WorldWideScience

Sample records for amber

  1. AMBER User's Manual

    International Nuclear Information System (INIS)

    AMBER is a Particle-In-Cell (PIC) code which models the evolution of a representative slice of a relativistic electron beam in a linear accelerator. The beam is modeled as a steady flow and therefore no electromagnetic waves: all the fields (external and self-fields) are electrostatic and magnetostatic fields (for a complete description, see chapter 5). The possible elements describing the accelerator lattice are solenoids, accelerating gaps, pipes and apertures. Several kinds of beam distribution can be loaded: KV, gaussian, semi-gaussian, etc. Alternatively, the user can reconstruct (or load) a distribution from the output of another codefile, for example, an interface generating the beam distribution from output produced from EGUN or LSP codes is available as an option. This documentation first describes in detail the input files needed to run AMBER and the procedure to start the executable. The possible data files and graphical output are explained in the two following chapters. The last chapter describes the physics model and numerical techniques used. An example of input files and the result obtained with these inputs are also given in the Appendix

  2. Insect frass in Baltic amber

    Directory of Open Access Journals (Sweden)

    Kari A. Kinnunen

    2008-01-01

    Full Text Available Inclusions of wood debris loosened from pine-like trees are abundant in Baltic amber of Eocene and Oligocene age. The possibilities to find insect frass and excrement among wood debris are outlined and some examples are given. Comparison with the frass and excrement produced by present-day insects provide a possibility to identify insects even though their fossils are lacking. This information can be used to characterize former forest environments. Amber forests may have also covered Southern Finland, and this possibility is discussed. Furthermore, the presence of wood debris may be utilized to recognize amber fakes, which is important for both gem trade and paleontology. It is proposed that databases and identification keys of frass and excrement should be constructed.

  3. Further AMBER and Ecolego Intercomparisons

    International Nuclear Information System (INIS)

    The AMBER compartmental modelling software is used by Quintessa in undertaking Performance Assessment (PA) calculations for SKI. SSI and NRPA are supporting the development of Ecolego which is based on the Matlab/Simulink general purpose modelling software for undertaking PA calculations. Intercomparison calculations using AMBER and Ecolego have been undertaken based on calculation cases considered in SKB's SR97 assessment. The reasons for undertaking such intercomparisons included: 1. to give confidence in the use of AMBER and Ecolego for whole system PA calculations for a deep repository; and 2. to provide SKI and SSI with an understanding of some of the technical issues raised by seeking to repeat the SR97 calculations with different models and software. Conclusions drawn from these intercomparisons included: 1. Both modelling packages successfully reproduced SKB's SR97 calculations for the near field, geosphere and biosphere. 2. AMBER and Ecolego calculations were typically in agreement to within one significant figure, but in several instances the SR97 documentation was not sufficiently clear to enable the implementation of the models in AMBER and Ecolego to be unambiguous. In order to gain more information on the comparisons between the two codes, additional intercomparisons have been undertaken using input data from the Vault Safety Case originally undertaken as part of an IAEA research project (ISAM). The comparisons between the AMBER and Ecolego calculations for the ISAM vault safety case have shown excellent agreement. Calculations at specified times generally agree to around three significant figures, and calculations of peak radionuclide fluxes and concentrations agree to two significant figures. This agreement is particularly good given the large number of model compartments and the inclusion of decay changes of up to six members. The most important situation where agreement may not be as good as that generally found is where radionuclides have been

  4. Provenance studies of amber by PIXE

    International Nuclear Information System (INIS)

    Analyses by Infrared Spectroscopy and 13 C Nuclear Magnetic Resonance are suitable to determine the paleobotanic source of amber, but cannot differentiate between beds of the same paleobotanic source. Particle Induced X-ray Emission (PIXE) using an external set-up is presented as a new and non-destructive semiquantitative method for provenance studies of amber. PIXE analysis is focused at inorganic contents of amber, considering that the composition of microscopic inclusions depends on the sedimentation environment and it can be used to determine similarities and differences between amber samples and correlate them with amber beds. Results of analyses on amber samples from several world regions and a group of archaeological samples from Chiapas, Mexico, are presented. Amber from different regions have specific inorganic elemental contents; archaeological samples can be associated with beds, even if they have the same paleobotanic origin. (Author)

  5. Further AMBER and Ecolego Intercomparisons

    Energy Technology Data Exchange (ETDEWEB)

    Maul, Philip; Robinson, Peter [Quintessa Limited, Henley-on-Thames (United Kingdom); Broed, Robert [Stockholm Univ. (Sweden). Center of Physics, Astronomy and Biotechnology; Avila, Rodolfo [Facilia AB, Bromma (Sweden)

    2004-01-01

    The AMBER compartmental modelling software is used by Quintessa in undertaking Performance Assessment (PA) calculations for SKI. SSI and NRPA are supporting the development of Ecolego which is based on the Matlab/Simulink general purpose modelling software for undertaking PA calculations. Intercomparison calculations using AMBER and Ecolego have been undertaken based on calculation cases considered in SKB's SR97 assessment. The reasons for undertaking such intercomparisons included: 1. to give confidence in the use of AMBER and Ecolego for whole system PA calculations for a deep repository; and 2. to provide SKI and SSI with an understanding of some of the technical issues raised by seeking to repeat the SR97 calculations with different models and software. Conclusions drawn from these intercomparisons included: 1. Both modelling packages successfully reproduced SKB's SR97 calculations for the near field, geosphere and biosphere. 2. AMBER and Ecolego calculations were typically in agreement to within one significant figure, but in several instances the SR97 documentation was not sufficiently clear to enable the implementation of the models in AMBER and Ecolego to be unambiguous. In order to gain more information on the comparisons between the two codes, additional intercomparisons have been undertaken using input data from the Vault Safety Case originally undertaken as part of an IAEA research project (ISAM). The comparisons between the AMBER and Ecolego calculations for the ISAM vault safety case have shown excellent agreement. Calculations at specified times generally agree to around three significant figures, and calculations of peak radionuclide fluxes and concentrations agree to two significant figures. This agreement is particularly good given the large number of model compartments and the inclusion of decay changes of up to six members. The most important situation where agreement may not be as good as that generally found is where radionuclides

  6. Optical characterization of amber from Chiapas, Mexico

    Science.gov (United States)

    López-Morales, Guadalupe; Espinosa-Luna, Rafael; Frausto-Reyes, Claudio

    2013-09-01

    An optical characterization of amber samples from México, the Baltic Sea and fake samples is presented, with the aim of discriminate between genuine and fake samples. We sought to identify the physical variables that could serve as the basis for the development of a device whose operation was able to discriminate between samples of genuine and fake amber. The optical refractive index was determined by Spectroscopic Ellipsometry, Abbe refractometry, and by the Brewster angle. The Raman spectra and the fluorescence optical responses were also determined. The results obtained indicate that the refractive index is not a robust variable that can differentiate between genuine amber and a fake sample. On the other hand, the Raman spectra and the fluorescence responses provide information that allows discriminating between both types of samples. For this reason, we used the results obtained by fluorescence as a basis for the design and construction of a prototype simple, reliable, portable, and affordable for authentication of the Mexican amber.

  7. Manufacturing of amber particles suitable for composite fibre melt spinning

    Directory of Open Access Journals (Sweden)

    Ļašenko Inga Ļ

    2016-04-01

    Full Text Available Polyamide fibre containing amber particles was fabricated. The amber particles were obtained by grinding technology using planetary ball-mills. Scanning electron microscopy and granulometry testing were used to characterise the structure and the size of prepared amber particles. Fourier transform infrared spectroscopy was used to analyse the chemical structure of the amber particles. The amber particles were characterised with average size up to 3 μm. The chemical composition of amber before and after the grinding remained unchanged. The amber particles were melt-extruded using polyamide 6 as the matrix. Melt spinning processing was used to fabricate polyamide-amber filaments. Pre-oriented yarns and fully drawn yarns were obtained after hotdrawing experiments. Reported experimental findings of amber composite fibre could be important for textile applications.

  8. Lipid14: The Amber Lipid Force Field

    OpenAIRE

    Dickson, Callum J.; Madej, Benjamin D.; Skjevik, Åge A.; Betz, Robin M.; Teigen, Knut; Gould, Ian R.; Walker, Ross C.

    2014-01-01

    The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by si...

  9. Penis morphology in a Burmese amber harvestman

    Science.gov (United States)

    Dunlop, Jason A.; Selden, Paul A.; Giribet, Gonzalo

    2016-02-01

    A unique specimen of the fossil harvestman Halitherses grimaldii Giribet and Dunlop, 2005 (Arachnida: Opiliones) from the Cretaceous (ca. 99 Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in H. grimaldii appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which H. grimaldii was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that H. grimaldii represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.

  10. OHANA, the AMBER/VLTI Snapshot Survey

    CERN Document Server

    Rivinius, Th; Demers, Z; Quirrenbach, A

    2016-01-01

    We report on the OHANA interferometric snapshot survey, carried out by the VLTI group at the Paranal observatory. It makes use of observing time not useful for any other scheduled scientific or technical tasks in the sense of a backup programme, to characterize the mass-loss for early-type stars. The survey employs the combination of AMBER's high spectral and spatial resolution. The spatially unresolved central object provides a reference frame for the fringe properties observed in the light of the continuum.

  11. Tetracycline-Regulated Suppression of Amber Codons in Mammalian Cells

    OpenAIRE

    Park, Ho-Jin; RajBhandary, Uttam L.

    1998-01-01

    As an approach to inducible suppression of nonsense mutations in mammalian cells, we described recently an amber suppression system in mammalian cells dependent on coexpression of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) along with the E. coli glutamine-inserting amber suppressor tRNA. Here, we report on tetracycline-regulated expression of the E. coli GlnRS gene and, thereby, tetracycline-regulated suppression of amber codons in mammalian HeLa and COS-1 cells. The E. coli GlnRS co...

  12. Mammalian hairs in Early Cretaceous amber

    Science.gov (United States)

    Vullo, Romain; Girard, Vincent; Azar, Dany; Néraudeau, Didier

    2010-07-01

    Two mammalian hairs have been found in association with an empty puparium in a ˜100-million-year-old amber (Early Cretaceous) from France. Although hair is known to be an ancestral, ubiquitous feature in the crown Mammalia, the structure of Mesozoic hair has never been described. In contrast to fur and hair of some Jurassic and Cretaceous mammals preserved as carbonized filaments, the exceptional preservation of the fossils described here allows for the study of the cuticular structure. Results show the oldest direct evidence of hair with a modern scale pattern. This discovery implies that the morphology of hair cuticula may have remained unchanged throughout most of mammalian evolution. The association of these hairs with a possible fly puparium provides paleoecological information and indicates peculiar taphonomic conditions.

  13. An asterid flower from neotropical mid-Tertiary amber.

    Science.gov (United States)

    Poinar, George O; Struwe, Lena

    2016-01-01

    Fossils preserved in amber may provide significant palaeoevolutionary and biogeographical data regarding the evolution of life on Earth(1). Although amber is particularly noted for its detailed preservation of arthropods, the same degree of preservation can be found for vascular plant remains(2). Mid-Tertiary Dominican amber is a rich source for such fossils, and representatives of several angiosperm families have been described. However, no fossilized examples of the large asterid plant clade have yet been reported. Here we describe the first fossil neotropical flowers found in amber from a representative of the asterids. The asterids are one of the largest lineages of flowering plants, containing groups such as the sunflower, potato, coffee and mint families, totalling over 80,000 species(3). The new fossils are only known as flowers, more precisely corollas with stamens and styles. We here describe them as a new species, Strychnos electri sp. nov, in the plant family Loganiaceae (Gentianales). PMID:27249345

  14. First AMBER/VLTI observations of hot massive stars

    CERN Document Server

    Petrov, R; Chesneau, O; Weigelt, G; Bonneau, D; Stee, P; Kraus, S; Mourard, D; Meilland, A; Malbet, F; Lisi, F; Kern, P; Beckmann, U; Lagarde, S; Gennari, S; Lecoarer, E; Driebe, T; Accardo, M; Robbe-Dubois, S; Ohnaka, K; Busoni, S; Roussel, A; Zins, G; Behrend, J; Ferruzi, D; Bresson, Y; Duvert, G; Nussbaum, E; Marconi, A; Feautrier, P; Dugu'e, M; Chelli, A; Tatulli, E; Heininger, M; Delboulbé, A; Bonhomme, S; Schertl, D; Testi, L; Mathias, P; Monin, J L; Gluck, L; Hofmann, Karl Heinrich; Salinari, P; Puget, P; Clausse, J M; Fraix-Burnet, D; Foy, R; Isella, A; Stee, Ph.; Driebe, Th.; Feautrier, Ph.; Mathias, Ph.

    2005-01-01

    AMBER is the first near infrared focal instrument of the VLTI. It combines three telescopes and produces spectrally resolved interferometric measures. This paper discusses some preliminary results of the first scientific observations of AMBER with three Unit Telescopes at medium (1500) and high (12000) spectral resolution. We derive a first set of constraints on the structure of the circumstellar material around the Wolf Rayet Gamma2 Velorum and the LBV Eta Carinae.

  15. Impact Amber, Popcorn, and Pathology: The Biology of Impact Melt Breccias and Implications for Astrobiology

    Science.gov (United States)

    Harris, R. S.; Schultz, P. H.

    2007-03-01

    We present evidence that superheated impact melts can trap and preserve both floral and faunal remains forming "impact amber." We discuss terrestrial occurrences of impact amber and the strategy it suggests in searching for evidence of past life on other

  16. Optical configuration and analysis of the AMBER/VLTI instrument

    CERN Document Server

    Robbe-Dubois, S; Petrov, R G; Lisi, F; Beckmann, U; Antonelli, P; Bresson, Y; Martinot-Lagarde, G; Roussel, A; Salinari, P; Vannier, M; Chelli, A; Dugué, M; Duvert, G; Gennari, S; Gluck, L; Kern, P; LeCoarer, E; Malbet, F; Millour, F; Perraut, K; Puget, P; Rantakyro, F; Tatulli, E; Weigelt, G; Zins, G

    2008-01-01

    This paper describes the design goals and engineering efforts that led to the realization of AMBER (Astronomical Multi BEam combineR) and to the achievement of its present performance. On the basis of the general instrumental concept, AMBER was decomposed into modules whose functions and detailed characteristics are given. Emphasis is put on the spatial filtering system, a key element of the instrument. We established a budget for transmission and contrast degradation through the different modules, and made the detailed optical design. The latter confirmed the overall performance of the instrument and defined the exact implementation of the AMBER optics. The performance was assessed with laboratory measurements and commissionings at the VLTI, in terms of spectral coverage and resolution, instrumental contrast higher than 0.80, minimum magnitude of 11 in K, absolute visibility accuracy of 1%, and differential phase stability of 1E-3 rad over one minute.

  17. IOT Overview: Calibrations of the VLTI Instruments (MIDI and AMBER)

    Science.gov (United States)

    Morel, S.; Rantakyrö, F.; Rivinius, T.; Stefl, S.; Hummel, C.; Brillant, S.; Schöller, M.; Percheron, I.; Wittkowski, M.; Richichi, A.; Ballester, P.

    We present here a short review of the calibration processes that are currently applied to the instruments AMBER and MIDI of the VLTI (Very Large Telescope Interferometer) at Paranal. We first introduce the general principles to calibrate the raw data (the "visibilities") that have been measured by long-baseline optical interferometry. Then, we focus on the specific case of the scientific operation of the VLTI instruments. We explain the criteria that have been used to select calibrator stars for the observations with the VLTI instruments, as well as the routine internal calibration techniques. Among these techniques, the "P2VM" (Pixel-to-Visibility Matrix) in the case of AMBER is explained. Also, the daily monitoring of AMBER and MIDI, that has recently been implemented, is shortly introduced.

  18. First Psocodean (Psocodea,Empheriidae) from the Cretaceous Amber of New Jersey

    Institute of Scientific and Technical Information of China (English)

    Dany AZAR; André NEL; Julian F.PETRULEVI(C)IUS

    2010-01-01

    Representatives of the extinct psocid family Empheriidae are known from Eocene Baltic amber,Lowermost Eocene French amber (Oise),and Lower Cretaceous Spanish amber (Alava).We report herein the first discovery of an empheriid psocid from the Cretaceous amber of New Jersey as Jerseyempheria grimaldii gen.et sp.nov.The fossil is figured and described.The new species is distinguished from related taxa.A discussion and checklist of Empheriidae are provided.

  19. Amber Trust on ostmas Tallinna Külmhoone emafirmat / Liis Kängsepp

    Index Scriptorium Estoniae

    Kängsepp, Liis, 1981-

    2005-01-01

    Skandinaavia-USA investeerimisfond Amber Trust loodab enne aasta lõppu allkirjastada Tallinna Külmhoone emafirma Kauno Pieno Centras ostulepingu. Diagramm: Tallinna Külmhoone majandusnäitajad. Vt. samas: Amber Trust tahab investeerida üle 2 miljardi krooni; Amber laiendas tegevust Vetteli kaudu Soome

  20. Chemotaxonomical aspects of lower Cretaceous amber from Reconcavo Basin, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Ricardo; Azevedo, Debora A., E-mail: ricardopereira@iq.ufrj.b, E-mail: debora@iq.ufrj.b [Universidade Federal do Rio de Janeiro (IQ/UFRJ), RJ (Brazil). Inst. de Quimica; Carvalho, Ismar S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Geociencias; Fernandes, Antonio Carlos S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Museu Nacional. Dept. de Geologia e Paleontologia

    2011-07-01

    The chemical composition of Lower Cretaceous amber samples from Reconcavo Basin (Salvador, Bahia) was performed by GC-MS to characterize possible botanical sources. The compounds identified were hydrocarbonic and polar diterpenoids, such as abietane, dehydroabietane, tetrahydroretene, dehydroabietol, dehydroabietic acid, ferruginol and sugiol. Other diterpenoid classes were not detected as well as triterpenoids. The composition of the extracts and chemosystematic data allows relating the samples to conifers of Podocarpaceae or Cheirolepidiaceae families due to detection of ferruginol, a specific biomarker to these families. The data concerning Cretaceous amber in the Reconcavo Basin provided information concerning the presence of a resinous flora in the Maracangalha Formation sediments during the Lower Cretaceous. (author)

  1. Structural changes in amber due to uranium mineralization.

    Science.gov (United States)

    Havelcová, Martina; Machovič, Vladimír; Mizera, Jiří; Sýkorová, Ivana; René, Miloš; Borecká, Lenka; Lapčák, Ladislav; Bičáková, Olga; Janeček, Oldřich; Dvořák, Zdeněk

    2016-07-01

    The presence of uranium, with a bulk mass fraction of about 1.5 wt% and radiolytic alterations are a feature of Cenomanian amber from Křižany, at the northeastern edge of the North Bohemian Cretaceous uranium ore district. Pores and microcracks in the amber were filled with a mineral admixture, mainly in the form of Zr-Y-REE enriched uraninite. As a result of radiolytic alterations due to the presence of uranium, structural changes were observed in the Křižany amber in comparison with a reference amber from Nové Strašecí in central Bohemia; this was of similar age and botanical origin but did not contain elevated levels of uranium. Structural changes involved an increase in aromaticity due to dehydroaromatization of aliphatic cyclic hydrocarbons, loss of oxygen functional groups, an increase in the degree of polymerization, crosslinking of CC bonds, formation of a three-dimensional hydrocarbon network in the bulk organic matrix, and carbonization of the organic matrix around the uraninite infill. PMID:27085038

  2. Entrapment Bias of Arthropods in Miocene Amber Revealed by Trapping Experiments in a Tropical Forest in Chiapas, Mexico

    OpenAIRE

    Solórzano Kraemer, Mónica M.; Kraemer, Atahualpa S.; Stebner, Frauke; Bickel, Daniel J.; Rust, Jes

    2015-01-01

    All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measu...

  3. AMBER and Ecolego Intercomparisons using Calculations from SR 97

    International Nuclear Information System (INIS)

    The AMBER compartmental modelling software has been used by Quintessa in undertaking Performance Assessment (PA) calculations for SKI for the last four years. In particular, it was used in helping to identify key issues in the safety case for SFR 1. SSI and the Norwegian Radiation Protection Authority (NRPA) are supporting the development of Ecolego which is based on the Matlab/Simulink general purpose modelling software and provides a user-friendly Graphical User Interface which is particularly suitable for undertaking PA calculations. At SKI/SSI expert group meetings in September 2002, Quintessa presented some radionuclide transport calculations for a deep repository for spent fuel using AMBER. Comparisons were presented with calculations undertaken by SKB in their SR 97 study. It was agreed that it would be useful to undertake some intercomparison calculations using AMBER and Ecolego based on calculation cases considered in SR 97. The reasons for undertaking such intercomparisons include: 1. to give confidence in the use of AMBER and Ecolego for whole system PA calculations for a deep repository; and 2. to provide SKI and SSI with an understanding of some of the technical issues raised by seeking to repeat the SR 97 calculations with different models and software. This report documents the intercomparison calculations that have been undertaken. The main conclusions that have been drawn are: 1. Both modelling packages could successfully reproduce SKB's SR 97 calculations for the near field, geosphere and biosphere. 2. The results of the deterministic calculations for the near field and both deterministic and probabilistic calculations for the biosphere, where AMBER and Ecolego used compartment models, were typically in agreement to within one significant figure. The identical results for the calculated equilibrium inventories in Bay sediments illustrate that the calculations by AMBER and Ecolego are essentially the same when the compartment models are identical

  4. Review of the El Soplao Amber Outcrop,Early Cretaceous of Cantabria,Spain

    Institute of Scientific and Technical Information of China (English)

    María NAJARRO; Francisco VELASCO; Fernando TORNOS; Véronique DAVIERO-GOMEZ; Bernard GOMEZ; Xavier DELCL(O)S; Enrique PE(N)ALVER; Ricardo P(E)REZ-DE LA FUENTE; Jaime ORTEGA-BLANCO; Cesar MENOR-SALV(A)N; Eduardo BARR(O)N; Carmen SORIANO; Idoia ROSALES; Rafael L(O)PEZ DEL VALLE

    2010-01-01

    El Soplao outcrop,an Early Cretaceous amber deposit recently discovered in northern Spain(Cantabria),has been shown to be the largest site of amber with arthropod inclusions that has been found in Spain so far.Relevant data provided herein for biogeochemistry of the amber,palynology,taphonomy and arthropod bioinclusious complement those previously published.This set of data suggests at least two botanical sources for the amber of El Soplao deposit.The first(type A amber)strongly supports a source related to Cheirolepidiaceae,and the second(type B amber)shows non-specific conifer biomarkers.Comparison of molecular composition of type A amber with Frenelopsis leaves(Cheicolepidiaceae)strongly suggests a biochemical affinity and a common botanical origin.A preliminary palynologlcal study indicates a regional high taxonomical diversity,mainly of pteridophyte spores and gymnosperm pollen grains.According to the preliminary palynological data,the region was inhabited by conifer forests adapted to a dry season under a subtropical climate.The abundant charcoalified wood associated with the amber in the same beds is evidence of paleofires that most likely promoted both the resin production and an intensive erosion of the litter,and subsequent great accumulation of amber plus plant cuticles.In addition,for the first time in the fossil record,charcoalified plant fibers as bioinclusious in amber are reported.Other relevant taphonomic data are the exceptional presence of serpulids and bryozoans on the surfaces of some amber pieces indicating both a long exposure on marine or brackish-water and a mixed assemblage of amber.Lastly,new findings of insect bioinclusions,some of them uncommon in the fossil record or showing remarkable adaptations,are reported.In conclusion,a documented scenario for the origin of the El Soplao amber outcrop is provided.

  5. Solid state 13C NMR analysis of Brazilian cretaceous ambers

    International Nuclear Information System (INIS)

    13C cross polarization with magic angle spinning nuclear magnetic resonance (13C CPMAS NMR) spectra have been obtained for the first time to three Cretaceous amber samples from South America. The samples were dated to Lower Cretaceous and collected in sediments from the Amazonas, Araripe and Reconcavo basins, Brazil. All samples have very similar spectra, consistent with a common paleobotanical source. Some aspects of the spectra suggest a relationship between Brazilian ambers and Araucariaceae family, such as intense resonances at 38-39 ppm. All samples are constituted by polylabdane structure associated to Class Ib resins, constituted by polymers of labdanoid diterpenes. Finally, information concerning some structural changes during maturation, such as isomerization of Δ8(17) and Δ12(13) unsaturations, were obtained by 13C NMR analyses. The results concerning botanical affinities are in accordance with previous results obtained by gas chromatography-mass spectrometry (GC-MS). (author)

  6. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

    OpenAIRE

    Pabis, Anna; Geronimo, Inacrist; York, Darrin M.; Paneth, Piotr

    2014-01-01

    Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specif...

  7. AMBER : a near infrared focal instrument for the VLTI

    OpenAIRE

    Petrov, R. G.; Malbet, F.; Richichi, A.; Hofmann, K.H.; Mourard, Denis; Agabi, Karim; Antonelli, P.; Aristidi, Eric; Baffa, Carlo; Beckmann, Udo; Berio, Philippe; Bresson, Yves; Cassaing, Frederic; Chelli, Alain; Dreiss, Albrecht

    2001-01-01

    AMBER is the General User near-infrared focal instrument of the Very Large Telescope interferometer. Its specifications are based on three key programs on Young Stellar Objects, Active Galactic Nuclei central regions, masses and spectra of hot Extra Solar Planets. It has an imaging capacity because it combines up to three beams and very high accuracy measurement are expected from the spatial filtering of beams by single mode fibers and the comparison of measurements made simultaneously in dif...

  8. Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber

    Directory of Open Access Journals (Sweden)

    Alonso Jesús

    2009-02-01

    Full Text Available Abstract Background Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Pyritization is the most important and extensive mode of preservation of animals and especially of plants. Entrapping in amber, a fossilized resin, is considered an alternative mode of biological preservation. For the first time, the internal organization of 114-million-year-old microfossils entrapped in Lower Cretaceous amber is described and analyzed, using adapted scanning electron microscopy in backscattered electron mode in association with energy dispersive X-ray spectroscopy microanalysis. Double fossilization of several protists included in diverse taxonomical groups and some vegetal debris is described and analyzed. Results In protists without an exoskeleton or shell (ciliates, naked amoebae, flagellates, determinate structures, including the nuclei, surface envelopes (cortex or cytoplasmic membrane and hyaloplasm are the main sites of pyritization. In protists with a biomineralized skeleton (diatoms, silicon was replaced by pyrite. Permineralization was the main mode of pyritization. Framboidal, subhedral and microcrystalline are the predominant pyrite textures detected in the cells. Abundant pyritized vegetal debris have also been found inside the amber nuggets and the surrounding sediments. This vegetal debris usually contained numerous pyrite framboids and very densely packed polycrystalline pyrite formations infilled with different elements of the secondary xylem. Conclusion Embedding in amber and pyritization are not always alternative modes of biological preservation during geological times, but double fossilization is possible under certain environmental conditions. Pyritization in protists shows a quite different pattern with regard to plants, due to the different composition and cellular architecture in these microorganisms and organisms. Anaerobic sulphate

  9. Webspinners in Early Eocene amber from western India (Insecta, Embiodea

    Directory of Open Access Journals (Sweden)

    Michael Engel

    2011-11-01

    Full Text Available The family Scelembiidae (Neoembiodea: Embiomorpha: Archembioidea is recorded from Asia for the first time, based on two individuals preserved in Early Eocene amber from the Cambay Basin, western India. Kumarembia hurleyi Engel & Grimaldi, gen. n. et sp. n., is described, figured, and distinguished from other archembioid genera. The genus shares male genitalic features with scelembiids, otherwise known from South America and Africa.

  10. Seeking carotenoid pigments in amber-preserved fossil feathers

    Science.gov (United States)

    Thomas, Daniel B.; Nascimbene, Paul C.; Dove, Carla J.; Grimaldi, David A.; James, Helen F.

    2014-06-01

    Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

  11. Amber bearing deposit in SW Saaremaa, Estonia - sedimentary environment and palaeogeography

    Science.gov (United States)

    Post, Triine; Ots, Mirja; Rosentau, Alar

    2015-04-01

    The paper describes a deposit of natural amber found form Estonia. Finds of natural amber are important in the context of the Bronze Age archaeology, because the amount of Bronze Age archaeological amber found in Estonia is very small. Most of the amber is from the Late Bronze Age and is mainly discovered from the fortified settlements in Saaremaa, some also from burials of the same time. Now, the discovery of the deposit of natural amber in the island of Saaremaa makes us reconsider the general opinion that all archaeological amber items found in Estonia have been imported. The aim of this study is to clarify the origin and age of the natural amber using scientific methods. A layer of buried organic matter (BOM) containing pieces of natural amber was discovered in Holocene coastal plain on Sõrve peninsula, island of Saaremaa. The BOM layer is buried under ca 90 cm-thick sandy coastal deposits and consists of remains of coastal plants and pieces of driftwood. Palaeogeographic reconstructions and sediment composition indicate that the layer was deposited in the coastal zone and buried quickly by sandy marine sediments. According to radiocarbon dating of the seeds of Polygonum lapathifolium the formation of the BOM layer remained in the Late Bronze Age (2480 ± 30 14C yr BP). Amber finds have been characterized using ATR-FTIR spectroscopy and isotope analysis of light elements (H and C) - both are referring to Baltic amber. Therefore it is probable that amber was transported to Saaremaa within organic matter from the Latvian-Lithuanian coastal zone where secondary Baltic amber deposits are widely known.

  12. Game Theory Model of Traffic Participants within Amber Time at Signalized Intersection

    OpenAIRE

    2014-01-01

    The traffic light scheme is composed of red, green, and amber lights, and it has been defined clearly for the traffic access of red and green lights; however, the definition of that for the amber light is indistinct, which leads to the appearance of uncertainty factors and serious traffic conflicts during the amber light. At present, the traffic administrations are faced with the decision of whether to forbid passing or not during the amber light in the cities of China. On one hand, it will g...

  13. IR and py/GC/MS examination of amber relics excavated from 6th century royal tomb in Korean Peninsula

    Science.gov (United States)

    Park, Jongseo; Yun, Eunyoung; Kang, Hyungtae; Ahn, Jooyoung; Kim, Gyuho

    2016-08-01

    Relics of amber were excavated from King Muryeong's tomb constructed in the 6th century on the Korean peninsula. To estimate the provenance, FTIR (Fourier transform infrared spectroscopy) and py/GC/MS (pyrolysis/gas chromatography/mass spectrometry) analysis were utilized. The reference Baltic amber sample was also analyzed with the same method for comparison. The relics were confirmed to be amber from the FTIR analysis where an absorption band near 1150 cm- 1, characteristic one in Baltic amber, was also observed. In py/GC/MS analysis, pyrolyzed products like butanedioic acid and dehydroabietic acid, known constituents of amber, were observed. In addition, D-fenchyl alcohol, camphor, borneol and butanedioic acid, typical constituents of Baltic amber, were observed in some samples. From this, it appears that some of relics were made from Baltic amber and that Baltic amber was transported to the Korean peninsula in the time of tomb construction.

  14. IR and py/GC/MS examination of amber relics excavated from 6th century royal tomb in Korean Peninsula.

    Science.gov (United States)

    Park, Jongseo; Yun, Eunyoung; Kang, Hyungtae; Ahn, Jooyoung; Kim, Gyuho

    2016-08-01

    Relics of amber were excavated from King Muryeong's tomb constructed in the 6th century on the Korean peninsula. To estimate the provenance, FTIR (Fourier transform infrared spectroscopy) and py/GC/MS (pyrolysis/gas chromatography/mass spectrometry) analysis were utilized. The reference Baltic amber sample was also analyzed with the same method for comparison. The relics were confirmed to be amber from the FTIR analysis where an absorption band near 1150cm(-1), characteristic one in Baltic amber, was also observed. In py/GC/MS analysis, pyrolyzed products like butanedioic acid and dehydroabietic acid, known constituents of amber, were observed. In addition, d-fenchyl alcohol, camphor, borneol and butanedioic acid, typical constituents of Baltic amber, were observed in some samples. From this, it appears that some of relics were made from Baltic amber and that Baltic amber was transported to the Korean peninsula in the time of tomb construction. PMID:27116473

  15. A gilled mushroom, Gerontomyces lepidotus gen. et sp. nov. (Basidiomycota: Agaricales), in Baltic amber.

    Science.gov (United States)

    Poinar, George

    2016-09-01

    A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. PMID:27567715

  16. Blue ghosts: a new method for isolating amber mutants defective in essential genes of Escherichia coli

    DEFF Research Database (Denmark)

    Brown, S; Brickman, E R; Beckwith, J

    1981-01-01

    We describe a technique which permits an easy screening for amber mutants defective in essential genes of Escherichia coli. Using this approach, we have isolated three amber mutants defective in the rho gene. An extension of the technique allows the detection of ochre mutants and transposon inser...

  17. Historical survey of the internal use of unprocessed amber.

    Science.gov (United States)

    Duffin, Christofer J

    2015-01-01

    The organic mineraloid gemstone, amber, a fossilized resin collected from Eocene deposits laid down around 44 million years old on the Baltic coast, has been an important geopharmaceutical in the western materia medica since classical times. Once rendered into powdered form, it could be delivered into the body using a wide range of vehicles including lozenges, pills, tablets, troches, electuaries, solutions and lohochs (lick-pots), and with toast and poached eggs. Acting either alone or in combination with a wide range of botanical, zoological and other geological ingredients, it was employed in the treatment of a huge range of diseases. Most prominent among these were various vascular disorders (e.g. haemoptysis, haemorrhage, excessive menstrual bleeding), problems with the urogenital system (e.g. tendency towards miscarriage, impotence, venereal diseases, strangury, dysuria and bladder stones) and alimentary conditions, particularly dysentery. A variety of infectious diseases, including plague, gonorrhoea, measles and fevers could be targeted with amber-containing preparations, as could epilepsy, melancholy and the ravages of old age. Rather more unusual applications included its use in the treatment of impotence, halitosis, drunkenness and a weak back. PMID:26203539

  18. The aquatic and semiaquatic biota in Miocene amber from the Campo LA Granja mine (Chiapas, Mexico): Paleoenvironmental implications

    Science.gov (United States)

    Serrano-Sánchez, María de Lourdes; Hegna, Thomas A.; Schaaf, Peter; Pérez, Liseth; Centeno-García, Elena; Vega, Francisco J.

    2015-10-01

    Amber from the Campo La Granja mine in Chiapas, Mexico, is distinct from other sources of amber in Chiapas. Campo La Granja amber has distinct layers created by successive flows of resin with thin layers of sand on most surfaces. Aquatic and semi-aquatic arthropods are commonly found. Together these pieces of evidence suggest an estuarine environment similar to modern mangrove communities. The aquatic crustaceans are the most intriguing aspect of the biota. A large number of ostracods have been found in the amber-many with their carapaces open, suggesting that they were alive and submerged in water at the time of entombment. The only known examples of brachyuran crabs preserved in amber are found in the Campo La Granja amber. Amphipods, copepods, isopods, and tanaids are also members of the crustacean fauna preserved in amber.

  19. Entrapment Bias of Arthropods in Miocene Amber Revealed by Trapping Experiments in a Tropical Forest in Chiapas, Mexico

    Science.gov (United States)

    Solórzano Kraemer, Mónica M.; Kraemer, Atahualpa S.; Stebner, Frauke; Bickel, Daniel J.; Rust, Jes

    2015-01-01

    All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measurements of the trapped arthropods, and guild distribution, that the amber trap is a complex entomological trap not comparable with a single artificial trap. At the order level, the most similar trap to amber is the sticky trap. However, in the case of Diptera, at the family level, the Malaise trap is also very similar to amber. Amber captured a higher diversity of arthropods than each of the artificial traps, based on our study of Mexican amber from the Middle Miocene, a time of climate optimum, where temperature and humidity were probably higher than in modern Central America. We conclude that the size bias is qualitatively independent of the kind of trap for non–extreme values. We suggest that frequent specimens in amber were not necessarily the most frequent arthropods in the former amber forest. Selected taxa with higher numbers of specimens appear in amber because of their ecology and behavior, usually closely related with a tree–inhabiting life. Finally, changes of diversity from the Middle Miocene to Recent time in Central and South America can be analyzed by comparing the rich amber faunas from Mexico and the Dominican Republic with the fauna trapped using sticky and Malaise traps in Central America. PMID:25785584

  20. A new genus of Podonominae (Diptera: Chironomidae) in Late Eocene Rovno amber from Ukraine

    OpenAIRE

    Baranov, Viktor; Andersen, Trond; Perkovsky, Evgeny

    2014-01-01

    The genus Palaeoboreochlus Baranov et Andersen, n. gen. is erected based on P. inornatus Baranov et Andersen, n. sp. described from a male found in Late Eocene Rovno amber. The new genus groups with Boreochlus Edwards in the tribe "Boreochlini".

  1. Implementation of project Safe in Amber. Verification study for SFR 1 SAR-08

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Gavin; Herben, Martin; Lloyd, Pam; Rose, Danny; Smith, Chris; Barraclough, Ian (Enviros Consulting Ltd (GB))

    2008-03-15

    This report documents an exercise in which AMBER has been used to represent the models used in Project SAFE, a safety assessment undertaken on SFR 1. (AMBER is a flexible, graphical-user-interface based tool that allows users to build their own dynamic compartmental models to represent the migration, degradation and fate of contaminants in an environmental system. AMBER allows the user to assess routine, accidental and long-term contaminant release.) AMBER has been used to undertake assessment calculations on all of the disposal system, including all disposal tunnels and the Silo, the geosphere and several biosphere modules. The near-field conceptual models were implemented with minimal changes to the approach undertaken previously in Project SAFE. Model complexity varied significantly between individual disposal facilities increasing significantly from the BLA to the BTF and BMA tunnels and Silo. Radionuclide transport through the fractured granite geosphere was approximated using a compartment model approach in AMBER. Several biosphere models were implemented in AMBER including reasonable biosphere development, which considered the evolution of the Forsmark area from coastal to lacustrine to agricultural environments in response to land uplift. Parameters were sampled from distributions and simulations were run for 1,000 realisations. In undertaking the comparison of AMBER with the various codes and calculation tools used in Project SAFE it was necessary to undertake a detailed analysis of the modelling approach previously adopted, with particular focus given to the near-field models. As a result some discrepancies in the implementation of the models and documentation were noted. The exercise demonstrates that AMBER is fully capable of representing the features of the SFR 1 disposal system in a safety assessment suitable for SAR-08

  2. Implementation of project Safe in Amber. Verification study for SFR 1 SAR-08

    International Nuclear Information System (INIS)

    This report documents an exercise in which AMBER has been used to represent the models used in Project SAFE, a safety assessment undertaken on SFR 1. (AMBER is a flexible, graphical-user-interface based tool that allows users to build their own dynamic compartmental models to represent the migration, degradation and fate of contaminants in an environmental system. AMBER allows the user to assess routine, accidental and long-term contaminant release.) AMBER has been used to undertake assessment calculations on all of the disposal system, including all disposal tunnels and the Silo, the geosphere and several biosphere modules. The near-field conceptual models were implemented with minimal changes to the approach undertaken previously in Project SAFE. Model complexity varied significantly between individual disposal facilities increasing significantly from the BLA to the BTF and BMA tunnels and Silo. Radionuclide transport through the fractured granite geosphere was approximated using a compartment model approach in AMBER. Several biosphere models were implemented in AMBER including reasonable biosphere development, which considered the evolution of the Forsmark area from coastal to lacustrine to agricultural environments in response to land uplift. Parameters were sampled from distributions and simulations were run for 1,000 realisations. In undertaking the comparison of AMBER with the various codes and calculation tools used in Project SAFE it was necessary to undertake a detailed analysis of the modelling approach previously adopted, with particular focus given to the near-field models. As a result some discrepancies in the implementation of the models and documentation were noted. The exercise demonstrates that AMBER is fully capable of representing the features of the SFR 1 disposal system in a safety assessment suitable for SAR-08

  3. Terpenoid compositions and botanical origins of Late Cretaceous and Miocene amber from China.

    Directory of Open Access Journals (Sweden)

    Gongle Shi

    Full Text Available The terpenoid compositions of the Late Cretaceous Xixia amber from Central China and the middle Miocene Zhangpu amber from Southeast China were analyzed by gas chromatography-mass spectrometry (GC-MS to elucidate their botanical origins. The Xixia amber is characterized by sesquiterpenoids, abietane and phyllocladane type diterpenoids, but lacks phenolic abietanes and labdane derivatives. The molecular compositions indicate that the Xixia amber is most likely contributed by the conifer family Araucariaceae, which is today distributed primarily in the Southern Hemisphere, but widely occurred in the Northern Hemisphere during the Mesozoic according to paleobotanical evidence. The middle Miocene Zhangpu amber is characterized by amyrin and amyrone-based triterpenoids and cadalene-based sesquiterpenoids. It is considered derived from the tropical angiosperm family Dipterocarpaceae based on these compounds and the co-occurring fossil winged fruits of the family in Zhangpu. This provides new evidence for the occurrence of a dipterocarp forest in the middle Miocene of Southeast China. It is the first detailed biomarker study for amber from East Asia.

  4. Game Theory Model of Traffic Participants within Amber Time at Signalized Intersection

    Directory of Open Access Journals (Sweden)

    Weiwei Qi

    2014-01-01

    Full Text Available The traffic light scheme is composed of red, green, and amber lights, and it has been defined clearly for the traffic access of red and green lights; however, the definition of that for the amber light is indistinct, which leads to the appearance of uncertainty factors and serious traffic conflicts during the amber light. At present, the traffic administrations are faced with the decision of whether to forbid passing or not during the amber light in the cities of China. On one hand, it will go against the purpose of setting amber lights if forbidding passing; on the other hand, it may lead to a mess of traffic flow running if not. And meanwhile the drivers are faced with the decision of passing the intersection or stopping during the amber light as well. So the decision-making behavior of traffic administrations and drivers can be converted into a double game model. And through quantification of their earnings in different choice conditions, the optimum decision-making plan under specific conditions could be solved via the Nash equilibrium solution concept. Thus the results will provide a basis for the formulation of the traffic management strategy.

  5. Game theory model of traffic participants within amber time at signalized intersection.

    Science.gov (United States)

    Qi, Weiwei; Wen, Huiying; Fu, Chuanyun; Song, Mo

    2014-01-01

    The traffic light scheme is composed of red, green, and amber lights, and it has been defined clearly for the traffic access of red and green lights; however, the definition of that for the amber light is indistinct, which leads to the appearance of uncertainty factors and serious traffic conflicts during the amber light. At present, the traffic administrations are faced with the decision of whether to forbid passing or not during the amber light in the cities of China. On one hand, it will go against the purpose of setting amber lights if forbidding passing; on the other hand, it may lead to a mess of traffic flow running if not. And meanwhile the drivers are faced with the decision of passing the intersection or stopping during the amber light as well. So the decision-making behavior of traffic administrations and drivers can be converted into a double game model. And through quantification of their earnings in different choice conditions, the optimum decision-making plan under specific conditions could be solved via the Nash equilibrium solution concept. Thus the results will provide a basis for the formulation of the traffic management strategy. PMID:25580108

  6. The value of advanced multiple beam equalization radiography (AMBER) and storage phosphor radiography in chest X-rays; Zur Validierung des AMBER-Systems und der digitalen Speicherfolienradiographie fuer Thoraxaufnahmen

    Energy Technology Data Exchange (ETDEWEB)

    Richter, C.S. [Strahlenklinik und Poliklinik, Klinikum Rudolf Virchow, Freie Univ. Berlin (Germany); Richter, K. [Franz-Volhard-Klinik, Klinikum Rudolf Virchow, Freie Univ. Berlin, Berlin-Buch (Germany); Stein, R. [Franz-Volhard-Klinik, Klinikum Rudolf Virchow, Freie Univ. Berlin, Berlin-Buch (Germany); Busch, H.P. [Inst. fuer Klinische Radiologie, Heidelberg Univ., Klinikum Mannheim (Germany)

    1993-12-31

    The study compared the quality of roentgenologic criteria in the evaluation of the heart and pulmonary vessels on chest X-rays obtained with different imaging systems. Fifty patients had four different chest radiographs, i.e. conventional chest X-rays, AMBER images, digital storage phosphor images, and digital storage radiographs that were obtained with the AMBER system. Comparison of techniques was based on 12 well-defined quality criteria of chest X-rays. Four radiologists with expertise reviewed the films according to these criteria. The AMBER technique was found to be superior to the remaining imaging modalities in visualization of the central pulmonary vessels, the descending aorta, and the left atrium. Peripheral pulmonary vessels were best appreciated with AMBER technique combined with storage phosphor technique. The same technique was superior in the assessment of all cardiovascular criteria. The superiority of this technique versus conventional chest X-rays can be explained on the basis of the linear slope of the gradation curve of AMBER and digital techniques. (orig.) [Deutsch] Es wurde ein Guetevergleich der roentgenologischen Kriterien des Herzens und der Pulmonalgefaesse auf Thoraxaufnahmen unterschiedlicher Bilderzeugungssysteme durchgefuehrt. Von 50 Patienten lagen jeweils 4 miteinander zu vergleichende Aufnahmen vor, und zwar jeweils eine konventionelle Filmfolienaufnahme, eine Aufnahme am AMBER (Advanced Multiple Beam Equalization Radiography)-System, eine digitale Phosphorspeicherfolienaufnahme und eine am AMBER-System angefertigte Speicherfolienaufnahme. Der Vergleich erfolgte anhand von 12 definierten Merkmalen der Thoraxaufnahme. Vier erfahrene Radiologen gaben fuer jedes dieser Kriterien ein Gueteurteil ab. Resultate: Die AMBER-Technik wurde fuer die Darstellung der zentralen Pulmonalgefaesse, der Aorta descendens und des linken Vorhofs als beste Methode eingeschaetzt. Die periphere Lungengefaesszeichnung erhielt die beste Guetebewertung bei

  7. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.

    Science.gov (United States)

    Zheng, Suqing; Tang, Qing; He, Jian; Du, Shiyu; Xu, Shaofang; Wang, Chaojie; Xu, Yong; Lin, Fu

    2016-04-25

    Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools. PMID:26998926

  8. Direct constraint on the distance of Gamma2 Velorum from AMBER/VLTI observations.

    OpenAIRE

    Millour, F.; G. Petrov, R.; Chesneau, O.; Bonneau, D.; Dessart, L.; Béchet, Clémentine; Tallon-Bosc, Isabelle; Tallon, Michel; Thiébaut, Éric; Thiébaut, Eric; Vakili, F.; Malbet, F.; Mourard, D.; Zins, G.; Roussel, A.

    2007-01-01

    In this work, we present the first AMBER observations, of the Wolf-Rayet and O (WR+O) star binary system y2 Velorum. The AMBER instrument was used with the telescopes UT2, UT3, and UT4 on baselines ranging from 46m to 85m. It delivered spectrally dispersed visibilities, as well as differential and closure phases, with a resolution R = 1500 in the spectral band 1.95-2.17 micron. We interpret these data in the context of a binary system with unresolved components, neglecting in a first approxim...

  9. First Record of Anisoptera (Insecta: Odonata) from mid-Cretaceous Burmese Amber.

    Science.gov (United States)

    Schädel, Mario; Bechly, Günter

    2016-01-01

    The fossil dragonfly Burmalindenia imperfecta gen. et sp. nov. is described from mid-Cretaceous Burmese amber as the first record of the odonate suborder Anisoptera for this locality and one of the few records from amber in general. The inclusion comprises two fragments of the two hind wings of a dragonfly. The fossil can be attributed to a new genus and species of the family Gomphidae, presumably in the subfamily Lindeniinae, and features a strange teratological phenomenon in its wing venation. PMID:27394756

  10. Cyclic terpenoids of contemporary resinous plant detritus and of fossil woods, ambers and coals

    Energy Technology Data Exchange (ETDEWEB)

    Simoneit, B.R.T.; Grimalt, J.O.; Wang, T.G.; Cox, R.E.; Hatcher, P.G.; Nissenbaum, A.

    1986-01-01

    Cyclic terpenoids present in the solvent extractable material of fossil woods, ambers and brown coals have been analyzed. The sample series chosen consisted of wood remains preserved in Holocene in Jurassic sediments and a set of ambers from the Philippines (copalite), Israel, Canada and Dominican Republic. The brown coals selected were from the Fortuna Garsdorf Mine and Miocene formations on Fiji. The fossil wood extracts contained dominant diterpenoid or sesquiterpenoid skeletons, and aromatized species were present at high concentrations, with a major amount of two-ring aromatic compounds. Tricyclic diterpenoids were the predominant compounds in the ambers. The brown coal extracts were composed of major amounts of one- and two-ring aromatized terpenoids, with a greater proportion of triterpenoid derivatives than in the case of the woods and ambers. This was especially noticeable for the German coal, where the triterpenoids were predominant. Open C-ring aromatized structures were also present in this coal. Steroid compounds were not detectable, but some hopanes were found as minor components in the German brown coal. An overview of the skeletal structure classes identified in each sample, as well as the general mass spectrometric characteristics of the unknown compounds are included in the present paper. It can be concluded from these structural distributions that aromatization is the main process for the transformation of terrestrial cyclic terpenoids during diagenesis, constituting a general pathway for all terpenoids.

  11. Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field

    Directory of Open Access Journals (Sweden)

    W. Wongsinlatam

    2013-01-01

    Full Text Available Nonbonding parameters of AMBER force field have been refined based on ab initio binding energies of CO2–[C7H5N2]− complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 for ε and σ parameters, respectively. Molecular dynamics simulations of CO2 molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I and refined parameters (SIM II, respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2 molecules. One slight but notable difference is that CO2 molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV are not much different from those obtained in SIM II.

  12. New predatory cockroaches (Insecta: Blattaria: Manipulatoridae fam.n.) from the Upper Cretaceous Myanmar amber

    Science.gov (United States)

    Vršanský, Peter; Bechly, Günter

    2015-04-01

    We describe a new extinct lineage Manipulatoridae (new family) of cockroaches from the Upper Cretaceous (Cenomanian) amber of Myanmar. Manipulator modificaputis gen. et sp. n. is a morphologically unique extinct cockroach that represents the first (of a total of 29 known worldwide) cockroach family reported exclusively from the Myanmar amber. This family represents an early side branch of the stem group of Mantodea (most probably a sister group of Eadiidae within Blattaria/Corydioidea) because it has some synapomorphies with the Mantodea (including the stem group and Eadiidae). This family also retains symplesiomorphies that exclude a position in the crown group, and furthermore has unique autapomorphies that exclude a position as a direct ancestor of Mantodea. The unique adaptations such as strongly elongated extremities and freely movable head on a long neck suggest that these animals were pursuit predators. Five additional specimens (including two immatures) reported from the Myanmar amber suggest that this group was relatively rare but belonged to the indigenous and autochthonous inhabitants of the ancient amber forest of the Myanmar region.

  13. A swarm of whiteflies—the first record of gregarious behavior from Eocene Baltic amber

    Science.gov (United States)

    Szwedo, Jacek; Drohojowska, Jowita

    2016-04-01

    A new whitefly Snotra christelae gen. et sp. n. is characterized, illustrated, and described from the Baltic amber. It represents the first record of gregarious behavior of Aleyrodinae (Aleyrodidae) whiteflies in fossil state. Implications of this finding on interpretation of whiteflies and their host-plant relationships and evolutionary traits of the group are discussed.

  14. A swarm of whiteflies-the first record of gregarious behavior from Eocene Baltic amber.

    Science.gov (United States)

    Szwedo, Jacek; Drohojowska, Jowita

    2016-04-01

    A new whitefly Snotra christelae gen. et sp. n. is characterized, illustrated, and described from the Baltic amber. It represents the first record of gregarious behavior of Aleyrodinae (Aleyrodidae) whiteflies in fossil state. Implications of this finding on interpretation of whiteflies and their host-plant relationships and evolutionary traits of the group are discussed. PMID:27023734

  15. A New Thorny Lacewing (Insecta:Neuroptera:Rhachiberothidae) from the Early Cretaceous Amber of Lebanon

    Institute of Scientific and Technical Information of China (English)

    Julian F.PETRULEVI(C)IUS; Dany AZAR; André NEL

    2010-01-01

    A new genus and species of Rhachiberothidae,Raptorapax terribilissima gen.et sp.nov.from the Cretaceous amber of Lebanon is described.The new genus is assigned to the subfamily Paraberothinae.The new material confirms the great diversity of the group in the Cretaceous age and its decrease in diversity in recent times.

  16. ASSESMENT OF FACTORS AFFECTING THE PRODUCTIVITY OF AMBER CHARKHA AND ERGONOMIC EVALUATION OF WORKERS

    Directory of Open Access Journals (Sweden)

    G. V. THAKRE

    2011-11-01

    Full Text Available Increasing demands of the cotton fabrics, now a day has made it necessary to increase the production of cotton fabrics. To increase the production it is necessary to study the factors affecting the performance of the women workers working on Amber charkha. Most of the Amber charkha in rural areas are hand operated (i.e. they runwith the help of human energy input. There are various medical, technical and environmental factors which affect the productivity of women workers working on Amber charkha. This paper discusses some of those factors which are responsible for this. The various factors that are affecting the productivity are health factors,sitting posture, working environment, raw material properties, and man machine system. Each of these factors plays an important role in the overall performance of the women workers. Analysis is carried out by comparing the actual readings with the standard norms available in the literature. The detailed project work is carried out to study the different factors affecting the productivity of Amber charkha. The basic necessity of this study is to provide comfortable sitting arrangement and good working environment which would help the workers for achieving better productivity with work satisfaction.

  17. A new genus of nemonychid weevil from Burmese amber (Coleoptera, Curculionoidea

    Directory of Open Access Journals (Sweden)

    Steve Davis

    2014-04-01

    Full Text Available The first fossil nemonychid (Nemonychidae in Burmese amber, belonging to the subfamily Rhinorhynchinae, is described and figured as Burmonyx zigrasi Davis and Engel, gen. n. and sp. n. While this specimen also comprises the first definitive record of the subfamily in the Asian continent, other compression fossils exist at least from the Yixian Formation of China and the Karatau site of Kazakhstan which may also deserve placement within this group. Although several important areas of the body are obscured by the shape and fragmented condition of the amber piece, a sufficient number of features are visible to consider adequate placement within Rhinorhynchinae, including the fairly strongly punctate elytral striae and appendiculate, nearly bifid pretarsal claws.

  18. Solid state {sup 13}C NMR analysis of Brazilian cretaceous ambers

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Ricardo; Azevedo, Debora A., E-mail: ricardopereira@iq.ufrj.b, E-mail: debora@iq.ufrj.b [Universidade Federal do Rio de Janeiro (IQ/UFRJ), Rio de Janeiro, RJ (Brazil). Inst. de Quimica. Lab. de Geoquimica Organica Molecular e Ambiental; San Gil, Rosane A.S. [Universidade Federal do Rio de Janeiro (IQ/UFRJ), RJ (Brazil). Inst. de Quimica. Lab. de RMN de Solidos; Carvalho, Ismar S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Geociencias. Dept. de Geologia; Fernandes, Antonio Carlos S. [Museu Nacional (MN/UFRJ), RJ (Brazil). Dept. de Geologia e Paleontologia

    2011-07-01

    {sup 13}C cross polarization with magic angle spinning nuclear magnetic resonance ({sup 13}C CPMAS NMR) spectra have been obtained for the first time to three Cretaceous amber samples from South America. The samples were dated to Lower Cretaceous and collected in sediments from the Amazonas, Araripe and Reconcavo basins, Brazil. All samples have very similar spectra, consistent with a common paleobotanical source. Some aspects of the spectra suggest a relationship between Brazilian ambers and Araucariaceae family, such as intense resonances at 38-39 ppm. All samples are constituted by polylabdane structure associated to Class Ib resins, constituted by polymers of labdanoid diterpenes. Finally, information concerning some structural changes during maturation, such as isomerization of {Delta}{sup 8(17)} and {Delta}{sup 12(13)} unsaturations, were obtained by {sup 13}C NMR analyses. The results concerning botanical affinities are in accordance with previous results obtained by gas chromatography-mass spectrometry (GC-MS). (author)

  19. New fossil bee flies (Diptera : Bombylioidea) in the Lowermost Eocene amber of the Paris Basin

    OpenAIRE

    A. Nel; Ploëg, G. de

    2004-01-01

    A new genus and two new species of bee flies are described from the Lowermost Eocene amber of the Paris basin: Paradolichomyia eocenica n. gen, n. sp. (Bombyliidae: Toxophorinae) and Proplatypygus matilei n. sp. (Mythicomyiidae). Paradolichomyia eocenica n. gen, n. sp. represents the oldest fossil record of Bombyliidae. It is closely related to the two modern genera Dolichomyia WIEDEMANN 1830 and Zaclava HULL 1973 (Toxophorinae: Systropodini). This discovery suggests that the present Gondwana...

  20. Improved side-chain torsion potentials for the Amber ff99SB protein force field

    OpenAIRE

    Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L.; Dror, Ron O.; Shaw, David E.

    2010-01-01

    Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving t...

  1. The oldest micropepline beetle from Cretaceous Burmese amber and its phylogenetic implications (Coleoptera: Staphylinidae)

    Science.gov (United States)

    Cai, Chen-Yang; Huang, Di-Ying

    2014-10-01

    The staphylinid subfamily Micropeplinae includes small strongly sclerotized beetles with truncate elytra leaving the most part of abdomen exposed. Fossil micropeplines are rare and confined to Cenozoic representatives of extant genera. Here, we describe the oldest micropepline, Protopeplus cretaceus gen. and sp. n., from the Upper Cretaceous Burmese amber. Fluorescence microscope and confocal laser scanning microscopy (CLSM) were both used to reveal diagnostic features of Micropeplinae and some primitive traits that place Protopeplus very basally within Micropeplinae.

  2. Description of an ancient social bee trapped in amber using diagnostic radioentomology

    OpenAIRE

    Greco, Mark; Welz, Patricia M; Siegrist, Mark; Ferguson, Stephen J.; Gallmann, Peter; Roubik, David W.; Engel, Michael S.

    2011-01-01

    The application of non-invasive imaging technologies using X-radiation (diagnostic radioentomology, ‘DR’) is demonstrated for the study of amber-entombed social bees. Here, we examine the external and internal morphology of an Early Miocene (Burdigalian) stingless bee (Apinae: Meliponini) from the Dominican Republic using non-destructive X-ray microtomography analysis. The study permits the accurate reconstruction of features otherwise obscured or impossible to visualize without destroying th...

  3. A new genus of alderflies (Megaloptera: Sialidae) in Upper Cretaceous Burmese amber

    OpenAIRE

    Huang, Diying; Azar, Dany; Michael S. Engel; Cai, Chenyang; Garrouste, Romain; Nel, André

    2016-01-01

    International audience A new genus and species of Mesozoic alderfly is described as Haplosialodes liui gen. et sp. nov., and from an adult male preserved in Cretaceous Burmese amber. The new genus is closely related to the genera Haplosialis Navás (Recent fauna of Madagascar), Indosialis Lestage (Recent fauna of Southeast Asia), and Eosialis Nel et al. (Eocene of France), suggesting a possible Early Cretaceous age for the clade that comprises these groups.

  4. DNA Changes in Tissues Entrapped in Plant Resins (the Precursors of Amber)

    Science.gov (United States)

    Rogers, S. O.; Langenegger, K.; Holdenrieder, O.

    There have been many reports characterizing DNA from amber, which is a fossil version of plant resin. Here we report an investigation of the effects of plant resin (from Pseudotsuga menziesii) and drying conditions on the preservation of DNA in biological tissues. We examined the degree of degradation of the DNA by agarose gel electrophoresis of extracted DNA, by polymerase chain reaction, and by DNA sequencing. The plant resin alone appeared to cause little or no damage to DNA. Tissue immersed in plant resin that dried rapidly (exposed to sunlight) contained DNA with little apparent damage. Tissue immersed in the resin that was dried slowly (in shade without sunlight) contained DNA with some degradation (3.5% nucleotide changes). The tissue that was immersed in the resin that was constantly hydrated (by immersion in water) yielded DNA that was severely damaged (50-62% nucleotide changes). Transversions outnumbered transitions in these samples by a ratio of 1.4 : 1. A piece of Baltic amber immersed in water for 5days appeared to be impervious to the water. Thus amber inclusions that initially dried rapidly have the potential to yield undamaged DNA. Those that dried slowly may contain damaged DNA and may be unsuitable for phylogenetic and other studies.

  5. The anamorphic genus Monotosporella (Ascomycota) from Eocene amber and from modern Agathis resin.

    Science.gov (United States)

    Sadowski, Eva-Maria; Beimforde, Christina; Gube, Matthias; Rikkinen, Jouko; Singh, Hukam; Seyfullah, Leyla J; Heinrichs, Jochen; Nascimbene, Paul C; Reitner, Joachim; Schmidt, Alexander R

    2012-10-01

    The anamorphic fungal genus Monotosporella (Ascomycota, Sordariomycetes) has been reco-vered from a piece of Early Eocene Indian amber, as well as from the surface of extant resin flows in New Caledonia. The fossil fungus was obtained from the Tarkeshwar Lignite Mine of Gujarat State, western India, and was part of the biota of an early tropical angiosperm rainforest. The amber inclusion represents the second fossil record of Sordariomycetes, as well as the first fossil of its particular order (either Savoryellales or Chaetosphaeriales). The fossil fungus is distinguished from extant representatives by possessing both short conidiophores and small two-septate pyriform conidia, and is described as Monotosporella doerfeltii sp. nov. Inside the amber, the anamorph is attached to its substrate, which is likely the degraded thallus of a cladoniform lichen. The extant New Caledonian species is assigned to Monotosporella setosa. It was found growing on semi-solidified resin flows of Agathis ovata (Araucariaceae), and is the first record of Monotosporella from modern resin substrates. PMID:23063189

  6. The value of advanced multiple beam equalization radiography (AMBER) and storage phosphor radiography in chest X-rays

    International Nuclear Information System (INIS)

    The study compared the quality of roentgenologic criteria in the evaluation of the heart and pulmonary vessels on chest X-rays obtained with different imaging systems. Fifty patients had four different chest radiographs, i.e. conventional chest X-rays, AMBER images, digital storage phosphor images, and digital storage radiographs that were obtained with the AMBER system. Comparison of techniques was based on 12 well-defined quality criteria of chest X-rays. Four radiologists with expertise reviewed the films according to these criteria. The AMBER technique was found to be superior to the remaining imaging modalities in visualization of the central pulmonary vessels, the descending aorta, and the left atrium. Peripheral pulmonary vessels were best appreciated with AMBER technique combined with storage phosphor technique. The same technique was superior in the assessment of all cardiovascular criteria. The superiority of this technique versus conventional chest X-rays can be explained on the basis of the linear slope of the gradation curve of AMBER and digital techniques. (orig.)

  7. A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation.

    Science.gov (United States)

    Okamoto, Takuya; Yamada, Kenta; Koyano, Yoshiyuki; Asada, Toshio; Koga, Nobuaki; Nagaoka, Masataka

    2011-04-15

    For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces. PMID:20949515

  8. Parameters for the AMBER force field for the molecular mechanics modeling of the cobalt corrinoids

    Science.gov (United States)

    Marques, H. M.; Ngoma, B.; Egan, T. J.; Brown, K. L.

    2001-04-01

    Additional parameters for the AMBER force field have been developed for the molecular mechanics modeling of the cobalt corrinoids. Parameter development was based on a statistical analysis of the reported structures of these compounds. The resulting force field reproduces bond lengths, bond angles, and torsional angles within 0.01 Å, 0.8°, and 4.0° of the mean crystallographic values, respectively. Parameters for the Co-C bond length and the Co-C-C bond angle for modeling the alkylcobalamins were developed by modeling six alkylcobalamins. The validity of the force field was tested by comparing the results obtained with known experimental features of the structures of the cobalt corrinoids as well as with the results from their modeling using a parameter set for the MM2 force field that has been previously developed and extensively tested. The AMBER force field reproduces the structures of the cobalt corrinoids as well as the MM2 force field, although it tends to underestimate the corrin fold angle, the angle between mean planes through the corrin atoms in the northern and southern half of the molecules, respectively. The force field was applied to a study of the structures of 5'-deoxy-5'-(3-isoadenosyl)cobalamin, 2',5'-dideoxy-5'-adenosylcobalamin and 2',3',5'-trideoxy-5'-adenosylcobalamin. This expansion of the standard AMBER force field provides a force field that can be used for modeling the structures of the B 12-dependent proteins, the structures of some of which are now beginning to emerge. This was verified in a preliminary modeling of the coenzyme B 12 binding site of methylmalonyl coenzyme A mutase.

  9. Eonandeva gen. nov., a new distinctive genus from Eocene Baltic amber (Diptera: Chironomidae).

    Science.gov (United States)

    Zakrzewska, Marta; Giłka, Wojciech

    2015-01-01

    A new fossil genus, Eonandeva gen. nov., with two new species: E. helva sp. nov. (type for the genus) and E. latistyla sp. nov., is described from Eocene Baltic amber (~45-40 Ma). Adult males of both new species show the wing venation pattern, shape and chaetotaxy typical for the tribe Tanytarsini. The characters defined as prior apomorphies for the new genus--the gonostylus with a subapical flattened lobe and the stout, strongly elongated superior volsella--separate Eonandeva from the closely related extant genus Nandeva Wiedenbrug, Reiss et Fittkau, 1998. PMID:26624727

  10. An asymmetry detected in the disk of Kappa CMa with the AMBER/VLTI

    OpenAIRE

    Meilland, Anthony; Millour, Florentin; Stee, Philippe; Domiciano De Souza, Armando; Petrov, Romain; Mourard, Denis; Jankov, Slobodan; Robbe-Dubois, Sylvie; Spang, Alain; Arisitidi, Eric; Antonelli, P.; Beckmann, U.; Bresson, Y.; Chelli, A.; Dugué, M.

    2006-01-01

    Aims. We study the geometry and kinematics of the circumstellar environment of the Be star Kappa CMa in the Br gamma emission line and its nearby continuum. Methods. We use the VLTI/AMBER instrument operating in the K band which provides a spatial resolution of about 6 mas with a spectral resolution of 1500 to study the kinematics within the disk and to infer its rotation law. In order to obtain more kinematical constraints we also use an high spectral resolution Pa beta line profile obtain i...

  11. An AMBER/DYANA/MOLMOL Phosphorylated Amino Acid Library Set and Incorporation into NMR Structure Calculations

    International Nuclear Information System (INIS)

    Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in libraries used by structure calculation programs such as DYANA and AMBER. However, only a few non-standard amino acid library sets are included in these programs or the molecular visualization program MOLMOL. Our laboratory is calculating the phosphorylated and non-phosphorylated states of peptides and proteins using NMR methods. To calculate chemically correct structures, we have extended the available molecular libraries for these programs to include the modified amino acids phosphoserine, phosphothreonine, and phosphotyrosine

  12. The first Mesozoic microwhip scorpion (Palpigradi): a new genus and species in mid-Cretaceous amber from Myanmar

    Science.gov (United States)

    Engel, Michael S.; Breitkreuz, Laura C. V.; Cai, Chenyang; Alvarado, Mabel; Azar, Dany; Huang, Diying

    2016-04-01

    A fossil palpigrade is described and figured from mid-Cretaceous (Cenomanian) amber from northern Myanmar. Electrokoenenia yaksha Engel and Huang, gen. n. et sp. n., is the first Mesozoic fossil of its order and the only one known as an inclusion in amber, the only other fossil being a series of individuals encased in Pliocene onyx marble and 94-97 million years younger than E. yaksha. The genus is distinguished from other members of the order but is remarkably consistent in observable morphological details when compared to extant relatives, likely reflecting a consistent microhabitat and biological preferences over the last 100 million years.

  13. Disk and wind interaction in the young stellar object MWC 297 spatially resolved with VLTI/AMBER

    OpenAIRE

    Malbet, F.; Benisty, M.; de Wit, W. J.; Kraus, S.; Meilland, A.; Millour, F.; Tatulli, E.; Berger, J.P.; Chesneau, O.; Hofmann, K.H.; Isella, A.; Natta, A.; Petrov, R.; Preibisch, T.; Stee, P.

    2007-01-01

    The young stellar object MWC 297 is an embedded B1.5Ve star exhibiting strong hydrogen emission lines and a strong near-infrared continuum excess. This object has been observed with the VLT interferometer equipped with the AMBER instrument during its first commissioning run. VLTI/AMBER is currently the only near infrared interferometer which can observe spectrally dispersed visibilities. MWC 297 has been spatially resolved in the continuum with a visibility of $0.50^{+0.08}_{-0.10}$ as well a...

  14. Effect of some parameters in the response of the Perspex 3042, Lot L amber dosemeters

    International Nuclear Information System (INIS)

    The answer of the dosimetric systems is affected by several factors, for what should know as these factors they influence in each one of the different dosimetric systems and by this way to minimize its effect in the value of the absorbed dose and to obtain exact dose values. One of the dosimetric systems more used in the high dose dosimetry like routine dosemeter for the control of the irradiation process are the Perspex dosemeters, for their speed in the obtaining the information, their easy manipulation and the precision that they present. To this dosemeters group they belong the same as the Red and Clear the Amber, which are adequate for the measurement of the radiation dose in the range of high doses. The objective of the present work is to obtain the calibration curves of the dosemeters Amber Perspex 3042, Lot L under our work conditions, like they are the irradiation temperatures and of storage and to know the influence of the rate dose in the value of the absorbed dose for different measurement wavelengths, as well as, the relationship among the one post-irradiation time and the specific absorbance value induced in function of the absorbed dose. (Author)

  15. Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber

    Science.gov (United States)

    Heinrichs, Jochen; Scheben, Armin; Bechteler, Julia; Lee, Gaik Ee; Schäfer-Verwimp, Alfons; Hedenäs, Lars; Singh, Hukam; Pócs, Tamás; Nascimbene, Paul C.; Peralta, Denilson F.; Renner, Matt; Schmidt, Alexander R.

    2016-01-01

    Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea). We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae. PMID:27244582

  16. A binary engine fuelling HD87643' s complex circumstellar environment, using AMBER/VLTI

    CERN Document Server

    Millour, Florentin; Borges-Fernandes, Marcelo; Meilland, Anthony; Mars, Gilbert; Benoist, C; Thiébaut, E; Stee, Philippe; Hofmann, K -H; Baron, Fabien; Young, John R; Bendjoya, Philippe; Carciofi, A C; De Souza, Armando Domiciano; Driebe, Thomas; Jankov, Slobodan; Kervella, Pierre; Petrov, R G; Robbe-Dubois, Sylvie; Vakili, Farrokh; Waters, L B F M; Weigelt, Gerd

    2009-01-01

    Context. The star HD 87643, exhibiting the ?B[e] phenomenon?, has one of the most extreme infrared excesses for this object class. It harbours a large amount of both hot and cold dust, and is surrounded by an extended re?ection nebula. Aims. One of our major goals was to investigate the presence of a companion in HD87643. In addition, the presence of close dusty material was tested through a combination of multi-wavelength high spatial resolution observations. Methods. We observed HD 87643 with high spatial resolution techniques, using the near-IR AMBER/VLTI interferometer with baselines ranging from 60 m to 130 m and the mid-IR MIDI/VLTI interferometer with baselines ranging from 25 m to 65 m. These observations are complemented by NACO/VLT adaptive-optics-corrected images in the K and L-bands, ESO-2.2m optical Wide-Field Imager large-scale images in the B, V and R-bands, Results. We report the direct detection of a companion to HD 87643 by means of image synthesis using the AMBER/VLTI instrument. The presen...

  17. Mesozoic Evaniidae (Insecta:Hymenoptera) in Spanish Amber:Reanalysis of the Phylogeny of the Evanioidea

    Institute of Scientific and Technical Information of China (English)

    Enrique PE(N)ALVER; Jaime ORTEGA-BLANCO; André NEL; Xavier DELCL(O)S

    2010-01-01

    One new genus and five new species of the family Evaniidae are described from the Early Cretaceous (Albian) Spanish amber of Pe(n)acerrada-Ⅰ (Province of Burgos),San Just and Arroyo de la Pascueta (both in the Province of Teruel):Cretevania alonsoi sp.nov.,C.montoyai sp.nov.,C.alcalai sp.nov.,C.rubusensis sp.nov.,and Iberoevania roblesi gen.and sp.nov.Taxonomic changes include Cretevania pristina (Zhang and Zhang,2000)comb.nov.,C.exquisita (Zhang,Rasnitsyn,Wang and Zhang,2007) comb.nov.,C.vesca (Zhang,Rasnitsyn,Wang and Zhang,2007) comb.nov.,and C.cyrtocerca (Deans,2004) comb.nov.,as a result of the reinterpretation of the genera Procretevania and Eovernevania.The new well preserved specimens of the genus Cretevania,together with the characters shown by the type specimens of the synonymized genera,give new information about their anatomical characters of taxonomical importance,and the genus Cretevania Rasnitsyn,1975 is re-diagnosed.The holotypes of the Russian species in amber have been revised.A cladistic analysis of fossil and extant groups of the superfamily Evanioidea is included.Cretevania had a wide palaeogeographic distribution,with the highest diversity known from Spain.The 13 known Cretevania species show a high interspecific variation mainly in wing characteristics,and a wide range of body and wing size.

  18. Description of Pintomyia (Pifanomyia falcaorum sp. n. (Diptera: Psychodidae: Phlebotominae, a Fossil Sand Fly from Dominican Amber

    Directory of Open Access Journals (Sweden)

    Reginaldo Peçanha Brazil

    2002-06-01

    Full Text Available A new species of sand fly, Pintomyia (Pifanomyia falcaorum is described from an amber originated from the northern mountain range of Dominican Republic. The male sand fly specimen is well preserved and most features used in Phlebotominae taxonomy are seen with remarkable clarity.

  19. Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

    DEFF Research Database (Denmark)

    Reichert, David E.; Norrby, Per-Ola; Welch, Michael J.

    2001-01-01

    In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER* force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new pa...

  20. Microbe-like inclusions in tree resins and implications for the fossil record of protists in amber.

    Science.gov (United States)

    Thiel, V; Lausmaa, J; Sjövall, P; Ragazzi, E; Seyfullah, L J; Schmidt, A R

    2016-07-01

    During the past two decades, a plethora of fossil micro-organisms have been described from various Triassic to Miocene ambers. However, in addition to entrapped microbes, ambers commonly contain microscopic inclusions that sometimes resemble amoebae, ciliates, microfungi, and unicellular algae in size and shape, but do not provide further diagnostic features thereof. For a better assessment of the actual fossil record of unicellular eukaryotes in amber, we studied equivalent inclusions in modern resin of the Araucariaceae; this conifer family comprises important amber-producers in Earth history. Using time-of-flight secondary ion mass spectrometry (ToF-SIMS), we investigated the chemical nature of the inclusion matter and the resin matrix. Whereas the matrix, as expected, showed a more hydrocarbon/aromatic-dominated composition, the inclusions contain abundant salt ions and polar organics. However, the absence of signals characteristic for cellular biomass, namely distinctive proteinaceous amino acids and lipid moieties, indicates that the inclusions do not contain microbial cellular matter but salts and hydrophilic organic substances that probably derived from the plant itself. Rather than representing protists or their remains, these microbe-like inclusions, for which we propose the term 'pseudoinclusions', consist of compounds that are immiscible with the terpenoid resin matrix and were probably secreted in small amounts together with the actual resin by the plant tissue. Consequently, reports of protists from amber that are only based on the similarity of the overall shape and size to extant taxa, but do not provide relevant features at light-microscopical and ultrastructural level, cannot be accepted as unambiguous fossil evidence for these particular groups. PMID:27027519

  1. Insights into molecular chemistry of Chiapas amber using infrared-light microscopy, PIXE/RBS, and sulfur K-edge XANES spectroscopy

    Science.gov (United States)

    Riquelme, Francisco; Northrup, Paul; Ruvalcaba-Sil, José Luis; Stojanoff, Vivian; Peter Siddons, D.; Alvarado-Ortega, Jesús

    2014-07-01

    Chiapas amber is a natural occurring fossil resin structurally composed of long macromolecule chains with semicrystalline phases associated with both fossil and polymerization process. The most conspicuous characteristic of this fossil polymer is that it preserves ancient organic inclusions. In the present work, PIXE/RBS spectrometry (particle-induced X-ray emission/Rutherford backscattering) were combined with complementary K-edge XANES spectroscopy (X-ray absorption near-edge structure) to identify the amount of sulfur in Chiapas amber. Initially, the amber samples were examined using infrared reflected photomicrography. Amber is transparent to infrared light and so embedded plants and animals are easily visible, showing them in extraordinary detail, as if they were immersed in a water-like solution. The PIXE/RBS data show that the proportion of sulfur in amber is significantly higher than that found in recently formed resins, consistent with the biogeochemical process that transforms the resin into amber during long-term burial in geological deposits. The sulfur K-edge XANES spectra from amber confirm the sulfur abundance and reveal sulfur species in the reduced and intermediate oxidation states in amber. Almost no oxidized sulfur was found, whereas the recent resins show mostly oxidized sulfur fractions. This indicates that labile oxidized sulfur decays during fossilization and resin maturation must occur under conditions of oxygen depletion. The implications of the presence of sulfur in amber for organic preservation is also discussed here. Sulfur compounds work as a polymer additive that promotes intense resin solidification. This restricts the early oxidant-specific biodegradation of the embedded biomatter and, over geological time, provides greater stability against chemical changes.

  2. Interferometric data reduction with AMBER/VLTI Principle,estimators and illustration

    CERN Document Server

    Tatulli, E

    2006-01-01

    We present in this paper an innovative data reduction method for single-mode interferometry. It has been specifically developed for the AMBER instrument, the three-beam combiner of the Very Large Telescope Interferometer, but can be derived for any single-mode interferometer. The algorithm is based on a direct modelling of the fringes in the detector plane. As such, it requires a preliminary calibration of the instrument in order to obtain the calibration matrix which builds the linear relationship between the interferogram and the interferometric observable, that is the complex visibility. Once the calibration procedure has been performed, the signal processing appears to be a classical least square determination of a linear inverse problem. From the estimated complex visibility, we derive the squared visibility, the closure phase and the spectral differential phase. The data reduction procedures are gathered into the so-called amdlib software, now available for the community, and presented in this paper. Fu...

  3. Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards.

    Science.gov (United States)

    Daza, Juan D; Stanley, Edward L; Wagner, Philipp; Bauer, Aaron M; Grimaldi, David A

    2016-03-01

    Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships. PMID:26973870

  4. Empirical corrections to the Amber RNA force field with Target Metadynamics

    CERN Document Server

    Gil-Ley, Alejandro; Bussi, Giovanni

    2016-01-01

    The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the alpha and beta backbone angles on the modulation of ...

  5. Sooty moulds from European tertiary amber, with notes on the systematic position of Rosaria ('Cyanobacteria').

    Science.gov (United States)

    Rikkinen, Jouko; Dörfelt, Heinrich; Schmidt, Alexander R; Wunderlich, Jörg

    2003-02-01

    Sooty moulds are described and illustrated from European amber dating back to 22-54 Myr. All the fossils are fragments of superficial subicula composed of brown moniliform hyphae with markedly tapering distal ends. The subglobose cells are identical to those of extant Metacapnodium (Metacapnodiaceae, Capnodiales) species. Also other preserved features, like the type of apical growth, wide-angled branching and the production of two distinctive conidial states, supports a placement in this genus. The fossils demonstrate that Metacapnodium hyphae have remained unchanged for tens of millions of years. This confirms that hyphal morphology and conidial states should be accorded considerable classificatory significance in this group of fungi. The following nomenclatural change is made: Metacapnodium succinum comb. nov. (syn. Rosaria succina). The type specimen was initially described as a filamentous cyanobacterium, due to similarities with Rosaria ramosa. Also the systematic position of this attribute is shortly discussed. PMID:12747338

  6. Modeling of Closure Phase Measurements with AMBER/VLTI - Towards Characterization of Exoplanetary Atmospheres

    CERN Document Server

    Jörgens, V; Joergens, Viki; Quirrenbach, Andreas

    2004-01-01

    Differential phase observations with a near-IR interferometer offer a way to obtain spectra of extrasolar planets. The method makes use of the wavelength dependence of the interferometer phase of the planet/star system, which depends both on the interferometer geometry and on the brightness ratio between the planet and the star. The differential phase is strongly affected by instrumental and atmospheric dispersion effects. Difficulties in calibrating these effects might prevent the application of the differential phase method to systems with a very high contrast, such as extrasolar planets. A promising alternative is the use of spectrally resolved closure phases, which are immune to many of the systematic and random errors affecting the single-baseline phases. We have modeled the response of the AMBER instrument at the VLTI to realistic models of known extrasolar planetary systems, taking into account their theoretical spectra as well as the geometry of the VLTI. We present a strategy to determine the geometr...

  7. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

    Science.gov (United States)

    Ramsey, Steven; Nguyen, Crystal; Salomon-Ferrer, Romelia; Walker, Ross C; Gilson, Michael K; Kurtzman, Tom

    2016-08-01

    The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc. PMID:27317094

  8. The Tanytarsini (Diptera: Chironomidae) in the collection of the Museum of Amber Inclusions, University of Gdańsk.

    Science.gov (United States)

    Zakrzewska, Marta; Giłka, Wojciech

    2015-01-01

    Non-biting midges of the tribe Tanytarsini collected in the Museum of Amber Inclusions, University of Gdańsk, Poland, are reviewed. Among over 1500 chironomid specimens examined (inclusions in Baltic amber), 44 Tanytarsini individuals were found, of which 27 well preserved specimens were determined to 7 species, including 3 species described as new. Stempellinella electra sp. nov. (male) displays morphological hypopygial characters unique for the genus, and the antenna composed of 13 flagellomeres. A new checklist of fossil and extant species of this genus is also given, including Stempellinella sofiae (Fusari et Lamas, 2014) comb. nov. Tanytarsus glaesarius sp. nov. (male) is the only Eocene species of the genus with a reduced number of antennal flagellomeres. Tanytarsus protogregarius sp. nov. (male) is the oldest known representative of the gregarius species group. Notes on phylogenetic relations of the new species with their extant congeners are also provided. PMID:25947696

  9. Parisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier

    OpenAIRE

    Vladimir Blagoderov; Heikki Hippa; André Nel

    2010-01-01

    Abstract A new genus and a new species of Lygistorrhinidae, Parisognoriste eocenica is described from the Eocene Oise amber of the Paris Basin. Parisognoriste sciariforme Meunier, 1904 and Parisognoriste affine Meunier, 1912 are re-described. Lectotypes are designated for both species of Palaeognoriste. The phylogenetic positions of the new genus and Palaeognoriste Meunier are discussed. The paper is an example demonstrating a new approach in cybertaxonomy including automatic generation of ma...

  10. Fundamental parameters of 16 late-type stars derived from their angular diameter measured with VLTI/AMBER

    OpenAIRE

    Cruzalèbes, P.; Jorissen, A.; Rabbia, Y.; Sacuto, S.; Chiavassa, A.; Pasquato, E.; Plez, B.; Eriksson, K; Spang, A.; Chesneau, O.

    2013-01-01

    Thanks to their large angular dimension and brightness, red giants and supergiants are privileged targets for optical long-baseline interferometers. Sixteen red giants and supergiants have been observed with the VLTI/AMBER facility over a two-years period, at medium spectral resolution (R=1500) in the K band. The limb-darkened angular diameters are derived from fits of stellar atmospheric models on the visibility and the triple product data. The angular diameters do not show any significant t...

  11. Otroacizzia soriae sp. nov., a new Miocene psyllid (Insecta, Hemiptera, Psyllidae from Dominican amber

    Directory of Open Access Journals (Sweden)

    García-Gimeno, V.

    2006-12-01

    Full Text Available new species of the fossil genus Otroacizzia Klimaszewski, 1996 (Hemiptera, Psyllidae is described as Otroacizzia soriae sp. nov. on the basis of a female specimen. This species is preserved in mid-Miocene amber from La Toca mines, Dominican Republic. The genus Otroacizzia is the most diverse psylloid genus in Dominican amber, with four known species. The new species differs from the three previously known species by the presence of a subapical dark band in the fore wing from the anterior part of the end of vein Rs to the end of vein Cu1b, which has a gap in the middle of the cell c1. Other differences in the fore wing are the presence of a strongly curved vein Cu1b and a cell c1 clearly longer than cell m1. Finally, the antennal segment 3 of the new species is one and a half times longer than segment 4.Se describe una nueva especie del género fósil Otroacizzia Klimaszewski, 1996 (Hemiptera, Psyllidae a partir de un ejemplar hembra: Otroacizzia soriae sp. nov. Esta especie está conservada en ámbar del Mioceno medio de las minas de La Toca en República Dominicana. Con cuatro especies conocidas, el género Otroacizzia es el género de psiloideo con mayor diversidad en el ámbar dominicano. La nueva especie difiere de las tres especies ya conocidas por la presencia de una banda oscura subapical en el ala anterior desde la parte anterior del final de la vena Rs hasta el final de la vena Cu1b, la cual presenta una discontinuidad en el medio de la celda c1. Otras diferencias en el ala anterior son la presencia de una vena Cu1b fuertemente curvada y una celda c1 claramente más larga que la celda m1. Finalmente, el tercer segmento antenal de la nueva especie es una vez y media más largo que el cuarto segmento.

  12. An asymmetry detected in the disk of Kappa CMa with the AMBER/VLTI

    CERN Document Server

    Meilland, A; Stee, P; De Souza, A D; Petrov, R; Mourard, D; Jankov, S; Robbe-Dubois, S; Spang, A; Arisitidi, E; Meilland, Anthony; Millour, Florentin; Stee, Philippe; Souza, Armando Domiciano De; Petrov, Romain; Mourard, Denis; Jankov, Slobodan; Robbe-Dubois, Sylvie; Spang, Alain; Arisitidi, Eric; al, et

    2006-01-01

    Aims. We study the geometry and kinematics of the circumstellar environment of the Be star Kappa CMa in the Br gamma emission line and its nearby continuum. Methods. We use the VLTI/AMBER instrument operating in the K band which provides a spatial resolution of about 6 mas with a spectral resolution of 1500 to study the kinematics within the disk and to infer its rotation law. In order to obtain more kinematical constraints we also use an high spectral resolution Pa beta line profile obtain in December 2005 at the Observatorio do Pico do Dios, Brazil and we compile V/R line profile variations and spectral energy distribution data points from the literature. Results. Using differential visibilities and differential phases across the Br gamma line we detect an asymmetry in the disk. Moreover, we found that kappa CMa seems difficult to fit within the classical scenario for Be stars, illustrated recently by alpha Arae observations, i.e. a fast rotating B star close to its breakup velocity surrounded by a Kepleria...

  13. Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM,...

  14. Afro-Asian cockroach from Chiapas amber and the lost Tertiary American entomofauna

    Science.gov (United States)

    Vršanský, Peter; Cifuentes-Ruiz, Paulina; Vidlička, Ľubomír; Čiampor, Fedor; Vega, Francisco J.

    2011-10-01

    Cockroach genera with synanthropic species (Blattella, Ectobius, Supella, Periplaneta, Diploptera and ?Blatta), as well as other insects such as honeybees, although natively limited to certain continents nowadays, had circumtropic distribution in the past. The ease of their reintroduction into their former range suggests a post-Early Miocene environmental stress which led to the extinction of cosmopolitan Tertiary entomofauna in the Americas, whilst in Eurasia, Africa and Australia this fauna survived. This phenomenon is demonstrated here on a low diversity (10 spp.) living cockroach genus Supella, which is peculiar for the circumtropical synanthropic brownbanded cockroach S. longipalpa and also for its exclusively free-living cavicolous species restricted to Africa. S. (Nemosupella) miocenica sp. nov. from the Miocene amber of Chiapas in Mexico is a sister species to the living S. mirabilis from the Lower Guinea forests and adjacent savannas. The difference is restricted to the shape of the central macula on the pronotum, and size, which may indicate the around-Miocene origin of the living, extremely polymorphic Supella species and possibly also the isochronic invasion into the Americas. The species also has a number of characteristics of the Asian (and possibly also Australian) uniform genus Allacta (falling within the generic variability of Supella) suggesting Supella is a direct ancestor of the former. The present species is the first significant evidence for incomplete hiati between well defined cockroach genera — a result of the extensive fossil record of the group. The reported specimen is covered by a mycelium of a parasitic fungus Cordyceps or Entomophthora.

  15. Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

    Science.gov (United States)

    Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

    2016-04-01

    We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

  16. VLTI/AMBER spectro-interferometric imaging of VX Sgr's inhomogenous outer atmosphere

    CERN Document Server

    Chiavassa, A; Millour, F; Driebe, T; Wittkowski, M; Plez, B; Thiebeaut, E; Josselin, E; Freytag, B; Scholz, M; Haubois, X

    2009-01-01

    Aims. We aim to explore the photosphere of the very cool late-type star VX Sgr and in particular the existence and characterization of molecular layers above the continuum forming photosphere. Methods. We obtained interferometric observations with the VLTI/AMBER interferometer using the fringe tracker FINITO in the spectral domain 1.45-2.50 micron with a spectral resolution of about 35 and baselines ranging from 15 to 88 meters.We perform independent image reconstruction for different wavelength bins and fit the interferometric data with a geometrical toy model.We also compare the data to 1D dynamical models of Miras atmosphere and to 3D hydrodynamical simulations of red supergiant (RSG) and asymptotic giant branch (AGB) stars. Results. Reconstructed images and visibilities show a strong wavelength dependence. The H-band images display two bright spots whose positions are confirmed by the geometrical toy model. The inhomogeneities are qualitatively predicted by 3D simulations. At about 2,00 micron and in the ...

  17. Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.

    Science.gov (United States)

    Smith, Micholas Dean; Rao, J Srinivasa; Segelken, Elizabeth; Cruz, Luis

    2015-12-28

    In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide. PMID:26629886

  18. Immersion mode ice nucleation measurements with the new Portable Immersion Mode Cooling chAmber (PIMCA)

    Science.gov (United States)

    Kohn, Monika; Lohmann, Ulrike; Welti, André; Kanji, Zamin A.

    2016-05-01

    The new Portable Immersion Mode Cooling chAmber (PIMCA) has been developed for online immersion freezing of single-immersed aerosol particles. PIMCA is a vertical extension of the established Portable Ice Nucleation Chamber (PINC). PIMCA immerses aerosol particles into cloud droplets before they enter PINC. Immersion freezing experiments on cloud droplets with a radius of 5-7 μm at a prescribed supercooled temperature (T) and water saturation can be conducted, while other ice nucleation mechanisms (deposition, condensation, and contact mode) are excluded. Validation experiments on reference aerosol (kaolinite, ammonium sulfate, and ammonium nitrate) showed good agreement with theory and literature. The PIMCA-PINC setup was tested in the field during the Zurich AMBient Immersion freezing Study (ZAMBIS) in spring 2014 in Zurich, Switzerland. Significant concentrations of submicron ambient aerosol triggering immersion freezing at T > 236 K were rare. The mean frozen cloud droplet number concentration was estimated to be 7.22·105 L-1 for T condensation nuclei (CCN) concentrations predicted for the site at a typical supersaturation of SS = 0.3%. This value should be considered as an upper limit of cloud droplet freezing via immersion and homogeneous freezing processes. The predicted ice nucleating particle (INP) concentration based on measured total aerosol larger than 0.5 μm and the parameterization by DeMott et al. (2010) at T = 238 K is INPD10=54 ± 39 L-1. This is a lower limit as supermicron particles were not sampled with PIMCA-PINC during ZAMBIS.

  19. Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

    DEFF Research Database (Denmark)

    Reichert, David E.; Norrby, Per-Ola; Welch, Michael J.

    2001-01-01

    In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER* force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new pa...... utilized to examine the conformational effects caused by the conjugation of InDTPA (DTPA = diethylenetriaminepentaacetic acid) and CuDOTA (DOTA 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to the cyclic octapeptide octreotide....

  20. Enhanced light output power of InGaN-based amber LEDs by strain-compensating AlN/AlGaN barriers

    Science.gov (United States)

    Iida, Daisuke; Lu, Shen; Hirahara, Sota; Niwa, Kazumasa; Kamiyama, Satoshi; Ohkawa, Kazuhiro

    2016-08-01

    We investigated the effect of a combined AlN/Al0.03Ga0.97N barrier on InGaN-based amber light-emitting diodes (LEDs) grown by metalorganic vapor-phase epitaxy. InGaN-based multiple quantum wells with a combined AlN/Al0.03Ga0.97N barrier showed intense photoluminescence with a narrow full-width at half-maximum. The amber LEDs with a combined AlN/Al0.03Ga0.97N barrier achieved a light output power enhanced approximately 2.5-fold at 20 mA compared to that of the LED with a combined AlN/GaN barrier, owing to the reduction of defects in InGaN active layers. Thus, the efficiency of high-In-content InGaN-based LEDs can be improved in the spectrum range of amber.

  1. 琥珀酸酐生产新工艺探讨%The Study of New Technology of Producing Amber Anhydride

    Institute of Scientific and Technical Information of China (English)

    吕杨

    2012-01-01

    It introduced the properties of Amber Anhydride and widely used in every field.Introducing the major technology of producing Amber Anhydride.Reviewing new tecnology of producing Amber Anhydride and comparing the major technology with new technology to explaining the superiority of new technology.%介绍了琥珀酸酐的性质及在各个领域的广泛用途,介绍了目前国内琥珀酸酐的主要生产工艺技术方案,综述了琥珀酸酐生产新技术,并对目前国内琥珀酸酐的主要生产工艺和琥珀酸酐生产新工艺进行了比较,突出了新工艺的优势。

  2. Molecular composition, chemotaxonomical aspects and botanical origin of Brazilian amber [Composição molecular, aspectos quimiotaxonômicos e origem botânica de âmbares brasileiros

    Directory of Open Access Journals (Sweden)

    Débora A. Azevedo

    2011-06-01

    Full Text Available Amber is a plant fossil resin constituted mainly by diterpenes of several classes, such as abietanes, labdanes, pimaranes and kauranes. The botanical origin of amber is related to angiosperms and gymnosperms, depending on the geological period and where it was produced. The analysis of its chemical composition performed using gas chromatography coupled to mass spectrometry and carbon 13 nuclear magnetic resonance allows the determination of the possible botanical sources, allowing obtaining important information regarding the resinous flora on the geological past of the Earth. Although amber samples are studied primarily by geochemists and paleontologists in the context of paleobotany and paleozoology, the research about its molecular composition is directly related to chemotaxonomy and phytochemistry. The results obtained to Brazilian amber samples until this moment allowed the determination of three possible amber botanical sources in Cretaceous period – Araucariaceae, Podocarpaceae e Cheirolepidiaceae.

  3. Modelling the interaction of several bisphosphonates with hydroxyapatite using the generalised AMBER force field

    Science.gov (United States)

    Robinson, Janine; Cukrowski, Ignacy; Marques, Helder M.

    2006-12-01

    The ability of the Generalised AMBER Force Field (GAFF) of Kollman and co-workers to model the structures of bisphosphonate ligands, C(R 1)(R 2)(PO 32-) 2, important compounds in the treatment of bone cancer, by molecular mechanics methods is evaluated. The structure of 50 bisphosphonates and nine bisphosphonate esters were predicted and compared to their crystal structures. Partial charges were assigned from a RHF/6-31G ∗ single point calculation at the geometry of the crystal structure. Additional parameters required for GAFF were determined using the methods of the force field's developers. The structures were found to be well replicated with virtually all bond lengths reproduced to within 0.015 Å, or within 1.2 σ of the crystallographic mean. Bond angles were reproduced to within 1.9° (0.8 σ). The observed gauche or anti conformation of the molecules was reproduced, although in several instances gauche conformations observed in the solid state energy-minimised into anti conformations, and vice versa. The interaction of MDP (R 1 = R 2 = H), HEDP (R 1 = OH, R 2 = CH 3), APD (R 1 = OH, R 2 = (CH 2) 2NH 3+), alendronate (R 1 = OH, R 2 = (CH 2) 3NH 3+) and neridronate (R 1 = OH, R 2 = (CH 2) 5NH 3+) with the (001), (010) and (100) faces of hydroxyapaptite was examined by energy-minimising 20 random orientations of each ligand 20 Å from the mineral (where there is no interaction), and then at about 8 Å from the surface whereupon the ligand relaxes onto the surface. The difference in energy between the two systems is the interaction energy. In all cases interaction with hydroxyapatite caused a decrease in energy. When modelled with a dielectric constant of 78 ɛo, non-bonded interactions dominate; electrostatic interactions become important when the dielectric constant is nature of the side chain and is similar to the magnitude of the interaction energy on the other two faces. The magnitude of the second conformation increases with the size of the Cα side

  4. Disk and wind interaction in the young stellar object MWC 297 spatially resolved with VLTI/AMBER

    CERN Document Server

    Malbet, F; De Wit, W J; Kraus, S; Meilland, A; Millour, F; Tatulli, E; Berger, J P; Chesneau, O; Hofmann, Karl Heinrich; Isella, A; Natta, A; Petrov, R; Preibisch, T; Stee, P; Testi, L; Weigelt, G; Antonelli, P; Beckmann, U; Bresson, Y; Chelli, A; Duvert, G; Gluck, L; Kern, P; Lagarde, S; Le Coarer, E; Lisi, F; Perraut, K; Robbe-Dubois, S; Roussel, A; Zins, G; Accardo, M; Acke, B; Agabi, K; Arezki, B; Aristidi, E; Baffa, C; Behrend, J; Blöcker, T; Bonhomme, S; Busoni, S; Cassaing, F; Clausse, J M; Colin, J; Connot, C; Delboulbé, A; Driebe, T; Dugué, M; Feautrier, P; Ferruzzi, D; Forveille, T; Fossat, E; Foy, R; Fraix-Burnet, D; Gallardo, A; Gennari, S; Glentzlin, A; Giani, E; Gil, C; Heiden, M; Heininger, M; Kamm, D; Le Contel, D; Le Contel, J M; López, B; Magnard, Y; Marconi, A; Mars, G; Martinot-Lagarde, G; Mathias, P; Monin, J L; Mouillet, D; Mourard, D; Mege, P; Nussbaum, E; Ohnaka, K; Pacheco, J; Pacini, F; Perrier, C; Puget, P; Rabbia, Y; Rebattu, S; Reynaud, F; Richichi, A; Sacchettini, M; Salinari, P; Schertl, D; Solscheid, W; Stefanini, P; Tallon, M; Tallon-Bosc, I; Tasso, D; Valtier, J C; Vannier, M; Ventura, N; Kiekebusch, M; Rantakyro, F; Schöller, M

    2005-01-01

    The young stellar object MWC 297 has been observed with the VLT interferometer equipped with the AMBER instrument. MWC 297 has been spatially resolved in the continuum with a visibility of 0.50 as well as in the Br gamma emission line where the visibility decrease to a lower value of 0.33. This change in the visibility with the wavelength can be interpreted by the presence of an optically thick disk responsible for the visibility in the continuum and of a stellar wind traced by Br gamma and whose apparent size is 40% larger. We validate this interpretation by building a model of the stellar environment that combines a geometrically thin, optically thick accretion disk model consisting of gas and dust, and a latitude-dependent stellar wind outflowing above the disk surface. The continuum emission and visibilities obtained from this model are fully consistent with the interferometric AMBER data. They agree also with existing optical, near-infrared spectra and other broad-band near-infrared interferometric visib...

  5. Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides

    Science.gov (United States)

    WANG, ZHI-XIANG; ZHANG, WEI; WU, CHUN; LEI, HONGXING; CIEPLAK, PIOTR; DUAN, YONG

    2014-01-01

    Based on the AMBER polarizable model (ff02), we have reoptimized the parameters related to the main-chain (Φ, Ψ) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., β, PII, αR, and αL regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the β, PII and αR regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)7-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization. PMID:16526038

  6. Description of a new species, Pintomyia dissimilis nov. sp., a phlebotomine fossil from Dominican Republic amber (Diptera: Psychodidae: Phlebotominae

    Directory of Open Access Journals (Sweden)

    Sanguinette Cristiani

    2009-05-01

    Full Text Available Abstract Background Phlebotomine sandflies are the vectors of etiological agents of leishmaniases in several areas of the world. In the Neotropical Region, the biodiversity of these insects is more than other regions, probably due the long evolutionary period of this group. Miocene amber from Dominican Republic, currently, has a record of 14 extinct species of Phlebotomine sandflies. Results This paper describes a new fossil species of phlebotomine sandfly from amber found in Dominican Republic. This new species is based on morphological characters of a male such as 5° palpomere longer than 3° + 4°, three well-developed spines in the gonostyle, lateral lobe longer than gonocoxite and permit inclusion of the new species in the genus Pintomyia, series serrana. The paramere, with a curvature in the ventral margin, of the middle of the structure, separates the new species from the others fossils or extant species. Conclusion The new species described in the present study named Pintomyia dissimilis nov. sp. is well differenciated from all known species in this genus.

  7. Synthesis of bacteriophage-coded gene products during infection of Escherichia coli with amber mutants of T3 and T7 defective in gene 1

    DEFF Research Database (Denmark)

    Issinger, O G; Hausmann, R

    1973-01-01

    During nonpermissive infection by a T7 amber mutant in gene 1 (phage RNA polymerase-deficient), synthesis of the products of the phage genes 3 (endonuclease), 3, 5 (lysozyme), 5 (DNA polymerase), and 17 (serum blocking power) was shown to occur at about half the rate as during wild-type infection...

  8. At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2015-03-06

    High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The

  9. At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields

    International Nuclear Information System (INIS)

    High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The

  10. Performance Analysis Cluster Computing Environments on Molecular Dynamic Simulation of RAD GTPase and LOXCurcumin Molecules with AMBER

    Directory of Open Access Journals (Sweden)

    Heru Suhartanto

    2012-03-01

    Full Text Available Implementation of virtual laboratory on scientific research has produced huge acceleration. One of the virtual scientific research activity is molecular dynamic simulation. The virtual experiments need high computing resources to solve the problem. AMBER is one of the software that provides molecular dynamic simulation that can utilize the parallel computing facilities. In this paper, we conduct the molecular dynamic experiments in order to know reliability of cluster computing environment. The results show that an implicit solvent simulation takes longer time than that in vacuum scenario since one has to consider existence of solvent surround the molecules so the computation is much longer than in vacuum; that the speed up will likely to remain constant on certain additional number of processors; and that there is no significant speed up for case in the LOX-Curcumin explicit solvent simulation.

  11. Internal quantum efficiency in yellow-amber light emitting AlGaN-InGaN-GaN heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Thi Huong; Gil, Bernard; Valvin, Pierre [Laboratoire Charles Coulomb – UMR 5221, CNRS and University Montpellier, Case courier 074, 34095 Montpellier Cedex 5 (France); Damilano, Benjamin; Lekhal, Kaddour; De Mierry, Philippe [CRHEA-CNRS Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, rue Bernard Gregory, 06560 Valbonne (France)

    2015-09-21

    We determine the internal quantum efficiency of strain-balanced AlGaN-InGaN-GaN hetero-structures designed for yellow-amber light emission, by using a recent model based on the kinetics of the photoluminescence decay initiated by Iwata et al. [J. Appl. Phys. 117, 075701 (2015)]. Our results indicate that low temperature internal quantum efficiencies sit in the 50% range and we measure that adding an AlGaN layer increases the internal quantum efficiency from 50% up to 57% with respect to the GaN-InGaN case. More dramatic, it almost doubles from 2.5% up to 4.3% at room temperature.

  12. Highly improved reliability of amber light emitting diode with Ca -α-SiAlON phosphor in glass formed by gas pressure sintering for automotive applications.

    Science.gov (United States)

    Yoon, Chang-Bun; Kim, Sanghyun; Choi, Sung-Woo; Yoon, Chulsoo; Ahn, Sang Hyeon; Chung, Woon Jin

    2016-04-01

    Phosphor in glass (PiG) with 40 wt% of Ca-α-SiAlON phosphor and 60 wt% of Pb-free silicate glass was synthesized and mounted on a high-power blue LED to make an amber LED for automotive applications. Gas pressure sintering was applied after the conventional sintering process was used to achieve fully dense PiG plates. Changes in photoluminescence spectra and color coordination were inspected by varying the thickness of the plates that were mounted after optical polishing and machining. A trade-off between luminous flux and color purity was observed. The commercial feasibility of amber PiG packaged LED, which can satisfy international regulations for automotive components, was successfully demonstrated by examining the practical reliability under 85% humidity at an 85°C condition. PMID:27192294

  13. A New Species Group in the Genus Tanytarsus van der Wulp(Diptera:Chironomidae)Based on a Fossil Record from Baltic Amber

    Institute of Scientific and Technical Information of China (English)

    Wojciech GI(L)KA

    2010-01-01

    A new fossil chironomid,Tanytarsus serafini,found in Baltic amber is described and illustrated based on adult males.The new species and similar extant species of the genus Tanytarsus van der Wulp are compared.Due to several distinct characters of wing,legs and hypopygium,a new species group for Tanytarsus serafini is proposed,and its diagnostic features are evaluated.

  14. Traitement du signal en interferometrie monomode dans le cadre du projet AMBER. Application a l'observation interferometrique de l'environnement > circumstellaire des etoiles jeunes

    OpenAIRE

    Tatulli, Eric

    2004-01-01

    Recent progresses of optical interferometry, in terms of spatial resolution, sensitivity and precision of the measurements, made this technique particularly well suited to study the close environment of young stars which hold the keys of stellar and planet formation. As a matter of fact, the first interferometric observations have unveiled many essential informations on the physical nature of the surrounding structure of these objects. The AMBER instrument, the near infrared three beams recom...

  15. Clumpy dust clouds and extended atmosphere of the AGB star W Hya revealed with VLT/SPHERE-ZIMPOL and VLTI/AMBER

    CERN Document Server

    Ohnaka, Keiichi; Hofmann, Karl-Heinz

    2016-01-01

    We present visible polarimetric imaging observations of the well-studied AGB star W Hya taken with VLT/SPHERE-ZIMPOL as well as high spectral resolution long-baseline interferometric observations with the AMBER instrument of the Very Large Telescope Interferometer (VLTI). We observed W Hya with VLT/SPHERE-ZIMPOL at three wavelengths in the continuum (645, 748, and 820 nm), in the Halpha line at 656.3 nm, and in the TiO band at 717 nm. The VLTI/AMBER observations were carried out in the wavelength region of the CO first overtone lines near 2.3 micron with a spectral resolution of 12000. Taking advantage of the polarimetric imaging capability of SPHERE-ZIMPOL combined with the superb adaptive optics performance, we have succeeded in spatially resolving three clumpy dust clouds located at ~50 mas (~2 Rstar) from the central star, revealing dust formation very close to the star. The AMBER data in the individual CO lines suggest a molecular outer atmosphere extending to ~3 Rstar. Furthermore, the SPHERE-ZIMPOL ima...

  16. The analysis of the kinetics of extraction of resinoids and hypericines from the amber, Hypericum perforatum L.

    Directory of Open Access Journals (Sweden)

    ANDRIJA A. SMELCEROVIC

    2002-06-01

    Full Text Available The kinetics of the extraction of the overall extracted materials (resinoids, total hypericine, hypericine and pseudohypericine from amber (Hypericum perforatum L. was investigated by the procedure of maceration both with and without ultra-sound, using methanol as the extractant. It was found that the period of fast extraction with intensification of the extraction of resinoid by ultra-sound was significantly shorter (about 20 minutes than was needed for the extraction without ultra-sound (about 5 h. Similar results were also obtained for the extraction of the other tested substances. It can be concluded that better drug exploitation can be achieved in a much shorter extraction time by intensification of the extraction using ultra-sound. By preparation of herbal material through pulverization, a significant grade of herbal tissue structure disintegration was achieved, so that turbulent mass transfer plays a dominant role in the extraction. The results show that the coefficient values of fast extraction (b are approximately the same for all the investigated kinetics.

  17. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

    Science.gov (United States)

    Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

    2014-01-14

    The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development. PMID:26579910

  18. Vetufebrus ovatus n. gen., n. sp. (Haemospororida: Plasmodiidae vectored by a streblid bat fly (Diptera: Streblidae in Dominican amber

    Directory of Open Access Journals (Sweden)

    Poinar George O

    2011-12-01

    Full Text Available Abstract Background Both sexes of bat flies in the families Nycteribiidae and Streblidae (Diptera: Hippoboscoidea reside in the hair or on the wing membranes of bats and feed on blood. Members of the Nycteribiidae transmit bat malaria globally however extant streblids have never been implemented as vectors of bat malaria. The present study shows that during the Tertiary, streblids also were vectors of bat malaria. Results A new haemospororidan, Vetufebrus ovatus, n. gen., n. sp., (Haemospororida: Plasmodiidae is described from two oocysts attached to the midgut wall and sporozoites in salivary glands and ducts of a fossil bat fly (Diptera: Streblidae in Dominican amber. The new genus is characterized by ovoid oocysts, short, stubby sporozoites with rounded ends and its occurrence in a fossil streblid. This is the first haemosporidian reported from a streblid bat fly and shows that representatives of the Hippoboscoidea were vectoring bat malaria in the New World by the mid-Tertiary. Conclusions This report is the first evidence of an extant or extinct streblid bat fly transmitting malaria. Discovering a mid-tertiary malarial parasite in a fossil streblid that closely resembles members of a malarial genus found in nycteribiid bat flies today shows how little we know about the vector associations of streblids. While no malaria parasites have been found in extant streblids, they probably occur and it is possible that streblids were the earliest lineage of flies that transmitted bat malaria to Chiroptera.

  19. Fundamental parameters of 16 late-type stars derived from their angular diameter measured with VLTI/AMBER

    CERN Document Server

    Cruzalèbes, P; Rabbia, Y; Sacuto, S; Chiavassa, A; Pasquato, E; Plez, B; Eriksson, K; Spang, A; Chesneau, O

    2013-01-01

    Thanks to their large angular dimension and brightness, red giants and supergiants are privileged targets for optical long-baseline interferometers. Sixteen red giants and supergiants have been observed with the VLTI/AMBER facility over a two-years period, at medium spectral resolution (R=1500) in the K band. The limb-darkened angular diameters are derived from fits of stellar atmospheric models on the visibility and the triple product data. The angular diameters do not show any significant temporal variation, except for one target: TX Psc, which shows a variation of 4% using visibility data. For the eight targets previously measured by Long-Baseline Interferometry (LBI) in the same spectral range, the difference between our diameters and the literature values is less than 5%, except for TX Psc, which shows a difference of 11%. For the 8 other targets, the present angular diameters are the first measured from LBI. Angular diameters are then used to determine several fundamental stellar parameters, and to loca...

  20. The Adaptive Buffered Force QM/MM method in the CP2K and AMBER software packages

    CERN Document Server

    Mones, Letif; Götz, Andreas W; Laino, Teodoro; Walker, Ross C; Leimkuhler, Ben; Csányi, Gábor; Bernstein, Noam

    2014-01-01

    The implementation and validation of the adaptive buffered force QM/MM method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the adaptive buffered-force QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reprod...

  1. Growth and Properties of Blue and Amber Complex Light Emitting InGaN/GaN Multi-Quantum Wells

    Institute of Scientific and Technical Information of China (English)

    XIE Zi-Li; HAN Ping; SHI Yi; ZHENG You-Dou; ZHANG Rong; LIU Bin; XIU Xiang-Qian; SU Hui; LI Yi; HUA Xue-Mei; ZHAO Hong; CHEN Peng

    2011-01-01

    @@ Blue-red complex light emitting InGaN/GaN multi-quantum well(MQW) structures are fabricated by metal organic chemical vapor deposition(MOCVD).The structures are grown on a 2-inch diameter(0001) oriented (c-face) sapphire substrate, which consists of an approximately 2-Etm-thick GaN template and a five-period layer consisting of a 4.9-nm-thick In0.18Ga0.82N well layer and a GaN barrier layer.The surface morphology of the MQW structures is observed by an atomic force microscope(AFM), which indicates the presence of islands of several tens of nanometers in height on the surface.The high resolution x-ray diffraction(XRD)θ/2θ scan is carried out on the symmetric(0002) of the InGaN/GaN MQW structures.At least four order satellite peaks presented in the XRD spectrum indicate that the thickness and alloy compositions of the individual quantum wells are repeatable throughout the active region.Besides the 364 nm GaN band edge emission, two main emissions of blue and amber light from these MQWs are found, which possibly originate from the carrier recombinations in the InGaN/GaN QWs and InGaN quasi-quantum dots embedded in the QWs.

  2. Properties of the CO and H$_2$O MOLsphere of the red supergiant Betelgeuse from VLTI/AMBER observations

    CERN Document Server

    Montargès, Miguel; Perrin, Guy; Ohnaka, Keiichi; Chiavassa, Andrea; Ridgway, Stephen T; Lacour, Sylvestre

    2014-01-01

    Context. Betelgeuse is the closest red supergiant (RSG), therefore it is well suited to study the complex processes in its atmosphere that lead to the chemical enrichment of the interstellar medium. Aims. We intend to investigate the shape and composition of the close molecular layer (also known as the MOLsphere) that surrounds the star. This analysis is part of a wider program that aims at understanding the dynamics of the circumstellar envelope of Betelgeuse. Methods. On January and February 2011, Betelgeuse was observed using the VLTI/AMBER interferometer in the H and K bands. Using the medium spectral resolution of the instrument ($R \\sim 1500$), we were able to investigate the carbon monoxide band heads and the water-vapor bands. We used two different approaches to analyse our data: model fitting both in the continuum and absorption lines and then fit with a RHD simulation. Results. Using the continuum data we derive a uniform disk diameter of $41.01 \\pm 0.41$ mas, a power law type limb-darkened disk dia...

  3. Fundamental properties and atmospheric structure of the red supergiant VY CMa based on VLTI/AMBER spectro-interferometry

    CERN Document Server

    Wittkowski, M; Torres, B Arroyo; Marcaide, J M

    2012-01-01

    We investigate the atmospheric structure and fundamental properties of the red supergiant VY CMa. We obtained near-infrared spectro-interferometric observations of VY CMa with spectral resolutions of 35 and 1500 using the AMBER instrument at the VLTI. The visibility data indicate the presence of molecular layers of water vapor and CO in the extended atmosphere with an asymmetric morphology. The uniform disk diameter in the water band around 2.0 mu is increased by \\sim20% compared to the near-continuum bandpass at 2.20-2.25 mu and in the CO band at 2.3-2.5 mu it is increased by up to \\sim50%. The closure phases indicate relatively small deviations from point symmetry close to the photospheric layer, and stronger deviations in the extended H2O and CO layers. Making use of the high spatial and spectral resolution, a near-continuum bandpass can be isolated from contamination by molecular and dusty layers, and the Rosseland-mean photospheric angular diameter is estimated to 11.3 +/- 0.3 mas based on a PHOENIX atmo...

  4. The use of a GIS Red-Amber-Green (RAG) system to define search priorities for burials

    Science.gov (United States)

    Somma, Roberta; Silvestro, Massimiliano; Cascio, Maria; Dawson, Lorna; Donnelly, Laurance; Harrison, Mark; McKinley, Jennifer; Ruffell, Alastair

    2016-04-01

    The aim of this research is to promote among the Italian police, magistrates, and geologists, the applications of a Geographical Information System (GIS)-based RAG system for use in ground searches for burials. To date the RAG system has not been used and documented in Italy and would potentially be useful for searches related to clandestine burial sites. This technique, was originally documented by the British Army in the 1st World War. The RAG method is based on the construction of theme maps. RAG maps can facilitate the deployment of appropriate search assets (such as geophysics, probe or search dogs) and therefore applied to ground searches for the potential location of homicide graves or other buried objects (including weapons, explosives, etc.). RAG maps also may assist in the management of resources such as the deployment of search personnel, search teams and dogs. A GIS RAG (Red-Amber-Green) system related to a search for a homicide grave was applied to a test site in Italy, simulating the concealment of a victim in the area of Alì. This is an area of hill in Sicily, characterized by Palaeozoic phyllites. It was assumed during this test that information was provided by an observer who saw a suspect carrying tools on his land during daylight hours. A desktop study of the rural area was first implemented. Data was collated from previous geological, geomorphological, hydrogeological, geophysical and land use surveys. All these data were stored and independently analysed in a GIS using ArcGIS software. For the development of the GIS-based RAG map a digital elevation model (DEM) including a digital surface model (DTS) and digital terrain model (DTM) types were used. These were integrated with data from soil surveys to provide a preliminary assessment of "diggability" - including the possible thickness of loose superficial deposits and soils. Data were stored in different layers within the GIS. These included the delineation of the search area with consideration

  5. Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Aubert Sylvie

    2009-03-01

    Full Text Available Abstract Background Presenilin proteins are part of a complex of proteins that can cleave many type I transmembrane proteins, including Notch Receptors and the Amyloid Precursor Protein, in the middle of the transmembrane domain. Dominant mutations in the human presenilin genes PS1 and PS2 lead to Familial Alzheimer's disease. Mutations in the Caenorhabditis elegans sel-12 presenilin gene cause a highly penetrant egg-laying defect due to reduction of signalling through the lin-12/Notch receptor. Mutations in six spr genes (for suppressor of presenilin are known to strongly suppress sel-12. Mutations in most strong spr genes suppress sel-12 by de-repressing the transcription of the largely functionally equivalent hop-1 presenilin gene. However, how mutations in the spr-2 gene suppress sel-12 is unknown. Results We show that spr-2 mutations increase the levels of sel-12 transcripts with Premature translation Termination Codons (PTCs in embryos and L1 larvae. mRNA transcripts from sel-12 alleles with PTCs undergo degradation by a process known as Nonsense Mediated Decay (NMD. However, spr-2 mutations do not appear to affect NMD. Mutations in the smg genes, which are required for NMD, can restore sel-12(PTC transcript levels and ameliorate the phenotype of sel-12 mutants with amber PTCs. However, the phenotypic suppression of sel-12 by smg genes is nowhere near as strong as the effect of previously characterized spr mutations including spr-2. Consistent with this, we have identified only two mutations in smg genes among the more than 100 spr mutations recovered in genetic screens. Conclusion spr-2 mutations do not suppress sel-12 by affecting NMD of sel-12(PTC transcripts and appear to have a novel mechanism of suppression. The fact that mutations in smg genes can ameliorate the phenotype of sel-12 alleles with amber PTCs suggests that some read-through of sel-12(amber alleles occurs in smg backgrounds.

  6. Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Otyepka, M.; Šponer, Jiří; Hobza, P.; Jurečka, P.

    2010-01-01

    Roč. 12, č. 35 (2010), s. 10476-10493. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA203/09/1476 Grant ostatní: GA MŠk(CZ) LC512; GA MŠk(CZ) GD203/09/H046 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : amber empirical potential * DFT-SAPT * compensation of errors Subject RIV: BO - Biophysics Impact factor: 3.454, year: 2010

  7. A New Subfamily of Aphids(Hemiptera,Aphidomorpha)from the Early Cretaceous Lebanese Amber with a Description of the Oldest Apterous Morphs

    Institute of Scientific and Technical Information of China (English)

    Piotr WEGIEREK; David A.GRIMALDI

    2010-01-01

    Aphids are marked by their high polymorphism,but species reported from the Early Cretaceous are known only from alate morphs.The discovery of an apterous adult morph in Lebanese amber and a larva of the same species are very important for the understanding of both the morphological and biological evolution of this insect group at the very early stage of development.Gondvanoaphis estephani new subfamily,new genus and species of the recent aphids family Thelaxidae is described.The characters of the new genus in respect to other genera placed in Thelaxidae are reviewed.The palaeoecologicai and palaeogeographical data concerning Gondvanoaphis new genus are also discussed.

  8. The Alberta moving beyond breast cancer (AMBER cohort study: a prospective study of physical activity and health-related fitness in breast cancer survivors

    Directory of Open Access Journals (Sweden)

    Courneya Kerry S

    2012-11-01

    Full Text Available Abstract Background Limited research has examined the association between physical activity, health-related fitness, and disease outcomes in breast cancer survivors. Here, we present the rationale and design of the Alberta Moving Beyond Breast Cancer (AMBER Study, a prospective cohort study designed specifically to examine the role of physical activity and health-related fitness in breast cancer survivorship from the time of diagnosis and for the balance of life. The AMBER Study will examine the role of physical activity and health-related fitness in facilitating treatment completion, alleviating treatment side effects, hastening recovery after treatments, improving long term quality of life, and reducing the risks of disease recurrence, other chronic diseases, and premature death. Methods/Design The AMBER Study will enroll 1500 newly diagnosed, incident, stage I-IIIc breast cancer survivors in Alberta, Canada over a 5 year period. Assessments will be made at baseline (within 90 days of surgery, 1 year, and 3 years consisting of objective and self-reported measurements of physical activity, health-related fitness, blood collection, lymphedema, patient-reported outcomes, and determinants of physical activity. A final assessment at 5 years will measure patient-reported data only. The cohort members will be followed for an additional 5 years for disease outcomes. Discussion The AMBER cohort will answer key questions related to physical activity and health-related fitness in breast cancer survivors including: (1 the independent and interactive associations of physical activity and health-related fitness with disease outcomes (e.g., recurrence, breast cancer-specific mortality, overall survival, treatment completion rates, symptoms and side effects (e.g., pain, lymphedema, fatigue, neuropathy, quality of life, and psychosocial functioning (e.g., anxiety, depression, self-esteem, happiness, (2 the determinants of physical activity and

  9. High spectral resolution imaging of the dynamical atmosphere of the red supergiant Antares in the CO first overtone lines with VLTI/AMBER

    CERN Document Server

    Ohnaka, Keiichi; Schertl, Dieter; Weigelt, Gerd; Baffa, Carlo; Chelli, Alain; Petrov, Romain; Robbe-Dubois, Sylvie

    2013-01-01

    We present high spectral resolution aperture-synthesis imaging of the red supergiant Antares (alpha Sco) in individual CO first overtone lines with VLTI/AMBER. The reconstructed images reveal that the star appears differently in the blue wing, line center, and red wing and shows an asymmetrically extended component. The appearance of the star within the CO lines changes drastically within one year, implying a significant change in the velocity field in the atmosphere. Our modeling suggests an outer atmosphere (MOLsphere) extending to 1.2--1.4 stellar radii with CO column densities of (0.5--1)x10^{20} cm^{-2} and a temperature of ~2000 K. While the velocity field in 2009 is characterized by strong upwelling motions at 20--30 km/s, it changed to strong downdrafts in 2010. On the other hand, the AMBER data in the continuum show only a slight deviation from limb-darkened disks and only marginal time variations. We derive a limb-darkened disk diameter of 37.38+/-0.06 mas and a power-law-type limb-darkening paramet...

  10. AMBER-NACO aperture-synthesis imaging of the half-obscured central star and the edge-on disk of the red giant L2 Pup

    CERN Document Server

    Ohnaka, Keiichi; Hofmann, Karl-Heinz; Weigelt, Gerd

    2015-01-01

    The red giant L2 Pup started a dimming event in 1994, which is considered to be caused by the ejection of dust clouds. We present near-IR aperture-synthesis imaging of L2 Pup achieved by combining data from VLT/NACO speckle observations and long-baseline interferometric observations with the AMBER instrument of the Very Large Telescope Interferometer (VLTI). We also extracted an 8.7 micron image from the mid-IR VLTI instrument MIDI. Our aim is to spatially resolve the innermost region of the circumstellar environment. The diffraction-limited image at 2.27 micron obtained by bispectrum speckle interferometry with NACO with a spatial resolution of 57 mas shows an elongated component. The aperture-synthesis imaging combining the NACO speckle data and AMBER data (2.2--2.29 micron) with a spatial resolution of 5.6x7.3 mas further resolves not only this elongated component, but also the central star. The reconstructed image reveals that the elongated component is a nearly edge-on disk with a size of ~180x50 mas lyi...

  11. AMBER/VLTI high spectral resolution observations of the Br$\\gamma$ emitting region in HD 98922. A compact disc wind launched from the inner disc region

    CERN Document Server

    Garatti, A Caratti o; Lopez, R Garcia; Kraus, S; Schertl, D; Grinin, V P; Weigelt, G; Hofmann, K -H; Massi, F; Lagarde, S; Vannier, M; Malbet, F

    2015-01-01

    We analyse the main physical parameters and the circumstellar environment of the young Herbig Be star HD 98922. We present AMBER/VLTI high spectral resolution (R =12000) interferometric observations across the Br$\\gamma$ line, accompanied by UVES high-resolution spectroscopy and SINFONI-AO assisted near-infrared integral field spectroscopic data. To interpret our observations, we develop a magneto-centrifugally driven disc-wind model. Our analysis of the UVES spectrum shows that HD 98922 is a young (~5x10^5 yr) Herbig Be star (SpT=B9V), located at a distance of 440(+60-50) pc, with a mass accretion rate of ~9+/-3x10^(-7) M_sun yr^(-1). SINFONI K-band AO-assisted imaging shows a spatially resolved circumstellar disc-like region (~140 AU in diameter) with asymmetric brightness distribution. Our AMBER/VLTI UT observations indicate that the Br$\\gamma$ emitting region (radius ~0.31+/-0.04 AU) is smaller than the continuum emitting region (inner dust radius ~0.7+/-0.2 AU), showing significant non-zero V-shaped diff...

  12. New genus and species of broad-nosed weevils from Baltic amber and notes on fossils of the subfamily Entiminae (Coleoptera, Curculionidae

    Directory of Open Access Journals (Sweden)

    Nikolai Yunakov

    2011-12-01

    Full Text Available Arostropsis groehni gen. et sp. n. is described from Baltic amber and temporarily placed in the tribe Naupactini. It differs from all recent Naupactini genera with open corbels by very short and flattened scape, distinct lateral carina of the pronotum and elytra, and the rostrum distinctly narrower than the head capsule. The shape of head in the extinct genus is somewhat similar to that of the extant Naupactini genera with enclosed corbels (Platyomus Sahlberg, 1823 and Aptolemus Schoenherr, 1842, but differs in the slender body, open corbels, very short antennal scape and epifrons without a median sulcus (only a longitudinal depression is slightly visible. It is also similar to the Tanymecine genus Pandeleteius Schoenherr, 1834 in general appearance, but distinct by the straight anterior edge of the pronotum, lack of postocular spurs, lobes, and vibrissae, a slightly sloping elytral declivity, lateral ridges on the pronotum, subflattened antennal scape, elongate rostrum, and sparsely setose epistome. A new synonymy of the generic names Protonaupactus Zherikhin, 1971 and Sucinophyllobius Wanat & Borowiec, 1986, syn. n., is established. The Madagascan genus Corecaulus Fairmaire, 1903 is transferred from the tribe Naupactini to the Brachyderini because of its connate claws and the similarity in chaetotaxy of the epistomal area with African and Madagascar Brachyderini genera. A key to the identification of known Baltic amber genera of Entiminae is proposed. A checklist of the prepleistocene fossil Entiminae, based on V.V. Zherikhin’s data, with remarks and corrections, is presented.

  13. Tracing jet emission at the base of a high-mass YSO. First AMBER/VLTI observations of the Br\\gamma emission in IRAS 13481-6124

    CERN Document Server

    Garatti, A Caratti o; Weigelt, G; Schertl, D; Hofmann, K -H; Kraus, S; Oudmaijer, R D; de Wit, W J; Sanna, A; Lopez, R Garcia; Kreplin, A; Ray, T P

    2016-01-01

    To probe the circumstellar environment of IRAS 13481-6124, a 20 M_sun high-mass young stellar object (HMYSO) with a parsec-scale jet and accretion disc, we investigate the origin of its Br\\gamma-emission line through NIR interferometry. We present the first AMBER/VLTI observations of the Br\\gamma-emitting region in an HMYSO at R~1500. Our AMBER/VLTI observations reveal a spatially and spectrally resolved Br\\gamma-line in emission with a strong P Cygni profile, indicating outflowing matter with a terminal velocity of ~500 km/s. Visibilities, differential phases, and closure phases are detected in our observations within the spectral line and in the adjacent continuum. Both total visibilities (continuum plus line emitting region) and pure-line visibilities indicate that the Br\\gamma-emitting region is more compact (2-4 mas in diameter or ~6-13 au at 3.2 kpc) than the continuum-emitting region (~5.4 mas or ~17 au). The absorption feature is also spatially resolved at the longest baselines (81 and 85 m) and has a...

  14. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

    Science.gov (United States)

    Debiec, Karl T; Cerutti, David S; Baker, Lewis R; Gronenborn, Angela M; Case, David A; Chong, Lillian T

    2016-08-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides-all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  15. Amber Hey!Beautiful!

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    AMBER作为组合f(x)第一个出solo专辑的成员,发行了首张个人作品《Beautiful》,这是一张完全展现她个人魅力的专辑,对她来说同样显得相当的有意义。

  16. Stable carbon isotopes of C3 plant resins and ambers record changes in atmospheric oxygen since the Triassic

    Science.gov (United States)

    Tappert, Ralf; McKellar, Ryan C.; Wolfe, Alexander P.; Tappert, Michelle C.; Ortega-Blanco, Jaime; Muehlenbachs, Karlis

    2013-11-01

    Estimating the partial pressure of atmospheric oxygen (pO2) in the geological past has been challenging because of the lack of reliable proxies. Here we develop a technique to estimate paleo-pO2 using the stable carbon isotope composition (δ13C) of plant resins-including amber, copal, and resinite-from a wide range of localities and ages (Triassic to modern). Plant resins are particularly suitable as proxies because their highly cross-linked terpenoid structures allow the preservation of pristine δ13C signatures over geological timescales. The distribution of δ13C values of modern resins (n = 126) indicates that (a) resin-producing plant families generally have a similar fractionation behavior during resin biosynthesis, and (b) the fractionation observed in resins is similar to that of bulk plant matter. Resins exhibit a natural variability in δ13C of around 8‰ (δ13C range: -31‰ to -23‰, mean: -27‰), which is caused by local environmental and ecological factors (e.g., water availability, water composition, light exposure, temperature, nutrient availability). To minimize the effects of local conditions and to determine long-term changes in the δ13C of resins, we used mean δ13C values (δ13Cmeanresin) for each geological resin deposit. Fossil resins (n = 412) are generally enriched in 13C compared to their modern counterparts, with shifts in δ13Cmeanresin of up to 6‰. These isotopic shifts follow distinctive trends through time, which are unrelated to post-depositional processes including polymerization and diagenesis. The most enriched fossil resin samples, with a δ13Cmeanresin between -22‰ and -21‰, formed during the Triassic, the mid-Cretaceous, and the early Eocene. Experimental evidence and theoretical considerations suggest that neither change in pCO2 nor in the δ13C of atmospheric CO2 can account for the observed shifts in δ13Cmeanresin. The fractionation of 13C in resin-producing plants (Δ13C), instead, is primarily influenced by

  17. A new species of Phyllopsora (Lecanorales, lichen-forming Ascomycota) from Dominican amber, with remarks on the fossil history of lichens.

    Science.gov (United States)

    Rikkinen, Jouko; Poinar, George O

    2008-01-01

    Phyllopsora dominicanus sp. nov. (Bacidiaceae, Lecanorales, lichen-forming Ascomycota) is described and illustrated from Dominican amber. The diagnostic features of the lichen include a minute subfolious thallus of lacinulate, ascending squamules, a well-developed upper cortex, and a net-like pseudocortex on the lower surface. The algal symbionts are unicellular green algae, forming a distinct layer immediately below the upper cortex. The fossil demonstrates that distinguishing features of Phyllopsora have remained unchanged for tens of millions of years. The fossil also provides the first detailed views of mycobiont-photobiont contacts in Tertiary green algal lichens. The mycobiont hyphae formed apical and intercalary appressoria by pressing closely against the photobiont cells. This indicates that a conserved maintenance of structure is also seen in the fine details of the fungal-algal interface. PMID:18319239

  18. Clumpy dust clouds and extended atmosphere of the AGB star W Hydrae revealed with VLT/SPHERE-ZIMPOL and VLTI/AMBER

    Science.gov (United States)

    Ohnaka, K.; Weigelt, G.; Hofmann, K.-H.

    2016-05-01

    Context. Dust formation is thought to play an important role in the mass loss from stars at the asymptotic giant branch (AGB); however, where and how dust forms is still open to debate. Aims: We present visible polarimetric imaging observations of the well-studied AGB star W Hya taken with VLT/SPHERE-ZIMPOL as well as high spectral resolution long-baseline interferometric observations taken with the AMBER instrument at the Very Large Telescope Interferometer (VLTI). Our goal is to spatially resolve the dust and molecule formation region within a few stellar radii. Methods: We observed W Hya with VLT/SPHERE-ZIMPOL at three wavelengths in the continuum (645, 748, and 820 nm), in the Hα line at 656.3 nm, and in the TiO band at 717 nm. The VLTI/AMBER observations were carried out in the wavelength region of the CO first overtone lines near 2.3 μm with a spectral resolution of 12000. Results: Taking advantage of the polarimetric imaging capability of SPHERE-ZIMPOL combined with the superb adaptive optics performance, we succeeded in spatially resolving three clumpy dust clouds located at ~50 mas (~2 R⋆) from the central star, revealing dust formation very close to the star. The AMBER data in the individual CO lines suggest a molecular outer atmosphere extending to ~3 R⋆. Furthermore, the SPHERE-ZIMPOL image taken over the Hα line shows emission with a radius of up to ~160 mas (~7 R⋆). We found that dust, molecular gas, and Hα-emitting hot gas coexist within 2-3 R⋆. Our modeling suggests that the observed polarized intensity maps can reasonably be explained by large (0.4-0.5 μm) grains of Al2O3, Mg2SiO4, or MgSiO3 in an optically thin shell (τ550nm = 0.1 ± 0.02) with an inner and outer boundary radius of 1.9-2.0 R⋆ and 3 ± 0.5R⋆, respectively. The observed clumpy structure can be reproduced by a density enhancement of a factor of 4 ± 1. Conclusions: The grain size derived from our modeling of the SPHERE-ZIMPOL polarimetric images is consistent with

  19. Strain-compensated (Ga,In)N/(Al,Ga)N/GaN multiple quantum wells for improved yellow/amber light emission

    Energy Technology Data Exchange (ETDEWEB)

    Lekhal, K.; Damilano, B., E-mail: bd@crhea.cnrs.fr; De Mierry, P.; Vennéguès, P. [CRHEA-CNRS, Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, Valbonne 06560 (France); Ngo, H. T.; Rosales, D.; Gil, B. [Laboratoire Charles Coulomb, CNRS-INP-UMR 5221, Université Montpellier 2, F-34095 Montpellier (France); Hussain, S. [CRHEA-CNRS, Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, Valbonne 06560 (France); Université de Nice Sophia Antipolis, Parc Valrose, 28 av. Valrose, 06108 Nice cedex 2 (France)

    2015-04-06

    Yellow/amber (570–600 nm) emitting In{sub x}Ga{sub 1−x}N/Al{sub y}Ga{sub 1−y}N/GaN multiple quantum wells (QWs) have been grown by metal organic chemical vapor deposition on GaN-on- sapphire templates. When the (Al,Ga)N thickness of the barrier increases, the room temperature photoluminescence is red-shifted while its yield increases. This is attributed to an increase of the QW internal electric field and an improvement of the material quality due to the compensation of the compressive strain of the In{sub x}Ga{sub 1−x}N QWs by the Al{sub y}Ga{sub 1−y}N layers, respectively.

  20. Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors.

    Science.gov (United States)

    Su, Pin-Chih; Johnson, Michael E

    2016-04-01

    Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc. PMID:26666582

  1. The nature and fate of natural resins in the geosphere. XII. Investigation of C-ring aromatic diterpenoids in Raritan amber by pyrolysis-GC-matrix isolation FTIR-MS

    Directory of Open Access Journals (Sweden)

    Anderson Ken B

    2006-03-01

    Full Text Available Abstract Upper Cretaceous amber from the Raritan Formation (Sayerville, New Jersey has been investigated by Pyrolysis-GC-MS and Pyrolysis-GC-matrix isolation FTIR-MS. Results establish the existence of two distinct forms of amber in this deposit. Both forms are Class Ib ambers, but they are unambiguously differentiated on the basis of their (intact diterpenoid composition. The presence of callitrisate in both forms, and cupraene in samples designated form 1, strongly suggest that both derive from related-but-distinct species within the Cupressaceae. In addition to callitrisate, dehydroabietate and analogous 17-nor-, 16,17-dinor- and 15,16,17-trinor- analogues of these compounds are also observed. The distributions of these products in multiple samples suggest that they are the result of biological emplacement, rather than diagenetic modification of the parent compounds. This indicates that the distributions of diterpenes observed in these samples are representative of the original bioterpenoids and, hence, are useful for chemotaxonomic analyses.

  2. (11-22) semipolar InGaN emitters from green to amber on overgrown GaN on micro-rod templates

    International Nuclear Information System (INIS)

    We demonstrate semipolar InGaN single-quantum-well light emitting diodes (LEDs) in the green, yellow-green, yellow and amber spectral region. The LEDs are grown on our overgrown semipolar (11-22) GaN on micro-rod array templates, which are fabricated on (11-22) GaN grown on m-plane sapphire. Electroluminescence measurements on the (11-22) green LED show a reduced blue-shift in the emission wavelength with increasing driving current, compared to a reference commercial c-plane LED. The blue-shifts for the yellow-green and yellow LEDs are also significantly reduced. All these suggest an effective suppression in quantum confined Stark effect in our (11-22) LEDs. On-wafer measurements yield a linear increase in the light output with the current, and external quantum efficiency demonstrates a significant improvement in the efficiency-droop compared to a commercial c-plane LED. Electro-luminescence polarization measurements show a polarization ratio of about 25% in our semipolar LEDs

  3. Amber Light (590 nm) Induces the Breakdown of Lipid Droplets through Autophagy-Related Lysosomal Degradation in Differentiated Adipocytes.

    Science.gov (United States)

    Choi, Min Sik; Kim, Hyoung-June; Ham, Mira; Choi, Dong-Hwa; Lee, Tae Ryong; Shin, Dong Wook

    2016-01-01

    Lipolysis in the adipocytes provides free fatty acids for other tissues in response to the energy demand. With the rapid increase in obesity-related diseases, finding novel stimuli or mechanisms that regulate lipid metabolism becomes important. We examined the effects of visible light (410, 457, 505, 530, 590, and 660 nm) irradiation on lipolysis regulation in adipocytes differentiated from human adipose-derived stem cells (ADSCs). Interestingly, 590 nm (amber) light irradiation significantly reduced the concentration of lipid droplets (LDs). We further investigated the lipolytic signaling pathways that are involved in 590 nm light irradiation-induced breakdown of LDs. Immunoblot analysis revealed that 590 nm light irradiation-induced phosphorylation of hormone-sensitive lipase (HSL) was insufficient to promote reduction of LDs. We observed that 590 nm light irradiation decreased the expression of perilipin 1. We found that 590 nm light irradiation, but not 505 nm, induced conversion of LC3 I to LC3 II, a representative autophagic marker. We further demonstrated that the lysosomal inhibitors leupeptin/NH4Cl inhibited 590 nm light irradiation-induced reduction of LDs in differentiated adipocytes. Our data suggest that 590 nm light irradiation-induced LD breakdown is partially mediated by autophagy-related lysosomal degradation, and can be applied in clinical settings to reduce obesity. PMID:27346059

  4. (11-22) semipolar InGaN emitters from green to amber on overgrown GaN on micro-rod templates

    Energy Technology Data Exchange (ETDEWEB)

    Bai, J., E-mail: j.bai@sheffield.ac.uk; Xu, B.; Guzman, F. G.; Xing, K.; Gong, Y.; Hou, Y.; Wang, T., E-mail: t.wang@sheffield.ac.uk [Department of Electronic and Electrical Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD (United Kingdom)

    2015-12-28

    We demonstrate semipolar InGaN single-quantum-well light emitting diodes (LEDs) in the green, yellow-green, yellow and amber spectral region. The LEDs are grown on our overgrown semipolar (11-22) GaN on micro-rod array templates, which are fabricated on (11-22) GaN grown on m-plane sapphire. Electroluminescence measurements on the (11-22) green LED show a reduced blue-shift in the emission wavelength with increasing driving current, compared to a reference commercial c-plane LED. The blue-shifts for the yellow-green and yellow LEDs are also significantly reduced. All these suggest an effective suppression in quantum confined Stark effect in our (11-22) LEDs. On-wafer measurements yield a linear increase in the light output with the current, and external quantum efficiency demonstrates a significant improvement in the efficiency-droop compared to a commercial c-plane LED. Electro-luminescence polarization measurements show a polarization ratio of about 25% in our semipolar LEDs.

  5. The influence of dose rate, irradiation temperature and post-irradiation storage conditions on the radiation response of Harwell Amber 3042 PMMA dosimeters

    International Nuclear Information System (INIS)

    The response of routine dosimeters is not independent of radiation dose rate, and environmental conditions such as humidity and temperature. In Harwell Amber 3042 dosimeters these influences are minimised by careful conditioning, and the use of special packaging material to maintain humidity. This paper describes studies carried out on the influences of irradiation dose rate and temperature, on two batches of dosimeters. Firstly, this paper gives gamma irradiation response data for dose rates of 6.1, 1.3 and 0.5 Gy·s-1 with irradiation temperatures of 20, 30, 40 and 50 deg. C. Dosimeters were irradiated, to doses of 3, 5, 7, 10 and 15 kGy. Secondly, this paper considers irradiation plus post irradiation storage temperatures, at a fixed dose rate of 1.5 Gy·s-1. Dosimeters were irradiated, to doses of 10 and 20 kGy; at temperatures of 30, 40 and 50 deg. C. The dosimeters were stored at these temperatures for 1, 24 and 48 hours before measurement. Results at both of the recommended measurement wavelengths, 603 nm and 651 nm, are presented. The choice of wavelength is discussed, in order to aid the optimum choice for the conditions prevailing. (author)

  6. Effect of some parameters in the response of the Perspex 3042, Lot L amber dosemeters; Efectos de algunos parametros en la respuesta de los dosimetros ambar Perspex 3042, Lote L

    Energy Technology Data Exchange (ETDEWEB)

    Prieto M, E.F.; Barrera G, G. [Centro de Aplicaciones Tecnologicas y Desarrollo Nuclear (CEADEN). Calle 30, No. 502, esq. 5ta. Avenida, Playa, Ciudad de La Habana (Cuba)]. e-mail: efprieto@ceaden.edu.cu

    2004-07-01

    The answer of the dosimetric systems is affected by several factors, for what should know as these factors they influence in each one of the different dosimetric systems and by this way to minimize its effect in the value of the absorbed dose and to obtain exact dose values. One of the dosimetric systems more used in the high dose dosimetry like routine dosemeter for the control of the irradiation process are the Perspex dosemeters, for their speed in the obtaining the information, their easy manipulation and the precision that they present. To this dosemeters group they belong the same as the Red and Clear the Amber, which are adequate for the measurement of the radiation dose in the range of high doses. The objective of the present work is to obtain the calibration curves of the dosemeters Amber Perspex 3042, Lot L under our work conditions, like they are the irradiation temperatures and of storage and to know the influence of the rate dose in the value of the absorbed dose for different measurement wavelengths, as well as, the relationship among the one post-irradiation time and the specific absorbance value induced in function of the absorbed dose. (Author)

  7. The close environment of high-mass X-ray binaries at high angular resolution I. VLTI/AMBER and VLTI/PIONIER near-infrared interferometric observations of Vela X-1

    CERN Document Server

    Choquet, E; Bouquin, J -B Le; Merand, A; Berger, J -P; Haubois, X; Perrin, G; Petrucci, P -O; Lazareff, B; Pott, J -U

    2013-01-01

    Recent improvements on the sensitivity and spectral resolution of X-ray observations have led to a better understanding of the properties of matter in the vicinity of High Mass X-ray Binaries hosting a supergiant star and a compact object. However the geometry and physical properties of their environment at larger scales are currently only predicted by simulations. We aim at exploring the environment of Vela X-1 at a few stellar radii of the supergiant using spatially resolved observations in the near-infrared and at studying its dynamical evolution along the 9-day orbital period of the system. We observed Vela X-1 in 2010 and 2012 using long baseline interferometry at VLTI, respectively with the AMBER instrument in the K band and the PIONIER instrument in the H band. The PIONIER observations span through one orbital period to monitor possible evolutions in the geometry of the system. We resolved a structure of $8\\pm3~R_\\star$ from the AMBER data and $2.0\\,_{-1.2}^{+0.7}~R_\\star$ from the PIONIER data. From t...

  8. When Green and Amber Meet

    Institute of Scientific and Technical Information of China (English)

    Francisco; Little

    2013-01-01

    Through the ages Scotch whisky has been the drink of kings, politicians, entertainers and those who aspire to the finer things in life.It’s traditionally drunk with a splash of water,straight up or with the debonair "on the rocks" by-line.

  9. Las dos versiones de la De Psalterii Anglicani exemplari animaduersio de Benito Arias Montano en la Biblia Políglota de Amberes

    Directory of Open Access Journals (Sweden)

    Dávila Pérez, Antonio

    2014-06-01

    Full Text Available In the eighth and final volume of the Antwerp Polyglot Arias Montano published a short text titled De Psalterii Anglicani Exemplari Animaduersio. In his defense of the Hebrew original of the Old Testament, Montano set out to warn the reader that some of the more esteemed manuscripts by the so-called Hebrew-haters of his time were of little value. For this purpose, Arias Montano examined a Hebrew manuscript of the Psalter considered to be of particular antiquity and significance by the powerful bishop Wilhelm D. Lindanus, and concluded that it was in fact recent and quite worthless in many aspects, thereby fiercely attacking the latter’s scholarly reputation. This attack, based in part on a false accusation, was the beginning of a scholarly controversy lasting over fifteen years. The present essay calls attention to the fact that two versions of the Animaduersio, very different from each other, can be found in surviving copies of the Polyglot Bible. In order to illuminate the circumstances that led to these versions, the author proposes a threefold goal: (1 to gather the Latin text and the Spanish translation of the two versions of the Animaduersio; (2 to examine the reasons why Arias Montano rewrote his text in the light of the private correspondence of both scholars; (3 and to propose an approximate date for each of the versions.En el octavo y último volumen de la Biblia Regia de Amberes Benito Arias Montano publicaba un breve texto titulado De Psalterii Anglicani exemplari animaduersio. En el marco de su defensa del original hebreo del Antiguo Testamento, su autor consideraba necesario advertir al lector de que algunos de los manuscritos más apreciados por los llamados «misohebreos» de su tiempo carecían de todo valor. Para ello, Arias Montano examinó un manuscrito hebreo del salterio elogiado como muy antiguo y relevante por el poderoso obispo Guillermo D. Lindano, y concluía que el códice era reciente y de escaso valor, cargando de

  10. Deoxyhexanucleotide containing a vinyl chloride induced DNA lesion, 1,N6-ethenoadenine: synthesis, physical characterization, and incorporation into a duplex bacteriophage M13 genome as part of an amber codon

    International Nuclear Information System (INIS)

    Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N6-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d[GCT(epsilon A)GC] was chemically synthesized by the phosphotriester method. Physical studies involving fluorescence, circular dichroism , and 1H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed in the genome of an M13mp19 insertion mutant. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer [5'-32P]d-[GCT(epsilon A)GC], after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli

  11. Sylvie Germaın’in gecelerin kitabı ve amber- gece adlı yapıtlarında büyülü gerçekçilik

    OpenAIRE

    YILDIRIM, Ceylan

    2011-01-01

    ÖZET Çalışmamız, Germain’in Gecelerin Kitabı ve Amber-Gece adlı yapıtlarının Büyülü Gerçekçi anlatım tarzına göre incelenmesi ve yazarın her iki yapıtında kullanılan Büyülü Gerçekçi öğelerin örneklerle açıklanmasını kapsar. Germain’in söz konusu iki yapıtında hangi Büyülü Gerçekçi anlatım tekniklerini kullandığı, bu tarzın anlatım tekniklerini kullanırken hangi unsurlardan ya da kişilerden esinlenmiş olabileceği gösterilmeye çalışılmıştır. Germain’in iki yapıtının Büyülü Gerçek...

  12. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification.

    Directory of Open Access Journals (Sweden)

    James A J Arpino

    Full Text Available Expanded genetic code approaches are a powerful means to add new and useful chemistry to proteins at defined residues positions. One such use is the introduction of non-biological reactive chemical handles for site-specific biocompatible orthogonal conjugation of proteins. Due to our currently limited information on the impact of non-canonical amino acids (nAAs on the protein structure-function relationship, rational protein engineering is a "hit and miss" approach to selecting suitable sites. Furthermore, dogma suggests surface exposed native residues should be the primary focus for introducing new conjugation chemistry. Here we describe a directed evolution approach to introduce and select for in-frame codon replacement to facilitate engineering proteins with nAAs. To demonstrate the approach, the commonly reprogrammed amber stop codon (TAG was randomly introduced in-frame in two different proteins: the bionanotechnologically important cyt b(562 and therapeutic protein KGF. The target protein is linked at the gene level to sfGFP via a TEV protease site. In absence of a nAA, an in-frame TAG will terminate translation resulting in a non-fluorescent cell phenotype. In the presence of a nAA, TAG will encode for nAA incorporation so instilling a green fluorescence phenotype on E. coli. The presence of endogenously expressed TEV proteases separates in vivo target protein from its fusion to sfGFP if expressed as a soluble fusion product. Using this approach, we incorporated an azide reactive handle and identified residue positions amenable to conjugation with a fluorescence dye via strain-promoted azide-alkyne cycloaddition (SPAAC. Interestingly, best positions for efficient conjugation via SPAAC were residues whose native side chain were buried through analysis of their determined 3D structures and thus may not have been chosen through rational protein engineering. Molecular modeling suggests these buried native residues could become partially

  13. Retractación o pertinacia. Vicisitudes de un tratado parcialmente perdido de Arias Montano al hilo de la polémica en torno a la Biblia Políglota de Amberes

    Directory of Open Access Journals (Sweden)

    Dávila Pérez, Antonio

    2011-12-01

    Full Text Available The aim of this article is to bring to light the origin, chronology and possible contents of a treatise by Arias Montano, partially lost until today. That treatise was the culmination of the long and fierce controversy that Arias Montano and Wilhem van der Lindt were involved in the last quarter of the 16th Century in the context of the polemics between supporters and detractors of the Hebrew original text of the Bible. Yet the main cause of this scientific enmity was a defamatory writing against Lindano published by Arias Montano in the Polyglot Bible of Antwerp. Taking as a starting point Arias Montano’s and Lindano’s Latin correspondence we will try to reconstruct a non-well-known story of complaints and retractions between two theologians whose ultimate goal is to preserve their own fame.

    El objetivo de este artículo es dar a conocer el origen, cronología y posibles contenidos de un tratado de Arias Montano parcialmente perdido hasta el día de hoy. Dicho tratado fue el colofón de la larga controversia que Arias Montano y Guillermo Lindano mantuvieron en el último cuarto del siglo XVI en el marco de la polémica entre defensores y detractores del original hebreo de la Biblia. Pero la causa principal de esta enemistad científica es un escrito difamatorio contra Lindano publicado por Arias Montano en la Biblia Políglota de Amberes. Tomando como punto de partida el epistolario latino de Arias Montano y Lindano se reconstruye aquí una historia no bien conocida de denuncias y retractaciones entre dos teólogos cuyo fin último es velar por su propia fama.

  14. Multichannel imaging with the AMBER FMCW SAR

    NARCIS (Netherlands)

    Otten, M.P.G.; Rossum, W.L. van; Graaf, M.W. van der; Vlothuizen, W.J.; Tan, R.G.

    2014-01-01

    An X-band Digital Array Synthetic Aperture Radar for a Short Range Tactical UAV is presented. The Frequency Modulated Continuous Wave radar principle in combination with digital beam forming over 24 receive channels is used to achieve low power and advanced imaging SAR capabilities on small platform

  15. High resolution radiography of ambers with pixel detectors

    Czech Academy of Sciences Publication Activity Database

    Dammer, J.; Weyda, F.; Beneš, J.; Sopko, V.; Jandejsek, I.; Pflegerová, Jitka

    2013-01-01

    Roč. 8, č. 3 (2013), C03024. ISSN 1748-0221. [Conference: International Workshop on Radiation Imaging Detector s /14./. Figueira da Foz, 01.07.2012-05.07.2012] Grant ostatní: GA ČR(CZ) GA103/09/2101; GA Mšk(CZ) LA08032 Institutional support: RVO:60077344 Keywords : X-ray detector s * Inspection with x-rays * X-ray radiography and digital radiography (DR) Subject RIV: EA - Cell Biology Impact factor: 1.526, year: 2013 http://iopscience.iop.org/1748-0221/8/03/C03024/

  16. The early evolution of feathers: fossil evidence from Cretaceous amber of France

    OpenAIRE

    Perrichot, Vincent; Marion, Loïc; Néraudeau, Didier; Vullo, Romain; Tafforeau, Paul

    2008-01-01

    The developmental stages of feathers are of major importance in the evolution of body covering and the origin of avian flight. Until now, there were significant gaps in knowledge of early morphologies in theoretical stages of feathers as well as in palaeontological material. Here we report fossil evidence of an intermediate and critical stage in the incremental evolution of feathers which has been predicted by developmental theories but hitherto undocumented by evidence from both the recent a...

  17. Latridius Usovae, a new Species of the Minute Brown Scavenger Beetles (Coleoptera, Latridiidae from Rovno Amber

    Directory of Open Access Journals (Sweden)

    Sergi T. A.

    2014-08-01

    Full Text Available Из позднеэоценового ровенского янтаря описан Latridius usovae Sergi et Perkovsky, sp. n. Новый вид отличается от Latridius alexeevi Bukejs, Kirejtshuk et Rucker, 2011 и L. jantaricus Borowiec, 1985 из балтийского янтаря формой переднеспинки, надкрыльев, средних и задних голеней.

  18. Toponyms and Ethnonyms in the Names of Rovno Amber Animals and Plants

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2015-10-01

    Full Text Available Из 49 названий таксонов родового ранга, описанных из ровенского янтаря, с украинскими топонимами связано 10 (20,4 %. Так или иначе с украинскими топонимами и этнонимами связаны названия 15,7 % из 217 описанных из ровенского янтаря видов животных и 67 % из 6 описанных видов растений. На сегодняшний день лишь 8 из 217 видов, описанных из ровенского янтаря, известны из балтийского янтаря. Соотношение украинских и балтийских топонимов в названиях ровенских представителей того или иного семейства прямо связано как со степенью изученности семейства в соответствующих фаунах и флорах, так и с тем, насколько семейство связано с экосистемой самого янтарного леса. Муравей Formica paleopolonica Dlussky впервые указан для ровенского янтаря.

  19. soLenoid and time projectioN chAmber for neutron lifetime measurement -- LINA

    CERN Document Server

    Otono, Hidetoshi

    2016-01-01

    Among measurements of the neutron lifetime, there is a 1% difference between proton-counting methods and neutron-counting methods. In this paper, a new electron-counting method with a magnetic field aiming for a 0.1% accuracy is proposed, which would have a possibility to probe the discrepancy.

  20. VLTI/AMBER Studies of the Atmospheric Structure and Fundamental Parameters of Red Giant and Supergiant Stars

    Science.gov (United States)

    Arroyo-Torres, B.; Wittkowski, M.; Marcaide, J. M.; Abellan, F. J.; Chiavassa, A.; Fabregat, J.; Freytag, B.; Guirado, J. C.; Hauschildt, P. H.; Marti-Vidal, I.; Quirrenbach, A.; Scholz, M.; Wood, P. R.

    2015-08-01

    We present recent near-IR interferometric studies of red giant and supergiant stars, which are aimed at obtaining information on the structure of the atmospheric layers and constraining the fundamental parameters of these objects. The observed visibilities of six red supergiants (RSGs), and also of one of the five red giants observed, indicate large extensions of the molecular layers, as previously observed for Mira stars. These extensions are not predicted by hydrostatic PHOENIX model atmospheres, hydrodynamical (RHD) simulations of stellar convection, or self-excited pulsation models. All these models based on parameters of RSGs lead to atmospheric structures that are too compact compared to our observations. We discuss how alternative processes might explain the atmospheric extensions for these objects. As the continuum appears to be largely free of contamination by molecular layers, we can estimate reliable Rosseland angular radii for our stars. Together with distances and bolometric fluxes, we estimate the effective temperatures and luminosities of our targets, locate them in the HR diagram, and compare their positions to recent evolutionary tracks.

  1. On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Berka, K.; Jurečka, P.; Hobza, P.

    2010-01-01

    Roč. 11, č. 11 (2010), s. 2399-2408. ISSN 1439-4235 R&D Projects: GA MŠk LC512; GA ČR GA203/06/1727 Institutional research plan: CEZ:AV0Z40550506 Keywords : dispersion energy * SAPT * noncovalent complex Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.339, year: 2010

  2. VLTI/AMBER differential interferometry of the broad-line region of the quasar 3C273

    CERN Document Server

    Petrov, Romain G; Lagarde, Stéphane; Vannier, Martin; Rakshit, Suvendu; Marconi, Alessandro; Weigelt, Gerd

    2014-01-01

    Unveiling the structure of the Broad Line Region (BLR) of AGNs is critical to understand the quasar phenomenon. Resolving a few BLRs by optical interferometry will bring decisive information to confront, complement and calibrate the reverberation mapping technique, basis of the mass-luminosity relation in quasars. BLRs are much smaller than the angular resolution of the VLT and Keck interferometers and they can be resolved only by differential interferometry very accurate measurements of differential visibility and phase as a function of wavelength. The latter yields the photocenter variation with wavelength, and constrains the size, position and velocity law of various regions of the BLR. AGNs are below the magnitude limit for spectrally resolved interferometry set by currently available fringe trackers. A new "blind" observation method and a data processing based on the accumulation of 2D Fourier power and cross spectra permitted us to obtain the first spectrally resolved interferometric observation of a BL...

  3. VLTI/AMBER differential interferometry of the broad-line region of the quasar 3C273

    OpenAIRE

    Petrov, Romain G.; Millour, Florentin; Lagarde, Stéphane; Vannier, Martin; Rakshit, Suvendu; Marconi, Alessandro; Weigelt, Gerd

    2014-01-01

    Unveiling the structure of the Broad Line Region (BLR) of AGNs is critical to understand the quasar phenomenon. Resolving a few BLRs by optical interferometry will bring decisive information to confront, complement and calibrate the reverberation mapping technique, basis of the mass-luminosity relation in quasars. BLRs are much smaller than the angular resolution of the VLT and Keck interferometers and they can be resolved only by differential interferometry very accurate measurements of diff...

  4. VLTI/AMBER differential interferometry of the broad-line region of the quasar 3C273

    Science.gov (United States)

    Petrov, Romain G.; Millour, Florentin; Lagarde, Stéphane; Vannier, Martin; Rakshit, Suvendu; Marconi, Alessandro; weigelt, Gerd

    2012-07-01

    Unveiling the structure of the Broad Line Region (BLR) of AGNs is critical to understand the quasar phenomenon. Resolving a few BLRs by optical interferometry will bring decisive information to confront, complement and calibrate the reverberation mapping technique, seed of the mass-luminosity relation in quasars. BLRs are much smaller than the angular resolution of the VLT and Keck interferometers and they can be resolved only by differential interferometry very accurate measurements of differential visibility and phase. The latest yields the photocenter variation with λ, and constrains the size, position and velocity law of various regions of the BLR. AGNs are below the magnitude limit for spectrally resolved interferometry set by currently available fringe trackers. A new “blind” observation method and a data processing based on the accumulation of 2D Fourier power and cross spectra permitted us the first spectrally resolved interferometric observation of a BLR, on the K=10 quasar 3C273. A careful bias analysis is still in progress, but we report strong evidence that, as the baseline increases, the differential visibility decreases in the Paα line. Combined with a differential phase certainly smaller than 3°, this yields an angular radius of the BLR larger than 0.4 milliarcseconds, or 1000 light days at the distance of 3C273, much larger than the reverberation mapping radius of 300 light days. Explaining the coexistence of these two different scales, and possibly structures and mechanisms, implies very new insights about the BLR of 3C273.

  5. A case-control analysis of smoking and breast cancer in African American women: findings from the AMBER Consortium.

    Science.gov (United States)

    Park, Song-Yi; Palmer, Julie R; Rosenberg, Lynn; Haiman, Christopher A; Bandera, Elisa V; Bethea, Traci N; Troester, Melissa A; Viscidi, Emma; Kolonel, Laurence N; Olshan, Andrew F; Ambrosone, Christine B

    2016-06-01

    Recent population studies suggest a role of smoking in the etiology of breast cancer, but few have been conducted among African American women. In a collaborative project of four large studies, we examined associations between smoking measures and breast cancer risk by menopause and hormone receptor status [estrogen receptor-positive (ER+), ER-negative (ER-) and triple-negative (ER-, PR-, HER2-)]. The study included 5791 African American women with breast cancer and 17376 African American controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in multivariable logistic regression analysis with adjustment for study and risk factors. Results differed by menopausal status. Among postmenopausal women, positive associations were observed for long duration and greater pack-years of smoking: relative to never smoking, fully adjusted ORs were 1.14 (95% CI: 1.03-1.26) for duration ≥20 years and 1.16 (95% CI: 1.01-1.33) for ≥20 pack-years. By contrast, inverse associations were observed among premenopausal women, with ORs of 0.80 (95% CI: 0.68-95) for current smoking and 0.81 (95% CI: 0.69-0.96) for former smoking, without trends by duration. Associations among postmenopausal women were somewhat stronger for ER+ breast cancer. The findings suggest that the relation of cigarette smoking to breast cancer risk in African American women may vary by menopausal status and breast cancer subtype. PMID:27207658

  6. Improved Parameterization of Amine-Carboxyate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

    CERN Document Server

    Yoo, Jejoong

    2015-01-01

    Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which have been developed and validated using relatively short simulations of small molecules---become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge--charge interactions. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine--carboxylate and amine--phosphate interactions, which brings MD simulations of basic peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better agreement with experiment. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing additional artifacts.

  7. Recent applications of a QM/MM scheme at the CASPT2//CASSCF/AMBER (or CHARMM) level of theory in photochemistry and photobiology

    Science.gov (United States)

    Sinicropi, A.; Basosi, R.; Olivucci, M.

    2008-02-01

    The excited-state properties of chemically different chromophores embedded in diverse protein environments or in solution can be nowadays correctly evaluated by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) computational strategy based on multiconfigurational perturbation theory and complete-active-space-self-consistent-field geometry optimization. In particular, in this article we show how a QM/MM strategy has been recently developed in our laboratory and has been successfully applied to the investigation of the fluorescence of the green fluorescent protein (GFP) and how the same strategy (embedding the chromophores in methanol solution) has been combined with retrosynthetic analysis to design a prototype light-driven Z/E molecular switch featuring a single reactive double bond and the same electronic structure and photoisomerization mechanism of the chromophore of the visual pigment Rhodopsin.

  8. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    Energy Technology Data Exchange (ETDEWEB)

    MacElrevey, Celeste; Wedekind, Joseph E., E-mail: joseph-wedekind@urmc.rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States)

    2005-12-01

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.

  9. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    International Nuclear Information System (INIS)

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P41212 or P43212. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported

  10. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Šponer, Jiří; Otyepka, M.; Cheatham III, T. E.; Galindo-Murillo, R.; Jurečka, P.

    2015-01-01

    Roč. 11, č. 12 (2015), s. 5723-5736. ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : MOLECULAR- DYNAMICS SIMULATIONS * NUCLEIC-ACID STRUCTURES * QUANTUM -CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  11. 78 FR 5870 - Community Development Financial Institutions Fund: Proposed Collection; Comment Request

    Science.gov (United States)

    2013-01-28

    ... consideration. ADDRESSES: Direct all comments to Amber Kuchar, Associate Program ] Manager, at the Community... information should be directed to Amber Kuchar, Associate Program Manager, at the Community Development... Community Development Financial Institutions Fund: Proposed Collection; Comment Request ACTION: Notice...

  12. Kaks miljardit jaotub Balti riikides paljude sektorite vahel / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2004-01-01

    Soome investeerimisfondi Danske Capital Finland loodud investeerimisfond Amber Trust II investeerib Balti riikidesse 2 miljardit krooni. Diagramm: Amber Trust S.C.A. fondi osalused Balti riikide ettevõtetes. Lisa: Turg täis, aga fonde tuleb juurde

  13. Salva pistab rinda hiiglastega / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2006-01-01

    Peamiselt eestlastele kuuluv Salva Kindlustus on turul edukas olnud. Diagrammid: Aktsionärid; Majandusnäitajad. Kommenteerib Peeter Teder. Vt. samas: Amber Trust: Salva Kindlustus on meile korralikult dividende maksnud. Diagramm: Fondi Amber Trust investeeringud

  14. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří

    2015-01-01

    Roč. 119, č. 49 (2015), s. 15176-15190. ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.302, year: 2014

  15. Irving Independent School District, Petitioner v. Henri Tatro, et Ux., Individually and as Next Friend of Amber Tatro, a Minor. On Writ of Certiorari to the United States Court of Appeals for the Fifth Circiut. No. 83-558.

    Science.gov (United States)

    Supreme Court of the U. S., Washington, DC.

    A Supreme Court ruling is presented regarding the provision of clean intermittent catheterization as part of related services mandated under P.L. 94-142, the Education for All Handicapped Children Act. The case argued focused on the needs of a young girl with spina bifida for intermittent catheterization to remove urine from her bladder. The court…

  16. Teledokumentalistika hiilgusest ja viletsusest / Maria Ulfsak

    Index Scriptorium Estoniae

    Ulfsak, Maria, 1981-

    2004-01-01

    Leedu teleprogrammide ja -filmide festivalil "Amber arch" ("Merevaigust arkaad") võitis peapreemia Priit Valkna dokumentaalfilm "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja. Ka teistest festivali filmidest

  17. The Dependence of Amyloid‐β Dynamics on Protein Force Fields and Water Models

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2015-01-01

    We studied the dynamics of Aβ40, involved in Alzheimer's disease, by using 21 methods combined from Amber03, Amber99sb‐ILDN, Charmm27, Charmm22*, OPLS‐2001, OPLS‐2006, OPLS‐2008, Gromos96‐43a1, Gromos96‐53a6, Gromos96‐54a7, and the water models SPC, TIP3P, TIP4P. Major differences in the structural...... ensembles were systematized: Amber03, Charmm27, and Gromos96‐54a7 stabilize the helices; Gromos96‐43a1 and Gromos53a6 favor the β‐strands (with Charmm22* and Amber99sb‐ILDN in between), and OPLS produces unstructured ensembles. The accuracy of the NMR chemical shifts was in the order: Charmm22*>Amber99sb...... circular dichroism data, providing a model for the real Aβ monomer ensemble. Also, the polar water model TIP3P significantly favored helix and compact conformations....

  18. Expression of the cloned uvr B gene of Escherichia coli: dependency on nonsense suppressors

    International Nuclear Information System (INIS)

    Recombinant plasmid pNP5, consisting of plasmid pMB9 on which the uvrB gene is cloned, fully complements for the defects due to chromosomal uvrB mutations in the presence of the amber suppressor sup-6 or supF. Correndonuclease II activity was also completely restored in UvrB strains containing both plasmid pNP5 and amber suppressor sup-6, as compared with the parental UvrB+ strain. It is shown that the amber mutation which interferes with the expression of the cloned uvrB gene is located outside this gene. Apparently, the amber mutation exerts a polar effect on uvrB expression that is relieved by sup-6 or supF. Introduction of a rho mutation into suppressor-free UvrB strains, harboring pNP5, did not relieve the polarity caused by the amber mutation

  19. Evaluating molecular mechanical potentials for helical peptides and proteins.

    Directory of Open Access Journals (Sweden)

    Erik J Thompson

    Full Text Available Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A(21 and F(s helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i predicts an unexpected decrease in helicity with ALA-->ARG(+ substitution, (ii lacks experimentally observed 3(10 helical content, and (iii deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99phi force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.

  20. Nonsense Mutations in the Maltose A Region of the Genetic Map of Escherichia coli

    Science.gov (United States)

    Hatfield, Dolph; Hofnung, Maurice; Schwartz, Maxime

    1969-01-01

    The isolation of one amber mutation in malQ, one ochre mutation in malP, and seven amber mutations in malT is reported. A study of their phenotypic expressions in the presence of the amber suppressor suIII and the ochre suppressor suc suggests that (i) malQ is the structural gene for amylomaltase; (ii) malQ and the structural gene for maltodextrin phosphorylase, malP, belong to the same operon; (iii) the malT product, which promotes the expression of the malP-malQ operon, is a protein synthesized in limiting amounts by the wild-type strain. PMID:4902812

  1. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda.

    OpenAIRE

    Phadnis, S H; Huang, H V; Berg, D E

    1989-01-01

    We constructed a derivative of transposon Tn5 called Tn5supF for insertion mutagenesis and sequencing DNAs cloned in phage lambda. This element carries a supF amber-suppressor tRNA gene. Its insertion into lambda can be selected by plaque formation by using nonsuppressing (sup0) Escherichia coli for amber mutant lambda phage and sup0 dnaB-amber E. coli for nonamber lambda phage. Tn5supF is just 264 base pairs long. It transposes efficiently and inserts quasi-randomly into DNA targets. The uni...

  2. The shelf life of dyed polymethylmethacrylate dosimeters

    International Nuclear Information System (INIS)

    The long-term stability of the radiation response of Harwell Red 4034 and Amber 3042 Perspex Dosimeters has been monitored for more than 15 years, and the resulting data used in the justification of their shelf-life specifications

  3. Vaja on professionaalseid oskusi! / Tiina Lokk ; interv. Maria Ulfsak

    Index Scriptorium Estoniae

    Lokk, Tiina, 1955-

    2004-01-01

    Eesti poolt Leedu teleprogrammide ja -filmide festivalil "Amber arch" žüriis osalenud T. Lokk nähtud filmidest ja peapreemia võitnud Priit Valkna dokumentaalfilmist "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja

  4. Palaeontology: The Point of No Return in the Fossil Record of Eusociality.

    Science.gov (United States)

    Rust, Jes; Wappler, Torsten

    2016-02-22

    The evolution of eusociality is one of the major transitions in the history of life, particularly in the insects. Now, fossil termites and ants from Burmese amber offer insights into early stages of eusociality in the Lower Cretaceous. PMID:26906485

  5. Energetics of infinite homopolypeptide chains: a new look at commonly used force fields.

    Science.gov (United States)

    Penev, Evgeni; Ireta, Joel; Shea, Joan-Emma

    2008-06-01

    We present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors. We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (pi, alpha, and 3(10)). PMID:18476737

  6. Recreation and Quality of Life

    Science.gov (United States)

    ... inbox. Sign up You can help find a cure for glaucoma Give now Recreation & Quality of Life ... wear sunglasses. Gray-colored lenses provide the most natural colors, while lenses tinted amber may boost your ...

  7. 33 CFR 334.590 - Atlantic Ocean off Cape Canaveral, Fla.; Air Force missile testing area, Patrick Air Force Base...

    Science.gov (United States)

    2010-07-01

    .... These signals will be in the form of a large red ball and a red flashing high intensity beacon. One... of the danger zone. An amber rotating beacon and warning sign will be erected on the north side...

  8. Chemical signatures of fossilized resins and recent plant exudates.

    Science.gov (United States)

    Lambert, Joseph B; Santiago-Blay, Jorge A; Anderson, Ken B

    2008-01-01

    Amber is one of the few gemstones based on an organic structure. Found over most of the world, it is the fossil form of sticky plant exudates called resins. Investigation of amber by modern analytical techniques provides structural information and insight into the identity of the ancient plants that produced the source resin. Mass spectrometric analysis of materials separated by gas chromatography has identified specific compounds that are the basis of a reliable classification of the different types of amber. NMR spectroscopy of bulk, solid amber provides a complementary classification. NMR spectroscopy also can be used to characterize modern resins as well as other types of plant exudates such as gums, gum resins, and kinos, which strongly resemble resins in appearance but have very different molecular constitutions. PMID:18925589

  9. Propriétés du miel produit par Tetragonisca angustula fiebrigi et Plebeia wittmanni en Argentine

    OpenAIRE

    Sgariglia, Melina Araceli; Vattuone, Marta Amelia; Sampietro Vattuone, María Marta; Soberón, José Rodolfo; Sampietro, Diego Alejandro

    2010-01-01

    The composition of honey samples of Plebeia wittmanni (n = 10) and Tetragonisca angustula fiebrigi (n = 12) was analysed. The colours of all collected honeys were amber to dark amber and the pH varied. Moisture was lower than reported for other stingless bee honeys. Conductivity and ash content of P. wittmanni honey were higher than for T. angustula fiebrigi. Acidity of P. wittmanni honey was the highest ever mentioned for all other Plebeia species. Total sugars and sucrose were higher in T. ...

  10. Diterpenoid Biopolymers: New Directions for Renewable Materials Engineering

    OpenAIRE

    Hillwig, Matthew L.; Mann, Francis M.; Peters, Reuben J.

    2010-01-01

    Most types of ambers are naturally occurring, relatively hard, durable resinite polymers derived from the exudates of trees. This resource has been coveted for thousands of years due to its numerous useful properties in industrial processes, beauty, and purported medicinal properties. Labdane diterpenoid based ambers represent the most abundant and important resinites on earth. These resinites are a dwindling, non-renewable natural resource, so a new source of such materials needs to be estab...

  11. Yellow light dilemma zone researches: a review

    OpenAIRE

    Yaping Zhang; Chuanyun Fu; Liwei Hu

    2014-01-01

    The yellow light dilemma zone is widely known as an area on the high-speed intersection approach, where vehicles neither safely stop before the stop line nor proceed through the intersection during amber interval. Within such an area, a vehicle might be involved in a right-angle crash or rear-end collision. This issue has been extensively discussed over five decades in traffic engineering field, covering from theory to practice. However, few comprehensive review literatures on the amber signa...

  12. Observations et modélisations spectro-interférométriques longue base des étoiles et de leur environnement proche

    OpenAIRE

    Hadjara, Macinissa

    2015-01-01

    This thesis presents the results of rapidly rotating stars observations conducted on the AMBER spectro-interferometer VLTI in its high average spectral modes and resolutions. The measurements are estimated on three simultaneous visibility bases, differential phases depending on the wavelength and closure phases, with good coverage of the (u, v) plane for some nights. The data used are from several observation campaigns. These were highly degraded by the optical defects of AMBER, and assigned ...

  13. Changes in Driver Behavior Resulting from Pedestrian Countdown Signals

    OpenAIRE

    Huey, S. Brian; Ragland, David

    2007-01-01

    This paper explores the effects that pedestrian countdown signals have on driver behavior. Observations of two intersections, one with pedestrian signals and one without, were made focusing specifically on driver behavior during the amber and red phases. It was found that drivers at the pedestrian countdown intersection were less likely to enter the intersection at the end of the amber phase than those at the traditional pedestrian signal intersection. It was also found that drivers at the in...

  14. The nature and fate of natural resins in the geosphere VI. Analysis of fossil resins from Axel Heiberg Island Canadian Arctic

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, K.B. [Argonne National Lab., IL (United States)]|[Amoco Oil Co., Naperville, IL (United States); LePage, B.A. [Univ. of Alberta, Edmonton (Canada). Dept. of Biological Sciences

    1995-06-01

    Ambers are well known and abundant in terrestrial sediments all over the world; however, due largely to the absence of definite morphological characteristics, the precise botanical origin of most amber samples, are at best, often a matter of speculation. This has severely restricted the usefulness of amber in paleobotanical and paleoecological interpretations. The molecular composition and structural characteristics of fossil resins however, may preserve evidence of their botanical origin, which could be of great value in both geochemical, paleobotanical, and paleoenvironmental studies. The remains of a number of exceptionally well-preserved Taxodiaceae-dominated swamp-forest communities have been identified in the sediments of the middle Eocene (45 million years old) Buchanan Lake Formation of Axel Heiberg Island, Canadian Arctic Archipelago. The amber collected from these ancient in situ forests provides a unique opportunity to characterize these resins chemically and taxonomically. Resinite associated with Metasequoia, Pinus and Pseudolarix has been characterized using Pyrolysis-Gas Chromatography-Mass Spectrometry. This method provides a direct analysis of the molecular structure and composition of the resin. In several cases, both bled resin and cone-resin samples have been characterized. The results of these analyses are presented and discussed. The implications of these results for the botanical origins of other ambers represented in the fossil record (including succinite) will also be discussed.

  15. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

    Science.gov (United States)

    Duan, Li L.; Feng, Guo Q.; Zhang, Qing G.

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  16. Combining ability analysis for yield and its components in popcorn (Zea mays var. everta Sturt.

    Directory of Open Access Journals (Sweden)

    Vijayabharathi A

    2009-12-01

    Full Text Available A line x tester set was obtained by crossing 8 lines with 3 testers in popcorn. The resultant 24 derived F1s were evaluatedalong with 11 parents to estimate general and specific combining ability variances and effects for 14 characters. The resultsshowed predominant role of non-additive gene action for all the characters studied. Based on both per se and gca, thegenotypes UPC 5, UPC 4, UPC 1 among lines and Amber popcorn, Bangalore popcorn among the testers were proved asgood general combiners for yield and quality traits. High per se, significant sca, standard heterosis exhibited by three hybridsviz., UPC 9 x Amber popcorn, UPC 8 x Amber popcorn and UPC 1 x UPC 6 could be used for exploitation of heterosis foryield and quality characters.

  17. Structure and shaping processes within the extended atmospheres of AGB stars

    CERN Document Server

    Wittkowski, M; Karovicova, I; Ohnaka, K; Ruiz-Velasco, A E; Scholz, M; Zijlstra, A

    2011-01-01

    We present recent studies using the near-infrared instrument AMBER of the VLT Interferometer (VLTI) to investigate the structure and shaping processes within the extended atmosphere of AGB stars. Spectrally resolved near-infrared AMBER observations of the Mira variable S Ori have revealed wavelength-dependent apparent angular sizes. These data were successfully compared to dynamic model atmospheres, which predict wavelength-dependent radii because of geometrically extended molecular layers. Most recently, AMBER closure phase measurements of several AGB stars have also revealed wavelength-dependent deviations from 0/180 deg., indicating deviations from point symmetry. The variation of closure phase with wavelength indicates a complex non-spherical stratification of the extended atmosphere, and may reveal whether observed asymmetries are located near the photosphere or in the outer molecular layers. Concurrent observations of SiO masers located within the extended molecular layers provide us with additional inf...

  18. B[e] stars at the highest angular resolution: the case of HD87643

    CERN Document Server

    Millour, Florentin; Borges-Fernandes, Marcelo; Meilland, Anthony

    2009-01-01

    New results on the B[e] star HD87643 are presented here. They were obtained with a wide range of di?erent instruments, from wide-?eld imaging with the WFI camera, high resolution spectroscopy with the FEROS instrument, high angular resolution imaging with the adaptive optics camera NACO, to the highest angular resolution available with AMBER on the VLTI. We report the detection of a companion to HD87643 with AMBER, subsequently con?rmed in the NACO data. Implications of that discovery to some of the previously di?cult-to-understand data-sets are then presented.

  19. Sub-Area. 2.5 Demonstration of Promising Energy Storage Technologies Project Type. Flywheel Energy Storage Demonstration Revision: V1.0

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2015-12-30

    In this program, Amber Kinetics designed, built, and tested a sub-­scale 5 kWh engineering prototype flywheel system. Applying lessons learned from the engineering prototype, Amber Kinetics then designed, built and tested full-­size, commercial-­scale 25 kWh flywheel systems. The systems underwent basic functional qualification testing before being installed, sequentially, at the company’s outdoor test site in Alameda, CA for full-­speed field-testing. The primary considerations in testing the prototype units were to demonstrate the functionality of the system, verify the frequencies of resonant modes, and quantify spinning losses and motor/generator efficiency.

  20. Pop-Up Store

    OpenAIRE

    Castiñeira Fernández, Agustín

    2016-01-01

    El presente proyecto muestra el proceso de diseño y conceptualización de una tienda “Pop-Up” que será la re-localización temporal para distintos comercios. Los negocios presentes en la calle Meir (Amberes) tendrán que renovar sus edificios para que la ciudad de Amberes sea zona de cero emisiones de CO2 en 2050. Por esta razón el proyecto explora las posibilidades de ofrecer un espacio que sea flexible y móvil, y que pueda adaptarse a distintos tipos de comercios dependiendo de sus necesidades...

  1. Neutral and ionized gas around the post-Red Supergiant IRC+10420 at au size scales

    CERN Document Server

    Oudmaijer, Rene

    2012-01-01

    IRC +10420 is one of the few known massive stars in rapid transition from the Red Supergiant phase to the Wolf-Rayet or Luminous Blue Variable phase. The star has an ionised wind and using the Br gamma hydrogen recombination emission we assess the mass-loss on spatial scales of order 1 au. We present new VLT Interferometer AMBER data which are combined with all other AMBER data in the literature. The final dataset covers a position angle range of 180 degrees and baselines up to 110 meters. The spectrally dispersed visibilities, differential phases and line flux are conjointly analyzed and modelled. We also present AMBER/FINITO observations which cover a larger wavelength range and allow us to observe the Na I doublet at 2.2 micron. The data are complemented by X-Shooter data, which provide a higher spectral resolution view. The Brackett gamma line and the Na I doublet are both spatially resolved. After correcting the AMBER data for the fact that the lines are not spectrally resolved, we find that Br gamma tra...

  2. 32 CFR 707.7 - Submarine identification light.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false Submarine identification light. 707.7 Section... RULES WITH RESPECT TO ADDITIONAL STATION AND SIGNAL LIGHTS § 707.7 Submarine identification light. Submarines may display, as a distinctive means of identification, an intermittent flashing amber beacon...

  3. Råmaterialer, forarbejder, spild

    DEFF Research Database (Denmark)

    Roesdahl, Else; Dobat, Andres S.; Pedersen, Unn;

    2014-01-01

    Finds from Aggersborg: raw iron, off-cuts and a ?bar, hammer-scale, slag, rough-outs of arrow-heads and leister-prongs, lead waste, copper-alloy raw material and waste, gold and amber waste, raw material, rough-outs and waste of bone, antler and horn, soapstone, pigment?...

  4. Building Knowledge by Design.

    OpenAIRE

    Foqué, Richard

    2012-01-01

    Ponencia inaugural de las IV Jornadas Internacionales sobre Investigación en Arquitectura y Urbanismo, a cargo de Richard Foqué, profesor emérito de la Henry van de Velde Higher Institute of Architecture, Universidad de Amberes, Bélgica.

  5. New ways to boost molecular dynamics simulations

    NARCIS (Netherlands)

    Krieger, E.; Vriend, G.

    2015-01-01

    We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 A cutoff, correct

  6. Development and evaluation of dosimeters from locally available perspex for high dose measurement in industrial radiation processing. Final report for the period December 1985 - December 1989

    International Nuclear Information System (INIS)

    The objective of the study was to find, develop and evaluate suitable low cost perspex materials to be used as routine dosemeters for high dose measurements, particularly in industrial radiation processing. Red, amber and white perspex materials of local origin were investigated for their dosimetric properties and evaluated against Harwell red perspex, Fricke and ethanol-monochlorobenzene dosemeters. 5 refs, 13 figs, 5 tabs

  7. Geochemistry of anomalous uranium enrichment in fossil resin

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Machovič, Vladimír; Mizera, Jiří; Sýkorová, Ivana; Dvořák, Z.

    Leoben : Montanauniversität Leoben, 2015. s. 49. [Geoanalysis 2015. 09.08.2015-14.08.2015, Leoben] R&D Projects: GA ČR(CZ) GA13-18482S Institutional support: RVO:67985891 Keywords : fossil resin * amber * uranium Subject RIV: DD - Geochemistry http://2015.geoanalysis.info/documents/abstract_volume_geoanalysis2015.pdf

  8. Polymeric, Metallic, and Other Glasses in Introductory Chemistry

    Science.gov (United States)

    Hawkes, Stephen J.

    2008-01-01

    Non-ceramic glasses are not adequately discussed in introductory chemistry. Such glasses include polycarbonate, which many corrective lenses are made of, amber, enamel, gelatin, hard candy, coal, refrigerated glycerol, and metallic glasses that have been marketed in recent decades. What is usually discussed in elementary texts is siliceous glass,…

  9. A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

    Czech Academy of Sciences Publication Activity Database

    Ohnmacht, S.A.; Marchetti, C.; Gunaratnam, M.; Besser, R.J.; Haider, S.M.; Di Vita, G.; Lowe, H.L.; Mellinas-Gomez, M.; Diocou, S.; Robson, M.; Šponer, Jiří

    2015-01-01

    Roč. 5, JUN 2015 (2015). ISSN 2045-2322 R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : NAPHTHALENE DIIMIDE LIGANDS * AMBER FORCE-FIELD * DNA G-QUADRUPLEX Subject RIV: BO - Biophysics Impact factor: 5.578, year: 2014

  10. Integrating Zooarchaeology and Paleoethnobotany: A Consideration of Issues, Methods, and Cases

    OpenAIRE

    Butler, Virginia L.

    2010-01-01

    Review of Integrating Zooarchaeology and Paleoethnobotany: A Consideration of Issues, Methods, and Cases. Amber M. VanDerwarker and Tanya M. Peres, eds. 2010. Springer, New York. Pp. 317, 13 color illustrations, 13 black-and-white illustrations. $129.00 (hardback). ISBN 9781441909343.

  11. Poliitik: vajame Lähis-Ida gaasi / Jerzy Buzek ; intervjueerinud Jan Jõgis-Laats

    Index Scriptorium Estoniae

    Buzek, Jerzy, 1940-

    2009-01-01

    Poola endise peaministri sõnul on vaja energiaühendust Poola ja Leedu vahel, arutada tuleks projekte, nagu Baltimaade ja Poola kaudu Euroopasse suunduv gaasitorustik Amber, samuti lõunapoolseid gaasiühendusi. Poola peab läbirääkimisi veeldatud gaasi saamiseks ning hakkab seejärel rajama sadamat

  12. Kak estonski oboroten litovskuju korovu ukral / Jevgenia Garanzha

    Index Scriptorium Estoniae

    Garanža, Jevgenija, 1979-

    2004-01-01

    Leedu teleprogrammide ja -filmide festivalil "Amber arch" ("Merevaigust arkaad") võitis peapreemia Priit Valkna dokumentaalfilm "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja. Osales ka Vahur Laiapea telesari setudest "Veere pääl". Ulatuslik ülevaade festivalist

  13. 21 CFR 184.1685 - Rennet (animal-derived) and chymosin preparation (fermentation-derived).

    Science.gov (United States)

    2010-04-01

    ... (fermentation-derived). 184.1685 Section 184.1685 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... (animal-derived) and chymosin preparation (fermentation-derived). (a)(1) Rennet and bovine rennet are... clear amber to dark brown liquid preparations or white to tan powders. (2) Chymosin preparation is...

  14. Orchestrating the Biosynthesis of an Unnatural Pyrrolysine Amino Acid for Its Direct Incorporation into Proteins Inside Living Cells

    Czech Academy of Sciences Publication Activity Database

    Ehrlich, M.; Gattner, M. J.; Viverge, B.; Bretzler, J.; Eisen, D.; Stadlmeier, M.; Vrábel, Milan; Carell, T.

    2015-01-01

    Roč. 21, č. 21 (2015), s. 7701-7704. ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : amber suppression * bioorganic chemistry * pyrrolysine * synthetic biology * unnatural amino acid Subject RIV: CC - Organic Chemistry Impact factor: 5.731, year: 2014

  15. 78 FR 38319 - Pesticide Maintenance Fee: Notice of Receipt of Requests to Voluntarily Cancel Certain Pesticide...

    Science.gov (United States)

    2013-06-26

    ...--Registrations With Pending Requests for Cancellation EPA company Registration No. No. Product name Chemical name 000100-00701 100 Amber Herbicide Triasulfuron. 000100-00800 100 Ridomil Gold Bravo......... D-Alanine, N.... Herbicide. CA040018 66222 Galigan 2E Oxyfluorfen Oxyfluorfen. Herbicide. CA040019 100 Subdue Maxx...

  16. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří; Banáš, P.; Jurečka, P.; Zgarbová, M.; Kührová, P.; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, M.

    2014-01-01

    Roč. 5, č. 10 (2014), s. 1771-1782. ISSN 1948-7185 R&D Projects: GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : DELTA-VIRUS RIBOZYME * AMBER FORCE-FIELD * REPLICA-EXCHANGE METHOD Subject RIV: BO - Biophysics Impact factor: 7.458, year: 2014

  17. INFRARED INTERFEROMETRY OF MASSIVE YOUNG STELLAR OBJECTS

    Directory of Open Access Journals (Sweden)

    W. J. de Wit

    2010-01-01

    Full Text Available Se discuten la interferometría de AMBER y MIDI, además de observaciones de disco-simple en Subaru de objetos estelares masivos jóvenes. Las observaciones muestran tamaños de escalas lineales entre 10 y 100UA como distancia promedio de nuestras fuentes.

  18. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  19. Organic geochemistry of fossil resins from the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Sýkorová, Ivana; Mach, K.; Dvořák, Z.

    2014-01-01

    Roč. 10, August (2014), s. 303-312. ISSN 1878-5220. [Geochemistry of the Earth's Surface (GES) Meeting /10./. Paris, 18.08.2014-23.08.2014] R&D Projects: GA ČR(CZ) GA13-18482S Institutional support: RVO:67985891 Keywords : fossil resin * amber * resinite * TMAH-Py-GC/MS Subject RIV: DD - Geochemistry

  20. Escherichia coli and Salmonella typhimurium supX genes specify deoxyribonucleic acid topoisomerase I.

    OpenAIRE

    Trucksis, M; Golub, E. I.; Zabel, D J; Depew, R E

    1981-01-01

    Mutations of the Escherichia coli or Salmonella typhimurium supX genes eliminated deoxyribonucleic acid topoisomerase I. Suppression of a supX amber mutation partially restored the topoisomerase. Multicopy plasmids carrying supX+ caused overproduction of topoisomerase. Thus, these supX genes were identified as topA genes which specify deoxyribonucleic acid topoisomerase I.

  1. The Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection

    Science.gov (United States)

    Potato leafroll virus (PLRV) produces a readthrough protein (RTP) via translational readthrough of the coat protein amber stop codon. The RTP functions as a structural component of the virion and as a non-incorporated protein in concert with numerous insect and plant proteins to regulate virus movem...

  2. A nonsense mutation in the tyrosinase gene of Afghan patients with tyrosinase negative (type IA) oculocutaneous albinism.

    OpenAIRE

    Giebel, L.B.; Musarella, M A; Spritz, R.A.

    1991-01-01

    We detected a nonsense mutation in the tyrosinase gene of two Afghan sibs with classical tyrosinase negative (type IA) oculocutaneous albinism. The mutation, a single base substitution at codon 178, creates an amber termination codon that truncates the 529 amino acid tyrosinase polypeptide at this position. The patients' parents are first cousins, and the patients are therefore homoallelic for this mutation.

  3. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper

    Science.gov (United States)

    Heli, B.; Morales-Narváez, E.; Golmohammadi, H.; Ajji, A.; Merkoçi, A.

    2016-04-01

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and

  4. New chest imaging techniques: a comparison of five analogue and digital methods

    International Nuclear Information System (INIS)

    In recent years new analogue and digital techniques have become available for chest imaging. This study compares conventional film/screen, asymmetric film/screen (InSight), equalization (Amber), storage phosphor and digital image intensifier techniques by phantom exposures and patient examinations. The quality of chest images of 43 patients was classified by seven observers in four different hospitals. According to the results of phantom measurements and a previous study, digital image intensifier radiography was excluded from the patient examinations because of its low image quality. The Amber system had the best image quality. Images of the storage phosphor system were of good quality in both mediastinal and peripheral fields of the chest. Compared to conventional film/screen, the asymmetric film/screen (InSight) was graded higher in the mediastinal field, but lower in the peripheral field. (orig.)

  5. Yellow light dilemma zone researches: a review

    Directory of Open Access Journals (Sweden)

    Yaping Zhang

    2014-10-01

    Full Text Available The yellow light dilemma zone is widely known as an area on the high-speed intersection approach, where vehicles neither safely stop before the stop line nor proceed through the intersection during amber interval. Within such an area, a vehicle might be involved in a right-angle crash or rear-end collision. This issue has been extensively discussed over five decades in traffic engineering field, covering from theory to practice. However, few comprehensive review literatures on the amber signal dilemma zone problems can be found. The objective of this paper is to summarize the evolution of yellow light dilemma zone researches. Basic definition and boundary of dilemma zone followed by driver behavior and dilemma zone hazard measurement are depicted. At last, the future directions of yellow light dilemma zone research are discussed.

  6. Migraine photophobia originating in cone-driven retinal pathways.

    Science.gov (United States)

    Noseda, Rodrigo; Bernstein, Carolyn A; Nir, Rony-Reuven; Lee, Alice J; Fulton, Anne B; Bertisch, Suzanne M; Hovaguimian, Alexandra; Cestari, Dean M; Saavedra-Walker, Rodrigo; Borsook, David; Doran, Bruce L; Buettner, Catherine; Burstein, Rami

    2016-07-01

    Migraine headache is uniquely exacerbated by light. Using psychophysical assessments in patients with normal eyesight we found that green light exacerbates migraine headache significantly less than white, blue, amber or red lights. To delineate mechanisms, we used electroretinography and visual evoked potential recording in patients, and multi-unit recording of dura- and light-sensitive thalamic neurons in rats to show that green activates cone-driven retinal pathways to a lesser extent than white, blue and red; that thalamic neurons are most responsive to blue and least responsive to green; and that cortical responses to green are significantly smaller than those generated by blue, amber and red lights. These findings suggest that patients' experience with colour and migraine photophobia could originate in cone-driven retinal pathways, fine-tuned in relay thalamic neurons outside the main visual pathway, and preserved by the cortex. Additionally, the findings provide substrate for the soothing effects of green light. PMID:27190022

  7. Implementation of a protein reduced point charge model toward molecular dynamics applications.

    Science.gov (United States)

    Leherte, Laurence; Vercauteren, Daniel P

    2011-11-17

    A reduced point charge model was developed in a previous work from the study of extrema in smoothed charge density distribution functions generated from the Amber99 molecular electrostatic potential. In the present work, such a point charge distribution is coupled with the Amber99 force field and implemented in the program TINKER to allow molecular dynamics (MD) simulations of proteins. First applications to two polypeptides that involve α-helix and β-sheet motifs are analyzed and compared to all-atom MD simulations. Two types of coarse-grained (CG)-based trajectories are generated using, on one hand, harmonic bond stretching terms and, on the other hand, distance restraints. Results show that the use of the unrestrained CG conditions are sufficient to preserve most of the secondary structure characteristics but restraints lead to a better agreement between CG and all-atom simulation results such as rmsd, dipole moment, and time-dependent mean square deviation functions. PMID:21800922

  8. Autofluorescence imaging system to discriminate and quantify the distribution of benthic cyanobacteria and diatoms

    DEFF Research Database (Denmark)

    Carreira, Cátia; Staal, Marc Jaap; Middelboe, Mathias;

    2015-01-01

    Observation of benthic photoautotrophs on sediment surfaces shows a single algal layer without distinction between photosynthetic groups. Until now it has not been possible to distinguish between benthic photosynthetic microorganisms, i.e. cyanobacteria and diatoms, at μm to mm scales using...... a single nondisruptive system. Chlorophyll autofluorescence can be used to distinguish different photoautotrophic groups if the correct excitation light is applied. Using this principle, a nonintrusive technique was developed to study the spatial distribution of benthic cyanobacteria and diatoms. By means...... of a charge coupled device camera, diatoms and cyanobacteria could be identified by blue light (470 nm) excitation and amber light (600 nm) excitation, respectively. By this approach, diatom or cyanobacterial dominance could be easily distinguished using the blue over amber ratio. We applied this method...

  9. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket".

    Science.gov (United States)

    McClain, W H; Foss, K

    1988-09-30

    The specificity of tRNA(Arg) (arginine transfer RNA) for aminoacylation (its acceptor identity) were first identified by computer analysis and then examined with amber suppressor tRNAs in Escherichia coli. On replacing two nucleotides in tRNA(Phe) (phenylalanine transfer RNA) with the corresponding nucleotides from tRNA(Arg), the acceptor identity of the resulting tRNA was changed to that of tRNA(Arg). The nucleotides used in the identity transformation occupy a "variable pocket" structure on the surface of the tRNA molecule where two single-stranded loop segments interact. The middle nucleotide in the anticodon also probably contributes to the interaction, since an amber suppressor of tRNA(Arg) had an acceptor identity for lysine as well as arginine. PMID:2459773

  10. Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability

    CERN Document Server

    Sakae, Yoshitake

    2013-01-01

    We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $\\psi$ (N-C$^{\\alpha}$-C-N) and $\\zeta$ (C$^{\\beta}$-C$^{\\alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $\\alpha$-helical and $\\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.

  11. Technological development of injectable cisplatin solution

    International Nuclear Information System (INIS)

    To develop a cisplatin formulation at 1mg/mL concentration by setting the solution preparation procedure for parenteral administration, with good physical, chemical, biological and microbiological stability. two formulation variants of cisplatin: one solution with and the other without acetate buffer. Both were followed in terms of physical and chemical stability for 3 months. The formulations used raw material from IMPEX SA company, which has 99.74 % power as certified by the manufacturer analysis. Three batches of 10mg cistoplatin at pilot scale in amber 10 R vials, 3 batches of 50 mg cisplatin in amber 50 H vials and the dose was 1mg/ml. Excipients were used to give isotony and stability to the formulation with 0.1 N chlorhydric acid and injection water for vehicle. The high performance liquid chromatography allowed evaluating the stability to determine the expiry date of the drug. The biological and microbiological methods determined lack of pyrogens and sterility respectively

  12. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    Science.gov (United States)

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  13. Tunable translational control using site-specific unnatural amino acid incorporation in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Yusuke Kato

    2015-04-01

    Full Text Available Translation of target gene transcripts in Escherichia coli harboring UAG amber stop codons can be switched on by the amber-codon-specific incorporation of an exogenously supplied unnatural amino acid, 3-iodo-L-tyrosine. Here, we report that this translational switch can control the translational efficiency at any intermediate magnitude by adjustment of the 3-iodo-L-tyrosine concentration in the medium, as a tunable translational controller. The translational efficiency of a target gene reached maximum levels with 10−5 M 3-iodo-L-tyrosine, and intermediate levels were observed with suboptimal concentrations (approximately spanning a 2-log10 concentration range, 10−7–10−5 M. Such intermediate-level expression was also confirmed in individual bacteria.

  14. Belege für die Anwesenheit von Eliten des 6./5. Jahrhunderts v. Chr. am Zusammenfluss von Elbe und Moldau in Mittelböhmen

    Czech Academy of Sciences Publication Activity Database

    Chytráček, Miloslav

    2015-01-01

    Roč. 90, č. 1-2 (2015), s. 271-300. ISSN 0079-4848 Grant ostatní: Rada Programu interní podpory projektů mezinárodní spolupráce AV ČR(CZ) M300021201 Institutional support: RVO:67985912 Keywords : Bohemia * Late Hallstatt * Early La Tène * cemetery * settlement * Etruscan bronze basins * drinking horns * amber routes * wreath * cult Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 0.278, year: 2014

  15. OPTIMIZATION OF ULTRASOUND-ASSISTED EXTRACTION OF TOTAL FLAVONOIDS AND ANTIOXIDANT PROPERTIES FROM TRIGONELLA FOENUM-GRAECUM SEEDS WITH RESPONSE SURFACE METHODOLOGY

    OpenAIRE

    Shaileyee Das

    2013-01-01

    Trigonella foenum-graecum is an annual plant in the family Fabaceae. The distinctive cuboid-shaped, yellow to amber coloured fenugreek seeds are frequently encountered in the cuisines of the Indian subcontinent. In this study, Trigonella foenum-graecum is used as an experimental matrix. Ultrasound-assisted extraction (UAE) of total flavonoids from Trigonella foenum-graecum is studied with dual wavelength UV-VIS spectrophotometer. Effects of various factors including ratio of material to liqui...

  16. Once upon a time in a fantasy : a study of fairytale elements in fantasy

    OpenAIRE

    Opheim, Anna Patricia T.

    2010-01-01

    This thesis has looked at the different fairy tales elements in fantasy literature, by analyzing the main characters in the following books, Coraline, Harry Potter and the Philosopher’s Stone and The Amber Spyglass. These books were chosen because they are written within the same time period, from 1997-2002. They were the books used for my close reading. As for the secondary literature, Propp has been used through out the thesis. Bettelheim has been an important source as well....

  17. Gemstones

    Science.gov (United States)

    Olson, D.W.

    2006-01-01

    During 2005, the estimated value of natural gemstones produced from US deposits was $13.9 million. Production included agates, amber, beryl, coral, garnet, jade, jasper, opal, pearl, quartz, sapphire, shell, topaz, tourmaline, and torquoise among others. For the year, the US gemstone trade with all countries and territories exceeded $26 billion. There are indication that there may be continued growth in the US diamond and jewelry markets in 2006.

  18. Mineral resource of the month: gemstones

    Science.gov (United States)

    Olson, Donald W.

    2008-01-01

    Humans have been intrigued by gemstones since prehistoric times. Gemstones have been valued as treasured objects throughout history by all societies in all parts of the world. The first stones known to have been used for making jewelry include amber, amethyst, coral, diamond, emerald, garnet, jade, jasper, lapis lazuli, pearl, rock crystal, ruby, serpentine and turquoise. These stones served as status symbols for the wealthy. Today, arguably, gems are worn more for pleasure and in appreciation of their beauty than to demonstrate wealth.

  19. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

    OpenAIRE

    Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M.; GONZÁLEZ-OUTEIRIÑO, JORGE; DANIELS, CHARLISA R.; Foley, B. Lachele; Woods, Robert J.

    2008-01-01

    A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present wo...

  20. QSAR Studies of Copper Azamacrocycles and Thiosemicarbazones: MM3 Parameter Development and Prediction of Biological Properties

    OpenAIRE

    Wolohan, Peter; Yoo, Jeongsoo; Welch, Michael J.; Reichert, David E.

    2005-01-01

    Genetic algorithms (GA) were used to develop specific copper metal-ligand force field parameters for the MM3 force field, from a combination of crystallographic structures and ab initio calculations. These new parameters produced results in good agreement with experiment and previously reported copper metal-ligand parameters for the AMBER force field. The MM3 parameters were then used to develop several Quantitative Structure Activity Relationship (QSAR) models. A successful QSAR for predicti...

  1. Importance of low carbohydrate diets in diabetes management

    OpenAIRE

    RM Hall; Parry Strong A; Krebs JD

    2016-01-01

    Rosemary M Hall, Amber Parry Strong, Jeremy D KrebsCentre for Endocrine, Diabetes and Obesity Research, Capital and Coast District Health Board, Wellington, New Zealand Abstract: Dietary strategies are fundamental in the management of diabetes. Historically, strict dietary control with a low carbohydrate diet was the only treatment option. With increasingly effective medications, the importance of dietary change decreased. Recommendations focused on reducing dietary fat to prevent atheroscle...

  2. The use of metformin is associated with decreased lumbar radiculopathy pain

    OpenAIRE

    Taylor A; Westveld AH; Szkudlinska M; Guruguri P; Annabi E; Patwardhan A; Price TJ; Yassine HN

    2013-01-01

    Amber Taylor,1 Anton H Westveld,2,6 Magdalena Szkudlinska,1 Prathima Guruguri,1 Emil Annabi,3 Amol Patwardhan,3 Theodore J Price,4 Hussein N Yassine51Department of Medicine, University of Arizona, Tucson, AZ, USA; 2Statistics Laboratory, Bio5 Institute, Statistics GIDP, University of Arizona, Tucson, AZ, USA; 3Department of Anesthesia, University of Arizona, Tucson, AZ, USA; 4Department of Pharmacology, University of Arizona, Tucson, AZ, USA; 5Department of Medicine, University of Southern Ca...

  3. A large parasitengonid mite (Acari, Erythraeoidea from the Early Cretaceous Crato Formation of Brazil

    Directory of Open Access Journals (Sweden)

    J. A. Dunlop

    2007-08-01

    Full Text Available A new large, fossil mite (Arachnida: Acari, Pararainbowia martilli n. gen. n. sp., is described from the Early Cretaceous (Aptian Crato Formation from Ceará State, Brazil. It is assigned to the Cohort Parasitengona and the superfamily Erythraeoidea, some extant members of which can reach up to seven millimetres in body length. Given that doubts have been raised about the identity of putative Crato feather mite eggs, this new fossil represents the first unequivocal record of Acari from the Crato Formation, the first non-amber record of an erythraeoid mite and the oldest named example of this superfamily. Fossil erythraeoids from Mesozoic and Tertiary ambers are briefly reviewed – including a widely overlooked Late Cretaceous species – with comments on Mesozoic mites in general. Thirteen Baltic amber erythraeoids have been formally described, but much unstudied material from various amber sources remains. Ein neues großes Milbenfossil (Arachnida: Acari, Pararainbowia martilli n. gen. n. sp., wird aus der Crato Formation (Unterkreide, Aptium des Ceará Gebietes in Brasilien beschrieben. Es wird der Kohorte Parasitengona und der Überfamilie Erythraeoidea zugeordnet; die modernen Vertreter erreichen eine Körperlänge bis zu sieben mm. Weil die Identität von Federmilbeneiern aus der Crato Formation in Frage gestellt wurde, ist dieser Neufund der erste klare Hinweis von Acari aus der Crato Formation. Es ist die erste erythraeoide Milbe, die nicht aus dem Bernstein stammt sowie das älteste genannte Beispiel dieser Überfamilie. Fossile erythraeoide Milben aus dem Bernstein des Mesozoikum und des Tertiärs werden kurz zusammengefasst – u. a. eine weitgehend übersehene Art aus der Oberkreide – mit allgemeinen Anmerkungen zu den mesozoischen Milben. Dreizehn erythraeoide Milbenarten sind aus dem baltischen Bernstein genannt und beschrieben worden, aber weiteres unbearbeitetes Material von verschiedenen Bernstein-Fundpunkten liegt noch vor

  4. Excluding Latino immigrant families from the social safety net hurts their children’s educational outcomes – and effects spill over onto Latino children who are not excluded

    OpenAIRE

    Condon, Meghan; Filindra, Alexandra; Wichowsky, Amber

    2016-01-01

    Recent years have seen growing discussion in media, academic, and policy circles about the problems of inequality in America. What often does not get a great deal of attention is that inequality among families with children has grown much faster than inequality overall. In new research Meghan Condon, Alexandra Filindra, and Amber Wichowsky look at how being excluded from social safety nets affects low-income Latino children. They find that not only does such exclusion lead to poorer education...

  5. Disciplines on Domestic Support in the Doha Round

    OpenAIRE

    Blandford, David

    2005-01-01

    The elements of a new agreement relating to domestic support for agriculture are set out in the WTO Framework document of July 2004. This introduces the concept of the Overall Trade Distorting Support (OTDS), which is to be disciplined and subject to reduction. In addition, some of the individual components of the OTDS will be subject to minimum required reductions and other elements will be capped. The caps and reduction percentages will define each country's future "entitlement" to Amber an...

  6. Triplex hydration: nanosecond molecular dynamics simulation of the solvated triplex formed by mixed sequences

    OpenAIRE

    Ojha, Rajendra P.; Tiwari, Rakesh K.

    2003-01-01

    A theoretical model for the hydration pattern and motion of ions around the triple helical DNA with mixed sequences d(GACTGGTGAC)d(GTCACCAGTC)*d(GACTGGTGAC) in solution, during MD simulation, using the particle mesh Ewald sum method, is elaborated here. The AMBER 5.0 force field has been used during the simulation in solvent. The simulation studies support a dynamically stable atmosphere around the DNA triplex in solution over the entire length of the trajectory. The results have been compare...

  7. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    OpenAIRE

    Andrzej Koliński; Maksim Kouza; Dominik Gront; Sebastian Kmiecik; Jacek Wabik

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combi...

  8. A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein interaction partners

    OpenAIRE

    Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Michael H. Peters

    2014-01-01

    A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, “OpenContact” provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases f...

  9. Impact of attentional demand on visual processing during simulated driving: a MEG study

    OpenAIRE

    Alexandra Fort; Robert Martin; Armelle Jacquet-Andrieu; Claude Delpuech

    2010-01-01

    The aim of this study was to assess the impact of attentional demand on car drivers’ cerebral activities using magnetoencephalography (MEG). A car simulator was designed according to the MEG constraints. It included a steering wheel, a turn indicator, a brake pedal and an accelerator pedal. An interactive virtual urban environment was projected onto a screen in front of the subject. Two stimuli of interest were defined: traffic light turning from green to amber and occurrence of left or...

  10. Izdevuma "Description de l'Égypte" oriģinālgravīras

    OpenAIRE

    Saviča, Mārīte

    2014-01-01

    Raksts par izstādē "Tutanhamona dzintars : Senā Ēģipte = The Amber of Tutankhamun : Ancient Egypt" (Rīgas birža, 2014.g. 14. novembris - 2015.g. 25. janvāris) eksponētajām senajām gravīrām no Latvijas Universitātes Bibliotēkas krājuma.

  11. Nucleotide sequence and genome organization of carnation mottle virus RNA.

    OpenAIRE

    Guilley, H; Carrington, J C; Balàzs, E; Jonard, G; Richards, K; Morris, T J

    1985-01-01

    The complete nucleotide sequence of carnation mottle genomic RNA (4003 nucleotides) is presented. The sequence was determined for cloned cDNA copies of viral RNA containing over 99% of the sequence and was completed by direct sequence analysis of RNA and cDNA transcripts. The sequence contains two long open reading frames which together can account for observed translation products. One translation product would arise by suppression of an amber termination codon and the sequence raises the po...

  12. Conquiliomorfologia de Tamayoa (Tamayops) banghaasi (Thiele) (Gastropoda, Systrophiidae) Conchomorphological aspects of Tamayoa (Tamayops) banghaasi (Thiele) (Gastropoda, Systrophiidae) as a contribution to Systrophiidae systematic

    OpenAIRE

    Daniele Pedrosa Monteiro; Sônia Barbosa dos Santos

    2001-01-01

    Thirty shells of Tamayoa (Tamayops) banghaasi (Thiele, 1927) from Ilha Grande, Rio de Janeiro, were analyzed with a stereomicroscop showing the following characteristics: discoid shell, without macrosculptures; ovate-lunate aperture without teeth. Thin, sharp and not-reflected lip; umbilicus with 1/5 of the shell's diameter; impressed suture, total whorls from 4 to 5.5; protoconch with 1.5 to 2 whorls; yellowish-amber, translucent and glossy periostracum. The morphology of the shells were dis...

  13. Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label

    Czech Academy of Sciences Publication Activity Database

    Zhang, X.J.; Xu, C.X.; Di Felice, R.; Šponer, Jiří; Islam, B.; Stadlbauer, Petr; Ding, Y.; Mao, L.; Mao, Z.W.; Qin, P.Z.

    2016-01-01

    Roč. 55, č. 2 (2016), s. 360-372. ISSN 0006-2960 R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : PARAMAGNETIC-RESONANCE SPECTROSCOPY * AMBER FORCE-FIELD * NUCLEIC-ACIDS Subject RIV: BO - Biophysics Impact factor: 3.015, year: 2014

  14. Luminescent ceramics for LED conversion

    Science.gov (United States)

    Raukas, M.; Wei, G.; Bergenek, K.; Kelso, J.; Zink, N.; Zheng, Y.; Hannah, M.; Stough, M.; Wirth, R.; Linkov, A.; Jermann, F.; Eisert, D.

    2011-03-01

    Many LED-based applications would benefit from more efficient and/or high lumen output devices that enable usage in both white and single color illumination schemes. In the present article we briefly review the materials research history leading to optical ceramic converters and discuss their typical characteristics. Recently demonstrated high performance values in terms of efficacy and external quantum efficiency in orange (amber) spectral region are described.

  15. Archaeometric study of glass beads from the 2nd century BC cemetery of Numantia

    OpenAIRE

    García Heras, Manuel; Rincoón López, Jesús M.; Alfredo JIMENO MARTÍNEZ; Villegas Broncano, María Angeles

    2003-01-01

    Recent archaeologícalf ieldwork undertaken in the Celtiberian cremation necropolis of Numantia (Soria, Spain) has provided a group of glass beads from the 2nd century BC. Such glass beads were part, together with other metallic and ceramic items, of the offerings deposited with the dead. They are ring-shaped in typology and deep-blue, amber, or semitransparent white in colour. This paper reports results derived from the chemical and microstructural characterization carried out on a representa...

  16. New fossil insect order Permopsocida elucidates major radiation and evolution of suction feeding in hemimetabolous insects (Hexapoda: Acercaria)

    OpenAIRE

    Di-Ying Huang; Günter Bechly; Patricia Nel; Michael S. Engel; Jakub Prokop; Dany Azar; Chen-Yang Cai; Thomas van de Kamp; Staniczek, Arnold H.; Romain Garrouste; Lars Krogmann; Tomy dos Santos Rolo; Tilo Baumbach; Rainer Ohlhoff; Shmakov, Alexey S.

    2016-01-01

    With nearly 100,000 species, the Acercaria (lice, plant lices, thrips, bugs) including number of economically important species is one of the most successful insect lineages. However, its phylogeny and evolution of mouthparts among other issues remain debatable. Here new methods of preparation permitted the comprehensive anatomical description of insect inclusions from mid-Cretaceous Burmese amber in astonishing detail. These “missing links” fossils, attributed to a new order Permopsocida, pr...

  17. Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method.

    OpenAIRE

    Perera, L; Li, L.; Darden, T.; Monroe, D M; Pedersen, L G

    1997-01-01

    The solution structures of the N-terminal domains of protein S, a plasma vitamin K-dependent glycoprotein, and its homolog growth arrest specific protein 6 (Gas6) were predicted by molecular dynamics computer simulations. The initial structures were based on the x-ray crystallographic structure of the corresponding region of bovine prothrombin fragment 1. The subsequent molecular dynamics trajectories were calculated using the second-generation AMBER force field. The long-range electrostatic ...

  18. Local Foods Marketing Channels Encompass a Wide Range of Producers

    OpenAIRE

    Low, Sarah A.; Vogel, Stephen J.

    2011-01-01

    Farmers selling locally grown food through farmers’ markets, roadside stands, and other local food outlets account for a small, but growing, segment of U.S. agriculture. Consumer demand for locally produced food is driven by demand for freshness, support for the local economy, and personal communication with the producer (see “Varied Interests Drive Growing Popularity of Local Foods†in the December 2010 issue of Amber Waves).

  19. Bernstein und der Zusammenbruch der klassischen Aunjetitzer Kultur in Böhmen

    Czech Academy of Sciences Publication Activity Database

    Ernée, Michal

    Halle (Saale) : Landesmuseum für Vorgeschichte Halle, 2013 - (Meller, H.; Bertemes, F.; Bork, H.; Risch, R.), s. 453-467 ISBN 978-3-944507-00-2. ISSN 1867-4402. - (Tagungen des Landesmuseums für Vorgeschichte Halle. 9). [Mitteldeutscher Archäologentag /4./. Halle (Saale) (DE), 14.10.2011-16.10.2011] Institutional support: RVO:67985912 Keywords : Early Bronze Age * amber * Aunjetitz Culture Subject RIV: AC - Archeology, Anthropology, Ethnology

  20. Influence of the extraction method and storage time on the physicochemical properties and carotenoid levels of pequi (Caryocar brasiliense Camb.) oil

    OpenAIRE

    Milton Cosme Ribeiro; Eduardo Valério de Barros Vilas Boas; Tania Regina Riul; Lílian Pantoja; Helyde Albuquerque Marinho; Alexandre Soares dos Santos

    2012-01-01

    The objective of this study was to analyze the physicochemical properties and carotenoid levels of pequi oil obtained by different extraction methods and to evaluate the preservation of these properties and pigments during storage time. The pequi oil was obtained by solvent extraction, mechanical extraction, and hot water flotation. It was stored for over 180 days in an amber bottle at ambient conditions. Analyses for the determination of the acidity, peroxide, saponification and iodine value...

  1. DHPLC technology for high-throughput detection of mutations in a durum wheat TILLING population

    OpenAIRE

    Colasuonno, Pasqualina; Incerti, Ornella; Lozito, Maria Luisa; Simeone, Rosanna; Gadaleta, Agata; Blanco, Antonio

    2016-01-01

    Background Durum wheat (Triticum turgidum L.) is a cereal crop widely grown in the Mediterranean regions; the amber grain is mainly used for the production of pasta, couscous and typical breads. Single nucleotide polymorphism (SNP) detection technologies and high-throughput mutation induction represent a new challenge in wheat breeding to identify allelic variation in large populations. The TILLING strategy makes use of traditional chemical mutagenesis followed by screening for single base mi...

  2. Colemanus keeleyorum (Braconidae, Ichneutinae s. l.: a new genus and species of Eocene wasp from the Green River Formation of western North America

    Directory of Open Access Journals (Sweden)

    J. Fisher

    2015-06-01

    Full Text Available A new genus and species of Ichneutinae s. l., Colemanus keeleyorum Fisher, is described from the Eocene Green River Formation in Colorado, USA. Colemanus was placed on a phylogenetic hypothesis using morphological data. Using a parsimony criterion, Colemanus is placed within Proteropini (Ichneutinae s. l.. Reconstructions of well-preserved regions (mesosomal dorsum and wings are included. A previously described species from lower Oligocene Baltic amber is transferred to Colemanus, resulting in the new combination C. contortus (Brues, 1933.

  3. Radiation monitoring of imported food to Saudi Arabia after Chernobyl accident

    International Nuclear Information System (INIS)

    Reports the results of radiation monitoring of food imports through ports of Jeddah, Yanbu and Jizan and Jeddah airport during June 1986 to February 1987. Monitoring procedure followed is detailed. Only meat and milk powder samples showed increased radioactivity above background upto September. Mainly cesium 137 and 134 were observed. From September, biscuits, mushrooms and fertilizer also showed radioactive contamination. Nuts, fruits, grain products, macaroni, amber and some indoor plants also showed contamination from October

  4. Stranicy institucional'noj jekonomicheskoj istorii Kjonigsberga/Kaliningrada [Chapters of the institutional economic history of Königsberg/Kaliningrad

    OpenAIRE

    Nureev Rustem; Latov Yuri

    2010-01-01

    This article consists of a series of short essays dedicated to a certain period of the 'popular' socioeconomic history (with a particular focus on the institutional development problems) of the former East Prussia from Antiquity to present days. The authors tackle the issues of the economic history of amber, the role of the Hansa League in the development of medieval trade, the QWERTY-effects in the rail gauge standards, and the peculiarities of the development of the Kaliningrad region in th...

  5. Chapters of the institutional economic history of Königsberg/Kaliningrad

    OpenAIRE

    Nureev R.; Latov Yu.

    2010-01-01

    This article consists of a series of short essays dedicated to a certain period of the 'popular' socioeconomic history (with a particular focus on the institutional development problems) of the former East Prussia from Antiquity to present days. The authors tackle the issues of the economic history of amber, the role of the Hansa League in the development of medieval trade, the QWERTY-effects in the rail gauge standards, and the peculiarities of the development of the Kaliningrad region in th...

  6. A LITERATURE REVIEW ON ARGYREIA NERVOSA (BURM. F.) BOJER

    OpenAIRE

    Meher Ashutosh; Agrahari Anuj kumar; Padhan Amiya Ranjan

    2011-01-01

    Various herbal drugs individually or in combination have been recommended for the treatment of different diseases. Argyreia nervosa Burm. F. (Syn. Argyreia speciosa) commonly known as ‘Vridha daraka’ in Sanskrit belongs to family Convolvulaceae has been used in different system of traditional medication for the treatment of diseases and ailments of human beings. It is reported to contain several phytochemical constituents like Alkaloids, Carbohydrate, Tannins, amber-colored resin, Sterols, Sa...

  7. A fast and efficient procedure to produce scFvs specific for large macromolecular complexes

    OpenAIRE

    Wu, Si; Ke, Ailong; Doudna, Jennifer A.

    2006-01-01

    We have expanded the application of antibody phage display to a new type of antigen: ribonucleoprotein (RNP) complexes. We describe a simple and efficient method for screening antibodies specific for large intact RNPs and individual components. We also describe a fast and easy method to overcome the abundance of amber stop codons in the positive phage clones. The resulting antibodies have been used in ELISA and Western blot analysis.

  8. Whole-brain functional hypoconnectivity as an endophenotype of autism in adolescents

    OpenAIRE

    Moseley, R.L.; Ypma, R.J.F.; Holt, R J; Floris, D.; Chura, L.R.; M.D. Spencer; Baron-Cohen, S; Suckling, J; Bullmore, E; Rubinov, M.

    2015-01-01

    The authors wish to thank the participants and their families for their participation and the autism support organisations who assisted with recruitment. We thank colleagues at the Brain Mapping Unit for methodological discussions and thank Meng-Chuan Lai, Amber Ruigrok and Richard Bethlehem for the same. Data collection was funded by a Clinical Scientist Fellowship from the UK Medical Research Council (MRC) (G0701919) to MDS. LRC was supported by the Gates Cambridge Scholarship Trust. The st...

  9. Patterning of a compound eye on an extinct dipteran wing

    OpenAIRE

    Dinwiddie, April; Rachootin, Stan

    2010-01-01

    We have discovered unexpected similarities between a novel and characteristic wing organ in an extinct biting midge from Baltic amber, Eohelea petrunkevitchi, and the surface of a dipteran's compound eye. Scanning electron microscope images now reveal vestigial mechanoreceptors between the facets of the organ. We interpret Eohelea's wing organ as the blending of these two developmental systems: the formation and patterning of the cuticle in the eye and of the wing.

  10. Sleep disorders in Parkinson’s disease

    OpenAIRE

    Israt Jahan; Hauser, Robert A; Kelly L. Sullivan; Amber Miller; et al, ...

    2009-01-01

    Israt Jahan1, Robert A Hauser2, Kelly L Sullivan1, Amber Miller1, Theresa A Zesiewicz11Department of Neurology, Parkinson’s Research Foundation, 2Departments of Neurology, Molecular Pharmacology, and Physiology, University of South Florida, Parkinson’s Disease and Movement Disorders Center, Tampa, FL, USAAbstract: Sleep disorders occur commonly in Parkinson’s disease (PD), and reduce quality of life. Sleep-related problems in PD include insomnia, restless legs sy...

  11. Pintura flamenca

    OpenAIRE

    Vergara Sharp, Alejandro; Checa, Fernando

    2015-01-01

    Contiene: Madrid, capital de la pintura flamenca (pp. 15-16).--Entrevista con Alejandro Vergara, Jefe de Conservación de Pintura Flamenca y Escuelas del Norte del Museo Nacional del Prado. Profesor del Curso de Estudios Hispánicos de la UC3M (pp. 18-19).-- Entrevista con Fernando Checa, Asesor Científico del Museo Carlos de Amberes de Madrid (pp. 20-21)

  12. Monophyly and extensive extinction of advanced eusocial bees: Insights from an unexpected Eocene diversity

    OpenAIRE

    Engel, Michael S.

    2001-01-01

    Advanced eusociality sometimes is given credit for the ecological success of termites, ants, some wasps, and some bees. Comprehensive study of bees fossilized in Baltic amber has revealed an unsuspected middle Eocene (ca. 45 million years ago) diversity of eusocial bee lineages. Advanced eusociality arose once in the bees with significant post-Eocene losses in diversity, leaving today only two advanced eusocial tribes comprising less than 2% of the total bee divers...

  13. Transitions between secondary structures in isolated polyalanines

    OpenAIRE

    Calvo, Florent; Poulain, Pierre

    2009-01-01

    Monte Carlo simulations of gas-phase polyalanine peptides have been carried out with the Amber ff96 force field. A low-temperature structural transition takes place between the α-helix stable conformation and β-sheet structures, followed by the unfolding phase change. The transition state ensembles connect- ing the helix and sheet conformations are investigated by sampling the energy landscape along specific geometric order parameters as putative reaction coordinates, namely the electric dipo...

  14. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Otyepka, Michal; Šponer, Jiří; Lankaš, Filip; Jurečka, P.

    2014-01-01

    Roč. 10, č. 8 (2014), s. 3177-3189. ISSN 1549-9618 R&D Projects: GA ČR(CZ) GP14-29874P Institutional support: RVO:68081707 ; RVO:61388963 Keywords : QUANTUM-CHEMICAL COMPUTATIONS * NUCLEIC-ACID STRUCTURES * AMBER FORCE-FIELD Subject RIV: BO - Biophysics; CC - Organic Chemistry (UOCHB-X) Impact factor: 5.498, year: 2014

  15. How a Huottuja (Piaroa community perceives genuine and false honey from the Venezuelan Amazon, by free-choice profi le sensory method

    Directory of Open Access Journals (Sweden)

    Patricia Vit

    2011-10-01

    Full Text Available Pot honey is the most abundant honey in the forest, produced by many species of stingless bees (Meliponini of the Huottuja (Piaroa community in Paria Grande, Venezuela. However, the commercialization of this honey is low, and false honeys, which are sold in labelled bottles, are easily found in the market. This study has investigated the ability of an untrained panel of Piaroa assessors to differentiate the genuine from the false pot honey using the Free-choice profile. This sensory method allows consumers to use their own words to describe and to quantify sensory attributes of a product. The genuine honeys, light amber Melipona fuscopilosa "isabitto" and dark amber Tetragona clavipes "ajavitte", the false light and dark "angelita" honeys, and the amber Apis mellifera honey, were evaluated. Sensory attributes related to the appearance, color, odor, flavor and mouthfeel were elicited in a qualitative session and were quantified in 10-cm unstructured line scales using individual score sheets. The data were analyzed by Generalized Procrustes Analysis (GPA. The bidimensional plot successfully separated genuine from false pot honeys. The first dimension (39.50% was represented by the low viscosity, fermented odor and sour taste, whereas the second dimension (24.69% was related to fruity and honey odor and flavor. Huottuja assessors differentiated the five honey types in terms of the perceived sensory characteristics.

  16. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract.

    Science.gov (United States)

    Ogawa, Atsushi; Tabuchi, Junichiro; Doi, Yasunori; Takamatsu, Masashi

    2016-08-01

    We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity. PMID:27289318

  17. Ectomycorrhizas from a Lower Eocene angiosperm forest.

    Science.gov (United States)

    Beimforde, Christina; Schäfer, Nadine; Dörfelt, Heinrich; Nascimbene, Paul C; Singh, Hukam; Heinrichs, Jochen; Reitner, Joachim; Rana, Rajendra S; Schmidt, Alexander R

    2011-12-01

    The development of mycorrhizal associations is considered a key innovation that enabled vascular plants to extensively colonize terrestrial habitats. Here, we present the first known fossil ectomycorrhizas from an angiosperm forest. Our fossils are preserved in a 52 million-yr-old piece of amber from the Tadkeshwar Lignite Mine of Gujarat State, western India. The amber was produced by representatives of Dipterocarpaceae in an early tropical broadleaf forest. The ectomycorrhizas were investigated using light microscopy and field emission scanning electron microscopy. Dissolving the amber surrounding one of the fossils allowed ultrastructural analyses and Raman spectroscopy. Approx. 20 unramified, cruciform and monopodial-pinnate ectomycorrhizas are fossilized adjacent to rootlets, and different developmental stages of the fossil mycorrhizas are delicately preserved in the ancient resin. Compounds of melanins were detectable in the dark hyphae. The mycobiont, Eomelanomyces cenococcoides gen. et spec. nov., is considered to be an ascomycete; the host is most likely a dipterocarp representative. An early ectomycorrhizal association may have conferred an evolutionary advantage on dipterocarps. Our find indicates that ectomycorrhizas occurred contemporaneously within both gymnosperms (Pinaceae) and angiosperms (Dipterocarpaceae) by the Lower Eocene. PMID:22074339

  18. Structure of human insulin monomer in water/acetonitrile solution

    Energy Technology Data Exchange (ETDEWEB)

    Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elzbieta [National Medicines Institute (Poland); Tarnowska, Anna; Kawecki, Robert [Institute of Organic Chemistry Polish Academy of Sciences (Poland); Kozerski, Lech [National Medicines Institute (Poland)], E-mail: lkoz@icho.edu.pl

    2008-01-15

    Here we present evidence that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. An NMR-derived human insulin monomer structure in H{sub 2}O/CD{sub 3}CN, 65/35 vol%, pH 3.6 is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Acta Crystallogr. 2003 Sec. D59, 474) and with NMR structures in water and organic cosolvent. Detailed analysis using PFGSE NMR, temperature-dependent NMR, dilution experiments and CSI proves that the structure is monomeric in the concentration and temperature ranges 0.1-3 mM and 10-30 deg. C, respectively. The presence of long-range interstrand NOEs, as found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Starting from structures calculated by the program CYANA, two different molecular dynamics simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER{sub V}C), or including a generalized Born solvent model (AMBER{sub G}B)

  19. The Sky Through Three Giant Eyes

    Science.gov (United States)

    2007-02-01

    AMBER Instrument on VLT Delivers a Wealth of Results The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns

  20. The Great Cometary Show

    Science.gov (United States)

    2007-01-01

    The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns the enigmatic object Eta Carinae. Using AMBER with

  1. Performance analysis of orthogonal pairs designed for an expanded eukaryotic genetic code.

    Directory of Open Access Journals (Sweden)

    Sebastian Nehring

    Full Text Available BACKGROUND: The suppression of amber stop codons with non-canonical amino acids (ncAAs is used for the site-specific introduction of many unusual functions into proteins. Specific orthogonal aminoacyl-tRNA synthetase (o-aaRS/amber suppressor tRNA(CUA pairs (o-pairs for the incorporation of ncAAs in S. cerevisiae were previously selected from an E. coli tyrosyl-tRNA synthetase/tRNA(CUA mutant library. Incorporation fidelity relies on the specificity of the o-aaRSs for their ncAAs and the ability to effectively discriminate against their natural substrate Tyr or any other canonical amino acid. METHODOLOGY/PRINCIPAL FINDINGS: We used o-pairs previously developed for ncAAs carrying reactive alkyne-, azido-, or photocrosslinker side chains to suppress an amber mutant of human superoxide dismutase 1 in S. cerevisiae. We found worse incorporation efficiencies of the alkyne- and the photocrosslinker ncAAs than reported earlier. In our hands, amber suppression with the ncAA containing the azido group did not occur at all. In addition to the incorporation experiments in S. cerevisiae, we analyzed the catalytic properties of the o-aaRSs in vitro. Surprisingly, all o-aaRSs showed much higher preference for their natural substrate Tyr than for any of the tested ncAAs. While it is unclear why efficiently recognized Tyr is not inserted at amber codons, we speculate that metabolically inert ncAAs accumulate in the cell, and for this reason they are incorporated despite being weak substrates for the o-aaRSs. CONCLUSIONS/SIGNIFICANCE: O-pairs have been developed for a whole plethora of ncAAs. However, a systematic and detailed analysis of their catalytic properties is still missing. Our study provides a comprehensive scrutiny of o-pairs developed for the site-specific incorporation of reactive ncAAs in S. cerevisiae. It suggests that future development of o-pairs as efficient biotechnological tools will greatly benefit from sound characterization in vivo and in

  2. Nanodefects in ultrahard crystalline cubic boron nitride

    International Nuclear Information System (INIS)

    Cubic boron nitride (cBN), the second hardest known material after diamond, exhibits high thermal conductivity and an excellent ability to be n or p doped, which makes it a strong candidate for the next generation of high-temperature micro optical and micro electronic devices. According to recent studies, cBN exhibits a better resistance to radiation damage than diamond, which suggests potential applications in extreme radiation environments. Crystalline cBN powders of up to 0.5 mm linear size is obtained in a similar way as diamond, by catalytic conversion of hexagonal BN (hBN) to cBN at even higher pressures (> 5GPa) and temperatures (∼ 1900 K). Considering the essential role played by the nanodefects (point defects and impurities) in determining its physical properties, it is surprising how limited is the amount of published data concerning the properties of nanodefects in this material, especially by Electron Paramagnetic Resonance (EPR) spectroscopy, the most powerful method for identification and characterization of nanodefects in both insulators and semiconductors. This seems to be due mainly to the absence of natural cBN gems and the extreme difficulties in producing even mm3 sized synthetic crystals. We shall present our recent EPR studies on cBN crystalline powders, performed in a broad temperature range from room temperature (RT) down to 1.2 K on several sorts of large size cBN powder grits of yellow and amber color for industrial applications. Previous multifrequency (9.3 GHz and 95 GHz) EPR studies of brown to black cBN crystallites prepared with excess of boron, resulted in the discovery of two new types of paramagnetic point defects with different spectral properties, called the D1 and D2 centers. Our X(9.3 GHz)-band EPR investigations resulted in the observation in amber cBN crystalline powders of a spectrum with a strong temperature dependence of the lineshape. It was found that for high and low temperatures, respectively, the numerical

  3. CT screening for lung cancer: Is the evidence strong enough?

    Science.gov (United States)

    Field, J K; Devaraj, A; Duffy, S W; Baldwin, D R

    2016-01-01

    The prevailing questions at this time in both the public mind and the clinical establishment is, do we have sufficient evidence to implement lung cancer Computed Tomography (CT) screening in Europe? If not, what is outstanding? This review addresses the twelve major areas, which are critical to any decision to implement CT screening and where we need to assess whether we have sufficient evidence to proceed to a recommendation for implementation in Europe. The readiness level of these twelve categories in 2015 have been with colour coded, where green indicates we have sufficient evidence, amber is borderline evidence and red requires further evidence. Recruitment from the 'Hard to Reach' community still remains at red, while mortality data, cost effectiveness and screening interval are all categorised as amber. The integration of smoking cessation into CT screening programmes is still considered to be category amber. The US Preventive Services Task Force have recommended that CT screening is implemented in the USA utilising the NLST criteria, apart from continuing screening to 80 years of age. The cost effectiveness of the NLST was calculated to be $81,000/QALY, however, its well recognised that the costs of medical care in the USA, is far higher than that of Europe. Medicare have agreed to cover the cost of screening but have stipulated a number of stringent requirements for inclusion. To date we do not have good CT screening mortality data available in Europe and eagerly await the publication of the NELSON trial data in 2016 and then the pooled UKLS and NELSON data thereafter. However in the meantime we should start planning for implementation in Europe, especially in the areas of the radiological service provision and accreditation, as well as identifying novel mechanisms to recruit from the hardest to reach communities. PMID:26711931

  4. TRIBUTOS E IMPUESTOS EN DIEGO DE AVENDAÑO. UN CAPÍTULO DE ÉTICA COLONIAL

    Directory of Open Access Journals (Sweden)

    Angel Garcia

    2001-01-01

    Full Text Available En 1668, Diego de Avendaño, jesuita peruano, publicaba en Amberes su Thesaurus Indicus, obra de contenido ético-jurídico, que –en intención del autor– pretendía ser guía para el Consejo de Indias en referencia al recto gobierno de las colonias americanas. El presente trabajo expone la visión que el jesuita presenta en su obra, sobre los diferentes impuestos y tributos en las colonias.

  5. Work in support of biosphere assessments for solid radioactive waste disposal. 2. biosphere FEP list and biosphere modelling

    International Nuclear Information System (INIS)

    In order to assist SSI in its reappraisal of the SFR safety case, QuantiSci has been appointed to develop a systematic framework within which to conduct the review of SKB's post-closure performance assessment (PA). The biosphere FEP list presented here was developed for use as reference material in conducting the review. SSI wishes to develop an independent PA capability for a time-dependent biosphere in preparation for the examination of the revised SFR safety case. This report documents the model development that has been undertaken by QuantiSci using the Amber computer code

  6. A new species of Oeda (Hemiptera: Membracidae: Stegaspidinae from Madre de Dios, Peru

    Directory of Open Access Journals (Sweden)

    Albino M. Sakakibara

    2014-12-01

    Full Text Available A new species of Oeda Amyot & Serville, 1843 - Oeda (Oeda mielkei sp. nov. from Peru, Madre de Dios, 12°52'S, 71°22'W - is described. It differs from the other species of O. (Oeda in having the inflated pronotal process more elongate, and amber color; the suprahumeral horns are much more developed, club-shaped, about as long as the width of head, forming an arch with the tips touching each other; the metopidium, in lateral view, is almost vertical above head. A key, including images of all species (except O. mirandai Fonseca are also provided.

  7. The Employee Diversity Team Wants to Take You around the World in Film | Poster

    Science.gov (United States)

    By Andrea Frydl, Contributing Writer The NCI at Frederick Employee Diversity Team (EDT) has prepared a new display that features a sample of the foreign films from the team’s collection in the Scientific Library. “Foreign films really help stimulate an awareness of different cultures and countries. I think it is a great celebration of diversity to have the Employee Diversity Team promote films from across the globe and make them available to our employees,” said Amber Elia, program analyst, NCI at Frederick Office of Scientific Operations, and member of the EDT.

  8. Combining ability analysis for yield and its components in popcorn (Zea mays var. everta Sturt.)

    OpenAIRE

    Vijayabharathi A; Anandakumar CR; Gnanamalar RP

    2009-01-01

    A line x tester set was obtained by crossing 8 lines with 3 testers in popcorn. The resultant 24 derived F1s were evaluatedalong with 11 parents to estimate general and specific combining ability variances and effects for 14 characters. The resultsshowed predominant role of non-additive gene action for all the characters studied. Based on both per se and gca, thegenotypes UPC 5, UPC 4, UPC 1 among lines and Amber popcorn, Bangalore popcorn among the testers were proved asgood general combiner...

  9. Study of dosimetric systems in commercial applications of radition

    International Nuclear Information System (INIS)

    Application of differents dosimeter systems: Standard Frickie, Modify Frickie, Yellow Perspex, Amber Perspex, Red Perspex and Clear Prespex, for industrial irradiation were studied. Dosimeter expositions in the range 0.05 KGy to 10 KGy were applied using both a Gammacell 220 source and a semi-industrial irradiator of Co-60, with dosis rates of 0.2 KGy/hr and 4 KGy/hr respectivily. During the experiment variables like storage temperature with 20, 35 and 45 degC were studied. Experimental results point out that Standard Frickie and Perspex dosimeter system can be used successfully with a very low dependence upon storage temperature and storage time

  10. El escultor Sebastián de Salinas y las pervivencias siloesco-vigarnianas en los años centrales del siglo XVI

    OpenAIRE

    Payo Hernanz, René Jesús

    2012-01-01

    El escultor Sebastián de Salinas, formado en el taller de Felipe Vigarny, desarrolló una importante actividad artística en Burgos y su comarca en los años centrales del siglo XVI. Relacionado con los principales artistas burgaleses del momento, como Diego Guillén, Nicolás París y Domingo de Amberes, mantuvo vivos en sus producciones los rasgos estéticos de Felipe Vigarny y de Diego de Siloé, siendo uno de los últimos representantes de la escultura burgalesa del primer Renacimiento. The scu...

  11. The colour and golden shine of early silver Islamic lustre

    OpenAIRE

    Gutierrez Neira, Carolina; Pradell Cara, Trinitat; Molera Marimon, Judit; Smith, Andrew D; Climent Font, Aurelio; Tite, Michael S.

    2014-01-01

    A selection of lustres including 9th century AD polychrome and 10th century AD monochrome Abbasid lustres from Iraq, and 10th to 12th centuries AD Fatimid lustres from Egypt and Syria is studied in the present paper. The selection is based on previous studies that demonstrated that all of them contain metal silver nanoparticles and copper, which, when present, appears either as Cuþ or Cu2þ dissolved in the glaze. They show different colours, green, yellow, amber, and brown, and...

  12. INFLUENCE OF GLASS CULLET IN CEMENT PASTES

    Institute of Scientific and Technical Information of China (English)

    A.Karamberi; E.Chaniotakis; D.Papageorgiou; A.Moutsatsou

    2006-01-01

    The present study investigates glass and cement compatibility with a view to use glass as a cement replacement. Amber, flint and green glasses were chosen due to their prevalence in the Greek market as packaging materials. The factors under investigation were the pozzolanicity of the glass cullet, the hydration rate and the mechanical strength development of the cement pastes, as well as the expansion of the specimens due to alkali-silica reaction.Moreover, the potential enhancement of glass pozzolanic activity was examined. The results of the study were encouraging to show the potentiality of utilising glass cullet in cementitious products.

  13. Prikazivanje čudovišno-ženskoga u odabranim djelima C. S. Lewisa, Roalda Dahla i Philipa Pullmana

    OpenAIRE

    Tso, Anna Wing Bo

    2012-01-01

    Rad istražuje načine prikazivanja ženskih likova u ulozi protivnika u trima popularnim književnim pripovijedima za djecu – u ciklusu Chronicles of Narnia [Kronike iz Narnije] C. S. Lewisa te u romanima The Witches [Vještice] Roalda Dahla i The Amber Spyglass [Jantarni dalekozor] Philipa Pullmana – pozivajući se na teoriju abjekcije Julije Kristeve i na raspravu o čudovišno-ženskom Barbare Creed. I u ciklusu o Narniji i u romanu Vještice, ženski su protivnički likovi pojednostavljeni, stereoti...

  14. REV7, a new gene concerned with UV mutagenesis in yeast

    International Nuclear Information System (INIS)

    Three allelic mutations of a new yeast gene, which we have named REV7, have been isolated by testing 313 methyl methane sulfonate sensitive mutants for UV-induced reversion of a lys2 allele. Rev7 mutants are markedly deficient with respect to UV-induced reversion of lys2, are slightly sensitive to UV and appear to be in the RAD6 epistasis group for UV survival. Rev7-1, which is probably an amber mutation, does not appear to affect sporulation in homozygous diploids. The REV7 gene is located about 12 cM distal to HIS5 on chromosome IX. (orig.)

  15. Work in support of biosphere assessments for solid radioactive waste disposal. 2. biosphere FEP list and biosphere modelling

    Energy Technology Data Exchange (ETDEWEB)

    Egan, M.J.; Maul, P.R.; Watkins, B.M.; Venter, A. [QuantiSci Ltd., Henley-on-Thames (United Kingdom)

    2001-10-01

    In order to assist SSI in its reappraisal of the SFR safety case, QuantiSci has been appointed to develop a systematic framework within which to conduct the review of SKB's post-closure performance assessment (PA). The biosphere FEP list presented here was developed for use as reference material in conducting the review. SSI wishes to develop an independent PA capability for a time-dependent biosphere in preparation for the examination of the revised SFR safety case. This report documents the model development that has been undertaken by QuantiSci using the Amber computer code.

  16. Coarse Point Charge Models For Proteins From Smoothed Molecular Electrostatic Potentials.

    Science.gov (United States)

    Leherte, Laurence; Vercauteren, Daniel P

    2009-12-01

    To generate coarse electrostatic models of proteins, we developed an original approach to hierarchically locate maxima and minima in smoothed molecular electrostatic potentials. A charge-fitting program was used to assign charges to the so-obtained reduced representations. Templates are defined to easily generate coarse point charge models for protein structures, in the particular cases of the Amber99 and Gromos43A1 force fields. Applications to four small peptides and to the ion channel KcsA are presented. Electrostatic potential values generated by the reduced models are compared with the corresponding values obtained using the original sets of atomic charges. PMID:26602509

  17. The Investigation of Different Properties of Clonidine Drug Binding to Carbon Nanotube: A Theoretical Study

    OpenAIRE

    Z. Yousefian

    2014-01-01

    In this study, we investigated the binding of Clonidine Drug (C9H9Cl2N3) with zigzag single walled Carbon Nanotubes (SWCNTs) (5, 0) and a length of 5ᵒA by theoretical methods of theory (NMR,NBO, HOMO- LUMO Gap energy,…calculations) using Gaussian ­09 software package. Then, Simulation was done in MM+, AMBER and OPLS force fields by Monte Carlo method in HyperChem. Three important energy parameters – Potential Energy, Kinetic Energy and Total Energy-calculated in five different simulating temp...

  18. The Investigation of Different Properties of Clonidine Drug Binding to Carbon Nanotube: A Theoretical Study

    Directory of Open Access Journals (Sweden)

    Z. Yousefian

    2014-12-01

    Full Text Available In this study, we investigated the binding of Clonidine Drug (C9H9Cl2N3 with zigzag single walled Carbon Nanotubes (SWCNTs (5, 0 and a length of 5ᵒA by theoretical methods of theory (NMR,NBO, HOMO- LUMO Gap energy,…calculations using Gaussian ­09 software package. Then, Simulation was done in MM+, AMBER and OPLS force fields by Monte Carlo method in HyperChem. Three important energy parameters – Potential Energy, Kinetic Energy and Total Energy-calculated in five different simulating temperatures (308, 310, 312, 314 and 316 Kelvin were used for computation and good results were obtained.

  19. Jeho temné esence: Ateismus v trilogii Philipa Pullmana

    OpenAIRE

    ERTELOVÁ, Jitka

    2013-01-01

    The aim of this bachelor thesis is to analyse atheistic elements in Philip Pullman´ s fantasy trilogy His Dark Materials (The Golden Compass, The Subtle Knife, The Amber Spyglass). The introductory parts of the thesis briefly describe the life of the writer, his literary output, inspirational sources of the trilogy and a critical reception of His Dark Materials. The middle parts of the thesis deal with various types of atheism and describe the contents of the volumes of Pullman´ s trilogy. Th...

  20. Symptom report in detecting breast cancer-related lymphedema

    OpenAIRE

    Fu; Axelrod D; Clel; CM; Qiu Z; Guth AA; Kleinman R; Scagliola J; Haber J

    2015-01-01

    Mei R Fu,1 Deborah Axelrod,2,3 Charles M Cleland,1 Zeyuan Qiu,4 Amber A Guth,2,3 Robin Kleinman,2 Joan Scagliola,2 Judith Haber1 1College of Nursing, New York University, 2Department of Surgery, NYU School of Medicine, 3NYU Clinical Cancer Center, New York, NY, 4Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, USA Abstract: Breast cancer-related lymphedema is a syndrome of abnormal swelling coupled with multiple symptoms resulting from obstru...

  1. VLTI status update: a decade of operations and beyond

    CERN Document Server

    Merand, Antoine; Aller-Carpentier, Emmanuel; Andolfato, Luigi; Alonso, Jaime; Berger, Jean-Philippe; Blanchard, Guillaume; Boffin, Henri; Bourget, Pierre; Bristow, Paul; Cid, Claudia; de Wit, Willem-Jan; del Valle, Diego; Delplancke-Stroebele, Franccoise; Derie, Frederic; Faundez, Lorena; Ertel, Steve; Grellmann, Rebekka; Gitton, Philippe; Glindemann, Andreas; Guajardo, Patricia; Guieu, Sylvain; Guisard, Stephane; Guniat, Serge; Haguenauer, Pierre; Herrera, Christian; Hummel, Christian; La Fuente, Carlos; Lopez, Marcelo; Mardones, Pedro; Morel, Sebastien; Mueller, Andre; Percheron, Isabelle; Duc, Than Phan; Pino, Andres; Poupar, Sebastien; Pozna, Eszter; Ramirez, Andres; Rengaswamy, Sridharan; Rivas, Lionel; Rivinius, Thomas; Segovia, Alex; Schmid, Christian; Schoeller, Markus; Schuhler, Nicolas; Woillez, Julien; Wittkowski, Markus

    2014-01-01

    We present the latest update of the European Southern Observatory's Very Large Telescope interferometer (VLTI). The operations of VLTI have greatly improved in the past years: reduction of the execution time; better offering of telescopes configurations; improvements on AMBER limiting magnitudes; study of polarization effects and control for single mode fibres; fringe tracking real time data, etc. We present some of these improvements and also quantify the operational improvements using a performance metric. We take the opportunity of the first decade of operations to reflect on the VLTI community which is analyzed quantitatively and qualitatively. Finally, we present briefly the preparatory work for the arrival of the second generation instruments GRAVITY and MATISSE.

  2. Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Zambach, Sine; Christiansen, Henning

    2013-01-01

    suggested, but the structure does not seem to be present in all pyrrolysine incorporating genes. Results We propose a strategy to predict pyrrolysine encoding genes in genomes of archaea and bacteria. We cluster open reading frames interrupted by the amber codon based on sequence similarity. We rank these...... prediction of pyrrolysine incorporating genes in genomes of bacteria and archaea leading to insights about the factors driving pyrrolysine translation and identification of new gene candidates. The method predicts known conserved genes with high recall and predicts several other promising candidates for...... experimental verification. The method is implemented as a computational pipeline which is available on request....

  3. Význam evropských obchodních cest a jejich vazby k turismu

    OpenAIRE

    Zemková, Kateřina

    2014-01-01

    This diploma thesis is focused on the importance of European trade routes and their links to tourism. It is divided into two main parts, theoretical and practical. The first part is a processed literary review on the history and development of ancient trade routes, as well as the development of trails in selected area, the development of transport and the oldest ways of traveling. The second part deals with selected Amber trail (specifically Břeclavská route in eastern Moravia), which is cons...

  4. Evaluating the effect of domestic support on international trade

    DEFF Research Database (Denmark)

    Urban, Kirsten; Brockmeier, Martina; Jensen, Hans Grinsted

    We use the Mercantilist Trade Restrictiveness Index (MTRI) to develop an extended index that measures the overall trade effects of domestic support payments in a general equilibrium framework environment. Our index is capable of analyzing the development of the trade restrictiveness of domestic...... 2004 to 2007, the results indicate a decrease in trade distortion stemming from the implementation of decoupled support in the EU. The trade-equivalent protection rate determined under the index shows that domestic support payments restrict trade more than tariffs and export subsidies. Additionally......, the index indicates that reducing WTO amber box domestic support payments would lead to decreased trade restrictiveness....

  5. NUTRITION VALUE OF PLUM TREE FOR HEALTH

    OpenAIRE

    Prajapati P M.; Solanki A S.; Sen D J.

    2012-01-01

    A Plum is a fruit that belongs to the family of peaches and cherries. This fruit is generally round in shape and at times can be oval or heart shaped as well. In addition to the health benefits of peaches and cherrie, it is rich in dietary fiber, which helps improving the digestive system. There are many different varieties of plums available, these are found in different colors like red, blue-black, purple, yellow, green or amber. This is a very delicious and juicy fruit. The plum is a tree,...

  6. Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

    Czech Academy of Sciences Publication Activity Database

    Kabeláč, Martin; Kroutil, O.; Předota, M.; Lankaš, Filip; Šíp, M.

    2012-01-01

    Roč. 14, č. 12 (2012), s. 4217-4229. ISSN 1463-9076 R&D Projects: GA ČR GC204/09/J010; GA MŠk LC512; GA AV ČR IAA400550808 Grant ostatní: GA ČR(CZ) GA203/08/0094; GA MŠk(CZ) LM2010005 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA * graphene * charge density * molecular dynamics * Amber Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.829, year: 2012

  7. Anticodon loop mutations perturb reading frame maintenance by the E site tRNA

    OpenAIRE

    Sanders, Christina L.; Lohr, Kristin J.; Gambill, Holly L.; Curran, Ryan B.; Curran, James F.

    2008-01-01

    The ribosomal E site helps hold the reading frame. Certain tRNA mutations affect translation, and anticodon loop mutations can be especially detrimental. We studied the effects of mutations saturating the anticodon loop of the amber suppressor tRNA, Su7, on the ability to help hold the reading frame when in the E site. We also tested three mutations in the anticodon stem, as well as a mutation in the D stem (the “Hirsh” mutation). We used the Escherichia coli RF2 programmed frameshift site to...

  8. “COLATURA DI ALICI “ CETARESE: EVALUATION OF AMINIC PROFILE

    OpenAIRE

    Anastasio, A; A. Citro; C Chirollo; Felice, A. de (Andrea); R. D’Ambrosio; R. Mercogliano

    2008-01-01

    “Colatura d’alici”is a speciality made in Cetara, a clear ,amber-coloured liquid that has sharp taste, prepared with the juice coming from the anchovy salting process. The anchovies are caught in the Gulf of Salerno between the mounths of March and July. The colatura is ready at the beginning of December. Histamine poisoning, a food-borne chemical intoxication caused by the consumption of food containing toxic levels of histamine, is a syndrome commonly associated with the c...

  9. Suppression of Recj Exonuclease Mutants of Escherichia Coli by Alterations in DNA Helicases II (Uvrd) and IV (Held)

    OpenAIRE

    Lovett, S T; Sutera-Jr., V. A.

    1995-01-01

    The recJ gene encodes a single-strand DNA-specific exonuclease involved in homologous recombination. We have isolated a pseudorevertant strain in which recJ mutant phenotypes were alleviated. Suppression of recJ was due to at least three mutations, two of which we have identified as alterations in DNA helicase genes. A recessive amber mutation, ``uvrD517(am),'' at codon 503 of the gene encoding helicase II was sufficient to suppress recJ partially. The uvrD517(am) mutation does not eliminate ...

  10. Genetically Encoded Cyclopropene Directs Rapid, Photoclick Chemistry-Mediated Protein Labeling in Mammalian Cells

    OpenAIRE

    Yu, Zhipeng; Pan, Yanchao; Wang, Zhiyong; Wang, Jiangyun; Lin, Qing

    2012-01-01

    Genetic incorporation of a cyclopropene amino acid, Nε-(1-methylcycloprop-2-enecarboxamido)-lysine (CpK), into sperm whale myoglobin site-specifically in E. coli as well as enhanced green fluorescent protein in mammalian cells was achieved through amber codon suppression employing an orthogonal aminoacyl-tRNA synthetase/tRNACUA pair. Because of its high ring strain, cyclopropene exhibited fast reaction kinetics (up to 58 ± 16 M−1 s−1) in the photoclick reaction and allowed rapid (~ 2 min) bio...

  11. Structure and aggregation in model tetramethylurea solutions

    International Nuclear Information System (INIS)

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, Xt, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at Xt = 0.005, aggregation is a well established feature of the solution at Xt = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (Xt ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At Xt = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations

  12. Modulation of allele leakiness and adaptive mutability in Escherichia coli

    Indian Academy of Sciences (India)

    R. Jayaraman

    2000-08-01

    It is shown that partial phenotypic suppression of two ochre mutations (argE3 and lacZU118) and an amber mutation (in argE) by sublethal concentrations of streptomycin in an rpsL+ (streptomycin-sensitive) derivative of the Escherichia coli strain AB1157 greatly enhances their adaptive mutability under selection. Streptomycin also increases adaptive mutability brought about by the ppm mutation described earlier. Inactivation of recA affects neither phenotypic suppression by streptomycin nor replication-associated mutagenesis but abolishes adaptive mutagenesis. These results indicate a causal relationship between allele leakiness and adaptive mutability.

  13. Free energy profile of RNA hairpins: a molecular dynamics simulation study.

    Science.gov (United States)

    Deng, Nan-Jie; Cieplak, Piotr

    2010-02-17

    RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted

  14. Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study

    OpenAIRE

    Deng, Nan-Jie; Cieplak, Piotr

    2010-01-01

    RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, t...

  15. J, H, K spectro-interferometry of the Mira variable S Orionis

    OpenAIRE

    Wittkowski, M.; Boboltz, D. A.; Driebe, T.; Bouquin, J. -B. Le; Millour, F.; Ohnaka, K.; Scholz, M.

    2008-01-01

    Aims: We present J, H, K interferometry with a spectral resolution of 35 for the Mira variable S Orionis. We aim at measuring the diameter variation as a function of wavelength that is expected due to molecular layers lying above the continuum-forming photosphere. Methods: Visibility data of S Ori were obtained at phase 0.78 with the VLTI/AMBER instrument using the fringe tracker FINITO at 29 spectral channels between 1.29 and 2.32 mu. Apparent uniform disk (UD) diameters were computed for ea...

  16. Early ontogenesis of the angelfish, Pterophyllum scalare Schultze, 1823 (Cichlidae)

    OpenAIRE

    Agata Korzelecka-Orkisz; Zuzanna Szalast; Dorota Pawlos; Izabella Smaruj; Adam Tañski; Joanna Szulc; Krzysztof Formicki

    2012-01-01

    This study describes the egg membrane structures of angelfish (Pterophyllum scalare), morpho-physiological changes during angelfish embryogenesis from activation to hatching under optimal conditions (28°C; pH 6.8), the developing larvae and fry, the effect of alkaline pH on the early developmental stages of the species, the relationship between food item size and fry survival. Egg membranes (thin, transparent, 1.67-2.18 µm thick) are covered by a sticky substance. The amber-coloured angelfish...

  17. Characterization of two mutant metJ proteins with reduced, temperature-dependent capacity to regulate Escherichia coli K-12 met regulon elements.

    OpenAIRE

    Bala, G A; Collier, C D; Emmett, M R; Johnson, J R

    1989-01-01

    At 28 degrees C, but not at 34 or 42 degrees C, strains with the metJ193 allele repressed chromosomal met genes but not a plasmid-borne met promoter. Increasing the metJ193 gene dosage to two copies resulted in overrepression of chromosomal and plasmid-borne met promoters at 28 degrees C. Suppressing the metJ185 amber mutation with supF (tRNATyr) produced the MetJ185F protein. Strains producing MetJ185F repressed chromosomal met promoters but not a plasmid-borne met promoter at 42 degrees C. ...

  18. Estudio de Diferentes Estrategias en el Almacenamiento Frigorífico Prolongado de tres Variedades de Ciruelo Japones

    OpenAIRE

    VENDRELL VERDÚ, MARIO

    2014-01-01

    [ES] El almacenamiento frigorífico prolongado en ciruelo es cada vez una opción más interesante, no únicamente para desestacionalizar la venta de producto en el mercado doméstico, sino también para poder acceder a mercados lejanos (ultramar,…), con la menor perdida de calidad del producto. A tal efecto se planteó un ensayo con tres variedades de ciruelo japonés (Black Amber, Black Diamond y Black Gold) expuestos a tres tratamientos con objeto de mitigar los daños que el almacen...

  19. Chemische und biochemische Synthesen zur Funktionsuntersuchung von Membranproteinen

    OpenAIRE

    Mak, Ellen

    2014-01-01

    Die vorliegende Arbeit besteht aus drei Teilprojekten. Das erste Projekt umfasst die Etablierung der nonsense-Suppression Methode zum Einbau von unnatürlichen Aminosäuren in Proteine. Dafür wurden die beiden Bausteine, das Dinukleotid pdCpa (5’-Phospho-2’-desoxycytidylyl(3’-5’)adenosin) und die verkürzte tRNA(-CA) mit dem amber Anticodon, zur Herstellung der vollständigen, misacylierten tRNA CUAuaa hergestellt. Das Dinukleotid konnte in sieben Stufen synthetisiert werden. Die verkürzte tRN...

  20. Chapters of the institutional economic history of Königsberg/Kaliningrad

    Directory of Open Access Journals (Sweden)

    Nureev R.

    2010-01-01

    Full Text Available This article consists of a series of short essays dedicated to a certain period of the 'popular' socioeconomic history (with a particular focus on the institutional development problems of the former East Prussia from Antiquity to present days. The authors tackle the issues of the economic history of amber, the role of the Hansa League in the development of medieval trade, the QWERTY-effects in the rail gauge standards, and the peculiarities of the development of the Kaliningrad region in the post-Soviet period.

  1. Stranicy institucional'noj jekonomicheskoj istorii Kjonigsberga/Kaliningrada [Chapters of the institutional economic history of Königsberg/Kaliningrad

    Directory of Open Access Journals (Sweden)

    Nureev Rustem

    2010-01-01

    Full Text Available This article consists of a series of short essays dedicated to a certain period of the 'popular' socioeconomic history (with a particular focus on the institutional development problems of the former East Prussia from Antiquity to present days. The authors tackle the issues of the economic history of amber, the role of the Hansa League in the development of medieval trade, the QWERTY-effects in the rail gauge standards, and the peculiarities of the development of the Kaliningrad region in the post-Soviet period.

  2. Carta de André Jansen a Alain Guy. Fernelmont, 14 de octubre de 1993

    OpenAIRE

    Jansen, André, 1922-

    1993-01-01

    Carta de André Jansen, profesor emérito de literatura iberoamericana en la Universidad de Amberes, a Alain Guy comentándole que acaba de adquirir “Panorama de la philosophie ibéro-américaine” y que sabe que preparó un “Panorama de la pensée ibero-américaine”; preguntándole que si dicho libro está en las librerías.Se conserva el sobre de la carta.

  3. The spin-orbit alignment of the Fomalhaut planetary system probed by optical long baseline interferometry

    OpenAIRE

    Le Bouquin, J.-B.; Absil, Olivier; Benisty, M.; Massi, F.; Mérand, A.; Stefl, S.

    2009-01-01

    Aims. We discuss the spin-orbit orientation of the Fomalhaut planetary system composed of a central A4V star, a debris disk, and a recently discovered planetary companion. Methods: We use spectrally resolved, near-IR long baseline interferometry to obtain precise spectro-astrometric measurements across the Br-gamma absorption line. The achieved astrometric accuracy of ±3 muas and the spectral resolution R=1500 from the AMBER/VLTI instrument allow us to spatially and spectrally resolve the rot...

  4. Effects of Polytypism on Optical Properties and Band Structure of Individual Ga(N)P Nanowires from Correlative Spatially Resolved Structural and Optical Studies.

    Science.gov (United States)

    Dobrovolsky, Alexander; Persson, Per O Å; Sukrittanon, Supanee; Kuang, Yanjin; Tu, Charles W; Chen, Weimin M; Buyanova, Irina A

    2015-06-10

    III-V semiconductor nanowires (NWs) have gained significant interest as building blocks in novel nanoscale devices. The one-dimensional (1D) nanostructure architecture allows one to extend band structure engineering beyond quantum confinement effects by utilizing formation of different crystal phases that are thermodynamically unfavorable in bulk materials. It is therefore of crucial importance to understand the influence of variations in the NWs crystal structure on their fundamental physical properties. In this work we investigate effects of structural polytypism on the optical properties of gallium phosphide and GaP/GaNP core/shell NW structures by a correlative investigation on the structural and optical properties of individual NWs. The former is monitored by transmission electron microscopy, whereas the latter is studied via cathodoluminescence (CL) mapping. It is found that structural defects, such as rotational twins in zinc blende (ZB) GaNP, have detrimental effects on light emission intensity at low temperatures by promoting nonradiative recombination processes. On the other hand, formation of the wurtzite (WZ) phase does not notably affect the CL intensity neither in GaP nor in the GaNP alloy. This suggests that zone folding in WZ GaP does not enhance its radiative efficiency, consistent with theoretical predictions. We also show that the change in the lattice structure have negligible effects on the bandgap energies of the GaNP alloys, at least within the range of the investigated nitrogen compositions of light emitters within the desirable amber-red spectral range. PMID:25988267

  5. Influences of Cross Pollination on Pollen Tube Growth and Fruit Set in Zuili Plums (Prunus salicina)

    Institute of Scientific and Technical Information of China (English)

    Hui-Juan Jia; Feng-Jie He; Cai-Zhen Xiong; Fu-Rong Zhu; Goro Okamoto

    2008-01-01

    Zuill plum (Prunus salicina L.) trees usually set fruit poorly, although they produce high quality fruit. To elucidate the causes of the poor fruit set, pollen tube growth Into pistils and fruit set percentage were investigated after cross-, self- and open-pollination. Ovule development in Zuili pistils was also investigated. Pollen tube penetration into the ovules via the obturator and micropyle was best when Zuili pistils were pollinated by cv. Black Amber (P. domestica) pollen grains, although cross-pollinations with Hongxinli and Miili (P. salicina) pollen were more effective than self- and open-pollination. The fruit set percentage was also highest In pistils pollinated with Black Amber pollen grains. Morphological observation of Zuili pistils revealed that the trees produce "double pistils", developing two ovaries from a basal pistil, at a rate as high as 28%. In such abnormal pistils, most ovules were lacking an embryo sac or were entirely degenerated. The percentage of normally developed ovules was 24.3% and 8.9% in normal and double pistils, respectively. From these results, we conclude that the main causes of poor fruit set of Zuili plums are a lack of effective cross-pollination and the production of high percentages of double pistils in which normally developed ovules are scarcely formed.

  6. New long-proboscid lacewings of the mid-Cretaceous provide insights into ancient plant-pollinator interactions.

    Science.gov (United States)

    Lu, Xiu-Mei; Zhang, Wei-Wei; Liu, Xing-Yue

    2016-01-01

    Many insects with long-proboscid mouthparts are among the pollinators of seed plants. Several cases of the long-proboscid pollination mode are known between fossil insects (e.g., true flies, scorpionflies, and lacewings) and various extinct gymnosperm lineages, beginning in the Early Permian and increasing during the Middle Jurassic to Early Cretaceous. However, details on the morphology of lacewing proboscides and the relevant pollination habit are largely lacking. Here we report on three lacewing species that belong to two new genera and a described genus from mid-Cretaceous (Albian-Cenomanian) amber of Myanmar. All these species possess relatively long proboscides, which are considered to be modified from maxillary and labial elements, probably functioning as a temporary siphon for feeding on nectar. Remarkably, these proboscides range from 0.4-1.0 mm in length and are attributed to the most diminutive ones among the contemporary long-proboscid insect pollinators. Further, they clearly differ from other long-proboscid lacewings which have a much longer siphon. The phylogenetic analysis indicates that these Burmese long-proboscid lacewings belong to the superfamily Psychopsoidea but cannot be placed into any known family. The present findings represent the first description of the mouthparts of long-proboscid lacewings preserved in amber and highlight the evolutionary diversification of the ancient plant-pollinator interactions. PMID:27149436

  7. The production and isolation of Cu-64 and Cu-67 from zinc target material and other radionuclides

    Science.gov (United States)

    Dolley, S. G.; van der Walt, T. N.; Steyn, G. F.; Szelecsényi, F.; Kovács, Z.

    2006-01-01

    A two-stage method is described for the purification of Cu radionuclides from up to 5 g of natZn and other radionuclides. After proton bombardment, co-produced 66,67Ga is removed by passing the dissolved zinc in 7 M HCl through a 2.5 ml column of AmberChrom CG-71, a methacrylate-based polymeric resin. This first column eluate, which contains 65Zn, 64,67Cu, and 56,57,58Co, is taken to incipient dryness and reconstituted in 300 ml 0.05 M HCl. This solution is then pumped through a novel 10 ml column of dithizone impregnated AmberChrom CG-71, where Cu radionuclides are efficiently retained with no breakthrough. Zinc and Co radionuclides elute smoothly during washing with no tailing. More than 97% Cu is eluted by washing with 40 ml 5 M HNO3 warmed to 50 °C. No dithizone is detected in this eluate.

  8. Advanced Strategies for Outdoor LED Lighting Applications and Technologies to Curtail Regional Light Pollution Effects

    Science.gov (United States)

    Monrad, Christian Karl; Benya, James R.

    2015-08-01

    LED lighting systems for outdoor lighting applications continue to evolve as do strategies to mitigate related effects upon regional astronomical and ecological assets. The improving availability and relative lumen-per-watt efficiencies of blue-suppressed low correlated color temperature emitters, narrow band amber, phosphor converted amber, and various combinations of broadband emitters and sub-550NM and sub-500NM filters allow for a wide palette of choices to be assessed to suit site-specific and task-specific lighting needs. In addition to static spectral content options, readily available luminaire designs also include precise geometric beam shape selections and adaptive controls to include dimming, dynamic spectral shifting, motion detection, and dynamic beam shaping to minimize total environmental lumen emissions throughout the course of the nighttime hours.Regional and international light pollution mitigation regulations will also be briefly addressed in the context of luminaire shielding and spectral content control efforts to better protect human quality of life issues as well as astronomical and ecological interests.The presentation will include numerous spectral content graphs for various luminaire options as well as project-specific case studies to document comparisons of legacy lighting systems versus high-performance LED systems with regard to total lumen emissions, skyglow contributions, energy efficiency, and end-user satisfaction with the installed LED lighting systems. Physical samples of various luminaires will also be available for hands-on assessments.

  9. Evidence for non-diverging time-scales in glass-forming liquids

    Science.gov (United States)

    McKenna, Gregory

    2013-03-01

    One perceived important signature of the ``ideal'' glass transition and of the complex fluid nature of glass-forming liquids remains the apparent divergence of the dynamics at temperatures above zero Kelvin. Recently, however, this perception has been increasingly challenged both through experiments and in new theories of the dynamics of glass forming systems. In this presentation we summarize some of the prior evidence suggesting that time scales actually do not diverge in glasses that are aged into equilibrium, perhaps 15 K below the conventional glass transition temperature Tg. We then show new results from an extremely densified glass, 20 Ma old Jamaican amber, in which we were able to obtain the upper bound to the relaxation times through a step-wise temperature scan in which the stress relaxation response of the amber was measured both below and above the fictive temperature TF . We find that in the case of the upper bound responses at T>TF , there is a strong deviation of the response from the Super-Arrhenius Vogel-Fulcher behavior and this persists to the fictive temperature which is some 33.8 K below Tg. The results are compared to the parabolic model of Chandler and co-workers and we find the model to be consistent with our results if the value of Tx in the model is taken to be the calorimetric glass transition temperature. The significance of the results will be discussed. We acknowledge NSF grants DMR-0804438 and DMR-1207070 for support of this work

  10. Palaeoanellus dimorphus gen. et sp. nov. (Deuteromycotina): a Cretaceous predatory fungus.

    Science.gov (United States)

    Schmidt, Alexander R; Dörfelt, Heinrich; Perrichot, Vincent

    2008-10-01

    In habitats where nitrogen is the limiting factor, carnivorous fungi gain an advantage by preying on nematodes and other microorganisms. These fungi are abundant in modern terrestrial ecosystems, but they are not predestined for preservation as fossils. Conclusions on their evolutionary history are therefore mainly based on molecular studies that are generally limited to those taxa that have survived until today. Here we present a fossil dimorphic fungus that was found in Late Albian amber from southwestern France. This fungus possessed unicellular hyphal rings as trapping devices and formed blastospores from which a yeast stage developed. The fossil probably represents an anamorph of an ascomycete and is described as Palaeoanellus dimorphus gen. et sp. nov. Because predatory fungi with regular yeast stages are not known from modern ecosystems, the fungus is assumed to not be related to any Recent carnivorous fungus and to belong to an extinct lineage of carnivorous fungi. The inclusions represent the only record of fossil fungi that developed trapping devices, so far. The fungus lived c. 100 million years ago in a limnetic-terrestrial microhabitat, and it was a part of a highly diverse biocenosis at the forest floor of a Cretaceous coastal amber forest. PMID:21632336

  11. Fossil evidence for the early ant evolution

    Science.gov (United States)

    Perrichot, Vincent; Lacau, Sébastien; Néraudeau, Didier; Nel, André

    2008-02-01

    Ants are one of the most studied insects in the world; and the literature devoted to their origin and evolution, systematics, ecology, or interactions with plants, fungi and other organisms is prolific. However, no consensus yet exists on the age estimate of the first Formicidae or on the origin of their eusociality. We review the fossil and biogeographical record of all known Cretaceous ants. We discuss the possible origin of the Formicidae with emphasis on the most primitive subfamily Sphecomyrminae according to its distribution and the Early Cretaceous palaeogeography. And we review the evidence of true castes and eusociality of the early ants regarding their morphological features and their manner of preservation in amber. The mid-Cretaceous amber forest from south-western France where some of the oldest known ants lived, corresponded to a moist tropical forest close to the shore with a dominance of gymnosperm trees but where angiosperms (flowering plants) were already diversified. This palaeoenvironmental reconstruction supports an initial radiation of ants in forest ground litter coincident with the rise of angiosperms, as recently proposed as an ecological explanation for their origin and successful evolution.

  12. The inner circumstellar disk of the UX Ori star V1026 Sco

    CERN Document Server

    Vural, J; Kishimoto, M; Weigelt, G; Hofmann, K -H; Kraus, S; Schertl, D; Dugué, M; Duvert, G; Lagarde, S; Massi, F

    2014-01-01

    The UX Ori type variables (named after the prototype of their class) are intermediate-mass pre-main sequence objects. One of the most likely causes of their variability is the obscuration of the central star by orbiting dust clouds. We investigate the structure of the circumstellar environment of the UX~Ori star V1026 Sco (HD 142666) and test whether the disk inclination is large enough to explain the UX Ori variability. We observed the object in the low-resolution mode of the near-infrared interferometric VLTI/AMBER instrument and derived H- and K-band visibilities and closure phases. We modeled our AMBER observations, published Keck Interferometer observations, archival MIDI/VLTI visibilities, and the spectral energy distribution using geometric and temperature-gradient models. Employing a geometric inclined-ring disk model, we find a ring radius of 0.15 +- 0.06 AU in the H band and 0.18 +- 0.06 AU in the K band. The best-fit temperature-gradient model consists of a star and two concentric, ring-shaped disk...

  13. Exploiting molecular dynamics in Nested Sampling simulations of small peptides

    Science.gov (United States)

    Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

    2016-04-01

    Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

  14. The production and isolation of Cu-64 and Cu-67 from zinc target material and other radionuclides

    International Nuclear Information System (INIS)

    A two-stage method is described for the purification of Cu radionuclides from up to 5 g of natZn and other radionuclides. After proton bombardment, co-produced 66,67Ga is removed by passing the dissolved zinc in 7 M HCl through a 2.5 ml column of AmberChrom CG-71, methacrylate-based polymeric resin. This first column eluate, which contains 65Zn, 64,67Cu, and 56,57,58Co, is taken to incipient dryness and reconstituted in 300 ml 0.05 M HCl. This solution is then pumped through a novel 10 ml column of dithizone impregnated AmberChrom CG-71, where Cu radionuclides are efficiently retained with no breakthrough. Zinc and Co radionuclides elute smoothly during washing with no tailing. More than 97 % Cu is eluted by washing with 40 ml 5 M HNO3 warmed to 50 degC. No dithizone is detected in this eluate. (author)

  15. The Change in the Parameters of Blood Plasma Infrared Spectra of Animals-carriers of Tumours Against the Background of Dietary Supplement Administration

    Directory of Open Access Journals (Sweden)

    Krasnikova О.V.

    2011-12-01

    Full Text Available The aim of the investigation is to study the dynamics of blood plasma IR-spectra parameters of animals-carriers of tumours against the background of dietary supplement administration. Materials and Methods. White non-pedigree male rats (n=30 with Pliss lymphosarcoma (РL have been administered the solutions of the substances under test (amber acid, oligosaccharide chitosan succinate, oligosaccharide chitosan succinate-ascorbate by probe into the stomach in a dose of 100 mg per kg of an animal’s mass, within seven days starting with the 6th day after strain transplantation. For IR-spectrum parameters there have been taken particular values resulted from the division of absorption bands peaks heights by each other: X=1165/1070, Y=1165/1150, Z=1165/1125. Results. The change of blood plasma infrared spectra (p≤0.05 has showed that in tumour carriers the content of glucose in blood plasma increases. The administration of amber acid and its derivatives contributes to the accumulation of glucose, as well as monophosphates (AMP, etc and the reduction of nucleoside triphosphates (ATP, GTP and others, that can be explained by energy imbalance in animals-carriers of tumours, being potentially dangerous and contributing to the acceleration of tumour growth.

  16. Radio detection of extensive air showers at the Pierre Auger Observatory

    International Nuclear Information System (INIS)

    The Pierre Auger Observatory explores the potential of radio-detection techniques to measure extensive air showers (EAS) induced by ultra-high energy cosmic rays. To study in detail the mechanisms responsible for radio emission in the MHz range, the Auger Engineering Radio Array has been installed at the Observatory. Presently consisting of 24 radio-detection stations, this number will grow to 150 units covering an area of almost 20 km2. Novel detection techniques based on the GHz emission from the EAS are currently being studied. AMBER (Air-shower Microwave Bremsstrahlung Experimental Radiometer) and MIDAS (Microwave Detection of Air Showers) are prototypes for a large imaging dish antenna. In EASIER (Extensive Air Shower Identification using Electron Radiometer), the microwave emission is detected by antenna horns located on each surface detector. MIDAS is a self-triggering system while AMBER and EASIER use the trigger from the Auger detectors to record the emission. The status of these radio-detection R and D efforts at the Pierre Auger Observatory will be reported

  17. Comparative studies on the structural proteins of T3 and T7 phages

    DEFF Research Database (Denmark)

    Issinger, O G; Falk, H

    1976-01-01

    A comparison of the coat protein patterns of the wild types of the related phages T3 and T7 on SDS polyacrylamide gel electrophoresis was carried out. After infection of the nonpermissive host with T7 amber mutants in genes 7, 11, 12, 13 or 17 and T3 amber mutants in genes 11, 12, 13 and 17...... respectively, noninfectious, DNA containing particles were produced. The protein pattern, as well as electron microscopy of defective particles of T3 and T7 led to the conclusion that the proteins specified by genes 11, 12, 13 and 17 are tail proteins whereas the proteins coded by genes 7, 8, 10, 14, 15 and 16...... enter the head structure. The "serum blocking protein" (gene 17 product) seems to play a different role in the assembly of T3 and T7 tails, since T3 particles defective in gene 17 did not show any tail structure connected with the head whereas T7 particles defective in gene 17 had a tail which looked...

  18. Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.

    Science.gov (United States)

    Hammerling, Michael J; Gollihar, Jimmy; Mortensen, Catherine; Alnahhas, Razan N; Ellington, Andrew D; Barrick, Jeffrey E

    2016-08-01

    Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to experimentally study the impact of alternative genetic codes on the evolution of biological systems. We explored how Escherichia coli strains that incorporate a 21st nonstandard amino acid (nsAA) at the recoded amber (TAG) stop codon evolve resistance to the antibiotic rifampicin. Resistance to rifampicin arises from chromosomal mutations in the β subunit of RNA polymerase (RpoB). We found that a variety of mutations that lead to substitutions of nsAAs in the essential RpoB protein confer robust rifampicin resistance. We interpret these results in a framework in which an expanded code can increase evolvability in two distinct ways: by adding a new letter with unique chemical properties to the protein alphabet and by altering the mutational connectivity of amber-adjacent codons by converting a lethal nonsense mutation into a missense mutation. Finally, we consider the implications of these results for the evolution of alternative genetic codes. In our experiments, reliance on a mutation to a reassigned codon for a vital trait is not required for the long-term maintenance of an expanded genetic code and may even destabilize incorporation of an nsAA, a result that is consistent with the codon capture model of genetic code evolution. PMID:27189550

  19. Debris-carrying camouflage among diverse lineages of Cretaceous insects.

    Science.gov (United States)

    Wang, Bo; Xia, Fangyuan; Engel, Michael S; Perrichot, Vincent; Shi, Gongle; Zhang, Haichun; Chen, Jun; Jarzembowski, Edmund A; Wappler, Torsten; Rust, Jes

    2016-06-01

    Insects have evolved diverse methods of camouflage that have played an important role in their evolutionary success. Debris-carrying, a behavior of actively harvesting and carrying exogenous materials, is among the most fascinating and complex behaviors because it requires not only an ability to recognize, collect, and carry materials but also evolutionary adaptations in related morphological characteristics. However, the fossil record of such behavior is extremely scarce, and only a single Mesozoic example from Spanish amber has been recorded; therefore, little is known about the early evolution of this complicated behavior and its underlying anatomy. We report a diverse insect assemblage of exceptionally preserved debris carriers from Cretaceous Burmese, French, and Lebanese ambers, including the earliest known chrysopoid larvae (green lacewings), myrmeleontoid larvae (split-footed lacewings and owlflies), and reduviids (assassin bugs). These ancient insects used a variety of debris material, including insect exoskeletons, sand grains, soil dust, leaf trichomes of gleicheniacean ferns, wood fibers, and other vegetal debris. They convergently evolved their debris-carrying behavior through multiple pathways, which expressed a high degree of evolutionary plasticity. We demonstrate that the behavioral repertoire, which is associated with considerable morphological adaptations, was already widespread among insects by at least the Mid-Cretaceous. Together with the previously known Spanish specimen, these fossils are the oldest direct evidence of camouflaging behavior in the fossil record. Our findings provide a novel insight into early evolution of camouflage in insects and ancient ecological associations among plants and insects. PMID:27386568

  20. Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.

    Science.gov (United States)

    Chang, Le; Ishikawa, Takeshi; Kuwata, Kazuo; Takada, Shoji

    2013-05-30

    Accurate computational estimate of the protein-ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein-ligand simulations, we use a protein-specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO-RESP method to two proteins, dodecin, and lysozyme, we found that protein-specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO-RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. PMID:23420697

  1. Inhomogeneities in molecular layers of Mira atmospheres

    CERN Document Server

    Wittkowski, M; Ireland, M; Karovicova, I; Ohnaka, K; Scholz, M; van Wyk, F; Whitelock, P; Wood, P R; Zijlstra, A A

    2011-01-01

    We obtained K-band spectro-interferometric observations of the Miras R Cnc, X Hya, W Vel, and RW Vel with a spectral resolution of 1500 using the VLTI/AMBER instrument. We obtained concurrent JHKL photometry using the the Mk II instrument at the SAAO. Our sources have wavelength-dependent visibility values that are consistent with earlier low-resolution AMBER observations of S Ori and with the predictions of dynamic model atmosphere series based on self-excited pulsation models. The wavelength-dependent UD diameters show a minimum near the near-continuum bandpass at 2.25 um. They increase by up to 30% toward the H2O band at 2.0 um and by up to 70% at the CO bandheads. The dynamic model atmosphere series show a consistent wavelength-dependence, and their parameters such as the visual phase, effective temperature, and distances are consistent with independent estimates. The closure phases have significantly wavelength-dependent non-zero values indicating deviations from point symmetry. For example, the R Cnc cl...

  2. Molecular dynamics simulations of coalescence in TBP/n-dodecane and water

    International Nuclear Information System (INIS)

    Tri-n-butylphosphate (TBP) is regarded as the work horse of nuclear fuel cycle. The PUREX process involving the extraction of U (VI) and Pu (IV) from the dissolver solution using a solution of 1.1 M TBP in n-dodecane (n-DD). The physiochemical changes such as dispersion, coalescence and phase disengagement occurring at the interphase during the extraction of metal ion is a complex process. Understanding the phase disengagement at molecular level is essential for understanding the hydrodynamics of solvent extraction process. In this context, MD simulations of coalescence and phase disengagement of the organic phase (TBP or 1.1 M TBP/n-DD) and aqueous phase using AMBER-II (Assisted Model Building with Energy Refinement) are carried out. GAFF Amber force field was used for all energy minimization calculations. The corresponding potential energy is given by equation 1, and the significances of various terms are described elsewhere. All the simulations were carried out by applying suitable periodic boundary conditions with constant pressure coupling. The simulations were performed for 100 ns

  3. MCPB.py: A Python Based Metal Center Parameter Builder.

    Science.gov (United States)

    Li, Pengfei; Merz, Kenneth M

    2016-04-25

    MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling. PMID:26913476

  4. Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini Mägdefrau

    Science.gov (United States)

    Kaasalainen, Ulla; Heinrichs, Jochen; Krings, Michael; Myllys, Leena; Grabenhorst, Heinrich; Rikkinen, Jouko; Schmidt, Alexander R.

    2015-01-01

    One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon. PMID:26053106

  5. Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette

    Directory of Open Access Journals (Sweden)

    Guillaume Borrel

    2014-01-01

    Full Text Available Pyrrolysine (Pyl, the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber   tRNAPyl with an imperfect anticodon stem and a shortened tRNAPyl synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.

  6. Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.

    Science.gov (United States)

    Perez, Alberto; MacCallum, Justin L; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A

    2015-10-13

    Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments. PMID:26574266

  7. Effect of Organic and Conventional Management on Bio-Functional Quality of Thirteen Plum Cultivars (Prunus salicina Lindl..

    Directory of Open Access Journals (Sweden)

    Francisco Julián Cuevas

    Full Text Available In this study, thirteen Japanese plum cultivars (Prunus salicina Lindl. grown under conventional and organic conditions were compared to evaluate the influence of the culture system on bioactive compounds. Their organic acids content (malic, citric, tartaric, succinic, shikimic, ascorbic and fumaric acid, total polyphenols, total anthocyanins, total carotenoids and antioxidant capacity (FRAP, ABTS were evaluated. The study was performed during two consecutive seasons (2012 and 2013 in two experimental orchards located at the IFAPA centre Las Torres-Tomejil (Seville, SW Spain. The culture system affected all the studied parameters except for total carotenoid content. The organic plums had significantly higher polyphenol and anthocyanin concentrations and a greater antioxidant capacity. Additionally, significant differences between cultivars were also found. 'Showtime' and 'Friar' were the cultivars with the highest polyphenol concentration and antioxidant capacity. 'Black Amber' had the highest anthocyanin content and 'Larry Ann' and 'Songold' the highest carotenoid content. 'Sapphire' and 'Black amber' were the cultivars with the highest concentration of ascorbic acid. Our results showed a strong year effect. In conclusion, organic management had an impact on the production of phytochemical compounds in plums.

  8. Photoluminescence spectroscopy of electron-irradiation induced defects in cubic boron nitride (cBN)

    International Nuclear Information System (INIS)

    Cubic boron nitride is an ultra-hard material that is widely used in industrial applications where its specific mechanical properties make it the material of choice. Compared to diamond, which has similar applications, relatively little is known about the defects in cBN, their structure, electronic properties and their possible effects on the mechanical properties. We present results of photoluminescence spectroscopy at low temperature (<10 K) of two types of cBN irradiated at ambient temperature with 1.9 MeV electrons. All the samples were small (<1 mm diameter) single crystals of cBN. Three defect centres (with narrow lines at 2.28 eV, 2.15 eV and 1.98 eV) are introduced in both the amber-coloured and black-brown coloured samples by the irradiation. The amber coloured sample also shows a defect centre (at 1.65 eV) that is present before and after irradiation. Line shape analysis of the zero phonon lines of all three irradiation-induced centres shows that the lines are predominantly Gaussian in character, suggesting that line-type defects such as dislocations are a prevalent characteristic of these crystals. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    Science.gov (United States)

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-01

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419

  10. The spin-orbit alignment of the Fomalhaut planetary system probed by optical long baseline interferometry

    Science.gov (United States)

    Le Bouquin, J.-B.; Absil, O.; Benisty, M.; Massi, F.; Mérand, A.; Stefl, S.

    2009-05-01

    Aims: We discuss the spin-orbit orientation of the Fomalhaut planetary system composed of a central A4V star, a debris disk, and a recently discovered planetary companion. Methods: We use spectrally resolved, near-IR long baseline interferometry to obtain precise spectro-astrometric measurements across the Br-γ absorption line. The achieved astrometric accuracy of ±3 μas and the spectral resolution R=1500 from the AMBER/VLTI instrument allow us to spatially and spectrally resolve the rotating photosphere. Results: We find a position angle {PAstar}=65° ± 3° for the stellar rotation axis, perpendicular to the literature measurement for the disk position angle ({PAdisk}=156.0 ° ± 0.3°). This is the first time such a test could be performed for a debris disk, and in a non-eclipsing system. Additionally, our measurements suggest unexpected backward-scattering properties for the circumstellar dust grains. Conclusions: Our observations validate the standard scenario for star and planet formation in which the angular momentum of the planetary systems are expected to be colinear with the stellar spins. Based on observations collected at the VLTI (ESO Paranal, Chile), with the 082.C-0376 program from the AMBER Guaranteed Time of the Osservatorio Astrofisico di Arcetri (INAF, Italy).

  11. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

    Science.gov (United States)

    O'Brien, Evan S; Wand, A Joshua; Sharp, Kim A

    2016-06-01

    Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O(2) values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R(2) of 0.8. PMID:26990788

  12. New long-proboscid lacewings of the mid-Cretaceous provide insights into ancient plant-pollinator interactions

    Science.gov (United States)

    Lu, Xiu-Mei; Zhang, Wei-Wei; Liu, Xing-Yue

    2016-01-01

    Many insects with long-proboscid mouthparts are among the pollinators of seed plants. Several cases of the long-proboscid pollination mode are known between fossil insects (e.g., true flies, scorpionflies, and lacewings) and various extinct gymnosperm lineages, beginning in the Early Permian and increasing during the Middle Jurassic to Early Cretaceous. However, details on the morphology of lacewing proboscides and the relevant pollination habit are largely lacking. Here we report on three lacewing species that belong to two new genera and a described genus from mid-Cretaceous (Albian-Cenomanian) amber of Myanmar. All these species possess relatively long proboscides, which are considered to be modified from maxillary and labial elements, probably functioning as a temporary siphon for feeding on nectar. Remarkably, these proboscides range from 0.4–1.0 mm in length and are attributed to the most diminutive ones among the contemporary long-proboscid insect pollinators. Further, they clearly differ from other long-proboscid lacewings which have a much longer siphon. The phylogenetic analysis indicates that these Burmese long-proboscid lacewings belong to the superfamily Psychopsoidea but cannot be placed into any known family. The present findings represent the first description of the mouthparts of long-proboscid lacewings preserved in amber and highlight the evolutionary diversification of the ancient plant-pollinator interactions. PMID:27149436

  13. Assessing the levels of food shortage using the traffic light metaphor by analyzing the gathering and consumption of wild food plants, crop parts and crop residues in Konso, Ethiopia

    Directory of Open Access Journals (Sweden)

    Ocho Dechassa

    2012-08-01

    Full Text Available Abstract Background Humanitarian relief agencies use scales to assess levels of critical food shortage to efficiently target and allocate food to the neediest. These scales are often labor-intensive. A lesser used approach is assessing gathering and consumption of wild food plants. This gathering per se is not a reliable signal of emerging food stress. However, the gathering and consumption of some specific plant species could be considered markers of food shortage, as it indicates that people are compelled to eat very poor or even health-threatening food. Methods We used the traffic light metaphor to indicate normal (green, alarmingly low (amber and fully depleted (red food supplies and identified these conditions for Konso (Ethiopia on the basis of wild food plants (WFPs, crop parts (crop parts not used for human consumption under normal conditions; CPs and crop residues (CRs being gathered and consumed. Plant specimens were collected for expert identification and deposition in the National Herbarium. Two hundred twenty individual households free-listed WFPs, CPs, and CRs gathered and consumed during times of food stress. Through focus group discussions, the species list from the free-listing that was further enriched through key informants interviews and own field observations was categorized into species used for green, amber and red conditions. Results The study identified 113 WFPs (120 products/food items whose gathering and consumption reflect the three traffic light metaphors: red, amber and green. We identified 25 food items for the red, 30 food items for the amber and 65 food items for the green metaphor. We also obtained reliable information on 21 different products/food items (from 17 crops normally not consumed as food, reflecting the red or amber metaphor and 10 crop residues (from various crops, plus one recycled stuff which are used as emergency foods in the study area clearly indicating the severity of food stress (red metaphor

  14. Douglas flight deck design philosophy

    Science.gov (United States)

    Oldale, Paul

    1990-01-01

    The systems experience gained from 17 years of DC-10 operation was used during the design of the MD-11 to automate system operation and reduce crew workload. All functions, from preflight to shutdown at the termination of flight, require little input from the crew. The MD-11 aircraft systems are monitored for proper operation by the Aircraft Systems Controllers (ASC). In most cases, system reconfiguration as a result of a malfunction is automated. Manual input is required for irreversible actions such as engine shutdown, fuel dump, fire agent discharge, or Integrated Drive Generator (IDG) disconnect. During normal operations, when the cockpit is configured for flight, all annunciators on the overhead panel will be extinguished. This Dark Cockpit immediately confirms to the crew that the panels are correctly configured and that no abnormalities are present. Primary systems annunciations are shown in text on the Alert Area of the Engine and Alert Display (EAD). This eliminates the need to scan the overhead. The MD-11 aircraft systems can be manually controlled from the overhead area of the cockpit. The center portion of the overhead panel is composed of the primary aircraft systems panels, which include FUEL, AIR, Electrical (ELEC) and Hydraulic (HYD) systems, which are easily accessible from both flight crew positions. Each Aircraft Systems Controller (ASC) has two automatic channels and a manual mode. All rectangular lights are annunciators. All square lights are combined switches and annunciators called switch/lights. Red switch/lights on the overhead (Level 3 alerts) are for conditions requiring immediate crew action. Amber (Level 2 or Level 1 alerts) indicates a fault or switch out of position requiring awareness or crew interaction. Overhead switches used in normal operating conditions will illuminate blue when in use (Level 0 alerts) such as WING ANTI-ICE - ON. An overhead switch/light with BLACK LETTERING on an amber or red background indicates a system

  15. STONEWORK OF THE ALTAI POPULATION AT THE 2nd CENTURY B.C. – THE 5 th CENTURY AD

    Directory of Open Access Journals (Sweden)

    V. I. SOENOV

    2015-01-01

    Full Text Available In this work we generalize the results of our study of stonework in Altai at the Hun-Sarmat period, based on the researches of the archaeological sources. It is noted that this craft is represented in the region only by products of stone cutting manufacture, which are basically tools and adornments, among which the most common ones are spindles, grinding bars or whetstones, beads and pendants from various types of stones. Findings of other stone products (incenseburner, stone graters, and plaques are rare. A set of technological operations and tools was quite diverse: to make stone adornments the Altai ancient masters used such operations as cutting, grinding, drilling, and polishing. As a result of the study, we conclude that tools and part of adornments were made of local rocks: rock crystal, calcite, fine-grained white marble, microcrystalgreen slates. Types of stone, from which were made the rest of the found adornments (carnelian, sard, sapphirine, amber, jade etc. were imported. Studies of geological formations in Altai did not show deposits of carnelian, sarder and sapphirine. Deposits of carnelian (serdolik are widespread throughout the world: they are known in the Trans-Baikal region, Yakutia, the Far East, the Crimea, India and Central America. Sard is usually found along with carnelian. In Russia, significant reserves of sard have been found only in the Trans-Baikal region. Sapphirine is a rare variety of chalcedony, its deposits have been found only in India. Natural amber has not been found in Altai; its nearest deposit is located in Burma and the Baltic-Dnepr amber-bearing area. Jade is a widespread decorative stone. The deposits of jade are known in Yakutia, Tuva, China and many other areas, but it was not mined in Altai. Adornments from these types of stones appeared in Altai rather as finished products, than raw materials. The place of their production is to be identified.

  16. Technical Feasibility Assessment of LED Roadway Lighting on the Golden Gate Bridge

    Energy Technology Data Exchange (ETDEWEB)

    Tuenge, Jason R.

    2012-09-01

    Subsequent to preliminary investigations by the Golden Gate Bridge Highway & Transportation District (GGB), in coordination with Pacific Gas & Electric (PG&E), the GATEWAY Demonstration program was asked to evaluate the technical feasibility of replacing existing roadway lighting on the bridge with products utilizing LED technology. GGB and PG&E also indicated interest in induction (i.e., electrodeless fluorescent) technology, since both light source types feature rated lifetimes significantly exceeding those of the existing high-pressure sodium (HPS) and low-pressure sodium (LPS) products. The goal of the study was to identify any solutions which would reduce energy use and maintenance without compromising the quantity or quality of existing illumination. Products used for roadway lighting on the historic bridge must be installed within the existing amber-lensed shoebox-style luminaire housings. It was determined that induction technology does not appear to represent a viable alternative for the roadway luminaires in this application; any energy savings would be attributable to a reduction in light levels. Although no suitable LED retrofit kits were identified for installation within existing luminaire housings, several complete LED luminaires were found to offer energy savings of 6-18%, suggesting custom LED retrofit kits could be developed to match or exceed the performance of the existing shoeboxes. Luminaires utilizing ceramic metal halide (CMH) were also evaluated, and some were found to offer 28% energy savings, but these products might actually increase maintenance due to the shorter rated lamp life. Plasma technology was evaluated, as well, but no suitable products were identified. Analysis provided in this report was completed in May 2012. Although LED technologies are expected to become increasingly viable over time, and product mock-ups may reveal near-term solutions, some options not currently considered by GGB may ultimately merit evaluation. For

  17. The core and O-polysaccharide structure of the Caulobacter crescentus lipopolysaccharide.

    Science.gov (United States)

    Jones, Michael D; Vinogradov, Evgeny; Nomellini, John F; Smit, John

    2015-01-30

    Here we describe the analysis of the structure of the lipopolysaccharide (LPS) from Caulobacter crescentus strain JS1025, a derivative of C. crescentus CB15 NA1000 with an engineered amber mutation in rsaA, leading to the loss of the protein S-layer and gene CCNA_00471 encoding a putative GDP-L-fucose synthase. LPS was isolated using an aqueous membrane disruption method. Polysaccharide and core oligosaccharide were produced by mild acid hydrolysis and analyzed by nuclear magnetic resonance spectroscopy and chemical methods. Spectra revealed the presence of two polysaccharides, one of them, a rhamnan, could be removed using periodate oxidation. Another polymer, built from 4-amino-4-deoxy-D-rhamnose (perosamine), mannose, and 3-O-methyl-glucose, should be the O-chain of the LPS according to genetic data. The attribution of the rhamnan as a part of LPS or a separate polymer was not possible. PMID:25498010

  18. HD139614: the interferometric case for a group-Ib pre-transitional young disk

    CERN Document Server

    Labadie, Lucas; Kreplin, Alexander; Lopez, Bruno; Wolf, Sebastian; Weigelt, Gerd; Ertel, Steve; Berger, Jean-Philippe; Pott, Jorg-Uwe; Danchi, William C

    2014-01-01

    The Herbig Ae star HD 139614 is a group-Ib object, which featureless SED indicates disk flaring and a possible pre-transitional evolutionary stage. We present mid- and near-IR interferometric results collected with MIDI, AMBER and PIONIER with the aim of constraining the spatial structure of the 0.1-10 AU disk region and assess its possible multi-component structure. A two-component disk model composed of an optically thin 2-AU wide inner disk and an outer temperature-gradient disk starting at 5.6 AU reproduces well the observations. This is an additional argument to the idea that group-I HAeBe inner disks could be already in the disk-clearing transient stage. HD 139614 will become a prime target for mid-IR interferometric imaging with the second-generation instrument MATISSE of the VLTI.

  19. The conditions of respect of rules in young and elderly drivers: An exploratory study

    Directory of Open Access Journals (Sweden)

    Didier Le-Gall

    2011-01-01

    Full Text Available This study is concerned with the theoretical field of social representations and conditionality of norms. The aim is to study the perception of driving norms by structuring them around individual and group behaviours. We propose to evaluate driving conditionality with the questionnaire based on conditional scenarios. The tool has been proposed to 40 young drivers and 48 elderly drivers. Results show that the driving representation is conditional for the 2 groups, except with the scenario of wearing seat belt. The more conditional scenarios are the same for the 2 groups (scenarios of speed limit and amber light, with higher scores of conditionality for young drivers. The representation of the driving shows that with the system of legal norms (Highway Code, there is a system of social norms related to the actual practices of the users. This study illustrates an important aspect of road safety: the social perception of rules and its impact on driver behaviour.

  20. Infrared source test

    Energy Technology Data Exchange (ETDEWEB)

    Ott, L.

    1994-11-15

    The purpose of the Infrared Source Test (IRST) is to demonstrate the ability to track a ground target with an infrared sensor from an airplane. The system is being developed within the Advance Technology Program`s Theater Missile Defense/Unmanned Aerial Vehicle (UAV) section. The IRST payload consists of an Amber Radiance 1 infrared camera system, a computer, a gimbaled mirror, and a hard disk. The processor is a custom R3000 CPU board made by Risq Modular Systems, Inc. for LLNL. The board has ethernet, SCSI, parallel I/O, and serial ports, a DMA channel, a video (frame buffer) interface, and eight MBytes of main memory. The real-time operating system VxWorks has been ported to the processor. The application code is written in C on a host SUN 4 UNIX workstation. The IRST is the result of a combined effort by physicists, electrical and mechanical engineers, and computer scientists.

  1. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes

    Science.gov (United States)

    Pineda De Castro, Luis Felipe; Dopson, Mark

    2016-01-01

    In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow. PMID:27167213

  2. Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

    DEFF Research Database (Denmark)

    Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas;

    2014-01-01

    binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce the...... photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact with a...

  3. INFRARED INTERFEROMETRY OF YOUNG STELLAR OBJECTS

    Directory of Open Access Journals (Sweden)

    S. Kraus

    2010-01-01

    Full Text Available Discos circunestelares alrededor de objetos estelares jovenes desempeñan un rol fundamental en el proceso de formación de estrellas y proporcionan una etapa para la formación de planetas. Desde recientemente, la interferometría infrarroja proporciona la resolución espacial requerida para estudiar directamente la distribución del gas y del polvo en la Unidad astroóomica más cercana alrededor de la estrella en formación. Presentamos investigaciones recientes en las cuales empleamos el VLTI e interferométros en infrarrojo cercano y lejano AMBER y MIDI para restringir la geometría y condiciones físicas de discos alrededor de estrellas Herbig Ae/Be y estudiar los procesos del acreción y decreción que ocurren cerca de la estrella central.

  4. Organic matter of fossil origin in the amberine speleothems from El Soplao Cave (Cantabria, Northern Spain

    Directory of Open Access Journals (Sweden)

    Gázquez Fernando

    2012-01-01

    Full Text Available Unusual amberine-coloured speleothems were recently found in El Soplao Cave (Cantabria, Spain. Chromophore elements such as Fe, Mn, Cd, Co or Ti were not present in significant quantities. Rather, our data show that their colour comes from leachates of fossilized organic material hosted in the carbonaceous Urgonian facies of the host rock. These leachates are related to the Cretaceous amber deposit that has been recently discovered in the vicinity of El Soplao Cave. The presence of humic and fulvic acids of fossil origin were confirmed by IR and Raman spectroscopic analysis of the carbonaceous strata and the speleothems. In addition, the mineralogy of the amberine speleothems was studied. Alternating bands made of calcite and aragonite reveal that periods of humidity and aridity occurred within the cave during the speleothem genesis.

  5. Potential Optical Counterparts to High Mass X-Ray and γ-Ray Binaries

    Science.gov (United States)

    Mitchell, Carl; McSwain, M. V.

    2011-01-01

    We seek to identify optical counterparts to several previously discovered high mass X-ray binaries and γ-ray sources from the Liu et al. and Fermi first year catalogues. Observations were taken with the CTIO 0.9-meter telescope, operated by the SMARTS Consortium. Photometric data were taken in the Strömgren b and y filters, as well as a narrow-band Hα filter. We present color-color diagrams of y-Hα vs. b-y for each field, and candidates for optical counterparts were selected based on their excesses of Hα emission. We also present spectral energy distributions for select candidates. This work is supported by the NSF REU site grant PHY-0849416, NASA DPR No. NNX09AT67G, and Lehigh University. We also thank the SMARTS Consortium, Rachael Roettenbacher, Tina Aragona, and Amber Marsh.

  6. Toward transferable interatomic van der Waals potentials: The role of multipole electrostatics and many-body dispersion without electrons

    CERN Document Server

    Bereau, Tristan

    2014-01-01

    We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi partitioning approach instead. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular potential from dispersion and electrostatics for more than 1,300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. Overall, the method achieves an accuracy well within sophisticated empirical force fields, such as OPLS and Amber FF03, while exhibiting a simple parametrization protocol without the need for experimental inp...

  7. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

    Directory of Open Access Journals (Sweden)

    Andrew T Fenley

    Full Text Available Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS, an open-source software package for computing atomic resolution stresses from molecular dynamics (MD simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.

  8. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    CERN Document Server

    Beauchamp, Kyle A; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using t...

  9. Induced mutations in bread wheat (Triticum aestivum L.) cv. Kharchia 65

    International Nuclear Information System (INIS)

    Through mutagenesis with gamma rays, mutants characterized by reduced plant height, square head, awnless ear, semisterile, amber seed colour and bold seeds were induced in bread wheat (Triticum aeastivum L.) cv. Kharchia 65. They were isolated in M2 derived from dry seeds treated with 20 kR, 30 kR and 40 kR of gamma rays of M1 population. In the M3 generation, some progenies with morphological mutants were also recovered. The pattern of segregation was found to be controlled by monogenic recessive control of mutant phenotypes, and showed a good fit for 3 normal: 1 mutant and 1 normal: 2 segregating and 1 mutant between and within the progenies respectively. (author)

  10. Molecular dynamics simulations of a single stranded (ss) DNA

    CERN Document Server

    Chatterjee, Subhasish; Thakur, Siddarth; Burin, Alexander

    2012-01-01

    The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.

  11. An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water

    Energy Technology Data Exchange (ETDEWEB)

    Stauffer, D.; Dragneva, N.; Floriano, W. B.; Rubel, O. [Thunder Bay Regional Research Institute, 290 Munro St, Thunder Bay, Ontario P7B 6V4 (Canada); Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Mawhinney, R. C. [Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Fanchini, G. [Physics and Astronomy, University of Western Ontario, 1151 Richmond St, London, Ontario N6A 3K7 (Canada); French, S. [University of Calgary, South Health Campus, 4448 Front St. SE, Calgary, Alberta T3M 1M4 (Canada)

    2014-07-28

    Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

  12. Binarity of the LBV HR Car

    CERN Document Server

    Rivinius, Th; de Wit, W J; Mehner, A; Martayan, Ch; Guieu, S; Bouquin, J -B Le

    2014-01-01

    VLTI/AMBER and VLTI/PIONIER observations of the LBV HR Car show an interferometric signature that could not possibly be explained by an extended wind, more or less symmetrically distributed around a single object. Instead, observations both in the Br$\\gamma$ line and the H-band continuum are best explained by two point sources (or alternatively one point source and one slightly extended source) at about 2 mas separation and a contrast ratio of about 1:5. These observations establish that HR Car is a binary, but further interpretation will only be possible with future observations to constrain the orbit. Under the assumption that the current separation is close to the maximum one, the orbital period can be estimated to be of the order of 5 years, similar as in the $\\eta$ Car system. This would make HR Car the second such LBV binary.

  13. S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

    DEFF Research Database (Denmark)

    Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

    2002-01-01

    computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes with......S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR and...... sulfonium sulfur is near an electronegative oxygen in the ribose ring is common. Comparisons of NMR results for AdoMet with those for the uncharged S-adenosylhomocysteine and 5'-methylthioadenosine, and the anionic ATP, indicate that the solution conformations are not dictated mainly by molecular charge. In...

  14. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach to the...... the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The...... structural differences between the eight enzyme-substrate complexes were studied with particular emphasis on the active site, and possible sites for obtaining selectivity among the MMP's are discussed. Differences in the P1' pocket are well-documented and have been extensively exploited in inhibitor design...

  15. Fuel formula for lighters

    Energy Technology Data Exchange (ETDEWEB)

    Iwayama, I.; Iwayama, A.

    1982-04-10

    A fuel formula that includes a homogenous mixture of benzine, aromatic ether oils, perfume and other perfuming agents, as well as the lowest possible aliphatic alcohol as a component solvent, surfactant, and possibly, a soluble pigment that colors the formula an appropriate color. This formula is used as an aromatic fuel for cigarette lights. The ether oils can be musk, amber, camomille, lavender, mint, anise, rose, camphor, and other aromatic oils; the perfuming agents are: geraniol, linalool, menthol, camphor, benzyl or phenetyl alcohols, phenylacetaldehyde, vanillin, coumarin, and so forth; the pigments are: beta-carotene, sudan dyes, etc.; the low aliphatic alcohols are EtOH, iso-PrOH. Example: 70 parts benzine, 10 parts EtOH, 15 parts oxide mezithylene and 5 parts borneol form a clear liquid that has a camphor aroma when it is lit.

  16. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.

    Directory of Open Access Journals (Sweden)

    Luis Felipe Pineda De Castro

    Full Text Available In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.

  17. The Influence of Waste Glass Slurry on the Properties of Concrete

    OpenAIRE

    Kara, P.

    2013-01-01

    The grinding of glass waste chips in a wet environment for 120 minutes gives possibility to obtain particles finer in size in comparison to glass waste chips ground in dry environment. The particle distribution analysis showed that borosilicate glass lamp waste slurry has particle size in the range of 0.713 μm to 8.088 μm, fluorescent lamp glass waste slurry - from 2.473 μm to 20.088 μm, amber glass cullet slurry - from 1.435 μm to 21.118 μm, green glass cullet slurry - from 0.903 μm to 23.12...

  18. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.

    Science.gov (United States)

    Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G

    2016-04-12

    Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features. PMID:26949976

  19. Assessment of Some Density Functional Theory Methods and Force Field Models in Describing Various Interaction Modes of Benzene Dimer

    Science.gov (United States)

    Zhou, Yu-wei; Zhang, Igor Ying; Wu, Jian-ming; Wu, An-an; Xu, Xin

    2011-12-01

    Benzene dimer (bz2) is the simplest prototype of the π-π interactions. Such interactions are ubiquitous in diverse areas of science and molecular engineering. In the present work, we have made assessment on some modern density functional methods including B97-D, BLYP-D3, M06-2X, XYG3, and force field models including CHARMM, AMBER, MM3, AMOEBA on six important interaction modes of bz2. Our results not only highlight the usefulness of these cost-effective methods, which can be used as economic substitutes of the expensive CCSD(T) for complex real-world systems, but also indicate their weakness in the description of the π-π interactions, which points to the future direction for further improvements.

  20. Cooltour

    OpenAIRE

    Del Castillo Sánchez, Elena

    2015-01-01

    Nuestro proyecto trata de agrupar los lugares más significativos del barrio sur de la ciudad de Amberes, conocida por su riqueza cultural y social, y de recrear un tour autoguiado centrado en niños de 10 a 12 años. A través de una serie de actividades, una página web donde encontrar todo el material e información necesarios, los niños se sumergen en una aventura en la que gracias a un librito que llevarán todo el camino, sus ganas, emoción y curiosidad, les guiarán para aprender acerca de la...

  1. Estudo comparativo do aspecto da hemolinfa de algumas espécies de carrapatos (Acari, Ixodidae: descrição da variação hemocitária de adultos de Amblyomma cajennense (Fabricius Koch Comparative study of the hemolymph aspect from a few ticks species (Acari, Ixodidae: description of the hemocyte variation of adults of Amblyomma cajennense (Fabricius Koch

    Directory of Open Access Journals (Sweden)

    Maria Elisa Carneiro

    2002-07-01

    Full Text Available The hemocyte composition of adults of Amblyomma cajennense (Fabricius, 1787 Koch, 1844 adults consisted of three basic cellular types: prahemocyte I (PR I, plasmatocyte (PL and spherulocyte (ES II. Among the ixodids observed (A. cajennense; A. dissimile Koch, 1844; Rhipicephalus sanguineus Latreille, 1806; Anocentor nitens (Neumann, 1897 Schulze, 1937; Boophilus microplus Canestrini, 1887 and Haemaphysalis sp. only A. cajennense was different in the adult hemolymph colour. It changed from amber to deep blue as the ixodid age advanced. This fact could be associated with the presence of hemocyanin in the hemolymph and points out the need to develop further investigations about the Ixodidae hemolymph pratein composition as well as the function of all the types found in it. This information could aid the studies on ticks control.

  2. Potencial hidrogeniônico de soluções de cloridrato de dobutamina expostas a condições ambientais de unidades de cuidados intensivos neonatais Hydrogen-ion potential of dobutamine hydrochloride solutions exposed to environmental conditions of neonatal intensive care units

    Directory of Open Access Journals (Sweden)

    Lidiane L. Reis

    2009-12-01

    Full Text Available OBJETIVO: Verificar o potencial hidrogeniônico (pH de soluções de cloridrato de dobutamina sob condições ambientais que mimetizam unidades de cuidados intensivos neonatais. MÉTODOS: Analisou-se pH do fármaco em solução glicosada 5% ou NaCl 0,9% segundo temperatura (22 e 37 °C, luz (escuro, lâmpadas fluorescentes ambiente e equipamento de fototerapia e equipos (incolor e âmbar em intervalos de tempo (0, 1, 24, 48, 72 e 96 horas. RESULTADOS: Evidenciaram-se valores próximos de pH do fármaco na apresentação comercial e diluído. Obteve-se média de pH de 3,45±0,19 a 22 °C e de 3,55±0,20 a 37 °C. A média de pH das soluções mantidas no escuro foi de 3,62±0,09, na luz ambiente, de 3,63±0,07, e sob fototerapia, de 3,31±0,16. Soluções em equipos incolores tiveram média menor (3,41±0,24 do que em âmbares (3,52±0,15. Obtiveram-se menores valores de pH nas soluções sob fototerapia em equipos incolores (3,17±0,03 do que em âmbares (3,55±0,03. CONCLUSÃO: Sob a luz da fototerapia houve maior variação do pH das soluções, e o emprego de equipos âmbares minimizou tal efeito.OBJECTIVE: To verify the hydrogen-ion potential (pH of dobutamine hydrochloride solutions under environmental conditions similar to those of neonatal intensive care units. METHODS: We analyzed the pH of the drug diluted in 5% dextrose in water or 0.9% NaCl under different conditions of temperature (22 and 37 °C and light (dark, fluorescent light bulbs, and phototherapy equipment, using colorless and amber intravenous sets at time intervals of 0, 1, 24, 48, 72, and 96 hours. RESULTS: The pH values of the marketed form of the drug and the diluted drug were similar. The pH means were 3.45±0.19 at 22 °C and 3.55±0.20 at 37 °C. The average of the pH according to light conditions were as follows: in the dark = 3.62±0.09, under room light = 3.63±0.07, and exposed to phototherapy = 3.31±0.16. Solutions stored in colorless intravenous sets had a lower

  3. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  4. Competency mapping in quality management of foundation training.

    Science.gov (United States)

    Ruddlesdin, Jennifer; Wentworth, Lauren; Bhat, Sarita; Baker, Paul

    2010-12-01

    Competency-based curricula focus on outcomes in terms of application of knowledge and acquisition of competencies. The aim of this exercise was to analyse posts and programmes for potential training outcomes. A mapping process against the UK foundation curriculum was designed. Data were gathered from foundation directors using red/amber/green judgements for each post. After submission no correspondence was needed on any programme about educational arrangements, suggesting the process had a significant formative effect as well as assessing outcomes. Certain competencies were problematic across the majority of host providers, allowing programme directors to ensure deficiencies are compensated by planned teaching or simulation training. Widespread difficulty in achieving these competencies raises the question of whether they should be included within the national curricula. Development of competency-based training is a complex, multistep process. However, it is possible to analyse it in a large programme of trainees in the setting of the modern, busy NHS. PMID:21413479

  5. Measuring starspots on magnetically active stars with the VLTI

    CERN Document Server

    Wittkowski, M; Hubrig, S; Posselt, B; Von der Lühe, O

    2002-01-01

    We present feasibility studies to directly image stellar surface features, which are caused by magnetic activity, with the Very Large Telescope Interferometer (VLTI). We concentrate on late type magnetically active stars, for which the distribution of starspots on the surface has been inferred from photometric and spectroscopic imaging analysis. The study of the surface spot evolution during consecutive rotation cycles will allow first direct measurements (apart from the Sun) of differential rotation which is the central ingredient of magnetic dynamo processes. The VLTI will provide baselines of up to 200 m, and two scientific instruments for interferometric studies at near- and mid-infrared wavelengths. Imaging capabilities will be made possible by closure-phase techniques. We conclude that a realistically modeled cool surface spot can be detected on stars with angular diameters exceeding ~2 mas using the VLTI with the first generation instrument AMBER. The spot parameters can then be derived with reasonable...

  6. Mutagenesis of ultraviolet-irradiated lambda phage by host cell irradiation: induction of Weigle mutagenesis is not an all-or-none process

    International Nuclear Information System (INIS)

    Ultraviolet mutagenesis of lambda phage to clear plaque formers is the same in the total phage population and in subpopulations of phage which have also mutated to gam- or at an amber codon. This is true for phage assayed in host cells in which Weigle mutagenesis has been either partially induced by low levels of ultraviolet irradiation, or fully induced by higher levels. If induction of Weigle mutagenesis were all-or-none, clear plaque formers in phage subpopulations selected for another mutation elsewhere would come mainly from induced cells; then the clear plaque mutation rate would always be that for fully induced host cells. Therefore, induction requires more than one lesion in host cell DNA. Although thymine starvation of cells induces synthesis of recA protein, it does not induce Weigle mutagenesis; in fact starvation inhibits induction of this process on subsequent ultraviolet irradiation of the cells. (orig.) 891 AJ/orig. 892 BRE

  7. Towards characterization of exoplanetary atmospheres with the VLT Interferometer

    CERN Document Server

    Jörgens, V; Joergens, Viki; Quirrenbach, Andreas

    2004-01-01

    The direct observation of extrasolar planets and their spectra is coming into reach with the new generation of ground-based near-IR interferometers, like the Very Large Telescope Interferometer (VLTI). The high contrast between star and planet requires an excellent calibration of atmospheric distortions. Proposed techniques are the observation of color-differential or closure phases. The differential phase, however, is only in a first order approximation independent of atmospheric influences because of dispersion effects. This might prevent differential phase observations of extrasolar planets. The closure phase, on the other hand, is immune to atmospheric phase errors and is therefore a promising alternative. We have modeled the response of the closure phase instrument AMBER at the VLTI to realistic models of known extrasolar planetary systems taking into account their theoretical spectra as well as the geometry of the VLTI. We present a strategy to determine the geometry of the planetary system and the spec...

  8. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei [Institute of High Performance Computing, A*STAR, 138632 (Singapore)

    2015-12-31

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  9. Chemical stabilities of isoetharine hydrochloride, metaproterenol sulphate and terbutaline sulphate after mixing with normal saline for respiratory therapy.

    Science.gov (United States)

    Das Gupta, V; Parasrampuria, J; Gardner, S N

    1988-04-01

    The chemical stabilities of isoetharine hydrochloride inhalation solution, metaproterenol sulphate inhalation solution and terbutaline sulphate injection, after diluting 1 in 10 with sodium chloride 0.9% injection were studied. On storing the solutions in amber-coloured syringes, they were stable for at least 120 days at 5 degrees C. At 25 degrees C they were also stable for 120 days except that isoetharine solution discoloured and lost 7.8% of its potency after 90 days of storage. There was a new peak in the chromatogram from the decomposition product. All other solutions remained clear for 120 days at both temperatures. The initial and final pH values were similar except that after 120 days at both temperatures. The initial and final pH values were similar except that after 120 days at 25 degrees C, the pH value of terbutaline solution had increased from 4.9 to 5.4. PMID:3392129

  10. Andromorphic female of the dragonfly Neurothemis tullia tullia (Drury (Odonata: Libellulidae, central India

    Directory of Open Access Journals (Sweden)

    R.J. Andrew

    2013-01-01

    Full Text Available Neurothemis tullia tullia (Drury is a common dragonfly which occurs in large colonies in swamps and heavily- weeded tanks in different parts of India. It exhibits striking sexual dimorphism in colour and wing spot patterns. The male is dark with a large blue-black spot on the wing base while the female is dull olivaceous and the wing base is amber yellow. The sexes can be easily identified from quite a far distance. Andromorphic females are very rarely found in anisopteran dragonflies. This paper describes and compares not only the coloration and wing spots of the normal male and female with this andromorphic female but also reports about its sexual fitness to produce viable eggs.

  11. Pollen spectrum and physicochemical attributes of sulla (Hedysarum coronarium honeys of Médéa region (Algeria

    Directory of Open Access Journals (Sweden)

    Salim Zerrouk

    2013-09-01

    Full Text Available The qualities of Sulla honey samples of Médéa region (Algeria were evaluated by determing the pollen spectrum and physicochemical attributes. It is generally accepted that a minimum content of 45% of Hedysarum coronarium (Sulla pollen is necessary to classify an Sulla honey as unifloral. The samples were analysed for parameters including moisture, electrical conductivity, hydroxymethylfurfural, pH, acidity (free, lactone and total, sugars (fructose, glucose, sucrose and total sugar, fructose+glucose, fructose/glucose, glucose/moisture, proteins and colour. Qualitative pollen analysis showed the presence of 76 types from 35 families, with Fabaceae, Cistaceae, Asteraceae, and Myrtaceae being the most frequent. The overall pollen content can be considered as medium. All the samples presented low values of hydroxymethylfurfural and lactone acidity. The degree of colour varied from white to amber. Moisture, proteins content, fructose, glucose, sucrose and electrical conductivity were according to international standards.

  12. The oldest fossil bee: Apoid history, evolutionary stasis, and antiquity of social behavior.

    Science.gov (United States)

    Michener, C D; Grimaldi, D A

    1988-09-01

    Trigona prisca, a stingless honey bee (Apidae; Meliponinae), is reported from Cretaceous New Jersey amber (96-74 million years before present). This is about twice the age of the oldest previously known fossil bee, although Trigona is one of the most derived bee genera. T. prisca is closely similar to modern neotropical species. Most of bee evolution probably occurred during the approximately 50 million years between the beginning of the Cretaceous when flowering plants (on which bees depend) appeared and the time of T. prisca. Since then, in this phyletic line of Meliponinae, there has been almost no morphological evolution. Since the fossil is a worker, social organization had arisen by its time. PMID:16593976

  13. “COLATURA DI ALICI “ CETARESE: EVALUATION OF AMINIC PROFILE

    Directory of Open Access Journals (Sweden)

    A Anastasio

    2008-12-01

    Full Text Available “Colatura d’alici”is a speciality made in Cetara, a clear ,amber-coloured liquid that has sharp taste, prepared with the juice coming from the anchovy salting process. The anchovies are caught in the Gulf of Salerno between the mounths of March and July. The colatura is ready at the beginning of December. Histamine poisoning, a food-borne chemical intoxication caused by the consumption of food containing toxic levels of histamine, is a syndrome commonly associated with the consumption of seafood beloging to the Engraulidae and some fish families. Histamine and biogenic amine levels were determined in “colatura di alici di Cetara”. The amine was separated in a HPLC/FL system. Histamine level were lower than the law limits only in one of the examinated products. A reduction of the histamine and amine levels in colatura cetarese can be obtained using a determinate salt concentrations and changing way of seasoning.

  14. Using Colored Cullet for Making Beautiful Glassware

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong-Sang; Matyas, Josef

    2003-03-14

    Eight colored glasses from Fire and Light Originals (FLO) and three container cullet glasses were characterized for the viscosity, density, and thermal expansion, glass transition temperature, dilatometer softening temperature, color chromaticity, Fe(II)/Fe(total) redox ratio, and chemical composition. The results of the characterization were used to evaluate the options for the glass formulation development of colored glasses aimed at increasing the use of recycled container glass cullet. Out of several options considered, the possibility of using clear cullet for FLO’s Citrus colored glass was selected and investigated in this study. It was shown that it is possible to use clear cullet to produce Citrus glass at the cullet oxide ratio of 90 mass% and the final color can be adjusted by controlling the nitrate level and alkali concentrations. From the present study, recommendations for further development efforts are provided to increase the container cullet usage or to replace partially or entirely the clear cullet by the amber cullet.

  15. Resolved astrometric orbits of ten O-type binaries

    CERN Document Server

    Bouquin, J -B Le; Gosset, E; De Becker, M; Duvert, G; Absil, O; Anthonioz, F; Berger, J -P; Ertel, S; Grellmann, R; Guieu, S; Kervella, P; Rabus, M; Willson, M

    2016-01-01

    Our long term aim is to derive model-independent stellar masses and distances for long period massive binaries by combining apparent astrometric orbit with double-lined radial velocity amplitudes (SB2). We follow-up ten O+O binaries with AMBER, PIONIER and GRAVITY at the VLTI. Here, we report about 130 astrometric observations over the last 7 years. We combine this dataset with distance estimates to compute the total mass of the systems. We also compute preliminary individual component masses for the five systems with available SB2 radial velocities. Nine over the ten binaries have their three dimensional orbit well constrained. Four of them are known colliding wind, non-thermal radio emitters, and thus constitute valuable targets for future high angular resolution radio imaging. Two binaries break the correlation between period and eccentricity tentatively observed in previous studies. It suggests either that massive star formation produce a wide range of systems, or that several binary formation mechanisms ...

  16. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  17. Safety assessment of Novi Han radioactive waste repository - features, problems, results and perspectives

    International Nuclear Information System (INIS)

    This paper summarizes the work done and the achievements reached in the Novi Han radioactive waste repository safety assessment within the IAEA Model Project 'Increasing the safety of Novi Han radioactive waste repository BUL 4/005'. The overall safety assessment has a wide context, but the work reported here relates only to some details and results concerning the development and implementation of the appropriate methodology approach, model and computer code used for the calculations. Different steps and procedures are included for a better practical understanding of the obtained results during the safety assessment performance. The methodology approach is widely based on an international experience in safety analysis and implemented for evaluation computer code AMBER, which is one of the recommended from the safety assessments experts. (author)

  18. Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases

    CERN Document Server

    Lino, J; Deriabina, A; Velasco, M; Poltev, V

    2013-01-01

    DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values ...

  19. Monte Carlo simulation for dose distribution calculations in a CT-based phantom at the Portuguese gamma irradiation facility

    Science.gov (United States)

    Oliveira, Carlos; Yoriyaz, Hélio; Oliveira, M. Carmo; Ferreira, L. M.

    2004-01-01

    In preview works the Portuguese Gamma Irradiation Facility, UTR, has been simulated using the MCNP code and the product to be irradiated has been drawn using the boolean operators with the MCNP surfaces. However, sometimes the product to be irradiated could have an irregular shape. The paper describes an alternative way for drawing the corresponding volume based on CT image data in a format of a 3D matrix of voxels. This data are read by a specific code called SCMS which transforms it into a MCNP input file. The dimensions of each MCNP voxel depend on the number of elements in the CT-based matrix. Additionally, the new approach allows one to know dose distributions anywhere without extra definitions of surfaces or volumes. Experimental dose measurements were carried out using Amber Perspex dosimeters. This work presents the results of MCNP simulations using both modeling modes - the standard mode and the voxel mode.

  20. Development of Polarizable Models for Molecular Mechanical Calculations III: Polarizable Water Models Conforming to Thole Polarization Screening Schemes

    Science.gov (United States)

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong

    2012-01-01

    As an integrated step towards a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well, but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations. PMID:22712654

  1. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

    Science.gov (United States)

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Luo, Ray

    2012-07-19

    As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations. PMID:22712654

  2. Extemporaneous Compounding of Oral Acitretin Suspension for Pediatric Patient with Generalized Pustular Psoriasis.

    Science.gov (United States)

    Choo, Winnie

    2016-01-01

    Generalized pustular psoriasis is rare in children, but it can occur and affect an extensive body surface area of a child. Treatment regimens can include medications that are not available in pediatric dosage form. Acitretin is considered one of the treatment options for acute generalized pustular psoriasis in children, but, in Singapore, it is only available as Neotigason capsules. Extemporaneous compounding of the powder content in the capsules was developed for formulating the oral acitretin suspension with a standardized formulation table and compounding process at National Skin Centre. An appropriate beyond-use date of the extemporaneous preparation was assigned after reviewing the photostability data of acitretin, compatibility of the active ingredient and excipients, and United States Pharmacopeia guidelines. It is deemed appropriate to assign a beyond-use date of 14 days when the extemporaneous preparation is stored in amber glass bottles at 2 degrees C to 8 degrees C. PMID:27125051

  3. An endoparasitoid Cretaceous fly and the evolution of parasitoidism

    Science.gov (United States)

    Zhang, Qingqing; Zhang, Junfeng; Feng, Yitao; Zhang, Haichun; Wang, Bo

    2016-02-01

    Parasitoidism is a key innovation in insect evolution, and parasitoid insects, nowadays, play a significant role in structuring ecological communities. Despite their diversity and ecological impact, little is known about the early evolution and ecology of parasitoid insects, especially parasitoid true flies (Diptera). Here, we describe a bizarre fly, Zhenia xiai gen. et sp. nov., from Late Cretaceous Burmese amber (about 99 million years old) that represents the latest occurrence of the family Eremochaetidae. Z. xiai is an endoparasitoid insect as evidenced by a highly developed, hypodermic-like ovipositor formed by abdominal tergites VIII + IX that was used for injecting eggs into hosts and enlarged tridactylous claws supposedly for clasping hosts. Our results suggest that eremochaetids are among the earliest definite records of parasitoid insects. Our findings reveal an unexpected morphological specialization of flies and broaden our understanding of the evolution and diversity of ancient parasitoid insects.

  4. A GoldSim Model for Colloid Facilitated Nuclide Transport

    International Nuclear Information System (INIS)

    Recently several total system performance assessment (TSPA) programs, called 'template' programs, ready for the safety assessment of radioactive waste repository systems which are conceptually modeled have been developed by utilizing GoldSim and AMBER at KAERI. It is generally believed that chelating agents (chelators) that could be disposed of together with radioactive wastes in the repository and natural colloids available in the geological media affect on nuclides by enhancing their transport in the geological media. A simple GoldSim module to evaluate such quantitative effects, by which colloid and chelator-facilitated nuclide release cases could be modeled and evaluated is introduced. Effects of the chelators alone are illustrated with the case associated with well pumping scenario in a hypothetical repository system

  5. Magnetic resonance spectroscopy and imaging for the study of fossils.

    Science.gov (United States)

    Giovannetti, Giulio; Guerrini, Andrea; Salvadori, Piero A

    2016-07-01

    Computed tomography (CT) has long been used for investigating palaeontological specimens, as it is a nondestructive technique which avoids the need to dissolve or ionize the fossil sample. However, magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) have recently gained ground as analytical tools for examination of palaeontological samples, by nondestructively providing information about the structure and composition of fossils. While MRI techniques are able to reveal the three-dimensional geometry of the trace fossil, MRS can provide information on the chemical composition of the samples. The multidimensional nature of MR (magnetic resonance) signals has potential to provide rich three-dimensional data on the palaeontological specimens and also to help in elucidating paleopathological and paleoecological questions. In this work the verified applications and the emerging uses of MRI and MRS in paleontology are reviewed, with particular attention to fossil spores, fossil plants, ambers, fossil invertebrates, and fossil vertebrate studies. PMID:26979538

  6. Self-organised criticality in base-pair breathing in DNA with a defect

    CERN Document Server

    Duduiala, Ciprian-Ionut; Laughton, Charles A

    2011-01-01

    We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

  7. Occurrence, distribution and characteristics of beached plastic production pellets on the island of Malta (central Mediterranean).

    Science.gov (United States)

    Turner, Andrew; Holmes, Luke

    2011-02-01

    The distribution, abundance and chemical characteristics of plastic production pellets on beaches of the island of Malta have been determined. Pellets were observed at all locations visited and were generally most abundant (> 1000m⁻² at the surface) on the backshores of beaches with a westerly aspect. Most pellets were disc-shaped or flattened cylinders and could be categorised as white, yellow, amber or brown. The polymeric matrix of all pellets analysed by infrared spectroscopy was polyethylene and the degree of yellowing or darkening was associated with an increase in the carbonyl index, hence extent of photo-oxidation or aging. Qualitatively, pellets are similar to those reported for other regions of the Mediterranean in surveys spanning three decades, suggesting that they are a general and persistent characteristic of the region. PMID:21030052

  8. Performance Characteristics of Waste Glass Powder Substituting Portland Cement in Mortar Mixtures

    Science.gov (United States)

    Kara, P.; Csetényi, L. J.; Borosnyói, A.

    2016-04-01

    In the present work, soda-lime glass cullet (flint, amber, green) and special glass cullet (soda-alkaline earth-silicate glass coming from low pressure mercury-discharge lamp cullet and incandescent light bulb borosilicate glass waste cullet) were ground into fine powders in a laboratory planetary ball mill for 30 minutes. CEM I 42.5N Portland cement was applied in mortar mixtures, substituted with waste glass powder at levels of 20% and 30%. Characterisation and testing of waste glass powders included fineness by laser diffraction particle size analysis, specific surface area by nitrogen adsorption technique, particle density by pycnometry and chemical analysis by X-ray fluorescence spectrophotometry. Compressive strength, early age shrinkage cracking and drying shrinkage tests, heat of hydration of mortars, temperature of hydration, X-ray diffraction analysis and volume stability tests were performed to observe the influence of waste glass powder substitution for Portland cement on physical and engineering properties of mortar mixtures.

  9. Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach.

    Science.gov (United States)

    Segev, Elad; Grumbach, Mikael; Gerber, Robert Benny

    2006-11-14

    The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the beta hairpin to alpha helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results. PMID:17066182

  10. Hydrogen Lines in Mira Stars Through Interferometry and Polarimetry

    Science.gov (United States)

    Fabas, N.; Chiavassa, A.; Millour, F.; Wittkowski, M.

    2015-12-01

    Balmer lines in emission are the most prominent features in Mira stars spectra and have a strong potential as a proxy to study the lower atmosphere's dynamics. In Fabas et al. ([1]), we accumulated spectropolarimetric observations of Balmer lines in emission. As the shock is propagating outwards, linear polarization rate increases and the angle of this polarization evolves. Assuming that linear polarization arises from anisotropic scattering, it has the potential of telling us about the geometric structure of the shock as it propagates and the study of such atmospheric structures can typically be performed with interferometry. In 2012, AMBER data on the Mira star omicron Ceti were collected in which the Brackett γ line is studied. The data show signatures in the interferometric observables around this line. Olivier Chesneau was in the jury evaluating the PhD thesis of N. Fabas and he was seduced by the idea to study these shock waves with interferometry and use polarimetry as a complementary study.

  11. Site-specific Incorporation of 3-Iodo-L-tyrosine into Proteins and Single-wavelength Anomalous Dispersion Phasing with Soft X-ray in Protein Crystallography

    Science.gov (United States)

    Murayama, Kazutaka; Sakamoto, Kensaku

    Iodine is a good anomalous scatter for radiations from in-house X-ray generators (Cu/CrKα). Non-natural amino acid, 3-iodo-L-tyrosine, is able to be site-specifically incorporated into proteins with amber suppresser tRNA and mutated TyrRS from M. jannaschii in the E. coli expression system. To determine the crystal structure of acetyl transferase from T. thermophilus, iodotyrosine-containing proteins were prepared and crystallized. Structure determination was successfully conducted with the protein variant with iodotyrosine at position 111. Anomalous signals from iodotyrosine with Cu/CrKα radiations were both sufficient to calculate clear electron density map. In the crystal structure, iodotyrosine did not significantly disturb the native structure.

  12. Radionuclide release calculations for SAR-08

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Gavin; Miller, Alex; Smith, Graham; Jackson, Duncan (Enviros Consulting Ltd, Wolverhampton (United Kingdom))

    2008-04-15

    Following a review by the Swedish regulatory authorities of the post-closure safety assessment of the SFR 1 disposal facility for low and intermediate waste (L/ILW), SAFE, the SKB has prepared an updated assessment called SAR-08. This report describes the radionuclide release calculations that have been undertaken as part of SAR-08. The information, assumptions and data used in the calculations are reported and the results are presented. The calculations address issues raised in the regulatory review, but also take account of new information including revised inventory data. The scenarios considered include the main case of expected behaviour of the system, with variants; low probability releases, and so-called residual scenarios. Apart from these scenario uncertainties, data uncertainties have been examined using a probabilistic approach. Calculations have been made using the AMBER software. This allows all the component features of the assessment model to be included in one place. AMBER has been previously used to reproduce results the corresponding calculations in the SAFE assessment. It is also used in demonstration of the IAEA's near surface disposal assessment methodology ISAM and has been subject to very substantial verification tests and has been used in verifying other assessment codes. Results are presented as a function of time for the release of radionuclides from the near field, and then from the far field into the biosphere. Radiological impacts of the releases are reported elsewhere. Consideration is given to each radionuclide and to each component part of the repository. The releases from the entire repository are also presented. The peak releases rates are, for most scenarios, due to organic C-14. Other radionuclides which contribute to peak release rates include inorganic C-14, Ni-59 and Ni-63. (author)

  13. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

    Science.gov (United States)

    Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

    2016-10-01

    Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470

  14. A resolved, au-scale gas disk around the B[e] star HD 50138

    Science.gov (United States)

    Ellerbroek, L. E.; Benisty, M.; Kraus, S.; Perraut, K.; Kluska, J.; le Bouquin, J. B.; Borges Fernandes, M.; Domiciano de Souza, A.; Maaskant, K. M.; Kaper, L.; Tramper, F.; Mourard, D.; Tallon-Bosc, I.; ten Brummelaar, T.; Sitko, M. L.; Lynch, D. K.; Russell, R. W.

    2015-01-01

    HD 50138 is a B[e] star surrounded by a large amount of circumstellar gas and dust. Its spectrum shows characteristics which may indicate either a pre- or a post-main-sequence system. Mapping the kinematics of the gas in the inner few au of the system contributes to a better understanding of its physical nature. We present the first high spatial and spectral resolution interferometric observations of the Brγ line of HD 50138, obtained with VLTI/AMBER. The line emission originates in a region more compact (up to 3 au) than the continuum-emitting region. Blue- and red-shifted emission originates from the two different hemispheres of an elongated structure perpendicular to the polarization angle. The velocity of the emitting medium decreases radially. An overall offset along the NW direction between the line- and continuum-emitting regions is observed. We compare the data with a geometric model of a thin Keplerian disk and a spherical halo on top of a Gaussian continuum. Most of the data are well reproduced by this model, except for the variability, the global offset and the visibility at the systemic velocity. The evolutionary state of the system is discussed; most diagnostics are ambiguous and may point either to a post-main-sequence or a pre-main-sequence nature. Based on observations performed with X-Shooter (program 090.D-0212) and CRIRES (program 084.C-0668), mounted on the ESO Very Large Telescope, on Cerro Paranal, Chile, and AMBER mounted on the Very Large Telescope Interferometer (programs 082.C-0621, 082.C-0657, 083.C-0144, 084.C-0187, 084.C-0668, 084.C-0983, 384.D-0482, and 092.C-0376(B)).Figure 4 and Appendix A are available in electronic form at http://www.aanda.org

  15. Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy.

    Science.gov (United States)

    Cheluvaraja, Srinath; Meirovitch, Hagai

    2008-01-01

    The hypothetical scanning molecular dynamics (HSMD) method is a relatively new technique for calculating the absolute entropy, S, and free energy, F, from a given sample generated by any simulation procedure. Thus, each sample conformation, i, is reconstructed by calculating transition probabilities that their product leads to the probability of i, hence to the entropy. HSMD is an exact method where all interactions are considered, and the only approximation is due to insufficient sampling. In previous studies HSMD (and HS Monte Carlo - HSMC) has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks, and peptides in a α-helix, extended, and hairpin microstates. In this paper HSMD is developed further as applied to the flexible 7-residue surface loop, 304-310 (Gly-His-Gly-Ala-Gly-Gly-Ser) of the enzyme porcine pancreatic α-amylase. We are mainly interested in entropy and free energy differences ΔS = Sfree - Sbound (and ΔF=Ffree-Fbound) between the free and bound microstates of the loop, which are obtained from two separate MD samples of these microstates without the need to carry out thermodynamic integration. As for peptides, we find that relatively large systematic errors in Sfree and Sbound (and Ffree and Fbound) are cancelled in ΔS (ΔF) which is thus obtained efficiently with high accuracy, i.e., with a statistical error of 0.1-0.2 kcal/mol (T=300 K) using the AMBER force field and AMBER with the implicit solvation GB/SA. We provide theoretical arguments in support of this cancellation, discuss in detail the problems involved in the computational definition of a microstate in conformational space, suggest potential ways for enhancing efficiency further, and describe the next development where explicit water will replace implicit solvation. PMID:26619992

  16. Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal.

    Directory of Open Access Journals (Sweden)

    David Penney

    Full Text Available Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.

  17. Safety case for Baita-Bihor facility

    International Nuclear Information System (INIS)

    Radioactive wastes need to be disposed in the special facilities, in a safe manner, that protects human health and the environment. During the licensing process of radioactive waste disposal facilities, scientific studies and experimental analyses, safety analyses and environmental impact studies are required to demonstrate both confinement capability and radioactive protection of repository. As basis of these studies and analyses, an evolution scenario system must be developed. During the licensing process, from this evolution scenario system, the representative scenarios will be chosen and evaluated, in the specific Safety Cases. The generic purpose of a Safety Case is to calculate concentration of representative radionuclides, which could be released from repository into biosphere, and doses for public. For Baita Bihor Facility, the paper presents 3 scenarios, based on the FEP List for this Facility, described as follows: - Migration through near field, far field and biosphere of a representative radionuclide from Repository, Cs-137; - Transport of Cs-137 with water, by a rock fracture, in a river; - In the river, a part of flow river is used as drinking water for human and animals and we consider also evaporation of water and deposition of radionuclide on sediments; - Migration of Cs -137 in biosphere. Generic exposure pathways taking into account are: - Consumption of drinking water by human and animals; - Consumption of animal products (milk and meat) by human; - Ingestion of contaminated material (sediments) by animals; - External exposure from soil (sediments). The assessment of scenarios is obtained AMBER computer code. AMBER is a flexible software tool that allows users to build their own dynamic behavior models to represent the migration and pathways of contaminants in a system. This computer code can be used to assess normal and abnormal evolution scenario. Taking into account the above described scenarios, radionuclide concentration in water and food

  18. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

    Science.gov (United States)

    Kmunícek, J; Luengo, S; Gago, F; Ortiz, A R; Wade, R C; Damborský, J

    2001-07-31

    Comparative binding energy (COMBINE) analysis was conducted for 18 substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA): 1-chlorobutane, 1-chlorohexane, dichloromethane, 1,2-dichloroethane, 1,2-dichloropropane, 2-chloroethanol, epichlorohydrine, 2-chloroacetonitrile, 2-chloroacetamide, and their brominated analogues. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91% (73% cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93% (74% cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223, and Leu263. These residues are suitable targets for modification by site-directed mutagenesis. PMID

  19. Stability of Commercially Available Grape and Compounded Cherry Oral Vancomycin Preparations Stored in Syringes and Cups.

    Science.gov (United States)

    Kirk, Loren; Lewis, Paul; Luu, Yao; Brown, Stacy

    2016-01-01

    The purpose of this study was to evaluate the stability of two preparations of vancomycin oral solution in two different storage containers, capped amber oral-dosing syringes and heat-sealed oral-dosing cups, stored under refrigerated conditions. Commercially available grape-flavored vancomycin oral preparation and compounded vancomycin for intravenous use in cherry syrup oral preparation were divided into 5-mL aliquots into heat-sealed plastic dosing cups and capped oral-dosing syringes. All samples were stored under refrigeration (2°C to 8°C) and evaluated at days 0, 3, 7, 14, 30, 60, and 90. For each evaluation, samples were visually inspected and analyzed for potency using a stability-indicating high-performance liquid chromatographic method with ultraviolet detection. Over the study period, at least 90% of the initial concentrations for the preparation and the product in both storage containers were retained at 60 days. The commercially available oral vancomycin further demonstrated stability within 90% out to 90 days in the syringe and the unit-dose cups. Visual inspection revealed no changes in the grape-flavored vancomycin oral preparation, but a detectable red-dye precipitate could be seen in the crevices of the dosing cups from the vancomycin in cherry syrup oral preparation after 60 days. Commercially available grape-flavored vancomycin oral preparation was stable up to 90 days, and com- pounded vancomycin for intravenous use in cherry syrup oral preparation maintained stability for 60 days when dispensed in capped amber polypropylene oral-dosing syringes and heat-sealed plastic dosing cups when stored at refrigerated conditions. PMID:27323427

  20. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

    Directory of Open Access Journals (Sweden)

    Chun Wu

    Full Text Available FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96 coupled with the implicit solvent model (IGB = 5, we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition. The breadth of the folding transition arises from the spread in the melting temperatures (from ∼325 K to ∼302 K of the individual transitions: formation of the hydrophobic core, β-hairpin and tertiary fold, with the helix formed earlier. Our simulations initiated from an extended chain accurately predict the native structure, provide a reasonable estimate of the transition barrier height, and explicitly demonstrate the existence of multiple pathways and multiple transition states for folding. Our exhaustive sampling enables us to assess the quality of the Amber ff96/igb5 combination and reveals that while this force field can predict the correct native fold, it nonetheless overstabilizes the α-helix portion of the protein (Tm = ∼387K as well as the denatured structures.

  1. AGN BLR structure, luminosity and mass from combined reverberation mapping and optical interferometry observations

    Science.gov (United States)

    Rakshit, Suvendu; Petrov, Romain G.

    2014-07-01

    Unveiling the structure of the Broad-Line Region (BLR) of AGN is critical to understand the quasar phenomenon. Detail study of the geometry and kinematic of these objects can answer the basic questions about the central BH mass, accretion mechanism and rate, growth and evolution history. Observing the response of the BLR clouds to continuum variations, Reverberation Mapping (RM) provides size-luminosity and mass-luminosity relations for QSOs and Sy1 AGNs with the goal to use these objects as standard candles and mass tags. However, the RM size can receive different interpretations depending on the assumed geometry and the corresponding mass depends on an unknown geometrical factor as well on the possible confusion between local and global velocity dispersion. From RM alone, the scatter around the mean mass is as large as a factor 3. Though BLRs are expected to be much smaller than the current spatial resolution of large optical interferometers (OI), we show that differential interferometry with AMBER, GRAVITY and successors can measure the size and constrain the geometry and kinematics on a large sample of QSOs and Sy1 AGNs. AMBER and GRAVITY (K_ 10:5) could be easily extended up to K= 13 by an external coherencer or by advanced "ncoherent" data processing. Future VLTI instrument could reach K~ 15. This opens a large AGN BLR program intended to obtain a very accurate calibration of mass, luminosity and distance measurements from RM data which will allow using many QSOs as standard candles and mass tags to study the general evolution of mass accretion in the Universe. This program is analyzed with our BLR model allowing predicting and interpreting RM and OI measures together and illustrated with the results of our observations of 3C273 with the VLTI.

  2. Radionuclide release calculations for SAR-08

    International Nuclear Information System (INIS)

    Following a review by the Swedish regulatory authorities of the post-closure safety assessment of the SFR 1 disposal facility for low and intermediate waste (L/ILW), SAFE, the SKB has prepared an updated assessment called SAR-08. This report describes the radionuclide release calculations that have been undertaken as part of SAR-08. The information, assumptions and data used in the calculations are reported and the results are presented. The calculations address issues raised in the regulatory review, but also take account of new information including revised inventory data. The scenarios considered include the main case of expected behaviour of the system, with variants; low probability releases, and so-called residual scenarios. Apart from these scenario uncertainties, data uncertainties have been examined using a probabilistic approach. Calculations have been made using the AMBER software. This allows all the component features of the assessment model to be included in one place. AMBER has been previously used to reproduce results the corresponding calculations in the SAFE assessment. It is also used in demonstration of the IAEA's near surface disposal assessment methodology ISAM and has been subject to very substantial verification tests and has been used in verifying other assessment codes. Results are presented as a function of time for the release of radionuclides from the near field, and then from the far field into the biosphere. Radiological impacts of the releases are reported elsewhere. Consideration is given to each radionuclide and to each component part of the repository. The releases from the entire repository are also presented. The peak releases rates are, for most scenarios, due to organic C-14. Other radionuclides which contribute to peak release rates include inorganic C-14, Ni-59 and Ni-63. (author)

  3. Simulaid: a simulation facilitator and analysis program.

    Science.gov (United States)

    Mezei, Mihaly

    2010-11-15

    Simulaid performs a large number of simulation-related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB (Berman et al., Nucleic Acids Res 2000, 28, 235), Charmm (Brooks et al., J Comput Chem 4, 187) CRD, Amber (Case et al.), Macromodel (Mohamadi et al., J Comput Chem 1990, 11, 440), Gromos/Gromacs (Hess et al.), InsightII (InsightII. Accelrys Inc.: San Diego, 2005), Grasp (Nicholls et al., Proteins: Struct Funct Genet 1991, 11, 281) .crg, Tripos (Tripos International, S. H. R., St. Louis, MO) .mol2 (input only), and in the MMC (Mezei, M.; MMC: Monte Carlo program for molecular assemblies. Available at: http://inka.mssm.edu/~mezei/mmc) formats; and trajectories in the formats of Charmm, Amber, Macromodel, and MMC. Analysis features include (but are not limited to): (1) simple distance calculations and hydrogen-bond analysis, (2) calculation of 2-D RMSD maps (produced both as text file with the data and as a color-coded matrix) and cross RMSD maps between trajectories, (3) clustering based on RMSD maps, (4) analysis of torsion angles, Ramachandran (Ramachandran and Sasiskharan, Adv Protein Chem 1968, 23, 283) angles, proline kink (Visiers et al., Protein Eng 2000, 13, 603) angles, pseudorotational (Altona and Sundaralingam, J Am Chem Soc 1972, 94, 8205; Cremer and Pople, J Am Chem Soc 1975, 97, 1354) angles, and (5) analysis based on circular variance (Mezei, J Mol Graphics Model 2003, 21, 463). Torsion angle evolutions are presented in dial plots (Ravishanker et al., J Biomol Struct Dyn 1989, 6, 669). Several of these features are unique to Simulaid. PMID:20740566

  4. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    International Nuclear Information System (INIS)

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology

  5. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  6. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  7. Conformational Interconversions of Amino Acid Derivatives.

    Science.gov (United States)

    Kaminský, Jakub; Jensen, Frank

    2016-02-01

    Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields. PMID:26691979

  8. Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal

    Science.gov (United States)

    Penney, David; Wadsworth, Caroline; Fox, Graeme; Kennedy, Sandra L.; Preziosi, Richard F.; Brown, Terence A.

    2013-01-01

    Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in ‘Anthropocene’ Colombian copal, dated to ‘post-Bomb’ and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal. PMID:24039876

  9. Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal.

    Science.gov (United States)

    Penney, David; Wadsworth, Caroline; Fox, Graeme; Kennedy, Sandra L; Preziosi, Richard F; Brown, Terence A

    2013-01-01

    Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal. PMID:24039876

  10. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

    Science.gov (United States)

    Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri

    2015-10-13

    We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283

  11. The clinical effectiveness of reflectance optical spectroscopy for the in vivo diagnosis of oral lesions

    Institute of Scientific and Technical Information of China (English)

    Diana VMessadi; Fariba SYounai; Hong-Hu Liu; Gao Guo; Cun-Yu Wang

    2014-01-01

    Optical spectroscopy devices are being developed and tested for the screening and diagnosis of oral precancer and cancer lesions. This study reports a device that uses white light for detection of suspicious lesions and green-amber light at 545 nm that detect tissue vascularity on patients with several suspicious oral lesions. The clinical grading of vascularity was compared to the histological grading of the biopsied lesions using specific biomarkers. Such a device, in the hands of dentists and other health professionals, could greatly increase the number of oral cancerous lesions detected in early phase. The purpose of this study is to correlate the clinical grading of tissue vascularity in several oral suspicious lesions using the IdentafiH system with the histological grading of the biopsied lesions using specific vascular markers. Twenty-one patients with various oral lesions were enrolled in the study. The lesions were visualized using IdentafiH device with white light illumination, followed by visualization of tissue autofluorescence and tissue reflectance. Tissue biopsied was obtained from the all lesions and both histopathological and immunohistochemical studies using a vascular endothelial biomarker (CD34) were performed on these tissue samples. The clinical vascular grading using the green-amber light at 545 nm and the expression pattern and intensity of staining for CD34 in the different biopsies varied depending on lesions, grading ranged from 1 to 3. The increase in vascularity was observed in abnormal tissues when compared to normal mucosa, but this increase was not limited to carcinoma only as hyperkeratosis and other oral diseases, such as lichen planus, also showed increase in vascularity. Optical spectroscopy is a promising technology for the detection of oral mucosal abnormalities;however, further investigations with a larger population group is required to evaluate the usefulness of these devices in differentiating benign lesions from

  12. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  13. Critical Dose of Internal Organs Internal Exposure - 13471

    Energy Technology Data Exchange (ETDEWEB)

    Grigoryan, G.; Amirjanyan, A. [Nuclear and Radiation Safety Centre (Armenia); Grigoryan, N. [Yerevan State Medical University 4Tigran Mets,375010 Yerevan (Armenia)

    2013-07-01

    radionuclides that have intake into the organism or absorbed into blood. Transport of different radionuclides between compartments is assumed to follow first order kinetics provided the concentration in red blood cells (RBCs) stays below a nonlinear threshold concentration. When the concentration in RBCs exceeds that threshold, the transfer rate from diffusible plasma to RBCs is assumed to decrease as the concentration in RBCs increases. For the calculations used capabilities AMBER by using the traces of radionuclides in the body. Model for the transfer of radionuclides in the body has been built on the basis of existing models at AMBER for lead. (authors)

  14. Critical Dose of Internal Organs Internal Exposure - 13471

    International Nuclear Information System (INIS)

    radionuclides that have intake into the organism or absorbed into blood. Transport of different radionuclides between compartments is assumed to follow first order kinetics provided the concentration in red blood cells (RBCs) stays below a nonlinear threshold concentration. When the concentration in RBCs exceeds that threshold, the transfer rate from diffusible plasma to RBCs is assumed to decrease as the concentration in RBCs increases. For the calculations used capabilities AMBER by using the traces of radionuclides in the body. Model for the transfer of radionuclides in the body has been built on the basis of existing models at AMBER for lead. (authors)

  15. Ground-based Instrumentations in Africa and its Scientific and Societal Benefits to the region

    Science.gov (United States)

    Yizengaw, Endawoke

    2012-07-01

    Much of what we know about equatorial physics is based on Jicamarca Incoherent Scattering Radar (ISR) observations. However, Jicamarca is in the American sector where the geomagnetic equator dips with a fairly large excursion between the geomagnetic and geodetic equator. On the other hand, in the African sector the geomagnetic equator is fairly well aligned with the geodetic equator. Satellites (e.g. ROCSAT, DMSP, C/NOFS) observations have also indicated that the equatorial ionosphere in the African sector responds differently than other sectors. However, these satellite observations have not been confirmed, validated or studied in detail by observations from the ground due to lack of suitable ground-based instrumentation in the region. Thus, the question of what causes or drives these unique density irregularities in the region is still not yet fully understood, leading the investigation of the physics behind each effect into speculative dead ends. During the past couple of years very few (compared to the land-mass that Africa covers) small instruments, like GPS receivers, magnetometers, VHF, and VLF have been either deployed in the region or in process. However, to understand the most dynamic region in terms of ionospheric irregularities, those few instruments are far from enough. Recently, significant progress has been emerging in securing more ground-based instrument into the region, and thus three ionosondes are either deployed or in process. In this paper, results from AMBER magnetometer network, ionosonde, and GPS receivers will be presented. By combining the multi instrument independent observations, this paper will show a cause and effect of space weather impact in the region for the first time. While the magnetometer network, such as those operated under the umbrella of AMBER project, estimates the fundamental electrodynamics that governs equatorial ionospheric motion, the GPS receivers will track the structure and dynamics of the ionosphere. In addition

  16. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    ) and amber (587 nm peak) LEDs it achieves 8 m lateral resolution using a CMOS imaging chip (as configured for serial data speeds) or 4 m resolution using USB imaging chips. The imager consists of a modified commercial off-the-shelf CMOS chip camera, amber, blue and white LEDs, as well as a relay lens and dual-band filters to obviate moving parts while supporting both fluorescence wavelengths.

  17. Total System Performance Assessment

    International Nuclear Information System (INIS)

    Based on the KAERI FEP list developed through the previous studies, the KAERI FEP Encyclopedia has been developed. Current version is 1.0 which includes all relevant FEPs to compose of two references and all alternative scenarios. Many interaction FEPs between scenario defining FEP(SDF) are created throughout the study. FEPs are classified into many Integrated FEP(IFEP) which eventually become the elements of the RES matrix. The FEAS program one of the component of the KAERI's CYPRUS information system is added to develop the FEP, RES, AC, AMF and finally scenarios. It assists to create transparent way to deal with assessment from the stage of the planning of the R and D to the final stage of the external audit and regulatory body review. Even though MASCOT-K and compartment analysis codes such as AMBER, GoldSim and Ecolego are excellent for TSPA they by in heritage possess a certain limitation especially to identify a proper migration cross sectional area when a relatively big component intersects with a tiny one such as a fracture. It is truly 3D phenomena in nature. MDPSA code is developed which is expected to overcome limitations in compartment models while successfully deals with natural disruptive events. The R and D target for the TSPA is to develop the sufficient scenarios and their variation cases to understand the safety of KRS in every possible aspect. For this, reference scenarios, alternative scenarios covering engineered barrier failure and natural events are developed and assessed respectively for around 100 cases. The stylized template to assess the Korean reference biosphere is developed using the AMBER. Three critical groups, agricultural, freshwater and marine water fishing groups are identified to assess the DCF following the guidelines of ICRP. Based on the QA principles of T2R3, the web based QA system is developed using the procedures in the USNRC 10CFR50 Appendix B. The QA system is combined with the PAID and FEAS to create the comprehensive

  18. Modelling approach to LILW-SL repository safety evaluation for different waste packing options

    International Nuclear Information System (INIS)

    The key objective of the work described here was to support the identification of a preferred disposal concept and packaging option for low and short-lived intermediate level waste (LILW-SL). The emphasis of the assessment, conducted on behalf of the Slovenian radioactive waste management agency (ARAO), was the consideration of several waste treatment and packaging options in an attempt to identify optimised containment characteristics that would result in safe disposal, taking into account the cost-benefit of alternative safety measures. Waste streams for which alternative treatment and packaging solutions were developed and evaluated include decommissioning waste and NPP operational wastes, including drums with unconditioned ion exchange resins in over-packed tube type containers (TTCs). For decommissioning wastes, the disposal options under consideration were either direct disposal of loose pieces grouted into a vault or use of high integrity containers (HIC). In relation to operational wastes, three main options were foreseen. The first is over-packing of resin containing TTCs grouted into high integrity containers, the second option is complete treatment with hydration, neutralization, and cementation of the dry resins into drums grouted into high integrity containers and the third is direct disposal of TTCs into high integrity containers without additional treatment. The long-term safety of radioactive waste repositories is usually demonstrated with the support of a safety assessment. This normally includes modelling of radionuclide release from a multi-barrier near-surface or deep repository to the geosphere and biosphere. For the current work, performance assessment models were developed for each combination of siting option, repository design and waste packaging option. Modelling of releases from the engineered containment system (the 'near-field') was undertaken using the AMBER code. Detailed unsaturated water flow modelling was undertaken using the

  19. Enhancing effects of organic acids on saltiness of low-sodium salt%有机酸味剂对低钠盐增咸作用的研究

    Institute of Scientific and Technical Information of China (English)

    王仕钰; 张立彦

    2012-01-01

    The combination effects between low-sodium salt and L-malic acid,amber acid,citric acid ,fumaric acid and other organic acids were researched.Using ].0% (w/w)of sodium chloride solution as standard,the sourness and saltiness of the combination solution was evaluated by a special panel.The results showed that= L-malic acid, amber acid,citric acid and fumaric acid all had an obvious effect to enhance the saltiness of low-sodium salt at ].6% ,0.8%, 2.4%, 0.8% (w/w) addition level, respectively.The combination solution which had been added into ].6% L-malic acid had a pure saltiness and good taste,and the saltiness could be increased by 1.33 times.%以1.0%(w/w)的氯化钠溶液为标准参照,重点研究了L一苹果酸、琥珀酸、柠檬酸、富马酸等有机酸味剂与低钠盐的复配效果。通过品尝小组对复配溶液的成度、酸度等进行感官评定,结果表明:当单独添加L-苹果酸、琥珀酸、柠檬酸、富马酸的量依次分别为1.6%、0.8%、2.4%、0.8%(w/w)时,对低钠盐有明显的掩盖苦味及增成效果,其中添加1.6%L-苹果酸的复配溶液成味纯正,综合口感良好,增成效果可达1.33倍。

  20. Nutrient Contents per Serving of Twelve Varieties of Cooked Rice Marketed in Jordan

    Directory of Open Access Journals (Sweden)

    Jafar M. El-Qudah

    2008-01-01

    Full Text Available Jordan imports rice from different countries without any quality preferences. Twelve varieties of cooked rice marketed in Jordan were analyzed. The content per serving of these varieties were computed for energy, protein, carbohydrates, fat, calcium, sodium, potassium, magnesium, manganese, copper, iron and phosphorous. The protein content per serving found to range from 0.49 g for La Cigala rice to 6.2 g for Harvest rice. The fat content for all rice brands was less than 0.37 g per serving. The energy content ranged from 172.12 g/serving for Basmati rice to 212.25 g/serving for Sun White rice. Generally, all rice varieties contain significant amounts of minerals per serving. Ruzzana found to contain the highest level of calcium (38.2 mg/serving and Amber the lowest calcium content (6.7 mg/serving. Magnesium content found to range from 5.7 mg/serving for Royal Umberella rice to 16.3 mg/serving for Ruzzana rice. Consumption of one serving of Harvest cooked rice will cover 13.5% of the daily requirement of protein for females and 11.1% for males. Manganese content of one serving of Harvest, Sun White, Abu bent and La Cigala will cover 22.2% of the daily requirements for females and 14.7% for males, while consumption of one of Basmati, Sos rice or Amber will cover only 11.1% and 8.75 of requirement for females and males respectively. Planning a healthful diet is not a simple task. Dietary Reference Intake planning and assessing the diets of individuals or groups of healthy individuals according to their stage of life and sex. Food choice is a function of many factors, including personal preferences, habits, ethnic heritage and tradition. Dietary guidelines for Americans, consider whole grain products like rice are among the food groups that form the basis of a healthy diet. Including rice as part of a healthy, balanced diet can be linked to overall healthier eating patterns. Rice eaters are more likely to eat a diet consistent with the 2005 Dietary

  1. The environment of the fast rotating star Achernar. III. Photospheric parameters revealed by the VLTI

    Science.gov (United States)

    Domiciano de Souza, A.; Kervella, P.; Moser Faes, D.; Dalla Vedova, G.; Mérand, A.; Le Bouquin, J.-B.; Espinosa Lara, F.; Rieutord, M.; Bendjoya, P.; Carciofi, A. C.; Hadjara, M.; Millour, F.; Vakili, F.

    2014-09-01

    Context. Rotation significantly impacts on the structure and life of stars. In phases of high rotation velocity (close to critical), the photospheric structure can be highly modified, and present in particular geometrical deformation (rotation flattening) and latitudinal-dependent flux (gravity darkening). The fastest known rotators among the nondegenerate stars close to the main sequence, Be stars, are key targets for studying the effects of fast rotation on stellar photospheres. Aims: We seek to determine the purely photospheric parameters of Achernar based on observations recorded during an emission-free phase (normal B phase). Methods: Several recent works proved that optical/IR long-baseline interferometry is the only technique able to sufficiently spatially resolve and measure photospheric parameters of fast rotating stars. We thus analyzed ESO-VLTI (PIONIER and AMBER) interferometric observations of Achernar to measure its photospheric parameters by fitting our physical model CHARRON using a Markov chain Monte Carlo method. This analysis was also complemented by spectroscopic, polarimetric, and photometric observations to investigate the status of the circumstellar environment of Achernar during the VLTI observations and to cross-check our model-fitting results. Results: Based on VLTI observations that partially resolve Achernar, we simultaneously measured five photospheric parameters of a Be star for the first time: equatorial radius (equatorial angular diameter), equatorial rotation velocity, polar inclination, position angle of the rotation axis projected on the sky, and the gravity darkening β coefficient (effective temperature distribution). The close circumstellar environment of Achernar was also investigated based on contemporaneous polarimetry, spectroscopy, and interferometry, including image reconstruction. This analysis did not reveal any important circumstellar contribution, so that Achernar was essentially in a normal B phase at least from mid

  2. Colour-rendition properties of solid-state lamps

    Energy Technology Data Exchange (ETDEWEB)

    Zukauskas, A [Institute of Applied Research, Vilnius University, Sauletekio al. 9, bldg. III, Vilnius, LT-10222 (Lithuania); Vaicekauskas, R [Department of Computer Science, Vilnius University, Naugarduko g. 24, Vilnius, LT-03225 (Lithuania); Shur, M S, E-mail: arturas.zukauskas@ff.vu.l [Department of Electrical, Computer, and System Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 (United States)

    2010-09-08

    The applicability of colour-quality metrics to solid-state light sources is validated and the results of the assessment of colour-rendition characteristics of various lamps are presented. The standard colour-rendering index metric or a refined colour-quality scale metric fails to distinguish between two principle colour-rendition properties of illumination: the ability to render object colours with high fidelity and the ability to increase chromatic contrast, especially when the spectra of light sources contain a few narrow-band electroluminescence components. Supplementing these metrics by the known figures of merit that measure the gamut area of a small number of test colour samples does not completely resolve this issue. In contrast, the statistical approach, which is based on sorting a very large number of test colour samples in respect of just-perceivable colour distortions of several kinds, offers a comprehensive assessment of colour-rendition properties of solid-state light sources. In particular, two statistical indices, colour-fidelity index (CFI) and colour-saturation index (CSI), which are the relative numbers of object colours rendered with high fidelity and increased saturation, respectively, are sufficient to reveal and assess three distinct types of solid-state light sources. These are (i) high-fidelity lamps, which cover the entire spectrum with the spectral components present in the wavelength ranges of both 530-610 nm and beyond 610 nm (e.g. trichromatic warm white phosphor-converted (pc) light-emitting diodes (LEDs), red-amber-green-blue LED clusters, complementary clusters of white and coloured LEDs); (ii) colour-saturating lamps, which lack power in the 530-610 nm wavelength range (e.g. red-green-blue or red-cyan-blue LED clusters) and (iii) colour-dulling lamps, which lack power for wavelengths longer than 610 nm (dichromatic daylight pc LEDs and amber-green-blue LED clusters). Owing to a single statistical format, CSI and CFI can be used for

  3. Conformational solution studies of neuropeptide gamma using CD and NMR spectroscopy.

    Science.gov (United States)

    Rodziewicz-Motowidło, Sylwia; Brzozowskl, Krzysztof; Legowska, Anna; Liwo, Adam; Silbering, Jerzy; Smoluch, Marek; Rolka, Krzysztof

    2002-05-01

    Neuropeptide gamma is one of the largest members of the tachykinin family of peptides, exhibiting strong agonistic activity towards the NK-2 tachykinin receptor. This peptide was synthesized by the solid-phase method using the Fmoc chemistry. Circular-dichroism spectroscopy (CD) investigations of this peptide were performed in phosphate buffer, in the presence of sodium dodecylsulphate (SDS) micelles and trifluoroethanol (TFE) solutions and in DMSO-d6 using the 2D NMR technique in conjunction with two different theoretical approaches. The first assumes multiconformational equilibrium of the peptide studied characterized by the values of statistical weights of low-energy conformations. These calculations were performed using three different force fields ECEPP/3, AMBER4.1 and CHARMM (implemented in the X-PLOR program). The second method incorporates interproton distance and dihedral angle constraints into the starting conformation using the Simulated Annealing algorithm (X-PLOR program). The CD experiments revealed that although the peptide studied is flexible in polar solvents, a tendency to adopt a helical structure was observed in the hydrophobic environment. The NMR data (NOE effects) indicate a helical or reverse structure in the Ile7-His12 fragment of the peptide studied in DMSO-d6 solution. The results obtained cannot be interpreted in terms of a single conformation. Most of the conformations obtained with the ECEPP/3 force field possess a high content of a helical structure. None of the conformers, obtained with the AMBER4.1 and CHARMM force fields, can be considered as the dominant one. In all conformations several beta-turns were detected and in some cases gamma-turns were also found. But in fact, it is rather difficult to select the position of the secondary element(s) present in the structure of NPgamma in solution. All conformers calculated with the X-PLOR program (with using NMR derived distance and torsion angle constraints) are stabilized by several

  4. Total System Performance Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Yong Soo; Kang, Chul Hyung; Lee, Youn Myoung; Han, Ji Woong; Choi, Jong Won; Hahn, Pil Soo; Park, Jeong Hwa; Jeong, Mi Seon

    2007-06-15

    Based on the KAERI FEP list developed through the previous studies, the KAERI FEP Encyclopedia has been developed. Current version is 1.0 which includes all relevant FEPs to compose of two references and all alternative scenarios. Many interaction FEPs between scenario defining FEP(SDF) are created throughout the study. FEPs are classified into many Integrated FEP(IFEP) which eventually become the elements of the RES matrix. The FEAS program one of the component of the KAERI's CYPRUS information system is added to develop the FEP, RES, AC, AMF and finally scenarios. It assists to create transparent way to deal with assessment from the stage of the planning of the R and D to the final stage of the external audit and regulatory body review. Even though MASCOT-K and compartment analysis codes such as AMBER, GoldSim and Ecolego are excellent for TSPA they by in heritage possess a certain limitation especially to identify a proper migration cross sectional area when a relatively big component intersects with a tiny one such as a fracture. It is truly 3D phenomena in nature. MDPSA code is developed which is expected to overcome limitations in compartment models while successfully deals with natural disruptive events. The R and D target for the TSPA is to develop the sufficient scenarios and their variation cases to understand the safety of KRS in every possible aspect. For this, reference scenarios, alternative scenarios covering engineered barrier failure and natural events are developed and assessed respectively for around 100 cases. The stylized template to assess the Korean reference biosphere is developed using the AMBER. Three critical groups, agricultural, freshwater and marine water fishing groups are identified to assess the DCF following the guidelines of ICRP. Based on the QA principles of T2R3, the web based QA system is developed using the procedures in the USNRC 10CFR50 Appendix B. The QA system is combined with the PAID and FEAS to create the

  5. El (reconocimiento de la madre en La mitad del alma

    Directory of Open Access Journals (Sweden)

    Sandra J. Schumm

    2011-01-01

    Full Text Available Resumen: La mitad del alma de Carme Riera, en que C rememora a su madre, enfatiza la importancia del reconocimiento de las mujeres en la memoria histórica. Desde el mito griego de Atena, quien ignoraba a su madre Metis, la sociedad patriarcal ha excluido a la madre, lo cual promete que la hija conlleve negación también, según Amber Jacobs en On Matricide. Jacobs observa que en La Oresteia hay crímenes sancionados contra las mujeres, las hijas están deprimidas, existe incesto contra la hija, la reproducción familiar se paraliza, toda la sociedad sufre y la hija se desperdicia también cuando la madre es menospreciada. Jacobs afirma que este desprecio de la madre que transcurría en los mitos griegos continúa en la sociedad y la psicología hoy en día. En esta novela de Riera, la hija protagonista, quien desconoce a su madre, sufre de un estado depresivo, la falta de creatividad y una conexión demasiado fuerte con su padre, semejante a lo que Jacobs observa en los mitos, pero la escritura de C sobre su madre la integrará en la consciencia y mejorará la situación de la hija y, últimamente, la de toda la civilización.Summary: Carme Riera‟s La mitad del alma, in which C recollects her mother, emphasizes the importance of the recognition of women in historic memory. Ever since the Greek myth of Athena, who was ignorant of the existence of her mother, Metis, patriarchal society has excluded the mother, a fact which promises that the daughter will also experience negation, according to Amber Jacobs in On Matricide. Jacobs observes that in La Oresteia there are sanctioned crimes against women, the daughters are depressed, there is incest against the daughter, she is dishonored, family reproduction stops, and all of society suffers when the mother is not appreciated. Jacobs affirms that the distain of the mother that took place in Greek myths continues in society and psychology today. In this novel by Riera, the protagonist/daughter, who

  6. Development of Polarizable Models for Molecular Mechanical Calculations IV: van der Waals parameterization

    Science.gov (United States)

    Wang, Junmei; Cieplak, Piotr; Li, Jie; Cai, Qin; Hsieh, MengJuei; Luo, Ray; Duan, Yong

    2012-01-01

    In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of “chromosomes” which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set as indicated by the reduction in errors of the calculated pure liquid density (d), heat of vaporization (Hvap) and hydration energy. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33% to 2.97%; the RMSE of Hvap was reduced from 1.98 kcal/mol to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 kcal/mol to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable

  7. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

    Science.gov (United States)

    Wang, Junmei; Cieplak, Piotr; Li, Jie; Cai, Qin; Hsieh, Meng-Juei; Luo, Ray; Duan, Yong

    2012-06-21

    In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H(vap)), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H(vap) was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was

  8. Archaeometric study of glass beads from the 2nd century BC cemetery of Numantia

    Directory of Open Access Journals (Sweden)

    García Heras, Manuel

    2003-06-01

    Full Text Available Recent archaeologícalf ieldwork undertaken in the Celtiberian cremation necropolis of Numantia (Soria, Spain has provided a group of glass beads from the 2nd century BC. Such glass beads were part, together with other metallic and ceramic items, of the offerings deposited with the dead. They are ring-shaped in typology and deep-blue, amber, or semitransparent white in colour. This paper reports results derived from the chemical and microstructural characterization carried out on a representative sample set of this group of beads. The main goal of the research was to find out about their production technology to explore their probable provenance. In addítion, corrosion mechanisms were also assessed to determine the influence of crematíon on the beads' structure. The resulting data suggest that these blue and amber beads were made using soda-lime silicate glass, whereas semi-transparent white ones were manufactured from alumino-silicate glass. It has also determined that some transition metal oxides were used as chromophores, as well as lead oxide for decoration.

    La reciente excavación de la necrópolis celtibérica de Numancia (Garray, Soria ha permitido recuperar un conjunto de cuentas de vidrio del siglo II a.C. Las cuentas, junto con otros objetos de metaly cerámica, formaban parte de las ofrendas depositadas con el difunto, siendo de tipología anular y coloreadas en azul oscuro, ambar y blanco semitransparente. Este trabajo presenta los resultados obtenidos en la caracterización química y microestructural de una muestra representativa de este conjunto. El objetivo principal de la investigación consistió en recabar información sobre su tecnología de manufactura y evaluar su posible procedencia. Asimismo, también se investigaron sus mecanismos de corrosión para determinar si la cremación había inducido cambios en su estructura. Los resultados indican que las cuentas azules y ámbar se realizaron con vidrio de silicato s

  9. Strong near-infrared emission in the sub-AU disk of the Herbig Ae star HD 163296: evidence of refractory dust?

    Science.gov (United States)

    Benisty, M.; Natta, A.; Isella, A.; Berger, J.-P.; Massi, F.; Le Bouquin, J.-B.; Mérand, A.; Duvert, G.; Kraus, S.; Malbet, F.; Olofsson, J.; Robbe-Dubois, S.; Testi, L.; Vannier, M.; Weigelt, G.

    2010-02-01

    We present new long-baseline spectro-interferometric observations of the Herbig Ae star HD 163296 (MWC 275) obtained in the H and K bands with the AMBER instrument at the VLTI. The observations cover a range of spatial resolutions between ~3 and ~12 milliarcseconds, with a spectral resolution of ~30. With a total of 1481 visibilities and 432 closure phases, they represent the most comprehensive (u,v) coverage achieved so far for a young star. The circumstellar material is resolved at the sub-AU spatial scale and closure phase measurements indicate a small but significant deviation from point-symmetry. We discuss the results assuming that the near-infrared excess in HD 163296 is dominated by the emission of a circumstellar disk. A successful fit to the spectral energy distribution, near-infrared visibilities and closure phases is found with a model in which a dominant contribution to the H and K band emission originates in an optically thin, smooth and point-symmetric region extending from about 0.1 to 0.45 AU. At a distance of 0.45 AU from the star, silicates condense, the disk becomes optically thick and develops a puffed-up rim, whose skewed emission can account for the non-zero closure phases. We discuss the source of the inner disk emission and tentatively exclude dense molecular gas as well as optically thin atomic or ionized gas as its possible origin. We propose instead that the smooth inner emission is produced by very refractory grains in a partially cleared region, extending to at least ~0.5 AU. If so, we may be observing the disk of HD 163296 just before it reaches the transition disk phase. However, we note that the nature of the refractory grains or, in fact, even the possibility of any grain surviving at the very high temperatures we require (~2100-2300 K at 0.1 AU from the star) is unclear and should be investigated further. Based on AMBER observations collected at the VLTI (European Southern Observatory, Paranal, Chile) with Arcetri Guaranteed Time

  10. Colour-rendition properties of solid-state lamps

    International Nuclear Information System (INIS)

    The applicability of colour-quality metrics to solid-state light sources is validated and the results of the assessment of colour-rendition characteristics of various lamps are presented. The standard colour-rendering index metric or a refined colour-quality scale metric fails to distinguish between two principle colour-rendition properties of illumination: the ability to render object colours with high fidelity and the ability to increase chromatic contrast, especially when the spectra of light sources contain a few narrow-band electroluminescence components. Supplementing these metrics by the known figures of merit that measure the gamut area of a small number of test colour samples does not completely resolve this issue. In contrast, the statistical approach, which is based on sorting a very large number of test colour samples in respect of just-perceivable colour distortions of several kinds, offers a comprehensive assessment of colour-rendition properties of solid-state light sources. In particular, two statistical indices, colour-fidelity index (CFI) and colour-saturation index (CSI), which are the relative numbers of object colours rendered with high fidelity and increased saturation, respectively, are sufficient to reveal and assess three distinct types of solid-state light sources. These are (i) high-fidelity lamps, which cover the entire spectrum with the spectral components present in the wavelength ranges of both 530-610 nm and beyond 610 nm (e.g. trichromatic warm white phosphor-converted (pc) light-emitting diodes (LEDs), red-amber-green-blue LED clusters, complementary clusters of white and coloured LEDs); (ii) colour-saturating lamps, which lack power in the 530-610 nm wavelength range (e.g. red-green-blue or red-cyan-blue LED clusters) and (iii) colour-dulling lamps, which lack power for wavelengths longer than 610 nm (dichromatic daylight pc LEDs and amber-green-blue LED clusters). Owing to a single statistical format, CSI and CFI can be used for

  11. 浅表脂肪瘤样痣1例%A Case of Nevus Lipomatosus Superficialis

    Institute of Scientific and Technical Information of China (English)

    李俊峰; 徐佳; 李鑫; 姜秋霞; 刘杰; 马俊平

    2012-01-01

    A 10-year-old girl had presented with papulae and plaque on the sacrococcygeal region for 9 years. Physical examination showed clustered soft papulae on die aacrococcygeal region with amber color,and anastomosis inequality of size. Two cicatrix were appearanced on center of erylhra with 1.0cm × 1.5cm. Histopathological examination showed hyperkeratinizalion, stratum spinosum hyperplasia, abnormal position adipocytes distributed in lamina superficialis and intercellular layer of dermis. A diagnosis of nevus lipomatosus superfi-cialis was established.%患者女,10岁.骶尾部丘疹、融合性斑块9年余.皮肤科情况:骶尾部可见簇集分布的米粒大淡黄色丘疹,质地柔软,融合成多处大小不等斑块或斑片,皮疹中央可见2处1.0cm×1.5cm大瘢痕增生.皮损组织病理示:表皮轻度角化过度,棘细胞层增生,真皮浅中层胶原束间可见成群分布异位脂肪细胞.诊断:浅表脂肪瘤样痣.

  12. Accounting for electronic polarization in nonpolarizable force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole $\\mu$~3D reported in recent ab initio and experimental s...

  13. Distribution and carbon isotope patterns of diterpenoids and triterpenoids in modern temperate C3 trees and their geochemical significance

    Science.gov (United States)

    Diefendorf, Aaron F.; Freeman, Katherine H.; Wing, Scott L.

    2012-05-01

    Tricyclic diterpenoids and pentacyclic triterpenoids are nearly exclusively produced by gymnosperms and angiosperms, respectively. Even though both classes of terpenoids have long been recognized as plant biomarkers, their potential use as phylogenetically specific δ13C proxies remains largely unexplored. Little is known of how terpenoid abundance and carbon isotope composition vary either with plant phylogenetic position, functional group, or during synthesis. Here, we report terpenoid abundances and isotopic data for 44 tree species in 21 families, representing both angiosperms and gymnosperms, and both deciduous and evergreen leaf habits. Di- and triterpenoid abundances are significantly higher in evergreens compared to deciduous species, reflecting differences in growth strategies and increased chemical investment in longer-lived leaves. Carbon isotope abundances of terpenoid lipids are similar to leaf tissues, indicating biosynthetic isotope effects are small for both the MVA (-0.4‰) and MEP (-0.6‰) pathways. Leaf and molecular isotopic patterns for modern plants are consistent with observations of amber, resins and plant biomarkers in ancient sediments. The δ13C values of ancient diterpenoids are higher than triterpenoids by 2-5‰, consistent with observed isotopic differences between gymnosperms and angiosperms leaves, and support the relatively small lipid biosynthetic effects reported here. All other factors being equal, evergreen plants will dominate the abundance of terpenoids contributed to soils, sediments and ancient archives, with similar inputs estimated for angiosperm and gymnosperm trees when scaled by litter flux.

  14. Polychromatic solid-state lamps versus tungsten radiator: hue changes of Munsell samples

    International Nuclear Information System (INIS)

    Colour-perception differences under illumination by two quadrichromatic solid-state sources of light have been studied with respect to a tungsten radiator with the same correlated colour temperature (2600 K). A virtual RYgCB source (illuminant), which contains red, yellow-green, cyan and blue components with the line width typical of AlGaInP and AlInGaN light-emitting diodes (LEDs), was fully optimized for the highest value of the general colour-rendering index (CRI) (Ra = 98.3). An implemented RAGB source (lamp) contained commercially available red, amber, green and blue LEDs (Ra 79.4). Colorimetric calculations in the Commission Internationale de l'Eclairage 1976 (u',v') colour plane for 40 Munsell colour samples (value 6, chroma/6, hue increment 2.5) revealed the differences in hue discrimination and distortion for both sources in the yellow-green and blue-cyan ranges. These differences were not revealed by the standard analysis of the special CRIs and were lower for the RYgCB illuminant, which contained primary LEDs in the sensitive ranges. A psychophysical experiment on seven subjects was performed using the RAGB lamp stabilized against thermal and ageing drifts. Despite different colour-perception abilities of the subjects under investigation, the experiment confirmed the calculation results. Methods of obtaining composite white light with high subjective ratings are discussed, based on the obtained data

  15. Establishment of technological parameters for disinfestation of dried fruits

    International Nuclear Information System (INIS)

    A study to determine the irradiation parameters for disinfestation of dried fruits: figs, pine nuts, raisins and walnuts, has been carried out in the UTR cobalt-60 facility. The dose distribution in the UTR boxes was measured. Low doses for disinfestation (150 Gy - 300 Gy) were studied, for the commercial practice simulation/validation higher doses were used (15 kGy - 20 kGy). The absorbed dose uniformity ratio (U = Dmax/Dmin) determined was 1.16 up to 1.33 for the dried fruits studied. Different dosimetric systems were tested. Low dose range dosimeters: reference standard Fricke dosimeter, routine dosimeters: Harwell YR Gammachrome and China PMMAYL dosimeter. High dose range dosimeters: routine dosimeters: Harwell Amber Perspex and Clear Perspex purchased at the local market. Label STERIN indicators of 125 Gy and of 300 Gy were assayed to establish a simple and direct process for verification, by customs inspectors, of a prior irradiation treatment. These indicators change their visual message if the threshold dose has been delivered. The performance of STERIN 125 and STERIN 300 suggested that these label indicators could properly be used for doses of 125 Gy and 300 Gy respectively, or higher than these ones. (author)

  16. Resolving asymmetries along the pulsation cycle of the Mira star X Hya

    CERN Document Server

    Haubois, X; Perrin, G; Kervella, P; Mérand, A; Thiébaut, E; Ridgway, S T; Ireland, M; Scholz, M

    2015-01-01

    The mass-loss process in Mira stars probably occurs in an asymmetric way where dust can form in inhomogeneous circumstellar molecular clumps. Following asymmetries along the pulsation cycle can give us clues about these mass-loss processes. We imaged the Mira star X Hya and its environnement at different epochs to follow the evolution of the morphology in the continuum and in the molecular bands. We observed X Hya with AMBER in J-H-K at low resolution at two epochs. We modelled squared visibilities with geometrical and physical models. We also present imaging reconstruction results obtained with MiRA and based on the physical a priori images. We report on the angular scale change of X Hya between the two epochs. 1D CODEX profiles allowed us to understand and model the spectral variation of squared visibilities and constrain the stellar parameters. Reconstructed model-dependent images enabled us to reproduce closure phase signals and the azimuthal dependence of squared visibilities. They show evidence for mate...

  17. Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.

    Science.gov (United States)

    Debolt, Stephen Edward

    Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

  18. Vectorization, parallelization and porting of nuclear codes (porting). Progress report fiscal 1999

    International Nuclear Information System (INIS)

    Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system, the AP3000 system, the SX-4 system and the Paragon system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 18 codes in fiscal 1999. These results are reported in 3 parts, i.e., the vectorization and the parallelization part on vector processors, the parallelization port on scalar processors and the porting part. In this report, we describe the porting. In this porting part, the porting of Assisted Model Building with Energy Refinement code version 5 (AMBER5), general purpose Monte Carlo codes far neutron and photon transport calculations based on continuous energy and multigroup methods (MVP/GMVP), automatic editing system for MCNP library code (autonj), neutron damage calculations for materials irradiations and neutron damage calculations for compounds code (SPECTER/SPECOMP), severe accident analysis code (MELCOR) and COolant Boiling in Rod Arrays, Two-Fluid code (COBRA-TF) on the VPP500 system and/or the AP3000 system are described. (author)

  19. Kirkwood-Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies.

    Science.gov (United States)

    Chiba, Shuntaro; Furuta, Tadaomi; Shimizu, Seishi

    2016-08-11

    Cosolvents, such as urea, affect protein folding and binding, and the solubility of solutes. The modeling of cosolvents has been facilitated significantly by the rigorous Kirkwood-Buff (KB) theory of solutions, which can describe structural thermodynamics over the entire composition range of aqueous cosolvent mixtures based only on the solution density and the KB integrals (KBIs), i.e., the net excess radial distribution functions from the bulk. Using KBIs to describe solution thermodynamics has given rise to a clear guideline that an accurate prediction of KBIs is equivalent to accurate modeling of cosolvents. Taking urea as an example, here we demonstrate that an improvement in the prediction of KBIs comes from an improved reproduction of high-level quantum chemical (QC) electrostatic potential and molecular pairwise interaction energies. This rational approach to the improvement of the KBI prediction stems from a comparison of existing force fields, AMOEBA, and the generalized AMBER force field, as well as the further optimization of the former to enable better agreement with QC interaction energies. Such improvements would pave the way toward a rational and systematic determination of the transferable force field parameters for a number of important small molecule cosolvents. PMID:27434200

  20. A molecular mechanical model for N-heterocyclic carbenes.

    Science.gov (United States)

    Gehrke, Sascha; Hollóczki, Oldamur

    2016-08-10

    In this work we present a set of force fields for nine synthetically relevant and/or structurally interesting N-heterocyclic carbenes, including imidazol-, thiazol-, triazol-, imidazolidin-, and pyridine-ylidenes. The bonding parameters were calculated by using a series of geometry optimizations by ab initio methods. For fitting the non-bonding interactions, a water molecule was employed as a probe. The interaction energy between the carbene and the probe molecule was sampled along two coordinates for each carbene, representing the interaction through the lone pair, or the π system of the molecule. The corresponding reference interaction energies were obtained by CCSD(T)/CBS calculations. To describe the direction dependence of the intermolecular potential energy, an extra, massless Coulombic interaction site was included for all carbenes, which represents the lone pair of the divalent carbon atom. The resulting fitted carbene force field (CaFF) showed a robust behavior regarding probe molecule, as changing the molecular mechanical water model, or employing, instead, an OPLS methanol molecule did not introduce significant deviations in the potential energies. The obtained CaFF models are easy to merge with standard OPLS or AMBER force fields, therefore the molecular simulations of a large number of N-heterocyclic carbenes becomes available. PMID:27426687

  1. Formation and use of coal combustion residues from three types of power plants burning Illinois coals

    Science.gov (United States)

    Demir, I.; Hughes, R.E.; DeMaris, P.J.

    2001-01-01

    Coal, ash, and limestone samples from a fluidized bed combustion (FBC) plant, a pulverized coal combustion (PC) plant, and a cyclone (CYC) plant in Illinois were analyzed to determine the combustion behavior of mineral matter, and to propose beneficial uses for the power plant ashes. Pyrite and marcasite in coal were converted during combustion to glass, hematite and magnetite. Calcite was converted to lime and anhydrite. The clay minerals were altered to mullite and glass. Quartz was partially altered to glass. Trace elements in coal were partially mobilized during combustion and, as a result, emitted into the atmosphere or adsorbed on fly ash or on hardware on the cool side of the power plants. Overall, the mobilities of 15 trace elements investigated were lower at the FBC plant than at the other plants. Only F and Mn at the FBC plant, F, Hg, and Se at the PC plant and Be, F, Hg, and Se at the CYC plant had over 50% of their concentrations mobilized. Se and Ge could be commercially recovered from some of the combustion ashes. The FBC ashes could be used as acid neutralizing agents in agriculture and waste treatment, and to produce sulfate fertilizers, gypsum wall boards, concrete, and cement. The PC and CYC fly ashes can potentially be used in the production of cement, concrete, ceramics, and zeolites. The PC and CYC bottom ashes could be used in stabilized road bases, as frits in roof shingles, and perhaps in manufacturing amber glass. ?? 2001 Elsevier Science Ltd. All rights reserved.

  2. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase.

    Science.gov (United States)

    Wang, Xianwei; Zhang, John Z H; He, Xiao

    2015-11-14

    Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties. PMID:26567650

  3. Differential interferometry of QSO broad line regions I: improving the reverberation mapping model fits and black hole mass estimates

    CERN Document Server

    Rakshit, Suvendu; Meilland, Anthony; Hönig, Sebastian F

    2014-01-01

    We investigate the general constraints that differential interferometry (DI) can yield on BLRs and discuss the signatures of different BLR parameters, such as black hole mass, BLR size, thickness, distribution of clouds, local micro or macroturbulence versus global velocity, rotation versus inflow and outflow, and cloud optical thickness, on both DI and reverberation mapping (RM) observables, describing a 3D geometrical and kinematic BLR model that can simulate all DI and RM observables. Combination of DI and RM not only constrain the BLR geometry and kinematics, but also provide a way to use BLRs as standard candles. It appears that DI can constrain the RM projection factor and decrease the number of fixed model parameters. We use a SNR analysis of DI, updated and calibrated on our actual 3C273 data, to evaluate the number of targets accessible to current (AMBER+), upcoming (GRAVITY) and possible VLTI instruments, that suggest the full potential of the VLTI exceeds 60 targets with known improvements of instr...

  4. AGN BLR structure, luminosity and mass from combined Reverberation Mapping and Optical Interferometry observations

    CERN Document Server

    Rakshit, Suvendu

    2014-01-01

    Unveiling the structure of the Broad Line Region (BLR) of AGN is critical to understand the quasar phenomenon. Detail study of the geometry and kinematic of these objects can answer the basic questions about the central BH mass, accretion mechanism and rate, growth and evolution history. Observing the response of the BLR clouds to continuum variations, Reverberation Mapping (RM) provides size vs luminosity and mass vs luminosity relations for QSOs and Sy1 AGNs with the goal to use these objects as standard candles and mass tags. However, the RM size can receive different interpretations depending on the assumed geometry and the corresponding mass depends on an unknown geometrical factor as well on the possible confusion between local and global velocity dispersion. From RM alone, the scatter around the mean mass is as large as a factor 3. Though BLRs are expected to be much smaller than the current spatial resolution of large optical interferometers (OI), we show that differential interferometry with AMBER, G...

  5. Shell Bed Identification of Kaliwangu Formation and its Sedimentary Cycle Significance, Sumedang, West Java

    Directory of Open Access Journals (Sweden)

    Aswan Aswan

    2014-07-01

    Full Text Available DOI: 10.17014/ijog.v8i1.151Kaliwangu Formation cropping out around Sumedang area contains mollusk fossils dominated by gastropods and bivalves. In terms of sequence stratigraphy, each sedimentary cycle generally consists of four shell bed types: Early Transgressive Systems Tract (Early TST deposited above an erosional surface or sequence boundary, that is characterized by shell disarticulation, trace fossils, gravelly content, no fossil orientation direction, and concretion at the bottom; Late Transgressive Systems Tract (Late TST identified by articulated (conjoined specimen in its life position, that shows a low level abration and fragmentation, adult specimen with complete shells, and variation of taxa; Early Highstand Systems Tract (Early HST characterized by adult taxa that was found locally in their life position with individual articulation, juvenile specimens frequently occured; Late Highstand Systems Tract (Late HST determined as multiple-event concentrations, disarticulated shell domination, and some carbon or amber intercalation indicating terrestrial influence. Shell bed identification done on this rock unit identified nineteen sedimentary cycles.

  6. Origin and properties of Oltu gemstone coal

    Energy Technology Data Exchange (ETDEWEB)

    Karayigit, A.I. [University of Hacettepe, Ankara (Turkey)

    2007-07-01

    This study focuses on the origin and properties of the Oltu gemstone or Oltustone. The Oltu gemstone known as 'Black Amber' is dull-bright black color, and is very low ash, high volatile matter, total sulfur and calorific value. Very high volatile matter content on a dry-ash free basis (66.52%) and non-agglomerating character imply that its coal rank is very low. The Oltu gemstone includes abundant organic (amorphous) matter and trace amounts of quartz and pyrite. Petrographic study indicated that pyrite and quartz generally finely disseminated the organic matter. Major and trace element data have low concentrations. The trace element concentrations fall within the range values for the most world coals, except for Bi that exceeds range values (0.1-0.5-g/ g) in most world coals. Petrographic observations on the polished briquette have shown that the gemstone was made of xylite including mainly textinite and corpohuminite, minor amounts of resinite and liptodetrinite. Mean values of random reflectance (% Rr) measurements on the textinite and corpohuminite are 0.23 and 0.30% Rr, respectively. These values indicate very low coal rank, in agreement with the volatile matter.

  7. Lithium cobalt oxide thin film and its electrochromism

    Science.gov (United States)

    Wei, Guang; Haas, Terry E.; Goldner, Ronald B.

    1989-06-01

    Thin films of lithium cobalt oxide have been prepared by RF-sputtering from powdered LiCoO2. These films permit reversible electrolytic removal of lithium ions upon application of an anodic voltage in a propylene carbonate-lithium perchlorate electrolyte, the films changing in color from a pale amber transparent state to a dark brown. A polycrystalline columnar film structure was revealed with SEM and TEM. X ray examination of the films suggests that the layered rhombohedral LiCoO2 structure is the major crystalline phase present. Oxidation-reduction titration and atomic absorption were used for the determination of the film stoichiometry. The results show that the as deposited-films on glass slides are lithium deficient (relative to the starting material) and show a high average cobalt oxidation state near +3.5. The measurements of dc conductivity suggest a band to band conduction at high temperature (300 to 430 K) and hopping conduction in localized states at low temperature (4 to 270 K). The thermoelectric power data show that the films behave as p-type semiconductors. Transmission and reflectance measurements from 400 nm to 2500 nm show significant near-IR reflectivity.

  8. Investigating risky, distracting, and protective peer passenger effects in a dual process framework.

    Science.gov (United States)

    Ross, Veerle; Jongen, Ellen M M; Brijs, Kris; Brijs, Tom; Wets, Geert

    2016-08-01

    Prior studies indicated higher collision rates among young novice drivers with peer passengers. This driving simulator study provided a test for a dual process theory of risky driving by examining social rewards (peer passengers) and cognitive control (inhibitory control). The analyses included age (17-18 yrs, n=30; 21-24 yrs, n=20). Risky, distracting, and protective effects were classified by underlying driver error mechanisms. In the first drive, participants drove alone. In the second, participants drove with a peer passenger. Red-light running (violation) was more prevalent in the presence of peer passengers, which provided initial support for a dual process theory of risk driving. In a subgroup with low inhibitory control, speeding (violation) was more prevalent in the presence of peer passengers. Reduced lane-keeping variability reflected distracting effects. Nevertheless, possible protective effects for amber-light running and hazard handling (cognition and decision-making) were found in the drive with peer passengers. Avenues for further research and possible implications for targets of future driver training programs are discussed. PMID:27218409

  9. Improved detection of induced seismicity using beamforming techniques: application to traffic light systems

    Science.gov (United States)

    Hicks, Stephen; Verdon, James; Kendal, J.-Michael; Hill, Phil

    2016-04-01

    Unconventional methods of hydrocarbon extraction, such as hydraulic fracturing, have the potential to reactivate existing faults, causing induced seismicity. Traffic Light Schemes have been implemented in some regions; these systems ensure that drilling activities are paused or shut-down if seismic events larger than a given magnitude are induced. In particular, the United Kingdom has imposed a traffic light scheme based on magnitude thresholds of Ml = 0.0 and Ml = 0.5 for the amber and red limits, respectively. Therefore, an effective traffic light scheme in the UK requires monitoring arrays capable of detecting events with Ml detection thresholds can be challenging where ambient noise levels are high, such as in the UK. We have developed an algorithm capable of robustly detecting and locating small magnitude events, which are characterised by very low signal-to-noise ratios using small arrays of surface broadband seismometers. We compute STA/LTA functions for each trace, time shift them by theoretical travel-times for a given event location, and combine them via a linear stack. We test our method using a dataset from a surface array of Güralp 3T broadband seismometers that recorded hydraulic fracturing activities in the central United States. Our beamforming and stacking approach identified a total of 20 events, compared to only 4 events detected by traditional picking methods. We therefore suggest that our approach is suitable for use with low magnitude traffic light schemes, especially in noisy environments.

  10. Functional analysis of three amino acid residues of purR re-pressor, Trp147, Gln-218 and Gln-292 in Salmonella typhi-murium

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The amber mutation sites of 6 purR(am) mutants were determined bycloning and DNA sequencing. The results showed that the mutations were distributed at three different sites in PurR coding region, G721(→A), C933(→T) and C1155(→T), which respectively turn Trp-147,Gln-218 and Gln-292 of PurR into TAG terminal codon. To determine the effect of the three amino acid residues on regulatory function of PurR protein 5 different kinds of tRNA suppressor genes, Su3, Su4, Su6, Su7 and Su9 were used for creating the PurR protein variants with single amino acid substitution. The results indicated that Cys, Glu, Gly, His and Arg which substituted Trp-147 respectively all could not recover the regulation function of PurR. It confirmed that Trp-147 is a critical amino acid for the PurR function. Gln-292 substituted respectively by the same amino acids also could not recover the PurR function, demonstrating that Gln-292 is also an important amino acid residue in PurR.

  11. Morphologically Specialized Termite Castes and Advanced Sociality in the Early Cretaceous.

    Science.gov (United States)

    Engel, Michael S; Barden, Phillip; Riccio, Mark L; Grimaldi, David A

    2016-02-22

    A hallmark of animals that are eusocial, or those with advanced sociality, is reproductive specialization into worker and queen castes. In the most derived societies, these divisions are essentially fixed and in some arthropods, include further specialization--a tripartite system with a soldier caste that defends the colony. Eusociality has originated numerous times among insects but is believed to have appeared first in the termites (Isoptera), in the Early Cretaceous. However, all termites known from the Cretaceous have, until now, only been winged reproductives (alates and dealates); the earliest soldiers and definitive workers were known from just the Miocene (ca. 17-20 million years ago [mya]). Here, we report six termite species preserved in Early Cretaceous (ca. 100 mya) amber from Myanmar, one described as Krishnatermes yoddha gen. et sp. nov., comprising the worker/pseudergate, winged reproductive, and soldier, and a second species, Gigantotermes rex gen. et sp. nov., based on one of the largest soldier termites yet known. Phylogenetic analysis indicates that Krishnatermes are in the basal "Meiatermes-grade" of Cretaceous termites. Workers/pseudergates of another four species are briefly described, but not named. One of these workers/pseudergates reveals that ants--the most serious enemies of modern termites--lived in close proximity to termites in the Burmese paleofauna. These discoveries demonstrate the Mesozoic antiquity of specialized termite caste systems and corroborate that among all social species, termites probably had the original societies. PMID:26877085

  12. Cockroach as the Earliest Eusocial Animal

    Institute of Scientific and Technical Information of China (English)

    Peter VR(S)ANSK(Y)

    2010-01-01

    A completely preserved cockroach Sociala perlucida gen.et sp.nov.(Blattida:Socialidae fam.nov.) is described from the Mesozoic (Albian Early Cretaceous) amber of Archingeay in France.It is categorized within the new family Socialidae,originating from the Mesozoic cockroach family Liberiblattinidae,and representing the sister group to the most basal known eutermite families.Numerous direct and indirect morphological evidence (such as a unique narrow body and pronotum with reduced coloration,legs without carination and with numerous sensiilar pitts (forelegs) as adaptations to life in nests analogical to the living termitophillous species;enlarged head,long paips for communication,a general venation modified in a direction towards termites (subcosta and radial vein [R] approximated,R branches approximated,simplified,cross-veins reduced),and possibly also the development of the breaking forewing sutura for detaching wings after marriage flight),suggest its eusociai mode of life.Thus,the first eusociality originated within cockroaches,prior to giving birth to termites;termites and Cryptocercus are not directly related.The group of eusocial cockroaches makes termite morphotaxon polyphyletic,but also in this case,the erection of a new order for mastotermites (including Cratomastotermitidae) and/or the inclusion of eusocial,morphological cockroaches within termites appears counterproductive,thus an example of such a general exception to the taxonomical procedure is provided.

  13. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

    Science.gov (United States)

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-04-12

    Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol. PMID:26914292

  14. Influence of the extraction method and storage time on the physicochemical properties and carotenoid levels of pequi (Caryocar brasiliense Camb. oil

    Directory of Open Access Journals (Sweden)

    Milton Cosme Ribeiro

    2012-06-01

    Full Text Available The objective of this study was to analyze the physicochemical properties and carotenoid levels of pequi oil obtained by different extraction methods and to evaluate the preservation of these properties and pigments during storage time. The pequi oil was obtained by solvent extraction, mechanical extraction, and hot water flotation. It was stored for over 180 days in an amber bottle at ambient conditions. Analyses for the determination of the acidity, peroxide, saponification and iodine values, coloration, total carotenoids, and β-carotene levels were conducted. The oil extraction with solvents produced the best yield and carotenoid levels. The oil obtained by mechanical extraction presented higher acidity (5.44 mg KOH.g-1 and peroxide values (1.07 mEq.kg-1. During the storage of pequi oil, there was an increase in the acidity and the peroxide values, darkening of the oil coloration, and a reduction of the carotenoid levels. Mechanical extraction is the less advantageous method for the conservation of the physicochemical properties and carotenoid levels in pequi oil.

  15. A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[N]arenes as carriers for Bosutinib and Sorafenib.

    Science.gov (United States)

    Galindo-Murillo, Rodrigo; Aguilar-Suárez, Luis Enrique; Barroso-Flores, Joaquín

    2016-04-15

    Interaction energies between a family of 36 calix[n]arenes, their corresponding thia- analogues, and two commercially available second generation tyrosine kinase III inhibitors-Bosutinib and Sorafenib-were calculated through DFT methods at the B97D/6-31G(d,p) level of theory, based on Natural Population Analysis, for the in silico development of suitable drug carriers based on the aforementioned macrocycles which can increase their bioavailability and in turn their pharmaceutical efficiency. Molecular Dynamics simulations (production runs: +500 ns) using the General Amber Force Field were also carried out in order to assess the releasing process of these drugs in an explicit aqueous environment. In total, 144 host-guest complexes are examined. According to our results, five-membered SO3 H and i-Pr functionalized-calixarenes are the best candidates for Sorafenib-carriers while six-membered ones SO3 H and C2 H4 NH2 functionalized- are the lead candidates for Bosutinib-carriers. © 2015 Wiley Periodicals, Inc. PMID:26714797

  16. Molecular dynamics of sialic acid analogues and their interaction with influenza hemagglutinin

    Directory of Open Access Journals (Sweden)

    Blessia T

    2010-01-01

    Full Text Available Synthetic sialic acid analogues with multiple modifications at different positions(C-1/C-2/C-4/C-8/C-9 are investigated by molecular mechanics and molecular dynamics to determine their conformational preferences and structural stability to interact with their natural receptors. Sialic acids with multiple modifications are soaked in a periodic box of water as solvent. Molecular mechanics and a 2 nanosecond molecular dynamics are done using amber force fields with 30 picosecond equilibrium. Direct and water mediated hydrogen bonds existing in the sialic acid analogues, aiding for their structural stabilization are identified in this study. The accessible conformations of side chain linkages of sialic acid analogues holding multiple substituents are determined from molecular dynamics trajectory at every 1ps interval. Transitions between different minimum energy regions in conformational maps are also noticed in C-1, C-2, C-4, C-8 and C-9 substituents. Docking studies were done to find the binding mode of the sialic acid analogues with Influenza hemagglutinin. This finding provides stereo chemical explanation and conformational preference of sialic acid analogues which may be crucial for the design of sialic acid analogues as inhibitors for different sialic acid specific pathogenic proteins such as influenza toxins and neuraminidases.

  17. The Use of Chlorophyll Fluorescence Lifetime to Assess Phytoplankton Physiology within a River-Dominated Environment

    Science.gov (United States)

    Hall, Callie M.; Miller, Richard L.; Redalje, Donald G.; Fernandez, Salvador M.

    2002-01-01

    Chlorophyll a fluorescence lifetime was measured for phytoplankton populations inhabiting the three physical zones surrounding the Mississippi River's terminus in the Gulf of Mexico. Observations of river discharge volume, nitrate + nitrite, silicate, phosphate, PAR (Photosynthetically Active Radiation) diffuse attenuation within the water column, salinity, temperature, SPM, and chl a concentration were used to characterize the distribution of chl fluorescence lifetime within a given region within restricted periods of time. 33 stations extending from the Mississippi River plume to the shelf break of the Louisiana coast were surveyed for analysis of chlorophyll fluorescence lifetime during two cruises conducted March 31 - April 6, 2000, and October 24 - November 1, 2000. At each station, two to three depths were chosen for fluorescence lifetime measurement to represent the vertical characteristics of the water column. Where possible, samples were taken from just below the surface and from just above and below the pycnocline. All samples collected were within the 1% light level of the water column (the euphotic zone). Upon collection, samples were transferred to amber Nalgene bottles and left in the dark for at least 15 minutes to reduce the effects of non-photochemical quenching and to insure that photosynthetic reaction centers were open. Before measurements within the phase fluorometer were begun, the instrument was allowed to warm up for no less than one hour.

  18. High-resolution Br-gamma spectro-interferometry of the transitional Herbig Ae/Be star HD 100546: a Keplerian gaseous disc inside the inner rim

    CERN Document Server

    Mendigutía, I; Oudmaijer, R D; Fairlamb, J R; Carciofi, A C; Ilee, J D; Vieira, R G

    2015-01-01

    We present spatially and spectrally resolved Br-gamma emission around the planet-hosting, transitional Herbig Ae/Be star HD 100546. Aiming to gain insight into the physical origin of the line in possible relation to accretion processes, we carried out Br-gamma spectro-interferometry using AMBER/VLTI from three different baselines achieving spatial and spectral resolutions of 2-4 mas and 12000. The Br-gamma visibility is larger than that of the continuum for all baselines. Differential phases reveal a shift between the photocentre of the Br-gamma line -displaced 0.6 mas (0.06 au at 100 pc) NE from the star- and that of the K-band continuum emission -displaced 0.3 mas NE from the star. The photocentres of the redshifted and blueshifted components of the Br-gamma line are located NW and SE from the photocentre of the peak line emission, respectively. Moreover, the photocentre of the fastest velocity bins within the spectral line tends to be closer to that of the peak emission than the photocentre of the slowest ...

  19. Hierarchical atom type definitions and extensible all-atom force fields.

    Science.gov (United States)

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. PMID:26537332

  20. Inclusion compounds between α-, β- and γ-cyclodextrins: iron II lactate: a theoretical and experimental study using diffusion coefficients and molecular mechanics

    Science.gov (United States)

    Leite, Rosiley A.; Lino, Antonio C. S.; Takahata, Yuji

    2003-01-01

    The inclusion compounds between iron II lactate and three different cyclodextrins (CDs) were studied by means of experimental and theoretical data. The importance of iron II in the human metabolism effort the necessity of a minimum concentration to the human life. Malnutrition is one great problem in social politics of many countries on the world. The possibility to the development of novel medicines with the iron II species stable look for an increase on the efficiency for this kind of aid. Kinetics measurements confirm the possibility to stop the oxidation reaction. It was the first indication of efficient molecular encapsulation. Diffusion coefficient measurements were carried out by Taylor-Aris diffusion technique. The decrease of diffusion coefficients measured for iron II lactate when alone and forming the inclusion complexes was obtained for all hosts molecules used. Molecular Mechanics calculations were performed to elucidate the perfect arrange of iron II lactate inside CDs cavity. No great differences were obtained to the binding energy for the different hosts. Using the software HyperChem6.03v MM+, AMBER94 and OPLS Forced Fields for iron atom in two chemical environments (a) vacuum and (b) with addition of 250 water molecules (MM+). The solvent treatment was decisive to the order of stability. This order was β-CD>γ-CD>α-CD, the same order of solubility in water. The results contained in this work confirm the possibility to protect iron II lactate against oxidation.

  1. Coarse-grained DNA model capable of simulating ribose flexibility

    CERN Document Server

    Kovaleva, Natalya A; Mazo, Mikhail A; Zubova, Elena A

    2014-01-01

    We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA forms. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the sugar CG DNA model are: (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one non-harmonic potential and one three-particle potential, (2) explicit representation of sodium counterions and (3) implicit solvent approach. Effects of solvation and of partial charge screening at small distances are taken into account through the shape of potentials of interactions between charged particles. We obtain parameters of the sugar CG DNA model from the all-atom AMBER model. The suggested model allows adequate simulation of the transitions between A- and B-DNA forms, as well as of large deformations of long DNA molecules, for example, in binding with proteins. Small modifications of the model can provide th...

  2. Some illustrative examples from parametric studies for a reference HLW repository using ACGEO

    International Nuclear Information System (INIS)

    Spent fuels are to be directly disposed of and the only type of HLW in Korea. According to the basic repository design, which is similar to Swedish KBS-3 repository concept, spent fuel is encapsulated in corrosion resistant canisters, and then emplaced into the deposition holes surrounded by high density bentonite clay in tunnels at a depth of ∼500 m in a plutonic rock (Fig. 1). The objective of this paper is to show how we could show reliability of radiological safety assessment through probabilistic calculation with parameters having uncertainties associated with safety of HLW system. To demonstrate a typical way, possibly among many others, some probabilistic calculation results for nuclide release and transport in the near- and farfield of the repository when such selected key parameters as buffer thickness, nuclide travel length in the fractured rock medium, and initial number of defective canisters are varying are presented. ACGEO, a case file developed by utilizing AMBER, a compartment modeling software package was used for calculation

  3. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    Science.gov (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments. PMID:22247593

  4. The RAG Model: A New Paradigm for Genetic Risk Stratification in Multiple Myeloma

    Directory of Open Access Journals (Sweden)

    Steven M. Prideaux

    2014-01-01

    Full Text Available Molecular studies have shown that multiple myeloma is a highly genetically heterogonous disease which may manifest itself as any number of diverse subtypes each with variable clinicopathological features and outcomes. Given this genetic heterogeneity, a universal approach to treatment of myeloma is unlikely to be successful for all patients and instead we should strive for the goal of personalised therapy using rationally informed targeted strategies. Current DNA sequencing technologies allow for whole genome and exome analysis of patient myeloma samples that yield vast amounts of genetic data and provide a mutational overview of the disease. However, the clinical utility of this information currently lags far behind the sequencing technology which is increasingly being incorporated into clinical practice. This paper attempts to address this shortcoming by proposing a novel genetically based “traffic-light” risk stratification system for myeloma, termed the RAG (Red, Amber, Green model, which represents a simplified concept of how complex genetic data may be compressed into an aggregate risk score. The model aims to incorporate all known clinically important trisomies, translocations, and mutations in myeloma and utilise these to produce a score between 1.0 and 3.0 that can be incorporated into diagnostic, prognostic, and treatment algorithms for the patient.

  5. Investigating the origin and spectroscopic variability of the near-infrared HI lines in the Herbig star VV Ser

    CERN Document Server

    López, Rebeca García; Garatti, Alessio Caratti o; Kreplin, Alexander; Weigelt, Gerd; Tambovtseva, Larisa V; Grinin, Vladimir P; Ray, Thomas P

    2015-01-01

    The origin of the near-infrared (NIR) HI emission lines in young stellar objects are not yet understood. To probe it, we present multi-epoch LBT-LUCIFER spectroscopic observations of the Pa{\\delta}, Pa{\\beta}, and Br{\\gamma} lines observed in the Herbig star VVSer, along with VLTI-AMBER Br{\\gamma} spectro-interferometric observations at medium resolution. Our spectroscopic observations show line profile variability in all the HI lines. The strongest variability is observed in the redshifted part of the line profiles. The Br{\\gamma} spectro-interferometric observations indicate that the Br{\\gamma} line emitting region is smaller than the continuum emitting region. To interpret our results, we employed radiative transfer models with three different flow configurations: magnetospheric accretion, a magneto-centrifugally driven disc wind, and a schematic bipolar outflow. Our models suggest that the HI line emission in VVSer is dominated by the contribution of an extended wind, perhaps a bipolar outflow. Although t...

  6. RAD6 gene of Saccharomyces cerevisiae encodes a protein containing a tract of 13 consecutive aspartates

    International Nuclear Information System (INIS)

    The RAD6 gene of Saccharomyces cerevisiae is required for postreplication repair of UV-damaged DNA, for induced mutagenesis, and for sporulation. The authors have mapped the transcripts and determined the nucleotide sequence of the cloned RAD6 gene. The RAD6 gene encodes two transcripts of 0.98 and 0.86 kilobases which differ only in their 3' termini. The transcribed region contains an open reading frame of 516 nucleotides. The rad6-1 and rad6-3 mutant alleles, which the authors have cloned and sequenced, introduce amber and ochre nonsense mutations, respectively into the open reading frame, proving that it encodes the RAD6 protein. The RAD6 protein predicted by the nucleotide sequence is 172 amino acids long, has a molecular weight of 19,704, and contains 23.3% acidic and 11.6% basic residues. Its most striking feature is the highly acidic carboxyl terminus: 20 of the 23 terminal amino acids are acidic, including 13 consecutive aspartates. RAD6 protein thus resembles high mobility group proteins HMG-1 and HMG-2, which each contain a carboxyl-proximal tract of acidic amino acids. 48 references, 6 figures

  7. The LBV HR Car has a partner: Discovery of a companion with the VLTI

    CERN Document Server

    Boffin, Henri M J; Merand, Antoine; Mehner, Andrea; LeBouquin, Jean-Baptiste; Pourbaix, Dimitri; de Wit, Willem-Jan; Martayan, Christophe; Guieu, Sylvain

    2016-01-01

    Luminous Blue Variables (LBVs) are massive stars caught in a post-main sequence phase, during which they are losing a significant amount of mass. As, on one hand, it is thought that the majority of massive stars are close binaries that will interact during their lifetime, and on the other, the most dramatic example of an LBV, Eta Car, is a binary, it would be useful to find other binary LBVs. We present here interferometric observations of the LBV HR Car done with the AMBER and PIONIER instruments attached to ESO's Very Large Telescope Interferometer (VLTI). Our observations, spanning two years, clearly reveal that HR Car is a binary star. It is not yet possible to constrain fully the orbit, and the orbital period may lie between a few years and several hundred years. We derive a radius for the primary in the system and possibly resolve as well the companion. The luminosity ratio in the H-band between the two components is changing with time, going from about 6 to 9. We also tentatively detect the presence of...

  8. Gemstones and geosciences in space and time. Digital maps to the "Chessboard classification scheme of mineral deposits"

    Science.gov (United States)

    Dill, Harald G.; Weber, Berthold

    2013-12-01

    The gemstones, covering the spectrum from jeweler's to showcase quality, have been presented in a tripartite subdivision, by country, geology and geomorphology realized in 99 digital maps with more than 2600 mineralized sites. The various maps were designed based on the "Chessboard classification scheme of mineral deposits" proposed by Dill (2010a, 2010b) to reveal the interrelations between gemstone deposits and mineral deposits of other commodities and direct our thoughts to potential new target areas for exploration. A number of 33 categories were used for these digital maps: chromium, nickel, titanium, iron, manganese, copper, tin-tungsten, beryllium, lithium, zinc, calcium, boron, fluorine, strontium, phosphorus, zirconium, silica, feldspar, feldspathoids, zeolite, amphibole (tiger's eye), olivine, pyroxenoid, garnet, epidote, sillimanite-andalusite, corundum-spinel - diaspore, diamond, vermiculite-pagodite, prehnite, sepiolite, jet, and amber. Besides the political base map (gems by country) the mineral deposit is drawn on a geological map, illustrating the main lithologies, stratigraphic units and tectonic structure to unravel the evolution of primary gemstone deposits in time and space. The geomorphological map is to show the control of climate and subaerial and submarine hydrography on the deposition of secondary gemstone deposits. The digital maps are designed so as to be plotted as a paper version of different scale and to upgrade them for an interactive use and link them to gemological databases.

  9. Ilex paraguariensis Pellets from a Spray-Dried Extract: Development, Characterization, and Stability.

    Science.gov (United States)

    Yatsu, Francini K J; Borghetti, Greice S; Magalhães, Fagner; Ferraz, Humberto G; Schenkel, Eloir Paulo; Bassani, Valquiria L

    2016-04-01

    Several studies have shown the potential use of Ilex paraguariensis in developing products with the aim to protect biological systems against oxidative stress-mediated damages. In the same way, technological studies have demonstrated the feasibility of obtaining dry products, by spray-drying process, from aqueous extracts of I. paraguariensis in laboratory. The present work was designed to develop pellets by extrusion/spheronization process, from an I. paraguariensis spray-dried powder. The pellets were characterized with respect to their chemical, physical, and technological properties, and the thermal and the photostability of the main polyphenol constituents were investigated. The pellets exhibited adequate size, shape, and high process yield (78.7%), as well as a good recovery of the total polyphenols (>95%) and a good dissolution in water (89.44 to 100.05%). The polyphenols were stable against light when conditioned in amber glass bottles; unstable against heat when the samples were conditioned either in open glass bottles or in hermetically sealed glass bottles and demonstrated to be hygroscopic and sensible to the temperature, especially when stored in permeable flasks. These findings pointed to the relevance of reducing the residual moisture content of pellets as well as of conditioning them in opaque humidity tight packages under low temperatures. The feasibility of obtaining pellets from an I. paraguariensis spray-dried powder using extrusion/spheronization technique was, for the first time, demonstrated. This finding represents a novelty for the herbal products in both pharmaceutical and food fields. PMID:26162976

  10. Alcohol solutions of triphenyl-tetrazolium chloride as high-dose radiochromic dosimeters

    International Nuclear Information System (INIS)

    The radiolytic reduction of colorless tetrazolium salts in aqueous solution to the highly colored formazan dye is a well-known acid-forming radiation chemical reaction. Radiochromic thin films and three-dimensional hydrocolloid gels have been used for imaging and mapping absorbed dose distributions. The high solubility of 2,3,5-triphenyl-tetrazolium chloride (TTC) in alcohols provides a useful liquid dosimeter (45 nM TTC in aerated ethanol) and shows a linear response of absorbance increase (λmax = 480 nm) with dose over the range 1-16 kGy. The linear molar absorption coefficient (εm) for the formazan at the absorption peak is 1.5 x 103 m2 mol-1, and the radiation chemical yield for the above solution is G (formazan) = 0.014 μmol J-1. The irradiation temperature coefficient is about 0.8 percent per degree Celsius rise in temperature over the temperature range 0-30oC but is much larger between 30oC and 60oC. The unirradiated and irradiated solutions are stable over at least five days storage at normal laboratory temperature in the dark, but when stored in daylight at elevated temperature, the unirradiated solution in sealed amber glass ampoules undergoes slow photolytic dye formation, and the irradiated solution experiences initial fading and subsequent reversal (photochromism) when exposed to direct sunlight. (author)

  11. Parameterization of AZT-A widely used nucleoside inhibitor of HIV-1 reverse transcriptase

    Science.gov (United States)

    Carvalho, Alexandra T. P.; Fernandes, Pedro A.; Ramos, Maria J.

    Seven nucleoside reverse transcriptase (RT) inhibitors are currently used in the clinical treatment of acquired immunodeficiency syndrome (AIDS). These substrate analogues block DNA synthesis by the viral enzyme RT. However, the emergence of resistant variants of RT allied to their long-term toxicity requires the design of new and better RT inhibitors, with long-term in vivo efficacy. In this work we used density functional theory (DFT) calculations to develop a set of molecular mechanics (MM) parameters committed to the AMBER force field for one of the most used in the clinic nucleoside reverse transcriptase inhibitors (NRTIs): zidovudine (AZT). These parameters were tested by comparing the optimized geometries of AZT at both the DFT and MM levels of theory. The ability of the new parameters to reproduce the torsional energy of the azide group was also verified by scanning the surface in MM with the new parameters and comparing the results with the same potential energy surface (PES) at the DFT level. Finally, the parameters were validated through classical MD simulations of AZT in aqueous environment.

  12. Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.

    Science.gov (United States)

    Leherte, Laurence; Vercauteren, Daniel P

    2011-10-01

    To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge values to the so-obtained reduced representations. In continuation to a previous work, the Amber99 force field was selected. To easily generate reduced point charge models for protein structures, a library of amino acid templates was designed. Applications to four small peptides, a set of 53 protein structures, and four KcsA ion channel models, are presented. Electrostatic potential and solvation free energy values generated by the reduced models are compared with the corresponding values obtained using the original set of atomic charges. Results are in closer agreement with the original all-atom electrostatic properties than those obtained with a previous reduced model that was directly built from the smoothed MEP functions [Leherte and Vercauteren in J Chem Theory Comput 5:3279-3298, 2009]. PMID:21915750

  13. Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

    Science.gov (United States)

    Leherte, Laurence; Vercauteren, Daniel P

    2014-02-01

    Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation. PMID:24316938

  14. A resolved, au-scale gas disk around the B[e] star HD 50138

    CERN Document Server

    Ellerbroek, L E; Kraus, S; Perraut, K; Kluska, J; Bouquin, J B le; Fernandes, M Borges; de Souza, A Domiciano; Maaskant, K M; Kaper, L; Tramper, F; Mourard, D; Tallon-Bosc, I; Brummelaar, T ten; Sitko, M L; Lynch, D K; Russell, R W

    2014-01-01

    HD 50138 is a B[e] star surrounded by a large amount of circumstellar gas and dust. Its spectrum shows characteristics which may indicate either a pre- or a post-main-sequence system. Mapping the kinematics of the gas in the inner few au of the system contributes to a better understanding of its physical nature. We present the first high spatial and spectral resolution interferometric observations of the Br-gamma line of HD~50138, obtained with VLTI/AMBER. The line emission originates from a region more compact (up to 3 au) than the continuum-emitting region. Blue- and red-shifted emission originates from the two different hemispheres of an elongated structure perpendicular to the polarization angle. The velocity of the emitting medium decreases radially. An overall offset along the NW direction between the line- and continuum-emitting regions is observed. We compare the data with a geometric model of a thin Keplerian disk and a spherical halo on top of a Gaussian continuum. Most of the data are well reproduc...

  15. Structure of human insulin monomer in water/acetonitrile solution

    International Nuclear Information System (INIS)

    Here we present evidence that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. An NMR-derived human insulin monomer structure in H2O/CD3CN, 65/35 vol%, pH 3.6 is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Acta Crystallogr. 2003 Sec. D59, 474) and with NMR structures in water and organic cosolvent. Detailed analysis using PFGSE NMR, temperature-dependent NMR, dilution experiments and CSI proves that the structure is monomeric in the concentration and temperature ranges 0.1-3 mM and 10-30 deg. C, respectively. The presence of long-range interstrand NOEs, as found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Starting from structures calculated by the program CYANA, two different molecular dynamics simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBERVC), or including a generalized Born solvent model (AMBERGB)

  16. Synthesis and Characterization of Poly (Arylene Ether Benzimidazole) Oligomers

    Science.gov (United States)

    Leonard, Michael J.

    1995-01-01

    Several poly(arylene ether benzimidazole) oligomers were prepared by the nucleophilic aromatic substitution reaction of a bisphenol benzimidazole and various alkyl-substituted aromatic bisphenols with an activated aromatic dihalide in N, N-dimethylacetarnide. Moderate to high molecular weight terpolymers were obtained in all cases, as shown by their inherent viscosities, which ranged from 0.50 to 0.87 dL g(sup -1). Glass transition temperatures (T(sub g)s) of polymer powders ranged from 267-280 C. Air-dried unoriented thin film T(sub g)s were markedly lower than those of the powders, whereas T(sub g)s of films dried in a nitrogen atmosphere were identical to those of the corresponding powders. In addition, air-dried films were dark amber and brittle, whereas nitrogen-dried films were yellow and creasable. Nitrogen-dried films showed slightly higher thin-film tensile properties than the air-dried films, as well.

  17. Radio detection of cosmic ray induced air showers at the Pierre Auger Observatory

    International Nuclear Information System (INIS)

    AERA - the Auger Engineering Radio Array - is currently being set up at the southern site of the Pierre Auger Observatory. AERA will explore the potential of the radio-detection technique to cosmic ray induced air showers with respect to the next generation of large-scale surface detectors. As AERA is co-located with the low-energy enhancements of the Pierre Auger Observatory, the observation of air showers in coincidence with the Auger surface and fluorescence detector will allow to study the radio emission processes in detail and to calibrate the radio signal. Finally, the combined reconstruction of shower parameters with three independent techniques promises new insights into the nature of cosmic rays in the transition region from 1017 to 1019 eV. Besides the detection of coherent radiation in the MHz frequency range, the setups AMBER - Air-shower Microwave Bremsstrahlung Experimental Radiometer - and MIDAS - MIcrowave Detection of Air Showers - prepare to check the possibility to detect air showers due the emission of molecular bremsstrahlung in the GHz range at the Auger site. This article presents the status of the radio-detection setups and discusses their physics potential as well as experimental challenges. Special focus is laid on the first stage of AERA which is the startup to the construction of a 20 km2 radio array.

  18. Use of generic safety assessment in demonstration of safety

    International Nuclear Information System (INIS)

    Safety assessment is made for the proposed Afra project for borehole disposal facility for disused sealed sources. ISAM technology is used. Different types of biosphere and geosphere are considered and five variations of the normal scenario are assessed. Conceptual and mathematical models are established and 63 combinations using AMBER code are calculated. For the vast majority of disposal system combinations the peak dose for the design scenario is below 3E-4 Sv.y-1Near field provides an effective barrier to the release of radionuclides even for the poor quality control scenario. The use of lead and copper as a containment barrier does not reduces peak doses for the most restrictive case and they increase in an order of magnitude for the poor quality control scenario. Four of the six calculation cases for the alternative scenarios (other than the poor quality control scenario) result in the dose constraint being exceeded by up a factor of 30. They are for the seismic event, societal change (fish farmer) and human intrusion (site dweller) scenarios. However, these calculations have been undertaken for the most restrictive combination of disposal system characteristics. It can be expected that for many of the other combinations of disposal system characteristics, the dose constraint will not be exceeded

  19. Understanding the effect of side groups in ionic liquids on carbon-capture properties: a combined experimental and theoretical effort

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Fangyong [Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engingeering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Lartey, Michael [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); Damodaran, Krishnan [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); Univ. of Pittsburgh, PA (United States). Dept. of Chemistry; Albenze, Erik [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); URS Corporation, South Park, PA (United States); Thompson, Robert L. [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); URS Corporation, South Park, PA (United States); Kim, Jihan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Science Div.; Harancyzk, Maciel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Div.; Nulwala, Hunaid B. [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); Carnegie Mellon Univ., Pittsburgh, PA (United States); Luebke, David R. [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); Smit, Berend [Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engingeering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division

    2013-01-01

    Ionic liquids are an emerging class of materials with applications in a variety of fields. Steady progress has been made in the creation of ionic liquids tailored to specific applications. However, the understanding of the underlying structure–property relationships has been slower to develop. As a step in the effort to alleviate this deficiency, the influence of side groups on ionic liquid properties has been studied through an integrated approach utilizing synthesis, experimental determination of properties, and simulation techniques. To achieve this goal, a classical force field in the framework of OPLS/Amber force fields has been developed to predict ionic liquid properties accurately. Cu(I)-catalyzed click chemistry was employed to synthesize triazolium-based ionic liquids with diverse side groups. Values of densities were predicted within 3% of experimental values, whereas self-diffusion coefficients were underestimated by about an order of magnitude though the trends were in excellent agreement, the activation energy calculated in simulation correlates well with experimental values. The predicted Henry coefficient for CO{sub 2} solubility reproduced the experimentally observed trends. This study highlights the importance of integrating experimental and computational approaches in property prediction and materials development, which is not only useful in the development of ionic liquids for CO{sub 2} capture but has application in many technological fields.

  20. Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.

    Science.gov (United States)

    Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto

    2014-07-24

    We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions. PMID:25020237