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Sample records for amber

  1. Where Does Amber Come from?

    Science.gov (United States)

    Booth, Bibi

    2005-01-01

    Amber is the fossilized resin of now-extinct trees, primarily ancient conifers but also some flowering tropical trees. An aromatic, soft, sticky substance, resin in extinct trees probably served the same purposes as resin in modern trees: to protect the plant by sealing cuts and by excluding bacteria, fungi, and insects.

  2. Amber : Een revolutie in Radar

    NARCIS (Netherlands)

    Huizing, A.G.

    2011-01-01

    Eind dit jaar verwachtTNO versie 4.0 op te leveren van zijn betaalbare digitale multibeamradar Amber. Het systeem is oorcpronkelijk ontwikkeld voor kleine toestellen die vliegen zonder hulp van de verkeersleiding. lnmiddels kijken de TN0'ers naar veel meer toepassingen, van havenbewaking tot zorg op

  3. 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)

  4. The molecular composition of ambers

    Science.gov (United States)

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

    1988-01-01

    Bulk (elemental composition, IR, CP/MAS 13C NMR) and molecular (GC-MS) analyses have been performed on a series of ambers and resins derived from different locations (Dominican Republic, Philippines, Canada, Israel, New Zealand, Chile) having diverse botanical affinities (Araucariaceae, Hymenaea) and variable age (from Holocene to Early Cretaceous). No major differences have been observed from the elemental composition and the spectroscopic data; however, the molecular analyses of the solvent extractable fraction show that a specific mixture of components is present in each sample. These are mainly diterpenoid products that in general are also found abundantly in the higher plants from which the ambers and resins originate. Nevertheless, a direct relationship between major terpenoid constituents in fossil resins and precursor plant materials can only be established for the younger samples. Irrespective of the geographical or botanical origin of the ambers and resins, several common age-dependent molecular transformation trends can be recognized: (1) progressive loss of olefinic bonds (especially those located in exocyclic positions), (2) decrease of functionalized products, and (3) increasing proportion of aromatized components. However, even in the samples of older age (Cretaceous) the degree of aromatization is very low when compared with that of other higher-plant related materials such as fossilized woods or low rank coals. This indicates that maturation must involve essentially olefin polymerization processes instead of extensive aromatization. ?? 1988.

  5. The identity of Romanian amber (rumanite) with Baltic amber (succinite).

    Energy Technology Data Exchange (ETDEWEB)

    Stout, E. C.; Beck, C. W.; Anderson, K. B.; Chemistry; Vassar Coll.

    2000-11-01

    Romanian amber (rumanite) has been considered to be a separate species of fossil resin for more than a century. While earlier investigators held it to be very similar to succinite (Baltic amber), modern scholars have assigned it a distinctly different botanical origin. We have found that almost all of the constituents of the ether-soluble fractions of 13 specimens of authentic rumanite identified by gas chromatography-mass spectrometry have previously been reported in the soluble fraction of succinite, including succinic acid and its monoterpene esters. Additionally and significantly, the soluble fraction of rumanite contains a number defunctionalized compounds that do not preexist in succinite, but that are produced by pyrolysis of whole succinite or of its insoluble polymeric fraction. Simultaneous methylation pyrolysis-gas chromatography-mass spectrometry of the polymeric fraction of seven of the rumanite specimens yielded further copious amounts of dimethyl succinate, a number of diterpene resin acid methyl esters, and additional defunctionalized compounds known to be pyrolysis products of succinite. The evidence shows conclusively that the botanical origin of rumanite is not distinct from that of succinite. Rather, rumanite is a succinite that has suffered partial thermal degradation in the course of the folding of the Oligocene Kliwa sandstone formation in which it is most commonly found.

  6. Technology for melting amber chips to produce a solid block

    Science.gov (United States)

    Vikhareva, A. S.; Melnikov, A. G.; Utyev, O. M.

    2016-04-01

    This research is relevant, because the bulk of the mined amber comes in amber chips. Therefore, we have decided to review the current ways of melting amber chips to develop the most technologically efficient algorithm and to use it further for producing decorative items. The purpose of the work is to perfect the technology of obtaining whole-piece amber from amber chips and to explore the usability of the obtained material in decorative items and jewelry.

  7. NEW POSSIBILITY FOR THE USE OF PLASMA DISCHARGES TO IDENTIFY AMBER AND CHANGES IN AMBER STRUCTURE

    Directory of Open Access Journals (Sweden)

    Sebastian Gnapowski

    2012-12-01

    Full Text Available Pulsed power discharge applied in air to the amber surface was found to cause improvement in its appearance and color changes such as to red, a color not natural to amber but attractive for jewelry. Needle and plate electrodes were used during experiments. Pulsed power discharges in air particularly turned amber red at the edges and around the needle electrode. Discharges in water did not change amber structure because discharge occurring on the surface does not cross the amber structure. Discharges in silicone oil had a different effect, with most discharge passing through the amber structure, causing fine cracks. Unfortunately, the absence of a consistent amber structure causes difficulty in selecting the correct discharge (shock wave power. Using new technology, we have changed the appearance a very old material-amber (about 40 – 60 million years old – to make it more attractive for customers; this technology is also useful for detecting artificial amber (costume jewellery without causing damage to the product.

  8. 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.

  9. 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.

  10. Carnivorous leaves from Baltic amber.

    Science.gov (United States)

    Sadowski, Eva-Maria; Seyfullah, Leyla J; Sadowski, Friederike; Fleischmann, Andreas; Behling, Hermann; Schmidt, Alexander R

    2015-01-01

    The fossil record of carnivorous plants is very scarce and macrofossil evidence has been restricted to seeds of the extant aquatic genus Aldrovanda of the Droseraceae family. No case of carnivorous plant traps has so far been reported from the fossil record. Here, we present two angiosperm leaves enclosed in a piece of Eocene Baltic amber that share relevant morphological features with extant Roridulaceae, a carnivorous plant family that is today endemic to the Cape flora of South Africa. Modern Roridula species are unique among carnivorous plants as they digest prey in a complex mutualistic association in which the prey-derived nutrient uptake depends on heteropteran insects. As in extant Roridula, the fossil leaves possess two types of plant trichomes, including unicellular hairs and five size classes of multicellular stalked glands (or tentacles) with an apical pore. The apices of the narrow and perfectly tapered fossil leaves end in a single tentacle, as in both modern Roridula species. The glandular hairs of the fossils are restricted to the leaf margins and to the abaxial lamina, as in extant Roridula gorgonias. Our discovery supports current molecular age estimates for Roridulaceae and suggests a wide Eocene distribution of roridulid plants. PMID:25453067

  11. 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.

  12. New taxa of Tanyderidae (Diptera) from Eocene Baltic amber.

    Science.gov (United States)

    Krzeminski, Wiesław; Krzeminska, Ewa; Kania, Iwona; Ross, Andrew J

    2013-01-01

    Macrochile hornei sp. nov. from Baltic amber (Upper Eocene) is described and illustrated. Podemacrochile gen. nov. is described with Podemacrochile baltica (Podenas, 1997) as type species. A key to the genera and species of Tanyderidae known from Baltic amber is presented. PMID:24583815

  13. AMBER: Uma linguagem para o desenvolvimento de sistemas distribuidos

    NARCIS (Netherlands)

    Ferreira Pires, L.; Guareis de Farias, C.R.; Farines, J.M.; Westphall, C.

    2001-01-01

    This paper presents the architectural model AMBER for the design of distributed systems developed at the University of Twente. This model allows the specification of distributed systems in terms of structures of functional entities and their corresponding behaviour. AMBER was originally developed to

  14. 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.

  15. 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...

  16. 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.

  17. 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

  18. 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.

  19. An enigmatic spiny harvestman from Baltic amber

    Directory of Open Access Journals (Sweden)

    J. A. Dunlop

    2012-08-01

    Full Text Available A new harvestman (Arachnida: Opiliones from Baltic amber (Palaeogene: Eocene; ca. 44–49 Ma is described as Piankhi steineri n. gen., n. sp. This enigmatic fossil expresses long, slender pedipalps without a tarsal claw, which is characteristic for the suborder Dyspnoi. The chelicerae are notably enlarged and the dorsal body surface is formed from a carapace with a separate prosomatic tergite (metapeltidium, plus a large opisthosomal scute (or scutum parvum. However these characters, combined with the distinctly spiny limbs and further rows of spines across the fossil's opisthosoma, have no parallel among the modern dyspnoid harvestmen that we are aware of. The fossil resolves features reminiscent of modern members of the dyspnoid families Ceratolasmatidae, Nipponopsalididae, Ischyropsalididae and Sabaconidae, but does not show unequivocal apomorphies of any one particular family. We must entertain the possibility that this is an extinct body plan from the Eocene of north-central Europe, and we tentatively refer the fossil to a new genus in an unresolved position among the Ischyropsalidoidea (Dyspnoi. An amorphous triangular structure behind the anal region is assumed to be faecal matter, rather than part of the original anatomy. doi:10.1002/mmng.201200007

  20. Identification of rumanite (Romanian amber) as thermally altered succinite (Baltic amber)

    Science.gov (United States)

    Stout, E. C.; Beck, C. W.; Anderson, K. B.

    Romanian amber (rumanite) has been considered to be a separate species of fossil resin for more than a century. While earlier investigators held it to be very similar to succinite (Baltic amber), modern scholars have assigned it a distinctly different botanical origin. We have found that almost all of the constituents of the ether-soluble fractions of 13 specimens of authentic rumanite identified by gas chromatography-mass spectrometry have previously been reported in the soluble fraction of succinite, including succinic acid and its monoterpene esters. Additionally and significantly, the soluble fraction of rumanite contains a number defunctionalized compounds that do not preexist in succinite, but that are produced by pyrolysis of whole succinite or of its insoluble polymeric fraction. Simultaneous methylation pyrolysis-gas chromatography-mass spectrometry of the polymeric fraction of seven of the rumanite specimens yielded further copious amounts of dimethyl succinate, a number of diterpene resin acid methyl esters, and additional defunctionalized compounds known to be pyrolysis products of succinite. The evidence shows conclusively that the botanical origin of rumanite is not distinct from that of succinite. Rather, rumanite is a succinite that has suffered partial thermal degradation in the course of the folding of the Oligocene Kliwa sandstone formation in which it is most commonly found.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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)

  7. 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

  8. Bird's nest fungi (Nidulariales: Nidulariaceae) in Baltic and Dominican amber.

    Science.gov (United States)

    Poinar, George

    2014-03-01

    Nidula baltica sp. nov. and Cyathus dominicanus sp. nov. are described from Cenozoic Baltic and Dominican amber. These are the first fossil members of the Family Nidulariaceae and show that the basic characteristics of this group were already established some 40-50 million years ago. PMID:24607356

  9. 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...

  10. 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.

  11. Mummified precocial bird wings in mid-Cretaceous Burmese amber.

    Science.gov (United States)

    Xing, Lida; McKellar, Ryan C; Wang, Min; Bai, Ming; O'Connor, Jingmai K; Benton, Michael J; Zhang, Jianping; Wang, Yan; Tseng, Kuowei; Lockley, Martin G; Li, Gang; Zhang, Weiwei; Xu, Xing

    2016-01-01

    Our knowledge of Cretaceous plumage is limited by the fossil record itself: compression fossils surrounding skeletons lack the finest morphological details and seldom preserve visible traces of colour, while discoveries in amber have been disassociated from their source animals. Here we report the osteology, plumage and pterylosis of two exceptionally preserved theropod wings from Burmese amber, with vestiges of soft tissues. The extremely small size and osteological development of the wings, combined with their digit proportions, strongly suggests that the remains represent precocial hatchlings of enantiornithine birds. These specimens demonstrate that the plumage types associated with modern birds were present within single individuals of Enantiornithes by the Cenomanian (99 million years ago), providing insights into plumage arrangement and microstructure alongside immature skeletal remains. This finding brings new detail to our understanding of infrequently preserved juveniles, including the first concrete examples of follicles, feather tracts and apteria in Cretaceous avialans. PMID:27352215

  12. 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)

  13. 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

  14. 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...

  15. 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...

  16. 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.

  17. 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.

  18. A New Species Of Globicornis (Hadrotoma (Coleoptera, Dermestidae, Megatominae From Baltic Amber

    Directory of Open Access Journals (Sweden)

    Háva J.

    2015-08-01

    Full Text Available The species Globicornis (Hadrotoma ingelehmannae sp. n. from Baltic amber is described, illustrated and compared with all known amber species of Globicornis Latreille, 1829. New species differs by the shape of antennae and black setation on dorsal and ventral surfaces.

  19. 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

  20. 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...

  1. New Records Of The Dipteran Genera Triphleba (Phoridae And Prosphyracephala (Diopsidae In Rovno And Baltic Ambers

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2015-06-01

    Full Text Available Dipteran insects constitute 51 % among arthropods of the Rovno Amber. There are 99 species and 23 genera of the Diptera described from the Rovno Amber; however, to date only 32 species are shared with the Baltic Amber fauna, including two species that are treated in this paper. Triphleba schulmanae Brown, 2003 (Phoridae, originally described from the Baltic Amber, is recorded in the Rovno Amber for the first time and its amended description is supplied. Genus Prosphyracephala Hennig, 1965 (Diopsidae, earlier known from the Baltic and Saxonian ambers, the Upper Eocene of Ruby River (Montana, USA and the Lower Oligocene of Céreste (France, is recorded in the Rovno Amber for the first time. Prosphyracephala aff. succini (Loew, 1873 is the first diopsid record from Ukraine. A second specimen of Prosphyracephala kerneggeri Kotrba, 2009 is found in the Baltic amber; the complete wing venation is described for the first time for this species. Vast majority of the Old World Diopsidae are strictly thermophilous. In fact, all of them but the five species of brevicornis group of Sphyracephala Say (three Palearctic and two Nearctic ones frequent tropic and the warmest subtropic areas, however the thermophilous Diopsidae are known in the New World neither in past nor in contemporary fauna.

  2. 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.

  3. Entrapment bias of arthropods in Miocene amber revealed by trapping experiments in a tropical forest in Chiapas, Mexico.

    Directory of Open Access Journals (Sweden)

    Mónica M Solórzano Kraemer

    Full Text Available 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.

  4. Band structure and optical properties of amber studied by first principles

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Zhi-Fan, E-mail: raozhifan@163.com [Analysis and Testing Center of Yunnan, Kunming University of Science and Technology, Kunming 650093 (China); Zhou, Rong-Feng [Analysis and Testing Center of Yunnan, Kunming University of Science and Technology, Kunming 650093 (China)

    2013-03-01

    The band structure and density of states of amber is studied by the first principles calculation based on density of functional theory. The complex structure of amber has 214 atoms and the band gap is 5.0 eV. The covalent bond is combined C/O atoms with H atoms. The O 2p orbital is the biggest effect near the Fermi level. The optical properties' results show that the reflectivity is low, and the refractive index is 1.65 in visible light range. The highest absorption coefficient peak is at 172 nm and another higher peak is at 136 nm. These convince that the amber would have a pretty sheen and that amber is a good and suitable crystal for jewelry and ornaments.

  5. 13C Solid State Nuclear Magnetic Resonance and µ-Raman Spectroscopic Characterization of Sicilian Amber.

    Science.gov (United States)

    Barone, Germana; Capitani, Donatella; Mazzoleni, Paolo; Proietti, Noemi; Raneri, Simona; Longobardo, Ugo; Di Tullio, Valeria

    2016-08-01

    (13)C cross-polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) and µ-Raman spectroscopy were applied to characterize Sicilian amber samples. The main goal of this work was to supply a complete study of simetite, highlighting discriminating criteria useful to distinguish Sicilian amber from fossil resins from other regions and laying the foundations for building a spectroscopic database of Sicilian amber. With this aim, a private collection of unrefined simetite samples and fossil resins from the Baltic region and Dominican Republic was analyzed. Overall, the obtained spectra permitted simetite to be distinguished from the other resins. In addition, principal component analysis (PCA) was applied to the spectroscopic data, allowing the clustering of simetite samples with respect to the Baltic and Dominican samples and to group the simetite samples in two sets, depending on their maturity. Finally, the analysis of loadings allowed for a better understanding of the spectral features that mainly influenced the discriminating characteristics of the investigated ambers.

  6. 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

  7. Computer simulations of interferometric imaging with the VLT interferometer and its AMBER instrument

    OpenAIRE

    Przygodda, F.; Bloecker, T.; Hofmann, K.-H; Weigelt, G.

    2001-01-01

    We present computer simulations of interferometric imaging with the Very Large Telescope Interferometer (VLTI) of the European Southern Observatory (ESO) and the Astronomical MultiBEam Recombiner (AMBER) phase-closure instrument. These simulations include both the astrophysical modelling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon ...

  8. 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.

  9. 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.

  10. 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

  11. Deuterium isotopic exchangeability of resin and amber at low thermal stress under hydrous conditions

    Science.gov (United States)

    Gonzalez, G.; Tappert, R.; Wolfe, A. P.; Muehlenbachs, K.

    2012-04-01

    Hydrous deuterium-exchange experiments have shown that a significant fraction of the original D/H composition of bulk kerogens, bitumens and expelled oils may participate in isotopic exchange reactions during burial diagenesis. However, it is unknown to what extent plant-derived secondary metabolites, namely resins and their fossil counterpart amber, exchange hydrogen isotopes following their biosynthesis. This situation hinders the application of resin D/H measurements in paleoenvironmental reconstruction. Here, we assess explicitly hydrogen exchange in resins and ambers using a series of immersion experiments in deuterated (D-enriched) waters over a period of several months at several temperatures. We are especially interested in assessing whether significant H-isotopic exchange occurs between resins and meteoric waters during early thermal maturation and polymerization. At 90°C, equivalent to ~3km of burial in most diagenetic regimes, modern conifer and angiosperm resins have an average post-metabolic H exchange of 4.6%, compared to only 1.1% for mature, polymerized ambers. At 55°C the degree of exchange is considerably lower: 1.9% for resins and 0.6% for ambers. These results indicate that most D/H isotopic exchange occurs prior to polymerization reactions, thereby confirming that D/H measurements from amber constitute a potentially sensitive proxy for environmental change.

  12. Fossil mesostigmatid mites (Mesostigmata: Gamasina, Microgyniina, Uropodina), associated with longhorn beetles (Coleoptera: Cerambycidae) in Baltic amber

    Science.gov (United States)

    Dunlop, Jason A.; Kontschán, Jenő; Zwanzig, Michael

    2013-04-01

    Fossil mesostigmatid mites are extremely rare. Inclusions assignable to the tortoise mites (Mesostigmata, Uropodina) are described here for the first time from Eocene (ca. 44-49 Ma) Baltic amber. This is the oldest record of Uropodina and documents the first unequivocal amber examples potentially assignable to the extant genus Uroobovella Berlese, 1903 (Uropodoidea: Urodinychidae). Further mites in the same amber pieces are tentatively assigned to Microgynioidea (Microgyniina) and Ascidae (Gamasina), both potentially representing the oldest records of their respective superfamily and family groups. This new material also preserves behavioural ecology in the form of phoretic deutonymphs attached to their carriers via a characteristic anal pedicel. These deutonymphs in amber are intimately associated with longhorn beetles (Coleoptera: Cerambycidae), probably belonging to the extinct species Nothorhina granulicollis Zang, 1905. Modern uropodines have been recorded phoretic on species belonging to several beetle families, including records of living Uroobovella spp. occurring on longhorn beetles. Through these amber inclusions, a uropodine-cerambycid association can now be dated back to at least the Eocene.

  13. Coordinated AMBER and MIDI observations of the Mira variable RR Aql

    CERN Document Server

    Karovicova, Iva; Boboltz, David A; Scholz, Michael

    2008-01-01

    We have used near- and mid-infrared interferometry to investigate the pulsating atmosphere and the circumstellar environment of the Mira variable RR Aql. Observations were taken with the VLTI/AMBER (near infrared) and the VLTI/MIDI (mid infrared) instruments. We have obtained a total of 15 MIDI epochs between Apr 9, 2004 and Jul 28, 2007 covering 4 pulsation cycles and one AMBER epoch on Sep 9, 2006 at phase 2.82. This work is also part of an ongoing project of joint VLTI and VLBA observations to study the connection between stellar pulsation and the mass loss process. Here we present a comparison of the AMBER visibility data to a simple uniform disk model as well as to predictions by recent self-excited dynamic model atmospheres. The best fitting photospheric angular diameter of the model atmosphere at phase 2.82 is 9.9 +/- 2.4 mas.

  14. 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

  15. Ancient Ephemeroptera-Collembola symbiosis fossilized in amber predicts contemporary phoretic associations.

    Directory of Open Access Journals (Sweden)

    David Penney

    Full Text Available X-ray computed tomography is used to identify a unique example of fossilized phoresy in 16 million-year-old Miocene Dominican amber involving a springtail being transported by a mayfly. It represents the first evidence (fossil or extant of phoresy in adult Ephemeroptera and only the second record in Collembola (the first is also preserved in amber. This is the first record of Collembola using winged insects for dispersal. This fossil predicts the occurrence of similar behaviour in living springtails and helps explain the global distribution of Collembola today.

  16. Ancient Ephemeroptera-Collembola symbiosis fossilized in amber predicts contemporary phoretic associations.

    Science.gov (United States)

    Penney, David; McNeil, Andrew; Green, David I; Bradley, Robert S; Jepson, James E; Withers, Philip J; Preziosi, Richard F

    2012-01-01

    X-ray computed tomography is used to identify a unique example of fossilized phoresy in 16 million-year-old Miocene Dominican amber involving a springtail being transported by a mayfly. It represents the first evidence (fossil or extant) of phoresy in adult Ephemeroptera and only the second record in Collembola (the first is also preserved in amber). This is the first record of Collembola using winged insects for dispersal. This fossil predicts the occurrence of similar behaviour in living springtails and helps explain the global distribution of Collembola today. PMID:23082186

  17. 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...

  18. A New Species of Dactylolabis (Eobothrophorus) from Baltic Amber (Diptera:Limoniidae)

    Institute of Scientific and Technical Information of China (English)

    Wies(l)aw KRZEMINSKI; Iwona KANIA; Ewa KRZEMINSKA

    2010-01-01

    A new species,Dactylolabis (Eobothrophorus) hoffeinsorum sp.nov.from the Baltic amber is described,based on one male.The distinctive characters are the shape of the discal cell in the wing and the shape of the process on tergite Ⅸ.The description of Dactylolabis (Eobothrophorus) lauryni Podenas,2003 is amended,based on an additional specimen.With the new species added herein,the number of species of this subgenus totals four.The wing venation,antennae,and tergai processes of all four species of the subgenus described from the Baltic amber are compared.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Photoageing of Baltic amber-influence of daylight radiation behind window glass on surface colour and chemistry

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2011-01-01

    in colour and chemical properties. Prism-shaped samples, obtained from a large amber piece, were exposed to different microclimatic conditions, subjected to accelerated photoageing and analysed by spectrocolorimetry, infrared spectroscopy and Raman spectroscopy. The experiments provided results about...

  6. 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)

  7. Amino acid racemization in amber-entombed insects: implications for DNA preservation

    Science.gov (United States)

    Bada, J. L.; Wang, X. S.; Poinar, H. N.; Paabo, S.; Poinar, G. O.

    1994-01-01

    DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from 10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

  8. 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...

  9. 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.

  10. 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.

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

    Science.gov (United States)

    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 to Jurassic sediments and a set of 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. Aromatized derivatives were the major components, consisting of one or two aromatic ring species with the abietane and occasionally pimarane skeletons. The saturated structures were comprised primarily of the abietane and pimarane skeletons having from three to five carbon (C1, C2, etc.) substituents. Kaurane and phyllocladane isomers were present in only minor amounts. Bicyclic sesquiterpenoids as saturated and partial or fully aromatized forms were also common in these samples, but only traces of sesterterpenoids and triterpenoid derivatives were found. 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

  12. 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

  13. Amberes-Bogotá: interpretaciones de lo doméstico en Ernesto Volkening

    OpenAIRE

    Carlos-Roberto Peña-Barrera

    2010-01-01

    Ernesto Volkening (1908-1983) fue un inmigrante alemán recordado en Colombia desde el ámbito de la crítica y el ensayo. Aunque sus producciones hablan de diversos temas, uno en particular es especial: las impresiones que dejó de su ciudad natal Amberes y algunas añadiduras poéticas de su vivir en Bogotá. En ese sentido, esta investigación tuvo por objeto conocer si en su obra podían encontrarse ideas, pensamientos y fragmentos que pudieran analizarse e interpretarse desde el punto de vista de...

  14. Subfamily Limoniinae Speiser, 1909 (Diptera, Limoniidae from Baltic amber (Eocene: the genus Elephantomyia Osten Sacken, 1860.

    Directory of Open Access Journals (Sweden)

    Iwona Kania

    Full Text Available A revision of the genus Elephantomyia Osten Sacken (Diptera: Limoniidae from Baltic amber (Eocene is presented. Four species--E. baltica Alexander, E. brevipalpa Loew, E. longirostris Loew, and E. pulchella Loew--are redescribed and documented with photographs and drawings. In addition, two new species of the genus are described: Elephantomyia bozenae sp. nov., and Elephantomyia irinae sp. nov. All these fossil species are placed within the subgenus Elephantomyia. A key to the extinct species of Elephantomyia is provided, and the genus' ecological pattern and evolutionary aspects are discussed.

  15. 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...

  16. Sucinolivolia torpida--a new genus and species of flea-beetles (Coleoptera: Chrysomelidae: Galerucinae) from Baltic amber.

    Science.gov (United States)

    Bukejs, Andris; Biondi, Maurizio; Alekseev, Vitalii I

    2015-12-15

    Sucinolivolia torpida gen. nov. et sp. nov. (Coleoptera: Chrysomelidae: Galerucinae: Alticini) is described and illustrated from Eocene Baltic amber. The new monotypic genus is compared with fossil and extant flea-beetle genera. Sucinolivolia gen. nov. is similar to the extant Livolia Jacoby and Orthaltica Crotch, but difference include the absence of an antebasal pronotal sulcus, not crenulate lateral pronotal margins, possessing very short genae, more robust legs, and the shape of tibiae. Including this new record, six described species of Alticini are known from Baltic amber.

  17. 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...

  18. 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.

  19. Compression fossil Mymaridae (Hymenoptera from Kishenehn oil shales, with description of two new genera and review of Tertiary amber genera

    Directory of Open Access Journals (Sweden)

    John Huber

    2011-09-01

    Full Text Available Compression fossils of three genera and six species of Mymaridae (Hymenoptera: Chalcidoidea are described from 46 million year old Kishenehn oil shales in Montana, USA. Two new genera are described: Eoeustochus Huber, gen. n., with two included species, E. kishenehn Huber (type species and E. borchersi Huber, sp. n., and Eoanaphes., gen. n., with E. stethynioides Huber, sp. n. Three new species of Gonatocerus are also described, G. greenwalti Huber, sp. n. , G. kootenai Huber, sp. n., and G. rasnitsyni Huber, sp.n. Previously described amber fossil genera are discussed and five genera in Baltic amber are tentatively recorded as fossils: Anagroidea, Camptoptera, Dorya, Eustochus, and Mimalaptus.

  20. Near-infrared interferometric observation of the Herbig Ae star HD144432 with VLTI/AMBER

    CERN Document Server

    Chen, Lei; Wang, Yang; Weigelt, Gerd; Hofmann, Karl-Heinz; Kraus, Stefan; Schertl, Dieter; Lagarde, Stephane; Natta, Antonella; Petrov, Roman; Robbe-Dubois, Sylvie; Tatulli, Eric

    2012-01-01

    We study the sub-AU-scale circumstellar environment of the Herbig Ae star HD144432 with near-infrared (NIR) VLTI/AMBER observations to investigate the structure of its inner dust disk. The interferometric observations were carried out with the AMBER instrument in the H and K band. We interpret the measured H- and K-band visibilities, the near- and mid-infrared visibilities from the literature, and the SED of HD144432 by using geometric ring models and ring-shaped temperature-gradient disk models with power-law temperature distributions. We derived a K-band ring-fit radius of 0.17 \\pm 0.01 AU and an H-band radius of 0.18 \\pm 0.01 AU (for a distance of 145 pc). This measured K-band radius of \\sim0.17 AU lies in the range between the dust sublimation radius of \\sim0.13 AU (predicted for a dust sublimation temperature of 1500 K and gray dust) and the prediction of models including backwarming (\\sim0.27 AU). We found that an additional extended halo component is required in both the geometric and temperature-gradi...

  1. 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...

  2. 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.

  3. Bulk carbon, oxygen, and hydrogen stable isotope composition of recent resins from amber-producing Hymenaea.

    Science.gov (United States)

    Nissenbaum, Arie; Yakir, Dan; Langenheim, Jean H

    2005-01-01

    Resins of Hymenaea, an angiosperm tree genus known to be a copious resin producer and a major source of amber since the Oligo-Miocene, were collected from a wide range of tropical environments from Latin America and Africa, and analyzed for their carbon, hydrogen, and oxygen stable isotope composition. The average value for delta13C in the resins was found to be -27.0+/-1.3 per thousand, which is very similar to the values reported for resins in other studies. Delta18O values for the Hymenaea resins averaged +11.2+/-1.6 per thousand, or about 20 per thousand more depleted than normal plant cellulose. DeltaD values of the resins ranged from -196 to -319 per thousand, with an average of -243+/-30 per thousand. Rough estimates suggest a fractionation of -200 to -210 per thousand between the resins and the environmental water. This value is similar to the -200 per thousand value observed for the fractionation between other plant lipids and environmental water. The present study suggests that the stable isotope composition of fossil resins (amber) has the potential to provide information on ancient environmental waters.

  4. Computer simulations of interferometric imaging with the VLT interferometer and its AMBER instrument

    CERN Document Server

    Przygodda, F; Hofmann, Karl Heinrich; Weigelt, G

    2001-01-01

    We present computer simulations of interferometric imaging with the Very Large Telescope Interferometer (VLTI) of the European Southern Observatory (ESO) and the Astronomical MultiBEam Recombiner (AMBER) phase-closure instrument. These simulations include both the astrophysical modelling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector read-out noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r_0,object and r_0,ref ranging between 0.9m and 1.2m), different residual tip-tilt error (delta_tt,object and delta_tt,ref ranging between 0.1% and 20% of the Airy disk diameter), and object brightness (K_object=0.7mag to 10.2mag, K_ref=0.7mag). Exem...

  5. 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.

  6. 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...

  7. 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.

  8. 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

  9. 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...

  10. 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

  11. 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

  12. A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals

    Science.gov (United States)

    Bergh, Magnus; Caleman, Carl

    2016-01-01

    Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.

  13. 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 ...

  14. Amberes-Bogotá: interpretaciones de lo doméstico en Ernesto Volkening

    Directory of Open Access Journals (Sweden)

    Carlos-Roberto Peña-Barrera

    2010-12-01

    Full Text Available Ernesto Volkening (1908-1983 fue un inmigrante alemán recordado en Colombia desde el ámbito de la crítica y el ensayo. Aunque sus producciones hablan de diversos temas, uno en particular es especial: las impresiones que dejó de su ciudad natal Amberes y algunas añadiduras poéticas de su vivir en Bogotá. En ese sentido, esta investigación tuvo por objeto conocer si en su obra podían encontrarse ideas, pensamientos y fragmentos que pudieran analizarse e interpretarse desde el punto de vista de lo doméstico. Para ello se abordó su producción, se seleccionaron escritos pertinentes, se resaltaron frases exactas y se comparara todo ello, al final, con algunos argumentos de otros autores. En efecto, su dialéctica y poesía argumentan sobre ello: la ciudad puede ser aprehendida como perteneciente a lo doméstico, porque “desde muy niño había sido para él la cosa más natural del mundo asociar la imagen paterna a la de Amberes; tanto así que el viaje que pensaba emprender le pareció otra manera de encontrarse con su padre”. Tan relevantes son sus pensamientos que siguen siendo vigentes y merecedores de posteriores reflexiones sobre la ciudad, el territorio y lo doméstico de la actualidad.

  15. Effects of Clear and Amber Cullet on Physical and Mechanical Properties of Glass-Ceramics Containing Zinc Hydrometallurgy Waste

    Science.gov (United States)

    Hanpongpun, Wilasinee; Jiemsirilers, Sirithan; Thavorniti, Parjaree

    The effect of glass cullet on physical and mechanical properties of glass-ceramics developed from zinc hydrometallurgy waste and glass cullet was investigated. The glass-ceramics were prepared by mixing zinc hydrometallurgy waste with glass cullet through vitrification process. Two difference types of glass cullet (clear and amber cullet) were used. The parent glasses were ground and pressed into bars and sintered at low temperature (850°C) for 2 hours. The obtained glass-ceramics had low porosity. The glass-ceramics with clear cullet exhibited higher density and strength, comparing with the glass-ceramics with amber cullet. The type and the amount of the glass cullet present in the glass-ceramics have strong effect on their properties.

  16. 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...

  17. 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.

  18. 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 ...

  19. 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,...

  20. Bridging the gap between chewing and sucking in the hemipteroid insects: new insights from Cretaceous amber.

    Science.gov (United States)

    Yoshizawa, Kazunori; Lienhard, Charles

    2016-01-01

    The diversity of feeding apparatuses in insects far exceeds that observed in any other animal group. Consequently, tracking mouthpart innovation in insects is one of the keys toward understanding their diversification. In hemipteroid insects (clade Paraneoptera or Acercaria: lice, thrips, aphids, cicadas, bugs, etc.), the transition from chewing to piercing-and-sucking mouthparts is widely regarded as the turning point that enabled hyperdiversification of the Hemiptera, the fifth largest insect order. However, the transitional process from chewing to piercing-and-sucking in the Paraneoptera was hitherto completely unknown. In this paper, we report a well preserved mid Cretaceous amber fossil of the paraneopteran insect family Archipsyllidae and describe it as Mydiognathus eviohlhoffae gen. et sp. n. This species has elongate mandibles and styliform laciniae similar to Hemiptera but retains functional chewing mouthparts. A number of morphological characters place the Archipsyllidae as the sister group of the thrips plus hemipterans, which strongly suggests that the mouthparts of M. eviohlhoffae represent a transitional condition from primitive chewing to derived piercing-and-sucking mouthparts. The clade composed of Archipsyllidae, thrips, and hemipterans is here named Pancondylognatha, a new supra-ordinal taxon. Based on newly obtained information, we also assess the monophyly of the Paraneoptera, which was called into question by recent phylogenomic analyses. A phylogenetic analysis that includes Mydiognathus strongly supports the monophyly of the Paraneoptera. PMID:27396002

  1. 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.

  2. Angular diameter estimation of interferometric calibrators. Example of λ Gruis, calibrator for VLTI-AMBER

    Science.gov (United States)

    Cruzalèbes, P.; Jorissen, A.; Sacuto, S.; Bonneau, D.

    2010-06-01

    Context. Accurate long-baseline interferometric measurements require careful calibration with reference stars. Small calibrators with high angular diameter accuracy ensure the true visibility uncertainty to be dominated by the measurement errors. Aims: We review some indirect methods for estimating angular diameter, using various types of input data. Each diameter estimate, obtained for the test-case calibrator star λ Gru, is compared with the value 2.71 mas found in the Bordé calibrator catalogue published in 2002. Methods: Angular size estimations from spectral type, spectral index, in-band magnitude, broadband photometry, and spectrophotometry give close estimates of the angular diameter, with slightly variable uncertainties. Fits on photometry and spectrophotometry need physical atmosphere models with “plausible” stellar parameters. Angular diameter uncertainties were estimated by means of residual bootstrapping confidence intervals. All numerical results and graphical outputs presented in this paper were obtained using the routines developed under PV-WAVE®, which compose the modular software suite SPIDAST, created to calibrate and interprete spectroscopic and interferometric measurements, particularly those obtained with VLTI-AMBER. Results: The final angular diameter estimate 2.70 mas of λ Gru, with 68% confidence interval 2.65-2.81 mas, is obtained by fit of the MARCS model on the ISO-SWS 2.38-27.5 μm spectrum, with the stellar parameters Te = 4250 K, log g = 2.0, z = 0.0 dex, M = 1.0 M⊙, and ξ_t = 2.0 km s-1.

  3. 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 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.

  4. 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.

  5. Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber

    Directory of Open Access Journals (Sweden)

    Leyla J. Seyfullah

    2015-07-01

    Full Text Available Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers, to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.

  6. Yeast Ca(2+)-signal transduction inhibitors isolated from Dominican amber prevent the degranulation of RBL-2H3 cells through the inhibition of Ca(2+)-influx.

    Science.gov (United States)

    Abe, Tomomi; Kobayashi, Miki; Okawa, Yusuke; Inui, Tomoki; Yoshida, Jun; Higashio, Hironori; Shinden, Hisao; Uesugi, Shota; Koshino, Hiroyuki; Kimura, Ken-Ichi

    2016-09-01

    A new norlabdane compound, named kujigamberol has previously been isolated from Kuji amber (but not from Baltic amber) by activity guided fractionation. However, there has been no study of biological compounds in Dominican amber. Biological activities were examined using the hypersensitive mutant yeast (zds1Δ erg3Δ pdr1Δ pdr3Δ) with respect to Ca(2+)-signal transduction, enzymes and rat basophilic leukemia (RBL)-2H3 cells. The structures were elucidated on the basis of spectral analysis including high resolution (HR)-EI-MS, 1D NMR and 2D NMR. Three diterpenoid compounds, 5(10)-halimen-15-oic acid (1), 3-cleroden-15-oic acid (2) and 8-labden-15-oic acid (3), which are different from the bioactive compounds in Kuji and Baltic ambers, were isolated from Dominican amber. They inhibited both calcineurin (CN) (IC50=40.0, 21.2 and 34.2μM) and glycogen synthase kinase-3β (GSK-3β) (IC50=48.9, 43.8 and 41.1μM) which are involved in the growth restored activity against the mutant yeast. The most abundant compound 2 showed inhibitory activity against both degranulation and Ca(2+)-influx in RBL-2H3 cells. The compounds having the growth restoring activity against the mutant yeast have potential as anti-allergic compounds.

  7. Yeast Ca(2+)-signal transduction inhibitors isolated from Dominican amber prevent the degranulation of RBL-2H3 cells through the inhibition of Ca(2+)-influx.

    Science.gov (United States)

    Abe, Tomomi; Kobayashi, Miki; Okawa, Yusuke; Inui, Tomoki; Yoshida, Jun; Higashio, Hironori; Shinden, Hisao; Uesugi, Shota; Koshino, Hiroyuki; Kimura, Ken-Ichi

    2016-09-01

    A new norlabdane compound, named kujigamberol has previously been isolated from Kuji amber (but not from Baltic amber) by activity guided fractionation. However, there has been no study of biological compounds in Dominican amber. Biological activities were examined using the hypersensitive mutant yeast (zds1Δ erg3Δ pdr1Δ pdr3Δ) with respect to Ca(2+)-signal transduction, enzymes and rat basophilic leukemia (RBL)-2H3 cells. The structures were elucidated on the basis of spectral analysis including high resolution (HR)-EI-MS, 1D NMR and 2D NMR. Three diterpenoid compounds, 5(10)-halimen-15-oic acid (1), 3-cleroden-15-oic acid (2) and 8-labden-15-oic acid (3), which are different from the bioactive compounds in Kuji and Baltic ambers, were isolated from Dominican amber. They inhibited both calcineurin (CN) (IC50=40.0, 21.2 and 34.2μM) and glycogen synthase kinase-3β (GSK-3β) (IC50=48.9, 43.8 and 41.1μM) which are involved in the growth restored activity against the mutant yeast. The most abundant compound 2 showed inhibitory activity against both degranulation and Ca(2+)-influx in RBL-2H3 cells. The compounds having the growth restoring activity against the mutant yeast have potential as anti-allergic compounds. PMID:27491756

  8. 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

  9. Stability of dacarbazine in amber glass vials and polyvinyl chloride bags.

    Science.gov (United States)

    El Aatmani, Mohamed; Poujol, Sylvain; Astre, Cecile; Malosse, Françoise; Pinguet, Frederic

    2002-07-15

    The stability of dacarbazine in commercial glass vials and polyvinyl chloride (PVC) bags in various storage conditions and the emergence of 2-azahypoxanthine, a major degradation product possibly linked with some adverse effects, were studied. Triplicate samples of reconstituted (11 mg/mL) and diluted (1.40 mg/mL) dacarbazine admixtures were prepared and stored at 4 degrees C or at 25 degrees C in daylight, fluorescent light, or the dark. The effect of several light-protective measures (amber glass vials, aluminum foil wrapping, and opaque tubing) on dacarbazine stability in a simulated i.v. infusion system was also evaluated. Dacarbazine quantification and main degradation product determination were performed by high-performance liquid chromatography. Stability was defined as conservation of 90-105% of initial dacarbazine concentration without major variations in clarity, color, or pH and without precipitate formation. Reconstituted dacarbazine solutions were stable for 24 hours at room temperature and during light exposure and stable for at least 96 hours at 2-6 degrees C when stored in the dark. After dilution in PVC bags, stability time increased from 2 hours in daylight to 24 hours in fluorescent light and to 72 hours when covered with aluminum foil. After two hours of simulated infusion, dacarbazine remained stable. Diluted dacarbazine solutions stored at 2-6 degrees C were stable for at least 168 hours. The only degradation product found was 2-azahypoxanthine, which was detected in every sample. The storage and handling of dacarbazine should take into account both the loss of the drug and the production of its potentially toxic degradation product. Dacarbazine must be carefully protected from light, administered using opaque infusion tubing, and, if necessary, refrigerated before administration to reduce 2-azahypoxanthine formation. PMID:12132562

  10. Resolving the stellar components of the massive multiple system Herschel 36 with AMBER/VLTI

    Science.gov (United States)

    Sanchez-Bermudez, J.; Alberdi, A.; Schödel, R.; Hummel, C. A.; Arias, J. I.; Barbá, R. H.; Maíz Apellániz, J.; Pott, J.-U.

    2014-12-01

    Context. Massive stars are extremely important for the evolution of the galaxies; there are large gaps in our understanding of their properties and formation, however, mainly because they evolve rapidly, are rare, and distant. Recent findings suggest that most O-stars belong to multiple systems. It may well be that almost all massive stars are born as triples or higher multiples, but their large distances require very high angular resolution to directly detect the companions at milliarcsecond scales. Aims: Herschel 36 is a young massive system located at 1.3 kpc. It has a combined smallest predicted mass of 45 M⊙. Multi-epoch spectroscopic data suggest the existence of at least three gravitationally bound components. Two of them, system Ab, are tightly bound in a spectroscopic binary, and the third one, component Aa, orbits in a wider orbit. Our aim was to image and obtain astrometric and photometric measurements of components Aa and Ab using, for the first time, long-baseline optical interferometry to further constrain its nature. Methods: We observed Herschel 36 with the near-infrared instrument AMBER attached to the ESO VLT Interferometer, which provides an angular resolution of ~2 mas. We used the code BSMEM to perform the interferometric image reconstruction. We fitted the interferometric observables using proprietary IDL routines and the code LitPro. Results: We imaged the Aa + Ab components of Herschel 36 in H and K filters. Component Ab is located at a projected distance of 1.81 mas, at a position angle of ~222° east of north, the flux ratio between components Aa and Ab is close to one. These findings agree with previous predictions about the properties of Herschel 36. The small measured angular separation indicates that system Ab and Ab may be approaching the periastron of their orbits. These results, only achievable with long-baseline near-infrared interferometry, constitute the first step toward a thorough understanding of this massive triple system.

  11. 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。

  12. 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.

  13. 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...

  14. 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.

  15. 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

  16. 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.

  17. 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...

  18. 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...

  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. 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

  1. 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...

  2. 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...

  3. 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.

  4. 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.

  5. 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...

  6. 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

  7. Genetic variations in vitamin D-related pathways and breast cancer risk in African American women in the AMBER consortium.

    Science.gov (United States)

    Yao, Song; Haddad, Stephen A; Hu, Qiang; Liu, Song; Lunetta, Kathryn L; Ruiz-Narvaez, Edward A; Hong, Chi-Chen; Zhu, Qianqian; Sucheston-Campbell, Lara; Cheng, Ting-Yuan David; Bensen, Jeannette T; Johnson, Candace S; Trump, Donald L; Haiman, Christopher A; Olshan, Andrew F; Palmer, Julie R; Ambrosone, Christine B

    2016-05-01

    Studies of genetic variations in vitamin D-related pathways and breast cancer risk have been conducted mostly in populations of European ancestry, and only sparsely in African Americans (AA), who are known for a high prevalence of vitamin D deficiency. We analyzed 24,445 germline variants in 63 genes from vitamin D-related pathways in the African American Breast Cancer Epidemiology and Risk (AMBER) consortium, including 3,663 breast cancer cases and 4,687 controls. Odds ratios (OR) were derived from logistic regression models for overall breast cancer, by estrogen receptor (ER) status (1,983 ER positive and 1,098 ER negative), and for case-only analyses of ER status. None of the three vitamin D-related pathways were associated with breast cancer risk overall or by ER status. Gene-level analyses identified associations with risk for several genes at a nominal p ≤ 0.05, particularly for ER- breast cancer, including rs4647707 in DDB2. In case-only analyses, vitamin D metabolism and signaling pathways were associated with ER- cancer (pathway-level p = 0.02), driven by a single gene CASR (gene-level p = 0.001). The top SNP in CASR was rs112594756 (p = 7 × 10(-5), gene-wide corrected p = 0.01), followed by a second signal from a nearby SNP rs6799828 (p = 1 × 10(-4), corrected p = 0.03). In summary, several variants in vitamin D pathways were associated with breast cancer risk in AA women. In addition, CASR may be related to tumor ER status, supporting a role of vitamin D or calcium in modifying breast cancer phenotypes.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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...

  13. 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...

  14. 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...

  15. 琥珀散在妇科疾病中的治疗应用%Therapeutic applications of amber scattered in treating gynecological diseases

    Institute of Scientific and Technical Information of China (English)

    闫伟; 于燕; 张艳; 张明珠

    2012-01-01

      Amber scattered is TCM classic recipe, the whole side played to warm the blood stasis and relieve pain efficiency, as early as for the treatment of blood stasis dysmenorrhea and significant effect. Due to poor blood, air-block can lead to a variety of gynecological diseases: Such as dysmenorrhea, pelvic mass. In recent years, many physicians applications amber scattered for the treatment of a variety of blood stasis gynecological diseases, received a significant effect.%  琥珀散是中医经典方剂,全方共奏温经活血、祛瘀止痛之效,早用于治疗血瘀型痛经且疗效显著。因血行不畅,气机阻滞可导致多种妇科疾病:如痛经、癥瘕等。近年来众多医家应用琥珀散加减治疗多种血瘀型妇科疾病,疗效显著。

  16. 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

  17. 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。

  18. 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

  19. X-shooter, NACO, and AMBER observations of the LBV Pistol Star \\footnote{Based on ESO runs 85.D-0182A, 085.D-0625AC}

    CERN Document Server

    Martayan, Christophe; Bouquin, Jean-Baptiste Le; Merand, Antoine; Montagnier, Guillaume; Selman, Fernando; Girard, Julien; Fox, Andrew; Baade, Dietrich; Fremat, Yves; Lobel, Alex; Martins, Fabrice; Patru, Fabien; Rivinius, Thomas; Sana, Hugues; Stefl, Stan; Zorec, Jean; Semaan, Thierry

    2010-01-01

    We present multi-instruments and multi-wavelengths observations of the famous LBV star Pistol Star. These observations are part of a larger program about early O stars at different metallicities. The Pistol star has been claimed as the most massive star known, with 250 solar masses. We present the preliminary results based on X-Shooter spectra, as well as the observations performed with the VLTI-AMBER and the VLT-NACO adaptive optics. The X-shooter spectrograph allows to obtain simultaneously a spectrum from the UV to the K-band with a resolving power of $\\sim$15000. The preliminary results obtained indicate that Pistol Star has similar properties of Eta Car, including shells of matter, but also the binarity. Other objects of the program, here briefly presented, were selected for their particular nature: early O stars with mass discrepancies between stellar evolution models and observations, discrepancies with the wind momentum luminosity relation.

  20. 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.

  1. 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

  2. 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.

  3. (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

  4. 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

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

    Science.gov (United States)

    Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jurečka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

  6. (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.

  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. 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)

  9. 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.

  10. 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

  11. Non-invasive determination of ethanol, propylene glycol and water in a multi-component pharmaceutical oral liquid by direct measurement through amber plastic bottles using Fourier transform near-infrared spectroscopy.

    Science.gov (United States)

    Broad, N W; Jee, R D; Moffat, A C; Eaves, M J; Mann, W C; Dziki, W

    2000-11-01

    Fourier transform near-infrared (FT-NIR) spectroscopy was used to quantify rapidly the ethanol (34-49% v/v), propylene glycol (20-35% v/v) and water (11-20% m/m) contents within a multi-component pharmaceutical oral liquid by measurement directly through the amber plastic bottle packaging. Spectra were collected in the range 7302-12,000 cm-1 and calibration models set-up using partial least-squares regression (PLSR) and multiple linear regression. Reference values for the three components were measured using capillary gas chromatography (ethanol and propylene glycol) and Karl Fischer (water) assay procedures. The calibration and test sets consisted of production as well as laboratory batches that were made to extend the concentration ranges beyond the natural production variation. The PLSR models developed gave standard errors of prediction (SEP) of 1.1% v/v for ethanol, 0.9% v/v for propylene glycol and 0.3% m/m for water. For each component the calibration model was validated in terms of: linearity, repeatability, intermediate precision and robustness. All the methods produced statistically favourable outcomes. Ten production batches independent of the calibration and test sets were also challenged against the PLSR models, giving SEP values of 1.3% v/v (ethanol), 1.0% v/v (propylene glycol) and 0.2% m/m (water). NIR transmission spectroscopy allowed all three liquid constituents to be non-invasively measured in under 1 min.

  12. VLTI-AMBER velocity-resolved aperture-synthesis imaging of Eta Carinae with a spectral resolution of 12000. Studies of the primary star wind and innermost wind-wind collision

    CERN Document Server

    Weigelt, G; Schertl, D; Clementel, N; Corcoran, M F; Damineli, A; de Wit, W -J; Grellmann, R; Groh, J; Guieu, S; Gull, T; Heininger, M; Hillier, D J; Hummel, C A; Kraus, S; Madura, T; Mehner, A; Mérand, A; Millour, F; Moffat, A F J; Ohnaka, K; Patru, F; Petrov, R G; Rengaswamy, S; Richardson, N D; Rivinius, T; Schöller, M; Teodoro, M; Wittkowski, M

    2016-01-01

    Context. The mass loss from massive stars is not understood well. Eta Car is a unique object for studying the massive stellar wind during the LBV phase. It is also an eccentric binary with a period of 5.54 yr. The nature of both stars is uncertain, although we know from X-ray studies that there is a wind-wind collision whose properties change with orbital phase. Methods. Observations of Eta Car were carried out with the ESO VLTI and the AMBER instrument between approximately five and seven months before the August 2014 periastron passage. Velocity-resolved aperture-synthesis images were reconstructed from the spectrally dispersed interferograms. Interferometric studies can provide information on the binary orbit, the primary wind, and the wind collision. Results. We present velocity-resolved aperture-synthesis images reconstructed in more than 100 different spectral channels distributed across the Br Gamma 2.166 micrometer emission line. The intensity distribution of the images strongly depends on wavelength....

  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. VLTI-AMBER velocity-resolved aperture-synthesis imaging of η Carinae with a spectral resolution of 12 000. Studies of the primary star wind and innermost wind-wind collision zone

    Science.gov (United States)

    Weigelt, G.; Hofmann, K.-H.; Schertl, D.; Clementel, N.; Corcoran, M. F.; Damineli, A.; de Wit, W.-J.; Grellmann, R.; Groh, J.; Guieu, S.; Gull, T.; Heininger, M.; Hillier, D. J.; Hummel, C. A.; Kraus, S.; Madura, T.; Mehner, A.; Mérand, A.; Millour, F.; Moffat, A. F. J.; Ohnaka, K.; Patru, F.; Petrov, R. G.; Rengaswamy, S.; Richardson, N. D.; Rivinius, T.; Schöller, M.; Teodoro, M.; Wittkowski, M.

    2016-10-01

    Context. The mass loss from massive stars is not understood well. η Carinae is a unique object for studying the massive stellar wind during the luminous blue variable phase. It is also an eccentric binary with a period of 5.54 yr. The nature of both stars is uncertain, although we know from X-ray studies that there is a wind-wind collision whose properties change with orbital phase. Aims: We want to investigate the structure and kinematics of η Car's primary star wind and wind-wind collision zone with a high spatial resolution of ~6 mas (~14 au) and high spectral resolution of R = 12 000. Methods: Observations of η Car were carried out with the ESO Very Large Telescope Interferometer (VLTI) and the AMBER instrument between approximately five and seven months before the August 2014 periastron passage. Velocity-resolved aperture-synthesis images were reconstructed from the spectrally dispersed interferograms. Interferometric studies can provide information on the binary orbit, the primary wind, and the wind collision. Results: We present velocity-resolved aperture-synthesis images reconstructed in more than 100 different spectral channels distributed across the Brγ 2.166 μm emission line. The intensity distribution of the images strongly depends on wavelength. At wavelengths corresponding to radial velocities of approximately -140 to - 376 km s-1 measured relative to line center, the intensity distribution has a fan-shaped structure. At the velocity of - 277 km s-1, the position angle of the symmetry axis of the fan is ~126°. The fan-shaped structure extends approximately 8.0 mas (~18.8 au) to the southeast and 5.8 mas (~13.6 au) to the northwest, measured along the symmetry axis at the 16% intensity contour. The shape of the intensity distributions suggests that the obtained images are the first direct images of the innermost wind-wind collision zone. Therefore, the observations provide velocity-dependent image structures that can be used to test three

  15. 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

  16. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.

    Science.gov (United States)

    Yildirim, Ilyas; Kierzek, Elzbieta; Kierzek, Ryszard; Schatz, George C

    2014-12-11

    When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both

  17. Fútbol e identidades: la actuación de la selección española de fútbol en los Juegos Olímpicos de Amberes y París a través de su impacto en la prensa

    Directory of Open Access Journals (Sweden)

    Juan Antonio Simón Sanjurjo

    2014-03-01

    Full Text Available El presente artículo aborda el análisis histórico de las importantes transformaciones que vivirá el fútbol español en la primera mitad de los años veinte, a partir del estudio de la actuación de la selección española en los Juegos Olímpicos de Amberes (1920 y París (1924. Este estudio también pretende analizar el rol que la prensa y el fútbol tendrá en la construcción de la identidad nacional, así como en la creación de los nuevos ídolos deportivos, en un periodo de progresiva implantación del profesionalismo y en pleno proceso de desarrollo de la sociedad de masas.

  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. 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...

  20. First fossil record of Ischaliidae Blair, 1920 (Coleoptera) from Eocene Baltic amber.

    Science.gov (United States)

    Alekseev, Vitalii I; Telnov, Dmitry

    2016-01-01

    Ischalia Pascoe, 1860, the monotypic genus of Ischaliidae, was placed as a subfamily among Pyrochroidae or Anthicidae by earlier authors. Nikitsky (1992) raised the status of Ischaliidae to the family rank. This position has been largely accepted and consequently followed by recent authors dealing with Ischalia, as well as in our paper. Ischaliidae is known from the Palaearctic (the Himalayas, East Asia: easternmost Russia, Japan, E China), South East Asia (southwards to Java, Borneo and the Philippines), and the Nearctic region (southern Canada, U.S.A.). No recent European representatives of Ischalia are known. At present, this genus is composed of 43 species worldwide (Gusakov & Telnov 2007; Saitô 2011; Young 2011; Young 2014; Saitô & Young 2015) placed in three subgenera (Young 2011): Ischalia s. str.-37 species, Eupleurida LeConte, 1862-5 species, Nitidischalia Young, 2011-1 species. Ischaliidae is most diverse in tropical rainforests, but many species are also known from subtropical to temperate zones. Adults and larvae of two Nearctic Ischalia feed on fungal mycelium growing on decaying wood of coniferous and broad-leaved trees (e.g. Pinus ponderosa, Lithocarpus densiflora) (Young 1985). Mimicry has been described among Bornean Ischaliidae, Tenebrionidae and Chrysomelidae (Telnov 2005) and also among Ischaliidae, Omalisidae, Lycidae and Endomychidae (Kazantsev & Young 2010). PMID:27394890

  1. Angular diameter estimation of interferometric calibrators - Example of lambda Gruis, calibrator for VLTI-AMBER

    CERN Document Server

    Cruzalebes, P; Sacuto, S; Bonneau, D; 10.1051/0004-6361/200913686

    2010-01-01

    Context. Accurate long-baseline interferometric measurements require careful calibration with reference stars. Small calibrators with high angular diameter accuracy ensure the true visibility uncertainty to be dominated by the measurement errors. Aims. We review some indirect methods for estimating angular diameter, using various types of input data. Each diameter estimate, obtained for the test-case calibrator star lambda Gru, is compared with the value 2.71 mas found in the Bord\\'e calibrator catalogue published in 2002. Methods. Angular size estimations from spectral type, spectral index, in-band magnitude, broadband photometry, and spectrophotometry give close estimates of the angular diameter, with slightly variable uncertainties. Fits on photometry and spectrophotometry need physical atmosphere models with "plausible" stellar parameters. Angular diameter uncertainties were estimated by means of residual bootstrapping confidence intervals. All numerical results and graphical outputs presented in this pap...

  2. 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.

  3. Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium.

    Science.gov (United States)

    Zhang, Jianmin; Yao, Song; Hu, Qiang; Zhu, Qianqian; Liu, Song; Lunetta, Kathryn L; Haddad, Stephen A; Yang, Nuo; Shen, He; Hong, Chi-Chen; Sucheston-Campbell, Lara; Ruiz-Narvaez, Edward A; Bensen, Jeannette T; Troester, Melissa A; Bandera, Elisa V; Rosenberg, Lynn; Haiman, Christopher A; Olshan, Andrew F; Palmer, Julie R; Ambrosone, Christine B

    2016-10-01

    The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. Dysfunction of the Hippo pathway components has been linked with breast cancer stem cell regulation, as well as breast tumor progression and metastasis. TAZ, a key component of the Hippo pathway, is highly expressed in triple negative breast cancer; however, the associations of genetic variations in this important pathway with breast cancer risk remain largely unexplored. Here, we analyzed 8309 germline variants in 15 genes from the Hippo pathway with a total of 3663 cases and 4687 controls from the African American Breast Cancer Epidemiology and Risk Consortium. Odds ratios (ORs) were estimated using logistic regression for overall breast cancer, by estrogen receptor (ER) status (1983 ER positive and 1098 ER negative), and for case-only analyses by ER status. The Hippo signaling pathway was significantly associated with ER-negative breast cancer (pathway level P = 0.02). Gene-based analyses revealed that CDH1 was responsible for the pathway association (P CDH1 statistically significant after gene-level adjustment for multiple comparisons (P = 9.2×10(-5), corrected P = 0.02). rs142697907 in PTPN14 was associated with ER-positive breast cancer and rs2456773 in CDK1 with ER-negativity in case-only analysis after gene-level correction for multiple comparisons (corrected P < 0.05). In conclusion, common genetic variations in the Hippo signaling pathway may contribute to both ER-negative and ER+ breast cancer risk in AA women.

  4. 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

  5. Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair.

    Science.gov (United States)

    Ko, Jae-hyeong; Llopis, Paula Montero; Heinritz, Jennifer; Jacobs-Wagner, Christine; Söll, Dieter

    2013-01-01

    While translational read-through of stop codons by suppressor tRNAs is common in many bacteria, archaea and eukaryotes, this phenomenon has not yet been observed in the α-proteobacterium Caulobacter crescentus. Based on a previous report that C. crescentus and Escherichia coli tRNA(His) have distinctive identity elements, we constructed E. coli tRNA(His) CUA, a UAG suppressor tRNA for C. crescentus. By examining the expression of three UAG codon- containing reporter genes (encoding a β-lactamase, the fluorescent mCherry protein, or the C. crescentus xylonate dehydratase), we demonstrated that the E. coli histidyl-tRNA synthetase/tRNA(His) CUA pair enables in vivo UAG suppression in C. crescentus. E. coli histidyl-tRNA synthetase (HisRS) or tRNA(His) CUA alone did not achieve suppression; this indicates that the E. coli HisRS/tRNA(His) CUA pair is orthogonal in C. crescentus. These results illustrate that UAG suppression can be achieved in C. crescentus with an orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pair.

  6. Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair.

    Directory of Open Access Journals (Sweden)

    Jae-hyeong Ko

    Full Text Available While translational read-through of stop codons by suppressor tRNAs is common in many bacteria, archaea and eukaryotes, this phenomenon has not yet been observed in the α-proteobacterium Caulobacter crescentus. Based on a previous report that C. crescentus and Escherichia coli tRNA(His have distinctive identity elements, we constructed E. coli tRNA(His CUA, a UAG suppressor tRNA for C. crescentus. By examining the expression of three UAG codon- containing reporter genes (encoding a β-lactamase, the fluorescent mCherry protein, or the C. crescentus xylonate dehydratase, we demonstrated that the E. coli histidyl-tRNA synthetase/tRNA(His CUA pair enables in vivo UAG suppression in C. crescentus. E. coli histidyl-tRNA synthetase (HisRS or tRNA(His CUA alone did not achieve suppression; this indicates that the E. coli HisRS/tRNA(His CUA pair is orthogonal in C. crescentus. These results illustrate that UAG suppression can be achieved in C. crescentus with an orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pair.

  7. VLTI/AMBER spectro-interferometry of the late-type supergiants V766 Cen (=HR 5171 A), sigma Oph, BM Sco, and HD 206859

    CERN Document Server

    Wittkowski, M; Marcaide, J M; Abellan, F J; Chiavassa, A; Guirado, J C

    2016-01-01

    We add four warmer late-type supergiants to our previous spectro-interferometric studies of red giants and supergiants. V766 Cen (=HR 5171 A) is found to be a high-luminosity log(L/L_sun)=5.8+-0.4 source of Teff 4290+-760 K and radius 1490+-540 Rsun located close to both the Hayashi and Eddington limits; this source is consistent with a 40 Msun evolutionary track without rotation and current mass 27-36 Msun. It exhibits NaI in emission arising from a shell of radius 1.5 Rphot and a photocenter displacement of about 0.1 Rphot. V766 Cen shows strong extended molecular (CO) layers and a dusty circumstellar background component. This suggest an optically thick pseudo-photosphere at about 1.5 Rphot at the onset of the wind. V766 Cen is a red supergiant located close to the Hayashi limit instead of a yellow hypergiant already evolving back toward warmer Teff as previously discussed. The stars sigma Oph, BM Sco, and HD 206859 are found to have lower luminosities of about log(L/Lsun)=3.4-3.5 and Teff of 3900-5300 K, ...

  8. 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.

  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. 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.

  11. 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.

  12. Application of Argonne's Glass Furnace Model to longhorn glass corporation oxy-fuel furnace for the production of amber glass.

    Energy Technology Data Exchange (ETDEWEB)

    Golchert, B.; Shell, J.; Jones, S.; Energy Systems; Shell Glass Consulting; Anheuser-Busch Packaging Group

    2006-09-06

    The objective of this project is to apply the Argonne National Laboratory's Glass Furnace Model (GFM) to the Longhorn oxy-fuel furnace to improve energy efficiency and to investigate the transport of gases released from the batch/melt into the exhaust. The model will make preliminary estimates of the local concentrations of water, carbon dioxide, elemental oxygen, and other subspecies in the entire combustion space as well as the concentration of these species in the furnace exhaust gas. This information, along with the computed temperature distribution in the combustion space may give indications on possible locations of crown corrosion. An investigation into the optimization of the furnace will be performed by varying several key parameters such as the burner firing pattern, exhaust number/size, and the boost usage (amount and distribution). Results from these parametric studies will be analyzed to determine more efficient methods of operating the furnace that reduce crown corrosion. Finally, computed results from the GFM will be qualitatively correlated to measured values, thus augmenting the validation of the GFM.

  13. 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

  14. 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

  15. Revision of fossil Metretopodidae (Insecta: Ephemeroptera) in Baltic amber-Part 3: Description of two new species of Siphloplecton Clemens, 1915, with notes on the re-discovered lectotype of Siphloplecton macrops (Pictet-Baraban & Hagen, 1856).

    Science.gov (United States)

    Staniczek, Arnold H; Godunko, Roman J

    2016-01-01

    In this contribution, we provide a complementary description of the re-discovered lectotype of Siphloplecton macrops (Pictet-Baraban & Hagen, 1856). Additionally, complementary descriptions of S. barabani Staniczek & Godunko, 2012 and S. picteti Staniczek & Godunko, 2012 based on new material are given. Two new species, S. sartorii sp. nov. and S. gattolliati sp. nov., are described from male imagines and attributed to two newly defined species groups within Siphloplecton. PMID:27394609

  16. 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…

  17. 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

  18. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Science.gov (United States)

    2010-10-01

    ... REGULATIONS PARTS AND ACCESSORIES NECESSARY FOR SAFE OPERATION Lamps, Reflective Devices, and Electrical... lamps; school bus warning lamps; amber warning lamps or flashing warning lamps on tow trucks...

  19. 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

  20. 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....

  1. 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...

  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. 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

  4. 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

  5. Huntington's Disease Society of America

    Science.gov (United States)

    ... Andrews HDSA Researcher Spotlight- Dr. Amber Southwell Advocacy Huntington’s Disease Parity Act Affordable Care Act Social Security ... 08.30.16 HD Support & Care Network and Huntington’s Disease Society of America Partner for Stronger HD ...

  6. Balti riikide firmadesse voolab veel 2 miljardit krooni / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2004-01-01

    Ilmunud ka: Delovõje Vedomosti 15. dets. lk. 33. Fondist Amber Trust II S.C.A., mis hakkab investeerima Balti riikidesse. Lisa: Firebirdi fondid ja Danske Capital praegu Tallinna börsil ligi 400 mln krooniga. Diagrammid

  7. Uudised : Ain Anger tuli ooperilauljate konkursil esikohale. Elton Johni fotokogu näitus

    Index Scriptorium Estoniae

    2000-01-01

    A. Anger võitis 11.-14. juuliniu Lätis Jurmalas toimunud rahvusvahelise noorte ooperilauljate konkursi "Amber Sea Voices". E. John korraldab novembris Ameerikas Atlantas oma fotokogu avaliku näituse "Chorus of Light"

  8. Kuni 30. IV on rahvusraamatukogu haruldaste raamatute saalis...

    Index Scriptorium Estoniae

    2005-01-01

    Näitus "Balti merevaik Palanga merevaigumuuseumist". 21.-24. III oli merevaigufirma Amber näitusmüük raamatukogu fuajees, firma skulptuurikollektsiooni põhjal avati 1996. a. Vilniuses merevaiguskulptuuride muuseum

  9. 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 ...

  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. Could submarine groundwater discharge be a significant carbon source to the southern Baltic Sea?** The study reports the results obtained within the framework of the following projects: the statutory activities of the Institute of Oceanology Polish Academy of Sciences theme 2.2, research project No. 2012/05/N/ST10/02761 sponsored by the National Science Centre, and AMBER, the BONUS+EU FP6 Project.

    Directory of Open Access Journals (Sweden)

    Beata Szymczycha

    2014-01-01

    Full Text Available Submarine Groundwater Discharge (SGD is an important yet poorly recognised pathway of material transport to the marine environment. This work reports on the results of dissolved inorganic carbon (DIC and dissolved organic carbon (DOC concentrations and loads in the groundwater seeping into the southern Baltic Sea. Most of the research was carried out in the Bay of Puck (2009–2010, while in 2013 the study was extended to include several other groundwater seepage impacted areas situated along the Polish coastline. The annual average concentrations of DIC and DOC in the groundwater were equal to 64.5±10.0 mg C L−1 and 5.8±0.9 mg C L−1 respectively. The carbon specific flux into the Bay of Puck was estimated at 850 mg m−2 yr−1. The loads of carbon via SGD were scaled up for the Baltic Sea sub-basins and the entire Baltic Sea. The DIC and DOC fluxes via SGD to the Baltic Sea were estimated at 283.6±66.7 kt yr−1 and 25.5±4.2 kt yr−1. The SGD derived carbon load to the Baltic Sea is an important component of the carbon budget, which gives the sea a firmly heterotrophic status.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Understanding the Longitudinal Variability of Equatorial Electrodynamics using integrated Ground- and Space-based Observations

    Science.gov (United States)

    Yizengaw, E.; Moldwin, M.; Zesta, E.

    2015-12-01

    The currently funded African Meridian B-Field Education and Research (AMBER) magnetometer array comprises more than thirteen magnetometers stationed globally in the vicinity of geomagnetic equator. One of the main objectives of AMBER network is to understand the longitudinal variability of equatorial electrodynamics as function of local time, magnetic activity, and season. While providing complete meridian observation in the region and filling the largest land-based gap in global magnetometer coverage, the AMBER array addresses two fundamental areas of space physics: first, the processes governing electrodynamics of the equatorial ionosphere as a function of latitude (or L-shell), local time, longitude, magnetic activity, and season, and second, ULF pulsation strength at low/mid-latitude regions and its connection with equatorial electrojet and density fluctuation. The global AMBER network can also be used to augment observations from space-based instruments, such us the triplet SWARM mission and the upcoming ICON missions. Thus, in coordination with space-based and other ground-based observations, the AMBER magnetometer network provides a great opportunity to understand the electrodynamics that governs equatorial ionosphere motions. In this paper we present the longitudinal variability of the equatorial electrodynamics using the combination of instruments onboard SWARM and C/NOFS satellites and ground-based AMBER network. Both ground- and pace-based observations show stronger dayside and evening sector equatorial electrodynamics in the American and Asian sectors compared to the African sector. On the other hand, the African sector is home to stronger and year-round ionospheric bubbles/irregularities compared to the American and Asian sectors. This raises the question if the evening sector equatorial electrodynamics (vertical drift), which is believed to be the main cause for the enhancement of Rayleigh-Taylor (RT) instability growth rate, is stronger in the

  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. 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.

  2. 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?......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?...

  3. 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.

  4. [The effect of phospholipid hepatoprotectors on lipid peroxidation in liver and content of cytokines in the blood in experimental pathology caused by isoniazid].

    Science.gov (United States)

    Udut, V V; Vengerovskiĭ, A I; Burkova, V N; Vaizova, O E; Korshunov, D A

    2012-01-01

    The purpose--to investigate the influence of hepatoprotective agents of phospholipids'structure essentiale, eplir and its combinations with amber acid on rats liver functional state, lipoperoxidation and bioenergetics, also tumor necrosis factor-a and interleukin-10 blood content in experimental isoniazid intoxication. These agents demonstrated antioxidant action, decreased the common and indirect bilirubine, tumor necrosis factor-alpha blood content, aminotransferase and alkaline phosphatase activity, increased the interleukin-10 blood content. Isonoazid uncoupled the substrate oxidation with ADP phosphorylation and inhibited the respiratory activity of liver mitochondrions. Essentiale and eplir increased the coupling of oxidation with ATP synthesis, in combination with amber acid improved kinetic characteristics of liver mitochondrions.

  5. Gemstones

    Science.gov (United States)

    Olson, D.W.

    2013-01-01

    The estimated value of natural gemstones produced from U.S. deposits during 2012 was $11.1 million, a slight increase from 2011. U.S. gemstone production included agate, amber, beryl, coral, garnet, jade, jasper, opal, pearl, quartz, sapphire, shell, topaz, tourmaline, turquoise and many other gem materials.

  6. 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,…

  7. Teaching Integration with Layers and Representations: A Case Study

    Science.gov (United States)

    Von Korff, Joshua; Rebello, N. Sanjay

    2012-01-01

    We designed a sequence of seven lessons to facilitate learning of integration in a physics context. We implemented this sequence with a single college sophomore, "Amber," who was concurrently enrolled in a first-semester calculus-based introductory physics course which covered topics in mechanics. We outline the philosophy underpinning these…

  8. ASPRO and its user's support: the JMMC tools for preparing VLTI Observations

    Science.gov (United States)

    Duchene, Gaspard; Berger, Jean-Philippe; Zins, Gerard; Duvert, Gilles

    2004-12-01

    We will present an overview of the main features of the current and next (to be released at the end of the summer) versions of the ASPRO software that are being developed by the JMMC to prepare VLTI observing programs. To help ASPRO users prepare their AMBER and MIDI proposals, an active helpdesk will also be available.

  9. 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.

  10. 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

  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. 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.

  14. Novel artificial metalloenzymes by in vivo incorporation of metal-binding unnatural amino acids

    NARCIS (Netherlands)

    Drienovska, Ivana; Rioz-Martinez, Ana; Draksharapu, Apparao; Roelfes, Gerard

    2015-01-01

    Artificial metalloenzymes have emerged as an attractive new approach to enantioselective catalysis. Herein, we introduce a novel strategy for preparation of artificial metalloenzymes utilizing amber stop codon suppression methodology for the in vivo incorporation of metal-binding unnatural amino aci

  15. Comparisons of experiment with cellulose models based on electronic structure and empirical force field theories

    Science.gov (United States)

    Studies of cellobiose conformations with HF/6-31G* and B3LYP/6-31+G*quantum theory [1] gave a reference for studies with the much faster empirical methods such as MM3, MM4, CHARMM and AMBER. The quantum studies also enable a substantial reduction in the number of exo-cyclic group orientations that...

  16. The Growing of Grids

    Science.gov (United States)

    Architectural Record, 1977

    1977-01-01

    The Central Building for the School of Art and Physical Education at Tsukuba University uses eight-inch-square amber-colored glass blocks, steel framing and floor decking, plus pured concrete, to provide simple and flexible spaces for athletes and artists. (Author/MLF)

  17. The nature and fate of natural resins in the geosphere XIII: a probable pinaceous resin from the early Cretaceous (Barremian, Isle of Wight

    Directory of Open Access Journals (Sweden)

    Anderson Ken B

    2008-01-01

    Full Text Available Abstract Terpenoid resin is produced by all families and most genera of the order Coniferales (the conifers, and the distribution of terpenes present in most conifer resins is characteristic of the originating family. Analyses of early Cretaceous (Barremian amber (fossil resin from the English Wealden, Isle of Wight, southern England, by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS, indicate a terpene distribution dominated by abietane- and labdane-type terpenes. Similar distributions are observed in some species of the extant family Pinaceae. The Pinaceae are well represented within the Wealden deposits of southern England, by only one (known species, Pityites solmsii (Seward Seward, whereas the macro-fossil record of these deposits is dominated by the extinct conifer family Cheirolepidiaceae, for which no resin chemistry has been reported. By analogy with modern materials, it is probable that the ambers found in these deposits are derived from an extinct member of the Pinaceae, but given the absence of evidence concerning the chemotaxonomy of the Cheirolepidiaceae, this family cannot be excluded a priori as a possible paleobotanical source. These ambers may therefore be assigned to either the Pinaceae or to the Cheirolepidiaceae. These samples are the oldest ambers to date to yield useful chemotaxonomic data.

  18. India's People, Country, and Great Religions: Two Instructional Learning Packages.

    Science.gov (United States)

    Wales, Largo Ann

    Divided into two parts, this slide narration covers India's history, people, religions, geography, and architecture. The first part, "Introduction: Country, People, and History," covers the general history of India and its people. The history is presented through: (1) the architecture, including the Palace of Winds, the Amber Fort, the Taj Mahal,…

  19. 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

  20. 40 CFR 262.85 - Contracts.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Contracts. 262.85 Section 262.85 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) STANDARDS... the OECD § 262.85 Contracts. (a) Transfrontier movements of hazardous wastes subject to amber or...

  1. Baltikum ja Poola juhiks Vene gaasi mööda maad / Lauri Linnamäe

    Index Scriptorium Estoniae

    Linnamäe, Lauri

    2007-01-01

    Balti riigid ja Poola taotlevad Euroopa Komisjonilt toetust uuringu läbiviimiseks, mis keskenduks 2004. aastal välja pakutud Lätit, Leedut ja Poolat läbiva gaasijuhtme Amber projekti võrdlusele Nord Streami projektiga. Lisa: Nord Stream

  2. 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...

  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. 假眼小绿叶蝉对不同颜色偏嗜性的研究%Study on Preference of Green Leafhopper Empoasca (Empoasca) vitis (G  o¨the) for Different Colors

    Institute of Scientific and Technical Information of China (English)

    赵冬香; 陈宗懋; 程家安

    2001-01-01

    Experiments were made both in laboratory and in tea field aboutthe preference of green leafhopper Empoasca (Empoasca) vitis (G o¨the) to different colors. The result showed that yellow is the most attractive color. Under laboratory conditions,amber yellow was the strongest to attract the leafhoppers. There were no significant difference among amber yellow,lake water blue and gem green,but there showed significant difference between amber yellow and emerald green,snow white ,reddish orange respectively(p<0.05). Among different yellow plates,there had no significant difference in attracting green leafhoppers,but among different yellows and emerald green,indigo-blue and sea-blue,there had significant difference (p<0.05) in attracting. In tea field,amber yellow was the strongest to attract the leafhoppers,there had no significant difference between amber yellow and gem green,and between amber yellow to lake water blue,there were significant difference(p<0.05). The laboratory and field experiments showed that the green leafhopper had a preference for yellow green and pale green.%作者进行了茶树害虫假眼小绿叶蝉对不同颜色偏嗜性的室内和田间试验。结果表明:假眼小绿叶蝉最偏嗜黄色。室内试验中,琥珀黄诱集的虫数最多,且与湖水蓝和宝石绿间的虫数差异不显著,与翠绿、雪白和橘橙间的虫数差异显著(p<0.05)。琥珀黄、油菜花黄和麦杆黄三种不同黄色间诱集的虫数无差异,它们与翠绿、靛青和海青间的虫数达差异显著性水平(p<0.05)。茶园试验中,琥珀黄诱集的虫数最多,与宝石绿间的虫数差异不显著,而与湖水蓝间虫数差异达显著水平(p<0.05)。室内外试验的结果基本一致,即假眼小绿叶蝉偏嗜黄绿色、浅绿色。

  5. 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.)

  6. 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...

  7. 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.

  8. 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.

  9. 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

  10. Botanical origin, colour, granulation, and sensory properties of the Harenna forest honey, Bale, Ethiopia.

    Science.gov (United States)

    Belay, Abera; Solomon, W K; Bultossa, Geremew; Adgaba, Nuru; Melaku, Samuel

    2015-01-15

    In this study, the Harenna forest honey samples were investigated with respect to their botanical origin, granulation, colour and sensory properties. Sixteen honey samples were collected from two representative sites (Chiri, C, and Wabero, W) using random sampling techniques. Botanical origin was investigated using qualitative pollen analysis by counting 500 pollen grains using harmonised methods of melissopalynology. Granulation, colour, and sensory properties of honey were determined by visual observation, using Pfund grader, acceptability and preference tests, respectively. Honey samples were also tested for tetracycline. Honey obtained from Wabero is originated dominantly from Syzygium guineense while Chiri was multifloral. The colour of honey ranged from 34 to 85 with light amber and extra light amber colours. The honey samples were free from tetracycline residue and form coarse granules slowly. Significant variation (p>0.05) in sensory preference and acceptability tests not observed due to hive types and locations.

  11. 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...

  12. 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.

  13. Baltorussus total makeover:rejuvenation and sex change in an ancient parasitoid wasp lineage

    OpenAIRE

    Lars Vilhelmsen; Dominique Zimmermann

    2014-01-01

    The Orussidae is a small and rare but phylogenetically important family of parasitoid wasps. The fossil record of the family is also very poor. Baltorussus velteni was described from Baltic amber from an allegedly female specimen. This and another recently discovered specimen are examined with microCT scanning and standard microscopy. We reveal that both the holotype and the new specimen are actually males. Furthermore, the results of the microCT scanning allow us to integrate the fossils in ...

  14. 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...

  15. Deposit Formation on Cylinder Liner Surface in medium-speed Engines

    OpenAIRE

    Buhaug, Øyvind

    2003-01-01

    The presence of deposits in the honing grooves in diesel engine cylinder liners can cause a severe increase in the consumption of lubricating oil. These deposits may appear amber in which case they may be referred to as 'liner lacquerer' or be nearly invisible in which case they are often referred to as 'transparent glaze' or 'bore glaze' in the marine sector. The formation of these deposits is believed to be influenced by engine design, engine load, fuel composition and lubricating oil compo...

  16. 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...

  17. 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....

  18. 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...

  19. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.

    Science.gov (United States)

    Wang, Jinan; Shao, Qiang; Cossins, Benjamin P; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang

    2016-01-01

    The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design.

  20. 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

  1. 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.

  2. 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...

  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. 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...

  5. 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.

  6. 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...

  7. 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...

  8. 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.

  9. 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...

  10. When using nutritional labels, less is better

    OpenAIRE

    Prevost, Marie; Hot, Pascal; Baciu, Monica; Ruffieux, Bernard; Meary, David; Crosetto, Paolo; Muller, Laurent

    2015-01-01

    New colorful nutrional labels are now used in some countries to help people better evaluate how healthy are food products. But little is known about how we understand and manipulate colored information to evaluate food products. The authors test how people evaluate anonymous food products from nutritional information displayed as numbers (% of daily amount) or as colors (red, amber, green). They anticipate that people will categorize food as bad for their health as soon as the color red is pr...

  11. The Effects of Lamp Spectral Distribution on Sky Glow over Observatories

    Science.gov (United States)

    Luginbuhl, C. B.; Boley, P. A.; Davis, D. R.; Duriscoe, D. M.

    2015-03-01

    Using a wavelength-generalized version of the Garstang (1991) model, we evaluate overhead sky glow as a function of distance up to 300 km, from a variety of lamp types, including common gas discharge lamps and several types of LED lamps. We conclude for both professional, and especially cultural (visual), astronomy, that low-pressure sodium and narrow-spectrum amber LED lamps cause much less sky glow than all broad-spectrum sources.

  12. 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.

  13. 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...

  14. 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...

  15. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

    Science.gov (United States)

    Zhou, Y; Wang, S; Li, Y; Zhang, Y

    2016-01-01

    There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636

  16. New paradigm of multi-chip white LEDs: combination of an InGaN blue LED and full down-converted phosphor-converted LEDs.

    Science.gov (United States)

    Oh, Ji Hye; Oh, Jeong Rok; Park, Hoo Keun; Sung, Yeon-Goog; Do, Young Rag

    2011-05-01

    This study introduces innovative multi-chip white LED systems that combine an InGaN blue LED and green/red or green/amber/red full down-converted, phosphor-conversion LEDs (pc-LEDs). Efficient green, amber, and red full down-converted pc-LEDs were fabricated by simply capping a long-wave pass filter (LWPF) on top of LED packing associated with each corresponding powder phosphor. The principal advantage of this type of color-mixing approach in newly developed multi-chip white LEDs based on colored pc-LEDs is thought to be dynamic control of the chromaticity and better light quality. In addition, the color-mixing approach improves the low efficacy of green/amber LEDs in the "green gap" wavelength; reduces the wide color/efficacy variations of each primary LED with at different temperatures and currents; and improves the low color rendering indexes of the traditional color-mixing approach in red, green, and blue (RGB) multi-chip white LEDs.

  17. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    Science.gov (United States)

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Teaching integration with layers and representations: A case study

    Directory of Open Access Journals (Sweden)

    Joshua Von Korff

    2012-05-01

    Full Text Available We designed a sequence of seven lessons to facilitate learning of integration in a physics context. We implemented this sequence with a single college sophomore, “Amber,” who was concurrently enrolled in a first-semester calculus-based introductory physics course which covered topics in mechanics. We outline the philosophy underpinning these lessons, which characterizes integration in terms of layers and representations. We describe how Amber learned to give oral presentations in which she told a story about how integration comes from products, sums, and limits in a variety of physics contexts. We conclude that by the end of our lessons, Amber was able to conceptualize and explain integrals using multiple representations. In one case, she was able to solve a novel problem about integration in an unfamiliar context (center of mass. Based on our previous research about integration, we suggest that these achievements would have been unattainable with the use of a single one or two hour lesson.

  3. 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)

  4. Erstnachweis von Taiwania, Cryptomeria und Liquidambar aus dem Bitterfelder und Baltischen Bernstein

    Directory of Open Access Journals (Sweden)

    H. Jähnichen

    1998-01-01

    Full Text Available Aus dem untermiozänen Bernstein von Bitterfeld (Sachsen-Anhalt werden erstmalig ein strukturzeigender Zweig von Taiwania schaeferi, ein isoliertes Nadel-Fragment von Cryptomeria sp. sowie ein Fruchtstand von Liquidambar europaea beschrieben. Außerdem muß “Widdringtonites oblongifolius” (Goeppert & Menge Caspary & Klebs 1906/07 pro parte aus dem obereozänen Baltischen Bernstein nach morphologisch-anatomischen Merkmalskomplexen ebenfalls zu Taiwania schaeferi gestellt werden. “Enormicutis eoconferta” — aff. Cryptomeria spec. (Schneider 1986 aus der obereozänen Braunkohle von Nordwestsachsen muß nach morphologisch-anatomischen Details zu Athrotaxis couttsiae (Heer Gardner revidiert werden. First record of Taiwania, Cryptomeria and Liquidambar from Bitterfeld and Baltic amber A structure-bearing twig of Taiwania schaeferi, an isolated needle-fragment of Cryptomeria spec. as also an aggregate fruit of Liquidambar europaea are firstly described from the Lower Miocene amber of Bitterfeld (Saxony-Anhalt. Moreover “Widdringtonites oblongifolius” (Goeppert & Menge Caspary & Klebs 1906/07 p.p. from the Upper Eocene Baltic amber after morphological-anatomical features must be also assigned to Taiwania schaeferi. “Enormicutis eoconferta” — aff. Cryptomeria sp. (Schneider 1986 from the Upper Eocene brown-coal of North Western Saxony after morphological-anatomical details must be revised to Athrotaxis couttsiae (Heer Gardner. doi:10.1002/mmng.19980010112

  5. 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

  6. Optimisation of a system for the co-translational incorporation of a keto amino acid and its application to a tumour-specific Anticalin.

    Science.gov (United States)

    Reichert, Andreas J; Poxleitner, Gabriele; Dauner, Martin; Skerra, Arne

    2015-12-01

    The bioorthogonal keto group has attracted interest for the site-specific chemical conjugation of recombinant proteins under mild conditions, e.g. with aminooxy-functionalised fluorescent probes, radiometal chelates, toxins or polymers. However, the cotranslational incorporation of the corresponding non-canonical amino acid p-acetyl-L-phenylalanine (Apa) into proteins expressed in Escherichia coli by means of amber suppression using a previously described system with a mutated tRNA and an engineered tyrosyl-tRNA synthetase from Methanococcus jannaschii shows limited efficiency and considerable promiscuity towards endogenous amino acids. Employing a one-plasmid system that encodes all three components required for selection, i.e. the modified aminoacyl-tRNA synthetase (aaRS), the cognate amber suppressor tRNA and the enhanced green fluorescent protein equipped with an amber stop codon and serving as reporter, we have generated an Apa-specific aaRS&tRNA pair with considerably improved efficiency (17-fold increased expression) and also fidelity (6-fold). To this end, both the aaRS and the tRNA were subjected to doped random mutagenesis and selection in altogether four evolutionary cycles using fluorescence-activated bacterial cell sorting as well as automated screening of microcultures. The resulting aaRS&tRNA pair was applied to the functionalisation of an Anticalin with specificity towards oncofetal fibronectin by introducing a keto group at a permissible site for subsequent conjugation with a fluorescent dye, thus allowing visualisation of this tumour target under the microscope.

  7. Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl pairs in the Escherichia coli BL21(DE3 cell strain.

    Directory of Open Access Journals (Sweden)

    Keturah A Odoi

    Full Text Available Systematic studies of nonsense and sense suppression of the original and three derivative Methanosarcina mazei PylRS-tRNA(Pyl pairs and cross recognition between nonsense codons and various tRNA(Pyl anticodons in the Escherichia coli BL21(DE3 cell strain are reported. tRNA(CUA(Pyl is orthogonal in E. coli and able to induce strong amber suppression when it is co-expressed with pyrrolysyl-tRNA synthetase (PylRS and charged with a PylRS substrate, N(ε-tert-butoxycarbonyl-L-lysine (BocK. Similar to tRNA(CUA(Pyl, tRNA(UUA(Pyl is also orthogonal in E. coli and can be coupled with PylRS to genetically incorporate BocK at an ochre mutation site. Although tRNA(UUA(Pyl is expected to recognize a UAG codon based on the wobble hypothesis, the PylRS-tRNA(UUA(Pyl pair does not give rise to amber suppression that surpasses the basal amber suppression level in E. coli. E. coli itself displays a relatively high opal suppression level and tryptophan (Trp is incorporated at an opal mutation site. Although the PylRS-tRNA(UCA(Pyl pair can be used to encode BocK at an opal codon, the pair fails to suppress the incorporation of Trp at the same site. tRNA(CCU(Pyl fails to deliver BocK at an AGG codon when co-expressed with PylRS in E. coli.

  8. 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

  9. 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.

  10. 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...

  11. 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...

  12. 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

  13. Sleep disorders in Parkinson’s disease

    Directory of Open Access Journals (Sweden)

    Israt Jahan

    2009-10-01

    Full Text Available 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 syndrome, rapid eye movement sleep behavior disorder, sleep apnea, parasomnias, excessive daytime sleepiness, and sleep attacks. This article reviews sleep disorders and their treatment in PD. Keywords: insomnia, restless legs syndrome, sleep apnea

  14. 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

  15. Catalogue of type materials of springtails (Hexapoda, Collembola) in the Canadian National Collection of Insects, Arachnids & Nematodes.

    Science.gov (United States)

    Stebaeva, Sophya; Lonsdale, Owen; Babenko, Anatoly

    2016-01-01

    The catalogue assembles and updates all data concerning the type material of Collembola kept in the Canadian National Collection of Insects, Arachnids & Nematodes in Ottawa (CNC). Information is provided for type material of 69 species. Included are holotypes of 31 species (together with 5 ones from Cretaceous amber), syntypes of 26 species (four of them are presently considered to be junior synonyms) and paratypes of 32 species (one of which is considered a junior synonym). Essential label data, references to original descriptions, and modern status including synonyms are given. PMID:27394350

  16. Lesion presenting with a “blue amber” pattern

    Science.gov (United States)

    Pagliarello, Calogero; Peccerillo, Francesca; Zucchi, Alfredo; Tortorella, Rocco Giuseppe; Ricci, Roberto; Stanganelli, Ignazio; Feliciani, Claudio; Di Nuzzo, Sergio

    2016-01-01

    Atypical fibroxanthoma (AFX) is a spindle cell neoplasm with low metastatic potential but high tendency to recur after surgery. Because of the rarity of this lesion and its aspecific clinical features, AFX could be easily misdiagnosed and undertreated by many clinicians who encounter them. Dermoscopy represents a valuable tool for easily assessing skin lesions, even though histological examination is required for final diagnosis. We report a case of a cheek lesion with dermoscopic “blue amber pattern”, easily recognisable and not observed in others skin tumours, which could represent an additional feature useful in differentiating this tumour from other skin neoplasms. PMID:27803916

  17. 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...

  18. Generic control software connecting astronomical instruments to the reflective memory data recording system of VLTI - bossvlti

    Science.gov (United States)

    Pozna, E.; Ramirez, A.; Mérand, A.; Mueller, A.; Abuter, R.; Frahm, R.; Morel, S.; Schmid, C.; Duc, T. Phan; Delplancke-Ströbele, F.

    2014-07-01

    The quality of data obtained by VLTI instruments may be refined by analyzing the continuous data supplied by the Reflective Memory Network (RMN). Based on 5 years experience providing VLTI instruments (PACMAN, AMBER, MIDI) with RMN data, the procedure has been generalized to make the synchronization with observation trouble-free. The present software interface saves not only months of efforts for each instrument but also provides the benefits of software frameworks. Recent applications (GRAVITY, MATISSE) supply feedback for the software to evolve. The paper highlights the way common features been identified to be able to offer reusable code in due course.

  19. 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....

  20. 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...

  1. Phase Closure Nulling: A "Lyot Mask" on correlated flux of stars

    Science.gov (United States)

    Duvert, G.; Chelli, A.; Malbet F.; Kern, P.

    2010-10-01

    "Phase closure nulling" (PCN in short) is a technique which consists of observing fully resolved stars around the spatial frequency regions where the interferometric visibility amplitude is close to zero. Chelli et al. (2009) have shown that the phase closure in these regions is dominated by the signature of close and faint companions (if present), as if a "Lyot mask" was blocking the correlated flux of the star. This contribution will present the theory of PCN and results obtained on recent AMBER/VLTI and CHARA/MIRC observations, showing the high detection dynamics achieved by this observational technique.

  2. The Cretaceous Fossil Burmaculex antiquus Confirmed as the Earliest Known Lineage of Mosquitoes (Diptera: Culicidae).

    Science.gov (United States)

    Borkent, Art; Grimaldi, David A

    2016-01-01

    A second female of mid-Cretaceous Burmaculex antiquus Borkent & Grimaldi, preserved in 99 myo Burmese amber, and the oldest known member of the Culicidae, is described in detail. Although generally opaque and distorted, some character states are added or refined. The discovery of well-developed scales on the legs shows that this feature must now be considered a synapomorphy of both the fossil and all extant members of the family. Previously described synapomorphies and further interpretation here confirm the phylogenetic position of this fossil as the sister group to extant and all known fossil Culicidae. It is placed in the new subfamily Burmaculicinae.

  3. 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.

  4. 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 ...

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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...

  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. Alustava ettevõtja rahaallikad / Eva Palu

    Index Scriptorium Estoniae

    Palu, Eva

    2005-01-01

    Võimalikest finantseerimisallikatest ettevõtte rajamisel. Lisa: Noppeid uuringu "Eesti elanike ettevõtlikkus" järeldustest. Alustavatele ettevõtetele pakutavaid finantseerimisvariante tutvustavad Hansapanga ettevõtete panganduse analüüsi- ja arendusosakonna juhataja Raul Kivari, Eesti Ühispanga ärilaenude arendusjuht Helen Saare, Nordea Panga äriklientide osakonna juhataja Ingo Põder, Parex Panga müügi- ja marketingidirektor Andres Pärloja, BIG-i juhatuse esimees Targo Raus, MTVP tegevjuht Allan Martinson, BaltCapi finantsjuht Martin Kõdar, Amber Trusti nõustaja Indrek Kasela. Diagrammid: Ettevõtlus Eestis

  12. 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. ...

  13. Characteristics of phospholipase A2 mutant of the starfish Asterina pectinifera

    OpenAIRE

    Kishimura, Hideki; ANDO, Seiichi

    2007-01-01

    Site-directed mutagenesis study of phospholipase A2 (PLA2) from the pyloric ceca of starfish Asterina pectinifera was used to probe the relationship between polar-group specificity and structure of the pancreatic loop region. The sequence of the cDNA encoding the starfish PLA2 was exchanged by the oligonucleotide-directed dual amber-long and accurate polymerase chain reaction method to insert Lys residue between Cys-62 and Gly-63. The modified cDNA was inserted into the expression plasmid pET...

  14. The first mesozoic ants.

    Science.gov (United States)

    Wilson, E O; Carpenter, F M; Brown, W L

    1967-09-01

    Two worker ants preserved in amber of Upper Cretaceous age have been found in New Jersey. They are the first undisputed remains of social insects of Mesozoic age, extending the existence of social life in insects back to approximately 100 million years. They are also the earliest known fossils that can be assigned with certainty to aculeate Hymenoptera. The species, Sphecomyrma freyi, is considered to represent a new subfamily (Sphecomyrminae), more primitive than any previously known ant group. It forms a near-perfect link between certain nonsocial tiphiid wasps and the most primitive myrmecioid ants.

  15. 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...

  16. NUTRITION VALUE OF PLUM TREE FOR HEALTH

    Directory of Open Access Journals (Sweden)

    Prajapati P M.

    2012-05-01

    Full Text Available 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, much like the peach but more erect growing. It is more beneficial to the health.

  17. 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,...

  18. 与交通有关的词汇

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    交通规则traffic regulation 路标guide post 红绿灯traffic light 红灯red light 绿灯green light 黄灯amber light 岗亭police box 斑马线zebra stripes 车行道cariage-way 此路不通blocked 不准驶入no entry 安全岛safety jsland 停车处parking place 不准停车restricted stop 不准滞留restricted waiting

  19. “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...

  20. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.

    Science.gov (United States)

    Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2013-01-01

    Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.

  1. 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.

  2. VizieR Online Data Catalog: eta Car velocity-resolved imaging (Weigelt+, 2016)

    Science.gov (United States)

    Weigelt, G.; Hofmann, K.-H.; Schertl, D.; Clementel, N.; Corcoran, M. F.; Damineli, A.; de Wit, W.-J.; Grellmann, R.; Groh, J.; Guieu, S.; Gull, T.; Heininger, M.; Hillier, D. J.; Hummel, C. A.; Kraus, S.; Madura, T.; Mehner, A.; Merand, A.; Millour, F.; Moffat, A. F. J.; Ohnaka, K.; Patru, F.; Petrov, R. G.; Rengaswamy, S.; Richardson, N. D.; Rivinius, T.; Schoeller, M.; Teodoro, M.; Wittkowski, M.

    2016-09-01

    We present the reconstructed images from Fig. 4 of the paper. The interferometric data were taken with the ESO VLTI and the AMBER instrument with high spectral resolution (R=12000) in many spectral channels across the Brackett Gamma line at 2.166 micron. 96 images were reconstructed at velocity channels from -663km/s to 520km/s. The velocity of each channel is coded into the filename. Plate scale is 0.781mas/pixel. North is up, and east to the left. FOV is 50mas. The resolution of the images is ~6 mas. (2 data files).

  3. A first record of Cretaceous aphids (Hemiptera, Sternorrhyncha, Aphidomorpha) in Australia, from the Lower Cretaceous Koonwarra Fossil Bed, Victoria.

    Science.gov (United States)

    Martin, Sarah K; Skidmore, Luke I; Stilwell, Jeffrey D

    2016-01-01

    This paper describes the first species of aphid from the Lower Cretaceous Koonwarra Fossil Bed of the Gippsland Basin, southeastern Victoria, Australia. This aphid, herein named Koonwarraphis rotundafrons gen. & sp. nov., is assigned to the cosmopolitan Cretaceous superfamily Tajmyraphidoidea, which has been previously described from the Lebanese, Taimyrian, Canadian, Myanmar (Burmese), and Spanish ambers. Koonwarraphis rotundafrons is the first aphid recorded from the eastern Gondwanan landmass during the Cretaceous, and represents the only tajmyraphidoid preserved as a compression fossil, rather than as an amber inclusion. Due to the nature of the fossil's preservation, Koonwarraphis cannot be firmly placed in any of the described tajmyraphidoid families; however, all observable morphological features suggest that the genus is broadly typical of the superfamily and Cretaceous aphids in general. Koonwarraphis' shortened rostrum, a feature also seen in other tajmyraphidoids, suggests an association with the more herbaceous aspects of the Early Cretaceous Victorian flora. Considering the modern aphid preference for angiosperm plants, it is possible that this aphid was living upon the herbaceous early angiosperms recorded previously from the Koonwarra macrofloral assemblage. PMID:27395744

  4. 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

  5. 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

  6. Occurrences of dendritic gold at the McLaughlin Mine hot-spring gold deposit

    Science.gov (United States)

    Sherlock, R. L.; Lehrman, N. J.

    1995-06-01

    Two styles of gold dendrites are variably developed at the McLaughlin Mine. The most abundant occurrence is hosted by amber-coloured hydrocarbon-rich opal. Silica likely precipitated from a boiling hydrothermal fluid and complexed with immiscible hydrocarbons forming an amorphous hydrocarbon-silica phase. This phase likely scavenged particulate gold by electrostatic attraction to the hydrocarbon-silica phase. The dendritic nature of the gold is secondary and is the result of dewatering of the amorphous hydrocarbon-silica phase and crystallization of gold into syneresis fractures. The second style of dendritic gold is hosted within vein swarms that focused large volumes of fluid flow. The dendrites occur along with hydrocarbon-rich silica at the upper contact of the vein margins which isolated the dendrites allowing sufficient time for them to grow. In a manner similar to the amber-coloured opal, the dendrites may have formed by scavenging particulate gold by electrostatic attraction to the hydrocarbon-silica phase.

  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. 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

  10. After-effects of TFT-LCD display polarity and display colour on the detection of low-contrast objects.

    Science.gov (United States)

    Mayr, Susanne; Buchner, Axel

    2010-07-01

    Participants performed a word-non-word discrimination task within a car control display emulated on a thin film transistor liquid-crystal display (TFT-LCD). The task simulated an information read-out from a TFT-LCD-based instrument panel. Subsequently, participants performed a low-contrast object detection task that simulated the detection of objects during night-time driving. In experiment 1, words/non-words were presented black-on-white (positive polarity) or white-on-black (negative polarity). In experiments 2 and 3, display colour was additionally manipulated. A positive polarity advantage in the discrimination task was consistently observed. In contrast, positive displays interfered more than negative displays with subsequent detection. The detrimental after-effect of positive polarity displays was strong with white and blue, reduced with amber and absent with red displays. Subjective measures showed a preference for blue over red, but a slight advantage for amber over blue. Implications for TFT-LCD design are derived from the results. STATEMENT OF RELEVANCE: When using TFT-LCDs as car instrument panels, positive polarity red TFT-LCDs are very likely to lead to good instrument readability while at the same time minimising - relative to other colours - the negative effects of an illuminated display on low-contrast object detection during night-time driving.

  11. V838 Monocerotis: the central star and its environment a decade after outburst

    CERN Document Server

    Chesneau, Olivier; De Marco, Orsola; Bright, S N; Spang, Alain; Banerjee, D P K; Ashok, N M; Kaminski, T; Wisniewski, John P; Meilland, Anthony; Lagadec, Eric

    2014-01-01

    Aims. V838 Monocerotis erupted in 2002, brightened in a series of outbursts, and eventually developed a spectacular light echo. A very red star emerged a few months after the outburst. The whole event has been interpreted as the result of a merger. Methods. We obtained near-IR and mid-IR interferometric observations of V838 Mon with the AMBER and MIDI recombiners located at the Very Large Telescope Interferometer (VLTI) array. The MIDI two-beam observations were obtained with the 8m Unit Telescopes between October 2011 and February 2012. The AMBER three-beam observations were obtained with the compact array (B≤35m) in April 2013 and the long array (B≤140m) in May 2014, using the 1.8m Auxiliary Telescopes. Results. A significant new result is the detection of a compact structure around V838 Mon, as seen from MIDI data. The extension of the structure increases from a FWHM of 25 mas at 8 {\\mu}m to 70 mas at 13 {\\mu}m. At the adopted distance of D = 6.1 $\\pm$ 0.6 kpc, the dust is distributed from about ...

  12. 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.

  13. 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...

  14. 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

  15. Diterpenoid Biopolymers: New Directions for Renewable Materials Engineering

    Science.gov (United States)

    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 established. Recent advances in sequencing technologies and biochemical engineering are rapidly accelerating the rate of identifying and assigning function to genes involved in terpenoid biosynthesis, as well as producing industrial-scale quantities of desired small-molecules in bacteria and yeast. This has provided new tools for engineering metabolic pathways capable of producing diterpenoid monomers that will enable the production of custom-tailored resinite-like polymers. Furthermore, this biosynthetic toolbox is continuously expanding, providing new possibilities for renewing dwindling stocks of naturally occurring resinite materials and engineering new materials for future applications. PMID:20857504

  16. 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

  17. 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

    2016-01-01

    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

  18. Nutritional value of cold-pressed rapeseed oil during long term storage as influenced by the type of packaging material, exposure to light & oxygen and storage temperature.

    Science.gov (United States)

    Wroniak, Małgorzata; Rękas, Agnieszka

    2016-02-01

    The effect of various conditions (storage temperature, exposure to light, access of oxygen) and different packaging material (amber glass, amber polyethylene terephthalate) on the nutritional value of cold-pressed rapeseed oil during 12 months of storage was investigated. Quantified quality parameters included: acidity, peroxide value, spectrophotometric indices (K 232 , K 268 ), fatty acid composition, tocopherols and sterols. Storage of oil at 4 °C was found to be most appropriate for maintaining the quality of cold-pressed rapeseed oil. Exposure of oil samples stored at room temperature to light in combination with the access of oxygen caused the most pronounced losses in the total tocopherols (ca. 90-91 % of α-T, and ca. 80-81 % of γ-T), total phytosterols (ca. 15-16 %) and substantial deterioration in oil qualitative properties. Although storage at room temperature is common for use in households, storage of at low temperatures (4 °C) significantly increases the possibility of prolonged shelf life of cold-pressed rapeseed oil. PMID:27162415

  19. Applying visual attention theory to transportation safety research and design: evaluation of alternative automobile rear lighting systems.

    Science.gov (United States)

    McIntyre, Scott E; Gugerty, Leo

    2014-06-01

    This field experiment takes a novel approach in applying methodologies and theories of visual search to the subject of conspicuity in automobile rear lighting. Traditional rear lighting research has not used the visual search paradigm in experimental design. It is our claim that the visual search design uniquely uncovers visual attention processes operating when drivers search the visual field that current designs fail to capture. This experiment is a validation and extension of previous simulator research on this same topic and demonstrates that detection of red automobile brake lamps will be improved if tail lamps are another color (in this test, amber) rather than the currently mandated red. Results indicate that when drivers miss brake lamp onset in low ambient light, RT and error are reduced in detecting the presence and absence of red brake lamps with multiple lead vehicles when tail lamps are not red compared to current rear lighting which mandates red tail lamps. This performance improvement is attributed to efficient visual processing that automatically segregates tail (amber) and brake (red) lamp colors into distractors and targets respectively.

  20. 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

  1. 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

  2. The life of massive stars seen through optical/infrared interferometry

    Science.gov (United States)

    Sanchez-Bermudez, J.; Alberdi, A.; Schödel, R.

    2015-05-01

    During the last decade, optical/infrared interferometry has become an essential tool to contribute to the understanding of stellar astrophysics. We present our results in the study of different aspects in the life of massive stars using optical interferometry. Particularly, we focused the discussion in our findings about multiplicity, interactions of the massive stars with the interstellar medium, and the early stages of high-mass stars. Our near-infrared observations comprise both: (i) long-baseline interferometry making use of AMBER/VLTI, and (ii) sparse aperture masking with VLT/NACO/SAM. These data have been obtained by our research group in the previous years, and the results have been published in several peer-reviewed papers. The principles of the optical/near-infrared interferometry are briefly presented. Particularly, we describe how to get the calibrated Interferometric observables. Henceforth, we present our results of two massive systems (HD150136 and Herschel 36) for which we discovered their triple nature using AMBER/VLTI. Finally, we will present the recently found evidence of a disk and a binary system in a very massive young stellar object known as IRS 9A in the NGC 3603 region.

  3. 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.

  4. Characterization of Plys-proximal morphogenetic genes of transposable bacteriophage Mu.

    Science.gov (United States)

    Siboo, I R; Sieder, F; Kumar, K; Howe, M M; DuBow, M S

    2004-02-01

    Late during the bacteriophage Mu lytic cycle, Mu DNA must be matured and packaged from its dispersed integration sites in the host DNA in order to produce progeny virions. Whereas control of late gene transcription in Mu is becoming well understood, less is known about the phage morphogenetic process. To investigate the latter, we cloned and sequenced a approximately 4.3-kb region of the phage DNA beginning just upstream of the leftmost late promoter Plys. Previous mapping of amber mutations had located the lysis (lys) and proposed DNA maturation genes D and E in this region. When the DNA sequence was analyzed, seven potential open reading frames were found. DNA sequence analysis of amber mutations in genes D and E identified the sixth and seventh open reading frames as D and E, respectively. Cloning and expression of this region enabled production of cell-free protein extracts that specifically recognize the phage-encoded packaging sequence (pac), a characteristic exhibited by phage maturation enzymes. In addition, the E protein was found to share homology with the large subunit of many phage DNA maturation enzymes. These results support the hypothesis that D and E encode subunits of the Mu DNA maturation enzyme.

  5. 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

  6. 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.

  7. 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

  8. 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...

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools.

    Science.gov (United States)

    Boström, J

    2001-12-01

    Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution (Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*\\GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed. PMID:12160095

  16. 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.

  17. Path integral evaluation of equilibrium isotope effects

    CERN Document Server

    Zimmermann, Tomas

    2009-01-01

    A general and rigorous methodology to compute the quantum equilibrium isotope effect is described. Unlike standard approaches, ours does not assume separability of rotational and vibrational motions and does not make the harmonic approximation for vibrations or rigid rotor approximation for the rotations. In particular, zero point energy and anharmonicity effects are described correctly quantum mechanically. The approach is based on the thermodynamic integration with respect to the mass of isotopes and on the Feynman path integral representation of the partition function. An efficient estimator for the derivative of free energy is used whose statistical error is independent of the number of imaginary time slices in the path integral, speeding up calculations by a factor of 60 at 500 K. We describe the implementation of the methodology in the molecular dynamics package Amber 10. The method is tested on three [1,5] sigmatropic hydrogen shift reactions. Because of the computational expense, we use ab initio pote...

  18. 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.

  19. CHARRON: Code for High Angular Resolution of Rotating Objects in Nature

    Science.gov (United States)

    Domiciano de Souza, A.; Zorec, J.; Vakili, F.

    2012-12-01

    Rotation is one of the fundamental physical parameters governing stellar physics and evolution. At the same time, spectrally resolved optical/IR long-baseline interferometry has proven to be an important observing tool to measure many physical effects linked to rotation, in particular, stellar flattening, gravity darkening, differential rotation. In order to interpret the high angular resolution observations from modern spectro-interferometers, such as VLTI/AMBER and VEGA/CHARA, we have developed an interferometry-oriented numerical model: CHARRON (Code for High Angular Resolution of Rotating Objects in Nature). We present here the characteristics of CHARRON, which is faster (≃q10-30 s per model) and thus more adapted to model-fitting than the first version of the code presented by Domiciano de Souza et al. (2002).

  20. 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.

  1. 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.

  2. 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.

  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. “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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Assessment of Some Density Functional Theory Methods and Force Field Models in Describing Various Interaction Modes of Benzene Dimer

    Institute of Scientific and Technical Information of China (English)

    Yu-wei Zhou; Igor Ying Zhang; Jian-ming Wu; An-an Wu; Xin Xu

    2011-01-01

    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.

  10. Dentinogenesis imperfecta associated with osteogenesis imperfecta: report of two cases.

    Science.gov (United States)

    Tsai, Chia-Ling; Lin, Yng-Tzer; Lin, Yai-Tin

    2003-02-01

    Osteogenesis imperfecta (OI) is a heritable systemic disorder of the connective tissue. Dentinogenesis imperfecta (DI), which is sometimes an accompanying symptom of OI, belongs to a group of genetically conditioned dentin dysplasias and is characterized clinically by an opalescent amber appearance of the dentin. Although the teeth of DI cases wear more easily and excessively compared to normal teeth, they do not appear to be more susceptible to dental caries than normal teeth. Two cases of DI associated with OI are presented in this paper, with 1 case suffering from nursing bottle caries. The purposes of this paper are to present the dental and skeletal characteristics of moderately and mildly involved DI associated with OI, and to discuss the possible methods of dental treatment. Patients with OI and opalescent teeth should be evaluated as soon as the deciduous teeth erupt; immediate dental involvement and oral hygiene instruction can be of help in reducing the necessity of extensive dental care.

  11. 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...

  12. 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...

  13. Development of a combined system for identification and classification of adverse drug reactions: Alerts Based on ADR Causality and Severity (ABACUS).

    Science.gov (United States)

    Koh, Yvonne; Yap, Chun Wei; Li, Shu-Chuen

    2010-01-01

    Currently, adverse drug reaction (ADR) causality and severity are assessed using different systems but there is no standard method to combine the results. In this work, a combined ADR causality and severity assessment system, including an online version, was developed. Logical rules were defined to translate the score obtained from the system into three alert zones: green, amber, and red. The alert zones are useful for triaging ADR cases as they help define the seriousness of the ADR and the urgency of the responses required. This new scoring system may be useful for clinicians, investigators, and regulators seeking information on the likelihood of a drug causing an adverse reaction, and whether an adverse reaction is sufficiently dangerous for the drug to be withheld or undergo further investigation.

  14. 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.

  15. 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

  16. Variable Message Signs for road tunnel emergency evacuations.

    Science.gov (United States)

    Ronchi, Enrico; Nilsson, Daniel; Modig, Henric; Walter, Anders Lindgren

    2016-01-01

    This paper investigates the design of Variable Message Signs (VMS) as a way-finding aid for road tunnel emergency evacuations. The use of the Theory of Affordances is suggested to provide recommendations on the design of VMS. A preliminary evaluation of 11 selected VMS systems was performed and 6 of them were further evaluated using an affordance-based within subject stated-preference questionnaire administered to a sample of 62 participants. Results are used to provide recommendations on the characteristics of the VMS systems, such as (1) size of the sign (large or small); (2) use of flashing lights; (3) colour scheme; (4) message coding (i.e., text, pictograms or a combination of them). The best performing VMS features for road tunnel emergency evacuation included the use of larger signs, flashing lights, the combination of emergency exit pictorial symbol in green in one panel and text in amber in the other panel.

  17. Phase closure nulling: results from the 2009 campaign

    Science.gov (United States)

    Duvert, Gilles; Malbet, Fabien; Chelli, Alain; Millan-Gabet, Rafael; Monnier, John D.; Schaefer, Gail H.

    2010-07-01

    We present here a new observational technique, Phase Closure Nulling (PCN), which has the potential to obtain very high contrast detection and spectroscopy of faint companions to bright stars. PCN consists in measuring closure phases of fully resolved objects with a baseline triplet where one of the baselines crosses a null of the object visibility function. For scenes dominated by the presence of a stellar disk, the correlated flux of the star around nulls is essentially canceled out, and in these regions the signature of fainter, unresolved, scene object(s) dominates the imaginary part of the visibility in particular the closure phase. We present here the basics of the PCN method, the initial proof-of-concept observation, the envisioned science cases and report about the first observing campaign made on VLTI/AMBER and CHARA/MIRC using this technique.

  18. 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.

  19. Phase Closure Nulling: results from the 2009 campaign

    CERN Document Server

    Duvert, Gilles; Chelli, Alain; Millan-Gabet, Rafael; Monnier, John D; Schaefer, Gail H

    2010-01-01

    We present here a new observational technique, Phase Closure Nulling (PCN), which has the potential to obtain very high contrast detection and spectroscopy of faint companions to bright stars. PCN consists in measuring closure phases of fully resolved objects with a baseline triplet where one of the baselines crosses a null of the object visibility function. For scenes dominated by the presence of a stellar disk, the correlated flux of the star around nulls is essentially canceled out, and in these regions the signature of fainter, unresolved, scene object(s) dominates the imaginary part of the visibility in particular the closure phase. We present here the basics of the PCN method, the initial proof-of-concept observation, the envisioned science cases and report about the first observing campaign made on VLTI/AMBER and CHARA/MIRC using this technique.

  20. 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.

  1. 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...

  2. 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

  3. 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

    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 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 proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

  4. 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.

  5. 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 ...

  6. Brood care in a 100-million-year-old scale insect.

    Science.gov (United States)

    Wang, Bo; Xia, Fangyuan; Wappler, Torsten; Simon, Ewa; Zhang, Haichun; Jarzembowski, Edmund A; Szwedo, Jacek

    2015-01-01

    Behavior of extinct organisms can be inferred only indirectly, but occasionally rare fossils document particular behaviors directly. Brood care, a remarkable behavior promoting the survival of the next generation, has evolved independently numerous times among animals including insects. However, fossil evidence of such a complex behavior is exceptionally scarce. Here, we report an ensign scale insect (Hemiptera: Ortheziidae), Wathondara kotejai gen. et sp. nov., from mid-Cretaceous Burmese amber, which preserves eggs within a wax ovisac, and several freshly hatched nymphs. The new fossil is the only Mesozoic record of an adult female scale insect. More importantly, our finding represents the earliest unequivocal direct evidence of brood care in the insect fossil record and demonstrates a remarkably conserved egg-brooding reproductive strategy within scale insects in stasis for nearly 100 million years.

  7. 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.

  8. Synthesis and Site-Specific Incorporation of Red-Shifted Azobenzene Amino Acids into Proteins.

    Science.gov (United States)

    John, Alford A; Ramil, Carlo P; Tian, Yulin; Cheng, Gang; Lin, Qing

    2015-12-18

    A series of red-shifted azobenzene amino acids were synthesized in moderate-to-excellent yields via a two-step procedure in which tyrosine derivatives were first oxidized to the corresponding quinonoidal spirolactones followed by ceric ammonium nitrate-catalyzed azo formation with the substituted phenylhydrazines. The resulting azobenzene-alanine derivatives exhibited efficient trans/cis photoswitching upon irradiation with a blue (448 nm) or green (530 nm) LED light. Moreover, nine superfolder green fluorescent protein (sfGFP) mutants carrying the azobenzene-alanine analogues were expressed in E. coli in good yields via amber codon suppression with an orthogonal tRNA/PylRS pair, and one of the mutants showed durable photoswitching with the LED light.

  9. 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

  10. Simulations on the kindling mechanism of the asFP595 fluorescent protein

    Science.gov (United States)

    Grigorenko, Bella L.; Nemukhin, Alexander V.; Savitsky, Alexander P.

    2008-02-01

    We report the results of quantum mechanical - molecular mechanical (QM/MM) simulations aiming to elucidate the mechanism of kindling of the initially non-fluorescent protein asFP595, which is a mutated variant of the chromoprotein asCP from the sea anemone Anemonia sulcata. asFP595 becomes brightly fluorescent (kindles) with emission at 595 nm in response to intense light irradiation at 568 nm. In simulations, we use the flexible effective fragment QM/MM method with the complete active space self-consistent field (CASSCF) wavefunctions in the quantum part and the AMBER force field parameters in the molecular mechanical part. We analyze the computed scans over potential energy surfaces of the ground and excited electronic states and consider details of the working hypothesis that the trans-cis isomerization of the chromophore group inside the protein is responsible for kindling.

  11. Review and update of the applications of organic petrology: Part 2, geological and multidisciplinary applications

    Science.gov (United States)

    Suarez-Ruiz, Isabel; Flores, Deolinda; Mendonça Filho, João Graciano; Hackley, Paul C.

    2012-01-01

    The present paper is focused on organic petrology applied to unconventional and multidisciplinary investigations and is the second part of a two part review that describes the geological applications and uses of this branch of earth sciences. Therefore, this paper reviews the use of organic petrology in investigations of: (i) ore genesis when organic matter occurs associated with mineralization; (ii) the behavior of organic matter in coal fires (self-heating and self-combustion); (iii) environmental and anthropogenic impacts associated with the management and industrial utilization of coal; (iv) archeology and the nature and geographical provenance of objects of organic nature such as jet, amber, other artifacts and coal from archeological sites; and (v) forensic science connected with criminal behavior or disasters. This second part of the review outlines the most recent research and applications of organic petrology in those fields.

  12. 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.

  13. 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.

  14. 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...

  15. 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.

  16. Molecular dynamics simulations of glycerol glass-forming liquid

    Energy Technology Data Exchange (ETDEWEB)

    Blieck, J. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Lerbret, A. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2005-10-31

    Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q {approx} 0.6 A{sup -1} are observed. Our results are also found compatible with predictions of the Mode Coupling Theory.

  17. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    Energy Technology Data Exchange (ETDEWEB)

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  18. Stability of carotenoids recovered from shrimp waste and their use as colorant in fish sausage.

    Science.gov (United States)

    Sachindra, N M; Mahendrakar, N S

    2010-01-01

    The stability of carotenoids recovered from shrimp waste using organic solvents and vegetable oils as affected by antioxidants and pigment carriers was evaluated during storage under different conditions. Solvent extracted carotenoid incorporated into alginate and starch as carriers was stored in metallised polyester and polypropylene pouches. Oil extracted carotenoids were stored in transparent and amber bottles. Also the use of recovered pigments as colorants in fish sausage was evaluated. Antioxidants, packaging material and storage period had a significant effect (p≤0.001) on the reduction of carotenoid content, while type of carrier had marginal effect (p≥0.05) on solvent extracted carotenoids during storage. Carotenoid content in pigmented oil was significantly affected by antioxidants (p≤0.001), packaging material (p≤0.05) and storage period (p≤0.001). Addition of carotenoid to the sausage enhanced the sensory colour, flavour and overall quality score of sausage and the added carotenoid was stable during processing.

  19. 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.

  20. 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...

  1. Force-field parameters for beryllium complexes in amorphous layers.

    Science.gov (United States)

    Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander

    2016-09-01

    Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data. Graphical Abstract Beryllium complexes in amorphous layersᅟ. PMID:27550375

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  7. 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.

  8. NEESPI focus issues in Environmental Research Letters

    Science.gov (United States)

    Norman, Julian; Groisman, Pavel; Soja, Amber J.

    2010-05-01

    In 2007 and 2009 Environmental Research Letters published focus issues (edited by Pavel Groisman and Amber J Soja) made up of work carried out by NEESPI participants. Here, we present the content of those focus issues as an invaluable resource for researchers working in the NEESPI study area. The first of the two issues, published in 2007 with title 'Northern Hemisphere High Latitude Climate and Environmental Change', presents a diverse collection of articles that are assembled into five groups devoted to studies of climate and hydrology, land cover and land use, the biogeochemical cycle and its feedbacks, the cryosphere, and human dimensions. The second issue, published in 2009, with title 'Climatic and Environmental Change in Northern Eurasia' presents diverse, assorted studies of different aspects of contemporary change, representing the diversity of climates and ecosystems across Northern Eurasia.

  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. 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.

  11. 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

  12. 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.

  13. Analysis of the secondary structure of a protein's N-terminal

    Science.gov (United States)

    Floare, C. G.; Bogdan, M.; Horovitz, O.; Mocanu, A.; Tomoaia-Cotisel, M.

    2009-08-01

    The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

  14. Analysis of the secondary structure of a protein's N-terminal

    Energy Technology Data Exchange (ETDEWEB)

    Floare, C G; Bogdan, M [National Institute for R and D of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Horovitz, O; Mocanu, A; Tomoaia-Cotisel, M, E-mail: calin.floare@itim-cj.r [Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Department of Physical Chemistry, 11 Arany Janos, 400028 Cluj-Napoca (Romania)

    2009-08-01

    The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

  15. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools.

    Science.gov (United States)

    Boström, J

    2001-12-01

    Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution (Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*\\GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.

  16. Predicting Model forComplex Production Process Based on Dynamic Neural Network

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Based on the comparison of several methods of time series predicting, this paper points out that it is nec-essary to use dynamic neural network in modeling of complex production process. Because self-feedback and mutu-al-feedback are adopted among nodes at the same layer in Elman network, it has stronger ability of dynamic ap-proximation, and can describe any non-linear dynamic system. After the structure and mathematical description be-ing given, dynamic back-propagation (BP) algorithm of training weights of Elman neural network is deduced. Atlast, the network is used to predict ash content of black amber in jigging production process. The results show thatthis neural network is powerful in predicting and suitable for modeling, predicting, and controling of complex pro-duction process.

  17. 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 ...

  18. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    Science.gov (United States)

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419

  19. 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.

  20. 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)

  1. 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

  2. Differential interferometry of QSO broad-line regions - I. Improving the reverberation mapping model fits and black hole mass estimates

    Science.gov (United States)

    Rakshit, Suvendu; Petrov, Romain G.; Meilland, Anthony; Hönig, Sebastian F.

    2015-03-01

    Reverberation mapping (RM) estimates the size and kinematics of broad-line regions (BLR) in quasars and type I AGNs. It yields size-luminosity relation to make QSOs standard cosmological candles, and mass-luminosity relation to study the evolution of black holes and galaxies. The accuracy of these relations is limited by the unknown geometry of the BLR clouds distribution and velocities. We analyse the independent BLR structure constraints given by super-resolving differential interferometry. We developed a three-dimensional BLR model to compute all differential interferometry and RM signals. We extrapolate realistic noises from our successful observations of the QSO 3C 273 with AMBER on the VLTI. These signals and noises quantify the differential interferometry capacity to discriminate and measure BLR parameters including angular size, thickness, spatial distribution of clouds, local-to-global and radial-to-rotation velocity ratios, and finally central black hole mass and BLR distance. A Markov Chain Monte Carlo model-fit, of data simulated for various VLTI instruments, gives mass accuracies between 0.06 and 0.13 dex, to be compared to 0.44 dex for RM mass-luminosity fits. We evaluate the number of QSOs accessible to observe with current (AMBER), upcoming (GRAVITY) and possible (OASIS with new generation fringe trackers) VLTI instruments. With available technology, the VLTI could resolve more than 60 BLRs, with a luminosity range larger than four decades, sufficient for a good calibration of RM mass-luminosity laws, from an analysis of the variation of BLR parameters with luminosity.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Effects of flashing green on driver’s stop/go decision at signalized intersection

    Institute of Scientific and Technical Information of China (English)

    沈家军; 王炜

    2015-01-01

    The primary objective of this work is to explore how drivers react to flashing green at signalized intersections. Through video taping and data procession based on photogrammetry, the operating speeds of vehicles before and after the moment when flashing green started was compared using paired-samples T-test. The critical distances between go and stop decisions was defined through cumulative percentage curve. The boundary of dilemma zone was determined by comparing stop distance and travel distance. Amber-running violation was analyzed on the basis of the travel time to the stop line. And finally, a logistic model for stop and go decisions was constructed. The results shows that the stopping ratios of the first vehicles of west-bound and east-bound approaches are 41.3% and 39.8%, respectively; the amber-light running violation ratios of two approaches are 31.6% and 25.4%, respectively; the operating speed growth ratios of first vehicles selecting to cross intersection after the moment when flashing green started are 26.7% and 17.7%, respectively; and the critical distances are 48 m and 46 m, respectively, which are close to 44 m, the boundary of dilemma zone. The developed decision models demonstrate that the probability of go decision is higher when the distance from the stop line is shorter or operating speed is higher. This indicates that flashing green is an effective way to enhance intersection safety, but it should work together with a strict enforcement. In addition, traffic signs near critical distance and reasonable speed limitation are also beneficial to the safety of intersections.

  12. 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)

  13. 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

  14. 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

  15. The luminous blue variable HR Carinae has a partner. Discovery of a companion with the VLTI

    Science.gov (United States)

    Boffin, Henri M. J.; Rivinius, Thomas; Mérand, Antoine; Mehner, Andrea; LeBouquin, Jean-Baptiste; Pourbaix, Dimitri; de Wit, Willem-Jan; Martayan, Christophe; Guieu, Sylvain

    2016-09-01

    Luminous blue variables (LBVs) are massive stars caught in a post-main sequence phase, during which they lose a significant amount of mass. Since, 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, η 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 fully constrain 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 also resolve 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 some background flux which remained at the 2% level until January 2016, but then increased to 6% in April 2016. Our AMBER results show that the emission line-forming region of Brγ is more extended than the continuum-emitting region as seen by PIONIER and may indicate some wind-wind interaction. Most importantly, we constrain the total masses of both components, with the most likely range being 33.6 M⊙ and 45 M⊙. Our results show that the LBV HR Car is possibly an η Car analog binary system with smaller masses, with variable components, and further monitoring of this object is definitively called for. Based on data obtained with ESO programmes 092.C-0243, 092.D-0289, 092.D-0296, 094.D-0069, and 596.D-0335.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study.

    Science.gov (United States)

    Zhu, Shun; Travis, Sue M; Elcock, Adrian H

    2013-07-01

    A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant

  3. 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。

  4. Bacteriophage lambda as a cloning vector.

    Science.gov (United States)

    Chauthaiwale, V M; Therwath, A; Deshpande, V V

    1992-12-01

    Extensive research has been directed toward the development of multipurpose lambda vectors for cloning ever since the potential of using coliphage lambda as a cloning vector was recognized in the late 1970s. An understanding of the intrinsic molecular organization and of the genetic events which determine lysis or lysogeny in lambda has allowed investigators to modify it to suit the specific requirements of gene manipulations. Unwanted restriction sites have been altered and arranged together into suitable polylinkers. The development of a highly efficient in vitro packaging system has permitted the introduction of chimeric molecules into hosts. Biological containment of recombinants has been achieved by introducing amber mutations into the lambda genome and by using specific amber suppressor hosts. Taking advantage of the limited range of genome size (78 to 105% of the wild-type size) for its efficient packaging, an array of vectors has been devised to accommodate inserts of a wide size range, the limit being 24 kbp in Charon 40. The central dispensable fragment of the lambda genome can be replaced by a fragment of heterologous DNA, leading to the construction of replacement vectors such as Charon and EMBL. Alternatively, small DNA fragments can be inserted without removing the dispensable region of the lambda genome, as in lambda gt10 and lambda gt11 vectors. In addition, the introduction of many other desirable properties, such as NotI and SfiI sites in polylinkers (e.g., lambda gt22), T7 and T3 promoters for the in vitro transcription (e.g., lambda DASH), and the mechanism for in vivo excision of the intact insert (e.g., lambda ZAP), has facilitated both cloning and subsequent analysis. In most cases, the recombinants can be differentiated from the parental phages by their altered phenotype. Libraries constructed in lambda vectors are screened easily with antibody or nucleic acid probes since several thousand clones can be plated on a single petri dish. Besides

  5. Las relaciones financieras entre España y Portugal, 1563-1580

    Directory of Open Access Journals (Sweden)

    Óscar LUCAS VILLANUEVA

    2009-12-01

    Full Text Available RESUMEN: Las economías de Castilla y Portugal durante la segunda mitad del siglo XVI estaban estrechamente ligadas por vínculos financieros. Un espacio económico en desarrollo, el del Atlántico septentrional, comprendía ambos territorios y se organizaba a partir de los grandes centros feriales de Amberes, Lyon y Medina. El gran tráfico mercantil transoceánico se hacía presente en este escenario europeo gracias a la intervención de España y Portugal, pero con papeles bien distintos: España, incontinente, drenando el oro y la plata americanos hacia Europa, Portugal suministrando las apreciadas mercancías orientales. Las ferias de Medina del Campo y los mercaderes castellanos como Simón Ruiz se convierten en colaboradores necesarios de los mercaderes portugueses, pues a través de éstos negociaban los reembolsos o inversiones financieras en las plazas europeas; sin embargo, para ello era preciso un buen conocimiento de los negocios cambiarlos y su oportunidad, atendiendo a la cotización de las distintas monedas y a demanda de dinero en las ferias europeas. De la mano del mercader medinense entran los lisboetas en las grandes finanzas y la concertación de asientos con la Corona, aunque tal vez sin la pujanza que Felipe II hubiese deseado.ABSTRACT: The correspondence studied shows the importance that had, for this period of time (1563-1580, the relationship between Castille and Portugal. The vigorous economic space of the Northern Atlantic, the space in which were inscribed both territories, was organised from the three great market centres of Amberes, Lyon and Medina del Campo. The big transoceanic commercial trade was present in this European scenery thanks to the supervision of Spain an Portugal, but playing a very different role: Spain, draining gold and silver to Europe; and Portugal, supplying the appreciated oriental goods. The fairs of Medina and the Castilian merchants, like Simon Ruiz, were converted in necessary

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Direct detection of the tertiary component in the massive multiple HD 150136 with VLTI

    Science.gov (United States)

    Sanchez-Bermudez, J.; Schödel, R.; Alberdi, A.; Barbá, R. H.; Hummel, C. A.; Maíz Apellániz, J.; Pott, J.-U.

    2013-06-01

    Context. Massive stars are of fundamental importance for almost all aspects of astrophysics, but there still exist large gaps in our understanding of their properties and formation because they are rare and therefore distant. It has been found that most O-stars are multiples. It may well be that almost all massive stars are born as triples or higher multiples, but their large distances require milliarcsecond angular resolution for a direct detection of the companions. Aims: HD 150136 is the nearest system to Earth with >100 M⊙ and provides a unique opportunity to study an extremely massive system. Recently, evidence for the existence of a third component in HD 150136, in addition to the tight spectroscopic binary that forms the main component, was found in spectroscopic observations. Our aim was to image and obtain astrometric and photometric measurements of this component using long-baseline optical interferometry to further constrain the nature of this component. Methods: We observed HD 150136 with the near-infrared instrument AMBER attached to the ESO VLT Interferometer, which provides an angular resolution of 2 mas. The recovered closure phases are robust to systematic errors and provide unique information on the source asymmetry. Therefore, they are of crucial relevance for both image reconstruction and model fitting of the source structure. Results: The third component in HD 150136 is clearly detected in the high-quality data from AMBER. It is located at a projected angular distance of 7.3 mas, or about 13 AU at the line-of-sight distance of HD 150136, at a position angle of 209 degrees east of north, and has a flux ratio of 0.25 with respect to the inner binary. Our findings agree with previous results and have permitted us to improve the orbital solutions of the tertiary around the inner system. Conclusions: We resolved the third component of HD 150136 in J, H and K filters. The luminosity and color of the tertiary agrees with the predictions and shows

  11. The inner circumstellar disk of the UX Orionis star V1026 Scorpii

    Science.gov (United States)

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

    2014-04-01

    Context. 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. Aims: 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. Methods: 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. Results: 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 disks. The inner disk has a temperature of 1257+133-53 K at the inner rim and extends from 0.19 ± 0.01 AU to 0.23 ± 0.02 AU. The outer disk begins at 1.35+0.19-0.20 AU and has an inner temperature of 334+35-17 K. The derived inclination of 48.6+2.9-3.6° approximately agrees with the inclination derived with the geometric model (49 ± 5° in the K band and 50 ± 11° in the H band). The position angle of the fitted geometric and temperature-gradient models are 163 ± 9° (K band; 179 ± 17° in the H band) and 169.3+4.2-6.7°, respectively. Conclusions: The narrow width of the inner ring-shaped model disk and the disk gap might be an indication for a puffed-up inner rim shadowing outer parts of the disk. The intermediate inclination of ~50° is consistent with models of UX Ori objects where dust clouds in the inclined disk obscure the central star. Based on observations made with ESO telescopes at the La Silla Paranal Observatory

  12. [GEOLOGICAL OVERVIEW OF THE VILNIUS REGION BY J. E. GILIBERT (1741-1814), THE FIRST PROFESSOR OF NATURAL HISTORY AT THE UNIVERSITY OF VILNIUS].

    Science.gov (United States)

    Tarkowski, Radosław

    2015-01-01

    In 1775-1783, Jean-Emmanuel Gilibert (1741-1814) stayed in Respublica Poloniae to oranize a veterinary school, the Royal Botanic Garden and the Royal School of Physicians in Grodno, and since 1781 he worked in Vilnius as Professor of Natural History at the Principal School of the Grand Duchy of Lithuania. Little is known about his work conducted in Lithuania in the field of geology and earth sciences. The author has decided, on the basis of Gilibert's publications and analysis of the literature (works of J. Garbowska and P. Daszkiewicz and others), to present his teaching and research activities in this field. In Grodno, Gilibert looked after and multiplied the collections of the natural history cabinet at the Royal School of Physicians, renowned for its rich mineralogical and fossil collections watched and admired by, among others, King Stanisław August, J. Bernoulli (1744-1807) and M. Patrin (1742-1815) who mentions the amber rosary with a different species of insects preserved in each bead. Gilibert's tours around Lithuania were the opportunity to enlarge the geological collections and to adapt them to the needs of the school. He also appreciated the importance of ordinary specimens representing the geology of the area. These specimens not only enriched the natural history cabinet, but also defined the way of working and collecting. Ha was the first to found and gather fossil animals from near Grodno. The signs of mineralogical and geological interests of Gilibert can be found in the works of other authors of that epoch (L. Viteta (1736-1809) and J. Bernoulli). In Vilnius, Gilibert conducted a one year-long full lecture on natural history (zoology, botany and mineralogy). In his lectures on mineralogy, he presented not only the systematics, but also emphasized the usefulness of minerals in medicine, for the production of ornamental items and in different sectors of the economy. He adapted the process of teaching to the needs of practical life, based on

  13. Post-processing the VLTI fringe-tracking data: First measurements of stars

    CERN Document Server

    Bouquin, Jean-Baptiste Le; Haguenauer, Pierre; Bauvir, Bertrand; Popovic, Daniel; Pozna, Ester

    2008-01-01

    At the Very Large Telescope Interferometer, the purpose of the fringe-tracker FINITO is to stabilize the optical path differences between the beams, allowing longer integration times on the scientific instruments AMBER and MIDI. Our goal is to demonstrate the potential of FINITO for providing H-band interferometric visibilities, simultaneously and in addition to its normal fringe-tracking role. We use data obtained during the commissioning of the Reflective Memory Network Recorder at the Paranal observatory. This device has permitted the first recording of all relevant real-time data needed for a proper data-reduction. We show that post-processing the FINITO data allows valuable scientific visibilities to be measured. Over the several hours of our engineering experiment, the intrinsic transfer function is stable at the level of 2%. Such stability would lead to robust measurements of science stars even without the observation of a calibration star within a short period of time. We briefly discuss the current l...

  14. Deep near-infrared interferometric search for low-mass companions around beta Pictoris

    CERN Document Server

    Absil, Olivier; Lebreton, Jeremy; Augereau, Jean-Charles; Benisty, Myriam; Chauvin, Gael; Hanot, Charles; Merand, Antoine; Montagnier, Guillaume

    2010-01-01

    Aims. We search for low-mass companions in the innermost region (<300 mas, i.e., 6 AU) of the beta Pic planetary system. Methods. We obtained interferometric closure phase measurements in the K-band with the VLTI/AMBER instrument used in its medium spectral resolution mode. Fringe stabilization was provided by the FINITO fringe tracker. Results. In a search region of between 2 and 60 mas in radius, our observations exclude at 3 sigma significance the presence of companions with K-band contrasts greater than 5e-3 for 90% of the possible positions in the search zone (i.e., 90% completeness). The median 1-sigma error bar in the contrast of potential companions within our search region is 1.2e-3. The best fit to our data set using a binary model is found for a faint companion located at about 14.4 mas from beta Pic, which has a contrast of 1.8e-3 \\pm 1.1e-3 (a result consistent with the absence of companions). For angular separations larger than 60 mas, both time smearing and field-of-view limitations reduce t...

  15. Effects of the interruption of the irradiation process on PMMA Harwell Industry Dosimetry Systems

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Paulo S.; Vasquez, Pablo A.S., E-mail: psantos@ipen.br, E-mail: pavsalva@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    Nowadays, the use of dyed-polymethylmethacrylate dosimetry systems in measurements at industrial irradiations has been broadly, despite the use of alanine dosimeters. Accurate dosimetry measurements are essential for the sterilization applications of medical products as well as the preservation of food by ionizing radiation. Regulations in many countries require in-plant dosimetry to ensure that the specified radiation dose has been delivered to the product. Harwell commercial dosimeters commonly are built to work with measurements between 1 kGy to 50 kGy, this means that a same dosimeter could be used until reach these values. Radiation processing demands partial measurements of the absorbed dose to guarantee the final desired applied absorbed dose depending to the dose rate. In this sense, the total absorbed dose corresponds to the cumulative partial values. In this study, several dosimeters were irradiated at the Multipurpose Gamma Irradiation Facility at IPEN - CNEN/SP to evaluate the response to the interruption of the irradiation process in the total cumulative absorbed dose values considering statistical changes and some processing parameters. When studied the Harwell dyed-polymethylmethacrylate dosimeters Red 4034 and Amber 3042, applying processing interruptions, results shown a coefficient of variation under 7% for industrial irradiation conditions to the total cumulative absorbed dose. (author)

  16. ACPYPE - AnteChamber PYthon Parser interfacE

    Directory of Open Access Journals (Sweden)

    Sousa da Silva Alan W

    2012-07-01

    Full Text Available Abstract Background ACPYPE (or AnteChamber PYthon Parser interfacE is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis and ARIA (for structure calculations from NMR data. ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. Findings We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. Conclusions ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

  17. QM/MM studies of cisplatin complexes with DNA dimer and octamer

    KAUST Repository

    Gkionis, Konstantinos

    2012-08-01

    Hybrid QM/MM calculations on adducts of cisplatin with DNA dimer and octamer are reported. Starting from the crystal structure of a cisplatin-DNA dimer complex and an NMR structure of a cisplatin-DNA octamer complex, several variants of the ONIOM approach are tested, all employing BHandH for the QM part and AMBER for MM. We demonstrate that a generic set of molecular mechanics parameters for description of Pt-coordination can be used within the subtractive ONIOM scheme without loss of accuracy, such that dedicated parameters for new platinum complexes may not be required. Comparison of optimised structures obtained with different strategies indicates that electrostatic embedding is vital for proper description of the complex, while inclusion of water molecules as explicit solvent further improves performance. The resulting DNA structural parameters are in good general agreement with the experimental structure obtained, particularly when the inherent variability in NMR-derived parameters is taken into account. © 2012 Elsevier B.V.

  18. Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: comparison with distance geometry calculations.

    Science.gov (United States)

    Beckers, M L; Buydens, L M; Pikkemaat, J A; Altona, C

    1997-01-01

    The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer present in a 10 basepair (bp) sense-antisense DNA duplex was studied with a genetic algorithm designed to interpret NOE distance restraints. Trial solutions were represented by torsion angles. This means that bond angles for the dimer trial structures are kept fixed during the genetic algorithm optimization. Bond angle values were extracted from a 10 bp sense-antisense duplex model that was subjected to energy minimization by means of a modified AMBER force field. A set of 63 proton-proton distance restraints defining the methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizes the difference between distances in the trial structures and distance restraints. A large conformational search space could be covered in the genetic algorithm optimization by allowing a wide range of torsion angles. The genetic algorithm optimization in all cases led to one family of structures. This family of the methylene-acetal-linked thymine dimer in the duplex differs from the family that was suggested from distance geometry calculations. It is demonstrated that the bond angle geometry around the methylene-acetal linkage plays an important role in the optimization. PMID:9081542

  19. Ámbar en la Meseta Oriental durante el Bronce Final: yacimientos locales e importaciones bálticas

    Directory of Open Access Journals (Sweden)

    Luisa Cerdeño, M.ª

    2012-12-01

    Full Text Available This paper shows the results of the analysis done with two amber beads coming of the cemetery of Herrería II (Molina de Aragón, Guadalajara; it is dated in Late Bronze Age, preceding the Celtiberian period. The Baltic origin of the raw material has been confirmed by the analysis and this origin provides the evidence that continental cultural influences arrived to the meseta during mentioned period.

    En el presente trabajo se dan a conocer los resultados de los análisis de espectroscopía infrarroja realizados a dos cuentas de ámbar procedentes de la fase II de la necrópolis de Herrería (Molina de Aragón, Guadalajara, fechada a finales del Bronce Final y precedente inmediato de la primera fase celtibérica de dicho cementerio. Los resultados confirman la procedencia báltica de esta materia prima. Ello la convierte en una nueva evidencia +de la llegada de elementos continentales hasta la Meseta oriental, donde dicho substrato cultural desempeñó un papel importante en la gestación de los posteriores pueblos prerromanos.

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

    CERN Document Server

    Wittkowski, M; 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 each spectral channel. In addition, the visibility data were directly compared to predictions by recent self-excited dynamic model atmospheres. Results: S Ori shows significant variations in the visibility values as a function of spectral channel that can only be described by a clear variation in the apparent angular size with wavelength. The closure phase values are close to zero at all spectral channels, indicating the absence of asymmetric intensity features. The apparent UD angular diameter is smallest at about 1.3 and ...

  1. Evaluation of non-volatile metabolites in beer stored at high temperature and utility as an accelerated method to predict flavour stability.

    Science.gov (United States)

    Heuberger, Adam L; Broeckling, Corey D; Sedin, Dana; Holbrook, Christian; Barr, Lindsay; Kirkpatrick, Kaylyn; Prenni, Jessica E

    2016-06-01

    Flavour stability is vital to the brewing industry as beer is often stored for an extended time under variable conditions. Developing an accelerated model to evaluate brewing techniques that affect flavour stability is an important area of research. Here, we performed metabolomics on non-volatile compounds in beer stored at 37 °C between 1 and 14 days for two beer types: an amber ale and an India pale ale. The experiment determined high temperature to influence non-volatile metabolites, including the purine 5-methylthioadenosine (5-MTA). In a second experiment, three brewing techniques were evaluated for improved flavour stability: use of antioxidant crowns, chelation of pro-oxidants, and varying plant content in hops. Sensory analysis determined the hop method was associated with improved flavour stability, and this was consistent with reduced 5-MTA at both regular and high temperature storage. Future studies are warranted to understand the influence of 5-MTA on flavour and aging within different beer types.

  2. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  3. Free Energy Landscape of GAGA and UUCG RNA Tetraloops

    CERN Document Server

    Bottaro, Sandro; Sponer, Jiri; Bussi, Giovanni

    2016-01-01

    We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber\\c{hi}OL3 force field. The estimated folding free energies are 30.2kJ/mol for UUCG and 7.5 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche+ region of {\\alpha} and {\\zeta} angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experim...

  4. What causes the large extensions of red-supergiant atmospheres? Comparisons of interferometric observations with 1-D hydrostatic, 3-D convection, and 1-D pulsating model atmospheres

    CERN Document Server

    Arroyo-Torres, B; Chiavassa, A; Scholz, M; Freytag, B; Marcaide, J M; Hauschildt, P H; Wood, P R; Abellan, F J

    2015-01-01

    We present the atmospheric structure and the fundamental parameters of three red supergiants, increasing the sample of RSGs observed by near-infrared spectro-interferometry. Additionally, we test possible mechanisms that may explain the large observed atmospheric extensions of RSGs. We carried out spectro-interferometric observations of 3 RSGs in the near-infrared K-band with the VLTI/AMBER instrument at medium spectral resolution. To comprehend the extended atmospheres, we compared our observational results to predictions by available hydrostatic PHOENIX, available 3-D convection, and new 1-D self-excited pulsation models of RSGs. Our near-infrared flux spectra are well reproduced by the PHOENIX model atmospheres. The continuum visibility values are consistent with a limb-darkened disk as predicted by the PHOENIX models, allowing us to determine the angular diameter and the fundamental parameters of our sources. Nonetheless, in the case of V602 Car and HD 95686, the PHOENIX model visibilities do not predict ...

  5. 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.

  6. Characterization of four-color multi-package white light-emitting diodes combined with various green monochromatic phosphor-converted light-emitting diodes

    Science.gov (United States)

    Oh, Ji Hye; Lee, Keyong Nam; Do, Young Rag

    2012-03-01

    In this study, several combinations of multi-package white light-emitting diodes (LEDs), which combine an InGaN blue LED with green, amber, and red phosphor-converted LEDs (pc-LEDs), were characterized by changing the peak wavelength of green pc-LEDs between 515nm and 560nm (515, 521, 530, 540, 550, 560nm) in color temperature of 6,500K and 3,500K. Various green monochromatic pc-LEDs were fabricated by capping a long-wave pass-filter (LWPF) on top of pc-LEDs to improve luminous efficacy and color purity. LWPF-capped green monochromatic pc-LED can address the drawback of green semiconductor-type III-V LED, such as low luminous efficacy in the region of green gap wavelength. Luminous efficacy and color rendering index (CRI) of multi-package white LEDs are compared with changing the driving current of individual LED in various multi-package white LEDs. This study provides a best combination of four-color multi-package white LEDs which has high luminous efficacy and good CRI.

  7. Color temperature tunable white-light light-emitting diode clusters with high color rendering index.

    Science.gov (United States)

    He, Guoxing; Zheng, Lihong

    2010-08-20

    A model for LED spectra at different drive currents is established. The simulation program of color rendering of a white-light LED cluster is developed according to the principle of additive color mixtures. The program can predict not only the spectral power distribution, chromaticity coordinates, correlated color temperature (CCT), and color rendering index (CRI), but also the drive currents of LEDs, luminous flux, input power, and luminous efficacy of white-light LED clusters. Three types of CCT tunable white-light LED clusters [warm-white/red/green/blue (WW/R/G/B), neutral-white (NW)/R/G/B, and cool-white/R/amber/G clusters] with high CRI are found by simulation analysis and realized in our laboratory. The experimental results show that the WW/R/G/B cluster can realize CCT tunable white light with high CRIs (above 90) but lower luminous efficacies (below 65 lm/W), and that the NW/R/G/B cluster can realize CCT tunable white light with high CRIs (above 86), as well as high luminous efficacies (above 64 lm/W). PMID:20733639

  8. Color temperature tunable white light LED system

    Science.gov (United States)

    Speier, Ingo; Salsbury, Marc

    2006-08-01

    Efficient white light LED systems with continuously tunable color temperature (CT) over a range of 3000 K to 6500 K are reviewed. Typically, white light sources have a fixed CT and color rendering index (CRI). White light with user-specified color temperatures is currently generated by solid-state systems with red green blue ("R/G/B"), red green blue amber ("R/G/B/A"), and warm white cool white ("WW/CW") LED combinations, but their performance is suboptimal for architectural lighting applications. We propose and discuss an LED module with a combination of warm white, green and blue ("WW/G/B") LEDs. In this scenario, the white LEDs have fixed intensity, while the blue and green LED intensities are adjusted to shift the LED module chromaticity along the blackbody locus. We also propose and discuss an LED module with a combination of red, green, blue, and cool white ("R/G/B/CW") LEDs. The white LEDs still have a fixed intensity, while the intensities of the red, green, and blue LEDs are again adjusted to shift the LED module chromaticity along the blackbody locus. The white LEDs ensure that an improved CRI is maintained in comparison to a simple "R/G/B" solution.

  9. Raman spectroscopic study on archaeological glasses in Thailand: Ancient Thai Glass

    Science.gov (United States)

    Won-in, K.; Thongkam, Y.; Pongkrapan, S.; Intarasiri, S.; Thongleurm, C.; Kamwanna, T.; Leelawathanasuk, T.; Dararutana, P.

    2011-12-01

    Glasses have been used as ornamental and decorative objects in Thailand for several hundred years as seen in archaeological artifacts, such as glass beads found throughout the regions. Decorative glasses can generally be seen as architectural components in Buddhist temples and old-styled palaces. They came in various colors ranging from transparent to amber, blue, green and red of different shades and tones. Fragments of archaeological glass samples were characterized for the first time using Raman spectrophotometer with the aim of obtaining information that would lead to the identification of the glass samples by means of laser scattering. The samples were also investigated using other techniques, such as proton induced X-ray emission spectroscopy, scanning electron microscopy cooperated with energy dispersive X-ray fluorescence spectrometer and synchrotron radiation to induced X-ray fluorescence. The results showed that they were mostly lead-silica based glasses whose colors were induced by metal ions. The differences in chemical compositions were confirmed by Raman signature spectra.

  10. The interaction of single walled carbon nanotube (SWCNT with phospholipids membrane: in point view of solvent effect

    Directory of Open Access Journals (Sweden)

    Akbar Elsagh

    2015-03-01

    Full Text Available In this research, we have studied the structural properties of phospholipids, surrounding single-walled carbon nanotube (SWCNT, by using ab-inition and molecular dynamics simulation. Carbon nanotubes (SWCNTs are very common in medical research and are being highly studied in the fields of biosensing methods for disease treatment and efficient drug delivery and health monitoring. The transportation of SWCNT through the cell membrane widely investigated because of many advantages. Because of the differences among force fields, the energy of a molecule calculated using two different force fields will not be the same. In this study difference in force field illustrated by comparing the energy of calculated by using force fields, MM+, Amber and OPLS. The quantum Mechanics (QM calculations were carried out with the GAUSSIAN 09 program based on density functional theory (DFT at B1LYP/6-31G* level. In our recent study the electronic structure of open-end of SWCNT and transportation of SWCNT through the phospholipids in skin cell membrane have been discussed for both vacuum and solvent media.

  11. Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

    Science.gov (United States)

    Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

    2016-08-23

    Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. PMID:27558719

  12. Complete nucleotide sequence of rose yellow leaf virus, a new member of the family Tombusviridae.

    Science.gov (United States)

    Mollov, Dimitre; Lockhart, Ben; Zlesak, David C

    2014-10-01

    The genome of the rose yellow leaf virus (RYLV) has been determined to be 3918 nucleotides long and to contain seven open reading frames (ORFs). ORF1 encodes a 27-kDa peptide (p27). ORF2 shares a common start codon with ORF1 and continues through the amber stop codon of p27 to encode an 87-kDa (p87) protein that has amino acid similarity to the RNA-dependent RNA polymerase (RdRp) of members of the family Tombusviridae. ORFs 3 and 4 have no significant amino acid similarity to known functional viral ORFs. ORF5 encodes a 6-kDa (p6) protein that has similarity to movement proteins of members of the Tombusviridae. ORF5A has no conventional start codon and overlaps with p6. A putative +1 frameshift mechanism allows p6 translation to continue through the stop codon and results in a 12-kDa protein that has high homology to the carmovirus p13 movement protein. The 37-kDa protein encoded by ORF6 has amino acid sequence similarity to coat proteins (CP) of members of the Tombusviridae. ORF7 has no significant amino acid similarity to known viral ORFs. Phylogenetic analysis of the RdRp amino acid sequences grouped RYLV together with the unclassified Rosa rugosa leaf distortion virus (RrLDV), pelargonium line pattern virus (PLPV), and pelargonium chlorotic ring pattern virus (PCRPV) in a distinct subgroup of the family Tombusviridae. PMID:24838852

  13. The gp41659 - 671 HIV-1 antibody epitope: a structurally challenging small peptide

    Science.gov (United States)

    Zhang, Yuan; Sagui, Celeste

    2014-03-01

    We present the results of extensive Molecular Dynamics (MD) simulations of the tridecapeptide corresponding to residues 659-671 of the envelope glycoprotein gp41 of HIV-1, which spans the 2F5 monoclonal antibody epitope ELDKWA. The most recent AMBER force fields ff99SB and ff12SB in both implicit and explicit solvents have been used for a cumulative time longer than 7.2 μs . We have analyzed the conformational ensembles of the peptide both with and without applied tensile restraints, and found that: (1) The amount of helical populations is important in aqueous solution, but this structure forms part of a flexible conformational ensemble with a rugged free energy landscape with shallow minima, which agrees well with the bulk of the experimental observations; (2) our results are more consistent with the experimental results than those from previous simulations; (3) under uniaxial tension, the disordered peptide first becomes fully helical before melting into turns, loops and 310-helices.

  14. 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".

  15. DNA repair and mutagenesis of singlestranded bacteriophages

    Energy Technology Data Exchange (ETDEWEB)

    Doubleday, O.P.; Brandenburger, A.; Wagner, R. Jr.; Radman, M. (Brussels Univ. (Belgium)); Godson, G.N.

    1981-01-01

    Virtually all radiation-induced mutagenesis is believed to result from an error-prone repair activity (SOS repair) and to involve mutations occurring both at the site of radiation-induced lesions (targeted mutations) and in undamaged DNA (untargeted mutations). To examine the relative contributions of targeted and untargeted mutations to ..gamma.. and ultraviolet (UV) radiation mutagenesis we have determined the DNA sequences of 174 M13 revertant phages isolated from stocks of irradiated or unirradiated amber mutants grown in irradiated or unirradiated host bacteria. We have detected no obvious specificity of mutagenesis and find no evidence of a predominance of targeted mutations associated with either UV- or ..gamma..-irradiation of the phages or with the induction of the host SOS repair system. In particular, pyrimidine dimers do not appear to be the principal sites of UV-induced bare substitution mutagenesis, suggesting that such UV-induced mutagenesis may be untargeted or occur at sites of lesions other than pyrimidine dimers.

  16. 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

  17. 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

  18. 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.

  19. Environmental transformations and cultural changes: A multidisciplinary case study for the Late Glacial and Final Palaeolithic from Northern Germany

    Science.gov (United States)

    Turner, F.; Tolksdorf, J. F.; Viehberg, F.; Schwarz, A.; von Bramann, U.; Bittmann, F.; Kaiser, K.; Schwalb, A.; Staesche, U.; Breest, K.; Pott, R.; Veil, S.

    2012-04-01

    In contrast to younger periods, studies integrating archaeological and environmental records for the Palaeolithic are still rare. Especially our knowledge about interactions between the drastic climatic/environmental changes and cultural developments during the Late Glacial is very limited. This multidisciplinary case study from river Jeetzel, a western Elbe tributary in Northern Germany, combines high resolution palaeoenvironmental investigations with fine-scaled archaeological research on stratified and surface sites. Various dating methods (palynostratigraphy, radiocarbon- and OSL-dating) and analyses of environmental and climatological proxies (pollen and plant macro-remains, ostracods, diatoms and green algae) on river palaeochannel sediments allow detailed reconstruction of interactions between Late Glacial climate, vegetation and fluvial developments. Biostratigraphical analyses on stratified archaeological sites and dating of charcoal / bone fragments from artefact scatters place the Late Palaeolithic occupation of Early Federmesser groups in an environmental context. Thus the former production of hitherto unknown amber art (amongst others a figurine representing a moose) can be ascribed to the Older Dryas and Early Allerød, which are the periods of main Late Glacial afforestation. Therewith our investigations suggest that Final Palaeolithic cultural changes may have been triggered by climatic and environmental transformations.

  20. 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.

  1. Preliminary investigation of the elemental variation and diagenesis of a tabular uranium deposit, La Sal Mine, San Juan County, Utah

    Science.gov (United States)

    Brooks, Robert A.; Campbell, John A.

    1976-01-01

    Ore in the La Sal mine, San Juan County, Utah, occurs as a typical tabular-type uranium deposit of the-Colorado Plateau. Uranium-vanadium occurs in the Salt Wash Member of the Jurassic Morrison Formation. Chemical and petrographic analyses were used to determine elemental variation and diagenetic aspects across the orebody. Vanadium is concentrated in the dark clay matrix, which constitutes visible ore. Uranium content is greater above the vanadium zone. Calcium, carbonate carbon, and lead show greater than fifty-fold increase across the ore zone, whereas copper and organic carbon show only a several-fold increase. Large molybdenum concentrations are present in and above the tabular layer, and large selenium concentrations occur below the uranium zone within the richest vanadium zone. Iron is enriched in the vanadium horizon. Chromium is depleted from above the ore and strongly enriched below. Elements that vary directly with the vanadium content include magnesium, iron, selenium, zirconium, strontium, titanium, lead, boron, yttrium, and scandium. The diagenetic sequence is as follows: (1) formation of secondary quartz overgrowths as cement; (2) infilling and lining of remaining pores with amber opaline material; (3) formation of vanadium-rich clay matrix, which has replaced overgrowths as well as quartz grains; (4) replacement of overgrowths and detrital grains by calcite; (5) infilling of pores with barite and the introduction of pyrite and marcasite.

  2. 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...

  3. 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.

  4. 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

  5. Non-small-cell lung cancer: molecular targeted therapy and personalized medicine – drug resistance, mechanisms, and strategies

    Directory of Open Access Journals (Sweden)

    Sechler M

    2013-04-01

    Full Text Available Marybeth Sechler,1,2 Amber D Cizmic,3 Sreedevi Avasarala,1 Michelle Van Scoyk,1 Christine Brzezinski,1 Nicole Kelley,1 Rama Kamesh Bikkavilli,1 Robert A Winn1–3 1Division of Pulmonary Sciences and Critical Care, 2Program in Cancer Biology, University of Colorado, Aurora, CO, USA; 3Veterans Affairs Medical Center, Denver, CO, USA Abstract: Targeted therapies for cancer bring the hope of specific treatment, providing high efficacy and in some cases lower toxicity than conventional treatment. Although targeted therapeutics have helped immensely in the treatment of several cancers, like chronic myelogenous leukemia, colon cancer, and breast cancer, the benefit of these agents in the treatment of lung cancer remains limited, in part due to the development of drug resistance. In this review, we discuss the mechanisms of drug resistance and the current strategies used to treat lung cancer. A better understanding of these drug-resistance mechanisms could potentially benefit from the development of a more robust personalized medicine approach for the treatment of lung cancer. Keywords: lung cancer, drug targets, personalized medicine, NSCLC

  6. Topical Review: Development of overgrown semi-polar GaN for high efficiency green/yellow emission

    Science.gov (United States)

    Wang, T.

    2016-09-01

    The most successful example of large lattice-mismatched epitaxial growth of semiconductors is the growth of III-nitrides on sapphire, leading to the award of the Nobel Prize in 2014 and great success in developing InGaN-based blue emitters. However, the majority of achievements in the field of III-nitride optoelectronics are mainly limited to polar GaN grown on c-plane (0001) sapphire. This polar orientation poses a number of fundamental issues, such as reduced quantum efficiency, efficiency droop, green and yellow gap in wavelength coverage, etc. To date, it is still a great challenge to develop longer wavelength devices such as green and yellow emitters. One clear way forward would be to grow III-nitride device structures along a semi-/non-polar direction, in particular, a semi-polar orientation, which potentially leads to both enhanced indium incorporation into GaN and reduced quantum confined Stark effects. This review presents recent progress on developing semi-polar GaN overgrowth technologies on sapphire or Si substrates, the two kinds of major substrates which are cost-effective and thus industry-compatible, and also demonstrates the latest achievements on electrically injected InGaN emitters with long emission wavelengths up to and including amber on overgrown semi-polar GaN. Finally, this review presents a summary and outlook on further developments for semi-polar GaN based optoelectronics.

  7. 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.

  8. Time dependence of immersion freezing: an experimental study on size selected kaolinite particles

    Directory of Open Access Journals (Sweden)

    A. Welti

    2012-10-01

    Full Text Available The time dependence of immersion freezing was studied for temperatures between 236 K and 243 K. Droplets with single immersed, size-selected 400 nm and 800 nm kaolinite particles were produced at 300 K, cooled down to supercooled temperatures, and the fraction of frozen droplets with increasing residence time was detected. To simulate the conditions of immersion freezing in mixed-phase clouds we used the Zurich Ice Nucleation Chamber (ZINC and its vertical extension, the Immersion Mode Cooling chAmber (IMCA. We observed that the frozen fraction of droplets increased with increasing residence time in the chamber. This suggests that there is a time dependence of immersion freezing and supports the importance of a stochastic component in the ice nucleation process. The rate at which droplets freeze was observed to decrease towards higher temperatures and smaller particle sizes. Comparison of the laboratory data with four different ice nucleation models, three based on classical nucleation theory with different representations of the particle surface properties and one singular, suggest that the classical, stochastic approach combined with a distribution of contact angles is able to reproduce the ice nucleation observed in these experiments most accurately. Using the models to calculate the increase in frozen fraction at typical mixed-phase cloud temperatures over an extended period of time, yields an equivalent effect of −1 K temperature shift for an increase in times scale by one order of magnitude. This suggests that temperature is more important than time.

  9. Time dependence of immersion freezing

    Directory of Open Access Journals (Sweden)

    A. Welti

    2012-05-01

    Full Text Available The time dependence of immersion freezing was studied for temperatures between 236 K and 243 K. Droplets with single immersed, size-selected 400 nm and 800 nm kaolinite particles were produced at 300 K, cooled down to supercooled temperatures typical for mixed-phase cloud conditions, and the fraction of frozen droplets with increasing residence time was detected. To simulate the conditions of immersion freezing in mixed-phase clouds we used the Zurich Ice Nucleation Chamber (ZINC and its vertical extension, the Immersion Mode Cooling chAmber (IMCA. We observed that the frozen fraction of droplets increased with increasing residence time in the chamber. This suggests that there is a time dependence of immersion freezing and supports the importance of a stochastic component in the ice nucleation process. The rate at which droplets freeze was observed to decrease towards higher temperatures and smaller particle sizes. Comparison of the laboratory data with four different ice nucleation models, three based on classical nucleation theory with different representations of the particle surface properties and one singular, suggest that the classical, stochastic approach combined with a distribution of contact angles is able to reproduce the ice nucleation observed in these experiments most accurately. Using the models to calculate the increase in frozen fraction at typical mixed-phase cloud temperatures over an extended period of time, yields an equivalent effect of −1 K temperature shift and an increase in time scale by a factor of ~10.

  10. A Bronze Age Pre-Historic Dolmen: Laser Cleaning Techniques of Paintings and Graffiti (The Bisceglie Dolmen Case Study)

    Science.gov (United States)

    Daurelio, G.

    The whole building was included and covered by an elliptical plan tumulus as reported for other similar monuments situated in the same territory of BISCEGLIE and GIOVINAZZO (in South of Italy). The monument was built by a community established in that area to mark their territory. It has a typical funerary character (funeral urn) and it was destined to the collective sepulture in the Middle Bronze Age, as indicated by the ceramic finds, accompanying the rich dead men, copper objects and ornaments, bones and amber recovered inside together with human rests. Degradation Mapping and Laser Cleaning with Photographs, during and after the process in-situ were carried out. Black incrustations and writings (by some different felt pens, marking pens, permanent black and colored ink pigments — fluorescent and no, as well as permanent text liner markings and spayed black paint) were cleaned by using a portable Nd:YAG Laser (λ 1.06 μm — 0.53 μm, in N-Mode and Q-Switch Mode, Laser pulse duration 150 μs or 6ns — f 1 to 10Hz — E max. 500 mJ per pulse in 1st harmonic and 200 mJ per pulse in 2nd harmonic). So, according to the different ink types three different laser cleaning techniques were used.

  11. 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...

  12. Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides.

    Science.gov (United States)

    Grubišić, Sonja; Chandramouli, Balasubramanian; Barone, Vincenzo; Brancato, Giuseppe

    2016-07-27

    Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides. PMID:27402118

  13. 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.

  14. Observatories of Sawai Jai Singh II

    Science.gov (United States)

    Johnson-Roehr, Susan N.

    Sawai Jai Singh II, Maharaja of Amber and Jaipur, constructed five observatories in the second quarter of the eighteenth century in the north Indian cities of Shahjahanabad (Delhi), Jaipur, Ujjain, Mathura, and Varanasi. Believing the accuracy of his naked-eye observations would improve with larger, more stable instruments, Jai Singh reengineered common brass instruments using stone construction methods. His applied ingenuity led to the invention of several outsize masonry instruments, the majority of which were used to determine the coordinates of celestial objects with reference to the local horizon. During Jai Singh's lifetime, the observatories were used to make observations in order to update existing ephemerides such as the Zīj-i Ulugh Begī. Jai Singh established communications with European astronomers through a number of Jesuits living and working in India. In addition to dispatching ambassadorial parties to Portugal, he invited French and Bavarian Jesuits to visit and make use of the observatories in Shahjahanabad and Jaipur. The observatories were abandoned after Jai Singh's death in 1743 CE. The Mathura observatory was disassembled completely before 1857. The instruments at the remaining observatories were restored extensively during the nineteenth and twentieth centuries.

  15. An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media

    Energy Technology Data Exchange (ETDEWEB)

    Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR field. Here, we describe a novel protocol for incorporating unnatural amino acids into fully deuterated proteins using glucose-based media (which are relevant to the production, for example, of amino acid-specific methyl-labeled proteins used in the study of large molecular weight systems). The method consists of pre-induction of the pEVOL plasmid encoding the tRNA/aminoacyl-tRNA synthetase pair in a rich, H{sub 2}O-based medium prior to exchanging the culture into a D{sub 2}O-based medium. Our protocol results in high level of isotopic incorporation ({approx}95%) and retains the high expression level of the target protein observed in Luria-Bertani medium.

  16. Origin of origami cockroach reveals long-lasting (11 Ma) phenotype instability following viviparity

    Science.gov (United States)

    Vršanský, Peter V.; Šmídová, Lucia; Valaška, Daniel; Barna, Peter; Vidlička, Ľubomír; Takáč, Peter; Pavlik, Lubomir; Kúdelová, Tatiana; Karim, Talia S.; Zelagin, David; Smith, Dena

    2016-10-01

    Viviparity evolved in bacteria, plants, ˃141 vertebrate lineages (ichthyosaurs, lizards, fishes, mammals, and others), and in 11 of 44 insect orders. Live-birth cockroaches preserved with brood sac (3D recovered two times optically) included Diploptera vladimir, Diploptera savba, Diploptera gemini spp.n., D. sp.1-2, and Stegoblatta irmgardgroehni from Green River, Colorado; Quilchena, Republic; McAbee, Canada; and Baltic amber, Russia (49, 54, and 45 Ma). They evolved from rare and newly evolved Blaberidae; they radiated circumtropically, later expanded into SE Asia, and have now spread to Hawaii and the SE USA. Association of autapomorphic characters that allow for passive and active protections from parasitic insects (unique wing origami pleating identical with its egg case-attacking wasp) suggest a response to high parasitic loads. Synchronized with global reorganization of the biota, morphotype destabilization in roaches lasted approximately 11-22 Ma, including both the adaptation of novel characters and the reduction of others. Thus, while viviparity can be disadvantageous, in association with new Bauplans and/or behaviors, it can contribute to the evolution of taxa with viviparous representatives that are slightly selectively preferred.

  17. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  18. Phenotypic variation in dentinogenesis imperfecta/dentin dysplasia linked to 4q21.

    Science.gov (United States)

    Beattie, M L; Kim, J-W; Gong, S-G; Murdoch-Kinch, C A; Simmer, J P; Hu, J C-C

    2006-04-01

    Dentinogenesis imperfecta (DGI) and dentin dysplasia (DD) are allelic disorders that primarily affect the formation of tooth dentin. Both conditions are autosomal-dominant and can be caused by mutations in the dentin sialophosphoprotein gene (DSPP, 4q21.3). We recruited 23 members of a four-generation kindred, including ten persons with dentin defects, and tested the hypothesis that these defects are linked to DSPP. The primary dentition showed amber discoloration, pulp obliteration, and severe attrition. The secondary dentition showed either pulp obliteration with bulbous crowns and gray discoloration or thistle-tube pulp configurations, normal crowns, and mild gray discoloration. Haplotype analyses showed no recombination between three 4q21-q24 markers and the disease locus. Mutational analyses identified no coding or intron junction sequence variations associated with affection status in DMP1, MEPE, or the DSP portion of DSPP. The defects in the permanent dentition were typically mild and consistent with a diagnosis of DD-II, but some dental features associated with DGI-II were also present. We conclude that DD-II and DGI-II are milder and more severe forms, respectively, of the same disease.

  19. Manifestasi Klinis, Aspek Genetica Molekuler dan Management Dentinogenesis Imperfekta

    Directory of Open Access Journals (Sweden)

    Olivia Bratanata

    2015-10-01

    Full Text Available Dentinogenesis imperfecta (DGI is an autosomal dominant disorder in which both the primary and the permanent teeth are affected. It occurs with an incidence of 1:8.000 live births. In DGI, the teeth are amber and opalescent, and the pulp chamber is obliterated by abnormal dentin. The enamel, although otherwise unaffected, tends to fracture, which leads to rapid attrition of dentin and marked shortening of the teeth. There are three types of DGI with similar dental abnormalities. Type I occurs in people with osteogenesis imperfecta, a genetic condition in which bones are brittle and easily broken. DGI types II and III occur in people without other ingerited disorders than mutations mapped to the 6.6-cM D4S2691-D4S2696 interval at $q21, which is the locus for the dentin sialophosphoprotein (DSPP gene. It is now believed that the DGI types II and III may be the same disorder. This paper reviews clinical manifestation, aspects of molecular genetics, and management of DGI.

  20. Dentin phosphoprotein compound mutation in dentin sialophosphoprotein causes dentinogenesis imperfecta type III.

    Science.gov (United States)

    Dong, Juan; Gu, TingTing; Jeffords, Leticia; MacDougall, Mary

    2005-01-30

    A rare compound mutation involving a 36 bp deletion and 18 bp insertion within exon 5 of the dentin sialophosphoprotein (DSPP) gene has been identified in a family with dentinogenesis imperfecta type III (DGI-III). The DSPP gene encodes two major tooth matrix proteins dentin sialoprotein (DSP) and dentin phosphoprotein (DPP). DSPP mutations associated with DGI-III results in an in frame truncation of the serine aspartic acid triplet repeat found in DPP near the highly conserved carboxyl terminal region shortening the protein by six amino acids. Clinically this family presents with discolored amber opalescent teeth and severe attrition of the tooth structure. This study is the first report of a mutation within DPP associated with a genetic dentin disease. Our study indicates that DGI-III is allelic with some forms of DGI-II with and without progressive hearing loss and dentin dysplasia type II that have been shown to be caused by mutations within the DSP coding or signal peptide regions.

  1. 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.

  2. 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

  3. 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.

  4. Carbamato de etila em bebidas alcoólicas (cachaça, tiquira, uísque e grapa

    Directory of Open Access Journals (Sweden)

    Andrade-Sobrinho Luiz Gualberto de

    2002-01-01

    Full Text Available The presence of ethyl carbamate in cachaças, tiquiras, whiskies and grapes was investigated by GC-MS, monitoring the m/z 62 ion. The external standard method was used for quantitation in 188 samples (126 cachaças, 37 tiquiras, 6 grappas and 19 whiskies. The results of the study for cachaça were analysed considering the geographic origin, distillation type (still or column, bottle coloration (amber or transparent and ageing. The average contents of ethyl carbamate in cachaças and tiquiras were 0.77 and 2.4 mg L-1, respectively. These values were higher than the mean concentration found in grapes (0.045 mg L-1 and whiskies (0.14 mg L-1. On average the cachaças distilled in column tend to present higher values of ethyl carbamate than those from still. In the sampling studied it was not possible to define a correlation between content of ethyl carbamate, bottle coloration and ageing time.

  5. Computer-aided identification of potential TYK2 inhibitors from drug database

    Science.gov (United States)

    Zhang, Wei; Li, Jianzong; Huang, Zhixin; Wang, Haiyang; Luo, Hao; Wang, Xin; Zhou, Nan; Wu, Chuanfang; Bao, Jinku

    2016-10-01

    TYK2 is a member of JAKs family protein tyrosine kinase activated in response to various cytokines. It plays a crucial role in transducing signals downstream of various cytokine receptors, which are involved in proinflammatory responses associated with immunological diseases. Thus, the study of selective TYK2 inhibitors is one of the most popular fields in anti-inflammation drug development. Herein, we adopted molecular docking, molecular dynamics simulation and MM-PBSA binding free energy calculation to screen potential TYK2-selective inhibitors from ZINC Drug Database. Finally, three small molecule drugs ZINC12503271 (Gemifloxacin), ZINC05844792 (Nebivolol) and ZINC00537805 (Glyburide) were selected as potential TYK2-selective inhibitors. Compared to known inhibitor 2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide, these three candidates had better Grid score and Amber score from molecular docking and preferable results from binding free energy calculation as well. What's more, the ATP-binding site and A-loop motif had been identified to play key roles in TYK2-targeted inhibitor discovery. It is expected that our study will pave the way for the design of potent TYK2 inhibitors of new drugs to treat a wide variety of immunological diseases such as inflammatory diseases, multiple sclerosis, psoriasis inflammatory bowel disease (IBD) and so on.

  6. Variation and correlation of properties in different grades of maple syrup.

    Science.gov (United States)

    Singh, Amritpal S; Jones, A Maxwell P; Saxena, Praveen K

    2014-03-01

    Thirty five commercial maple syrups from twelve producers in Southern Ontario were evaluated for properties including light transmittance, autofluorescence, density, pH, total soluble solids (TSS), glucose and fructose content, total phenol content, antioxidant potential and mineral content (Mg, Mn, P, Zn, Ca, K, Fe and Pb). A high degree of variability was found in many characteristics, often exceeding an order of magnitude. Syrups were categorized based on light transmission at 560 nm into amber (12), dark (13) and very dark (10) using International Maple Syrup Institute (IMSI) guidelines. No statistical differences were found among grades of syrup for density, pH, TSS, glucose, fructose, total reducing sugars, glucose:fructose ratio, magnesium, manganese or potassium. Darker syrups showed significantly higher autofluorescence, total phenol content, antioxidant potential, phosphorous, calcium and total mineral content. Significant negative correlations of percent transmission with total phenol content, antioxidant potential and total mineral content are reported. Significant positive correlations among total phenol content, antioxidant potential and total mineral content are also described. The results from this study suggest that darker syrups tend to contain more beneficial traits and may be applied in developing functional foods and value added products.

  7. Pathogenicity Of Mycogone Perniciosa Isolates Collected On Polish Mushroom Farms

    Directory of Open Access Journals (Sweden)

    Szumigaj-Tarnowska Joanna

    2015-06-01

    Full Text Available Mycogone perniciosa is the fungal pathogen causing the wet bubble of white button mushrooms (Agaricus bisporus. The main symptoms of disease are undifferentiated, irregular forms of mushroom tissue, cap spotting and development of amber liquid droplets on the distorted mushrooms. The aim of the research was to assess the pathogenicity of M. perniciosa isolates that were obtained from the infected sporophores. Six isolates from Polish mushroom farms as well reference strain of Hypomyces perniciosus CBS 322.52 were used in this study. The pathogenicity of isolates was assessed on the basis of severity of disease symptoms and crop reduction in the first flush. Mushroom crop was infected with different suspensions containing of M. perniciosa aleuriospores. Significant variability was shown between tested isolates. It was stated that the pathogenicity of isolates and concentration of conidia had a significant influence on the mushroom yield. The isolate of high pathogenicity caused significant yield losses, after inoculation with 1.3 × 104·m−2, whereas the isolate with fairly pathogenicity did not produce symptoms of wet bubble disease or caused slight deformation of single sporophores, even when the casing soil was inoculated with 1.3 × 106·m−2 spores.

  8. 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...

  9. 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...

  10. Partial hessian fitting for determining force constant parameters in molecular mechanics.

    Science.gov (United States)

    Wang, Ruixing; Ozhgibesov, Mikhail; Hirao, Hajime

    2016-10-01

    We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond-stretching, angle-bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least-squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER-type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM-calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal-organic frameworks, the MM-optimized geometry sometimes deviates significantly from the QM-optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond-stretching and angle-bending terms. © 2016 Wiley Periodicals, Inc.

  11. GPU-enabled molecular dynamics simulations of ankyrin kinase complex

    Science.gov (United States)

    Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

    2014-10-01

    The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

  12. Pre-main-sequence binaries with tidally disrupted discs: the Br gamma in HD 104237

    CERN Document Server

    Garcia, P J V; Dougados, C; Bacciotti, F; Clausse, J -M; Massi, F; Mérand, A; Petrov, R; Weigelt, G

    2013-01-01

    Active pre-main-sequence binaries with separations of around ten stellar radii present a wealth of phenomena unobserved in common systems. The study of these objects is extended from Classical T Tauri stars to the Herbig Ae star HD 104237. Spectro-interferometry with the VLTI/AMBER is presented. It is found that the K-band continuum squared visibilities are compatible with a circumbinary disc with a radius of ~0.5 AU. However, a significant fraction (~50 per cent) of the flux is unresolved and not fully accounted by the stellar photospheres. The stars probably don't hold circumstellar discs, in addition to the circumbinary disk, due to the combined effects of inner magnetospheric truncation and outer tidal truncation. This unresolved flux likely arises in compact structures inside the tidally disrupted circumbinary disc. Most ($\\gtrsim 90$ per cent) of the Br gamma line emission is unresolved. The line-to-continuum spectro-astrometry shifts in time, along the direction of the Ly alpha jet known to be driven b...

  13. Un San Jerónimo penitente del Maestro del Papagayo en colección privada madrileña

    Directory of Open Access Journals (Sweden)

    Sanzsalazar, Jahel

    2005-12-01

    Full Text Available El Maestro del Papagayo es pintor vinculado por su estilo y personalidad a la escuela de Brujas. Fue dado a conocer por Friedlander, quien lo denominó así por el pájaro exótico que sostiene Jesús en algunas tablas con la Virgen y el Niño. Como numerosos pintores de Brujas de principios del siglo xvi, debió partir a Amberes, llamado por su floreciente comercio, dedicando buena parte de su producción a la exportación, a juzgar por las pinturas de su mano localizadas en España. Un retrato fechado en 1524 permite situarlo cronológicamente pero se desconoce cualquier dato sobre su biografía. La tabla con San Jerónimo penitente que damos hoy a conocer [48.7 x 38.1 cm; Fig. 1] fue adquirida en el coleccionismo madrileño con atribución al Maestro de las Medias Figuras, con quien comparte modelos y fuentes de inspiración.

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

    Directory of Open Access Journals (Sweden)

    Shaileyee Das

    2013-11-01

    Full Text Available 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 liquid, ultrasonic time, methanol concentration and extraction times on extraction yield of total flavonoids are evaluated. Then, optimization of total flavonoid compound (TFC extraction from Trigonella foenum-graecum seed is investigated using response surface methodology (RSM in this paper. Statistical analysis of the experiments indicated that Ratio of material to liquid and methanol concentration significantly affected TFC extraction (p < 0.01. The Box-Behnken experiment design shows that polynomial regression models are in good agreement with the experimental results, with the coefficients of multiple determination of 0.9758 for TFC yield. The optimal conditions for maximum TFC yield are 70% methanol, 50min and 30 (v/w liquid to solid ratios with a 2 time extraction time. Extracts from these conditions showed a moderate antioxidant value from 1,1-diphenyl-2-picrylhydrazyl (DPPH assay, Ferric chloride reducing assay and hydrogen peroxide reducing assay. Fenugreek flavonoids have direct and potent antioxidant activities, might be developed and utilized as natural antioxidant.

  15. Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy.

    Science.gov (United States)

    Panieri, G; Lugli, S; Manzi, V; Roveri, M; Schreiber, B C; Palinska, K A

    2010-03-01

    Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep-sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north-eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910-5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo-reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean. PMID:20059556

  16. Identification of the date-rape drug GHB and its precursor GBL by Raman spectroscopy.

    Science.gov (United States)

    Brewster, Victoria L; Edwards, Howell G M; Hargreaves, Michael D; Munshi, Tasnim

    2009-01-01

    Gamma hydroxybutyric acid (GHB), also known as 'liquid ecstasy', has recently become associated with drug-facilitated sexual assaults, known colloquially as 'date rape', due to the ability of the drug to cause loss of consciousness. The drug is commonly found 'spiked' into alcoholic beverages, as alcohol increases its sedative effects. Gamma hydroxybutyric acid and the corresponding lactone gamma-butyrolactone (GBL) will reach an equilibrium in solution which favours the lactone in basic conditions and GHB in acidic conditions (less than pH 4). Therefore, we have studied both GHB and GBL, as a mildly acidic beverage 'spiked' with GHB will contain both GHB and GBL. We report the analysis of GHB as a sodium salt and GBL, its precursor, using bench-top and portable Raman spectroscopy. It has been demonstrated that we are able to detect GHB and GBL in a variety of containers including colourless and amber glass vials, plastic vials and polythene bags. We have also demonstrated the ability to detect both GBL and GHB in a range of liquid matrices simulating 'spiked' beverages.

  17. 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...

  18. Inner disk clearing around the Herbig Ae star HD\\,139614: Evidence for a planet-induced gap ?

    CERN Document Server

    Matter, A; Augereau, J -C; Kluska, J; Crida, A; Carmona, A; Gonzalez, J F; Thi, W F; Bouquin, J -B Le; Olofsson, J; Lopez, B

    2016-01-01

    Spatially resolving the inner dust cavity of the transitional disks is a key to understanding the connection between planetary formation and disk dispersal. The disk around the Herbig star HD 139614 is of particular interest since it presents a pretransitional nature with an au-sized gap, in the dust, that was spatially resolved by mid-IR interferometry. Using new NIR interferometric observations, we aim to characterize the 0.1-10~au region of the HD~139614 disk further and identify viable mechanisms for the inner disk clearing. We report the first multiwavelength radiative transfer modeling of the interferometric data acquired on HD~139614 with PIONIER, AMBER, and MIDI, complemented by Herschel/PACS photometries. We confirm a gap structure in the um-sized dust, extending from about 2.5 au to 6 au, and constrained the properties of the inner dust component: e.g., a radially increasing surface density profile, and a depletion of 10^3 relative to the outer disk. Since self-shadowing and photoevaporation appears...

  19. 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 ...

  20. Progress in characterizing the multidimensional color quality properties of white LED light sources

    Science.gov (United States)

    Teunissen, Kees; Hoelen, Christoph

    2016-03-01

    With the introduction of solid state light sources, the variety in emission spectra is almost unlimited. However, the set of standardized parameters to characterize a white LED light source, such as correlated color temperature (CCT) and CIE general color rendering index (Ra), is known to be limited and insufficient for describing perceived differences between light sources. Several characterization methods have been proposed over the past decades, but their contribution to perceived color quality has not always been validated. To gain more insight in the relevant characteristics of the emission spectra for specific applications, we have conducted a perception experiment to rate the attractiveness of three sets of objects, including fresh food, packaging materials and skin tones. The objects were illuminated with seven different combinations of Red, Green, Blue, Amber and White LEDs, all with the same CCT and illumination level, but with differences in Ra and color saturation. The results show that, in general, object attractiveness does not correlate well with Ra, but shows a positive correlation with saturation increase for two out of three applications. There is no clear relation between saturation and skin tone attractiveness, partly due to differences in preference between males and females. A relative gamut area index (Ga) represents the average change in saturation and a complementary color vector graphic shows the direction and magnitude of chromatic differences for the eight CIE-1974 test-color samples. Together with the CIE general color rendering index (Ra) they provide useful information for designing and optimizing application specific emission spectra.