Sample records for amber verification study

  1. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2010-09-30

    Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

  2. A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

    NASA Astrophysics Data System (ADS)

    Gao, Ya; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong

    2017-07-01

    We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    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.

  5. Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

    PubMed Central

    Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, Bingbing; Zhang, John Z. H.; Mei, Ye

    2015-01-01

    A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. PMID:26039188

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

    PubMed Central

    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. PMID:28076427

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

    PubMed

    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.

  8. The levantine amber belt

    NASA Astrophysics Data System (ADS)

    Nissenbaum, A.; Horowitz, A.

    1992-02-01

    Amber, a fossil resin, is found in Early Cretaceous sanstones and fine clastics in Lebanon, Jordan, and Israel. The term "Levantine amber belt" is coined for this amber-containing sediment belt. The amber occurs as small nodules of various colors and frequently contains inclusions of macro- and microorganisms. The Lebanese amber contains Lepidoptera and the amber from southern Israel is rich in fungal remains. The source of the amber, based on geochemical and palynological evidence, is assumed to be from a conifer belonging to the Araucariaceae. The resins were produced by trees growing in a tropical near shore environment. The amber was transported into small swamps and was preserved there together with lignite. Later reworking of those deposits resulted in redeposition of the amber in oxidized sandstones.

  9. Hydrolysis of Baltic amber during thermal ageing--an infrared spectroscopic approach.

    PubMed

    Pastorelli, Gianluca; Shashoua, Yvonne; Richter, Jane

    2013-04-01

    To enable conservation of amber in museums, understanding of chemical changes is crucial. While oxidation has been investigated particularly well for this natural polymer, further degradation phenomena in relation to humidity and pollutants are poorly studied or still unknown. Attenuated total reflectance-Fourier transform infrared spectroscopy was explored with regard to Baltic amber. A systematic spectroscopic survey of a wide range of thermally aged model amber samples, exposed to different microclimatic conditions, showed significant changes in their spectra. Samples aged in a humid and acidic environment or exposed to a humid and alkaline atmosphere generally exhibited a higher absorbance intensity of carbonyl groups at frequencies assigned to acids than unaged samples, samples aged in drier conditions and samples immersed in an alkaline solution. Baltic amber comprises succinate ester, which may be hydrolysed into communol and succinic acid. The survey thus provided evidence about the progress of hydrolytic reactions during degradation of Baltic amber. Infrared spectroscopy was shown to have significant potential for providing qualitative and quantitative chemical information on hydrolysis of amber, which will be of interest for the development of preventive conservation techniques for museum collections of amber objects. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. AM Broadcast Emergency Relay (AMBER)

    DTIC Science & Technology

    1990-07-01

    might be for an end-to-end error probability of 10- 6 for a 4The onlN difference between a real and a % irtual circuit in AMBER is that a real circuit...automation, the initial AMBER feasibility study was awarded to Altran Electronics, which had developed and marketed this concept (Martinez, 1981). The

  11. Ambered kernels in stenospermocarpic fruit of eastern black walnut

    Treesearch

    Michele R. Warmund; J.W. Van Sambeek

    2014-01-01

    "Ambers" is a term used to describe poorly filled, shriveled eastern black walnut (Juglans nigra L.) kernels with a dark brown or black-colored pellicle that are unmarketable. Studies were conducted to determine the incidence of ambered black walnut kernels and to ascertain when symptoms were apparent in specific tissues. The occurrence of...

  12. LIPID11: A Modular Framework for Lipid Simulations using Amber

    PubMed Central

    Skjevik, Åge A.; Madej, Benjamin D.; Walker, Ross C.; eigen, Knut T

    2013-01-01

    Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach, and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that Lipid11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field. PMID:22916730

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

    PubMed

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

    2016-08-05

    Relics of amber were excavated from King Muryeong's tomb constructed in the 6th century on the Korean peninsula. To estimate the provenance, FTIR (Fourier transform infrared spectroscopy) and py/GC/MS (pyrolysis/gas chromatography/mass spectrometry) analysis were utilized. The reference Baltic amber sample was also analyzed with the same method for comparison. The relics were confirmed to be amber from the FTIR analysis where an absorption band near 1150cm(-1), characteristic one in Baltic amber, was also observed. In py/GC/MS analysis, pyrolyzed products like butanedioic acid and dehydroabietic acid, known constituents of amber, were observed. In addition, d-fenchyl alcohol, camphor, borneol and butanedioic acid, typical constituents of Baltic amber, were observed in some samples. From this, it appears that some of relics were made from Baltic amber and that Baltic amber was transported to the Korean peninsula in the time of tomb construction. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed

    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.

  15. 40Ar/39Ar systematics and argon diffusion in amber: implications for ancient earth atmospheres

    USGS Publications Warehouse

    Landis, G.P.; Snee, L.W.

    1991-01-01

    Argon isotope data indicate retained argon in bulk amber (matrix gas) is radiogenic [40Ar/39Ar ???32o] than the much more abundant surface absorbed argon [40Ar/39Ar ???295.5]. Neutron-induced 39Ar is retained in amber during heating experiments to 150?? -250??C, with no evidence of recoiled 39Ar found after irradiation. A maximum permissible volume diffusion coefficient of argon in amber (at ambient temperature) D???1.5 x 10-17 cm2S-1 is calculated from 39Ar retention. 40Ar/39Ar age calculations indicate Dominican Republic amber is ??? 45 Ma and North Dakota amber is ??? 89 Ma, both at least reasonable ages for the amber based upon stratigraphic and paleontological constraints and upon the small amount of radiogenic 40Ar. To date, over 300 gas analyses of ambers and resins of Cretaceous to Recent age that are geographically distributed among fifteen noted world locations identify mixtures of gases in different sites within amber (Berner and Landis, 1988). The presence of multiple mixing trends between compositionally distinct end-members gases within the same sample and evidence for retained radiogenic argon within the amber argue persuasivley against rapid exchange by diffusion of amber-contained gases with moder air. Only gas in primary bubbles entrapped between successive flows of tree resin has been interpreted as original "ancient air", which is an O2-rich end-member gas with air-like N2/Ar ratios. Gas analyses of these primary bubbles indicate atmospheric O2 levels in the Late Cretaceous of ??? 35%, and that atmospheric O2 dropped by early Tertiary time to near a present atmospheric level of 21% O2. A very low argon diffusion coefficient in amber persuasively argues for a gas in primary bubbles trapped in amber being ancient air (possibly modified only by O2 reaction with amber). ?? 1991.

  16. Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

    PubMed

    Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

    2010-05-11

    A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

  17. Evidence for marine microfossils from amber.

    PubMed

    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.

  18. First fossil representatives of Pharaxonothinae Crowson (Coleoptera: Erotylidae): indirect evidence for cycads existence in Baltic amber forest.

    PubMed

    Alekseev, Vitalii I; Bukejs, Andris

    2017-10-19

    A new species of Erotylidae, Cycadophila (s. str.) mumia sp. nov., the first fossil representative of the subfamily Pharaxo-nothinae, is described and illustrated from Eocene Baltic amber. A second closely related specimen is reported but not described as new due to poor preservation in amber. The occurrence of representatives of the Recent cycad-specialized genus in Baltic amber can indirectly indicate the presence of their host plants (Cycadales: Cycadophyta: Cycadopsida) in the Eocene amber forest.

  19. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator

    NASA Astrophysics Data System (ADS)

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T.; Singh, Hukam; Hammel, Jörg U.; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-10-01

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

  20. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator.

    PubMed

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T; Singh, Hukam; Hammel, Jörg U; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-10-04

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

  1. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator

    PubMed Central

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T.; Singh, Hukam; Hammel, Jörg U.; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-01-01

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far. PMID:27698490

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

    PubMed

    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.

  3. Full down-conversion of amber-emitting phosphor-converted light-emitting diodes with powder phosphors and a long-wave pass filter.

    PubMed

    Oh, Jeong Rok; Cho, Sang-Hwan; Park, Hoo Keun; Oh, Ji Hye; Lee, Yong-Hee; Do, Young Rag

    2010-05-24

    This paper reports the possibility of a facile optical structure to realize a highly efficient monochromatic amber-emitting light-emitting diode (LED) using a powder-based phosphor-converted LED combined with a long-wave pass filter (LWPF). The capping of a blue-reflecting and amber-passing LWPF enhances both the amber emission from the silicate amber phosphor layer and the color purity due to the blocking and recycling of the pumping blue light from the InGaN LED. The enhancement of the luminous efficacy of the amber pc-LED with a LWPF (phosphor concentration 20 wt%, 39.4 lm/W) is 34% over that of an amber pc-LED without a LWPF (phosphor concentration 55 wt%, 29.4 lm/W) at 100 mA and a high color purity (>96%) with Commission International d'Eclairage (CIE) color coordinates of x=0.57 and y=0.42.

  4. 7 CFR 52.1006 - Color.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., with respect to dates that are predominantly light amber in color, there may be not more than 5 percent... dark amber in color, there may be not more than 5 percent by count of dates that are light amber in... reasonably uniform for the type; and, with respect to dates that are predominantly light amber in color...

  5. 7 CFR 52.1006 - Color.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., with respect to dates that are predominantly light amber in color, there may be not more than 5 percent... dark amber in color, there may be not more than 5 percent by count of dates that are light amber in... reasonably uniform for the type; and, with respect to dates that are predominantly light amber in color...

  6. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa.

    PubMed

    Grimaldi, David A; Arillo, Antonio; Cumming, Jeffrey M; Hauser, Martin

    2011-01-01

    Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. etsp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa significantly expand the Mesozoic fossil record of rare and phylogenetically significant taxa of lower Brachycera.

  7. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber

    NASA Astrophysics Data System (ADS)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan C.; Alonso, Jesús; Ascaso, Carmen

    2009-05-01

    Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.

  8. Free energy landscape of protein folding in water: explicit vs. implicit solvent.

    PubMed

    Zhou, Ruhong

    2003-11-01

    The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt-bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt-bridge effect results in an overweighting of a non-native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the beta-hairpin in to an alpha-helix, and the alpha-helical content is much higher than the previously reported alpha-helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt-bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, alpha-helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models. Copyright 2003 Wiley-Liss, Inc.

  9. 7 CFR 52.1006 - Color.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... predominantly light amber in color, there may be not more than 5 percent by count of dates that are dark amber... more than 5 percent by count of dates that are light amber in color. (b) (B) classification. If the...; and, with respect to dates that are predominantly light amber in color, there may be not more than 10...

  10. 7 CFR 52.1006 - Color.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... predominantly light amber in color, there may be not more than 5 percent by count of dates that are dark amber... more than 5 percent by count of dates that are light amber in color. (b) (B) classification. If the...; and, with respect to dates that are predominantly light amber in color, there may be not more than 10...

  11. 78 FR 40175 - Exempt Chemical Preparations Under the Controlled Substances Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-03

    ..., Chloral hydrate..... Amber ampule: 1 mL...... 1/28/2013 AccuStandard, Inc CLP-HC-X1, Composite Mix Amber......... 1/28/2013 products. AccuStandard, Inc M-551B-2, Chloral hydrate..... Amber ampule: 1 mL...... 1/28...Standard, Inc M-E-1179-M, Chloral hydrate... Amber ampule: 1 mL...... 1/28/2013 Agilent Technologies...

  12. Potentiating effects of honey on antioxidant properties of lemon-flavoured black tea.

    PubMed

    Pereira, Carla; Barros, Lillian; Vilas-Boas, Miguel; Ferreira, Isabel C F R

    2013-03-01

    Health benefits including antioxidant potential of black tea (Camellia sinensis), lemon (Citrus limon) and honey bees (Apis mellifera) have been extensively reported. Nevertheless, nothing is reported about the effects of their concomitant use. Herein, those effects were evaluated in infusions of lemon-flavoured black tea with three different kinds of honey (light amber, amber and dark amber) from Lavandula stoechas, Erica sp. pl. and other indigenous floral species from north-east Portugal, a region with high amounts of this food product. Data obtained showed that the use of honey (dark amber>amber>light amber) potentiates the antioxidant activity of lemon-flavoured black tea, increasing the reducing power and lipid peroxidation inhibition properties, as also the antioxidant contents such as phenolics, flavonoids and organic acids including ascorbic acid.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. New records and species of Crepidodera Chevrolat (Coleoptera: Chrysomelidae) in Eocene European amber, with a brief review of described fossil beetles from Bitterfeld amber.

    PubMed

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

    2016-11-15

    Based on six relatively well-preserved specimens from Eocene Baltic amber, Crepidodera tertiotertiaria sp. nov. is described. The new species is illustrated and compared with morphologically similar extant and fossil relatives. It is the third described fossil species of Crepidodera Chevrolat. In addition to the new taxon, new fossil records of C. decolorata Nadein & Perkovsky from Baltic and Bitterfeld amber are presented. A key to species of Crepidodera described from fossil resins is provided, and a checklist of Coleoptera described from Bitterfeld amber is compiled.

  15. First early Mesozoic amber in the Western Hemisphere

    USGS Publications Warehouse

    Litwin, R.J.; Ash, S.R.

    1991-01-01

    Detrital amber pebbles and granules have been discovered in Upper Triassic strata on the Colorado Plateau. Although amber previously has been reported from Pennsylvanian, Jurassic, Cretaceous, and Tertiary strata, we know of no other reported Triassic occurrence in North America or the Western Hemisphere. The new discovered occurrences of amber are at two localities in the lower part of the Petrified Forest Member of the Upper Triassic Chinle Formation in Petrified Forest National Park, Arizona. The paper coals and carbonaceous paper shales containing the amber also contain fossil palynomorph assemblages that indicate a late Carnian age for these occurrences. -Authors

  16. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa

    PubMed Central

    Grimaldi, David A.; Arillo, Antonio; Cumming, Jeffrey M.; Hauser, Martin

    2011-01-01

    Abstract Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. et sp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa significantly expand the Mesozoic fossil record of rare and phylogenetically significant taxa of lower Brachycera. PMID:22287902

  17. Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.

    PubMed

    Project, Elad; Nachliel, Esther; Gutman, Menachem

    2010-07-15

    The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. Copyright 2009 Wiley Periodicals, Inc.

  18. AmberAlert / DPS / DHSEM / AAB

    Science.gov Websites

    cooperative public service alert to aid in the safe recovery of abducted children. The Alaska AMBER Alert children to aid in their safe return. AMBER Alert Hotline: 866-AKAMBER - (866-252-6237) State of Alaska

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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 information about botanical source and environmental growing conditions of the fossil plant material will probably allow a more faithful interpretation of amber δ13C records and a wider understanding of the composition of the past atmosphere.

  1. Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

    PubMed

    Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

    2004-07-15

    Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

  2. New Fossil Scorpion from the Chiapas Amber Lagerstätte

    PubMed Central

    Riquelme, Francisco; Villegas-Guzmán, Gabriel; González-Santillán, Edmundo; Córdova-Tabares, Víctor; Francke, Oscar F.; Piedra-Jiménez, Dulce; Estrada-Ruiz, Emilio; Luna-Castro, Bibiano

    2015-01-01

    A new species of scorpion is described based on a rare entire adult male preserved in a cloudy amber from Miocene rocks in the Chiapas Highlands, south of Mexico. The amber-bearing beds in Chiapas constitute a Conservation Lagerstätte with outstanding organic preservation inside plant resin. The new species is diagnosed as having putative characters that largely correspond with the genus Tityus Koch, 1836 (Scorpiones, Buthidae). Accordingly, it is now referred to as Tityus apozonalli sp. nov. Its previously unclear phylogenetic relationship among fossil taxa of the family Buthidae from both Dominican and Mexican amber is also examined herein. Preliminarily results indicate a basal condition of T. apozonalli regarding to Tityus geratus Santiago-Blay and Poinar, 1988, Tityus (Brazilotityus) hartkorni Lourenço, 2009, and Tityus azari Lourenço, 2013 from Dominican amber, as was Tityus (Brazilotityus) knodeli Lourenço, 2014 from Mexican amber. Its close relationships with extant Neotropic Tityus-like subclades such as ‘Tityus clathratus’ and the subgenus Tityus (Archaeotityus) are also discussed. This new taxon adds to the knowledge of New World scorpions from the Miocene that are rarely found trapped in amber. PMID:26244974

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

    PubMed

    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.

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

    PubMed Central

    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

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

    USDA-ARS?s Scientific Manuscript database

    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. ...

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  7. Amber Plug-In for Protein Shop

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oliva, Ricardo

    2004-05-10

    The Amber Plug-in for ProteinShop has two main components: an AmberEngine library to compute the protein energy models, and a module to solve the energy minimization problem using an optimization algorithm in the OPTI-+ library. Together, these components allow the visualization of the protein folding process in ProteinShop. AmberEngine is a object-oriented library to compute molecular energies based on the Amber model. The main class is called ProteinEnergy. Its main interface methods are (1) "init" to initialize internal variables needed to compute the energy. (2) "eval" to evaluate the total energy given a vector of coordinates. Additional methods allow themore » user to evaluate the individual components of the energy model (bond, angle, dihedral, non-bonded-1-4, and non-bonded energies) and to obtain the energy of each individual atom. The Amber Engine library source code includes examples and test routines that illustrate the use of the library in stand alone programs. The energy minimization module uses the AmberEngine library and the nonlinear optimization library OPT++. OPT++ is open source software available under the GNU Lesser General Public License. The minimization module currently makes use of the LBFGS optimization algorithm in OPT++ to perform the energy minimization. Future releases may give the user a choice of other algorithms available in OPT++.« less

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

    PubMed

    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.

  9. Monitoring the Assembly of a Secreted Bacterial Virulence Factor Using Site-specific Crosslinking

    PubMed Central

    Pavlova, Olga; Ieva, Raffaele; Bernstein, Harris D

    2013-01-01

    This article describes a method to detect and analyze dynamic interactions between a protein of interest and other factors in vivo. Our method is based on the amber suppression technology that was originally developed by Peter Schultz and colleagues1. An amber mutation is first introduced at a specific codon of the gene encoding the protein of interest. The amber mutant is then expressed in E. coli together with genes encoding an amber suppressor tRNA and an amino acyl-tRNA synthetase derived from Methanococcus jannaschii. Using this system, the photo activatable amino acid analog p-benzoylphenylalanine (Bpa) is incorporated at the amber codon. Cells are then irradiated with ultraviolet light to covalently link the Bpa residue to proteins that are located within 3-8 Å. Photocrosslinking is performed in combination with pulse-chase labeling and immunoprecipitation of the protein of interest in order to monitor changes in protein-protein interactions that occur over a time scale of seconds to minutes. We optimized the procedure to study the assembly of a bacterial virulence factor that consists of two independent domains, a domain that is integrated into the outer membrane and a domain that is translocated into the extracellular space, but the method can be used to study many different assembly processes and biological pathways in both prokaryotic and eukaryotic cells. In principle interacting factors and even specific residues of interacting factors that bind to a protein of interest can be identified by mass spectrometry. PMID:24378574

  10. 7 CFR 51.2282 - Tolerances for color.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... classification Tolerances for color Darker than extra light 1 Darker than light 1 Darker than light amber 1... (included in 15 percent darker than light amber). Amber 10 percent. 1 See illustration of this term on color... 7 Agriculture 2 2013-01-01 2013-01-01 false Tolerances for color. 51.2282 Section 51.2282...

  11. 7 CFR 51.2282 - Tolerances for color.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... classification Tolerances for color Darker than extra light 1 Darker than light 1 Darker than light amber 1... (included in 15 percent darker than light amber). Amber 10 percent. 1 See illustration of this term on color... 7 Agriculture 2 2014-01-01 2014-01-01 false Tolerances for color. 51.2282 Section 51.2282...

  12. The search for new amber ingredients.

    PubMed

    Narula, Anubhav P S

    2014-10-01

    There is a constant need for developing new fragrance ingredients in the flavor and fragrance industry, as it allows perfumers to create unique and differentiating perfumes for fine as well as functional products. Among all the categories of notes used in perfume creation, amber notes are indispensible and ubiquitous in their presence in all perfumes. Not only amber notes impart high performance and substantivity to fragrances, but they are paramount in the development of classic and legendary fragrances. This article is based on the plenary lecture delivered at the flavor & fragrance 2013 conference of the German Chemical Society in Leipzig, Germany. The strategy, rationale, and the various synthetic approaches that led to the discovery of two new very powerful, woody, amber materials, Amber Xtreme(®) (1) and Trisamber(®) (2), are delineated. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

  13. Spatial dynamics of the invasive defoliator amber-marked birch leafminer across the Anchorage landscape

    Treesearch

    J.E. Lundquist; R.M. Reich; M. Tuffly

    2012-01-01

    The amber-marked birch leafminer has caused severe infestations of birch species in Anchorage, AK, since 2002. Its spatial distribution has been monitored since 2006 and summarized using interpolated surfaces based on simple kriging. In this study, we developed methods of assessing and describing spatial distribution of the leafminer as they vary from year to year, and...

  14. 7 CFR 52.1847 - Colors of golden seedless raisins.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... raisins are practically uniform in color and may range from yellow or golden to light amber color with a... uniform in color and may range from yellow or golden or greenish yellow to light amber wherein the predominating color may be greenish yellow or light amber and that not more than 3 percent, by weight, of all...

  15. 7 CFR 52.1847 - Colors of golden seedless raisins.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... raisins are practically uniform in color and may range from yellow or golden to light amber color with a... uniform in color and may range from yellow or golden or greenish yellow to light amber wherein the predominating color may be greenish yellow or light amber and that not more than 3 percent, by weight, of all...

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

    PubMed Central

    Sadowski, Eva-Maria; Schmidt, Alexander R.

    2015-01-01

    Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers), to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR) spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene) resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age. PMID:26157631

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

    PubMed

    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.

  18. The semi-aquatic pondweed bugs of a Cretaceous swamp

    PubMed Central

    Sánchez-García, Alba; Nel, André; Arillo, Antonio

    2017-01-01

    Pondweed bugs (Hemiptera: Mesoveliidae), considered a sister group to all other Gerromorpha, are exceedingly rare as fossils. Therefore, each new discovery of a fossil mesoveliid is of high interest, giving new insight into their early evolutionary history and diversity and enabling the testing of their proposed relationships. Here, we report the discovery of new mesoveliid material from Spanish Lower Cretaceous (Albian) amber, which is the first such find in Spanish amber. To date, fossil records of this family only include one species from French Kimmeridgian as compression fossils, two species in French amber (Albian-Cenomanian boundary), and one in Dominican amber (Miocene). The discovery of two males and one female described and figured as Glaesivelia pulcherrima Sánchez-García & Solórzano Kraemer gen. et sp. n., and a single female described and figured as Iberovelia quisquilia Sánchez-García & Nel, gen. et sp. n., reveals novel combinations of traits related to some genera currently in the subfamily Mesoveliinae. Brief comments about challenges facing the study of fossil mesoveliids are provided, showing the necessity for a revision of the existing phylogenetic hypotheses. Some of the specimens were studied using infrared microscopy, a promising alternative to the systematic study of organisms preserved in amber that cannot be clearly visualised. The new taxa significantly expand the fossil record of the family and shed new light on its palaeoecology. The fossils indicate that Mesoveliidae were certainly diverse by the Cretaceous and that numerous tiny cryptic species living in humid terrestrial to marginal aquatic habitats remain to be discovered. Furthermore, the finding of several specimens as syninclusions suggests aggregative behaviour, thereby representing the earliest documented evidence of such ethology. PMID:28890856

  19. The semi-aquatic pondweed bugs of a Cretaceous swamp.

    PubMed

    Sánchez-García, Alba; Nel, André; Arillo, Antonio; Solórzano Kraemer, Mónica M

    2017-01-01

    Pondweed bugs (Hemiptera: Mesoveliidae), considered a sister group to all other Gerromorpha, are exceedingly rare as fossils. Therefore, each new discovery of a fossil mesoveliid is of high interest, giving new insight into their early evolutionary history and diversity and enabling the testing of their proposed relationships. Here, we report the discovery of new mesoveliid material from Spanish Lower Cretaceous (Albian) amber, which is the first such find in Spanish amber. To date, fossil records of this family only include one species from French Kimmeridgian as compression fossils, two species in French amber (Albian-Cenomanian boundary), and one in Dominican amber (Miocene). The discovery of two males and one female described and figured as Glaesivelia pulcherrima Sánchez-García & Solórzano Kraemer gen. et sp. n., and a single female described and figured as Iberovelia quisquilia Sánchez-García & Nel, gen. et sp. n., reveals novel combinations of traits related to some genera currently in the subfamily Mesoveliinae. Brief comments about challenges facing the study of fossil mesoveliids are provided, showing the necessity for a revision of the existing phylogenetic hypotheses. Some of the specimens were studied using infrared microscopy, a promising alternative to the systematic study of organisms preserved in amber that cannot be clearly visualised. The new taxa significantly expand the fossil record of the family and shed new light on its palaeoecology. The fossils indicate that Mesoveliidae were certainly diverse by the Cretaceous and that numerous tiny cryptic species living in humid terrestrial to marginal aquatic habitats remain to be discovered. Furthermore, the finding of several specimens as syninclusions suggests aggregative behaviour, thereby representing the earliest documented evidence of such ethology.

  20. In vitro incorporation of nonnatural amino acids into protein using tRNACys-derived opal, ochre, and amber suppressor tRNAs

    PubMed Central

    Gubbens, Jacob; Kim, Soo Jung; Yang, Zhongying; Johnson, Arthur E.; Skach, William R.

    2010-01-01

    Amber suppressor tRNAs are widely used to incorporate nonnatural amino acids into proteins to serve as probes of structure, environment, and function. The utility of this approach would be greatly enhanced if multiple probes could be simultaneously incorporated at different locations in the same protein without other modifications. Toward this end, we have developed amber, opal, and ochre suppressor tRNAs derived from Escherichia coli, and yeast tRNACys that incorporate a chemically modified cysteine residue with high selectivity at the cognate UAG, UGA, and UAA stop codons in an in vitro translation system. These synthetic tRNAs were aminoacylated in vitro, and the labile aminoacyl bond was stabilized by covalently attaching a fluorescent dye to the cysteine sulfhydryl group. Readthrough efficiency (amber > opal > ochre) was substantially improved by eRF1/eRF3 inhibition with an RNA aptamer, thus overcoming an intrinsic hierarchy in stop codon selection that limits UGA and UAA termination suppression in higher eukaryotic translation systems. This approach now allows concurrent incorporation of two different modified amino acids at amber and opal codons with a combined apparent readthrough efficiency of up to 25% when compared with the parent protein lacking a stop codon. As such, it significantly expands the possibilities for incorporating nonnative amino acids for protein structure/function studies. PMID:20581130

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Anderson, K.B.; LePage, B.A.

    1995-06-01

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

  2. 78 FR 4446 - Exempt Chemical Preparations Under the Controlled Substances Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-22

    ... Laboratories Liquichek Immunoassay Plus Amber Vial: 10 mL; Box: 12/22/2011 Control Levels 1, 2, and 3. 12 vials. Bio-Rad Laboratories Liquichek Immunoassay Plus Amber Vial: 10 mL; Box: 12/22/2011 Control Trilevel. 12 vials. Bio-Rad Laboratories Liquichek Immunoassay Plus Amber Vial: 5 mL; Box: 3 12/22/2011 Control...

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

    PubMed

    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.

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

    PubMed Central

    Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew

    2013-01-01

    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. PMID:24185531

  5. The price for reduced light toxicity: Do endoilluminator spectral filters decrease color contrast during Brilliant Blue G-assisted chromovitrectomy?

    PubMed

    Henrich, Paul B; Valmaggia, Christophe; Lang, Corina; Cattin, Philippe C

    2014-03-01

    Vitreoretinal surgeons have been slow to adopt the use of spectral filters for endoillumination to reduce retinal light toxicity. This study shows that spectral filters can be used without a loss in color contrast during brilliant blue G chromovitrectomy. To evaluate the influence of intra operative spectral light filters on perceivable contrast during Brilliant Blue G chromovitrectomy, a prospective, observational clinical study was carried out on 59 consecutive Brilliant Blue G chromovitrectomy interventions in 59 patients admitted for macular holes, macular pucker or vitreomacular traction syndromes. Subsequent to peeling of the internal limiting membrane, six different illumination modes were enabled consecutively: mercury vapor, mercury vapor/xenon, and xenon followed by xenon combined with an amber, green or yellow spectral filter. Main outcome measure was the chromaticity spread between stained internal limiting membrane and unstained retina as a measure for the color contrast perceived by the human eye. Mean chromaticity scores were similar for all light sources: mercury vapor 7.97, mercury vapor/xenon 7.96 (p = 0.96), and xenon 7.41 (p = 0.55). Compared to xenon, the additional use of endoillumination spectral filters did not change contrast recognizability: Chromaticity scores were 9.38 for the amber filter (p = 0.13), 6.63 for the green and 7.02 for the yellow filter (p = 0.37 and 0.64, respectively). When comparing the different filters head-to-head, the amber filter was superior to the green filter (p = 0.03), while the yellow was intermediate and not significantly different from either the amber (p = 0.08) or the green filter (p = 0.51). Color contrast perceptibility during Brilliant Blue G assisted chromovitrectomy is similar with mercury vapor, mercury vapor/xenon or xenon light sources. Spectral filters do not decrease color contrast recognizability. Head-to-head comparison shows a significant advantage for the amber over the green filter with respect to contrast generation, the yellow filter is intermediate. As spectral filters are known to greatly reduce retinal light toxicity, we suggest donor eye studies to validate whether the amber filter should be generally recommended for Brilliant Blue G chromovitrectomy.

  6. The termites of Early Eocene Cambay amber, with the earliest record of the Termitidae (Isoptera)

    PubMed Central

    Engel, Michael S.; Grimaldi, David A.; Nascimbene, Paul C.; Singh, Hukam

    2011-01-01

    Abstract The fauna of termites (Isoptera) preserved in Early Eocene amber from the Cambay Basin (Gujarat, India) are described and figured. Three new genera and four new species are recognized, all of them Neoisoptera – Parastylotermes krishnai Engel & Grimaldi, sp. n. (Stylotermitidae); Prostylotermes kamboja Engel & Grimaldi, gen. et sp. n. (Stylotermitidae?); Zophotermes Engel, gen. n., with Zophotermes ashoki Engel & Singh, sp. n. (Rhinotermitidae: Prorhinotermitinae); and Nanotermes isaacae Engel & Grimaldi, gen. et sp. n. (Termitidae: Termitinae?). Together these species represent the earliest Tertiary records of the Neoisoptera and the oldest definitive record of Termitidae, a family that comprises >75% of the living species of Isoptera. Interestingly, the affinities of the Cambay amber termites are with largely Laurasian lineages, in this regard paralleling relationships seen between the fauna of bees and some flies. Diversity of Neoisoptera in Indian amber may reflect origin of the amber deposit in Dipterocarpaceae forests formed at or near the paleoequator. PMID:22287892

  7. Lipid14: The Amber Lipid Force Field

    PubMed Central

    2015-01-01

    The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields. PMID:24803855

  8. First demonstration of green and amber LED-pumped Nd:YAG laser

    NASA Astrophysics Data System (ADS)

    Tarkashvand, M.; Farahbod, A. H.; Hashemizadeh, S. A.

    2018-05-01

    For the first time, to the best of our knowledge, a green (520 nm) and amber (592 nm) light emitting diode-pumped Nd:YAG laser is reported. The laser oscillator is a stable semi-planar resonator with a total length of 140 mm. The green (amber) light emitting diode-pumped laser produced a 107 (52) µJ laser energy, at 2.6 (0.7) J electrical pump energy. The oscillator operated at a low repetition rate (about 0.1 Hz) in free-running mode, where the laser spikes were initiated about 210–280 µs after the leading edge of the pump pulse. Moreover, the transverse mode profiles of the resonator, pump absorption efficiency, and optical gain have been studied in some detail.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  11. Suppression of Murine Retrovirus Polypeptide Termination: Effect of Amber Suppressor tRNA on the Cell-Free Translation of Rauscher Murine Leukemia Virus, Moloney Murine Leukemia Virus, and Moloney Murine Sarcoma Virus 124 RNA

    PubMed Central

    Murphy, Edwin C.; Wills, Norma; Arlinghaus, Ralph B.

    1980-01-01

    The effect of suppressor tRNA's on the cell-free translation of several leukemia and sarcoma virus RNAs was examined. Yeast amber suppressor tRNA (amber tRNA) enhanced the synthesis of the Rauscher murine leukemia virus and clone 1 Moloney murine leukemia virus Pr200gag-pol polypeptides by 10- to 45-fold, but at the same time depressed the synthesis of Rauscher murine leukemia virus Pr65gag and Moloney murine leukemia virus Pr63gag. Under suppressor-minus conditions, Moloney murine leukemia virus Pr70gag was present as a closely spaced doublet. Amber tRNA stimulated the synthesis of the “upper” Moloney murine leukemia virus Pr70gag polypeptide. Yeast ochre suppressor tRNA appeared to be ineffective. Quantitative analyses of the kinetics of viral precursor polypeptide accumulation in the presence of amber tRNA showed that during linear protein synthesis, the increase in accumulated Moloney murine leukemia virus Pr200gag-pol coincided closely with the molar loss of Pr63gag. Enhancement of Pr200gag-pol and Pr70gag by amber tRNA persisted in the presence of pactamycin, a drug which blocks the initiation of protein synthesis, thus arguing for the addition of amino acids to the C terminus of Pr63gag as the mechanism behind the amber tRNA effect. Moloney murine sarcoma virus 124 30S RNA was translated into four major polypeptides, Pr63gag, P42, P38, and P23. In the presence of amber tRNA, a new polypeptide, Pr67gag, appeared, whereas Pr63gag synthesis was decreased. Quantitative estimates indicated that for every 1 mol of Pr67gag which appeared, 1 mol of Pr63gag was lost. Images PMID:7373716

  12. The Great Cometary Show

    NASA Astrophysics Data System (ADS)

    2007-01-01

    The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns the enigmatic object Eta Carinae. Using AMBER with its high spatial and spectral resolution, it was possible to zoom into the very heart of this very massive star. In this innermost region, the observations are dominated by the extremely dense stellar wind that totally obscures the underlying central star. The AMBER observations show that this dense stellar wind is not spherically symmetric, but exhibits a clearly elongated structure. Overall, the AMBER observations confirm that the extremely high mass loss of Eta Carinae's massive central star is non-spherical and much stronger along the poles than in the equatorial plane. This is in agreement with theoretical models that predict such an enhanced polar mass-loss in the case of rapidly rotating stars. ESO PR Photo 06c/07 ESO PR Photo 06c/07 RS Ophiuchi in Outburst Several papers from this special feature focus on the later stages in a star's life. One looks at the binary system Gamma 2 Velorum, which contains the closest example of a star known as a Wolf-Rayet. A single AMBER observation allowed the astronomers to separate the spectra of the two components, offering new insights in the modeling of Wolf-Rayet stars, but made it also possible to measure the separation between the two stars. This led to a new determination of the distance of the system, showing that previous estimates were incorrect. The observations also revealed information on the region where the winds from the two stars collide. The famous binary system RS Ophiuchi, an example of a recurrent nova, was observed just 5 days after it was discovered to be in outburst on 12 February 2006, an event that has been expected for 21 years. AMBER was able to detect the extension of the expanding nova emission. These observations show a complex geometry and kinematics, far from the simple interpretation of a spherical fireball in extension. AMBER has detected a high velocity jet probably perpendicular to the orbital plane of the binary system, and allowed a precise and careful study of the wind and the shockwave coming from the nova. The stream of results from the VLTI and AMBER is no doubt going to increase in the coming years with the availability of new functionalities. "In addition to the 8.2-m Unit Telescopes, the VLTI can also combine the light from up to 4 movable 1.8-m Auxiliary Telescopes. AMBER fed by three of these AT's will be offered to the user community as of April this year, and from October we will also make FINITO available," said Melnick. "This 'fringe-tracking' device allows us to stabilise changes in the atmospheric conditions and thus to substantially improve the efficiency of the observations. By effectively 'freezing' the interferometric fringes, FINITO allows astronomers to significantly increase the exposure times." The Astronomy & Astrophysics special feature (volume 464 - March II 2007) on AMBER first results includes 11 articles. They are freely available on the A&A web site.

  13. Residue-Specific α-Helix Propensities from Molecular Simulation

    PubMed Central

    Best, Robert B.; de Sancho, David; Mittal, Jeetain

    2012-01-01

    Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w and Amber ff99SB∗. Encouragingly, we find that the overall helix propensity of many residues is captured well by both energy functions, with Amber ff99SB∗ being more accurate. Nonetheless, there are some residues that deviate considerably from experiment, which can be attributed to two aspects of the energy function: i), variations of the charge model used to determine the atomic partial charges, with residues whose backbone charges differ most from alanine tending to have the largest error; ii), side-chain torsion potentials, as illustrated by the effect of modifications to the torsion angles of I, L, D, N. We find that constrained refitting of residue charges for charged residues in Amber ff99SB∗ significantly improves their helix propensity. The resulting parameters should more faithfully reproduce helix propensities in simulations of protein folding and disordered proteins. PMID:22455930

  14. The Sky Through Three Giant Eyes

    NASA Astrophysics Data System (ADS)

    2007-02-01

    AMBER Instrument on VLT Delivers a Wealth of Results The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns the enigmatic object Eta Carinae. Using AMBER with its high spatial and spectral resolution, it was possible to zoom into the very heart of this very massive star. In this innermost region, the observations are dominated by the extremely dense stellar wind that totally obscures the underlying central star. The AMBER observations show that this dense stellar wind is not spherically symmetric, but exhibits a clearly elongated structure. Overall, the AMBER observations confirm that the extremely high mass loss of Eta Carinae's massive central star is non-spherical and much stronger along the poles than in the equatorial plane. This is in agreement with theoretical models that predict such an enhanced polar mass-loss in the case of rapidly rotating stars. ESO PR Photo 06c/07 ESO PR Photo 06c/07 RS Ophiuchi in Outburst Several papers from this special feature focus on the later stages in a star's life. One looks at the binary system Gamma 2 Velorum, which contains the closest example of a star known as a Wolf-Rayet. A single AMBER observation allowed the astronomers to separate the spectra of the two components, offering new insights in the modeling of Wolf-Rayet stars, but made it also possible to measure the separation between the two stars. This led to a new determination of the distance of the system, showing that previous estimates were incorrect. The observations also revealed information on the region where the winds from the two stars collide. The famous binary system RS Ophiuchi, an example of a recurrent nova, was observed just 5 days after it was discovered to be in outburst on 12 February 2006, an event that has been expected for 21 years. AMBER was able to detect the extension of the expanding nova emission. These observations show a complex geometry and kinematics, far from the simple interpretation of a spherical fireball in extension. AMBER has detected a high velocity jet probably perpendicular to the orbital plane of the binary system, and allowed a precise and careful study of the wind and the shockwave coming from the nova. The stream of results from the VLTI and AMBER is no doubt going to increase in the coming years with the availability of new functionalities. "In addition to the 8.2-m Unit Telescopes, the VLTI can also combine the light from up to 4 movable 1.8-m Auxiliary Telescopes. AMBER fed by three of these AT's will be offered to the user community as of April this year, and from October we will also make FINITO available," said Melnick. "This 'fringe-tracking' device allows us to stabilise changes in the atmospheric conditions and thus to substantially improve the efficiency of the observations. By effectively 'freezing' the interferometric fringes, FINITO allows astronomers to significantly increase the exposure times." The Astronomy & Astrophysics special feature (volume 464 - March II 2007) on AMBER first results includes 11 articles. They are freely available on the A&A web site. More Information The AMBER consortium, led by Romain Petrov (Nice, France), includes researchers from the Laboratoire d'Astrophysique de Grenoble (France), Laboratoire d'Astrophysique Universitaire de Nice (France), Max-Planck Institut für Radioastronomie (Bonn, Germany), INAF-Osservatorio Astrofisico di Arcetri (Italy), and the Observatoire de la Côte d'Azur (Nice, France). In March 2004, the first on-line tests of AMBER (Astronomical Multiple BEam Recombiner) were completed, when astronomers combined the two beams of light from the southern star Theta Centauri from two test 40-cm aperture telescopes (ESO 07/04). It was later used to combine light from two, then three Unit Telescopes of ESO's VLT and light from the Auxiliary Telescopes. AMBER is part of the VLT Interferometer (VLTI) and completes the planned set of first-generation instruments for this facility. It continues the success story of the interferometric mode of the VLT, following the unique initial scientific results obtained by the VINCI and MIDI instruments, the installation of the four MACAO adaptive optics systems and the recent arrival of the last of the four 1.8-m Auxiliary Telescopes at Paranal. The principle of the interferometric technique is to combine the light collected by two or more telescopes. The greater the distance between the telescopes, the more details one can detect. For the VLTI, this distance can be up to 200 metres, providing observers with milli-arcsecond spatial resolution. With such a high spatial resolution, one would be able to distinguish between the headlights of a car located on the Moon. In addition, AMBER also provides astronomers with spectroscopic measurements, allowing the structure and the physics of the source to be constrained by comparing the measures at different wavelengths. AMBER combines the light beams from three telescopes - this is a world first for large telescopes such as the VLT. The ability to combine three beams, rather than just two as in a conventional interferometer, provides a substantial increase in the efficiency of observations, permitting astronomers to obtain three baselines simultaneously instead of one. The combination of these three baselines also permits the computation of the so-called closure phase, an important mathematical quantity that can be used in imaging applications. The AMBER instrument is mounted on a 4.2 x 1.5-m precision optical table, placed in the VLT Interferometric Laboratory at the top of the Paranal mountain. The total shipping weight of the instrument and its extensive associated electronics was almost 4 tons. Two of the results discussed here were already presented as ESO press releases in ESO 29/05 and 35/06.

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

    PubMed

    Poinar, George

    2016-09-01

    A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from <100 years to 130 million years. The amino acids present in 40 to 130 million year old amber-entombed insects resemble those in a modern fly and are probably the most ancient, unaltered amino acids found so far on Earth. In comparison to other geochemical environments on the surface of the Earth, the amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

  18. Structural changes in amber due to uranium mineralization.

    PubMed

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

    2016-07-01

    The presence of uranium, with a bulk mass fraction of about 1.5 wt% and radiolytic alterations are a feature of Cenomanian amber from Křižany, at the northeastern edge of the North Bohemian Cretaceous uranium ore district. Pores and microcracks in the amber were filled with a mineral admixture, mainly in the form of Zr-Y-REE enriched uraninite. As a result of radiolytic alterations due to the presence of uranium, structural changes were observed in the Křižany amber in comparison with a reference amber from Nové Strašecí in central Bohemia; this was of similar age and botanical origin but did not contain elevated levels of uranium. Structural changes involved an increase in aromaticity due to dehydroaromatization of aliphatic cyclic hydrocarbons, loss of oxygen functional groups, an increase in the degree of polymerization, crosslinking of CC bonds, formation of a three-dimensional hydrocarbon network in the bulk organic matrix, and carbonization of the organic matrix around the uraninite infill. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Short Blue Light Pulses (30 Min) in the Morning Support a Sleep-Advancing Protocol in a Home Setting.

    PubMed

    Geerdink, Moniek; Walbeek, Thijs J; Beersma, Domien G M; Hommes, Vanja; Gordijn, Marijke C M

    2016-10-01

    Many people in our modern civilized society sleep later on free days compared to work days. This discrepancy in sleep timing will lead to so-called 'social jetlag' on work days with negative consequences for performance and health. Light therapy in the morning is often proposed as the most effective method to advance the circadian rhythm and sleep phase. However, most studies focus on direct effects on the circadian system and not on posttreatment effects on sleep phase and sleep integrity. In this placebo-controlled home study we investigated if blue light, rather than amber light therapy, can phase shift the sleep phase along with the circadian rhythm with preservation of sleep integrity and performance. We selected 42 participants who suffered from 'social jetlag' on workdays. Participants were randomly assigned to either high-intensity blue light exposure or amber light exposure (placebo) with similar photopic illuminance. The protocol consisted of 14 baseline days without sleep restrictions, 9 treatment days with either 30-min blue light pulses or 30-min amber light pulses in the morning along with a sleep advancing scheme and 7 posttreatment days without sleep restrictions. Melatonin samples were taken at days 1, 7, 14 (baseline), day 23 (effect treatment), and day 30 (posttreatment). Light exposure was recorded continuously. Sleep was monitored through actigraphy. Performance was measured with a reaction time task. As expected, the phase advance of the melatonin rhythm from day 14 to day 23 was significantly larger in the blue light exposure group, compared to the amber light group (84 min ± 51 (SD) and 48 min ± 47 (SD) respectively; t36 = 2.23, p < 0.05). Wake-up time during the posttreatment days was slightly earlier compared to baseline in the blue light group compared to slightly later in the amber light group (-21 min ± 33 (SD) and +12 min ± 33 (SD) respectively; F1,35 = 9.20, p < 0.01). The number of sleep bouts was significantly higher in the amber light group compared to the blue light group during sleep in the treatment period (F1,32 = 4.40, p < 0.05). Performance was significantly worse compared to baseline at all times during (F1,13 = 10.1, p < 0.01) and after amber light treatment (F1,13 = 17.1, p < 0.01), while only in the morning during posttreatment in the blue light condition (F1,10 = 9.8, p < 0.05). The data support the conclusion that blue light was able to compensate for the sleep integrity reduction and to a large extent for the performance decrement that was observed in the amber light condition, both probably as a consequence of the advancing sleep schedule. This study shows that blue light therapy in the morning, applied in a home setting, supports a sleep advancing protocol by phase advancing the circadian rhythm as well as sleep timing. © 2016 The Author(s).

  20. [Genetic study of bacteriophage phi81. I. Isolation, study of complementation and preliminary mapping of amber-mutants of bacteriophage phi81].

    PubMed

    Sineokiĭ, S P; Pogosov, V Z; Iankovskiĭ, N K; Krylov, V N

    1976-01-01

    123 Amber mutants of lambdoid bacteriophage phi81 are isolated and distributed into 19 complementation groups. Deletion mapping made possible to locate 5 gene groups on the genetic map of bacteriophage phi81 and to determine a region of possible location of mm' sticky ends on the prophage genetic map. A gene of phage phi81 is localized, which controls the adsorption specificity, and which functional similarity to a respective gene of phage phi80 is demonstrated.

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

    PubMed

    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.

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

    PubMed

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

    2008-01-01

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

  3. Recent results from the SIMECA code and VLTI observations

    NASA Astrophysics Data System (ADS)

    Meilland, A.; Stee, Ph.

    We present recent results on active hot stars using the first VLTI/MIDI and VLTI/AMBER observations, and the SIMECA code developed by Stee (1994). α Arae was the first classical Be star observed with MIDI (June 2003) and AMBER (February 2005). The size of its circumstellar envelope was measured and thanks to the spectrally-resolved interferometric AMBER observations, we were able, for the first time to evidence the Keplerian rotation of the circumstellar disc. MWC 297 is one of the brightest Herbig Be star, and it was then observed during the first commissioning run of AMBER in May 2004. The data obtained were good enough to allow us to infer the accretion disc extension, as well as to put strong constraints on the stellar wind geometry and kinematics.

  4. Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field.

    PubMed

    Stachura, Slawomir S; Malajczuk, Chris J; Mancera, Ricardo L

    2018-06-25

    Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields. Graphical abstract Hydration structure within hydrogen-bonding distance around a DMSOmolecule.

  5. Method for the preparation of photochromic insulating crystals

    DOEpatents

    Abraham, Marvin M.; Boldu, Jose L.; Chen, Yok; Orera, Victor M.

    1986-01-01

    A method for preparing reversible-photochromic magnesium oxide (MgO) crystals. Single crystals of MgO doped with both lithium (Li) and nickel (Ni) are grown by a conventional arc fusion method. The as-grown crystals are characterized by an amber coloration. The crystals lose the amber coloration and become photochromic when they are thermochemically reduced by heating at temperatures greater than 1000.degree. K. in a hydrogen atmosphere. Alternate irradiation with UV and visible light result in rejuvenation and bleaching of the amber coloration, respectively.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging. Electronic supplementary information (ESI) available: Details on the estimations of evaporation rates and limits of detection, ESI figures and author contributions. See DOI: 10.1039/c6nr00537c

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  11. Method for the preparation of photochromic insulating crystals

    DOEpatents

    Abraham, M.M.; Boldu, J.L.; Chen, Y.; Orera, V.M.

    1984-09-28

    A method for preparing reversible-photochromic magnesium oxide (MgO) crystals is disclosed. Single crystals of MgO doped with both lithium (Li) and nickel (Ni) are grown by a conventional arc fusion method. The as-grown crystals are characterized by an amber coloration. The crystals lose the amber coloration and become photochromic when they are thermochemically reduced by heating at temperatures greater then 1000/sup 0/K in a hydrogen atmosphere. Alternate irradiation with uv and visible light result in rejuvenation and bleaching of the amber coloration, respectively.

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

    DTIC Science & Technology

    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

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

    PubMed

    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.

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

    PubMed

    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.

  15. AMBER instrument control software

    NASA Astrophysics Data System (ADS)

    Le Coarer, Etienne P.; Zins, Gerard; Gluck, Laurence; Duvert, Gilles; Driebe, Thomas; Ohnaka, Keiichi; Heininger, Matthias; Connot, Claus; Behrend, Jan; Dugue, Michel; Clausse, Jean Michel; Millour, Florentin

    2004-09-01

    AMBER (Astronomical Multiple BEam Recombiner) is a 3 aperture interferometric recombiner operating between 1 and 2.5 um, for the Very Large Telescope Interferometer (VLTI). The control software of the instrument, based on the VLT Common Software, has been written to comply with specific features of the AMBER hardware, such as the Infrared detector read out modes or piezo stage drivers, as well as with the very specific operation modes of an interferomtric instrument. In this respect, the AMBER control software was designed to insure that all operations, from the preparation of the observations to the control/command of the instrument during the observations, would be kept as simple as possible for the users and operators, opening the use of an interferometric instrument to the largest community of astronomers. Peculiar attention was given to internal checks and calibration procedures both to evaluate data quality in real time, and improve the successes of long term UV plane coverage observations.

  16. Blind life in the Baltic amber forests: description of an eyeless species of the ground beetle genus Trechus Clairville, 1806 (Coleoptera: Carabidae: Trechini).

    PubMed

    Schmidt, Joachim; Hoffmann, Hannes; Michalik, Peter

    2016-02-22

    The first eyeless beetle known from Baltic amber, Trechus eoanophthalmus sp. n., is described and imaged using light microscopy and X-ray micro-computed tomography. Based on external characters, the new species is most similar to species of the Palaearctic Trechus sensu stricto clade and seems to be closely related to the Baltic amber fossil T. balticus Schmidt & Faille, 2015. Due to the poor conservation of the internal parts of the body, no information on the genital characters can be provided. Therefore, the systematic position of this fossil within the megadiverse genus Trechus remains dubious. The occurrence of the blind and flightless T. eoanophthalmus sp. n. in the Baltic amber forests supports a previous hypothesis that these forests were located in an area partly characterised by mountainous habitats with temperate climatic conditions.

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

    PubMed

    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.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19570786

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

    PubMed Central

    2012-01-01

    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 health-related fitness including demographic, medical, social cognitive, and environmental variables, (3) the mediators of any observed associations between physical activity, health-related fitness, and health outcomes including biological, functional, and psychosocial, and (4) the moderators of any observed associations including demographic, medical, and biological/disease factors. Taken together, these data will provide a comprehensive inquiry into the outcomes, determinants, mechanisms, and moderators of physical activity and health-related fitness in breast cancer survivors. PMID:23153358

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

    PubMed

    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.

  1. Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

    PubMed

    Kashefolgheta, Sadra; Vila Verde, Ana

    2017-08-09

    We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

  2. How accurately do force fields represent protein side chain ensembles?

    PubMed

    Petrović, Dušan; Wang, Xue; Strodel, Birgit

    2018-05-23

    Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  3. Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 2: Evaluating suppression efficiency

    PubMed Central

    Rodriguez, Erik A.; Lester, Henry A.; Dougherty, Dennis A.

    2007-01-01

    The incorporation of unnatural amino acids into proteins is a valuable tool for addition of biophysical probes, bio-orthogonal functionalities, and photoreactive cross-linking agents, although these approaches often require quantities of protein that are difficult to access with chemically aminoacylated tRNAs. THG73 is an amber suppressor tRNA that has been used extensively, incorporating over 100 residues in 20 proteins. In vitro studies have shown that the Escherichia coli Asn amber suppressor (ENAS) suppresses better than THG73. However, we report here that ENAS suppresses with <26% of the efficiency of THG73 in Xenopus oocytes. We then tested the newly developed Tetrahymena thermophila Gln amber suppressor (TQAS) tRNA library, which contains mutations in the second to fourth positions of the acceptor stem. The acceptor stem mutations have no adverse effect on suppression efficiency and, in fact, can increase the suppression efficiency. Combining mutations causes an averaging of suppression efficiency, and increased suppression efficiency does not correlate with increased ΔG of the acceptor stem. We created a T. thermophila opal suppressor, TQOpS′, which shows ∼50% suppression efficiency relative to THG73. The TQAS tRNA library, composed of functional suppressor tRNAs, has been created and will allow for screening in eukaryotic cells, where rapid analysis of large libraries is not feasible. PMID:17698637

  4. Effect of polarization on the stability of a helix dimer

    NASA Astrophysics Data System (ADS)

    Wang, Xing Y.; Zhang, John Z. H.

    2011-01-01

    Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.

  5. Comparison of imaging characteristics of multiple-beam equalization and storage phosphor direct digitizer radiographic systems

    NASA Astrophysics Data System (ADS)

    Sankaran, A.; Chuang, Keh-Shih; Yonekawa, Hisashi; Huang, H. K.

    1992-06-01

    The imaging characteristics of two chest radiographic equipment, Advanced Multiple Beam Equalization Radiography (AMBER) and Konica Direct Digitizer [using a storage phosphor (SP) plate] systems have been compared. The variables affecting image quality and the computer display/reading systems used are detailed. Utilizing specially designed wedge, geometric, and anthropomorphic phantoms, studies were conducted on: exposure and energy response of detectors; nodule detectability; different exposure techniques; various look- up tables (LUTs), gray scale displays and laser printers. Methods for scatter estimation and reduction were investigated. It is concluded that AMBER with screen-film and equalization techniques provides better nodule detectability than SP plates. However, SP plates have other advantages such as flexibility in the selection of exposure techniques, image processing features, and excellent sensitivity when combined with optimum reader operating modes. The equalization feature of AMBER provides better nodule detectability under the denser regions of the chest. Results of diagnostic accuracy are demonstrated with nodule detectability plots and analysis of images obtained with phantoms.

  6. Interferometric observations of main-sequence stars: fundamental stellar astrophysics, circumstellar matter, and kinematics

    NASA Astrophysics Data System (ADS)

    Bakker, Eric J.; Eiroa, Carlos

    2003-10-01

    With our minds focussed on the direct detection of planets using the space interferometry mission DARWIN/TPF, we have made an attempt to identify how the set of ESO Very Large Telescope Interferometer instruments available now, and in the near future (VINCI, MIDI, AMBER, GENIE, FINITO and PRIMA) could contribute to the DARWIN/TPF precursory science program. In particular related to the identification of a short list of science stars to be observed with DARWIN/TPF. We have identified two research projects which can be viewed as DARWIN/TPF precursory science and can be embarked upon shortly using the available VLTI instruments: (1) the direct measurement of stellar angular diameters of a statistically meaningful sample of main-sequence stars with AMBER; (2) an interferometric study of those main-sequence stars that exhibit an infrared excess with either AMBER or MIDI. On the longer run, VLTI can obviously make a significant impact through the exploitation of the infrared nuller GENIE and the astrometric facility PRIMA.

  7. Seeking carotenoid pigments in amber-preserved fossil feathers.

    PubMed

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

    2014-06-09

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

  8. Seeking carotenoid pigments in amber-preserved fossil feathers

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  9. 7 CFR 51.2282 - Tolerances for color.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... than light amber). Amber 10 percent. 1 See illustration of this term on color chart. ... 7 Agriculture 2 2012-01-01 2012-01-01 false Tolerances for color. 51.2282 Section 51.2282... STANDARDS) United States Standards for Shelled English Walnuts (Juglans Regia) Color Requirements § 51.2282...

  10. 7 CFR 51.2282 - Tolerances for color.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... than light amber). Amber 10 percent. 1 See illustration of this term on color chart. ... 7 Agriculture 2 2011-01-01 2011-01-01 false Tolerances for color. 51.2282 Section 51.2282... STANDARDS) United States Standards for Shelled English Walnuts (Juglans Regia) Color Requirements § 51.2282...

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Where Does Amber Come from?

    ERIC Educational Resources Information Center

    Booth, Bibi

    2005-01-01

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

  14. 78 FR 32081 - Airworthiness Directives; Aircraft Industries a.s. Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    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...

  15. A new species of Diochus from Baltic amber (Coleoptera, Staphylinidae, Diochini)

    PubMed Central

    Chatzimanolis, Stylianos; Engel, Michael S.

    2011-01-01

    Abstract The first fossil of the staphylinine tribe Diochini Casey is described and figured from an inclusion in mid-Eocene (Lutetian) Baltic amber. Diochus electrus sp. n. is distinguished from its congeners and the diversity of rove beetles (Staphylinidae s.l.) is summarized briefly. PMID:22144854

  16. Novel recombinant insulin analogue with flexible C-terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water/acetonitrile solution.

    PubMed

    Borowicz, Piotr; Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elżbieta; Mikiewicz-Syguła, Diana; Błażej-Sosnowska, Sylwia; Bogiel, Monika; Rusek, Dorota; Kurzynoga, Dariusz; Kozerski, Lech

    2011-11-01

    A tertiary structure of recombinant A22(G)-B31(K)-B32(R)-human insulin monomer (insulin GKR) has been characterized by (1)H, (13)C NMR at natural isotopic abundance using NOESY, TOCSY, (1)H/(13)C-GHSQC, and (1)H/(13)C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculations an ensemble of 20 structures of lowest energy was chosen which represents the tertiary structure of studied insulin. Here we present novel insulin with added A22(G) amino acid which interacts with β-turn environment resulting in high flexibility of B chain C-terminus. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Stability of gabapentin in extemporaneously compounded oral suspensions.

    PubMed

    Friciu, Mihaela; Roullin, V Gaëlle; Leclair, Grégoire

    2017-01-01

    This study reports the stability of extemporaneously prepared gabapentin oral suspensions prepared at 100 mg/mL from bulk drug and capsules in either Oral Mix or Oral Mix SF suspending vehicles. Suspensions were packaged in amber plastic bottles and amber plastic syringes at 25°C / 60%RH for up to 90 days. Throughout the study period, the following tests were performed to evaluate the stability of the preparations: organoleptic inspection to detect homogeneity, color or odor changes; pH measurements; and gabapentin assay using a stability-indicating HPLC-UV method. As crystallization was observed at 5°C, storage at this temperature condition is not recommended. All preparations stored at 25°C / 60%RH remained stable for the whole study duration of 90 days.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. 7 CFR 52.1847 - Colors of golden seedless raisins.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... range from yellow or golden to light amber color with a predominating yellow or golden color and that... golden or greenish yellow to light amber wherein the predominating color may be greenish yellow or light... 7 Agriculture 2 2011-01-01 2011-01-01 false Colors of golden seedless raisins. 52.1847 Section 52...

  20. 7 CFR 52.1847 - Colors of golden seedless raisins.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... range from yellow or golden to light amber color with a predominating yellow or golden color and that... golden or greenish yellow to light amber wherein the predominating color may be greenish yellow or light... 7 Agriculture 2 2012-01-01 2012-01-01 false Colors of golden seedless raisins. 52.1847 Section 52...

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

    PubMed

    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.

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

    PubMed Central

    Anderson, Ken B

    2006-01-01

    Upper Cretaceous amber from the Raritan Formation (Sayerville, New Jersey) has been investigated by Pyrolysis-GC-MS and Pyrolysis-GC-matrix isolation FTIR-MS. Results establish the existence of two distinct forms of amber in this deposit. Both forms are Class Ib ambers, but they are unambiguously differentiated on the basis of their (intact) diterpenoid composition. The presence of callitrisate in both forms, and cupraene in samples designated form 1, strongly suggest that both derive from related-but-distinct species within the Cupressaceae. In addition to callitrisate, dehydroabietate and analogous 17-nor-, 16,17-dinor- and 15,16,17-trinor- analogues of these compounds are also observed. The distributions of these products in multiple samples suggest that they are the result of biological emplacement, rather than diagenetic modification of the parent compounds. This indicates that the distributions of diterpenes observed in these samples are representative of the original bioterpenoids and, hence, are useful for chemotaxonomic analyses. PMID:16759406

  3. Snakefly diversity in Early Cretaceous amber from Spain (Neuropterida, Raphidioptera)

    PubMed Central

    la Fuente, Ricardo Pérez-de; Peñalver, Enrique; Delclòs, Xavier; Engel, Michael S.

    2012-01-01

    Abstract The Albian amber from Spain presently harbors the greatest number and diversity of amber adult fossil snakeflies (Raphidioptera). Within Baissopteridae, Baissoptera? cretaceoelectra sp. n., from the Peñacerrada I outcrop (Moraza, Burgos), is the first amber inclusion belonging to the family and described from western Eurasia, thus substantially expanding the paleogeographical range of the family formerly known from the Cretaceous of Brazil and eastern Asia. Within the family Mesoraphidiidae, Necroraphidia arcuata gen. et sp. n. and Amarantoraphidia ventolina gen. et sp. n. are described from the El Soplao outcrop (Rábago, Cantabria), whereas Styporaphidia? hispanica sp. n. and Alavaraphidia imperterrita gen. et sp. n. are describedfrom Peñacerrada I. In addition, three morphospecies are recognized from fragmentary remains. The following combinations are restored: Yanoraphidia gaoi Ren, 1995, stat. rest., Mesoraphidia durlstonensis Jepson, Coram and Jarzembowski, 2009, stat. rest., and Mesoraphidia heteroneura Ren, 1997, stat. rest. The singularity of this rich paleodiversity could be due to the paleogeographic isolation of the Iberian territory and also the prevalence of wildfires during the Cretaceous. PMID:22787417

  4. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

    PubMed

    Mermelstein, Daniel J; Lin, Charles; Nelson, Gard; Kretsch, Rachael; McCammon, J Andrew; Walker, Ross C

    2018-07-15

    Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  5. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

    PubMed

    Salomon-Ferrer, Romelia; Götz, Andreas W; Poole, Duncan; Le Grand, Scott; Walker, Ross C

    2013-09-10

    We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

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

    NASA Astrophysics Data System (ADS)

    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 American sector and weaker in the African sector - why are the occurrence and amplitude of equatorial irregularities stronger in the African sector?

  7. Amber: Using "Tree Tears Turned to Stone" to Teach Biology, Ecology, and More!

    ERIC Educational Resources Information Center

    Clary, Renee M.; Wandersee, James H.

    2009-01-01

    Amber is a fossil by itself, and can also contain plants and animals that lived millions of years ago. Some of these perfectly preserved specimens give scientists a convenient window to past environments, including the biology, ecology, geology, and chemistry of Earth's past. By using an interdisciplinary approach, we can demonstrate to students a…

  8. Story as a Bridge to Transformation: The Way beyond Death in Philip Pullman's "The Amber Spyglass."

    ERIC Educational Resources Information Center

    Lenz, Millicent

    2003-01-01

    Explains that in "The Amber Spyglass," Philip Pullman extends the psychological depth of literature for young readers by presenting in palpable terms a confrontation with death met by the human capacity for dealing creatively, through story, with personal mortality. Contends that Pullman's portrayal of the power of storytelling is placed within…

  9. A new species of the genus Orchesia Latreille (Coleoptera: Melandryidae) from Baltic amber with a key to species described from fossil resins.

    PubMed

    Alekseev, Vitalii I; Bukejs, Andris

    2015-04-17

    Orchesia (Orchestera) canaliculata sp. nov. is described and illustrated from Eocene Baltic amber (Kaliningrad Region, Russia). New fossil records on O. turkini Alekseev & Bukejs and O. rasnitzyni Nikitsky are presented. A key to species of Orchesia Latreille, described from fossil resins, is provided.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    Huber, John T.; Greenwalt, Dale

    2011-01-01

    Abstract Compression fossils of three genera and six species of Mymaridae (Hymenoptera: Chalcidoidea) are described from 46 million year old Kishenehn oil shales in Montana, USA. Two new genera are described: Eoeustochus Huber, gen. n., with two included species, Eoeustochus kishenehn Huber (type species) and Eoeustochus borchersi Huber, sp. n., and Eoanaphes, gen. n., with Eoanaphes stethynioides Huber, sp. n. Three new species of Gonatocerus are also described, Gonatocerus greenwalti Huber, sp. n. , Gonatocerus kootenai Huber, sp. n., and Gonatocerus rasnitsyni Huber, sp. n. Previously described amber fossil genera are discussed and five genera in Baltic amber are tentatively recorded as fossils: Anagroidea, Camptoptera, Dorya, Eustochus, and Mimalaptus. PMID:22259294

  12. Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car Parrinello) molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hammond, Philip S.; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J.; Car, Roberto; Schmitt, Jeffrey D.

    2005-01-01

    A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

  13. Stability of gabapentin in extemporaneously compounded oral suspensions

    PubMed Central

    Friciu, Mihaela; Roullin, V. Gaëlle

    2017-01-01

    This study reports the stability of extemporaneously prepared gabapentin oral suspensions prepared at 100 mg/mL from bulk drug and capsules in either Oral Mix or Oral Mix SF suspending vehicles. Suspensions were packaged in amber plastic bottles and amber plastic syringes at 25°C / 60%RH for up to 90 days. Throughout the study period, the following tests were performed to evaluate the stability of the preparations: organoleptic inspection to detect homogeneity, color or odor changes; pH measurements; and gabapentin assay using a stability-indicating HPLC-UV method. As crystallization was observed at 5°C, storage at this temperature condition is not recommended. All preparations stored at 25°C / 60%RH remained stable for the whole study duration of 90 days. PMID:28414771

  14. A functionally significant SNP in TP53 and breast cancer risk in African-American women.

    PubMed

    Murphy, Maureen E; Liu, Song; Yao, Song; Huo, Dezheng; Liu, Qin; Dolfi, Sonia C; Hirshfield, Kim M; Hong, Chi-Chen; Hu, Qiang; Olshan, Andrew F; Ogundiran, Temidayo O; Adebamowo, Clement; Domchek, Susan M; Nathanson, Katherine L; Nemesure, Barbara; Ambs, Stefan; Blot, William J; Feng, Ye; John, Esther M; Bernstein, Leslie; Zheng, Wei; Hu, Jennifer J; Ziegler, Regina G; Nyante, Sarah; Ingles, Sue A; Press, Michael F; Deming, Sandra L; Rodriguez-Gil, Jorge L; Haiman, Christopher A; Olopade, Olufunmilayo I; Lunetta, Kathryn L; Palmer, Julie R; Ambrosone, Christine B

    2017-01-01

    A coding region polymorphism exists in the TP53 gene (Pro47Ser; rs1800371) in individuals of African descent, which reduces p53 tumor suppressor function in a mouse model. It has been unclear whether this functionally significant polymorphism alters cancer risk in humans. This analysis included 6907 women with breast cancer and 7644 controls from the AMBER, ROOT, and AABC consortia. We used multivariable logistic regression to estimate associations between the TP53 Pro47Ser allele and overall breast cancer risk. Because polymorphisms in TP53 tend to be associated with cancer risk in pre-menopausal women, we also limited our analyses to this population in the AMBER and ROOT consortia, where menopausal status was known, and conducted a fixed effects meta-analysis. In an analysis of all women in the AMBER, ROOT, and AABC consortia, we found no evidence for association of the Pro47Ser variant with breast cancer risk. However, when we restricted our analysis to only pre-menopausal women from the AMBER and ROOT consortia, there was a per allele odds ratio of 1.72 (95% confidence interval 1.08-2.76; p -value = 0.023). Although the Pro47Ser variant was not associated with overall breast cancer risk, it may increase risk among pre-menopausal women of African ancestry. Following up on more studies in human populations may better elucidate the role of this variant in breast cancer etiology. However, because of the low frequency of the polymorphism in women of African ancestry, its impact at a population level may be minimal.

  15. Cretaceous origin of the unique prey-capture apparatus in mega-diverse genus: stem lineage of Steninae rove beetles discovered in Burmese amber

    PubMed Central

    Żyła, Dagmara; Yamamoto, Shûhei; Wolf-Schwenninger, Karin; Solodovnikov, Alexey

    2017-01-01

    Stenus is the largest genus of rove beetles and the second largest among animals. Its evolutionary success was associated with the adhesive labial prey-capture apparatus, a unique apomorphy of that genus. Definite Stenus with prey-capture apparatus are known from the Cenozoic fossils, while the age and early evolution of Steninae was hardly ever hypothesized. Our study of several Cretaceous Burmese amber inclusions revealed a stem lineage of Steninae that possibly possesses the Stenus-like prey-capture apparatus. Phylogenetic analysis of extinct and extant taxa of Steninae and putatively allied subfamilies of Staphylinidae with parsimony and Bayesian approaches resolved the Burmese amber lineage as a member of Steninae. It justified the description of a new extinct stenine genus Festenus with two new species, F. robustus and F. gracilis. The Late Cretaceous age of Festenus suggests an early origin of prey-capture apparatus in Steninae that, perhaps, drove the evolution towards the crown Stenus. Our analysis confirmed the well-established sister relationships between Steninae and Euaesthetinae and resolved Scydmaeninae as their next closest relative, the latter having no stable position in recent phylogenetic studies of rove beetles. Close affiliation of Megalopsidiinae, a subfamily often considered as a sister group to Euaesthetinae + Steninae clade, is rejected. PMID:28397786

  16. 7 CFR 917.459 - California Peach Grade and Size Regulation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Column B maturity guide Angelus I August Dream J August Lady L Autumn Flame J Autumn Gem I Autumn Lady H... Supechfour (Amber Crest) G Super Chief H Super Rich H Sweet Amber J Sweet Blaze J Sweet Crest H Sweet Dream J..., Summer Dragon, Summer Fling, Summer Lady, Summer Sweet, Summer Zee, Sweet Blaze, Sweet Dream, Sweet Henry...

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

    PubMed

    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.

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

    PubMed

    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.

  19. Gas bubbles in fossil amber as possible indicators of the major gas composition of ancient air

    USGS Publications Warehouse

    Berner, R.A.; Landis, G.P.

    1988-01-01

    Gases trapped in Miocene to Upper Cretaceous amber were released by gently crushing the amber under vacuum and were analyzed by quadrupole mass spectrometry. After discounting the possibility that the major gases N2, O2, and CO2 underwent appreciable diffusion and diagenetic exchange with their surroundings or reaction with the amber, it has been concluded that in primary bubbles (gas released during initial breakage) these gases represent mainly original ancient air modified by the aerobic respiration of microorganisms. Values of N2/(CO2+O2) for each time period give consistent results despite varying O2/CO2 ratios that presumably were due to varying degrees of respiration. This allows calculation of original oxygen concentrations, which, on the basis of these preliminary results, appear to have changed from greater than 30 percent O2 during one part ofthe Late Cretaceous (between 75 and 95 million years ago) to 21 percent during the Eocene-Oligocene and for present-day samples, with possibly lower values during the Oligocene-Early Miocene. Variable O2 levels over time in general confirm theoretical isotope-mass balance calculations and suggest that the atmosphere has evolved over Phanerozoic time.

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

    PubMed Central

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

    2010-01-01

    Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

  1. A new fossil soldier beetle (Coleoptera, Cantharidae, Silinae) from Eocene Baltic amber.

    PubMed

    Fanti, Fabrizio; Pankowski, Michael J

    2018-01-09

    A new genus and species of fossil soldier beetle Markus karenae gen. et sp. nov. is described and illustrated from Eocene Baltic amber. Its morphological characteristics place it in the taxonomic position of the subfamily Silinae. It is characterized by a particular lateral pronotal shape with two difform processes, pronotum slightly longer than wide, with a blunt and evident angle near the basal angles, anterior and posterior margins flat and with shallow punctation, and lateral margin strongly granulose and in relief. Furthermore, each of its legs has a claw with one acute tooth at the base, except for the posterior legs where the tooth appears to be blunt. The new taxon is morphologically compared with the other fossil representatives of Silinae from Baltic amber, and with extant Palearctic genera.

  2. The effect on drink sales of removal of unhealthy drinks from display in a self-service café.

    PubMed

    Huse, Oliver; Blake, Miranda R; Brooks, Ruby; Corben, Kirstan; Peeters, Anna

    2016-12-01

    The present study assessed the impact of the retailer-led removal of unhealthy beverages from display at a self-service café within a major health service. While unhealthy beverages remained available from behind the counter upon request, this was not communicated directly to customers. Drinks were categorised based on the state government nutrient profiling system, classifying drinks as 'green' (best choices), 'amber' (choose carefully) and 'red' (limit). Total drink sales (as number of items sold per week) in the café were measured for five weeks. All unhealthy 'red' beverages were removed from display (but were still available for purchase) and the sales of all beverages were measured for another six weeks. We found that, in response to this strategy, the proportion of 'red' drinks sold decreased from 33 % to 10 % of total drink sales. As 'amber' and 'green' drink sales increased in response to this strategy, total retailer sales remained steady. Most consumers appeared to switch to purchasing 'amber' drinks rather than the healthiest option, 'green' drinks. The removal of unhealthy beverages from display can result in consumers making healthier purchases, while not significantly affecting retailers' sales.

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

    PubMed

    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.

  4. The context of transcription start site regions is crucial for transcription of a plant tRNA(Lys)(UUU) gene group both in vitro and in vivo.

    PubMed

    Yukawa, Yasushi; Akama, Kazuhito; Noguchi, Kanta; Komiya, Masaaki; Sugiura, Masahiro

    2013-01-10

    Nuclear tRNA genes are transcribed by RNA polymerase III. The A- and B-boxes located within the transcribed regions are essential promoter elements for nuclear tRNA gene transcription. The Arabidopsis genome contains ten annotated genes encoding identical tRNA(Lys)(UUU) molecules, which are scattered on the five chromosomes. In this study, we prepared ten tDNA constructs including each of the tRNA(Lys)(UUU) coding sequences with their individual 5' and 3' flanking sequences, and assayed tRNA expression using an in vitro RNA polymerase III-dependent transcription system. Transcription levels differed significantly among the ten genes and two of the tRNA genes were transcribed at a very low level, despite possessing A- and B-boxes identical to those of the other tRNA genes. To examine whether the in vitro results were reproducible in vivo, the 5' flanking sequence of an amber suppressor tRNA gene was then replaced with those of the ten tRNA(Lys) genes. An in vivo experiment based on an amber suppressor tRNA that mediates suppression of a premature amber codon in a β-glucuronidase (GUS) reporter gene in plant tissues generated nearly identical results to those obtained in vitro. Analysis of mutated versions of the amber suppressor tRNA gene, which contained base substitutions around the transcription start site (TSS), showed that the context around the transcription start sites is a crucial determinant for transcription of plant tRNA(Lys)(UUU) both in vitro and in vivo. The above transcription regulation by context around TSS differed between tRNA genes and other Pol III-dependent genes. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

    2015-08-06

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna–Matthews–Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbitalmore » (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.« less

  6. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA.

    PubMed

    Karakas, Esra; Taveneau, Cyntia; Bressanelli, Stéphane; Marchi, Massimo; Robert, Bruno; Abel, Stéphane

    2017-01-01

    In this paper, we describe the derivation and the validation of original RESP atomic partial charges for the N, N-dimethyl-dodecylamine oxide (LDAO) surfactant. These charges, designed to be fully compatible with all the AMBER force fields, are at first tested against molecular dynamics simulations of pure LDAO micelles and with a fragment of the lipid kinase PIK4A (DI) modeled with the QUARK molecular modeling server. To model the micelle, we used two distinct AMBER force fields (i.e. Amber99SB and Lipid14) and a variety of starting conditions. We find that the micelle structural properties (such as the shape, size, the LDAO headgroup hydration, and alkyl chain conformation) slightly depend on the force field but not on the starting conditions and more importantly are in good agreement with experiments and previous simulations. We also show that the Lipid14 force field should be used instead of the Amber99SB one to better reproduce the C(sp3)C(sp3)C(sp3)C(sp3) conformation in the surfactant alkyl chain. Concerning the simulations with LDAO-DI protein, we carried out different runs at two NaCl concentrations (i.e. 0 and 300 mM) to mimic, in the latter case, the experimental conditions. We notice a small dependence of the simulation results with the LDAO parameters and the salt concentration. However, we find that in the simulations, three out of four tryptophans of the DI protein are not accessible to water in agreement with our fluorescence spectroscopy experiments reported in the paper.

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

    PubMed

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

    2013-01-01

    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.

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

    PubMed

    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).

  9. The Amber Biomolecular Simulation Programs

    PubMed Central

    CASE, DAVID A.; CHEATHAM, THOMAS E.; DARDEN, TOM; GOHLKE, HOLGER; LUO, RAY; MERZ, KENNETH M.; ONUFRIEV, ALEXEY; SIMMERLING, CARLOS; WANG, BING; WOODS, ROBERT J.

    2006-01-01

    We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. PMID:16200636

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

    PubMed

    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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dunlop, Jason A.; Apanaskevich, Dmitry A.; Lehmann, Jens

    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 Ixodesmore » 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.« less

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

    PubMed Central

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

    2016-01-01

    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. PMID:27731321

  14. Penis morphology in a Burmese amber harvestman

    NASA Astrophysics Data System (ADS)

    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.

  15. The molecular composition of ambers

    USGS Publications Warehouse

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

    1988-01-01

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

  16. Penis morphology in a Burmese amber harvestman.

    PubMed

    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.

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

    PubMed

    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.

  18. Microcomputer Selection Guide for Construction Field Offices. Revision.

    DTIC Science & Technology

    1984-09-01

    the system, and the monitor displays information on a video display screen. Microcomputer systems today are available in a variety of configura- tions...background. White on black monitors report- edly caule more eye fatigue, while amber is reported to cause the least eye fatigue. Reverse video ...The video should be amber or green display with a resolution of at least 640 x 200 dots per in. Additional features of the monitor include an

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

    PubMed

    Zakrzewska, Marta; Giłka, Wojciech

    2015-04-10

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-06-28

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

  2. Computer simulations of interferometric imaging with the VLT Interferometer and the AMBER instrument

    NASA Astrophysics Data System (ADS)

    Bloecker, Thomas; Hofmann, Karl-Heinz; Przygodda, Frank; Weigelt, Gerd

    2000-07-01

    We present computer simulations of interferometric imaging with the VLT interferometer and the AMBER instrument. These simulations include both the astrophysical modeling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector read- out noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r0,object equals 2.4 m, r0,ref. equals 2.5 m), different residual tip- tilt error ((delta) tt,object equals 2% of the Airy disk diameter, (delta) tt,ref. equals 0.1%), and object brightness (Kobject equals 3.5 mag and 11 mag, Kref. equals 3.5 mag). Exemplarily, we focus on stars in late stages of stellar evolution and study one of its key objects, the dusty supergiant IRC + 10420 that is rapidly evolving on human timescales. We show computer simulations of VLTI interferometry of IRC + 10420 with two ATs (wide-field mode, i.e. without fiber optics spatial filters) and discuss whether the visibility accuracy is sufficient to distinguish between different theoretical model predictions.

  3. The VLT Interferometer and its AMBER Instrument: Simulations of Interferometric Imaging in the Wide-Field Mode

    NASA Astrophysics Data System (ADS)

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

    We present computer simulations of interferometric imaging with the VLT interferometer and the AMBER instrument. These simulations include both the astrophysical modelling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector read-out noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r0,object and r0,ref. ranging between 0.9 m and 1.2 m), different residual tip-tilt error (δtt,object and δtt,ref. ranging between 0.1% and 20% of the Airy disk diameter), and object brightness (Kobject=3.5 mag to 13 mag, Kref.=3.5 mag). Exemplarily, we focus on stars in late stages of stellar evolution and study one of its key objects, the dusty supergiant IRC +10 420 that is rapidly evolving on human timescales. We show computer simulations of VLT interferometry of IRC +10 420 with two ATs (wide-field mode, i.e. without fiber optics spatial filters) and discuss whether the visibility accuracy is sufficient to distinguish between different theoretical model predictions.

  4. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions

    PubMed Central

    Zhou, Yanzi; Wang, Shenglong; Li, Yongle; Zhang, Yingkai

    2016-01-01

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

  5. Wearing blue light-blocking glasses in the evening advances circadian rhythms in the patients with delayed sleep phase disorder: An open-label trial.

    PubMed

    Esaki, Yuichi; Kitajima, Tsuyoshi; Ito, Yasuhiro; Koike, Shigefumi; Nakao, Yasumi; Tsuchiya, Akiko; Hirose, Marina; Iwata, Nakao

    2016-01-01

    It has been recently discovered that blue wavelengths form the portion of the visible electromagnetic spectrum that most potently regulates circadian rhythm. We investigated the effect of blue light-blocking glasses in subjects with delayed sleep phase disorder (DSPD). This open-label trial was conducted over 4 consecutive weeks. The DSPD patients were instructed to wear blue light-blocking amber glasses from 21:00 p.m. to bedtime, every evening for 2 weeks. To ascertain the outcome of this intervention, we measured dim light melatonin onset (DLMO) and actigraphic sleep data at baseline and after the treatment. Nine consecutive DSPD patients participated in this study. Most subjects could complete the treatment with the exception of one patient who hoped for changing to drug therapy before the treatment was completed. The patients who used amber lens showed an advance of 78 min in DLMO value, although the change was not statistically significant (p = 0.145). Nevertheless, the sleep onset time measured by actigraph was advanced by 132 min after the treatment (p = 0.034). These data suggest that wearing amber lenses may be an effective and safe intervention for the patients with DSPD. These findings also warrant replication in a larger patient cohort with controlled observations.

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

    DOEpatents

    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.

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

    PubMed Central

    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

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

    PubMed

    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.

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

    PubMed

    Deng, Nan-Jie; Cieplak, Piotr

    2010-02-17

    RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted to be thermodynamically stable in solution. This finding is further supported by separate unrestrained CHARMM27 simulations, in which the UUCG hairpin unfolds spontaneously within 10 ns. The instability of the UUCG hairpin originates from the loop region, and propagates to the stem. The results of this study provide a molecular picture of RNA hairpin unfolding and reveal problems in the force field descriptions for the conformational energy of certain RNA hairpin. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Stability of Extemporaneously Prepared Hydroxychloroquine Sulfate 25-mg/mL Suspensions in Plastic Bottles and Syringes.

    PubMed

    McHenry, Adam R; Wempe, Michael F; Rice, Peter J

    2017-01-01

    This study evaluated the stability of the antimalarial and anti-rheumatic drug hydroxychloroquine sulfate in two commercially available suspension vehicles, Oral Mix and Oral Mix SF (Medisca Pharmaceutique Inc.). Hydroxychloroquine sulfate (25 mg/mL) suspension was prepared, packaged in amber 50-mL polyethylene terephthalate bottles and amber 3-mL syringes, and stored at room temperature or at 4°C. Samples were collected and analyzed over a 16-week period by high-performance liquid chromatography with ultraviolet detection at 340 nm. Approximately 99.8% of the hydroxychloroquine remained at the conclusion of the study, with no observable difference between room temperature and refrigerated storage. Hydroxychloroquine sulfate is stable for at least 90 days in Medisca Oral Mix or Oral Mix SF suspension media at 25°C and 4°C. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

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

    USGS Publications Warehouse

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

    1986-01-01

    Cyclic terpenoids present in the solvent extractable material of fossil woods, ambers and brown coals have been analyzed. The sample series chosen consisted of wood remains preserved in Holocene to Jurassic sediments and a set of of ambers from the Philippines (copalite), Israel, Canada and Dominican Republic. The brown coals selected were from the Fortuna Garsdorf Mine and Miocene formations on Fiji. The fossil wood extracts contained dominant diterpenoid or sesquiterpenoid skeletons, and aromatized species were present at high concentrations, with a major amount of two-ring aromatic compounds. Tricyclic diterpenoids were the predominant compounds in the ambers. Aromatized derivatives were the major components, consisting of one or two aromatic ring species with the abietane and occasionally pimarane skeletons. The saturated structures were comprised primarily of the abietane and pimarane skeletons having from three to five carbon (C1, C2, etc.) substituents. Kaurane and phyllocladane isomers were present in only minor amounts. Bicyclic sesquiterpenoids as saturated and partial or fully aromatized forms were also common in these samples, but only traces of sesterterpenoids and triterpenoid derivatives were found. The brown coal extracts were composed of major amounts of one- and two-ring aromatized terpenoids, with a greater proportion of triterpenoid derivatives than in the case of the woods and ambers. This was especially noticeable for the German coal, where the triterpenoids were predominant. Open C-ring aromatized structures were also present in this coal. Steroid compounds were not detectable, but some hopanes were found as minor components in the German brown coal. An overview of the skeletal structure classes identified in each sample, as well as the general mass spectrometric characteristics of the unknown compounds are included in the present paper. It can be concluded from these structural distributions that aromatization is the main process for the transformation of terrestrial cyclic terpenoids during diagenesis, constituting a general pathway for all terpenoids. ?? 1986 Pergamon Journals Ltd.

  12. Assessment of sample preservation techniques for pharmaceuticals, personal care products, and steroids in surface and drinking water.

    PubMed

    Vanderford, Brett J; Mawhinney, Douglas B; Trenholm, Rebecca A; Zeigler-Holady, Janie C; Snyder, Shane A

    2011-02-01

    Proper collection and preservation techniques are necessary to ensure sample integrity and maintain the stability of analytes until analysis. Data from improperly collected and preserved samples could lead to faulty conclusions and misinterpretation of the occurrence and fate of the compounds being studied. Because contaminants of emerging concern, such as pharmaceuticals and personal care products (PPCPs) and steroids, generally occur in surface and drinking water at ng/L levels, these compounds in particular require such protocols to accurately assess their concentrations. In this study, sample bottle types, residual oxidant quenching agents, preservation agents, and hold times were assessed for 21 PPCPs and steroids in surface water and finished drinking water. Amber glass bottles were found to have the least effect on target analyte concentrations, while high-density polyethylene bottles had the most impact. Ascorbic acid, sodium thiosulfate, and sodium sulfite were determined to be acceptable quenching agents and preservation with sodium azide at 4 °C led to the stability of the most target compounds. A combination of amber glass bottles, ascorbic acid, and sodium azide preserved analyte concentrations for 28 days in the tested matrices when held at 4 °C. Samples without a preservation agent were determined to be stable for all but two of the analytes when stored in amber glass bottles at 4 °C for 72 h. Results suggest that if improper protocols are utilized, reported concentrations of target PPCPs and steroids may be inaccurate.

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

    NASA Astrophysics Data System (ADS)

    Cai, Chen-Yang; Huang, Di-Ying

    2014-10-01

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

  14. Beckerite

    NASA Astrophysics Data System (ADS)

    Beck, Curt W.; Lambert, Joseph B.; Frye, James S.

    1986-11-01

    Beckerite, a minor component of the amber fossil resins of northern Europe, has previously been classified as being mineralogically distinct from common Baltic amber or succinite on the basis of physical properties such as density and chemical properties such as saponification number. We show that beckerite and succinite are spectroscopically identical, according to infrared and carbon-13 nuclear magnetic resonance methods. Following the suggestion of Schubert, we attribute the deviations of beckerite to the presence of low levels of contaminants, such as decomposed wood and insect excrement.

  15. Mitigation of Atmospheric Effects on Imaging Systems

    DTIC Science & Technology

    2004-03-31

    focal length. The imaging system had two cameras: an Electrim camera sensitive in the visible (0.6 µ m) waveband and an Amber QWIP infrared camera...sensitive in the 9–micron region. The Amber QWIP infrared camera had 256x256 pixels, pixel pitch 38 mµ , focal length of 1.8 m, FOV of 5.4 x5.4 mr...each day. Unfortunately, signals from the different read ports of the Electrim camera picked up noise on their way to the digitizer, and this resulted

  16. A new lineage of braconid wasps in Burmese Cenomanian amber (Hymenoptera, Braconidae).

    PubMed

    Engel, Michael S; Huang, Diying; Cai, Chenyang; Alqarni, Abdulaziz S

    2018-01-01

    A new braconid wasp from the Upper Cretaceous (Cenomanian) amber of the Hukawng Valley in Kachin State, Myanmar is described and figured from a unique female. Seneciobracon novalatus Engel & Huang, gen. et sp. n. , is placed in a distinct subfamily, Seneciobraconinae Engel & Huang, subfam. n. , owing to the presence of a unique combination of primitive protorhyssaline-like traits, with an otherwise more derived wing venation. The fossil is discussed in the context of other Cretaceous Braconidae.

  17. A new lineage of braconid wasps in Burmese Cenomanian amber (Hymenoptera, Braconidae)

    PubMed Central

    Engel, Michael S.; Huang, Diying; Cai, Chenyang; Alqarni, Abdulaziz S.

    2018-01-01

    Abstract A new braconid wasp from the Upper Cretaceous (Cenomanian) amber of the Hukawng Valley in Kachin State, Myanmar is described and figured from a unique female. Seneciobracon novalatus Engel & Huang, gen. et sp. n., is placed in a distinct subfamily, Seneciobraconinae Engel & Huang, subfam. n., owing to the presence of a unique combination of primitive protorhyssaline-like traits, with an otherwise more derived wing venation. The fossil is discussed in the context of other Cretaceous Braconidae. PMID:29416397

  18. Structure and aggregation in model tetramethylurea solutions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gupta, Rini; Patey, G. N., E-mail: patey@chem.ubc.ca

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

  19. New Small Polypeptides Associated with DNA-Dependent RNA Polymerase of Escherichia coli after Infection with Bacteriophage T4

    PubMed Central

    Stevens, Audrey

    1972-01-01

    Four new small polypeptides are associated with DNA-dependent RNA polymerase from E. coli after infection with T4 phage. The new polypeptides are easily detected in RNA polymerase from E. coli cells labeled with amino acids after phage infection. Their molecular weights range from 10,000 to 22,000, as detected by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. All four polypeptides are found after infection with either wild-type T4 phage or T4 early amber mutants in genes 44, 42, 47, and 46. None of the polypeptides is labeled significantly before 5 min after infection at 30°. When two maturation-defective amber mutants in gene 55 of T4 phage are used for infection, a polypeptide with a molecular weight of 22,000 is absent. When a maturation-defective amber mutant in gene 33 of T4 phage is used, another small protein is absent. PMID:4551978

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

    PubMed

    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.

  1. Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU)

    PubMed Central

    2013-01-01

    Locked Nucleic Acids (LNAs) are RNA analogues with an O2′-C4′ methylene bridge which locks the sugar into a C3′-endo conformation. This enhances hybridization to DNA and RNA, making LNAs useful in microarrays and potential therapeutics. Here, the LNA, L(CAAU), provides a simplified benchmark for testing the ability of molecular dynamics (MD) to approximate nucleic acid properties. LNA χ torsions and partial charges were parametrized to create AMBER parm99_LNA. The revisions were tested by comparing MD predictions with AMBER parm99 and parm99_LNA against a 200 ms NOESY NMR spectrum of L(CAAU). NMR indicates an A-Form equilibrium ensemble. In 3000 ns simulations starting with an A-form structure, parm99_LNA and parm99 provide 66% and 35% agreement, respectively, with NMR NOE volumes and 3J-couplings. In simulations of L(CAAU) starting with all χ torsions in a syn conformation, only parm99_LNA is able to repair the structure. This implies methods for parametrizing force fields for nucleic acid mimics can reasonably approximate key interactions and that parm99_LNA will improve reliability of MD studies for systems with LNA. A method for approximating χ population distribution on the basis of base to sugar NOEs is also introduced. PMID:24377321

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    Aims: The red giant L2 Pup started a dimming event in 1994, which is considered to be caused by the ejection of dust clouds. We present near-IR aperture-synthesis imaging of L2 Pup achieved by combining data from VLT/NACO and the AMBER instrument of the Very Large Telescope Interferometer (VLTI). Our aim is to spatially resolve the innermost region of the circumstellar environment. Methods: We carried out speckle interferometric observations at 2.27 μm with VLT/NACO and long-baseline interferometric observations with VLTI/AMBER at 2.2-2.35 μm with baselines of 15-81 m. We also extracted an 8.7 μm image from the mid-IR VLTI instrument MIDI. Results: The diffraction-limited image obtained by bispectrum speckle interferometry with NACO with a spatial resolution of 57 mas shows an elongated component. The aperture-synthesis imaging combining the NACO speckle data and AMBER data with a spatial resolution of 5.6 × 7.3 mas further resolves not only this elongated component, but also the central star. The reconstructed image reveals that the elongated component is a nearly edge-on disk with a size of ~180 × 50 mas lying in the E-W direction, and furthermore, that the southern hemisphere of the central star is severely obscured by the equatorial dust lane of the disk. The angular size of the disk is consistent with the distance that the dust clouds that were ejected at the onset of the dimming event should have traveled by the time of our observations, if we assume that the dust clouds moved radially. This implies that the formation of the disk may be responsible for the dimming event. The 8.7 μm image with a spatial resolution of 220 mas extracted from the MIDI data taken in 2004 (seven years before the AMBER and NACO observations) shows an approximately spherical envelope without a signature of the disk. This suggests that the mass loss before the dimming event may have been spherical. Based on AMBER, NACO, and MIDI observations made with the Very Large Telescope and Very Large Telescope Interferometer of the European Southern Observatory. Program ID: 074.D-0075(A), 074.D-0101(A), 074.D-0198(B), 088.D-0150(A/B), and 288.D-5041(A). Appendices are available in electronic form at http://www.aanda.org

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

    PubMed

    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.

  4. Near-infrared interferometry of η Carinae with spectral resolutions of 1 500 and 12 000 using AMBER/VLTI

    NASA Astrophysics Data System (ADS)

    Weigelt, G.; Kraus, S.; Driebe, T.; Petrov, R. G.; Hofmann, K.-H.; Millour, F.; Chesneau, O.; Schertl, D.; Malbet, F.; Hillier, J. D.; Gull, T.; Davidson, K.; Domiciano de Souza, A.; Antonelli, P.; Beckmann, U.; Bresson, Y.; Chelli, A.; Dugué, M.; Duvert, G.; Gennari, S.; Glück, L.; Kern, P.; Lagarde, S.; Le Coarer, E.; Lisi, F.; Perraut, K.; Puget, P.; Rantakyrö, F.; Robbe-Dubois, S.; Roussel, A.; Tatulli, E.; Zins, G.; Accardo, M.; Acke, B.; Agabi, K.; Altariba, E.; Arezki, B.; Aristidi, E.; Baffa, C.; Behrend, J.; Blöcker, T.; Bonhomme, S.; Busoni, S.; Cassaing, F.; Clausse, J.-M.; Colin, J.; Connot, C.; Delboulbé, A.; Feautrier, P.; Ferruzzi, D.; Forveille, T.; Fossat, E.; Foy, R.; Fraix-Burnet, D.; Gallardo, A.; Giani, E.; Gil, C.; Glentzlin, A.; Heiden, M.; Heininger, M.; Hernandez Utrera, O.; Kamm, D.; Kiekebusch, M.; Le Contel, D.; Le Contel, J.-M.; Lesourd, T.; Lopez, B.; Lopez, M.; Magnard, Y.; Marconi, A.; Mars, G.; Martinot-Lagarde, G.; Mathias, P.; Mège, P.; Monin, J.-L.; Mouillet, D.; Mourard, D.; Nussbaum, E.; Ohnaka, K.; Pacheco, J.; Perrier, C.; Rabbia, Y.; Rebattu, S.; Reynaud, F.; Richichi, A.; Robini, A.; Sacchettini, M.; Schöller, M.; Solscheid, W.; Spang, A.; Stee, P.; Stefanini, P.; Tallon, M.; Tallon-Bosc, I.; Tasso, D.; Testi, L.; Vakili, F.; von der Lühe, O.; Valtier, J.-C.; Vannier, M.; Ventura, N.; Weis, K.; Wittkowski, M.

    2007-03-01

    Aims: We present the first NIR spectro-interferometry of the LBV η Carinae. The observations were performed with the AMBER instrument of the ESO Very Large Telescope Interferometer (VLTI) using baselines from 42 to 89 m. The aim of this work is to study the wavelength dependence of η Car's optically thick wind region with a high spatial resolution of 5 mas (11 AU) and high spectral resolution. Methods: The observations were carried out with three 8.2 m Unit Telescopes in the K-band. The raw data are spectrally dispersed interferograms obtained with spectral resolutions of 1500 (MR-K mode) and 12 000 (HR-K mode). The MR-K observations were performed in the wavelength range around both the He I 2.059 μm and the Brγ 2.166 μm emission lines, the HR-K observations only in the Brγ line region. Results: The spectrally dispersed AMBER interferograms allow the investigation of the wavelength dependence of the visibility, differential phase, and closure phase of η Car. In the K-band continuum, a diameter of 4.0±0.2 mas (Gaussian FWHM, fit range 28-89 m baseline length) was measured for η Car's optically thick wind region. If we fit Hillier et al. (2001, ApJ, 553, 837) model visibilities to the observed AMBER visibilities, we obtain 50% encircled-energy diameters of 4.2, 6.5 and 9.6 mas in the 2.17 μm continuum, the He I, and the Brγ emission lines, respectively. In the continuum near the Brγ line, an elongation along a position angle of 120°±15° was found, consistent with previous VINCI/VLTI measurements by van Boekel et al. (2003, A&A, 410, L37). We compare the measured visibilities with predictions of the radiative transfer model of Hillier et al. (2001), finding good agreement. Furthermore, we discuss the detectability of the hypothetical hot binary companion. For the interpretation of the non-zero differential and closure phases measured within the Brγ line, we present a simple geometric model of an inclined, latitude-dependent wind zone. Our observations support theoretical models of anisotropic winds from fast-rotating, luminous hot stars with enhanced high-velocity mass loss near the polar regions. Based on observations collected at the European Southern Observatory, Paranal, Chile, within the AMBER guaranteed time programme 074.A-9025 and the VLTI science demonstration programme 074.A-9024.

  5. Department of Defense Chemical and Biological Defense Programs. Annual Report to Congress 2007

    DTIC Science & Technology

    2007-04-01

    Bio aerosol Detection GREEN CB.37 CB agent Water monitor AMBER CB.42 environmental Fate of agents GREEN CB.45 Self -Detoxifying materials AMBER CB.46...nano-Closure Systems • Self -Detoxifying Surfaces/materials 32 C h a P t e r 2 C he m ic al a nd B io lo gi ca l D ef en se r eq ui re m en ts...resistant, selective permeable materials, and aerosol and vapor-resistant breathable materials. The addition of a self -detoxification component is

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

    PubMed

    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.

  7. A new species of the genus Disogmus Förster (Hymenoptera, Proctotrupoidea, Proctotrupidae) from the Eocene Rovno amber

    PubMed Central

    Kolyada, V.; Perkovsky, E.

    2011-01-01

    Abstract Disogmus rasnitsyni Kolyada & Perkovsky, sp. n. is described from a fossil inclusion of Late Eocene amber (Ukraine). The new species is most similar to Disogmus basalis (Thomson, 1857), in particular, in the shape of the tyloids and the general shortening of the segments of antennae, but distinctly differs from it and the other species of the genus by having tyloids on flagellar segments 2–4 compared to 3–6 and 4–7 in other species. PMID:22259292

  8. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

    NASA Astrophysics Data System (ADS)

    Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

    2015-07-01

    Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

  9. AMBER: a PIC slice code for DARHT

    NASA Astrophysics Data System (ADS)

    Vay, Jean-Luc; Fawley, William

    1999-11-01

    The accelerator for the second axis of the Dual Axis Radiographic Hydrodynamic Test (DARHT) facility will produce a 4-kA, 20-MeV, 2-μ s output electron beam with a design goal of less than 1000 π mm-mrad normalized transverse emittance and less than 0.5-mm beam centroid motion. In order to study the beam dynamics throughout the accelerator, we have developed a slice Particle-In-Cell code named AMBER, in which the beam is modeled as a time-steady flow, subject to self, as well as external, electrostatic and magnetostatic fields. The code follows the evolution of a slice of the beam as it propagates through the DARHT accelerator lattice, modeled as an assembly of pipes, solenoids and gaps. In particular, we have paid careful attention to non-paraxial phenomena that can contribute to nonlinear forces and possible emittance growth. We will present the model and the numerical techniques implemented, as well as some test cases and some preliminary results obtained when studying emittance growth during the beam propagation.

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

    NASA Astrophysics Data System (ADS)

    Berat, C.

    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 km2. Novel detection techniques based on the GHz emission from the EAS are currently being studied. AMBER (Air-shower Microwave Bremsstrahlung Experimental Radiometer) and MIDAS (Microwave Detection of Air Showers) are prototypes for a large imaging dish antenna. In EASIER (Extensive Air Shower Identification using Electron Radiometer), the microwave emission is detected by antenna horns located on each surface detector. MIDAS is a self-triggering system while AMBER and EASIER use the trigger from the Auger detectors to record the emission. The status of these radio-detection R&D efforts at the Pierre Auger Observatory will be reported.

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

    PubMed Central

    Solórzano Kraemer, Mónica M.; Ibáñez-Bernal, Sergio; Wagner, Rüdiger

    2015-01-01

    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. PMID:26401462

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

    PubMed

    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. Computer simulations of interferometric imaging with the Very Large Telescope Interferometer and its Astronomical Multibeam Recombiner instrument

    NASA Astrophysics Data System (ADS)

    Przygodda, Frank; Bloecker, Thomas; Hofmann, Karl-Heinz; Weigelt, Gerd

    2001-05-01

    We present computer simulations of interferometric imaging with the Very Large Telescope Interferometer (VLTI) of the European Southern Observatory and the Astronomical Multibeam Recombiner (AMBER) phase-closure instrument. These simulations include both the astrophysical modeling of a stellar object by radiative-transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector readout noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r0,object and r0,ref ranging between 0.9 and 1.2 m), different residual tip-tilt error ((delta) tt,object and (delta) tt,ref ranging between 0.1% and 20% of the Airy-disk diameter), and object brightness (Kobject equals 0.7 to 10.2 mag, Kref equals 0.7 mag). As an example, we focus on stars in late stages of stellar evolution and study one of the key objects of that kind, the dusty super-giant IRC + 10420, which is rapidly evolving on human time scales. We show computer simulations of VLT interferometer (visibility and phase-closure measurements) of IRC + 10420 with two and three auxiliary telescopes (in AMBER wide-field mode, i.e., without fiber optic spatial filters) and discuss whether the visibility accuracy is sufficient to distinguish between different theoretical model predictions.

  14. Electronic polarization stabilizes tertiary structure prediction of HP-36.

    PubMed

    Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

    2014-04-01

    Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

  15. A mid-Cretaceous Eccrinales infesting a primitive wasp in Myanmar amber.

    PubMed

    Poinar, George

    2016-12-01

    A mid-Cretaceous Eccrinales in Myanmar amber is described as Paleocadus burmiticus gen. et sp. nov. in the family Eccrinaceae. The fossil is represented by two types of sporangiospores formed on different thalli protruding from the anus of a primitive wasp, with secondary infestation spores multinucleate and thin walled. Its presence establishes the Eccrinales in the mid-Cretaceous and shows that at that time, lineages of this group parasitized wasps, an association unknown with extant members of the Order. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  16. A new fossil cricket of the genus Proanaxipha in Miocene amber from the Dominican Republic (Orthoptera, Gryllidae, Pentacentrinae).

    PubMed

    Heads, Sam W; Penney, David; Green, David I

    2012-01-01

    A new species of the cricket genus Proanaxipha Vickery & Poinar (Orthoptera: Gryllidae: Pentacentrinae) from Early Miocene Dominican amber is described and illustrated. Proanaxipha madgesuttonaesp. n. is distinguished from congeners by: (1) head capsule bearing a distinctive posteriorly bilobed colour spot on the vertex; (2) presence of crossveins in the proximal part of the mediocubital area; (3) apical field of tegmen entirely dark; and (4) median process of epiphallus short. The poorly known Proanaxipha bicolorata Vickery & Poinar, of questionable affinity and status, is herein regarded as a nomen inquirendum.

  17. A new fossil cricket of the genus Proanaxipha in Miocene amber from the Dominican Republic (Orthoptera, Gryllidae, Pentacentrinae)

    PubMed Central

    Heads, Sam W.; Penney, David; Green, David I.

    2012-01-01

    Abstract A new species of the cricket genus Proanaxipha Vickery & Poinar (Orthoptera: Gryllidae: Pentacentrinae) from Early Miocene Dominican amber is described and illustrated. Proanaxipha madgesuttonae sp. n. is distinguished from congeners by: (1) head capsule bearing a distinctive posteriorly bilobed colour spot on the vertex; (2) presence of crossveins in the proximal part of the mediocubital area; (3) apical field of tegmen entirely dark; and (4) median process of epiphallus short. The poorly known Proanaxipha bicolorata Vickery & Poinar, of questionable affinity and status, is herein regarded as a nomen inquirendum. PMID:23166475

  18. Description of the second fossil Baltic amber species of Monotomidae (Coleoptera: Cucujoidea).

    PubMed

    Bukejs, Andris; Alekseev, Vitalii I

    2015-04-10

    Based on a specimen from the Upper Eocene Baltic amber (Kaliningrad Region, Russia), Aneurops daugpilensis sp. nov. is described. The new species is similar to the extant A. convergens (Sharp, 1900) and A. championi Sharp, 1900 distributed in North and Central America, but differs in the larger punctation of pronotum, and shorter and sparser setation of the median plaque on ventrite 1. Aneurops daugpilensis sp. nov. is distinguished from Europs insterburgensis Alekseev, 2014 by having a median plaque on ventrite 1, a larger body size, and distinctly sparser punctation of the forebody.

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

    PubMed Central

    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

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

    PubMed

    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.

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

    PubMed Central

    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

  2. NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer.

    PubMed

    Bocian, Wojciech; Borowicz, Piotr; Mikołajczyk, Jerzy; Sitkowski, Jerzy; Tarnowska, Anna; Bednarek, Elzbieta; Głabski, Tadeusz; Tejchman-Małecka, Bozena; Bogiel, Monika; Kozerski, Lech

    2008-10-01

    A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, 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 (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), 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. (c) 2008 Wiley Periodicals, Inc.

  3. Evaluating Thermodynamic Integration Performance of the New Amber Molecular Dynamics Package and Assess Potential Halogen Bonds of Enoyl-ACP Reductase (FabI) Benzimidazole Inhibitors

    PubMed Central

    Su, Pin-Chih; Johnson, Michael E.

    2015-01-01

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

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

    PubMed

    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.

  5. First direct detection of a Keplerian rotating disk around the Be star α Arae using AMBER/VLTI

    NASA Astrophysics Data System (ADS)

    Meilland, A.; Stee, P.; Vannier, M.; Millour, F.; Domiciano de Souza, A.; Malbet, F.; Martayan, C.; Paresce, F.; Petrov, R. G.; Richichi, A.; Spang, A.

    2007-03-01

    Aims:We aim to study the geometry and kinematics of the disk around the Be star α Arae as a function of wavelength, especially across the Brγ emission line. The main purpose of this paper is to understand the nature of the disk rotation around Be stars. Methods: We use the AMBER/VLTI instrument operating in the K-band, which provides a gain by a factor of 5 in spatial resolution compared to previous MIDI/VLTI observations. Moreover, it is possible to combine the high angular resolution provided with the (medium) spectral resolution of AMBER to study the kinematics of the inner part of the disk and to infer its rotation law. Results: For the first time, we obtain direct evidence that the disk is in Keplerian rotation, answering a question that has existed since the discovery of the first Be star γ Cas by Father Secchi in 1866. We also present the global geometry of the disk, showing that it is compatible with a thin disk and polar enhanced winds modeled with the SIMECA code. We found that the disk around α Arae is compatible with a dense equatorial matter confined to the central region, whereas a polar wind is contributing along the rotational axis of the central star. Between these two regions, the density must be low enough to reproduce the large visibility modulus (small extension) obtained for two of the four VLTI baselines. Moreover, we obtain that α Arae is rotating very close to its critical rotation. This scenario is also compatible with the previous MIDI measurements. Based on observations collected at the European Southern Observatory, Paranal, Chile, within the science demonstration time programme 074.A-9026(A).

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

    ERIC Educational Resources Information Center

    Von Korff, Joshua; Rebello, N. Sanjay

    2012-01-01

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

  7. Assessing the levels of food shortage using the traffic light metaphor by analyzing the gathering and consumption of wild food plants, crop parts and crop residues in Konso, Ethiopia

    PubMed Central

    2012-01-01

    Background Humanitarian relief agencies use scales to assess levels of critical food shortage to efficiently target and allocate food to the neediest. These scales are often labor-intensive. A lesser used approach is assessing gathering and consumption of wild food plants. This gathering per se is not a reliable signal of emerging food stress. However, the gathering and consumption of some specific plant species could be considered markers of food shortage, as it indicates that people are compelled to eat very poor or even health-threatening food. Methods We used the traffic light metaphor to indicate normal (green), alarmingly low (amber) and fully depleted (red) food supplies and identified these conditions for Konso (Ethiopia) on the basis of wild food plants (WFPs), crop parts (crop parts not used for human consumption under normal conditions; CPs) and crop residues (CRs) being gathered and consumed. Plant specimens were collected for expert identification and deposition in the National Herbarium. Two hundred twenty individual households free-listed WFPs, CPs, and CRs gathered and consumed during times of food stress. Through focus group discussions, the species list from the free-listing that was further enriched through key informants interviews and own field observations was categorized into species used for green, amber and red conditions. Results The study identified 113 WFPs (120 products/food items) whose gathering and consumption reflect the three traffic light metaphors: red, amber and green. We identified 25 food items for the red, 30 food items for the amber and 65 food items for the green metaphor. We also obtained reliable information on 21 different products/food items (from 17 crops) normally not consumed as food, reflecting the red or amber metaphor and 10 crop residues (from various crops), plus one recycled stuff which are used as emergency foods in the study area clearly indicating the severity of food stress (red metaphor) households are dealing with. Our traffic light metaphor proved useful to identify and closely monitor the types of WFPs, CPs, and CRs collected and consumed and their time of collection by subsistence households in rural settings. Examples of plant material only consumed under severe food stress included WFPs with health-threatening features like Dobera glabra (Forssk.) Juss. ex Poir. and inkutayata, parts of 17 crops with 21 food items conventionally not used as food (for example, maize tassels, husks, empty pods), ten crop residues (for example bran from various crops) and one recycled food item (tata). Conclusions We have complemented the conventional seasonal food security assessment tool used by humanitarian partners by providing an easy, cheap tool to scale food stress encountered by subsistence farmers. In cognizance of environmental, socio-cultural differences in Ethiopia and other parts of the globe, we recommend analogous studies in other parts of Ethiopia and elsewhere in the world where recurrent food stress also occurs and where communities intensively use WFPs, CPs, and CRs to cope with food stress. PMID:22871123

  8. Spatially resolving the outer atmosphere of the M giant BK Virginis in the CO first overtone lines with VLTI/AMBER

    NASA Astrophysics Data System (ADS)

    Ohnaka, K.; Hofmann, K.-H.; Schertl, D.; Weigelt, G.; Malbet, F.; Massi, F.; Meilland, A.; Stee, Ph.

    2012-01-01

    Context. The mass-loss mechanism in normal K-M giant stars with small variability amplitudes is not yet understood, although the majority among red giant stars are precisely of this type. Aims: We present high-spatial and high-spectral resolution observations of the M7 giant BK Vir with AMBER at the Very Large Telescope Interferometer (VLTI). Our aim is to probe the physical properties of the outer atmosphere by spatially resolving the star in the individual CO first overtone lines. Methods: BK Vir was observed between 2.26 and 2.31 μm using the 16-32-48 m telescope configuration with an angular resolution of 9.8 mas and a spectral resolution of 12 000. Results: The uniform-disk diameters observed in the CO first overtone lines are 12 - 31% larger than those measured in the continuum. We also detected asymmetry in the CO line-forming region, which manifests itself as non-zero/non-π differential and closure phases. The data taken 1.5 months apart show possible time variation on a spatial scale of 30 mas (corresponding to 3 × stellar diameter) at the CO band head. Comparison of the observed data with the MARCS photospheric model shows that whereas the observed CO line spectrum can be satisfactorily reproduced by the model, the angular sizes observed in the CO lines are much larger than predicted by the model. Our model with two additional CO layers above the MARCS photosphere reproduces the observed spectrum and interferometric data in the CO lines simultaneously. This model suggests that the inner CO layer at ~1.2 R⋆ is very dense and warm with a CO column density of ~1022 cm-2 and temperatures of 1900 - 2100 K, while the outer CO layer at 2.5-3.0 R⋆ is characterized by column densities of 1019-1020 cm-2 and temperatures of 1500 - 2100 K. Conclusions: Our AMBER observations of BK Vir have spatially resolved the extended molecular outer atmosphere of a normal M giant in the individual CO lines for the first time. The temperatures derived for the CO layers are higher than, or equal to, the uppermost layer of the MARCS photospheric model, implying the operation of some heating mechanism in the outer atmosphere. This study also illustrates that testing photospheric models only with the spectra of strong molecular or atomic features can be misleading. Based on AMBER observations made with the Very Large Telescope Interferometer of the European Southern Observatory. Program ID: 081.D-0233(A) (AMBER Guaranteed Time Observation).

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

    PubMed

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

    2015-03-01

    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://group.bmj.com/group/rights-licensing/permissions.

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

    PubMed

    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/

  11. Beyond-use dating of lidocaine alone and in two "magic mouthwash" preparations.

    PubMed

    Kirk, Loren Madden; Brown, Stacy D; Luu, Yao; Ogle, Amanda; Huffman, Jessica; Lewis, Paul O

    2017-05-01

    Beyond-use dating (BUD) of lidocaine alone and in two "magic mouthwash" preparations stored in amber oral syringes at room temperature was determined. Two formulations of mouthwash containing oral topical lidocaine 2% (viscous), diphenhydramine 2.5 mg/mL, and aluminum hydroxide-magnesium hydroxide-simethicone were prepared in 1:1:1 and 1:2.5:2.5 ratios, divided into 3-mL samples, and stored in unit-dose oral amber syringes. Unit-dose single-product lidocaine samples were also prepared to serve as controls and stored in oral amber syringes. The lidocaine concentrations in these samples were measured periodically for 90 days. A stability-indicating high-performance liquid chromatographic method was developed and validated for system suitability, accuracy, repeatability, intermediate precision, specificity, linearity, and robustness. Based on the calculated percentages versus the initial concentration and the results from an analysis of variance comparing the two formulations, a BUD of 21 days is deemed appropriate for both magic mouthwash formulations. Based on the stability data, published safety concerns, and lack of efficacy in combination, packaging and dispensing lidocaine separately from other ingredients are recommended when administering magic mouthwash mixtures. Utilizing a 90-day BUD, lidocaine can be packaged separately from other magic mouthwash ingredients in individual dosage units and applied to the oral cavity using the swish-and-spit method. The delivery of the diphenhydramine and aluminum hydroxide-magnesium hydroxide-simethicone could be separated, allowing for a swish-and-swallow method of administration. A BUD of 21 days is recommended for lidocaine prepared with diphenhydramine and aluminum hydroxide-magnesium hydroxide-simethicone in ratios of 1:1:1 and 1:2.5:2.5 and stored at room temperature in amber oral plastic syringes. Copyright © 2017 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

  12. A Feathered Dinosaur Tail with Primitive Plumage Trapped in Mid-Cretaceous Amber.

    PubMed

    Xing, Lida; McKellar, Ryan C; Xu, Xing; Li, Gang; Bai, Ming; Persons, W Scott; Miyashita, Tetsuto; Benton, Michael J; Zhang, Jianping; Wolfe, Alexander P; Yi, Qiru; Tseng, Kuowei; Ran, Hao; Currie, Philip J

    2016-12-19

    In the two decades since the discovery of feathered dinosaurs [1-3], the range of plumage known from non-avialan theropods has expanded significantly, confirming several features predicted by developmentally informed models of feather evolution [4-10]. However, three-dimensional feather morphology and evolutionary patterns remain difficult to interpret, due to compression in sedimentary rocks [9, 11]. Recent discoveries in Cretaceous amber from Canada, France, Japan, Lebanon, Myanmar, and the United States [12-18] reveal much finer levels of structural detail, but taxonomic placement is uncertain because plumage is rarely associated with identifiable skeletal material [14]. Here we describe the feathered tail of a non-avialan theropod preserved in mid-Cretaceous (∼99 Ma) amber from Kachin State, Myanmar [17], with plumage structure that directly informs the evolutionary developmental pathway of feathers. This specimen provides an opportunity to document pristine feathers in direct association with a putative juvenile coelurosaur, preserving fine morphological details, including the spatial arrangement of follicles and feathers on the body, and micrometer-scale features of the plumage. Many feathers exhibit a short, slender rachis with alternating barbs and a uniform series of contiguous barbules, supporting the developmental hypothesis that barbs already possessed barbules when they fused to form the rachis [19]. Beneath the feathers, carbonized soft tissues offer a glimpse of preservational potential and history for the inclusion; abundant Fe 2+ suggests that vestiges of primary hemoglobin and ferritin remain trapped within the tail. The new finding highlights the unique preservation potential of amber for understanding the morphology and evolution of coelurosaurian integumentary structures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. First identifiable Mesozoic harvestman (Opiliones: Dyspnoi) from Cretaceous Burmese amber

    PubMed Central

    Giribet, Gonzalo; Dunlop, Jason A

    2005-01-01

    Two inclusions in a piece of Upper Cretaceous (Albian) Burmese amber from Myanmar are described as a harvestman (Arachnida: Opiliones), Halitherses grimaldii new genus and species. The first Mesozoic harvestman to be named can be referred to the suborder Dyspnoi for the following reasons: prosoma divided into two regions, the posterior formed by the fusion of the meso- and metapeltidium; palp lacking a terminal claw, with clavate setae, and tarsus considerably shorter than the tibia. The bilobed, anteriorly projecting ocular tubercle is reminiscent of that of ortholasmatine nemastomatids. The status of other Mesozoic fossils referred to Opiliones is briefly reviewed. PMID:16024358

  14. Amber from western Amazonia reveals Neotropical diversity during the middle Miocene

    PubMed Central

    Antoine, Pierre-Olivier; De Franceschi, Dario; Flynn, John J.; Nel, André; Baby, Patrice; Benammi, Mouloud; Calderón, Ysabel; Espurt, Nicolas; Goswami, Anjali; Salas-Gismondi, Rodolfo

    2006-01-01

    Tertiary insects and arachnids have been virtually unknown from the vast western Amazonian basin. We report here the discovery of amber from this region containing a diverse fossil arthropod fauna (13 hexapod families and 3 arachnid species) and abundant microfossil inclusions (pollen, spores, algae, and cyanophyceae). This unique fossil assemblage, recovered from middle Miocene deposits of northeastern Peru, greatly increases the known diversity of Cenozoic tropical–equatorial arthropods and microorganisms and provides insights into the biogeography and evolutionary history of modern Neotropical biota. It also strengthens evidence for the presence of more modern, high-diversity tropical rainforest ecosystems during the middle Miocene in western Amazonia. PMID:16950875

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

    PubMed

    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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    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 < 0.01). For 75% of primary and 57% of secondary schools, the selected 'less healthy' lunch item was cheaper than the 'healthy' lunch item. For 41% of primary and 48% of secondary schools, the selected 'less healthy' 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.

  18. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

    PubMed

    Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

    2011-01-01

    To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

  19. Genetic Incorporation of Twelve meta-Substituted Phenylalanine Derivatives Using A Single Pyrrolysyl-tRNA Synthetase

    PubMed Central

    Wang, Yane-Shih; Fang, Xinqiang; Chen, Hsueh-Ying; Wu, Bo; Wang, Zhiyong U.; Hilty, Christian; Liu, Wenshe R.

    2012-01-01

    When coexpressed with its cognate amber suppressing tRNACUAPyl, a pyrrolysyl-tRNA synthetase mutant N346A/C348A is able to genetically incorporate twelve meta-substituted phenylalanine derivatives into proteins site-specifically at amber mutation sites in Escherichia coli. These genetically encoded noncanonical amino acids resemble phenylalanine in size and contain diverse bioorthogonal functional groups such as halide, trifluoromethyl, nitrile, nitro, ketone, alkyne, and azide moieties. The genetic installation of these functional groups in proteins provides multiple ways to site-selectively label proteins with biophysical and biochemical probes for their functional investigations. We demonstrate that a genetically incorporated trifluoromethyl group can be used as a sensitive 19F NMR probe to study protein folding/unfolding, and that genetically incorporated reactive functional groups such as ketone, alkyne, and azide moieties can be applied to site-specifically label proteins with florescent probes. This critical discovery allows the synthesis of proteins with diverse bioorthogonal functional groups for a variety of basic studies and biotechnology development using a single recombinant expression system. PMID:23138887

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

    PubMed

    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.

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

    PubMed

    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.

  2. Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

    PubMed

    Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

    2017-01-01

    Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

  3. Deoxyhexanucleotide containing a vinyl chloride induced DNA lesion, 1,N/sup 6/-ethenoadenine: synthesis, physical characterization, and incorporation into a duplex bacteriophage M13 genome as part of an amber codon

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Basu, A.K.; Niedernhofer, L.J.; Essigmann, J.M.

    Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N/sup 6/-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d(GCT(epsilon A)GC) was chemically synthesized by the phosphotriester method. Physical studies involving fluorescence, circular dichroism , and /sup 1/H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed inmore » the genome of an M13mp19 insertion mutant. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer (5'-/sup 32/P)d-(GCT(epsilon A)GC), after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli.« less

  4. Effect of Organic and Conventional Management on Bio-Functional Quality of Thirteen Plum Cultivars (Prunus salicina Lindl.).

    PubMed

    Cuevas, Francisco Julián; Pradas, Inmaculada; Ruiz-Moreno, María José; Arroyo, Francisco Teodoro; Perez-Romero, Luis Felipe; Montenegro, José Carlos; Moreno-Rojas, José Manuel

    2015-01-01

    In this study, thirteen Japanese plum cultivars (Prunus salicina Lindl.) grown under conventional and organic conditions were compared to evaluate the influence of the culture system on bioactive compounds. Their organic acids content (malic, citric, tartaric, succinic, shikimic, ascorbic and fumaric acid), total polyphenols, total anthocyanins, total carotenoids and antioxidant capacity (FRAP, ABTS) were evaluated. The study was performed during two consecutive seasons (2012 and 2013) in two experimental orchards located at the IFAPA centre Las Torres-Tomejil (Seville, SW Spain). The culture system affected all the studied parameters except for total carotenoid content. The organic plums had significantly higher polyphenol and anthocyanin concentrations and a greater antioxidant capacity. Additionally, significant differences between cultivars were also found. 'Showtime' and 'Friar' were the cultivars with the highest polyphenol concentration and antioxidant capacity. 'Black Amber' had the highest anthocyanin content and 'Larry Ann' and 'Songold' the highest carotenoid content. 'Sapphire' and 'Black amber' were the cultivars with the highest concentration of ascorbic acid. Our results showed a strong year effect. In conclusion, organic management had an impact on the production of phytochemical compounds in plums.

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

    PubMed

    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.

  6. Electrical apparatus used in medicine before 1900.

    PubMed Central

    Cambridge, N A

    1977-01-01

    The Ancients had at their disposal torpedo fish, amber and magnets. It was not until the sixteenth century that ideas on the strange behaviour of amber and magnets were put forward. The eighteenth century saw the application of Newton's theories of matter and the introduction of the electrostatic machine, Galvanism and Volta's battery. In the nineteenth century there was extensive application of electricity in medical practice, with the development of electrocautery apparatus and illuminated cystoscopes, the pioneering of the electrocardiogram and the discovery of X-rays. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 Fig 8 Fig 9 Fig 10 Fig 11 Fig 12 PMID:335397

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ngo, Thi Huong; Gil, Bernard; Valvin, Pierre

    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.

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

    ERIC Educational Resources Information Center

    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,…

  9. Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

    PubMed

    Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

    2014-02-01

    We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

  10. FF12MC: A revised AMBER forcefield and new protein simulation protocol

    PubMed Central

    2016-01-01

    ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C—H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric–isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left‐ and right‐handed configurations for C14–C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp‐cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general‐purpose AMBER forcefield FF14SB locks the C14–C38 bond to the right‐handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric–isothermal MD simulations 2–4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490–1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27348292

  11. Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

    NASA Astrophysics Data System (ADS)

    Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

    2014-11-01

    The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

  12. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    DOE PAGES

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; ...

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

  13. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

    PubMed

    Lee, Jumin; Cheng, Xi; Swails, Jason M; Yeom, Min Sun; Eastman, Peter K; Lemkul, Justin A; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S; Case, David A; Brooks, Charles L; MacKerell, Alexander D; Klauda, Jeffery B; Im, Wonpil

    2016-01-12

    Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

  14. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

    PubMed

    Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

    2017-06-05

    Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. Characterization of suppressible mutations in the viomycin phosphotransferase gene of the Streptomyces enteric plasmid pVE138.

    PubMed Central

    Paradiso, M J; Roberts, G; Streicher, S L; Goldberg, R B

    1987-01-01

    The viomycin phosphotransferase gene (vph) is expressed and confers resistance to viomycin in both Streptomyces spp. and members of the family Enterobacteriaceae. We report the isolation of UGA (opal) and UAG (amber) mutations in the vph gene of shuttle plasmid pVE138. We found that the five UGA mutations in vph resulted in a temperature-sensitive phenotype in Salmonella typhimurium. Su- strains are Vior at 28 degrees C and Vios at 37 degrees C, whereas Su+UGA strains are Vior at both 28 and 37 degrees C. The single amber mutation isolated was not temperature sensitive and resulted in the expected Vios phenotype in Su- strains and Vior in Su+UAG strains. PMID:3029035

  16. Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion

    PubMed Central

    O’Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U.; Ling, Jiqiang; Odoi, Keturah; Liu, Wenshe R.; Söll, Dieter

    2012-01-01

    Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to ‘statistical protein’ that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNAPyl orthogonal pair cannot completely outcompete contamination by natural amino acids. PMID:23036644

  17. The genus Macroteleia Westwood in Middle Miocene amber from Peru (Hymenoptera, Platygastridae s.l., Scelioninae)

    PubMed Central

    Perrichot, Vincent; Antoine, Pierre-Olivier; Salas-Gismondi, Rodolfo; Flynn, John J.; Engel, Michael S.

    2014-01-01

    Abstract A new species of the scelionine genus Macroteleia Westwood (Platygastridae s.l., Scelioninae) is described and figured from a female beautifully preserved in Middle Miocene amber from Peru. Macroteleia yaguarum Perrichot & Engel, sp. n., shows a unique combination of characters otherwise seen independently within its congeners. It is most similar to the modern M. surfacei Brues, but differs from it by the non-foveolate notauli, the contiguous punctures of the vertex, and the continuous propodeum. The new species is the first New World fossil of the genus, suggesting a Cretaceous origin for the group and a relatively old age of the South American, tropical African, and Australian faunas, and a younger age of the modern Holarctic faunas. PMID:25147461

  18. 76 FR 68500 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-04

    ... following endangered species; Etowah darter (Etheostoma etowahae), amber darter (Percina antesella... for identification purposes, the tuxedo (duskytail) darter (Etheostoma lemniscatum) and the spotfin...

  19. Direct folding simulation of helical proteins using an effective polarizable bond force field.

    PubMed

    Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John Z H

    2017-06-14

    We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

  20. Stability of Metronidazole Suspensions.

    PubMed

    Donnelly, Ronald F; Ying, James

    2015-01-01

    Metronidazole is an antiprotozoal agent used in the treatment of bacterial and protozoal anaerobic infections. The objectives of this study were to develop concentrated metronidazole suspensions that are inexpensive and easy to prepare and determine the stability of these suspensions after storage in amber polyvinyl chloride bottles at room temperature (23°C) and under refrigeration (5°C). Metronidazole suspensions (50 mg/mL) were prepared from powder using Ora-Blend or simple syrup as the vehicles. Samples were collected in triplicate from each container on days 0, 7, 14, 28, 56, and 93. Samples were assayed using a high-performance liquid chromatography method that had been validated as stability indicating. Color, change in physical appearance, and pH were also monitored at each time interval. There was no apparent change in color or physical appearance. The pH values changed by less than 0.20 units over the 93 days. The stability of metronidazole suspensions compounded from United States Pharmacopeia powder using Ora-Blend or simple syrup and packaged in amber polyvinyl chloride bottles was determined to be 93 days when stored at either room temperature or under refrigeration.

  1. Influence of daytime running lamps on visual reaction time of pedestrians when detecting turn indicators.

    PubMed

    Peña-García, Antonio; de Oña Lopez, Rocío; Espín Estrella, Antonio; Aznar Dols, Fernando; Calvo Poyo, Franscisco J; Molero Mesa, Evaristo; de Oña López, Juan

    2010-10-01

    This article describes one experiment that studied the influence of Daytime Running Lamps (DRL) on pedestrian detection of turn indicators. An experimental device including one DRL and one turn indicator was used in order to determine Visual Reaction Times (VRT) of 148 observers in different situations involving turn indicator activation. Such situations were combinations of three main variables: color of DRL, separation between DRL and Turn Indicator, and observation angle. Significant changes in VRT were found depending on the configurations above, especially the observation angle and the color of DRL. This second result demonstrates that amber DRLs inhibit the detection of Turn Indicators. One of the main targets of this paper is to recommend that carmakers introduce only white DRLs on new vehicles. We also intend to advise regulatory bodies working on automotive regulation about the consequences of allowing amber DRLs and also about the danger of introducing constrains on the distance between DRL and Turn Indicator without further experimental evidences. Copyright © 2010 Elsevier Ltd and National Safety Council. All rights reserved.

  2. Fossil evidence for the early ant evolution

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

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

  3. STUDIES ON MAMMALIAN AND HUMAN PYRUVATE AND ALPHA-KETOGLUTARATE DEHYDROGENATION COMPLEXES.

    DTIC Science & Technology

    The pig heart pyruvate and alpha - ketoglutarate dehydrogenase complex were isolated in highly purified state as multienzyme units with molecular...weights of approximately 9 million and 2.8 million, respectively. The aims were to resolve the pig heart pyruvate and alpha - ketoglutarate dehydrogenase...complexes was isolated from three sources; (1) pyruvate dehydrogenase complex, (2) alpha - ketoglutarate dehydrogenase, and (3) amber-color extract free

  4. Presidential Green Chemistry Challenge: 2011 Small Business Award

    EPA Pesticide Factsheets

    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.

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

    PubMed

    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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lekhal, K.; Damilano, B., E-mail: bd@crhea.cnrs.fr; De Mierry, P.

    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.

  7. Taxonomic notes on Babinskaiidae from the Cretaceous Burmese amber, with the description of a new species (Insecta, Neuroptera).

    PubMed

    Hu, Jiahui; Lu, Xiumei; Wang, Bo; Liu, Xingyue

    2018-01-01

    Babinskaiidae is an extinct lacewing family of the superfamily Myrmeleontoidea. Hitherto, nine species of seven genera are described from the Lower and mid-Cretaceous. Here a new species of Babinskaiidae is described from Cretaceous Burmese amber, namely Parababinskaia makarkini sp. n. The new species possesses an A2 vein in the hind wing, suggesting that the loss of this vein might not be an autapomorphy of Babinskaiidae. The female of Electrobabinskaia burmana Lu, Zhang & Liu, 2017 is also described for the first time based on two specimens with their abdomens perfectly preserved, exhibiting a specialised sternum VI with paired elongate projections. A brief discussion of female genital characters is provided, which may increase our understanding of the morphology and phylogenetic position of Babinskaiidae.

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

    PubMed

    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.

  9. 32 CFR 707.7 - Submarine identification light.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RULES WITH RESPECT TO ADDITIONAL STATION AND SIGNAL LIGHTS § 707.7 Submarine identification light. Submarines may display, as a distinctive means of identification, an intermittent flashing amber beacon with...

  10. Self-verification motives at the collective level of self-definition.

    PubMed

    Chen, Serena; Chen, Karen Y; Shaw, Lindsay

    2004-01-01

    Three studies examined self-verification motives in relation to collective aspects of the self. Several moderators of collective self-verification were also examined--namely, the certainty with which collective self-views are held, the nature of one's ties to a source of self-verification, the salience of the collective self, and the importance of group identification. Evidence for collective self-verification emerged across all studies, particularly when collective self-views were held with high certainty (Studies 1 and 2), perceivers were somehow tied to the source of self-verification (Study 1), the collective self was salient (Study 2), and group identification was important (Study 3). To the authors' knowledge, these studies are the first to examine self-verification at the collective level of self-definition. The parallel and distinct ways in which self-verification processes may operate at different levels of self-definition are discussed.

  11. Expression of Recombinant Phosphoproteins for Signal Transduction Studies.

    PubMed

    Barber, Karl W; Rinehart, Jesse

    2017-01-01

    Complex signaling cascades are difficult to study in vitro without phosphorylated proteins. Here, we describe a technique for the routine production of recombinant phosphoproteins by directly incorporating phosphoserine as a nonstandard amino acid. This protocol utilizes an optimized phosphoserine orthogonal translation system and an engineered strain of E. coli containing no genomic amber codons. This approach has been used to generate a variety of phosphorylated proteins to understand the role of protein phosphorylation in cell signaling.

  12. Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

    PubMed Central

    Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

    2014-01-01

    We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

  13. The fossil record and macroevolutionary history of the beetles

    PubMed Central

    Smith, Dena M.; Marcot, Jonathan D.

    2015-01-01

    Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today. PMID:25788597

  14. Visitor's Guide | FNLCR Staging

    Cancer.gov

    The Frederick National Laboratory for Cancer Research is located within theFort Detrick U.S. Army facilityin Frederick, Maryland. All visitors must enter through Nallin Gate, which is located onOpossumtown Pike at Amber Road. The Na

  15. 76 FR 14682 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-17

    ... Tennessee yellow-eyed grass Xyris tennesseensis Etowah Darter Etheostoma etowahae Amber Darter Percina.... Applicant: Dr. J.H. Carter III and Assoc., TE-807672. The applicant requests renewal of authorization for...

  16. Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

    NASA Astrophysics Data System (ADS)

    Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

    We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

  17. Electrolichas circumbalticus gen. et sp. nov. (Coleoptera: Byrrhoidea: Ptilodactylidae) from Baltic amber, the first anchytarsine toed-winged beetle described from Europe.

    PubMed

    Alekseev, Vitalii I; Jäch, Manfred A

    2016-07-07

    A new genus and species of Ptilodactylidae, Electrolichas circumbalticus gen. et sp. nov., the first fossil representative of the subfamily Anchytarsinae, is described from Baltic amber. This Eocene beetle can be distinguished from the extant genera of Anchytarsinae by the combination of the following characters: labrum transverse, terminal segment of maxillary palps cylindrical, antennae with non-articulated rami, basal pronotal margin only very finely crenulate, lacking a median denticle, anterior margin of scutellum not excised medially, elytra not striate, tarsi not pseudotetramerous, proportional lengths: 1.5: 1.2: 1.2: 1.1: 1.5, flashy pads on apex of first tarsomere as well as on tarsomeres 2-4. A list of the extant species of Anchytarsinae is provided. Both hitherto described fossil ptilodactylid genera are briefly discussed.

  18. Taxonomic notes on Babinskaiidae from the Cretaceous Burmese amber, with the description of a new species (Insecta, Neuroptera)

    PubMed Central

    Hu, Jiahui; Lu, Xiumei; Wang, Bo; Liu, Xingyue

    2018-01-01

    Abstract Babinskaiidae is an extinct lacewing family of the superfamily Myrmeleontoidea. Hitherto, nine species of seven genera are described from the Lower and mid-Cretaceous. Here a new species of Babinskaiidae is described from Cretaceous Burmese amber, namely Parababinskaia makarkini sp. n. The new species possesses an A2 vein in the hind wing, suggesting that the loss of this vein might not be an autapomorphy of Babinskaiidae. The female of Electrobabinskaia burmana Lu, Zhang & Liu, 2017 is also described for the first time based on two specimens with their abdomens perfectly preserved, exhibiting a specialised sternum VI with paired elongate projections. A brief discussion of female genital characters is provided, which may increase our understanding of the morphology and phylogenetic position of Babinskaiidae. PMID:29674912

  19. Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity.

    PubMed Central

    Martin, F; Reinbolt, J; Dirheimer, G; Gangloff, J; Eriani, G

    1996-01-01

    Elements that confer identity to a tRNA in the cellular environment, where all aminoacyl-tRNA synthetases are competing for substrates, may be delineated by in vivo experiments using suppressor tRNAs. Here we describe the selection of active Escherichia coli tRNAAsp amber mutants and analyze their identity. Starting from a library containing randomly mutated tRNA(CUA)Asp genes, we isolated four amber suppressors presenting either lysine, alanine, or glutamine activity. Two of them, presenting mainly alanine or lysine activity, were further submitted to a second round of mutagenesis selection in order to improve their efficiency of suppression. Eleven suppressors were isolated, each containing two or three mutations. Ten presented identities of the two parental mutants, whereas one had switched from lysine to arginine identity. Analysis of the different mutants revealed (or confirmed for some nucleotides) their role as positive and/or negative determinants in AlaRS, LysRS, and ArgRS recognition. More generally, it appears that tRNAAsp presents identity characteristics closely related to those of tRNALys, as well as a structural basis for acquiring alanine or arginine identity upon moderate mutational changes; these consist of addition or suppression of the corresponding positive or negative determinants, as well as tertiary interactions. Failure to isolate aspartic acid-inserting suppressors is probably due to elimination of the important G34 identity element and its replacement by an antideterminant when changing the anticodon of the tRNAAsp to the CUA triplet. PMID:8809018

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

    PubMed Central

    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

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

    PubMed Central

    Krell, Frank-Thorsten; Dimitrov, Dimitar

    2016-01-01

    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. PMID:27547512

  2. A Multi-spectroscopic Investigation of Sulphur Speciation in Silicate Glasses and Slags

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bingham, P.; Connelly, A; Hand, R

    2010-01-01

    Sulphur K-edge x-ray absorption near-edge structure (XANES), sulphur K{sub {alpha}} and K{sub {beta}} high resolution x-ray emission spectroscopies (XES), electron paramagnetic resonance (EPR) and optical absorption spectroscopies have been used to study the speciation of sulphur in a range of soda-lime-silica glasses and silicate slags. Several inorganic standards with known sulphur oxidation states and structural environments have also been analysed. Results confirm that the average oxidation state of sulphur in glasses decreases, as expected, in the order (colourless>light olive>dark olive>light amber>dark amber). This behaviour is consistent with decreasing S{sup 6+}/{Sigma}S ratio, which has been quantified by linear combination fitting ofmore » XES S K{alpha} spectra, and with analysed sulphur contents which exhibit a characteristic relationship with oxygen partial pressure, pO{sub 2}. A combination of S{sup 6+}, S{sup 5+}, S{sup 4+} and more reduced sulphur species has been detected in olive and amber glasses. The S{sup 4+} and S{sup 5+} species are most evident in olive-coloured glasses produced under moderately reducing conditions that coincide with minimum sulphur solubilities. The reduced form of sulphur, present in all reduced glasses, is interpreted as being present as S{sup 2-} on the basis of XANES, XES, EPR and optical measurements. An alternative interpretation of the data is that there is a continuum of less strongly reduced species, primarily S{sup +} and S{sup 2+}; this interpretation has less merit. In this paper we show that the established relationship that describes sulphur redox only in terms of S{sup 6+} and S{sup 2-}, and which states that only these two species co-exist over a narrow, moderately reducing range of pO{sub 2}, does not fully describe the behaviour of S in the industrial, non-equilibrated glasses studied. Hence this relationship requires slight modification for non-equilibrated systems to explain the existence of intermediate sulphur oxidation states such as S{sup 4+} and S{sup 5+}, particularly within the intermediate pO{sub 2} range that corresponds with sulphur solubility minima.« less

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

    PubMed

    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.

  4. Imaging reconstruction for infrared interferometry: first images of YSOs environment

    NASA Astrophysics Data System (ADS)

    Renard, S.; Malbet, F.; Thiébaut, E.; Berger, J.-P.

    2008-07-01

    The study of protoplanetary disks, where the planets are believed to form, will certainly allow the formation of our Solar System to be understood. To conduct observations of these objects at the milli-arcsecond scale, infrared interferometry provides the right performances for T Tauri, FU Ori or Herbig Ae/Be stars. However, the only information obtained so far are scarce visibility measurements which are directly tested with models. With the outcome of recent interferometers, one can foresee obtaining images reconstructed independently of the models. In fact, several interferometers including IOTA and AMBER on the VLTI already provide the possibility to recombine three telescopes at once and thus to obtain the data necessary to reconstruct images. In this paper, we describe the use of MIRA, an image reconstruction algorithm developed for optical interferometry data (squared visibilities and closure phases) by E. Thiébaut. We foresee also to use the spectral information given by AMBER data to constrain even better the reconstructed images. We describe the use of MIRA to reconstruct images of young stellar objects out of actual data, in particular the multiple system GW Orionis (IOTA, 2004), and discuss the encountered difficulties.

  5. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... well cured; (e) Poorly developed kernels; (f) Kernels which are dark amber in color; (g) Kernel spots when more than one dark spot is present on either half of the kernel, or when any such spot is more...

  6. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... well cured; (e) Poorly developed kernels; (f) Kernels which are dark amber in color; (g) Kernel spots when more than one dark spot is present on either half of the kernel, or when any such spot is more...

  7. 75 FR 67201 - Flightcrew Alerting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-02

    ... airplanes concerning flightcrew alerting. These standards update definitions, prioritization, color... addressed regulations regarding definitions, prioritization, color requirements, and performance for... proposal: Reserving and limiting the use of alerting colors red, amber, or yellow on the flight deck...

  8. 75 FR 30794 - Notice of Intent To Grant Exclusive Patent License; AmberWave Systems Corporation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-02

    ..., power transistor devices, and power devices in the United States, the Government-owned inventions... amplifiers, radio frequency power transistor devices, and power devices and their use for the fabrication of...

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

    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

  11. The earliest direct evidence of frogs in wet tropical forests from Cretaceous Burmese amber.

    PubMed

    Xing, Lida; Stanley, Edward L; Bai, Ming; Blackburn, David C

    2018-06-14

    Frogs are a familiar and diverse component of tropical forests around the world. Yet there is little direct evidence from the fossil record for the antiquity of this association. We describe four fossil frog specimens from mid-Cretaceous (~99 mya) amber deposits from Kachin State, Myanmar for which the associated fauna provides rich paleoenvironmental context. Microcomputed tomographic analysis provides detailed three-dimensional anatomy for these small frogs, which is generally unavailable for articulated anurans in the Mesozoic. These crown-group anuran specimens provide the earliest direct evidence for anurans in a wet tropical forest. Based on a distinct combination of skeletal characters, at least one specimen has clear similarities to living alytoid frogs as well as several Mesozoic taxa known from the Jehol Biota in China. Whereas many Mesozoic frogs are from seasonal and mesic paleoenvironments, these fossils provide the earliest direct evidence of anurans in wet tropical forests.

  12. A critical examination of Escherichia coli esterase activity.

    PubMed

    Antonczak, Alicja K; Simova, Zuzana; Tippmann, Eric M

    2009-10-16

    The ability of Escherichia coli to grow on a series of acetylated and glycosylated compounds has been investigated. It is surmised that E. coli maintains low levels of nonspecific esterase activity. This observation may have ramifications for previous reports that relied on nonspecific esterases from E. coli to genetically encode nonnatural amino acids. It had been reported that nonspecific esterases from E. coli deacetylate tri-acetyl O-linked glycosylated serine and threonine in vivo. The glycosylated amino acids were reported to have been genetically encoded into proteins in response to the amber stop codon. However, it is our contention that such amino acids are not utilized in this manner within E. coli. The current results report in vitro analysis of the original enzyme and an in vivo analysis of a glycosylated amino acid. It is concluded that the amber suppression method with nonnatural amino acids may require a caveat for use in certain instances.

  13. A Critical Examination of Escherichia coli Esterase Activity*

    PubMed Central

    Antonczak, Alicja K.; Simova, Zuzana; Tippmann, Eric M.

    2009-01-01

    The ability of Escherichia coli to grow on a series of acetylated and glycosylated compounds has been investigated. It is surmised that E. coli maintains low levels of nonspecific esterase activity. This observation may have ramifications for previous reports that relied on nonspecific esterases from E. coli to genetically encode nonnatural amino acids. It had been reported that nonspecific esterases from E. coli deacetylate tri-acetyl O-linked glycosylated serine and threonine in vivo. The glycosylated amino acids were reported to have been genetically encoded into proteins in response to the amber stop codon. However, it is our contention that such amino acids are not utilized in this manner within E. coli. The current results report in vitro analysis of the original enzyme and an in vivo analysis of a glycosylated amino acid. It is concluded that the amber suppression method with nonnatural amino acids may require a caveat for use in certain instances. PMID:19666472

  14. ssaD1, a suppressor of secA51(Ts) that renders growth of Escherichia coli cold sensitive, is an early amber mutation in the transcription factor gene nusB.

    PubMed Central

    Rajapandi, T.; Oliver, D.

    1994-01-01

    Complementation analysis of the ssaD1 mutation, isolated as a suppressor of the secA51(Ts) mutation that renders growth of Escherichia coli cold sensitive, was used to show that ssaD corresponds to nusB, a gene known to be important in transcription antitermination. DNA sequence analysis of the ssaD1 allele showed that it creates an amber mutation in the 15th codon of nusB. Analysis of the effect of different levels of NusB protein on secA transcription and translation suggested that NusB plays little or no role in the control of secA expression. Accordingly, mechanisms by which nusB inactivation can lead to suppression of secA51(Ts) and secY24(Ts) mutations without affecting secA expression need to be considered. PMID:8021230

  15. pmx: Automated protein structure and topology generation for alchemical perturbations

    PubMed Central

    Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

    2015-01-01

    Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36. PMID:25487359

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

    PubMed

    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.

  17. Simulation verification techniques study

    NASA Technical Reports Server (NTRS)

    Schoonmaker, P. B.; Wenglinski, T. H.

    1975-01-01

    Results are summarized of the simulation verification techniques study which consisted of two tasks: to develop techniques for simulator hardware checkout and to develop techniques for simulation performance verification (validation). The hardware verification task involved definition of simulation hardware (hardware units and integrated simulator configurations), survey of current hardware self-test techniques, and definition of hardware and software techniques for checkout of simulator subsystems. The performance verification task included definition of simulation performance parameters (and critical performance parameters), definition of methods for establishing standards of performance (sources of reference data or validation), and definition of methods for validating performance. Both major tasks included definition of verification software and assessment of verification data base impact. An annotated bibliography of all documents generated during this study is provided.

  18. Study of techniques for redundancy verification without disrupting systems, phases 1-3

    NASA Technical Reports Server (NTRS)

    1970-01-01

    The problem of verifying the operational integrity of redundant equipment and the impact of a requirement for verification on such equipment are considered. Redundant circuits are examined and the characteristics which determine adaptability to verification are identified. Mutually exclusive and exhaustive categories for verification approaches are established. The range of applicability of these techniques is defined in terms of signal characteristics and redundancy features. Verification approaches are discussed and a methodology for the design of redundancy verification is developed. A case study is presented which involves the design of a verification system for a hypothetical communications system. Design criteria for redundant equipment are presented. Recommendations for the development of technological areas pertinent to the goal of increased verification capabilities are given.

  19. Stability of Extemporaneously Prepared Hydroxycarbamide Oral Suspensions.

    PubMed

    Kabiche, Djamila; Balde, Issa-Bella; Majoul, Elyes; Kabiche, Sofiane; Bourguignon, Elodie; Fontan, Jean-Eudes; Cisternino, Salvatore; Schlatter, Jöel

    2017-01-01

    Hydroxycarbamide, available as tablets, is a pharmacological agent for fetal hemoglobin induction such as sickle cell anemia. The need for alternative dosage form options for patients unable to take tablets led hospital pharmacies to prepare solutions and suspensions. The objective of this study was to determine the stability of hydroxycarbamide in Ora-Plus in combination with either Ora-Sweet or Ora-Sweet SF, Ora-Blend, or Ora-Blend SF suspending agents. The studied samples were compounded into 100-mg/mL suspensions and stored in 60-mL amber glass bottles at room (22°C to 25°C) or refrigerated (4°C to 8°C) temperature. Samples were assayed at each time point out to 120 days by a stability-indicating high-performance liquid chromatography method. The samples were examined for any change in color, odor, visual microbiology, and pH on initial and final day of analysis. At least 90% of hydroxycarbamide concentration remained in all suspensions at the end of the 120-day study period in both conditions. There was no appreciable change in color, odor, or taste. The pH values of suspensions stored at 25°C changed by at least 1 unit at the end of the study period. Based on the data collected, the beyond-use date of these suspensions is 120 days when stored in 60-mL amber glass bottles at both temperature storage conditions. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

  20. Low-temperature thermal properties of a hyperaged geological glass.

    PubMed

    Pérez-Castañeda, Tomás; Jiménez Riobóo, Rafael J; Ramos, Miguel A

    2013-07-24

    We have measured the specific heat of amber from the Dominican Republic, an ancient geological glass about 20 million years old, in the low-temperature range 0.6 K ≤ T ≤ 26 K, in order to assess the effects of its natural stabilization (hyperageing) process on the low-temperature glassy properties, i.e. boson peak and two-level systems. We have also conducted modulated differential scanning calorimetry experiments to characterize the thermodynamic state of our samples. We found that calorimetric curves exhibit a huge ageing signal ΔH ≈ 5 J g(-1) in the first upscan at the glass transition Tg = 389 K, that completely disappears after heating up (rejuvenating) the sample to T = 395 K for 3 h. To independently evaluate the phonon contribution to the specific heat, Brillouin spectroscopy was performed in the temperature range 80 K ≤ T ≤ 300 K. An expected increase in the Debye level was observed after rejuvenating the Dominican amber. However, no significant change was observed in the low-temperature specific heat of glassy amber after erasing its thermal history: both its boson peak (i.e., the maximum in the Cp/T(3) representation) and the density of tunnelling two-level systems (i.e., the Cp ∼ T contribution at the lowest temperatures) remained essentially the same. Also, a consistent analysis using the soft-potential model of our Cp data and earlier thermal-conductivity data found in the literature further supports our main conclusion, namely, that these glassy 'anomalous' properties at low temperatures remain essentially invariant after strong relaxational processes such as hyperageing.

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

    NASA Astrophysics Data System (ADS)

    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 (<3.5 kA cm-2) the blueshift is attributable to both the 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.

  2. A DATABASE FOR TRACKING REPRODUCTIVE TOXICOGENOMIC DATA

    EPA Science Inventory

    A Database for Tracking Reproductive Toxicogenomic Data
    Wenjun Bao, Judy Schmid, Amber Goetz, Hongzu Ren and David Dix
    Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Pr...

  3. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) Kernels which are dark amber in color; (g) Kernel spots when more than one dark spot is present on either half of the kernel, or when any such spot is more than one-eighth inch (3 mm) in greatest dimension; (h...

  4. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) Kernels which are dark amber in color; (g) Kernel spots when more than one dark spot is present on either half of the kernel, or when any such spot is more than one-eighth inch (3 mm) in greatest dimension; (h...

  5. Tracing the young massive high-eccentricity binary system θ^1Orionis C through periastron passage

    NASA Astrophysics Data System (ADS)

    Kraus, S.; Weigelt, G.; Balega, Y. Y.; Docobo, J. A.; Hofmann, K.-H.; Preibisch, T.; Schertl, D.; Tamazian, V. S.; Driebe, T.; Ohnaka, K.; Petrov, R.; Schöller, M.; Smith, M.

    2009-04-01

    Context: The nearby high-mass star binary system θ^1Ori C is the brightest and most massive of the Trapezium OB stars at the core of the Orion Nebula Cluster, and it represents a perfect laboratory to determine the fundamental parameters of young hot stars and to constrain the distance of the Orion Trapezium Cluster. Aims: By tracing the orbital motion of the θ^1Ori C components, we aim to refine the dynamical orbit of this important binary system. Methods: Between January 2007 and March 2008, we observed θ^1Ori C with VLTI/AMBER near-infrared (H- and K-band) long-baseline interferometry, as well as with bispectrum speckle interferometry with the ESO 3.6 m and the BTA 6 m telescopes (B'- and V'-band). Combining AMBER data taken with three different 3-telescope array configurations, we reconstructed the first VLTI/AMBER closure-phase aperture synthesis image, showing the θ^1Ori C system with a resolution of ˜ 2 mas. To extract the astrometric data from our spectrally dispersed AMBER data, we employed a new algorithm, which fits the wavelength-differential visibility and closure phase modulations along the H- and K-band and is insensitive to calibration errors induced, for instance, by changing atmospheric conditions. Results: Our new astrometric measurements show that the companion has nearly completed one orbital revolution since its discovery in 1997. The derived orbital elements imply a short-period (P ≈ 11.3 yr) and high-eccentricity orbit (e ≈ 0.6) with periastron passage around 2002.6. The new orbit is consistent with recently published radial velocity measurements, from which we can also derive the first direct constraints on the mass ratio of the binary components. We employ various methods to derive the system mass (M_system = 44 ± 7 M⊙) and the dynamical distance (d = 410 ± 20 pc), which is in remarkably good agreement with recently published trigonometric parallax measurements obtained with radio interferometry. Based on observations made with ESO telescopes at the La Silla Paranal Observatory under the OT and VISA-MPG GTO programme IDs 078.C-0360(A), 080.C-0541(A,B,C,D), 080.D-0225(B), and 080.C-0388(A).

  6. Mineralogical Characterization of Hispano-Moresque Glazes: A µ-Raman and Scanning Electron Microscopy with X-Ray Energy Dispersive Spectrometry (SEM-EDS) Study.

    PubMed

    Coentro, Susana; da Silva, Rui C; Relvas, Cátia; Ferreira, Teresa; Mirão, José; Pleguezuelo, Alfonso; Trindade, Rui; Muralha, Vânia S F

    2018-06-05

    This work explores the combination of µ-Raman spectroscopy and scanning electron microscopy with X-ray energy dispersive spectrometry (SEM-EDS) for the study of the glazes in 15th-16th century Hispano-Moresque architectural tiles. These are high lead glazes that can be tin-opacified or transparent, and present five colors: tin-white, cobalt-blue, copper-green, iron-amber, and manganese-brown. They are generally homogenous and mineral inclusions are mostly concentrated in the glaze-ceramic interface. Through SEM-EDS, these inclusions were observed and chemically analyzed, whereas µ-Raman allowed their identification on a molecular level. K-feldspars, wollastonite and diopside were the most common compounds, as well as cassiterite agglomerates that render the glaze opaque. Malayaite was identified in green glazes, and andradite and magnesioferrite in amber glazes. Co-Ni-ferrites were identified in blue glazes, as well as Ni-Fe-olivines. Manganese-brown is the color where most compounds were identified: bustamite, jacobsite, hausmannite, braunite, and kentrolite. Through the µ-Raman analysis of different areas in large inclusions previously observed by SEM, it was possible to identify intermediate phases that illustrate the reaction process that occurs between the color-conferring compounds and the surrounding lead glaze. Furthermore, the obtained results allowed inference of the raw materials and firing temperatures used on the manufacture of these tiles.

  7. Gemstones

    USGS Publications Warehouse

    Olson, D.W.

    2012-01-01

    The estimated value of natural gemstones produced from U.S. deposits during 2011 was $10.6 million, a 6-percent increase from 2010. 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.

  8. Gemstones

    USGS Publications Warehouse

    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.

  9. Gemstones

    USGS Publications Warehouse

    Olson, D.W.

    2011-01-01

    The estimated value of natural gemstones produced from U.S. deposits during 2010 was $8.5 million, a slight increase from 2009. 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.

  10. 47 CFR 10.410 - Prioritization.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Prioritization. 10.410 Section 10.410 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMERCIAL MOBILE ALERT SYSTEM Alert Message... required to transmit Imminent Threat Alerts and AMBER Alerts on a first in-first out (FIFO) basis. ...

  11. Electronic Portfolios. [SITE 2002 Section].

    ERIC Educational Resources Information Center

    Barrett, Helen C., Ed.

    This document contains the following papers on electronic portfolios from the SITE (Society for Information Technology & Teacher Education) 2002 conference: (1) "What Is the Perceived Value of Creating Electronic Portfolios to Teacher Credential Candidates?" (Valerie Amber and Brenda Czech); (2) "Development and Use of…

  12. Frequent Questions on International Agreements on Transboundary Shipments of Waste

    EPA Pesticide Factsheets

    Answers FAQs such as How does the OECD control the shipment of hazardous waste between Member countries? Where do I find the green and amber lists of waste? Why hasn't the United States ratified the Basel Convention?

  13. ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

    PubMed Central

    Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng

    2017-01-01

    Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738

  14. Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

    PubMed

    Forouzesh, Negin; Izadi, Saeed; Onufriev, Alexey V

    2017-10-23

    Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG pol ) and binding free energies (ΔΔG pol ). The model tolerates a relatively coarse grid size h = 0.5 Å, where the grid artifact error in computing ΔΔG pol remains in the range of k B T ∼ 0.6 kcal/mol. The estimated ΔΔG pol s are well correlated (r 2 = 0.97) with the numerical Poisson-Boltzmann reference, while showing virtually no systematic bias and RMSE = 1.43 kcal/mol. The grid-based GBNSR6 model is available in Amber (AmberTools) package of molecular simulation programs.

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

    PubMed

    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.

  16. 40 CFR 262.82 - General conditions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., other Federal environmental statutes (e.g., the Toxic Substances Control Act) restrict certain waste... to EPA in accordance with § 262.87(b). (e) Duty to return wastes subject to the Amber control....82 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED...

  17. 40 CFR 262.82 - General conditions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (e.g., the Toxic Substances Control Act) restrict certain waste imports or exports. Such restrictions... to EPA in accordance with § 262.87(b). (e) Duty to return wastes subject to the Amber control....82 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED...

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

    DTIC Science & Technology

    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

  19. Stability of extemporaneously compounded dexamethasone in glass and plastic bottles and plastic syringes.

    PubMed

    Ensom, Mary H H; Décarie, Diane

    2014-07-01

    Dexamethasone is widely used to treat rheumatic and endocrine disorders and chemotherapy-induced nausea and vomiting. A palatable, alcohol-free liquid formulation, with a suitable concentration to allow reasonable administration volume, is available only via extemporaneous compounding. To evaluate the stability of dexamethasone suspensions in commercially available vehicles (Oral Mix and Oral Mix SF) in various types of containers after storage at 25°C and 4°C for up to 91 days. Dexamethasone suspensions (1 mg/mL) were prepared in Oral Mix and Oral Mix SF and then transferred to amber glass and plastic prescription bottles and plastic oral syringes. Suspensions in all 3 types of containers were stored at 25°C; suspensions in glass and plastic bottles were also stored at 4°C. Samples were collected weekly from each container up to 28 days and then every 2 weeks up to 91 days. The samples were analyzed by a validated, stability-indicating high-performance liquid chromatography - ultraviolet detection method. A suspension was considered stable if it maintained at least 90% of its initial dexamethasone concentration. Changes in colour, taste, odour, precipitation (and ease of resuspension), and pH were used to assess physical compatibility. All suspensions maintained at least 96% of the original concentration for up to 91 days with storage at 25°C or at 4°C. No notable changes in colour, taste, odour, precipitation, or pH were observed over the 91-day period. Dexamethasone suspensions (1 mg/mL) in Oral Mix and Oral Mix SF, stored in amber glass or plastic bottles or plastic syringes at 25°C or in amber glass or plastic bottles at 4°C can be expected to remain stable for up to 91 days.

  20. AMBER/VLTI and MIDI/VLTI spectro-interferometric observations of the B[e] supergiant CPD-57°2874. Size and geometry of the circumstellar envelope in the near- and mid-IR

    NASA Astrophysics Data System (ADS)

    Domiciano de Souza, A.; Driebe, T.; Chesneau, O.; Hofmann, K.-H.; Kraus, S.; Miroshnichenko, A. S.; Ohnaka, K.; Petrov, R. G.; Preisbisch, T.; Stee, P.; Weigelt, G.; Lisi, F.; Malbet, F.; Richichi, A.

    2007-03-01

    We present the first high spatial and spectral resolution observations of the circumstellar envelope (CSE) of a B[e] supergiant (CPD-57°2874), performed with the Very Large Telescope Interferometer (VLTI). Spectra, visibilities and closure phase were obtained using the beam-combiner instruments AMBER (near-IR interferometry with three 8.3 m Unit Telescopes or UTs) and MIDI (mid-IR interferometry with two UTs). The interferometric observations of the CSE are well fitted by an elliptical Gaussian model with FWHM diameters varying linearly with wavelength. Typical diameters measured are ≃1.8×3.4 mas or ≃4.5×8.5 AU (adopting a distance of 2.5 kpc) at 2.2 μm, and ≃12×15 mas or ≃30×38 AU at 12 μm. The size of the region emitting the Brγ flux is ≃2.8×5.2 mas or ≃7.0×13.0 AU. The major-axis position angle of the elongated CSE in the mid-IR (≃144°) agrees well with previous polarimetric data, hinting that the hot-dust emission originates in a disk-like structure. In addition to the interferometric observations we also present new optical (UBVR_cI_c) and near-IR (JHKL) broadband photometric observations of CPD-57°2874. Our spectro-interferometric VLTI observations and data analysis support the non-spherical CSE paradigm for B[e] supergiants. Based on observations collected at the European Southern Observatory, Paranal, Chile, within the AMBER science demonstration time programme 074.A-9026 and the MIDI open time programme 074.D-0101.

  1. Verification of performance specifications for a US Food and Drug Administration-approved molecular microbiology test: Clostridium difficile cytotoxin B using the Becton, Dickinson and Company GeneOhm Cdiff assay.

    PubMed

    Schlaberg, Robert; Mitchell, Michael J; Taggart, Edward W; She, Rosemary C

    2012-01-01

    US Food and Drug Administration (FDA)-approved diagnostic tests based on molecular genetic technologies are becoming available for an increasing number of microbial pathogens. Advances in technology and lower costs have moved molecular diagnostic tests formerly performed for research purposes only into much wider use in clinical microbiology laboratories. To provide an example of laboratory studies performed to verify the performance of an FDA-approved assay for the detection of Clostridium difficile cytotoxin B compared with the manufacturer's performance standards. We describe the process and protocols used by a laboratory for verification of an FDA-approved assay, assess data from the verification studies, and implement the assay after verification. Performance data from the verification studies conducted by the laboratory were consistent with the manufacturer's performance standards and the assay was implemented into the laboratory's test menu. Verification studies are required for FDA-approved diagnostic assays prior to use in patient care. Laboratories should develop a standardized approach to verification studies that can be adapted and applied to different types of assays. We describe the verification of an FDA-approved real-time polymerase chain reaction assay for the detection of a toxin gene in a bacterial pathogen.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  4. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  5. The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of L-phenylalanine and its derivatives.

    PubMed

    Wang, Yane-Shih; Russell, William K; Wang, Zhiyong; Wan, Wei; Dodd, Lindsey E; Pai, Pei-Jing; Russell, David H; Liu, Wenshe R

    2011-03-01

    Using evolved pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs, L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine have been genetically incorporated into proteins at amber mutation sites in E. coli.

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

    NASA Astrophysics Data System (ADS)

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

    1995-06-01

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

  7. Amber fossils demonstrate deep-time stability of Caribbean lizard communities.

    PubMed

    Sherratt, Emma; del Rosario Castañeda, María; Garwood, Russell J; Mahler, D Luke; Sanger, Thomas J; Herrel, Anthony; de Queiroz, Kevin; Losos, Jonathan B

    2015-08-11

    Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils--only three have been described to date--has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15-20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.

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

    PubMed Central

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

    2008-01-01

    The developmental stages of feathers are of major importance in the evolution of body covering and the origin of avian flight. Until now, there were significant gaps in knowledge of early morphologies in theoretical stages of feathers as well as in palaeontological material. Here we report fossil evidence of an intermediate and critical stage in the incremental evolution of feathers which has been predicted by developmental theories but hitherto undocumented by evidence from both the recent and the fossil records. Seven feathers have been found in an Early Cretaceous (Late Albian, ca 100 Myr) amber of western France, which display a flattened shaft composed by the still distinct and incompletely fused bases of the barbs forming two irregular vanes. Considering their remarkably primitive features, and since recent discoveries have yielded feathers of modern type in some derived theropod dinosaurs, the Albian feathers from France might have been derived either from an early bird or from a non-avian dinosaur. PMID:18285280

  9. Taxonomic notes on Cretarophalis patrickmuelleri Wichard, 2017 (Insecta: Neuroptera: Nevrorthidae) from the mid-Cretaceous of Myanmar, and its phylogenetic significance.

    PubMed

    Lu, Xiumei; Xia, Fangyuan; Wang, Bo; AspÖck, Ulrike; Liu, Xingyue

    2018-01-15

    Nevrorthidae is a family of Neuroptera with low species diversity, disjunct geographic distributions, and a controversial phylogenetic status. Previous fossil records of the family are from the Eocene except for the recently described species Cretarophalis patrickmuelleri Wichard, 2017 from mid-Cretaceous Burmese amber, following earlier records of an undescribed species. However, such a significant finding of this family from Mesozoic was originally presented only with a preliminary description. Here we re-describe the species based on exquisitely preserved materials from mid-Cretaceous Burmese amber that provides for a much more detailed description, in particular of the hindwing, female genitalia, and larval head. Furthermore, distinctive morphological characters of C. patrickmuelleri with significant phylogenetic relevance are discussed. The general morphology, particularly that of the larva, has changed little between the Mesozoic and Cenozoic, and it reflects an evolutionary stasis that might correspond to their aquatic larval life-style. The present finding also supports the relictual nature of the modern nevrorthids.

  10. Stability of extemporaneously prepared moxifloxacin oral suspensions.

    PubMed

    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.

  11. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... booms, backhoes, and winches) prevents compliance with this paragraph by any required lamp, an auxiliary... SAE J845—Optical Warning Devices for Authorized Emergency, Maintenance and Service Vehicles, May 1997... Authorized Emergency, Maintenance and Service Vehicles, January 2005. Amber gaseous discharge warning lamps...

  12. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... booms, backhoes, and winches) prevents compliance with this paragraph by any required lamp, an auxiliary... SAE J845—Optical Warning Devices for Authorized Emergency, Maintenance and Service Vehicles, May 1997... Authorized Emergency, Maintenance and Service Vehicles, January 2005. Amber gaseous discharge warning lamps...

  13. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... booms, backhoes, and winches) prevents compliance with this paragraph by any required lamp, an auxiliary... SAE J845—Optical Warning Devices for Authorized Emergency, Maintenance and Service Vehicles, May 1997... Authorized Emergency, Maintenance and Service Vehicles, January 2005. Amber gaseous discharge warning lamps...

  14. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... booms, backhoes, and winches) prevents compliance with this paragraph by any required lamp, an auxiliary... SAE J845—Optical Warning Devices for Authorized Emergency, Maintenance and Service Vehicles, May 1997... Authorized Emergency, Maintenance and Service Vehicles, January 2005. Amber gaseous discharge warning lamps...

  15. 49 CFR 393.25 - Requirements for lamps other than head lamps.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... booms, backhoes, and winches) prevents compliance with this paragraph by any required lamp, an auxiliary... SAE J845—Optical Warning Devices for Authorized Emergency, Maintenance and Service Vehicles, May 1997... Authorized Emergency, Maintenance and Service Vehicles, January 2005. Amber gaseous discharge warning lamps...

  16. Thermal Modeling of Millimeter Wave Energy and Heat Transfer in Skin

    DTIC Science & Technology

    2008-11-25

    34 29* Annual Meeting of the Bioelectromagnetics Society, Kanazawa, Japan. (W. Hubert , N. Millenbaugh, C. Roth, R. Sypniewska, V. Chan, J. Eggers, R...Research Student) - 100% Fall 2007. i. Marcos Lopez (Undergraduate Research Student) - 25% Spring 2006; 100% Summer 2006. j. Amber MacDonald

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

    PubMed

    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.

  18. Working Memory Mechanism in Proportional Quantifier Verification

    ERIC Educational Resources Information Center

    Zajenkowski, Marcin; Szymanik, Jakub; Garraffa, Maria

    2014-01-01

    The paper explores the cognitive mechanisms involved in the verification of sentences with proportional quantifiers (e.g. "More than half of the dots are blue"). The first study shows that the verification of proportional sentences is more demanding than the verification of sentences such as: "There are seven blue and eight yellow…

  19. Adjusting for partial verification or workup bias in meta-analyses of diagnostic accuracy studies.

    PubMed

    de Groot, Joris A H; Dendukuri, Nandini; Janssen, Kristel J M; Reitsma, Johannes B; Brophy, James; Joseph, Lawrence; Bossuyt, Patrick M M; Moons, Karel G M

    2012-04-15

    A key requirement in the design of diagnostic accuracy studies is that all study participants receive both the test under evaluation and the reference standard test. For a variety of practical and ethical reasons, sometimes only a proportion of patients receive the reference standard, which can bias the accuracy estimates. Numerous methods have been described for correcting this partial verification bias or workup bias in individual studies. In this article, the authors describe a Bayesian method for obtaining adjusted results from a diagnostic meta-analysis when partial verification or workup bias is present in a subset of the primary studies. The method corrects for verification bias without having to exclude primary studies with verification bias, thus preserving the main advantages of a meta-analysis: increased precision and better generalizability. The results of this method are compared with the existing methods for dealing with verification bias in diagnostic meta-analyses. For illustration, the authors use empirical data from a systematic review of studies of the accuracy of the immunohistochemistry test for diagnosis of human epidermal growth factor receptor 2 status in breast cancer patients.

  20. Hormone-Related Pathways and Risk of Breast Cancer Subtypes in African American Women

    PubMed Central

    Haddad, Stephen A.; Lunetta, Kathryn L.; Ruiz-Narváez, Edward A.; Bensen, Jeannette T.; Hong, Chi-Chen; Sucheston-Campbell, Lara E.; Yao, Song; Bandera, Elisa V.; Rosenberg, Lynn; Haiman, Christopher A.; Troester, Melissa A.; Ambrosone, Christine B.; Palmer, Julie R.

    2016-01-01

    Purpose We sought to investigate genetic variation in hormone pathways in relation to risk of overall and subtype-specific breast cancer in women of African ancestry (AA). Methods Genotyping and imputation yielded data on 143,934 SNPs in 308 hormone-related genes for 3663 breast cancer cases (1098 ER-, 1983 ER+, 582 ER unknown) and 4687 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium. AMBER includes data from four large studies of AA women: the Carolina Breast Cancer Study, the Women's Circle of Health Study, the Black Women's Health Study, and the Multiethnic Cohort Study. Pathway- and gene-based analyses were conducted, and single SNP tests were run for the top genes. Results There were no strong associations at the pathway level. The most significantly associated genes were GHRH, CALM2, CETP, and AKR1C1 for overall breast cancer (gene-based nominal p ≤0.01); NR0B1, IGF2R, CALM2, CYP1B1, and GRB2 for ER+ breast cancer (p ≤0.02); and PGR, MAPK3, MAP3K1, and LHCGR for ER- disease (p ≤0.02). Single-SNP tests for SNPs with pairwise linkage disequilibrium r2 <0.8 in the top genes identified 12 common SNPs (in CALM2, CETP, NR0B1, IGF2R, CYP1B1, PGR, MAPK3, and MAP3K1) associated with overall or subtype-specific breast cancer after gene-level correction for multiple testing. Rs11571215 in PGR (progesterone receptor) was the SNP most strongly associated with ER- disease. Conclusion We identified eight genes in hormone pathways that contain common variants associated with breast cancer in AA women after gene-level correction for multiple testing. PMID:26458823

  1. Development of Extemporaneously Compounded Aripiprazole Oral Suspensions for Use in Children.

    PubMed

    Pramann, Lance A; Davidow, Lawrence W; van Haandel, Leon; Funk, Ryan S

    2016-01-01

    The purpose of this study was to develop extemporaneously compounded oral liquid formulations of aripiprazole for use in pediatric patients and those patients unable to swallow the solid oral dosage forms. Aripiprazole tablets(30 mg) were ground to a fine powder and suspended at a concentration of 1.0 mg/mL in either a 1:1 blend of Ora-Plus and Ora-Sweet, or 1% methylcellulose and Simple Syrup NF. Five amber, plastic liquid prescription bottles of each formulation were stored at 4°C, and aripiprazole content was measured by ultra-performance liquid chromatography time-of-flight mass spectrometry at 0, 14, 32, 67, and 91 days. Formulations were visually inspected at each time point for color change and precipitation. Forced degradation studies were conducted under oxidizing, acidic, basic, and thermal conditions. Concentrations of aripiprazole in the formulation containing 1:1 Ora-Plus and Ora-Sweet were unchanged over the study period with no signs of degradation over 91 days. In the 1:1 1% methylcellulose and Simple Syrup NF formulation, aripiprazole concentrations were 95% of labeled levels at 67 days, but failed to maintain greater than 90% of labeled levels at 91 days, with an average of only 84% of the labeled content. No apparent physical changes in the formulations were noted over the study period. In the forced degradation studies, loss of aripiprazole was notable under extreme oxidizing and alkaline conditions. Extemporaneously compounded oral suspensions of 1.0 mg/mL aripiprazole in 1:1 Ora-Plus and Ora-Sweet are stable for at least 91 days when stored in amber, plastic prescription bottles at 4°C, whereas suspensions in 1:1 1% methylcellulose and Simple Syrup NF are stable for up to 67 days. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

  2. The politics of verification and the control of nuclear tests, 1945-1980

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gallagher, N.W.

    1990-01-01

    This dissertation addresses two questions: (1) why has agreement been reached on verification regimes to support some arms control accords but not others; and (2) what determines the extent to which verification arrangements promote stable cooperation. This study develops an alternative framework for analysis by examining the politics of verification at two levels. The logical politics of verification are shaped by the structure of the problem of evaluating cooperation under semi-anarchical conditions. The practical politics of verification are driven by players' attempts to use verification arguments to promote their desired security outcome. The historical material shows that agreements on verificationmore » regimes are reached when key domestic and international players desire an arms control accord and believe that workable verification will not have intolerable costs. Clearer understanding of how verification is itself a political problem, and how players manipulate it to promote other goals is necessary if the politics of verification are to support rather than undermine the development of stable cooperation.« less

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

    ERIC Educational Resources Information Center

    Hawkes, Stephen J.

    2008-01-01

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

  4. Archaeoteleia Masner in the Cretaceous and a new species of Proteroscelio Brues (Hymenoptera, Platygastroidea)

    USDA-ARS?s Scientific Manuscript database

    The generic concepts of Archaeoteleia Masner and Proteroscelio Brues are expanded to accommodate two new species that are here described: Archaeoteleia astropulvis Talamas sp. n. and Proteroscelio nexus Talamas sp. n. A specimen of Archaeoteleia from Baltic amber is illustrated and discussed. Diagno...

  5. GENE EXPRESSION PROFILING OF ACCESSIBLE SURROGATE TISSUES TO MONITOR MOLECULAR CHANGES IN INACCESSIBLE TARGET TISSUES FOLLOWING TOXICANT EXPOSURE

    EPA Science Inventory

    Gene Expression Profiling Of Accessible Surrogate Tissues To Monitor Molecular Changes In Inaccessible Target Tissues Following Toxicant Exposure
    John C. Rockett, Chad R. Blystone, Amber K. Goetz, Rachel N. Murrell, Judith E. Schmid and David J. Dix
    Reproductive Toxicology ...

  6. Changing Times for Rural Prosperity through Wine, Food, and Art

    ERIC Educational Resources Information Center

    VanAusdle, Steven L.

    2005-01-01

    The landscape of rural America is changing. Rural areas have been described as the country's "bread basket"--feeding citizens of the United States and many countries abroad. But these areas are struggling with declining crop prices, escalating production costs, and increased competition from overseas producers. Where amber waves of…

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

    ERIC Educational Resources Information Center

    Wales, Largo Ann

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

  8. GENOMIC ANALYSIS OF SURROGATE TISSUES FOR ASSESSING ENVIRONMENTAL EXPOSURES AND FUTURE DISEASE STATES

    EPA Science Inventory

    Genomic Analysis of Surrogate Tissues for Assessing Environmental Exposures and Future Disease States

    John C. Rockett, Chad R. Blystone, Amber K. Goetz, Rachel N. Murrell, Hongzu Ren, Judith E. Schmid, Jessica Stapelfeldt, Lillian F. Strader, Kary E. Thompson, Douglas B. T...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  10. One hundred million year old ergot: psychotropic compounds in the Cretaceous?

    USDA-ARS?s Scientific Manuscript database

    A fungal sclerotium similar to sclerotia of the genus Claviceps, commonly known as ergot, was found infecting a grass kernel in Early Cretaceous Myanmar amber. This represents the first fossil record of ergot dating as far back as the Cretaceous period. The fungus, described as Palaeoclaviceps para...

  11. 21 CFR 184.1595 - Pepsin.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Substances Affirmed as GRAS § 184.1595 Pepsin. (a) Pepsin (CAS Reg. No. 9001-75-6) is an enzyme preparation... amber to brown liquid. Its characterizing enzyme activity is that of a peptide hydrolase (EC 3.4.23.1). (b) The ingredient meets the general requirements and additional requirements for enzyme preparations...

  12. 78 FR 38319 - Pesticide Maintenance Fee: Notice of Receipt of Requests to Voluntarily Cancel Certain Pesticide...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-26

    ... 100 Amber Herbicide Triasulfuron. 000100-00800 100 Ridomil Gold Bravo......... D-Alanine, N-(2,6- dimethylphenyl-N- (methoxyacetyl)-,methyl ester; Chlorothalonil. 000100-00848 100 Zorial Rapid 80 Herbicide...-00735 264 Sencor 4 Flowable Herbicide Metribuzin. 000264-00737 264 Bayleton 50% Dry Flowable Triadimefon...

  13. Anthropomorphic Portraits

    ERIC Educational Resources Information Center

    DeSimone, Jana

    2012-01-01

    Sepia tones range from pale neutral cream, tan, and amber all the way to deep chocolate brown; some even have dark green undertones. Sepia tones are used primarily by photographers. Photographers opt to print their photos in sepia because of the warmer, almost old-fashioned look it has. Art is considered "anthropomorphic" when an object or an…

  14. 75 FR 34139 - Ocean Transportation Intermediary License Applicants

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-16

    ... Service. A.W.L.I. Group, Inc. dba Amber Worldwide Logistics, Inc. (OFF & NVO), 1358 NW 78th Avenue, Miami... President, Application Type: Add NVO Service. Aztec Marine Agencies, Inc. dba Beaumont Logistics Group (OFF... Logistics, LLC (OFF & NVO), 6133 Edith Blvd., NE., Albuquerque, NM 87107, Officers: Terry L. Strohl...

  15. High Brightness OLED Lighting

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Spindler, Jeffrey; Kondakova, Marina; Boroson, Michael

    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.

  16. Acute exposure to blue wavelength light during memory consolidation improves verbal memory performance.

    PubMed

    Alkozei, Anna; Smith, Ryan; Dailey, Natalie S; Bajaj, Sahil; Killgore, William D S

    2017-01-01

    Acute exposure to light within the blue wavelengths has been shown to enhance alertness and vigilance, and lead to improved speed on reaction time tasks, possibly due to activation of the noradrenergic system. It remains unclear, however, whether the effects of blue light extend beyond simple alertness processes to also enhance other aspects of cognition, such as memory performance. The aim of this study was to investigate the effects of a thirty minute pulse of blue light versus placebo (amber light) exposure in healthy normally rested individuals in the morning during verbal memory consolidation (i.e., 1.5 hours after memory acquisition) using an abbreviated version of the California Verbal Learning Test (CVLT-II). At delayed recall, individuals who received blue light (n = 12) during the consolidation period showed significantly better long-delay verbal recall than individuals who received amber light exposure (n = 18), while controlling for the effects of general intelligence, depressive symptoms and habitual wake time. These findings extend previous work demonstrating the effect of blue light on brain activation and alertness to further demonstrate its effectiveness at facilitating better memory consolidation and subsequent retention of verbal material. Although preliminary, these findings point to a potential application of blue wavelength light to optimize memory performance in healthy populations. It remains to be determined whether blue light exposure may also enhance performance in clinical populations with memory deficits.

  17. Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

    PubMed

    Kundu, Sangeeta

    2018-02-01

    The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. Influence of the Redundant Verification and the Non-Redundant Verification on the Hydraulic Tomography

    NASA Astrophysics Data System (ADS)

    Wei, T. B.; Chen, Y. L.; Lin, H. R.; Huang, S. Y.; Yeh, T. C. J.; Wen, J. C.

    2016-12-01

    In the groundwater study, it estimated the heterogeneous spatial distribution of hydraulic Properties, there were many scholars use to hydraulic tomography (HT) from field site pumping tests to estimate inverse of heterogeneous spatial distribution of hydraulic Properties, to prove the most of most field site aquifer was heterogeneous hydrogeological parameters spatial distribution field. Many scholars had proposed a method of hydraulic tomography to estimate heterogeneous spatial distribution of hydraulic Properties of aquifer, the Huang et al. [2011] was used the non-redundant verification analysis of pumping wells changed, observation wells fixed on the inverse and the forward, to reflect the feasibility of the heterogeneous spatial distribution of hydraulic Properties of field site aquifer of the non-redundant verification analysis on steady-state model.From post literature, finding only in steady state, non-redundant verification analysis of pumping well changed location and observation wells fixed location for inverse and forward. But the studies had not yet pumping wells fixed or changed location, and observation wells fixed location for redundant verification or observation wells change location for non-redundant verification of the various combinations may to explore of influences of hydraulic tomography method. In this study, it carried out redundant verification method and non-redundant verification method for forward to influences of hydraulic tomography method in transient. And it discuss above mentioned in NYUST campus sites the actual case, to prove the effectiveness of hydraulic tomography methods, and confirmed the feasibility on inverse and forward analysis from analysis results.Keywords: Hydraulic Tomography, Redundant Verification, Heterogeneous, Inverse, Forward

  20. Modality Switching in a Property Verification Task: An ERP Study of What Happens When Candles Flicker after High Heels Click

    PubMed Central

    Collins, Jennifer; Pecher, Diane; Zeelenberg, René; Coulson, Seana

    2011-01-01

    The perceptual modalities associated with property words, such as flicker or click, have previously been demonstrated to affect subsequent property verification judgments (Pecher et al., 2003). Known as the conceptual modality switch effect, this finding supports the claim that brain systems for perception and action help subserve the representation of concepts. The present study addressed the cognitive and neural substrate of this effect by recording event-related potentials (ERPs) as participants performed a property verification task with visual or auditory properties in key trials. We found that for visual property verifications, modality switching was associated with an increased amplitude N400. For auditory verifications, switching led to a larger late positive complex. Observed ERP effects of modality switching suggest property words access perceptual brain systems. Moreover, the timing and pattern of the effects suggest perceptual systems impact the decision-making stage in the verification of auditory properties, and the semantic stage in the verification of visual properties. PMID:21713128

  1. Modality Switching in a Property Verification Task: An ERP Study of What Happens When Candles Flicker after High Heels Click.

    PubMed

    Collins, Jennifer; Pecher, Diane; Zeelenberg, René; Coulson, Seana

    2011-01-01

    The perceptual modalities associated with property words, such as flicker or click, have previously been demonstrated to affect subsequent property verification judgments (Pecher et al., 2003). Known as the conceptual modality switch effect, this finding supports the claim that brain systems for perception and action help subserve the representation of concepts. The present study addressed the cognitive and neural substrate of this effect by recording event-related potentials (ERPs) as participants performed a property verification task with visual or auditory properties in key trials. We found that for visual property verifications, modality switching was associated with an increased amplitude N400. For auditory verifications, switching led to a larger late positive complex. Observed ERP effects of modality switching suggest property words access perceptual brain systems. Moreover, the timing and pattern of the effects suggest perceptual systems impact the decision-making stage in the verification of auditory properties, and the semantic stage in the verification of visual properties.

  2. A Collaborative Study of the Etiology of Breast Cancer Subtypes in African American Women: the AMBER Consortium

    PubMed Central

    Palmer, Julie R.; Ambrosone, Christine B.; Olshan, Andrew F.

    2014-01-01

    Purpose Breast cancer is a heterogeneous disease, with at least five intrinsic subtypes defined by molecular characteristics. Tumors that express the estrogen receptor (ER+) have better outcomes than ER− tumors, due in part to the success of hormonal therapies that target ER+ tumors. The incidence of ER− breast cancer, and the subset of ER− cancers that are basal-like, is about twice as high among African American (AA) women as among U.S. women of European descent (EA). This disparity appears to explain, in part, the disproportionately high mortality from breast cancer that occurs in AA women. Epidemiologic research on breast cancer in AA women lags behind research in EA women. Here, we review differences in the etiology of breast cancer subtypes among AA women and describe a new consortium of ongoing studies of breast cancer in AA women. Methods We combined samples and data from four large epidemiologic studies of breast cancer in AA women, two cohort and two case-control, creating the AMBER consortium. Tumor tissue is obtained and stored in tissue microarrays, with assays of molecular markers carried out at a pathology core. Genotyping, carried out centrally, includes a whole exome SNP array and over 180,000 custom SNPs for fine-mapping of GWAS loci and candidate pathways. Results To date, questionnaire data from 5,739 breast cancer cases and 14,273 controls have been harmonized. Genotyping of the first 3,200 cases and 3,700 controls is underway, with a total of 6,000 each expected by the end of the study period. Conclusions The new consortium will likely have sufficient statistical power to assess potential risk factors, both genetic and non-genetic in relation to specific subtypes of breast cancer in AA women. PMID:24343304

  3. Application of mobile phone technology for managing chemotherapy-associated side-effects.

    PubMed

    Weaver, A; Young, A M; Rowntree, J; Townsend, N; Pearson, S; Smith, J; Gibson, O; Cobern, W; Larsen, M; Tarassenko, L

    2007-11-01

    Novel mobile phone technology linked to a server that communicates patients' symptoms to healthcare professionals has been adapted to register the side- effects of chemotherapy and provide advice on management of toxicity. We report a feasibility study to examine the utility of home monitoring of patients' symptoms via a mobile phone. Six colon cancer patients receiving adjuvant chemotherapy, entered symptom data onto user friendly screens on a mobile phone twice daily. This 'real time' self assessment of nausea, vomiting, mucositis, diarrhoea and hand-foot syndrome and measurement of temperature was sent via a secured connection to a remote computer. In the event of moderate or severe symptoms (generating amber and red alerts respectively), the nurse was immediately alerted by the computer, via a pager. The nurse then contacted the patient to reinforce the automatic advice sent to the patient on their phone and to assess the patient using clinical algorithms. The patient used the mobile phones during the first two cycles of chemotherapy. The data were successfully analysed by the server software and alerts were generated alerting the study nurses to patients' symptoms at the appropriate time. There were 91 alerts-54 red and 37 amber; 54% (29/54) of the red alerts were data delay and transmission problems which were swiftly rectified. The remaining red alerts were managed appropriately by the study nurses. Both patients and staff felt confident in this approach to symptom management. This study demonstrates that the technology for monitoring patients' symptoms worked well. The patients felt secure in the knowledge that their symptoms were being closely monitored and that they were participating effectively in their own care management.

  4. NANOGOLD decorated by pHLIP peptide: comparative force field study.

    PubMed

    Kyrychenko, A

    2015-05-21

    The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP.

  5. Admixture Mapping of African-American Women in the AMBER Consortium Identifies New Loci for Breast Cancer and Estrogen-Receptor Subtypes.

    PubMed

    Ruiz-Narváez, Edward A; Sucheston-Campbell, Lara; Bensen, Jeannette T; Yao, Song; Haddad, Stephen; Haiman, Christopher A; Bandera, Elisa V; John, Esther M; Bernstein, Leslie; Hu, Jennifer J; Ziegler, Regina G; Deming, Sandra L; Olshan, Andrew F; Ambrosone, Christine B; Palmer, Julie R; Lunetta, Kathryn L

    2016-01-01

    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.

  6. Functions of social support and self-verification in association with loneliness, depression, and stress.

    PubMed

    Wright, Kevin B; King, Shawn; Rosenberg, Jenny

    2014-01-01

    This study investigated the influence of social support and self-verification on loneliness, depression, and stress among 477 college students. The authors propose and test a theoretical model using structural equation modeling. The results indicated empirical support for the model, with self-verification mediating the relation between social support and health outcomes. The results have implications for social support and self-verification research, which are discussed along with directions for future research and limitations of the study.

  7. Exploring the Possible Use of Information Barriers for future Biological Weapons Verification Regimes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luke, S J

    2011-12-20

    This report describes a path forward for implementing information barriers in a future generic biological arms-control verification regime. Information barriers have become a staple of discussion in the area of arms control verification approaches for nuclear weapons and components. Information barriers when used with a measurement system allow for the determination that an item has sensitive characteristics without releasing any of the sensitive information. Over the last 15 years the United States (with the Russian Federation) has led on the development of information barriers in the area of the verification of nuclear weapons and nuclear components. The work of themore » US and the Russian Federation has prompted other states (e.g., UK and Norway) to consider the merits of information barriers for possible verification regimes. In the context of a biological weapons control verification regime, the dual-use nature of the biotechnology will require protection of sensitive information while allowing for the verification of treaty commitments. A major question that has arisen is whether - in a biological weapons verification regime - the presence or absence of a weapon pathogen can be determined without revealing any information about possible sensitive or proprietary information contained in the genetic materials being declared under a verification regime. This study indicates that a verification regime could be constructed using a small number of pathogens that spans the range of known biological weapons agents. Since the number of possible pathogens is small it is possible and prudent to treat these pathogens as analogies to attributes in a nuclear verification regime. This study has determined that there may be some information that needs to be protected in a biological weapons control verification regime. To protect this information, the study concludes that the Lawrence Livermore Microbial Detection Array may be a suitable technology for the detection of the genetic information associated with the various pathogens. In addition, it has been determined that a suitable information barrier could be applied to this technology when the verification regime has been defined. Finally, the report posits a path forward for additional development of information barriers in a biological weapons verification regime. This path forward has shown that a new analysis approach coined as Information Loss Analysis might need to be pursued so that a numerical understanding of how information can be lost in specific measurement systems can be achieved.« less

  8. Space Station automated systems testing/verification and the Galileo Orbiter fault protection design/verification

    NASA Technical Reports Server (NTRS)

    Landano, M. R.; Easter, R. W.

    1984-01-01

    Aspects of Space Station automated systems testing and verification are discussed, taking into account several program requirements. It is found that these requirements lead to a number of issues of uncertainties which require study and resolution during the Space Station definition phase. Most, if not all, of the considered uncertainties have implications for the overall testing and verification strategy adopted by the Space Station Program. A description is given of the Galileo Orbiter fault protection design/verification approach. Attention is given to a mission description, an Orbiter description, the design approach and process, the fault protection design verification approach/process, and problems of 'stress' testing.

  9. Screen Color and Reading Performance on Closed-Circuit Television.

    ERIC Educational Resources Information Center

    Jacobs, R. J.

    1990-01-01

    To investigate whether screen color is an important variable in the prescription of closed circuit television (CCTV) systems, 16 adults with low vision were assessed on reading performance on white, green, and amber screens. When the screen luminance and contrast were equated for each CCTV, subjects' reading performance was unaffected by screen…

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

    USDA-ARS?s Scientific Manuscript database

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

  11. MICROARRAY DATA ANALYSIS USING MULTIPLE STATISTICAL MODELS

    EPA Science Inventory

    Microarray Data Analysis Using Multiple Statistical Models

    Wenjun Bao1, Judith E. Schmid1, Amber K. Goetz1, Ming Ouyang2, William J. Welsh2,Andrew I. Brooks3,4, ChiYi Chu3,Mitsunori Ogihara3,4, Yinhe Cheng5, David J. Dix1. 1National Health and Environmental Effects Researc...

  12. 77 FR 61452 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Designation of Longer...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-09

    ...; Letter from Daniel G. Weaver, Ph.D., Professor of Finance, Rutgers Business School, dated April 26, 2012; Letter from Amber Anand, Associate Professor of Finance, Syracuse University, dated April 29, 2012; Letter from Albert J. Menkveld, Associate Professor of Finance, VU University Amsterdam, dated May 2...

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

    ERIC Educational Resources Information Center

    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…

  14. Silver Alerts and the Problem of Missing Adults with Dementia

    ERIC Educational Resources Information Center

    Carr, Dawn; Muschert, Glenn W.; Kinney, Jennifer; Robbins, Emily; Petonito, Gina; Manning, Lydia; Brown, J. Scott

    2010-01-01

    In the months following the introduction of the National AMBER (America's Missing: Broadcast Emergency Response) Alert plan used to locate missing and abducted children, Silver Alert programs began to emerge. These programs use the same infrastructure and approach to find a different missing population, cognitively impaired older adults. By late…

  15. Cleopatra's Bedroom west facade with 12' scale (in tenths) with ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Cleopatra's Bedroom west facade with 12' scale (in tenths) with picture tube wall along walkway. Structure is made solely of amber colored bottles. Roof supported by telephone poles. Areas of wall collapsed in the 1994 Northridge earthquake. Camera facing east. - Grandma Prisbrey's Bottle Village, 4595 Cochran Street, Simi Valley, Ventura County, CA

  16. Cleopatra's Bedroom oblique with picture tube wall along walkway. Structure ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Cleopatra's Bedroom oblique with picture tube wall along walkway. Structure is made solely of amber colored bottles. Roof supported by telephone poles. Areas of bottle wall above window opening collapsed in the 1994 Northridge earthquake. Camera facing northeast. - Grandma Prisbrey's Bottle Village, 4595 Cochran Street, Simi Valley, Ventura County, CA

  17. (11-22) semipolar InGaN emitters from green to amber on overgrown GaN on micro-rod templates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bai, J., E-mail: j.bai@sheffield.ac.uk; Xu, B.; Guzman, F. G.

    2015-12-28

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

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

    PubMed

    Li, Pengfei; Merz, Kenneth M

    2016-04-25

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

  19. Maternally inherited architecture in tertiary leaf beetles: paleoichnology of cryptocephaline fecal cases in Dominican and Baltic amber.

    PubMed

    Chaboo, Caroline S; Engel, Michael S; Chamorro-Lacayo, Maria Lourdes

    2009-09-01

    Complex ethological adaptations and intraspecific interactions leave few fossil traces. We document three Dominican (20 million years old [myo]) and Baltic (45 myo) amber fossils that exhibit firm evidence of highly integrated interactions between mothers and offspring in the diverse camptosomate lineage of beetles (Chrysomelidae, leaf beetles). As in contemporary species, these hard cases were initially constructed by mothers, then inherited and retained by offspring, which then elaborate this protective domicile with an unusual but economical building material, their feces. The three fossils are classified in the Subfamily Cryptocephalinae; two are classified in the tribe Chlamisini based on morphological evidence-the flattened head lacking a sharp keel and long legs with simple recurved untoothed claws. These diagnostic features are not clearly visible in the third specimen to permit more refined identification. These fossils provide more precise paleontological dating of tribal nodes within the cryptocephaline radiation of leaf beetles. These fossils are the first and earliest evidence of mother-offspring interaction, building behavior, and fecal recycling in Camptosomata beetles and of inheritance of architectural structures in beetles.

  20. For whom the bell tolls: Silver Alerts raise concerns regarding individual rights and governmental interests.

    PubMed

    Wasser, Tobias D; Fox, Patrick K

    2013-01-01

    The Silver Alert system was initially created to help protect missing persons who have cognitive impairments, particularly the elderly. The Silver Alert is modeled after the Amber Alert, created to help locate and safeguard missing children. Unlike the Amber Alert, however, in most states the Silver Alert applies to the elderly, adults with a mental impairment, or both, depending on the state. The goal of the Silver Alert system is the quick dissemination of information about missing persons to law enforcement personnel as well as to the general public. Previously, states notified law enforcement personnel of missing persons through teletype to other public safety jurisdictions to enlist their assistance in the retrieval of the missing person. Silver Alert programs substantially expand the notification to include the general public, who receive information through radio and television broadcasts as well as highway billboards. The programs serve a legitimate governmental interest by protecting a vulnerable population from possible harm. Yet, the implementation of these alerts can have unintended consequences, including the possible violation of an individual's right to privacy. Such consequences require careful consideration.

  1. Amber fossils demonstrate deep-time stability of Caribbean lizard communities

    PubMed Central

    Sherratt, Emma; del Rosario Castañeda, María; Garwood, Russell J.; Mahler, D. Luke; Sanger, Thomas J.; Herrel, Anthony; de Queiroz, Kevin; Losos, Jonathan B.

    2015-01-01

    Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils—only three have been described to date—has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales. PMID:26216976

  2. The influence of rear turn-signal characteristics on crash risk.

    PubMed

    Sullivan, John M; Flannagan, Michael J

    2012-02-01

    The relationship between the relative risk of a rear-end collision during a turn, merge, or lane change maneuver and the characteristics of the rear turn-signal configuration was examined using crash data from seven states in the United States. Rear turn-signal characteristics-including color, optics, separation, and light source-were identified for 55 vehicle models and used in a logistic regression analysis to model the odds of a rear-end collision. Additional variables including driver demographics (gender, age), vehicle age, and light condition were also modeled. Risk was assessed using a contrast group of striking vehicles in similar collisions. The results suggest that the odds of being the struck vehicle were 3% to 28% lower among vehicles equipped with amber versus red turn signals. Although the analysis suggests that there may be a safety benefit associated with amber rear turn signals, it is unclear whether turn-signal color alone is responsible. The results suggest that aspects of a vehicle's rear signal characteristics may influence crash risk. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

    PubMed

    Mittal, Jeetain; Best, Robert B

    2010-08-04

    The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Maternally inherited architecture in tertiary leaf beetles: paleoichnology of cryptocephaline fecal cases in Dominican and Baltic amber

    NASA Astrophysics Data System (ADS)

    Chaboo, Caroline S.; Engel, Michael S.; Chamorro-Lacayo, Maria Lourdes

    2009-09-01

    Complex ethological adaptations and intraspecific interactions leave few fossil traces. We document three Dominican (20 million years old [myo]) and Baltic (45 myo) amber fossils that exhibit firm evidence of highly integrated interactions between mothers and offspring in the diverse camptosomate lineage of beetles (Chrysomelidae, leaf beetles). As in contemporary species, these hard cases were initially constructed by mothers, then inherited and retained by offspring, which then elaborate this protective domicile with an unusual but economical building material, their feces. The three fossils are classified in the Subfamily Cryptocephalinae; two are classified in the tribe Chlamisini based on morphological evidence—the flattened head lacking a sharp keel and long legs with simple recurved untoothed claws. These diagnostic features are not clearly visible in the third specimen to permit more refined identification. These fossils provide more precise paleontological dating of tribal nodes within the cryptocephaline radiation of leaf beetles. These fossils are the first and earliest evidence of mother-offspring interaction, building behavior, and fecal recycling in Camptosomata beetles and of inheritance of architectural structures in beetles.

  5. Simulation of carbohydrates, from molecular docking to dynamics in water.

    PubMed

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

    Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

  6. Modeling the mechanism of CLN025 beta-hairpin formation

    NASA Astrophysics Data System (ADS)

    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.

  7. Study on verifying the angle measurement performance of the rotary-laser system

    NASA Astrophysics Data System (ADS)

    Zhao, Jin; Ren, Yongjie; Lin, Jiarui; Yin, Shibin; Zhu, Jigui

    2018-04-01

    An angle verification method to verify the angle measurement performance of the rotary-laser system was developed. Angle measurement performance has a great impact on measuring accuracy. Although there is some previous research on the verification of angle measuring uncertainty for the rotary-laser system, there are still some limitations. High-precision reference angles are used in the study of the method, and an integrated verification platform is set up to evaluate the performance of the system. This paper also probes the error that has biggest influence on the verification system. Some errors of the verification system are avoided via the experimental method, and some are compensated through the computational formula and curve fitting. Experimental results show that the angle measurement performance meets the requirement for coordinate measurement. The verification platform can evaluate the uncertainty of angle measurement for the rotary-laser system efficiently.

  8. Experimental verification of the kinetic theory of FRET using optical microspectroscopy and obligate oligomers.

    PubMed

    Patowary, Suparna; Pisterzi, Luca F; Biener, Gabriel; Holz, Jessica D; Oliver, Julie A; Wells, James W; Raicu, Valerică

    2015-04-07

    Förster resonance energy transfer (FRET) is a nonradiative process for the transfer of energy from an optically excited donor molecule (D) to an acceptor molecule (A) in the ground state. The underlying theory predicting the dependence of the FRET efficiency on the sixth power of the distance between D and A has stood the test of time. In contrast, a comprehensive kinetic-based theory developed recently for FRET efficiencies among multiple donors and acceptors in multimeric arrays has waited for further testing. That theory has been tested in the work described in this article using linked fluorescent proteins located in the cytoplasm and at the plasma membrane of living cells. The cytoplasmic constructs were fused combinations of Cerulean as donor (D), Venus as acceptor (A), and a photo-insensitive molecule (Amber) as a nonfluorescent (N) place holder: namely, NDAN, NDNA, and ADNN duplexes, and the fully fluorescent quadruplex ADAA. The membrane-bound constructs were fused combinations of GFP2 as donor (D) and eYFP as acceptor (A): namely, two fluorescent duplexes (i.e., DA and AD) and a fluorescent triplex (ADA). According to the theory, the FRET efficiency of a multiplex such as ADAA or ADA can be predicted from that of analogs containing a single acceptor (e.g., NDAN, NDNA, and ADNN, or DA and AD, respectively). Relatively small but statistically significant differences were observed between the measured and predicted FRET efficiencies of the two multiplexes. While elucidation of the cause of this mismatch could be a worthy endeavor, the discrepancy does not appear to question the theoretical underpinnings of a large family of FRET-based methods for determining the stoichiometry and quaternary structure of complexes of macromolecules in living cells. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. Verification bias: an under-recognized source of error in assessing the efficacy of MRI of the meniscii.

    PubMed

    Richardson, Michael L; Petscavage, Jonelle M

    2011-11-01

    The sensitivity and specificity of magnetic resonance imaging (MRI) for diagnosis of meniscal tears has been studied extensively, with tears usually verified by surgery. However, surgically unverified cases are often not considered in these studies, leading to verification bias, which can falsely increase the sensitivity and decrease the specificity estimates. Our study suggests that such bias may be very common in the meniscal MRI literature, and illustrates techniques to detect and correct for such bias. PubMed was searched for articles estimating sensitivity and specificity of MRI for meniscal tears. These were assessed for verification bias, deemed potentially present if a study included any patients whose MRI findings were not surgically verified. Retrospective global sensitivity analysis (GSA) was performed when possible. Thirty-nine of the 314 studies retrieved from PubMed specifically dealt with meniscal tears. All 39 included unverified patients, and hence, potential verification bias. Only seven articles included sufficient information to perform GSA. Of these, one showed definite verification bias, two showed no bias, and four others showed bias within certain ranges of disease prevalence. Only 9 of 39 acknowledged the possibility of verification bias. Verification bias is underrecognized and potentially common in published estimates of the sensitivity and specificity of MRI for the diagnosis of meniscal tears. When possible, it should be avoided by proper study design. If unavoidable, it should be acknowledged. Investigators should tabulate unverified as well as verified data. Finally, verification bias should be estimated; if present, corrected estimates of sensitivity and specificity should be used. Our online web-based calculator makes this process relatively easy. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

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

    PubMed Central

    Nouvel, Laurent X; Vultos, Tiago Dos; Kassa-Kelembho, Eric; Rauzier, Jean; Gicquel, Brigitte

    2007-01-01

    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. PMID:17506895

  11. Stability of an extemporaneously prepared thalidomide suspension.

    PubMed

    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.

  12. Stability of an extemporaneous alcohol-free melatonin suspension.

    PubMed

    Johnson, Cary E; Cober, Mary Petrea; Thome, Tennille; Rouse, Emily

    2011-03-01

    The stability of alcohol-free oral suspensions of melatonin 1 mg/mL, extemporaneously prepared from two commercially available melatonin tablet products, was studied. Four 1-mg/mL melatonin suspensions were prepared. Formulations A and B contained 20 crushed 3-mg tablets of melatonin combined with a 1:1 mixture of Ora-Plus and either Ora-Sweet or Ora-Sweet SF to produce a volume of 60 mL. Formulations C and D were prepared by crushing 20 combination tablets containing melatonin 3 mg and pyridoxine hydrochloride 10 mg and then combining the powder with a 1:1 mixture of Ora-Plus and either Ora-Sweet or Ora-Sweet SF to produce a 60-mL volume. The suspensions were prepared in triplicate and stored at room temperature in amber plastic prescription bottles. Immediately after preparation and on days 7, 15, 30, 60, and 90, the samples were assayed in duplicate by stability-indicating high-performance liquid chromatography (HPLC). The samples were also evaluated for any changes in color, odor, and taste. HPLC analysis demonstrated that at least 94% of the initial melatonin concentration in formulations A and B, and at least 98% of that in formulations C and D, remained throughout the 90-day study period. Detectable changes in color, odor, or taste occurred in all of the formulations. Extemporaneously prepared, alcohol-free, 1-mg/mL suspensions of melatonin and melatonin-pyridoxine hydrochloride in a 1:1 mixture of Ora-Plus and either Ora Sweet or Ora Sweet SF were stable for at least 90 days when stored in 2-oz amber plastic bottles at room temperature.

  13. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

    PubMed

    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.

  14. The phylogeny of fossil whip spiders.

    PubMed

    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 broad phylogenetic framework for both the fossil and Recent whip spiders against which future discoveries can be tested.

  15. Stability of Extemporaneously Compounded Dexamethasone in Glass and Plastic Bottles and Plastic Syringes

    PubMed Central

    Ensom, Mary H H; Décarie, Diane

    2014-01-01

    Background Dexamethasone is widely used to treat rheumatic and endocrine disorders and chemotherapy-induced nausea and vomiting. A palatable, alcohol-free liquid formulation, with a suitable concentration to allow reasonable administration volume, is available only via extemporaneous compounding. Objective: To evaluate the stability of dexamethasone suspensions in commercially available vehicles (Oral Mix and Oral Mix SF) in various types of containers after storage at 25°C and 4°C for up to 91 days. Methods: Dexamethasone suspensions (1 mg/mL) were prepared in Oral Mix and Oral Mix SF and then transferred to amber glass and plastic prescription bottles and plastic oral syringes. Suspensions in all 3 types of containers were stored at 25°C; suspensions in glass and plastic bottles were also stored at 4°C. Samples were collected weekly from each container up to 28 days and then every 2 weeks up to 91 days. The samples were analyzed by a validated, stability-indicating high-performance liquid chromatography − ultraviolet detection method. A suspension was considered stable if it maintained at least 90% of its initial dexamethasone concentration. Changes in colour, taste, odour, precipitation (and ease of resuspension), and pH were used to assess physical compatibility. Results: All suspensions maintained at least 96% of the original concentration for up to 91 days with storage at 25°C or at 4°C. No notable changes in colour, taste, odour, precipitation, or pH were observed over the 91-day period. Conclusion: Dexamethasone suspensions (1 mg/mL) in Oral Mix and Oral Mix SF, stored in amber glass or plastic bottles or plastic syringes at 25°C or in amber glass or plastic bottles at 4°C can be expected to remain stable for up to 91 days. PMID:25214658

  16. Selective-area nanoheteroepitaxy for light emitting diode (LED) applications

    NASA Astrophysics Data System (ADS)

    Wildeson, Isaac H.

    Over 20% of the electricity in the United States is consumed for lighting, and the majority of this energy is wasted as heat during the lighting process. A solid-state (or light emitting diode (LED)-based) light source has the potential of saving the United States billions of dollars in electricity and reducing megatons of global CO2 emissions annually. While white light LEDs are currently on the market with efficiencies that are superior to incandescent and fluorescent light sources, their high up-front cost is inhibiting mass adoption. One reason for the high cost is the inefficiency of green and amber LEDs that can used to make white light. The inefficiency of green and amber LEDs results in more of these chips being required, and thus a higher cost. Improvements in the performance of green and amber LEDs is also required in order to realize the full potential of solid-state lighting. Nanoheteroepitaxy is an interesting route towards achieving efficient green and amber LEDs as it resolves major challenges that are currently plaguing III-nitride LEDs such as high dislocation densities and limited active region critical thicknesses. A method for fabricating III-nitride nanopyramid LEDs is presented that employs conventional processing used in industry. The present document begins with an overview of the current challenges in III-nitride LEDs and the benefits of nanoheteroepitaxy. A process for controlled selective-area growth of nanopyramid LEDs by organometallic vapor phase epitaxy has been developed throughout the course of this work. Dielectric templates used for the selective-area growth are patterned by two methods, namely porous anodic alumina and electron-beam lithography. The dielectric templates serve as efficient dislocation filters; however, planar defects are initiated during lower temperature growth on the nanopyramids. The quantum wells outline six semipolar planes that form each hexagonal pyramid. Quantum wells grown on these semipolar planes generate built-in electric fields with magnitudes that are one-tenth those on the polar c-plane with the same (In,Ga)N composition. The lateral strain relaxation innate in the nanoheterostructures allows greater coherent InN incorporation in the nanopyramids as compared to thin-film heterostructures, as confirmed by electroluminescence and transmission electron microscopy. In addition to applications for light emitting diodes, selective area growth of GaN nanostructures is also important for biological and sensing applications. A process for fabricating porous GaN nanorods is presented that also relies on selective-area organometallic vapor phase epitaxy. The nanopore walls are primarily outlined by nonpolar planes, and the diameter of the nanopore can be controlled by the diameter of the opening in the dielectric template and the growth time. The lining of the nanopore walls is comprised of crystalline GaN, which makes these structures interesting for sensing, electrical and optical applications.

  17. Stability of extemporaneously prepared oxandrolone oral suspensions.

    PubMed

    Johnson, Cary E; Cober, Mary Petrea; Hawkins, Katherine A; Julian, Justin D

    2011-03-15

    The stability of extemporaneously prepared oxandrolone oral suspensions was studied. Oxandrolone oral suspension (1 mg/mL) was prepared using oxandrolone tablets, Ora-Plus, and either Ora-Sweet or Ora-Sweet SF. Three identical samples of each formulation were prepared and stored in 2-oz amber plastic bottles with child-resistant caps at room temperature (23-25 °C). After thorough but gentle shaking by hand to prevent foaming, a 1-mL sample was withdrawn from each of the six bottles, diluted with mobile phase to an expected concentration of 200 μg/mL, and assayed in duplicate by injecting 5 μL into the high-performance liquid chromatography system immediately after preparation and at 7, 14, 35, 60, and 90 days. The samples were examined for any change in color or pH on each day of analysis. The stability of the suspensions was determined by calculating the percentage of the initial oxandrolone concentration remaining on each test day. Stability was defined as the retention of at least 90% of the initial oxandrolone concentration. At least 98% of the original oxandrolone concentration remained in both formulations at the end of the 90-day study period. There was no appreciable change in odor, taste, color, or pH. Both suspensions remained white in color and sweet with no aftertaste throughout the study period. The oxandrolone was easily resuspended with gentle shaking. Extemporaneously prepared suspensions of oxandrolone 1 mg/mL in 1:1 mixtures of Ora-Plus and either Ora-Sweet or Ora-Sweet SF were stable for at least 90 days when stored in 2-oz amber plastic bottles at room temperature.

  18. Stability of an extemporaneously prepared tadalafil suspension.

    PubMed

    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.

  19. Verification of EPA's " Preliminary remediation goals for radionuclides" (PRG) electronic calculator

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stagich, B. H.

    The U.S. Environmental Protection Agency (EPA) requested an external, independent verification study of their “Preliminary Remediation Goals for Radionuclides” (PRG) electronic calculator. The calculator provides information on establishing PRGs for radionuclides at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites with radioactive contamination (Verification Study Charge, Background). These risk-based PRGs set concentration limits using carcinogenic toxicity values under specific exposure conditions (PRG User’s Guide, Section 1). The purpose of this verification study is to ascertain that the computer codes has no inherit numerical problems with obtaining solutions as well as to ensure that the equations are programmed correctly.

  20. Fingerprint changes and verification failure among patients with hand dermatitis.

    PubMed

    Lee, Chew Kek; Chang, Choong Chor; Johar, Asmah; Puwira, Othman; Roshidah, Baba

    2013-03-01

    To determine the prevalence of fingerprint verification failure and to define and quantify the fingerprint changes associated with fingerprint verification failure. Case-control study. Referral public dermatology center. The study included 100 consecutive patients with clinical hand dermatitis involving the palmar distal phalanx of either thumb and 100 age-, sex-, and ethnicity-matched controls. Patients with an altered thumb print due to other causes and palmar hyperhidrosis were excluded. Fingerprint verification(pass/fail) and hand eczema severity index score. Twenty-seven percent of patients failed fingerprint verification compared with 2% of controls. Fingerprint verification failure was associated with a higher hand eczema severity index score (P.001). The main fingerprint abnormalities were fingerprint dystrophy (42.0%) and abnormal white lines (79.5%). The number of abnormal white lines was significantly higher among the patients with hand dermatitis compared with controls(P=.001). Among the patients with hand dermatitis, theodds of failing fingerprint verification with fingerprint dystrophy was 4.01. The presence of broad lines and long lines was associated with a greater odds of fingerprint verification failure (odds ratio [OR], 8.04; 95% CI, 3.56-18.17 and OR, 2.37; 95% CI, 1.31-4.27, respectively),while the presence of thin lines was protective of verification failure (OR, 0.45; 95% CI, 0.23-0.89). Fingerprint verification failure is a significant problem among patients with more severe hand dermatitis. It is mainly due to fingerprint dystrophy and abnormal white lines. Malaysian National Medical Research Register Identifier: NMRR-11-30-8226

  1. Response to "Improving Patient Safety With Error Identification in Chemotherapy Orders by Verification Nurses"
.

    PubMed

    Zhu, Ling-Ling; Lv, Na; Zhou, Quan

    2016-12-01

    We read, with great interest, the study by Baldwin and Rodriguez (2016), which described the role of the verification nurse and details the verification process in identifying errors related to chemotherapy orders. We strongly agree with their findings that a verification nurse, collaborating closely with the prescribing physician, pharmacist, and treating nurse, can better identify errors and maintain safety during chemotherapy administration.

  2. Being known, intimate, and valued: global self-verification and dyadic adjustment in couples and roommates.

    PubMed

    Katz, Jennifer; Joiner, Thomas E

    2002-02-01

    We contend that close relationships provide adults with optimal opportunities for personal growth when relationship partners provide accurate, honest feedback. Accordingly, it was predicted that young adults would experience the relationship quality with relationship partners who evaluated them in a manner consistent their own self-evaluations. Three empirical tests of this self-verification hypothesis as applied to close dyads were conducted. In Study 1, young adults in dating relationships were most intimate with and somewhat more committed to partners when they perceived that partners evaluated them as they evaluated themselves. Self-verification effects were pronounced for those involved in more serious dating relationships. In Study 2, men reported the greatest esteem for same-sex roommates who evaluated them in a self-verifying manner. Results from Study 2 were replicated and extended to both male and female roommate dyads in Study 3. Further, self-verification effects were most pronounced for young adults with high emotional empathy. Results suggest that self-verification theory is useful for understanding dyadic adjustment across a variety of relational contexts in young adulthood. Implications of self-verification processes for adult personal development are outlined within an identity negotiation framework.

  3. Alaska biological control program directed at amber-marked birch leaf miner.

    Treesearch

    J.E. Lundquist; K.F. Zogas; C.L. Snyder; B.K. Schulz

    2008-01-01

    Nonnative invasive insects are having major impacts on the economics and ecology of forests nationwide. Until recently, Alaska was fortunately mostly free of these pests. Because of the remoteness of much of Alaska's native forests, an invasive pest infestation would be extremely difficult to control. Global markets, global climate change, and the ever-increasing...

  4. The oldest fossil mushroom.

    PubMed

    Heads, Sam W; Miller, Andrew N; Crane, J Leland; Thomas, M Jared; Ruffatto, Danielle M; Methven, Andrew S; Raudabaugh, Daniel B; Wang, Yinan

    2017-01-01

    A new fossil mushroom is described and illustrated from the Lower Cretaceous Crato Formation of northeast Brazil. Gondwanagaricites magnificus gen. et sp. nov. is remarkable for its exceptional preservation as a mineralized replacement in laminated limestone, as all other fossil mushrooms are known from amber inclusions. Gondwanagaricites represents the oldest fossil mushroom to date and the first fossil mushroom from Gondwana.

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

    ERIC Educational Resources Information Center

    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…

  6. 49 CFR 221.14 - Marking devices.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... side of the horizontal center line as defined in terms of the 50 candela intensity points; (3) A color defined by the red-orange-amber color range; and (4) If a flashing light is used, a flash rate of not less... intensity of not less than 100 candela nor more than 1000 candela for flashing lights) as measured at the...

  7. 49 CFR 221.14 - Marking devices.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... side of the horizontal center line as defined in terms of the 50 candela intensity points; (3) A color defined by the red-orange-amber color range; and (4) If a flashing light is used, a flash rate of not less... intensity of not less than 100 candela nor more than 1000 candela for flashing lights) as measured at the...

  8. 49 CFR 221.14 - Marking devices.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... side of the horizontal center line as defined in terms of the 50 candela intensity points; (3) A color defined by the red-orange-amber color range; and (4) If a flashing light is used, a flash rate of not less... intensity of not less than 100 candela nor more than 1000 candela for flashing lights) as measured at the...

  9. 49 CFR 221.14 - Marking devices.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... side of the horizontal center line as defined in terms of the 50 candela intensity points; (3) A color defined by the red-orange-amber color range; and (4) If a flashing light is used, a flash rate of not less... intensity of not less than 100 candela nor more than 1000 candela for flashing lights) as measured at the...

  10. 75 FR 47025 - Endangered and Threatened Wildlife and Plants; Initiation of 5-Year Reviews of Five Listed...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-04

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R5-ES-2010-N148; 50120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Initiation of 5- Year Reviews of Five Listed Species: Delmarva Peninsula Fox Squirrel, Northeastern Bulrush, Furbish Lousewort, Chittenango Ovate Amber Snail, and Virginia...

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

    DTIC Science & Technology

    2011-07-01

    Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

  12. 2018 NDIA Precision Strike Annual Review (PSAR-18)

    DTIC Science & Technology

    2018-03-20

    Director for Space and Prompt Strike, OUSD for Acquisition and Sustainment (OUSD(A&S)) 1100 DARPA OPERATIONAL FIRES: Major Amber Walker, USA, Ph.D...Program Manager , Tactical Technology Office, Defense Advanced Research Projects Agency (DARPA) 1120 TURNING EXISTING TECHNOLOGIES AND WEAPONS INTO...SURPRISING NEW CAPABILITIES—FAST: Vincent Sabio—Program Manager , Advanced Technology Programs, Strategic Capabilities Office (SCO), OUSD for

  13. 33 CFR 117.393 - Illinois Waterway.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... light to indicate that vessels may pass. (2) When a vessel is approaching and the draw is in the open... remains open until passage is complete. (3) When a vessel is approaching and the draw is in the closed..., flashing amber lights are displayed. (4) When a train approaches the bridge and the draw is in the open...

  14. The oldest fossil mushroom

    PubMed Central

    Miller, Andrew N.; Crane, J. Leland; Thomas, M. Jared; Ruffatto, Danielle M.; Methven, Andrew S.; Raudabaugh, Daniel B.; Wang, Yinan

    2017-01-01

    A new fossil mushroom is described and illustrated from the Lower Cretaceous Crato Formation of northeast Brazil. Gondwanagaricites magnificus gen. et sp. nov. is remarkable for its exceptional preservation as a mineralized replacement in laminated limestone, as all other fossil mushrooms are known from amber inclusions. Gondwanagaricites represents the oldest fossil mushroom to date and the first fossil mushroom from Gondwana. PMID:28591180

  15. 49 CFR 221.14 - Marking devices.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... side of the horizontal center line as defined in terms of the 50 candela intensity points; (3) A color defined by the red-orange-amber color range; and (4) If a flashing light is used, a flash rate of not less... classification light on the rear of the locomotive, provided it complies with paragraph (a) of this section; or...

  16. 21 CFR 184.1595 - Pepsin.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... amber to brown liquid. Its characterizing enzyme activity is that of a peptide hydrolase (EC 3.4.23.1...) The ingredient is used as an enzyme as defined in § 170.3(o)(9) of this chapter to hydrolyze proteins... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Pepsin. 184.1595 Section 184.1595 Food and Drugs...

  17. 21 CFR 184.1595 - Pepsin.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... amber to brown liquid. Its characterizing enzyme activity is that of a peptide hydrolase (EC 3.4.23.1...) The ingredient is used as an enzyme as defined in § 170.3(o)(9) of this chapter to hydrolyze proteins... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Pepsin. 184.1595 Section 184.1595 Food and Drugs...

  18. 21 CFR 184.1595 - Pepsin.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... amber to brown liquid. Its characterizing enzyme activity is that of a peptide hydrolase (EC 3.4.23.1...) The ingredient is used as an enzyme as defined in § 170.3(o)(9) of this chapter to hydrolyze proteins... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Pepsin. 184.1595 Section 184.1595 Food and Drugs...

  19. Compromises produced by the dialectic between self-verification and self-enhancement.

    PubMed

    Morling, B; Epstein, S

    1997-12-01

    Three studies of people's reactions to evaluative feedback demonstrated that the dialectic between self-enhancement and self-verification results in compromises between these 2 motives, as hypothesized in cognitive-experiential self-theory. The demonstration was facilitated by 2 procedural improvements: Enhancement and verification were established by calibrating evaluative feedback against self appraisals, and degree of enhancement and of verification were varied along a continuum, rather than categorically. There was also support for the hypotheses that processing in an intuitive-experiential mode favors enhancement and processing in an analytical-rational mode favors verification in the kinds of situations investigated.

  20. Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

    PubMed Central

    2015-01-01

    Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

  1. Verification and Validation Studies for the LAVA CFD Solver

    NASA Technical Reports Server (NTRS)

    Moini-Yekta, Shayan; Barad, Michael F; Sozer, Emre; Brehm, Christoph; Housman, Jeffrey A.; Kiris, Cetin C.

    2013-01-01

    The verification and validation of the Launch Ascent and Vehicle Aerodynamics (LAVA) computational fluid dynamics (CFD) solver is presented. A modern strategy for verification and validation is described incorporating verification tests, validation benchmarks, continuous integration and version control methods for automated testing in a collaborative development environment. The purpose of the approach is to integrate the verification and validation process into the development of the solver and improve productivity. This paper uses the Method of Manufactured Solutions (MMS) for the verification of 2D Euler equations, 3D Navier-Stokes equations as well as turbulence models. A method for systematic refinement of unstructured grids is also presented. Verification using inviscid vortex propagation and flow over a flat plate is highlighted. Simulation results using laminar and turbulent flow past a NACA 0012 airfoil and ONERA M6 wing are validated against experimental and numerical data.

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

    PubMed

    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.

  3. Evaluation of Bacto TB hydrolysis reagent (Tween 80) for the identification of Branhamella catarrhalis.

    PubMed Central

    Weiner, M; Penha, P D

    1990-01-01

    An investigation of the hydrolysis of Tween 80 reagent by Branhamella catarrhalis and related organisms (Neisseria and Moraxella species) revealed that only B. catarrhalis gave a positive result. A total of 226 strains, including reference organisms and clinical isolates, were studied. B. catarrhalis changed the color of the reagent from amber to pink-red after overnight incubation. We recommend this simple and cost-effective test as an alternative procedure to DNase testing or tributyrin hydrolysis or as a supplemental procedure for the identification of B. catarrhalis in clinical specimens. PMID:2105335

  4. Studies on thermal decomposition behaviors of polypropylene using molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Huang, Jinbao; He, Chao; Tong, Hong; Pan, Guiying

    2017-11-01

    Polypropylene (PP) is one of the main components of waste plastics. In order to understand the mechanism of PP thermal decomposition, the pyrolysis behaviour of PP has been simulated from 300 to 1000 K in periodic boundary conditions by molecular dynamic method, based on AMBER force field. The simulation results show that the pyrolysis process of PP can mostly be divided into three stages: low temperature pyrolysis stage, intermediate temperature stage and high temperature pyrolysis stage. PP pyrolysis is typical of random main-chain scission, and the possible formation mechanism of major pyrolysis products was analyzed.

  5. 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.

    PubMed

    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.

  6. You Can't See the Real Me: Attachment Avoidance, Self-Verification, and Self-Concept Clarity.

    PubMed

    Emery, Lydia F; Gardner, Wendi L; Carswell, Kathleen L; Finkel, Eli J

    2018-03-01

    Attachment shapes people's experiences in their close relationships and their self-views. Although attachment avoidance and anxiety both undermine relationships, past research has primarily emphasized detrimental effects of anxiety on the self-concept. However, as partners can help people maintain stable self-views, avoidant individuals' negative views of others might place them at risk for self-concept confusion. We hypothesized that avoidance would predict lower self-concept clarity and that less self-verification from partners would mediate this association. Attachment avoidance was associated with lower self-concept clarity (Studies 1-5), an effect that was mediated by low self-verification (Studies 2-3). The association between avoidance and self-verification was mediated by less self-disclosure and less trust in partner feedback (Study 4). Longitudinally, avoidance predicted changes in self-verification, which in turn predicted changes in self-concept clarity (Study 5). Thus, avoidant individuals' reluctance to trust or become too close to others may result in hidden costs to the self-concept.

  7. Shuttle payload interface verification equipment study. Volume 2: Technical document, part 1

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The technical analysis is reported that was performed during the shuttle payload interface verification equipment study. It describes: (1) the background and intent of the study; (2) study approach and philosophy covering all facets of shuttle payload/cargo integration; (3)shuttle payload integration requirements; (4) preliminary design of the horizontal IVE; (5) vertical IVE concept; and (6) IVE program development plans, schedule and cost. Also included is a payload integration analysis task to identify potential uses in addition to payload interface verification.

  8. A Roadmap for the Implementation of Continued Process Verification.

    PubMed

    Boyer, Marcus; Gampfer, Joerg; Zamamiri, Abdel; Payne, Robin

    2016-01-01

    In 2014, the members of the BioPhorum Operations Group (BPOG) produced a 100-page continued process verification case study, entitled "Continued Process Verification: An Industry Position Paper with Example Protocol". This case study captures the thought processes involved in creating a continued process verification plan for a new product in response to the U.S. Food and Drug Administration's guidance on the subject introduced in 2011. In so doing, it provided the specific example of a plan developed for a new molecular antibody product based on the "A MAb Case Study" that preceded it in 2009.This document provides a roadmap that draws on the content of the continued process verification case study to provide a step-by-step guide in a more accessible form, with reference to a process map of the product life cycle. It could be used as a basis for continued process verification implementation in a number of different scenarios: For a single product and process;For a single site;To assist in the sharing of data monitoring responsibilities among sites;To assist in establishing data monitoring agreements between a customer company and a contract manufacturing organization. The U.S. Food and Drug Administration issued guidance on the management of manufacturing processes designed to improve quality and control of drug products. This involved increased focus on regular monitoring of manufacturing processes, reporting of the results, and the taking of opportunities to improve. The guidance and practice associated with it is known as continued process verification This paper summarizes good practice in responding to continued process verification guidance, gathered from subject matter experts in the biopharmaceutical industry. © PDA, Inc. 2016.

  9. Verification of operational solar flare forecast: Case of Regional Warning Center Japan

    NASA Astrophysics Data System (ADS)

    Kubo, Yûki; Den, Mitsue; Ishii, Mamoru

    2017-08-01

    In this article, we discuss a verification study of an operational solar flare forecast in the Regional Warning Center (RWC) Japan. The RWC Japan has been issuing four-categorical deterministic solar flare forecasts for a long time. In this forecast verification study, we used solar flare forecast data accumulated over 16 years (from 2000 to 2015). We compiled the forecast data together with solar flare data obtained with the Geostationary Operational Environmental Satellites (GOES). Using the compiled data sets, we estimated some conventional scalar verification measures with 95% confidence intervals. We also estimated a multi-categorical scalar verification measure. These scalar verification measures were compared with those obtained by the persistence method and recurrence method. As solar activity varied during the 16 years, we also applied verification analyses to four subsets of forecast-observation pair data with different solar activity levels. We cannot conclude definitely that there are significant performance differences between the forecasts of RWC Japan and the persistence method, although a slightly significant difference is found for some event definitions. We propose to use a scalar verification measure to assess the judgment skill of the operational solar flare forecast. Finally, we propose a verification strategy for deterministic operational solar flare forecasting. For dichotomous forecast, a set of proposed verification measures is a frequency bias for bias, proportion correct and critical success index for accuracy, probability of detection for discrimination, false alarm ratio for reliability, Peirce skill score for forecast skill, and symmetric extremal dependence index for association. For multi-categorical forecast, we propose a set of verification measures as marginal distributions of forecast and observation for bias, proportion correct for accuracy, correlation coefficient and joint probability distribution for association, the likelihood distribution for discrimination, the calibration distribution for reliability and resolution, and the Gandin-Murphy-Gerrity score and judgment skill score for skill.

  10. The influence of verification jig on framework fit for nonsegmented fixed implant-supported complete denture.

    PubMed

    Ercoli, Carlo; Geminiani, Alessandro; Feng, Changyong; Lee, Heeje

    2012-05-01

    The purpose of this retrospective study was to assess if there was a difference in the likelihood of achieving passive fit when an implant-supported full-arch prosthesis framework is fabricated with or without the aid of a verification jig. This investigation was approved by the University of Rochester Research Subject Review Board (protocol #RSRB00038482). Thirty edentulous patients, 49 to 73 years old (mean 61 years old), rehabilitated with a nonsegmented fixed implant-supported complete denture were included in the study. During the restorative process, final impressions were made using the pickup impression technique and elastomeric impression materials. For 16 patients, a verification jig was made (group J), while for the remaining 14 patients, a verification jig was not used (group NJ) and the framework was fabricated directly on the master cast. During the framework try-in appointment, the fit was assessed by clinical (Sheffield test) and radiographic inspection and recorded as passive or nonpassive. When a verification jig was used (group J, n = 16), all frameworks exhibited clinically passive fit, while when a verification jig was not used (group NJ, n = 14), only two frameworks fit. This difference was statistically significant (p < .001). Within the limitations of this retrospective study, the fabrication of a verification jig ensured clinically passive fit of metal frameworks in nonsegmented fixed implant-supported complete denture. © 2011 Wiley Periodicals, Inc.

  11. Identity Verification, Control, and Aggression in Marriage

    ERIC Educational Resources Information Center

    Stets, Jan E.; Burke, Peter J.

    2005-01-01

    In this research we study the identity verification process and its effects in marriage. Drawing on identity control theory, we hypothesize that a lack of verification in the spouse identity (1) threatens stable self-meanings and interaction patterns between spouses, and (2) challenges a (nonverified) spouse's perception of control over the…

  12. Students' Verification Strategies for Combinatorial Problems

    ERIC Educational Resources Information Center

    Mashiach Eizenberg, Michal; Zaslavsky, Orit

    2004-01-01

    We focus on a major difficulty in solving combinatorial problems, namely, on the verification of a solution. Our study aimed at identifying undergraduate students' tendencies to verify their solutions, and the verification strategies that they employ when solving these problems. In addition, an attempt was made to evaluate the level of efficiency…

  13. QPF verification using different radar-based analyses: a case study

    NASA Astrophysics Data System (ADS)

    Moré, J.; Sairouni, A.; Rigo, T.; Bravo, M.; Mercader, J.

    2009-09-01

    Verification of QPF in NWP models has been always challenging not only for knowing what scores are better to quantify a particular skill of a model but also for choosing the more appropriate methodology when comparing forecasts with observations. On the one hand, an objective verification technique can provide conclusions that are not in agreement with those ones obtained by the "eyeball" method. Consequently, QPF can provide valuable information to forecasters in spite of having poor scores. On the other hand, there are difficulties in knowing the "truth" so different results can be achieved depending on the procedures used to obtain the precipitation analysis. The aim of this study is to show the importance of combining different precipitation analyses and verification methodologies to obtain a better knowledge of the skills of a forecasting system. In particular, a short range precipitation forecasting system based on MM5 at 12 km coupled with LAPS is studied in a local convective precipitation event that took place in NE Iberian Peninsula on October 3rd 2008. For this purpose, a variety of verification methods (dichotomous, recalibration and object oriented methods) are used to verify this case study. At the same time, different precipitation analyses are used in the verification process obtained by interpolating radar data using different techniques.

  14. Mineral Time Capsules on Mars?

    NASA Technical Reports Server (NTRS)

    Schirber, Michael

    2006-01-01

    Like dinosaur-age insects trapped in amber, biomolecules sequestered in million-year-old sulfate minerals could provide a glimpse into the past, say researchers who've recently analyzed such minerals from N orth America. The same minerals have recently been discovered on Mars , so they may be a good place to look for traces of past life on the red planet, the researchers say.

  15. Gemstones

    USGS Publications Warehouse

    Olson, D.W.

    2006-01-01

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

  16. 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)

    USDA-ARS?s Scientific Manuscript database

    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 ...

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

    Treesearch

    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...

  18. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false 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...

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

    PubMed

    McIntyre, Scott E; Gugerty, Leo

    2014-06-01

    This field experiment takes a novel approach in applying methodologies and theories of visual search to the subject of conspicuity in automobile rear lighting. Traditional rear lighting research has not used the visual search paradigm in experimental design. It is our claim that the visual search design uniquely uncovers visual attention processes operating when drivers search the visual field that current designs fail to capture. This experiment is a validation and extension of previous simulator research on this same topic and demonstrates that detection of red automobile brake lamps will be improved if tail lamps are another color (in this test, amber) rather than the currently mandated red. Results indicate that when drivers miss brake lamp onset in low ambient light, RT and error are reduced in detecting the presence and absence of red brake lamps with multiple lead vehicles when tail lamps are not red compared to current rear lighting which mandates red tail lamps. This performance improvement is attributed to efficient visual processing that automatically segregates tail (amber) and brake (red) lamp colors into distractors and targets respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. The development of a standardised diet history tool to support the diagnosis of food allergy.

    PubMed

    Skypala, Isabel J; Venter, Carina; Meyer, Rosan; deJong, Nicolette W; Fox, Adam T; Groetch, Marion; Oude Elberink, J N; Sprikkelman, Aline; Diamandi, Louiza; Vlieg-Boerstra, Berber J

    2015-01-01

    The disparity between reported and diagnosed food allergy makes robust diagnosis imperative. The allergy-focussed history is an important starting point, but published literature on its efficacy is sparse. Using a structured approach to connect symptoms, suspected foods and dietary intake, a multi-disciplinary task force of the European Academy of Allergy and Clinical Immunology developed paediatric and adult diet history tools. Both tools are divided into stages using traffic light labelling (red, amber and green). The red stage requires the practitioner to gather relevant information on symptoms, atopic history, food triggers, foods eaten and nutritional issues. The amber stage facilitates interpretation of the responses to the red-stage questions, thus enabling the practitioner to prepare to move forward. The final green stage provides a summary template and test algorithm to support continuation down the diagnostic pathway. These tools will provide a standardised, practical approach to support food allergy diagnosis, ensuring that all relevant information is captured and interpreted in a robust manner. Future work is required to validate their use in diverse age groups, disease entities and in different countries, in order to account for differences in health care systems, food availability and dietary norms.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2014-01-14

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

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

    PubMed

    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.

  4. Extension of historical range of Betylobraconinae (Hymenoptera: Braconidae) into Palaearctic Region based on a Baltic amber fossil, and description of a new species of Mesocentrus Szépligeti from Papua New Guinea.

    PubMed

    Butcher, Buntika Areekul; Zaldivar-Riverón, Alejandro; Van de Kamp, Thomas; Rolo, Tomy Dos Santos; Baumbach, Tilo; Quicke, Donald L J

    2014-09-09

    Two new species of the parasitic wasp genus Mesocentrus Szépligeti (Betylobraconinae) are described. One based on a new species from Papua New Guinea, the other the first Palaearctic member of the subfamily based on a 30+ mya, species from Baltic amber. The second species is illustrated using synchrotron X-ray microtomography. Whereas the extant Betylobraconinae are restricted to Australia, New Guinea and New Caledonia, their ancestral distribution is now known to have extended considerably further. A key to the four species of Mesocentrus known from Papua New Guinea is provided. Both species possess some putatively plesiomorphic characters absent in other extant Mesocentrus spp. The new extant species differs in having a considerably larger number of antennal segments and a less laterally depressed frons, while the extinct one has the clypeus separated from the face dorsally and strongly developed hypoclypeal depression. Availability of sequence data for this species enabled further analysis of the relationships of the subfamily, which we present in a phylogenetic analysis additionally including the release of a number of new sequences of related taxa. 

  5. Carnivorous leaves from Baltic amber.

    PubMed

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

    2015-01-06

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

  6. Carnivorous leaves from Baltic amber

    PubMed Central

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

    2015-01-01

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

  7. Goddard Monitors Orions EFT-1 Test Flight

    NASA Image and Video Library

    2017-12-08

    NASA's Goddard Space Flight Center in Greenbelt, Maryland, played a critical role in the test flight of the #Orion spacecraft on Dec. 5, 2014. Goddard's Networks Integration Center, pictured here, coordinated the communications support for both the Orion vehicle and the Delta IV rocket, ensuring complete communications coverage through NASA's Space Network and Tracking and Data Relay Satellite. The Orion spacecraft lifted off from Cape Canaveral Air Force Station's Space Launch Complex 37 in Florida at 7:05 a.m. EST. The Orion capsule splashed down about four and a half hours later, at 11:29 a.m. EST, about 600 miles off the coast of San Diego, California. While no humans were aboard Orion for this test flight, in the future, Orion will allow humans to travel deeper in to space than ever before, including an asteroid and Mars. Credit: NASA/Goddard/Amber Jacobson Credit: NASA/Goddard/Amber Jacobson NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

  8. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

    PubMed

    Shirts, Michael R; Klein, Christoph; Swails, Jason M; Yin, Jian; Gilson, Michael K; Mobley, David L; Case, David A; Zhong, Ellen D

    2017-01-01

    We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

  9. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

    PubMed Central

    Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

    2017-01-01

    We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to a better than 0.1% relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb’s constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison. PMID:27787702

  10. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

    NASA Astrophysics Data System (ADS)

    Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

    2017-01-01

    We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

  11. Self-verification and contextualized self-views.

    PubMed

    Chen, Serena; English, Tammy; Peng, Kaiping

    2006-07-01

    Whereas most self-verification research has focused on people's desire to verify their global self-conceptions, the present studies examined self-verification with regard to contextualized selfviews-views of the self in particular situations and relationships. It was hypothesized that individuals whose core self-conceptions include contextualized self-views should seek to verify these self-views. In Study 1, the more individuals defined the self in dialectical terms, the more their judgments were biased in favor of verifying over nonverifying feedback about a negative, situation-specific self-view. In Study 2, consistent with research on gender differences in the importance of relationships to the self-concept, women but not men showed a similar bias toward feedback about a negative, relationship-specific self-view, a pattern not seen for global self-views. Together, the results support the notion that self-verification occurs for core self-conceptions, whatever form(s) they may take. Individual differences in self-verification and the nature of selfhood and authenticity are discussed.

  12. An exome-wide analysis of low frequency and rare variants in relation to risk of breast cancer in African American Women: the AMBER Consortium

    PubMed Central

    Haddad, Stephen A.; Ruiz-Narváez, Edward A.; Haiman, Christopher A.; Sucheston-Campbell, Lara E.; Bensen, Jeannette T.; Zhu, Qianqian; Liu, Song; Yao, Song; Bandera, Elisa V.; Rosenberg, Lynn; Olshan, Andrew F.; Ambrosone, Christine B.; Palmer, Julie R.; Lunetta, Kathryn L.

    2016-01-01

    A large percentage of breast cancer heritability remains unaccounted for, and most of the known susceptibility loci have been established in European and Asian populations. Rare variants may contribute to the unexplained heritability of this disease, including in women of African ancestry (AA). We conducted an exome-wide analysis of rare variants in relation to risk of overall and subtype-specific breast cancer in the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, which includes data from four large studies of AA women. Genotyping on the Illumina Human Exome Beadchip yielded data for 170 812 SNPs and 8287 subjects: 3629 cases (1093 estrogen receptor negative (ER−), 1968 ER+, 568 ER unknown) and 4658 controls, the largest exome chip study to date for AA breast cancer. Pooled gene-based association analyses were performed using the unified optimal sequence kernel association test (SKAT-O) for variants with minor allele frequency (MAF) ≤ 5%. In addition, each variant with MAF >0.5% was tested for association using logistic regression. There were no significant associations with overall breast cancer. However, a novel gene, FBXL22 (P = 8.2×10–6), and a gene previously identified in GWAS of European ancestry populations, PDE4D (P = 1.2×10–6), were significantly associated with ER− breast cancer after correction for multiple testing. Cases with the associated rare variants were also negative for progesterone and human epidermal growth factor receptors—thus, triple-negative cancer. Replication is required to confirm these gene-level associations, which are based on very small counts at extremely rare SNPs. PMID:27267999

  13. Exposure to Blue Light Increases Subsequent Functional Activation of the Prefrontal Cortex During Performance of a Working Memory Task.

    PubMed

    Alkozei, Anna; Smith, Ryan; Pisner, Derek A; Vanuk, John R; Berryhill, Sarah M; Fridman, Andrew; Shane, Bradley R; Knight, Sara A; Killgore, William D S

    2016-09-01

    Prolonged exposure to blue wavelength light has been shown to have an alerting effect, and enhances performance on cognitive tasks. A small number of studies have also shown that relatively short exposure to blue light leads to changes in functional brain responses during the period of exposure. The extent to which blue light continues to affect brain functioning during a cognitively challenging task after cessation of longer periods of exposure (i.e., roughly 30 minutes or longer), however, has not been fully investigated. A total of 35 healthy participants (18 female) were exposed to either blue (469 nm) (n = 17) or amber (578 nm) (n = 18) wavelength light for 30 minutes in a darkened room, followed immediately by functional magnetic resonance imaging (fMRI) while undergoing a working memory task (N-back task). Participants in the blue light condition were faster in their responses on the N-back task and showed increased activation in the dorsolateral (DLPFC) and ventrolateral (VLPFC) prefrontal cortex compared to those in the amber control light condition. Furthermore, greater activation within the VLPFC was correlated with faster N-back response times. This is the first study to suggest that a relatively brief, single exposure to blue light has a subsequent beneficial effect on working memory performance, even after cessation of exposure, and leads to temporarily persisting functional brain changes within prefrontal brain regions associated with executive functions. These findings may have broader implication for using blue-enriched light in a variety of work settings where alertness and quick decision-making are important. © 2016 Associated Professional Sleep Societies, LLC.

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

    PubMed

    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.

  15. Stability of extemporaneously prepared glycopyrrolate oral suspensions.

    PubMed

    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.

  16. Stability of extemporaneously prepared rifaximin oral suspensions.

    PubMed

    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.

  17. Self-verification and social anxiety: preference for negative social feedback and low social self-esteem.

    PubMed

    Valentiner, David P; Skowronski, John J; McGrath, Patrick B; Smith, Sarah A; Renner, Kerry A

    2011-10-01

    A self-verification model of social anxiety views negative social self-esteem as a core feature of social anxiety. This core feature is proposed to be maintained through self-verification processes, such as by leading individuals with negative social self-esteem to prefer negative social feedback. This model is tested in two studies. In Study 1, questionnaires were administered to a college sample (N = 317). In Study 2, questionnaires were administered to anxiety disordered patients (N = 62) before and after treatment. Study 1 developed measures of preference for negative social feedback and social self-esteem, and provided evidence of their incremental validity in a college sample. Study 2 found that these two variables are not strongly related to fears of evaluation, are relatively unaffected by a treatment that targets such fears, and predict residual social anxiety following treatment. Overall, these studies provide preliminary evidence for a self-verification model of social anxiety.

  18. Systematic study of source mask optimization and verification flows

    NASA Astrophysics Data System (ADS)

    Ben, Yu; Latypov, Azat; Chua, Gek Soon; Zou, Yi

    2012-06-01

    Source mask optimization (SMO) emerged as powerful resolution enhancement technique (RET) for advanced technology nodes. However, there is a plethora of flow and verification metrics in the field, confounding the end user of the technique. Systemic study of different flows and the possible unification thereof is missing. This contribution is intended to reveal the pros and cons of different SMO approaches and verification metrics, understand the commonality and difference, and provide a generic guideline for RET selection via SMO. The paper discusses 3 different type of variations commonly arise in SMO, namely pattern preparation & selection, availability of relevant OPC recipe for freeform source and finally the metrics used in source verification. Several pattern selection algorithms are compared and advantages of systematic pattern selection algorithms are discussed. In the absence of a full resist model for SMO, alternative SMO flow without full resist model is reviewed. Preferred verification flow with quality metrics of DOF and MEEF is examined.

  19. The Effect of Mystery Shopper Reports on Age Verification for Tobacco Purchases

    PubMed Central

    KREVOR, BRAD S.; PONICKI, WILLIAM R.; GRUBE, JOEL W.; DeJONG, WILLIAM

    2011-01-01

    Mystery shops (MS) involving attempted tobacco purchases by young buyers have been employed to monitor retail stores’ performance in refusing underage sales. Anecdotal evidence suggests that MS visits with immediate feedback to store personnel can improve age verification. This study investigated the impact of monthly and twice-monthly MS reports on age verification. Forty-five Walgreens stores were each visited 20 times by mystery shoppers. The stores were randomly assigned to one of three conditions. Control group stores received no feedback, whereas two treatment groups received feedback communications every visit (twice monthly) or every second visit (monthly) after baseline. Logit regression models tested whether each treatment group improved verification rates relative to the control group. Post-baseline verification rates were higher in both treatment groups than in the control group, but only the stores receiving monthly communications had a significantly greater improvement than control group stores. Verification rates increased significantly during the study period for all three groups, with delayed improvement among control group stores. Communication between managers regarding the MS program may account for the delayed age-verification improvements observed in the control group stores. Encouraging inter-store communication might extend the benefits of MS programs beyond those stores that receive this intervention. PMID:21541874

  20. The effect of mystery shopper reports on age verification for tobacco purchases.

    PubMed

    Krevor, Brad S; Ponicki, William R; Grube, Joel W; DeJong, William

    2011-09-01

    Mystery shops involving attempted tobacco purchases by young buyers have been implemented in order to monitor retail stores' performance in refusing underage sales. Anecdotal evidence suggests that mystery shop visits with immediate feedback to store personnel can improve age verification. This study investigated the effect of monthly and twice-monthly mystery shop reports on age verification. Mystery shoppers visited 45 Walgreens stores 20 times. The stores were randomly assigned to 1 of 3 conditions. Control group stores received no feedback, whereas 2 treatment groups received feedback communications on every visit (twice monthly) or on every second visit (monthly) after baseline. Logit regression models tested whether each treatment group improved verification rates relative to the control group. Postbaseline verification rates were higher in both treatment groups than in the control group, but only the stores receiving monthly communications had a significantly greater improvement compared with the control group stores. Verification rates increased significantly during the study period for all 3 groups, with delayed improvement among control group stores. Communication between managers regarding the mystery shop program may account for the delayed age-verification improvements observed in the control group stores. Encouraging interstore communication might extend the benefits of mystery shop programs beyond those stores that receive this intervention. Copyright © Taylor & Francis Group, LLC

  1. Calibration and verification of models of organic carbon removal kinetics in Aerated Submerged Fixed-Bed Biofilm Reactors (ASFBBR): a case study of wastewater from an oil-refinery.

    PubMed

    Trojanowicz, Karol; Wójcik, Włodzimierz

    2011-01-01

    The article presents a case-study on the calibration and verification of mathematical models of organic carbon removal kinetics in biofilm. The chosen Harremöes and Wanner & Reichert models were calibrated with a set of model parameters obtained both during dedicated studies conducted at pilot- and lab-scales for petrochemical wastewater conditions and from the literature. Next, the models were successfully verified through studies carried out utilizing a pilot ASFBBR type bioreactor installed in an oil-refinery wastewater treatment plant. During verification the pilot biofilm reactor worked under varying surface organic loading rates (SOL), dissolved oxygen concentrations and temperatures. The verification proved that the models can be applied in practice to petrochemical wastewater treatment engineering for e.g. biofilm bioreactor dimensioning.

  2. Verification bias an underrecognized source of error in assessing the efficacy of medical imaging.

    PubMed

    Petscavage, Jonelle M; Richardson, Michael L; Carr, Robert B

    2011-03-01

    Diagnostic tests are validated by comparison against a "gold standard" reference test. When the reference test is invasive or expensive, it may not be applied to all patients. This can result in biased estimates of the sensitivity and specificity of the diagnostic test. This type of bias is called "verification bias," and is a common problem in imaging research. The purpose of our study is to estimate the prevalence of verification bias in the recent radiology literature. All issues of the American Journal of Roentgenology (AJR), Academic Radiology, Radiology, and European Journal of Radiology (EJR) between November 2006 and October 2009 were reviewed for original research articles mentioning sensitivity or specificity as endpoints. Articles were read to determine whether verification bias was present and searched for author recognition of verification bias in the design. During 3 years, these journals published 2969 original research articles. A total of 776 articles used sensitivity or specificity as an outcome. Of these, 211 articles demonstrated potential verification bias. The fraction of articles with potential bias was respectively 36.4%, 23.4%, 29.5%, and 13.4% for AJR, Academic Radiology, Radiology, and EJR. The total fraction of papers with potential bias in which the authors acknowledged this bias was 17.1%. Verification bias is a common and frequently unacknowledged source of error in efficacy studies of diagnostic imaging. Bias can often be eliminated by proper study design. When it cannot be eliminated, it should be estimated and acknowledged. Published by Elsevier Inc.

  3. A robust method using propensity score stratification for correcting verification bias for binary tests

    PubMed Central

    He, Hua; McDermott, Michael P.

    2012-01-01

    Sensitivity and specificity are common measures of the accuracy of a diagnostic test. The usual estimators of these quantities are unbiased if data on the diagnostic test result and the true disease status are obtained from all subjects in an appropriately selected sample. In some studies, verification of the true disease status is performed only for a subset of subjects, possibly depending on the result of the diagnostic test and other characteristics of the subjects. Estimators of sensitivity and specificity based on this subset of subjects are typically biased; this is known as verification bias. Methods have been proposed to correct verification bias under the assumption that the missing data on disease status are missing at random (MAR), that is, the probability of missingness depends on the true (missing) disease status only through the test result and observed covariate information. When some of the covariates are continuous, or the number of covariates is relatively large, the existing methods require parametric models for the probability of disease or the probability of verification (given the test result and covariates), and hence are subject to model misspecification. We propose a new method for correcting verification bias based on the propensity score, defined as the predicted probability of verification given the test result and observed covariates. This is estimated separately for those with positive and negative test results. The new method classifies the verified sample into several subsamples that have homogeneous propensity scores and allows correction for verification bias. Simulation studies demonstrate that the new estimators are more robust to model misspecification than existing methods, but still perform well when the models for the probability of disease and probability of verification are correctly specified. PMID:21856650

  4. Can self-verification strivings fully transcend the self-other barrier? Seeking verification of ingroup identities.

    PubMed

    Gómez, Angel; Seyle, D Conor; Huici, Carmen; Swann, William B

    2009-12-01

    Recent research has demonstrated self-verification strivings in groups, such that people strive to verify collective identities, which are personal self-views (e.g., "sensitive") associated with group membership (e.g., "women"). Such demonstrations stop short of showing that the desire for self-verification can fully transcend the self-other barrier, as in people working to verify ingroup identities (e.g., "Americans are loud") even when such identities are not self-descriptive ("I am quiet and unassuming"). Five studies focus on such ingroup verification strivings. Results indicate that people prefer to interact with individuals who verify their ingroup identities over those who enhance these identities (Experiments 1-5). Strivings for ingroup identity verification were independent of the extent to which the identities were self-descriptive but were stronger among participants who were highly invested in their ingroup identities, as reflected in high certainty of these identities (Experiments 1-4) and high identification with the group (Experiments 1-5). In addition, whereas past demonstrations of self-verification strivings have been limited to efforts to verify the content of identities (Experiments 1 to 3), the findings also show that they strive to verify the valence of their identities (i.e., the extent to which the identities are valued; Experiments 4 and 5). Self-verification strivings, rather than self-enhancement strivings, appeared to motivate participants' strivings for ingroup identity verification. Links to collective self-verification strivings and social identity theory are discussed.

  5. Electronic cigarette sales to minors via the internet.

    PubMed

    Williams, Rebecca S; Derrick, Jason; Ribisl, Kurt M

    2015-03-01

    Electronic cigarettes (e-cigarettes) entered the US market in 2007 and, with little regulatory oversight, grew into a $2-billion-a-year industry by 2013. The Centers for Disease Control and Prevention has reported a trend of increasing e-cigarette use among teens, with use rates doubling from 2011 to 2012. While several studies have documented that teens can and do buy cigarettes online, to our knowledge, no studies have yet examined age verification among Internet tobacco vendors selling e-cigarettes. To estimate the extent to which minors can successfully purchase e-cigarettes online and assess compliance with North Carolina's 2013 e-cigarette age-verification law. In this cross-sectional study conducted from February 2014 to June 2014, 11 nonsmoking minors aged 14 to 17 years made supervised e-cigarette purchase attempts from 98 Internet e-cigarette vendors. Purchase attempts were made at the University of North Carolina Internet Tobacco Vendors Study project offices using credit cards. Rate at which minors can successfully purchase e-cigarettes on the Internet. Minors successfully received deliveries of e-cigarettes from 76.5% of purchase attempts, with no attempts by delivery companies to verify their ages at delivery and 95% of delivered orders simply left at the door. All delivered packages came from shipping companies that, according to company policy or federal regulation, do not ship cigarettes to consumers. Of the total orders, 18 failed for reasons unrelated to age verification. Only 5 of the remaining 80 youth purchase attempts were rejected owing to age verification, resulting in a youth buy rate of 93.7%. None of the vendors complied with North Carolina's e-cigarette age-verification law. Minors are easily able to purchase e-cigarettes from the Internet because of an absence of age-verification measures used by Internet e-cigarette vendors. Federal law should require and enforce rigorous age verification for all e-cigarette sales as with the federal PACT (Prevent All Cigarette Trafficking) Act's requirements for age verification in Internet cigarette sales.

  6. Designer proteins: applications of genetic code expansion in cell biology.

    PubMed

    Davis, Lloyd; Chin, Jason W

    2012-02-15

    Designer amino acids, beyond the canonical 20 that are normally used by cells, can now be site-specifically encoded into proteins in cells and organisms. This is achieved using 'orthogonal' aminoacyl-tRNA synthetase-tRNA pairs that direct amino acid incorporation in response to an amber stop codon (UAG) placed in a gene of interest. Using this approach, it is now possible to study biology in vitro and in vivo with an increased level of molecular precision. This has allowed new biological insights into protein conformational changes, protein interactions, elementary processes in signal transduction and the role of post-translational modifications.

  7. NASA Hubble Space Telescope (HST) Research Project Capstone Even

    NASA Image and Video Library

    2014-05-05

    Dr. Amber Straughn, Lead Scientist for James Webb Space Telescope Education & Public Outreach at NASA's Goddard Space Flight Center, speaks to students from Mapletown Jr/Sr High School and Margaret Bell Middle School during the NASA Hubble Space Telescope (HST) Research Project Capstone Event in the James E. Webb Auditorium at NASA Headquarters on Monday, May 5, 2014 Photo Credit: (NASA/Joel Kowsky)

  8. GENE EXPRESSION PROFILING IN TESTIS AND LIVER OF MICE TO IDENTIFY MODES OF ACTION OF CONAZOLE TOXICITIES

    EPA Science Inventory

    Gene Expression Profiling in Testis and Liver of Mice to Identify MODES OF ACTION OF Conazole TOXICITies

    Amber K. Goetz1, Wenjun Bao2, Judith E. Schmid2, Carmen Wood2, Hongzu Ren2, Deborah S. Best2, Rachel N. Murrell1, John C. Rockett2, Michael G. Narotsky2, Douglas C. Wol...

  9. Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach

    PubMed Central

    Zhu, Qianqian; Shepherd, Lori; Lunetta, Kathryn L.; Yao, Song; Liu, Qian; Hu, Qiang; Haddad, Stephen A.; Sucheston-Campbell, Lara; Bensen, Jeannette T.; Bandera, Elisa V.; Rosenberg, Lynn; Liu, Song; Haiman, Christopher A.; Olshan, Andrew F.; Palmer, Julie R.; Ambrosone, Christine B.

    2016-01-01

    Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal variants driving the GWAS signals within European-descent populations even when the causal variants were only weakly linked with the GWAS-discovered variants. To evaluate the performance of our approach in a trans-ethnic setting, we applied it to follow up breast cancer GWAS hits identified mostly from populations of European ancestry in African Americans (AA). We evaluated 74 breast cancer GWAS variants in 8,315 AA women from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Only 27% of them were associated with breast cancer risk at significance level α=0.05, suggesting race-specificity of the identified breast cancer risk loci. We followed up on those replicated GWAS hits in the AMBER consortium utilizing the preferential LD approach, to search for causal variants or better breast cancer markers from the 1000 Genomes variant catalog. Our approach identified stronger breast cancer markers for 80% of the GWAS hits with at least nominal breast cancer association, and in 81% of these cases, the marker identified was among the top 10 of all 1000 Genomes variants in the corresponding locus. The results support trans-ethnic application of the preferential LD approach in search for candidate causal variants, and may have implications for future genetic research of breast cancer in AA women. PMID:27825120

  10. Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface.

    PubMed

    Sandoval-Perez, Angelica; Pluhackova, Kristyna; Böckmann, Rainer A

    2017-05-09

    Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.

  11. Assessment of oral mucosal lesions with autofluorescence imaging and reflectance spectroscopy.

    PubMed

    Lalla, Yastira; Matias, Marie Anne T; Farah, Camile S

    2016-08-01

    The aim of this prospective study was to evaluate the efficacy of a new form of autofluorescence imaging and tissue reflectance spectroscopy (Identafi, DentalEZ) in examining patients with oral mucosal lesions. The authors examined 88 patients with 231 oral mucosal lesions by conventional oral examination (COE) using white-light illumination and ×2.5 magnification loupes, followed by examination using Identafi. The authors noted fluorescence visualization loss, the presence of blanching, and diffuseness of vasculature. They performed incisional biopsies to provide definitive histopathologic diagnosis. Identafi's white light produced lesion visibility and border distinctness equivalent to COE. Identafi's violet light displayed a sensitivity of 12.5% and specificity of 85.4% for detection of oral epithelial dysplasia (OED). The authors noted visible vasculature using the green-amber light in 40.9% of lesions. Identafi's intraoral white light provided detailed visualization of oral mucosal lesions comparable with examination using an extraoral white-light source with magnification. A high level of clinical experience is required to interpret the results of autofluorescence examination as the violet light displayed low sensitivity for detection of OED. The green-amber light provided additional clinical information in relation to underlying vasculature and inflammation of lesions. Examination using Identafi can provide clinicians with more clinical data than a standard COE with yellow incandescent light, but the clinical and optical findings should be interpreted as a whole and not in isolation. Clinicians should use the light features of Identafi in a sequential and differential manner. Copyright © 2016 American Dental Association. Published by Elsevier Inc. All rights reserved.

  12. Effects of Colored Enrichment Devices on Circadian Metabolism and Physiology in Male Sprague-Dawley Rats.

    PubMed

    Wren-Dail, Melissa A; Dauchy, Robert T; Ooms, Tara G; Baker, Kate C; Blask, David E; Hill, Steven M; Dupepe, Lynell M; Bohm, Rudolf P

    2016-01-01

    Environmental enrichment (EE) gives laboratory animals opportunities to engage in species-specific behaviors. However, the effects of EE devices on normal physiology and scientific outcomes must be evaluated. We hypothesized that the spectral transmittance (color) of light to which rats are exposed when inside colored enrichment devices (CED) affects the circadian rhythms of various plasma markers. Pair-housed male Crl:SD rats were maintained in ventilated racks under a 12:12-h light:dark environment (265.0 lx; lights on, 0600); room lighting intensity and schedule remained constant throughout the study. Treatment groups of 6 subjects were exposed for 25 d to a colored enrichment tunnel: amber, red, clear, or opaque. We measured the proportion of time rats spent inside their CED. Blood was collected at 0400, 0800, 1200, 1600, 2000, and 2400 and analyzed for plasma melatonin, total fatty acids, and corticosterone. Rats spent more time in amber, red, and opaque CED than in clear tunnels. All tubes were used significantly less after blood draws had started, except for the clear tunnel, which showed no change in use from before blood sampling began. Normal peak nighttime melatonin concentrations showed significant disruption in the opaque CED group. Food and water intakes and body weight change in rats with red-tinted CED and total fatty acid concentrations in the opaque CED group differed from those in other groups. These results demonstrate that the color of CED altered normal circadian rhythms of plasma measures of metabolism and physiology in rats and therefore might influence the outcomes of scientific investigations.

  13. Preparation and stability of extemporaneous oral liquid formulations of oseltamivir using commercially available capsules.

    PubMed

    Winiarski, Aleksander P; Infeld, Martin H; Tscherne, Ronald; Bachynsky, Maria; Rucki, Richard; Nagano-Mate, Kathy

    2007-01-01

    To develop a simple, standardized method for the extemporaneous compounding of an oral liquid form of oseltamivir from commercially available Tamiflu 75 mg capsules (Roche Pharmaceuticals) and to determine the stability of oseltamivir in this preparation. Chemical and microbial stability study. Laboratory. None. Extemporaneous oral liquid formulations of oseltamivir (15 mg/mL) were prepared in Cherry Syrup (Humco) and Ora-Sweet SF (Paddock Laboratories) using methods consistent with current compounding practice in a pharmacy setting. Preparations were stored in amber glass and amber polyethyleneterephthalate bottles at 5 degrees C +/- 2 degrees C (41 degrees F +/- 4 degrees F) and 25 degrees C +/- 2 degrees C (77 degrees F +/- 4 degrees F) at 60% +/- 5% relative humidity (RH) for 35 days and 30 degrees C +/- 2 degrees C (86 degrees F +/- 4 degrees F) at 65% +/- 5% RH for 13 days. Samples were monitored for appearance, pH, assay, degradation products, and microbiologic stability. The Cherry Syrup preparation, in either bottle type, was stable for up to 35 days under refrigeration (5 degrees C) and up to 5 days at room temperature (25 degrees C). It was not stable when stored at 30 degrees C for 5 days. The Ora-Sweet SF preparation was stable for up to 35 days at 5 degrees C or 25 degrees C and for up to 13 days at 30 degrees C in either bottle type. Both preparations maintained microbiologic stability for 35 days. Both preparations are stable under the described conditions and may provide an option in situations where the marketed suspension is unavailable.

  14. Stability of an extemporaneous oral liquid aprepitant formulation.

    PubMed

    Dupuis, L Lee; Lingertat-Walsh, Karen; Walker, Scott E

    2009-06-01

    Aprepitant is currently recommended for the prevention of acute antineoplastic-induced nausea and vomiting in adults receiving highly emetogenic therapy. The lack of an oral liquid dosage form is one barrier to its use in children. The purpose of this study was to develop a stable oral liquid formulation of aprepitant using the marketed aprepitant capsules. Aprepitant 20-mg/mL oral liquid was prepared from 125-mg capsule contents in Orablend(R). Twelve test samples were prepared: six packaged in amber glass and six in polyethylene terephthalate (PET) containers, three of each stored at either 23 degrees C or 4 degrees C. The physical characteristics of the oral aprepitant liquid stored in amber glass bottles were evaluated at the time of compounding and on days 7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, 84, and 91. The aprepitant content of three test solutions of each container type and storage temperature was determined using a stability-indicating assay at 5, 9, 14, 29, 48, 62, 73, and 111 days after compounding. All samples stored in glass demonstrated suitable physical characteristics and those stored in either glass or PET retained more than 94.0% of the initial concentration. Based on the higher limit of the 95% confidence interval of the degradation rate, suspensions stored at 23 degrees C achieved 10% loss within 66 to 85 days, compared to greater than 100 days when stored at 4 degrees C. The extemporaneous aprepitant oral suspension formulation described is physically and chemically stable for at least 90 days when refrigerated. The bioavailability of this formulation is unknown.

  15. Binding preference of carbon nanotube over proline-rich motif ligand on SH3-domain: a comparison with different force fields.

    PubMed

    Shi, Biyun; Zuo, Guanghong; Xiu, Peng; Zhou, Ruhong

    2013-04-04

    With the widespread applications of nanomaterials such as carbon nanotubes, there is a growing concern on the biosafety of these engineered nanoparticles, in particular their interactions with proteins. In molecular simulations of nanoparticle-protein interactions, the choice of empirical parameters (force fields) plays a decisive role, and thus is of great importance and should be examined carefully before wider applications. Here we compare three commonly used force fields, CHARMM, OPLSAA, and AMBER in study of the competitive binding of a single wall carbon nanotube (SWCNT) with a native proline-rich motif (PRM) ligand on its target protein SH3 domain, a ubiquitous protein-protein interaction mediator involved in signaling and regulatory pathways. We find that the SWCNT displays a general preference over the PRM in binding with SH3 domain in all the three force fields examined, although the degree of preference can be somewhat different, with the AMBER force field showing the highest preference. The SWCNT prevents the ligand from reaching its native binding pocket by (i) occupying the binding pocket directly, and (ii) binding with the ligand itself and then being trapped together onto some off-sites. The π-π stacking interactions between the SWCNT and aromatic residues are found to play a significant role in its binding to the SH3 domain in all the three force fields. Further analyses show that even the SWCNT-ligand binding can also be relatively more stable than the native ligand-protein binding, indicating a serious potential disruption to the protein SH3 function.

  16. Douglas flight deck design philosophy

    NASA Technical Reports Server (NTRS)

    Oldale, Paul

    1990-01-01

    The systems experience gained from 17 years of DC-10 operation was used during the design of the MD-11 to automate system operation and reduce crew workload. All functions, from preflight to shutdown at the termination of flight, require little input from the crew. The MD-11 aircraft systems are monitored for proper operation by the Aircraft Systems Controllers (ASC). In most cases, system reconfiguration as a result of a malfunction is automated. Manual input is required for irreversible actions such as engine shutdown, fuel dump, fire agent discharge, or Integrated Drive Generator (IDG) disconnect. During normal operations, when the cockpit is configured for flight, all annunciators on the overhead panel will be extinguished. This Dark Cockpit immediately confirms to the crew that the panels are correctly configured and that no abnormalities are present. Primary systems annunciations are shown in text on the Alert Area of the Engine and Alert Display (EAD). This eliminates the need to scan the overhead. The MD-11 aircraft systems can be manually controlled from the overhead area of the cockpit. The center portion of the overhead panel is composed of the primary aircraft systems panels, which include FUEL, AIR, Electrical (ELEC) and Hydraulic (HYD) systems, which are easily accessible from both flight crew positions. Each Aircraft Systems Controller (ASC) has two automatic channels and a manual mode. All rectangular lights are annunciators. All square lights are combined switches and annunciators called switch/lights. Red switch/lights on the overhead (Level 3 alerts) are for conditions requiring immediate crew action. Amber (Level 2 or Level 1 alerts) indicates a fault or switch out of position requiring awareness or crew interaction. Overhead switches used in normal operating conditions will illuminate blue when in use (Level 0 alerts) such as WING ANTI-ICE - ON. An overhead switch/light with BLACK LETTERING on an amber or red background indicates a system failure and that crew interaction is required. A switch/light with blue or amber lettering and a BLACK BACKGROUND indicates a switch out of normal position and that crew action is necessary only if the system is in manual operation.

  17. 1-D Imaging of the Dynamical Atmosphere of the Red Supergiant Betelgeuse in the CO First Overtone Lines with VLTI/AMBER

    NASA Astrophysics Data System (ADS)

    Ohnaka, K.

    2014-09-01

    We present high-spatial and high-spectral resolution observations of the red supergiant Betelgeuse in the CO first overtone lines near 2.3μm with the AMBER instrument at the Very Large Telescope Interferometer (VLTI). Our AMBER observations in 2008 spatially resolved the gas motions in a stellar atmosphere (photosphere and extended molecular outer atmosphere) for the first time other than the Sun. From our second observations one year later, we have reconstructed 1-D images in the individual CO lines with an angular resolution of 9.8 mas and a spectral resolution of 6000 by applying the self-calibration technique to restore the Fourier phase from the differential phase measurements. The reconstructed 1-D images reveal that the star appears different in the blue and red wing of the individual CO lines. In the blue wing, the star shows a pronounced, asymmetrically extended component at least up to 1.3 R⋆, while such a component does not appear in the red wing 1-D image. This can be explained by a model in which the CO gas patch (or clump) more than half as large as the star is moving slightly outward with 0-5 km s-1, while the gas in the remaining region is infalling fast with 20-30 km s-1. Comparison between the CO line data taken in 2008 and 2009 shows a significant time variation in the dynamics of the photosphere and outer atmosphere. However, the 1-D images in the continuum show only a slight deviation from a limb-darkened disk with an angular diameter of 42.49±0.06 mas, which leads to an effective temperature of 3690± 54 K. Moreover, the continuum data taken in 2008 and 2009 reveal no or only marginal time variations, much smaller than the maximum variation predicted by the current 3-D convection simulation. The derived continuum diameter also shows that the near-IR size of Betelgeuse has been nearly constant over the last 18 years, in marked contrast to the recently reported noticeable decrease in the mid-IR size.

  18. Effect of sport-tinted contact lenses for contrast enhancement on retinal straylight measurements.

    PubMed

    Cerviño, Alejandro; Gonzalez-Meijome, Jose M; Linhares, João M M; Hosking, Sarah L; Montes-Mico, Robert

    2008-03-01

    To investigate the effect of two tinted contact lenses (CL) designed for outdoor sports activity on the psychometric determination of retinal straylight using the compensation comparison method. Thirteen emmetropic subjects were randomly fitted with two different tinted Nike Maxsight (Bausch & Lomb, Rochester, NY, USA) CL in one eye, while the contralateral eye was fitted with a clear lens made of the same material (Optima 38, Bausch & Lomb). Three valid straylight measurements were taken on each eye before and a few minutes after lens insertion, when lens stabilization had occurred. The subjects' mean straylight values were 0.90 +/- 0.09 at baseline and 0.95 +/- 0.10 with the clear Optima 38 CL. Straylight values were 0.97 +/- 0.10 and 1.0 +/- 0.10 log units with the amber and grey-green tinted CL, respectively. Differences in straylight between baseline (without CL) and with the clear CL in place were neither statistically significant (p = 0.066) nor was there a significant difference between baseline and the amber CL (p = 0.052). However, the grey-green CL showed a statistically significant difference from baseline (p = 0.006). Differences in straylight with the clear CL compared with the grey-green CL were also statistically different from zero (p = 0.002) showing an increased straylight value for the tinted CL. These differences were variable, but consistent for each subject, thus those showing higher or lower changes with one tinted lens tended to show the same trend with the second lens (r(2) = 0.736). Despite increases having been found in straylight values with tinted contact lenses, those changes are not likely to induce clinically significant changes in visual function under photopic conditions, even for the grey-green CL, which seems to increase straylight values more significantly than the amber CL. This difference between the tinted CL could suggest a wavelength dependence of straylight values, although this should be investigated further by controlling for pupil size and subjects' pigmentation, as well as by using neutral density filters.

  19. A study of applications scribe frame data verifications using design rule check

    NASA Astrophysics Data System (ADS)

    Saito, Shoko; Miyazaki, Masaru; Sakurai, Mitsuo; Itoh, Takahisa; Doi, Kazumasa; Sakurai, Norioko; Okada, Tomoyuki

    2013-06-01

    In semiconductor manufacturing, scribe frame data generally is generated for each LSI product according to its specific process design. Scribe frame data is designed based on definition tables of scanner alignment, wafer inspection and customers specified marks. We check that scribe frame design is conforming to specification of alignment and inspection marks at the end. Recently, in COT (customer owned tooling) business or new technology development, there is no effective verification method for the scribe frame data, and we take a lot of time to work on verification. Therefore, we tried to establish new verification method of scribe frame data by applying pattern matching and DRC (Design Rule Check) which is used in device verification. We would like to show scheme of the scribe frame data verification using DRC which we tried to apply. First, verification rules are created based on specifications of scanner, inspection and others, and a mark library is also created for pattern matching. Next, DRC verification is performed to scribe frame data. Then the DRC verification includes pattern matching using mark library. As a result, our experiments demonstrated that by use of pattern matching and DRC verification our new method can yield speed improvements of more than 12 percent compared to the conventional mark checks by visual inspection and the inspection time can be reduced to less than 5 percent if multi-CPU processing is used. Our method delivers both short processing time and excellent accuracy when checking many marks. It is easy to maintain and provides an easy way for COT customers to use original marks. We believe that our new DRC verification method for scribe frame data is indispensable and mutually beneficial.

  20. Verification, Validation and Sensitivity Studies in Computational Biomechanics

    PubMed Central

    Anderson, Andrew E.; Ellis, Benjamin J.; Weiss, Jeffrey A.

    2012-01-01

    Computational techniques and software for the analysis of problems in mechanics have naturally moved from their origins in the traditional engineering disciplines to the study of cell, tissue and organ biomechanics. Increasingly complex models have been developed to describe and predict the mechanical behavior of such biological systems. While the availability of advanced computational tools has led to exciting research advances in the field, the utility of these models is often the subject of criticism due to inadequate model verification and validation. The objective of this review is to present the concepts of verification, validation and sensitivity studies with regard to the construction, analysis and interpretation of models in computational biomechanics. Specific examples from the field are discussed. It is hoped that this review will serve as a guide to the use of verification and validation principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques. PMID:17558646

  1. The effectiveness of ID readers and remote age verification in enhancing compliance with the legal age limit for alcohol.

    PubMed

    Van Hoof, Joris J

    2017-04-01

    Currently, two different age verification systems (AVS) are implemented to enhance compliance with legal age limits for the sale of alcohol in the Netherlands. In this study, we tested the operational procedures and effectiveness of ID readers and remote age verification technology in supermarkets during the sale of alcohol. Following a trained alcohol purchase protocol, eight mystery shoppers (both underage and in the branch's reference age) conducted 132 alcohol purchase attempts in stores that were equipped with ID readers or remote age verification or were part of a control group. In stores equipped with an ID reader, 34% of the purchases were conducted without any mistakes (full compliance). In stores with remote age verification, full compliance was achieved in 87% of the cases. The control group reached 57% compliance, which is in line with the national average. Stores with ID readers perform worse than stores with remote age verification, and also worse than stores without any AVS. For both systems, in addition to effectiveness, public support and user friendliness need to be investigated. This study shows that remote age verification technology is a promising intervention that increases vendor compliance during the sales of age restricted products. © The Author 2016. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

  2. The Maximal Oxygen Uptake Verification Phase: a Light at the End of the Tunnel?

    PubMed

    Schaun, Gustavo Z

    2017-12-08

    Commonly performed during an incremental test to exhaustion, maximal oxygen uptake (V̇O 2max ) assessment has become a recurring practice in clinical and experimental settings. To validate the test, several criteria were proposed. In this context, the plateau in oxygen uptake (V̇O 2 ) is inconsistent in its frequency, reducing its usefulness as a robust method to determine "true" V̇O 2max . Moreover, secondary criteria previously suggested, such as expiratory exchange ratios or percentages of maximal heart rate, are highly dependent on protocol design and often are achieved at V̇O 2 percentages well below V̇O 2max . Thus, an alternative method termed verification phase was proposed. Currently, it is clear that the verification phase can be a practical and sensitive method to confirm V̇O 2max ; however, procedures to conduct it are not standardized across the literature and no previous research tried to summarize how it has been employed. Therefore, in this review the knowledge on the verification phase was updated, while suggestions on how it can be performed (e.g. intensity, duration, recovery) were provided according to population and protocol design. Future studies should focus to identify a verification protocol feasible for different populations and to compare square-wave and multistage verification phases. Additionally, studies assessing verification phases in different patient populations are still warranted.

  3. Feasibility study on dosimetry verification of volumetric-modulated arc therapy-based total marrow irradiation.

    PubMed

    Liang, Yun; Kim, Gwe-Ya; Pawlicki, Todd; Mundt, Arno J; Mell, Loren K

    2013-03-04

    The purpose of this study was to develop dosimetry verification procedures for volumetric-modulated arc therapy (VMAT)-based total marrow irradiation (TMI). The VMAT based TMI plans were generated for three patients: one child and two adults. The planning target volume (PTV) was defined as bony skeleton, from head to mid-femur, with a 3 mm margin. The plan strategy similar to published studies was adopted. The PTV was divided into head and neck, chest, and pelvic regions, with separate plans each of which is composed of 2-3 arcs/fields. Multiple isocenters were evenly distributed along the patient's axial direction. The focus of this study is to establish a dosimetry quality assurance procedure involving both two-dimensional (2D) and three-dimensional (3D) volumetric verifications, which is desirable for a large PTV treated with multiple isocenters. The 2D dose verification was performed with film for gamma evaluation and absolute point dose was measured with ion chamber, with attention to the junction between neighboring plans regarding hot/cold spots. The 3D volumetric dose verification used commercial dose reconstruction software to reconstruct dose from electronic portal imaging devices (EPID) images. The gamma evaluation criteria in both 2D and 3D verification were 5% absolute point dose difference and 3 mm of distance to agreement. With film dosimetry, the overall average gamma passing rate was 98.2% and absolute dose difference was 3.9% in junction areas among the test patients; with volumetric portal dosimetry, the corresponding numbers were 90.7% and 2.4%. A dosimetry verification procedure involving both 2D and 3D was developed for VMAT-based TMI. The initial results are encouraging and warrant further investigation in clinical trials.

  4. NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR DATA ENTRY AND DATA VERIFICATION (HAND ENTRY) (UA-D-15.0)

    EPA Science Inventory

    The purpose of this SOP is to define the steps involved in data entry and data verification of physical forms. It applies to the data entry and data verification of all physical forms. The procedure defined herein was developed for use in the Arizona NHEXAS project and the "Bor...

  5. Verification of chemistry reference ranges using a simple method in sub-Saharan Africa

    PubMed Central

    Taylor, Douglas; Mandala, Justin; Nanda, Kavita; Van Campenhout, Christel; Agingu, Walter; Madurai, Lorna; Barsch, Eva-Maria; Deese, Jennifer; Van Damme, Lut; Crucitti, Tania

    2016-01-01

    Background Chemistry safety assessments are interpreted by using chemistry reference ranges (CRRs). Verification of CRRs is time consuming and often requires a statistical background. Objectives We report on an easy and cost-saving method to verify CRRs. Methods Using a former method introduced by Sigma Diagnostics, three study sites in sub-Saharan Africa, Bondo, Kenya, and Pretoria and Bloemfontein, South Africa, verified the CRRs for hepatic and renal biochemistry assays performed during a clinical trial of HIV antiretroviral pre-exposure prophylaxis. The aspartate aminotransferase/alanine aminotransferase, creatinine and phosphorus results from 10 clinically-healthy participants at the screening visit were used. In the event the CRRs did not pass the verification, new CRRs had to be calculated based on 40 clinically-healthy participants. Results Within a few weeks, the study sites accomplished verification of the CRRs without additional costs. The aspartate aminotransferase reference ranges for the Bondo, Kenya site and the alanine aminotransferase reference ranges for the Pretoria, South Africa site required adjustment. The phosphorus CRR passed verification and the creatinine CRR required adjustment at every site. The newly-established CRR intervals were narrower than the CRRs used previously at these study sites due to decreases in the upper limits of the reference ranges. As a result, more toxicities were detected. Conclusion To ensure the safety of clinical trial participants, verification of CRRs should be standard practice in clinical trials conducted in settings where the CRR has not been validated for the local population. This verification method is simple, inexpensive, and can be performed by any medical laboratory. PMID:28879112

  6. Verification of chemistry reference ranges using a simple method in sub-Saharan Africa.

    PubMed

    De Baetselier, Irith; Taylor, Douglas; Mandala, Justin; Nanda, Kavita; Van Campenhout, Christel; Agingu, Walter; Madurai, Lorna; Barsch, Eva-Maria; Deese, Jennifer; Van Damme, Lut; Crucitti, Tania

    2016-01-01

    Chemistry safety assessments are interpreted by using chemistry reference ranges (CRRs). Verification of CRRs is time consuming and often requires a statistical background. We report on an easy and cost-saving method to verify CRRs. Using a former method introduced by Sigma Diagnostics, three study sites in sub-Saharan Africa, Bondo, Kenya, and Pretoria and Bloemfontein, South Africa, verified the CRRs for hepatic and renal biochemistry assays performed during a clinical trial of HIV antiretroviral pre-exposure prophylaxis. The aspartate aminotransferase/alanine aminotransferase, creatinine and phosphorus results from 10 clinically-healthy participants at the screening visit were used. In the event the CRRs did not pass the verification, new CRRs had to be calculated based on 40 clinically-healthy participants. Within a few weeks, the study sites accomplished verification of the CRRs without additional costs. The aspartate aminotransferase reference ranges for the Bondo, Kenya site and the alanine aminotransferase reference ranges for the Pretoria, South Africa site required adjustment. The phosphorus CRR passed verification and the creatinine CRR required adjustment at every site. The newly-established CRR intervals were narrower than the CRRs used previously at these study sites due to decreases in the upper limits of the reference ranges. As a result, more toxicities were detected. To ensure the safety of clinical trial participants, verification of CRRs should be standard practice in clinical trials conducted in settings where the CRR has not been validated for the local population. This verification method is simple, inexpensive, and can be performed by any medical laboratory.

  7. Development of independent MU/treatment time verification algorithm for non-IMRT treatment planning: A clinical experience

    NASA Astrophysics Data System (ADS)

    Tatli, Hamza; Yucel, Derya; Yilmaz, Sercan; Fayda, Merdan

    2018-02-01

    The aim of this study is to develop an algorithm for independent MU/treatment time (TT) verification for non-IMRT treatment plans, as a part of QA program to ensure treatment delivery accuracy. Two radiotherapy delivery units and their treatment planning systems (TPS) were commissioned in Liv Hospital Radiation Medicine Center, Tbilisi, Georgia. Beam data were collected according to vendors' collection guidelines, and AAPM reports recommendations, and processed by Microsoft Excel during in-house algorithm development. The algorithm is designed and optimized for calculating SSD and SAD treatment plans, based on AAPM TG114 dose calculation recommendations, coded and embedded in MS Excel spreadsheet, as a preliminary verification algorithm (VA). Treatment verification plans were created by TPSs based on IAEA TRS 430 recommendations, also calculated by VA, and point measurements were collected by solid water phantom, and compared. Study showed that, in-house VA can be used for non-IMRT plans MU/TT verifications.

  8. Formal verification of medical monitoring software using Z language: a representative sample.

    PubMed

    Babamir, Seyed Morteza; Borhani, Mehdi

    2012-08-01

    Medical monitoring systems are useful aids assisting physicians in keeping patients under constant surveillance; however, taking sound decision by the systems is a physician concern. As a result, verification of the systems behavior in monitoring patients is a matter of significant. The patient monitoring is undertaken by software in modern medical systems; so, software verification of modern medial systems have been noticed. Such verification can be achieved by the Formal Languages having mathematical foundations. Among others, the Z language is a suitable formal language has been used to formal verification of systems. This study aims to present a constructive method to verify a representative sample of a medical system by which the system is visually specified and formally verified against patient constraints stated in Z Language. Exploiting our past experience in formal modeling Continuous Infusion Insulin Pump (CIIP), we think of the CIIP system as a representative sample of medical systems in proposing our present study. The system is responsible for monitoring diabetic's blood sugar.

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

    PubMed

    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.

  10. Block 2 SRM conceptual design studies. Volume 1, Book 2: Preliminary development and verification plan

    NASA Technical Reports Server (NTRS)

    1986-01-01

    Activities that will be conducted in support of the development and verification of the Block 2 Solid Rocket Motor (SRM) are described. Development includes design, fabrication, processing, and testing activities in which the results are fed back into the project. Verification includes analytical and test activities which demonstrate SRM component/subassembly/assembly capability to perform its intended function. The management organization responsible for formulating and implementing the verification program is introduced. It also identifies the controls which will monitor and track the verification program. Integral with the design and certification of the SRM are other pieces of equipment used in transportation, handling, and testing which influence the reliability and maintainability of the SRM configuration. The certification of this equipment is also discussed.

  11. MARATHON Verification (MARV)

    DTIC Science & Technology

    2017-08-01

    comparable with MARATHON 1 in terms of output. Rather, the MARATHON 2 verification cases were designed to ensure correct implementation of the new algorithms...DISCLAIMER The findings of this report are not to be construed as an official Department of the Army position, policy, or decision unless so designated by...for employment against demands. This study is a comparative verification of the functionality of MARATHON 4 (our newest implementation of MARATHON

  12. Study of space shuttle orbiter system management computer function. Volume 2: Automated performance verification concepts

    NASA Technical Reports Server (NTRS)

    1975-01-01

    The findings are presented of investigations on concepts and techniques in automated performance verification. The investigations were conducted to provide additional insight into the design methodology and to develop a consolidated technology base from which to analyze performance verification design approaches. Other topics discussed include data smoothing, function selection, flow diagrams, data storage, and shuttle hydraulic systems.

  13. Exploring implementation practices in results-based financing: the case of the verification in Benin.

    PubMed

    Antony, Matthieu; Bertone, Maria Paola; Barthes, Olivier

    2017-03-14

    Results-based financing (RBF) has been introduced in many countries across Africa and a growing literature is building around the assessment of their impact. These studies are usually quantitative and often silent on the paths and processes through which results are achieved and on the wider health system effects of RBF. To address this gap, our study aims at exploring the implementation of an RBF pilot in Benin, focusing on the verification of results. The study is based on action research carried out by authors involved in the pilot as part of the agency supporting the RBF implementation in Benin. While our participant observation and operational collaboration with project's stakeholders informed the study, the analysis is mostly based on quantitative and qualitative secondary data, collected throughout the project's implementation and documentation processes. Data include project documents, reports and budgets, RBF data on service outputs and on the outcome of the verification, daily activity timesheets of the technical assistants in the districts, as well as focus groups with Community-based Organizations and informal interviews with technical assistants and district medical officers. Our analysis focuses on the actual practices of quantitative, qualitative and community verification. Results show that the verification processes are complex, costly and time-consuming, and in practice they end up differing from what designed originally. We explore the consequences of this on the operation of the scheme, on its potential to generate the envisaged change. We find, for example, that the time taken up by verification procedures limits the time available for data analysis and feedback to facility staff, thus limiting the potential to improve service delivery. Verification challenges also result in delays in bonus payment, which delink effort and reward. Additionally, the limited integration of the verification activities of district teams with their routine tasks causes a further verticalization of the health system. Our results highlight the potential disconnect between the theory of change behind RBF and the actual scheme's implementation. The implications are relevant at methodological level, stressing the importance of analyzing implementation processes to fully understand results, as well as at operational level, pointing to the need to carefully adapt the design of RBF schemes (including verification and other key functions) to the context and to allow room to iteratively modify it during implementation. They also question whether the rationale for thorough and costly verification is justified, or rather adaptations are possible.

  14. A field study of the accuracy and reliability of a biometric iris recognition system.

    PubMed

    Latman, Neal S; Herb, Emily

    2013-06-01

    The iris of the eye appears to satisfy the criteria for a good anatomical characteristic for use in a biometric system. The purpose of this study was to evaluate a biometric iris recognition system: Mobile-Eyes™. The enrollment, verification, and identification applications were evaluated in a field study for accuracy and reliability using both irises of 277 subjects. Independent variables included a wide range of subject demographics, ambient light, and ambient temperature. A sub-set of 35 subjects had alcohol-induced nystagmus. There were 2710 identification and verification attempts, which resulted in 1,501,340 and 5540 iris comparisons respectively. In this study, the system successfully enrolled all subjects on the first attempt. All 277 subjects were successfully verified and identified on the first day of enrollment. None of the current or prior eye conditions prevented enrollment, verification, or identification. All 35 subjects with alcohol-induced nystagmus were successfully verified and identified. There were no false verifications or false identifications. Two conditions were identified that potentially could circumvent the use of iris recognitions systems in general. The Mobile-Eyes™ iris recognition system exhibited accurate and reliable enrollment, verification, and identification applications in this study. It may have special applications in subjects with nystagmus. Copyright © 2012 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  15. Predictors of fever-related admissions to a paediatric assessment unit, ward and reattendances in a South London emergency department: the CABIN 2 study.

    PubMed

    Bustinduy, Amaya L; Chis Ster, Irina; Shaw, Rebecca; Irwin, Adam; Thiagarajan, Jaiganesh; Beynon, Rhys; Ladhani, Shamez; Sharland, Mike

    2017-01-01

    To explore the risk factors for ward and paediatric assessment unit (PAU) admissions from the emergency department (ED). Prospective observational study. Febrile children attending a large tertiary care ED during the winter of 2014-2015. Ward and PAU admissions, National Institute for Health and Care Excellence (NICE) guidelines classification, reattendance to the ED within 28 days and antibiotic use. A total of 1097 children attending the children's ED with fever were analysed. Risk factors for PAU admission were tachycardia (RR=1.1, 95% CI (1 to 1.1)), ill-appearance (RR=2.2, 95% CI (1.2 to 4.2)), abnormal chest findings (RR=2.1, 95% CI (1.2 to 4.3)), categorised as NICE amber (RR 1.7 95% CI (1.2 to 2.5)). There was a 30% discordance between NICE categorisation at triage and statistical internal validation. Predictors of ward admission were a systemic (RR=6.9, 95% CI (2.4 to 19.8)) or gastrointestinal illness (RR=3.8, 95% (1.4 to 10.4)) and categorised as NICE Red (RR=5.9, 95% CI (2.2 to 15.3)). Only 51 children had probable bacterial pneumonia (4.6%), 52 children had a proven urinary tract infection (4.2%), with just 2 (0.2%) positive blood cultures out of 485 (44%) children who received an antibiotic. 15% of all children reattended by 28 days and were more likely to have been categorised as Amber and had investigations on initial visit. Risk factors for PAU and ward admissions are different in this setting with high reattendance rates and very low proportion of confirmed/probable serious bacterial infections. Future studies need to focus on reducing avoidable admissions and antibiotic treatment. 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/.

  16. Exposure to Blue Light Increases Subsequent Functional Activation of the Prefrontal Cortex During Performance of a Working Memory Task

    PubMed Central

    Alkozei, Anna; Smith, Ryan; Pisner, Derek A.; Vanuk, John R.; Berryhill, Sarah M.; Fridman, Andrew; Shane, Bradley R.; Knight, Sara A.; Killgore, William D.S.

    2016-01-01

    Study Objectives: Prolonged exposure to blue wavelength light has been shown to have an alerting effect, and enhances performance on cognitive tasks. A small number of studies have also shown that relatively short exposure to blue light leads to changes in functional brain responses during the period of exposure. The extent to which blue light continues to affect brain functioning during a cognitively challenging task after cessation of longer periods of exposure (i.e., roughly 30 minutes or longer), however, has not been fully investigated. Methods: A total of 35 healthy participants (18 female) were exposed to either blue (469 nm) (n = 17) or amber (578 nm) (n = 18) wavelength light for 30 minutes in a darkened room, followed immediately by functional magnetic resonance imaging (fMRI) while undergoing a working memory task (N-back task). Results: Participants in the blue light condition were faster in their responses on the N-back task and showed increased activation in the dorsolateral (DLPFC) and ventrolateral (VLPFC) prefrontal cortex compared to those in the amber control light condition. Furthermore, greater activation within the VLPFC was correlated with faster N-back response times. Conclusions: This is the first study to suggest that a relatively brief, single exposure to blue light has a subsequent beneficial effect on working memory performance, even after cessation of exposure, and leads to temporarily persisting functional brain changes within prefrontal brain regions associated with executive functions. These findings may have broader implication for using blue-enriched light in a variety of work settings where alertness and quick decision-making are important. Citation: Alkozei A, Smith R, Pisner DA, Vanuk JR, Berryhill SM, Fridman A, Shane BR, Knight SA, Killgore WD. Exposure to blue light increases subsequent functional activation of the prefrontal cortex during performance of a working memory task. SLEEP 2016;39(9):1671–1680. PMID:27253770

  17. The Eocene Thermal Maximum 2 (ETM-2) in a terrestrial section of the High Arctic: identification by U-Pb zircon ages of volcanic ashes and carbon isotope records of coal and amber (Stenkul Fiord, Ellesmere Island, Canada)

    NASA Astrophysics Data System (ADS)

    Reinhardt, Lutz; von Gosen, Werner; Piepjohn, Karsten; Lückge, Andreas; Schmitz, Mark

    2017-04-01

    The Stenkul Fiord section on southern Ellesmere Island reveals largely fluvial clastic sediments with intercalated coal seams of the Margaret Formation of Late Paleocene/Early Eocene age according to palynology and vertebrate remains. Field studies in recent years and interpretative mapping of a high-resolution satellite image of the area southeast of Stenkul Fiord revealed that the clastic deposits consist of at least four sedimentary units (Units 1 to 4) separated by unconformities. Several centimeter-thin volcanic ash layers, recognized within coal layers and preserved as crandallite group minerals (Ca-bearing goyazite), suggest an intense volcanic ash fall activity. Based on new U-Pb zircon ages (ID-TIMS) of three ash layers, the volcanic ash fall took place at 53.7 Ma in the Early Eocene, i.e. within the Eocene Thermal Maximum 2 (ETM-2) hyperthermal. The ETM-2 is bracketed further by discrete negative excursions of carbon isotope records of both bulk coal and amber droplets collected from individual coal layers of the section. The identification of the ETM-2 hyperthermal provides a stratigraphic tie-point in the terrestrial Margaret Formation sediments enabling assignment of the lowermost sedimentary Unit 1 to the Late Paleocene-earliest Eocene, Unit 2 to the Early Eocene, whereas Unit 3 and 4 might be Early to Middle Eocene in age. Thus the timing of syn-sedimentary movements of the Eurekan deformation causal for the observed unconformities in the section can be studied and the positions of further hyperthermals like the PETM or the ETM-3 in the section can be identified in the future. The integration of structural studies, new U-Pb zircon ages, and different carbon isotope records provides a new stratigraphic framework for further examination of the unique Early Eocene flora and fauna preserved in this high-latitude outcrop.

  18. Influence of Botanical Origin and Chemical Composition on the Protective Effect against Oxidative Damage and the Capacity to Reduce In Vitro Bacterial Biofilms of Monofloral Honeys from the Andean Region of Ecuador

    PubMed Central

    García-Tenesaca, Marilyn; Navarrete, Eillen S.; Iturralde, Gabriel A.; Villacrés Granda, Irina M.; Tejera, Eduardo; Beltrán-Ayala, Pablo

    2017-01-01

    Three types of monofloral honey from the Andean regions of Ecuador (Avocado, Eucalyptus, and Rapeseed honey) were analyzed to determine their floral origin, physicochemical parameters, chemical composition, antioxidant capacity, and their capacity to reduce in vitro bacterial biofilms. The chemical composition varied considerably depending on floral origin. The highest values of bioactive compounds were found in Avocado honey, classified as dark amber in color, while the lowest values were found in Eucalyptus honey followed by Rapeseed honey, both classified as extra light amber. When compared to Eucalyptus and Rapeseed honey, Avocado honey showed a more effective superoxide scavenging activity, chelating metal ions capacity, and a higher ability to protect human erythrocyte membranes against lipid peroxidation. For antimicrobial activity, the hydrogen peroxide content and the capacity to inhibit the biofilm formation, and to remove preformed biofilm from Staphylococcus aureus and Klebsiella pneumoniae was determined. Avocado honey showed the highest values of hydrogen peroxide content, as well as the highest capacity to reduce in vitro bacterial biofilms. A correlation between color vs. phenolics content vs. superoxide scavenging activity vs. chelating metal ions capacity, and the capacity to protect human erythrocyte membranes against lipid peroxidation was found. PMID:29295525

  19. Influence of Botanical Origin and Chemical Composition on the Protective Effect against Oxidative Damage and the Capacity to Reduce In Vitro Bacterial Biofilms of Monofloral Honeys from the Andean Region of Ecuador.

    PubMed

    García-Tenesaca, Marilyn; Navarrete, Eillen S; Iturralde, Gabriel A; Villacrés Granda, Irina M; Tejera, Eduardo; Beltrán-Ayala, Pablo; Giampieri, Francesca; Battino, Maurizio; Alvarez-Suarez, José M

    2017-12-23

    Three types of monofloral honey from the Andean regions of Ecuador (Avocado, Eucalyptus, and Rapeseed honey) were analyzed to determine their floral origin, physicochemical parameters, chemical composition, antioxidant capacity, and their capacity to reduce in vitro bacterial biofilms. The chemical composition varied considerably depending on floral origin. The highest values of bioactive compounds were found in Avocado honey, classified as dark amber in color, while the lowest values were found in Eucalyptus honey followed by Rapeseed honey, both classified as extra light amber. When compared to Eucalyptus and Rapeseed honey, Avocado honey showed a more effective superoxide scavenging activity, chelating metal ions capacity, and a higher ability to protect human erythrocyte membranes against lipid peroxidation. For antimicrobial activity, the hydrogen peroxide content and the capacity to inhibit the biofilm formation, and to remove preformed biofilm from Staphylococcus aureus and Klebsiella pneumoniae was determined. Avocado honey showed the highest values of hydrogen peroxide content, as well as the highest capacity to reduce in vitro bacterial biofilms. A correlation between color vs. phenolics content vs. superoxide scavenging activity vs. chelating metal ions capacity, and the capacity to protect human erythrocyte membranes against lipid peroxidation was found.

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

    PubMed

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

    2016-05-05

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

  1. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rod, M.L. Alam, K.Y.; Cunningham, P.R.; Clark, D.P.

    When grown at high osmotic pressure, some strains of Escherichia coli K-12 synthesized substantial levels of free sugar and accumulated proline if it was present in the growth medium. The sugar was identified as trehalose. Strains of E. coli K-12 could be divided into two major classes with respect of osmoregulation. Those of class A showed a large increase in trehalose levels with increasing medium osmolarity and also accumulated proline from the medium, whereas those in class B showed no accumulation of trehalose or proline. Most class A strains carried suppressor mutations which arose during their derivation from the wildmore » type, whereas the osmodefective strains of class B were suppressor free. When amber suppressor mutations at the supD, supE, or supF loci were introduced into such sup{sup o} osmodefective strains, they became osmotolerant and gained the ability to accumulate trehalose in response to elevated medium osmolarity. It appears that the original K-12 strain of E. coli carries an amber mutation in a gene affecting osmoregulation. Mutants lacking ADP-glucose synthetase (glgC) accumulated trehalose normally, whereas mutants lacking UDP-glucose synthetase (galU) did not make trehalose and grew poorly in medium of high osmolarity. Trehalose synthesis was repressed by exogenous glycine betaine but not by proline.« less

  2. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

    DOE PAGES

    Mones, Letif; Jones, Andrew; Götz, Andreas W.; ...

    2015-02-03

    We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

  3. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

    PubMed Central

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

    2015-01-01

    The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25649827

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

    PubMed

    Mayr, Susanne; Buchner, Axel

    2010-07-01

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

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

    PubMed Central

    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

  6. Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method.

    PubMed

    Parish, Carol A; Yarger, Matthew; Sinclair, Kent; Dure, Myrianne; Goldberg, Alla

    2004-09-23

    The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.

  7. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mones, Letif; Jones, Andrew; Götz, Andreas W.

    We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

  8. Mitigating errors caused by interruptions during medication verification and administration: interventions in a simulated ambulatory chemotherapy setting.

    PubMed

    Prakash, Varuna; Koczmara, Christine; Savage, Pamela; Trip, Katherine; Stewart, Janice; McCurdie, Tara; Cafazzo, Joseph A; Trbovich, Patricia

    2014-11-01

    Nurses are frequently interrupted during medication verification and administration; however, few interventions exist to mitigate resulting errors, and the impact of these interventions on medication safety is poorly understood. The study objectives were to (A) assess the effects of interruptions on medication verification and administration errors, and (B) design and test the effectiveness of targeted interventions at reducing these errors. The study focused on medication verification and administration in an ambulatory chemotherapy setting. A simulation laboratory experiment was conducted to determine interruption-related error rates during specific medication verification and administration tasks. Interventions to reduce these errors were developed through a participatory design process, and their error reduction effectiveness was assessed through a postintervention experiment. Significantly more nurses committed medication errors when interrupted than when uninterrupted. With use of interventions when interrupted, significantly fewer nurses made errors in verifying medication volumes contained in syringes (16/18; 89% preintervention error rate vs 11/19; 58% postintervention error rate; p=0.038; Fisher's exact test) and programmed in ambulatory pumps (17/18; 94% preintervention vs 11/19; 58% postintervention; p=0.012). The rate of error commission significantly decreased with use of interventions when interrupted during intravenous push (16/18; 89% preintervention vs 6/19; 32% postintervention; p=0.017) and pump programming (7/18; 39% preintervention vs 1/19; 5% postintervention; p=0.017). No statistically significant differences were observed for other medication verification tasks. Interruptions can lead to medication verification and administration errors. Interventions were highly effective at reducing unanticipated errors of commission in medication administration tasks, but showed mixed effectiveness at reducing predictable errors of detection in medication verification tasks. These findings can be generalised and adapted to mitigate interruption-related errors in other settings where medication verification and administration are required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  9. Mitigating errors caused by interruptions during medication verification and administration: interventions in a simulated ambulatory chemotherapy setting

    PubMed Central

    Prakash, Varuna; Koczmara, Christine; Savage, Pamela; Trip, Katherine; Stewart, Janice; McCurdie, Tara; Cafazzo, Joseph A; Trbovich, Patricia

    2014-01-01

    Background Nurses are frequently interrupted during medication verification and administration; however, few interventions exist to mitigate resulting errors, and the impact of these interventions on medication safety is poorly understood. Objective The study objectives were to (A) assess the effects of interruptions on medication verification and administration errors, and (B) design and test the effectiveness of targeted interventions at reducing these errors. Methods The study focused on medication verification and administration in an ambulatory chemotherapy setting. A simulation laboratory experiment was conducted to determine interruption-related error rates during specific medication verification and administration tasks. Interventions to reduce these errors were developed through a participatory design process, and their error reduction effectiveness was assessed through a postintervention experiment. Results Significantly more nurses committed medication errors when interrupted than when uninterrupted. With use of interventions when interrupted, significantly fewer nurses made errors in verifying medication volumes contained in syringes (16/18; 89% preintervention error rate vs 11/19; 58% postintervention error rate; p=0.038; Fisher's exact test) and programmed in ambulatory pumps (17/18; 94% preintervention vs 11/19; 58% postintervention; p=0.012). The rate of error commission significantly decreased with use of interventions when interrupted during intravenous push (16/18; 89% preintervention vs 6/19; 32% postintervention; p=0.017) and pump programming (7/18; 39% preintervention vs 1/19; 5% postintervention; p=0.017). No statistically significant differences were observed for other medication verification tasks. Conclusions Interruptions can lead to medication verification and administration errors. Interventions were highly effective at reducing unanticipated errors of commission in medication administration tasks, but showed mixed effectiveness at reducing predictable errors of detection in medication verification tasks. These findings can be generalised and adapted to mitigate interruption-related errors in other settings where medication verification and administration are required. PMID:24906806

  10. SU-F-T-494: A Multi-Institutional Study of Independent Dose Verification Using Golden Beam Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Itano, M; Yamazaki, T; Tachibana, R

    Purpose: In general, beam data of individual linac is measured for independent dose verification software program and the verification is performed as a secondary check. In this study, independent dose verification using golden beam data was compared to that using individual linac’s beam data. Methods: Six institutions were participated and three different beam data were prepared. The one was individual measured data (Original Beam Data, OBD) .The others were generated by all measurements from same linac model (Model-GBD) and all linac models (All-GBD). The three different beam data were registered to the independent verification software program for each institute. Subsequently,more » patient’s plans in eight sites (brain, head and neck, lung, esophagus, breast, abdomen, pelvis and bone) were analyzed using the verification program to compare doses calculated using the three different beam data. Results: 1116 plans were collected from six institutes. Compared to using the OBD, the results shows the variation using the Model-GBD based calculation and the All-GBD was 0.0 ± 0.3% and 0.0 ± 0.6%, respectively. The maximum variations were 1.2% and 2.3%, respectively. The plans with the variation over 1% shows the reference points were located away from the central axis with/without physical wedge. Conclusion: The confidence limit (2SD) using the Model-GBD and the All-GBD was within 0.6% and 1.2%, respectively. Thus, the use of golden beam data may be feasible for independent verification. In addition to it, the verification using golden beam data provide quality assurance of planning from the view of audit. This research is partially supported by Japan Agency for Medical Research and Development(AMED)« less

  11. Inverse probability weighting estimation of the volume under the ROC surface in the presence of verification bias.

    PubMed

    Zhang, Ying; Alonzo, Todd A

    2016-11-01

    In diagnostic medicine, the volume under the receiver operating characteristic (ROC) surface (VUS) is a commonly used index to quantify the ability of a continuous diagnostic test to discriminate between three disease states. In practice, verification of the true disease status may be performed only for a subset of subjects under study since the verification procedure is invasive, risky, or expensive. The selection for disease examination might depend on the results of the diagnostic test and other clinical characteristics of the patients, which in turn can cause bias in estimates of the VUS. This bias is referred to as verification bias. Existing verification bias correction in three-way ROC analysis focuses on ordinal tests. We propose verification bias-correction methods to construct ROC surface and estimate the VUS for a continuous diagnostic test, based on inverse probability weighting. By applying U-statistics theory, we develop asymptotic properties for the estimator. A Jackknife estimator of variance is also derived. Extensive simulation studies are performed to evaluate the performance of the new estimators in terms of bias correction and variance. The proposed methods are used to assess the ability of a biomarker to accurately identify stages of Alzheimer's disease. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Verification and classification bias interactions in diagnostic test accuracy studies for fine-needle aspiration biopsy.

    PubMed

    Schmidt, Robert L; Walker, Brandon S; Cohen, Michael B

    2015-03-01

    Reliable estimates of accuracy are important for any diagnostic test. Diagnostic accuracy studies are subject to unique sources of bias. Verification bias and classification bias are 2 sources of bias that commonly occur in diagnostic accuracy studies. Statistical methods are available to estimate the impact of these sources of bias when they occur alone. The impact of interactions when these types of bias occur together has not been investigated. We developed mathematical relationships to show the combined effect of verification bias and classification bias. A wide range of case scenarios were generated to assess the impact of bias components and interactions on total bias. Interactions between verification bias and classification bias caused overestimation of sensitivity and underestimation of specificity. Interactions had more effect on sensitivity than specificity. Sensitivity was overestimated by at least 7% in approximately 6% of the tested scenarios. Specificity was underestimated by at least 7% in less than 0.1% of the scenarios. Interactions between verification bias and classification bias create distortions in accuracy estimates that are greater than would be predicted from each source of bias acting independently. © 2014 American Cancer Society.

  13. Electronic Cigarette Sales to Minors via the Internet

    PubMed Central

    Williams, Rebecca S.; Derrick, Jason; Ribisl, Kurt M.

    2015-01-01

    Importance Electronic cigarettes (e-cigarettes) entered the US market in 2007 and, with little regulatory oversight, grew into a $2-billion-a-year industry by 2013. The Centers for Disease Control and Prevention has reported a trend of increasing e-cigarette use among teens, with use rates doubling from 2011 to 2012. While several studies have documented that teens can and do buy cigarettes online, to our knowledge, no studies have yet examined age verification among Internet tobacco vendors selling e-cigarettes. Objective To estimate the extent to which minors can successfully purchase e-cigarettes online and assess compliance with North Carolina's 2013 e-cigarette age-verification law. Design, Setting, and Participants In this cross-sectional study conducted from February 2014 to June 2014, 11 nonsmoking minors aged 14 to 17 years made supervised e-cigarette purchase attempts from 98 Internet e-cigarette vendors. Purchase attempts were made at the University of North Carolina Internet Tobacco Vendors Study project offices using credit cards. Main Outcome and Measure Rate at which minors can successfully purchase e-cigarettes on the Internet. Results Minors successfully received deliveries of e-cigarettes from 76.5% of purchase attempts, with no attempts by delivery companies to verify their ages at delivery and 95% of delivered orders simply left at the door. All delivered packages came from shipping companies that, according to company policy or federal regulation, do not ship cigarettes to consumers. Of the total orders, 18 failed for reasons unrelated to age verification. Only 5 of the remaining 80 youth purchase attempts were rejected owing to age verification, resulting in a youth buy rate of 93.7%. None of the vendors complied with North Carolina's e-cigarette age-verification law. Conclusions and Relevance Minors are easily able to purchase e-cigarettes from the Internet because of an absence of age-verification measures used by Internet e-cigarette vendors. Federal law should require and enforce rigorous age verification for all e-cigarette sales as with the federal PACT (Prevent All Cigarette Trafficking) Act's requirements for age verification in Internet cigarette sales. PMID:25730697

  14. Verification of the FtCayuga fault-tolerant microprocessor system. Volume 1: A case study in theorem prover-based verification

    NASA Technical Reports Server (NTRS)

    Srivas, Mandayam; Bickford, Mark

    1991-01-01

    The design and formal verification of a hardware system for a task that is an important component of a fault tolerant computer architecture for flight control systems is presented. The hardware system implements an algorithm for obtaining interactive consistancy (byzantine agreement) among four microprocessors as a special instruction on the processors. The property verified insures that an execution of the special instruction by the processors correctly accomplishes interactive consistency, provided certain preconditions hold. An assumption is made that the processors execute synchronously. For verification, the authors used a computer aided design hardware design verification tool, Spectool, and the theorem prover, Clio. A major contribution of the work is the demonstration of a significant fault tolerant hardware design that is mechanically verified by a theorem prover.

  15. 30 CFR 250.913 - When must I resubmit Platform Verification Program plans?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Structures Platform Verification Program § 250.913 When must I resubmit Platform Verification Program plans? (a) You must resubmit any design verification, fabrication verification, or installation verification... 30 Mineral Resources 2 2010-07-01 2010-07-01 false When must I resubmit Platform Verification...

  16. INF and IAEA: A comparative analysis of verification strategy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Scheinman, L.; Kratzer, M.

    1992-07-01

    This is the final report of a study on the relevance and possible lessons of Intermediate Range Nuclear Force (INF) verification to the International Atomic Energy Agency (IAEA) international safeguards activities.

  17. Spectro-Interferometry Studies of Velocity-Related Phenomena at the Surface of Stars: Pulsation and Rotation

    NASA Astrophysics Data System (ADS)

    Mérand, Antoine; Patru, Fabien; Aufdenberg, Jason

    We illustrate here two applications of spectro-interferometry to the study of velocity fields at the surface of stars: pulsation and rotation. Stellar pulsation has been resolved spectroscopically for a long time, and interferometry has resolved stellar diameters variations due to pulsation. Combining the two provides unique insights to the study of Cepheids, in particular regarding the structure of the photosphere or investigating the infamous projection factor which biases distances measured by the Baade-Wesselink method. On the other hand, resolving the surface velocity field of rotating stars offers a unique opportunity to potentially study differential rotation in other cases than for the Sun. We also present the model we have implemented recently, as well as two applications to VLTI/AMBER Data: the pulsation of Cepheids and the rotation of intermediate mass main sequence stars.

  18. A computational study of open-chain epothilone analogue

    NASA Astrophysics Data System (ADS)

    Kamel, Karol; Rusinska-Roszak, Danuta

    Molecular mechanics (MM/Ambers) calculations were applied to probe the conformational profile of open-chain epothilone analogue [Org Lett 2006, 8, 685], cytotoxic against some cell lines. Geometries of the most stable conformers were optimized at DFT level using the B3LYP functional and then compared to known both experimental and virtual conformers of epothilone. One of the most stable structures is III (1.47 kcal/mol above global minimum) which represents high similarity to the appropriate fragment of the Taylor's model of epothilone A, but two other conformers: XIV and XX, although they have almost the same conformation as the mother structure, are very unstable (6.7 and 12.4 kcal/mol above the global minimum).0

  19. A study of amber and copal samples using FT-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Brody, Rachel H.; Edwards, Howell G. M.; Pollard, A. Mark

    2001-05-01

    FT-Raman spectra were collected from fossil resins originating from a variety of geographical locations. The spectral profiles of most of the fossil resins could be related to modern resins containing diterpenoid components with predominantly labdane skeletons. The spectra collected from the fossil resin sample from Borneo differed from other fossil resins and was found to contain triterpenoid components. The differences in the spectral profile of fossil resins containing diterpenoid components are shown to relate to differences in level of maturation rather than geographical origin. FT-Raman spectra of fossil resins cannot be used to distinguish source although the degree of maturation can be used as an indicator to narrow the range of possible geographical origins.

  20. Independent verification and validation report of Washington state ferries' wireless high speed data project

    DOT National Transportation Integrated Search

    2008-06-30

    The following Independent Verification and Validation (IV&V) report documents and presents the results of a study of the Washington State Ferries Prototype Wireless High Speed Data Network. The purpose of the study was to evaluate and determine if re...

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