WorldWideScience

Sample records for amber

  1. light amber and dark amber

    African Journals Online (AJOL)

    Both samples showed high amount of carbohydrate, that of light amber being higher. The antioxidant vitamins (vitamins A, C and E) content of the two honeys are 4.08± 0.21, 2.22± 0.10and 0.28± 0.03(mg/dl), (for light amber), and 4.42± 0.06, 2.61± 0.11,and 0.26± 0.02 (mg/dl), (for dark amber) respectively. Both samples

  2. AMBER User's Manual

    International Nuclear Information System (INIS)

    Vay, J.L.; Fawley, W.

    2000-01-01

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

  3. Further AMBER and Ecolego Intercomparisons

    International Nuclear Information System (INIS)

    Maul, Philip; Robinson, Peter; Broed, Robert

    2004-01-01

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

  4. Organic geochemistry of Czech amber

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 11, č. 1 (2015), s. 146 ISSN 1336-7242. [Zjazd chemikov /67./. 07.09.2015-11.09.2015, Horný Smokovec] R&D Projects: GA ČR(CZ) GA13-18482S Institutional research plan: CEZ:AV0Z30460519 Keywords : fossil resin * amber * resinite Subject RIV: DD - Geochemistry

  5. Evidence for marine microfossils from amber.

    Science.gov (United States)

    Girard, Vincent; Schmidt, Alexander R; Saint Martin, Simona; Struwe, Steffi; Perrichot, Vincent; Saint Martin, Jean-Paul; Grosheny, Danièle; Breton, Gérard; Néraudeau, Didier

    2008-11-11

    Amber usually contains inclusions of terrestrial and rarely limnetic organisms that were embedded in the places were they lived in the amber forests. Therefore, it has been supposed that amber could not have preserved marine organisms. Here, we report the discovery amber-preserved marine microfossils. Diverse marine diatoms as well as radiolarians, sponge spicules, a foraminifer, and a spine of a larval echinoderm were found in Late Albian and Early Cenomanian amber samples of southwestern France. The highly fossiliferous resin samples solidified approximately 100 million years ago on the floor of coastal mixed forests dominated by conifers. The amber forests of southwestern France grew directly along the coast of the Atlantic Ocean and were influenced by the nearby sea: shells and remnants of marine organisms were probably introduced by wind, spray, or high tide from the beach or the sea onto the resin flows.

  6. Visualization of normal pleural sinuses with AMBER

    International Nuclear Information System (INIS)

    Aarts, N.J.; Kool, L.J.S.; Oestmann, J.W.

    1991-01-01

    This paper reports that ventral and dorsal pleural sinuses are frequently better appreciated with advanced modulated beam equalization radiography (AMBER) than with standard chest radiography. The visualization of the sinuses with both techniques was compared and their typical configuration studied. Four hundred patients without known chest disease were evaluated. Two groups of 200 patients were studied with either AMBER or standard chest radiography. Visualization was evaluated by three radiologists using a four-point scale. The shape of the sinus was traced if sufficiently visible. A significantly larger segment of the respective sinuses was seen with the AMBER technique. The dorsal sinus was significantly easier to trace than the ventral. Various sinus configurations were noted. AMBER improves the visibility of the pleural sinuses. Knowledge of their normal configuration is the precondition for correctly diagnosing lesions hitherto frequently overlooked

  7. The Amber Industry: Development Сhallenges and Combating Amber Trafficking in the Baltic Region

    Directory of Open Access Journals (Sweden)

    Volchetskaya Т. S.

    2017-12-01

    Full Text Available This article considers the current state and prospective development of the amber industry in the Baltic Sea region. The authors identify the main obstacles to the industry’s development in Russia — poor pricing mechanisms for raw amber, an imbalance between supply and demand, a slow pace of technological modernisation, and a delayed introduction of new technologies and processing techniques. The authors identify gaps in the regulatory framework and highlight problems of legal regulation and law enforcement as regards the amber industry. Combating illegal amber extraction and trafficking is a pressing problem in the Kaliningrad region (Russia and other Baltic region states. The article explores theoretical aspects of the legislative policy on combating illegal amber extraction and trafficking. The authors focus on the relevant law enforcement practices and hold that administrative sanctions for unauthorised amber extraction and trade are not fully effective in Russia. The authors stress the need for introducing criminal liability for a repeated offence and outline opportunities for using forensic gemological examination of amber and amber products.

  8. Protist-like inclusions in amber, as evidenced by Charentes amber.

    Science.gov (United States)

    Girard, Vincent; Néraudeau, Didier; Adl, Sina M; Breton, Gérard

    2011-05-01

    The mid-Cretaceous amber of France contains thousands of protist-like inclusions similar in shape to some ciliates, flagellates and amoebae. The sheer abundance of these inclusions and their size variation within a single amber piece are not concordant with true fossil protists. French amber is coniferous in origin, which generally does not preserve well protists without cell walls. Thus, it would be surprising if French Cretaceous amber had preserved millions of protists. Here, we present a survey of the protist-like inclusions from French amber and attempt to elucidate their origins. Diverse Cretaceous ambers (from Spain, Germany and Lebanon), also derived from conifer resins, contain thousands of protist-like inclusions. In contrast, Tertiary ambers and modern resins are poor in protist-like fossils. This suggests these inclusions originated from early Cretaceous plant resins, probably secreted with the resin by trees that did not survive after the Cretaceous (such as the Cheirolepidiaceae). A review of the recent literature on amber microfossils indicates several protist-like inclusions that are unlikely to have a biological origin have already been described as real fossil protists. This is problematic in that it will bias our understanding of protist evolution. Copyright © 2011 Elsevier GmbH. All rights reserved.

  9. Penis morphology in a Burmese amber harvestman

    Science.gov (United States)

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

    2016-02-01

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

  10. Leucine insertion caused by a yeast amber suppressor

    Energy Technology Data Exchange (ETDEWEB)

    Liebman, S W [Univ. of Rochester School of Medicine and Dentistry, NY; Stewart, J W; Parker, J H; Sherman, F

    1977-01-01

    The amber suppressor SUP52 can cause the production of approximately 15 to 20% of the normal amount of iso-l-cytochrome c when coupled to the amber (UAG) mutant cyc1-76. The suppressed iso-l-cytochrome c contains a residue of leucine at the position corresponding to the site of the amber codon. SUP52 also supresses another amber allele cyc1-179, but only with a low efficiency of approximately 2%. It does not appear to act at all on ochre (UAA) mutants. SUP52 was found to be on the left arm of chromosome X closely linked to the centromere.

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

    NARCIS (Netherlands)

    Ferreira Pires, Luis; Farines, J-M.; Westphall, C.; Guareis de farias, Cléver

    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

  12. Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea in early Eocene Cambay amber

    Directory of Open Access Journals (Sweden)

    Frauke Stebner

    2017-05-01

    Full Text Available One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.

  13. Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber.

    Science.gov (United States)

    Stebner, Frauke; Singh, Hukam; Rust, Jes; Grimaldi, David A

    2017-01-01

    One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina . Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.

  14. Tropical and Holarctic Ants in Late Eocene Ambers

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2016-04-01

    Full Text Available Based on representative collections, the ratio of tropical and Holarctic ant species in Priabonian (Late Eocene Baltic, Bitterfeld (Saxonian, Danish and Rovno ambers is analyzed for the first time. In surveyed representative collections of Baltic amber, the ratios of Holarctic and tropical ant species are from 1.1 to 1.5; with 10 Holarctic and 9 tropical species (out of 31 in the PIN-964 collection, and 9 and 5 species (out of 29 in the Giecewicz collection; the ratio in the representative collection of Saxonian amber is 0.9, 11 Holarctic species vs. 12 tropical species (out of 55; in the representative collection of Rovno amber it is 0.65, 15 vs. 23 species (out of 79; and in the representative collection of Danish amber it is 0.64, 7 vs. 11 species (out of 36. Hence, in representative collections of Baltic amber, Holarctic species clearly prevail not just in terms of the share of their specimens (by 9.8 to 19.6 times, but also by the number of species. In Bitterfeld amber, Holarctic species are somewhat less numerous than tropical ones, but their specimens are 6 times greater. In representative collections of Rovno and Danish ambers, the number of Holarctic species is 1.5 to 1.7 times smaller than that of tropical species, but the number of their specimens is 4.9 to 6.9 times greater. The numbers of tropical and Holarctic species represented by more than one specimen is similar in Priabonian ambers, 25 versus 22, but Holarctic species include four dominants or subdominants. The abundance of temperate elements in the Priabonian amber ant fauna along with the relatively small number of tropical elements greatly distinguishes it from the Middle European Lutetian ant faunas of Messel and Eckfeld in shale, which do not have temperate elements at all. Formica phaethusa Wheeler, Glaphyromyrmex oligocenicus Wheeler, Plagiolepis squamifera Mayr, Proceratium eocenicum Dlussky, Hypoponera atavia (Mayr, Ponera lobulifera Dlussky, Aphaenogaster mersa

  15. Applications of diamond crystal ATR FTIR spectroscopy to the characterization of ambers.

    Science.gov (United States)

    Guiliano, Michel; Asia, Laurence; Onoratini, Gérard; Mille, Gilbert

    2007-08-01

    Diamond crystal ATR FTIR spectroscopy is a rapid technique with virtually no sample preparation which requires small sample amounts and showed potential in the study of ambers. FTIR spectra of ambers present discriminating patterns and can be used to distinguish amber from immature resins as copal, to determine local or Baltic origin of archaeological ambers and to detect most of the falsifications encountered in the amber commercialisation.

  16. The first fossil cyphophthalmid harvestman from Baltic amber

    Directory of Open Access Journals (Sweden)

    Dunlop, Jason A.

    2011-01-01

    Full Text Available The first fossil cyphophthalmid harvestman (Opiliones: Cyphophthalmi from Palaeogene (Eocene Baltic amber is described. This is only the third fossil example of this basal harvestman lineage; the others being from the probably slightly younger Bitterfeld amber and the much older, early Cretaceous, Myanmar (Burmese amber. Although incomplete and lacking most of the appendages, the new Baltic amber fossil can be identified as a female. The somatic characters preserved, especially spiracle morphology and the coxo-genital region, allow it to be assigned with some confidence to the extant genus Siro Latreille, 1796 (Sironidae. This fossil is formally described here as Siro balticus sp. nov. It resembles modern North American Siro species more than modern European ones, and can be distinguished principally on its relatively large size and the outline form of the body.

  17. Analysis and Provenience of Minoan and Mycenaean Amber, I

    Directory of Open Access Journals (Sweden)

    Curt W. Beck

    2003-02-01

    Full Text Available Spectroscopic analysis of amber artifacts excavated in Greece, chiefly of the Bronze Age, can clarify the geographical origins of the material (chiefly Balkan and add to our understanding of trade routes.

  18. Evidence concerning oxidation as a surface reaction in Baltic amber

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2012-01-01

    , obtained from pressed amber powder, were subjected to accelerated thermal ageing. Cross-sections of the pellets were analyzed by infrared micro-spectroscopy, in order to identify and quantify changes in chemical properties. The experimental results showed strong oxidation exclusively at the exterior part...... of cross-sections from samples subjected to long-term thermal ageing, confirming that oxidation of Baltic amber starts from the surface....

  19. 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.

  20. A new proposal concerning the botanical origin of Baltic amber.

    Science.gov (United States)

    Wolfe, Alexander P; Tappert, Ralf; Muehlenbachs, Karlis; Boudreau, Marc; McKellar, Ryan C; Basinger, James F; Garrett, Amber

    2009-10-07

    Baltic amber constitutes the largest known deposit of fossil plant resin and the richest repository of fossil insects of any age. Despite a remarkable legacy of archaeological, geochemical and palaeobiological investigation, the botanical origin of this exceptional resource remains controversial. Here, we use taxonomically explicit applications of solid-state Fourier-transform infrared (FTIR) microspectroscopy, coupled with multivariate clustering and palaeobotanical observations, to propose that conifers of the family Sciadopityaceae, closely allied to the sole extant representative, Sciadopitys verticillata, were involved in the genesis of Baltic amber. The fidelity of FTIR-based chemotaxonomic inferences is upheld by modern-fossil comparisons of resins from additional conifer families and genera (Cupressaceae: Metasequoia; Pinaceae: Pinus and Pseudolarix). Our conclusions challenge hypotheses advocating members of either of the families Araucariaceae or Pinaceae as the primary amber-producing trees and correlate favourably with the progressive demise of subtropical forest biomes from northern Europe as palaeotemperatures cooled following the Eocene climate optimum.

  1. A new soldier beetle from Eocene Baltic amber

    Directory of Open Access Journals (Sweden)

    Fabrizio Fanti

    2017-11-01

    Full Text Available The family Cantharidae is a worldwide distributed group of flattened and soft-bodied beetles displaying aposematic colouration. These beetles, commonly known as soldier beetles, have an extensive fossil record dating back to the Lower Cretaceous. The majority of fossil material, referred to Cantharidae, is known from amber inclusions. In this paper we describe and illustrate a new soldier beetle Kuskaella macroptera gen. et sp. nov. from the Baltic amber. It is characterised by pronotum of the male parallel-sided in basal third and abruptly narrowed towards apex, and of the female gradually and steadily narrowing from the basal margin to the apex; globular head; unequal maxillary palpomeres with the last segment elongated-globular and pointed; long elytra slightly surpassing the last abdominal segment. This finding is the first described species of both sexes preserved in a single amber piece.

  2. Two new fossil species of Cryptocephalus Geoffroy (Coleoptera: Chrysomelidae) from Baltic and Dominican Amber

    Science.gov (United States)

    Two new species of Cryptocephalus Geoffroy (Coleoptera: Chrysomelidae) are described and illustrated from fossil resin: Cryptocephalus groehni sp. nov (Baltic amber) and Cryptocephalus kheelorum sp. nov. (Dominican amber). These are the first described species of Cryptocephalinae from fossil resin. ...

  3. 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

  4. Isolation and genetic analysis of amber uvrA and uvrB mutants

    International Nuclear Information System (INIS)

    Morimyo, M.; Shimazu, Y.; Ishii, N.

    1976-01-01

    Genetic properties of amber uvrA and uvrB mutants of Escherichia coli K-12 are described. The isolation of three amber uvrA and two amber uvrB mutants indicates that the products of these genes are proteins

  5. New fossil ants in French Cretaceous amber (Hymenoptera: Formicidae)

    Science.gov (United States)

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

    2008-02-01

    Recent studies on the ant phylogeny are mainly based on the molecular analyses of extant subfamilies and do not include the extinct, only Cretaceous subfamily Sphecomyrminae. However, the latter is of major importance for ant relationships, as it is considered the most basal subfamily. Therefore, each new discovery of a Mesozoic ant is of high interest for improving our understanding of their early history and basal relationships. In this paper, a new sphecomyrmine ant, allied to the Burmese amber genus Haidomyrmex, is described from mid-Cretaceous amber of France as Haidomyrmodes mammuthus gen. and sp. n. The diagnosis of the tribe Haidomyrmecini is emended based on the new type material, which includes a gyne (alate female) and two incomplete workers. The genus Sphecomyrmodes, hitherto known by a single species from Burmese amber, is also reported and a new species described as S. occidentalis sp. n. after two workers remarkably preserved in a single piece of Early Cenomanian French amber. The new fossils provide additional information on early ant diversity and relationships and demonstrate that the monophyly of the Sphecomyrminae, as currently defined, is still weakly supported.

  6. GPU acceleration of Dock6's Amber scoring computation.

    Science.gov (United States)

    Yang, Hailong; Zhou, Qiongqiong; Li, Bo; Wang, Yongjian; Luan, Zhongzhi; Qian, Depei; Li, Hanlu

    2010-01-01

    Dressing the problem of virtual screening is a long-term goal in the drug discovery field, which if properly solved, can significantly shorten new drugs' R&D cycle. The scoring functionality that evaluates the fitness of the docking result is one of the major challenges in virtual screening. In general, scoring functionality in docking requires a large amount of floating-point calculations, which usually takes several weeks or even months to be finished. This time-consuming procedure is unacceptable, especially when highly fatal and infectious virus arises such as SARS and H1N1, which forces the scoring task to be done in a limited time. This paper presents how to leverage the computational power of GPU to accelerate Dock6's (http://dock.compbio.ucsf.edu/DOCK_6/) Amber (J. Comput. Chem. 25: 1157-1174, 2004) scoring with NVIDIA CUDA (NVIDIA Corporation Technical Staff, Compute Unified Device Architecture - Programming Guide, NVIDIA Corporation, 2008) (Compute Unified Device Architecture) platform. We also discuss many factors that will greatly influence the performance after porting the Amber scoring to GPU, including thread management, data transfer, and divergence hidden. Our experiments show that the GPU-accelerated Amber scoring achieves a 6.5× speedup with respect to the original version running on AMD dual-core CPU for the same problem size. This acceleration makes the Amber scoring more competitive and efficient for large-scale virtual screening problems.

  7. AMBER and Ecolego Intercomparisons using Calculations from SR 97

    International Nuclear Information System (INIS)

    Maul, Philip; Robinson, Peter; Avila, Rodolfo; Broed, Robert; Pereira, Antonio

    2003-08-01

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

  8. Mid-infrared spectroscopy for characterization of Baltic amber (succinite)

    Science.gov (United States)

    Wagner-Wysiecka, Ewa

    2018-05-01

    Natural Baltic amber (succinite) is the most appreciated fossil resin of the rich cultural traditions dating back to prehistoric times. Its unequivocal identification is extremely important in many branches of science and trades including archeology, paleontology, chemistry and finally mineralogical and gemological societies. Current methods of modification of natural succinite are more and more sophisticated making the identification of natural Baltic amber often challenging. In article the systematic analytical approach for identification of natural and modified under different conditions succinite, using mid-infrared spectroscopy (transmission, Drifts and ATR techniques) is presented. The correlation between spectral characteristics and properties of succinite is discussed pointing that the understanding of the nature of changes is the key of identification of this precious material.

  9. Structural changes in amber due to uranium mineralization

    Czech Academy of Sciences Publication Activity Database

    Havelcová, M.; Machovič, V.; Mizera, Jiří; Sýkorová, I.; Rene, M.; Borecká, L.; Lapčák, L.; Bičáková, O.; Janeček, O.; Dvořák, Z.

    2016-01-01

    Roč. 158, JUL (2016), s. 89-101 ISSN 0265-931X R&D Projects: GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LM2011019 Institutional support: RVO:61389005 Keywords : fossil resin * amber * Uranium * radiolytic alteration * micro-FTIR * mapping * SEM/EDX Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.310, year: 2016

  10. Structural changes in amber due to uranium mineralization

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Machovič, Vladimír; Mizera, Jiří; Sýkorová, Ivana; René, Miloš; Borecká, Lenka; Lapčák, L.; Bičáková, Olga; Janeček, O.; Dvořák, Z.

    158-159, JUL (2016), s. 89-101 ISSN 0265-931X R&D Projects: GA ČR(CZ) GA13-18482S Grant - others:OPPK(XE) CZ.2.16/3.1.00/21538 Program:OPPK Institutional support: RVO:67985891 Keywords : fossil resin * amber * uranium * radiolytic alteration * micro-FTIR * mapping * SEM/EDX Subject RIV: DD - Geochemistry Impact factor: 2.310, year: 2016

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

    Directory of Open Access Journals (Sweden)

    Michael Engel

    2011-11-01

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

  12. Diversity of Scydmaeninae (Coleoptera: Staphylinidae) in Upper Eocene Rovno amber.

    Science.gov (United States)

    Jałoszyński, Paweł; Perkovsky, Evgeny

    2016-08-25

    Among nearly 1270 inclusions of Coleoptera found in Upper Eocene Rovno amber, 69 were identified as ant-like stone beetles (Scydmaeninae); 34 were possible to unambiguously determine to the tribal level and were studied in detail. Rovnoleptochromus ableptonoides gen. & sp. n. (Mastigitae: Clidicini), Vertheia quadrisetosa gen. & sp. n. (Cephenniitae: Eutheiini), Cephennomicrus giganteus sp. n. (Cephenniitae: Cephenniini), Glaesoconnus unicus gen. & sp. n. (Scydmaenitae: Glandulariini), Rovnoscydmus frontalis gen. & sp. n. (Scydmaenitae: Glandulariini; type species of Rovnoscydmus), Rovnoscydmus microscopicus sp. n., Euconnus (incertae sedis, near Cladoconnus) palaeogenus sp. n. (Scydmaenitae: Glandulariini), and Stenichnus (s. str.) proavus sp. n. (Scydmaenitae: Glandulariini) are described. Additionally, specimens representing one undescribed species of Vertheia, one of Cephennodes, five of Cephennomicrus, one of Euconnus, one of Microscydmus are recorded, and nine specimens representing an unknown number of species of Rovnoscydmus (and two putative Rovnoscydmus), one Euconnus (and one putative Euconnus), two putative Microscydmus and one putative Scydmoraphes were found in the studied material. The composition of Scydmaeninae fauna in Rovno amber is discussed in the context of ecological preferences and distribution of extant taxa. It is concluded that subtropical and tropical taxa were present in the region where Rovno amber has formed, most notably the second genus and species of the extant tribe Clidicini known from the Eocene of Europe, and six species of the extant genus Cephennomicrus, for the first time found in the fossil record. An annotated catalog of nominal species of Scydmaeninae known in the fossil record is given.

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

    OpenAIRE

    G. V. THAKRE; S. G. PATIL; D. N. AGRAWAL

    2011-01-01

    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 ch...

  14. Subfamily Limoniinae Speiser, 1909 (Diptera, Limoniidae) from Baltic amber (Eocene): the genus Helius Lepeletier & Serville, 1828.

    Science.gov (United States)

    Kania, Iwona

    2014-06-10

    A revision of the genus Helius Lepeletier & Serville, 1828 (Diptera: Limoniidae) from Baltic amber (Eocene) is presented. Redescriptions of 5 species, Helius formosus Krzemiński, 1993, Helius linus Podenas, 2002, Helius minutus (Loew, 1850), Helius mutus Podenas, 2002, Helius pulcher (Loew, 1850) of this genus from Baltic amber are given and documented by photographs and drawings. Four new species of the genus Helius from Baltic amber are described: Helius gedanicus sp. nov., Helius hoffeinsorum sp. nov., Helius similis sp. nov., Helius fossilis sp. nov. A key to species of Helius from Baltic amber is provided. Patterns morphological evolution and the aspects evolutionary history of Helius are discussed.

  15. 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...

  16. New and revised maimetshid wasps from Cretaceous ambers (Hymenoptera, Maimetshidae

    Directory of Open Access Journals (Sweden)

    Vincent Perrichot

    2011-09-01

    Full Text Available New material of the wasp family Maimetshidae (Apocrita is presented from four Cretaceous amber deposits – the Neocomian of Lebanon, the Early Albian of Spain, the latest Albian/earliest Cenomanian of France, and the Campanian of Canada. The new record from Canadian Cretaceous amber extends the temporal and paleogeographical range of the family. New material from France is assignable to Guyotemaimetsha enigmatica Perrichot et al. including the first females for the species, while a series of males and females from Spain are described and figured as Iberomaimetsha Ortega-Blanco, Perrichot, and Engel gen. n., with the two new species Iberomaimetsha rasnitsyni Ortega-Blanco, Perrichot, and Engel sp. n. and I. nihtmara Ortega-Blanco, Delclòs, and Engel sp. n.; a single female from Lebanon is described and figured as Ahiromaimetsha najlae Perrichot, Azar, Nel, and Engel gen. et sp. n., and a single male from Canada is described and figured as Ahstemiam cellula McKellar and Engel gen. et sp. n. The taxa are compared with other maimetshids, a key to genera and species is given, and brief comments made on the family.

  17. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

    Science.gov (United States)

    Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

    2017-06-20

    With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. The occurrence of amber and sub-amber (copal) in Costa Rica: the case of San Cristobal de Savegre

    International Nuclear Information System (INIS)

    Alvarado, Guillermo E.; Brenes, Jorge; Brenes, Jose

    2013-01-01

    In Costa Rica, small fragments of amber are found in the Miocene shallow marine clastic sedimentary rocks, such as Formacion Punta Judas (Middle Miocene), Formacion Santa Teresa (Middle Miocene), and Formacion Curre (Middle-Upper Miocene). Sub-amber or copal is found in relative abundance in certain localities in the residual soils in the mountains near San Cristobal de Savegre (Aguirre, Puntarenas). The copal samples have sub-rounded or pearly (21.3%), tabular or laminar (29.6%) and troncoidal (30.4%) forms, but some are intermediate or indefinite (18.7%). Its color varies between orange / red (57.4%), followed by yellow (31.0%) and less frequently light yellow to whitish (11.6%); some samples have insects incorporated. The age of the copal is in the age range of 1670-1780 A.D., based on a calibrated 14 C dating. Although these samples of copal seem to have no commercial value, they could be used by local artisans. (author) [es

  19. parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages.

    Science.gov (United States)

    Peñalver, Enrique; Arillo, Antonio; Delclòs, Xavier; Peris, David; Grimaldi, David A; Anderson, Scott R; Nascimbene, Paul C; Pérez-de la Fuente, Ricardo

    2017-12-12

    Ticks are currently among the most prevalent blood-feeding ectoparasites, but their feeding habits and hosts in deep time have long remained speculative. Here, we report direct and indirect evidence in 99 million-year-old Cretaceous amber showing that hard ticks and ticks of the extinct new family Deinocrotonidae fed on blood from feathered dinosaurs, non-avialan or avialan excluding crown-group birds. A †Cornupalpatum burmanicum hard tick is entangled in a pennaceous feather. Two deinocrotonids described as †Deinocroton draculi gen. et sp. nov. have specialised setae from dermestid beetle larvae (hastisetae) attached to their bodies, likely indicating cohabitation in a feathered dinosaur nest. A third conspecific specimen is blood-engorged, its anatomical features suggesting that deinocrotonids fed rapidly to engorgement and had multiple gonotrophic cycles. These findings provide insight into early tick evolution and ecology, and shed light on poorly known arthropod-vertebrate interactions and potential disease transmission during the Mesozoic.

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

    Science.gov (United States)

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

    2015-01-01

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

  1. Experimental analysis of motion artifacts in chest radiographs with the AMBER system

    International Nuclear Information System (INIS)

    Boetticher, H. von; Hofmann, K.; Luska, G.

    1999-01-01

    The prerequisites, mechanisms and principles of motion artifacts in AMBER radiographs were analysed. The experiments were performed using metronomes, a moving conventional mammography phantom, and arrangements of oscillating coil spring, spheroid and grid elements. A diagnostic dosimeter and TLDs, respectively, were used to measure exposure times and doses. The deree of distortion in AMBER radiographs depends on the direction of the object movement relative to the AMBER fan beam in a complex manner. The size of the motion artifacts depends on the local exposure time. The maximum value of this time is 75 ms and thus 1.5 times higher than specified by the manufacturer. To interpret AMBER radiographs possible system specific artifacts have to be considered to avoid misinterpretations of potentially significant details. (orig.) [de

  2. The range of bioinclusions and pseudoinclusions preserved in a new Turonian (~90 ma) amber occurrence from Southern Australia.

    Science.gov (United States)

    Quinney, Annie; Mays, Chris; Stilwell, Jeffrey D; Zelenitsky, Darla K; Therrien, François

    2015-01-01

    A new Turonian amber occurrence, representing the oldest in situ amber locality in Australia and the southern-most locality in Gondwana, has recently been discovered in the Otway Basin of Victoria. The amber was collected from petroleum cores and many pieces contain a range of inclusions that can provide information on the depositional history of the resin. To date, one species of fern spore (Cyathidites minor) and one species of lycophyte spore (Kraeuselisporites sp?) have been conclusively identified in the amber, along with filamentous microorganisms and degraded plant matter. Several samples are also rife with pseudoinclusions as reported recently in other ambers. The abundance of preserved particulate debris and wind dispersed spores suggest that the Otway amber formed subaerially. Furthermore, based on the range of bioinclusions and forms of pseudoinclusions preserved within a single piece of amber, the locus of hardening for individual samples is variably interpreted as occurring in the tree tops, on the tree trunk or on the ground surface. Notably, specific inclusion assemblages are associated with certain colours of amber. By extension, and in accordance with recent studies, amber colour may be indicative of depositional environment. Variation in the environment of solidification may, therefore, be sufficient to account for the broad range of morphological characteristics preserved in a single amber deposit.

  3. Vibrational spectroscopy with chromatographic methods in molecular analyses of Moravian amber samples (Czech Republic)

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Machovič, Vladimír; Linhartová, M.; Lapčák, L.; Přichystal, A.; Dvořák, Z.

    2016-01-01

    Roč. 128, SEP (2016), 153-160 ISSN 0026-265X R&D Projects: GA ČR(CZ) GA13-18482S Grant - others:OPPK(XE) CZ.2.16/3.1.00/21538 Program:OPPK Institutional support: RVO:67985891 Keywords : studlovite * valchovite * amber * fossil resin * Baltic amber Subject RIV: DD - Geochemistry Impact factor: 3.034, year: 2016

  4. 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

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

    International Nuclear Information System (INIS)

    Thomson, Gavin; Herben, Martin; Lloyd, Pam; Rose, Danny; Smith, Chris; Barra clough, Ian

    2008-03-01

    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

  6. Terpenoid Compositions and Botanical Origins of Late Cretaceous and Miocene Amber from China

    Science.gov (United States)

    Shi, Gongle; Dutta, Suryendu; Paul, Swagata; Wang, Bo; Jacques, Frédéric M. B.

    2014-01-01

    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. PMID:25354364

  7. 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.

  8. 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

  9. Evaluating amber force fields using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

    NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

  10. Eocene and not Cretaceous origin of spider wasps: Fossil evidence from amber

    Directory of Open Access Journals (Sweden)

    Juanita Rodriguez

    2016-02-01

    Full Text Available Spider wasps had long been proposed to originate in the mid-Cretaceous based on the Burmese amber fossil Bryopompilus interfector Engel and Grimaldi, 2006. We performed a morphological examination of this fossil and determined it does not belong to Pompilidae or any other described hymenopteran family. Instead, we place it in the new family Bryopompilidae. The oldest verifiable member of the Pompilidae is from Baltic amber, which suggests the family probably originated in the Eocene, not in the mid-Cretaceous as previously proposed. The origin of spider wasps appears to be correlated with an increase in spider familial diversity in the Cenozoic. We also we add two genera to the extinct pompilid fauna: Tainopompilus gen. nov., and Paleogenia gen. nov., and describe three new species of fossil spider wasps: Anoplius planeta sp. nov., from Dominican amber (Burdigalian to Langhian; Paleogenia wahisi sp. nov., from Baltic amber (Lutetian to Priabonian; and Tainopompilus argentum sp. nov, from Dominican amber (Chattian to Langhian.

  11. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

    Science.gov (United States)

    Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

    2013-09-10

    Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license.

  12. Influence of land-based Kaliningrad (Primorsky) amber mining on coastal zone.

    Science.gov (United States)

    Krek, Alexander; Ulyanova, Marina; Koschavets, Svetlana

    2018-06-01

    In this paper, we report on the pollution in the coastal zone of the South-Eastern Baltic Sea (Russian coast). It was studied through a range of methods, including analyses potential water quality indicators (WQIs) and potentially harmful elements (PHEs). A contamination factor and modified degree of contamination were used for describing the contamination of the sediments by toxic substances. Special attention was paid to activity of the Kaliningrad Amber Combine (KAC), the biggest world amber mining company, located onshore close to the coastal zone (Kaliningrad Region). The amber extraction contribution to the ecological state of the coastal zone was estimated. Contamination of the quarry by metals (Cr, Co, Ni, Cu, Pb, Zn) was comparable with contamination of abrasion bench. The pollution of the western coastal zone of the Sambia Peninsula is caused both by land-based anthropogenic developments (including KAC) and natural processes (coastal abrasion). Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Arthropods in modern resins reveal if amber accurately recorded forest arthropod communities.

    Science.gov (United States)

    Solórzano Kraemer, Mónica M; Delclòs, Xavier; Clapham, Matthew E; Arillo, Antonio; Peris, David; Jäger, Peter; Stebner, Frauke; Peñalver, Enrique

    2018-05-07

    Amber is an organic multicompound derivative from the polymerization of resin of diverse higher plants. Compared with other modes of fossil preservation, amber records the anatomy of and ecological interactions between ancient soft-bodied organisms with exceptional fidelity. However, it is currently suggested that ambers do not accurately record the composition of arthropod forest paleocommunities, due to crucial taphonomic biases. We evaluated the effects of taphonomic processes on arthropod entrapment by resin from the plant Hymenaea , one of the most important resin-producing trees and a producer of tropical Cenozoic ambers and Anthropocene (or subfossil) resins. We statistically compared natural entrapment by Hymenaea verrucosa tree resin with the ensemble of arthropods trapped by standardized entomological traps around the same tree species. Our results demonstrate that assemblages in resin are more similar to those from sticky traps than from malaise traps, providing an accurate representation of the arthropod fauna living in or near the resiniferous tree, but not of entire arthropod forest communities. Particularly, arthropod groups such as Lepidoptera, Collembola, and some Diptera are underrepresented in resins. However, resin assemblages differed slightly from sticky traps, perhaps because chemical compounds in the resins attract or repel specific insect groups. Ground-dwelling or flying arthropods that use the tree-trunk habitat for feeding or reproduction are also well represented in the resin assemblages, implying that fossil inclusions in amber can reveal fundamental information about biology of the past. These biases have implications for the paleoecological interpretation of the fossil record, principally of Cenozoic amber with angiosperm origin.

  14. Revival and Identification of Bacterial Spores in 25- to 40-Million-Year-Old Dominican Amber

    Science.gov (United States)

    Cano, Raul J.; Borucki, Monica K.

    1995-05-01

    A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.

  15. 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.

  16. Baltileuctra gen. nov., a new genus of Leuctridae (Insecta: Plecoptera) in Baltic amber.

    Science.gov (United States)

    Chen, Zhi-Teng

    2018-04-10

    A new genus and species of the stonefly family Leuctridae, Baltileuctra foraminis gen. et sp. nov., is described and illustrated based on a well-preserved male specimen from the Eocene Baltic amber. The new genus possesses typical characters of Leuctridae but has diagnostic characters of the thoracic sclerites and terminalia. The relationship between the new genus and other leuctrids is briefly discussed.

  17. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    DEFF Research Database (Denmark)

    Ou, Yiyu; Iida, Daisuke; Liu, Jin

    2018-01-01

    We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW) samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extr...

  18. Discovery of a new stonefly genus with three new species from mid-Cretaceous Burmese amber (Plecoptera: Perlidae).

    Science.gov (United States)

    Chen, Zhi-Teng; Wang, Bo; Du, Yu-Zhou

    2018-02-11

    A new fossil stonefly genus of the subfamily Acroneuriinae Klapálek, 1914 (Plecoptera: Perlidae), Largusoperla gen. nov. is reported based on three well-preserved specimens in mid-Cretaceous amber from northern Myanmar. Three new species of this new genus, L. acus sp. nov, L. flata sp. nov and L. arcus sp. nov. are described and illustrated. This is the first report of stonefly specimens from mid-Cretaceous Burmese amber. The taxonomic placement of the new genus is discussed.

  19. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    KAUST Repository

    Ou, Yiyu

    2017-09-09

    We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW) samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extraction efficiency. The size-dependent strain relaxation effect was characterized by photoluminescence, Raman spectroscopy and time-resolved photoluminescence measurements. In addition, the light extraction efficiency of different MQW samples was studied by finite-different time-domain simulations. Compared to the as-grown sample, the nanopillar amber MQW sample with a diameter of 300 nm has demonstrated an emission enhancement by a factor of 23.8.

  20. Development of ACBIO: A Biosphere Template Using AMBER for a Potential Radioactive Waste Repository

    International Nuclear Information System (INIS)

    Lee, Youn Myoung; Hwang, Yong Soo; Kang, Chul Hyung; Hahn, Pil Soo

    2005-01-01

    Nuclides in radioactive wastes are assumed to be transported in the geosphere by groundwater and probably discharged into the biosphere. Quantitative evaluation of doses to human beings due to nuclide transport in the geosphere and through the various pathways in the biosphere is the final step of safety assessment of the radioactive waste repository. To calculate the flux to dose conversion factors (DCFs) for nuclides appearing at GBIs with their decay chains, a template ACBIO which is an AMBER case file based on mathematical model for the mass transfer coefficients between the compartments has been developed considering material balance among the compartments in biosphere and then implementing to AMBER, a general and flexible software tool that allows to build dynamic compartment models. An illustrative calculation with ACBIO is shown.

  1. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    Directory of Open Access Journals (Sweden)

    Ou Yiyu

    2018-01-01

    Full Text Available We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extraction efficiency. The size-dependent strain relaxation effect was characterized by photoluminescence, Raman spectroscopy and time-resolved photoluminescence measurements. In addition, the light extraction efficiency of different MQW samples was studied by finite-different time-domain simulations. Compared to the as-grown sample, the nanopillar amber MQW sample with a diameter of 300 nm has demonstrated an emission enhancement by a factor of 23.8.

  2. A community intervention: AMBER: Arab American breast cancer education and referral program.

    Science.gov (United States)

    Ayash, Claudia; Axelrod, Deborah; Nejmeh-Khoury, Sana; Aziz, Arwa; Yusr, Afrah; Gany, Francesca M

    2011-12-01

    Although the number of Arab Americans is growing in the United States, there is very little data available on this population's cancer incidence and screening practices. Moreover, there are few interventions addressing their unique needs. This study aims to determine effective strategies for increasing breast cancer screening in at-risk underserved Arab American women. AMBER utilizes a community based participatory approach to conduct formative research and program interventions, including culturally appropriate Arabic language breast cancer education, screening coordination, and cultural competency training for healthcare professionals in New York City. In 2 years, 597 women were educated, 189 underserved women were identified as being in need of assistance, 68 were screened, one new case of breast cancer was detected, and four active cases in need of follow-up reconnected with care. The AMBER model is an important intervention for breast cancer screening and care in the underserved Arab American community.

  3. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    KAUST Repository

    Ou, Yiyu; Iida, Daisuke; Liu, Jin; Wu, Kaiyu; Ohkawa, Kazuhiro; Boisen, Anja; Petersen, Paul Michael; Ou, Haiyan

    2017-01-01

    We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW) samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extraction efficiency. The size-dependent strain relaxation effect was characterized by photoluminescence, Raman spectroscopy and time-resolved photoluminescence measurements. In addition, the light extraction efficiency of different MQW samples was studied by finite-different time-domain simulations. Compared to the as-grown sample, the nanopillar amber MQW sample with a diameter of 300 nm has demonstrated an emission enhancement by a factor of 23.8.

  4. Biting Midges (Diptera: Ceratopogonidae) from Cambay Amber Indicate that the Eocene Fauna of the Indian Subcontinent Was Not Isolated.

    Science.gov (United States)

    Stebner, Frauke; Szadziewski, Ryszard; Singh, Hukam; Gunkel, Simon; Rust, Jes

    2017-01-01

    India's unique and highly diverse biota combined with its unique geodynamical history has generated significant interest in the patterns and processes that have shaped the current distribution of India's flora and fauna and their biogeographical relationships. Fifty four million year old Cambay amber from northwestern India provides the opportunity to address questions relating to endemism and biogeographic history by studying fossil insects. Within the present study seven extant and three fossil genera of biting midges are recorded from Cambay amber and five new species are described: Eohelea indica Stebner & Szadziewski n. sp., Gedanohelea gerdesorum Stebner & Szadziewski n. sp., Meunierohelea cambayana Stebner & Szadziewski n. sp., Meunierohelea borkenti Stebner & Szadziewski n. sp., and Meunierohelea orientalis Stebner & Szadziewski n. sp. Fossils of species in the genera Leptoconops Skuse, 1889, Forcipomyia Meigen, 1818, Brachypogon Kieffer, 1899, Stilobezzia Kieffer, 1911, Serromyia Meigen, 1818, and Mantohelea Szadziewski, 1988 are recorded without formal description. Furthermore, one fossil belonging to the genus Camptopterohelea Wirth & Hubert, 1960 is included in the present study. Our study reveals faunal links among Ceratopogonidae from Cambay amber and contemporaneous amber from Fushun, China, Eocene Baltic amber from Europe, as well as the modern Australasian and the Oriental regions. These findings imply that faunal exchange between Europe, Asia and India took place before the formation of Cambay amber in the early Eocene.

  5. Early Cretaceous trypanosomatids associated with fossil sand fly larvae in Burmese amber

    Directory of Open Access Journals (Sweden)

    George Poinar Jr

    2007-08-01

    Full Text Available Early Cretaceous flagellates with characters typical of trypanosomatids were found in the gut of sand fly larvae, as well as in surrounding debris, in Burmese amber. This discovery supports a hypothesis in which free-living trypanosomatids could have been acquired by sand fly larvae in their feeding environment and then carried transtadially into the adult stage. At some point in time, specific genera were introduced into vertebrates, thus establishing a dixenous life cycle.

  6. A MODEL OF THE INNOVATIVE AMBER CLUSTER AS A CENTRE OF COOPERATION OF AUTHORITIES - BUSINESS - SCIENCE

    Directory of Open Access Journals (Sweden)

    Gleb B. Trifonov

    2015-01-01

    Full Text Available A mechanism of forming an innovative amber cluster was developed, including structural interconnections of cluster partners,a package of basic innovative technologies, which will createa new value chain, new vacancies, provide contributions to theregional budget.A method of analytical estimation was suggested to assess cluster synergism of partners: authorities, business, science/education, culture, which reflects potential possibilities of thecluster model of region development.

  7. Amber light-emitting diode comprising a group III-nitride nanowire active region

    Science.gov (United States)

    Wang, George T.; Li, Qiming; Wierer, Jr., Jonathan J.; Koleske, Daniel

    2014-07-22

    A temperature stable (color and efficiency) III-nitride based amber (585 nm) light-emitting diode is based on a novel hybrid nanowire-planar structure. The arrays of GaN nanowires enable radial InGaN/GaN quantum well LED structures with high indium content and high material quality. The high efficiency and temperature stable direct yellow and red phosphor-free emitters enable high efficiency white LEDs based on the RGYB color-mixing approach.

  8. Two cloned β thalassemia genes are associated with amber mutations at codon 39

    Science.gov (United States)

    Pergolizzi, Robert; Spritz, Richard A.; Spence, Sally; Goossens, Michel; Kan, Yuet Wai; Bank, Arthur

    1981-01-01

    Two β globin genes from patients with the β+ thalassemia phenotype have been cloned and sequenced. A single nucleotide change from CAG to TAG (an amber mutation) at codon 39 is the only difference from normal in both genes analyzed. The results are consistent with the assumption that both patients are doubly heterozygous for β+ and β° thalassemia, and that we have isolated and analyzed the β° thalassemia gene. Images PMID:6278453

  9. Microplastics in sea coastal zone: Lessons learned from the Baltic amber.

    Science.gov (United States)

    Chubarenko, Irina; Stepanova, Natalia

    2017-05-01

    Baltic amber, adored for its beauty already in Homer's Odyssey (ca. 800 B.C.E), has its material density close to that of wide-spread plastics like polyamide, polystyrene, or acrylic. Migrations of amber stones in the sea and their massive washing ashore have been monitored by Baltic citizens for ages. Based on the collected information, we present the hypothesis on the behaviour of microplastic particles in sea coastal zone. Fresh-to-strong winds generate surface waves, currents and roll-structures, whose joint effect washes ashore from the underwater slope both amber stones and plastics - and carries them back to the sea in a few days. Analysis of underlying hydrophysical processes suggests that sea coastal zone under stormy winds plays a role of a mill for plastics, and negatively buoyant pieces seem to repeatedly migrate between beaches and underwater slopes until they are broken into small enough fragments that can be transported by currents to deeper areas and deposited out of reach of stormy waves. Direct observations on microplastics migrations are urged to prove the hypothesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Early Miocene amber inclusions from Mexico reveal antiquity of mangrove-associated copepods.

    Science.gov (United States)

    Huys, Rony; Suárez-Morales, Eduardo; Serrano-Sánchez, María de Lourdes; Centeno-García, Elena; Vega, Francisco J

    2016-10-12

    Copepods are aquatic microcrustaceans and represent the most abundant metazoans on Earth, outnumbering insects and nematode worms. Their position of numerical world predominance can be attributed to three principal radiation events, i.e. their major habitat shift into the marine plankton, the colonization of freshwater and semiterrestrial environments, and the evolution of parasitism. Their variety of life strategies has generated an incredible morphological plasticity and disparity in body form and shape that are arguably unrivalled among the Crustacea. Although their chitinous exoskeleton is largely resistant to chemical degradation copepods are exceedingly scarce in the geological record with limited body fossil evidence being available for only three of the eight currently recognized orders. The preservation of aquatic arthropods in amber is unusual but offers a unique insight into ancient subtropical and tropical ecosystems. Here we report the first discovery of amber-preserved harpacticoid copepods, represented by ten putative species belonging to five families, based on Early Miocene (22.8 million years ago) samples from Chiapas, southeast Mexico. Their close resemblance to Recent mangrove-associated copepods highlights the antiquity of the specialized harpacticoid fauna living in this habitat. With the taxa reported herein, the Mexican amber holds the greatest diversity of fossil copepods worldwide.

  11. Improving care for patients whose recovery is uncertain. The AMBER care bundle: design and implementation.

    Science.gov (United States)

    Carey, Irene; Shouls, Susanna; Bristowe, Katherine; Morris, Michelle; Briant, Linda; Robinson, Carole; Caulkin, Ruth; Griffiths, Mathew; Clark, Kieron; Koffman, Jonathan; Hopper, Adrian

    2015-12-01

    Despite preferences to the contrary, 53% of deaths in England occur in hospital. Difficulties in managing clinical uncertainty can result in delayed recognition that a person may be approaching the end of life, and a failure to address his/her preferences. Planning and shared decision-making for hospital patients need to improve where an underlying condition responds poorly to acute medical treatment and there is a risk of dying in the next 1-2 months. This paper suggests an approach to improve this care. A care bundle (the AMBER care bundle) was designed by a multiprofessional development team, which included service users, utilising the model for improvement following an initial scoping exercise. The care bundle includes two identification questions, four subsequent time restricted actions and systematic daily follow-up. This paper describes the development and implementation of a care bundle. From August 2011 to July 2012, 638 patients received care supported by the AMBER care bundle. In total 42.8% died in hospital and a further 14.5% were readmitted as emergencies within 30 days of discharge. Clinical outcome measures are in development. It has been possible to develop a care bundle addressing a complex area of care which can be a lever for cultural change. The implementation of the AMBER care bundle has the potential to improve care of clinically uncertain hospital patients who may be approaching the end of life by supporting their recognition and prompting discussion of their preferences. Outcomes associated with its use are currently being formally evaluated. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

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

    Science.gov (United States)

    Zakrzewska, Marta; Giłka, Wojciech

    2015-11-20

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

  13. Ca2+-Signal Transduction Inhibitors, Kujiol A and Kujigamberol B, Isolated from Kuji Amber Using a Mutant Yeast.

    Science.gov (United States)

    Uchida, Takeshi; Koshino, Hiroyuki; Takahashi, Shunya; Shimizu, Eisaku; Takahashi, Honoka; Yoshida, Jun; Shinden, Hisao; Tsujimura, Maiko; Kofujita, Hisayoshi; Uesugi, Shota; Kimura, Ken-Ichi

    2018-04-27

    A podocarpatriene and a labdatriene derivative, named kujiol A [13-methyl-8,11,13-podocarpatrien-19-ol (1)] and kujigamberol B [15,20-dinor-5,7,9-labdatrien-13-ol (2)], respectively, were isolated from Kuji amber through detection with the aid of their growth-restoring activity against a mutant yeast strain ( zds1Δ erg3Δ pdr1Δ pdr3Δ), which is known to be hypersensitive with respect to Ca 2+ -signal transduction. The structures were elucidated by spectroscopic data analysis. Compounds 1 and 2 are rare organic compounds from Late Cretaceous amber, and the mutant yeast used seems useful for elucidating a variety of new compounds from Kuji amber specimens, produced before the K-Pg boundary.

  14. A comparative Study between GoldSim and AMBER Based Biosphere Assessment Models for an HLW Repository

    International Nuclear Information System (INIS)

    Lee, Youn-Myoung; Hwang, Yong-Soo

    2007-01-01

    To demonstrate the performance of a repository, the dose exposure rate to human being due to long-term nuclide releases from a high-level waste repository (HLW) should be evaluated and the results compared to the dose limit presented by the regulatory bodies. To evaluate such a dose rate to an individual, biosphere assessment models have been developed and implemented for a practical calculation with the aid of such commercial tools as AMBER and GoldSim, both of which are capable of probabilistic and deterministic calculation. AMBER is a general purpose compartment modeling tool and GoldSim is another multipurpose simulation tool for dynamically modeling complex systems, supporting a higher graphical user interface than AMBER and a postprocessing feature. And also unlike AMBER, any kind of compartment scheme can be rather simply constructed with an appropriate transition rate between compartments, GoldSim is designed to facilitate the object-oriented modules to address any specialized programs, similar to solving jig saw puzzles. During the last couple of years a compartment modeling approach for a biosphere has been mainly carried out with AMBER in KAERI in order to conservatively or rather roughly provide dose conversion factors to get the final exposure rate due to a nuclide flux into biosphere over various geosphere-biosphere interfaces (GBIs) calculated through nuclide transport modules. This caused a necessity for a newly devised biosphere model that could be coupled to a nuclide transport model with less conservatism in the frame of the development of a total system performance assessment modeling tool, which could be successfully done with the aid of GoldSim. Therefore, through the current study, some comparison results of the AMBER and the GoldSim approaches for the same case of a biosphere modeling without any consideration of geosphere transport are introduced by extending a previous study

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

    International Nuclear Information System (INIS)

    Prieto M, E.F.; Barrera G, G.

    2004-01-01

    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)

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

    Directory of Open Access Journals (Sweden)

    Jochen Heinrichs

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

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

    Science.gov (United States)

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

    2016-01-01

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

  18. Females of the genus Podmosta (Plecoptera: Nemouridae): comparison of terminalia and a new female record in Baltic Amber.

    Science.gov (United States)

    Chen, Zhi-Teng

    2018-04-10

    Based on a specimen preserved in Baltic amber from Lithuania, a new fossil female of the nemourid genus Podmosta Ricker, 1952 is described, illustrated and compared to other described species of the genus. The new female specimen is distinguished from other Podmosta females by the "rabbit-shaped" sclerite on sternum 8.

  19. 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

    The aim of this study was to provide evidence about the interaction between Baltic amber and daylight behind window glass, essential to understanding the mechanisms by which the material degrades in museum environments and to propose techniques for preventive conservation based on the control...

  20. 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.

  1. An unusual new species of Hallodapomimus Herczek, 2000 from the Eocene Baltic amber (Hemiptera, Heteroptera, Miridae, Phylinae

    Directory of Open Access Journals (Sweden)

    Aleksander Herczek

    2015-03-01

    Full Text Available Hallodapomimus antennatus sp. n. (Hemiptera: Heteroptera, Miridae, Phylinae, Hallodapini is described from a macropterous female found in Eocene Baltic amber. The new species can be recognized readily from the other species of the genus, mainly due to its unusual second antennal segment. A key for the identification of all known fossil Hallodapini is presented.

  2. Evaluating the use of amber in palaeoatmospheric reconstructions: The carbon-isotope variability of modern and Cretaceous conifer resins

    Science.gov (United States)

    Dal Corso, Jacopo; Schmidt, Alexander R.; Seyfullah, Leyla J.; Preto, Nereo; Ragazzi, Eugenio; Jenkyns, Hugh C.; Delclòs, Xavier; Néraudeau, Didier; Roghi, Guido

    2017-02-01

    Stable carbon-isotope geochemistry of fossilized tree resin (amber) potentially could be a very useful tool to infer the composition of past atmospheres. To test the reliability of amber as a proxy for the atmosphere, we studied the variability of modern resin δ13C at both local and global scales. An amber δ13C curve was then built for the Cretaceous, a period of abundant resin production, and interpreted in light of data from modern resins. Our data show that hardening changes the pristine δ13C value by causing a 13C-depletion in solid resin when compared to fresh liquid-viscous resin, probably due to the loss of 13C-enriched volatiles. Modern resin δ13C values vary as a function of physiological and environmental parameters in ways that are similar to those described for leaves and wood. Resin δ13C varies between plant species and localities, within the same tree and between different plant tissues by up to 6‰, and in general increases with increasing altitudes of the plant-growing site. We show that, as is the case with modern resin, Cretaceous amber δ13C has a high variability, generally higher than that of other fossil material. Despite the high natural variability, amber shows a negative 2.5-3‰ δ13C trend from the middle Early Cretaceous to the Maastrichtian that parallels published terrestrial δ13C records. This trend mirrors changes in the atmospheric δ13C calculated from the δ13C and δ18O of benthic foraminiferal tests, although the magnitude of the shift is larger in plant material than in the atmosphere. Increasing mean annual precipitation and pO2 could have enhanced plant carbon-isotope fractionation during the Late Cretaceous, whereas changing pCO2 levels seem to have had no effect on plant carbon-isotope fractionation. The results of this study suggest that amber is a powerful fossil plant material for palaeoenvironmental and palaeoclimatic reconstructions. Improvement of the resolution of the existing data coupled with more detailed

  3. 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. © 2016 John Wiley & Sons Ltd.

  4. Moth flies and sand flies (Diptera: Psychodidae in Cretaceous Burmese amber

    Directory of Open Access Journals (Sweden)

    Frauke Stebner

    2015-09-01

    Full Text Available One new subfamily, four new genera and 10 new species of Psychodidae are described from Burmese amber which significantly increases our knowledge about this group in the Cretaceous. Protopsychodinae n. subfam. probably represents the oldest known ancestor of modern Psychodinae and includes three species within two genera: Datzia setosa gen. et sp. n., Datzia bispina gen. et sp. n., and Mandalayia beumersorum gen. et sp. n. Sycoracinae and Phlebotominae are represented by two genera each in the studied material, Palaeoparasycorax globosus gen. et sp. n., Palaeoparasycorax suppus gen. et sp. n., Parasycorax simplex sp. n., and Phlebotomites aphoe sp. n. and Phlebotomus vetus sp. n., respectively. Bruchomyiinae is represented by Nemopalpus quadrispiculatus sp. n. Furthermore, one genus of an incertae sedis subfamily, Bamara groehni gen. et sp. n., is described. The systematic positions of the new taxa are discussed.

  5. Dose rate influence in the response of the amber 3042 perspex Dosimeter, batch l

    International Nuclear Information System (INIS)

    Prieto Miranda, E. F.; Barrera Gonzalez, G.

    2001-01-01

    The answer of the dosimetry systems is affected by several factors , as the temperature, humidity, light, concentration of oxygen, dose rate, energy spectrum and one can also add the technological conditions of the irradiation process. It should be known as these factors influence in each one of the different dosimetry systems and this way to minimize their effect in the value of the absorbed dose and to obtain exact values . The objective of this paper is to know the influence of the dose rate in the value of the absorbed dose in the Amber 3042 Perspex dosimeters, Batch L, for different measurement wavelengths, as well as, the relation between the post-irradiation time and the induced specific absorbance value in function of the absorbed dose

  6. ESR characterization of point defects in amber colored c-BN super abrasive powders

    International Nuclear Information System (INIS)

    Nistor, S.V.; Ghica, D.; Stefan, M.; Bouwen, A.; Goovaerts, E.

    2004-01-01

    Cubic boron nitride (c-BN) crystalline superabrasive powder (Borazon ** CBN 400), consisting of 200-300 microns sized amber colored crystallites prepared by HP/HT synthesis, has been examined from 2.1 K to 293 K by X-band ESR spectroscopy. The observed spectrum consists of a component line A1, visible in the whole temperature range, and two component lines A2 and A3, visible at high and low temperatures, respectively. The A1 and A3 lines originate from transitions inside S = 1/2 ground states of distinct paramagnetic species and A2 from transitions inside an excited state of another paramagnetic center. The intensity of the A1 and A3 lines changes differently during in situ low temperature illumination in the UV-VIS range. * Borazon is a registered trademark of Diamond Innovations, Inc. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  7. 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.

    2016-01-01

    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

  8. Rovno Amber Ant Assamblage: Bias toward Arboreal Strata or Sampling Effect?

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2016-06-01

    Full Text Available In 2015 B. Guenard with co-authors indicated that the Rovno amber ant assemblage, as described by G. Dlussky and A. Rasnitsyn (2009, showed modest support for a bias towards arboreal origin comparing the Baltic and Bitterfeld assemblages, although it is not clear whether this reflects a sampling error or a signal of real deviation. Since 2009, the Rovno ant collection has now grown more than twice in volume which makes possible to check if the above inference about the essentially arboreal character of the assemblage is real or due to a sampling error. The comparison provided suggests in favour of the latter reason for the bias revealed by B. Guenard and co-authors. The new and larger data on the Rovno assemblage show that the share of non-arboreal ants is now well comparable with those concerning the Baltic and Bitterfeld assemblages. This holds true for the both total assemblages and subassemblages of worker ants only.

  9. Stability of diclofenac sodium oral suspensions packaged in amber polyvinyl chloride bottles.

    Science.gov (United States)

    Donnelly, Ronald F; Pascuet, Elena; Ma, Carmen; Vaillancourt, Régis

    2010-01-01

    Prescribing of diclofenac for children usually involves a dose different from commercially available strengths. This drug is available only as tablets, which can be divided only so many times before the dose obtained becomes inaccurate. In addition, children may have difficulty swallowing tablets. For these reasons, a compounding formula for a liquid dosage form is essential to ensure effective delivery of the drug to pediatric patients. To develop a compounding formula for diclofenac sodium and to determine the extended physical and chemical stability of this compound when stored in amber polyvinyl chloride (PVC) prescription bottles under refrigeration and at room temperature. A suspension of diclofenac sodium (10 mg/mL) was prepared from commercially available diclofenac sodium tablets, with Ora-Blend as the suspending and flavouring agent. The suspension was packaged in 60-mL amber PVC prescription bottles and stored at either room temperature (23°C) or under refrigeration (5°C). Samples were collected on days 0, 7, 14, 21, 27, 56, and 93. Chemical stability was determined using a validated stability-indicating high-performance liquid chromatography method. At each sampling time, the suspensions were checked for changes in appearance (i.e., colour, layering, caking, ease of resuspension), odour, and pH. The diclofenac sodium suspensions were very stable, retaining at least 99.5% of the original concentration for up to 93 days, regardless of storage temperature. There were no apparent changes in the physical appearance of the suspensions, nor were there any substantial changes in odour or pH. Suspensions of diclofenac sodium (10 mg/mL) were quantitatively stable but difficult to prepare because of the enteric coating of the tablets. Therefore, it is recommended that diclofenac powder be used for the preparation of suspensions. For pediatric use, palatability is a consideration, and a masking agent should be added before administration. An expiry date of up to

  10. New Genus and Species of Gall Midges (Diptera, Cecidomyiidae, Porricondylinae, Holoneurini from the Late Eocene Amber of Olevsk (Zhitomir Region, Ukraine

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    Fedotova Z. A.

    2017-02-01

    Full Text Available Gall midges are reported for the first time in Late Eocene Rovno amber from the Olevsk, Zhitomir Region. This is the second amber locality to yield gall midges in the Zhitomir Region, after Gulyanka. Rovnoholoneurus gen. n. and two new species, Rovnoholoneurus davidi sp. n. and R. miyae sp. n. are described. Bryocrypta laqueata Fedotova, 2005 is transferred to the genus Rovnoholoneurus, and Rovnoholoneurus laqueatus (Fedotova, 2005, comb. n. is established. A key to the species of Rovnoholoneurus is provided.

  11. Using 20-million-year-old amber to test the super-Arrhenius behaviour of glass-forming systems

    Science.gov (United States)

    Zhao, Jing; Simon, Sindee L.; McKenna, Gregory B.

    2013-04-01

    Fossil amber offers the opportunity to investigate the dynamics of glass-forming materials far below the nominal glass transition temperature. This is important in the context of classical theory, as well as some new theories that challenge the idea of an ‘ideal’ glass transition. Here we report results from calorimetric and stress relaxation experiments using a 20-million-year-old Dominican amber. By performing the stress relaxation experiments in a step-wise fashion, we measured the relaxation time at each temperature and, above the fictive temperature of this 20-million-year-old glass, this is an upper bound to the equilibrium relaxation time. The results deviate dramatically from the expectation of classical theory and are consistent with some modern ideas, in which the diverging timescale signature of complex fluids disappears below the glass transition temperature.

  12. A new genus and species of micro bee fly from the Earliest Eocene French amber (Diptera: Mythicomyiidae: Psiloderoidinae).

    Science.gov (United States)

    Myskowiak, Justine; Garrouste, Romain; Nel, Andre

    2016-05-26

    Mythicomyiidae, or micro bee flies, are tiny flies (0.5-5.0 mm) that are found throughout most parts of the world except the highest altitudes and latitudes (Greathead & Evenhuis 2001). Including all extinct and extant taxa, the Mythicomyiidae currently comprise more than 380 valid taxonomic species distributed among 30 genera. The subfamily Psiloderoidinae is especially well represented among the fossil Mythicomyiidae by seven Cretaceous or Cenozoic genera. We here describe a new genus and a new species of this subfamily based on fossils from the Earliest Eocene of Oise (France). A Psiloderoidinae, Proplatypygus matilei Nel & DePloëg, 2004, is already described in this amber. Another mythicomyiid, Eurodoliopteryx inexpectatus Nel, 2006, is the most frequent bombylioid in this amber (Nel & DePloëg, 2004; Nel, 2006).

  13. Evolution and classification of Elaphoglossum and Asplenium ferns on Cuba, and discovery of a Miocene Elaphoglossum in Dominican amber

    OpenAIRE

    Lóriga Piñero, Josmaily

    2018-01-01

    This dissertation deals with the systematics and evolution of Neotropical ferns of the genera Elaphoglossum and Asplenium, with particular focus on the species of Cuba and the West Indies. It also includes an analysis and description of an Elaphoglossum frond fragment preserved in Miocene Dominican amber. The worldwide genera Elaphoglossum with 600 species and Asplenium with 685 species are the most species-rich groups of leptosporangiate ferns. On Cuba, Elaphoglossum has 34 species and Asple...

  14. A potential amber-emitting KCaVO4:Sm3+ nanophosphor for near-UV LEDs

    Science.gov (United States)

    Biswas, Pankaj; Kumar, Vinay

    2018-05-01

    The Sm3+ doped KCaVO4 phosphor powders were synthesized via combustion route. The powder X-ray diffraction (pXRD) analysis established the crystalline structure and phase of the phosphor material. Williamson-Hall technique was employed to approximate the mean grain size and lattice micro-strain. The transmission electron microscope (TEM) studies were carried out to confirm the nano-sized grain formation. On 405 nm excitation, the phosphor gave amber emission which was assigned to 4G5/2 → 6HJ/2 (J = 7/2, 9/2) transitions of the Sm3+ ion. The concentration quenching mechanism was studied and the optimum dopant concentration in the phosphor was obtained as 2.0 mol%. The diffuse reflectance (DR) studies were carried out to obtain optical band gap (Eg) and Urbach energy (Ec) of the KCaVO4 phosphor which were estimated as 3.63 eV and 98.6 meV, respectively. The color coordinates (x = 0.61, y = 0.39) of the nanophosphor signified the amber shade in the color gamut. The high luminescent properties of KCaVO4:Sm3+ phosphor suggests that the material can be explored as a potential phosphor to be profitably excited by near-UV LEDs to bridge the amber gap in light emitting diodes (LEDs) for solid state lighting (SSL) applications.

  15. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

    Directory of Open Access Journals (Sweden)

    Longhua Yang

    2016-09-01

    Full Text Available Cytochrome c oxidase (CcO is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F, we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.

  16. Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus

    Energy Technology Data Exchange (ETDEWEB)

    Dunlop, Jason A.; Apanaskevich, Dmitry A.; Lehmann, Jens; Hoffmann, René; Fusseis, Florian; Ehlke, Moritz; Zachow, Stefan; Xiao, Xianghui

    2016-10-10

    Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44–49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil’s referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner’s amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases.

  17. Molecular and Morphological Evidence Challenges the Records of the Extant Liverwort Ptilidium pulcherrimum in Eocene Baltic Amber.

    Science.gov (United States)

    Heinrichs, Jochen; Scheben, Armin; Lee, Gaik Ee; Váňa, Jiří; Schäfer-Verwimp, Alfons; Krings, Michael; Schmidt, Alexander R

    2015-01-01

    Preservation of liverworts in amber, a fossilized tree resin, is often exquisite. Twenty-three fossil species of liverworts have been described to date from Eocene (35-50 Ma) Baltic amber. In addition, two inclusions have been assigned to the extant species Ptilidium pulcherrimum (Ptilidiales or Porellales). However, the presence of the boreal P. pulcherrimum in the subtropical or warm-temperate Baltic amber forest challenges the phytogeographical interpretation of the Eocene flora. A re-investigation of one of the fossils believed to be P. pulcherrimum reveals that this specimen in fact represents the first fossil evidence of the genus Tetralophozia, and thus is re-described here as Tetralophozia groehnii sp. nov. A second fossil initially assigned to P. pulcherrimum is apparently lost, and can be reassessed only based on the original description and illustrations. This fossil is morphologically similar to the extant North Pacific endemic Ptilidium californicum, rather than P. pulcherrimum. Divergence time estimates based on chloroplast DNA sequences provide evidence of a Miocene origin of P. pulcherrimum, and thus also argue against the presence of this taxon in the Eocene. Ptilidium californicum originated 25-43 Ma ago. As a result, we cannot rule out that the Eocene fossil belongs to P. californicum. Alternatively, the fossil might represent a stem lineage element of Ptilidium or an early crown group species with morphological similarities to P. californicum.

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

    Science.gov (United States)

    Yoshizawa, Kazunori; Lienhard, Charles

    2016-02-11

    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.

  19. 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.

  20. Seryl-tRNA Synthetases from Methanogenic Archaea: Suppression of Bacterial Amber Mutation and Heterologous Toxicity

    Directory of Open Access Journals (Sweden)

    Drasko Boko

    2010-01-01

    Full Text Available Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS, evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.

  1. Two flat-backed polydesmidan millipedes from the Miocene Chiapas-amber Lagerstätte, Mexico.

    Directory of Open Access Journals (Sweden)

    Francisco Riquelme

    Full Text Available Two species of fossil polydesmidan millipedes (Diplopoda: Polydesmida embedded in amber are described from Miocene strata near Simojovel, in the Chiapas Highlands, Mexico. Maatidesmus paachtun gen. et sp. nov., placed into Chelodesmidae Cook, 1895, and Anbarrhacus adamantis gen. et sp. nov., assigned in the family Platyrhacidae Pocock, 1895. Morphological data from fossil specimens have been recovered using 3D X-ray micro-computed tomography and regular to infrared-reflected microscopy. Both fossil species are recognizable as new primarily but not exclusively, by collum margin modification and remarkable paranotal and metatergite dorsal sculpture.

  2. Two Flat-Backed Polydesmidan Millipedes from the Miocene Chiapas-Amber Lagerstätte, Mexico

    Science.gov (United States)

    Riquelme, Francisco; Hernández-Patricio, Miguel; Martínez-Dávalos, Arnulfo; Rodríguez-Villafuerte, Mercedes; Montejo-Cruz, Maira; Alvarado-Ortega, Jesús; Ruvalcaba-Sil, José L.; Zúñiga-Mijangos, Luis

    2014-01-01

    Two species of fossil polydesmidan millipedes (Diplopoda: Polydesmida) embedded in amber are described from Miocene strata near Simojovel, in the Chiapas Highlands, Mexico. Maatidesmus paachtun gen. et sp. nov., placed into Chelodesmidae Cook, 1895, and Anbarrhacus adamantis gen. et sp. nov., assigned in the family Platyrhacidae Pocock, 1895. Morphological data from fossil specimens have been recovered using 3D X-ray micro-computed tomography and regular to infrared-reflected microscopy. Both fossil species are recognizable as new primarily but not exclusively, by collum margin modification and remarkable paranotal and metatergite dorsal sculpture. PMID:25162220

  3. Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.

    Science.gov (United States)

    Snow, M E; Crippen, G M

    1991-08-01

    The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.

  4. Lutzomyia adiketis sp. n. (Diptera: Phlebotomidae, a vector of Paleoleishmania neotropicum sp. n. (Kinetoplastida: Trypanosomatidae in Dominican amber

    Directory of Open Access Journals (Sweden)

    Poinar George

    2008-07-01

    Full Text Available Abstract Background Amber fossils can be used to trace the history of disease-vector associations because microorganisms are preserved "in situ" inside the alimentary tract and body cavity of blood-sucking insects. Results Lutzomyia adiketis sp. n. (Phlebotomidae: Diptera is described from Dominican amber as a vector of Paleoleishmania neotropicum sp. n. (Kinetoplastida: Trypanosomatidae. The fossil sand fly differs from all previously described extinct and extant members of the genus by the following combination of characters: Sc forked with the branches meeting the costa and radius veins; wing L/W value of 4.1; a δ value of 18; a ratio β/α value of 0.86, and the shape and size of the spatulate rods on the ninth sternite. The trypanosomatid is characterized by the structure of its promastigotes, amastigotes and paramastigotes and its transmission by an extinct species of sand fly. Conclusion Morphological characters show that the fossil sand fly is a new extinct species and that it is host to a digenetic species of trypanosomatid. This study provides the first fossil evidence that Neotropical sand flies were vectors of trypanosomatids in the mid-Tertiary (20–30 mya.

  5. Potential of Sm3+ doped LiSrVO4 nanophosphor to fill amber gap in LEDs

    Science.gov (United States)

    Biswas, P.; Kumar, Vinay; Sharma, Vishal; Bedyal, A. K.; Padha, Naresh; Swart, H. C.

    2018-04-01

    The LiSrVO4:Sm3+ phosphor powders were synthesized by the combustion method by varying the concentration of the Sm3+ ions from 0.25 mol% to 2.5 mol%. The powder X-ray diffraction (XRD) studies confirmed that the phosphors were crystallized as monoclinic structure belonging to space group P2/m and the transmission electron microscopy (TEM) revealed nanosized grains of the powders. The Fourier transform infrared studies (FTIR) established the formation of non-hygroscopic vanadate powders. The photoluminescence (PL) and diffused reflectance studies (DRS) were also carried out and discussed. Under 401 nm excitation, the optimized phosphor exhibited the characteristic 568, 600, 646 and 704 nm emissions of Sm3+ which corresponded to the orange-red (amber) color with (0.59, 0.41) Commission Internationale de' Eclairage (CIE) chromaticity coordinates. Concentration quenching of phosphor intensity on account of non-radiative energy transfer was ascribed to dipole-dipole interaction between activators. DRS study reveals that the host of the phosphor is a wide bandgap material which accommodates the dopant successfully. The present results signify that the LiSrVO4:Sm3+ phosphor can suitably be excited by the GaN family of UV-LEDs chips for efficient amber LEDs applications.

  6. Remarkable preservation of terpenoids and record of volatile signalling in plant-animal interactions from Miocene amber.

    Science.gov (United States)

    Dutta, Suryendu; Mehrotra, Rakesh C; Paul, Swagata; Tiwari, R P; Bhattacharya, Sharmila; Srivastava, Gaurav; Ralte, V Z; Zoramthara, C

    2017-09-08

    Plants produce and release a large array of volatile organic compounds that play many ecological functions. These volatile plant metabolites serve as pollinator attractants, herbivore and pathogen repellents and protect plants from abiotic stresses. To date, the geological evolution of these organic compounds remains unknown. The preservation potential of these metabolites in the fossil record is very poor due to their low boiling points. Here we report a series of volatile sesquiterpenoids, including δ-elemene, α-copaene, β-elemene, β-caryophyllene, α-humulene, germacrene D, δ-cadiene and spathunenol, from early Miocene (~17 million year) amber from eastern India. The survival of these unaltered bioterpenoids can be attributed to the existence of extraordinary taphonomic conditions conducive to the preservation of volatile biomolecules through deep time. Furthermore, the occurrence of these volatiles in the early Miocene amber suggests that the plants from this period had evolved metabolic pathways to synthesize these organic molecules to play an active role in forest ecology, especially in plant-animal interactions.

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

    Directory of Open Access Journals (Sweden)

    Sanguinette Cristiani

    2009-05-01

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

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

    DEFF Research Database (Denmark)

    Issinger, O G; Hausmann, R

    1973-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-06

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

  10. 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.

  11. Extended Stability of Epinephrine Hydrochloride Injection in Polyvinyl Chloride Bags Stored in Amber Ultraviolet Light-Blocking Bags.

    Science.gov (United States)

    Van Matre, Edward T; Ho, Kang C; Lyda, Clark; Fullmer, Beth A; Oldland, Alan R; Kiser, Tyree H

    2017-09-01

    Objective: The objective of this study was to evaluate the stability of epinephrine hydrochloride in 0.9% sodium chloride in polyvinyl chloride bags for up to 60 days. Methods: Dilutions of epinephrine hydrochloride to concentrations of 16 and 64 µg/mL were performed under aseptic conditions. The bags were then placed into ultraviolet light-blocking bags and stored at room temperature (23°C-25°C) or under refrigeration (3°C-5°C). Three samples of each preparation and storage environment were analyzed on days 0, 30, 45, and 60. Physical stability was performed by visual examination. The pH was assessed at baseline and upon final degradation evaluation. Sterility of the samples was not assessed. Chemical stability of epinephrine hydrochloride was evaluated using high-performance liquid chromatography. To determine the stability-indicating nature of the assay, degradation 12 months following preparation was evaluated. Samples were considered stable if there was less than 10% degradation of the initial concentration. Results: Epinephrine hydrochloride diluted to 16 and 64 µg/mL with 0.9% sodium chloride injection and stored in amber ultraviolet light-blocking bags was physically stable throughout the study. No precipitation was observed. At days 30 and 45, all bags had less than 10% degradation. At day 60, all refrigerated bags had less than 10% degradation. Overall, the mean concentration of all measurements demonstrated less than 10% degradation at 60 days at room temperature and under refrigeration. Conclusion: Epinephrine hydrochloride diluted to 16 and 64 µg/mL with 0.9% sodium chloride injection in polyvinyl chloride bags stored in amber ultraviolet light-blocking bags was stable up to 45 days at room temperature and up to 60 days under refrigeration.

  12. Fundamental properties and atmospheric structure of the red supergiant VY Canis Majoris based on VLTI/AMBER spectro-interferometry

    Science.gov (United States)

    Wittkowski, M.; Hauschildt, P. H.; Arroyo-Torres, B.; Marcaide, J. M.

    2012-04-01

    Aims: We investigate the atmospheric structure and fundamental properties of the red supergiant VY CMa. Methods: We obtained near-infrared spectro-interferometric observations of VY CMa with spectral resolutions of 35 and 1500 using the AMBER instrument at the VLTI. Results: 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 μm is increased by ~20% compared to the near-continuum bandpass at 2.20-2.25 μm, and in the CO band at 2.3-2.5 μm it is increased by up to ~50%. 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 atmosphere model. Together with recent high-precision estimates of the distance and spectro-photometry, this estimate corresponds to a radius of 1420 ± 120 R⊙ and an effective temperature of 3490 ± 90 K. Conclusions: VY CMa exhibits asymmetric, possibly clumpy, atmospheric layers of H2O and CO, which are not co-spatial, within a larger elongated dusty envelope. Our revised fundamental parameters put VY CMa close to the Hayashi limit of recent evolutionary tracks of initial mass 25 M⊙ with rotation or 32 M⊙ without rotation, shortly before evolving blueward in the HR-diagram. Based on observations made with the VLT Interferometer (VLTI) at Paranal Observatory under programme ID 386.D-0012.Figures 2, 3 and 5 are available in electronic form at http://www.aanda.org

  13. 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.

    2016-01-01

    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. PMID:26650177

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

    Czech Academy of Sciences Publication Activity Database

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

    2010-01-01

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

  15. 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

  16. Electrical, spectral and optical performance of yellow-green and amber micro-pixelated InGaN light-emitting diodes

    Science.gov (United States)

    Gong, Z.; Liu, N. Y.; Tao, Y. B.; Massoubre, D.; Xie, E. Y.; Hu, X. D.; Chen, Z. Z.; Zhang, G. Y.; Pan, Y. B.; Hao, M. S.; Watson, I. M.; Gu, E.; Dawson, M. D.

    2012-01-01

    Micro-pixelated InGaN LED arrays operating at 560 and 600 nm, respectively, are demonstrated for what the authors believe to be the first time. Such devices offer applications in areas including bioinstrumentation, visible light communications and optoelectronic tweezers. The devices reported are based on new epitaxial structures, retaining conventional (0 0 0 1) orientation, but incorporating electron reservoir layers which enhance the efficiency of radiative combination in the active regions. A measured output optical power density up to 8 W cm-2 (4.4 W cm-2) has been achieved from a representative pixel of the yellow-green (amber) LED array, substantially higher than that from conventional broad-area reference LEDs fabricated from the same wafer material. Furthermore, these micro-LEDs can sustain a high current density, up to 4.5 kA cm-2, before thermal rollover. A significant blueshift of the emission wavelength with increasing injection current is observed, however. This blueshift saturates at 45 nm (50 nm) for the yellow-green (amber) LED array, and numerical simulations have been used to gain insight into the responsible mechanisms in this microstructured format of device. In the relatively low-current-density regime (screening of the piezoelectric field by the injected carriers and the band-filling effect, whereas in the high-current regime, it is mainly due to band-filling. Further development of the epitaxial wafer material is expected to improve the current-dependent spectral stability.

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

    Science.gov (United States)

    2016-01-01

    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

  18. 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.

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

    Science.gov (United States)

    Su, Pin-Chih; Johnson, Michael E

    2016-04-05

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

  20. A review and phylogeny of Scarabaeine dung beetle fossils (Coleoptera: Scarabaeidae: Scarabaeinae, with the description of two Canthochilum species from Dominican amber

    Directory of Open Access Journals (Sweden)

    Sergei Tarasov

    2016-05-01

    Full Text Available Despite the increasing rate of systematic research on scarabaeine dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae, their fossil record has remained largely unrevised. In this paper, we review all 33 named scarabaeine fossils and describe two new species from Dominican amber (Canthochilum alleni sp.n., Canthochilum philipsivieorum sp.n.. We provide a catalogue of all fossil Scarabaeinae and evaluate their assignment to this subfamily, based primarily on the original descriptions but also, where possible, by examining the type specimens. We suggest that only 21 fossil taxa can be reliably assigned to the Scarabaeinae, while the remaining 14 should be treated as doubtful Scarabaeinae. The doubtful scarabaeines include the two oldest dung beetle fossils known from the Cretaceous and we suggest excluding them from any assessments of the minimum age of scarabaeine dung beetles. The earliest reliably described scarabaeine fossil appears to be Lobateuchus parisii, known from Oise amber (France, which shifts the minimum age of the Scarabaeinae to the Eocene (53 Ma. We scored the best-preserved fossils, namely Lobateuchus and the two Canthochilum species described herein, into the character matrix used in a recent morphology-based study of dung beetles, and then inferred their phylogenetic relationships with Bayesian and parsimony methods. All analyses yielded consistent phylogenies where the two fossil Canthochilum are placed in a clade with the extant species of Canthochilum, and Lobateuchus is recovered in a clade with the extant genera Ateuchus and Aphengium. Additionally, we evaluated the distribution of dung beetle fossils in the light of current global dung beetle phylogenetic hypotheses, geological time and biogeography. The presence of only extant genera in the late Oligocene and all later records suggests that the main present-day dung beetle lineages had already been established by the late Oligocene–mid Miocene.

  1. The Green, Amber, Red Delineation of Risk and Need (GARDIAN) management system: a pragmatic approach to optimizing heart health from primary prevention to chronic disease management.

    Science.gov (United States)

    Carrington, Melinda J; Kok, Simone; Jansen, Kiki; Stewart, Simon

    2013-08-01

    A sustained epidemic of cardiovascular disease and related risk factors is a global phenomenon contributing significantly to premature deaths and costly morbidity. Preventative strategies across the full continuum of life, from a population to individual perspective, are not optimally applied. This paper describes a simple and adaptable 'traffic-light' system we have developed to systematically perform individual risk and need delineation in order to 'titrate' the intensity and frequency of healthcare intervention in a cost-effective manner. The GARDIAN (Green Amber Red Delineation of Risk and Need) system is an individual assessment of risk and need that modulates the frequency and intensity of future healthcare intervention. Individual assessment of risk and need for ongoing intervention and support is determined with reference to three domains: (1) clinical stability, (2) gold-standard management, and (3) a broader, holistic assessment of individual circumstance. This can be applied from a primary prevention, secondary prevention, or chronic disease management perspective. Our experience with applying and validating GARDIAN to titrate healthcare resources according to need has been extensive to date, with >5000 individuals profiled in a host of clinical settings. A series of clinical randomized trials will determine the impact of the GARDIAN system on important indices of healthcare utilization and health status. The GARDIAN model to delineating risk and need for varied intensity of management shows strong potential to cost effectively improve health outcomes for both individuals at risk of heart disease and those with established heart disease.

  2. Admixture mapping of African-American women in the AMBER Consortium identifies new loci for breast cancer and estrogen-receptor subtypes

    Directory of Open Access Journals (Sweden)

    Edward Antonio Ruiz-Narvaez

    2016-09-01

    Full Text Available Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative and 601 triple-negative and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.

  3. Museum Institutions in Monuments - Positive and Negative Aspects of Adaptation: The New Amber Museum and Museum of Science in Gdansk, Poland

    Science.gov (United States)

    Piatkowska, Ksenia

    2017-10-01

    The issue of the creation and location of new museums is a current topic. The decision of where and how to create new museum facilities will impact successful function in the future. Museums are either located in newly designed buildings or in existing buildings. In general, existing buildings adapted for museum use are either formally under conservational protection or not. With regard to museum location in preserved monuments, the author notes that the true impact on authentic monumental building structure still needs intense research. The adaptation of the Great Mill and St. Catherine’s Church - two preserved medieval objects located in the historical city center of Gdansk - provide case studies to investigate positive and negative aspects. In both cases, the author carried out architectural projects for the functional purposes of museums: The New Amber Museum and Museum of Science. The author concludes that mutual benefits of adaptation result from: the financial means of the museum institution to invest long-term; the institutional respect of the museum towards heritage, which translates into respect for conservational protection; and the competitive advantage created by the monumental features of the building and the privileged location in a well-established, branded space. Negative aspects result from: space limitations of monuments that disable the museum from extending its exposition and thus prevent institutional development; the overly restrictive requirements of restoration that take priority over the museum mission; and the lack of technically functional space required for contemporary museum technologies, which forces unconventional engineering solutions that are more expensive than the location of the museum in a newly constructed building.

  4. 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)

  5. AM Broadcast Emergency Relay (AMBER)

    Science.gov (United States)

    1990-07-01

    TIFTON GA US FC-n 3 5000 1000 31.456 -83.561 231 4989 1430 WMNC MORGANTOWN NC US F--n 3 5000 1000 35.752 -81.717 232 5080 1440 KODL THE DALLES OR US FC-n...Loring, ME Cutter, ME Alt. CINCSAC Plattsburgh, NY March AFB, CA Barksdale, LA Pease, Nil CINCLANT Griffiss, NY Norfolk, VA Sy Johnson, NC Robbins, GA ...retransmission. This process is repeated at AM stations located on the A k 0. AA 0o. .... - ° o" : 331 s os 0,u . psi risk area .. 001 0 00 ga Haqua

  6. 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

  7. Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions.

    Science.gov (United States)

    Vymětal, Jiří; Vondrášek, Jiří

    2014-09-04

    We present a novel force field model of 2,2,2-trifluoroethanol (TFE) based on the generalized AMBER force field. The model was exhaustively parametrized to reproduce liquid-state properties of pure TFE, namely, density, enthalpy of vaporization, self-diffusion coefficient, and population of trans and gauche conformers. The model predicts excellently other liquid-state properties such as shear viscosity, thermal expansion coefficient, and isotropic compressibility. The resulting model describes unexpectedly well the state equation of the liquid region in the range of 100 K and 10 MPa. More importantly, the proposed TFE model was optimized for use in combination with the TIP4P/Ew and TIP4P/2005 water models. It does not manifest excessive aggregation, which is known for other models, and therefore, it is supposed to more realistically describe the behavior of TFE/water mixtures. This was demonstrated by means of the Kirkwood-Buff theory of solutions and reasonable agreement with experimental data. We explored a considerable part of the parameter space and systematically tested individual combinations of parameters for performance in combination with the TIP4P/Ew and TIP4P/2005 water models. We observed ambiguity in parameters describing pure liquid TFE; however, most of them failed for TFE/water mixtures. We clearly demonstrated the necessity for balanced TFE-TFE, TFE-water, and water-water interactions which can be acquired only by employing implicit polarization correction in the course of parametrization.

  8. Durability of virologic response, risk of de novo hepatocellular carcinoma, liver function and stiffness two years after treatment with Ombitasvir/Paritaprevir/Ritonavir ±Dasabuvir ±Ribavirin in the AMBER, real-world experience study.

    Science.gov (United States)

    Flisiak, Robert; Janczewska, Ewa; Łucejko, Mariusz; Karpińska, Ewa; Zarębska-Michaluk, Dorota; Nazzal, Khalil; Bolewska, Beata; Białkowska, Jolanta; Berak, Hanna; Fleischer-Stępniewska, Katarzyna; Tomasiewicz, Krzysztof; Karwowska, Kornelia; Simon, Krzysztof; Piekarska, Anna; Tronina, Olga; Tuchendler, Ewelina; Garlicki, Aleksander

    2018-06-11

    We followed for 2 years patients treated with Direct Acting Agents (DAA) to assess long-term durability of virologic response, improvement of liver function, reduction of liver stiffness (LS), and risk of hepatocellular carcinoma (HCC).The study included patients from 16 hepatologic centers involved in the AMBER, investigators initiated study on treatment of chronic hepatitis C patients within a programme preceding EU registration of Ombitasvir/Paritaprevir/ritonavir±Dasabuvir±Ribavirin. A total of 204 patients among 209 from the primary study were enrolled; 200 with available testing at 2 years follow-up (2yFU) with undetectable HCV RNA (198 responders and 2 non-responders retreated). During 2yFU 4 patients died, 17 had hepatic decompensation and 3 needed liver transplantation. De novo hepatocellular carcinoma was diagnosed in 4 and its recurrence in 3 patients. Significant decreases in bilirubin, MELD, Child-Pugh scores and liver stiffness, and increases in albumin level were observed during 2yFU. Strengths of the study were a fixed period of post treatment follow-up, prospective character of the study and high proportion of available patients from the primary study. The major weaknesses was lack of a comparative arm and relatively insufficient number of patients for subsets analysis. In conclusion, two-years follow-up confirmed durability of virologic response after treatment of HCV infection with Ombitasvir/Paritaprevir/ritonavir±Dasabuvir±Ribavirin. It was accompanied by significant improvement of major measures of hepatic function and reduction of hepatic stiffness. Successful therapy did not prevent hepatic decompensation, HCC or death in cirrhotics, that support the need for longer than 2-year monitoring for possible disease progression. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. Role of quantum-confined stark effect on bias dependent photoluminescence of N-polar GaN/InGaN multi-quantum disk amber light emitting diodes

    Science.gov (United States)

    Tangi, Malleswararao; Mishra, Pawan; Janjua, Bilal; Prabaswara, Aditya; Zhao, Chao; Priante, Davide; Min, Jung-Wook; Ng, Tien Khee; Ooi, Boon S.

    2018-03-01

    We study the impact of quantum-confined stark effect (QCSE) on bias dependent micro-photoluminescence emission of the quantum disk (Q-disk) based nanowires light emitting diodes (NWs-LED) exhibiting the amber colored emission. The NWs are found to be nitrogen polar (N-polar) verified using KOH wet chemical etching and valence band spectrum analysis of high-resolution X-ray photoelectron spectroscopy. The crystal structure and quality of the NWs were investigated by high-angle annular dark field - scanning transmission electron microscopy. The LEDs were fabricated to acquire the bias dependent micro-photoluminescence spectra. We observe a redshift and a blueshift of the μPL peak in the forward and reverse bias conditions, respectively, with reference to zero bias, which is in contrast to the metal-polar InGaN well-based LEDs in the literature. Such opposite shifts of μPL peak emission observed for N-polar NWs-LEDs, in our study, are due to the change in the direction of the internal piezoelectric field. The quenching of PL intensity, under the reverse bias conditions, is ascribed to the reduction of electron-hole overlap. Furthermore, the blueshift of μPL emission with increasing excitation power reveals the suppression of QCSE resulting from the photo-generated carriers. Thereby, our study confirms the presence of QCSE for NWs-LEDs from both bias and power dependent μPL measurements. Thus, this study serves to understand the QCSE in N-polar InGaN Q-disk NWs-LEDs and other related wide-bandgap nitride nanowires, in general.

  10. Role of quantum-confined stark effect on bias dependent photoluminescence of N-polar GaN/InGaN multi-quantum disk amber light emitting diodes

    KAUST Repository

    Tangi, Malleswararao

    2018-03-09

    We study the impact of quantum-confined stark effect (QCSE) on bias dependent micro-photoluminescence emission of the quantum disk (Q-disk) based nanowires light emitting diodes (NWs-LED) exhibiting the amber colored emission. The NWs are found to be nitrogen polar (N-polar) verified using KOH wet chemical etching and valence band spectrum analysis of high-resolution X-ray photoelectron spectroscopy. The crystal structure and quality of the NWs were investigated by high-angle annular dark field - scanning transmission electron microscopy. The LEDs were fabricated to acquire the bias dependent micro-photoluminescence spectra. We observe a redshift and a blueshift of the μPL peak in the forward and reverse bias conditions, respectively, with reference to zero bias, which is in contrast to the metal-polar InGaN well-based LEDs in the literature. Such opposite shifts of μPL peak emission observed for N-polar NWs-LEDs, in our study, are due to the change in the direction of the internal piezoelectric field. The quenching of PL intensity, under the reverse bias conditions, is ascribed to the reduction of electron-hole overlap. Furthermore, the blueshift of μPL emission with increasing excitation power reveals the suppression of QCSE resulting from the photo-generated carriers. Thereby, our study confirms the presence of QCSE for NWs-LEDs from both bias and power dependent μPL measurements. Thus, this study serves to understand the QCSE in N-polar InGaN Q-disk NWs-LEDs and other related wide-bandgap nitride nanowires, in general.

  11. VLTI-AMBER Velocity-Resolved Aperture-Synthesis Imaging of Eta 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.; hide

    2016-01-01

    The mass loss from massive stars is not understood well. Eta 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 Car's primary star wind and wind-wind collision zone with a high spatial resolution of approx.6 mas (approx.14 au) and high spectral resolution of R = 12 000. Methods. Observations of 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 di erent spectral channels distributed across the Br(gamma) 2.166 micron 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 measured relative to line center, the intensity distribution has a fan-shaped structure. At the velocity of -277 km/s, the position angle of the symmetry axis of the fan is 126. The fan-shaped structure extends approximately 8.0 mas (approx.18:8 au) to the southeast and 5.8 mas (approx.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

  12. Estudios preliminares de estabilidad de un extracto lipídico de los frutos de Roystonea regia en frascos de vidrio ámbar Preliminary studies of a lipid extract stability from the fruits of Roystonea regia in amber glass flasks

    Directory of Open Access Journals (Sweden)

    Roxana de la Caridad Sierra Pérez

    2010-09-01

    Full Text Available El D004 es un nuevo ingrediente activo extraído de los frutos de la palma real cubana (Roystonea regia, promisorio en el tratamiento de la hiperplasia prostática benigna. Para determinar su estabilidad en frascos de vidrio ámbar, se realizaron estudios donde las muestras se sometieron a diferentes condiciones. En condiciones de estrés se observó que el D004 es susceptible a la degradación térmica y oxidativa. En condiciones aceleradas (40 ± 2 ºC y 75 ± 5 % humedad relativa no se observaron cambios significativos en ninguno de los parámetros evaluados durante 12 meses, lo que permitió predecir un tiempo de vida útil de al menos 2 años en condiciones menos drásticas. Esto fue corroborado en las condiciones de las zonas climáticas II (25 ± 2 ºC y 60 ± 5 % humedad relativa y IV (30 ± 2 ºC y 70 ± 5 % humedad relativa.The D004 is a new active ingredient extracted from the Cuban real palm (Roystonea regia, promising in the treatment of the benign prostatic hyperplasia. To determine its stability in amber glass flasks studies were conducted where samples underwent different conditions. In stress situations D004 is sensitive to the thermal and oxidative degradation. Under accelerated conditions (40 ± 2 ºC ad 75 ± 5 % of relative humidity there weren't significant changes in any assessed parameters during 12 months allowing predicting a useful life time of at least 2 years under less drastic conditions. It was corroborated under climatic conditions II (25 ± 2ºC and 60± 5% of relative humidity and IV (30 ± 2 ºC and 70 ± 5 % of relative humidity.

  13. Проблемы развития янтарной отрасли и противодействие незаконному обороту янтаря в Балтийском регионе=The Amber Industry: Development Сhallenges and Combating Amber Trafficking in the Baltic Region

    Directory of Open Access Journals (Sweden)

    Волчецкая Т. С.

    2017-12-01

    олной мере эффективны; предложено введение мер уголовной ответственности при повторном совершении этих противоправных деяний. Показаны возможности геммологической экспертизы в исследовании янтаря и изделий из него, проанализированы особенности ее назначения. This article considers the current state and prospective development of the amber industry in the Baltic Sea region. The authors identify the main obstacles to the industry’s development in Russia — poor pricing mechanisms for raw amber, an imbalance between supply and demand, a slow pace of technological modernisation, and a delayed introduction of new technologies and processing techniques. The authors identify gaps in the regulatory framework and highlight problems of legal regulation and law enforcement as regards the amber industry. Combating illegal amber extraction and trafficking is a pressing problem in the Kaliningrad region (Russia and other Baltic region states. The article explores theoretical aspects of the legislative policy on combating illegal amber extraction and trafficking. The authors focus on the relevant law enforcement practices and hold that administrative sanctions for unauthorised amber extraction and trade are not fully effective in Russia. The authors stress the need for introducing criminal liability for a repeated offence and outline opportunities for using forensic gemological examination of amber and amber products.

  14. High resolution radiography of ambers with pixel detectors

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

  15. New species of Compsocidae (Insecta, Psocodea) from Cretaceous Burmese amber

    Czech Academy of Sciences Publication Activity Database

    Sroka, Pavel; Nel, A.

    2017-01-01

    Roč. 4320, č. 3 (2017), s. 597-600 ISSN 1175-5326 Institutional support: RVO:60077344 Keywords : Psocoptera * Troctomorpha * Burmacompsocus Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 0.972, year: 2016 https://biotaxa.org/Zootaxa/article/view/zootaxa.4320.3.12

  16. Publisher Correction: Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages.

    Science.gov (United States)

    Peñalver, Enrique; Arillo, Antonio; Delclòs, Xavier; Peris, David; Grimaldi, David A; Anderson, Scott R; Nascimbene, Paul C; Fuente, Ricardo Pérez-de la

    2018-01-30

    The originally published version of this Article was updated shortly after publication to add the word 'Ticks' to the title, following its inadvertent removal during the production process. This has now been corrected in both the PDF and HTML versions of the Article.

  17. The generic HASKELL user's guide : version 0.99 - Amber release

    NARCIS (Netherlands)

    Clarke, D.; Hinze, R.; Jeuring, J.T.; Löh, A.; Wit, J. de

    2001-01-01

    Software development often consists of designing datatypes around which functionality is added. Some functionality is datatype specific, whereas other functionality is defined on almost all datatypes in such a way that it depends only on the structure of the datatype. A function that works on

  18. 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.

  19. Assessing the Current State of Amber Force Field Modifications for DNA

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

    Roč. 12, č. 8 (2016), s. 4114-4127 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * particle mesh ewald * pair opening kinetics Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016

  20. Development and evaluation of an algorithm-based tool for Medication Management in nursing homes: the AMBER study protocol.

    Science.gov (United States)

    Erzkamp, Susanne; Rose, Olaf

    2018-04-20

    Residents of nursing homes are susceptible to risks from medication. Medication Reviews (MR) can increase clinical outcomes and the quality of medication therapy. Limited resources and barriers between healthcare practitioners are potential obstructions to performing MR in nursing homes. Focusing on frequent and relevant problems can support pharmacists in the provision of pharmaceutical care services. This study aims to develop and evaluate an algorithm-based tool that facilitates the provision of Medication Management in clinical practice. This study is subdivided into three phases. In phase I, semistructured interviews with healthcare practitioners and patients will be performed, and a mixed methods approach will be chosen. Qualitative content analysis and the rating of the aspects concerning the frequency and relevance of problems in the medication process in nursing homes will be performed. In phase II, a systematic review of the current literature on problems and interventions will be conducted. The findings will be narratively presented. The results of both phases will be combined to develop an algorithm for MRs. For further refinement of the aspects detected, a Delphi survey will be conducted. In conclusion, a tool for clinical practice will be created. In phase III, the tool will be tested on MRs in nursing homes. In addition, effectiveness, acceptance, feasibility and reproducibility will be assessed. The primary outcome of phase III will be the reduction of drug-related problems (DRPs), which will be detected using the tool. The secondary outcomes will be the proportion of DRPs, the acceptance of pharmaceutical recommendations and the expenditure of time using the tool and inter-rater reliability. This study intervention is approved by the local Ethics Committee. The findings of the study will be presented at national and international scientific conferences and will be published in peer-reviewed journals. DRKS00010995. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  1. A new fossil mayfly species if the genus Borinquena Traver, 1938 (Insecta: Ephemeroptera: Leptophlebiidae: Atalophlebiinae) from Miocene Dominican amber

    Czech Academy of Sciences Publication Activity Database

    Staniczek, A. H.; Godunko, Roman J.; Krzemiński, W.

    2017-01-01

    Roč. 67, č. 1 (2017), s. 113-119 ISSN 0003-4541 Institutional support: RVO:60077344 Keywords : mayflies * Hagenulini * neotropics Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 0.699, year: 2016 http://www.bioone.org/doi/abs/10.3161/00034541ANZ2017.67.1.013

  2. Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field

    Czech Academy of Sciences Publication Activity Database

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

    2017-01-01

    Roč. 121, č. 11 (2017), s. 2420-2433 ISSN 1520-6106 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * sugar-phosphate backbone * free-energy landscape * ribosomal-rna Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

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

    International Nuclear Information System (INIS)

    Sinicropi, A; Basosi, R; Olivucci, M

    2008-01-01

    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

  4. Reference simulations of noncanonical nucleic acids with different chí variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Zgarbová, M.; Stadlbauer, Petr; Otyepka, M.; Banáš, P.; Koča, J.; Cheatham III, T.E.; Jurečka, P.; Šponer, Jiří

    2012-01-01

    Roč. 8, č. 7 (2012), s. 2506-2520 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : refinement of empirical force fields * DNA * Z-DNA backbone Subject RIV: BO - Biophysics Impact factor: 5.389, year: 2012

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 11, č. 12 (2015), s. 5723-5736 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * NUCLEIC-ACID STRUCTURES * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

  6. 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)

    MacElrevey, Celeste; Wedekind, Joseph E.

    2005-01-01

    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 1 2 1 2 or P4 3 2 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

  7. Excavating treasure from the amber of the prior art: why the public benefit doctrine is ill-suited to the pharmaceutical sciences.

    Science.gov (United States)

    Hess, Robert Alan

    2011-01-01

    This paper explores incongruities between patents and regulation as applied to the pharmaceutical industry in the United States. Research, development and marketing of a new pharmaceutical agent generally requires large, high-risk investments. The time and expense of conducting clinical trials to obtain pre-market approval from the Food and Drug Administration provides an additional barrier to entry. The patent system stimulates such investment by providing a legal barrier to appropriation of these investments by free-riders and increasing the likelihood of capital return on these investments. These two barriers are intertwined. For the most part, firms only attempt to clear the regulatory barrier when patent protection is certain. As a result of the uniquely challenging economic situation presented by the regulatory barrier, a common line of reasoning in patent policy and jurisprudence, that inventions which are barred from patenting benefit the public, is flawed. To the contrary, the patent/regulatory system forever traps pharmaceutical inventions, once placed in the public domain. Pharmaceutical companies cannot afford to invest the resources needed to clear the regulatory barrier if the investment is quickly appropriated by a free-riding manufacturer. Various implications of, and solutions to, this policy artifact are explored.

  8. Complementation Studies of Bacteriophage λ O Amber Mutants by Allelic Forms of O Expressed from Plasmid, and O-P Interaction Phenotypes.

    Science.gov (United States)

    Hayes, Sidney; Rajamanickam, Karthic; Hayes, Connie

    2018-04-05

    λ genes O and P are required for replication initiation from the bacteriophage λ origin site, ori λ, located within gene O . Questions have persisted for years about whether O-defects can indeed be complemented in trans . We show the effect of original null mutations in O and the influence of four origin mutations (three are in-frame deletions and one is a point mutation) on complementation. This is the first demonstration that O proteins with internal deletions can complement for O activity, and that expression of the N-terminal portion of gene P can completely prevent O complementation. We show that O-P co-expression can limit the lethal effect of P on cell growth. We explore the influence of the contiguous small RNA OOP on O complementation and P-lethality.

  9. 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

  10. 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

  11. 77 FR 74837 - President's Council of Advisors on Science and Technology (PCAST)

    Science.gov (United States)

    2012-12-18

    ... week of the meeting. Questions about the meeting should be directed to Dr. Amber Hartman Scholz, PCAST... accommodation to access this public meeting should contact Dr. Amber Hartman Scholz at least ten business days...

  12. Amber Particles as Living Plant Cell Markers in Flow Cytometry / Dzintara Daļiņas Kā Dzīvu Augu Šūnu Marķieri Plūsmas Citometrijā

    Directory of Open Access Journals (Sweden)

    Grauda Dace

    2015-08-01

    Full Text Available Labi zināma ir dzintara labvēlīgā ietekme uz dažādiem organismiem, tomēr ir ļoti maz pētījumu par dzintara ietekmi uz augu šūnām. Tādēļ šī pētījuma mērķis bija noskaidrot nano un mikro lieluma (5 nm-3 μm dzintara daļiņu un dzintara komponentu (spirtā šķīstošā dzintara frakcija un sukcināta ietekmi uz augu somatiskajām un gametiskajām šūnām, un noskaidrot dzintara daļiņu piemērotību dzīvu augu šūnu iezīmēšanai urbānās vides pētījumiem, izmantojot plūsmas citometriju. Relatīvā fluorescence, izmantojot BD FACSJazz® šūnu šķirotāju ar plūsmas citometra funkciju, tika noteikta èetru dažādu ģinšu sugu (Argyranthemum frutescens, Cyclamen persicum, Hordeum vulgare, Linum usitatissimum augu šūnām pēc 2 un 24 stundu kultivācijas barotnēs ar un bez dzintara daļiņām vai dzintara komponentiem. Konstatēts, ka dzintara daļiņu klātbūtne visām pētīto augu šūnām ievērojami palielināja relatīvo fluorescenci. Dzintara komponentu ietekme uz šūnu relatīvās fluorescences izmaiņām nebija būtiska, salīdzinot ar dzintara daļiņu ietekmi. Dzintara daļiņas nesamazināja dzīvo šūnu daudzumu paraugos. Konstatēts, ka dzintara daļiņas (5 nm-3 μm var izmantot kā marķierus dzīvo šūnu iezīmēšanai plūsmas citometrijas pētījumos.

  13. Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions

    Czech Academy of Sciences Publication Activity Database

    Vymětal, Jiří; Vondrášek, Jiří

    2014-01-01

    Roč. 118, č. 35 (2014), s. 10390-10404 ISSN 1520-6106 R&D Projects: GA MŠk(CZ) LH11020 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * alpha-helical structure * der Waals interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  15. Role of quantum-confined stark effect on bias dependent photoluminescence of N-polar GaN/InGaN multi-quantum disk amber light emitting diodes

    KAUST Repository

    Tangi, Malleswararao; Mishra, Pawan; Janjua, Bilal; Prabaswara, Aditya; Zhao, Chao; Priante, Davide; Min, Jung-Wook; Ng, Tien Khee; Ooi, Boon S.

    2018-01-01

    to be nitrogen polar (N-polar) verified using KOH wet chemical etching and valence band spectrum analysis of high-resolution X-ray photoelectron spectroscopy. The crystal structure and quality of the NWs were investigated by high-angle annular dark field

  16. Teledokumentalistika hiilgusest ja viletsusest / Maria Ulfsak

    Index Scriptorium Estoniae

    Ulfsak, Maria, 1981-

    2004-01-01

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

  17. 78 FR 32081 - Airworthiness Directives; Aircraft Industries a.s. Airplanes

    Science.gov (United States)

    2013-05-29

    ... Injection System WATER INJECTION circuit ON breakter. TCL TQ=min. 60% WATER INJECTION/ON push- Push and hold till amber button. WATER INJECTION signal comes on (on the front control panel) Before throttling back power: WATER INJECTION/OFF push- Push and check amber button. WATER INJECTION signal extinguishes...

  18. Verifying business processes using spin

    NARCIS (Netherlands)

    Janssen, W.; Mateescu, R.; Mauw, S.; Springintveld, J.; Holzmann, G.; Najm, E.; Serhrouchni, A.

    1998-01-01

    We present an application of the Spin model-checker in Testbed, a framework for business process reengineering. Business processes are described by end-users of Testbed in a graphi- cal language with a causality-based semantics, called Amber. The Amber language contains various constructs describing

  19. Jantar v české únětické kultuře - k počátkům jantarové stezky

    Czech Academy of Sciences Publication Activity Database

    Ernée, Michal

    2012-01-01

    Roč. 103, prosinec (2012), s. 71-172 ISSN 0031-0506 Institutional research plan: CEZ:AV0Z80020508 Institutional support: RVO:67985912 Keywords : amber * Early Bronze Age * Aunjetitz Culture * Bohemia * Amber Route Subject RIV: AC - Archeology, Anthropology, Ethnology

  20. Improvement of Head-Up Display Standards. Volume 5. Head Up Display ILS (Instrument Landing System) Accuracy Flight Tests.

    Science.gov (United States)

    1987-09-01

    amber system. The front canopy of the NT-33A is cov- ered with an amber plastic sheet; when the front seat pilot low- ers his blue visor, the...tigation of the effect of head-up display symbol dynamic response caracteristics on flying qualities; Task B was an investigation of symbol accuracy...An amber vinyl plastic sheet covered the in- side front half of the NT-33 canopy. Blue snap-on visors were pi ovided to the evaluation pilots. The

  1. 7 CFR 989.701 - Minimum grade and condition standards for natural condition raisins.

    Science.gov (United States)

    2010-01-01

    ...) Golden Seedless. Natural condition Golden Seedless raisins shall have been prepared from sound, wholesome.... Definitely dark berries means raisins which are definitely darker than dark amber and characteristic of...

  2. 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

  3. 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

  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. K.A.Subramanian (2005) Dragonflies and Damselflies of Peninsular ...

    Indian Academy of Sciences (India)

    K A Subramaniam

    K.A.Subramanian (2005) Dragonflies and Damselflies of Peninsular India-A Field Guide. .... This dragonfly is very common near marshes, ponds and big wells. .... black and yellow dragonfly with amber coloured wings. Male: Eyes: Eyes are.

  6. 75 FR 28682 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-05-21

    ... and devices showing standard red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some... T. Montoya, Doug L. Norman, Richard W. Pierce, Christopher A. Reineck, Carroll R. Rogers, Kevin L...

  7. 75 FR 9478 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-03-02

    ... and devices showing standard red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some..., Donald D. Overton, Willie L. Parks, Derrick A. Robinson, Clarence Robinshaw, Jr., Norman J. Watson and...

  8. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  9. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    NICO

    Trishomocubane, molecular dynamics, Amber, CLASICO, β-turn, α-helical. 1. Introduction .... MD simulations of Ac-Ala3-Tris-Ala3-NHMe explicitly in MEOH. 3. Results and .... worthwhile to group all conformations into clusters according to.

  10. The shelf life of dyed polymethylmethacrylate dosimeters

    International Nuclear Information System (INIS)

    Bett, R.; Watts, M.F.; Plested, M.E.

    2002-01-01

    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

  11. Biomass Characterization | Bioenergy | NREL

    Science.gov (United States)

    Characterization Biomass Characterization NREL provides high-quality analytical characterization of biomass feedstocks, intermediates, and products, a critical step in optimizing biomass conversion clear, amber liquid Standard Biomass Laboratory Analytical Procedures We maintain a library of

  12. In Silico Screening for Biothreat Countermeasures

    National Research Council Canada - National Science Library

    Westerhoff, Lance M

    2006-01-01

    The current state of the art of in silico drug discovery or computer aided drug discovery relies almost exclusively on molecular mechanics force fields, such as AMBER and CHARMM, and empirical potentials...

  13. Modeling of NAD+ analogues in horse liver alcohol dehydrogenase

    NARCIS (Netherlands)

    Beijer, N.A.; Buck, H.M.; Sluyterman, L.A.A.E.; Meijer, E.M.

    1990-01-01

    So far, the interactions of nicotinamide adenine dinucleotide (NAD+) derivatives with dehydrogenases are not very well understood. This hampers the introduction of NAD+ analogues with improved characteristics concerning industrial application. We have developed an AMBER molecular mechanics model in

  14. Presidential Green Chemistry Challenge: 2011 Small Business Award

    Science.gov (United States)

    Presidential Green Chemistry Challenge 2011 award winner, BioAmber, developed an integrated technology to produce large, commercial quantities of succinic acid by bacterial fermentation, replacing petroleum-based feedstocks.

  15. Resonance – Journal of Science Education | Indian Academy of ...

    Indian Academy of Sciences (India)

    article/fulltext/reso/011/02/0078-0087. Keywords. Sierpinski numbers; Fermat numbers; Chinese remainder theorem; covering set. Author Affiliations. Shailesh A Shirali1. Amber Valley Residential School, Chikmagalur Karnataka 577 101, India.

  16. Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

    OpenAIRE

    Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

    2002-01-01

    Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

  17. An Intensive Cultural Resources Survey and National Register Evaluation of Archaeological Sites at the Proposed River Ranch Resort in Lyman County, South Dakota

    Science.gov (United States)

    1990-02-01

    and other wet places (Barkley ed. 1986:289). Its bark can be used for medicinal purposes and also provides tannin . The buds, leaves and twigs are...was also very candid about the interest in certain types of liquid refreshments often consumed by Alfred, namely beer, wine and whiskey. This may...complete bottles include two 4/5 quart amber bottles, two colorless glass wine flasks, and two amber glass flasks which once held alcohol. The first

  18. Jantar starší doby železné a průběh jantarové stezky ve střední Evropě

    Czech Academy of Sciences Publication Activity Database

    Chytráček, Miloslav; Golec, M.; Chvojka, O.; Metlička, M.; Michálek, J.; Novotná, M.; Frolíková, Drahomíra

    2017-01-01

    Roč. 108, prosinec (2017), s. 121-256 ISSN 0031-0506 Grant - others:Rada Programu interní podpory projektů mezinárodní spolupráce AV ČR(CZ) M300021201 Program:M Institutional support: RVO:67985912 Keywords : amber * Hallstatt period * Early La Tène period * Bohemia * Moravia * Slovakia * Central Europe * Amber Road Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology

  19. 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 structur...

  20. The fossil history of pseudoscorpions (Arachnida: Pseudoscorpiones

    Directory of Open Access Journals (Sweden)

    D. Harms

    2017-08-01

    Full Text Available Pseudoscorpions, given their resemblance to scorpions, have attracted human attention since the time of Aristotle, although they are much smaller and lack the sting and elongated tail. These arachnids have a long evolutionary history but their origins and phylogenetic affinities are still being debated. Here, we summarise their fossil record based on a comprehensive review of the literature and data contained in other sources. Pseudoscorpions are one of the oldest colonisers of the land, with fossils known since the Middle Devonian (ca. 390 Ma. The only arachnid orders with an older fossil record are scorpions, harvestmen and acariform mites, plus two extinct groups. Pseudoscorpions do not fossilise easily, and records from the Mesozoic and Cenozoic consist almost exclusively of amber inclusions. Most Mesozoic fossils come from Archingeay and Burmese ambers (Late Cretaceous and those from the Cenozoic are primarily from Eocene Baltic amber, although additional fossils from, for example, Miocene Dominican and Mexican ambers, are known. Overall, 16 of the 26 families of living pseudoscorpions have been documented from fossils and 49 currently valid species are recognised in the literature. Pseudoscorpions represent a case of morphological stasis and even the Devonian fossils look rather modern. Indeed, most amber fossils are comparable to Recent groups despite a major gap in the fossil record of almost 250 Myr. Baltic amber inclusions indicate palaeofauna inhabiting much warmer climates than today and point to climatic shifts in central Europe since the Eocene. They also indicate that some groups (e.g. Feaellidae and Pseudogarypidae had much wider Eocene distributions. Their present-day occurrence is relictual and highlights past extinction events. Faunas from younger tropical amber deposits (e.g. Dominican and Mexican amber are comparable to Recent ones. Generally, there is a strong bias in the amber record towards groups that live under tree

  1. Signal treatments to reduce heavy vehicle crash-risk at metropolitan highway intersections.

    Science.gov (United States)

    Archer, Jeffery; Young, William

    2009-05-01

    Heavy vehicle red-light running at intersections is a common safety problem that has severe consequences. This paper investigates alternative signal treatments that address this issue. A micro-simulation analysis approach was adopted as a precursor to a field trial. The simulation model emulated traffic conditions at a known problem intersection and provided a baseline measure to compare the effects of: an extension of amber time; an extension of green for heavy vehicles detected in the dilemma zone at the onset of amber; an extension of the all-red safety-clearance time based on the detection of vehicles considered likely to run the red light at two detector locations during amber; an extension of the all-red safety-clearance time based on the detection of potential red-light runners during amber or red; and a combination of the second and fourth alternatives. Results suggested safety improvements for all treatments. An extension of amber provided the best safety effect but is known to be prone to behavioural adaptation effects and wastes traffic movement time unnecessarily. A green extension for heavy vehicles detected in the dilemma zone and an all-red extension for potential red-light runners were deemed to provide a sustainable safety improvement and operational efficiency.

  2. Durability of Mortar Made with Fine Glass Powdered Particles

    Directory of Open Access Journals (Sweden)

    Rosemary Bom Conselho Sales

    2017-01-01

    Full Text Available Different studies investigate the use of waste glass in Portland cement compounds, either as aggregates or as supplementary cementitious materials. Nevertheless, it seems that there is no consensus about the influence of particle color and size on the behavior of the compounds. This study addresses the influence of cement replacement by 10 and 20% of the colorless and amber soda-lime glass particles sized around 9.5 μm on the performance of Portland cement mortars. Results revealed that the partial replacement of cement could contribute to the production of durable mortars in relation to the inhibition of the alkali-aggregate reaction. This effect was more marked with 20% replacement using amber glass. Samples containing glass microparticles were more resistant to corrosion, in particular those made of colorless glass. The use of colorless and amber glass microparticles promoted a reduction in wear resistance.

  3. Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4 in ZIF-8

    Directory of Open Access Journals (Sweden)

    Phannika Kanthima

    2016-01-01

    Full Text Available The differential evolution (DE algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4 and 2-methylimidazolate ([C4N2H5]− using quantum binding energies of CH4-[C4N2H5]− complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD simulations of CH4 molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.

  4. Palaeontology of the upper Turonian paralic deposits of the Sainte-Mondane Formation, Aquitaine Basin, France

    Energy Technology Data Exchange (ETDEWEB)

    Neraudenau, D.; Saint Martin, S.; Battern, D.J.; Colin, J.P.; Daviero-Gomez, V.; Girard, V.; Gomez, B.; Nohra, Y.A.; Polette, F.; Platel, J.P.; Saint Martin, J.P.; Vullo, R.

    2016-07-01

    The upper Turonian lignite deposits of Sainte-Mondane, Dordogne (Aquitaine Basin, SW France), consist of clays bearing translucent, orange to red, amber micrograins. The amber exhibits different types of microbial inclusions. The clays contain several conifers including the genera Brachyphyllum, Frenelopsis and Glenrosa, and a few leaf fragments of eudicot angiosperms. Among the plant meso-fossils the occurrence of Costatheca, Spermatites and abundant, diverse, megaspores, including species of Ariadnaesporites, Bacutriletes, Echitriletes, Erlansonisporites, Maexisporites, Minerisporites and Verrutriletes, is noteworthy. Pollen grains of the Normapolles group are important components of the palynomorph assemblage. The clays were deposited in a calm, estuarine or lagoonal, muddy environment. The overlying lignitic sands contain large fossil wood pieces of the conifer Agathoxylon, small solitary corals, fragmentary oysters and pectinids, echinoid spines, a few teeth of marine selachians and bony fishes, but no amber is present. These sands were deposited in a high-energy coastal marine environment. (Author)

  5. 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

  6. Pacemaker wires

    International Nuclear Information System (INIS)

    Fransson, S.G.

    1993-01-01

    Evaluation of pacemaker wires were performed by comparing Advanced Multiple Beam Equalization Radiography (AMBER) with conventional chest radiography. The scanning equalization technique of the AMBER unit makes it superior to conventional technique in the depiction of different structures in the mediastinum or in the pleural sinuses. So far motion artifacts have not been considered clinically important. The longer exposure time, however, may impair the assessment of pacemaker wires. The motion artifact described may not only make adequate evaluation impossible but may even give a false impression of a lead fracture. The difference between the two systems was significant. (orig.)

  7. 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.

  8. 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

  9. 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

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  11. High Brightness OLED Lighting

    Energy Technology Data Exchange (ETDEWEB)

    Spindler, Jeffrey [OLEDWorks LLC; Kondakova, Marina [OLEDWorks LLC; Boroson, Michael [OLEDWorks LLC; Hamer, John [OLEDWorks LLC

    2016-05-25

    In this work we describe the technology developments behind our current and future generations of high brightness OLED lighting panels. We have developed white and amber OLEDs with excellent performance based on the stacking approach. Current products achieve 40-60 lm/W, while future developments focus on achieving 80 lm/W or higher.

  12. 29 CFR 1910.1044 - 1,2-dibromo-3-chloropropane.

    Science.gov (United States)

    2010-07-01

    ... occupational history including reproductive history. (ii) A physical examination, including examination of the... prohibited. C. Appearance and odor: Technical grade DBCP is a dense yellow or amber liquid with a pungent... laboratory animals and has been determined to constitute an increased risk of cancer in man. 3. Reporting...

  13. (Convolvulaceae) extracts and fractions on larvae of Spodoptera f

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... both seed extracts were isolated by gravity column chromatography over silica gel and analyzed for ... weighed and stored at 4°C in amber glass flasks before used. ..... probably had less energy for the production of biomass.

  14. Napodobenina červenofigurové keramiky z časně laténského sídliště v Chržíně s doklady kovolitectví a zpracování jantaru

    Czech Academy of Sciences Publication Activity Database

    Chytráček, Miloslav

    2007-01-01

    Roč. 59, č. 3 (2007), s. 461-516 ISSN 0323-1267 R&D Projects: GA AV ČR IAA8002204 Institutional research plan: CEZ:AV0Z80020508 Keywords : Bohemia * early La Tène period * imitations * red -figure decoration * metallurgy * amber * long-distance roads * imports * Attic ceramic Subject RIV: AC - Archeology, Anthropology, Ethnology

  15. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models

    Czech Academy of Sciences Publication Activity Database

    Rebic, M.; Laaksonen, A.; Šponer, Jiří; Uličný, J.; Mocci, F.

    2016-01-01

    Roč. 120, č. 30 (2016), s. 7380-7391 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : amber force-field * nucleic-acids * biomolecular simulations Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

  16. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

    Czech Academy of Sciences Publication Activity Database

    Stadlbauer, Petr; Mazzanti, L.; Cragnolini, T.; Wales, D.J.; Derreumaux, P.; Pasquali, C.; Sponer, Jiri

    2016-01-01

    Roč. 12, č. 12 (2016), s. 6077-6097 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : particle mesh ewald * amber force-field * free-energy profiles * binding dna aptamer Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016

  17. Circumventing Therapeutic Resistance and the Emergence of Disseminated Breast Cancer Cells Through Non-Invasive Optical Imaging

    Science.gov (United States)

    2015-06-01

    Investigator (1992-1994); National Science Foundation Young Investigator (1993-1998); E. I. DuPont de Nemours Young Faculty Award (1995-1997); Alfred P. Sloan...address of the Funding Agency’s Procuring Contracting/Grants Officer: Amber Stilh·ich U.S . Almy Medical Resem·ch Acquisition Activity, 820 Chandler

  18. case report endomyocardial fibrosis associated with schistosoma

    African Journals Online (AJOL)

    2014-12-01

    Dec 1, 2014 ... stored in containers and subsequently used for bathing. Both patients were ... His urine was amber and of adequate vol- ume. He had been ... schistosome specific antibody test for Schistosoma haematobium ... health problem, with the highest prevalence seen in communities ... newer drug targets.13,14.

  19. 77 FR 67808 - President's Council of Advisors on Science and Technology (PCAST)

    Science.gov (United States)

    2012-11-14

    ...-secondary science, technology, engineering, and mathematics (STEM) education. PCAST will also receive an... only for substantive commentary on PCAST's work, not for business marketing purposes. Oral Comments: To.... Amber Hartman Scholz at least ten business days prior to the meeting so that appropriate arrangements...

  20. A QM/MM–Based Computational Investigation on the Catalytic Mechanism of Saccharopine Reductase

    Directory of Open Access Journals (Sweden)

    James W. Gauld

    2011-10-01

    Full Text Available Saccharopine reductase from Magnaporthe grisea, an NADPH-containing enzyme in the α-aminoadipate pathway, catalyses the formation of saccharopine, a precursor to L-lysine, from the substrates glutamate and α-aminoadipate-δ-semialdehyde. Its catalytic mechanism has been investigated using quantum mechanics/molecular mechanics (QM/MM ONIOM-based approaches. In particular, the overall catalytic pathway has been elucidated and the effects of electron correlation and the anisotropic polar protein environment have been examined via the use of the ONIOM(HF/6-31G(d:AMBER94 and ONIOM(MP2/6-31G(d//HF/6-31G(d:AMBER94 methods within the mechanical embedding formulism and ONIOM(MP2/6-31G(d//HF/6-31G(d:AMBER94 and ONIOM(MP2/6-311G(d,p//HF/6-31G(d:AMBER94 within the electronic embedding formulism. The results of the present study suggest that saccharopine reductase utilises a substrate-assisted catalytic pathway in which acid/base groups within the cosubstrates themselves facilitate the mechanistically required proton transfers. Thus, the enzyme appears to act most likely by binding the three required reactant molecules glutamate, α-aminoadipate-δ-semialdehyde and NADPH in a manner and polar environment conducive to reaction.

  1. Modulation of allele leakiness and adaptive mutability in Escherichia ...

    Indian Academy of Sciences (India)

    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.

  2. 78 FR 52602 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2013-08-23

    ... showing requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do.... Thane (OH), Larry A. Tidwell (MO), Dale Torkelson (WI), Norman Vanderzyl (IA), John Vanek (MO), James D. Vorderbruggen (MN), Desmond Waldor (PA), Alicia Waters (IL), Norman R. Wilson (WA), James G. Witt (AZ), James L...

  3. Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay

    Czech Academy of Sciences Publication Activity Database

    Noureini, S.K.; Esmaeili, H.; Abachi, F.; Khiali, S.; Islam, Barira; Kuta, M.; Saboury, A.A.; Hoffillann, M.; Šponer, Jiří; Parkinson, G.; Haider, S.

    2017-01-01

    Roč. 1861, č. 8 (2017), s. 2020-2030 ISSN 0304-4165 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : prostate-cancer cells * amber force-field * nucleic-acids Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 4.702, year: 2016

  4. 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.

  5. An entomopathogenic fungus and nematode prove ineffective for biocontrol of an invasive leaf miner Profenusa thomsoni in Alaska

    Science.gov (United States)

    Robert Progar; J.J. Kruse; John Lundquist; K.P. Zogas; M.J. Rinella

    2015-01-01

    A non-native invasive sawfly, the amber-marked birch leaf miner Profenusa thomsoni (Konow), was first detected in south-central Alaska in 1996 and is now widely distributed throughout urban and wild birch trees in Alaska. Impacts have been considered primarily aesthetic because leaf miners cause leaves of birch trees (Betula...

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  7. Superovulation Response and In vivo Embryo Production Potential ...

    African Journals Online (AJOL)

    withdrawal to onset of estrus was 20.4±1.8 hours, and breed difference was not ... The total CL count was significantly higher (p=0.01) in Boran (10.1CL/cow/cycle) ..... All collected embryos were light amber colored cytoplasm, round shape,.

  8. 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)

    Amin, R.

    1989-11-01

    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

  9. A Simple Molecular Dynamics Lab to Calculate Viscosity as a Function of Temperature

    Science.gov (United States)

    Eckler, Logan H.; Nee, Matthew J.

    2016-01-01

    A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self-diffusion in "n"-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the…

  10. Can Social Networks Assist Analysts Fight Terrorism?

    Science.gov (United States)

    2011-06-01

    Facebook set up 53 AMBER alert pages, one for each of the 50 states, along with pages for the District of Columbia, Puerto Rico, and the U.S. Virgin ...was the commonplace name of massive blizzard-like storms that plagued the northeast during the 2009-2010 holidays . Ryan Ozimek and his team at PICnet

  11. Studies of base pair sequence effects on DNA solvation based on all

    Indian Academy of Sciences (India)

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization ...

  12. The ABCs of molecular dynamics simulations on B-DNA, circa 2012

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... Introduction ... methods and applications of MD simulations to nucleic acids. ... access to high-performance computing, all-atom MD on DNA ... Specifically, the focus in this article is (a) ... of MD on DNA using AMBER came with the development ..... python-based tool for managing this task on widely.

  13. Chemical composition and palaeobotanical origin of Miocene resins ...

    Indian Academy of Sciences (India)

    interest in the past few decades since the important contribution they can make ... rate of 3. ◦. C/min to 310. ◦. C maintained isothermally for a final 12 min. The carrier gas was ..... acterization of ambers from deposits in Poland; Appl. Geochem.

  14. 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?...

  15. Defining Strong State Accountability Systems: How Can Better Standards Gain Greater Traction? A First Look

    Science.gov (United States)

    Reed, Eileen; Scull, Janie; Slicker, Gerilyn; Winkler, Amber M.

    2012-01-01

    Rigorous standards and aligned assessments are vital tools for boosting education outcomes but they have little traction without strong accountability systems that attach consequences to performance. In this pilot study, Eileen Reed, Janie Scull, Gerilyn Slicker, and Amber Winkler lay out the essential features of such accountability systems,…

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 21, č. 21 (2015), s. 7701-7704 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : amber suppression * bioorganic chemistry * pyrrolysine * synthetic biology * unnatural amino acid Subject RIV: CC - Organic Chemistry Impact factor: 5.771, year: 2015

  17. Free Energy Landscape of GAGA and UUCG RNA Tetraloops

    Czech Academy of Sciences Publication Activity Database

    Bottaro, S.; Banáš, Pavel; Sponer, Jiri; Bussi, G.

    2016-01-01

    Roč. 7, č. 20 (2016), s. 4032-4038 ISSN 1948-7185 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * amber force-field * secondary structure * nmr relaxation Subject RIV: BO - Biophysics Impact factor: 9.353, year: 2016

  18. Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?

    Czech Academy of Sciences Publication Activity Database

    Islam, B.; Stadlbauer, Petr; Neidle, S.; Haider, S.; Šponer, Jiří

    2016-01-01

    Roč. 120, č. 11 (2016), s. 2899-2912 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * TELOMERIC G-QUADRUPLEX * AMBER FORCE-FIELD Subject RIV: BO - Biophysics Impact factor: 3.177, year: 2016

  19. Organic geochemistry of fossil resins from the Czech Republic

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  20. New genus and species of the extinct aphid family Szelegiewicziidae and their implications for aphid evolution

    DEFF Research Database (Denmark)

    Wegierek, Piotr; Zyła, Dagmara Maria; Homan, Agnieszka

    2017-01-01

    of the extinct groups. The extinct aphid family Szelegiewicziidae is supposed to be one of the oviparous lineages in aphid evolution. New material from the rock fossil deposits of Shar Teg (Upper Jurassic of Mongolia), Baissa (Lower Cretaceous of Siberia-Russia), and Burmese amber (Upper Cretaceous of Myanmar...

  1. 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

    Energy Technology Data Exchange (ETDEWEB)

    Amin, R [Atomic Energy Research Establishment, Dhaka (Bangladesh). Inst. of Food and Radiation Biology

    1989-11-01

    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.

  2. Ionising-radiation detector

    International Nuclear Information System (INIS)

    Hames, G.E.; Reed, J.; Robertson, D.S.

    1982-01-01

    A scintillation crystal/photodiode assembly for the detection of x- and γ-rays is described comprising a single crystal of zinc-tungstate grown from a melt and optically coupled to a photodiode. The crystal is doped with a trace element, for example Ag or Sb, to eliminate the characteristic rose/amber colour of the pure crystal. (U.K.)

  3. Fossil Platygastroidea in the National Museum of Natural History, Smithsonian Institution

    Science.gov (United States)

    Platygastroid wasps preserved in Dominican amber and oil shale from the Kishenehn formation (Montana, USA) in the National Museum of Natural History are catalogued. Compression fossils in Kishenehn oil shale yield a specimen of Fidiobia, a specimen of Telenominae, and a specimen with a Scelio-type o...

  4. The description of Rovnoeucoila tympanomorpha Buffington & Perkovsky, a new genus and species of fossil eucoiline,with observations on the asynchronous evolution of Diglyphosematini (Hymenoptera: Figitidae: Eucoilinae)

    Science.gov (United States)

    A new genus and species of Eucoilinae, Rovnoeucoila tympanomorpha Buffington & Perkovsky, from a Rovno Amber inclusion, is described. This new taxon differs from extant eucoilines by having a clearly segmented metasoma and singular flagellomere morphology in the antenna. The new taxon is included ...

  5. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

    Czech Academy of Sciences Publication Activity Database

    Islam, Barira; Stadlbauer, Petr; Gil-Ley, A.; Perez-Hernandez, J.A.; Haider, S.M.; Neidle, S.; Bussi, G.; Banáš, P.; Otyepka, Michal; Šponer, Jiří

    2017-01-01

    Roč. 13, č. 6 (2017), s. 2458-2480 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : amber force -field * particle mesh ewald Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 5.245, year: 2016

  6. 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

  7. Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

    Science.gov (United States)

    Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

    2018-01-01

    A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

  8. 78 FR 40175 - Exempt Chemical Preparations Under the Controlled Substances Act

    Science.gov (United States)

    2013-07-03

    ...Standard, Inc M-8270-04-ASL, Method 8270B-- Amber ampule: 1 mL...... 1/28/2013 Base/Neutrals Mix. Accu... CSA and its implementing regulations are designed to prevent, detect, and eliminate the diversion of... controlled substances and listed chemicals for legitimate medical, scientific, research, and industrial...

  9. 16 CFR 1500.91 - Determinations regarding lead content for certain materials or products under section 101 of the...

    Science.gov (United States)

    2010-01-01

    ... certain materials or products under section 101 of the Consumer Product Safety Improvement Act. 1500.91... Safety Improvement Act. (a) The Consumer Product Safety Improvement Act provides for specific lead limits..., flowers, bone, sea shell, coral, amber, feathers, fur, leather. (e) The following metals and alloys do not...

  10. The price of healthy and unhealthy foods in Australian primary school canteens.

    Science.gov (United States)

    Wyse, Rebecca; Wiggers, John; Delaney, Tessa; Ooi, Jia Ying; Marshall, Josephine; Clinton-McHarg, Tara; Wolfenden, Luke

    2017-02-01

    To describe the price of Australian school canteen foods according to their nutritional value. Primary school canteen menus were collected as part of a policy compliance randomised trial. For each menu item, dietitians classified its nutritional value; 'green' ('good sources of nutrients'), 'amber' ('some nutritional value'), 'red' ('lack adequate nutritional value') and assigned a food category (e.g. 'Drinks', 'Snacks'). Pricing information was extracted. Within each food category, ANOVAs assessed differences between the mean price of 'green', 'amber' and 'red' items, and post-hoc tests were conducted. Seventy of the 124 invited schools participated. There were significant differences in the mean price of 'green', 'amber' and 'red foods' across categories, with 'green' items more expensive than 'amber' items in main-meal categories ('Sandwiches' +$0.43, 'Hot Foods' +$0.71), and the reverse true for non-meal categories ('Drinks' -$0.13, 'Snacks' -$0.18, 'Frozen Snacks' -$0.25^). Current pricing may not encourage the purchasing of healthy main-meal items by and for students. Further investigation of pricing strategies that enhance the public health benefit of existing school canteen policies and practices are warranted. Implications for Public Health: Providing support to canteen managers regarding healthy canteen policies may have a positive impact on public health nutrition. © 2016 The Authors.

  11. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

    2018-03-01

    The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

  12. Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis.

    Science.gov (United States)

    Gan, Qinglei; Fan, Chenguang

    2017-11-01

    Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position. By removing three near cognate tRNA isoacceptors of the amber stop codon [tRNA Lys , tRNA Tyr , and tRNA Gln (CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved. Removal of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems. We provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Phototaxis of Propsilocerus akamusi (Diptera: Chironomidae) From a Shallow Eutrophic Lake in Response to Led Lamps.

    Science.gov (United States)

    Hirabayashi, Kimio; Nagai, Yoshinari; Mushya, Tetsuya; Higashino, Makoto; Taniguchi, Yoshio

    2017-06-01

    A study on the attraction of adult Propsilocerus akamusi midges to different-colored light traps was carried out from October 21 to November 15, 2013. The 6 colored lights used in light-emitting diode (LED) lamps were white, green, red, blue, amber, and ultraviolet (UV). The UV lamp attracted the most P. akamusi, followed by green, white, blue, amber, and red. A white pulsed LED light attracted only half the number of midges as did a continuous-emission white LED light. The result indicated that manipulation of light color, considering that the red LED light and/or pulsed LED light are not as attractive as the other colors, may be appropriate for the development of an overall integrated strategy to control nuisance P. akamusi in the Lake Suwa area.

  14. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Nonsense mutants in the bacteriophage T4D v gene

    Energy Technology Data Exchange (ETDEWEB)

    Minderhout, L van; Grimbergen, J; Groot, B de [Rijksuniversiteit Leiden (Netherlands). Lab. voor Stralengenetica en Chemische Mutagenese; Cohen (J.A.) Instituut voor Radiopathologie en Stralenbescherming, Leiden (Netherlands))

    1975-09-01

    Ten UV-sensitive mutants of T4D with the v phenotype were isolated. Of these ten mutants, two are amber and two opal. In UV curves and in photoreactivation and multiplicity reactivation experiments the nonsense mutants show the v phenotype in su/sup -/ hosts and almost the T4/sup +/ phenotype in su/sup +/ hosts. The mutations are located between rl and e and are alleles of v/sub 1/. In crosses with irradiated and non-irradiated phages the recombinant frequency is not reduced by uvs5. Amber uvs5 propagated in CR63 su/sup +/ is with B su/sup -/ just as sensitive to UV as uvs5 propagated in B su/sup -/, which permits the conclusion that the capsid of T4 phage particles does not contain the v gene product.

  16. 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.

  17. FESetup: Automating Setup for Alchemical Free Energy Simulations.

    Science.gov (United States)

    Loeffler, Hannes H; Michel, Julien; Woods, Christopher

    2015-12-28

    FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

  18. Stability of compounded trilostane suspension in cod liver oil.

    Science.gov (United States)

    Crosby, Jesse; Brown, Stacy

    2017-10-01

    Trilostane is a synthetic steroid analog used to treat canine hyperadrenocorticism. For small dogs, the dose found in commercially available dosage forms of trilostane is sometimes too high. Compounding trilostane in a liquid diluent provides an option for more precise dosing and adjustments, and can be easier to administer, versus a tablet or capsule. Trilostane suspends well in cod liver oil, which is generally palatable to dogs. The stability of a compounded trilostane suspension in cod liver oil stored at room temperature was investigated for 90 days. Compounded trilostane retained stability, defined as maintaining 90-105% labeled value, for 60 days when stored in amber glass bottles. However, drug potency fell >10% below the labeled value when stored in amber plastic bottles after 7 days. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Why Mycophoris is not an orchid seedling, and why Synaptomitus is not a fungal symbiont within this fossil

    DEFF Research Database (Denmark)

    Selosse, Marc-Andre; Brundrett, Mark; Dearnaley, John

    2017-01-01

    A recent publication in Botany introduced two new taxa: a fossil orchid seed (Mycophoris) and a fossilized basidiomycete fungus (Synaptomitus) in an alleged relationship with this orchid, encased in 15–20 million year old Dominican amber (Poinar, G. 2017. Two new genera, Mycophoris gen. nov......., (Orchidaceae) and Synaptomitus gen. nov. (Basidiomycota) based on a fossil seed with developing embryo and associated fungus in Dominican amber. Botany, 95: 1–8). From the working knowledge of extant orchid seeds, seedlings, and mycorrhiza shared among us, we cannot support these interpretations. Here we...... analyse: (i) why Mycophoris may not be an orchid seed, (ii) why Mycophoris is not a germinating seed, (iii) why fungal hyphae and a symbiotic fungus are absent in Mycophoris, and (iv) why Synaptomitus is likely not a fossil basidiomycete....

  20. Selected Blood Serum Elements in Van (Turkey Cats

    Directory of Open Access Journals (Sweden)

    V. Altunok

    2007-01-01

    Full Text Available The Turkish Van cat originates from eastern Turkey. One of the characteristic features of Van cats is the colour of their eyes, which can be both eyes blue, both eyes amber or one eye blue and the other amber. Serum essential trace, macro and industrial element concentrations of Van cats (n = 47 according to sex, age, hair length and eye colour differences were investigated. Serum aluminium, arsenic, boron, barium, cobalt, chromium, copper, gallium, indium, iron, lead, lithium, manganese, nickel, selenium, silver, sulphur, strontium, vanadium and zinc were measured with ICP-OES plasma optical atomic emission spectrometer. In result, serum aluminium, barium, copper, manganese and strontium levels in male cats were found higher (p p p p > 0.05 found in the age and hair length groups. Our results indicate that several of the blood serum elements of Van cats may be related to their eye colours and sex differences.

  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. Method or Madness: Federal Oversight Structures for Critical Infrastructure Protection

    Science.gov (United States)

    2007-12-01

    daughters, Amber and Lauren, who always say just the right things to keep this all in perspective. Bike rides and soccer games helped to provide just...security perspective, is shared by the U.S. Department of Agriculture and the Department of Health and Human Services. The USDA monitors the meat ... poultry , and egg sectors, while HHS oversees production of all other food products.90 HHS implements a two-prong strategy to achieve a safe and

  3. Visual performance with sport-tinted contact lenses in natural sunlight.

    Science.gov (United States)

    Erickson, Graham B; Horn, Fraser C; Barney, Tyler; Pexton, Brett; Baird, Richard Y

    2009-05-01

    The use of tinted and clear contact lenses (CLs) in all aspects of life is becoming a more popular occurrence, particularly in athletic activities. This study broadens previous research regarding performance-tinted CLs and their effects on measures of visual performance. Thirty-three subjects (14 male, 19 female) were fitted with clear B&L Optima 38, 50% visible light transmission Amber and 36% visible light transmission Gray-Green Nike Maxsight CLs in an individualized randomized sequence. Subjects were dark-adapted with welding goggles before testing and in between subtests involving a Bailey-Lovie chart and the Haynes Distance Rock test. The sequence of testing was repeated for each lens modality. The Amber and Gray-Green lenses enabled subjects to recover vision faster in bright sunlight compared with clear lenses. Also, subjects were able to achieve better visual recognition in bright sunlight when compared with clear lenses. Additionally, the lenses allowed the subjects to alternate fixation between a bright and shaded target at a more rapid rate in bright sunlight as compared with clear lenses. Subjects preferred both the Amber and Gray-Green lenses over clear lenses in the bright and shadowed target conditions. The results of the current study show that Maxsight Amber and Gray-Green lenses provide better contrast discrimination in bright sunlight, better contrast discrimination when alternating between bright and shaded target conditions, better speed of visual recovery in bright sunlight, and better overall visual performance in bright and shaded target conditions compared with clear lenses.

  4. Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

    Science.gov (United States)

    2011-07-01

    AMBER starting from the in-vacuum minimized Watson - Crick based paired 9-mer hairpin structures. These models were then used with NMR derived distance...the cell. The oligonucleotides studied adopt many different secondary structures such as Watson - Crick duplex, hairpin, quadruplex, and single...deoxyoligonucleotide. Although the mechanism(s) for this induction is unknown, our studies reveal key insights into the structural and sequence requirements for DNA

  5. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

    Czech Academy of Sciences Publication Activity Database

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

    2017-01-01

    Roč. 8, č. 3 (2017), č. článku e1405. ISSN 1757-7004 R&D Projects: GA ČR(CZ) GBP305/12/G034 Grant - others:GA MŠk(CZ) LO1305 Institutional support: RVO:68081707 Keywords : hepatitis-delta-virus * amber force-field * free-energy landscape * hdv ribozyme Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 4.838, year: 2016

  6. Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Stadlbauer, Petr; Islam, Barira; Otyepka, M.; Šponer, Jiří

    2017-01-01

    Roč. 13, č. 8 (2017), s. 3911-3926 ISSN 1549-9618 R&D Projects: GA MŠk EF15_003/0000477; GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : telomeric g-quadruplex * amber force-field * nucleic-acid quadruplexes Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 5.245, year: 2016

  7. Characterization of the Chemical Constitution and Profile of Pharmacological Activity of PGBx.

    Science.gov (United States)

    1980-04-30

    Mitochondrial Oxydative Phosphorylation System Columna Percent Activity- Comments Fractiorr 20 g 40 4g 7 50 100 slightly lower specific activity 8 115 115...amber alcoholic solution con- taining 155.6 mg of PGBx acid per ml. It was converted to the water- soluble sodium salt by us and both the freeze dried...salt and alcoholic solution were stored at 50C in a dessicator. For all biological studies, PGBx-Na was dissolved in appropriate volumes of Sorenson’s

  8. Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.

    Science.gov (United States)

    Lee, Tai-Sung; Hu, Yuan; Sherborne, Brad; Guo, Zhuyan; York, Darrin M

    2017-07-11

    We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.

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

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

    Roč. 55, č. 2 (2016), s. 360-372 ISSN 0006-2960 R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : PARAMAGNETIC-RESONANCE SPECTROSCOPY * AMBER FORCE-FIELD * NUCLEIC-ACIDS Subject RIV: BO - Biophysics Impact factor: 2.938, year: 2016

  10. Implications of Domestic Support Disciplines for Further Agricultural Trade Liberalization

    OpenAIRE

    Keith Walsh; Martina Brockmeier; Alan Matthews

    2005-01-01

    This paper employs the GTAP computable general equilibrium model and dataset to analyse the implications of domestic support reductions in the context of agricultural trade liberalisation. Three specific issues are addressed: overhang in domestic support, the accurate distinction of the boxes in the GTAP dataset and the treatment of market price support in the amber box. An extensive domestic support database is used to calculate the change in applied domestic support rates from a specified c...

  11. Ecuadorian honey types described by Kichwa community in Rio Chico, Pastaza province, Ecuador using Free-Choice Profiling

    Directory of Open Access Journals (Sweden)

    Patricia Vit

    Full Text Available Abstract Pastaza is the largest and least populated province in Ecuador, with seven native indigenous nationalities. The Kichwas from the Rio Chico community live near to the capital city Puyo, are recognized for their knowledge on stingless honey bees. From the 400 species of Neotropical Meliponini that make honey in cerumen pots, almost 100 thrive in Southern Ecuador, and confer such biodiversity to pot-honey. In this study sensory characteristics of Ecuadorian false and genuine honeys with diverse entomological origin: Apis mellifera – light amber and amber, Geotrigona leucogastra, Melipona grandis and Scaptotrigona sp. (S. ederi np Schwarz were investigated with Kichwa assessors (four female and four male, aged 18–62 years old. The panel was asked to taste and to identify sensory attributes of honey (appearance, taste, smell, aroma, mouthfeel, other tactile sensations, and to score their intensities in 10 cm unstructured line scales anchored with the words weak and strong, using the Free-Choice Profile methodology The Generalized Procrustes Analysis was used on the data. The first and second dimensions accounted for by 61.1% of the variance. In the descriptive sensory evaluation, darker honeys (amber A. mellifera, false and Geotrigona were separated from (light amber A. mellifera, Melipona and Scaptotrigona by the first dimension; whereas thicker honeys (A. mellifera and false were discriminated from thinner honeys (Geotrigona, Melipona and Scaptotrigona by the second dimension. The assessors were able to evaluate and differentiate honey types without previous sensory training. Remarkably, two Kichwa ladies immediately spit out the false honey, in contrast to an acceptance study on 18-honeys, where the false honey was scored among the preferred ones by 58 participants of the First Congress on Apiculture and Meliponiculture in Ecuador. Therefore, results suggest that Ecuadorian native Kichwas keep a sensory legacy of ancestral knowledge

  12. Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Jurečka, P.; Lankaš, F.; Cheatham, T. E.; Sponer, Jiri; Otyepka, M.

    2017-01-01

    Roč. 57, č. 2 (2017), s. 275-287 ISSN 1549-9596 Grant - others:GA ČR(CZ) GP14-29874P; GA MŠk(CZ) LO1305 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * amber force-field * t-g-g * b-dna Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.760, year: 2016

  13. Biting Deterrence, Repellency, and Larvicidal Activity of Ruta chalepensis (Sapindales: Rutaceae) Essential Oil and Its Major Individual Constituents Against Mosquitoes

    Science.gov (United States)

    2013-01-01

    anthraquinones, tannins , ßavonoids, cyanogenic glycosides, cardiac glycosides, triterpenes, saponins, sterols, furanocou- marins, and essential oils...and stored in sealed amber vial at 4C. Gas Chromatography–Mass Spectrometry Analysis Conditions. The gas chromatographyÐmass spectrom- etry(GCÐMS...Mass spectra were recorded at 70 with mass range of m/z 35Ð450. GCAnalyses.TheGC analysis was carried out using an Agilent 6890N GC system (SEM Ltd

  14. Nitrogen and Phosphorus Biomass-Kinetic Model for Chlorella vulgaris in a Biofuel Production Scheme

    Science.gov (United States)

    2010-03-01

    using a Hach DR-890 colorimeter and the cadmium reduction method (Method 8048). A Hach Nitra Ver 5 Nitrate reagent powder pillow was added to the...for testing purposes. Distilled water was used as the diluting agent; no reagent was used. This blank was used to zero the colorimeter prior to...to form an amber product. The colorimeter measurement of the treatment sample was converted to mg/L NO3-N. 31 PO4-P Uptake Phosphorus uptake

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

    OpenAIRE

    Engel, Michael S.

    2001-01-01

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

  16. Assessing the prevalence of autoimmune, endocrine, gynecologic, and psychiatric comorbidities in an ethnically diverse cohort of female fibromyalgia patients: does the time from hysterectomy provide a clue?

    OpenAIRE

    Brooks, Larry; Hadi, Joseph; Amber, Kyle T; Weiner, Michelle; La Riche, Christopher L; Ference, Tamar

    2015-01-01

    Larry Brooks,1 Joseph Hadi,2 Kyle T Amber,1 Michelle Weiner,3 Christopher L La Riche,4 Tamar Ference1 1Department of Rehabilitation Medicine, University of Miami Miller School of Medicine, Miami, 2Anesco Interventional Pain Institute, Margate, 3Miami Pain and Diagnostics, Miami, 4Department of Psychiatry and Behavioral Health, Florida International University Wertheim College of Medicine, University Park, FL, USABackground: This retrospective chart review investigated differences in the preva...

  17. Study of the Deposition of Ammonium Perchlorate Following the Static Firing of MK-58 Rocket Motors

    Science.gov (United States)

    2008-10-01

    hyperthyroidism , gas generators, electrolytes for lithium cells, and as chemical reagents. The occurrence of perchlorate in the environment is...and prevent their movement by the rocket motor plume (Fig. 5). The water in the traps was collected using 1-l amber glass containers and the exact...them. On day one, after the firing of the second motor, heavy rain and lightning prevented the collection of samples from the witness plates. Only

  18. 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

  19. Associations of Military Divorce with Mental, Behavioral, and Physical Health Outcomes

    Science.gov (United States)

    2015-06-19

    sion was similar among recent divorcees and those who were single. Understanding the temporal proximity of the association between a recent divorce ...Shapiro E. Alcohol consumption and divorce : Which causes which? J Divorce . 1988;12(1):127–36. 60. Lee MR, Chassin L, Mackinnon D. The effect of marriage...Naval Health Research Center Associations of Military Divorce With Mental, Behavioral, and Physical Health Outcomes Lawrence Wang Amber Seelig

  20. 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.

  1. Sensitivity of Nuclide Release Behavior to Groundwater Flow in an HLW Repository

    International Nuclear Information System (INIS)

    Lee, Youn-Myoung; Hwang, Yong-Soo

    2008-01-01

    Evaluation of the dose exposure rate to human being due to long-term nuclide releases from a high-level waste repository (HLW) is of importance to meet the dose limit presented by the regulatory bodies in order to ensure the performance of a repository. During the last few years, tools by which such a dose rate to an individual can be evaluated have been developed and implemented for a practical calculation to demonstrate the suitability of an HLW repository, with the aid of commercial tools such as AMBER and GoldSim, both of which are capable of probabilistic and deterministic calculations with their convenient user interface. Recently a migration from AMBER based models to GoldSim based ones has been made in accordance with a better feature of GoldSim, which is designed to facilitate the object-oriented modules to address any specialized programs, similar to solving jig saw puzzles and shows more advantage in a detailed complex modeling over AMBER. Recently a compartment modeling approach both for a geosphere and biosphere has been mainly carried out with AMBER in KAERI, which causes a necessity for a newly devised system performance evaluation model in which geosphere and biosphere models could be coupled organically together with less conservatism in the frame of the development of a total system performance assessment modeling tool, which could be successfully done with the aid of GoldSim. Therefore, through the current study, some probabilistic results of the GoldSim approach for a normal situation that could take place in a typical HLW repository are introduced

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

    Directory of Open Access Journals (Sweden)

    J. Fisher

    2015-06-01

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

  3. Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    The present report demonstrates that the conformational properties of DNA in solution are sensitive to the type of monovalent ion. Results are based on the ability of a polarizable force field using the classical Drude oscillator to reproduce experimental solution X-ray scattering data more accurately than two nonpolarizable DNA models, AMBER Parmbsc0 and CHARMM36. The polarizable model is then used to calculate scattering profiles of DNA in the presence of four different monovalent salts, Li...

  4. Distribution and Fate of Energetics on DoD Test and Training Ranges: Interim Report 6

    Science.gov (United States)

    2006-11-01

    Applied Research Associates, Inc.). The objective of this project was to develop a low-cost, fieldable process for the rapid decontamination of...DLE. Moreover, the DLE mandate includes the analysis of other types of range contaminants such as heavy metals, petroleum products, and radioactive ...ground material with a small stainless spatula and combined in a 2-oz amber jar with a Teflon-lined lid. In the case of the 12 samples selected for the

  5. 21 CFR 184.1091 - Succinic acid.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Succinic acid. 184.1091 Section 184.1091 Food and... Substances Affirmed as GRAS § 184.1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It is...

  6. Development and Validation of a Prototype Vacuum Sensing Unit for the DD2011 Chairside Amalgam Separators

    Science.gov (United States)

    2015-10-30

    amalgam separators , such as the DD2011, remove amalgam waste particulates by filtration and are attached to the vacuum system of dental chairs for...based upon the principle that solid particulate amalgam waste and dental debris accumulate and block the movement of water through the filtration...AMALGAM SEPARATORS JAY SHARTZER, B.S., SOPHIA JOHNSON, PH.D., AND AMBER NAGY, PH.D. CRANIOFACIAL HEALTH AND RESTORATIVE MEDICINE BIOMATERIALS AND

  7. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Mutations at the cysteine codons of the recA gene of Escherichia coli

    International Nuclear Information System (INIS)

    Weisemann, J.M.; Weinstock, G.M.

    1988-01-01

    Each of the three cysteine residues in the Escherichia coli RecA protein was replaced with a number of other amino acids. To do this, each cysteine codon was first converted to a chain-terminating amber codon by oligonucleotide-directed mutagenesis. These amber mutants were then either assayed for function in different suppressor strains or reverted by a second round of mutagenesis with oligonucleotides that had random sequences at the amber codon. Thirty-three different amino acid substitutions were obtained. Mutants were tested for three functions of RecA: survival following UV irradiation, homologous recombination, and induction of the SOS response. It was found that although none of the cysteines is essential for activity, mutations at each of these positions can affect one or more of the activities of RecA, depending on the particular amino acid substitution. In addition, the cysteine at position 116 appears to be involved in the RecA-promoted cleavage of the LexA protein

  9. The relative price of healthy and less healthy foods available in Australian school canteens.

    Science.gov (United States)

    Billich, Natassja; Adderley, Marijke; Ford, Laura; Keeton, Isabel; Palermo, Claire; Peeters, Anna; Woods, Julie; Backholer, Kathryn

    2018-04-12

    School canteens have an important role in modelling a healthy food environment. Price is a strong predictor of food and beverage choice. This study compared the relative price of healthy and less healthy lunch and snack items sold within Australian school canteens. A convenience sample of online canteen menus from five Australian states were selected (100 primary and 100 secondary schools). State-specific canteen guidelines were used to classify menu items into 'green' (eat most), 'amber' (select carefully) and 'red' (not recommended in schools). The price of the cheapest 'healthy' lunch (vegetable-based 'green') and snack ('green' fruit) item was compared to the cheapest 'less healthy' ('amber/red') lunch and snack item, respectively, using an un-paired t-test. The relative price of the 'healthy' items and the 'less healthy' items was calculated to determine the proportion of schools that sold the 'less healthy' item cheaper. The mean cost of the 'healthy' lunch items was greater than the 'less healthy' lunch items for both primary (AUD $0.70 greater) and secondary schools ($0.50 greater; p snack was cheaper than the 'healthy' snack. These proportions were greatest for primary schools located in more, compared to less, disadvantaged areas. The relative price of foods sold within Australian school canteens appears to favour less healthy foods. School canteen healthy food policies should consider the price of foods sold.

  10. QUALIDADE DO MEL DE ABELHA PRODUZIDOS PELOS INCUBADOS DA IAGRAM E COMERCIALIZADO NO MUNICIPIO DE MOSSORÓ/RN

    Directory of Open Access Journals (Sweden)

    Edna Maria Mendes Aroucha

    2008-01-01

    Full Text Available This experiment had for objective to evaluate some parameters of quality of the bee honey (Apis mellífera L. produced by IAGRAM and commercialized in the city of Mossoró-RN. For this, 19 honey samples had been collected in the local market, these were analyzed, in the Chemistry Laboratory of the Universidade Federal Rural do Semi-Árido (UFERSA, how much to the color, humidity, total acidity, reducing sugars, apparent sucrose and diastase activity. It was utilized districted statistics for analysis of date, with shunting line standard, reliable interval and distribution of frequency. The honeys sample presented the colors clearly extra amber (5,2%, amber (5,2% and dark amber (89,4%. The honey samples presented normal standard established for the Brazilian Legislation as humidity percentage (14,3 18.6% and reducing sugars (66,9 75.0%. About 5,2% and 42% of the analyzed honey samples, not presented, respectively, apparent sucrose content and total acidity, as the standard established for commercialization as floral honey. The diastase activity was remained inside of the quality standard.

  11. A minute fossil phoretic mite recovered by phase-contrast X-ray computed tomography

    Science.gov (United States)

    Dunlop, Jason A.; Wirth, Stefan; Penney, David; McNeil, Andrew; Bradley, Robert S.; Withers, Philip J.; Preziosi, Richard F.

    2012-01-01

    High-resolution phase-contrast X-ray computed tomography (CT) reveals the phoretic deutonymph of a fossil astigmatid mite (Acariformes: Astigmata) attached to a spider's carapace (Araneae: Dysderidae) in Eocene (44–49 Myr ago) Baltic amber. Details of appendages and a sucker plate were resolved, and the resulting three-dimensional model demonstrates the potential of tomography to recover morphological characters of systematic significance from even the tiniest amber inclusions without the need for a synchrotron. Astigmatids have an extremely sparse palaeontological record. We confirm one of the few convincing fossils, potentially the oldest record of Histiostomatidae. At 176 µm long, we believe this to be the smallest arthropod in amber to be CT-scanned as a complete body fossil, extending the boundaries for what can be recovered using this technique. We also demonstrate a minimum age for the evolution of phoretic behaviour among their deutonymphs, an ecological trait used by extant species to disperse into favourable environments. The occurrence of the fossil on a spider is noteworthy, as modern histiostomatids tend to favour other arthropods as carriers. PMID:22072283

  12. A minute fossil phoretic mite recovered by phase-contrast X-ray computed tomography.

    Science.gov (United States)

    Dunlop, Jason A; Wirth, Stefan; Penney, David; McNeil, Andrew; Bradley, Robert S; Withers, Philip J; Preziosi, Richard F

    2012-06-23

    High-resolution phase-contrast X-ray computed tomography (CT) reveals the phoretic deutonymph of a fossil astigmatid mite (Acariformes: Astigmata) attached to a spider's carapace (Araneae: Dysderidae) in Eocene (44-49 Myr ago) Baltic amber. Details of appendages and a sucker plate were resolved, and the resulting three-dimensional model demonstrates the potential of tomography to recover morphological characters of systematic significance from even the tiniest amber inclusions without the need for a synchrotron. Astigmatids have an extremely sparse palaeontological record. We confirm one of the few convincing fossils, potentially the oldest record of Histiostomatidae. At 176 µm long, we believe this to be the smallest arthropod in amber to be CT-scanned as a complete body fossil, extending the boundaries for what can be recovered using this technique. We also demonstrate a minimum age for the evolution of phoretic behaviour among their deutonymphs, an ecological trait used by extant species to disperse into favourable environments. The occurrence of the fossil on a spider is noteworthy, as modern histiostomatids tend to favour other arthropods as carriers.

  13. 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

    2011-06-01

    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.

  14. 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.

  15. A computational prospect to aspirin side effects: aspirin and COX-1 interaction analysis based on non-synonymous SNPs.

    Science.gov (United States)

    Marjan, Mojtabavi Naeini; Hamzeh, Mesrian Tanha; Rahman, Emamzadeh; Sadeq, Vallian

    2014-08-01

    Aspirin (ASA) is a commonly used nonsteroidal anti-inflammatory drug (NSAID), which exerts its therapeutic effects through inhibition of cyclooxygenase (COX) isoform 2 (COX-2), while the inhibition of COX-1 by ASA leads to apparent side effects. In the present study, the relationship between COX-1 non-synonymous single nucleotide polymorphisms (nsSNPs) and aspirin related side effects was investigated. The functional impacts of 37 nsSNPs on aspirin inhibition potency of COX-1 with COX-1/aspirin molecular docking were computationally analyzed, and each SNP was scored based on DOCK Amber score. The data predicted that 22 nsSNPs could reduce COX-1 inhibition, while 15 nsSNPs showed increasing inhibition level in comparison to the regular COX-1 protein. In order to perform a comparing state, the Amber scores for two Arg119 mutants (R119A and R119Q) were also calculated. Moreover, among nsSNP variants, rs117122585 represented the closest Amber score to R119A mutant. A separate docking computation validated the score and represented a new binding position for ASA that acetyl group was located within the distance of 3.86Å from Ser529 OH group. This could predict an associated loss of activity of ASA through this nsSNP variant. Our data represent a computational sub-population pattern for aspirin COX-1 related side effects, and provide basis for further research on COX-1/ASA interaction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. 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)

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

    International Nuclear Information System (INIS)

    Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elzbieta; Tarnowska, Anna; Kawecki, Robert; Kozerski, Lech

    2008-01-01

    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 2 O/CD 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 V C), or including a generalized Born solvent model (AMBER G B)

  18. Mutability of bacteriophage M13 by ultraviolet light: role of pyrimidine dimers

    International Nuclear Information System (INIS)

    Schaaper, R.M.; Glickman, B.W.

    1982-01-01

    The role of pyrimidine dimers in mutagenesis by ultraviolet light was examined by measuring the UV-induced reversion of six different bacteriophage M13 amber mutants for which the neighboring DNA sequences are known. The mutational response at amber (TAG) codons preceded by a guanine or adenine (where no pyrimidine dimer can be formed) were compared with those preceded by thymine or cytosine (where dimer formation is possible). Equivalent levels of UV-induced mutagenesis were observed at both kinds of sites. This observation demonstrates that there is no requirement for a pyrimidine dimer directly at the site of UV-induced mutation in this single-stranded DNA phage. UV irradiation of the phage was also performed in the presence of Ag + ions, which specifically sensitize the DNA to dimer formation. The two methods of irradiation, when compared at equal survival levels (and presumably equal dimer frequencies), produced equivalent frequencies of reversion of the amber phage. We believe these results indicate that while the presence of pyrimidine dimers may be a prerequisite for UV mutagenesis, the actual mutagenic event can occur at a site some distance removed from a dimer. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Sebastian Nehring

    Full Text Available 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.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.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 vitro in parallel to monitoring intracellular ncAA levels.

  20. Nanodefects in ultrahard crystalline cubic boron nitride

    International Nuclear Information System (INIS)

    Nistor, S. V.; Stefan, M.; Goovaerts, E.; Schoemaker, D.

    2002-01-01

    Cubic boron nitride (cBN), the second hardest known material after diamond, exhibits high thermal conductivity and an excellent ability to be n or p doped, which makes it a strong candidate for the next generation of high-temperature micro optical and micro electronic devices. According to recent studies, cBN exhibits a better resistance to radiation damage than diamond, which suggests potential applications in extreme radiation environments. Crystalline cBN powders of up to 0.5 mm linear size is obtained in a similar way as diamond, by catalytic conversion of hexagonal BN (hBN) to cBN at even higher pressures (> 5GPa) and temperatures (∼ 1900 K). Considering the essential role played by the nanodefects (point defects and impurities) in determining its physical properties, it is surprising how limited is the amount of published data concerning the properties of nanodefects in this material, especially by Electron Paramagnetic Resonance (EPR) spectroscopy, the most powerful method for identification and characterization of nanodefects in both insulators and semiconductors. This seems to be due mainly to the absence of natural cBN gems and the extreme difficulties in producing even mm 3 sized synthetic crystals. We shall present our recent EPR studies on cBN crystalline powders, performed in a broad temperature range from room temperature (RT) down to 1.2 K on several sorts of large size cBN powder grits of yellow and amber color for industrial applications. Previous multifrequency (9.3 GHz and 95 GHz) EPR studies of brown to black cBN crystallites prepared with excess of boron, resulted in the discovery of two new types of paramagnetic point defects with different spectral properties, called the D1 and D2 centers. Our X(9.3 GHz)-band EPR investigations resulted in the observation in amber cBN crystalline powders of a spectrum with a strong temperature dependence of the lineshape. It was found that for high and low temperatures, respectively, the numerical

  1. 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.

  2. Ultraviolet light protection, enhancement of ultraviolet light mutagenesis, and mutator effect of plasmid R46 in Salmonella typhimurium

    International Nuclear Information System (INIS)

    Mortelmans, K.E.; Stocker, B.A.D.

    1976-01-01

    Plasmid R46 partially protected Salmonella typhimurium, wild type or uvrB or polA, against the lethal effect of ultraviolet (uv) irradiation, but did not protect recA mutants. The plasmid also increased frequency of uv-induced reversion to His + in all tested his point mutants (wild type for uv sensitivity), including amber, ochre, UGA, missense, and frame-shift mutants. Plasmid R46 also increased uv-induced reversion to His + in uvrB and polA strains, but no uv mutagenic effect was detected in R - or R46-carrying recA derivatives of a his(amber) mutant. The spontaneous reversion frequency of his nonsense mutants of all classes, and of some his missense mutants, was increased about 10-fold when the strains carried R46, but the plasmid had no effect on the spontaneous reversion frequency of some other his missense mutations or of reversion rate of his frame-shift mutants (except for two uvrB derivatives of one single-base insertion mutant). The plasmid increased the ability of wild type, polA, and uvrB hosts to support plaque production by uv-irradiated phage, and made strain LT2 his G46 less sensitive to methyl methane sulfonate and to x rays and more responsive to the mutagenic effect of visible-light irradiation. R46 increased spontaneous reversion frequency of a his(amber) rec + strain, but had no such effect in its recA sublines. Since the plasmid in the absence of host recA function fails to produce its mutator effect, or to confer uv protection or to enhance uv mutagenesis, these three effects may be produced via some mechanism involved in recA-dependent deoxyribonucleic acid repair, perhaps by an increase in activity of the ''error-prone'' component of the inducible repair pathway

  3. Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection.

    Directory of Open Access Journals (Sweden)

    Maria Homs

    Full Text Available Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg. The amber codon encodes the small (unedited HDAg form and the W codon the large (edited HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (p<0.05. An accumulation of transition-type changes was found to be responsible for higher evolution rates. The percentages of unedited and edited genomes and the quasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.

  4. The phylogeny of fossil whip spiders.

    Science.gov (United States)

    Garwood, Russell J; Dunlop, Jason A; Knecht, Brian J; Hegna, Thomas A

    2017-04-21

    Arachnids are a highly successful group of land-dwelling arthropods. They are major contributors to modern terrestrial ecosystems, and have a deep evolutionary history. Whip spiders (Arachnida, Amblypygi), are one of the smaller arachnid orders with ca. 190 living species. Here we restudy one of the oldest fossil representatives of the group, Graeophonus anglicus Pocock, 1911 from the Late Carboniferous (Duckmantian, ca. 315 Ma) British Middle Coal Measures of the West Midlands, UK. Using X-ray microtomography, our principal aim was to resolve details of the limbs and mouthparts which would allow us to test whether this fossil belongs in the extant, relict family Paracharontidae; represented today by a single, blind species Paracharon caecus Hansen, 1921. Tomography reveals several novel and significant character states for G. anglicus; most notably in the chelicerae, pedipalps and walking legs. These allowed it to be scored into a phylogenetic analysis together with the recently described Paracharonopsis cambayensis Engel & Grimaldi, 2014 from the Eocene (ca. 52 Ma) Cambay amber, and Kronocharon prendinii Engel & Grimaldi, 2014 from Cretaceous (ca. 99 Ma) Burmese amber. We recovered relationships of the form ((Graeophonus (Paracharonopsis + Paracharon)) + (Charinus (Stygophrynus (Kronocharon (Charon (Musicodamon + Paraphrynus)))))). This tree largely reflects Peter Weygoldt's 1996 classification with its basic split into Paleoamblypygi and Euamblypygi lineages; we were able to score several of his characters for the first time in fossils. Our analysis draws into question the monophyly of the family Charontidae. Our data suggest that Graeophonus is a crown group amblypygid, and falls within a monophyletic Paleoamblypgi clade, but outside the family Paracharontidae (= Paracharonopsis + Paracharon). Our results also suggest a new placement for the Burmese amber genus Kronocharon, a node further down from its original position. Overall, we offer a

  5. 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.

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

    International Nuclear Information System (INIS)

    Lawrence, C.W.; Das, G.; Christensen, R.B.

    1985-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, C.W.; Das, G.; Christensen, R.B.

    1985-06-26

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

  8. Conformational Analysis of Indole Alkaloids Corynantheine and Dihydrocorynantheine by Dynamic 1H NMR Spectroscopy and Computational Methods: Steric Effects of Ethyl vs Vinyl Group

    DEFF Research Database (Denmark)

    Stærk, Dan; Norrby, Per-Ola; Jaroszewski, Jerzy W.

    2001-01-01

    H-1 NMR (400 MHz) spectra of the indole alkaloid dihydrocorynantheine recorded at room temperature show the presence of two conformers near coalescence. Low temperature H-1 NMR allowed characterization of the conformational equilibrium, which involves rotation of the 3-methoxypropenoate side chain...... bulk of the vinyl and the ethyl group. The conformational equilibria involving the side chain rotation as well as inversion of the bridgehead nitrogen in corynantheine and dihydrocorynantheine was studied by force-field (Amber(*) and MMFF) and ab initio (density-functional theory at the B3LYP/6-31G...

  9. Fires Readiness: The State of US Army Fires in Support of Combined Arms Maneuver at the Division Level

    Science.gov (United States)

    2016-06-10

    Synchronize JIM Assets 3-09.90 15 Target Mensuration 3-09.90 16 Collateral Damage Estimation 3-09.90 17 Assess (Munitions Effects Analysis / BDA ) 3-09.90 18...Assess (Munitions Effects Analysis / BDA ) X X X X 4 18 Recommand FA Organization for Combat X X X 3 19 Plan Fires X X X X X X X 7 20 Plan Positions...Estimation 3-09.90 Not evaluated 17 Assess (Munitions Effects Analysis / BDA ) 3-09.90 Amber 18 Recommand FA Organization for Combat 3-09.24 Green 19 Plan

  10. Mapping the Binding Site for Escitalopram and Paroxetine in the Human Serotonin Transporter Using Genetically Encoded Photo-Cross-Linkers

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Andersen, Jacob; Bang-Andersen, Benny

    2017-01-01

    amber codon suppression in hSERT to encode the photo-cross-linking unnatural amino acid p-azido-l-phenylalanine into the suggested high- and low-affinity binding sites. We then employ UV-induced cross-linking with azF to map the binding site of escitalopram and paroxetine, two prototypical selective...... serotonin reuptake inhibitors (SSRIs). We find that the two antidepressant drugs exclusively cross-link to azF incorporated at the high-affinity binding site of hSERT, while cross-linking is not observed at the low-affinity binding site. Combined with previous homology models and recent structural data on h...

  11. 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.

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

    Science.gov (United States)

    Engel, M S

    2001-02-13

    Advanced eusociality sometimes is given credit for the ecological success of termites, ants, some wasps, and some bees. Comprehensive study of bees fossilized in Baltic amber has revealed an unsuspected middle Eocene (ca. 45 million years ago) diversity of eusocial bee lineages. Advanced eusociality arose once in the bees with significant post-Eocene losses in diversity, leaving today only two advanced eusocial tribes comprising less than 2% of the total bee diversity, a trend analogous to that of hominid evolution. This pattern of changing diversity contradicts notions concerning the role of eusociality for evolutionary success in insects.

  13. Monte Carlo studies of the Portuguese gamma irradiation facility. The irradiator geometry and its influence on process parameters

    International Nuclear Information System (INIS)

    Oliveira, C.; Ferreira, L.; Salgado, J.

    2001-01-01

    The paper describes a Monte Carlo study of dose distributions, minimum dose and uniformity ratio for the Portuguese Gamma Irradiation Facility. These process parameters are calculated using the MCNP code for several irradiator geometries. The comparison of the simulated results with the experimental results carried out using Amber Perspex dosimeters in a routine process of the gamma facility for a given material composition and density reveals good agreement. The results already obtained allow to conclude that the dose uniformity is not very sensitive to the irradiator geometry for density value ρ = 0.1 and for a dynamic process. (orig.)

  14. pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

    Directory of Open Access Journals (Sweden)

    Ardita Shkurti

    2016-01-01

    Full Text Available The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced written in Python.

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

    Czech Academy of Sciences Publication Activity Database

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

    2012-01-01

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

  16. Triassic leech cocoon from Antarctica contains fossil bell animal

    DEFF Research Database (Denmark)

    Bomfleur, Benjamin; Kerp, Hans; Taylor, Thomas N.

    2012-01-01

    . The microfossil consists of a helically contractile stalk that attaches to a main body with a peristomial feeding apparatus and a large C-shaped macronucleus. It agrees in every aspect with the living bell animals, such as Vorticella. Vorticellids and similar peritrichs are vital constituents of aquatic...... ecosystems worldwide, but so far have lacked any fossil record. This discovery offers a glimpse of ancient soft-bodied protozoan biotas, and also highlights the potential of clitellate cocoons as microscopic "conservation traps" comparable to amber....

  17. COLOR THERAPY WITH CRYSTALS AND GEMSTONES

    OpenAIRE

    Dr.Jyoti Gupta

    2017-01-01

    Gems are well-compressed small pieces found in mineral deposits found inside earth. Pearls and amber are notable exceptions in that they are formed from organic materials. Most of the gemstones are crystalline. A crystalline mineral is formed by a distinct 3-dimensional atom and this is a unique characteristic of gemstones. They possess color, hardness, aesthetic beauty, clarity and they can be cut to give sparkle.According to David Marcum’s remarks in his book “The Dow Jones Irwin Guide to F...

  18. 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.

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

    International Nuclear Information System (INIS)

    Egan, M.J.; Maul, P.R.; Watkins, B.M.; Venter, A.

    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

  20. GOLDSIM application in modeling the potential radioactive impact of LILW at Saligny site

    International Nuclear Information System (INIS)

    Constantin, Alina; Diaconu, Daniela

    2009-01-01

    This paper presents the results of a model for the impact of potential contamination produced by radionuclide leaking due to long-term physical, chemical and hydrogeological processes occurring in a LILW repository and in the natural environment. The analysis contains a deterministic and also a probabilistic approach for uncertainty assessment. The input function, i.e., the source term was evaluated by using AMBER code and the entire analysis was accomplished by using GOLDSIM, a powerful tool to support probabilistic simulation in management and decision-making in engineering and science. The results obtained were compared to previous simulations and uncertainty analyses (FEHM). (authors)

  1. A Food-Grade Cloning System for Industrial Strains of Lactococcus lactis

    OpenAIRE

    Sørensen, Kim I.; Larsen, Rasmus; Kibenich, Annette; Junge, Mette P.; Johansen, Eric

    2000-01-01

    We have previously reported the construction of a food-grade cloning vector for Lactococcus using the ochre suppressor, supB, as the selective marker. This vector, pFG1, causes only a slight growth inhibition in the laboratory strain MG1363 but is unstable in the industrial strains tested. As supB suppresses both amber and ochre stop codons, which are present in 82% of all known lactococcal genes, this undesirable finding may result from the accumulation of elongated mistranslated polypeptide...

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

    Czech Academy of Sciences Publication Activity Database

    Chytráček, Miloslav

    2015-01-01

    Roč. 90, č. 1-2 (2015), s. 271-300 ISSN 0079-4848 Grant - others:Rada Programu interní podpory projektů mezinárodní spolupráce AV ČR(CZ) M300021201 Program:M Institutional support: RVO:67985912 Keywords : Bohemia * Late Hallstatt * Early La Tène * cemetery * settlement * Etruscan bronze basins * drinking horns * amber routes * wreath * cult Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 0.103, year: 2015

  3. RNase H and replication of ColE1 DNA in Escherichia coli.

    OpenAIRE

    Naito, S; Uchida, H

    1986-01-01

    Amber mutations within the rnh (RNase H) gene of Escherichia coli K-12 were isolated by selecting for bacteria capable of replicating in a sup+ background replication-defective cer-6 mutant of the ColE1 replicon. The cer-6 mutation is an alteration of one base pair located 160 nucleotides upstream of the unique replication origin of this plasmid. Subsequently, we determined the DNA alterations present within these mutants. ColE1 DNA replicated in rnh(Am) recA cells, indicating that (i) RNase ...

  4. Government food service policies and guidelines do not create healthy school canteens.

    Science.gov (United States)

    de Silva-Sanigorski, Andrea; Breheny, Tara; Jones, Laura; Lacy, Kathleen; Kremer, Peter; Carpenter, Lauren; Bolton, Kristy; Prosser, Lauren; Gibbs, Lisa; Waters, Elizabeth; Swinburn, Boyd

    2011-04-01

    In 2006, the Victorian Government adopted the School Canteens and other school Food Services (SCFS) Policy that bans the sale of sweet drinks and confectionary and recommends the proportions of menu items based on a traffic light system of food classification. This study aims to determine whether compliance with the policy improves the nutritional profile of the menus. Items from food service menus were assessed for compliance with the SCFS policy and categorised as 'everyday' ('green'), 'select carefully' ('amber') or 'occasionally' ('red') (n=106). Profile analysis assessed differences in the nutritional profile of the menus between sub-groups. Overall, 37% of menus contained items banned under the policy. The largest proportion of items on the assessed menus were from the 'amber' category (mean: 51.0%), followed by 'red' (29.3%) and 'green' (20.3%). No menus met the traffic light-based recommendations and there was no relationship between policy compliance and the proportion of items in each of the three categories. To increase the healthiness of the school food service we recommend a greater investment in resources and infrastructure to implement existing policies, and establishing stronger monitoring and support systems. © 2011 The Authors. ANZJPH © 2011 Public Health Association of Australia.

  5. Localization and regulation of bacteriophage Mu promoters

    International Nuclear Information System (INIS)

    Stoddard, S.F.; Howe, M.M.

    1989-01-01

    Mu promoters active during the lytic cycle were located by isolating RNA at various times after induction of Mu prophages, radiolabeling it by capping in vitro, and hybridizing it to Mu DNA fragments on Southern blots. Signals were detected from four new promoters in addition to the previously characterized P e (early), P cM (repressor), and P mom (late) promoters. A major signal upstream of C was first observed at 12 min and intensified thereafter with RNA from cts and C amber but not replication-defective prophages; these characteristics indicate that this signal arises from a middle promoter, which we designate P m . With 20- and 40-min RNA, four additional major signals originated in the C-lys, F-G-I, N-P, and com-mom regions. These signals were missing with RNA from C amber and replication-defective prophages and therefore reflected the activity of late promoters, one of which we presume was P mom . Uninduced lysogens showed weak signals from five regions, one from the early regulatory region, three between genes B and lys, and one near the late genes K, L, and M. The first of these probably resulted from P cM activity; the others remain to be identified

  6. 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.

  7. Confidence building on the total system performance assessment code, MASCOT-K for permanent disposal of HLW in Korea

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Y. S.; Kim, S. G.; Kang, C. H

    2002-12-01

    To perform Total System Performance Assessment(TSPA) of a potential HLW repository, it is necessary to develop the TSPA code. KAERI has developed the one-dimensional PSA code MASCOT-K since 1997 and verified special modules dedicated for the dissolution of spent nuclear fuel. In the second R and D phase, MASCOT-K is once again verified as a part of the confidence building for TSPA. The AMBER code based on the totally different mathematical approach, compartment theory is used together with MASCOT-K to assess the annual individual doses for given K- and Q- scenarios. Results indicate that both AMBER and MASCOT-K simulate the annual individual doses to a potential biosphere. And the MASCOT-K is more flexible to describe the natural barrier such as a fracture for sensitivity studies. In the third R and D phase, MASCOT-K will be actively used to check whether the proposed KAERI reference disposal concept is solid or not.

  8. Confidence building on the total system performance assessment code, MASCOT-K for permanent disposal of HLW in Korea

    International Nuclear Information System (INIS)

    Hwang, Y. S.; Kim, S. G.; Kang, C. H.

    2002-12-01

    To perform Total System Performance Assessment(TSPA) of a potential HLW repository, it is necessary to develop the TSPA code. KAERI has developed the one-dimensional PSA code MASCOT-K since 1997 and verified special modules dedicated for the dissolution of spent nuclear fuel. In the second R and D phase, MASCOT-K is once again verified as a part of the confidence building for TSPA. The AMBER code based on the totally different mathematical approach, compartment theory is used together with MASCOT-K to assess the annual individual doses for given K- and Q- scenarios. Results indicate that both AMBER and MASCOT-K simulate the annual individual doses to a potential biosphere. And the MASCOT-K is more flexible to describe the natural barrier such as a fracture for sensitivity studies. In the third R and D phase, MASCOT-K will be actively used to check whether the proposed KAERI reference disposal concept is solid or not

  9. Undoped poly (phenyl sulfone) for radiation detection

    International Nuclear Information System (INIS)

    Nakamura, Hidehito; Shirakawa, Yoshiyuki; Sato, Nobuhiro; Kitamura, Hisashi; Takahashi, Sentaro

    2015-01-01

    Undoped aromatic ring polymers are potential scintillation materials. Here, we characterise poly (phenyl sulfone) (PPSU) for radiation detection. The amber-coloured transparent resin emits bluish-white fluorescence with 390-nm maximum. It has an excitation maximum of 340 nm, and has a density of 1.29 g/cm 3 . The effective refractive index based on its emission spectrum is 1.75. The light yield is almost equal to that of poly (ethylene terephthalate), which is a transparent resin. These results demonstrate that PPSU can be used as a component substrate in polymer blends for altering optical characteristics. - Highlights: • Poly (phenyl sulfone) (PPSU) has suitable characteristics as a scintillation material. • PPSU is an amber-coloured transparent resin that emits bluish white fluorescence with 390-nm maximum. • The 1.75 effective refractive index over the emission spectrum is relatively high. • The light yield is 0.95 times that of poly (ethylene terephthalate), which is a transparent resin. • PPSU can potentially alter optical characteristics in polymer blends

  10. Modeling the mechanism of CLN025 beta-hairpin formation

    Science.gov (United States)

    McKiernan, Keri A.; Husic, Brooke E.; Pande, Vijay S.

    2017-09-01

    Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

  11. A negentropy minimization approach to adaptive equalization for digital communication systems.

    Science.gov (United States)

    Choi, Sooyong; Lee, Te-Won

    2004-07-01

    In this paper, we introduce and investigate a new adaptive equalization method based on minimizing approximate negentropy of the estimation error for a finite-length equalizer. We consider an approximate negentropy using nonpolynomial expansions of the estimation error as a new performance criterion to improve performance of a linear equalizer based on minimizing minimum mean squared error (MMSE). Negentropy includes higher order statistical information and its minimization provides improved converge, performance and accuracy compared to traditional methods such as MMSE in terms of bit error rate (BER). The proposed negentropy minimization (NEGMIN) equalizer has two kinds of solutions, the MMSE solution and the other one, depending on the ratio of the normalization parameters. The NEGMIN equalizer has best BER performance when the ratio of the normalization parameters is properly adjusted to maximize the output power(variance) of the NEGMIN equalizer. Simulation experiments show that BER performance of the NEGMIN equalizer with the other solution than the MMSE one has similar characteristics to the adaptive minimum bit error rate (AMBER) equalizer. The main advantage of the proposed equalizer is that it needs significantly fewer training symbols than the AMBER equalizer. Furthermore, the proposed equalizer is more robust to nonlinear distortions than the MMSE equalizer.

  12. 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.

  13. Stability of pyrimethamine in a liquid dosage formulation stored for three months.

    Science.gov (United States)

    Nahata, M C; Morosco, R S; Hipple, T F

    1997-12-01

    The stability of pyrimethamine in a liquid dosage formulation stored for up to three months was studies. Commercially available 25-mg pyrimethamine tablets were crushed with a mortar and pestle and mixed with a 1:1 mixture of Simple Syrup, NF, and 1% methylcellulose to yield a suspension with a pyrimethamine concentration of 2 mg/mL. The suspension was poured into 10 amber plastic and 10 amber glass prescription bottles; 5 plastic and 5 glass bottles were stored at 4 degrees C, and the remaining bottles were kept at 25 degrees C. Samples were collected at intervals up to 91 days and tested for pyrimethamine concentration by stability-indicating high-performance liquid chromatography. Pyrimethamine remained stable throughout the three-month study period under all conditions. At 4 degrees C, pyrimethamine concentrations remained above 96% of the initial concentration; at 25 degrees C, pyrimethamine concentrations remained above 91%. No substantial changes in pH were observed. Pyrimethamine was stable for at least 91 days in an oral suspension stored in plastic or glass prescription bottles at 4 or 25 degrees C.

  14. A GoldSim Based Biosphere Assessment Model for a HLW Repository

    International Nuclear Information System (INIS)

    Lee, Youn-Myoung; Hwang, Yong-Soo; Kang, Chul-Hyung

    2007-01-01

    To demonstrate the performance of a repository, the dose exposure to a human being due to nuclide releases from a repository should be evaluated and the results compared to the dose limit presented by the regulatory bodies. To evaluate a dose rate to an individual due to a long-term release of nuclides from a HLW repository, biosphere assessment models and their implemented codes such as ACBIO1 and ACBIO2 have been developed with the aid of AMBER during the last few years. BIOMASS methodology has been adopted for a HLW repository currently being considered in Korea, which has a similar concept to the Swedish KBS-3 HLW repository. Recently, not just only for verifying the purpose for biosphere assessment models but also for varying the possible alternatives to assess the consequences in a biosphere due to a HLW repository, another version of the assessment modesl has been newly developed in the frame of development programs for a total system performance assessment modeling tool by utilizing GoldSim. Through a current study, GoldSim approach for a biosphere modeling is introduced. Unlike AMBER by which a compartment scheme can be rather simply constructed with an appropriate transition rate between compartments, GoldSim was designed to facilitate the object-oriented modules by which specific models can be addressed in an additional manner, like solving jig saw puzzles

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

    International Nuclear Information System (INIS)

    Berat, C.

    2013-01-01

    The Pierre Auger Observatory explores the potential of radio-detection techniques to measure extensive air showers (EAS) induced by ultra-high energy cosmic rays. To study in detail the mechanisms responsible for radio emission in the MHz range, the Auger Engineering Radio Array has been installed at the Observatory. Presently consisting of 24 radio-detection stations, this number will grow to 150 units covering an area of almost 20 km 2 . Novel detection techniques based on the GHz emission from the EAS are currently being studied. AMBER (Air-shower Microwave Bremsstrahlung Experimental Radiometer) and MIDAS (Microwave Detection of Air Showers) are prototypes for a large imaging dish antenna. In EASIER (Extensive Air Shower Identification using Electron Radiometer), the microwave emission is detected by antenna horns located on each surface detector. MIDAS is a self-triggering system while AMBER and EASIER use the trigger from the Auger detectors to record the emission. The status of these radio-detection R and D efforts at the Pierre Auger Observatory will be reported

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

    Energy Technology Data Exchange (ETDEWEB)

    Berat, C., E-mail: berat@lpsc.in2p3.fr [LPSC, Université Joseph Fourier Grenoble 1, CNRS/IN2P3, Institut Polytechnique de Grenoble, 53 rue des Martyrs, 38000 Grenoble (France)

    2013-08-01

    The Pierre Auger Observatory explores the potential of radio-detection techniques to measure extensive air showers (EAS) induced by ultra-high energy cosmic rays. To study in detail the mechanisms responsible for radio emission in the MHz range, the Auger Engineering Radio Array has been installed at the Observatory. Presently consisting of 24 radio-detection stations, this number will grow to 150 units covering an area of almost 20 km{sup 2}. Novel detection techniques based on the GHz emission from the EAS are currently being studied. AMBER (Air-shower Microwave Bremsstrahlung Experimental Radiometer) and MIDAS (Microwave Detection of Air Showers) are prototypes for a large imaging dish antenna. In EASIER (Extensive Air Shower Identification using Electron Radiometer), the microwave emission is detected by antenna horns located on each surface detector. MIDAS is a self-triggering system while AMBER and EASIER use the trigger from the Auger detectors to record the emission. The status of these radio-detection R and D efforts at the Pierre Auger Observatory will be reported.

  17. Detection of pulmonary nodules. Improvement by new screen-film systems?

    International Nuclear Information System (INIS)

    Lehmann, K.J.; Himmighoefer, U.

    1994-01-01

    In addition to digital radiography and AMBER, the development of asymmetric screen-film systems is another attempt to optimize chest radiography. Due to reduced contrast in the parenchyma, the former asymmetric screen-film systems did not show sufficient image quality. Three new asymmetric systems with completely different composition are available now. In-Sight VHC (Kodak), High Light GUV (3M) and Opthos D (Agfa) were compared to standard chest films using densitometric curves, a chest phantom for high and low contrast detectability, a nodule detection phantom and patient studies. The sensitivity of nodule detection in the mediastinum has been 41-48% for L-films and 58-65% for the asymmetric screen-film systems. No differences could be demonstrated for nodule detection in the lung field. Contrast in the parenchyma is equivalent to L-films. There is no loss of diagnostic information in the lung field. Differences between the asymmetric systems concern speed, dynamic range and granularity. If AMBER and digital radiography are not available, new asymmetric screen-film systems can improve nodule detection without further investment costs. (orig.) [de

  18. Ultrastructural Comparison of Processing of Protein and Pigment in the Ink Gland of Four Species of Sea Hares

    Directory of Open Access Journals (Sweden)

    Jeffrey S. Prince

    2015-01-01

    Full Text Available The ink glands of four sea hare species (Aplysia californica, A. parvula, A. juliana, and Dolabrifera dolabrifera were compared to determine where ink protein is synthesized, how it is incorporated into protein storage vesicles, and the degree of variation in the structure of the ink gland. Ink protein was synthesized in RER cells and stored in amber and white vesicles. Lack of competent RER cells in the ink gland of D. dolabrifera was correlated with the absence of ink protein. Ink protein had similar characteristics in all three Aplysia species but, again, it was absent in D. dolabrifera. Its uptake involved pinocytosis by protein vesicle cell membranes. Granulate cells showed little variation in structure among the four species, the opposite was the case for RER cells. The conversion of the red algal pigment, phycoerythrin, to phycoerythrobilin (PEB occurs in the digestive gland but the change of PEB to aplysioviolin (APV, the form of pigment released by the ink gland, occurs in the ink gland itself by both granulate cells and pigment vesicles. The literature describes five types of vesicles based upon color and contents in the ink gland of these four species. We report only three types of vesicle: colored (purple, protein (white and amber, and transparent (includes clear vesicles.

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

    Science.gov (United States)

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

    2015-01-01

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

  20. The first fossil of a bolbitidoid fern belongs to the early-divergent lineages of Elaphoglossum (Dryopteridaceae).

    Science.gov (United States)

    Lóriga, Josmaily; Schmidt, Alexander R; Moran, Robbin C; Feldberg, Kathrin; Schneider, Harald; Heinrichs, Jochen

    2014-09-01

    • Closing gaps in the fossil record and elucidating phylogenetic relationships of mostly incomplete fossils are major challenges in the reconstruction of the diversification of fern lineages through time. The cosmopolitan family Dryopteridaceae represents one of the most species-rich families of leptosporangiate ferns, yet its fossil record is sparse and poorly understood. Here, we describe a fern inclusion in Miocene Dominican amber and investigate its relationships to extant Dryopteridaceae.• The morphology of the fossil was compared with descriptions of extant ferns, resulting in it being tentatively assigned to the bolbitidoid fern genus Elaphoglossum. This assignment was confirmed by reconstructing the evolution of the morphological characters preserved in the inclusion on a molecular phylogeny of 158 extant bolbitidoid ferns. To assess the morphology-based assignment of the fossil to Elaphoglossum, we examined DNA-calibrated divergence time estimates against the age of the amber deposits from which it came.• The fossil belongs to Elaphoglossum and is the first of a bolbitidoid fern. Its assignment to a particular section of Elaphoglossum could not be determined; however, sects. Lepidoglossa, Polytrichia, and Setosa can be discounted because the fossil lacks subulate scales or scales with acicular marginal hairs. Thus, the fossil might belong to either sects. Amygdalifolia, Wrightiana, Elaphoglossum, or Squamipedia or to an extinct lineage.• The discovery of a Miocene Elaphoglossum fossil provides remarkable support to current molecular clock-based estimates of the diversification of these ferns. © 2014 Botanical Society of America, Inc.

  1. A Food-Grade Cloning System for Industrial Strains of Lactococcus lactis

    Science.gov (United States)

    Sørensen, Kim I.; Larsen, Rasmus; Kibenich, Annette; Junge, Mette P.; Johansen, Eric

    2000-01-01

    We have previously reported the construction of a food-grade cloning vector for Lactococcus using the ochre suppressor, supB, as the selective marker. This vector, pFG1, causes only a slight growth inhibition in the laboratory strain MG1363 but is unstable in the industrial strains tested. As supB suppresses both amber and ochre stop codons, which are present in 82% of all known lactococcal genes, this undesirable finding may result from the accumulation of elongated mistranslated polypeptides. Here, we report the development of a new food-grade cloning vector, pFG200, which is suitable for overexpressing a variety of genes in industrial strains of Lactococcus lactis. The vector uses an amber suppressor, supD, as selectable marker and consists entirely of Lactococcus DNA, with the exception of a small polylinker region. Using suppressible pyrimidine auxotrophs, selection and maintenance are efficient in any pyrimidine-free medium including milk. Importantly, the presence of this vector in a variety of industrial strains has no significant effect on the growth rate or the rate of acidification in milk, making this an ideal system for food-grade modification of industrially relevant L. lactis strains. The usefulness of this system is demonstrated by overexpressing the pepN gene in a number of industrial backgrounds. PMID:10742196

  2. Artificial light pollution: Shifting spectral wavelengths to mitigate physiological and health consequences in a nocturnal marsupial mammal.

    Science.gov (United States)

    Dimovski, Alicia M; Robert, Kylie A

    2018-05-02

    The focus of sustainable lighting tends to be on reduced CO 2 emissions and cost savings, but not on the wider environmental effects. Ironically, the introduction of energy-efficient lighting, such as light emitting diodes (LEDs), may be having a great impact on the health of wildlife. These white LEDs are generated with a high content of short-wavelength 'blue' light. While light of any kind can suppress melatonin and the physiological processes it regulates, these short wavelengths are potent suppressors of melatonin. Here, we manipulated the spectral composition of LED lights and tested their capacity to mitigate the physiological and health consequences associated with their use. We experimentally investigated the impact of white LEDs (peak wavelength 448 nm; mean irradiance 2.87 W/m 2 ), long-wavelength shifted amber LEDs (peak wavelength 605 nm; mean irradiance 2.00 W/m 2 ), and no lighting (irradiance from sky glow light treatments. White LED exposed wallabies had significantly suppressed nocturnal melatonin compared to no light and amber LED exposed wallabies, while there was no difference in lipid peroxidation. Antioxidant capacity declined from baseline to week 10 under all treatments. These results provide further evidence that short-wavelength light at night is a potent suppressor of nocturnal melatonin. Importantly, we also illustrate that shifting the spectral output to longer wavelengths could mitigate these negative physiological impacts. © 2018 Wiley Periodicals, Inc.

  3. 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

  4. Nanobodies: Chemical Functionalization Strategies and Intracellular Applications

    Science.gov (United States)

    Schumacher, Dominik; Helma, Jonas; Schneider, Anselm F. L.; Leonhardt, Heinrich

    2018-01-01

    Abstract Nanobodies can be seen as next‐generation tools for the recognition and modulation of antigens that are inaccessible to conventional antibodies. Due to their compact structure and high stability, nanobodies see frequent usage in basic research, and their chemical functionalization opens the way towards promising diagnostic and therapeutic applications. In this Review, central aspects of nanobody functionalization are presented, together with selected applications. While early conjugation strategies relied on the random modification of natural amino acids, more recent studies have focused on the site‐specific attachment of functional moieties. Such techniques include chemoenzymatic approaches, expressed protein ligation, and amber suppression in combination with bioorthogonal modification strategies. Recent applications range from sophisticated imaging and mass spectrometry to the delivery of nanobodies into living cells for the visualization and manipulation of intracellular antigens. PMID:28913971

  5. Safety assessment of Novi Han radioactive waste repository - features, problems, results and perspectives

    International Nuclear Information System (INIS)

    Mateeva, M.

    2000-01-01

    This paper summarizes the work done and the achievements reached in the Novi Han radioactive waste repository safety assessment within the IAEA Model Project 'Increasing the safety of Novi Han radioactive waste repository BUL 4/005'. The overall safety assessment has a wide context, but the work reported here relates only to some details and results concerning the development and implementation of the appropriate methodology approach, model and computer code used for the calculations. Different steps and procedures are included for a better practical understanding of the obtained results during the safety assessment performance. The methodology approach is widely based on an international experience in safety analysis and implemented for evaluation computer code AMBER, which is one of the recommended from the safety assessments experts. (author)

  6. Potencial hidrogeniônico de soluções de cloridrato de dobutamina expostas a condições ambientais de unidades de cuidados intensivos neonatais Hydrogen-ion potential of dobutamine hydrochloride solutions exposed to environmental conditions of neonatal intensive care units

    Directory of Open Access Journals (Sweden)

    Lidiane L. Reis

    2009-12-01

    Full Text Available OBJETIVO: Verificar o potencial hidrogeniônico (pH de soluções de cloridrato de dobutamina sob condições ambientais que mimetizam unidades de cuidados intensivos neonatais. MÉTODOS: Analisou-se pH do fármaco em solução glicosada 5% ou NaCl 0,9% segundo temperatura (22 e 37 °C, luz (escuro, lâmpadas fluorescentes ambiente e equipamento de fototerapia e equipos (incolor e âmbar em intervalos de tempo (0, 1, 24, 48, 72 e 96 horas. RESULTADOS: Evidenciaram-se valores próximos de pH do fármaco na apresentação comercial e diluído. Obteve-se média de pH de 3,45±0,19 a 22 °C e de 3,55±0,20 a 37 °C. A média de pH das soluções mantidas no escuro foi de 3,62±0,09, na luz ambiente, de 3,63±0,07, e sob fototerapia, de 3,31±0,16. Soluções em equipos incolores tiveram média menor (3,41±0,24 do que em âmbares (3,52±0,15. Obtiveram-se menores valores de pH nas soluções sob fototerapia em equipos incolores (3,17±0,03 do que em âmbares (3,55±0,03. CONCLUSÃO: Sob a luz da fototerapia houve maior variação do pH das soluções, e o emprego de equipos âmbares minimizou tal efeito.OBJECTIVE: To verify the hydrogen-ion potential (pH of dobutamine hydrochloride solutions under environmental conditions similar to those of neonatal intensive care units. METHODS: We analyzed the pH of the drug diluted in 5% dextrose in water or 0.9% NaCl under different conditions of temperature (22 and 37 °C and light (dark, fluorescent light bulbs, and phototherapy equipment, using colorless and amber intravenous sets at time intervals of 0, 1, 24, 48, 72, and 96 hours. RESULTS: The pH values of the marketed form of the drug and the diluted drug were similar. The pH means were 3.45±0.19 at 22 °C and 3.55±0.20 at 37 °C. The average of the pH according to light conditions were as follows: in the dark = 3.62±0.09, under room light = 3.63±0.07, and exposed to phototherapy = 3.31±0.16. Solutions stored in colorless intravenous sets had a lower

  7. Growth of Bi 12SiO 20 single crystals by the pulling-down method with continuous feeding

    Science.gov (United States)

    Maida, Shigeru; Higuchi, Mikio; Kodaira, Kohei

    1999-09-01

    Bi 12SiO 20 single crystals were successfully grown by the pulling-down method with continuous feeding. As-grown crystals were amber in color and transparent, and had no cracks or inclusions. A crystal with homogeneous composition was obtained from Bi-rich feed powder having a composition of 14.1 mol% SiO 2, whereas precipitates of Bi 4Si 3O 12 were observed on the surface of a crystal grown with stoichiometric powder. The shape of the solid-liquid interface during the crystal growth was estimated to be almost flat, which was favorable to avoid core formation. Average dislocation density was 4×10 3/cm 2, which was comparable to that of Bi 12SiO 20 crystals grown by the Czochralski method.

  8. Phage Pl mutants with altered transducing abilities for Escherichia coli

    International Nuclear Information System (INIS)

    Wall, J.D.; Harriman, P.D.

    1974-01-01

    A search was made for mutants of the coliphage P1 with altered transducing frequencies. A method was developed for the rapid assay of transducing frequencies in single plaques using prophage lambda as the transduced bacterial marker. This procedure selects for mutants altered in their ability to package host DNA. Mutants with 5 to 10 times higher or 10 to 20 times lower frequencies than those of wild-type P1 were found. Not only are the markers used for the detection of the mutants affected, but all other markers are similarly affected (not always to the same extent). One of the high transducing frequency mutants is a suppressible amber, indicating that loss of a function increases P1's ability to package host DNA preferentially. (U.S.)

  9. Analog to digital workflow improvement: a quantitative study.

    Science.gov (United States)

    Wideman, Catherine; Gallet, Jacqueline

    2006-01-01

    This study tracked a radiology department's conversion from utilization of a Kodak Amber analog system to a Kodak DirectView DR 5100 digital system. Through the use of ProModel Optimization Suite, a workflow simulation software package, significant quantitative information was derived from workflow process data measured before and after the change to a digital system. Once the digital room was fully operational and the radiology staff comfortable with the new system, average patient examination time was reduced from 9.24 to 5.28 min, indicating that a higher patient throughput could be achieved. Compared to the analog system, chest examination time for modality specific activities was reduced by 43%. The percentage of repeat examinations experienced with the digital system also decreased to 8% vs. the level of 9.5% experienced with the analog system. The study indicated that it is possible to quantitatively study clinical workflow and productivity by using commercially available software.

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

    Science.gov (United States)

    Dinwiddie, April; Rachootin, Stan

    2011-04-23

    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. Typically, only females in the genus carry this distinctive, highly organized structure. Two species were studied (E. petrunkevitchi and E. sinuosa), and the structure differs in form between them. We examine Eohelea's wing structures for modes of fabrication, material properties and biological functions, and the effective ecological environment in which these midges lived. We argue that the current view of the wing organ's function in stridulation has been misconstrued since it was described half a century ago.

  11. Dentinogenesis imperfect a type II: A case report with 17 years of follow-up

    Energy Technology Data Exchange (ETDEWEB)

    Gama, Francisco Jose Reis; Correa, Isabella Sousa; Valerio, Claudia Scigliano; Fatima Ferreira, Emanuelle; Manzi, Flavio Ricardo [Pontifical Catholic University of Minas Gerais, Belo Horizonte (Brazil)

    2017-06-15

    Dentinogenesis imperfect a is a dominant autosomal hereditary disorder of dentin formation that affects the deciduous and permanent teeth. Its etiology is characterized by inadequate cell differentiation during odontogenesis. The clinical characteristics of dentinogenesis imperfect a are discolored teeth with a translucency that varies from gray to brown or amber. Radiographically, the teeth exhibit pulp obliteration, thin and short roots, bell-shaped crowns, and periapical bone rarefaction. The aim of this report was to present a case of dentinogenesis imperfect a type II that was followed up over a 17-year period. This report also presents scanning electron microscopy images of the enamel and dentin, showing that both were altered in the affected teeth. The disease characteristics and the treatments that were administered are reported in this study to guide dentists with respect to the need for early diagnosis and adequate follow-up to avoid major sequelae.

  12. Dentinogenesis imperfect a type II: A case report with 17 years of follow-up

    International Nuclear Information System (INIS)

    Gama, Francisco Jose Reis; Correa, Isabella Sousa; Valerio, Claudia Scigliano; Fatima Ferreira, Emanuelle; Manzi, Flavio Ricardo

    2017-01-01

    Dentinogenesis imperfect a is a dominant autosomal hereditary disorder of dentin formation that affects the deciduous and permanent teeth. Its etiology is characterized by inadequate cell differentiation during odontogenesis. The clinical characteristics of dentinogenesis imperfect a are discolored teeth with a translucency that varies from gray to brown or amber. Radiographically, the teeth exhibit pulp obliteration, thin and short roots, bell-shaped crowns, and periapical bone rarefaction. The aim of this report was to present a case of dentinogenesis imperfect a type II that was followed up over a 17-year period. This report also presents scanning electron microscopy images of the enamel and dentin, showing that both were altered in the affected teeth. The disease characteristics and the treatments that were administered are reported in this study to guide dentists with respect to the need for early diagnosis and adequate follow-up to avoid major sequelae

  13. 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.

  14. ForConX: A forcefield conversion tool based on XML.

    Science.gov (United States)

    Lesch, Volker; Diddens, Diddo; Bernardes, Carlos E S; Golub, Benjamin; Dequidt, Alain; Zeindlhofer, Veronika; Sega, Marcello; Schröder, Christian

    2017-04-05

    The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. Hidden flows and waste processing--an analysis of illustrative futures.

    Science.gov (United States)

    Schiller, F; Raffield, T; Angus, A; Herben, M; Young, P J; Longhurst, P J; Pollard, S J T

    2010-12-14

    An existing materials flow model is adapted (using Excel and AMBER model platforms) to account for waste and hidden material flows within a domestic environment. Supported by national waste data, the implications of legislative change, domestic resource depletion and waste technology advances are explored. The revised methodology offers additional functionality for economic parameters that influence waste generation and disposal. We explore this accounting system under hypothetical future waste and resource management scenarios, illustrating the utility of the model. A sensitivity analysis confirms that imports, domestic extraction and their associated hidden flows impact mostly on waste generation. The model offers enhanced utility for policy and decision makers with regard to economic mass balance and strategic waste flows, and may promote further discussion about waste technology choice in the context of reducing carbon budgets.

  16. Site-specific labeling of proteins with NMR-active unnatural amino acids

    International Nuclear Information System (INIS)

    Jones, David H.; Cellitti, Susan E.; Hao Xueshi; Zhang Qiong; Jahnz, Michael; Summerer, Daniel; Schultz, Peter G.; Uno, Tetsuo; Geierstanger, Bernhard H.

    2010-01-01

    A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

  17. 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.

  18. A deep-learning-based emergency alert system

    Directory of Open Access Journals (Sweden)

    Byungseok Kang

    2016-06-01

    Full Text Available Emergency alert systems serve as a critical link in the chain of crisis communication, and they are essential to minimize loss during emergencies. Acts of terrorism and violence, chemical spills, amber alerts, nuclear facility problems, weather-related emergencies, flu pandemics, and other emergencies all require those responsible such as government officials, building managers, and university administrators to be able to quickly and reliably distribute emergency information to the public. This paper presents our design of a deep-learning-based emergency warning system. The proposed system is considered suitable for application in existing infrastructure such as closed-circuit television and other monitoring devices. The experimental results show that in most cases, our system immediately detects emergencies such as car accidents and natural disasters.

  19. Dose measurements for characterization of a semi-industrial cobalt-60 gamma-irradiation facility

    International Nuclear Information System (INIS)

    Farah, K.; Jerbi, T.; Kuntz, F.; Kovacs, A.

    2006-01-01

    Cobalt-60 irradiation facility has been put into operation at the National Centre of Nuclear Sciences and Technology, Sidi-thabet, Tunisia. Its technical specifications were controlled by dosimetry commissioning experiments and compared to the data specified by the plant manufacturer. Installation qualification has been carried out to measure absorbed dose distribution in the irradiation cell and products. Two dosimeter systems were used for measurements: Red and Amber Perspex and Cellulose Triacetate (CTA). The regions of minimum and maximum absorbed dose within a homogeneous dummy product (sawdust) with a bulk density of 114kg/m 3 and the dose uniformity ratio were determined. The isodose curves and the three-dimensional views were built using an automatic geostatistical gridding method, the kriging method

  20. New documents on Samuel Usque, the author of the Consolaçam as tribulaçoens de Israel

    Directory of Open Access Journals (Sweden)

    Guerrini, Maria Teresa

    2001-06-01

    Full Text Available Samuel Usque was a sixteenth-century Ferrara merchant and man of letters. Usque and Beatriz de Luna [Gracia Nasi] collaborated in the well-known task of reeducating Marranos in the precepts of normative Judaism. In addition, he represented Brianda Mendes in business trading in Antwerp, Ferrara, Venice and Ancona.Samuel Usque, literato y mercader en Ferrara en el siglo XVI, compartió con Beatriz de Luna [Gracia Nasi] el ya bien conocido proyecto cultural de la reeducación de los marranos en el judaismo. Además, Samuel Usque estuvo también al servicio de Brianda Méndez como mercader en Amberes, Ferrara, Venezia y Ancona.

  1. 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.

  2. Radiation-induced base substitution mutagenesis in single-stranded DNA phage M13

    International Nuclear Information System (INIS)

    Brandenburger, A.; Godson, G.N.; Glickman, B.W.; Sluis, C.A. van

    1981-01-01

    To elucidate the relative contributions of targeted and untargeted mutations to γ and UV radiation mutagenesis, the DNA sequences of 174 M13 revertant phages isolated from stocks of irradiated or unirradiated amber mutants grown in irradiated (SOS-induced) or unirradiated (non-induced) host bacteria, have been determined. Differences in the spectra of base change mutations induced in the various conditions were apparent, but no obvious specificity of mutagenesis was detected. In particular, under the present conditions, pyrimidine dimers did not seem to be the principal sites of UV-induced base substitution mutagenesis, suggesting that such mutagenesis occurs at the sites of lesions other than pyrimidine dimers, or is untargeted. (U.K.)

  3. Development of materials of `bekko work` using horn; Gyukaku riyo ni yoru bekko daitai zairyo no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Mori, S.; Nagata, S. [Technology Center of Nagasaki, Nagasaki (Japan); Sakoguchi, A. [Kumamoto Institute of Technology, Kumamoto (Japan)

    1996-11-10

    The technical art `Bekko` is one of the traditional technologies in Japan, and the materials of `Bekko` are shells of hawksbills. However, the industry of `Bekko Work` has been facing a crisis recently, because the import of turtleshell is restricted. We have therefore tried to develop new materials as substitutes for the turtleshell by utilization of horn. The noteworthy aspects in this study are as follows: (a) It has been clearly established that the horn could be reformed with amber color similar to that of turtleshell by chemical treatment using hydrogen peroxide (H2O2). (b) It is also of interest that we produced new materials like `Bekko` by mixing horn powder and turtleshell powder at the appropriate ratio and molding them in the temperature range of 110-120{degree}C. 1 ref., 6 figs., 3 tabs.

  4. 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.

  5. Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

    DEFF Research Database (Denmark)

    Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas

    2014-01-01

    that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce...... the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact...

  6. Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1

    KAUST Repository

    Guan, Yue; Haroon, Mohamed; Alam, Intikhab; Ferry, James G.; Stingl, Ulrich

    2017-01-01

    Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea. Functional annotation of the MSBL1 single cell amplified genomes (SAGs) also revealed a complete corrinoid-dependent methyl-transfer pathway suggesting that members of MSBL1 may possibly be capable of synthesizing Pyl and metabolizing methylated amines. This article is protected by copyright. All rights reserved.

  7. Chemical stability of diphenhydramine hydrochloride from an elixir and lidocaine hydrochloride from a viscous solution when mixed together.

    Science.gov (United States)

    Gupta, Vishnu D

    2006-01-01

    The stability of diphenhydramine hydrochloride (from an elixir) and lidocaine hydrochloride (from a viscous solution) in a mixture (1:1) was studied using a stability-indicating high-peformance liquid chromatographic assay method. The concentrations of the drugs were related directly to peak heights and the percent relative standard deviations based on five injections were 1.4 for diphenhydramine and 1.3 for lidocaine. The products of hydrolysis from the both the drugs and a number of excipients present in the dosage forms did not interfere with the developed assay procedure. The mixture was stable for at least 21 days when stored in amber-colored bottles at room temperature. The pH value of the mixture remained constant, and the physical appearance did not change during the study period.

  8. A diverse ant fauna from the mid-cretaceous of Myanmar (Hymenoptera: Formicidae.

    Directory of Open Access Journals (Sweden)

    Phillip Barden

    Full Text Available A new collection of 24 wingless ant specimens from mid-Cretaceous Burmese amber (Albian-Cenomanian, 99 Ma comprises nine new species belonging to the genus Sphecomyrmodes Engel and Grimaldi. Described taxa vary considerably with regard to total size, head and body proportion, cuticular sculpturing, and petiole structure while all species are unified by a distinct shared character. The assemblage represents the largest known diversification of closely related Cretaceous ants with respect to species number. These stem-group ants exhibit some characteristics previously known only from their extant counterparts along with presumed plesiomorphic morphology. Consequently, their morphology may inform hypotheses relating to basal relationships and general patterns of ant evolution. These and other uncovered Cretaceous species indicate that stem-group ants are not simply wasp-like, transitional formicids, but rather a group of considerable adaptive diversity, exhibiting innovations analogous to what crown-group ants would echo 100 million years later.

  9. 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.

  10. Muscle and plastic equivalent glass dosimeter for high-dose dosimetry

    International Nuclear Information System (INIS)

    Abdel-Rehim, F.; Maged, A.F.; Morsy, M.A.; Hashad, A.M.

    1990-01-01

    The alkali-silicate glass dosimeter is made up of 66.8% SiO 2 , 31.2% Li 2 O, 2% K 2 O. It is nearly colourless before irradiation and then takes on an amber colour with increasing doses of gamma radiation. This colouration is represented by the appearance of broad absorption bands at 405 nm and 600 nm wavelengths. The change in absorbance is linear with the absorbed dose in the range of 0.1-4.5 kGy, when measured at its 405 nm absorption band maximum. This glass dosimeter simulates low-z plastics and muscle tissue in terms of gamma-ray absorption properties over broad radiation spectra (0.1 MeV to 10 MeV). (author) 22 refs.; 4 figs.; 2 tabs

  11. Safety assessment for radioactive waste disposal facility

    International Nuclear Information System (INIS)

    Thanaletchumy Karuppiah; Mohd Abdul Wahab Yusof; Nik Marzuki Nik Ibrahim; Nurul Wahida Ahmad Khairuddin

    2008-08-01

    Safety assessments are used to evaluate the performance of a radioactive waste disposal facility and its impact on human health and the environment. This paper presents the overall information and methodology to carry out the safety assessment for a long term performance of a disposal system. A case study was also conducted to gain hands-on experience in the development and justification of scenarios, the formulation and implementation of models and the analysis of results. AMBER code using compartmental modeling approach was used to represent the migration and fate of contaminants in this training. This safety assessment is purely illustrative and it serves as a starting point for each development stage of a disposal facility. This assessment ultimately becomes more detail and specific as the facility evolves. (Author)

  12. Nanobodies: Chemical Functionalization Strategies and Intracellular Applications.

    Science.gov (United States)

    Schumacher, Dominik; Helma, Jonas; Schneider, Anselm F L; Leonhardt, Heinrich; Hackenberger, Christian P R

    2018-02-23

    Nanobodies can be seen as next-generation tools for the recognition and modulation of antigens that are inaccessible to conventional antibodies. Due to their compact structure and high stability, nanobodies see frequent usage in basic research, and their chemical functionalization opens the way towards promising diagnostic and therapeutic applications. In this Review, central aspects of nanobody functionalization are presented, together with selected applications. While early conjugation strategies relied on the random modification of natural amino acids, more recent studies have focused on the site-specific attachment of functional moieties. Such techniques include chemoenzymatic approaches, expressed protein ligation, and amber suppression in combination with bioorthogonal modification strategies. Recent applications range from sophisticated imaging and mass spectrometry to the delivery of nanobodies into living cells for the visualization and manipulation of intracellular antigens. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  13. Transmission dynamic range in chest radiology

    International Nuclear Information System (INIS)

    Lemmers, H.E.A.S.J.; Schultze Kool, L.J.; van Elburg, H.J.; Boelens, F.

    1989-01-01

    Due to the large difference in transmission between the lung area and the mediastinum, the human chest is a challenging object for radiographic imaging. This study is performed in order to define the dynamic range needed for a chest imaging chain. Eight hundred seventy-five consecutive outpatients were imaged with a prototype AMBER (advanced multiple beam equalization radiography) unit at 141 kVp. The equalization facility was disabled, allowing for the simultaneous capture of a film image and a digital dataset representing the local patient transmission in fields of approximately 2x2 cm. The datasets were analyzed to obtain the relation between the average transmission distribution in a subset of the population and physical parameters characterizing this subset, such as body weight or length

  14. Use of lambda pMu bacteriophages to isolate lambda specialized transducing bacteriophages carrying genes for bacterial chemotaxis.

    Science.gov (United States)

    Kondoh, H; Paul, B R; Howe, M M

    1980-09-01

    A general method for constructing lambda specialized transducing phages is described. The method, which is potentially applicable to any gene of Escherichia coli, is based on using Mu DNA homology to direct the integration of a lambda pMu phage near the genes whose transduction is desired. With this method we isolated a lambda transducing phage carrying all 10 genes in the che gene cluster (map location, 41.5 to 42.5 min). The products of the cheA and tar genes were identified by using transducing phages with amber mutations in these genes. It was established that tar codes for methyl-accepting chemotaxis protein II (molecular weight, 62,000) and that cheA codes for two polypeptides (molecular weights, 76,000 and 66,000). Possible origins of the two cheA polypeptides are discussed.

  15. 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 homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in 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...

  16. Pristine Early Eocene wood buried deeply in kimberlite from northern Canada.

    Science.gov (United States)

    Wolfe, Alexander P; Csank, Adam Z; Reyes, Alberto V; McKellar, Ryan C; Tappert, Ralf; Muehlenbachs, Karlis

    2012-01-01

    We report exceptional preservation of fossil wood buried deeply in a kimberlite pipe that intruded northwestern Canada's Slave Province 53.3±0.6 million years ago (Ma), revealed during excavation of diamond source rock. The wood originated from forest surrounding the eruption zone and collapsed into the diatreme before resettling in volcaniclastic kimberlite to depths >300 m, where it was mummified in a sterile environment. Anatomy of the unpermineralized wood permits conclusive identification to the genus Metasequoia (Cupressaceae). The wood yields genuine cellulose and occluded amber, both of which have been characterized spectroscopically and isotopically. From cellulose δ(18)O and δ(2)H measurements, we infer that Early Eocene paleoclimates in the western Canadian subarctic were 12-17°C warmer and four times wetter than present. Canadian kimberlites offer Lagerstätte-quality preservation of wood from a region with limited alternate sources of paleobotanical information.

  17. Pristine Early Eocene wood buried deeply in kimberlite from northern Canada.

    Directory of Open Access Journals (Sweden)

    Alexander P Wolfe

    Full Text Available We report exceptional preservation of fossil wood buried deeply in a kimberlite pipe that intruded northwestern Canada's Slave Province 53.3±0.6 million years ago (Ma, revealed during excavation of diamond source rock. The wood originated from forest surrounding the eruption zone and collapsed into the diatreme before resettling in volcaniclastic kimberlite to depths >300 m, where it was mummified in a sterile environment. Anatomy of the unpermineralized wood permits conclusive identification to the genus Metasequoia (Cupressaceae. The wood yields genuine cellulose and occluded amber, both of which have been characterized spectroscopically and isotopically. From cellulose δ(18O and δ(2H measurements, we infer that Early Eocene paleoclimates in the western Canadian subarctic were 12-17°C warmer and four times wetter than present. Canadian kimberlites offer Lagerstätte-quality preservation of wood from a region with limited alternate sources of paleobotanical information.

  18. Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach.

    Science.gov (United States)

    Ahmed, Bilal; Ali Ashfaq, Usman; Usman Mirza, Muhammad

    2018-05-01

    Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding affinity. Finally, 10 molecules (Kushenol K, Rosmarinic acid, Reserpic acid, Munjistin, Leachianone G, Cephamycin C, Arctigenin, 3-O-acetylpadmatin, Geniposide and Obtusin) were selected that showed strong bonding with the pancreatic lipase. MD simulations were performed on top five compounds using AMBER16. The simulated complexes revealed stability and ligands remained inside the binding pocket. This study concluded that these finalised molecules can be used as drug candidate to control obesity.

  19. Chirality-dependent anisotropic elastic properties of a monolayer graphene nanosheet.

    Science.gov (United States)

    Guo, Jian-Gang; Zhou, Li-Jun; Kang, Yi-Lan

    2012-04-01

    An analytical approach is presented to predict the elastic properties of a monolayer graphene nanosheet based on interatomic potential energy and continuum mechanics. The elastic extension and torsional springs are utilized to simulate the stretching and angle variation of carbon-carbon bond, respectively. The constitutive equation of the graphene nanosheet is derived by using the strain energy density, and the analytical formulations for nonzero elastic constants are obtained. The in-plane elastic properties of the monolayer graphene nanosheet are proved to be anisotropic. In addition, Young's moduli, Poisson's ratios and shear modulus of the monolayer graphene nanosheet are calculated according to the force constants derived from Morse potential and AMBER force field, respectively, and they were proved to be chirality-dependent. The comparison with experimental results shows a very agreement.

  20. 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. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Raman Spectroscopic Study on Decorative Glasses in Thailand

    International Nuclear Information System (INIS)

    Won-In, K.; Ponkrapan, S.; Dararutana, P.

    2011-01-01

    Glasses have been used as decorative objects in Thailand for several hundred years. Decorative glasses can generally be seen as architectural components in old styled palaces and Buddhist objects. There were various colors ranging from transparent to amber, blue, green and red with different shades among glass of different colors. Fragments of archaeological glass samples were characterized for the first time using Raman microscopy with the aim of obtaining information that would lead to identification of the glass samples by means of laser scattering. The samples were also investigated using other techniques, such as particle induced X-ray emission spectroscopy and scanning electron microscope operated with energy dispersive X-ray fluorescence spectrometer. They were mostly lead-silica based glasses. The colors resulted from metal ions. The difference in chemical composition was confirmed by Raman signature spectra. (author)

  2. “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.

  3. Ultraviolet-induced reversion of cyc1 alleles in radiation-sensitive strains of yeast. III. rev 3 mutant strains

    International Nuclear Information System (INIS)

    Lawrence, C.W.; Crhistensen, R.B.

    1979-01-01

    The role of rev3 gene function in uv-induced mutagenesis in the yeast Saccharomyces cerevisiae has been examined by determining the reversion of 12 well-defined cyc1 mutations in diploid strains homozygous for the rev3-1 or rev3-3 allale. The 12 cyc1 alleles include one ochre, one amber, four initiation, two proline missense, and four frameshift mutations. We find that the rev3 mutations reduce the frequency of UV-induced reversion of all of the cyc1 alleles, though different classes of alleles respond to a different extent. These results imply that the rev3 gene function is required for the production of a wide variety of mutational events, though probably not all, and show that each of the three rev loci have different mutational phenotypes. Such diverse phenotypes are not predicted by the unitary model for bacterial mutagenes, suggesting that this is at best an incomplete description of eukaryotic mutagenesis

  4. 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.

  5. Molecular dynamics simulations of glycerol glass-forming liquid

    International Nuclear Information System (INIS)

    Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.

    2005-01-01

    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 ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory

  6. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

    2012-05-01

    MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

  7. [A new look at the tomb of the physician, Morlongo Venice].

    Science.gov (United States)

    Pardon-Labonnelie, Muriel

    2014-01-01

    The development of the inventory and synthetic study of collyrium stamps, commonly known as "oculist's stamps", includes the physico-chemical analysis of rare stamped collyrium's remains. The fragments of collyrium which were discovered in a tomb of Morlungo (Veneto) are all the more remarkable as the remedy's name stamped on two of them remains enigmatic at the moment and because of the association in a funerary context with an-other thirty-five finds. More specifically, they were discovered near surgical bronze instruments, a large amount of amber, a portable sundial and a seal box. Recent archaeological, textual and technological data thus make the study of the remains of collyriums of Morlungo particularly interesting for the history of medicine.

  8. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

    Science.gov (United States)

    Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

    2009-10-01

    This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

  9. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

    Science.gov (United States)

    Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

    2014-12-15

    LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. © 2014 Wiley Periodicals, Inc.

  10. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation

    Science.gov (United States)

    Paluch, Andrew S.; Parameswaran, Sreeja; Liu, Shuai; Kolavennu, Anasuya; Mobley, David L.

    2015-01-01

    We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.

  11. Plastic pollution on the Baltic beaches of Kaliningrad region, Russia.

    Science.gov (United States)

    Esiukova, Elena

    2017-01-30

    Contamination of sandy beaches of the Baltic Sea in Kaliningrad region is evaluated on the base of surveys carried out from June 2015 to January 2016. Quantity of macro/meso/microplastic objects in the upper 2cm of the sandy sediments of the wrack zone at 13 sampling sites all along the Russian coast is reported. Occurrence of paraffin and amber pieces at the same sites is pointed out. Special attention is paid to microplastics (range 0.5-5mm): its content ranges between 1.3 and 36.3 items per kg dry sediment. The prevailing found type is foamed plastic. No sound differences in contamination are discovered between beaches with high and low anthropogenic load. Mean level of contamination is of the same order of magnitude as has been reported by other authors for the Baltic Sea beaches. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1

    KAUST Repository

    Guan, Yue

    2017-05-11

    Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea. Functional annotation of the MSBL1 single cell amplified genomes (SAGs) also revealed a complete corrinoid-dependent methyl-transfer pathway suggesting that members of MSBL1 may possibly be capable of synthesizing Pyl and metabolizing methylated amines. This article is protected by copyright. All rights reserved.

  13. Evolution of Lower Brachyceran Flies (Diptera and Their Adaptive Radiation with Angiosperms

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2017-04-01

    Full Text Available The Diptera (true flies is one of the most species-abundant orders of Insecta, and it is also among the most important flower-visiting insects. Dipteran fossils are abundant in the Mesozoic, especially in the Late Jurassic and Early Cretaceous. Here, we review the fossil record and early evolution of some Mesozoic lower brachyceran flies together with new records in Burmese amber, including Tabanidae, Nemestrinidae, Bombyliidae, Eremochaetidae, and Zhangsolvidae. The fossil records reveal that some flower-visiting groups had diversified during the mid-Cretaceous, consistent with the rise of angiosperms to widespread floristic dominance. These brachyceran groups played an important role in the origin of co-evolutionary relationships with basal angiosperms. Moreover, the rise of angiosperms not only improved the diversity of flower-visiting flies, but also advanced the turnover and evolution of other specialized flies.

  14. An Ilustrative Nuclide Release Behavior from an HLW Repository due to an Earthquake Event

    International Nuclear Information System (INIS)

    Lee, Youn-Myoung; Hwang, Yong-Soo; Choi, Jong-Won

    2008-01-01

    Program for the evaluation of a high-level waste repository which is conceptually modeled. During the last few years, programs developed with the aid of AMBER and GoldSim by which nuclide transports in the near- and far-field of a repository as well as transport through the biosphere under various normal and disruptive release scenarios could be modeled and evaluated, have been continuously demonstrated. To show its usability, as similarly done for the natural groundwater flow scheme, influence of a possible disruptive event on a nuclide release behavior from an HLW repository system caused naturally due to an earthquake has been investigated and illustrated with the newly developed GoldSim program

  15. A GoldSim Model for Colloid Facilitated Nuclide Transport

    International Nuclear Information System (INIS)

    Lee, Youn Myoung; Jeong, Jong Tae

    2010-01-01

    Recently several total system performance assessment (TSPA) programs, called 'template' programs, ready for the safety assessment of radioactive waste repository systems which are conceptually modeled have been developed by utilizing GoldSim and AMBER at KAERI. It is generally believed that chelating agents (chelators) that could be disposed of together with radioactive wastes in the repository and natural colloids available in the geological media affect on nuclides by enhancing their transport in the geological media. A simple GoldSim module to evaluate such quantitative effects, by which colloid and chelator-facilitated nuclide release cases could be modeled and evaluated is introduced. Effects of the chelators alone are illustrated with the case associated with well pumping scenario in a hypothetical repository system

  16. A Nuclide Release Model for a Deep Well Scenario near a Repository

    International Nuclear Information System (INIS)

    Lee, Youn Myoung; Jung, Jong Tae; Choi, Jong Won

    2010-01-01

    Recently several template programs ready for the safety assessment of a high-level radioactive waste repository (HLW) and a low- and intermediate level radioactive waste repository (LILW) systems, that are conceptually modeled, have been developed by utilizing GoldSim and AMBER at KAERI. During the last few years, such template programs have been utilized for the evaluation of nuclide transports in the nearand far-field of a repository as well as transport through the biosphere under various normal and disruptive release scenarios with assumed data. The GoldSim program, another template program by which influence due to a well located very near to the repository has been modeled and evaluated for an assumed case in order to simulate the worst exposure scenario. This seems very useful to evaluate an accidental event a long time after closure of the repository has been developed and illustrated

  17. Study of the influence of chemical composition on the pozzolanicity of soda-lime glass microparticles

    International Nuclear Information System (INIS)

    Sales, R.B.C.; Mohallem, N.D.S.; Aguilar, M.T.P.

    2014-01-01

    The use of residues presents interesting possibilities for obtaining eco-efficient concretes. Research has investigated the use of glass residue in Portland cement composite, whether as an aggregate or a supplementary material. However, there is still no consensus on the influence of the chemical composition of glass on the behaviour of the composites in which it is used. This paper aims to analyse the influence of this composition on the performance of cement composites produced with microparticles of colourless and amber glass. Pozzolanicity was assessed by means of direct tests (modified Chapelle and electrical conductivity) and indirect tests (chemical characterization, X-ray diffraction, thermo analysis and pozzolanic activity index). Most of the results show that microparticles of both types of glass display pozzolanic activity, with no significant differences between them. This indicates the potential for the use of glass microparticles as a supplementary material in cement composites. (author)

  18. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

    2017-09-01

    We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

  19. Radiation Technician Scientist service

    International Nuclear Information System (INIS)

    Prieto Miranda, Enrique; Barrera Gonzalez, Gisela; Guerra Torres, Mercedes; Mora Lopez, Leonor; Altanes Valentin, Sonia; Rapado Paneque, Manuel; Plasencia Gutierrez, Manuel

    2003-01-01

    The irradiation service is part of the specialized technician scientist services of the Center of Technological Applications and Nuclear Development it belonging to the Radiobiological Department it provides a self shielded laboratory irradiator, PX y 30 type with Cobalt 60 sources, it destined for searches studies, so much basic as applying, in several branches of the science, like the radiobiology, the radiation chemistry, the solid state physics, the medicine, the agriculture and the Pharmaceutical- Medical Industry and besides offering the irradiation service properly with the which have been gotten significant economical outputs. The radiation processing is controlled by means of the dosimetric systems of Freckle, ceric cerous sulfate, Perspex (red, clear and Amber) and dose indicators

  20. Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA98-210) with damaged DNA.

    Science.gov (United States)

    Pradhan, Sushmita; Mattaparthi, Venkata Satish Kumar

    2017-10-25

    Nucleotide excision repair (NER) in higher organisms repair massive DNA abrasions caused by ultraviolet rays, and various mutagens, where Xeroderma pigmentosum group A (XPA) protein is known to be involved in damage recognition step. Any mutations in XPA cause classical Xeroderma pigmentosum disease. The extent to which XPA is required in the NER is still unclear. Here, we present the comparative study on the structural and conformational changes in globular DNA binding domain of XPA 98-210 in DNA bound and DNA free state. Atomistic molecular dynamics simulation was carried out for both XPA 98-210 systems using AMBER force fields. We observed that XPA 98-210 in presence of damaged DNA exhibited more structural changes compared to XPA 98-210 in its free form. When XPA is in contact with DNA, we found marked stability of the complex due to the formation of characteristic longer antiparallel β-sheets consisting mainly lysine residues.

  1. 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...

  2. Study of the influence of chemical composition on the pozzolanicity of soda-lime glass microparticles; Estudo da influencia da composicao quimica na pozolanicidade de microparticulas de vidro soda-cal

    Energy Technology Data Exchange (ETDEWEB)

    Sales, R.B.C. [Universidade do Estado de Minas Gerais (UEMG), MG (Brazil). Departamento de Ciencias e Tecnologia; Sales, F.A.; Correa, E.C.; Patricio, P. [Centro Federal de Educacao Tecnologica de Minas Gerais (CEFET-MG), MG (Brazil); Mohallem, N.D.S.; Aguilar, M.T.P., E-mail: teresa@ufmg.br [Universidade Federal de Minas Gerais (UFMG), MG (Brazil)

    2014-07-01

    The use of residues presents interesting possibilities for obtaining eco-efficient concretes. Research has investigated the use of glass residue in Portland cement composite, whether as an aggregate or a supplementary material. However, there is still no consensus on the influence of the chemical composition of glass on the behaviour of the composites in which it is used. This paper aims to analyse the influence of this composition on the performance of cement composites produced with microparticles of colourless and amber glass. Pozzolanicity was assessed by means of direct tests (modified Chapelle and electrical conductivity) and indirect tests (chemical characterization, X-ray diffraction, thermo analysis and pozzolanic activity index). Most of the results show that microparticles of both types of glass display pozzolanic activity, with no significant differences between them. This indicates the potential for the use of glass microparticles as a supplementary material in cement composites. (author)

  3. A non-sense mutation in the putative anti-mutator gene ada/alkA of Mycobacterium tuberculosis and M. bovis isolates suggests convergent evolution

    Directory of Open Access Journals (Sweden)

    Gicquel Brigitte

    2007-05-01

    Full Text Available Abstract Background Previous studies have suggested that variations in DNA repair genes of W-Beijing strains may have led to transient mutator phenotypes which in turn may have contributed to host adaptation of this strain family. Single nucleotide polymorphism (SNP in the DNA repair gene mutT1 was identified in MDR-prone strains from the Central African Republic. A Mycobacteriumtuberculosis H37Rv mutant inactivated in two DNA repair genes, namely ada/alkA and ogt, was shown to display a hypermutator phenotype. We then looked for polymorphisms in these genes in Central African Republic strains (CAR. Results In this study, 55 MDR and 194 non-MDR strains were analyzed. Variations in DNA repair genes ada/alkA and ogt were identified. Among them, by comparison to M. tuberculosis published sequences, we found a non-sense variation in ada/alkA gene which was also observed in M. bovis AF2122 strain. SNPs that are present in the adjacent regions to the amber variation are different in M. bovis and in M. tuberculosis strain. Conclusion An Amber codon was found in the ada/alkA locus of clustered M. tuberculosis isolates and in M. bovis strain AF2122. This is likely due to convergent evolution because SNP differences between strains are incompatible with horizontal transfer of an entire gene. This suggests that such a variation may confer a selective advantage and be implicated in hypermutator phenotype expression, which in turn contributes to adaptation to environmental changes.

  4. Fixed dose darunavir boosted with cobicistat combined with emtricitabine and tenofovir alafenamide fumarate.

    Science.gov (United States)

    Cevik, Muge; Orkin, Chloe

    2018-07-01

    In an era when virological efficacy approaches 100%, novel antiretroviral (ARV) therapies must deliver better tolerability, safety, and convenient coformulated regimens. We review the phase II and III clinical data on the fixed dose combination (FDC) darunavir (DRV) 800mg / cobicistat (COBI/C) 150 mg / emtricitabine (F/FTC) 200 mg / tenofovir alafenamide fumarate (TAF) 10mg (D/C/F/TAF) for the treatment of HIV-1 infection. In an exploratory phase II study, D/C/F/TAF FDC demonstrated similar virological efficacy to darunavir/cobicistat FDC + F /tenofovir disoproxil fumarate (TDF) FDC in treatment-naive HIV-1-infected individuals with favorable bone and renal outcomes. These findings led to two subsequent international phase III double-blind randomized controlled trials; AMBER and EMERALD. In the (treatment naïve) AMBER study, D/C/F/TAF FDC was noninferior to component regimen F/TDF + darunavir/cobicistat with favorable bone and renal outcomes at week 48. In the EMERALD study (switch study for virologically suppressed patients), D/C/F/TAF showed noninferior efficacy to F/TDF and boosted protease inhibitor (bPI) regimen at week 48 also with favorable renal and bone outcomes. No virological failure was observed, and no resistance to TDF or darunavir emerged in either study. In clinical trials, D/C/F/TAF FDC demonstrated excellent, noninferior virological efficacy, maintained a high genetic barrier and conferred the additional safety benefits of TAF. As the first one pill, once daily, protease inhibitor-based regimen, D/C/F/TAF FDC offers a new option for the treatment of HIV infection.

  5. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

    Science.gov (United States)

    Lara, A; Riquelme, M; Vöhringer-Martinez, E

    2018-05-11

    Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model

  6. Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2013-03-30

    We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free-energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica-exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local-minimum free-energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid-β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β-helix, α-helix, 3(10)-helix, β-hairpin, and β-sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free-energy landscape. Copyright © 2012 Wiley Periodicals, Inc.

  7. Labeling proteins on live mammalian cells using click chemistry.

    Science.gov (United States)

    Nikić, Ivana; Kang, Jun Hee; Girona, Gemma Estrada; Aramburu, Iker Valle; Lemke, Edward A

    2015-05-01

    We describe a protocol for the rapid labeling of cell-surface proteins in living mammalian cells using click chemistry. The labeling method is based on strain-promoted alkyne-azide cycloaddition (SPAAC) and strain-promoted inverse-electron-demand Diels-Alder cycloaddition (SPIEDAC) reactions, in which noncanonical amino acids (ncAAs) bearing ring-strained alkynes or alkenes react, respectively, with dyes containing azide or tetrazine groups. To introduce ncAAs site specifically into a protein of interest (POI), we use genetic code expansion technology. The protocol can be described as comprising two steps. In the first step, an Amber stop codon is introduced--by site-directed mutagenesis--at the desired site on the gene encoding the POI. This plasmid is then transfected into mammalian cells, along with another plasmid that encodes an aminoacyl-tRNA synthetase/tRNA (RS/tRNA) pair that is orthogonal to the host's translational machinery. In the presence of the ncAA, the orthogonal RS/tRNA pair specifically suppresses the Amber codon by incorporating the ncAA into the polypeptide chain of the POI. In the second step, the expressed POI is labeled with a suitably reactive dye derivative that is directly supplied to the growth medium. We provide a detailed protocol for using commercially available ncAAs and dyes for labeling the insulin receptor, and we discuss the optimal surface-labeling conditions and the limitations of labeling living mammalian cells. The protocol involves an initial cloning step that can take 4-7 d, followed by the described transfections and labeling reaction steps, which can take 3-4 d.

  8. SU-F-R-11: Designing Quality and Safety Informatics Through Implementation of a CT Radiation Dose Monitoring Program

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, JM [Clinical Imaging Physics Group and Carl E. Ravin Advanced Imaging Laboratories, Department of Radiology, Duke University Medical Center, Durham, NC (United States); Samei, E [Clinical Imaging Physics Group and Carl E. Ravin Advanced Imaging Laboratories, Department of Radiology, Duke University Medical Center, Durham, NC (United States); Departments of Physics, Electrical and Computer Engineering, and Biomedical Engineering, and Medical Physics Graduate Program, Duke University, Durham, NC (United States)

    2016-06-15

    Purpose: Recent legislative and accreditation requirements have driven rapid development and implementation of CT radiation dose monitoring solutions. Institutions must determine how to improve quality, safety, and consistency of their clinical performance. The purpose of this work was to design a strategy and meaningful characterization of results from an in-house, clinically-deployed dose monitoring solution. Methods: A dose monitoring platform was designed by our imaging physics group that focused on extracting protocol parameters, dose metrics, and patient demographics and size. Compared to most commercial solutions, which focus on individual exam alerts and global thresholds, the program sought to characterize overall consistency and targeted thresholds based on eight analytic interrogations. Those were based on explicit questions related to protocol application, national benchmarks, protocol and size-specific dose targets, operational consistency, outliers, temporal trends, intra-system variability, and consistent use of electronic protocols. Using historical data since the start of 2013, 95% and 99% intervals were used to establish yellow and amber parameterized dose alert thresholds, respectively, as a function of protocol, scanner, and size. Results: Quarterly reports have been generated for three hospitals for 3 quarters of 2015 totaling 27880, 28502, 30631 exams, respectively. Four adult and two pediatric protocols were higher than external institutional benchmarks. Four protocol dose levels were being inconsistently applied as a function of patient size. For the three hospitals, the minimum and maximum amber outlier percentages were [1.53%,2.28%], [0.76%,1.8%], [0.94%,1.17%], respectively. Compared with the electronic protocols, 10 protocols were found to be used with some inconsistency. Conclusion: Dose monitoring can satisfy requirements with global alert thresholds and patient dose records, but the real value is in optimizing patient

  9. Stability of three commonly compounded extemporaneous enrofloxacin suspensions for oral administration to exotic animals.

    Science.gov (United States)

    Petritz, Olivia A; Guzman, David Sanchez-Migallon; Wiebe, Valerie J; Papich, Mark G

    2013-07-01

    To evaluate the stability of 3 extemporaneous oral suspensions of enrofloxacin mixed with readily available flavoring vehicles when stored at room temperature (approx 22°C). Evaluation study. 3 commonly compounded oral suspensions of enrofloxacin. On day 0, commercially available enrofloxacin tablets were compounded with a mixture of distilled water and corn syrup (formulation A) or cherry syrup (formulation B) flavoring vehicles to create suspensions with a nominal enrofloxacin concentration of 22.95 mg/mL, and 2.27% enrofloxacin injectable solution was compounded with a liquid sweetener (formulation C) to create a suspension with a nominal enrofloxacin concentration of 11.35 mg/mL. Preparations were stored in amber-colored vials at room temperature for 56 days. For each preparation, the enrofloxacin concentration was evaluated with high-performance liquid chromatography at prespecified intervals during the study. The pH, odor, and consistency for all suspensions were recorded at the start and completion of the study. Relative to the nominal enrofloxacin concentration, the enrofloxacin concentration strength ranged from 95.80% to 100.69% for formulation A, 108.44% to 111.06% for formulation B, and 100.99% to 103.28% for formulation C. A mild pH increase was detected in all 3 suspensions during the study. Results indicated that, when stored in amber-colored vials at room temperature for 56 days, the enrofloxacin concentration strength in all 3 formulations was retained within acceptance criteria of 90% to 110%. Subjectively, cherry syrup flavoring was better at masking the smell and taste of enrofloxacin than were the other mixing vehicles.

  10. 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.

  11. 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.

  12. Formulation and stability of an extemporaneously compounded oral solution of chlorpromazine HCl.

    Science.gov (United States)

    Prohotsky, Daniel L; Juba, Katherine M; Zhao, Fang

    2014-12-01

    Chlorpromazine is a phenothiazine antipsychotic which is often used in hospice and palliative care to treat hiccups, delirium, and nausea. With the discontinuation of the commercial oral solution concentrate, there is a need to prepare this product by extemporaneous compounding. This study was initiated to identify an easy-to-prepare formulation for the compounding pharmacist. A stability study was also conducted to select the proper storage conditions and establish the beyond-use date. Chlorpromazine HCl powder and the Ora-Sweet® syrup vehicle were used to prepare the 100 mg/mL solution. Once the feasibility was established, a batch of the solution was prepared and packaged in amber plastic prescription bottles for a stability study. These samples were stored at refrigeration (2-8°C) or room temperature (20-25°C) for up to 3 months. At each monthly time point, the samples were evaluated by visual inspection, pH measurement, and high performance liquid chromatography (HPLC). A separate forced stability study was conducted to confirm that the HPLC method was stability indicating. A clear and colorless solution of 100 mg/mL chlorpromazine HCl was obtained by dissolving the drug powder in Ora-Sweet® with moderate agitation. The stability study results indicated that this solution product remained unchanged in visual appearance or pH at both refrigeration and room temperature for up to 3 months. The HPLC results also confirmed that all stability samples retained 93.6-101.4% of initial drug concentration. Chlorpromazine HCl solution 100 mg/mL can be compounded extemporaneously by dissolving chlorpromazine HCl drug powder in Ora-Sweet®. The resulting product is stable for at least three months in amber plastic prescription bottles stored at either refrigeration or room temperature.

  13. 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.

  14. Stability of an extemporaneously prepared thalidomide suspension.

    Science.gov (United States)

    Kraft, Shawna; Johnson, Cary E; Tyler, Ryan P

    2012-01-01

    The short-term physical and chemical stability of an oral suspension of thalidomide 20 mg/mL was studied. An oral suspension of thalidomide 20 mg/mL was prepared by emptying the contents of 12 100-mg thalidomide capsules into a glass mortar; 30 mL of Ora-Plus and 30 mL of Ora-Sweet were mixed and added to the thalidomide powder to make a final volume of 60 mL. Three identical samples of the formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and stored under refrigeration (3-5 °C). A 1-mL sample was withdrawn from each of the three samples with a micropipette immediately after preparation and at 7, 14, 21, 28, and 35 days. After further dilution to an expected concentration of 20 μg/mL with acetonitrile-methanol and then dilution with mobile phase, the samples were assayed in duplicate using stability-indicating high-performance liquid chromatography. Stability was determined by evaluating the percentage of the initial concentration remaining at each time point; stability was defined as the retention of at least 90% of the initial concentration of thalidomide. At least 92% of the initial thalidomide concentration remained throughout the 35-day study period. There were no detectable changes in color, odor, or pH and no visible microbial growth in any sample. An extemporaneously prepared suspension of thalidomide 20 mg/mL in a 1:1 mixture of Ora-Plus and Ora-Sweet was stable for at least 35 days when stored in 2-oz amber plastic bottles under refrigeration.

  15. Stability of extemporaneously prepared sodium phenylbutyrate oral suspensions.

    Science.gov (United States)

    Caruthers, Regine L; Johnson, Cary E

    2007-07-15

    In an effort to minimize barriers to compliance and adherence and to improve the accuracy of dosage measurement, sugar-containing and sugar-free sodium phenylbutyrate suspensions were formulated, and the stability of these products over a 90-day period was determined. An oral suspension of sodium phenylbutyrate 200 mg/mL was prepared by thoroughly grinding 12 g of Sodium Phenylbutyrate Powder, USP, in a glass mortar. Thirty milliliters of Ora-Plus and 30 mL of either Ora-Sweet or Ora-Sweet SF were mixed and added to the powder to make a final volume of 60 mL. Three identical samples of each formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and were stored at room temperature. A 500-microL sample was withdrawn from each of the six bottles with a micropipette immediately after preparation and at 7, 14, 28, 60, and 90 days. After further dilution to an expected concentration of 100 microg/mL with the mobile phase, the samples were assayed by high-performance liquid chromatography. Stability was defined as the retention of at least 90% of the initial concentration. At least 95% of the initial sodium phenylbutyrate concentration remained throughout the 90-day study period in both preparations. There were no detectable changes in color, odor, taste, and pH and no visible microbial growth in any sample. Extemporaneously compounded suspensions of sodium phenylbutyrate, 200 mg/mL, in a 1:1 mixture of Ora-Plus and Ora-Sweet or Ora-Sweet SF were stable for at least 90 days when stored in 2-oz amber plastic bottles at room temperature.

  16. Stability of an extemporaneously prepared alcohol-free phenobarbital suspension.

    Science.gov (United States)

    Cober, Mary Petrea; Johnson, Cary E

    2007-03-15

    The physical and chemical short-term stability of alcohol-free, oral suspensions of phenobarbital 10 mg/mL prepared from commercially available tablets in both a sugar and a sugar-free vehicle was assessed at room temperature. Phenobarbital oral suspension 10 mg/mL was prepared by crushing 10 60-mg tablets of phenobarbital with a mortar and pestle. A small amount of Ora-Plus was added to the phenobarbital powder to sufficiently wet the particles. A 1:1 mixture of Ora-Plus and either Ora-Sweet or Ora-Sweet SF was combined with the phenobarbital powder to produce a final volume of 60 mL. Three identical samples of each of the two different formulations were prepared and stored at room temperature in 2-oz amber plastic bottles. Immediately after preparation and at 15, 30, 60, and 115 days, the samples were assayed in duplicate by stability-indicating high-performance liquid chromatography. The samples were tasted and inspected for color and odor changes. The percent of the initial concentration remaining at each study time for each phenobarbital suspension was determined. Stability was defined as the retention of at least 90% of the initial concentration. There were no detectable changes in color, odor, and taste and no visible microbial growth in any sample. At least 98% of the initial phenobarbital concentration remained throughout the 115-day study period in both preparations. An extemporaneously prepared alcohol-free suspension of phenobarbital 10 mg/mL in a 1:1 mixture of Ora-Plus and Ora-Sweet or Ora-Sweet SF was stable for at least 115 days when stored in 2-oz amber plastic bottles at room temperature.

  17. Stability of an extemporaneously prepared tadalafil suspension.

    Science.gov (United States)

    Pettit, Rebecca S; Johnson, Cary E; Caruthers, Regine L

    2012-04-01

    The stability of an extemporaneously prepared tadalafil oral suspension was studied. An oral suspension of tadalafil 5 mg/mL was prepared by thoroughly grinding 15 20-mg tadalafil tablets in a glass mortar. Thirty milliliters of Ora-Plus and 30 mL of Ora-Sweet were mixed and added to the powder to make a final volume of 60 mL. Three identical samples of the formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and stored at room temperature (23-25 °C). A 1-mL sample was withdrawn from each of the three bottles with a micropipette immediately after preparation and at 7, 14, 28, 57, and 91 days. After double dilution (1:10 and 0.1:5 v/v) to an expected concentration of 10 μg/mL with methanol and mobile phase, respectively, the samples were assayed in duplicate using stability-indicating high-performance liquid chromatography. The samples were visually examined for any color change and evaluated for pH changes on each day of analysis. Taste evaluation was performed at the beginning and end of the study. Stability was defined as the retention of at least 90% of the initial concentration. At least 99% of the initial tadalafil concentration remained throughout the 91-day study period. There were no detectable changes in color, odor, taste, and pH, and no visible microbial growth was observed in any sample. An extemporaneously prepared suspension of tadalafil 5 mg/mL in a 1:1 mixture of Ora-Plus and Ora-Sweet was stable for at least 91 days when stored in amber plastic bottles at room temperature.

  18. Stability of extemporaneously prepared moxifloxacin oral suspensions.

    Science.gov (United States)

    Hutchinson, David J; Johnson, Cary E; Klein, Kristin C

    2009-04-01

    The stability of extemporaneously prepared moxifloxacin oral suspensions was studied. An oral suspension of moxifloxacin 20 mg/mL was prepared by thoroughly grinding three 400-mg tablets of moxifloxacin in a glass mortar. Thirty milliliters of Ora-Plus and 30 mL of either Ora-Sweet or Ora-Sweet SF were mixed and added to the powder to make a final volume of 60 mL. Three identical samples of each formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and were stored at room temperature (23-25 degrees C). A 1-mL sample was withdrawn from each of the six bottles with a micropipette immediately after preparation and at 7, 14, 28, 60, and 90 days. After further dilution to an expected concentration of 8 microg/ mL with sample diluent, the samples were assayed in duplicate by stability-indicating high-performance liquid chromatography. Stability was defined as the retention of at least 90% of the initial concentration. At least 99% of the initial moxifloxacin remained throughout the 90-day study period in both preparations. There were no detectable changes in color, odor, taste, and pH and no visible microbial growth in any sample. Extemporaneously compounded suspensions of moxifloxacin 20 mg/mL in a 1:1 mixture of Ora-Plus and Ora-Sweet or Ora-Sweet SF were stable for at least 90 days when stored in 2-oz amber plastic bottles at room temperature.

  19. Stability of extemporaneously prepared glycopyrrolate oral suspensions.

    Science.gov (United States)

    Cober, Mary Petrea; Johnson, Cary E; Sudekum, David; Penprase, Kimberly

    2011-05-01

    The stability of extemporaneously prepared glycopyrrolate 0.5-mg/mL suspensions was evaluated. An oral suspension of glycopyrrolate 0.5 mg/mL was prepared by thoroughly grinding 30 1-mg tablets of glycopyrrolate in a glass mortar. Thirty milliliters of Ora-Plus and 30 mL of either Ora-Sweet or Ora-Sweet SF were mixed and added to the powder to make a final volume of 60 mL. Three identical samples of the formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and stored at room temperature (23-25 °C). A 1-mL sample was withdrawn from each of the three bottles with a micropipette immediately after preparation and 7, 15, 30, 60, and 90 days afterward. After further dilution to an expected concentration of 50 μg/mL with sample diluent, the samples were assayed in duplicate by stability-indicating high-performance liquid chromatography. The samples were visually examined for any color change and evaluated for pH on each day of analysis. Taste evaluations were performed at the beginning and end of the study. Stability was defined as the retention of at least 90% of the initial concentration. At least 95% of the initial glycopyrrolate remained throughout the 90-day study period in both preparations. There were no detectable changes in color, odor, taste, and pH, and no visible microbial growth was observed in any sample. Extemporaneously compounded suspensions of glycopyrrolate 0.5 mg/mL in a 1:1 mixture of Ora-Plus/Ora-Sweet or Ora-Plus/Ora-Sweet SF were stable for at least 90 days when stored in amber plastic bottles at room temperature.

  20. Stability of extemporaneously prepared rifaximin oral suspensions.

    Science.gov (United States)

    Cober, Mary Petrea; Johnson, Cary E; Lee, Jordan; Currie, Kenne

    2010-02-15

    The stability of extemporaneously prepared rifaximin oral suspensions was studied. An oral suspension of rifaximin 20 mg/mL was prepared by thoroughly grinding six 200-mg tablets of rifaximin in a glass mortar. Thirty milliliters of Ora-Plus and 30 mL of either Ora-Sweet or Ora-Sweet SF were mixed and added to the powder to make a final volume of 60 mL. Three identical samples of each formulation were prepared and placed in 2-oz amber plastic bottles with child-resistant caps and were stored at room temperature (23-25 degrees C). A 1-mL sample was withdrawn from each of the six bottles with a micropipette immediately after preparation and at 7, 15, 30, and 60 days. After further dilution to an expected concentration of 20 microg/mL with mobile phase, the samples were assayed in duplicate using stability-indicating high-performance liquid chromatography. The samples were visually examined for any color change and pH was tested on each day of analysis. Stability was determined by evaluating the percentage of the initial concentration remaining at each time point and defined as retention of at least 90% of the initial concentration of rifaximin. At least 99% of the initial rifaximin remained throughout the 60-day study period in both preparations. There were no detectable changes in color, odor, taste, or pH and no visible microbial growth in any sample. Extemporaneously prepared suspensions of rifaximin 20 mg/mL in 1:1 mixtures of Ora-Plus with either Ora-Sweet or Ora-Sweet SF were stable for at least 60 days when stored in 2-oz amber plastic bottles at room temperature.

  1. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

    Directory of Open Access Journals (Sweden)

    Yusuke Kato

    2015-09-01

    Full Text Available Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8 per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.

  2. SU-F-R-11: Designing Quality and Safety Informatics Through Implementation of a CT Radiation Dose Monitoring Program

    International Nuclear Information System (INIS)

    Wilson, JM; Samei, E

    2016-01-01

    Purpose: Recent legislative and accreditation requirements have driven rapid development and implementation of CT radiation dose monitoring solutions. Institutions must determine how to improve quality, safety, and consistency of their clinical performance. The purpose of this work was to design a strategy and meaningful characterization of results from an in-house, clinically-deployed dose monitoring solution. Methods: A dose monitoring platform was designed by our imaging physics group that focused on extracting protocol parameters, dose metrics, and patient demographics and size. Compared to most commercial solutions, which focus on individual exam alerts and global thresholds, the program sought to characterize overall consistency and targeted thresholds based on eight analytic interrogations. Those were based on explicit questions related to protocol application, national benchmarks, protocol and size-specific dose targets, operational consistency, outliers, temporal trends, intra-system variability, and consistent use of electronic protocols. Using historical data since the start of 2013, 95% and 99% intervals were used to establish yellow and amber parameterized dose alert thresholds, respectively, as a function of protocol, scanner, and size. Results: Quarterly reports have been generated for three hospitals for 3 quarters of 2015 totaling 27880, 28502, 30631 exams, respectively. Four adult and two pediatric protocols were higher than external institutional benchmarks. Four protocol dose levels were being inconsistently applied as a function of patient size. For the three hospitals, the minimum and maximum amber outlier percentages were [1.53%,2.28%], [0.76%,1.8%], [0.94%,1.17%], respectively. Compared with the electronic protocols, 10 protocols were found to be used with some inconsistency. Conclusion: Dose monitoring can satisfy requirements with global alert thresholds and patient dose records, but the real value is in optimizing patient

  3. Quartz-Amethyst Hosted Hydrocarbon-Bearing Fluid Inclusions from the Green Ridge Breccia in the Snoqualmie Granite, North Cascades, WA, USA

    Directory of Open Access Journals (Sweden)

    Martin Feely

    2017-09-01

    Full Text Available The Green Ridge Breccia cuts the composite Miocene Snoqualmie Batholith in King County, WA, USA. The granite was emplaced at ~5 km depth between ~17 and 20 Ma and the crosscutting NW trending breccia contains large angular blocks of the host granite (<1 m in longest dimension. The brecciated granite blocks are cemented by quartz-amethyst euhedra (<10 cm in longest dimension bearing vugs. A notable feature is the presence of centimetric scale amber coloured oil inclusions within the quartz-amethyst crystals. Fluid inclusion studies using Transmitted Light Petrography, UV Microscopy, Microthermometry, Laser Raman Microspectroscopy and Gas Chromatography-Mass Spectrometry record the presence and the fluid composition of three fluid inclusion types hosted by the euhedra: primary Type 1 (liquid rich two-phase (L + V aqueous inclusions and secondary Type 2 bituminous two-phase (S + L inclusions and Type 3 amber coloured oil bearing two-phase immiscible liquid inclusions. The Green Ridge Breccia was the locus for convective hydrothermal fluid flow that formed the quartz-amethyst vugs formed at T~390 °C assuming a trapping pressure of ~1.65 kb. Later, hydrocarbon fluids migrated downwards from the roof source rock (e.g., the Guye Sedimentary Member and were trapped in the euhedra. This was followed by unroofing of the batholith and exposure of the Green Ridge Breccia. This study highlights the potential for other oil migrations into the Snoqualmie Batholith in areas where it forms the basement capped by the Guye Sedimentary Member.

  4. 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

  5. Radionuclide release calculations for SAR-08

    International Nuclear Information System (INIS)

    Thomson, Gavin; Miller, Alex; Smith, Graham; Jackson, Duncan

    2008-04-01

    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)

  6. A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

    Science.gov (United States)

    Giese, Timothy J; York, Darrin M

    2018-03-13

    There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg 2+ → Ca 2+ transformations than traditional linear alchemical pathways (with and without soft-core potentials). The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed (e.g., single call to particle-mesh Ewald) leading to better performance. In the case of AMBER, this enables all the performance benefits of GPU-acceleration to be realized, in addition to unlocking the full spectrum of features available within the MD software, such as Hamiltonian replica exchange (HREM). The TI derivative evaluation can be accomplished efficiently in a post-processing step by reanalyzing the statistically independent trajectory frames in parallel for high throughput. We also show how one can evaluate the particle mesh Ewald contribution to the TI derivative evaluation without needing to perform two reciprocal space calculations. We apply the PI-TI method with HREM on GPUs in AMBER to predict p K a values in double stranded RNA molecules and make comparison with experiments. Convergence to under 0.25 units for these systems required 100 ns or more of sampling per window and coupling of windows with HREM. We find that MM charges derived from ab initio QM/MM fragment calculations improve the agreement between calculation and experimental results.

  7. ESO Reflex: A Graphical Workflow Engine for Data Reduction

    Science.gov (United States)

    Hook, R.; Romaniello, M.; Péron, M.; Ballester, P.; Gabasch, A.; Izzo, C.; Ullgrén, M.; Maisala, S.; Oittinen, T.; Solin, O.; Savolainen, V.; Järveläinen, P.; Tyynelä, J.

    2008-08-01

    Sampo {http://www.eso.org/sampo} (Hook et al. 2005) is a project led by ESO and conducted by a software development team from Finland as an in-kind contribution to joining ESO. The goal is to assess the needs of the ESO community in the area of data reduction environments and to create pilot software products that illustrate critical steps along the road to a new system. Those prototypes will not only be used to validate concepts and understand requirements but will also be tools of immediate value for the community. Most of the raw data produced by ESO instruments can be reduced using CPL {http://www.eso.org/cpl} recipes: compiled C programs following an ESO standard and utilizing routines provided by the Common Pipeline Library. Currently reduction recipes are run in batch mode as part of the data flow system to generate the input to the ESO VLT/VLTI quality control process and are also made public for external users. Sampo has developed a prototype application called ESO Reflex {http://www.eso.org/sampo/reflex/} that integrates a graphical user interface and existing data reduction algorithms. ESO Reflex can invoke CPL-based recipes in a flexible way through a dedicated interface. ESO Reflex is based on the graphical workflow engine Taverna {http://taverna.sourceforge.net} that was originally developed by the UK eScience community, mostly for work in the life sciences. Workflows have been created so far for three VLT/VLTI instrument modes ( VIMOS/IFU {http://www.eso.org/instruments/vimos/}, FORS spectroscopy {http://www.eso.org/instruments/fors/} and AMBER {http://www.eso.org/instruments/amber/}), and the easy-to-use GUI allows the user to make changes to these or create workflows of their own. Python scripts and IDL procedures can be easily brought into workflows and a variety of visualisation and display options, including custom product inspection and validation steps, are available.

  8. 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)

  9. In Depth Modeling of Nuclide Transport in the Geosphere and the Biosphere to Reduce Uncertainty (Final Report)

    International Nuclear Information System (INIS)

    Lee, Youn Myoung; Kang, Chul Kyung; Hwang, Yong Soo; Lee, Sung Ho

    2010-08-01

    The Korea Radioactive Waste Management Center (KRMC) is conducting a research on a step by step development of a safety case for the Gyeongju low- and intermediate-level radioactive waste repository (WNEMC; Wolseong Nuclear Environment Management Center). A modeling study and development of a methodology, by which an assessment of safety and performance for a low- and intermediate level radioactive waste (LILW) repository could be effectively made has been carried out. With normal or abnormal nuclide release cases associated with the various FEPs and scenarios involved in the performance of the proposed repository in view of nuclide transport and transfer both in geosphere and biosphere, a total system performance assessment (TSPA) program has been developed by utilizing such commercial development tool programs as GoldSim, AMBER, MASCOT-K, and TOUGH2 in Korea Atomic Energy Research Institute (KAERI) under contract with KRMC. The final project report especially deals much with a detailed conceptual modeling scheme by which a GoldSim program modules, all of which are integrated into a TSPA program template kit as well as the input data set currently available. In-depth system models that are conceptually and rather practically described and then ready for implementing into a GoldSim TSPA program are introduced with plenty of illustrative conceptual schemes and evaluations with data currently available. The GoldSim TSPA tempalte program and the AMBER biosphere tempalte program as well as the TOUGH-2 gas migration template program developed through this project are expected to be successfully applied to the post closure safety assessment required for WNEMC by the regulatory body with increased practicality and much reduced uncertainty and conservatism

  10. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

    Science.gov (United States)

    Wu, Chun; Shea, Joan-Emma

    2010-11-18

    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.

  11. A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

    Science.gov (United States)

    Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

    2013-09-01

    Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

  12. Colour-rendition properties of solid-state lamps

    International Nuclear Information System (INIS)

    Zukauskas, A; Vaicekauskas, R; Shur, M S

    2010-01-01

    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

  13. Retailer-Led Sugar-Sweetened Beverage Price Increase Reduces Purchases in a Hospital Convenience Store in Melbourne, Australia: A Mixed Methods Evaluation.

    Science.gov (United States)

    Blake, Miranda R; Peeters, Anna; Lancsar, Emily; Boelsen-Robinson, Tara; Corben, Kirstan; Stevenson, Christopher E; Palermo, Claire; Backholer, Kathryn

    2018-06-01

    Limited evidence has been gathered on the real-world impact of sugar-sweetened beverage price changes on purchasing behavior over time or in community-retail settings. Our aim was to determine changes in beverage purchases, business outcomes, and customer and retailer satisfaction associated with a retailer-led sugar-sweetened beverage price increase in a convenience store. We hypothesized that purchases of less-healthy beverages would decrease compared to predicted sales. A convergent parallel mixed methods design complemented sales data (122 weeks pre-intervention, 17 weeks during intervention) with stakeholder interviews and customer surveys. Electronic beverage sales data were collected from a convenience store in Melbourne, Australia (August through November 2015). Convenience store staff completed semi-structured interviews (n=4) and adult customers exiting the store completed surveys (n=352). Beverages were classified using a state government framework. Prices of "red" beverages (eg, nondiet soft drinks, energy drinks) increased by 20%. Prices of "amber" (eg, diet soft drinks, small pure fruit juices) and "green" beverages (eg, water) were unchanged. Changes in beverage volume, item sales, and revenue during the intervention were compared with predicted sales. Sales data were analyzed using time series segmented regression while controlling for pre-intervention trends, autocorrelation in sales data, and seasonal fluctuations. Beverage volume sales of red (-27.6%; 95% CI -32.2 to -23.0) and amber (-26.7%; 95% CI -39.3 to -16.0) decreased, and volume of green beverages increased (+26.9%; 95% CI +14.1 to +39.7) in the 17th intervention week compared with predicted sales. Store manager and staff considered the intervention business-neutral, despite a small reduction in beverage revenue. Fifteen percent of customers noticed the price difference and 61% supported the intervention. A 20% sugar-sweetened beverage price increase was associated with a reduction

  14. 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.

  15. 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

  16. 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 comprehensive

  17. Total System Performance Assessment

    International Nuclear Information System (INIS)

    Hwang, Yong Soo; Kang, Chul Hyung; Lee, Youn Myoung; Han, Ji Woong; Choi, Jong Won; Hahn, Pil Soo; Park, Jeong Hwa; Jeong, Mi Seon

    2007-06-01

    Based on the KAERI FEP list developed through the previous studies, the KAERI FEP Encyclopedia has been developed. Current version is 1.0 which includes all relevant FEPs to compose of two references and all alternative scenarios. Many interaction FEPs between scenario defining FEP(SDF) are created throughout the study. FEPs are classified into many Integrated FEP(IFEP) which eventually become the elements of the RES matrix. The FEAS program one of the component of the KAERI's CYPRUS information system is added to develop the FEP, RES, AC, AMF and finally scenarios. It assists to create transparent way to deal with assessment from the stage of the planning of the R and D to the final stage of the external audit and regulatory body review. Even though MASCOT-K and compartment analysis codes such as AMBER, GoldSim and Ecolego are excellent for TSPA they by in heritage possess a certain limitation especially to identify a proper migration cross sectional area when a relatively big component intersects with a tiny one such as a fracture. It is truly 3D phenomena in nature. MDPSA code is developed which is expected to overcome limitations in compartment models while successfully deals with natural disruptive events. The R and D target for the TSPA is to develop the sufficient scenarios and their variation cases to understand the safety of KRS in every possible aspect. For this, reference scenarios, alternative scenarios covering engineered barrier failure and natural events are developed and assessed respectively for around 100 cases. The stylized template to assess the Korean reference biosphere is developed using the AMBER. Three critical groups, agricultural, freshwater and marine water fishing groups are identified to assess the DCF following the guidelines of ICRP. Based on the QA principles of T2R3, the web based QA system is developed using the procedures in the USNRC 10CFR50 Appendix B. The QA system is combined with the PAID and FEAS to create the comprehensive

  18. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    Science.gov (United States)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

  19. Modelling approach to LILW-SL repository safety evaluation for different waste packing options

    International Nuclear Information System (INIS)

    Perko, Janez; Mallants, Dirk; Volckaert, Geert; Towler, George; Egan, Mike; Virsek, Sandi; Hertl, Bojan

    2007-01-01

    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

  20. Stability of extemporaneously prepared rufinamide oral suspensions.

    Science.gov (United States)

    Hutchinson, David J; Liou, Yayin; Best, Robert; Zhao, Fang

    2010-03-01

    Rufinamide is an oral antiepileptic drug indicated for adjunctive therapy in treating generalized seizures associated with Lennox-Gastaut syndrome. Currently, rufinamide is available as 200-mg and 400-mg tablets. A liquid dosage form does not exist at the present time. Lack of a suspension formulation may present an administration problem for many children and adults who are unable to swallow tablets. The availability of a liquid dosage form will provide an easy and accurate way to measure and administer the medication. To determine the stability of both sugar-containing and sugar-free rufinamide suspensions over a 90-day period. A suspension of rufinamide 40 mg/mL was prepared by grinding twelve 400-mg tablets of rufinamide tablets in a glass mortar. Sixty milliliters of Ora-Plus and 60 mL of either Ora-Sweet or Ora-Sweet SF (sugar free) were mixed and added to the powder to make a final volume of 120 mL. Three identical samples of each formulation were prepared and placed in 60-mL amber plastic bottles and were stored at room temperature. A 1-mL sample was withdrawn from each of the 6 bottles with a micropipette immediately after preparation and at 7, 14, 28, 56, and 90 days. After further dilution to an expected concentration of 0.4 mg/mL, the samples were assayed using high-performance liquid chromatography. Stability was defined as the retention of at least 90% of the initial concentration. At least 90% of the initial rufinamide concentration remained throughout the 90-day study period in both preparations. There were no detectable changes in color, odor, taste, and pH and no visible microbial growth. Extemporaneously compounded suspensions of rufinamide 40 mg/mL in a 1:1 mixture of Ora-Plus and Ora-Sweet or Ora-Sweet SF were stable for at least 90 days when stored in 59-mL amber polypropylene plastic bottles at room temperature.

  1. 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

    2013-07-09

    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

  2. Colour-rendition properties of solid-state lamps

    Energy Technology Data Exchange (ETDEWEB)

    Zukauskas, A [Institute of Applied Research, Vilnius University, Sauletekio al. 9, bldg. III, Vilnius, LT-10222 (Lithuania); Vaicekauskas, R [Department of Computer Science, Vilnius University, Naugarduko g. 24, Vilnius, LT-03225 (Lithuania); Shur, M S, E-mail: arturas.zukauskas@ff.vu.l [Department of Electrical, Computer, and System Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 (United States)

    2010-09-08

    The applicability of colour-quality metrics to solid-state light sources is validated and the results of the assessment of colour-rendition characteristics of various lamps are presented. The standard colour-rendering index metric or a refined colour-quality scale metric fails to distinguish between two principle colour-rendition properties of illumination: the ability to render object colours with high fidelity and the ability to increase chromatic contrast, especially when the spectra of light sources contain a few narrow-band electroluminescence components. Supplementing these metrics by the known figures of merit that measure the gamut area of a small number of test colour samples does not completely resolve this issue. In contrast, the statistical approach, which is based on sorting a very large number of test colour samples in respect of just-perceivable colour distortions of several kinds, offers a comprehensive assessment of colour-rendition properties of solid-state light sources. In particular, two statistical indices, colour-fidelity index (CFI) and colour-saturation index (CSI), which are the relative numbers of object colours rendered with high fidelity and increased saturation, respectively, are sufficient to reveal and assess three distinct types of solid-state light sources. These are (i) high-fidelity lamps, which cover the entire spectrum with the spectral components present in the wavelength ranges of both 530-610 nm and beyond 610 nm (e.g. trichromatic warm white phosphor-converted (pc) light-emitting diodes (LEDs), red-amber-green-blue LED clusters, complementary clusters of white and coloured LEDs); (ii) colour-saturating lamps, which lack power in the 530-610 nm wavelength range (e.g. red-green-blue or red-cyan-blue LED clusters) and (iii) colour-dulling lamps, which lack power for wavelengths longer than 610 nm (dichromatic daylight pc LEDs and amber-green-blue LED clusters). Owing to a single statistical format, CSI and CFI can be used for

  3. Structural studies of the 5'-phenazinium-tethered matched and G-A-mismatched DNA duplexes by NMR spectroscopy.

    Science.gov (United States)

    Maltseva, T; Sandström, A; Ivanova, I M; Sergeyev, D S; Zarytova, V F; Chattopadhyaya, J

    1993-05-01

    The mechanism through which modified oligo-DNA analogues act as antisense repressors at the transcriptional and translational level of gene expression is based on the information content in the nucleotide sequence which is determined by the specific base pairing. The efficiency of such action is largely determined by the stability of the duplex formed between the oligonucleotide reagent and the target sequence and also by the mismatched base pairing, such as G-A, that occurs during replication or recombination. We herein report that the phenazinium (Pzn)-tethered matched duplex p(d(TGTTTGGC)):(Pzn)-p(d(CCAAACA)) (III) (Tm = 50 degrees C) has a much larger stability than the parent matched duplex p(d(TGTTTGGC)):p(d(CCAAACA)) (I) (Tm = 30 degrees C). On the other hand, the Pzn-tethered G-A-mismatched duplex p(d(TGTTTGGC)):(Pzn)-p(d(ACAAACA)) (IV) (Tm = 34 degrees C) is only slightly more stable than its parent mismatched duplex p(d(TGTTTGGC)):p(d(ACAAACA)) (Tm = 25 degrees C). A detailed 500 MHz NMR study and constrained MD refinements of NMR-derived structures have been undertaken for the DNA duplexes (I), (II), (III) and (IV) in order to understand the structural basis of stabilization of Pzn-tethered matched DNA duplex (delta Tm = 20 degrees C) compared to mismatched duplex (delta Tm = 9 degrees C). Assignment of the 1H-NMR (500 MHz) spectra of the duplexes has been carried out by 2D NOESY, HOHAHA and DQF-COSY experiments. The torsion angles have been extracted from the J-coupling constants obtained by simulation of most of the DQF-COSY cross-peaks using program SMART. The solution structure of the duplexes were assessed by an iterative hybride relaxation matrix method (MORASS) combined with NOESY distances and torsion angles restrained molecular dynamics (MD) using program Amber 4.0. The standard Amber 4.0 force-field parameters were used for the oligonucleotide in conjunction with the new parameters for Pzn residue which was obtained by full geometry

  4. 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

  5. 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

  6. Molecular insight on the non-covalent interactions between carbapenems and uc(l,d)-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

    Science.gov (United States)

    Ntombela, Thandokuhle; Fakhar, Zeynab; Ibeji, Collins U.; Govender, Thavendran; Maguire, Glenn E. M.; Lamichhane, Gyanu; Kruger, Hendrik G.; Honarparvar, Bahareh

    2018-05-01

    Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. uc(l,d)-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both uc(d,d)- and uc(l,d)-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit uc(d,d)-transpeptidases, while uc(l,d)-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and Ldt

  7. 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

  8. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

    Science.gov (United States)

    Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

    2010-12-30

    Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an

  9. Critical Dose of Internal Organs Internal Exposure - 13471

    Energy Technology Data Exchange (ETDEWEB)

    Grigoryan, G.; Amirjanyan, A. [Nuclear and Radiation Safety Centre (Armenia); Grigoryan, N. [Yerevan State Medical University 4Tigran Mets,375010 Yerevan (Armenia)

    2013-07-01

    radionuclides that have intake into the organism or absorbed into blood. Transport of different radionuclides between compartments is assumed to follow first order kinetics provided the concentration in red blood cells (RBCs) stays below a nonlinear threshold concentration. When the concentration in RBCs exceeds that threshold, the transfer rate from diffusible plasma to RBCs is assumed to decrease as the concentration in RBCs increases. For the calculations used capabilities AMBER by using the traces of radionuclides in the body. Model for the transfer of radionuclides in the body has been built on the basis of existing models at AMBER for lead. (authors)

  10. A GIS-based Quantitative Approach for the Search of Clandestine Graves, Italy.

    Science.gov (United States)

    Somma, Roberta; Cascio, Maria; Silvestro, Massimiliano; Torre, Eliana

    2018-05-01

    Previous research on the RAG color-coded prioritization systems for the discovery of clandestine graves has not considered all the factors influencing the burial site choice within a GIS project. The goal of this technical note was to discuss a GIS-based quantitative approach for the search of clandestine graves. The method is based on cross-referenced RAG maps with cumulative suitability factors to host a burial, leading to the editing of different search scenarios for ground searches showing high-(Red), medium-(Amber), and low-(Green) priority areas. The application of this procedure allowed several outcomes to be determined: If the concealment occurs at night, then the "search scenario without the visibility" will be the most effective one; if the concealment occurs in daylight, then the "search scenario with the DSM-based visibility" will be most appropriate; the different search scenarios may be cross-referenced with offender's confessions and eyewitnesses' testimonies to verify the veracity of their statements. © 2017 American Academy of Forensic Sciences.

  11. LED Street Lighting Solutions: Flagstaff, Arizona as a Case Study

    Science.gov (United States)

    Hall, Jeffrey C.

    2018-01-01

    Dark-sky protection in Flagstaff, Arizona extends back to 1958, with the first ordinance in the City banning advertising floodlights. The current ordinance, adopted in 1989, is comprehensive and has played a critical role in maintaining the quality of the night sky for astronomy, tourism, public enjoyment, and other purposes. Flagstaff, like many communities around the world, is now working on a transition from legacy bulb-based technology to LED for its outdoor lighting. The City, Lowell Observatory, the U. S. Naval Observatory, and the Flagstaff Dark Skies Coalition have been working intensively for two years to identify an LED-based street lighting solution that will preserve the City's dark skies while meeting municipal needs. We will soon be installing test fixtures for an innovative solution incorporating narrow-band amber LED and modest amounts of low-CCT white LED. In this talk, I will review the types of LEDs available for outdoor lighting and discuss the plans for Flagstaff's street lighting in the LED era, which we hope will be a model for communities worldwide.

  12. 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.

  13. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  14. 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.

  15. Vial freeze-drying, part 1: new insights into heat transfer characteristics of tubing and molded vials.

    Science.gov (United States)

    Hibler, Susanne; Wagner, Christophe; Gieseler, Henning

    2012-03-01

    In order to optimize a freeze-drying cycle, information regarding the heat transfer characteristics of the container system is imperative. Two most recently developed tubing (TopLyo™) and molded (EasyLyo™) vial designs were compared with a standard serum tubing and molded vial, a polymer vial (TopPac™), and an amber molded EasyLyo™. In addition, the impact of methodology on the determination of reliable vial heat transfer coefficient (K(v) ) data is examined in detail. All K(v) s were gravimetrically determined by sublimation tests with pure water at 50, 100, 200, and 400 mTorr. In contrast to the traditional assumption that molded vials exhibit inefficient heat transfer characteristics, these vials showed a very similar performance compared with their serum tubing counterparts in the relevant pressure range for freeze-drying. At 100 mTorr, the TopLyo™ center vials show only 4% higher K(v) values than the EasyLyo™ center vials. All glass vials outmatch the polymer vial in terms of heat transfer, up to 30% elevated heat transfer for the TopLyo™ center vials at 400 mTorr. Sublimation tests have demonstrated to be a valuable tool to investigate the heat transfer characteristics of vials, but results are dependent on methodology. New developments in molded vial manufacturing lead to improved heat transfer performance. Copyright © 2011 Wiley Periodicals, Inc.

  16. Cockroaches probably cleaned up after dinosaurs.

    Directory of Open Access Journals (Sweden)

    Peter Vršanský

    Full Text Available Dinosaurs undoubtedly produced huge quantities of excrements. But who cleaned up after them? Dung beetles and flies with rapid development were rare during most of the Mesozoic. Candidates for these duties are extinct cockroaches (Blattulidae, whose temporal range is associated with herbivorous dinosaurs. An opportunity to test this hypothesis arises from coprolites to some extent extruded from an immature cockroach preserved in the amber of Lebanon, studied using synchrotron X-ray microtomography. 1.06% of their volume is filled by particles of wood with smooth edges, in which size distribution directly supports their external pre-digestion. Because fungal pre-processing can be excluded based on the presence of large particles (combined with small total amount of wood and absence of damages on wood, the likely source of wood are herbivore feces. Smaller particles were broken down biochemically in the cockroach hind gut, which indicates that the recent lignin-decomposing termite and cockroach endosymbionts might have been transferred to the cockroach gut upon feeding on dinosaur feces.

  17. Adaptive resolution simulation of salt solutions

    International Nuclear Information System (INIS)

    Bevc, Staš; Praprotnik, Matej; Junghans, Christoph; Kremer, Kurt

    2013-01-01

    We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt. (paper)

  18. Investigating risky, distracting, and protective peer passenger effects in a dual process framework.

    Science.gov (United States)

    Ross, Veerle; Jongen, Ellen M M; Brijs, Kris; Brijs, Tom; Wets, Geert

    2016-08-01

    Prior studies indicated higher collision rates among young novice drivers with peer passengers. This driving simulator study provided a test for a dual process theory of risky driving by examining social rewards (peer passengers) and cognitive control (inhibitory control). The analyses included age (17-18 yrs, n=30; 21-24 yrs, n=20). Risky, distracting, and protective effects were classified by underlying driver error mechanisms. In the first drive, participants drove alone. In the second, participants drove with a peer passenger. Red-light running (violation) was more prevalent in the presence of peer passengers, which provided initial support for a dual process theory of risk driving. In a subgroup with low inhibitory control, speeding (violation) was more prevalent in the presence of peer passengers. Reduced lane-keeping variability reflected distracting effects. Nevertheless, possible protective effects for amber-light running and hazard handling (cognition and decision-making) were found in the drive with peer passengers. Avenues for further research and possible implications for targets of future driver training programs are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Modeling the effects of phosphor converted LED lighting to the night sky of the Haleakala Observatory, Hawaii

    Science.gov (United States)

    Aubé, M.; Simoneau, A.; Wainscoat, R.; Nelson, L.

    2018-05-01

    The goal of this study is to evaluate the current level of light pollution in the night sky at the Haleakala Observatory on the island of Maui in Hawaii. This is accomplished with a numerical model that was tested in the first International Dark Sky Reserve located in Mont-Mégantic National Park in Canada. The model uses ground data on the artificial light sources present in the region of study, geographical data, and remotely sensed data for: 1) the nightly upward radiance; 2) the terrain elevation; and, 3) the ground spectral reflectance of the region. The results of the model give a measure of the current state of the sky spectral radiance at the Haleakala Observatory. Then, using the current state as a reference point, multiple light conversion plans are elaborated and evaluated using the model. We can thus estimate the expected impact of each conversion plan on the night sky radiance spectrum. A complete conversion to white (LEDs) with (CCT) of 4000K and 3000K are contrasted with a conversion using (PC) amber (LEDs). We include recommendations concerning the street lamps to be used in sensitive areas like the cities of Kahului and Kihei and suggest best lighting practices related to the color of lamps used at night.

  1. Light emission ranging from blue to red from a series of Iguana/GaN single quantum wells

    International Nuclear Information System (INIS)

    Martin, R.W.; Edwards, P.R.; Pecharroman-Gallego, R.; O'Donnell, K.P.; Liu, C.; Deatcher, C.J.; Watson, I.M.

    2002-01-01

    In this paper, we describe the growth and characterization of InGaN single quantum wells with emission peaks in the blue, green, amber and red spectral regions, grown by metal-organic vapour phase epitaxy. Starting from the growth of a blue-emitting (peak ∼430 nm) InGaN quantum well at 860 deg. C the InGaN growth temperature was progressively reduced. The photoluminescence peak wavelength, measured at low temperature, shifts through the green and orange spectral regions and reaches 670 nm for an InGaN growth temperature of 760 deg. C. This corresponds to an energy lower than the currently accepted band-gap of the binary compound, InN. Spectral characteristics of the luminescence peaks will be discussed, including an analysis of the phonon-assisted contribution. Low energy secondary ion mass spectrometry analysis provides information on the indium content and thickness of the 'blue' and 'red' quantum wells. The results are combined to discuss the origin of the 'sub-band-gap' luminescence in terms of the combined influence of InN-GaN segregation and the effect of intense piezoelectric fields. (author)

  2. Closure Report for Corrective Action Unit 107: Low Impact Soil Sites, Nevada Test Site, Nevada

    International Nuclear Information System (INIS)

    2009-01-01

    Corrective Action Unit (CAU) 107 is identified in the Federal Facility Agreement and Consent Order (FFACO) as 'Low Impact Soil Sites' and consists of the following 15 Corrective Action Sites (CASs), located in Areas 1, 2, 3, 4, 5, 9, 10, and 18 of the Nevada Test Site: CAS 01-23-02, Atmospheric Test Site - High Alt; CAS 02-23-02, Contaminated Areas (2); CAS 02-23-03, Contaminated Berm; CAS 02-23-10, Gourd-Amber Contamination Area; CAS 02-23-11, Sappho Contamination Area; CAS 02-23-12, Scuttle Contamination Area; CAS 03-23-24, Seaweed B Contamination Area; CAS 03-23-27, Adze Contamination Area; CAS 03-23-28, Manzanas Contamination Area; CAS 03-23-29, Truchas-Chamisal Contamination Area; CAS 04-23-02, Atmospheric Test Site T4-a; CAS 05-23-06, Atmospheric Test Site; CAS 09-23-06, Mound of Contaminated Soil; CAS 10-23-04, Atmospheric Test Site M-10; and CAS 18-23-02, U-18d Crater (Sulky). Closure activities were conducted from February through April 2009 according to the FFACO (1996; as amended February 2008) and Revision 1 of the Streamlined Approach for Environmental Restoration Plan for CAU 107 (U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, 2009). The corrective action alternatives included No Further Action and Closure in Place with Administrative Controls. Closure activities are summarized.

  3. Driving deaths and injuries post-9/11

    Directory of Open Access Journals (Sweden)

    Deonandan R

    2011-12-01

    Full Text Available Raywat Deonandan, Amber BackwellInterdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, CanadaObjectives: In the days immediately following the terror attacks of 9/11, thousands of Americans chose to drive rather than to fly. We analyzed highway accident data to determine whether or not the number of fatalities and injuries following 9/11 differed from those in the same time period in 2000 and 2002.Methods: Motor crash data from the National Highway Traffic Safety Administration's Fatality Analysis Reporting System were analyzed to determine the numbers and rates of fatalities and injuries nationally and in selected states for the 20 days after September 11, in each of 2000, 2001, and 2002.Results: While the fatality rate did not change appreciably, the number of less severe injuries was statistically higher in 2001 than in 2000, both nationally and in New York State.Conclusions: The fear of terror attacks may have compelled Americans to drive instead of fly. They were thus exposed to the heightened risk of injury and death posed by driving. The need for public health to manage risk perception and communication is thus heightened in an era of global fear and terrorism.Keywords: public health, traffic, injuries, epidemiology

  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. Cathodoluminescence studies of chevron features in semi-polar (11 2 ¯ 2 ) InGaN/GaN multiple quantum well structures

    Science.gov (United States)

    Brasser, C.; Bruckbauer, J.; Gong, Y.; Jiu, L.; Bai, J.; Warzecha, M.; Edwards, P. R.; Wang, T.; Martin, R. W.

    2018-05-01

    Epitaxial overgrowth of semi-polar III-nitride layers and devices often leads to arrowhead-shaped surface features, referred to as chevrons. We report on a study into the optical, structural, and electrical properties of these features occurring in two very different semi-polar structures, a blue-emitting multiple quantum well structure, and an amber-emitting light-emitting diode. Cathodoluminescence (CL) hyperspectral imaging has highlighted shifts in their emission energy, occurring in the region of the chevron. These variations are due to different semi-polar planes introduced in the chevron arms resulting in a lack of uniformity in the InN incorporation across samples, and the disruption of the structure which could cause a narrowing of the quantum wells (QWs) in this region. Atomic force microscopy has revealed that chevrons can penetrate over 150 nm into the sample and quench light emission from the active layers. The dominance of non-radiative recombination in the chevron region was exposed by simultaneous measurement of CL and the electron beam-induced current. Overall, these results provide an overview of the nature and impact of chevrons on the luminescence of semi-polar devices.

  6. Prevention of GABA reduction during dough fermentation using a baker's yeast dal81 mutant.

    Science.gov (United States)

    Ando, Akira; Nakamura, Toshihide

    2016-10-01

    γ-Aminobutyric acid (GABA) is consumed by yeasts during fermentation. To prevent GABA reduction in bread dough, a baker's yeast mutant AY77 deficient in GABA assimilation was characterized and utilized for wheat dough fermentation. An amber mutation in the DAL81 gene, which codes for a positive regulator of multiple nitrogen degradation pathways, was found in the AY77 strain. The qPCR analyses of genes involved in nitrogen utilization showed that transcriptional levels of the UGA1 and DUR3 genes encoding GABA transaminase and urea transporter, respectively, are severely decreased in the AY77 cells. The AY77 strain cultivated by fed-batch culture using cane molasses exhibited inferior gas production during dough fermentation compared to that of wild-type strain AY13. However, when fed with molasses containing 0.5% ammonium sulfate, the mutant strain exhibited gas production comparable to that of the AY13 strain. In contrast to the AY13 strain, which completely consumed GABA in dough within 5 h, the AY77 strain consumed no GABA under either culture condition. Dough fermentation with the dal81 mutant strain should be useful for suppression of GABA reduction in breads. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  7. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

    Science.gov (United States)

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-04-12

    Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

  8. Radiation exposure control by estimation of multiplication factors for online remote radiation monitoring systems at vitrification plant

    International Nuclear Information System (INIS)

    Deokar, U.V.; Kulkarni, V.V.; Khot, A.R.; Mathew, P.; Kamlesh; Purohit, R.G.; Sarkar, P.K.

    2012-01-01

    Vitrification Plant is commissioned for vitrification of high level liquid waste (HLW) generated in nuclear fuel cycle operations by using Joule Heated Ceramic Melter first time in India. Exposure control is a major concern in operating plant. Therefore in addition to installed monitors, we have developed online remote radiation monitoring system to minimize number of entries in amber areas and to reduce the exposure to the surveyor and operator. This also helped in volume reduction of secondary waste. The reliability and accuracy of the online monitoring system is confirmed with actual measurements and by theoretical shielding calculations. The multiplication factors were estimated for remote on line monitoring of Melter Off Gas (MOG) filter, Hood filter, three exhaust filter banks, and over-pack monitoring. This paper summarizes - how the online remote monitoring system helped in saving of 128.52 person-mSv collective dose (14.28% of budgeted dose). The system also helped in the reduction of 2.6 m 3 of Cat-I waste. Our online remote monitoring system has helped the plant management to plan in advance for replacement of these filters, which resulted in considerable saving in collective dose and secondary waste

  9. Cultural responses to pain in UK children of primary school age: a mixed-methods study.

    Science.gov (United States)

    Azize, Pary M; Endacott, Ruth; Cattani, Allegra; Humphreys, Ann

    2014-06-01

    Pain-measurement tools are often criticized for not addressing the influence of culture and ethnicity on pain. This study examined how children who speak English as a primary or additional language discuss pain. Two methods were used in six focus group interviews with 34 children aged 4-7 years: (i) use of drawings from the Pediatric Pain Inventory to capture the language used by children to describe pain; and (ii) observation of the children's placing of pain drawings on red/amber/green paper to denote perceived severity of pain. The findings demonstrated that children with English as an additional language used less elaborate language when talking about pain, but tended to talk about the pictures prior to deciding where they should be placed. For these children, there was a positive significant relationship between language, age, and length of stay in the UK. The children's placement of pain drawings varied according to language background, sex, and age. The findings emphasize the need for sufficient time to assess pain adequately in children who do not speak English as a first language. © 2013 Wiley Publishing Asia Pty Ltd.

  10. Synergic effect of gamma radiation with thermal treatment for conserving natural apple juice from Gala variety

    International Nuclear Information System (INIS)

    Blumer, L.; Domarco, R.E.; Spoto, M.H.F.; Walder, J.M.M.; Matraia, C.

    1995-01-01

    This paper aims at the feasibility of a new method for conserving natural apple juice using no chemicals. The apple juice was extract from Gala apple variety and was bottled in sterile 100 ml amber vials. The samples were treated by: heat at 60 0 C for 20 minutes; heat at 80 0 C for 20 minutes; radiation; radiation plus heat (60 0 ); radiation plus heat 80 0 C. The radiation doses were 0,2,4 and 6 kGy at the dose rate of 1.6 kGy/h. The juice quality control was carried out by chemical analysis (total soluble solids, pH, acidity, ascorbic acid) following the AOAC methodology. The samples were stored under refrigeration conditions 5±3 0 C) up to 180 days. It was observed an alteration of the total soluble solids and the pH during the storage period for all treatments. The pH was also affected by the combined treatments (radiation plus heat). The acidity was affected by the interaction of storage period and heat temperature. The ascorbic acid was affected by the synergic effect of heat and radiation and by the interaction radiation and storage period. (author). 8 refs, 6 figs

  11. Transfer time estimation of 129I, 99Tc and 14C in the geological layers of the Saligny site

    International Nuclear Information System (INIS)

    Dogaru, Daniela; Niculae, Ortenzia; Terente, M.; Jinescu, Gh.; Duliu, O.G.

    2009-01-01

    The paper describes the assessment of transfer time of 129 I, 99 Tc and 14 C in the geological layers of Saligny site, selected as Near Surface Final Repository for short-lived low and intermediate level radioactive waste generated by the operation and decommissioning of the four units of Cernavoda NPP equipped with the CANDU-6 Canadian type reactors. The geological aspects of Saligny site are presented for which the transfer time of radio-nuclides is necessary to assess. The conceptual model of the repository as well as the associated mathematical model which describes the transfer of radio-nuclides from radioactive waste disposal system to aquifer is also presented in the paper. The transfer time of these radionuclides is derived from the time difference when a radionuclide reaches the highest peak value of concentration into two adjacent compartments. The transfer time is compared with the half-life of radio-nuclides in order to asses the role of geological layers of the site in delaying the transfer of radio-nuclides. The evaluation was performed using the AMBER computing code. also a comparison with results from HYDRUS computer code is done. (authors)

  12. Morphogenic variability of some autochthonous plum cultivars in western Serbia

    Directory of Open Access Journals (Sweden)

    Tomo Milosevic

    2010-12-01

    Full Text Available A study conducted over a period of two years in a Western Serbian valley included in situ identification of autochthonous plum cultivars. Observation and recording of their phenological and pomological traits were performed using IBPGR and UPOV methodologies. Fifteen cultivars derived from Prunus domestica L. and two cultivars derived from P. insititia L. were identified. Flowering started between 24 March and 7 April and fruit ripening between 12 July (Petrovača and 16 September (Trnovača. Fruit weight ranged from 6.79± 0.018 to 36.62± 0.251 g and stone weight from 0.14± 0.002 to 1.95± 0.023 g. The cultivars were classified as being extremely small in terms of fruit size. Rounded fruit shape and light-yellow ground colour were dominant. Skin colour ranged from amber to black. Yellow green was a dominant flesh colour and medium flesh firmness predominated. The fruits of the above cultivars could be processed, particularly into plum brandy, or they could be used fresh or dried. The selected plum cultivars can be used both in breeding programmes and as rootstocks as well as in further disease-related systematic studies under field and laboratory conditions.

  13. New genus and species of the extinct aphid family Szelegiewicziidae and their implications for aphid evolution.

    Science.gov (United States)

    Wegierek, Piotr; Żyła, Dagmara; Homan, Agnieszka; Cai, Chenyang; Huang, Diying

    2017-10-24

    Recently, we are witnessing an increased appreciation for the importance of the fossil record in phylogenetics and testing various evolutionary hypotheses. However, this approach brings many challenges, especially for such a complex group as aphids and requires a thorough morphological analysis of the extinct groups. The extinct aphid family Szelegiewicziidae is supposed to be one of the oviparous lineages in aphid evolution. New material from the rock fossil deposits of Shar Teg (Upper Jurassic of Mongolia), Baissa (Lower Cretaceous of Siberia-Russia), and Burmese amber (Upper Cretaceous of Myanmar) allowed us to undertake a more detailed examination of the morphological features and carry out an analysis of the taxonomical composition and evolution of the family. This led us to the conclusion that evolution of the body plan and wing structure was similar in different, often not closely related groups, probably as a result of convergence. Additionally, we present a description of a new genus and two species (Tinaphis mongolica Żyła &Wegierek, sp. nov., and Feroorbis burmensis Wegierek & Huang, gen. et sp. nov.) that belong to this family.

  14. Characterisation of varnishes used in violins by pyrolysis-gas chromatography/mass spectrometry.

    Science.gov (United States)

    Chiavari, Giuseppe; Montalbani, Simona; Otero, Vanessa

    2008-12-01

    The correct characterisation and a detailed knowledge of the materials originally used in violin varnishes, like natural resins, is crucial for the conservation in museums and for a suitable restoration technique. The study presented here reports on the potential of pyrolysis (Py) coupled with gas chromatography (GC) and mass spectrometry (MS) for the identification of chemical markers of each resin; this technique is very sensitive and selective, it needs a small quantity of sample and does not require chemical treatments. To improve the chromatographic behaviour of polar compounds the derivatising agent tetramethylammonium hydroxide (TMAH) in combination with pyrolysis has been used, in the so-called TMAH thermochemolysis or thermally assisted hydrolysis and methylation (THM), or more simply pyrolysis-methylation. The natural resins studied were colophony, sandarac, manila copal, elemi, amber and benzoin, mainly composed of terpenic compounds, with the exception of the latter, composed of aromatic compounds. Many compounds were identified; in particular, methyl esters of resinous acids that, individually or in a group, can be used as chemical markers. However, through this technique it was not possible to distinguish between the sandarac and manila copal resins because their chromatographic behaviour is very similar. Finally, the procedure applied has been employed in the characterisation of original varnish samples.

  15. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

    Science.gov (United States)

    Miller, Mark S.; Lay, Wesley K.

    2016-01-01

    Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

  16. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

    International Nuclear Information System (INIS)

    Henriksen, Niel M.; Davis, Darrell R.; Cheatham, Thomas E. III

    2012-01-01

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility—using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions—by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to “update” older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  17. Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts

    Science.gov (United States)

    Vea, Isabelle M.; Grimaldi, David A.

    2016-01-01

    The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228–273], and of the neococcoids 60 million years later [210–165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous. PMID:27000526

  18. 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.

  19. Specialized proteinine rove beetles shed light on insect-fungal associations in the Cretaceous.

    Science.gov (United States)

    Cai, Chenyang; Newton, Alfred F; Thayer, Margaret K; Leschen, Richard A B; Huang, Diying

    2016-12-28

    Insects and fungi have a long history of association in shared habitats. Fungus-feeding, or mycophagy, is remarkably widespread in beetles (Coleoptera) and appears to be a primitive feeding habit that preceded feeding on plant tissues. Numerous Mesozoic beetles belonging to extant fungus-associated families are known, but direct fossil evidence elucidating mycophagy in insects has remained elusive. Here, we report a remarkable genus and species, Vetuproteinus cretaceus gen. et sp. nov., belonging to a new tribe (Vetuproteinini trib. nov.) of the extant rove beetle subfamily Proteininae (Staphylinidae) in Mid-Cretaceous Burmese amber. The mouthparts of this beetle have a markedly enlarged protruding galea bearing an apparent spore brush, a specialized structure we infer was used to scrape spores off surfaces and direct them into the mouth, as in multiple modern spore-feeding beetles. Considering the long evolutionary history of Fungi, the Mid-Cretaceous beetles likely fed on ancient Basidiomycota and/or Ascomycota fungi or spore-producing organisms such as slime moulds (Myxomycetes). The discovery of the first Mesozoic proteinine illustrates the antiquity of the subfamily, and suggests that ancestral Proteininae were already diverse and widespread in Pangaea before the supercontinent broke up. © 2016 The Author(s).

  20. A golden orb-weaver spider (Araneae: Nephilidae: Nephila) from the Middle Jurassic of China.

    Science.gov (United States)

    Selden, Paul A; Shih, ChungKun; Ren, Dong

    2011-10-23

    Nephila are large, conspicuous weavers of orb webs composed of golden silk, in tropical and subtropical regions. Nephilids have a sparse fossil record, the oldest described hitherto being Cretaraneus vilaltae from the Cretaceous of Spain. Five species from Neogene Dominican amber and one from the Eocene of Florissant, CO, USA, have been referred to the extant genus Nephila. Here, we report the largest known fossil spider, Nephila jurassica sp. nov., from Middle Jurassic (approx. 165 Ma) strata of Daohugou, Inner Mongolia, China. The new species extends the fossil record of the family by approximately 35 Ma and of the genus Nephila by approximately 130 Ma, making it the longest ranging spider genus known. Nephilidae originated somewhere on Pangaea, possibly the North China block, followed by dispersal almost worldwide before the break-up of the supercontinent later in the Mesozoic. The find suggests that the palaeoclimate was warm and humid at this time. This giant fossil orb-weaver provides evidence of predation on medium to large insects, well known from the Daohugou beds, and would have played an important role in the evolution of these insects.

  1. Radiation exposure control by estimation of multiplication factors for online remote radiation monitoring systems at Vitrification Plant

    International Nuclear Information System (INIS)

    Deokar, Umesh V.; Kukarni, V.V.; Khot, A.R.; Mathew, P.; Kamlesh; Purohit, R.G.; Sarkar, P.K.

    2011-01-01

    Vitrification Plant is commissioned for vitrification of high-level liquid waste generated in Nuclear Fuel Cycle operations by using Joule Heated Ceramic Melter first time in India. Exposure control is a major concern in operating plant. Therefore, in addition to installed monitors, we have developed online remote radiation monitoring system to minimize number of entries in amber areas and to reduce the exposure to the surveyor and operator. This also helped in volume reduction of secondary waste. The reliability and accuracy of the online monitoring system is confirmed with actual measurements and by theoretical shielding calculations. The multiplication factors were estimated for remote online monitoring of Melter off Gas (MOG) filter, Hood filter, three exhaust filter banks, and overpack monitoring. This paper summarizes how the online remote monitoring system had helped in saving of 128.52 Person-mSv collective dose (14.28% of budgeted dose) and also there was 2.6 m 3 reduction in generation of Cat-I waste. (author)

  2. Feasibility of detection and intervention for alcohol-related liver disease in the community: the Alcohol and Liver Disease Detection study (ALDDeS).

    Science.gov (United States)

    Sheron, Nick; Moore, Michael; O'Brien, Wendy; Harris, Scott; Roderick, Paul

    2013-10-01

    In the past 15 years mortality rates from liver disease have doubled in the UK. Brief alcohol advice is cost effective, but clinically meaningful reductions in alcohol consumption only occur in around 1 in 10 individuals. To provide evidence that detecting early liver disease in the community is feasible, practical, and that feedback of liver risk can increase the proportion of subjects reducing alcohol consumption. A community feasibility study in nine general practice sites in Hampshire. Hazardous and harmful drinkers were identified by WHO AUDIT questionnaire and offered screening for liver fibrosis. In total, 4630 individuals responded, of whom 1128 (24%) hazardous or harmful drinkers were offered a liver fibrosis check using the Southampton Traffic Light (STL) test; 393 (38%) attended and test results were returned by post. The STL has a low threshold for liver fibrosis with 45 (11%) red, 157 (40%) amber, and 191 (49%) green results. Follow-up AUDIT data was obtained for 303/393 (77%) and 76/153 (50%) subjects with evidence of liver damage reduced drinking by at least one AUDIT category (harmful to hazardous, or hazardous to low risk) compared with 52/150 (35%, PAUDIT >15), 22/34 (65%) of STL positives, reduced drinking compared with 10/29 (35%, PDetection of liver disease in the community is feasible, and feedback of liver risk may reduce harmful drinking.

  3. UAS Air Traffic Controller Acceptability Study. 2; Evaluating Detect and Avoid Technology and Communication Delays in Simulation

    Science.gov (United States)

    Comstock, James R., Jr.; Ghatas, Rania W.; Consiglio, Maria C.; Chamberlain, James P.; Hoffler, Keith D.

    2015-01-01

    This study evaluated the effects of communications delays and winds on air traffic controller ratings of acceptability of horizontal miss distances (HMDs) for encounters between Unmanned Aircraft Systems (UAS) and manned aircraft in a simulation of the Dallas-Ft. Worth (DFW) airspace. Fourteen encounters per hour were staged in the presence of moderate background traffic. Seven recently retired controllers with experience at DFW served as subjects. Guidance provided to the UAS pilots for maintaining a given HMD was provided by information from Detect and Avoid (DAA) self-separation algorithms (Stratway+) displayed on the Multi-Aircraft Control System. This guidance consisted of amber "bands" on the heading scale of the UAS navigation display indicating headings that would result in a loss of well clear between the UAS and nearby traffic. Winds tested were successfully handled by the DAA algorithms and did not affect the controller acceptability ratings of the HMDs. Voice communications delays for the UAS were also tested and included one-way delay times of 0, 400, 1200, and 1800 msec. For longer communications delays, there were changes in strategy and communications flow that were observed and reported by the controllers. The aim of this work is to provide useful information for guiding future rules and regulations applicable to flying UAS in the NAS. Information from this study will also be of value to the Radio Technical Commission for Aeronautics (RTCA) Special Committee 228 - Minimum Performance Standards for UAS.

  4. New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

    Science.gov (United States)

    Sagui, Celeste

    2006-03-01

    An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

  5. Exposure to blue wavelength light modulates anterior cingulate cortex activation in response to 'uncertain' versus 'certain' anticipation of positive stimuli.

    Science.gov (United States)

    Alkozei, Anna; Smith, Ryan; Killgore, William D S

    2016-03-11

    Blue wavelength light has been used as an effective treatment for some types of mood disorders and circadian rhythm related sleep problems. We hypothesized that acute exposure to blue wavelength light would directly affect the functioning of neurocircuity implicated in emotion regulation (i.e., ventromedial prefrontal cortex, amygdala, insula, and anterior cingulate cortex [ACC]) during 'certain' and 'uncertain' anticipation of negative and positive stimuli. Thirty-five healthy adults were randomized to receive a thirty-minute exposure to either blue (active) or amber (placebo) light, immediately followed by an emotional anticipation task during functional magnetic resonance imaging (fMRI). In contrast to placebo, participants in the blue light group showed significantly reduced activation within the rostral ACC during 'uncertain' anticipation (i.e., uncertainty regarding whether a positive or negative stimulus would be shown) in comparison to 'certain' anticipation of a positive stimulus. These findings may be explicable in terms of interactions between blue light exposure and the influence of specific neuromodulators on ACC-mediated decision-making mechanisms. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Preliminary Molecular Dynamic Simulations of the Estrogen Receptor Alpha Ligand Binding Domain from Antagonist to Apo

    Directory of Open Access Journals (Sweden)

    Adrian E. Roitberg

    2008-06-01

    Full Text Available Estrogen receptors (ER are known as nuclear receptors. They exist in the cytoplasm of human cells and serves as a DNA binding transcription factor that regulates gene expression. However the estrogen receptor also has additional functions independent of DNA binding. The human estrogen receptor comes in two forms, alpha and beta. This work focuses on the alpha form of the estrogen receptor. The ERα is found in breast cancer cells, ovarian stroma cells, endometrium, and the hypothalamus. It has been suggested that exposure to DDE, a metabolite of DDT, and other pesticides causes conformational changes in the estrogen receptor. Before examining these factors, this work examines the protein unfolding from the antagonist form found in the 3ERT PDB crystal structure. The 3ERT PDB crystal structure has the estrogen receptor bound to the cancer drug 4-hydroxytamoxifen. The 4-hydroxytamoxifen ligand was extracted before the simulation, resulting in new conformational freedom due to absence of van der Waals contacts between the ligand and the receptor. The conformational changes that result expose the binding clef of the co peptide beside Helix 12 of the receptor forming an apo conformation. Two key conformations in the loops at either end of the H12 are produced resulting in the antagonist to apo conformation transformation. The results were produced over a 42ns Molecular Dynamics simulation using the AMBER FF99SB force field.

  7. New Mesozoic and Cenozoic fossils from Ecuador: Invertebrates, vertebrates, plants, and microfossils

    Science.gov (United States)

    Cadena, Edwin A.; Mejia-Molina, Alejandra; Brito, Carla M.; Peñafiel, Sofia; Sanmartin, Kleber J.; Sarmiento, Luis B.

    2018-04-01

    Ecuador is well known for its extensive extant biodiversity, however, its paleobiodiversity is still poorly explored. Here we report seven new Mesozoic and Cenozoic fossil localities from the Pacific coast, inter-Andean depression and Napo basin of Ecuador, including vertebrates, invertebrates, plants, and microfossils. The first of these localities is called El Refugio, located near the small town of Chota, Imbabura Province, from where we report several morphotypes of fossil leaves and a mycetopodid freshwater mussel of the Upper Miocene Chota Formation. A second site is also located near the town of Chota, corresponding to potentially Pleistocene to Holocene lake deposits from which we report the occurrence of leaves and fossil diatoms. A third locality is at the Pacific coast of the country, near Rocafuerte, a town in Esmeraldas Province, from which we report a late Miocene palm leaf. We also report the first partially articulated skull with teeth from a Miocene scombridid (Mackerels) fish from El Cruce locality, and completely preserved seeds from La Pila locality, both sites from Manabí Province. Two late Cretaceous fossil sites from the Napo Province, one near Puerto Napo showing a good record of fossil shrimps and a second near the town of Loreto shows the occurrence of granular amber and small gymnosperms seeds and cuticles. All these new sites and fossils show the high potential of the sedimentary sequences and basins of Ecuador for paleontological studies and for a better understanding of the fossil record of the country and northern South America.

  8. Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

    Science.gov (United States)

    Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

    2015-12-28

    Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

  9. Experimental Study on Behavior of Bow-tie Tree Generation by Using Heavy Water

    Science.gov (United States)

    Kumazawa, Takao; Nakagawa, Wataru; Tsurumaru, Hidekazu

    Bow-tie tree (BTT) generated from contaminant, e.g., metal, carbon, amber(over cured resin) or void in insulator is a significant deterioration factor of XLPE power cable. However, essential role of water in generation and progress of BTT is not yet sufficiently cleared. In order to investigate the role of water we paid attention to difference in chemical properties of light water (H2O) and heavy water (D2O), moreover we evaluated influence of isotopic effect due to hydrogen and deuterium on behavior of BTT generation. In accelerated aging test the number of BTT in XLPE sample, in which copper powder of 500ppm was contaminated as BTT cores, dipped in heavy water (D2O:100wt%) decreased to one third compared with light water(D2O:0wt%). Furthermore, the maximum length of BTT decreased with increase in concentration of heavy water. The experimental results show that heavy water exerted a depression effect on generation and progress of BTT. We considered that the depression effect due to hydrogen isotope appeared by inhibiting ionization and elution of BTT cores, because salt-solubility and ionic mobility of heavy water are about 15 to 20% smaller than those of light water. Therefore, the essential role of water seemed to be production and transport of ions in XLPE.

  10. Engineering a promiscuous pyrrolysyl-tRNA synthetase by a high throughput FACS screen

    KAUST Repository

    Hohl, Adrian

    2017-12-06

    The Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl are used to facilitate the incorporation of non-canonical amino acids (ncAAs) into the genetic code of bacterial and eukaryotic cells by orthogonally reassigning the amber codon. Currently, the incorporation of new ncAAs requires a cumbersome engineering process composed of several positive and negative selection rounds to select the appropriate PylRS/tRNAPyl pair. Our fast and sensitive engineering approach required only a single FACS selection round to identify 110 orthogonal PylRS variants for the aminoacylation of 20 ncAAs. Pocket-substrate relationship from these variants led to the design of a highly promiscuous PylRS (HpRS), which catalyzed the aminoacylation of 31 structurally diverse lysine derivatives bearing clickable, fluorinated, fluorescent, and biotinylated entities. The high speed and sensitivity of our approach provides a competitive alternative to existing screening methodologies, and delivers insights into the complex PylRS-substrate interactions to facilitate the generation of additional promiscuous variants.

  11. Evaluation of extra virgin olive oil stability by artificial neural network.

    Science.gov (United States)

    Silva, Simone Faria; Anjos, Carlos Alberto Rodrigues; Cavalcanti, Rodrigo Nunes; Celeghini, Renata Maria dos Santos

    2015-07-15

    The stability of extra virgin olive oil in polyethylene terephthalate bottles and tinplate cans stored for 6 months under dark and light conditions was evaluated. The following analyses were carried out: free fatty acids, peroxide value, specific extinction at 232 and 270 nm, chlorophyll, L(∗)C(∗)h color, total phenolic compounds, tocopherols and squalene. The physicochemical changes were evaluated by artificial neural network (ANN) modeling with respect to light exposure conditions and packaging material. The optimized ANN structure consists of 11 input neurons, 18 hidden neurons and 5 output neurons using hyperbolic tangent and softmax activation functions in hidden and output layers, respectively. The five output neurons correspond to five possible classifications according to packaging material (PET amber, PET transparent and tinplate can) and light exposure (dark and light storage). The predicted physicochemical changes agreed very well with the experimental data showing high classification accuracy for test (>90%) and training set (>85). Sensitivity analysis showed that free fatty acid content, peroxide value, L(∗)Cab(∗)hab(∗) color parameters, tocopherol and chlorophyll contents were the physicochemical attributes with the most discriminative power. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. 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.

  13. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

    Science.gov (United States)

    Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

    2011-01-01

    Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

  14. Using an original triage and on call management tool aids identification and assessment of the acutely unwell surgical patient.

    Science.gov (United States)

    Hodge, Stacie; Helliar, Sebastian; Macdonald, Hamish Ian; Mackey, Paul

    2018-01-01

    Until now, there have been no published surgical triage tools. We have developed the first such tool with a tiered escalation policy, aiming to improve identification and management of critically unwell patients. The existing sheet which is used to track new referrals and admissions to the surgical assessment unit was reviewed. The sheet was updated and a traffic light triage tool generated using National Early Warning Scores (NEWS), sepsis criteria and user discretion. A tiered escalation policy to guide urgency of assessment was introduced and education sessions for all staff undertaken, to ensure understanding and compliance. Through multiple 'plan-do-study-act' cycles, the new system and its efficiency have been analysed. Prior to intervention, documentation of NEWS did not occur and only 13% of admission observations were communicated to the surgical team. Following multiple cycles and interventions, 93% of patients were fully triaged, and 80% of 'red' and 'amber' patients' observations were communicated to the surgical team. The average time for a registrar to review a 'red' patient was 37 min and 79% of 'green' patients were reviewed within an hour of their presentation. Rapid identification of the unwell patient is crucial. Here we publish the first triage tool that enables early assessment of septic and otherwise potentially unwell surgical patients.

  15. Light emission ranging from blue to red from a series of Iguana/GaN single quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Martin, R.W. [Department of Physics, University of Strathclyde, Glasgow (United Kingdom)]. E-mail: r.w.martin@strath.ac.uk; Edwards, P.R.; Pecharroman-Gallego, R.; O' Donnell, K.P. [Department of Physics, University of Strathclyde, Glasgow (United Kingdom); Liu, C.; Deatcher, C.J.; Watson, I.M. [Institute of Photonics, University of Strathclyde, Glasgow (United Kingdom)

    2002-04-07

    In this paper, we describe the growth and characterization of InGaN single quantum wells with emission peaks in the blue, green, amber and red spectral regions, grown by metal-organic vapour phase epitaxy. Starting from the growth of a blue-emitting (peak {approx}430 nm) InGaN quantum well at 860 deg. C the InGaN growth temperature was progressively reduced. The photoluminescence peak wavelength, measured at low temperature, shifts through the green and orange spectral regions and reaches 670 nm for an InGaN growth temperature of 760 deg. C. This corresponds to an energy lower than the currently accepted band-gap of the binary compound, InN. Spectral characteristics of the luminescence peaks will be discussed, including an analysis of the phonon-assisted contribution. Low energy secondary ion mass spectrometry analysis provides information on the indium content and thickness of the 'blue' and 'red' quantum wells. The results are combined to discuss the origin of the 'sub-band-gap' luminescence in terms of the combined influence of InN-GaN segregation and the effect of intense piezoelectric fields. (author)

  16. Color, physicochemical parameters and antioxidant potential of whole grape juices subject to different UV-C radiation doses

    Directory of Open Access Journals (Sweden)

    Paôla de Castro Henrique

    2016-04-01

    Full Text Available ABSTRACT Knowing that moderate stress such as UV radiation can activate defense mechanisms in plants, the use of UV-C radiation appears as hypothesis of a promising technique that would help to stimulate and enhance beneficial compounds for health, through a clean and healthy technology. In this study, the possible induction of secondary metabolism, the increase in the content of phytochemical compounds and physicochemical changes through the use of UV-C radiation were evaluated on whole grape juices produced with Vitis labrusca grapes, cultivar Isabel Precoce. Grapes were harvested, sanitized, exposed to UV-C radiation at doses of 0, 2, 4 and 6 KJ m-2, and then the juices were prepared and packed into amber glass bottles at room temperature. Analyses were performed at 0, 30, 60, 90 and 120 days of storage. Based on results obtained and conditions in which the experiment was performed, UV-C treatment in grapes caused abiotic stress in the fruits, affecting color, titratable acidity, soluble solids/titratable acidity ratio, vitamin C and percentage of protection against oxidation. Application of UV-C did not change levels of phenolic compounds in fruit juices or the percentage of scavenging free radicals, pH and soluble solids.

  17. Air conditioning facilities in a fuel reprocessing plant

    International Nuclear Information System (INIS)

    Kawasaki, Michitaka; Oka, Tsutomu

    1987-01-01

    Reprocessing plants are the facilities for separating the plutonium produced by nuclear reaction and unconsumed remaining uranium from fission products in the spent fuel taken out of nuclear reactors and recovering them. The fuel reprocessing procedure is outlined. In order to ensure safety in handling radioactive substances, triple confinement using vessels, concrete cells and buildings is carried out in addition to the prevention of criticality and radiation shielding, and stainless steel linings and drip trays are installed as occasion demands. The ventilation system in a reprocessing plant is roughly divided into three systems, that is, tower and tank ventilation system to deal with offgas, cell ventilation system for the cells in which main towers and tanks are installed, and building ventilation system. Air pressure becomes higher from tower and tank system to building system. In a reprocessing plant, the areas in a building are classified according to dose rate. The building ventilation system deals with green and amber areas, and the cell ventilation system deals with red area. These three ventilation systems are explained. Radiation monitors are installed to monitor the radiation dose rate and air contamination in working places. The maintenance and checkup of ventilation systems are important. (Kako, I.)

  18. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

    Energy Technology Data Exchange (ETDEWEB)

    Henriksen, Niel M.; Davis, Darrell R.; Cheatham, Thomas E. III, E-mail: tec3@utah.edu [College of Pharmacy, University of Utah, Department of Medicinal Chemistry (United States)

    2012-08-15

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5{gamma} and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to 'update' older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  19. Characterization of NIES CRM No. 23 Tea Leaves II for the determination of multielements.

    Science.gov (United States)

    Mori, Ikuko; Ukachi, Miyuki; Nagano, Kimiyo; Ito, Hiroyasu; Yoshinaga, Jun; Nishikawa, Masataka

    2010-05-01

    A candidate environmental certified reference material (CRM) for the determination of multielements in tea leaves and materials of similar matrix, NIES CRM No. 23 Tea Leaves II, has been developed and characterized by the National Institute for Environmental Studies (NIES), Japan. The origin of the material was tea leaves, which were ground, sieved through a 106-microm mesh, homogenized, and then subdivided into amber glass bottles. The results of homogeneity and stability tests indicated that the material was sufficiently homogeneous and stable for use as a reference material. The property values of the material were statistically determined based on chemical analyses by a network of laboratories using a wide range of methods. Sixteen laboratories participated in the characterization, and nine certified values and five reference values were obtained. These property values of the candidate CRM, which are expressed as mass fractions, were close to the median and/or mean values of the mass fractions of elements in various tea products. The candidate CRM is appropriate for use in analytical quality control and in the evaluation of methods used in the analysis of tea and materials of similar matrix.

  20. Vectorization, parallelization and porting of nuclear codes (porting). Progress report fiscal 1999

    Energy Technology Data Exchange (ETDEWEB)

    Kawasaki, Nobuo; Nemoto, Toshiyuki; Kawai, Wataru; Ishizuki, Shigeru [Fujitsu Ltd., Tokyo (Japan); Ogasawara, Shinobu; Kume, Etsuo; Adachi, Masaaki [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Yatake, Yo-ichi [Hitachi Ltd., Tokyo (Japan)

    2001-01-01

    Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system, the AP3000 system, the SX-4 system and the Paragon system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 18 codes in fiscal 1999. These results are reported in 3 parts, i.e., the vectorization and the parallelization part on vector processors, the parallelization port on scalar processors and the porting part. In this report, we describe the porting. In this porting part, the porting of Assisted Model Building with Energy Refinement code version 5 (AMBER5), general purpose Monte Carlo codes far neutron and photon transport calculations based on continuous energy and multigroup methods (MVP/GMVP), automatic editing system for MCNP library code (autonj), neutron damage calculations for materials irradiations and neutron damage calculations for compounds code (SPECTER/SPECOMP), severe accident analysis code (MELCOR) and COolant Boiling in Rod Arrays, Two-Fluid code (COBRA-TF) on the VPP500 system and/or the AP3000 system are described. (author)

  1. A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments.

    Science.gov (United States)

    Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto

    2017-06-26

    Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.

  2. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase.

    Science.gov (United States)

    Wang, Xianwei; Zhang, John Z H; He, Xiao

    2015-11-14

    Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

  3. Diseño de una formulación antimicótica

    Directory of Open Access Journals (Sweden)

    Martha Gómez Carril

    1998-04-01

    Full Text Available Se desarrolló una formulación con nitrato de miconazol al 2 % en una crema hidrosoluble apropiada, la cual cumple con los requerimientos físicos, químicos, microbiológicos y biológicos para este tipo de forma farmacéutica. Se comprobó que el producto debe ser envasado en frascos de vidrio ámbar o en tubos de aluminio laqueado, además de presentar una estabilidad física adecuada durante 3 años. El contenido del principio activo se mantuvo dentro de los límites establecidos hasta los 16 meses. También se demostró la actividad antimicótica de la preparación y su efectividad terapéutica.A formulation with miconazole nitrate 2 % is developed in an appropiate hydrosoluble cream, which meets all the physical, chemical, microbiologic and biologic requirements for this type of pharmaceutical form. It was proved that the product should be put into amber glass flasks or into lacquered aluminum tubes. besides having an adecuate physical stability during three years. The content of the active principle was kept within the established limits up to the 16 months. The antifungal activity of the preparation as well as its therapeutic effectiveness were also demonstrated.

  4. Direct Growth of III-Nitride Nanowire-Based Yellow Light-Emitting Diode on Amorphous Quartz Using Thin Ti Interlayer

    KAUST Repository

    Prabaswara, Aditya

    2018-02-06

    Consumer electronics have increasingly relied on ultra-thin glass screen due to its transparency, scalability, and cost. In particular, display technology relies on integrating light-emitting diodes with display panel as a source for backlighting. In this study, we undertook the challenge of integrating light emitters onto amorphous quartz by demonstrating the direct growth and fabrication of a III-nitride nanowire-based light-emitting diode. The proof-of-concept device exhibits a low turn-on voltage of 2.6 V, on an amorphous quartz substrate. We achieved ~ 40% transparency across the visible wavelength while maintaining electrical conductivity by employing a TiN/Ti interlayer on quartz as a translucent conducting layer. The nanowire-on-quartz LED emits a broad linewidth spectrum of light centered at true yellow color (~ 590 nm), an important wavelength bridging the green-gap in solid-state lighting technology, with significantly less strain and dislocations compared to conventional planar quantum well nitride structures. Our endeavor highlighted the feasibility of fabricating III-nitride optoelectronic device on a scalable amorphous substrate through facile growth and fabrication steps. For practical demonstration, we demonstrated tunable correlated color temperature white light, leveraging on the broadly tunable nanowire spectral characteristics across red-amber-yellow color regime.

  5. Use of rice rusk ash and spent catalyst as a source of raw material for the production and characterization of soda-lime silicate glasses destined for packaging; Utilizacao de residuos de catalisador (ECAT) e cinzas da casca de arroz (CCA) na elaboracao de vidros silicatos soda-cal destinados ao setor de embalagem

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, M.S.; Martinelli, J.R.; Genova, L.A.; Prado, U.S. do, E-mail: araujo.mariaana@gmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil). Centro de Ciencia e Tecnologia de Materiais

    2016-07-01

    Study on the use of rice husk ash (RHA) and waste catalyst (ECAT), two industrial solid waste generated in large quantities in Brazil, getting soda-lime glass for the production of packaging. Both the waste may be classified as class II waste according to NBR 10,004. Samples were produced adding Na{sub 2}CO{sub 3} and CaO to obtain a composition within the range of commercial soda-lime glasses. The results showed that both can be used as received (without any previous treatment) replacing important raw materials, source of Al{sub 2}O{sub 3} and SiO2, necessary for glass formation. The produced samples were amber due to the presence of nickel (Ni2+ ions) from the ECAT and optical transmittance of 18%. These also showed good homogeneity, i.e., absence of bubbles and striae and dissolution rate higher than a commercial soda-lime glass. In general, the samples are presented suitable for applications that require low transmittance such as colored glass containers, which does not require perfect visibility and transparency. Finally, the waste level of incorporation was approximately 78 mass%. (author)

  6. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach.

    Science.gov (United States)

    Sanusi, Z K; Govender, T; Maguire, G E M; Maseko, S B; Lin, J; Kruger, H G; Honarparvar, B

    2017-09-01

    Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?G bind ) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide.

    Science.gov (United States)

    Turner, Matthew; Platts, James A; Deeth, Robert J

    2016-03-08

    Ligand field molecular mechanics (LFMM), density functional theory (DFT), and semiempirical PM7 methods are used to study the binding of two Pt(II)-L systems to an N-terminal fragment of the amyloid-β peptide, where L = 2,2-bipyridyl or 1,10-phenanthroline. Molecular dynamics simulations are used to explore the conformational freedom of the peptide using LFMM combined with AMBER molecular mechanics parameters. We establish a modeling protocol, allowing for identification and analysis of favorable platinum-binding modes and peptide conformations. Preferred binding modes are identified for each ligand investigated; metal coordination occurs via Nε in His residues for both ligands--His6ε-His13ε and His6ε-His14ε for the bipyridyl and phenanthroline ligands, respectively. The observed change in binding mode for the different ligands suggests that the binding mode of these platinum-based structures can be controlled by the choice of ligand. In the bipy systems, Boltzmann population at 310 K is dominated by a single conformer, while in the phenanthroline case, three conformations make significant contributions to the ensemble. The relative stability of these conformations is due to the inherent stability of binding platinum via Nε in addition to subtle H-bonding effects.

  8. Prediction of ligand effects in platinum-amyloid-β coordination.

    Science.gov (United States)

    Turner, Matthew; Deeth, Robert J; Platts, James A

    2017-08-01

    Ligand field molecular mechanics (LFMM) and semi-empirical Parametric Model 7 (PM7) methods are applied to a series of six Pt II -Ligand systems binding to the N-terminal domain of the amyloid-β (Aβ) peptide. Molecular dynamics using a combined LFMM/Assisted Model Building with Energy Refinement (AMBER) approach is used to explore the conformational freedom of the peptide fragment, and identifies favourable platinum binding modes and peptide conformations for each ligand investigated. Platinum coordination is found to depend on the nature of the ligand, providing evidence that binding mode may be controlled by suitable ligand design. Boltzmann populations at 310K indicate that each Pt-Aβ complex has a small number of thermodynamically accessible states. Ramachandran maps are constructed for the sampled Pt-Aβ conformations and secondary structural analysis of the obtained complex structures is performed and contrasted with the free peptide; coordination of these platinum complexes disrupts existing secondary structure in the Aβ peptide and promotes formation of ligand-specific turn-type secondary structure. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides.

    Science.gov (United States)

    Mutter, Shaun T; Deeth, Robert J; Turner, Matthew; Platts, James A

    2018-04-01

    Ligand field molecular mechanics (LFMM) parameters have been benchmarked for copper (II) bound to the amyloid-β 1-16 peptide fragment. Several density functional theory (DFT) optimised small test models, representative of different possible copper coordination modes, have been used to test the accuracy of the LFMM copper bond lengths and angles, resulting in errors typically less than 0.1 Å and 5°. Ligand field molecular dynamics (LFMD) simulations have been carried out on the copper bound amyloid-β 1-16 peptide and snapshots extracted from the subsequent trajectory. Snapshots have been optimised using DFT and the semi-empirical PM7 method resulting in good agreement against the LFMM calculated geometry. Analysis of substructures within snapshots shows that the larger contribution of geometrical difference, as measured by RMSD, lies within the peptide backbone, arising from differences in DFT and AMBER, and the copper coordination sphere is reproduced well by LFMM. PM7 performs excellently against LFMM with an average RMSD of 0.2 Å over 21 tested snapshots. Further analysis of the LFMD trajectory shows that copper bond lengths and angles have only small deviations from average values, with the exception of a carbonyl moiety from the N-terminus, which can act as a weakly bound fifth ligand.

  10. Nitrile bonds as infrared probes of electrostatics in ribonuclease S.

    Science.gov (United States)

    Fafarman, Aaron T; Boxer, Steven G

    2010-10-28

    Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.

  11. Early Cretaceous greenhouse pumped higher taxa diversification in spiders.

    Science.gov (United States)

    Shao, Lili; Li, Shuqiang

    2018-05-24

    The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganizations significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrences spider in amber deposits. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification. Copyright © 2018. Published by Elsevier Inc.

  12. Vision, eye disease, and art: 2015 Keeler Lecture.

    Science.gov (United States)

    Marmor, M F

    2016-02-01

    The purpose of this study was to examine normal vision and eye disease in relation to art. Ophthalmology cannot explain art, but vision is a tool for artists and its normal and abnormal characteristics may influence what an artist can do. The retina codes for contrast, and the impact of this is evident throughout art history from Asian brush painting, to Renaissance chiaroscuro, to Op Art. Art exists, and can portray day or night, only because of the way retina adjusts to light. Color processing is complex, but artists have exploited it to create shimmer (Seurat, Op Art), or to disconnect color from form (fauvists, expressionists, Andy Warhol). It is hazardous to diagnose eye disease from an artist's work, because artists have license to create as they wish. El Greco was not astigmatic; Monet was not myopic; Turner did not have cataracts. But when eye disease is documented, the effects can be analyzed. Color-blind artists limit their palette to ambers and blues, and avoid greens. Dense brown cataracts destroy color distinctions, and Monet's late canvases (before surgery) showed strange and intense uses of color. Degas had failing vision for 40 years, and his pastels grew coarser and coarser. He may have continued working because his blurred vision smoothed over the rough work. This paper can barely touch upon the complexity of either vision or art. However, it demonstrates some ways in which understanding vision and eye disease give insight into art, and thereby an appreciation of both art and ophthalmology.

  13. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

    Science.gov (United States)

    Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2000-10-01

    Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

  14. Condições de estabilidade para preparações magistrais contendo clorexidina

    Directory of Open Access Journals (Sweden)

    Paula Martinez Rodrigue

    2009-12-01

    Full Text Available The mouthwash containing chlorhexidine (CHX is a solution and aims to complement the oral hygiene. It is considered standard for judging of antimicrobial effectiveness compared to other chemical agents in dentistry. CHX used in low concentrations it has a bacteriostatic and bactericidal high. The mouthwash consisting of CHX has some side effects, including blackening of the teeth, tongue and resets, burning mouth and changes in taste and to reverse the process, no need of stopping treatment. There are several factors that may interfere with the stability of CHX, including pH, light, and presence of substances with anionic character in the composition and packing in containers inadequate. His prolonged substantivity accounts for their effectiveness, with a view that can be retained in the oral cavity for up to 12 hours. CHX has been considered an antimicrobial agent is extremely important to present many advantages, among them non-toxic and safety in addition to presenting properties fungicide, algicide and virucidal. The validity of a extemporaneous preparation containing CHX may be estimated at about six months, provided that all the conditions of stability of the active substance, among which stand out the pH of the final product should be between 5.5 and 7.0 avoiding chemical incompatibilities with other components of the solution, and the packing in plastic amber PET. Finally, it is suggested that extemporaneous solutions containing CHX can be effective in treating periodontal diseases, since the conditions for stability, packaging and storage.

  15. Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wen-Ting Chu

    Full Text Available Src-homology regions 3 (SH3 domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5, including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

  16. Purification-Free, Target-Selective Immobilization of a Protein from Cell Lysates.

    Science.gov (United States)

    Cha, Jaehyun; Kwon, Inchan

    2018-02-27

    Protein immobilization has been widely used for laboratory experiments and industrial processes. Preparation of a recombinant protein for immobilization usually requires laborious and expensive purification steps. Here, a novel purification-free, target-selective immobilization technique of a protein from cell lysates is reported. Purification steps are skipped by immobilizing a target protein containing a clickable non-natural amino acid (p-azidophenylalanine) in cell lysates onto alkyne-functionalized solid supports via bioorthogonal azide-alkyne cycloaddition. In order to achieve a target protein-selective immobilization, p-azidophenylalanine was introduced into an exogenous target protein, but not into endogenous non-target proteins using host cells with amber codon-free genomic DNAs. Immobilization of superfolder fluorescent protein (sfGFP) from cell lysates is as efficient as that of the purified sfGFP. Using two fluorescent proteins (sfGFP and mCherry), the authors also demonstrated that the target proteins are immobilized with a minimal immobilization of non-target proteins (target-selective immobilization). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

    Science.gov (United States)

    Sevgen, Emre; Giberti, Federico; Sidky, Hythem; Whitmer, Jonathan K; Galli, Giulia; Gygi, Francois; de Pablo, Juan J

    2018-05-14

    We present a seamless coupling of a suite of codes designed to perform advanced sampling simulations, with a first-principles molecular dynamics (MD) engine. As an illustrative example, we discuss results for the free energy and potential surfaces of the alanine dipeptide obtained using both local and hybrid density functionals (DFT), and we compare them with those of a widely used classical force field, Amber99sb. In our calculations, the efficiency of first-principles MD using hybrid functionals is augmented by hierarchical sampling, where hybrid free energy calculations are initiated using estimates obtained with local functionals. We find that the free energy surfaces obtained from classical and first-principles calculations differ. Compared to DFT results, the classical force field overestimates the internal energy contribution of high free energy states, and it underestimates the entropic contribution along the entire free energy profile. Using the string method, we illustrate how these differences lead to different transition pathways connecting the metastable minima of the alanine dipeptide. In larger peptides, those differences would lead to qualitatively different results for the equilibrium structure and conformation of these molecules.

  18. Effect of artificial shading on the tannin accumulation and aromatic composition of the Grillo cultivar (Vitis vinifera L.)

    Science.gov (United States)

    2013-01-01

    Background White wine quality, especially in warm climates, is affected by sunlight and heat stress. These factors increase the probability that ambering processes will occur and reduce the potential flavour compounds. This study aimed to investigate the effect of sunlight reduction on the accumulation of polyphenolic and aromatic compounds. Results This study was conducted in a commercial vineyard containing V. vinifera L. cv Grillo. Opaque polypropylene boxes (100% shading) and high-density polyethylene (HDPE) net bags (50% shading) were applied at fruit set. The effect of the shaded treatments was compared to the exposed fruit treatment. The shaded treatments resulted in heavier berries and lower must sugar contents than the exposed treatments. Proanthocyanidins and total polyphenol levels were similar in the exposed and bagged grapes; however, the levels were always lower in the boxed fruit. At harvest, the highest aroma level was measured in the boxed fruits. Conclusions The boxed fruit had less sugar, fewer proanthocyanidins and more flavours than the exposed grapes. The reduction in flavanols reactive to p-dimethylamino-cinnamaldehyde as (+)-catechin equivalents and total skin proanthocyanidins is an important result for the white winemaking process. In addition, the higher level of aromatic compounds in shaded grapes at harvest is an important contribution to the development of different wine styles. PMID:24195612

  19. 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.

  20. QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

    Energy Technology Data Exchange (ETDEWEB)

    Hagiwara, Yohsuke; Tateno, Masaru [Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571 (Japan); Ohta, Takehiro [Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8577 (Japan)], E-mail: tateno@ccs.tsukuba.ac.jp

    2009-02-11

    An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.