Anti-aliasing techniques in photon-counting depth imaging using GHz clock rates

NASA Astrophysics Data System (ADS)

Krichel, Nils J.; McCarthy, Aongus; Collins, Robert J.; Buller, Gerald S.

2010-04-01

Single-photon detection technologies in conjunction with low laser illumination powers allow for the eye-safe acquisition of time-of-flight range information on non-cooperative target surfaces. We previously presented a photon-counting depth imaging system designed for the rapid acquisition of three-dimensional target models by steering a single scanning pixel across the field angle of interest. To minimise the per-pixel dwelling times required to obtain sufficient photon statistics for accurate distance resolution, periodic illumination at multi- MHz repetition rates was applied. Modern time-correlated single-photon counting (TCSPC) hardware allowed for depth measurements with sub-mm precision. Resolving the absolute target range with a fast periodic signal is only possible at sufficiently short distances: if the round-trip time towards an object is extended beyond the timespan between two trigger pulses, the return signal cannot be assigned to an unambiguous range value. Whereas constructing a precise depth image based on relative results may still be possible, problems emerge for large or unknown pixel-by-pixel separations or in applications with a wide range of possible scene distances. We introduce a technique to avoid range ambiguity effects in time-of-flight depth imaging systems at high average pulse rates. A long pseudo-random bitstream is used to trigger the illuminating laser. A cyclic, fast-Fourier supported analysis algorithm is used to search for the pattern within return photon events. We demonstrate this approach at base clock rates of up to 2 GHz with varying pattern lengths, allowing for unambiguous distances of several kilometers. Scans at long stand-off distances and of scenes with large pixel-to-pixel range differences are presented. Numerical simulations are performed to investigate the relative merits of the technique.

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

Lindenmaier, Rodica; Tipton, Nicole; Sams, Robert L.

Hydroxyacetone (acetol) is a simple organic molecule of interest in both the astrophysical and atmospheric communities, having recently been observed in biomass burning events, as well as a known degradation product of isoprene oxidation. However, its vibrational assignment has never been fully completed, and few quantitative data are available for its detection via infrared spectroscopy. Our recent acquisition of both the pressure-broadened gas-phase data and the far-IR spectra now allow for unambiguous assignment of several (new) bands. In particular, the observed C-type bands of several fundamentals (particularly in the far-infrared) and a few combination bands demonstrate that the monomer ismore » in a planar (Cs) conformation, at least a majority of the time. As suggested by other researchers, the monomer is a cis-cis conformer stabilized by an intramolecular O—H···O=C hydrogen bond forming a five-membered planar ring structure. Band assignments in the Cs point group are justified (at least for a good fraction of the molecules in the ensemble) by the presence of the C-type bands. The results and band assignments are well confirmed by both ab initio MP2-ccpvtz calculations as well as GAMESS (B3LYP) theoretical calculations. In addition, using vetted methods for quantitative measurements, we report the first IR absorption band strengths of acetol (also in electronic format) that can be used for atmospheric monitoring and other applications.« less

Molecular origin of the vibrational structure of ice I h

DOE PAGES

Moberg, Daniel R.; Straight, Shelby C.; Knight, Christopher; ...

2017-05-25

Here, an unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the latticemore » vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.« less

Redefining the modular organization of the core Mediator complex.

PubMed

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-07-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.

Redefining the modular organization of the core Mediator complex

PubMed Central

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-01-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation. PMID:24810298

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

Implementation of generalized quantum measurements for unambiguous discrimination of multiple non-orthogonal coherent states.

PubMed

Becerra, F E; Fan, J; Migdall, A

2013-01-01

Generalized quantum measurements implemented to allow for measurement outcomes termed inconclusive can perform perfect discrimination of non-orthogonal states, a task which is impossible using only measurements with definitive outcomes. Here we demonstrate such generalized quantum measurements for unambiguous discrimination of four non-orthogonal coherent states and obtain their quantum mechanical description, the positive-operator valued measure. For practical realizations of this positive-operator valued measure, where noise and realistic imperfections prevent perfect unambiguous discrimination, we show that our experimental implementation outperforms any ideal standard-quantum-limited measurement performing the same non-ideal unambiguous state discrimination task for coherent states with low mean photon numbers.

Single-Molecule Spectroscopy Unmasks the Lowest Exciton State of the B850 Assembly in LH2 from Rps. acidophila

PubMed Central

Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J.; Freiberg, Arvi; Köhler, Jürgen

2014-01-01

We have recorded fluorescence-excitation and emission spectra from single LH2 complexes from Rhodopseudomonas (Rps.) acidophila. Both types of spectra show strong temporal spectral fluctuations that can be visualized as spectral diffusion plots. Comparison of the excitation and emission spectra reveals that for most of the complexes the lowest exciton transition is not observable in the excitation spectra due to the cutoff of the detection filter characteristics. However, from the spectral diffusion plots we have the full spectral and temporal information at hand and can select those complexes for which the excitation spectra are complete. Correlating the red most spectral feature of the excitation spectrum with the blue most spectral feature of the emission spectrum allows an unambiguous assignment of the lowest exciton state. Hence, application of fluorescence-excitation and emission spectroscopy on the same individual LH2 complex allows us to decipher spectral subtleties that are usually hidden in traditional ensemble spectroscopy. PMID:24806933

Rovibrational bound states of SO2 isotopologues. II: Total angular momentum J = 11-20

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Poirier, Bill

2015-11-01

In a two-part series, the rovibrational bound states of SO2 are investigated in comprehensive detail, for all four stable sulfur isotopes 32-34,36S. All low-lying rovibrational energy levels-both permutation-symmetry-allowed and not allowed-are computed, for all values of total angular momentum in the range J = 0-20. The calculations have carried out using the ScalIT suite of parallel codes. The present study (Paper II) examines the J = 11-20 rovibrational levels, providing symmetry and rovibrational labels for every computed state, relying on a new lambda-doublet splitting technique to make completely unambiguous assignments. Isotope shifts are analyzed, as is the validity of ;J-shifting; as a predictor of rotational fine structure. Among other ramifications, this work will facilitate understanding of mass-independent fractionation of sulfur isotopes (S-MIF) observed in the Archean rock record-particularly as this may have arisen from self shielding. S-MIF, in turn is highly relevant in the broader context of understanding the ;oxygen revolution;.

Electron transfer dissociation (ETD): The mass spectrometric breakthrough essential for O-GlcNAc protein site assignments – A study of the O-GlcNAcylated protein Host Cell Factor C1

PubMed Central

Myers, Samuel A.; Daou, Salima; Affar, El Bachir; Burlingame, AL

2014-01-01

The development of electron-based, unimolecular dissociation mass spectrometric methods, i.e. electron capture and electron transfer dissociation (ECD and ETD, respectively), has greatly increased the speed and reliability of labile post-translational modification (PTM) site assignment. The field of intracellular O-GlcNAc (O-linked N-acetylglucosamine) signaling has especially advanced with the advent of ETD mass spectrometry. Only within the last five years have proteomic-scale experiments utilizing ETD allowed the assignment of hundreds of O-GlcNAc sites within cells and subcellular structures. Our ability to identify and unambiguously assign the site of O-GlcNAc modifications using ETD is rapidly increasing our understanding of this regulatory glycosylation and its potential interaction with other PTMs. Here, we discuss the advantages of using ETD, complimented with collisional-activation mass spectrometry (CID/CAD), in a study of O-GlcNAc modified peptides of the extensively O-GlcNAcylated protein Host Cell Factor C1 (HCF-1). HCF-1 is a transcriptional co-regulator, forms a stable complex with O-GlcNAc transferase and is involved in control of cell cycle progression. ETD, along with higher energy collisional dissociation (HCD) mass spectrometry, was employed to assign the PTMs of the HCF-1 protein isolated from HEK293T cells. These include nineteen sites of O-GlcNAcylation, two sites of phosphorylation and two sites bearing dimethylarginine, and showcase the residue-specific, PTM complexity of this regulator of cell proliferation. PMID:23335398

Single-molecule spectroscopy unmasks the lowest exciton state of the B850 assembly in LH2 from Rps. acidophila.

PubMed

Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J; Freiberg, Arvi; Köhler, Jürgen

2014-05-06

We have recorded fluorescence-excitation and emission spectra from single LH2 complexes from Rhodopseudomonas (Rps.) acidophila. Both types of spectra show strong temporal spectral fluctuations that can be visualized as spectral diffusion plots. Comparison of the excitation and emission spectra reveals that for most of the complexes the lowest exciton transition is not observable in the excitation spectra due to the cutoff of the detection filter characteristics. However, from the spectral diffusion plots we have the full spectral and temporal information at hand and can select those complexes for which the excitation spectra are complete. Correlating the red most spectral feature of the excitation spectrum with the blue most spectral feature of the emission spectrum allows an unambiguous assignment of the lowest exciton state. Hence, application of fluorescence-excitation and emission spectroscopy on the same individual LH2 complex allows us to decipher spectral subtleties that are usually hidden in traditional ensemble spectroscopy. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Identification of Isomeric N-Glycan Structures by Mass Spectrometry with 157 nm Laser-Induced Photofragmentation

PubMed Central

Devakumar, Arugadoss; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Reilly, James P.

2008-01-01

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with CID experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion-trap facilitates MSn experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein utilized in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans. PMID:18487060

Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins

PubMed Central

Ichikawa, Muneyoshi; Liu, Dinan; Kastritis, Panagiotis L.; Basu, Kaustuv; Hsu, Tzu Chin; Yang, Shunkai; Bui, Khanh Huy

2017-01-01

Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule. PMID:28462916

Use of (S)-trans-gamma-monocyclofarnesol as a useful chiral building block for the stereoselective synthesis of diterpenic natural products.

PubMed

Serra, Stefano; Cominetti, Alessandra A; Lissoni, Veronica

2014-03-01

A comprehensive study of the exploitation of (S)-trans-gamma-monocyclofarnesol as a useful chiral building block for the stereoselective synthesis of natural diterpene derivatives is here described. The farnesol derivative (+)-1 was used as starting material in the preparation of the diterpenes (S)-dehydroambliol-A and (S)-trixagol, as well as for the syntheses of the dinorditerpene (S)-dinortrixagone and of the guanidine-interrupted terpenoid (S)-dotofide. Key steps of the presented syntheses were the cross-coupling between an allyl acetate and a Grignard reagent, the Wittig reaction, the selective preparation ofa diacylguanidine derivative and the alkylation of a sulfone derivative, followed by the reductive removal of the same functional group. It is worth noting that the natural products (+)-8, (+)-12 and (+)-15 were prepared stereoselectively for the first time, thus allowing the unambiguous assignment of their absolute configuration.

Differentiation of closely related isomers: application of data mining techniques in conjunction with variable wavelength infrared multiple photon dissociation mass spectrometry for identification of glucose-containing disaccharide ions.

PubMed

Stefan, Sarah E; Ehsan, Mohammad; Pearson, Wright L; Aksenov, Alexander; Boginski, Vladimir; Bendiak, Brad; Eyler, John R

2011-11-15

Data mining algorithms have been used to analyze the infrared multiple photon dissociation (IRMPD) patterns of gas-phase lithiated disaccharide isomers irradiated with either a line-tunable CO(2) laser or a free electron laser (FEL). The IR fragmentation patterns over the wavelength range of 9.2-10.6 μm have been shown in earlier work to correlate uniquely with the asymmetry at the anomeric carbon in each disaccharide. Application of data mining approaches for data analysis allowed unambiguous determination of the anomeric carbon configurations for each disaccharide isomer pair using fragmentation data at a single wavelength. In addition, the linkage positions were easily assigned. This combination of wavelength-selective IRMPD and data mining offers a powerful and convenient tool for differentiation of structurally closely related isomers, including those of gas-phase carbohydrate complexes.

Identification of the nucleophile catalytic residue of GH51 α-l-arabinofuranosidase from Pleurotus ostreatus

DOE PAGES

Amore, Antonella; Iadonisi, Alfonso; Vincent, Florence; ...

2015-12-21

In this paper, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involvedmore » in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.« less

Vibrational dynamics of rutile-type GeO2 from micro-Raman spectroscopy experiments and first-principles calculations

NASA Astrophysics Data System (ADS)

Sanson, A.; Pokrovski, G. S.; Giarola, M.; Mariotto, G.

2015-01-01

The vibrational dynamics of germanium dioxide in the rutile structure has been investigated by using polarized micro-Raman scattering spectroscopy coupled with first-principles calculations. Raman spectra were carried out in backscattering geometry at room temperature from micro-crystalline samples either unoriented or oriented by means of a micromanipulator, which enabled successful detection and identification of all the Raman active modes expected on the basis of the group theory. In particular, the Eg mode, incorrectly assigned or not detected in the literature, has been definitively observed by us and unambiguously identified at 525 \\text{cm}-1 under excitation by certain laser lines, thus revealing an unusual resonance phenomenon. First-principles calculations within the framework of the density functional theory allow quantifying both wave number and intensity of the Raman vibrational spectra. The excellent agreement between calculated and experimental data corroborates the reliability of our findings.

Optical third harmonic generation in the magnetic semiconductor EuSe

NASA Astrophysics Data System (ADS)

Lafrentz, M.; Brunne, D.; Kaminski, B.; Pavlov, V. V.; Pisarev, R. V.; Henriques, A. B.; Yakovlev, D. R.; Springholz, G.; Bauer, G.; Bayer, M.

2012-01-01

Third harmonic generation (THG) has been studied in europium selenide EuSe in the vicinity of the band gap at 2.1-2.6 eV and at higher energies up to 3.7 eV. EuSe is a magnetic semiconductor crystalizing in centrosymmetric structure of rock-salt type with the point group m3m. For this symmetry the crystallographic and magnetic-field-induced THG nonlinearities are allowed in the electric-dipole approximation. Using temperature, magnetic field, and rotational anisotropy measurements, the crystallographic and magnetic-field-induced contributions to THG were unambiguously separated. Strong resonant magnetic-field-induced THG signals were measured at energies in the range of 2.1-2.6 eV and 3.1-3.6 eV for which we assign to transitions from 4f7 to 4f65d1 bands, namely involving 5d(t2g) and 5d(eg) states.

Total mass difference statistics algorithm: a new approach to identification of high-mass building blocks in electrospray ionization Fourier transform ion cyclotron mass spectrometry data of natural organic matter.

PubMed

Kunenkov, Erast V; Kononikhin, Alexey S; Perminova, Irina V; Hertkorn, Norbert; Gaspar, Andras; Schmitt-Kopplin, Philippe; Popov, Igor A; Garmash, Andrew V; Nikolaev, Evgeniy N

2009-12-15

The ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrum of natural organic matter (NOM) contains several thousand peaks with dozens of molecules matching the same nominal mass. Such a complexity poses a significant challenge for automatic data interpretation, in which the most difficult task is molecular formula assignment, especially in the case of heavy and/or multielement ions. In this study, a new universal algorithm for automatic treatment of FTICR mass spectra of NOM and humic substances based on total mass difference statistics (TMDS) has been developed and implemented. The algorithm enables a blind search for unknown building blocks (instead of a priori known ones) by revealing repetitive patterns present in spectra. In this respect, it differs from all previously developed approaches. This algorithm was implemented in designing FIRAN-software for fully automated analysis of mass data with high peak density. The specific feature of FIRAN is its ability to assign formulas to heavy and/or multielement molecules using "virtual elements" approach. To verify the approach, it was used for processing mass spectra of sodium polystyrene sulfonate (PSS, M(w) = 2200 Da) and polymethacrylate (PMA, M(w) = 3290 Da) which produce heavy multielement and multiply-charged ions. Application of TMDS identified unambiguously monomers present in the polymers consistent with their structure: C(8)H(7)SO(3)Na for PSS and C(4)H(6)O(2) for PMA. It also allowed unambiguous formula assignment to all multiply-charged peaks including the heaviest peak in PMA spectrum at mass 4025.6625 with charge state 6- (mass bias -0.33 ppm). Application of the TMDS-algorithm to processing data on the Suwannee River FA has proven its unique capacities in analysis of spectra with high peak density: it has not only identified the known small building blocks in the structure of FA such as CH(2), H(2), C(2)H(2)O, O but the heavier unit at 154.027 amu. The latter was identified for the first time and assigned a formula C(7)H(6)O(4) consistent with the structure of dihydroxyl-benzoic acids. The presence of these compounds in the structure of FA has so far been numerically suggested but never proven directly. It was concluded that application of the TMDS-algorithm opens new horizons in unfolding molecular complexity of NOM and other natural products.

A new system for naming ribosomal proteins

PubMed Central

Ban, Nenad; Beckmann, Roland; Cate, Jamie HD; Dinman, Jonathan D; Dragon, François; Ellis, Steven R; Lafontaine, Denis LJ; Lindahl, Lasse; Liljas, Anders; Lipton, Jeffrey M; McAlear, Michael A; Moore, Peter B; Noller, Harry F; Ortega, Joaquin; Panse, Vikram Govind; Ramakrishnan, V; Spahn, Christian MT; Steitz, Thomas A; Tchorzewski, Marek; Tollervey, David; Warren, Alan J; Williamson, James R; Wilson, Daniel; Yonath, Ada; Yusupov, Marat

2015-01-01

A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as ‘new system’ names. PMID:24524803

Infrared spectroscopy of isoprene in noble gas matrices

NASA Astrophysics Data System (ADS)

Ito, Fumiyuki

2018-06-01

In this study, the infrared absorption spectra of 2-methyl-1,3-butadiene (isoprene) in noble gas matrices (Ar, Kr, and Xe) have been reported. The vibrational structure observed at cryogenic temperature, in combination with anharmonic vibrational calculations using density functional theory, helped in unambiguously assigning the fundamental modes of isoprene unresolved in the previous gas phase measurements, which would be of basic importance in the remote sensing of this molecule. A careful comparison with the most recent gas phase study [Brauer et al., Atmos. Meas. Tech. 7 (2014) 3839-3847.] led us to alternative assignments of the weak bands.

Chirped-Pulse Ftmw Spectroscopy of the Lactic ACID-H_2O System

NASA Astrophysics Data System (ADS)

Kisiel, Zbigniew; Białkowska-Jaworska, Ewa; Zaleski, Daniel P.; Neill, Justin L.; Steber, Amanda L.; Pate, Brooks H.

2011-06-01

The previous study of the rotational spectrum of lactic acid in supersonic expansion revealed rather temperamental behaviour of signal intensity suggestive of considerable clusterization. Lactic acid samples contain an appreciable amount of water so that the presence of clusters with water, as well as lactic dimers is suspected. Several, mainly computational, studies of such species have already been published. Investigation of the chirped-pulse rotational spectrum of a heated lactic acid (LA) sample diluted in Ne carrier gas allowed unambiguous assignment of the LA-H_2O, LA-(H_2O)_2, and LA-(H_2O)_3 species. In addition, the rotational spectrum of the AaT conformer of lactic acid has been assigned. This conformer involves an intramolecular hydrogen bond to the hydroxyl of the carboxylic group and it has been estimated to be less stable by ca 10 kJ/mol than the most stable SsC conformer. The evidence for the assignment and a discussion of the derived properties for the new species are presented. L.Pszczółkowski, E.Białkowska-Jaworska, Z.Kisiel, J. Mol. Spectrosc. 234, 106 (2005). J.Sadlej, J.Cz.Dobrowolski, J.E.Rode, M.H.Jamróz, PCCP 8, 101 (2006) M.Losada, H.Tran, Y.Xu, J. Chem. Phys. 128, 014508 (2008) A.Smaga, J.Sadlej, J. Phys. Chem. A 114, 4427 (2010). A.Borba, A.Gomez-Zavaglia, L.Łapinski, R.Fausto, PCCP 6, 2101 (2004).

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

Uncovering the Terahertz Spectrum of Copper Sulfate Pentahydrate.

PubMed

Ruggiero, Michael T; Korter, Timothy M

2016-01-21

Terahertz vibrational spectroscopy has evolved into a powerful tool for the detection and characterization of transition metal sulfate compounds, specifically for its ability to differentiate between various hydrated forms with high specificity. Copper(II) sulfate is one such system where multiple crystalline hydrates have had their terahertz spectra fully assigned, and the unique spectral fingerprints of the forms allows for characterization of multicomponent systems with relative ease. Yet the most commonly occurring form, copper(II) sulfate pentahydrate (CuSO4·5H2O), has proven elusive due to the presence of a broad absorption across much of the terahertz region, making the unambiguous identification of its spectral signature difficult. Here, it is shown that the sub-100 cm(-1) spectrum of CuSO4·5H2O is obscured by absorption from adsorbed water and that controlled drying reveals sharp underlying features. The crystalline composition of the samples was monitored in parallel by X-ray diffraction as a function of drying time, supporting the spectroscopic results. Finally, the terahertz spectrum of CuSO4·5H2O was fully assigned using solid-state density functional theory simulations, helping attribute the additional absorptions that appear after excessive drying to formation of CuSO4·3H2O.

Synthesis of robalzotan, ebalzotan, and rotigotine precursors via the stereoselective multienzymatic cascade reduction of α,β-unsaturated aldehydes.

PubMed

Brenna, Elisabetta; Gatti, Francesco G; Malpezzi, Luciana; Monti, Daniela; Parmeggiani, Fabio; Sacchetti, Alessandro

2013-05-17

A stereoselective synthesis of bicyclic primary or secondary amines, based on tetralin or chroman structural moieties, is reported. These amines are precursors of important active pharmaceutical ingredients such as rotigotine (Neupro), robalzotan, and ebalzotan. The key step is based on a multienzymatic reduction of an α,β-unsaturated aldehyde or ketone to give the saturated primary or secondary alcohol, in a high yield and with a high ee. The catalytic system consists of the combination of an ene-reductase (ER; i.e., OYE2 or OYE3 belonging to the Old Yellow Enzyme family) with an alcohol dehydrogenase (ADH), applying the in situ substrate feeding product removal technology. By this system the formation of the allylic alcohol side product and the racemization of the chirally unstable α-substituted aldehyde intermediate are minimized. The primary alcohols were elaborated via a Curtius rearrangement. The combination of OYE2 with a Prelog or an anti-Prelog ADH allowed the preparation of the secondary alcohols with ee > 99% and de > 87%. The absolute configuration of the primary amines was unambiguously assigned by comparison with authentic samples. The stereochemistry of secondary alcohols was assigned by X-ray crystal structure and NMR analysis of Mosher esters.

How Toddlers and Preschoolers Learn to Uniquely Identify Referents for Others: A Training Study

ERIC Educational Resources Information Center

Matthews, Danielle; Lieven, Elena; Tomasello, Michael

2007-01-01

This training study investigates how children learn to refer to things unambiguously. Two hundred twenty-four children aged 2.6, 3.6, and 4.6 years were pre- and post-tested for their ability to request stickers from a dense array. Between test sessions, children were assigned to a training condition in which they (a) asked for stickers from an…

HGVS Recommendations for the Description of Sequence Variants: 2016 Update.

PubMed

den Dunnen, Johan T; Dalgleish, Raymond; Maglott, Donna R; Hart, Reece K; Greenblatt, Marc S; McGowan-Jordan, Jean; Roux, Anne-Francoise; Smith, Timothy; Antonarakis, Stylianos E; Taschner, Peter E M

2016-06-01

The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD-WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD-WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here, we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen. © 2016 WILEY PERIODICALS, INC.

The Comprehensive AOCMF Classification System: Mandible Fractures- Level 2 Tutorial

PubMed Central

Cornelius, Carl-Peter; Audigé, Laurent; Kunz, Christoph; Rudderman, Randal; Buitrago-Téllez, Carlos H.; Frodel, John; Prein, Joachim

2014-01-01

This tutorial outlines the details of the AOCMF image-based classification system for fractures of the mandible at the precision level 2 allowing description of their topographical distribution. A short introduction about the anatomy is made. Mandibular fractures are classified by the anatomic regions involved. For this purpose, the mandible is delineated into an array of nine regions identified by letters: the symphysis/parasymphysis region anteriorly, two body regions on each lateral side, combined angle and ascending ramus regions, and finally the condylar and coronoid processes. A precise definition of the demarcation lines between these regions is given for the unambiguous allocation of fractures. Four transition zones allow an accurate topographic assignment if fractures end up in or run across the borders of anatomic regions. These zones are defined between angle/ramus and body, and between body and symphysis/parasymphysis. A fracture is classified as “confined” as long as it is located within a region, in contrast to a fracture being “nonconfined” when it extents to an adjoining region. Illustrations and case examples of mandible fractures are presented to become familiar with the classification procedure in daily routine. PMID:25489388

Preliminary neutron crystallographic analysis of selectively CH3-protonated, deuterated rubredoxin from Pyrococcus furiosus

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

Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew

2008-01-01

Neutron crystallography is used to locate hydrogen atoms in biological materials and can distinguish between negatively scattering hydrogen and positively scattering deuterium substituted positions in isomorphous neutron structures. Recently, Hauptman and Langs (2003) have shown that neutron diffraction data can be used to solve macromolecular structures by direct methods and that solution is aided by the presence of negatively scattering hydrogen atoms in the structure. Selective labeling protocols allow the design and production of H/D-labeled macromolecular structures in which the ratio of hydrogen to deuterium atoms can be precisely controlled. We have applied methyl-selective labeling protocols to introduce (1H-delta methyl)-leucinemore » and (1H-gamma methyl)-valine into deuterated rubredoxin from Pyrococcus furiosus (PfRd). Here we report on the production, crystallization, and preliminary neutron analysis of the selectively CH3-protonated, deuterated PfRd sample, which provided a high quality neutron data set extending to 1.75 resolution at the new LADI-III instrument at the Insititut Laue-Langevin. Preliminary analysis of neutron density maps allows unambiguous assignment of the positions of hydrogen atoms at the methyl groups of the valine and leucine residues in the otherwise deuterated rubredoxin structure.« less

Evaluation of gas chromatography-tandem quadrupole mass spectrometry for the determination of organochlorine pesticides in fats and oils.

PubMed

Patel, Katan; Fussell, Richard J; Hetmanski, Mike; Goodall, David M; Keely, Brendan J

2005-03-18

A gas chromatography-tandem quadrupole mass spectrometry multi-residue method for the analysis of 19 organochlorine pesticides in fats and oils has been developed. Gel permeation chromatography was employed to remove lipid material prior to GC-MS/MS analysis. Average recoveries of the pesticides spiked at 10 and 50 microg kg(-1) into fish oil, pork fat, olive oil and hydrogenated vegetable oil were typically in the range 70-110% with relative standard deviations generally less than 10%. Calculated limits of detection are between 0.1 and 2.0 microg kg(-1) and results obtained for the analysis of proficiency test materials are in good agreement with assigned values. The higher selectivity of the GC-MS/MS compared to electron capture detection and GC-MS in selective ion monitoring mode allowed unambiguous identification and confirmation of all the target pesticides at low microg kg(-1) levels in fats and oils in a single analysis.

Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.

DART - LTQ ORBITRAP as an expedient tool for the identification of synthetic cannabinoids.

PubMed

Habala, Ladislav; Valentová, Jindra; Pechová, Iveta; Fuknová, Mária; Devínsky, Ferdinand

2016-05-01

Synthetic cannabinoids as designer drugs constitute a major problem due to their rapid increase in number and the difficulties connected with their identification in complex mixtures. DART (Direct Analysis in Real Time) has emerged as an advantageous tool for the direct and rapid analysis of complex samples by mass spectrometry. Here we report on the identification of six synthetic cannabinoids originating from seized material in various matrices, employing the combination of ambient pressure ion source DART and hybrid ion trap - LTQ ORBITRAP mass spectrometer. This report also describes the sampling techniques for the provided herbal material containing the cannabinoids, either directly as plant parts or as an extract in methanol and their influence on the outcome of the analysis. The high resolution mass spectra supplied by the LTQ ORBITRAP instrument allowed for an unambiguous assignment of target compounds. The utilized instrumental coupling proved to be a convenient way for the identification of synthetic cannabinoids in real-world samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Temperature effect on the vibrational dynamics of cyclodextrin inclusion complexes: investigation by FTIR-ATR spectroscopy and numerical simulation.

PubMed

Crupi, Vincenza; Majolino, Domenico; Venuti, Valentina; Guella, Graziano; Mancini, Ines; Rossi, Barbara; Verrocchio, Paolo; Viliani, Gabriele; Stancanelli, Rosanna

2010-07-01

The vibrational dynamics of solid inclusion complexes of the nonsteroidal anti-inflammatory drug Ibuprofen (IBP) with beta-cyclodextrin (beta-CD) and methyl-beta-cyclodextrin (Me-beta-CD) has been investigated by using attenuated total reflection-Fourier transform infrared FTIR-ATR spectroscopy, in order to monitor the changes induced, as a consequence of complexation, on the vibrational spectrum of IBP, in the wavenumber range 600-4000 cm(-1). Quantum chemical calculations were performed on monomeric and dimeric structures of IBP, derived from symmetric hydrogen bonding of the two carboxylic groups, in order to unambiguously assign some characteristic IR bands in the IBP spectrum. The evolution in temperature from 250 to 340 K of the C horizontal lineO stretching vibration, described by a best-fit procedure, allowed us to extract the thermodynamic parameter DeltaH associated to the binding of IBP with betaCDs in the solid phase. By comparing these results, Me-beta-CD has been shown to be the most effective carrier for IBP.

Point defects in crystalline zircon (zirconium silicate), ZrSiO4: electron paramagnetic resonance studies

NASA Astrophysics Data System (ADS)

Tennant, W. C.; Claridge, R. F. C.; Walsby, C. J.; Lees, N. S.

This article outlines the present state of knowledge of paramagnetic defects in crystalline zircon as obtained mainly, but not exclusively, from electron paramagnetic resonance (EPR) studies in crystalline zircon (zirconium silicate, ZrSiO4). The emphasis is on single-crystal studies where, in principle, unambiguous analysis is possible. Firstly, the crystallography of zircon is presented. Secondly, the relationships between available crystal-site symmetries and the symmetries of observed paramagnetic species in zircon, and how these observations lead to unambiguous assignments of point-group symmetries for particular paramagnetic species are detailed. Next, spin-Hamiltonian (SH) analysis is discussed with emphasis on the symmetry relationships that necessarily exist amongst the Laue classes of the crystal sites in zircon, the paramagnetic species occupying those sites and the SH itself. The final sections of the article then survey the results of EPR studies on zircon over the period 1960-2002.

Redescription of Calyptosuchus (Stagonolepis) wellesi (Archosauria: Pseudosuchia: Aetosauria) from the Late Triassic of the Southwestern United States with a discussion of genera in vertebrate paleontology.

PubMed

Parker, William G

2018-01-01

Calyptosuchus wellesi is a medium-sized desmatosuchian aetosaur common in Adamanian (early to middle Norian) age rocks from the Chinle Formation and Dockum Group of the Western United States. Known chiefly from osteoderms, this taxon has never been fully described and non-osteoderm material assigned to Calyptosuchus has been done so based on questionable criteria. Mapping of aetosaurian elements from the Placerias Quarry allows for the recognition of associated material providing support for referrals of non-osteoderm material. Furthermore, another previously undescribed specimen from the Chinle Formation of Arizona provides more details about this taxon. Presently Calyptosuchus lacks discrete autapomorphies, but can be distinguished from other aetosaurs based on a unique combination of characters supported by a phylogenetic analysis. Calyptosuchus is one of the most common aetosaurians in the Western United States and an index taxon of the early Adamanian biozone. The name Calyptosuchus is retained and encouraged as the applicable genus name for the species wellesi rather than the often used Stagonolepis because assignments of taxa to multi-species genus names are problematic and in this case provides a proposed taxonomic relationship that cannot be unambiguously supported, even by phylogenetic analyses. Because of the inherent limitations of the fossil record, referral of specimens and species to species and genera respectively is an epistemological problem in vertebrate paleontology.

On the problem of resonance assignments in solid state NMR of uniformly 15N, 13C-labeled proteins

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

Some practical problems in implementing randomization.

PubMed

Downs, Matt; Tucker, Kathryn; Christ-Schmidt, Heidi; Wittes, Janet

2010-06-01

While often theoretically simple, implementing randomization to treatment in a masked, but confirmable, fashion can prove difficult in practice. At least three categories of problems occur in randomization: (1) bad judgment in the choice of method, (2) design and programming errors in implementing the method, and (3) human error during the conduct of the trial. This article focuses on these latter two types of errors, dealing operationally with what can go wrong after trial designers have selected the allocation method. We offer several case studies and corresponding recommendations for lessening the frequency of problems in allocating treatment or for mitigating the consequences of errors. Recommendations include: (1) reviewing the randomization schedule before starting a trial, (2) being especially cautious of systems that use on-demand random number generators, (3) drafting unambiguous randomization specifications, (4) performing thorough testing before entering a randomization system into production, (5) maintaining a dataset that captures the values investigators used to randomize participants, thereby allowing the process of treatment allocation to be reproduced and verified, (6) resisting the urge to correct errors that occur in individual treatment assignments, (7) preventing inadvertent unmasking to treatment assignments in kit allocations, and (8) checking a sample of study drug kits to allow detection of errors in drug packaging and labeling. Although we performed a literature search of documented randomization errors, the examples that we provide and the resultant recommendations are based largely on our own experience in industry-sponsored clinical trials. We do not know how representative our experience is or how common errors of the type we have seen occur. Our experience underscores the importance of verifying the integrity of the treatment allocation process before and during a trial. Clinical Trials 2010; 7: 235-245. http://ctj.sagepub.com.

Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF.

PubMed Central

Tolson, D A; Nicholson, N H

1998-01-01

The determination of DNA sequences by partial exonuclease digestion followed by Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF) is a well established method. When the same procedure is applied to RNA, difficulties arise due to the small (1 Da) mass difference between the nucleotides U and C, which makes unambiguous assignment difficult using a MALDI-TOF instrument. Here we report our experiences with sequence specific endonucleases and chemical methods followed by MALDI-TOF to resolve these sequence ambiguities. We have found chemical methods superior to endonucleases both in terms of correct specificity and extent of sequence coverage. This methodology can be used in combination with exonuclease digestion to rapidly assign RNA sequences. PMID:9421498

Negative ion formation in potassium-nitromethane collisions.

PubMed

Antunes, R; Almeida, D; Martins, G; Mason, N J; Garcia, G; Maneira, M J P; Nunes, Y; Limão-Vieira, P

2010-10-21

Ion-pair formation in gaseous nitromethane (CH(3)NO(2)) induced by electron transfer has been studied by investigating the products of collisions between fast potassium atoms and nitromethane molecules using a crossed molecular-beam technique. The negative ions formed in such collisions were analysed using time-of-flight mass spectroscopy. The six most dominant product anions are NO(2)(-), O(-), CH(3)NO(2)(-), OH(-), CH(2)NO(2)(-) and CNO(-). By using nitromethane-d(3) (CD(3)NO(2)), we found that previous mass 17 amu assignment to O(-) delayed fragment, is in the present experiment may be unambiguously assigned to OH(-). The formation of CH(2)NO(2)(-) may be explained in terms of dissociative electron attachment to highly vibrationally excited molecules.

Complete sequence of HLA-B27 cDNA identified through the characterization of structural markers unique to the HLA-A, -B, and -C allelic series

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

Szoets, H.; Reithmueller, G.; Weiss, E.

1986-03-01

Antigen HLA-B27 is a high-risk genetic factor with respect to a group of rheumatoid disorders, especially ankylosing spondylitis. A cDNA library was constructed from an autozygous B-cell line expressing HLA-B27, HLA-Cw1, and the previously cloned HLA-A2 antigen. Clones detected with an HLA probe were isolated and sorted into homology groups by differential hybridization and restriction maps. Nucleotide sequencing allowed the unambiguous assignment of cDNAs to HLA-A, -B, and -C loci. The HLA-B27 mRNA has the structure features and the codon variability typical of an HLA class I transcript but it specifies two uncommon amino acid replacements: a cysteine in positionmore » 67 and a serine in position 131. The latter substitution may have functional consequences, because it occurs in a conserved region and at a position invariably occupied by a species-specific arginine in humans and lysine in mice. The availability of the complete sequence of HLA-B27 and of the partial sequence of HLA-Cw1 allows the recognition of locus-specific sequence markers, particularly, but not exclusively, in the transmembrane and cytoplasmic domains.« less

Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

PubMed

Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

2016-02-18

Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

Re-Visiting the Electronic Energy Map of the Copper Dimer by Double-Resonant Four-Wave Mixing

NASA Astrophysics Data System (ADS)

Visser, Bradley; Bornhauser, Peter; Beck, Martin; Knopp, Gregor; Marquardt, Roberto; Gourlaouen, Christophe; van Bokhoven, Jeroen A.; Radi, Peter

2017-06-01

The copper dimer is one of the most studied transition metal (TM) diatomics due to its alkali-metal like electronic shell structure, strongly bound ground state and chemical reactivity. The high electronic promotion energy in the copper atom yields numerous low-lying electronic states compared to TM dimers with d)-hole electronic configurations. Thus, through extensive study the excited electronic structure of Cu_2 is relatively well known, however in practice few excited states have been investigated with rotational resolution or even assigned term symbols or dissociation limits. The spectroscopic methods that have been used to investigate the copper dimer until now have not possessed sufficient spectral selectivity, which has complicated the analysis of the often overlapping transitions. Resonant four-wave mixing is a non-linear absorption based spectroscopic method. In favorable cases, the two-color version (TC-RFWM) enables purely optical mass selective spectral measurements in a mixed molecular beam. Additionally, by labelling individual rotational levels in the common intermediate state the spectra are dramatically simplified. In this work, we report on the rotationally resolved characterization of low-lying electronic states of dicopper. Several term symbols have been assigned unambiguously. De-perturbation studies performed shed light on the complex electronic structure of the molecule. Furthermore, a new low-lying electronic state of Cu_2 is discovered and has important implications for the high-level theoretical structure calculations performed in parallel. In fact, the ab initio methods applied yield relative energies among the electronic levels that are almost quantitative and allow assignment of the newly observed state that is governed by spin-orbit interacting levels.

Unambiguous detection of astaxanthin and astaxanthin fatty acid esters in krill (Euphausia superba Dana).

PubMed

Grynbaum, Marc David; Hentschel, Petra; Putzbach, Karsten; Rehbein, Jens; Krucker, Manfred; Nicholson, Graeme; Albert, Klaus

2005-09-01

HPLC atmospheric pressure chemical ionization (APCI)/MS, GC MS, HPLC diode array detection (DAD), and NMR were used for the identification of astaxanthin and astaxanthin fatty acid esters in krill (Euphausia superba Dana). Matrix solid phase dispersion was applied for the extraction of the carotenoids. This gentle and expeditious extraction technique for solid and viscous samples leads to distinct higher enrichment rates than the conventional liquid-liquid extraction. The chromatographic separation was achieved employing a C30 RP column that allows the separation of shape-constrained geometrical isomers. A methanol/tert-butylmethyl ether/water gradient was applied. (all-E) Astaxanthin and the geometrical isomers were identified by HPLC APCI/MS, by coelution with isomerized authentical standard, by UV spectroscopy (DAD), and three isomers were unambiguously assigned by microcoil NMR spectroscopy. In this method, microcoils are transversally aligned to the magnetic field and have an increased sensitivity compared to the conventional double-saddle Helmholtz coils, thus enabling the measurement on small samples. The carotenol fatty acid esters were saponified enzymatically with Lipase type VII from Candida rugosa. The fatty acids were detected by GC MS after transesterification, but also without previous derivatization by HPLC APCI/MS. C14:0, C16:0, C16:1, C18:1, C20:0, C20:5, and C22:6 were found in astaxanthin monoesters and in astaxanthin diesters. (all-E) Astaxanthin was identified as the main isomer in six fatty acid ester fractions by NMR. Quantitation was carried out by the method of internal standard. (13-cis) Astaxanthin (70 microg/g), 542 microg/g (all-E) astaxanthin, 36 microg/g unidentified astaxanthin isomer, 62 microg/g (9-cis) astaxanthin, and 7842 microg/g astaxanthin fatty acid esters were found.

Magnetic nanoparticles formed in glasses co-doped with iron and larger radius elements

NASA Astrophysics Data System (ADS)

Edelman, I.; Ivanova, O.; Ivantsov, R.; Velikanov, D.; Zabluda, V.; Zubavichus, Y.; Veligzhanin, A.; Zaikovskiy, V.; Stepanov, S.; Artemenko, A.; Curély, J.; Kliava, J.

2012-10-01

A new type of nanoparticle-containing glasses based on borate glasses co-doped with low contents of iron and larger radius elements, Dy, Tb, Gd, Ho, Er, Y, and Bi, is studied. Heat treatment of these glasses results in formation of magnetic nanoparticles, radically changing their physical properties. Transmission electron microscopy and synchrotron radiation-based techniques: x-ray diffraction, extended x-ray absorption fine structure, x-ray absorption near-edge structure, and small-angle x-ray scattering, show a broad distribution of nanoparticle sizes with characteristics depending on the treatment regime; a crystalline structure of these nanoparticles is detected in heat treated samples. Magnetic circular dichroism (MCD) studies of samples subjected to heat treatment as well as of maghemite, magnetite, and iron garnet allow to unambiguously assign the nanoparticle structure to maghemite, independently of co-dopant nature and of heat treatment regime used. Different features observed in the MCD spectra are related to different electron transitions in Fe3+ ions gathered in the nanoparticles. The static magnetization in heat treated samples has non-linear dependence on the magnetizing field with hysteresis. Zero-field cooled magnetization curves show that at higher temperatures the nanoparticles occur in superparamagnetic state with blocking temperatures above 100 K. Below ca. 20 K, a considerable contribution to both zero field-cooled and field-cooled magnetizations occurs from diluted paramagnetic ions. Variable-temperature electron magnetic resonance (EMR) studies unambiguously show that in as-prepared glasses paramagnetic ions are in diluted state and confirm the formation of magnetic nanoparticles already at earlier stages of heat treatment. Computer simulations of the EMR spectra corroborate the broad distribution of nanoparticle sizes found by "direct" techniques as well as superparamagnetic nanoparticle behaviour demonstrated in the magnetization studies.

Identification and subspecific differentiation of Mycobacterium scrofulaceum by automated sequencing of a region of the gene (hsp65) encoding a 65-kilodalton heat shock protein.

PubMed Central

Swanson, D S; Pan, X; Musser, J M

1996-01-01

Mycobacterium scrofulaceum is most commonly recovered from children with cervical lymphadenitis, although it also accounts for approximately 2% of the mycobacterial infections in AIDS patients. Species assignment of M. scrofulaceum isolated by conventional techniques can be difficult and time-consuming. To develop a strategy for rapid species assignment of these organisms, a 360-bp region of the gene (hsp65) encoding a 65-kDa heat shock protein in 37 isolates from diverse sources was sequenced. Eight hsp65 alleles were identified, and these sequences formed phylogenetic clusters and lineages largely distinct from other Mycobacterium species. There was incomplete correlation between serovar designation and hsp65 allele assignment. The hsp65 data correlated strongly with the results of sequence analysis of the gene coding for 16S rRNA. Automated DNA sequencing of a 360-bp region of the hsp65 gene provides a rapid and unambiguous method for species assignment of these acid-fast organisms for diagnostic purposes. PMID:8940463

Cooperative use of VCD and XRD for the determination of tetrahydrobenzoisoquinolines absolute configuration: a reliable proof of memory of chirality and retention of configuration in enediyne rearrangements.

PubMed

Mondal, Shovan; Naubron, Jean-Valère; Campolo, Damien; Giorgi, Michel; Bertrand, Michéle P; Nechab, Malek

2013-12-01

The absolute configurations (AC) of azaheterocylic compounds resulting from the cascade rearrangement of enediynes involving only light atoms were unambiguously assigned by the joint use of vibrational circular dichroism (VCD) and copper radiation single crystal X-ray diffraction (XRD). These AC determinations proved that the rearrangements of enediynes proceeded with memory of chirality and retention of configuration. © 2013 Wiley Periodicals, Inc.

Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

2010-05-01

Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

A robust sparse-modeling framework for estimating schizophrenia biomarkers from fMRI.

PubMed

Dillon, Keith; Calhoun, Vince; Wang, Yu-Ping

2017-01-30

Our goal is to identify the brain regions most relevant to mental illness using neuroimaging. State of the art machine learning methods commonly suffer from repeatability difficulties in this application, particularly when using large and heterogeneous populations for samples. We revisit both dimensionality reduction and sparse modeling, and recast them in a common optimization-based framework. This allows us to combine the benefits of both types of methods in an approach which we call unambiguous components. We use this to estimate the image component with a constrained variability, which is best correlated with the unknown disease mechanism. We apply the method to the estimation of neuroimaging biomarkers for schizophrenia, using task fMRI data from a large multi-site study. The proposed approach yields an improvement in both robustness of the estimate and classification accuracy. We find that unambiguous components incorporate roughly two thirds of the same brain regions as sparsity-based methods LASSO and elastic net, while roughly one third of the selected regions differ. Further, unambiguous components achieve superior classification accuracy in differentiating cases from controls. Unambiguous components provide a robust way to estimate important regions of imaging data. Copyright © 2016 Elsevier B.V. All rights reserved.

Use of CID/ETD Mass Spectrometry to Analyze Glycopeptides

PubMed Central

Mechref, Yehia

2013-01-01

Collision-induced dissociation (CID) tandem mass spectrometry (MS) does not allow the characterization of glycopeptides because of the fragmentation of their glycan structures and limited fragmentation of peptide backbones. Electron-transfer dissociation (ETD) tandem MS, on the other hand, offers an alternative approach allowing the fragmentation of only peptide backbones of glycopeptides. Characterization of glycopeptides using both CID and ETD is summarized in this unit. While CID provide information related to the composition of glycan moiety attached to a peptide backbone, ETD permits de novo sequencing of peptides, since it prompts only peptide backbone fragmentation while keeping posttranslational modifications intact. Radical anions transfer of electrons to peptide backbone which induces cleavage of the N-Cα bond is observed in ETD. The glycan moiety is retained on the peptide backbone, largely unaffected by the ETD process. Accordingly, ETD allows not only the identification of the amino acid sequence of a glycopeptide, but also the unambiguous assignment of its glycosylation site. When data acquired from both fragmentation techniques are combined, it is possible to characterize comprehensively the entire glycopeptide. This is achieved using an instrument capable of alternating between CID and ETD experiments during an LC-MS/MS analysis. This unit discusses the different fragmentation of glycopeptides observed in CID and ETD. Tables of residue masses associated with oxonium ions observed in CID are provided to help in the interpretation of CID mass spectra. The utility of both CID and ETD for better characterization of glycopeptides are demonstrated for a model glycoprotein. PMID:22470127

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE PAGES

Zinke, Maximilian; Fricke, Pascal; Samson, Camille; ...

2017-07-07

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

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

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Gene Expression During the Development of Bacteriophage φ29 III. Analysis of Viral-Specific Protein Synthesis with Suppressible Mutants

PubMed Central

McGuire, Jeffrey C.; Pène, Jacques J.; Barrow-Carraway, Joyce

1974-01-01

Fifty-four suppressible mutants of bacteriophage φ29 have been isolated with a variety of mutagens and assigned to eight complementation groups. Viral-specific protein synthesis in UV light-irradiated, nonsuppressing Bacillus subtilis 60084 was analyzed with exponential acrylamide gels. Four additional φ29 proteins which were undetected on ordinary acrylamide gels are reported in this paper. Five phage φ29 proteins have been unambiguously assigned to specific cistrons. Two cistrons had pleiotropic effects on viral protein synthesis. Mutants in cistrons I or II were unable to synthesize DNA in nonsuppressing bacteria. Mutants in cistron I were unable to attach viral chromosomes to the host cell membrane, and the protein responsible for this function has been identified. The other viral protein playing a role in phage φ29 DNA synthesis is also identified and assigned to cistron II. Mutants in cistron II can attach viral chromosomes to membrane, but cannot synthesize DNA in nonsuppressing bacteria. Images PMID:4362871

Iron Carbides in Fischer–Tropsch Synthesis: Theoretical and Experimental Understanding in Epsilon-Iron Carbide Phase Assignment

DOE PAGES

Liu, Xing-Wu; Cao, Zhi; Zhao, Shu; ...

2017-09-11

As active phases in low-temperature Fischer–Tropsch synthesis for liquid fuel production, epsilon iron carbides are critically important industrial materials. However, the precise atomic structure of epsilon iron carbides remains unclear, leading to a half-century of debate on the phase assignment of the ε-Fe 2C and ε’-Fe 2.2C. Here, we resolve this decades-long question by a combining theoretical and experimental investigation to assign the phases unambiguously. First, we have investigated the equilibrium structures and thermal stabilities of ε-Fe xC, (x = 1, 2, 2.2, 3, 4, 6, 8) by first-principles calculations. We have also acquired X-ray diffraction patterns and Mössbauer spectramore » for these epsilon iron carbides, and compared them with the simulated results. These analyses indicate that the unit cell of ε-Fe 2C contains only one type of chemical environment for Fe atoms, while ε’-Fe 2.2C has six sets of chemically distinct Fe atoms.« less

Aperture Mask for Unambiguous Parity Determination in Long Wavelength Imagers

NASA Technical Reports Server (NTRS)

Bos, Brent

2011-01-01

A document discusses a new parity pupil mask design that allows users to unambiguously determine the image space coordinate system of all the James Webb Space Telescope (JWST) science instruments by using two out-of-focus images. This is an improvement over existing mask designs that could not completely eliminate the coordinate system parity ambiguity at a wavelength of 5.6 microns. To mitigate the problem of how the presence of diffraction artifacts can obscure the pupil mask detail, this innovation has been created with specifically designed edge features so that the image space coordinate system parity can be determined in the presence of diffraction, even at long wavelengths.

Raman fingerprints for unambiguous identification of organotin compounds.

PubMed

Pankin, Dmitrii; Kolesnikov, Ilya; Vasileva, Anna; Pilip, Anna; Zigel, Vladislav; Manshina, Alina

2018-06-13

Raman spectra of the different ecotoxicants such as perfluorooctane sulfonate acid, organotin compounds of different families tributyl-, and triphenyl-, as well as chemically close compounds belonging to the same family - such as mono-, di-, and tributyl organotin compounds were analyzed. The comprehensive Raman spectra analysis allowed suggesting the identification scheme for clear recognition of the toxins family and the following intra-group specification. Possibility of unambiguous toxins detection and identification was demonstrated also for complex mixtures of various toxins on a base of control of characteristic peak groups, which can be considered as Raman fingerprints of the listed environmentally hazardous substances. Copyright © 2018. Published by Elsevier B.V.

Concurrent Mass Measurement and Laser Spectroscopy for Unambiguous Isomeric State Assignment

NASA Astrophysics Data System (ADS)

Lascar, Daniel; Babcock, Carla; Henderson, Jack; Pearson, Matt

2017-09-01

Recent work by the TITAN group at TRIUMF on isomeric state mass measurements of odd-A, neutron-rich cadmium nuclei has shown a disconnect between experiment and theory in 127 g , mCd. The spin and parity assignments of the ground and isomeric states are assigned as 3/2+ and 11/2-, respectively, primarily via systematic arguments. Conversely, state of the art shell model and ab initio calculations show a reversal of the states, predicting a ground state of 11/2- and a 3/2+ isomer. Penning Trap Mass Spectrometry (PTMS) can measure the energy separation between the ground state and the isomer without ambiguity but cannot, on its own, comment on the spin and parity. Collinear Laser Spectroscopy (CLS) experiments have been performed on 127Cd and have elegantly demonstrated the existence of both 3/2+ and 11/2- states. What CLS cannot do, on its own, is assign an ordering to those states. If, however, a PTMS and CLS experiment could be performed concurrently using identical beams from the same facility then there exists sufficient information shared between both experiments that a definitive assignment can be made. We present a concept for a new slate of measurements using existing experimental facilities simultaneously, with shared resources, to definitively assign spin and parity for ground and isomeric states in short-lived nuclei.

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Synthesis of 24-phenyl-24-oxo steroids derived from bile acids by palladium-catalyzed cross coupling with phenylboronic acid. NMR characterization and X-ray structures.

PubMed

Mayorquín-Torres, Martha C; Romero-Ávila, Margarita; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

2013-11-01

Palladium-catalyzed cross coupling of phenyboronic acid with acetylated bile acids in which the carboxyl functions have been activated by formation of a mixed anhydride with pivalic anhydride afforded moderate to good yield of 24-phenyl-24-oxo-steroids. Unambiguous assignments of the NMR signals were made with the aid of combined 1D and 2D NMR techniques. X-ray diffraction studies confirmed the obtained structures. Copyright © 2013 Elsevier Inc. All rights reserved.

Combined distribution functions: A powerful tool to identify cation coordination geometries in liquid systems

NASA Astrophysics Data System (ADS)

Sessa, Francesco; D'Angelo, Paola; Migliorati, Valentina

2018-01-01

In this work we have developed an analytical procedure to identify metal ion coordination geometries in liquid media based on the calculation of Combined Distribution Functions (CDFs) starting from Molecular Dynamics (MD) simulations. CDFs provide a fingerprint which can be easily and unambiguously assigned to a reference polyhedron. The CDF analysis has been tested on five systems and has proven to reliably identify the correct geometries of several ion coordination complexes. This tool is simple and general and can be efficiently applied to different MD simulations of liquid systems.

A DNA barcode library for Germany's mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera).

PubMed

Morinière, Jérôme; Hendrich, Lars; Balke, Michael; Beermann, Arne J; König, Tobias; Hess, Monika; Koch, Stefan; Müller, Reinhard; Leese, Florian; Hebert, Paul D N; Hausmann, Axel; Schubart, Christoph D; Haszprunar, Gerhard

2017-11-01

Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well-curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient and reliable DNA-based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two-thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution. © 2017 John Wiley & Sons Ltd.

Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia.

PubMed

Hmaïed, F; Helel, S; Le Berre, V; François, J-M; Leclercq, A; Lecuit, M; Smaoui, H; Kechrid, A; Boudabous, A; Barkallah, I

2014-02-01

We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus. The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases. We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Comprehensive Fe-ligand vibration identification in {FeNO} 6 Hemes

DOE PAGES

Li, Jianfeng; Peng, Qian; Oliver, Allen G.; ...

2014-12-09

Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO} 6 porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO 4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO 4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO 4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quitemore » distinct from those found for CO or {FeNO} 7 heme species. This is the result of unchanging Fe–N NO bonding interactions in the {FeNO} 6 species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe–Im stretch in six-coordinate heme derivatives. Furthermore, NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O 2 reveal a strong correlation between the Fe–Im stretch and Fe–N Im bond distance that is detailed for the first time.« less

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

PubMed

Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

2015-12-10

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

Isolation and identification of lutein esters, including their regioisomers, in tritordeum (×Tritordeum Ascherson et Graebner) grains: Evidence for a preferential xanthophyll acyltransferase activity.

PubMed

Mellado-Ortega, Elena; Hornero-Méndez, Dámaso

2012-12-01

Liquid chromatography in conjunction with UV-visible spectroscopy and atmospheric pressure chemical ionisation (APCI) mass spectrometry has been used for the structural assignment of the lutein esters, including the regioisomeric forms, naturally occurring in the endosperm of tritordeum (×Tritordeum Ascherson et Graebner), a novel cereal. The distinctive mass spectrometry fragmentation pattern of lutein, characterized by a favored loss of the moieties at the position 3' of the ε-end ring, allowed an unambiguous structural identification of four monoesters (lutein 3'-O-linoleate, lutein 3-O-linoleate, lutein 3'-O-palmitate, lutein 3-O-palmitate) and four diesters (lutein dilinoleate, lutein 3'-O-linoleate-3-O-palmitate, lutein 3'-O-palmitate-3-O-linoleate, lutein dipalmitate). This is the first time that the regioisomers of carotenoid esters have been identified in a cereal. Evidences for a preferential xanthophyll acyltransferase activity regarding the position (3 or 3') and the acyl moiety are discussed. Further studies should be carried out in order to identify the acyltransferase enzymes and the acyl donor molecules involved in the xanthophyll esterification process. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-J rotational spectrum of toluene in |m| ⩽ 3 torsional states

NASA Astrophysics Data System (ADS)

Ilyushin, Vadim V.; Alekseev, Eugene A.; Kisiel, Zbigniew; Pszczółkowski, Lech

2017-09-01

The study of the rotational spectrum of toluene (C6H5CH3) is considerably extended to include transitions in |m| ⩽ 3 torsional states up to the onset of the submillimeter wave region. New data involving torsion-rotation transitions up to 336 GHz were combined with previously published measurements and fitted using the rho-axis-method torsion-rotation Hamiltonian. The final fit used 50 parameters to give an overall weighted root-mean-square deviation of 0.69 for a dataset consisting of 8924 transitions with J up to 94 and Ka up to 50. The new analysis allowed us to resolve all problems encountered previously for m = 0 transitions beyond a certain combination of quantum numbers J and Ka when many lines of appreciable intensity and unambiguous assignment deviated from the distorted asymmetric rotor treatment. Those discrepancies are now identified to result from m = 0 ↔ m = 3 and m = 0 ↔ m = -3 resonances, which have been successfully encompassed by the current fit. At the same time an analogous problem was discovered and fitted for m = 2 transitions, which were found to be affected by many m = 1 ↔ m = 2 resonances.

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

Liu, Xing-Wu; Cao, Zhi; Zhao, Shu

As active phases in low-temperature Fischer–Tropsch synthesis for liquid fuel production, epsilon iron carbides are critically important industrial materials. However, the precise atomic structure of epsilon iron carbides remains unclear, leading to a half-century of debate on the phase assignment of the ε-Fe 2C and ε’-Fe 2.2C. Here, we resolve this decades-long question by a combining theoretical and experimental investigation to assign the phases unambiguously. First, we have investigated the equilibrium structures and thermal stabilities of ε-Fe xC, (x = 1, 2, 2.2, 3, 4, 6, 8) by first-principles calculations. We have also acquired X-ray diffraction patterns and Mössbauer spectramore » for these epsilon iron carbides, and compared them with the simulated results. These analyses indicate that the unit cell of ε-Fe 2C contains only one type of chemical environment for Fe atoms, while ε’-Fe 2.2C has six sets of chemically distinct Fe atoms.« less

Xe-129 - Xe-128 and Ar-40 - Ar-39 chronology of two Antarctic enstatite meteorites

NASA Technical Reports Server (NTRS)

Honda, M.; Bernatowicz, T. J.; Podosek, F. A.

1983-01-01

Xe-129 - Xe-128 and Ar-40 - Ar-39 analyses has been performed on two Antarctic enstatite meteorites, the chondrite Y-691 and the aubrite (enstatite achondrite) ALH-78113. Both meteorites have complex Ar-40 - Ar-39 release patterns to which no unambiguous age assignment is possible. Both give apparently satisfactory Xe-129 - Xe-128 correlations corresponding to unusual ages. The I-Xe age of the chondrite Y-691 is 16 Ma after Bjurbole, not unusual for chondrites in general but 10 Ma later than previously known ages for enstatite chondrites. The I-Xe age of the aubrite ALH-78113 is 210 Ma after Bjurbole, the latest age (rather than a limit) so far observed by the I-Xe technique, but this age assignment must be considered tentative because of the possibility that it is significantly influenced by terrestrial I contamination.

Identification of ion-pair structures in solution by vibrational stark effects

DOE PAGES

Hack, John; Mani, Tomoyasu; Grills, David C.; ...

2016-01-25

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

Identification of ion-pair structures in solution by vibrational stark effects

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

Hack, John; Mani, Tomoyasu; Grills, David C.

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

41 CFR 302-3.207 - Am I eligible to receive relocation allowances for overseas assignment and return travel?

Code of Federal Regulations, 2011 CFR

2011-07-01

... relocation allowances for overseas assignment and return travel? 302-3.207 Section 302-3.207 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3... eligible to receive relocation allowances for overseas assignment and return travel? You may be eligible to...

41 CFR 302-3.207 - Am I eligible to receive relocation allowances for overseas assignment and return travel?

Code of Federal Regulations, 2013 CFR

2013-07-01

... relocation allowances for overseas assignment and return travel? 302-3.207 Section 302-3.207 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3... eligible to receive relocation allowances for overseas assignment and return travel? You may be eligible to...

41 CFR 302-3.207 - Am I eligible to receive relocation allowances for overseas assignment and return travel?

Code of Federal Regulations, 2012 CFR

2012-07-01

... relocation allowances for overseas assignment and return travel? 302-3.207 Section 302-3.207 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3... eligible to receive relocation allowances for overseas assignment and return travel? You may be eligible to...

41 CFR 302-3.207 - Am I eligible to receive relocation allowances for overseas assignment and return travel?

Code of Federal Regulations, 2010 CFR

2010-07-01

... relocation allowances for overseas assignment and return travel? 302-3.207 Section 302-3.207 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3... eligible to receive relocation allowances for overseas assignment and return travel? You may be eligible to...

CIDR

Science.gov Websites

NIH CIDR Program Studies For whole exome sequencing projects, we pretest all samples using a high -density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie

Trends in phosphorus loading to the western basin of Lake Erie

EPA Science Inventory

Dave Dolan spent much of his career computing and compiling phosphorus loads to the Great Lakes. None of his work in this area has been more valuable than his continued load estimates to Lake Erie, which has allowed us to unambiguously interpret the cyanobacteria blooms and hypox...

NEW METHODOLOGY FOR IDENTIFYING POTENTIAL HUMAN BIOMARKERS BY COLLECTION AND CONCENTRATION OF EXHALED BREATH CONDENSATE

EPA Science Inventory

In many studies of human exposure, the measurement of pollutant chemicals in the environment (air, water, food, soil, etc.) is being supplemented by their additional measurement in biological media such as human breath, blood, and urine. This allows an unambiguous confirmation...

In praise of hierarchy.

PubMed

Jaques, E

1990-01-01

Hierarchy has not had its day. After 3,000 years as the preferred structure for large organizations, managerial hierarchy is still the most natural and effective organizational form that a big company can employ. Now, as in the past, the key to organizational success is individual accountability, and hierarchy preserves unambiguous accountability for getting work done. Unfortunately, hierarchy is widely misunderstood and abused. Pay grades are confused with real layers of responsibility, for example, and incompetent bosses abound. As a result, many experts now urge us to adopt group-oriented or "flat" structures. But groups are never held accountable as groups for what they do or fail to do, and groups don't have careers. The proper use of hierarchy derives from the nature of work. As organizational tasks range from simple to very complex, there are sharp jumps in the level of difficulty and responsibility. Surprisingly, people in hundreds of companies in dozens of countries agree on where these jumps take place. They are tied to an objective measure-the time span of the longest task or program assigned to each managerial role-and they occur at 3 months, 1 year, 2 years, 5 years, 10 years, and 20 years. As the time span increases, so does the level of experience, knowledge, and mental stamina required to do the work. This increasing level of mental capacity lets companies put people in jobs they can do, it allows managers to add value to the work of their subordinates, it creates hierarchical layers acceptable to everyone in the organization, and it allows employees to be evaluated by people they accept as organizational superiors. Best of all, understanding hierarchy allows organizations to set up hierarchies with no more than seven layers-often fewer-and to know what the structure is good for and how it ought to perform.

Spectroscopic Characterization, Computational Investigation, and Comparisons of ECX – (E = As, P, and N; X = S and O) Anions

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

Hou, Gao-Lei; Chen, Bo; Transue, Wesley J.

Three newly-synthesized [Na+(221-kryptofix)] salts containing AsCO–, PCO–, and PCS– anions were successfully electrosprayed into the vacuum, and the ECX– (E = As, P; X = O, S) anions were investigated by negative ion photoelectron spectroscopy (NIPES) and high resolution photoelectron imaging spectroscopy. For each ECX– anion, a well-resolved NIPE spectrum was obtained, in which every major peak is split into a doublet. The splittings are attributed to spin-orbit coupling (SOC) in the ECX• radicals. Vibrational progressions in the NIPE spectra of ECX– were assigned to the symmetric and antisymmetric stretching modes in ECX• radicals. The electron affinities (EAs) and SOCmore » splittings of ECX• are determined from the NIPE spectra to be: AsCO•: EA = 2.414 ± 0.002 eV, SOC splitting = 988 cm-1; PCO•: EA = 2.670 ± 0.005 eV, SOC splitting = 175 cm-1; PCS•: EA = 2.850 ± 0.005 eV, SOC splitting = 300 cm-1. Calculations using the B3LYP, CASPT2, and CCSD(T) methods all predict linear geometries for both the anions and neutral radicals. The calculated EAs and SOC splittings for ECX• are in excellent agreement with the experimentally-measured values. The simulated NIPE spectra, based on the calculated Franck-Condon factors, and SOC splittings nicely reproduce all of the observed spectral peaks, thus allowing unambiguous spectral assignments. The finding that PCS has the greatest EA of the three triatomic molecules considered here is counterintuitive based upon electronegativity considerations, but understandable in terms of the HOMO of PCS– having the greatest degree of delocalization onto both terminal atoms.« less

Brillouin Study of the Quantization of Acoustic Modes in Nanospheres

NASA Astrophysics Data System (ADS)

Kuok, M. H.; Lim, H. S.; Ng, S. C.; Liu, N. N.; Wang, Z. K.

2003-06-01

The vibrational modes in three-dimensional ordered arrays of unembedded SiO2 nanospheres have been studied by Brillouin light scattering. Multiple distinct Brillouin peaks are observed whose frequencies are found to be inversely proportional to the diameter (≈200 340 nm) of the nanospheres, in agreement with Lamb’s theory. This is the first Brillouin observation of acoustic mode quantization in a nanoparticle arising from spatial confinement. The distinct spectral peaks measured afford an unambiguous assignment of seven surface and inner acoustic modes. Interestingly, the relative intensities and polarization dependence of the Brillouin spectrum do not agree with the predictions made for Raman scattering.

Brillouin study of the quantization of acoustic modes in nanospheres.

PubMed

Kuok, M H; Lim, H S; Ng, S C; Liu, N N; Wang, Z K

2003-06-27

The vibrational modes in three-dimensional ordered arrays of unembedded SiO2 nanospheres have been studied by Brillouin light scattering. Multiple distinct Brillouin peaks are observed whose frequencies are found to be inversely proportional to the diameter (approximately 200-340 nm) of the nanospheres, in agreement with Lamb's theory. This is the first Brillouin observation of acoustic mode quantization in a nanoparticle arising from spatial confinement. The distinct spectral peaks measured afford an unambiguous assignment of seven surface and inner acoustic modes. Interestingly, the relative intensities and polarization dependence of the Brillouin spectrum do not agree with the predictions made for Raman scattering.

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

Rh(I)-catalyzed Pauson-Khand-type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide (CO).

PubMed

Yuan, Wei; Dong, Xiang; Shi, Min; McDowell, Patrick; Li, Guigen

2012-11-02

An intramolecular Pauson-Khand type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide has been established by using [Rh(COD)Cl](2) as the catalyst. The reaction was found to be highly efficient in solvents of 1,2-dichloroethane and 1,1,2,2-tetrachloroethane to give excellent yields of 90-99%. The reaction provides easy access to a series of fused 6,5-ring structures containing spiro-cyclopropane units that are useful for drug design and development. A mechanism of this cycloaddition process has been proposed accounting for structures of resulting products that were unambiguously assigned by X-ray diffractional analysis.

Topology of OxlT, the oxalate transporter of Oxalobacter formigenes, determined by site-directed fluorescence labeling.

PubMed

Ye, L; Jia, Z; Jung, T; Maloney, P C

2001-04-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His(9)-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+ linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis.

Topology of OxlT, the Oxalate Transporter of Oxalobacter formigenes, Determined by Site-Directed Fluorescence Labeling

PubMed Central

Ye, Liwen; Jia, Zhenzhen; Jung, Thomas; Maloney, Peter C.

2001-01-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His9-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+-linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis. PMID:11274108

A proteomic analysis of leaf sheaths from rice.

PubMed

Shen, Shihua; Matsubae, Masami; Takao, Toshifumi; Tanaka, Naoki; Komatsu, Setsuko

2002-10-01

The proteins extracted from the leaf sheaths of rice seedlings were separated by 2-D PAGE, and analyzed by Edman sequencing and mass spectrometry, followed by database searching. Image analysis revealed 352 protein spots on 2-D PAGE after staining with Coomassie Brilliant Blue. The amino acid sequences of 44 of 84 proteins were determined; for 31 of these proteins, a clear function could be assigned, whereas for 12 proteins, no function could be assigned. Forty proteins did not yield amino acid sequence information, because they were N-terminally blocked, or the obtained sequences were too short and/or did not give unambiguous results. Fifty-nine proteins were analyzed by mass spectrometry; all of these proteins were identified by matching to the protein database. The amino acid sequences of 19 of 27 proteins analyzed by mass spectrometry were similar to the results of Edman sequencing. These results suggest that 2-D PAGE combined with Edman sequencing and mass spectrometry analysis can be effectively used to identify plant proteins.

Mechanochemical Cycloreversion of Cyclobutane Observed at the Single Molecule Level.

PubMed

Pill, Michael F; Holz, Katharina; Preußke, Nils; Berger, Florian; Clausen-Schaumann, Hauke; Lüning, Ulrich; Beyer, Martin K

2016-08-16

Mechanochemical cycloreversion of cyclobutane is known from ultrasound experiments. It is, however, not clear which forces are required to induce the cycloreversion. In atomic force microscopy (AFM) experiments, on the other hand, it is notoriously difficult to assign the ruptured bond. We have solved this problem through the synthesis of tailored macrocycles, in which the cyclobutane mechanophore is bypassed by an ethylene glycol chain of specific length. This macrocycle is covalently anchored between a glass substrate and an AFM cantilever by polyethylene glycol linkers. Upon mechanical stretching of the macrocycle, cycloreversion occurs, which is identified by a defined length increase of the stretched polymer. The measured length change agrees with the value calculated with the external force explicitly included (EFEI) method. By using two different lengths for the ethylene glycol safety line, the assignment becomes unambiguous. Mechanochemical cycloreversion of cyclobutane is observed at forces above 1.7 nN. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibrational spectra, NLO analysis, and HOMO-LUMO studies of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid by density functional method

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Arivazhagan, M.; Thangaraju, P.

2015-08-01

The FTIR and FT-Raman spectra of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid have been recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of fundamental modes of the compounds were carried out. The optimized molecular geometries, vibrational frequencies, thermodynamic properties and atomic charge of the compounds were calculated by using density functional theory (B3LYP) method with 6-311+G and 6-311++G basis sets. The difference between the observed and scaled wave number values of most of fundamentals is very small. Unambiguous vibration assignment of all the fundamentals is made up the total energy distribution (TED). The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules. Besides, molecular electro static potential (MESP), Mulliken's charge analysis, first order hyper polarizability and several thermodynamic properties were performed by the DFT method.

Competition between inter- and intra-molecular hydrogen bonding: An infrared spectroscopic study of jet-cooled amino-ethanol and its dimer

NASA Astrophysics Data System (ADS)

Asselin, Pierre; Madebène, Bruno; Soulard, Pascale; Georges, Robert; Goubet, Manuel; Huet, Thérèse R.; Pirali, Olivier; Zehnacker-Rentien, Anne

2016-12-01

The Fourier transform IR vibrational spectra of amino-ethanol (AE) and its dimer have been recorded at room temperature and under jet-cooled conditions over the far and mid infrared ranges (50-4000 cm-1) using the White-type cell and the supersonic jet of the Jet-AILES apparatus at the synchrotron facility SOLEIL. Assignment of the monomer experimental frequencies has been derived from anharmonic frequencies calculated at a hybrid CCSD(T)-F12/MP2 level. Various thermodynamical effects in the supersonic expansion conditions including molar dilution of AE and nature of carrier gas have been used to promote or not the formation of dimers. Four vibrational modes of the observed dimer have been unambiguously assigned using mode-specific scaling factors deduced from the ratio between experimental and computed frequencies for the monomer. The most stable g'Gg' monomer undergoes strong deformation upon dimerization, leading to a homochiral head to head dimer involving two strong hydrogen bonds.

The application of inelastic neutron scattering to explore the significance of a magnetic transition in an iron based Fischer-Tropsch catalyst that is active for the hydrogenation of CO

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

Warringham, Robbie; McFarlane, Andrew R.; Lennon, David, E-mail: David.Lennon@Glasgow.ac.uk

2015-11-07

An iron based Fischer-Tropsch synthesis catalyst is evaluated using CO hydrogenation at ambient pressure as a test reaction and is characterised by a combination of inelastic neutron scattering (INS), powder X-ray diffraction, temperature-programmed oxidation, Raman scattering, and transmission electron microscopy. The INS spectrum of the as-prepared bulk iron oxide pre-catalyst (hematite, α-Fe{sub 2}O{sub 3}) is distinguished by a relatively intense band at 810 cm{sup −1}, which has previously been tentatively assigned as a magnon (spinon) feature. An analysis of the neutron scattering intensity of this band as a function of momentum transfer unambiguously confirms this assignment. Post-reaction, the spinon featuremore » disappears and the INS spectrum is characterised by the presence of a hydrocarbonaceous overlayer. A role for the application of INS in magnetic characterisation of iron based FTS catalysts is briefly considered.« less

Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae).

PubMed

Pfeiffer, Tanja; Roschanski, Anna M; Pannell, John R; Korbecka, Grazyna; Schnittler, Martin

2011-01-01

For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.

Electronic Structure and Magnetic Interactions in the Radical Salt [BEDT-TTF]2[CuCl4].

PubMed

Calzado, Carmen J; Rodríguez-García, Bárbara; Galán Mascarós, José Ramón; Hernández, Norge Cruz

2018-06-07

The magnetic behavior and electric properties of the hybrid radical salt [BEDT-TTF] 2 [CuCl 4 ] have been revisited through extended experimental analyses and DDCI and periodic DFT plane waves calculations. Single crystal X-ray diffraction data have been collected at different temperatures, discovering a phase transition occurring in the 250-300 K range. The calculations indicate the presence of intradimer, interdimer, and organic-inorganic π-d interactions in the crystal, a magnetic pattern much more complex than the Bleaney-Bowers model initially assigned to this material. Although this simple model was good enough to reproduce the magnetic susceptibility data, our calculations demonstrate that the actual magnetic structure is significantly more intricate, with alternating antiferromagnetic 1D chains of the organic BEDT-TTF + radical, connected through weak antiferromagnetic interactions with the CuCl 4 2- ions. Combination of experiment and theory allowed us to unambiguously determine and quantify the leading magnetic interactions in the system. The density-of-states curves confirm the semiconductor nature of the system and the dominant organic contribution of the valence and conduction band edges. This general and combined approach appears to be fundamental in order to properly understand the magnetic structure of these complex materials, where experimental data can actually be fitted from a variety of models and parameters.

Using ambient ozone for assignment of double bond position in unsaturated lipids.

PubMed

Ellis, Shane R; Hughes, Jessica R; Mitchell, Todd W; in het Panhuis, Marc; Blanksby, Stephen J

2012-03-07

Unsaturated lipids deposited onto a range of materials are observed to react with the low concentrations of ozone present in normal laboratory air. Parent lipids and ozonolysis cleavage products are both detected directly from surfaces by desorption electrospray ionisation mass spectrometry (DESI-MS) with the resulting mass spectra providing clear evidence of the double bond position within these molecules. This serendipitous process has been coupled with thin-layer chromatography (TLC) to provide a simple but powerful approach for the detailed structural elucidation of lipids present in complex biological extracts. Lipid extracts from human lens were deposited onto normal phase TLC plates and then developed to separate components according to lipid class. Exposure of the developed plates to laboratory air for ca. 1 h prior to DESI-MS analysis gave rise to ozonolysis products allowing for the unambiguous identification of double bond positions in even low abundant, unsaturated lipids. In particular, the co-localization of intact unsaturated lactosylceramides (LacCer) with products from their oxidative cleavage provide the first evidence for the presence of three isomeric LacCer (d18:0/24:1) species in the ocular lens lipidome, i.e., variants with double bonds at the n-9, n-7 and n-5 positions.

Triprotic site-specific acid-base equilibria and related properties of fluoroquinolone antibacterials.

PubMed

Rusu, Aura; Tóth, Gergő; Szőcs, Levente; Kökösi, József; Kraszni, Márta; Gyéresi, Árpád; Noszál, Béla

2012-07-01

The complete macro- and microequilibrium analyses of six fluoroquinolone drugs - ciprofloxacin, enrofloxacin, norfloxacin, pefloxacin, ofloxacin and moxifloxacin - are presented. Previous controversial literature data are straightened up, the protonation centers are unambiguously identified, and the protonation macro- and microconstant values are reported. The macroconstants were determined by (1)H NMR-pH titrations while the microconstants were determined by a multi-modal spectroscopic-deductive methodology, in which methyl ester derivatives were synthesized and their NMR-pH titration data contributed to the evaluation of all the microconstants. The full (1)H, (13)C and (15)N NMR assignments, NMR-pH profiles, macro- and microprotonation schemes and species-specific diagrams are included. Our studies show that the fluoroquinolones have three protonation centers: the carboxylate group, the N-1' and N-4' piperazine nitrogens and concentration of the uncharged microspecies is way below the values published earlier. The results could be well interpreted in terms of structural properties. The protonation macro- and microconstant values allow the pre-planned method development in techniques such as capillary zone electrophoresis and also, the interpretation of fluoroquinolone mechanism of biological action, including the pharmacokinetic properties, and antibacterial activities that are all heavily influenced by the states of protonation. Copyright © 2012 Elsevier B.V. All rights reserved.

Application of Raman spectroscopy for direct analysis of Carlina acanthifolia subsp. utzka root essential oil.

PubMed

Strzemski, Maciej; Wójciak-Kosior, Magdalena; Sowa, Ireneusz; Agacka-Mołdoch, Monika; Drączkowski, Piotr; Matosiuk, Dariusz; Kurach, Łukasz; Kocjan, Ryszard; Dresler, Sławomir

2017-11-01

Carlina genus plants e.g. Carlina acanthifolia subsp. utzka have been still used in folk medicine of many European countries and its biological activity is mostly associated with root essential oils. In the present paper, Raman spectroscopy (RS) was applied for the first time for evaluation of essential oil distribution in root of C. acnthifolia subsp. utzka and identification of root structures containing the essential oil. Furthermore, RS technique was applied to assess chemical stability of oil during drying of plant material or distillation process. Gas chromatography-mass spectrometry was used for qualitative and quantitative analysis of the essential oil. The identity of compounds was confirmed using Raman, ATR-IR and NMR spectroscopy. Carlina oxide was found to be the main component of the oil (98.96% ± 0.15). The spectroscopic study showed the high stability of essential oil and Raman distribution analysis indicated that the oil reservoirs were localized mostly in the structures of outer layer of the root while the inner part showed nearly no signal assigned to the oil. Raman spectroscopy technique enabled rapid, non-destructive direct analysis of plant material with minimal sample preparation and allowed straightforward, unambiguous identification of the essential oil in the sample. Copyright © 2017. Published by Elsevier B.V.

Cloning and Functional Characterization of the Maize (Zea mays L.) Carotenoid Epsilon Hydroxylase Gene

PubMed Central

Sheng, Yanmin; Wang, Yingdian; Capell, Teresa; Shi, Lianxuan; Ni, Xiuzhen; Sandmann, Gerhard; Christou, Paul; Zhu, Changfu

2015-01-01

The assignment of functions to genes in the carotenoid biosynthesis pathway is necessary to understand how the pathway is regulated and to obtain the basic information required for metabolic engineering. Few carotenoid ε-hydroxylases have been functionally characterized in plants although this would provide insight into the hydroxylation steps in the pathway. We therefore isolated mRNA from the endosperm of maize (Zea mays L., inbred line B73) and cloned a full-length cDNA encoding CYP97C19, a putative heme-containing carotenoid ε hydroxylase and member of the cytochrome P450 family. The corresponding CYP97C19 genomic locus on chromosome 1 was found to comprise a single-copy gene with nine introns. We expressed CYP97C19 cDNA under the control of the constitutive CaMV 35S promoter in the Arabidopsis thaliana lut1 knockout mutant, which lacks a functional CYP97C1 (LUT1) gene. The analysis of carotenoid levels and composition showed that lutein accumulated to high levels in the rosette leaves of the transgenic lines but not in the untransformed lut1 mutants. These results allowed the unambiguous functional annotation of maize CYP97C19 as an enzyme with strong zeinoxanthin ε-ring hydroxylation activity. PMID:26030746

Barcode Identifiers as a Practical Tool for Reliable Species Assignment of Medically Important Black Yeast Species

PubMed Central

Heinrichs, Guido; de Hoog, G. Sybren

2012-01-01

Herpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives. PMID:22785187

New indolizines with phenanthroline skeleton: Synthesis, structure, antimycobacterial and anticancer evaluation.

PubMed

Danac, Ramona; Al Matarneh, Cristina M; Shova, Sergiu; Daniloaia, Teofil; Balan, Mihaela; Mangalagiu, Ionel I

2015-05-15

We report herein a feasible study concerning the design, synthesis, structure and in vitro antimycobacterial and anticancer activity of two new classes (containing four and five fused rings) of indolizine with phenanthroline skeleton. The preparation is straight and efficient, involving a Huisgen [3+2] dipolar cycloaddition of cycloimmonium ylides to alkynes or alkenes dipolarophiles. The cycloaddition reactions are highly stereo- or regioselective, according with the dipolarophiles nature. The structure of the new compounds was assigned unambiguously, X-ray analysis including. The primary antimycobacterial screening reveals that one of the thirteen tested compounds had a good activity against Mycobacterium tuberculosis H37Rv under aerobic conditions. The antiproliferative evaluation against a NCI 60 human tumor cell line panel, revealed that two indolizine with phenanthroline skeleton exhibit a selective and significant antitumor growth inhibitory activity against Breast Cancer (MCF7 and T-47D) and a slightly moderate activity against some forms of Leukemia, Non-Small Cell Lung Cancer, Renal Cancer and Breast Cancer (MDA-MB-468). The X-ray diffraction study of the indolizines with phenanthroline skeleton prove a flat coplanar structure which, corroborated with their anticancer activity, allow us to suggest that an interaction with DNA (via an intercalation mechanism) would be reasonable. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diagnostic games: from adequate formalization of clinical experience to structure discovery.

PubMed

Shifrin, Michael A; Kasparova, Eva I

2008-01-01

A method of obtaining well-founded and reproducible results in clinical decision making is presented. It is based on "diagnostic games", a procedure of elicitation and formalization of experts' knowledge and experience. The use of this procedure allows formulating decision rules in the terms of an adequate language, that are both unambiguous and clinically clear.

38 CFR 21.4146 - Assignments of benefits prohibited.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Administration of Educational Assistance Programs Payments; Educational Assistance Allowance § 21.4146 Assignments of benefits prohibited. (a) General... authorized by law. No law specifically authorizes assignments of educational assistance allowances payable...

38 CFR 21.4146 - Assignments of benefits prohibited.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Administration of Educational Assistance Programs Payments; Educational Assistance Allowance § 21.4146 Assignments of benefits prohibited. (a) General... authorized by law. No law specifically authorizes assignments of educational assistance allowances payable...

Female control of paternity in the sexually cannibalistic spider Argiope keyserlingi.

PubMed Central

Elgar, M A; Schneider, J M; Herberstein, M E

2000-01-01

Sexual conflict theory predicts an antagonistic coevolution, with each sex evolving adaptations and counter-adaptations to overcome a temporary dominance of the other sex over the control of paternity. Polyandry allows sexual selection to operate after mating has commenced, with male and female interests competing for control of fertilization. There are numerous examples of male control of paternity, but few studies have unambiguously revealed female control. Attributing variance in paternity to females is often difficult since male and female influences cannot be separated unambiguously. However, we show that polyandrous female orb-web spiders Argiope keserlingi (Arancidae) control the paternity of their offspring by adjusting the timing of sexual cannibalism. Our experiments reveal that females copulating with relatively smaller males delay sexual cannibalism, thereby prolonging the duration of copulation, and that these males consequently fertilize relatively more eggs. PMID:11133035

The Influence of the Level Structure of Sodium -20 upon the Stellar Reaction Rate for NEON-19(PROTON, PHOTON)(20)SODIUM.

NASA Astrophysics Data System (ADS)

Lamm, Larry Odell

The level structure of ^{20 }Na has been measured up to excitation energies of 3.33 MeV using the charge-exchange reaction 20Ne(^3He,t) 20Na. Angular distributions have been measured for 14 levels at laboratory angles ranging from 10 to 60 degrees. Assignments of spin and parities have been made for the levels based on DWBA analysis of the angular distributions and comparisons with the level structure of the analog nuclei. The reaction rate for ^{19 }Ne(p,gamma)^{20 }Na has been calculated to include the effects of the resonant levels of temperatures of interest in the operation of the hot CNO cycle. The result is an increase of nearly three orders of magnitude in the stellar reaction rate for 19Ne(p, gamma)20Na, as compared to previous estimates made before the measurement of the level structure of 20Na. This increase may indicate that 19 Ne(p,gamma)20 Na is the sought after breakout mechanism to allow for the transport of mass from the CNO region into the Ne-Na-Mg regions, with applications for the rp-process and the possible explanation of the observed neon overabundances in some nova events. A detailed description of the experiment is given, including a discussion of the development of a new type of position sensitive detector for use with the broad range magnetic spectrograph which has allowed, for the first time, the unambiguous identification to tritons within the spectrograph.

Single Stage Tandem Mass Spectrometry Assignment of the C-5 Uronic Acid Stereochemistry in Heparan Sulfate Tetrasaccharides using Electron Detachment Dissociation

NASA Astrophysics Data System (ADS)

Agyekum, Isaac; Zong, Chengli; Boons, Geert-Jan; Amster, I. Jonathan

2017-09-01

The analysis of heparan sulfate (HS) glycosaminoglycans presents many challenges, due to the high degree of structural heterogeneity arising from their non-template biosynthesis. Complete structural elucidation of glycosaminoglycans necessitates the unambiguous assignments of sulfo modifications and the C-5 uronic acid stereochemistry. Efforts to develop tandem mass spectrometric-based methods for the structural analysis of glycosaminoglycans have focused on the assignment of sulfo positions. The present work focuses on the assignment of the C-5 stereochemistry of the uronic acid that lies closest to the reducing end. Prior work with electron-based tandem mass spectrometry methods, specifically electron detachment dissociation (EDD), have shown great promise in providing stereo-specific product ions, such as the B3 ´ -CO2, which has been found to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) in some HS tetrasaccharides. The previously observed diagnostic ions are generally not observed with 2- O-sulfo uronic acids or for more highly sulfated heparan sulfate tetrasaccharides. A recent study using electron detachment dissociation and principal component analysis revealed a series of ions that correlate with GlcA versus IdoA for a set of 2- O-sulfo HS tetrasaccharide standards. The present work comprehensively investigates the efficacy of these ions for assigning the C-5 stereochemistry of the reducing end uronic acid in 33 HS tetrasaccharides. A diagnostic ratio can be computed from the sum of the ions that correlate to GlcA to those that correlate to IdoA. [Figure not available: see fulltext.

Advanced Microwave Precipitation Radiometer (AMPR) for remote observation of precipitation

NASA Technical Reports Server (NTRS)

Galliano, J. A.; Platt, R. H.

1990-01-01

The design, development, and tests of the Advanced Microwave Precipitation Radiometer (AMPR) operating in the 10 to 85 GHz range specifically for precipitation retrieval and mesoscale storm system studies from a high altitude aircraft platform (i.e., ER-2) are described. The primary goals of AMPR are the exploitation of the scattering signal of precipitation at frequencies near 10, 19, 37, and 85 GHz together to unambiguously retrieve precipitation and storm structure and intensity information in support of proposed and planned space sensors in geostationary and low earth orbit, as well as storm-related field experiments. The development of AMPR will have an important impact on the interpretation of microwave radiances for rain retrievals over both land and ocean for the following reasons: (1) A scanning instrument, such as AMPR, will allow the unambiguous detection and analysis of features in two dimensional space, allowing an improved interpretation of signals in terms of cloud features, and microphysical and radiative processes; (2) AMPR will offer more accurate comparisons with ground-based radar data by feature matching since the navigation of the ER-2 platform can be expected to drift 3 to 4 km per hour of flight time; and (3) AMPR will allow underflights of the SSM/I satellite instrument with enough spatial coverage at the same frequencies to make meaningful comparisons of the data for precipitation studies.

Structural study of ethyl 3-methyl-9-oxo-3-azabicyclo63.3.19nonane-1-carboxylate by two-dimensional NMR spectroscopy

NASA Astrophysics Data System (ADS)

Arias-Pérez, M. S.; Alejo, A.; Gálvez, E.; Pérez, S. M.; Santos, M. J.

1995-04-01

Ethyl 3-methyl-9-oxo-3-azabicyclo[3.3.1]nonane-1-carboxylate has been studied by 1H, 13C and 2D NMR spectroscopy in order to establish its conformational behaviour. The combined use of COSY and 1H- 13C correlation spectra helped in the unambiguous and complete assignment of the bicyclic carbon and proton resonances. It is found that the piperidone ring displays a slightly fattened chair conformation with the N-methyl group in the equatorial position, while a twist-chair form seems to be favoured for the cyclohexanone one. Two preferred orientations migth be proposed for the ethoxycarbonyl moiety.

Observation of interlayer excitons in MoSe2 single crystals

NASA Astrophysics Data System (ADS)

Horng, Jason; Stroucken, Tineke; Zhang, Long; Paik, Eunice Y.; Deng, Hui; Koch, Stephan W.

2018-06-01

Interlayer excitons with direct optical transitions are observed coexisting with intralayer excitons in the same K valleys in bilayer, few-layer, and bulk MoSe2 single crystals by confocal reflection contrast spectroscopy. Quantitative analysis using the Dirac-Bloch equations provides unambiguous state assignment of all the measured resonances. The interlayer excitons in bilayer MoSe2 have a large binding energy of 153 meV and a narrow linewidth of 20 meV. Their spectral weight is comparable to the commonly studied higher-order intralayer excitons. At the same time, the interlayer excitons are characterized by distinct transition energies and permanent dipole moments, providing a promising high temperature and optically accessible platform for dipolar exciton physics.

Absolute configuration determination through the unique intramolecular excitonic coupling in the circular dichroisms of o,p'-DDT and o,p'-DDD. A combined experimental and theoretical study.

PubMed

Tanaka, Hiroki; Inoue, Yoshihisa; Nakano, Takeshi; Mori, Tadashi

2017-04-12

Circular dichroisms (CDs) of the o,p'-isomers of 1,1,1-trichloro- and 1,1-dichloro-2,2-bis(chlorophenyl)ethanes (DDT and DDD) were investigated experimentally and theoretically. A series of strong Cotton effect peaks in a characteristic negative-negative-positive-negative, or its mirror-imaged, pattern were observed in the CD spectra of these persistent organic pollutants. The theoretical CD spectra at the SAC-CI/B95(d) and RI-CC2/def2-TZVPP levels well reproduced the experimental ones, enabling us to unambiguously assign the absolute configuration of (+)-DDT and (-)-DDD as S.

Rh(I)-catalyzed Pauson-Khand-type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide (CO)

PubMed Central

Yuan, Wei; Dong, Xiang; McDowell, Patrick

2012-01-01

An intramolecular Pauson-Khand type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide has been established by using [Rh(COD)Cl]2 as the catalyst. The reaction was found to be highly efficient in solvents of 1,2-dichloroethane and 1,1,2,2-tetrachloroethane to give excellent yields of 90 – 99%. The reaction provides easy access to a series of fused 6,5-ring structures containing spiro-cyclopropane units that are useful for drug design and development. A mechanism of this cycloaddition process has been proposed accounting for structures of resulting products that were unambiguously assigned by X-ray diffractional analysis. PMID:23098194

Boron environments in Pyrex® glass--a high resolution, Double-Rotation NMR and thermodynamic modelling study.

PubMed

Howes, A P; Vedishcheva, N M; Samoson, A; Hanna, J V; Smith, M E; Holland, D; Dupree, R

2011-07-07

It is shown, using the important technological glass Pyrex® as an example, that 1D and 2D (11)B Double-Rotation (DOR) NMR experiments, in combination with thermodynamic modelling, are able to provide unique structural information about complex glasses. (11)B DOR NMR has been applied to Pyrex® glass in order to remove both dipolar and quadrupolar broadening of the NMR lines, leading to high resolution spectra that allow unambiguous, accurate peak fitting to be carried out, of particular importance in the case of the 3-coordinated [BO(3)] (B3) trigonal planar environments. The data obtained are of sufficient quality that they can be used to test the distributions of borate and borosilicate superstructural units predicted by the thermodynamics-based Model of Associated Solutions. The model predicts the dominant boron-containing chemical groupings in Pyrex® glass to be those associated with B(2)O(3) and sodium tetraborate (with smaller amounts of sodium triborate, sodium diborate, sodium pentaborate, danburite and reedmergnerite). Excellent agreement is found between model and experiment provided the (11)B peaks with isotropic chemical shifts of -1.4 ppm and 0.5 ppm are assigned to B4 species from borosilicate units ([B(OSi)(4)] and [B(OSi)(3)(OB)]) and borate superstructural units (mainly triborate rings with some pentaborate and diborate) respectively. The peaks with isotropic shifts of 14 ppm and 18.1 ppm are then assigned to B3 in borate superstructural units (mainly triborate and pentaborate along with connecting B3) and boroxol rings respectively. The assignments of the DOR NMR peaks, are supported by the presence of cross-peaks in (11)B spin-diffusion DOR NMR spectra which can be used to develop a structural model in which B(2)O(3)-like regions are linked, via borate and borosilicate superstructural units, to the majority silica network. Pyrex® is thus shown to have a heterogeneous structure, with distinct molecular groupings that are far removed from a random distribution of network polyhedra with only short-range order. This journal is © the Owner Societies 2011

The metabolism of primaquine to its active metabolite is dependent on CYP 2D6.

PubMed

Pybus, Brandon S; Marcsisin, Sean R; Jin, Xiannu; Deye, Gregory; Sousa, Jason C; Li, Qigui; Caridha, Diana; Zeng, Qiang; Reichard, Gregory A; Ockenhouse, Christian; Bennett, Jason; Walker, Larry A; Ohrt, Colin; Melendez, Victor

2013-06-20

The efficacy of the 8-aminoquinoline (8AQ) drug primaquine (PQ) has been historically linked to CYP-mediated metabolism. Although to date no clear evidence exists in the literature that unambiguously assigns the metabolic pathway or specific metabolites necessary for activity, recent literature suggests a role for CYP 2D6 in the generation of redox active metabolites. In the present study, the specific CYP 2D6 inhibitor paroxetine was used to assess its effects on the production of specific phenolic metabolites thought to be involved in PQ efficacy. Further, PQ causal prophylactic (developing liver stage) efficacy against Plasmodium berghei in CYP 2D knockout mice was assessed in comparison with a normal C57 background and with humanized CYP 2D6 mice to determine the direct effects of CYP 2D6 metabolism on PQ activity. PQ exhibited no activity at 20 or 40 mg/kg in CYP 2D knockout mice, compared to 5/5 cures in normal mice at 20 mg/kg. The activity against developing liver stages was partially restored in humanized CYP 2D6 mice. These results unambiguously demonstrate that metabolism of PQ by CYP 2D6 is essential for anti-malarial causal prophylaxis efficacy.

Lattice modes of hexamethylbenzene studied by inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Stride, J. A.; Adams, J. M.; Johnson, M. R.

2005-10-01

The combination of inelastic neutron scattering and detailed ab initio calculations has been used to arrive at accurate assignments of the low energy lattice mode region of hexamethylbenzene (HMB) across the low temperature first order phase transition at 117.5 K. This was also extended well into the mid-infrared spectral region and a good agreement was found between observed and calculated frequencies, which were also confirmed with isotopically substituted d-HMB. At low temperature, the lattice region is dominated by the methyl group torsions around 15 and 20 meV, which soften dramatically on passing into the higher temperature phase. The lowest energy methyl torsion corresponds to a coherent gear wheel motion, observed here for the first time and predicted in previous numerical studies of HMB. The three acoustic phonons lie to lower energy, centered around 6-7 meV, whilst the three optic phonons are very close in energy to the lowest methyl torsions. Other assignments are found to be in accord with literature values and so an unambiguous assignment of all spectral modes has been obtained for the first time. We conclude that due to the behaviour of the lattice modes either side of the phase transition, its nature is predominantly that of a thermally activated dynamic order-disorder transition.

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

Using regime analysis to identify the contribution of clouds to surface temperature errors in weather and climate models

DOE PAGES

Van Weverberg, Kwinten; Morcrette, Cyril J.; Ma, Hsi -Yen; ...

2015-06-17

Many global circulation models (GCMs) exhibit a persistent bias in the 2 m temperature over the midlatitude continents, present in short-range forecasts as well as long-term climate simulations. A number of hypotheses have been proposed, revolving around deficiencies in the soil–vegetation–atmosphere energy exchange, poorly resolved low-level boundary-layer clouds or misrepresentations of deep-convective storms. A common approach to evaluating model biases focuses on the model-mean state. However, this makes difficult an unambiguous interpretation of the origins of a bias, given that biases are the result of the superposition of impacts of clouds and land-surface deficiencies over multiple time steps. This articlemore » presents a new methodology to objectively detect the role of clouds in the creation of a surface warm bias. A unique feature of this study is its focus on temperature-error growth at the time-step level. It is shown that compositing the temperature-error growth by the coinciding bias in total downwelling radiation provides unambiguous evidence for the role that clouds play in the creation of the surface warm bias during certain portions of the day. Furthermore, the application of an objective cloud-regime classification allows for the detection of the specific cloud regimes that matter most for the creation of the bias. We applied this method to two state-of-the-art GCMs that exhibit a distinct warm bias over the Southern Great Plains of the USA. Our analysis highlights that, in one GCM, biases in deep-convective and low-level clouds contribute most to the temperature-error growth in the afternoon and evening respectively. In the second GCM, deep clouds persist too long in the evening, leading to a growth of the temperature bias. In conclusion, the reduction of the temperature bias in both models in the morning and the growth of the bias in the second GCM in the afternoon could not be assigned to a cloud issue, but are more likely caused by a land-surface deficiency.« less

Deterministic and unambiguous dense coding

NASA Astrophysics Data System (ADS)

Wu, Shengjun; Cohen, Scott M.; Sun, Yuqing; Griffiths, Robert B.

2006-04-01

Optimal dense coding using a partially-entangled pure state of Schmidt rank Dmacr and a noiseless quantum channel of dimension D is studied both in the deterministic case where at most Ld messages can be transmitted with perfect fidelity, and in the unambiguous case where when the protocol succeeds (probability τx ) Bob knows for sure that Alice sent message x , and when it fails (probability 1-τx ) he knows it has failed. Alice is allowed any single-shot (one use) encoding procedure, and Bob any single-shot measurement. For Dmacr ⩽D a bound is obtained for Ld in terms of the largest Schmidt coefficient of the entangled state, and is compared with published results by Mozes [Phys. Rev. A71, 012311 (2005)]. For Dmacr >D it is shown that Ld is strictly less than D2 unless Dmacr is an integer multiple of D , in which case uniform (maximal) entanglement is not needed to achieve the optimal protocol. The unambiguous case is studied for Dmacr ⩽D , assuming τx>0 for a set of Dmacr D messages, and a bound is obtained for the average ⟨1/τ⟩ . A bound on the average ⟨τ⟩ requires an additional assumption of encoding by isometries (unitaries when Dmacr =D ) that are orthogonal for different messages. Both bounds are saturated when τx is a constant independent of x , by a protocol based on one-shot entanglement concentration. For Dmacr >D it is shown that (at least) D2 messages can be sent unambiguously. Whether unitary (isometric) encoding suffices for optimal protocols remains a major unanswered question, both for our work and for previous studies of dense coding using partially-entangled states, including noisy (mixed) states.

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia.

PubMed

Li, Cai-Xia; Pakstis, Andrew J; Jiang, Li; Wei, Yi-Liang; Sun, Qi-Fan; Wu, Hong; Bulbul, Ozlem; Wang, Ping; Kang, Long-Li; Kidd, Judith R; Kidd, Kenneth K

2016-07-01

Many ancestry informative SNP (AISNP) panels have been published. Ancestry resolution in them varies from three to eight continental clusters of populations depending on the panel used. However, none of these panels differentiates well among East Asian populations. To meet this need, we have developed a 74 AISNP panel after analyzing a much larger number of SNPs for Fst and allele frequency differences between two geographically close population groups within East Asia. The 74 AISNP panel can now distinguish at least 10 biogeographic groups of populations globally: Sub-Saharan Africa, North Africa, Europe, Southwest Asia, South Asia, North Asia, East Asia, Southeast Asia, Pacific and Americas. Compared with our previous 55-AISNP panel, Southeast Asia and North Asia are two newly assignable clusters. For individual ancestry assignment, the likelihood ratio and ancestry components were analyzed on a different set of 500 test individuals from 11 populations. All individuals from five of the test populations - Yoruba (YRI), European (CEU), Han Chinese in Henan (CHNH), Rondonian Surui (SUR) and Ticuna (TIC) - were assigned to their appropriate geographical regions unambiguously. For the other test populations, most of the individuals were assigned to their self-identified geographical regions with a certain degree of overlap with adjacent populations. These alternative ancestry components for each individual thus help give a clearer picture of the possible group origins of the individual. We have demonstrated that the new AISNP panel can achieve a deeper resolution of global ancestry. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Size Constancy in Bat Biosonar? Perceptual Interaction of Object Aperture and Distance

PubMed Central

Heinrich, Melina; Wiegrebe, Lutz

2013-01-01

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed “size constancy”. It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the ‘sonar aperture’, i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats. PMID:23630598

Size constancy in bat biosonar? Perceptual interaction of object aperture and distance.

PubMed

Heinrich, Melina; Wiegrebe, Lutz

2013-01-01

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed "size constancy". It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the 'sonar aperture', i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats.

Multiple band structures in 70Ge

NASA Astrophysics Data System (ADS)

Haring-Kaye, R. A.; Morrow, S. I.; Döring, J.; Tabor, S. L.; Le, K. Q.; Allegro, P. R. P.; Bender, P. C.; Elder, R. M.; Medina, N. H.; Oliveira, J. R. B.; Tripathi, Vandana

2018-02-01

High-spin states in 70Ge were studied using the 55Mn(18O,p 2 n ) fusion-evaporation reaction at a beam energy of 50 MeV. Prompt γ -γ coincidences were measured using the Florida State University Compton-suppressed Ge array consisting of three Clover detectors and seven single-crystal detectors. An investigation of these coincidences resulted in the addition of 31 new transitions and the rearrangement of four others in the 70Ge level scheme, providing a more complete picture of the high-spin decay pattern involving both positive- and negative-parity states with multiple band structures. Spins were assigned based on directional correlation of oriented nuclei ratios, which many times also led to unambiguous parity determinations based on the firm assignments for low-lying states made in previous work. Total Routhian surface calculations, along with the observed trends in the experimental kinematic moment of inertia with rotational frequency, support the multiquasiparticle configurations of the various crossing bands proposed in recent studies. The high-spin excitation spectra predicted by previous shell-model calculations compare favorably with the experimental one determined from this study.

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

PubMed Central

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

The Spatial and the Visual in Mental Spatial Reasoning: An Ill-Posed Distinction

NASA Astrophysics Data System (ADS)

Schultheis, Holger; Bertel, Sven; Barkowsky, Thomas; Seifert, Inessa

It is an ongoing and controversial debate in cognitive science which aspects of knowledge humans process visually and which ones they process spatially. Similarly, artificial intelligence (AI) and cognitive science research, in building computational cognitive systems, tended to use strictly spatial or strictly visual representations. The resulting systems, however, were suboptimal both with respect to computational efficiency and cognitive plau sibility. In this paper, we propose that the problems in both research strands stem from a mis conception of the visual and the spatial in mental spatial knowl edge pro cessing. Instead of viewing the visual and the spatial as two clearly separable categories, they should be conceptualized as the extremes of a con tinuous dimension of representation. Regarding psychology, a continuous di mension avoids the need to exclusively assign processes and representations to either one of the cate gories and, thus, facilitates a more unambiguous rating of processes and rep resentations. Regarding AI and cognitive science, the con cept of a continuous spatial / visual dimension provides the possibility of rep re sentation structures which can vary continuously along the spatial / visual di mension. As a first step in exploiting these potential advantages of the pro posed conception we (a) introduce criteria allowing for a non-dichotomic judgment of processes and representations and (b) present an approach towards rep re sentation structures that can flexibly vary along the spatial / visual dimension.

Successful Cleaning and Study of Contamination of Si(001) in Ultrahigh Vacuum

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

Gheorghe, N. G.; Lungu, G. A.; Husanu, M. A.

2011-10-03

This paper presents the very first surface physics experiment performed in ultrahigh vacuum (UHV) in Romania, using a new molecular beam epitaxy (MBE) installation. Cleaning of a Si(001) wafer was achieved by using a very simple technique: sequences of annealing at 900-1000 deg. C in ultrahigh vacuum: low 10{sup -8} mbar, with a base pressure of 1.5x10{sup -10} mbar. The preparation procedure is quite reproducible and allows repeated cleaning of the Si(001) after contamination in ultrahigh vacuum. The Si(001) single crystal surface is characterized by low energy electron diffraction (LEED), reflection high energy electron diffraction (RHEED), and Auger electron spectroscopymore » (AES). The latter technique is utilized in order to investigate the sample contamination by the residual gas in the UHV chamber, as determined by a residual gas analyzer (RGA). Unambiguous assignment of oxidized and unoxidized silicon is provided; also, an important feature is that the LVV Auger peak at 90-92 eV cannot be solely attributed to clean Si (i.e. Si surrounded only by Si), but also to silicon atoms bounded with carbon. Even with a sum of partial pressures of oxygen and carbon containing molecules in the range of 5x10{sup -10} mbar, the sample is contaminated very quickly, having a (1/e) lifetime of about 76 minutes.« less

Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

NASA Astrophysics Data System (ADS)

Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

2016-09-01

This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

In depth chemical investigation of Glycyrrhiza triphylla Fisch roots guided by a preliminary HPLC-ESIMSn profiling.

PubMed

Shakeri, Abolfazl; Masullo, Milena; D'Urso, Gilda; Iranshahi, Mehrdad; Montoro, Paola; Pizza, Cosimo; Piacente, Sonia

2018-05-15

Chemical investigations on Glycyrrhiza spp. have mostly been focused on G. glabra (typically cultivated in Europe, henceforth called European licorice), G. uralensis and G. inflata (known as Chinese licorice) with little information on the constituents of other Glycyrrhiza species. According to the growing interest in further Glycyrrhiza spp. to be used as sweeteners, the roots of G. triphylla have been investigated. The LC-ESI/LTQOrbitrap/MS profile of the methanolic extract of G. triphylla roots guided the isolation of 21 compounds, of which the structures were elucidated by 1D- and 2D-NMR experiments. Based on this approach, 6 previously unreported compounds including two isoflavones 7,5'-dihydroxy-6,3'-dimethoxy-isoflavone-7-O-β-d-glucopyranoside (4) and 7,5'-dihydroxy-6,3'-dimethoxy-isoflavone-7-O-(7,8-dihydro-p-hydroxycinnamoyl)-β-d-glucopyranoside (7) and four saponins, named licoricesaponins M3 (13), N2 (14), O2 (16) and P2 (18), have been characterized. It is to be noted that the accurate masses of some compounds here reported for the first time corresponded to those of compounds previously described in Glycyrrhiza spp. Thus an approach based only on MS analysis could be misleading; only isolation followed by NMR analysis allowed us to unambiguously assign the structures of these previously unreported compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

41 CFR 302-3.207 - Am I eligible to receive relocation allowances for overseas assignment and return travel?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false Am I eligible to receive... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.207 Am I...

Coupling of Excitons and Discrete Acoustic Phonons in Vibrationally Isolated Quantum Emitters.

PubMed

Werschler, Florian; Hinz, Christopher; Froning, Florian; Gumbsheimer, Pascal; Haase, Johannes; Negele, Carla; de Roo, Tjaard; Mecking, Stefan; Leitenstorfer, Alfred; Seletskiy, Denis V

2016-09-14

The photoluminescence emission by mesoscopic condensed matter is ultimately dictated by the fine-structure splitting of the fundamental exciton into optically allowed and dipole-forbidden states. In epitaxially grown semiconductor quantum dots, nonradiative equilibration between the fine-structure levels is mediated by bulk acoustic phonons, resulting in asymmetric spectral broadening of the excitonic luminescence. In isolated colloidal quantum dots, spatial confinement of the vibrational motion is expected to give rise to an interplay between the quantized electronic and phononic degrees of freedom. In most cases, however, zero-dimensional colloidal nanocrystals are strongly coupled to the substrate such that the charge relaxation processes are still effectively governed by the bulk properties. Here we show that encapsulation of single colloidal CdSe/CdS nanocrystals into individual organic polymer shells allows for systematic vibrational decoupling of the semiconductor nanospheres from the surroundings. In contrast to epitaxially grown quantum dots, simultaneous quantization of both electronic and vibrational degrees of freedom results in a series of strong and narrow acoustic phonon sidebands observed in the photoluminescence. Furthermore, an individual analysis of more than 200 compound particles reveals that enhancement or suppression of the radiative properties of the fundamental exciton is controlled by the interaction between fine-structure states via the discrete vibrational modes. For the first time, pronounced resonances in the scattering rate between the fine-structure states are directly observed, in good agreement with a quantum mechanical model. The unambiguous assignment of mediating acoustic modes to the observed scattering resonances complements the experimental findings. Thus, our results form an attractive basis for future studies on subterahertz quantum opto-mechanics and efficient laser cooling at the nanoscale.

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Enantiomeric characterization and structure elucidation of LH601A using vibrational circular dichroism spectroscopy

NASA Astrophysics Data System (ADS)

Shen, Jian; Magesh, Sadagopan; Chen, Lin; Hu, Longqin; He, Yanan

2018-03-01

LH601A is a novel non-reactive chiral molecule inhibiting Keap1-Nrf2 protein-protein interaction. The absolute configuration (AC) was independently determined in this study using vibrational circular dichroism (VCD) spectroscopy. Because of band overlapping and broadening in the IR spectrum, a direct VCD spectrum comparison method is devised without the conventional IR band alignment. Being an unbiased AC inquiry, all possible chiralities are evaluated based on the statistical analysis of VCD similarity, Sv. The AC of three-center stereoisomer LH601A is unambiguously assigned to (S,R,S). A comparative study was also carried out to investigate the structural and energy differences of calculated conformers using the polarized continuum model of dimethyl sulfoxide.

Synthesis of stereoarray isotope labeled (SAIL) lysine via the "head-to-tail" conversion of SAIL glutamic acid.

PubMed

Terauchi, Tsutomu; Kamikawai, Tomoe; Vinogradov, Maxim G; Starodubtseva, Eugenia V; Takeda, Mitsuhiro; Kainosho, Masatsune

2011-01-07

A stereoarray isotope labeled (SAIL) lysine, (2S,3R,4R,5S,6R)-[3,4,5,6-(2)H(4);1,2,3,4,5,6-(13)C(6);2,6-(15)N(2)]lysine, was synthesized by the "head-to-tail" conversion of SAIL-Glu, (2S,3S,4R)-[3,4-(2)H(2);1,2,3,4,5-(13)C(5);2-(15)N]glutamic acid, with high stereospecificities for all five chiral centers. With the SAIL-Lys in hand, the unambiguous simultaneous stereospecific assignments were able to be established for each of the prochiral protons within the four methylene groups of the Lys side chains in proteins.

Total Synthesis and Stereochemical Assignment of Nostosin B

PubMed Central

Wang, Xiaoji; Feng, Junmin; Xu, Zhengshuang; Ye, Tao; Meng, Yi; Zhang, Zhiyu

2017-01-01

Nostosins A and B were isolated from a hydrophilic extract of Nostoc sp. strain from Iran, which exhibits excellent trypsin inhibitory activity. Nostosin A was the most potent natural tripeptide aldehyde as trypsin inhibitor up to now. Both r- and s-2-hydroxy-4-(4-hydroxy-phenyl)butanoic acid (Hhpba) were prepared and incorporated into the total synthesis of nostosin B, respectively. Careful comparison of the NMR spectra and optical rotation data of synthetic nostosin B (1a and 1b) with the natural product led to the unambiguous identification of the r-configuration of the Hhpba fragment, which was further confirmed by co-injection with the authentic sample on HPLC using both reversed phase column and the chiral AD-RH column. PMID:28264450

Evidence for lysine acetylation in the coat protein of a polerovirus.

PubMed

Cilia, Michelle; Johnson, Richard; Sweeney, Michelle; DeBlasio, Stacy L; Bruce, James E; MacCoss, Michael J; Gray, Stewart M

2014-10-01

Virions of the RPV strain of Cereal yellow dwarf virus-RPV were purified from infected oat tissue and analysed by MS. Two conserved residues, K147 and K181, in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional data are available for K147, K181 lies within an interfacial region critical for virion assembly and stability. The signature immonium ion at m/z 126.0919 demonstrated the presence of N-acetyllysine, and the sequence fragment ions enabled an unambiguous assignment of the epsilon-N-acetyl modification on K181. We hypothesize that selection favours acetylation of K181 in a fraction of coat protein monomers to stabilize the capsid by promoting intermonomer salt bridge formation.

One-pot synthesis of novel 1-(1H-tetrazol-5-yl)-1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazine derivatives via an Ugi-azide 4CR process.

PubMed

Ghandi, Mehdi; Salahi, Saleh; Taheri, Abuzar; Abbasi, Alireza

2018-05-01

A facile one-pot method has been developed for the synthesis of novel pyrrolo[2,1-a]pyrazine scaffolds. A variety of 1-(1H-tetrazol-5-yl)-1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazine derivatives were obtained in moderate to high yields in methanol using a one-pot four-component condensation of 1-(2-bromoethyl)-1H-pyrrole-2-carbaldehyde, amine, isocyanide and sodium azide at room temperature. These reactions presumably proceed via a domino imine formation, intramolecular annulation and Ugi-azide reaction. Unambiguous assignment of the molecular structures was carried out by single-crystal X-ray diffraction.

Amoeba behavior of UO/sub 2/ coated particle fuel

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

Wagner-Loeffler, M.

1977-09-01

The data extracted from numerous irradiation tests were used to derive amoeba endurance parameters for UO/sub 2/. The data do not yet allow an unambiguous definition of the controlling mechanism, which may be due to either gaseous or solid-state diffusion processes. Adequate data on the amoeba effect are available for design of a steam-raising high-temperature gas-cooled reactor using UO/sub 2/ fuel.

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach

PubMed Central

Sternberg, Michael J.E.; Tamaddoni-Nezhad, Alireza; Lesk, Victor I.; Kay, Emily; Hitchen, Paul G.; Cootes, Adrian; van Alphen, Lieke B.; Lamoureux, Marc P.; Jarrell, Harold C.; Rawlings, Christopher J.; Soo, Evelyn C.; Szymanski, Christine M.; Dell, Anne; Wren, Brendan W.; Muggleton, Stephen H.

2013-01-01

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning—the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system. PMID:23103756

Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach.

PubMed

Sternberg, Michael J E; Tamaddoni-Nezhad, Alireza; Lesk, Victor I; Kay, Emily; Hitchen, Paul G; Cootes, Adrian; van Alphen, Lieke B; Lamoureux, Marc P; Jarrell, Harold C; Rawlings, Christopher J; Soo, Evelyn C; Szymanski, Christine M; Dell, Anne; Wren, Brendan W; Muggleton, Stephen H

2013-01-09

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning-the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system. Copyright © 2012 Elsevier Ltd. All rights reserved.

Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Basire, Marie; Mouhat, Félix; Fraux, Guillaume; Bordage, Amélie; Hazemann, Jean-Louis; Louvel, Marion; Spezia, Riccardo; Bonella, Sara; Vuilleumier, Rodolphe

2017-04-01

Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them.

Attractor concretion as a mechanism for the formation of context representations

PubMed Central

Rigotti, Mattia; Ben Dayan Rubin, Daniel; Morrison, Sara E.; Salzman, C. Daniel; Fusi, Stefano

2010-01-01

Complex tasks often require the memory of recent events, the knowledge about the context in which they occur, and the goals we intend to reach. All this information is stored in our mental states. Given a set of mental states, reinforcement learning (RL) algorithms predict the optimal policy that maximizes future reward. RL algorithms assign a value to each already-known state so that discovering the optimal policy reduces to selecting the action leading to the state with the highest value. But how does the brain create representations of these mental states in the first place? We propose a mechanism for the creation of mental states that contain information about the temporal statistics of the events in a particular context. We suggest that the mental states are represented by stable patterns of reverberating activity, which are attractors of the neural dynamics. These representations are built from neurons that are selective to specific combinations of external events (e.g. sensory stimuli) and pre-existent mental states. Consistent with this notion, we find that neurons in the amygdala and in orbito-frontal cortex (OFC) often exhibit this form of mixed selectivity. We propose that activating different mixed selectivity neurons in a fixed temporal order modifies synaptic connections so that conjunctions of events and mental states merge into a single pattern of reverberating activity. This process corresponds to the birth of a new different mental state that encodes a different temporal context. The concretion process depends on temporal contiguity, i.e. on the probability that a combination of an event and mental states follows or precedes the events and states that define a certain context. The information contained in the context thereby allows an animal to assign unambiguously a value to the events that initially appeared in different situations with different meanings. PMID:20100580

Unambiguous discrimination between linearly dependent equidistant states with multiple copies

NASA Astrophysics Data System (ADS)

Zhang, Wen-Hai; Ren, Gang

2018-07-01

Linearly independent quantum states can be unambiguously discriminated, but linearly dependent ones cannot. For linearly dependent quantum states, however, if C copies of the single states are available, then they may form linearly independent states, and can be unambiguously discriminated. We consider unambiguous discrimination among N = D + 1 linearly dependent states given that C copies are available and that the single copies span a D-dimensional space with equal inner products. The maximum unambiguous discrimination probability is derived for all C with equal a priori probabilities. For this classification of the linearly dependent equidistant states, our result shows that if C is even then adding a further copy fails to increase the maximum discrimination probability.

41 CFR 302-3.208 - What relocation expenses will my agency pay for my overseas assignment and return?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 41 Public Contracts and Property Management 4 2011-07-01 2011-07-01 false What relocation expenses... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.208 What...

41 CFR 302-3.208 - What relocation expenses will my agency pay for my overseas assignment and return?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false What relocation expenses... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.208 What...

41 CFR 302-3.208 - What relocation expenses will my agency pay for my overseas assignment and return?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true What relocation expenses... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.208 What...

41 CFR 302-3.208 - What relocation expenses will my agency pay for my overseas assignment and return?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 41 Public Contracts and Property Management 4 2012-07-01 2012-07-01 false What relocation expenses... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.208 What...

41 CFR 302-3.208 - What relocation expenses will my agency pay for my overseas assignment and return?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 4 2010-07-01 2010-07-01 false What relocation expenses... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Assignment and Return § 302-3.208 What...

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Rapid figure-ground responses to stereograms reveal an advantage for a convex foreground.

PubMed

Bertamini, Marco; Lawson, Rebecca

2008-01-01

Convexity has long been recognised as a factor that affects figure - ground segmentation, even when pitted against other factors such as symmetry [Kanizsa and Gerbino, 1976 Art and Artefacts Ed.M Henle (New York: Springer) pp 25-32]. It is accepted in the literature that the difference between concave and convex contours is important for the visual system, and that there is a prior expectation favouring convexities as figure. We used bipartite stimuli and a simple task in which observers had to report whether the foreground was on the left or the right. We report objective evidence that supports the idea that convexity affects figure-ground assignment, even though our stimuli were not pictorial in that depth order was specified unambiguously by binocular disparity.

Interaction of ammonium with birnessite: Evidence of a chemical and structural transformation in alkaline aqueous medium

NASA Astrophysics Data System (ADS)

Boumaiza, Hella; Coustel, Romain; Despas, Christelle; Ruby, Christian; Bergaoui, Latifa

2018-02-01

The ammonium cation interaction with Na-birnessite in aqueous alkaline medium was studied. Solution and solid analysis give evidence that birnessite is not only acting as a cationic exchanger toward NH4+. The surface analysis performed by XPS showed that N1s spectra are characterized by the existence of two different environments: one assignable to an interlayer NH4+ and the second to a chemisorbed N-species. Structural and chemical transformations were observed on birnessite with nitrogen mass balance deficit. The monitoring of NH4+, Na+, Mn2+, NO3- and NO2- and solid changes (average oxidation state of Mn, cation exchange capacity, solid nitrogen content and symmetry evolution identified by XRD and FTIR) indicate unambiguously that NH4+ reacts chemically with the birnessite.

On-line identification of lysergic acid diethylamide (LSD) in tablets using a combination of a sweeping technique and micellar electrokinetic chromatography/77 K fluorescence spectroscopy.

PubMed

Fang, Ching; Liu, Ju-Tsung; Lin, Cheng-Huang

2003-03-01

This work describes a novel method for the accurate determination of lysergic acid diethylamide (LSD) in tablets. A technique involving sweeping-micellar electrokinetic chromatography (MEKC) was used for the initial on-line concentration and separation, after which a cryogenic molecular fluorescence experiment was performed at 77 K. Using this approach, not only the separation of LSD from the tablet extract was achieved, but on-line spectra were readily distinguishable and could be unambiguously assigned. The results are in agreement with analyses by gas chromatography-mass spectrometry (GC-MS). Thus, this method, which was found to be accurate, sensitive and rapid, has the potential for use as a reliable complementary method to GC-MS in such analyses.

Ordinary dielectric function of corundumlike α -Ga2O3 from 40 meV to 20 eV

NASA Astrophysics Data System (ADS)

Feneberg, Martin; Nixdorf, Jakob; Neumann, Maciej D.; Esser, Norbert; Artús, Lluis; Cuscó, Ramon; Yamaguchi, Tomohiro; Goldhahn, Rüdiger

2018-04-01

The linear optical response of metastable α -Ga2O3 is investigated by spectroscopic ellipsometry. We determine the ordinary dielectric function from lattice vibrations up to the vacuum ultraviolet spectral range at room temperature for a sample with a (0001 ) surface. Three out of four Eu infrared-active phonon modes are unambiguously determined, and their frequencies are in good agreement with density functional theory calculations. The dispersion of the refractive index in the visible and ultraviolet part of the spectrum is determined. High-energy interband transitions are characterized up to 20 eV . By comparison with the optical response of α -Al2O3 and with theoretical results, a tentative assignment of interband transitions is proposed.

Identification of Excited States in the N=Z Nucleus 82Nb

NASA Astrophysics Data System (ADS)

Caceres, L. S.; Gorska, M.; Jungclaus, A.; Regan, P. H.; Garnsworthy, A. B.; Pietri, S.; Podolyak, Zs.; Rudolph, D.; Steer, S. J.; Grawe, H.; Balabanski, D. L.; Becker, F.; Bednarczyk, P.; Benzoni, G.; Blank, B.; Brandau, C.; Bruce, A. M.; Camera, F.; Catford, W. N.; Cullen, I. J.; Dombradi, Zs.; Doornenbal, P.; Estevez, E.; Geissel, H.; Gelletly, W.; Gerl, J.; Grebosz, J.; Heinz, A.; Hoischen, R.; Ilie, G.; Jolie, J.; Jones, G. A.; Kmiecik, M.; Kojouharov, I.; Kondev, F. G.; Kurtukian-Nieto, T.; Kurz, N.; Lalkowski, S.; Liu, L.; Maj, A.; Myalski, S.; Montes, F.; Pfuetzner, M.; Prokopowicz, W.; Saito, T.; Schaffner, H.; Schwertel, S.; Shizuma, T.; Simons, A. J.; Tashenov, S.; Walker, P. M.; Werner-Malento, E.; Wieland, O.; Wollersheim, H. J.

2007-04-01

Information on the first excited states in the N=Z=41 nucleus 82Nb sheds light on the competition of isospin T=0 and T=1 states in the A sim 80 region. The measurement was performed at the GSI laboratory using fragmentation of a 107Ag primary beam at 750 MeV/u on a 4 g/cm2 9Be target. The fragments were separated and identified unambiguously in the FRagment Separator. Three excited states were observed and the half-life estimate for the isomeric state was extracted. A tentative spin assignment based on the isobaric analogue states systematics in the Tz=1 nucleus 82Zr, and transition probabilities indicate T=1 character of the first two excited states, and T=0 for the isomeric state.

Rotational spectroscopy of pyridazine and its isotopologs from 235–360 GHz: Equilibrium structure and vibrational satellites

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

Esselman, Brian J.; Amberger, Brent K.; Shutter, Joshua D.

2013-12-14

The rotational spectrum of pyridazine (o-C{sub 4}H{sub 4}N{sub 2}), the ortho disubstituted nitrogen analog of benzene, has been measured and analyzed in the gas phase. For the ground vibrational state of the normal isotopolog, over 2000 individual rotational transitions have been identified between 238 and 360 GHz and have been fit to 13 parameters of a 6th-order centrifugal distortion Hamiltonian. All transitions in this frequency region can now be predicted from this model to near experimental accuracy, i.e., well enough for the purpose of any future radio-astronomical search for this species. Three isotopologs, [3-{sup 13}C]-C{sub 4}H{sub 4}N{sub 2}, [4-{sup 13}C]-C{sub 4}H{submore » 4}N{sub 2}, and [1-{sup 15}N]-C{sub 4}H{sub 4}N{sub 2}, have been detected in natural abundance, and several hundred lines have been measured for each of these species and fit to 6th-order Hamiltonians. Ten additional isotopologs were synthesized with enhanced deuterium substitution and analyzed to allow for a complete structure determination. The equilibrium structure (R{sub e}) of pyridazine was obtained by correcting the experimental rotational constants for the effects of vibration-rotation coupling using interaction constants predicted from CCSD(T) calculations with an ANO0 basis set and further correcting for the effect of electron mass. The final R{sub e} structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (I{sub a} and I{sub b} for 14 isotopologs) very well from 9 structural parameters. The rotational spectra of the six lowest-energy fundamental vibrational satellites of the main isotopolog have been detected. The rotational spectra of the five lowest-energy vibrational satellites have been assigned and fit to yield accurate rotational and distortion constants, while the fit and assignment for the sixth is less complete. The resultant vibration-rotation interaction (α) constants are found to be in excellent agreement with ones predicted from coupled-cluster calculations, which proved to be the key to unambiguous assignment of the satellite spectra to specific vibration modes.« less

Assignment Choice, Effort, and Assignment Completion: Does Work Ethic Predict Those Who Choose Higher-Effort Assignments?

ERIC Educational Resources Information Center

Parkhurst, John T.; Fleisher, Matthew S.; Skinner, Christopher H.; Woehr, David J.; Hawthorn-Embree, Meredith L.

2011-01-01

After completing the Multidimensional Work-Ethic Profile (MWEP), 98 college students were given a 20-problem math computation assignment and instructed to stop working on the assignment after completing 10 problems. Next, they were allowed to choose to finish either the partially completed assignment that had 10 problems remaining or a new…

Exciplex formation in bimolecular photoinduced electron-transfer investigated by ultrafast time-resolved infrared spectroscopy.

PubMed

Koch, Marius; Letrun, Romain; Vauthey, Eric

2014-03-12

The dynamics of bimolecular photoinduced electron-transfer reactions has been investigated with three donor/acceptor (D/A) pairs in tetrahydrofuran (THF) and acetonitrile (ACN) using a combination of ultrafast spectroscopic techniques, including time-resolved infrared absorption. For the D/A pairs with the highest driving force of electron transfer, all transient spectroscopic features can be unambiguously assigned to the excited reactant and the ionic products. For the pair with the lowest driving force, three additional transient infrared bands, more intense in THF than in ACN, with a time dependence that differs from those of the other bands are observed. From their frequency and solvent dependence, these bands can be assigned to an exciplex. Moreover, polarization-resolved measurements point to a relatively well-defined mutual orientation of the constituents and to a slower reorientational time compared to those of the individual reactants. Thanks to the minimal overlap of the infrared signature of all transient species in THF, a detailed reaction scheme including the relevant kinetic and thermodynamic parameters could be deduced for this pair. This analysis reveals that the formation and recombination of the ion pair occur almost exclusively via the exciplex.

High-resolution four-dimensional carbon-correlated 1H- 1H ROESY experiments employing isotags and the filter diagonalization method for effective assignment of glycosidic linkages in oligosaccharides

NASA Astrophysics Data System (ADS)

Armstrong, Geoffrey S.; Bendiak, Brad

2006-07-01

Four-dimensional nuclear magnetic resonance spectroscopy of oligosaccharides that correlates 1H-1H ROESY cross peaks to two additional 13C frequency dimensions is reported. The 13C frequencies were introduced by derivatization of all free hydroxyl groups with doubly 13C-labeled acetyl isotags. Pulse sequences were optimized for processing with the filter diagonalization method. The extensive overlap typically observed in 2D ROESY 1H-1H planes was alleviated by resolution of ROESY cross peaks in the two added dimensions associated with the carbon frequencies of the isotags. This enabled the interresidue 1H-1H ROESY cross peaks to be unambiguously assigned hence spatially proximate sugar spin systems across glycosidic bonds could be effectively ascertained. An experiment that selectively amplifies interresidue ROESY 1H-1H cross peaks is also reported. It moves the magnetization of an intraresidue proton normally correlated to a sugar H-1 signal orthogonally along the z axis prior to a Tr-ROESY mixing sequence. This virtually eliminates the incoherent intraresidue ROESY transfer, suppresses coherent TOCSY transfer, and markedly enhances the intensity of interresidue ROESY cross peaks.

High-resolution four-dimensional carbon-correlated 1H-1H ROESY experiments employing isotags and the filter diagonalization method for effective assignment of glycosidic linkages in oligosaccharides.

PubMed

Armstrong, Geoffrey S; Bendiak, Brad

2006-07-01

Four-dimensional nuclear magnetic resonance spectroscopy of oligosaccharides that correlates 1H-1H ROESY cross peaks to two additional 13C frequency dimensions is reported. The 13C frequencies were introduced by derivatization of all free hydroxyl groups with doubly 13C-labeled acetyl isotags. Pulse sequences were optimized for processing with the filter diagonalization method. The extensive overlap typically observed in 2D ROESY 1H-1H planes was alleviated by resolution of ROESY cross peaks in the two added dimensions associated with the carbon frequencies of the isotags. This enabled the interresidue 1H-1H ROESY cross peaks to be unambiguously assigned hence spatially proximate sugar spin systems across glycosidic bonds could be effectively ascertained. An experiment that selectively amplifies interresidue ROESY 1H-1H cross peaks is also reported. It moves the magnetization of an intraresidue proton normally correlated to a sugar H-1 signal orthogonally along the z axis prior to a Tr-ROESY mixing sequence. This virtually eliminates the incoherent intraresidue ROESY transfer, suppresses coherent TOCSY transfer, and markedly enhances the intensity of interresidue ROESY cross peaks.

Classification of DNA nucleotides with transverse tunneling currents

NASA Astrophysics Data System (ADS)

Nyvold Pedersen, Jonas; Boynton, Paul; Di Ventra, Massimiliano; Jauho, Antti-Pekka; Flyvbjerg, Henrik

2017-01-01

It has been theoretically suggested and experimentally demonstrated that fast and low-cost sequencing of DNA, RNA, and peptide molecules might be achieved by passing such molecules between electrodes embedded in a nanochannel. The experimental realization of this scheme faces major challenges, however. In realistic liquid environments, typical currents in tunneling devices are of the order of picoamps. This corresponds to only six electrons per microsecond, and this number affects the integration time required to do current measurements in real experiments. This limits the speed of sequencing, though current fluctuations due to Brownian motion of the molecule average out during the required integration time. Moreover, data acquisition equipment introduces noise, and electronic filters create correlations in time-series data. We discuss how these effects must be included in the analysis of, e.g., the assignment of specific nucleobases to current signals. As the signals from different molecules overlap, unambiguous classification is impossible with a single measurement. We argue that the assignment of molecules to a signal is a standard pattern classification problem and calculation of the error rates is straightforward. The ideas presented here can be extended to other sequencing approaches of current interest.

Structural Identification of 19 Purified Isomers of the OPV Acceptor Material bisPCBM by 13C NMR and UV-Vis Absorption Spectroscopy and High-Performance Liquid Chromatography.

PubMed

Liu, Tong; Abrahams, Isaac; Dennis, T John S

2018-04-26

The molecular structures of 19 purified isomers of bis-phenyl-C 62 -butyric acid methyl ester were identified by a combination of 13 C NMR and UV-vis absorption spectroscopies and high-performance liquid chromatography (HPLC) retention time analysis. All 19 isomers are dicyclopropafullerenes (none are homofullerenes). There were seven isomers with C 1 molecular point-group symmetry, four with C s , six with C 2 , one with C 2 v , and one with C 2 h symmetry. The C 2 h , C 2 v , and all five nonequatorial C 1 isomers were unambiguously assigned to their respective HPLC fractions. For the other 12 isomers, the 13 C NMR and UV-vis spectra placed them in six groups of two same-symmetry isomers. On the basis of the widely spaced HPLC retention times of the two isomers within each of these six groups, and the empirical inverse correlation between retention time and addend spacing, each isomer was assigned to its corresponding HPLC fraction. In addition, the missing trans-1 isomer was found, purified, and characterized.

Journeys through antigravity?

NASA Astrophysics Data System (ADS)

Carrasco, John Joseph M.; Chemissany, Wissam; Kallosh, Renata

2014-01-01

A possibility of journeys through antigravity has recently been proposed, with the suggestion that Weyl-invariant extension of scalars coupled to Einstein gravity allows for an unambiguous classical evolution through cosmological singularities in anisotropic spacetimes. We compute the Weyl invariant curvature squared and find that it blows up for the proposed anisotropic solution both at the Big Crunch as well as at the Big Bang. Therefore the cosmological singularities are not resolved by uplifting Einstein theory to a Weyl invariant model.

Kinetic Evidence of an Apparent Negative Activation Enthalpy in an Organocatalytic Process

PubMed Central

Han, Xiao; Lee, Richmond; Chen, Tao; Luo, Jie; Lu, Yixin; Huang, Kuo-Wei

2013-01-01

A combined kinetic and computational study on our tryptophan-based bifunctional thiourea catalyzed asymmetric Mannich reactions reveals an apparent negative activation enthalpy. The formation of the pre-transition state complex has been unambiguously confirmed and these observations provide an experimental support for the formation of multiple hydrogen bonding network between the substrates and the catalyst. Such interactions allow the creation of a binding cavity, a key factor to install high enantioselectivity. PMID:23990028

Non-Lethal Weapons in Noncombatant Evacuation Operations

DTIC Science & Technology

1999-12-01

against your small squad of peacekeepers. If any of the three men decides to shoot, your rules of engagement unambiguously allow you to shoot back in...personnel (Siegel, pp. 7-8). By 30 December, Mogadishu resembled a war zone, with shells being fired into tribal neighborhoods, and uncontrolled small arms...his sentiments changed during his New Year’s Day jog in the compound; the constant small arms fire outside the walls forced him to reconsider the

Evaluating the Use of Auditory Systems to Improve Performance in Combat Search and Rescue

DTIC Science & Technology

2012-03-01

take advantage of human binaural hearing to present spatial information through auditory stimuli as it would occur in the real world. This allows the...multiple operators unambiguously and in a short amount of time. Spatial audio basics Spatial audio works with human binaural hearing to generate... binaural recordings “sound better” when heard in the same location where the recordings were made. While this appears to be related to the acoustic

Determining thin film properties by fitting optical transmittance

NASA Astrophysics Data System (ADS)

Klein, J. D.; Yen, A.; Cogan, S. F.

1990-08-01

The optical transmission spectra of rf sputtered tungsten oxide films on glass substrates were modeled to determine absorption edge behavior, film thickness, and index of refraction. Removal of substrate reflection and absorption phenomena from the experimental spectra allowed direct examination of thin film optical characteristics. The interference fringe pattern allows determination of the film thickness and the dependence of the real index of refraction on wavelength. Knowledge of the interference fringe behavior in the vicinity of the absorption edge was found essential to unambiguous determination of the optical band gap. In particular, the apparently random deviations commonly observed in the extrapolation of as-acquired data are eliminated by explicitly considering interference fringe phenomena. The multivariable optimization fitting scheme employed allows air-film-substrate reflection losses to be compensated without making reflectance measurements.

DNA Barcoding Green Microalgae Isolated from Neotropical Inland Waters

PubMed Central

Hadi, Sámed I. I. A.; Santana, Hugo; Brunale, Patrícia P. M.; Gomes, Taísa G.; Oliveira, Márcia D.; Matthiensen, Alexandre; Oliveira, Marcos E. C.; Silva, Flávia C. P.; Brasil, Bruno S. A. F.

2016-01-01

This study evaluated the feasibility of using the Ribulose Bisphosphate Carboxylase Large subunit gene (rbcL) and the Internal Transcribed Spacers 1 and 2 of the nuclear rDNA (nuITS1 and nuITS2) markers for identifying a very diverse, albeit poorly known group, of green microalgae from neotropical inland waters. Fifty-one freshwater green microalgae strains isolated from Brazil, the largest biodiversity reservoir in the neotropics, were submitted to DNA barcoding. Currently available universal primers for ITS1-5.8S-ITS2 region amplification were sufficient to successfully amplify and sequence 47 (92%) of the samples. On the other hand, new sets of primers had to be designed for rbcL, which allowed 96% of the samples to be sequenced. Thirty-five percent of the strains could be unambiguously identified to the species level based either on nuITS1 or nuITS2 sequences’ using barcode gap calculations. nuITS2 Compensatory Base Change (CBC) and ITS1-5.8S-ITS2 region phylogenetic analysis, together with morphological inspection, confirmed the identification accuracy. In contrast, only 6% of the strains could be assigned to the correct species based solely on rbcL sequences. In conclusion, the data presented here indicates that either nuITS1 or nuITS2 are useful markers for DNA barcoding of freshwater green microalgae, with advantage for nuITS2 due to the larger availability of analytical tools and reference barcodes deposited at databases for this marker. PMID:26900844

The structure of poly(carbonsuboxide) on the atomic scale: a solid-state NMR study.

PubMed

Schmedt auf der Günne, Jörn; Beck, Johannes; Hoffbauer, Wilfried; Krieger-Beck, Petra

2005-07-18

In this contribution we present a study of the structure of amorphous poly(carbonsuboxide) (C3O2)x by 13C solid-state NMR spectroscopy supported by infrared spectroscopy and chemical analysis. Poly(carbonsuboxide) was obtained by polymerization of carbonsuboxide C3O2, which in turn was synthesized from malonic acid bis(trimethylsilylester). Two different 13C labeling schemes were applied to probe inter- and intramonomeric bonds in the polymer by dipolar solid-state NMR methods and also to allow quantitative 13C MAS NMR spectra. Four types of carbon environments can be distinguished in the NMR spectra. Double-quantum and triple-quantum 2D correlation experiments were used to assign the observed peaks using the through-space and through-bond dipolar coupling. In order to obtain distance constraints for the intermonomeric bonds, double-quantum constant-time experiments were performed. In these experiments an additional filter step was applied to suppress contributions from not directly bonded 13C,13C spin pairs. The 13C NMR intensities, chemical shifts, connectivities and distances gave constraints for both the polymerization mechanism and the short-range order of the polymer. The experimental results were complemented by bond lengths predicted by density functional theory methods for several previously suggested models. Based on the presented evidence we can unambiguously exclude models based on gamma-pyronic units and support models based on alpha-pyronic units. The possibility of planar ladder- and bracelet-like alpha-pyronic structures is discussed.

Pelvis morphology suggests that early Mesozoic birds were too heavy to contact incubate their eggs.

PubMed

Charles Deeming, D; Mayr, Gerald

2018-05-01

Numerous new fossils have driven an interest in reproduction of early birds, but direct evidence remains elusive. No Mesozoic avian eggs can be unambiguously assigned to a species, which hampers our understanding of the evolution of contact incubation, which is a defining feature of extant birds. Compared to living species, eggs of Mesozoic birds are relatively small, but whether the eggs of Mesozoic birds could actually have borne the weight of a breeding adult has not yet been investigated. We estimated maximal egg breadth for a range of Mesozoic avian taxa from the width of the pelvic canal defined by the pubic symphysis. Known elongation ratios of Mesozoic bird eggs allowed us to predict egg mass and hence the load mass an egg could endure before cracking. These values were compared to the predicted body masses of the adult birds based on skeletal remains. Based on 21 fossil species, we show that for nonornithothoracine birds body mass was 187% of the load mass of the eggs. For Enantiornithes, body mass was 127% greater than the egg load mass, but some early Cretaceous ornithuromorphs were 179% heavier than their eggs could support. Our indirect approach provides the best evidence yet that early birds could not have sat on their eggs without running the risk of causing damage. We suggest that contact incubation evolved comparatively late in birds. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Generation and Characterization of Six Recombinant Botulinum Neurotoxins as Reference Material to Serve in an International Proficiency Test.

PubMed

Weisemann, Jasmin; Krez, Nadja; Fiebig, Uwe; Worbs, Sylvia; Skiba, Martin; Endermann, Tanja; Dorner, Martin B; Bergström, Tomas; Muñoz, Amalia; Zegers, Ingrid; Müller, Christian; Jenkinson, Stephen P; Avondet, Marc-Andre; Delbrassinne, Laurence; Denayer, Sarah; Zeleny, Reinhard; Schimmel, Heinz; Åstot, Crister; Dorner, Brigitte G; Rummel, Andreas

2015-11-26

The detection and identification of botulinum neurotoxins (BoNT) is complex due to the existence of seven serotypes, derived mosaic toxins and more than 40 subtypes. Expert laboratories currently use different technical approaches to detect, identify and quantify BoNT, but due to the lack of (certified) reference materials, analytical results can hardly be compared. In this study, the six BoNT/A1-F1 prototypes were successfully produced by recombinant techniques, facilitating handling, as well as improving purity, yield, reproducibility and biosafety. All six BoNTs were quantitatively nicked into active di-chain toxins linked by a disulfide bridge. The materials were thoroughly characterized with respect to purity, identity, protein concentration, catalytic and biological activities. For BoNT/A₁, B₁ and E₁, serotypes pathogenic to humans, the catalytic activity and the precise protein concentration were determined by Endopep-mass spectrometry and validated amino acid analysis, respectively. In addition, BoNT/A₁, B₁, E₁ and F₁ were successfully detected by immunological assays, unambiguously identified by mass spectrometric-based methods, and their specific activities were assigned by the mouse LD50 bioassay. The potencies of all six BoNT/A1-F1 were quantified by the ex vivo mouse phrenic nerve hemidiaphragm assay, allowing a direct comparison. In conclusion, highly pure recombinant BoNT reference materials were produced, thoroughly characterized and employed as spiking material in a worldwide BoNT proficiency test organized by the EQuATox consortium.

VisFlow - Web-based Visualization Framework for Tabular Data with a Subset Flow Model.

PubMed

Yu, Bowen; Silva, Claudio T

2017-01-01

Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model. VisFlow focuses on interactive queries within the data flow, overcoming the limitation of interactivity from past computational data flow systems. In particular, VisFlow applies embedded visualizations and supports interactive selections, brushing and linking within a visualization-oriented data flow. The model requires all data transmitted by the flow to be a data item subset (i.e. groups of table rows) of some original input table, so that rendering properties can be assigned to the subset unambiguously for tracking and comparison. VisFlow features the analysis flexibility of a flow diagram, and at the same time reduces the diagram complexity and improves usability. We demonstrate the capability of VisFlow on two case studies with domain experts on real-world datasets showing that VisFlow is capable of accomplishing a considerable set of visualization and analysis tasks. The VisFlow system is available as open source on GitHub.

Assigning historic responsibility for extreme weather events

NASA Astrophysics Data System (ADS)

Otto, Friederike E. L.; Skeie, Ragnhild B.; Fuglestvedt, Jan S.; Berntsen, Terje; Allen, Myles R.

2017-11-01

Recent scientific advances make it possible to assign extreme events to human-induced climate change and historical emissions. These developments allow losses and damage associated with such events to be assigned country-level responsibility.

Evaluation of assigned-value uncertainty for complex calibrator value assignment processes: a prealbumin example.

PubMed

Middleton, John; Vaks, Jeffrey E

2007-04-01

Errors of calibrator-assigned values lead to errors in the testing of patient samples. The ability to estimate the uncertainties of calibrator-assigned values and other variables minimizes errors in testing processes. International Organization of Standardization guidelines provide simple equations for the estimation of calibrator uncertainty with simple value-assignment processes, but other methods are needed to estimate uncertainty in complex processes. We estimated the assigned-value uncertainty with a Monte Carlo computer simulation of a complex value-assignment process, based on a formalized description of the process, with measurement parameters estimated experimentally. This method was applied to study uncertainty of a multilevel calibrator value assignment for a prealbumin immunoassay. The simulation results showed that the component of the uncertainty added by the process of value transfer from the reference material CRM470 to the calibrator is smaller than that of the reference material itself (<0.8% vs 3.7%). Varying the process parameters in the simulation model allowed for optimizing the process, while keeping the added uncertainty small. The patient result uncertainty caused by the calibrator uncertainty was also found to be small. This method of estimating uncertainty is a powerful tool that allows for estimation of calibrator uncertainty for optimization of various value assignment processes, with a reduced number of measurements and reagent costs, while satisfying the requirements to uncertainty. The new method expands and augments existing methods to allow estimation of uncertainty in complex processes.

High energy conformers of M(+)(APE)(H2O)(0-1)Ar(0-1) clusters revealed by combined IR-PD and DFT-MD anharmonic vibrational spectroscopy.

PubMed

Brites, V; Nicely, A L; Sieffert, N; Gaigeot, M-P; Lisy, J M

2014-07-14

IR-PD vibrational spectroscopy and DFT-based molecular dynamics simulations are combined in order to unravel the structures of M(+)(APE)(H2O)0-1 ionic clusters (M = Na, K), where APE (2-amino-1-phenyl ethanol) is commonly used as an analogue for the noradrenaline neurotransmitter. The strength of the synergy between experiments and simulations presented here is that DFT-MD provides anharmonic vibrational spectra that unambiguously help assign the ionic clusters structures. Depending on the interacting cation, we have found that the lowest energy conformers of K(+)(APE)(H2O)0-1 clusters are formed, while the lowest energy conformers of Na(+)(APE)(H2O)0-1 clusters can only be observed through water loss channel (i.e. without argon tagged to the clusters). Trapping of higher energy conformers is observed when the argon loss channel is recorded in the experiment. This has been rationalized by transition state energies. The dynamical anharmonic vibrational spectra unambiguously provide the prominent OH stretch due to the OH···NH2 H-bond, within 10 cm(-1) of the experiment, hence reproducing the 240-300 cm(-1) red-shift (depending on the interacting cation) from bare neutral APE. When this H-bond is not present, the dynamical anharmonic spectra provide the water O-H stretches as well as the rotational motion of the water molecule at finite temperature, as observed in the experiment.

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

Hofmann, S.; Heinz, S.; Mann, R.

The reaction 54Cr$ + $248Cm was investigated at the velocity filter SHIP at GSI, Darmstadt, with the intention to study production and decay properties of isotopes of element 120. Three correlated signals were measured, which occurred within a period of 279ms. The heights of the signals correspond with the expectations for a decay sequence starting with an isotope of element 120. However, a complete decay chain cannot be established, since a signal from the implantation of the evaporation residue cannot be identified unambiguously. Measured properties of the event chain are discussed in detail. The result is compared with theoretical predictions.more » Previously measured decay properties of even element super-heavy nuclei were compiled in order to find arguments for an assignment from the systematics of experimental data. In the course of this review, a few tentatively assigned data could be corrected. New interpretations are given for results which could not be assigned definitely in previous studies. The discussion revealed that the cross-section for production of element 120 could be high enough so that a successful experiment seems possible with presently available techniques. However, a continuation of the experiment at SHIP for a necessary confirmation of the results obtained in a relatively short irradiation of five weeks is not possible at GSI presently. Furthermore, we decided to publish the results of the measurement and of the review as they exist now. In the summary and outlook section we also present concepts for the continuation of research in the field of super-heavy nuclei.« less

Gas-phase infrared spectra of vinyl selenol and vinyl tellurol.

PubMed

Benidar, Abdessamad; Khater, Brahim; Guillemin, Jean-Claude; Gámez, José A; Yáñez, Manuel

2009-11-19

The infrared spectra (3500-500 cm(-1)) of gaseous vinyl selenol and vinyl tellurol have been recorded at 0.1 cm(-1) resolution. For the latter the spectra were obtained at room temperature, but for the former a temperature of -40 degrees C was required because of the chemical instability of vinyl selenol at room temperature. To compensate the very weak vapor pressure of vinyl tellurol at room temperature, a long optical path up to 136 m was necessary to record its spectrum. B3LYP density functional theory (DFT) calculations have been performed to assign the different absorption bands. Since an unambiguous assignment of the absorption bands requires a precise knowledge on the relative abundance of the syn and gauche rotamers of these compounds, their relative energies and their anharmonic vibrational frequencies were obtained using a very extended Def2-QZVP basis set. Two rotamers, the syn, which is planar, and a nonplanar gauche, were found to be local minima for both compounds. The gauche rotamer presents two degenerate conformers, which differ by the position of the SeH (TeH) hydrogen atom above or below the molecular plane. Our theoretical results are in good agreement with the main features of the experimental spectra. Fundamental bands and some combination bands of vinyl selenol and vinyl tellurol were assigned and compared with those of vinyl alcohol and vinyl thiol, whose spectra had been reported previously in the literature.

Gas-Phase Infrared Spectra of Vinyl Selenol and Vinyl Tellurol

NASA Astrophysics Data System (ADS)

Benidar, Abdessamad; Khater, Brahim; Guillemin, Jean-Claude; Gámez, José A.; Yáñez, Manuel

2009-10-01

The infrared spectra (3500-500 cm-1) of gaseous vinyl selenol and vinyl tellurol have been recorded at 0.1 cm-1 resolution. For the latter the spectra were obtained at room temperature, but for the former a temperature of -40 °C was required because of the chemical instability of vinyl selenol at room temperature. To compensate the very weak vapor pressure of vinyl tellurol at room temperature, a long optical path up to 136 m was necessary to record its spectrum. B3LYP density functional theory (DFT) calculations have been performed to assign the different absorption bands. Since an unambiguous assignment of the absorption bands requires a precise knowledge on the relative abundance of the syn and gauche rotamers of these compounds, their relative energies and their anharmonic vibrational frequencies were obtained using a very extended Def2-QZVP basis set. Two rotamers, the syn, which is planar, and a nonplanar gauche, were found to be local minima for both compounds. The gauche rotamer presents two degenerate conformers, which differ by the position of the SeH (TeH) hydrogen atom above or below the molecular plane. Our theoretical results are in good agreement with the main features of the experimental spectra. Fundamental bands and some combination bands of vinyl selenol and vinyl tellurol were assigned and compared with those of vinyl alcohol and vinyl thiol, whose spectra had been reported previously in the literature.

Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: utility in exploration of endangered plants.

PubMed

Oh, Joonseok; Bowling, John J; Zou, Yike; Chittiboyina, Amar G; Doerksen, Robert J; Ferreira, Daneel; Leininger, Theodor D; Hamann, Mark T

2013-08-01

Endangered plant species are an important resource for new chemistry. Lindera melissifolia is native to the Southeastern U.S. and scarcely populates the edges of lakes and ponds. Quantum mechanics (QM) used in combination with NMR/ECD is a powerful tool for the assignment of absolute configuration in lieu of X-ray crystallography. The EtOAc extract of L. melissifolia was subject to chromatographic analysis by VLC and HPLC. Spin-spin coupling constant (SSCC) were calculated using DFT at the MPW1PW91/6-31G(d,p) level for all staggered rotamers. ECD calculations employed Amber* force fields followed by PM6 semi-empirical optimizations. Hetero- and homo-nuclear coupling constants were extracted from 1D (1)H, E.COSY and HETLOC experiments. Two meroterpenoids, melissifolianes A (1) and B (2) were purified and their 2-D structures elucidated using NMR and HRESIMS. The relative configuration of 1 was established using the combination of NOE-based distance restraints and the comparisons of experimental and calculated SSCCs. The comparison of calculated and experimental ECD assigned the absolute configuration of 1. The relative configuration of a racemic mixture, melissifoliane B (2) was established utilizing J-based analysis combined with QM and NMR techniques.Conclusion Our study of the Lindera melissifolia metabolome exemplifies how new chemistry remains undiscovered among the numerous endangered plant species and demonstrates how analysis by ECD and NMR combined with various QM calculations is a sensible approach to support the stereochemical assignment of molecules with conformationally restricted conformations. QM-NMR/ECD combined approaches are of utility for unambiguous assignment of 3-D structures, especially with limited plant material and when a molecule is conformationally restricted. Conservation of an endangered plant species can be supported through identification of its new chemistry and utilization of that chemistry for commercial purposes. Copyright © 2013. Published by Elsevier B.V.

Ultra-high Q terahertz whispering-gallery modes in a silicon resonator

NASA Astrophysics Data System (ADS)

Vogt, Dominik Walter; Leonhardt, Rainer

2018-05-01

We report on the first experimental demonstration of terahertz (THz) whispering-gallery modes (WGMs) with an ultra-high quality factor of 1.5 × 104 at 0.62 THz. The WGMs are observed in a high resistivity float zone silicon spherical resonator coupled to a sub-wavelength silica waveguide. A detailed analysis of the coherent continuous wave THz spectroscopy measurements combined with a numerical model based on Mie-Debye-Aden-Kerker theory allows us to unambiguously identify the observed higher order radial THz WGMs.

Peculiarities of data interpretation upon direct tissue analysis by Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Chagovets, Vtaliy; Kononikhin, Aleksey; Starodubtseva, Nataliia; Kostyukevich, Yury; Popov, Igor; Frankevich, Vladimir; Nikolaev, Eugene

2016-01-01

The importance of high-resolution mass spectrometry for the correct data interpretation of a direct tissue analysis is demonstrated with an example of its clinical application for an endometriosis study. Multivariate analysis of the data discovers lipid species differentially expressed in different tissues under investigation. High-resolution mass spectrometry allows unambiguous separation of peaks with close masses that correspond to proton and sodium adducts of phosphatidylcholines and to phosphatidylcholines differing in double bond number.

Human visual performance model for crewstation design

NASA Technical Reports Server (NTRS)

Larimer, James; Prevost, Michael; Arditi, Aries; Azueta, Steven; Bergen, James; Lubin, Jeffrey

1991-01-01

An account is given of a Visibility Modeling Tool (VMT) which furnishes a crew-station designer with the means to assess configurational tradeoffs, with a view to the impact of various options on the unambiguous access of information to the pilot. The interactive interface of the VMT allows the manipulation of cockpit geometry, ambient lighting, pilot ergonomics, and the displayed symbology. Performance data can be displayed in the form of 3D contours into the crewstation graphic model, thereby yielding an indication of the operator's visual capabilities.

Separation of spin Seebeck effect and anomalous Nernst effect in Co/Cu/YIG

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

Tian, Dai; State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433; Li, Yufan

2015-05-25

The spin Seebeck effect (SSE) and Anomalous Nernst effect (ANE) have been observed in Co/Cu/YIG (yttrium iron garnet) multi-layer structure, where the ferromagnetic insulator YIG acts as the pure spin injector and the ferromagnetic metal Co layer acts as the spin current detector. With the insertion of 5 nm Cu layer, the two ferromagnetic layers are decoupled, thus allowing unambiguous separation of the SSE and ANE contributions under the same experimental conditions in the same sample.

Separation of spin Seebeck effect and anomalous Nernst effect in Co/Cu/YIG

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

Tian, Dai; Li, Yufan; Qu, D.

2015-05-25

The spin Seebeck effect (SSE) and Anomalous Nernst effect (ANE) have been observed in Co/Cu/YIG (yttrium iron garnet) multi-layer structure, where the ferromagnetic insulator YIG acts as the pure spin injector and the ferromagnetic metal Co layer acts as the spin current detector. With the insertion of 5 nm Cu layer, the two ferromagnetic layers are decoupled, thus allowing unambiguous separation of the SSE and ANE contributions under the same experimental conditions in the same sample.

Internal energy flows in composite optical vortices

NASA Astrophysics Data System (ADS)

Ferrer-Garcia, Manuel F.; Lopez-Mago, Dorilian; Hernandez-Aranda, Raul I.

2016-09-01

We study the energy ow pattern in the superposition of two off-axis optical vortices with orthogonal polarization states. This system presents a rich structure of polarization singularities, which allows us to study the transverse spin and orbital angular momentum of different polarization morphologies, which includes C points (stars, lemons and monstars) and L lines. We perform numerical simulations of the optical forces acting on submicron particles and show interesting configurations. We provide the set of control parameters to unambiguously distinguish between the spin and orbital ow contributions.

The discovery of the appearance of νμ - ντ oscillations

NASA Astrophysics Data System (ADS)

Ereditato, Antonio

2016-07-01

Almost 20 years after the first conceptual design of the experiment, five years of running in the Gran Sasso underground laboratory (LNGS), and billions of billions muon-neutrinos sent from CERN along the CNGS beam, in 2015 the OPERA neutrino detector has allowed the long-awaited discovery of the direct transformation (oscillation) of muon-neutrinos into tau-neutrinos. This result unambiguously confirms the interpretation of the so-called atmospheric channel, after the discovery of neutrino oscillations by the Super-Kamiokande Collaboration in 1998.

Quantum interference effects on the intensity of the G modes in double-walled carbon nanotubes

DOE PAGES

Tran, Huy Nam; Blancon, Jean-Christophe Robert; Arenal, Raul; ...

2017-05-08

The effects of quantum interferences on the excitation dependence of the intensity of G modes have been investigated on single-walled carbon nanotubes [Duque et al., Phys. Rev. Lett.108, 117404 (2012)]. In this work, by combining optical absorption spectroscopy and Raman scattering on individual index identified double-walled carbon nanotubes, we examine the experimental excitation dependence of the intensity of longitudinal optical and transverse optical G modes of the constituent inner and outer single-walled carbon nanotubes. The observed striking dependencies are understood in terms of quantum interference effects. Considering such effects, the excitation dependence of the different components of the G modesmore » permit to unambiguously assign each of them as originating from the longitudinal or transverse G modes of inner and outer tubes.« less

Towards saturation of the electron-capture delayed fission probability: The new isotopes 240Es and 236Bk

NASA Astrophysics Data System (ADS)

Konki, J.; Khuyagbaatar, J.; Uusitalo, J.; Greenlees, P. T.; Auranen, K.; Badran, H.; Block, M.; Briselet, R.; Cox, D. M.; Dasgupta, M.; Di Nitto, A.; Düllmann, Ch. E.; Grahn, T.; Hauschild, K.; Herzán, A.; Herzberg, R.-D.; Heßberger, F. P.; Hinde, D. J.; Julin, R.; Juutinen, S.; Jäger, E.; Kindler, B.; Krier, J.; Leino, M.; Lommel, B.; Lopez-Martens, A.; Luong, D. H.; Mallaburn, M.; Nishio, K.; Pakarinen, J.; Papadakis, P.; Partanen, J.; Peura, P.; Rahkila, P.; Rezynkina, K.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Sorri, J.; Stolze, S.; Sulignano, B.; Theisen, Ch.; Ward, A.; Yakushev, A.; Yakusheva, V.

2017-01-01

The new neutron-deficient nuclei 240Es and 236Bk were synthesised at the gas-filled recoil separator RITU. They were identified by their radioactive decay chains starting from 240Es produced in the fusion-evaporation reaction 209Bi(34S,3n)240Es. Half-lives of 6 (2)s and 22-6+13s were obtained for 240Es and 236Bk, respectively. Two groups of α particles with energies Eα = 8.19 (3)MeV and 8.09 (3)MeV were unambiguously assigned to 240Es. Electron-capture delayed fission branches with probabilities of 0.16 (6) and 0.04 (2) were measured for 240Es and 236Bk, respectively. These new data show a continuation of the exponential increase of ECDF probabilities in more neutron-deficient isotopes.

Study of near-stability nuclei populated as fission fragments in heavy-ion fusion reactions

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

Fotiadis, Nikolaos; Nelson, Ronald O; Devlin, Matthew

2010-01-01

Examples are presented to illustrate the power of prompt {gamma}-ray spectroscopy of fission fragments from compound nuclei with A {approx} 200 formed in fusion-evaporation reactions in experiments using the Gammasphere Ge-detector array. Complementary methods, such as Coulomb excitation and deep-inelastic processes, are also discussed. In other cases (n, xn{gamma}) reactions on stable isotopes have been used to establish neutron excitation functions for {gamma}-rays using a pulsed 'white'-neutron source, coupled to a high-energy-resolution germanium-detector array. The excitation functions can unambiguously assign {gamma}-rays to a specific reaction product. Results from all these methods bridge the gaps in the systematics of high-spin statesmore » between the neutron-deficient and neutron-rich nuclei. Results near shell closures should motivate new shell model calculations.« less

Against the naming of fungi.

PubMed

Money, Nicholas P

2013-01-01

The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence. Copyright © 2013 The Author. Published by Elsevier Ltd.. All rights reserved.

Quantum interference effects on the intensity of the G modes in double-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Tran, H. N.; Blancon, J.-C.; Arenal, R.; Parret, R.; Zahab, A. A.; Ayari, A.; Vallée, F.; Del Fatti, N.; Sauvajol, J.-L.; Paillet, M.

2017-05-01

The effects of quantum interferences on the excitation dependence of the intensity of G modes have been investigated on single-walled carbon nanotubes [Duque et al., Phys. Rev. Lett. 108, 117404 (2012), 10.1103/PhysRevLett.108.117404]. In this work, by combining optical absorption spectroscopy and Raman scattering on individual index identified double-walled carbon nanotubes, we examine the experimental excitation dependence of the intensity of longitudinal optical and transverse optical G modes of the constituent inner and outer single-walled carbon nanotubes. The observed striking dependencies are understood in terms of quantum interference effects. Considering such effects, the excitation dependence of the different components of the G modes permits us to unambiguously assign each of them as originating from the longitudinal or transverse G modes of inner and outer tubes.

A Domain-Specific Terminology for Retinopathy of Prematurity and Its Applications in Clinical Settings.

PubMed

Zhang, Yinsheng; Zhang, Guoming

2018-01-01

A terminology (or coding system) is a formal set of controlled vocabulary in a specific domain. With a well-defined terminology, each concept in the target domain is assigned with a unique code, which can be identified and processed across different medical systems in an unambiguous way. Though there are lots of well-known biomedical terminologies, there is currently no domain-specific terminology for ROP (retinopathy of prematurity). Based on a collection of historical ROP patients' data in the electronic medical record system, we extracted the most frequent terms in the domain and organized them into a hierarchical coding system-ROP Minimal Standard Terminology, which contains 62 core concepts in 4 categories. This terminology has been successfully used to provide highly structured and semantic-rich clinical data in several ROP-related applications.

Quantum interference effects on the intensity of the G modes in double-walled carbon nanotubes

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

Tran, Huy Nam; Blancon, Jean-Christophe Robert; Arenal, Raul

The effects of quantum interferences on the excitation dependence of the intensity of G modes have been investigated on single-walled carbon nanotubes [Duque et al., Phys. Rev. Lett.108, 117404 (2012)]. In this work, by combining optical absorption spectroscopy and Raman scattering on individual index identified double-walled carbon nanotubes, we examine the experimental excitation dependence of the intensity of longitudinal optical and transverse optical G modes of the constituent inner and outer single-walled carbon nanotubes. The observed striking dependencies are understood in terms of quantum interference effects. Considering such effects, the excitation dependence of the different components of the G modesmore » permit to unambiguously assign each of them as originating from the longitudinal or transverse G modes of inner and outer tubes.« less

The structure, vibrational spectra and nonlinear optical properties of the L-lysine × tartaric acid complex—Theoretical studies

NASA Astrophysics Data System (ADS)

Drozd, M.; Marchewka, M. K.

2006-05-01

The room temperature X-ray studies of L-lysine × tartaric acid complex are not unambiguous. The disorder of three atoms of carbon in L-lysine molecule is observed. These X-ray studies are ambiguous. The theoretical geometry study performed by DFT methods explain the most doubts which are connected with crystallographic measurements. The theoretical vibrational frequencies and potential energy distribution (PED) of L-lysine × tartaric acid were calculated by B3LYP method. The calculated frequencies were compared with experimental measured IR spectra. The complete assignment of the bands has been made on the basis of the calculated PED. The restricted Hartee-Fock (RHF) methods were used for calculation of the hyperpolarizability for investigated compound. The theoretical results are compared with experimental value of β.

41 CFR 302-8.200 - Am I eligible for extended storage during assignment OCONUS?

Code of Federal Regulations, 2012 CFR

2012-07-01

... extended storage during assignment OCONUS? 302-8.200 Section 302-8.200 Public Contracts and Property...-ALLOWANCES FOR EXTENDED STORAGE OF HOUSEHOLD GOODS (HHG) Extended Storage During Assignment Outside the Continental United States (OCONUS) § 302-8.200 Am I eligible for extended storage during assignment OCONUS...

41 CFR 302-8.200 - Am I eligible for extended storage during assignment OCONUS?

Code of Federal Regulations, 2010 CFR

2010-07-01

... extended storage during assignment OCONUS? 302-8.200 Section 302-8.200 Public Contracts and Property...-ALLOWANCES FOR EXTENDED STORAGE OF HOUSEHOLD GOODS (HHG) Extended Storage During Assignment Outside the Continental United States (OCONUS) § 302-8.200 Am I eligible for extended storage during assignment OCONUS...

41 CFR 302-8.200 - Am I eligible for extended storage during assignment OCONUS?

Code of Federal Regulations, 2011 CFR

2011-07-01

... extended storage during assignment OCONUS? 302-8.200 Section 302-8.200 Public Contracts and Property...-ALLOWANCES FOR EXTENDED STORAGE OF HOUSEHOLD GOODS (HHG) Extended Storage During Assignment Outside the Continental United States (OCONUS) § 302-8.200 Am I eligible for extended storage during assignment OCONUS...

What is Novel About Novel Ecosystems: Managing Change in an Ever-Changing World

NASA Astrophysics Data System (ADS)

Truitt, Amy M.; Granek, Elise F.; Duveneck, Matthew J.; Goldsmith, Kaitlin A.; Jordan, Meredith P.; Yazzie, Kimberly C.

2015-06-01

Influenced by natural climatic, geological, and evolutionary changes, landscapes and the ecosystems within are continuously changing. In addition to these natural pressures, anthropogenic drivers have increasingly influenced ecosystems. Whether affected by natural or anthropogenic processes, ecosystems, ecological communities, and ecosystem functioning are dynamic and can lead to "novel" or "emerging" ecosystems. Current literature identifies several definitions of these ecosystems but lacks an unambiguous definition and framework for categorizing what constitutes a novel ecosystem and for informing decisions around best management practices. Here we explore the various definitions used for novel ecosystems, present an unambiguous definition, and propose a framework for identifying the most appropriate management option. We identify and discuss three approaches for managing novel ecosystems: managing against, tolerating, and managing for these systems, and we provide real-world examples of each approach. We suggest that this framework will allow managers to make thoughtful decisions about which strategy is most appropriate for each unique situation, to determine whether the strategy is working, and to facilitate decision-making when it is time to modify the management approach.

Statistical benchmark for BosonSampling

NASA Astrophysics Data System (ADS)

Walschaers, Mattia; Kuipers, Jack; Urbina, Juan-Diego; Mayer, Klaus; Tichy, Malte Christopher; Richter, Klaus; Buchleitner, Andreas

2016-03-01

Boson samplers—set-ups that generate complex many-particle output states through the transmission of elementary many-particle input states across a multitude of mutually coupled modes—promise the efficient quantum simulation of a classically intractable computational task, and challenge the extended Church-Turing thesis, one of the fundamental dogmas of computer science. However, as in all experimental quantum simulations of truly complex systems, one crucial problem remains: how to certify that a given experimental measurement record unambiguously results from enforcing the claimed dynamics, on bosons, fermions or distinguishable particles? Here we offer a statistical solution to the certification problem, identifying an unambiguous statistical signature of many-body quantum interference upon transmission across a multimode, random scattering device. We show that statistical analysis of only partial information on the output state allows to characterise the imparted dynamics through particle type-specific features of the emerging interference patterns. The relevant statistical quantifiers are classically computable, define a falsifiable benchmark for BosonSampling, and reveal distinctive features of many-particle quantum dynamics, which go much beyond mere bunching or anti-bunching effects.

What is Novel About Novel Ecosystems: Managing Change in an Ever-Changing World.

PubMed

Truitt, Amy M; Granek, Elise F; Duveneck, Matthew J; Goldsmith, Kaitlin A; Jordan, Meredith P; Yazzie, Kimberly C

2015-06-01

Influenced by natural climatic, geological, and evolutionary changes, landscapes and the ecosystems within are continuously changing. In addition to these natural pressures, anthropogenic drivers have increasingly influenced ecosystems. Whether affected by natural or anthropogenic processes, ecosystems, ecological communities, and ecosystem functioning are dynamic and can lead to "novel" or "emerging" ecosystems. Current literature identifies several definitions of these ecosystems but lacks an unambiguous definition and framework for categorizing what constitutes a novel ecosystem and for informing decisions around best management practices. Here we explore the various definitions used for novel ecosystems, present an unambiguous definition, and propose a framework for identifying the most appropriate management option. We identify and discuss three approaches for managing novel ecosystems: managing against, tolerating, and managing for these systems, and we provide real-world examples of each approach. We suggest that this framework will allow managers to make thoughtful decisions about which strategy is most appropriate for each unique situation, to determine whether the strategy is working, and to facilitate decision-making when it is time to modify the management approach.

Guidelines for assigning allowable properties to visually graded foreign species based on test data from full sized specimens

Treesearch

David W. Green; Bradley E. Shelley

2006-01-01

The objective of this document is to provide philosophy and guidelines for the assignment of allowable properties to visually graded dimension lumber produced from trees not grown in the United States. This document assumes, as a starting point, the procedures of ASTM D 1990.

Attention affects visual perceptual processing near the hand.

PubMed

Cosman, Joshua D; Vecera, Shaun P

2010-09-01

Specialized, bimodal neural systems integrate visual and tactile information in the space near the hand. Here, we show that visuo-tactile representations allow attention to influence early perceptual processing, namely, figure-ground assignment. Regions that were reached toward were more likely than other regions to be assigned as foreground figures, and hand position competed with image-based information to bias figure-ground assignment. Our findings suggest that hand position allows attention to influence visual perceptual processing and that visual processes typically viewed as unimodal can be influenced by bimodal visuo-tactile representations.

Single machine scheduling with slack due dates assignment

NASA Astrophysics Data System (ADS)

Liu, Weiguo; Hu, Xiangpei; Wang, Xuyin

2017-04-01

This paper considers a single machine scheduling problem in which each job is assigned an individual due date based on a common flow allowance (i.e. all jobs have slack due date). The goal is to find a sequence for jobs, together with a due date assignment, that minimizes a non-regular criterion comprising the total weighted absolute lateness value and common flow allowance cost, where the weight is a position-dependent weight. In order to solve this problem, an ? time algorithm is proposed. Some extensions of the problem are also shown.

41 CFR 302-8.202 - Do provisions for the place, choice, or type of storage, allowable costs, or partial storage...

Code of Federal Regulations, 2010 CFR

2010-07-01

... place, choice, or type of storage, allowable costs, or partial storage during assignment OCONUS differ from those prescribed for storage during assignment to isolated locations in CONUS? 302-8.202 Section 302-8.202 Public Contracts and Property Management Federal Travel Regulation System RELOCATION...

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

Reduction theorems for optimal unambiguous state discrimination of density matrices

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

Raynal, Philippe; Luetkenhaus, Norbert; Enk, Steven J. van

2003-08-01

We present reduction theorems for the problem of optimal unambiguous state discrimination of two general density matrices. We show that this problem can be reduced to that of two density matrices that have the same rank n and are described in a Hilbert space of dimensions 2n. We also show how to use the reduction theorems to discriminate unambiguously between N mixed states (N{>=}2)

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

NASA Astrophysics Data System (ADS)

Morard, Raphaël; Lejzerowicz, Franck; Darling, Kate F.; Lecroq-Bennet, Béatrice; Winther Pedersen, Mikkel; Orlando, Ludovic; Pawlowski, Jan; Mulitza, Stefan; de Vargas, Colomban; Kucera, Michal

2017-06-01

Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.

Osteology of a new specimen of Macrocnemus aff. M. fuyuanensis (Archosauromorpha, Protorosauria) from the Middle Triassic of Europe: potential implications for species recognition and paleogeography of tanystropheid protorosaurs

NASA Astrophysics Data System (ADS)

Jaquier, Vivien P.; Fraser, Nicholas C.; Furrer, Heinz; Scheyer, Torsten M.

2017-11-01

Over the past two decades, a wealth of marine and terrestrial reptiles, including protorosaurian archosauromorphs, has been described from Triassic shales and limestone layers in southern China. Recovered from the eastern margin of the Tethys Ocean, these forms often show remarkable similarities to taxa that were previously known and described from Europe, i.e., the western Tethyan margin. One protorosaurian that is known from the western and the eastern Tethyan province is the genus Macrocnemus, with currently three recognized species: 1) M. bassanii from the Middle Triassic Besano Formation and Meride Limestone (late Anisian – early Ladinian), UNESCO World Heritage Site Monte San Giorgio, Ticino, Switzerland; 2) M. obristi from the Prosanto Formation (early Ladinian) of the Ducan area, Grisons, Switzerland; and 3) M. fuyuanensis from the Falang Formation (Ladinian), Yunnan Province, southern China. Recently a new specimen, PIMUZ T 1559, from the upper Besano Formation at Meride, Ticino, Switzerland, was prepared, revealing a disarticulated skeleton which includes most of the cranium and lower jaw, pre-caudal vertebral column and ribs, the forelimbs, and girdle elements. Unambiguously assignable to the genus Macrocnemus, it evinces particularly gracile elongated cervical ribs, as well as a humerus/radius ratio that is comparable only to that of M. fuyuanensis from southern China. Based on this feature we tentatively recognize the new specimen as M. aff. fuyuanensis from Europe. The position and exquisite preservation of the clavicle and interclavicle in this specimen allows a revision of the shoulder girdle of Macrocnemus when articulated, which also has implications for closely related protorosaurian taxa, such as the long-necked Tanystropheus. Furthermore, differences in the shape and morphology of the interclavicle including pointed wing-like lateral processes and a short, fusiform caudal process represent rare discrete characters that allow separation of the specimens of M. bassanii from the new specimen of M. aff. fuyuanensis.

Probing polariton dynamics in trapped ions with phase-coherent two-dimensional spectroscopy

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

Gessner, Manuel; Schlawin, Frank; Buchleitner, Andreas

2015-06-07

We devise a phase-coherent three-pulse protocol to probe the polariton dynamics in a trapped-ion quantum simulation. In contrast to conventional nonlinear signals, the presented scheme does not change the number of excitations in the system, allowing for the investigation of the dynamics within an N-excitation manifold. In the particular case of a filling factor one (N excitations in an N-ion chain), the proposed interaction induces coherent transitions between a delocalized phonon superfluid and a localized atomic insulator phase. Numerical simulations of a two-ion chain demonstrate that the resulting two-dimensional spectra allow for the unambiguous identification of the distinct phases, andmore » the two-dimensional line shapes efficiently characterize the relevant decoherence mechanism.« less

PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications.

PubMed

Pasquier, C; Promponas, V J; Hamodrakas, S J

2001-08-15

A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED-CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLASS.

Cysteine S-linked N-acetylglucosamine (S-GlcNAcylation), A New Post-translational Modification in Mammals.

PubMed

Maynard, Jason C; Burlingame, Alma L; Medzihradszky, Katalin F

2016-11-01

Intracellular GlcNAcylation of Ser and Thr residues is a well-known and widely investigated post-translational modification. This post-translational modification has been shown to play a significant role in cell signaling and in many regulatory processes within cells. O-GlcNAc transferase is the enzyme responsible for glycosylating cytosolic and nuclear proteins with a single GlcNAc residue on Ser and Thr side-chains. Here we report that the same enzyme may also be responsible for S-GlcNAcylation, i.e. for linking the GlcNAc unit to the peptide by modifying a cysteine side-chain. We also report that O-GlcNAcase, the enzyme responsible for removal of O-GlcNAcylation does not appear to remove the S-linked sugar. Such Cys modifications have been detected and identified in mouse and rat samples. This work has established the occurrence of 14 modification sites assigned to 11 proteins unambiguously. We have also identified S-GlcNAcylation from human Host Cell Factor 1 isolated from HEK-cells. Although these site assignments are primarily based on electron-transfer dissociation mass spectra, we also report that S-linked GlcNAc is more stable under collisional activation than O-linked GlcNAc derivatives. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Triplet energy differences and the low lying structure of 62Ga

NASA Astrophysics Data System (ADS)

Henry, T. W.; Bentley, M. A.; Clark, R. M.; Davies, P. J.; Bader, V. M.; Baugher, T.; Bazin, D.; Beausang, C. W.; Berryman, J. S.; Bruce, A. M.; Campbell, C. M.; Crawford, H. L.; Cromaz, M.; Fallon, P.; Gade, A.; Henderson, J.; Iwasaki, H.; Jenkins, D. G.; Lee, I. Y.; Lemasson, A.; Lenzi, S. M.; Macchiavelli, A. O.; Napoli, D. R.; Nichols, A. J.; Paschalis, S.; Petri, M.; Recchia, F.; Rissanen, J.; Simpson, E. C.; Stroberg, S. R.; Wadsworth, R.; Weisshaar, D.; Wiens, A.; Walz, C.

2015-08-01

Background: Triplet energy differences (TED) can be studied to yield information on isospin-non-conserving interactions in nuclei. Purpose: The systematic behavior of triplet energy differences (TED) of T =1 , Jπ=2+ states is examined. The A =62 isobar is identified as having a TED value that deviates significantly from an otherwise very consistent trend. This deviation can be attributed to the tentative assignments of the pertinent states in 62Ga and 62Ge . Methods: An in-beam γ -ray spectroscopy experiment was performed to identify excited states in 62Ga using Gamma-Ray Energy Tracking In-Beam Nuclear Array with the S800 spectrometer at NSCL using a two-nucleon knockout approach. Cross-section calculations for the knockout process and shell-model calculations have been performed to interpret the population and decay properties observed. Results: Using the systematics as a guide, a candidate for the transition from the T =1 , 2+ state is identified. However, previous work has identified similar states with different Jπ assignments. Cross-section calculations indicate that the relevant T =1 , 2+ state should be one of the states directly populated in this reaction. Conclusions: As spins and parities were not measurable, it is concluded that an unambiguous identification of the first T =1 , 2+ state is required to reconcile our understanding of TED systematics.

A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature

PubMed Central

Song, Yuhyun; Leman, Scotland; Monteil, Caroline L.; Heath, Lenwood S.; Vinatzer, Boris A.

2014-01-01

A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today’s speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research. PMID:24586551

Changes to International Nonproprietary Names for antibody therapeutics 2017 and beyond: of mice, men and more.

PubMed

Parren, Paul W H I; Carter, Paul J; Plückthun, Andreas

Active pharmaceutical substances require an International Nonproprietary Name (INN) assigned by the World Health Organization (WHO) to obtain market authorization as a medicinal product. INNs are selected to represent a unique, generic name for a drug enabling unambiguous identification by stakeholders worldwide. INNs may be requested after initiating clinical development of an investigational drug. Pharmaceutical classes are indicated by a common stem or suffix. Currently, INNs for monoclonal antibody-based drugs are recognized by the suffix, -mab, preceded by a source infix such as -xi- (chimeric), -zu- (humanized) or -u- (human) designating the species from which the antibody was derived. However, many technological advances have made it increasingly difficult to accurately capture an antibody's source in its name. In 2014, the WHO and the United States Adopted Names (USAN) Council approached this challenge by implementing changes to antibody source infix definitions. Unfortunately, gaps and ambiguities in the definitions and procedures resulted in inconsistent source category assignments and widespread confusion. The Antibody Society, extensively supported by academic and industry scientists, voiced concerns leading to constructive dialog during scheduled consultations with WHO and USAN Council representatives. In June 2017, the WHO announced that use of the source infix will be discontinued for new antibody INNs effective immediately. We fully support this change as it better aligns antibody INNs with current and foreseeable future innovations in antibody therapeutics. Here we review the changes implemented. Additionally, we analyzed antibody INNs recently assigned under the previous 2014 definitions and provide recommendations for further alignment.

Review of even element super-heavy nuclei and search for element 120

DOE PAGES

Hofmann, S.; Heinz, S.; Mann, R.; ...

2016-06-28

The reaction 54Cr$ + $248Cm was investigated at the velocity filter SHIP at GSI, Darmstadt, with the intention to study production and decay properties of isotopes of element 120. Three correlated signals were measured, which occurred within a period of 279ms. The heights of the signals correspond with the expectations for a decay sequence starting with an isotope of element 120. However, a complete decay chain cannot be established, since a signal from the implantation of the evaporation residue cannot be identified unambiguously. Measured properties of the event chain are discussed in detail. The result is compared with theoretical predictions.more » Previously measured decay properties of even element super-heavy nuclei were compiled in order to find arguments for an assignment from the systematics of experimental data. In the course of this review, a few tentatively assigned data could be corrected. New interpretations are given for results which could not be assigned definitely in previous studies. The discussion revealed that the cross-section for production of element 120 could be high enough so that a successful experiment seems possible with presently available techniques. However, a continuation of the experiment at SHIP for a necessary confirmation of the results obtained in a relatively short irradiation of five weeks is not possible at GSI presently. Furthermore, we decided to publish the results of the measurement and of the review as they exist now. In the summary and outlook section we also present concepts for the continuation of research in the field of super-heavy nuclei.« less

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

PubMed Central

Jakob, Sabine S.; Rödder, Dennis; Engler, Jan O.; Shaaf, Salar; Özkan, Hakan; Blattner, Frank R.; Kilian, Benjamin

2014-01-01

Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included. PMID:24586028

Interactive visual exploration and refinement of cluster assignments.

PubMed

Kern, Michael; Lex, Alexander; Gehlenborg, Nils; Johnson, Chris R

2017-09-12

With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

PubMed

Al Hasan, Naila M; Johnson, Grant E; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy(n-) and VxOyCl(n-) ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N(+), tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCl(n-) and VxOyCl(L)((n-1)-) clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl((1-2)-) and VxOy ((1-2)-) anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Identifying guanosine self assembly at natural isotopic abundance by high-resolution 1H and 13C solid-state NMR spectroscopy.

PubMed

Webber, Amy L; Masiero, Stefano; Pieraccini, Silvia; Burley, Jonathan C; Tatton, Andrew S; Iuga, Dinu; Pham, Tran N; Spada, Gian Piero; Brown, Steven P

2011-12-14

By means of the (1)H chemical shifts and the proton-proton proximities as identified in (1)H double-quantum (DQ) combined rotation and multiple-pulse spectroscopy (CRAMPS) solid-state NMR correlation spectra, ribbon-like and quartet-like self-assembly can be identified for guanosine derivatives without isotopic labeling for which it was not possible to obtain single crystals suitable for diffraction. Specifically, characteristic spectral fingerprints are observed for dG(C10)(2) and dG(C3)(2) derivatives, for which quartet-like and ribbon-like self-assembly has been unambiguously identified by (15)N refocused INADEQUATE spectra in a previous study of (15)N-labeled derivatives (Pham, T. N.; et al. J. Am. Chem. Soc.2005, 127, 16018). The NH (1)H chemical shift is observed to be higher (13-15 ppm) for ribbon-like self-assembly as compared to 10-11 ppm for a quartet-like arrangement, corresponding to a change from NH···N to NH···O intermolecular hydrogen bonding. The order of the two NH(2)(1)H chemical shifts is also inverted, with the NH(2) proton closest in space to the NH proton having a higher or lower (1)H chemical shift than that of the other NH(2) proton for ribbon-like as opposed to quartet-like self-assembly. For the dG(C3)(2) derivative for which a single-crystal diffraction structure is available, the distinct resonances and DQ peaks are assigned by means of gauge-including projector-augmented wave (GIPAW) chemical shift calculations. In addition, (14)N-(1)H correlation spectra obtained at 850 MHz under fast (60 kHz) magic-angle spinning (MAS) confirm the assignment of the NH and NH(2) chemical shifts for the dG(C3)(2) derivative and allow longer range through-space N···H proximities to be identified, notably to the N7 nitrogens on the opposite hydrogen-bonding face. © 2011 American Chemical Society

Unambiguous quantum-state filtering

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

Takeoka, Masahiro; Sasaki, Masahide; CREST, Japan Science and Technology Corporation, Tokyo,

2003-07-01

In this paper, we consider a generalized measurement where one particular quantum signal is unambiguously extracted from a set of noncommutative quantum signals and the other signals are filtered out. Simple expressions for the maximum detection probability and its positive operator valued measure are derived. We apply such unambiguous quantum state filtering to evaluation of the sensing of decoherence channels. The bounds of the precision limit for a given quantum state of probes and possible device implementations are discussed.

41 CFR 302-9.171 - If circumstances warrant an authorization to transport a POV to my post of duty after my...

Code of Federal Regulations, 2014 CFR

2014-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... Transportation Subsequent to the Time of Assignment § 302-9.171 If circumstances warrant an authorization to... signed at the time of your assignment to the post of duty. Violation of that service agreement, however...

41 CFR 302-9.171 - If circumstances warrant an authorization to transport a POV to my post of duty after my...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... Transportation Subsequent to the Time of Assignment § 302-9.171 If circumstances warrant an authorization to... signed at the time of your assignment to the post of duty. Violation of that service agreement, however...

41 CFR 302-9.171 - If circumstances warrant an authorization to transport a POV to my post of duty after my...

Code of Federal Regulations, 2013 CFR

2013-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... Transportation Subsequent to the Time of Assignment § 302-9.171 If circumstances warrant an authorization to... signed at the time of your assignment to the post of duty. Violation of that service agreement, however...

41 CFR 302-9.171 - If circumstances warrant an authorization to transport a POV to my post of duty after my...

Code of Federal Regulations, 2011 CFR

2011-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... Transportation Subsequent to the Time of Assignment § 302-9.171 If circumstances warrant an authorization to... signed at the time of your assignment to the post of duty. Violation of that service agreement, however...

41 CFR 302-9.171 - If circumstances warrant an authorization to transport a POV to my post of duty after my...

Code of Federal Regulations, 2012 CFR

2012-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... Transportation Subsequent to the Time of Assignment § 302-9.171 If circumstances warrant an authorization to... signed at the time of your assignment to the post of duty. Violation of that service agreement, however...

Total angular momenta of high-lying odd levels of U I at ∼ 4 eV using resonance ionization laser polarization spectroscopy

NASA Astrophysics Data System (ADS)

Rath, Asawari D.; Kundu, S.; Ray, A. K.

2018-02-01

Laser induced photoionization of atoms shows significant dependence on the choice of polarizations of lasers. In multi-step, multi-photon excitation and subsequent ionization of atoms different polarization combinations of the exciting lasers lead to distinctly different ion yields. This fact is exploited in this work to determine total angular momenta of odd-parity energy levels of U I lying at ∼ 4 eV from its ground level using resonance ionization laser polarization spectroscopy in time of flight mass spectrometer. These levels are populated by two-step resonant excitation using two pulsed dye lasers with preset polarizations of choice followed by nonresonant ionization by third laser. The dependence of ionization yield on specific polarizations of the first two lasers is studied experimentally for each level under consideration. This dependence when compared to simulations makes possible unambiguous assignment of J angular momenta to these levels.

Synthesis, stereochemical, structural, and biological studies of a series of N‧-(2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ylidene)pyrazine-2-carbohydrazides

NASA Astrophysics Data System (ADS)

Mangalam, M.; Sebastian Antony Selvan, C.; Sankar, C.

2017-02-01

A new series of N‧-(2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ylidene)pyrazine-2-carbohydrazides (8-14) were synthesized by the corresponding 2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ones (1-7) reaction with pyrazine-2-carbohydrazide. The stereochemistry of the newly synthesized compounds were unambiguously assigned using FT-IR, 1H, 13C, and 2D (COSY, HSQC, HMBC, ROESY) nuclear magnetic resonance (NMR) spectral data. The chemical shifts suggest that all these compounds adopt twin-chair conformation with equatorial orientation of aryl substitutions in solution. Hydrazones were screened for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv and antibacterial activity against a set of pathogenic bacteria. Most of the halogenated compounds showed promising antitubercular and antibacterial activities.

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

PubMed

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Unraveling different chemical fingerprints between a champagne wine and its aerosols.

PubMed

Liger-Belair, Gérard; Cilindre, Clara; Gougeon, Régis D; Lucio, Marianna; Gebefügi, Istvan; Jeandet, Philippe; Schmitt-Kopplin, Philippe

2009-09-29

As champagne or sparkling wine is poured into a glass, the myriad of ascending bubbles collapse and radiate a multitude of tiny droplets above the free surface into the form of very characteristic and refreshing aerosols. Ultrahigh-resolution MS was used as a nontargeted approach to discriminate hundreds of surface active compounds that are preferentially partitioning in champagne aerosols; thus, unraveling different chemical fingerprints between the champagne bulk and its aerosols. Based on accurate exact mass analysis and database search, tens of these compounds overconcentrating in champagne aerosols were unambiguously discriminated and assigned to compounds showing organoleptic interest or being aromas precursors. By drawing a parallel between the fizz of the ocean and the fizz in Champagne wines, our results closely link bursting bubbles and flavor release; thus, supporting the idea that rising and collapsing bubbles act as a continuous paternoster lift for aromas in every glass of champagne.

Towards monitoring the sandflies (Diptera: Psychodidae) of Thailand: DNA barcoding the sandflies of Wihan Cave, Uttaradit.

PubMed

Polseela, Raxsina; Jaturas, Narong; Thanwisai, Aunchalee; Sing, Kong-Wah; Wilson, John-James

2016-09-01

Sandflies vary in their distributions and role in pathogen transmission. Attempts to record distributions of sandflies in Thailand have faced difficulties due to their high abundance and diversity. We aim to provide an insight into the diversity of sandflies in Thailand by (i) conducting a literature review, and (ii) DNA barcoding sandflies collected from Wihan Cave where eight morphologically characterized species were recorded. DNA barcodes generated for 193 sandflies fell into 13 distinct species clusters under four genera (Chinius, Idiophlebotomus, Phlebotomus and Sergentomyia). Five of these species could be assigned Linnaean species names unambiguously and two others corresponded to characterized morphospecies. Two species represented a complex under the name Sergentomyia barraudi while the remaining four had not been recognized before in any form. The resulting species checklist and DNA barcode library contribute to a growing set of records for sandflies which is useful for monitoring and vector control.

Synthesis of highly functionalized macrocycles by the peripheral functionalization of macrocyclic diimines.

PubMed

Sierra, Miguel A; Pellico, Daniel; Gómez-Gallego, Mar; Mancheño, María José; Torres, Rosario

2006-11-10

The easily available macrocyclic diimines 4-7 can be stereoselectively transformed to macrocyclic bis-beta-amino acids 13-17, macrocyclic bisazetidines 18-20, and macrocyclic bisamides 21 and 22 by means of the corresponding bis-beta-lactam scaffolds 8-12. These key intermediates are available through standard Staudinger reaction and obtained as the cis-cis diastereomers, exclusively. An interesting relation between the proximity of the reactive C=N bonds and the selectivity in the formation of the bis-beta-lactams 8-12 is observed. Thus, diimine 4 leads to low selectivities, producing a 1:1 mixture of cis-syn-cis and cis-anti-cis diastereomers, while diimines 5-7 having the diimine sites more separated lead almost exclusively to the cis-anti-cis diastereomers. The stereochemistry of all the products was unambiguously assigned by X-ray diffraction analysis of compounds cis-syn-cis 8 and cis-anti-cis 12-Co2CO6 complex.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts III. 1H, 13C and 15N NMR studies at natural isotope abundance.

PubMed Central

Kozerski, L; Sierzputowska-Gracz, H; Krzyzosiak, W; Bratek-Wiewiórowska, M; Jaskólski, M; Wiewiórowski, M

1984-01-01

The 1H, 13C, 15N NMR spectra of cytidine /Cyd/, ethenocytidine /epsilon Cyd/ and their hydrochlorides /Cyd X HC1/ and /epsilon Cyd X HC1/ have been analysed to compare structural differences observed in solution with those existing in the crystalline state. The effects of ethenobridging and protonation of the hertero-aromatic base on the intramolecular stereochemistry, intermolecular interactions and electronic structure of the whole molecule are discussed on the basis of the NMR studies in DMSO solutions. Particular interest is devoted to the discussion of the conformation of the ribose ring, the presence of the intramolecular C-5'-0...H-6-C hydrogen bond, unambiguous assignment of the site of protonation, the mechanism of the 5C-H deuterium exchange in Cyd X HC1, and the intermolecular interactions in solution. PMID:6701098

Standardized reference ideogram for physical mapping in the saltwater crocodile (Crocodylus porosus).

PubMed

Dalzell, P; Miles, L G; Isberg, S R; Glenn, T C; King, C; Murtagh, V; Moran, C

2009-01-01

Basic cytogenetic data, such as diploid number and general chromosome morphology, are available for many reptilian species. Here we present a detailed cytogenetic examination of the saltwater crocodile (Crocodylus porosus) karyotype, including the creation of the first fully annotated G-band standard ideogram for any crocodilian species. The C. porosus karyotype contains macrochromosomes and has a diploid number of 34. This study presents a detailed description of each chromosome, permitting unambiguous chromosome identification. The fully annotated standardized C. porosus ideogram provides the backbone to a standard nomenclature system which can be used to accurately identify specific band locations. Seven microsatellite containing fosmid clones were fluorescently labeled and used as fluorescent in situ hybridization (FISH) probes for physical localization. Chromosome locations for each of these FISH probes were successfully assigned, demonstrating the utility of the fully annotated ideogram for genome mapping. Copyright 2010 S. Karger AG, Basel.

H2BC: a new technique for NMR analysis of complex carbohydrates.

PubMed

Petersen, Bent O; Vinogradov, Evguenii; Kay, William; Würtz, Peter; Nyberg, Nils T; Duus, Jens Ø; Sørensen, Ole W

2006-03-20

It is demonstrated that the H2BC NMR pulse sequence (J. Am. Chem. Soc.2005, 127, 6154, Magn. Reson. Chem.2005, 43, 971-974) offers unambiguous assignments and significant simplification of NMR spectra of large and complex carbohydrates compared to other techniques for the establishment of correlations over more than one bond. H2BC almost exclusively correlates protons and proton-bearing carbon spins separated by two covalent bonds and is independent of occasionally vanishing (2)J(CH) coupling constants, which alleviates the problem of missing two-bond correlations in HMBC spectra. H2BC also solves the problem of distinguishing two- and three-bond correlations in HSQC-TOCSY or HMBC. It is a further asset of H2BC that the experiment is significantly shorter than HMBC and HSQC-TOCSY, and hence less sensitive to transverse relaxation. The H2BC experiment is demonstrated on an approximately 30-residue oligosaccharide from Francisella victoria.

Unraveling different chemical fingerprints between a champagne wine and its aerosols

PubMed Central

Liger-Belair, Gérard; Cilindre, Clara; Gougeon, Régis D.; Lucio, Marianna; Gebefügi, Istvan; Jeandet, Philippe; Schmitt-Kopplin, Philippe

2009-01-01

As champagne or sparkling wine is poured into a glass, the myriad of ascending bubbles collapse and radiate a multitude of tiny droplets above the free surface into the form of very characteristic and refreshing aerosols. Ultrahigh-resolution MS was used as a nontargeted approach to discriminate hundreds of surface active compounds that are preferentially partitioning in champagne aerosols; thus, unraveling different chemical fingerprints between the champagne bulk and its aerosols. Based on accurate exact mass analysis and database search, tens of these compounds overconcentrating in champagne aerosols were unambiguously discriminated and assigned to compounds showing organoleptic interest or being aromas precursors. By drawing a parallel between the fizz of the ocean and the fizz in Champagne wines, our results closely link bursting bubbles and flavor release; thus, supporting the idea that rising and collapsing bubbles act as a continuous paternoster lift for aromas in every glass of champagne. PMID:19805335

Rotational band on a three-quasineutron isomer in 127Xe

NASA Astrophysics Data System (ADS)

Chakraborty, S.; Sharma, H. P.; Tiwary, S. S.; Majumder, C.; Banerjee, P.; Ganguly, S.; Rai, S.; Pragati, Modi, Swati; Arumugam, P.; Mayank, Kumar, S.; Palit, R.; Kumar, A.; Bhattacharjee, S. S.; Singh, R. P.; Muralithar, S.

2018-05-01

Excited states in 127Xe were populated via 122Sn(9Be,4 n γ ) fusion-evaporation reaction at Ebeam=48 MeV. A rotational band above an isomeric state at 2730.3 keV has been established. Jπ=23 /2+ has been assigned unambiguously to the bandhead. Structural features, configuration, and reduced hindrance factor per degree of K -forbiddenness (fν) have been discussed in the context of neighboring nuclei. Half-lives of 7 /2+ (t1 /2=37 ±1 ns) and 23 /2+ (t1 /2=28 ±1 ns) isomeric states have also been estimated and found to be consistent with the earlier reported values. The experimentally observed energy levels of the rotational band have been reproduced successfully by theoretical calculations carried out using the modified particle rotor model (MPRM) with β2˜0.22 and 15∘≲γ ≲22∘ .

Are the islets of Langerhans neuro-paraneuronal control centers of the exocrine pancreas?

PubMed

Radke, R; Stach, W

1986-10-01

The authors investigate whether the islets of Langerhans can actually be regarded as "neuro-paraneuronal control centers of the exocrine pancreas" as was first suggested by Fujita and Kobayashi (1979). The question is discussed on the basis of the authors' electron microscopic findings regarding pancreatic innervation before and after truncular vagotomy. The results do not seem to support the above hypothesis which advocates that the intrainsular axons are principally engaged in the release of their transmitters into the capillaries in order to regulate, via the insuloacinar portal vessels, the exocrine function of the pancreas. On the contrary, the present data draw attention to the unambiguous assignation of intrainsular axons to endocrine cells, a point of question in line with several findings published in the literature including papers by the first supporters of this hypothesis. No change was observed in the innervation pattern of the effector cells after vagotomy.

A software for managing after-hours activities in research user facilities

DOE PAGES

Camino, F. E.

2017-05-01

Here, we present an afterhours activity management program for shared facilities, which handles the processes required for afterhours access (request, approval, extension, etc.). It implements the concept of permitted afterhours activities, which consists of a list of well-defined activities that each user can perform afterhours. The program provides an easy and unambiguous way for users to know which activities they are allowed to perform afterhours. In addition, the program can enhance its safety efficacy by interacting with lab and instrument access control systems commonly present in user facilities.

Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem.

PubMed

Charleston, M A

1995-01-01

This article introduces a coherent language base for describing and working with characteristics of combinatorial optimization problems, which is at once general enough to be used in all such problems and precise enough to allow subtle concepts in this field to be discussed unambiguously. An example is provided of how this nomenclature is applied to an instance of the phylogeny problem. Also noted is the beneficial effect, on the landscape of the solution space, of transforming the observed data to account for multiple changes of character state.

A software for managing after-hours activities in research user facilities

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

Camino, F. E.

Here, we present an afterhours activity management program for shared facilities, which handles the processes required for afterhours access (request, approval, extension, etc.). It implements the concept of permitted afterhours activities, which consists of a list of well-defined activities that each user can perform afterhours. The program provides an easy and unambiguous way for users to know which activities they are allowed to perform afterhours. In addition, the program can enhance its safety efficacy by interacting with lab and instrument access control systems commonly present in user facilities.

Probing Majorana modes in the tunneling spectra of a resonant level.

PubMed

Korytár, R; Schmitteckert, P

2013-11-27

Unambiguous identification of Majorana physics presents an outstanding problem whose solution could render topological quantum computing feasible. We develop a numerical approach to treat finite-size superconducting chains supporting Majorana modes, which is based on iterative application of a two-site Bogoliubov transformation. We demonstrate the applicability of the method by studying a resonant level attached to the superconductor subject to external perturbations. In the topological phase, we show that the spectrum of a single resonant level allows us to distinguish peaks coming from Majorana physics from the Kondo resonance.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

Real-time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers.

PubMed

Godinho, Raquel; López-Bao, José Vicente; Castro, Diana; Llaneza, Luís; Lopes, Susana; Silva, Pedro; Ferrand, Nuno

2015-03-01

Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations. © 2014 John Wiley & Sons Ltd.

Infrared spectroscopic study of the synthetic Mg-Ni talc series

NASA Astrophysics Data System (ADS)

Blanchard, Marc; Méheut, Merlin; Delon, Louise; Poirier, Mathilde; Micoud, Pierre; Le Roux, Christophe; Martin, François

2018-05-01

Five talc samples [(Mg,Ni)3Si4O10(OH)2] covering the entire Mg-Ni solid solution were synthesized following a recently developed and patented process (Dumas et al., Process for preparing a composition comprising synthetic mineral particles and composition, 2013a; Procédé de préparation d'une composition comprenant des particules minérales synthétiques et composition, 2013b), which produces sub-micron talc particles replying to industrial needs. Near- and mid-infrared spectra were collected and compared to infrared spectra modeled from first-principles calculations based on density functional theory. The good agreement between experimental and theoretical spectra allowed assigning unambiguously all absorption bands. We focused in particular on the four main OH stretching bands, which represent good probes of their local physical and chemical environment. The description of the vibrational modes at the origin of these absorption bands and the theoretical determination of absorption coefficients provide a firm basis for quantifying the talc chemical composition from infrared spectroscopy and for discussing the distribution of divalent cations in the octahedral sheet. Results confirm that these synthetic talc samples have a similar structure as natural talc, with a random distribution of Mg and Ni atoms. They only differ from natural talc by their hydrophilic character, which is due to their large proportion of reactive sites on sheet edges due to sub-micronic size of the particles. Therefore, the contribution on infrared spectra of hydroxyls adsorbed on edge sites has also been investigated by computing the infrared signature of hydroxyls of surface models.

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci.

PubMed

Martín, Virginia; Mediano, Pilar; Del Campo, Rosa; Rodríguez, Juan M; Marín, María

2016-11-01

The genus Streptococcus is 1 of the dominant bacterial groups in human milk, but the taxonomic identification of some species remains difficult. The objective of this study was to investigate the discriminatory ability of different methods to identify streptococcal species in order to perform an assessment of the streptococcal diversity of human milk microbiota as accurately as possible. The identification of 105 streptococcal strains from human milk was performed by 16S rRNA, tuf, and sodA gene sequencing, phylogenetic analysis, and Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry. Streptococcus salivarius, Streptococcus mitis, and Streptococcus parasanguinis were the streptococcal dominant species in the human milk microbiota. Sequencing of housekeeping genes allowed the classification of 96.2% (16S rRNA), 84.8% ( sodA), and 88.6% ( tuf) of the isolates. Phylogenetic analysis showed 3 main streptococcal clusters corresponding with the mitis (73 isolates), salivarius (29), mutans (1)-pyogenic (2) groups, but many of the mitis group isolates (36) could not be assigned to any species. The application of the MALDI-TOF Bruker Biotyper system resulted in the identification of 56 isolates (53.33%) at the species level, but it could not discriminate between S pneumoniae and S mitis isolates, in contrast to the Vitek-MS system. There was a good agreement among the different methods assessed in this study to identify those isolates of the salivarius, mutans, and pyogenic groups, whereas unambiguous discrimination could not be achieved concerning some species of the mitis group ( S mitis, S pneumoniae, S pseudopneumoniae, S oralis).

Slow aging in Secondary Organic Aerosol observed by Liquid Chromatography coupled with High-Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bones, D. L.; Bateman, A. P.; Nguyen, T. B.; Laskin, J.; Laskin, A.; Nizkorodov, S.

2009-12-01

This study investigated long term changes in the chemical composition of model biogenic secondary organic aerosol (SOA) prepared via ozonolysis of the terpene limonene. This SOA has been observed to turn brown when exposed to NH4+. Our hypothesis is that the chromophoric compounds responsible for this color change are suspected to be imidazole-like or pyridinium-like compounds. These compounds are only present in small relative amounts, hence standard mass spectrometry is insufficient to unambiguously detect these compounds. However, a combination of HPLC and high resolution electrospray ionization mass spectrometry allows assignments of chemical formulae to individual peaks. These and other experiments confirm the presence of N-containing compounds in treated SOA. We are in the process of determining the exact identity of these species by MS/MS methods. LC-MS can also provide information about the polarity of the compounds in SOA. Most compounds in limonene-O3 SOA are polar and are detected at short retention times; peaks suggesting trimeric species appear at longer retention times in the case of fresh SOA, but at shorter times with the bulk of the components for aged SOA. Limonene SOA has been shown to be composed of monomers, dimers, trimers and larger oligomers. The appearance of trimers in specific regions of the chromatogram suggests these species are genuine SOA components and not an artifact of electrospray ionization. Changes in biogenic SOA over time are important because of the propensity of SOA to affect direct and indirect radiative forcing.

Generation and Characterization of Six Recombinant Botulinum Neurotoxins as Reference Material to Serve in an International Proficiency Test

PubMed Central

Weisemann, Jasmin; Krez, Nadja; Fiebig, Uwe; Worbs, Sylvia; Skiba, Martin; Endermann, Tanja; Dorner, Martin B.; Bergström, Tomas; Muñoz, Amalia; Zegers, Ingrid; Müller, Christian; Jenkinson, Stephen P.; Avondet, Marc-Andre; Delbrassinne, Laurence; Denayer, Sarah; Zeleny, Reinhard; Schimmel, Heinz; Åstot, Crister; Dorner, Brigitte G.; Rummel, Andreas

2015-01-01

The detection and identification of botulinum neurotoxins (BoNT) is complex due to the existence of seven serotypes, derived mosaic toxins and more than 40 subtypes. Expert laboratories currently use different technical approaches to detect, identify and quantify BoNT, but due to the lack of (certified) reference materials, analytical results can hardly be compared. In this study, the six BoNT/A1–F1 prototypes were successfully produced by recombinant techniques, facilitating handling, as well as improving purity, yield, reproducibility and biosafety. All six BoNTs were quantitatively nicked into active di-chain toxins linked by a disulfide bridge. The materials were thoroughly characterized with respect to purity, identity, protein concentration, catalytic and biological activities. For BoNT/A1, B1 and E1, serotypes pathogenic to humans, the catalytic activity and the precise protein concentration were determined by Endopep-mass spectrometry and validated amino acid analysis, respectively. In addition, BoNT/A1, B1, E1 and F1 were successfully detected by immunological assays, unambiguously identified by mass spectrometric-based methods, and their specific activities were assigned by the mouse LD50 bioassay. The potencies of all six BoNT/A1–F1 were quantified by the ex vivo mouse phrenic nerve hemidiaphragm assay, allowing a direct comparison. In conclusion, highly pure recombinant BoNT reference materials were produced, thoroughly characterized and employed as spiking material in a worldwide BoNT proficiency test organized by the EQuATox consortium. PMID:26703728

A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

NASA Astrophysics Data System (ADS)

Iacobucci, Claudio; Hage, Christoph; Schäfer, Mathias; Sinz, Andrea

2017-10-01

The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. [Figure not available: see fulltext.

77 FR 52705 - Notice of Submission for OMB Review; Federal Student Aid; Federal Perkins Loan Program/NDSL...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... DEPARTMENT OF EDUCATION Notice of Submission for OMB Review; Federal Student Aid; Federal Perkins Loan Program/NDSL Assignment Form SUMMARY: The Federal Perkins Loan Program allows for assignment of... its efforts in recovering an outstanding loan. The Perkins Assignment Form serves as the transmittal...

Teaching Complaint and Adjustment Letters--And Tact (My Favorite Assignment).

ERIC Educational Resources Information Center

Deimling, Paula

1992-01-01

Describes a three-part assignment in which each student writes a complaint letter and an adjustment letter responding to another student's complaint letter. Discusses how the third part of the assignment--journal entries--allows students to formulate their own criteria for excellent letters based upon their reactions to the letters they receive.…

Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.

PubMed

Nakabayashi, Ryo; Sawada, Yuji; Yamada, Yutaka; Suzuki, Makoto; Hirai, Masami Yokota; Sakurai, Tetsuya; Saito, Kazuki

2013-02-05

Phytochemicals containing heteroatoms (N, O, S, and halogens) often have biological activities that are beneficial to humans. Although targeted profiling methods for such phytochemicals are expected to contribute to rapid chemical assignments, thus making phytochemical genomics and crop breeding much more efficient, there are few profiling methods for the metabolites. Here, as an ultrahigh performance approach, we propose a practical profiling method for S-containing metabolites (S-omics) using onions (Allium cepa) as a representative species and (12)C- and (13)C-based mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses by liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FTICR-MS). Use of the ultrahigh quality data from FTICR-MS enabled simplifying the previous methods to determine specific elemental compositions. MS analysis with a resolution of >250,000 full width at half-maximum and a mass accuracy of <1 ppm can distinguish S-containing monoisotopic ions from other ions on the basis of the natural abundance of (32)S and (34)S and the mass differences among the S isotopes. Comprehensive peak picking using the theoretical mass difference (1.99579 Da) between (32)S-containing monoisotopic ions and their (34)S-substituted counterparts led to the assignment of 67 S-containing monoisotopic ions from the (12)C-based MS spectra, which contained 4693 chromatographic ions. The unambiguous elemental composition of 22 ions was identified through comparative analysis of the (12)C- and (13)C-based MS spectra. Finally, of these, six ions were found to be derived from S-alk(en)ylcysteine sulfoxides and glutathione derivatives. This S-atom-driven approach afforded an efficient chemical assignment of S-containing metabolites, suggesting its potential application for screening not only S but also other heteroatom-containing metabolites in MS-based metabolomics.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Direct Observation of Two Proton Radioactivity Using Digital Photography

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

Rykaczewski, Krzysztof Piotr; Pfutzner, M.; Dominik, Wojciech

2007-01-01

Recently the observation of a new type of spontaneous radioactive decay has been claimed in which two protons are simultaneously ejected by an atomic nucleus from the ground state1,2,3. Experimental data obtained for the extremely neutron-deficient nuclei 45Fe and 54Zn, were interpreted as the first evidence of such a decay mode which has been sought since 1960.4 However, the technique applied in those studies allowed only measurements of the decay time and the total energy released. Particles emitted in the decay were not identified and the conclusions had to be supported by theoretical arguments. Here we show for the firstmore » time, directly and unambiguously, that 45Fe indeed disintegrates by two-proton decay. Furthermore, we demonstrate that the decay branch of this isotope leads to various particle emission channels including two-proton and three-proton emission. To achieve this result we have developed a new type of detector V the Optical Time Projection Chamber (OTPC) in which digital photography is applied to nuclear physics for the first time. The detector records images of tracks from charged particles, allowing for their unambiguous identification and the reconstruction of decay events in three dimensions. This new and simple technique provides a powerful method to identify exotic decay channels involving emission of charged particles. It is expected that further studies with the OTPC device will yield important information on nuclei located at and beyond the proton drip-line, thus providing new material for testing and improving models of very unstable atomic nuclei.« less

Gamma-ray follow-up studies on η Carinae

DOE PAGES

Reitberger, K.; Reimer, O.; Reimer, A.; ...

2012-08-01

Observations of high-energy γ-rays recently revealed a persistent source in spatial coincidence with the binary system η Carinae. Since modulation of the observed γ-ray flux on orbital time scales has not been reported so far, an unambiguous identification was hitherto not possible. In particular, the observations made by the Fermi Large Area Telescope (LAT) posed additional questions regarding the actual emission scenario. Analyses show two energetically distinct components in the γ-ray spectrum, which are best described by an exponentially cutoff power-law function (CPL) at energies below 10 GeV and a power-law (PL) component dominant at higher energies. The increased exposuremore » in conjunction with the improved instrumental response functions of the LAT now allow us to perform a more detailed investigation of location, spectral shape, and flux time history of the observed γ-ray emission. Furthermore, we detect a weak but regular flux decrease over time. This can be understood and interpreted in a colliding-wind binary scenario for orbital modulation of the γ-ray emission. We find that the spectral shape of the γ-ray signal agrees with a single emitting particle population in combination with significant absorption by γ-γ pair production. We are able to report on the first unambiguous detection of GeV γ-ray emission from a colliding-wind massive star binary. By studying the correlation of the flux decrease with the orbital separation of the binary components allows us to predict the behaviour up to the next periastron passage in 2014.« less

Immune to Situation: The Self-Serving Bias in Unambiguous Contexts

PubMed Central

Wang, Xiaoyan; Zheng, Li; Li, Lin; Zheng, Yijie; Sun, Peng; Zhou, Fanzhi A.; Guo, Xiuyan

2017-01-01

Traditionally, the self-serving bias has been investigated in ambiguous contexts in which participants work on tasks that measure novel abilities before making attributions without clear criteria for success or failure feedback. Prior studies have confirmed that the self-serving bias is pervasive in the general population, yet it varies significantly across situations involving ambiguous contexts. The present study features an unambiguous context encompassing interpersonal events that involved implicit causality (with the “self” as an actor or recipient), the inherent logic of which indicated attribution criteria. The aim of this study was to explore whether there is a self-serving bias in unambiguous contexts and to examine whether it is as sensitive to situation as it has been shown to be in ambiguous contexts. The results showed that, in an unambiguous context, participants exhibited self-serving bias in relation to attribution associated with negative interpersonal events. Additionally, the self-serving bias was greater in the actor condition relative to the recipient condition (Study 1), and this effect was not affected by the level of self-awareness, which was manipulated by the use or otherwise of a camera during the experiment (Study 2). Our findings provide evidence for the existence of the self-serving bias in unambiguous contexts. Moreover, the self-serving bias was shown to be immune to situation in unambiguous contexts, but it did depend on factors associated with the events per se, such as the actor versus recipient role that the self played in interpersonal events. PMID:28588532

Multilocus sequence typing (MLST) for lineage assignment and high resolution diversity studies in Trypanosoma cruzi.

PubMed

Yeo, Matthew; Mauricio, Isabel L; Messenger, Louisa A; Lewis, Michael D; Llewellyn, Martin S; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernan J; Miles, Michael A

2011-06-01

Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes.

A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.

PubMed

Hendrich, Lars; Morinière, Jérôme; Haszprunar, Gerhard; Hebert, Paul D N; Hausmann, Axel; Köhler, Frank; Balke, Michael

2015-07-01

Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. © 2014 John Wiley & Sons Ltd.

One-pot microwave assisted synthesis under green chemistry conditions, antioxidant screening, and cytotoxicity assessments of benzimidazole Schiff bases and pyrimido[1,2-a]benzimidazol-3(4H)-ones.

PubMed

Neochoritis, Constantinos G; Zarganes-Tzitzikas, Tryfon; Tsoleridis, Constantinos A; Stephanidou-Stephanatou, Julia; Kontogiorgis, Christos A; Hadjipavlou-Litina, Dimitra J; Choli-Papadopoulou, Theodora

2011-01-01

The synthesis of a number of benzimidazole Schiff bases 3 and 3-oxo-pyrimido[1,2-a]benzimidazoles 4 in excellent yields by a one-step sequence from the reaction of 2-aminobenzimidazole under green chemistry conditions is described. Structural assignments of the new compounds as well as complete assignment of (1)H and (13)C NMR signals have been unambiguously achieved based on the analysis of their (1)H and (13)C NMR (1D and 2D), IR, MS and elemental analysis data. To the synthesized Schiff bases the E-configuration was assigned on the basis of comparison of experimental and calculated (DFT) (13)C NMR chemical shifts. Compounds 3 and 4 were evaluated as inhibitors of lipoxygenase (LOX) and of lipid peroxidation (LPO). All the tested derivatives showed inhibition of lipid peroxidation, whereas most of them were found to have higher activation than the reference compound trolox; The Schiff bases 3e, 3h, and 3i, and the pyrimidobenzimidazoles 4a, 4e and 4f were found to be the most potent. The most potent LOX inhibitor within the subset of Schiff bases was found compound 3i, followed by 3f, whereas compounds 4a and 4g were found the most potent of the 3-oxo-pyrimido[1,2-a]benzimidazole group. Moreover, some cytotoxicity assessments were undertaken, whereupon it was found that Schiff base 3i and pyrimidobenzimidazoles 4e and 4f did not exhibit cytotoxicity at similar concentrations resembling thus the inhibitory activity of lipid peroxidation. The most cytotoxic Schiff base and pyrimidobenzimidazole were found to be 3d and 4c, respectively. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

DFT analysis of the structure and IR spectrum of potassium salt of diphenylsulfophthalide - A model compound for polydiphenylenesulfophthalide salts

NASA Astrophysics Data System (ADS)

Shishlov, N. M.; Akhmetzyanov, Sh S.; Khursan, S. L.

2017-02-01

Experimental IR spectra of crystalline dried and non-dried potassium diphenylsulfophthalide (TAC-K) as a model compound for polymeric salts are presented. DFT analysis (B3LYP/6-311G(d,p)) of the structure and IR spectra of a series of compounds similar in structure to TAC-K as well as their dimers indicates that the sulfonate group environment strongly affects the positions of absorption bands (ABs) of vibrations of Ssbnd O bonds and demonstrates that information on the exact structure of ion clusters is needed for reliable and unambiguous assignment of the ABs in experimental IR spectra of real sulfonate ion containing systems to particular vibrational modes. Various ways of metal ion coordination with sulfonate ion, as well as their reflection in IR spectra of model compounds, are considered and discussed. Using TAC-K as an example, the effect of an intramolecular hydrogen bond on the vibrational modes of sulfonate group and hydroxy group is considered. The effect of ion aggregation on the shape of the IR spectrum of TAC-K is analyzed for an energetically favorable dimer of this salt as an example. Based on a combination of calculated, literature and reference data, a number of ABs in the IR spectra of TAC-K have been tentatively assigned. In particular, the bands in the region of 3230-3180 cm-1 have been assigned to ν(Osbnd H); those at 1240-1160 cm-1, to νas(SO3-); the AB at 1080 cm-1, to νs(SO3-); that at 616 cm-1, to δ(oop)s(SO3-); and that at 570 cm-1, to δ(ip)as(SO3-).

Excited states of neutral donor bound excitons in GaN

NASA Astrophysics Data System (ADS)

Callsen, G.; Kure, T.; Wagner, M. R.; Butté, R.; Grandjean, N.

2018-06-01

We investigate the excited states of a neutral donor bound exciton (D0X) in bulk GaN by means of high-resolution, polychromatic photoluminescence excitation (PLE) spectroscopy. The optically most prominent donor in our sample is silicon accompanied by only a minor contribution of oxygen—the key for an unambiguous assignment of excited states. Consequently, we can observe a multitude of Si0X-related excitation channels with linewidths down to 200 μeV. Two groups of excitation channels are identified, belonging either to rotational-vibrational or electronic excited states of the hole in the Si0X complex. Such identification is achieved by modeling the excited states based on the equations of motion for a Kratzer potential, taking into account the particularly large anisotropy of effective hole masses in GaN. Furthermore, several ground- and excited states of the exciton-polaritons and the dominant bound exciton are observed in the photoluminescence (PL) and PLE spectra, facilitating an estimate of the associated complex binding energies. Our data clearly show that great care must be taken if only PL spectra of D0X centers in GaN are analyzed. Every PL feature we observe at higher emission energies with regard to the Si0X ground state corresponds to an excited state. Hence, any unambiguous peak identification renders PLE spectra highly valuable, as important spectral features are obscured in common PL spectra. Here, GaN represents a particular case among the wide-bandgap, wurtzite semiconductors, as comparably low localization energies for common D0X centers are usually paired with large emission linewidths and the prominent optical signature of exciton-polaritons, making the sole analysis of PL spectra a challenging task.

Direct spectroscopic evidence for isolated silanols in SiO x/Al 2O 3 and their formation mechanism

DOE PAGES

Mouat, Aidan R.; Kobayashi, Takeshi; Pruski, Marek; ...

2017-02-27

Here, the preparation and unambiguous characterization of isolated Brønsted-acidic silanol species on silica–alumina catalysts presents a key challenge in the rational design of solid acid catalysts. In this report, atomic layer deposition (ALD) and liquid-phase preparation (chemical liquid deposition, CLD) are used to install the SiO x sites on Al 2O 3 catalysts using the same Si source (tetraethylorthosilicate, TEOS). The ALD-derived and CLD-derived SiO x sites are probed with dynamic nuclear polarization (DNP)-enhanced 29Si– 29Si double-quantum/single-quantum (DQ/SQ) correlation NMR spectroscopy. The investigation reveals conclusively that the SiO x/Al 2O 3 material prepared by ALD and CLD, followed by calcinationmore » under an O 2 stream, contains fully spatially isolated Si species, in contrast with those resulting from the calcination under static air, which is widely accepted as a postgrafting treatment for CLD. Insight into the formation mechanism of these sites is obtained via in situ monitoring of the TEOS + γ-Al 2O 3 reaction in an environmental diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) cell. Upon calcination, the DRIFTS spectra of SiO x/Al 2O 3 reveal a signature unambiguously assignable to isolated Brønsted-acidic silanol species. Surprisingly, the results of this study indicate that the method of preparing SiO x/Al 2O 3 catalysts is less important to the final structure of the silanol sites than the post-treatment conditions. This finding should greatly simplify the methods for synthesizing site-isolated, Brønsted-acidic SiO x/Al 2O 3 catalysts.« less

Reference Manual for the Ada Programming Language

DTIC Science & Technology

1983-01-01

Convercions 4-21 4.7 Qualified Expresclions 4-24 4.8 Allocators 4-24 4.9 Static Expressions and Static Subtypes 4-26 , 4.10 Universal Expressions 4-27 5...record type.•: • 2 Access types allow the construction of linked data structures created by the evaluation of / allocators . They allow several...the following: A * An assignment (In assignment statements and Initializations), an allocator , a membership test, or a short-circuit control form, * A

Test of the X(3872) structure in antiproton-nucleus collisions

NASA Astrophysics Data System (ADS)

Larionov, Alexei; Strikman, Mark; Bleicher, Marcus

2016-05-01

The present day experimental data on the X(3872) decays do not allow us to make clear conclusions about the dominant structure of this state. We discuss here an alternative way to study its structure by means of the two-step D¯* (or D) production in p ¯A reactions. If this process is mediated by X(3872), the characteristic narrow peaks of the D¯* (or D) distributions in the light cone momentum fraction at small transverse momenta will appear. This would unambiguously signal the DD¯* + c.c. molecular composition of the X(3872) state.

Three-dimensional magnetic bubble memory system

NASA Technical Reports Server (NTRS)

Stadler, Henry L. (Inventor); Katti, Romney R. (Inventor); Wu, Jiin-Chuan (Inventor)

1994-01-01

A compact memory uses magnetic bubble technology for providing data storage. A three-dimensional arrangement, in the form of stacks of magnetic bubble layers, is used to achieve high volumetric storage density. Output tracks are used within each layer to allow data to be accessed uniquely and unambiguously. Storage can be achieved using either current access or field access magnetic bubble technology. Optical sensing via the Faraday effect is used to detect data. Optical sensing facilitates the accessing of data from within the three-dimensional package and lends itself to parallel operation for supporting high data rates and vector and parallel processing.

DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds.

PubMed

Banlaki, Zsofia; Cimarelli, Giulia; Viranyi, Zsofia; Kubinyi, Eniko; Sasvari-Szekely, Maria; Ronai, Zsolt

2017-06-01

A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf. Altogether, 79 CpG sites constituting the 65 so-called CpG units located in the promoter regions of genes affecting behavioral and temperamental traits (COMT, HTR1A, MAOA, OXTR, SLC6A4, TPH1, WFS1)-regions putatively targeted during domestication and breed selection. Methylation status of buccal cells was assessed using EpiTYPER technology. Significant inter-population methylation differences were found in 52.3% of all CpG units investigated. DNA methylation profile-based hierarchical cluster analysis indicated an unambiguous segregation of wolf from domestic dog. In addition, one of the three dog breeds (Golden Retriever) investigated also formed a separate, autonomous group. The findings support that population segregation is interrelated with shifts in DNA methylation patterns, at least in putative selection target regions, and also imply that epigenetic profiles could provide a sufficient basis for population assignment of individuals.

Precision spectroscopy of high rotational states in H2 investigated by Doppler-free two-photon laser spectroscopy in the EF 1Σg+-X 1Σg+ system

NASA Astrophysics Data System (ADS)

Dickenson, G. D.; Salumbides, E. J.; Niu, M.; Jungen, Ch.; Ross, S. C.; Ubachs, W.

2012-09-01

Recently a high precision spectroscopic investigation of the EF1Σg+-X1Σg+ system of molecular hydrogen was reported yielding information on QED and relativistic effects in a sequence of rotational quantum states in the X1Σg+ ground state of the H2 molecule [Salumbides , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.043005 107, 043005 (2011)]. The present paper presents a more detailed description of the methods and results. Furthermore, the paper serves as a stepping stone towards a continuation of the previous study by extending the known level structure of the EF1Σg+ state to highly excited rovibrational levels through Doppler-free two-photon spectroscopy. Based on combination differences between vibrational levels in the ground state, and between three rotational branches (O, Q, and S branches) assignments of excited EF1Σg+ levels, involving high vibrational and rotational quantum numbers, can be unambiguously made. For the higher EF1Σg+ levels, where no combination differences are available, calculations were performed using the multichannel quantum defect method, for a broad class of vibrational and rotational levels up to J=19. These predictions were used for assigning high-J EF levels and are found to be accurate within 5 cm-1.

Structural characterization, vibrational study, NLO and DFT calculations of a novel organic sulfate monohydrate templated with (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole

NASA Astrophysics Data System (ADS)

Barhoumi, Abir; Mhiri, Tahar; Dammak, Thameur; Suñol, Joan Josep; Belhouchet, Mohamed

2017-01-01

A single crystal of (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole sulfate monohydrate has been synthesized and grown at room temperature by slow evaporation of aqueous solution. The studied compound crystallizes in the space group P212121 of the orthorhombic system with cell parameters a = 7.0014(12), b = 8.7631(15), c = 19.773(3) Å. We report the molecular structure and the theoretical and experimental vibrational spectra of the synthesized compound. The atomic arrangement, which is an alternation of organic inorganic layers linked together through hydrogen bonds, gives rise to three types of rings formed by the interconnection of organic-inorganic entities. The experimental FT-IR and the Raman spectra the synthesized compound were recorded and analyzed. The peaks assignment has been made unambiguously from the literature. To confirm the assignment, the experimental spectra were compared with theoretical spectra obtained with the Gaussian 98 program by the Density Functional Theory (DFT) method using B3LYP function with the LanL2DZ basis set. Moreover, to study the nonlinear optical (NLO) property of this compound, the hyperpolarizability βtot, the electric dipole μtot and the polarizability αtot were calculated using the DFT. Based on our calculation the synthesized compound has a non-zero hyperpolarizability suggesting that it may be used in some NLO applications.

High-resolution solid-state 13C NMR spectroscopy of the paramagnetic metal-organic frameworks, STAM-1 and HKUST-1.

PubMed

Dawson, Daniel M; Jamieson, Lauren E; Mohideen, M Infas H; McKinlay, Alistair C; Smellie, Iain A; Cadou, Romain; Keddie, Neil S; Morris, Russell E; Ashbrook, Sharon E

2013-01-21

Solid-state (13)C magic-angle spinning (MAS) NMR spectroscopy is used to investigate the structure of the Cu(II)-based metal-organic frameworks (MOFs), HKUST-1 and STAM-1, and the structural changes occurring within these MOFs upon activation (dehydration). NMR spectroscopy is an attractive technique for the investigation of these materials, owing to its high sensitivity to local structure, without any requirement for longer-range order. However, interactions between nuclei and unpaired electrons in paramagnetic systems (e.g., Cu(II)-based MOFs) pose a considerable challenge, not only for spectral acquisition, but also in the assignment and interpretation of the spectral resonances. Here, we exploit the rapid T(1) relaxation of these materials to obtain (13)C NMR spectra using a spin-echo pulse sequence at natural abundance levels, and employ frequency-stepped acquisition to ensure uniform excitation of resonances over a wide frequency range. We then utilise selective (13)C isotopic labelling of the organic linker molecules to enable an unambiguous assignment of NMR spectra of both MOFs for the first time. We show that the monomethylated linker can be recovered from STAM-1 intact, demonstrating not only the interesting use of this MOF as a protecting group, but also the ability (for both STAM-1 and HKUST-1) to recover isotopically-enriched linkers, thereby reducing significantly the overall cost of the approach.

Assigning the low lying vibronic states of CH3O and CD3O

NASA Astrophysics Data System (ADS)

Johnson, Britta A.; Sibert, Edwin L.

2017-05-01

The assignment of lines in vibrational spectra in strongly mixing systems is considered. Several low lying vibrational states of the ground electronic X˜ 2E state of the CH3O and CD3O radicals are assigned. Jahn-Teller, spin-orbit, and Fermi couplings mix the normal mode states. The mixing complicates the assignment of the infrared spectra using a zero-order normal mode representation. Alternative zero-order representations, which include specific Jahn-Teller couplings, are explored. These representations allow for definitive assignments. In many instances it is possible to plot the wavefunctions on which the assignments are based. The plots, which are shown in the adiabatic representation, allow one to visualize the effects of various higher order couplings. The plots also enable one to visualize the conical seam and its effect on the wavefunctions. The first and the second order Jahn-Teller couplings in the rocking motion dominate the spectral features in CH3O, while first order and modulated first order couplings dominate the spectral features in CD3O. The methods described here are general and can be applied to other Jahn-Teller systems.

Assignment of the Internal Vibrational Modes of C70 by Inelastic Neutron Scattering Spectroscopy and Periodic-DFT

PubMed Central

Refson, Keith; Parker, Stewart F

2015-01-01

The fullerene C70 may be considered as the shortest possible nanotube capped by a hemisphere of C60 at each end. Vibrational spectroscopy is a key tool in characterising fullerenes, and C70 has been studied several times and spectral assignments proposed. Unfortunately, many of the modes are either forbidden or have very low infrared or Raman intensity, even if allowed. Inelastic neutron scattering (INS) spectroscopy is not subject to selection rules, and all the modes are allowed. We have obtained a new INS spectrum from a large sample recorded at the highest resolution available. An advantage of INS spectroscopy is that it is straightforward to calculate the spectral intensity from a model. We demonstrate that all previous assignments are incorrect in at least some respects and propose a new assignment based on periodic density functional theory (DFT) that successfully reproduces the INS, infrared, and Raman spectra. PMID:26491642

Vibrational Spectroscopy as a Promising Toolbox for Analyzing Functionalized Ceramic Membranes.

PubMed

Kiefer, Johannes; Bartels, Julia; Kroll, Stephen; Rezwan, Kurosch

2018-01-01

Ceramic materials find use in many fields including the life sciences and environmental engineering. For example, ceramic membranes have shown to be promising filters for water treatment and virus retention. The analysis of such materials, however, remains challenging. In the present study, the potential of three vibrational spectroscopic methods for characterizing functionalized ceramic membranes for water treatment is evaluated. For this purpose, Raman scattering, infrared (IR) absorption, and solvent infrared spectroscopy (SIRS) were employed. The data were analyzed with respect to spectral changes as well as using principal component analysis (PCA). The Raman spectra allow an unambiguous discrimination of the sample types. The IR spectra do not change systematically with functionalization state of the material. Solvent infrared spectroscopy allows a systematic distinction and enables studying the molecular interactions between the membrane surface and the solvent.

Using Ontologies to Formalize Services Specifications in Multi-Agent Systems

NASA Technical Reports Server (NTRS)

Breitman, Karin Koogan; Filho, Aluizio Haendchen; Haeusler, Edward Hermann

2004-01-01

One key issue in multi-agent systems (MAS) is their ability to interact and exchange information autonomously across applications. To secure agent interoperability, designers must rely on a communication protocol that allows software agents to exchange meaningful information. In this paper we propose using ontologies as such communication protocol. Ontologies capture the semantics of the operations and services provided by agents, allowing interoperability and information exchange in a MAS. Ontologies are a formal, machine processable, representation that allows to capture the semantics of a domain and, to derive meaningful information by way of logical inference. In our proposal we use a formal knowledge representation language (OWL) that translates into Description Logics (a subset of first order logic), thus eliminating ambiguities and providing a solid base for machine based inference. The main contribution of this approach is to make the requirements explicit, centralize the specification in a single document (the ontology itself), at the same that it provides a formal, unambiguous representation that can be processed by automated inference machines.

Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase

PubMed Central

Buttet, Géraldine F.; Holliger, Christof

2013-01-01

Reductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present in Sulfurospirillum spp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme of Sulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed. PMID:23995945

Molecular beam electric resonance study of KCN, K 13CN and KC 15N

NASA Astrophysics Data System (ADS)

van Vaals, J. J.; Leo Meerts, W.; Dymanus, A.

1984-08-01

The microwave spectra of the isotopic species K 13CN and KC 15N have been investigated by molecular beam electric resonance spectroscopy, using the seeded beam technique. For both isotopic species about 20 rotational transitions originating in the ground vibrational state were observed in the frequency range 9-38 GHz. The observed transitions were fitted to an asymmetric rotor model to determine the three rotational, as well as the five quartic and three sextic centrifugal distortion constants. The hyperfine spectrum of KCN has been unravelled with the help of microwave-microwave double-resonance techniques. One hundred and forty hyperfine transitions in 11 rotational transitions have been assigned. The hyperfine structures of K 13CN and KC 15N were also studied. For all three isotopic species the quadrupole coupling constants and some spin-rotation coupling constants could be deduced. The rotational constants of the 13C and 15N isotopically substituted species of potassium cyanide, combined with those of the normal isotopic species (determined more accurately in this work), allowed an accurate and unambiguous evaluation of the structure, which was confirmed to be T shaped. Both the effective structure of the ground vibrational state and the substitution structure were evaluated. The results for the effective structural parameters are r CN = 1.169(3) Å, r KC = 2.716(9) Å, and r KN = 2.549(9) Å. The values obtained for the principal hyperfine coupling constant eQqz(N), the angle between the CN axis and zN, and the bond length rCN indicate that in gaseous potassium cyanide the CN group can be considered as an almost unperturbed CN - ion.

High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA.

PubMed

De Barba, M; Miquel, C; Lobréaux, S; Quenette, P Y; Swenson, J E; Taberlet, P

2017-05-01

Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies. © 2016 John Wiley & Sons Ltd.

Tunneling Out of the Darkness: Rescuing Rare Samples and Data from the Geologic Survey of New York City Water Tunnel #3

NASA Astrophysics Data System (ADS)

Block, K. A.; Randel, C.; Ismail, A.; Palumbo, R. V.; Cai, Y.; Carter, M.; Lehnert, K.

2016-12-01

Most geologic samples of New York City (NYC) have been collected during city construction projects. Studies of these samples are essential for our understanding of the local geology as well as the tectonic processes that shaped the entire Appalachian region. Among these is a suite of rare high-grade granulite samples collected during the construction of the Brooklyn-Queens section of NYC Water Tunnel #3 have been resting dormant in the basement of the City College of New York (CCNY), studied by a small group of investigators with institutional knowledge, but largely undiscoverable and inaccessible to the broader scientific community. Data derived from these samples remain in disparate places, at best in analog format in publications or theses or, at worst, in spreadsheets stored on local machines or on old media, such as CDs and even floppy disks. As part of the Interdisciplinary Earth Data Alliance - CCNY joint internship program, 3 undergraduate students inventoried hundreds of samples and archived sample metadata in the System for Earth Sample Registration (SESAR), a sample metadata registry. Upon registration, each sample was assigned an International GeoSample Number (IGSN) ‒ a globally-unique and persistent identifier that allows unambiguous citation of samples and linking of disparate analytical data across the literature. The students also compiled geochemical analyses, thin-section images, and associated analytical metadata for publication in the EarthChem Library, where the dataset will be openly and persistently accessible and citable via a DOI (Digital Object Identifier). Not only did the internship result in the illumination of countless dark samples and data values, but it also provided the students with valuable lessons in responsible sample and data management, training that should serve them well in their future scientific endeavors.

Characterization of Encapsulated and Noncapsulated Haemophilus influenzae and Determination of Phylogenetic Relationships by Multilocus Sequence Typing

PubMed Central

Meats, Emma; Feil, Edward J.; Stringer, Suzanna; Cody, Alison J.; Goldstein, Richard; Kroll, J. Simon; Popovic, Tanja; Spratt, Brian G.

2003-01-01

A multilocus sequence typing (MLST) scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated Haemophilus influenzae isolates. The sequences of internal fragments of seven housekeeping genes were determined for 131 isolates, comprising a diverse set of 104 serotype a, b, c, d, e, and f isolates and 27 noncapsulated isolates. Many of the encapsulated isolates had previously been characterized by multilocus enzyme electrophoresis (MLEE), and the validity of the MLST scheme was established by the very similar clustering of isolates obtained by these methods. Isolates of serotypes c, d, e, and f formed monophyletic groups on a dendrogram constructed from the differences in the allelic profiles of the isolates, whereas there were highly divergent lineages of both serotype a and b isolates. Noncapsulated isolates were distinct from encapsulated isolates and, with one exception, were within two highly divergent clusters. The relationships between the major lineages of encapsulated H. influenzae inferred from MLEE data could not be discerned on a dendrogram constructed from differences in the allelic profiles, but were apparent on a tree reconstructed from the concatenated nucleotide sequences. Recombination has not therefore completely eliminated phylogenetic signal, and in support of this, for encapsulated isolates, there was significant congruence between many of the trees reconstructed from the sequences of the seven individual loci. Congruence was less apparent for noncapsulated isolates, suggesting that the impact of recombination is greater among noncapsulated than encapsulated isolates. The H. influenzae MLST scheme is available at www.mlst.net, it allows any isolate to be compared with those in the MLST database, and (for encapsulated isolates) it assigns isolates to their phylogenetic lineage, via the Internet. PMID:12682154

Preconception Brief: Occupational/Environmental Exposures

PubMed Central

Gehle, Kim

2006-01-01

In the last decade, more than half of U.S. children were born to working mothers and 65% of working men and women were of reproductive age. In 2004 more than 28 million women age 18–44 were employed full time. This implies the need for clinicians to possess an awareness about the impact of work on the health of their patients and their future offspring. Most chemicals in the workplace have not been evaluated for reproductive toxicity, and where exposure limits do exist, they were generally not designed to mitigate reproductive risk. Therefore, many toxicants with unambiguous reproductive and developmental effects are still in regular commercial or therapeutic use and thus present exposure potential to workers. Examples of these include heavy metals, (lead, cadmium), organic solvents (glycol ethers, percholoroethylene), pesticides and herbicides (ethylene dibromide) and sterilants, anesthetic gases and anti-cancer drugs used in healthcare. Surprisingly, many of these reproductive toxicants are well represented in traditional employment sectors of women, such as healthcare and cosmetology. Environmental exposures also figure prominently in evaluating a woman’s health risk and that to a pregnancy. Food and water quality and pesticide and solvent usage are increasingly topics raised by women and men contemplating pregnancy. The microenvironment of a woman, such as her choices of hobbies and leisure time activities also come into play. Caregivers must be aware of their patients’ potential environmental and workplace exposures and weigh any risk of exposure in the context of the time-dependent window of reproductive susceptibility. This will allow informed decision-making about the need for changes in behavior, diet, hobbies or the need for added protections on the job or alternative duty assignment. Examples of such environmental and occupational history elements will be presented together with counseling strategies for the clinician. PMID:16897370

Infrared-Vacuum Ultraviolet Pulsed Field Ionization-Photoelectron Study of C₂H₄ + Using a High-Resolution Infrared Laser

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

Xing, Xi; Reed, Beth; Bahng, Mi-Kyung

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The infrared (IR)-vacuum ultraviolet (VUV)-pulsed field ionization-photoelectron (IR-VUV-PFI-PE) spectrum for C₂H₄(X 1A g, V 11 = 1, N' Ka' Kc'=3₀₃) in the VUV range of 83 000-84 800 cm -1 obtained using a single mode infrared laser revealed 24 rotationally resolved vibrational bands for the ion C₂H₄ +(X 2B 3u) ground state. The frequencies and symmetry of the vibrational bandsmore » thus determined, together with the anharmonic frequency predictions calculated at the CCSD(T)/aug-cc-pVQZ level, have allowed the unambiguous assignment of these vibrational bands. These bands are mostly combination bands. The measured frequencies of these bands yield the fundamental frequencies for V 8 + ) 1103± ( 10 cm -1 and V 10 + ) 813 ( 10 cm -1 of C₂H₄ +(X 2B 3u), which have not been determined previously. The present IR-VUV-PFI-PE study also provides truly rovibrationally selected and resolved state-to-state cross sections for the photoionization transitions C₂H₄(X~ 1A g; V 11, N' Ka' Kc') → C₂H₄ +(X ~ 2B 3u; V i +, N + Ka + Kc +), where N' Ka' Kc' denotes the rotational level of C₂H₄(X ~ 1Ag; V 11), and V i + and N + Ka + Kc + represent the vibrational and rotational states of the cation.« less

The pattern and diagnostic criteria of sensory neuronopathy: a case–control study

PubMed Central

Camdessanché, Jean-Philippe; Jousserand, Guillemette; Ferraud, Karine; Vial, Christophe; Petiot, Philippe; Honnorat, Jérôme

2009-01-01

Acquired sensory neuronopathies encompass a group of paraneoplastic, dysimmune, toxic or idiopathic disorders characterized by degeneration of peripheral sensory neurons in dorsal root ganglia. As dorsal root ganglia cannot easily be explored, the clinical diagnosis of these disorders may be difficult. The question as to whether there exists a common clinical pattern of sensory neuronopathies, allowing the establishment of validated and easy-to-use diagnostic criteria, has not yet been addressed. In this study, logistic regression was used to construct diagnostic criteria on a retrospective study population of 78 patients with sensory neuronopathies and 56 with other sensory neuropathies. For this, sensory neuronopathy was provisionally considered as unambiguous in 44 patients with paraneoplastic disorder or cisplatin treatment and likely in 34 with a dysimmune or idiopathic setting who may theoretically have another form of neuropathy. To test the homogeneity of the sensory neuronopathy population, likely candidates were compared with unambiguous cases and then the whole population was compared with the other sensory neuropathies population. Criteria accuracy was checked on 37 prospective patients referred for diagnosis of sensory neuropathy. In the study population, sensory neuronopathy showed a common clinical and electrophysiological pattern that was independent of the underlying cause, including unusual forms with only patchy sensory loss, mild electrical motor nerve abnormalities and predominant small fibre or isolated lower limb involvement. Logistic regression allowed the construction of a set of criteria that gave fair results with the following combination: ataxia in the lower or upper limbs + asymmetrical distribution + sensory loss not restricted to the lower limbs + at least one sensory action potential absent or three sensory action potentials <30% of the lower limit of normal in the upper limbs + less than two nerves with abnormal motor nerve conduction study in the lower limbs. PMID:19506068

Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru

PubMed Central

Aguilar, César; Wood Jr, Perry L.; Cusi, Juan C.; Guzmán, Alfredo; Huari, Frank; Lundberg, Mikael; Mortensen, Emma; Ramírez, César; Robles, Daniel; Suárez, Juana; Ticona, Andres; Vargas, Víctor J.; Venegas, Pablo J.; Sites Jr, Jack W.

2013-01-01

Abstract Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes) to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided. PMID:24453545

Crystallization of the photosystem II core complex and its chlorophyll binding subunit CP43 from transplastomic plants of Nicotiana tabacum.

PubMed

Piano, Dario; El Alaoui, Sabah; Korza, Henryk J; Filipek, Renata; Sabala, Izabela; Haniewicz, Patrycja; Buechel, Claudia; De Sanctis, Daniele; Bochtler, Matthias

2010-12-01

Photosystem II from transplastomic plants of Nicotiana tabacum with a hexahistidine tag at the N-terminal end of the PsbE subunit (α-chain of the cytochrome b(559)) was purified according to the protocol of Fey et al. (BBA 12:1501-1509, 2008). The protein sample was then subjected to two additional gel filtration runs in order to increase its homogeneity and to standardize the amount of detergent. Large three dimensional crystals of the core complex were obtained. Crystals of one of its chlorophyll binding subunits (CP43) in isolation grew in very similar conditions that differed only in the concentration of the detergent. Diffraction of Photosystem II and CP43 crystals at various synchrotron beamlines was limited to a resolution of 7 and 14 Å, respectively. In both cases the diffraction quality was insufficient for an unambiguous assignment of the crystallographic lattice or space group.

Unambiguous Metabolite Identification in High-Throughput Metabolomics by Hybrid 1H-NMR/ESI-MS1 Approach

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

The invention improves accuracy of metabolite identification by combining direct infusion ESI-MS with one-dimensional 1H-NMR spectroscopy. First, we apply a standard 1H-NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in a metabolomics reference libraries. This generates a list of candidate metabolites. The list contains both false positive and ambiguous identifications. The software tool (the invention) takes the list of candidate metabolites, generated from NMRbased metabolite identification, and then calculates, for each of the candidate metabolites, the monoisotopic mass-tocharge (m/z) ratios for each commonly observedmore » ion, fragment and adduct feature. These are then used to assign m/z ratios in experimental ESI-MS spectra of the same sample. Detection of the signals of a given metabolite in both NMR and MS spectra resolves the ambiguities, and therefore, significantly improves the confidence of the identification.« less

Supercomputer description of human lung morphology for imaging analysis.

PubMed

Martonen, T B; Hwang, D; Guan, X; Fleming, J S

1998-04-01

A supercomputer code that describes the three-dimensional branching structure of the human lung has been developed. The algorithm was written for the Cray C94. In our simulations, the human lung was divided into a matrix containing discrete volumes (voxels) so as to be compatible with analyses of SPECT images. The matrix has 3840 voxels. The matrix can be segmented into transverse, sagittal and coronal layers analogous to human subject examinations. The compositions of individual voxels were identified by the type and respective number of airways present. The code provides a mapping of the spatial positions of the almost 17 million airways in human lungs and unambiguously assigns each airway to a voxel. Thus, the clinician and research scientist in the medical arena have a powerful new tool to be used in imaging analyses. The code was designed to be integrated into diverse applications, including the interpretation of SPECT images, the design of inhalation exposure experiments and the targeted delivery of inhaled pharmacologic drugs.

Enantioselective inhibition of microbial lipolytic enzymes by nonracemic monocyclic enolphosphonate analogues of cyclophostin.

PubMed

Point, Vanessa; Malla, Raj K; Carrière, Frederic; Canaan, Stéphane; Spilling, Christopher D; Cavalier, Jean-François

2013-06-13

Four nonracemic enolphosphonate analogues of Cyclophostin were obtained by asymmetric synthesis, and their absolute configurations at both phosphorus and C-5 carbon chiral centers were unambiguously assigned. The influence of chirality was studied by testing the inhibitory effects of these four stereoisomers toward the lipolytic activity of three microbial lipases: Fusarium solani cutinase, Rv0183, and LipY from Mycobacterium tuberculosis . Cutinase was highly diastereoselective for the (Sp) configuration using (Sc) inhibitors, whereas no obvious stereopreference at phosphorus was observed with (Rc) compounds. Conversely, Rv0183 exhibited strong enantioselective discrimination for (Sp) configuration regardless of the chirality at the asymmetric carbon atom. Lastly, LipY discriminated only the unusual diastereoisomeric configuration (Rc, Rp) leading to the most potent inhibitor. This work, which provides a fundamental premise for the understanding of the stereoselective relationships between nonracemic enolphosphonates and their inhibitory activity, also opens new prospects on the design and synthesis of highly specific enantioselective antimicrobial agents.

Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

PubMed

Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

2014-01-15

Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

Rovibrational bound states of SO2 isotopologues. I: Total angular momentum J = 0-10

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Ellis, Joseph; Poirier, Bill

2015-04-01

Isotopic variation of the rovibrational bound states of SO2 for the four stable sulfur isotopes 32-34,36S is investigated in comprehensive detail. In a two-part series, we compute the low-lying energy levels for all values of total angular momentum in the range J = 0-20. All rovibrational levels are computed, to an extremely high level of numerical convergence. The calculations have been carried out using the ScalIT suite of parallel codes. The present study (Paper I) examines the J = 0-10 rovibrational levels, providing unambiguous symmetry and rovibrational label assignments for each computed state. The calculated vibrational energy levels exhibit very good agreement with previously reported experimental and theoretical data. Rovibrational energy levels, calculated without any Coriolis approximations, are reported here for the first time. Among other potential ramifications, this data will facilitate understanding of the origin of mass-independent fractionation of sulfur isotopes in the Archean rock record-of great relevance for understanding the "oxygen revolution".

Direct determination of phosphate sugars in biological material by (1)H high-resolution magic-angle-spinning NMR spectroscopy.

PubMed

Diserens, Gaëlle; Vermathen, Martina; Gjuroski, Ilche; Eggimann, Sandra; Precht, Christina; Boesch, Chris; Vermathen, Peter

2016-08-01

The study aim was to unambiguously assign nucleotide sugars, mainly UDP-X that are known to be important in glycosylation processes as sugar donors, and glucose-phosphates that are important intermediate metabolites for storage and transfer of energy directly in spectra of intact cells, as well as in skeletal muscle biopsies by (1)H high-resolution magic-angle-spinning (HR-MAS) NMR. The results demonstrate that sugar phosphates can be determined quickly and non-destructively in cells and biopsies by HR-MAS, which may prove valuable considering the importance of phosphate sugars in cell metabolism for nucleic acid synthesis. As proof of principle, an example of phosphate-sugar reaction and degradation kinetics after unfreezing the sample is shown for a cardiac muscle, suggesting the possibility to follow by HR-MAS NMR some metabolic pathways. Graphical abstract Glucose-phosphate sugars (Glc-1P and Glc-6P) detected in muscle by 1H HR-MAS NMR.

Probing the electronic structure of UO+ with high-resolution photoelectron spectroscopy.

PubMed

Goncharov, Vasiliy; Kaledin, Leonid A; Heaven, Michael C

2006-10-07

The pulsed field ionization-zero kinetic energy photoelectron technique has been used to observe the low-lying energy levels of UO+. Rotationally resolved spectra were recorded for the ground state and the first nine electronically excited states. Extensive vibrational progressions were characterized. Omega+ assignments were unambiguously determined from the first rotational lines identified in each vibronic band. Term energies, vibrational frequencies, and anharmonicity constants for low-lying energy levels of UO+ are reported. In addition, accurate values for the ionization energies for UO [48,643.8(2) cm(-1)] and U [49,957.6(2) cm(-1)] were determined. The pattern of low-lying electronic states for UO+ indicates that they originate from the U3+(5f3)O2- configuration, where the uranium ion-centered interactions between the 5f electrons are significantly stronger than interactions with the intramolecular electric field. The latter lifts the degeneracy of U3+ ion-core states, but the atomic angular momentum quantum numbers remain reasonably well defined.

Structural and quantum chemical analysis of exciton coupling in homo- and heteroaggregate stacks of merocyanines

NASA Astrophysics Data System (ADS)

Bialas, David; Zitzler-Kunkel, André; Kirchner, Eva; Schmidt, David; Würthner, Frank

2016-09-01

Exciton coupling is of fundamental importance and determines functional properties of organic dyes in (opto-)electronic and photovoltaic devices. Here we show that strong exciton coupling is not limited to the situation of equal chromophores as often assumed. Quadruple dye stacks were obtained from two bis(merocyanine) dyes with same or different chromophores, respectively, which dimerize in less-polar solvents resulting in the respective homo- and heteroaggregates. The structures of the quadruple dye stacks were assigned by NMR techniques and unambiguously confirmed by single-crystal X-ray analysis. The heteroaggregate stack formed from the bis(merocyanine) bearing two different chromophores exhibits remarkably different ultraviolet/vis absorption bands compared with those of the homoaggregate of the bis(merocyanine) comprising two identical chromophores. Quantum chemical analysis based on an extension of Kasha's exciton theory appropriately describes the absorption properties of both types of stacks revealing strong exciton coupling also between different chromophores within the heteroaggregate.

Millimeter and submillimeter wave spectroscopy of propanal

NASA Astrophysics Data System (ADS)

Zingsheim, Oliver; Müller, Holger S. P.; Lewen, Frank; Jørgensen, Jes K.; Schlemmer, Stephan

2017-12-01

The rotational spectra of the two stable conformers syn- and gauche-propanal (CH3CH2CHO) were studied in the millimeter and submillimeter wave regions from 75 to 500 GHz with the Cologne (Sub-)Millimeter wave Spectrometer. Furthermore, the first excited states associated with the aldehyde torsion and with the methyl torsion, respectively, of the syn-conformer were analyzed. The newly obtained spectroscopic parameters yield better predictions, thus fulfill sensitivity and resolution requirements in new astronomical observations in order to unambiguously assign pure rotational transitions of propanal. This is demonstrated on a radio astronomical spectrum from the Atacama Large Millimeter/submillimeter Array Protostellar Interferometric Line Survey (ALMA-PILS). In particular, an accurate description of observed splittings, caused by internal rotation of the methyl group in the syn-conformer and by tunneling rotation interaction from two stable degenerate gauche-conformers, is reported. The rotational spectrum of propanal is of additional interest because of its two large amplitude motions pertaining to the methyl and the aldehyde group, respectively.

Government Projects and Teaching the Technical Proposal.

ERIC Educational Resources Information Center

Butler, Douglas R.

1987-01-01

Describes a technical proposal writing assignment modeled after the conditions in industry. Provides a paradigm of government project proposals and then outlines the stages of the assignment that allow student to rework and revise, thereby discouraging students from writing formulaic and superficial proposals. (SRT)

42 CFR 432.55 - Reporting training and administrative costs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... training (with no assigned agency duties): Salaries, fringe benefits, dependency allowances, travel, tuition, books, and educational supplies. (2) For part-time training: Travel, per diem, tuition, books and... supporting staff) assigned fulltime training functions: Salaries, fringe benefits, travel, and per diem...

Gamma activity modulated by naming of ambiguous and unambiguous images: intracranial recording

PubMed Central

Cho-Hisamoto, Yoshimi; Kojima, Katsuaki; Brown, Erik C; Matsuzaki, Naoyuki; Asano, Eishi

2014-01-01

OBJECTIVE Humans sometimes need to recognize objects based on vague and ambiguous silhouettes. Recognition of such images may require an intuitive guess. We determined the spatial-temporal characteristics of intracranially-recorded gamma activity (at 50–120 Hz) augmented differentially by naming of ambiguous and unambiguous images. METHODS We studied ten patients who underwent epilepsy surgery. Ambiguous and unambiguous images were presented during extraoperative electrocorticography recording, and patients were instructed to overtly name the object as it is first perceived. RESULTS Both naming tasks were commonly associated with gamma-augmentation sequentially involving the occipital and occipital-temporal regions, bilaterally, within 200 ms after the onset of image presentation. Naming of ambiguous images elicited gamma-augmentation specifically involving portions of the inferior-frontal, orbitofrontal, and inferior-parietal regions at 400 ms and after. Unambiguous images were associated with more intense gamma-augmentation in portions of the occipital and occipital-temporal regions. CONCLUSIONS Frontal-parietal gamma-augmentation specific to ambiguous images may reflect the additional cortical processing involved in exerting intuitive guess. Occipital gamma-augmentation enhanced during naming of unambiguous images can be explained by visual processing of stimuli with richer detail. SIGNIFICANCE Our results support the theoretical model that guessing processes in visual domain occur following the accumulation of sensory evidence resulting from the bottom-up processing in the occipital-temporal visual pathways. PMID:24815577

Discrimination of microbiological samples using femtosecond laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Baudelet, Matthieu; Yu, Jin; Bossu, Myriam; Jovelet, Julien; Wolf, Jean-Pierre; Amodeo, Tanguy; Fréjafon, Emeric; Laloi, Patrick

2006-10-01

Using femtosecond laser-induced breakdown spectroscopy, the authors have analyzed five different species of bacterium. Line emissions from six trace mineral elements, Na, Mg, P, K, Ca, and Fe, have been clearly detected. Their intensities correspond to relative concentrations of these elements contained in the analyzed samples. The authors demonstrate that the concentration profile of trace elements allows unambiguous discrimination of different bacteria. Quantitative differentiation has been made by representing bacteria in a six-dimension hyperspace with each of its axis representing a detected trace element. In such hyperspace, representative points of different species of bacterium are gathered in different and distinct volumes.

Detection of fractional solitons in quantum spin Hall systems

NASA Astrophysics Data System (ADS)

Fleckenstein, C.; Traverso Ziani, N.; Trauzettel, B.

2018-03-01

We propose two experimental setups that allow for the implementation and the detection of fractional solitons of the Goldstone-Wilczek type. The first setup is based on two magnetic barriers at the edge of a quantum spin Hall system for generating the fractional soliton. If then a quantum point contact is created with the other edge, the linear conductance shows evidence of the fractional soliton. The second setup consists of a single magnetic barrier covering both edges and implementing a long quantum point contact. In this case, the fractional soliton can unambiguously be detected as a dip in the conductance without the need to control the magnetization of the barrier.

The conformation of cyclo(-D-Pro-Ala4-) as a model for cyclic pentapeptides of the DL4 type.

PubMed

Heller, Markus; Sukopp, Martin; Tsomaia, Natia; John, Michael; Mierke, Dale F; Reif, Bernd; Kessler, Horst

2006-10-25

The conformation of the cyclic pentapeptide cyclo(-D-Pro-Ala(4)-) in solution and in the solid state was reinvestigated using modern NMR techniques. To allow unequivocal characterization of hydrogen bonds, relaxation behavior, and intramolecular distances, differently labeled isotopomers were synthesized. The NMR results, supported by extensive MD simulations, demonstrate unambiguously that the preferred conformation previously described by us, but recently questioned, is indeed correct. The validation of the conformational preferences of this cyclic peptide is important given that this system is a template for several bioactive compounds and for controlled "spatial screening" for the search of bioactive conformations.

PERMANENT GENETIC RESOURCES: Consensus primers of cyp73 genes discriminate willow species and hybrids (Salix, Salicaceae).

PubMed

Trung, Le Quang; VAN Puyvelde, Karolien; Triest, Ludwig

2008-03-01

Consensus primers, based on exon sequences of the cyp73 gene family coding for cinnamate 4-hydroxylase (C4H) of the lignin biosynthesis pathway, were designed for the tetraploid willow species Salix alba and Salix fragilis. Diagnostic alleles at species level were observed among introns of three cyp73 genes and allowed unambiguous detection of the first generation and introgressed hybrids in populations. Progeny analysis of a female S. alba with a male introgressed hybrid confirmed the codominant inheritance of each intron. Sequences of the diagnostic alleles of both species were similar to those found in the hybrids. © 2007 The Authors.

Quantification of major flavonoids in carnation tissues (Dianthus caryophyllus) as a tool for cultivar discrimination.

PubMed

Galeotti, Francesco; Barile, Elisa; Lanzotti, Virginia; Dolci, Marcello; Curir, Paolo

2008-01-01

One flavone-C-glycoside and two flavonol-O-glycosides were recognized and isolated as the main flavonoidal components in nine different carnation cultivars, and their chemical structures have been determined by spectroscopic methods, including UV detection, MS and NMR. The distribution of these three compounds in flowers, leaves, stems, young sprouts, and roots of each cultivar was evaluated by a simple HPLC-UV method: the graphic representation of their content in the different tissues allows to identify and characterize unambiguously each considered carnation cultivar. The presented method could be an easy, inexpensive and reliable tool for carnation cultivar discrimination.

Fission Fragment Studies by Gamma-Ray Spectrometry with the Mass Separator Lohengrin

NASA Astrophysics Data System (ADS)

Materna, T.; Amouroux, C.; Bail, A.; Bideau, A.; Chabod, S.; Faust, H.; Capellan, N.; Kessedjian, G.; Köster, U.; Letourneau, A.; Litaize, O.; Martin, F.; Mathieu, L.; Méplan, O.; Panebianco, S.; Régis, J.-M.; Rudigier, M.; Sage, C.; Serot, O.; Urban, W.

2014-09-01

A gamma spectrometric technique was implemented at the exit of the fission fragment separator of the ILL. It allows a precise measurement of isotopic yields of most important actinides in the heavy fragment region by an unambiguous identification of the nuclear charge of the fragments selected by the mass spectrometer. The status of the project and last results are reviewed. A spin-off of this activity is the identification of unknown nanosecond isomers in exotic nuclei through the observation of a disturbed ionic charge distribution. This technique has been improved to provide an estimation of the lifetime of the isomeric state.

Gravitational corrections to Higgs potentials

NASA Astrophysics Data System (ADS)

Bounakis, Marios; Moss, Ian G.

2018-04-01

Understanding the Higgs potential at large field values corresponding to scales in the range above 1010GeV is important for questions of vacuum stability, particularly in the early universe where survival of the Higgs vacuum can be an issue. In this paper we show that the Higgs potential can be derived in away which is independent of the choice of conformal frame for the spacetime metric. Questions about vacuum stability can therefore be answered unambiguously. We show that frame independence leads to new relations between the beta functions of the theory and we give improved limits on the allowed values of the Higgs curvature coupling for stability.

The cosmic X-ray experiment aboard HEAO-1

NASA Technical Reports Server (NTRS)

Rothschild, R. E.; Bolt, E.; Holt, S.; Serlemitsos, P. J.; Garmire, G.; Agrawal, P.; Reigler, G.; Bowyer, C. S.; Lampton, M.

1978-01-01

The HEAO-1 A-2 experiment, designed to study the large scale structure of the galaxy and the universe at X-ray energies is described. The instrument consists of six gas proportional counters of three types nominally covering the energy ranges of 0.15-3 keV, 1.2-20 keV, and 2.5-60 keV. The two low energy detectors have about 400 sq cm open area each while the four others have about 800 sq cm each. Dual field of view collimators allow the unambiguous determination of instrument internal background and diffuse X-ray brightness. Instrument characteristics and early performance are discussed.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

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

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-07-02

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including V xO y n– and V xO yCl n– ions (x = 1–14, y = 2–36, n = 1–3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V 14O 36Cl(L) 5 (L = Et 4N +, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged V xO yCl n– and V xOmore » yCl(L) (n–1)– clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller V xO yCl (1–2)– and V xO y (1–2)– anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged V xO yCl and V xO y species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of V xO yCl and V xO y anions through low-energy CID. Finally and furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.« less

Spectroscopic and Magnetic Investigations of Rhenium(i)chlorine(carbon MONOXIDE)(3)(ALPHA, - Complexes and Group (1B, 8B) Bimetallic Complexes.

NASA Astrophysics Data System (ADS)

Striplin, Durwin Ray

Complexes with the generic formula, Re(I)Cl(CO) _3(alpha,alpha-diimine), where alpha,alpha-diimine = 2,2^'-bipyridine, 1,10 -phenanthroline, or methyl-substituted analogs, were subjected to detailed optical investigations in the 77-4 K range, both in rigid glasses and in PMMA plastics. Excitation spectra, absorption spectra, and decay kinetics of the phosphorescing manifolds were complemented by detailed measurements of polarization ratios to arrive at a coherent picture of the emitting manifolds. Symmetry assignments and energy orderings of the ^3MLCT (metal-to-ligand charge transfer) spin sublevels were made. Analogous assignments for the ^3MLCT spin -sublevels of Ru(alpha, alpha -diimine)_3^{2+} and Os(alpha,alpha-diimine) _{3}^{2+} ions are implied by this analysis. Increases in luminescence decay rates and emission intensities with increasing external magnetic field strength were observed at 4 K. The decay rates were found to be non-quadratic with respect to magnetic field strength. A simple parametric model that includes spin-orbit coupling and a magnetic field perturbation was developed to describe the MLCT excited states. The energies, symmetry assignments, and magnetic field mixing of the ^3MLCT states were rationalized by the model. Fluorescence, phosphorescence, and excitation spectra were measured on a series of mu -bridged bis(diphenylphosphinomethane) homo- and heterobimetallic compounds of Rh(I), Ir(I), Pt(II), and Au(I). These results were augmented with polarization ratios obtained at 77 K and detailed studies of the temperature dependence of the phosphorescence in the 77-4 K range. The triplet manifold is split by spin-orbit coupling into a forbidden state lying lowest in energy followed by a quasi-degenerate pair lying a few wavenumbers higher that decays two orders of magnitude faster. A quadratic dependence of the decay rate on magnetic field strength was recorded at 4 K for ail complexes. The results are consistent with a rm d_{sigma*}to p_sigma orbital promotion, and the direction of charge-transfer for heterobimetallic complexes was unambiguously assigned. Electronic structural models based on D_{rm 4h}, D_{rm 2h}, and C _{rm 2v} micro-symmetries about the axial chromophore were employed to make explicit symmetry assignments of the excited states.

5 CFR 591.401 - Purpose and applicability.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Section 591.401 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ALLOWANCES AND DIFFERENTIALS Separate Maintenance Allowance for Duty at Johnston Island § 591.401 Purpose and... States Code, to authorize payment of a separate maintenance allowance to assist an employee assigned to...

Quantum mechanics as classical statistical mechanics with an ontic extension and an epistemic restriction.

PubMed

Budiyono, Agung; Rohrlich, Daniel

2017-11-03

Where does quantum mechanics part ways with classical mechanics? How does quantum randomness differ fundamentally from classical randomness? We cannot fully explain how the theories differ until we can derive them within a single axiomatic framework, allowing an unambiguous account of how one theory is the limit of the other. Here we derive non-relativistic quantum mechanics and classical statistical mechanics within a common framework. The common axioms include conservation of average energy and conservation of probability current. But two axioms distinguish quantum mechanics from classical statistical mechanics: an "ontic extension" defines a nonseparable (global) random variable that generates physical correlations, and an "epistemic restriction" constrains allowed phase space distributions. The ontic extension and epistemic restriction, with strength on the order of Planck's constant, imply quantum entanglement and uncertainty relations. This framework suggests that the wave function is epistemic, yet it does not provide an ontic dynamics for individual systems.

[Thin filament elasticity and its role in the muscle contraction].

PubMed

Skubiszak, L

2006-01-01

The available experimental methods do not allow one to establish unambiguously the molecular structural events during muscle contraction. To resolve the existing controversies, I have devised an unconventional original computer program. The new approach allows the reconstruction of the hexagonal lattice of the sarcomere for different muscle states and verification of the structure by comparison of the calculated Fourier spectra with the real diffraction patterns. Previously, by the use of this approach, the real structure of a myosin filament from vertebrate striated muscle has been reconstructed (http://zope.ibib.waw.pl/pspk). In this work, a reconstruction for the thin filament is presented for three states: relaxed, after activation, and during contraction. Good consistency of the calculated Fourier spectra with the real diffraction patterns available in the literature suggests that the thin filament, due to flexibility, plays an active part in muscle contraction, as myosin cross-bridges do.

High capacity low delay packet broadcasting multiaccess schemes for satellite repeater systems

NASA Astrophysics Data System (ADS)

Bose, S. K.

1980-12-01

Demand assigned packet radio schemes using satellite repeaters can achieve high capacities but often exhibit relatively large delays under low traffic conditions when compared to random access. Several schemes which improve delay performance at low traffic but which have high capacity are presented and analyzed. These schemes allow random acess attempts by users, who are waiting for channel assignments. The performance of these are considered in the context of a multiple point communication system carrying fixed length messages between geographically distributed (ground) user terminals which are linked via a satellite repeater. Channel assignments are done following a BCC queueing discipline by a (ground) central controller on the basis of requests correctly received over a collision type access channel. In TBACR Scheme A, some of the forward message channels are set aside for random access transmissions; the rest are used in a demand assigned mode. Schemes B and C operate all their forward message channels in a demand assignment mode but, by means of appropriate algorithms for trailer channel selection, allow random access attempts on unassigned channels. The latter scheme also introduces framing and slotting of the time axis to implement a more efficient algorithm for trailer channel selection than the former.

Designing Effective Classroom Assignments: Intellectual Work Worth Sharing

ERIC Educational Resources Information Center

Hutchings, Pat; Jankowski, Natasha A.; Schultz, Kathryn E.

2016-01-01

The National Institute for Learning Outcomes Assessment's (NILOA's) online library of faculty-created assignments that both produce and demonstrate learning makes pedagogical work visible and available for colleagues to learn from, build on, and reward. This online library allows faculty to collaborate in sharing, critiquing, and improving…

Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ(2) conformation by intra-residue NOEs.

PubMed

Miyanoiri, Yohei; Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

2011-12-01

Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U-(13)C,(15)N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the (13)C-(13)C and (13)C-(1)H spin coupling networks (Kainosho et al. in Nature 440:52-57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3-(2)H(2); δ1,ε3,η2-(13)C(3); ε1-(15)N]-indole ring ([(12)C (γ,) ( 12) C(ε2)] SAIL-Trp), which provides a more robust way to correlate the (1)H(β), (1)H(α), and (1)H(N) to the (1)H(δ1) and (1)H(ε3) through the intra-residue NOEs. The assignment of the (1)H(δ1)/(13)C(δ1) and (1)H(ε3)/(13)C(ε3) signals can thus be transferred to the (1)H(ε1)/(15)N(ε1) and (1)H(η2)/(13)C(η2) signals, as with the previous type of SAIL-Trp, which has an extra (13)C at the C(γ) of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was (1)H(β2) in this experiment, one can determine the side-chain conformation of the Trp residue including the χ(2) angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [(12)C(γ),(12)C(ε2)] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

Pf1 bacteriophage hydration by magic angle spinning solid-state NMR

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

Sergeyev, Ivan V.; Bahri, Salima; McDermott, Ann E., E-mail: aem5@columbia.edu

2014-12-14

High resolution two- and three-dimensional heteronuclear correlation spectroscopy ({sup 1}H–{sup 13}C, {sup 1}H–{sup 15}N, and {sup 1}H–{sup 13}C–{sup 13}C HETCOR) has provided a detailed characterization of the internal and external hydration water of the Pf1 virion. This long and slender virion (2000 nm × 7 nm) contains highly stretched DNA within a capsid of small protein subunits, each only 46 amino acid residues. HETCOR cross-peaks have been unambiguously assigned to 25 amino acids, including most external residues 1–21 as well as residues 39–40 and 43–46 deep inside the virion. In addition, the deoxyribose rings of the DNA near the virionmore » axis are in contact with water. The sets of cross-peaks to the DNA and to all 25 amino acid residues were from the same hydration water {sup 1}H resonance; some of the assigned residues do not have exchangeable side-chain protons. A mapping of the contacts onto structural models indicates the presence of water “tunnels” through a highly hydrophobic region of the capsid. The present results significantly extend and modify results from a lower resolution study, and yield a comprehensive hydration surface map of Pf1. In addition, the internal water could be distinguished from external hydration water by means of paramagnetic relaxation enhancement. The internal water population may serve as a conveniently localized magnetization reservoir for structural studies.« less

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

NASA Astrophysics Data System (ADS)

Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

The lowest ionization potentials of Al2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Barnes, Leslie A.; Taylor, Peter R.

1988-01-01

Potential curves for the lowest two electronic states (X 2 sigma g + and A 2 pi u) of Al2(+) were computed using complete active space SCF/multireference CI wave functions and large Gaussian basis sets. The lowest observable vertical ionization potential (to Al2(+) X 2 sigma g +) of the Al2 X 3 pi u ground state is calculated to occur around 6.1 eV, in excellent agreement with the experimental range of 6.0 to 6.42 eV obtained in recent cluster ionization studies by Cox and co-workers. The second vertical ionization potential (to Al2(+) A 2 pi u) occurs near 6.4 eV, also within the experimental range. The adiabatic IP of 5.90 eV is in good agreement with the value of 5.8 to 6.1 eV deduced by Hanley and co-workers from the difference in thresholds between collision induced dissociation processes of Al3(+). The computed IP values are somewhat larger than those deduced from branching ratios in cluster fragmentation experiments by Jarrold and co-workers. The observation of an ionization threshold below 6.42 eV is shown to be incompatible with an Al2 ground electronic state assignment of 3 sigma g -, but the separation between the two lowest states of Al2 is so small that it is likely that both are populated in the experiments, so that this does not provide unambiguous support for the recent theoretical assignment of the ground state as 3 pi u.

Automated glycopeptide analysis—review of current state and future directions

PubMed Central

Dallas, David C.; Martin, William F.; Hua, Serenus

2013-01-01

Glycosylation of proteins is involved in immune defense, cell–cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins—glycoproteomics—remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software—advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available. PMID:22843980

In silico identification of functional regions in proteins.

PubMed

Nimrod, Guy; Glaser, Fabian; Steinberg, David; Ben-Tal, Nir; Pupko, Tal

2005-06-01

In silico prediction of functional regions on protein surfaces, i.e. sites of interaction with DNA, ligands, substrates and other proteins, is of utmost importance in various applications in the emerging fields of proteomics and structural genomics. When a sufficient number of homologs is found, powerful prediction schemes can be based on the observation that evolutionarily conserved regions are often functionally important, typically, only the principal functionally important region of the protein is detected, while secondary functional regions with weaker conservation signals are overlooked. Moreover, it is challenging to unambiguously identify the boundaries of the functional regions. We present a new methodology, called PatchFinder, that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1) Assignment of conservation scores to each amino acid position on the protein surface. (2) Assignment of a score to each putative patch, based on its likelihood to be functionally important. The patch of maximum likelihood is considered to be the main functionally important region, and the search is continued for non-overlapping patches of secondary importance. We examined the accuracy of the method using the IGPS enzyme, the SH2 domain and a benchmark set of 112 proteins. These examples demonstrated that PatchFinder is capable of identifying both the main and secondary functional patches. The PatchFinder program is available at: http://ashtoret.tau.ac.il/~nimrodg/

Spectroscopy of Ncncs at the Canadian Light Source: the Far-Infrared Spectrum of the ν_7 Region from 60-140 wn

NASA Astrophysics Data System (ADS)

Tokaryk, Dennis; Ross, Stephen Cary; Winnewisser, Brenda P.; Winnewisser, Manfred; De Lucia, Frank C.; Billinghurst, Brant E.

2014-06-01

We report on the analysis of our spectrum from 60-140 wn of the ν_7 bending fundamental and associated hot band sequence of NCNCS, obtained on the far-infrared beamline at the Canadian Light Source synchrotron. The data were collected in May 2013, building upon what we learned conducting experiments in May 2011 and 2012 on this molecule. Calculations indicated that the ν_7 system was very weak (one of the four weakest fundamental bands, all of comparable strength), but its spectrum became evident when 30 mTorr of NCNCS was admitted into the 2-m-long sample cell, through which the synchrotron beam passed 40 times. The best spectrum so far has been obtained with 121 mTorr of gas. Loomis-Wood plots reveal many branches, some of which were unambiguously assignable to Δ ν_7 = +1 subbands for ν_7" = 0, 1, 2, 3 and for K_a = 0, 1,2 with Δ K_a = 0 (a-type subbands) by comparison of lower-state combination differences with those obtained from the published pure-rotational data. We will continue the analysis by assigning as many a-type subbands as possible and by searching for b-type subbands with Δ K_a = ± 1 so that the connections between K_a-stacks can be measured. Finally, we will simultaneously fit the infrared and rotational data with a generalized semi-rigid bender Hamiltonian.

Do the Wrong Thing: How Toddlers Tell a Joke from a Mistake

ERIC Educational Resources Information Center

Hoicka, Elena; Gattis, Merideth

2008-01-01

We investigated whether 19-36-month-olds (1) differentiate mistakes from jokes, and (2) understand humorous intentions. The experimenter demonstrated unambiguous jokes accompanied by laughter, unambiguous mistakes accompanied by the experimenter saying, "Woops!", and ambiguous actions that could either be a mistake or a joke, accompanied by either…

Using a Course Management System to Improve Classroom Communication

ERIC Educational Resources Information Center

Perkins, Matthew; Pfaffman, Jay

2006-01-01

Course management systems (CMSs) enable teachers to easily post assignments, lesson plans, announcements, and course documents. They also allow students to participate in online discussions and chats and turn in assignments online. Unfortunately, commercial systems are often expensive to purchase and maintain, removing them from the reach of many…

28 CFR 545.23 - Inmate work/program assignment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Inmate work/program assignment. 545.23... involvement is mandated by Bureau policy or statute (for example, the Literacy Program). Where such participation is not required by either policy or statute, exception may be made to allow an inmate to...

75 FR 9797 - Policies To Promote Rural Radio Service and To Streamline Allotment and Assignment Procedures

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... Media Bureau and the Wireless Telecommunications Bureau (collectively, the ``Bureaus'') delegated... relationship with the federal government as domestic dependent nations with inherent sovereign powers over... suggested by commenters. First, the Commission will allow assignments or transfers within the four-year...

18 CFR 301.7 - Average System Cost methodology functionalization.

Code of Federal Regulations, 2010 CFR

2010-04-01

... SYSTEM COST METHODOLOGY FOR SALES FROM UTILITIES TO BONNEVILLE POWER ADMINISTRATION UNDER NORTHWEST POWER... functionalization under its Direct Analysis assigns costs, revenues, debits or credits based upon the actual and/or...) Functionalization methods. (1) Direct analysis, if allowed or required by Table 1, assigns costs, revenues, debits...

BrainLiner: A Neuroinformatics Platform for Sharing Time-Aligned Brain-Behavior Data

PubMed Central

Takemiya, Makoto; Majima, Kei; Tsukamoto, Mitsuaki; Kamitani, Yukiyasu

2016-01-01

Data-driven neuroscience aims to find statistical relationships between brain activity and task behavior from large-scale datasets. To facilitate high-throughput data processing and modeling, we created BrainLiner as a web platform for sharing time-aligned, brain-behavior data. Using an HDF5-based data format, BrainLiner treats brain activity and data related to behavior with the same salience, aligning both behavioral and brain activity data on a common time axis. This facilitates learning the relationship between behavior and brain activity. Using a common data file format also simplifies data processing and analyses. Properties describing data are unambiguously defined using a schema, allowing machine-readable definition of data. The BrainLiner platform allows users to upload and download data, as well as to explore and search for data from the web platform. A WebGL-based data explorer can visualize highly detailed neurophysiological data from within the web browser, and a data-driven search feature allows users to search for similar time windows of data. This increases transparency, and allows for visual inspection of neural coding. BrainLiner thus provides an essential set of tools for data sharing and data-driven modeling. PMID:26858636

Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach.

PubMed

Marco-Ruiz, Luis; Pedrinaci, Carlos; Maldonado, J A; Panziera, Luca; Chen, Rong; Bellika, J Gustav

2016-08-01

The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data. They aim to provide semantic descriptions over SOA implementations to overcome the limitations derived from the syntactic nature of Web services technologies. To facilitate the publication, discovery and interoperability of CDS services by evolving them into Linked Services that expose their interfaces as Linked Data. We developed methods and models to enhance CDS SOA as Linked Services that define a rich semantic layer based on machine interpretable ontologies that powers their interoperability and reuse. These ontologies provided unambiguous descriptions of CDS services properties to expose them to the Web of Data. We developed models compliant with Linked Data principles to create a semantic representation of the components that compose CDS services. To evaluate our approach we implemented a set of CDS Linked Services using a Web service definition ontology. The definitions of Web services were linked to the models developed in order to attach unambiguous semantics to the service components. All models were bound to SNOMED-CT and public ontologies (e.g. Dublin Core) in order to count on a lingua franca to explore them. Discovery and analysis of CDS services based on machine interpretable models was performed reasoning over the ontologies built. Linked Services can be used effectively to expose CDS services to the Web of Data by building on current CDS standards. This allows building shared Linked Knowledge Bases to provide machine interpretable semantics to the CDS service description alleviating the challenges on interoperability and reuse. Linked Services allow for building 'digital libraries' of distributed CDS services that can be hosted and maintained in different organizations. Copyright © 2016 Elsevier Inc. All rights reserved.

5 CFR 591.402 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... receiving a similar allowance. Johnston Island, also called Johnston Atoll, is a possession of the United... Separate Maintenance Allowance for Duty at Johnston Island § 591.402 Definitions. Adult, a term used in the... allowance to assist an employee assigned to Johnston Island who is compelled by reason of dangerous, notably...

5 CFR 591.402 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... receiving a similar allowance. Johnston Island, also called Johnston Atoll, is a possession of the United... Separate Maintenance Allowance for Duty at Johnston Island § 591.402 Definitions. Adult, a term used in the... allowance to assist an employee assigned to Johnston Island who is compelled by reason of dangerous, notably...

Colliders as a simultaneous probe of supersymmetric dark matter and Terascale cosmology

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

Barenboim, Gabriela; /Valencia U.; Lykken, Joseph D.

2006-08-01

Terascale supersymmetry has the potential to provide a natural explanation of the dominant dark matter component of the standard {Lambda}CDM cosmology. However once we impose the constraints on minimal supersymmetry parameters from current particle physics data, a satisfactory dark matter abundance is no longer prima facie natural. This Neutralino Tuning Problem could be a hint of nonstandard cosmology during and/or after the Terascale era. To quantify this possibility, we introduce an alternative cosmological benchmark based upon a simple model of quintessential inflation. This benchmark has no free parameters, so for a given supersymmetry model it allows an unambiguous prediction ofmore » the dark matter relic density. As a example, we scan over the parameter space of the CMSSM, comparing the neutralino relic density predictions with the bounds from WMAP. We find that the WMAP-allowed regions of the CMSSM are an order of magnitude larger if we use the alternative cosmological benchmark, as opposed to {Lambda}CDM. Initial results from the CERN Large Hadron Collider will distinguish between the two allowed regions.« less

Colliders as a simultaneous probe of supersymmetric dark matter and Terascale cosmology

NASA Astrophysics Data System (ADS)

Barenboim, Gabriela; Lykken, Joseph D.

2006-12-01

Terascale supersymmetry has the potential to provide a natural explanation of the dominant dark matter component of the standard ΛCDM cosmology. However once we impose the constraints on minimal supersymmetry parameters from current particle physics data, a satisfactory dark matter abundance is no longer prima facie natural. This Neutralino Tuning Problem could be a hint of nonstandard cosmology during and/or after the Terascale era. To quantify this possibility, we introduce an alternative cosmological benchmark based upon a simple model of quintessential inflation. This benchmark has no free parameters, so for a given supersymmetry model it allows an unambiguous prediction of the dark matter relic density. As a example, we scan over the parameter space of the CMSSM, comparing the neutralino relic density predictions with the bounds from WMAP. We find that the WMAP allowed regions of the CMSSM are an order of magnitude larger if we use the alternative cosmological benchmark, as opposed to ΛCDM. Initial results from the CERN Large Hadron Collider will distinguish between the two allowed regions.

Children's Trait and Emotion Attributions in Socially Ambiguous and Unambiguous Situations

ERIC Educational Resources Information Center

Boseovski, Janet J.; Lapan, Candace; Bosacki, Sandra

2013-01-01

Children's attributions about story characters in ambiguous and unambiguous social situations were assessed. One hundred and forty-four 6-7-year-olds and 10-11-year-olds heard about actors who slighted a recipient intentionally or for an undetermined reason and then made causal attributions about the events, an emotion attribution about the…

Optimum measurement for unambiguously discriminating two mixed states: General considerations and special cases

NASA Astrophysics Data System (ADS)

Herzog, Ulrike; Bergou, János A.

2006-04-01

Based on our previous publication [U. Herzog and J. A. Bergou, Phys. Rev. A 71, 050301(R)(2005)] we investigate the optimum measurement for the unambiguous discrimination of two mixed quantum states that occur with given prior probabilities. Unambiguous discrimination of nonorthogonal states is possible in a probabilistic way, at the expense of a nonzero probability of inconclusive results, where the measurement fails. Along with a discussion of the general problem, we give an example illustrating our method of solution. We also provide general inequalities for the minimum achievable failure probability and discuss in more detail the necessary conditions that must be fulfilled when its absolute lower bound, proportional to the fidelity of the states, can be reached.

Don’t Get Me Wrong: ERP Evidence from Cueing Communicative Intentions

PubMed Central

Regel, Stefanie; Gunter, Thomas C.

2017-01-01

How to make sure that one’s utterances are understood as intended when not facing each other? In order to convey communicative intentions, in digital communication emoticons and pragmatic cues are frequently used. Such cueing becomes even more crucial for implied interpretations (e.g., irony) that cannot be understood literally, but require extra information. Sentences, such as ‘That’s fantastic,’ may achieve either a literal or ironic meaning depending on the contextual constraints. In two experiments using event-related brain potentials (ERPs), we examined the effects of cueing communicative intentions (i.e., by means of quotation marks) on ironic and literal language comprehension. An impact of cueing on language processing was seen as early as 200 ms post-stimulus onset by the emergence of a P300 preceding a sustained positivity for cued irony relative to literal language, while for uncued irony a P200-P600 pattern was obtained. In presence of additional information for ironic intentions, pragmatic reanalysis allowing inferences on the message level may have occured immediately. Moreover, by examining the way of cueing (i.e., ambiguous vs. unambiguous cueing) this type of information for communicative intentions appeared to be only effective when the cues were unambiguous by matching pragmatic conventions. The findings suggest that cueing communicative intentions may immediately affect language comprehension, albeit depending on pragmatic conventions of the cues’ usage. PMID:28955258

Top-down and bottom-up characterization of nitrated birch pollen allergen Bet v 1a with CZE hyphenated to an Orbitrap mass spectrometer.

PubMed

Gusenkov, Sergey; Stutz, Hanno

2018-02-01

Tyrosine (Tyr) residues of the major pollen allergen of birch Betula verrucosa, Bet v 1a, were nitrated by peroxynitrite. This modification enhances the allergenicity. Modified tyrosines were identified by analyzing intact allergen variants in combination with top-down and bottom-up approaches. Therefore, a laboratory-built sheath-liquid assisted ESI interface was applied for hyphenation of CE to an Orbitrap mass spectrometer to localize individual nitration sites. The major focus was on identification of primary nitration sites. The top-down approach unambiguously identified Tyr 5 as the most prominent modification site. Fragments from the allergen core and the C-terminal part carried up to three potential nitration sites, respectively. Thus, a bottom-up approach with tryptic digest was used as a complementary strategy which allowed for the unambiguous localization of nitration sites within the respective peptides. Nitration propensity for individual Tyr residues was addressed by comparison of MS signals of nitrated peptides relative to all cognates of homolog primary sequence. Combined data identified surface exposed Tyr 5 and Tyr 66 as major nitration sites followed by less accessible Tyr 158 whereas Tyr 81, 83 and 150 possess a lower nitration tendency and are apparently modified in variants with higher nitration levels. © 2018 The Authors. Electrophoresis published by Wiley-VCH Verlag GmbH & Co. KGaA.

The "COLD-PCR approach" for early and cost-effective detection of tyrosine kinase inhibitor resistance mutations in EGFR-positive non-small cell lung cancer.

PubMed

Mairinger, Fabian D; Vollbrecht, Claudia; Streubel, Anna; Roth, Andreas; Landt, Olfert; Walter, Henry F R; Kollmeier, Jens; Mairinger, Thomas

2014-01-01

Activating epidermal growth factor receptor (EGFR) gene mutations can be successfully treated by EGFR tyrosine kinase inhibitors (EGFR-TKIs), but nearly 50% of all patients' exhibit progression of the disease until treatment because of T790M mutations. It is proposed that this is mostly caused by therapy-resistant tumor clones harboring a T790M mutation. Until now no cost-effective routine-diagnostic method for EGFR-resistance mutation status analysis is available leaving long-time response to TKI treatment to chance. Unambiguous identification of T790M EGFR mutations is mandatory to optimize initial treatment strategies. Artificial EGFR T790M mutations and human wild-type gDNA were prepared in several dilution series. Preferential amplification using coamplification at lower denaturation temperature-PCR (COLD-PCR) of the mutant sequence and subsequent HybProbe melting curve detection or pyrosequencing were performed in comparison to normal processing. COLD-PCR-based amplification allowed the detection of 0.125% T790M mutant DNA in a background of wild-type DNA in comparison to 5% while normal processing. These results were reproducible. COLD-PCR is a powerful and cost-effective tool for routine diagnostic to detect underrepresented tumor clones in clinical samples. A diagnostic tool for unambiguous identification of T790M-mutated minor tumor clones is now available enabling optimized therapy.

76 FR 71888 - Federal Travel Regulation (FTR); Storage of a Privately Owned Vehicle When Assigned a Temporary...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-21

...This final rule amends the Federal Travel Regulation (FTR), and allows agencies to establish internal policy and procedures for storage of a privately owned vehicle (POV) when an employee is assigned a temporary change of station (TCS) in support of a contingency operation.

"I'm Not so Sure…": Teacher Educator Action Research into Uncertainty

ERIC Educational Resources Information Center

Rogers, Carrie

2016-01-01

Using a framework of uncertainty that is informed by Hannah Arendt's philosophy this four-semester action research project describes the creation and analysis of an assignment that allows teacher candidates to explore their own uncertainties in regards to the teaching profession. This action research project examines the assignment and its…

77 FR 38784 - Notice of Proposed Information Collection Requests; Federal Student Aid; Federal Perkins Loan...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-29

...; Federal Perkins Loan Program/NDSL Assignment Form SUMMARY: The Federal Perkins Loan Program allows for... exhausted all of its efforts in recovering an outstanding loan. The Perkins Assignment Form serves as the... to this notice will be considered public records. Title of Collection: Federal Perkins Loan Program...

[Work and health status of workers of shoe manufacturing industries].

PubMed

Mironov, A I; Kirillov, V F; Bul'bulian, M A; Golubeva, A P; Kraeva, G K; Kuznetsova, A I; Nikolaeva, G M

2001-01-01

According to work conditions, severity and intensity, the main shoe-making occupations are assigned to III class of I-II jeopardy grade. If new technology applied, the work is assigned to I-II jeopardy class, being optimal--allowable. Increased mortality with liver cancer and lympholeucosis was revealed among workers contacting chloroprene.

"Yes, a T-Shirt!": Assessing Visual Composition in the "Writing" Class

ERIC Educational Resources Information Center

Odell, Lee; Katz, Susan M.

2009-01-01

Computer technology is expanding our profession's conception of composing, allowing visual information to play a substantial role in an increasing variety of composition assignments. This expansion, however, creates a major problem: How does one assess student work on these assignments? Current work in assessment provides only partial answers to…

Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

PubMed

Sborgi, Lorenzo; Verma, Abhinav; Muñoz, Victor; de Alba, Eva

2011-01-01

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

Two simple models of classical heat pumps.

PubMed

Marathe, Rahul; Jayannavar, A M; Dhar, Abhishek

2007-03-01

Motivated by recent studies of models of particle and heat quantum pumps, we study similar simple classical models and examine the possibility of heat pumping. Unlike many of the usual ratchet models of molecular engines, the models we study do not have particle transport. We consider a two-spin system and a coupled oscillator system which exchange heat with multiple heat reservoirs and which are acted upon by periodic forces. The simplicity of our models allows accurate numerical and exact solutions and unambiguous interpretation of results. We demonstrate that while both our models seem to be built on similar principles, one is able to function as a heat pump (or engine) while the other is not.

Theoretical study of the hyperfine parameters of OH

NASA Technical Reports Server (NTRS)

Chong, Delano P.; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

1991-01-01

In the present study of the hyperfine parameters of O-17H as a function of the one- and n-particle spaces, all of the parameters except oxygen's spin density, b sub F(O), are sufficiently easily tractable to allow concentration on the computational requirements for accurate determination of b sub F(O). Full configuration-interaction (FCI) calculations in six Gaussian basis sets yield unambiguous results for (1) the effect of uncontracting the O s and p basis sets; (2) that of adding diffuse s and p functions; and (3) that of adding polarization functions to O. The size-extensive modified coupled-pair functional method yields b sub F values which are in fair agreement with FCI results.

Antigravity and the big crunch/big bang transition

NASA Astrophysics Data System (ADS)

Bars, Itzhak; Chen, Shih-Hung; Steinhardt, Paul J.; Turok, Neil

2012-08-01

We point out a new phenomenon which seems to be generic in 4d effective theories of scalar fields coupled to Einstein gravity, when applied to cosmology. A lift of such theories to a Weyl-invariant extension allows one to define classical evolution through cosmological singularities unambiguously, and hence construct geodesically complete background spacetimes. An attractor mechanism ensures that, at the level of the effective theory, generic solutions undergo a big crunch/big bang transition by contracting to zero size, passing through a brief antigravity phase, shrinking to zero size again, and re-emerging into an expanding normal gravity phase. The result may be useful for the construction of complete bouncing cosmologies like the cyclic model.

An MBE growth facility for real-time in situ synchrotron x-ray topography studies of strained-layer III-V epitaxial materials

NASA Astrophysics Data System (ADS)

Whitehouse, C. R.; Barnett, S. J.; Soley, D. E. J.; Quarrell, J.; Aldridge, S. J.; Cullis, A. G.; Emeny, M. T.; Johnson, A. D.; Clarke, G. F.; Lamb, W.; Tanner, B. K.; Cottrell, S.; Lunn, B.; Hogg, C.; Hagston, W.

1992-01-01

This paper describes a unique combined UHV MBE growth x-ray topography facility designed to allow the first real-time synchrotron radiation x-ray topography study of strained-layer III-V growth processes. This system will enable unambiguous determination of dislocation nucleation and multiplication processes as a function of controlled variations in growth conditions, and also during post-growth thermal processing. The planned experiments have placed very stringent demands upon the engineering design of the system, and design details regarding the growth chamber; sample manipulator, x-ray optics, and real-time imaging systems are described. Results obtained during a feasibility study are also presented.

An MBE growth facility for real-time in situ synchrotron x-ray topography studies of strained-layer III--V epitaxial materials

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

Whitehouse, C.R.; Barnett, S.J.; Soley, D.E.J.

1992-01-01

This paper describes a unique combined UHV MBE growth x-ray topography facility designed to allow the first real-time synchrotron radiation x-ray topography study of strained-layer III--V growth processes. This system will enable unambiguous determination of dislocation nucleation and multiplication processes as a function of controlled variations in growth conditions, and also during post-growth thermal processing. The planned experiments have placed very stringent demands upon the engineering design of the system, and design details regarding the growth chamber; sample manipulator, x-ray optics, and real-time imaging systems are described. Results obtained during a feasibility study are also presented.

Subparsec-scale structure and evolution of Centaurus A (NGC5128).

PubMed Central

Jauncey, D L; Tingay, S J; Preston, R A; Reynolds, J E; Lovell, J E; McCulloch, P M; Tzioumis, A K; Costa, M E; Murphy, D W; Meier, D L; Jones, D L; Amy, S W; Biggs, J D; Blair, D G; Clay, R W; Edwards, P G; Ellingsen, S P; Ferris, R H; Gough, R G; Harbison, P; Jones, P A; King, E A; Kemball, A J; Migenes, V; Nicolson, G D; Sinclair, M W; Van Ommen, T; Wark, R M; White, G L

1995-01-01

We present a series of 8.4-GHz very-long-baseline radio interferometry images of the nucleus of Centaurus A (NGC5128) made with a Southern Hemisphere array, representing a 3.3-year monitoring effort. The nuclear radio jet is approximately 50 milliarcseconds in extent, or at the 3.5-megaparsec distance of NGC5128, approximately 1 parsec in length. Subluminal motion is seen and structural changes are observed on time scales shorter than 4 months. High-resolution observations at 4.8 and 8.4 GHz made in November 1992 reveal a complex morphology and allow us to unambiguously identify the self-absorbed core located at the southwestern end of the jet. PMID:11607599

Subparsec-scale structure and evolution of Centaurus A (NGC5128).

PubMed

Jauncey, D L; Tingay, S J; Preston, R A; Reynolds, J E; Lovell, J E; McCulloch, P M; Tzioumis, A K; Costa, M E; Murphy, D W; Meier, D L; Jones, D L; Amy, S W; Biggs, J D; Blair, D G; Clay, R W; Edwards, P G; Ellingsen, S P; Ferris, R H; Gough, R G; Harbison, P; Jones, P A; King, E A; Kemball, A J; Migenes, V; Nicolson, G D; Sinclair, M W; Van Ommen, T; Wark, R M; White, G L

1995-12-05

We present a series of 8.4-GHz very-long-baseline radio interferometry images of the nucleus of Centaurus A (NGC5128) made with a Southern Hemisphere array, representing a 3.3-year monitoring effort. The nuclear radio jet is approximately 50 milliarcseconds in extent, or at the 3.5-megaparsec distance of NGC5128, approximately 1 parsec in length. Subluminal motion is seen and structural changes are observed on time scales shorter than 4 months. High-resolution observations at 4.8 and 8.4 GHz made in November 1992 reveal a complex morphology and allow us to unambiguously identify the self-absorbed core located at the southwestern end of the jet.

MultiLaue: A Technique to Extract d-spacings from Laue XRD

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

Gainsforth, Zack; Marcus, Matthew A.; Tamura, Nobumichi

We present that broad spectrum X-ray Diffraction (XRD) is named Laue after Max von Laue, and is the original XRD technique. Today, monochromatic XRD is more common because Bragg's equation allows determination of d-spacings where Laue does not. Laue still remains in use for single crystal systems because it can be used to make very accurate unit cell determinations as well as for strain and orientation mapping. Lastly, a Laue technique which could provide unambiguous determination of lattice spacings, a la Bragg's equation would be a huge leap forward, especially for multiphase samples such as meteorites, interplanetary dust particles andmore » some geological specimens.« less

Detection of hexamethonium-perchlorate association complexes using NACE-MS.

PubMed

Groom, Carl A; Hawari, Jalal

2007-02-01

Perchlorate (ClO(4) (+)) and other chlorine oxide anions were observed to complex weakly with hexamethonium (1,6-bis-(trimethylammonium)-hexane) in both aqueous and polar nonaqueous solvents. The resultant positively charged complexes were resolved by NACE using 2-propanol/acetone electrolytes prior to mass spectrometric detection using an Agilent(3D)CE system coupled to a Bruker Esquire 3000+ quadrupole IT mass detector. Using electrokinetic injection, the method detection limit for perchlorate in nonaqueous media was 10 microg/L. The isotope patterns due to the presence of (35)Cl and (37)Cl in complex mass spectra allowed for unambiguous identification of perchlorate, chlorate (ClO(3) (+)), chlorite (ClO(2) (+)), and chloride (Cl(+)) in photoreaction samples.

Synthesis of syn-4,6-dimethyldodecanal, the male sex pheromone and trail-following pheromone of two species of the termite Zootermopsis.

PubMed

Ghostin, J; Bordereau, C; Braekman, J C

2011-03-01

Recently, we reported that syn-4,6-dimethyldodecanal is the male sex pheromone and the trail-following pheromone of the Termopsidae Zootermopsis nevadensis and Zootermopsis angusticollis. In this article, we describe the syntheses of the mixture of the four stereoisomers of 4,6-dimethyldodecanal using a synthetic pathway where the key step is a Wittig reaction between methyl 4-methyl-5-oxo-pentanoate and 1-methylheptyl-triphenylphosphonium iodide, and of (±)-syn-4,6-dimethyldodecanal starting from 3,5-dimethyl-2-cyclohexen-1-one. Direct GC-MS comparison of these synthetic samples with the natural pheromone allowed its unambiguous identification.

MultiLaue: A Technique to Extract d-spacings from Laue XRD

DOE PAGES

Gainsforth, Zack; Marcus, Matthew A.; Tamura, Nobumichi; ...

2016-07-25

We present that broad spectrum X-ray Diffraction (XRD) is named Laue after Max von Laue, and is the original XRD technique. Today, monochromatic XRD is more common because Bragg's equation allows determination of d-spacings where Laue does not. Laue still remains in use for single crystal systems because it can be used to make very accurate unit cell determinations as well as for strain and orientation mapping. Lastly, a Laue technique which could provide unambiguous determination of lattice spacings, a la Bragg's equation would be a huge leap forward, especially for multiphase samples such as meteorites, interplanetary dust particles andmore » some geological specimens.« less

Sampling Versus Filtering in Large-Eddy Simulations

NASA Technical Reports Server (NTRS)

Debliquy, O.; Knaepen, B.; Carati, D.; Wray, A. A.

2004-01-01

A LES formalism in which the filter operator is replaced by a sampling operator is proposed. The unknown quantities that appear in the LES equations originate only from inadequate resolution (Discretization errors). The resulting viewpoint seems to make a link between finite difference approaches and finite element methods. Sampling operators are shown to commute with nonlinearities and to be purely projective. Moreover, their use allows an unambiguous definition of the LES numerical grid. The price to pay is that sampling never commutes with spatial derivatives and the commutation errors must be modeled. It is shown that models for the discretization errors may be treated using the dynamic procedure. Preliminary results, using the Smagorinsky model, are very encouraging.

Strong electron-hole exchange in coherently coupled quantum dots.

PubMed

Fält, Stefan; Atatüre, Mete; Türeci, Hakan E; Zhao, Yong; Badolato, Antonio; Imamoglu, Atac

2008-03-14

We have investigated few-body states in vertically stacked quantum dots. Because of a small interdot tunneling rate, the coupling in our system is in a previously unexplored regime where electron-hole exchange plays a prominent role. By tuning the gate bias, we are able to turn this coupling off and study a complementary regime where total electron spin is a good quantum number. The use of differential transmission allows us to obtain unambiguous signatures of the interplay between electron and hole-spin interactions. Small tunnel coupling also enables us to demonstrate all-optical charge sensing, where a conditional exciton energy shift in one dot identifies the charging state of the coupled partner.

Artificially Expanded Genetic Information Systems for New Aptamer Technologies.

PubMed

Biondi, Elisa; Benner, Steven A

2018-05-09

Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”.

A High Throughput Single Nucleotide Polymorphism Multiplex Assay for Parentage Assignment in New Zealand Sheep

PubMed Central

Clarke, Shannon M.; Henry, Hannah M.; Dodds, Ken G.; Jowett, Timothy W. D.; Manley, Tim R.; Anderson, Rayna M.; McEwan, John C.

2014-01-01

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development- firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 “parentage SNP panel” was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test’s suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry. PMID:24740141

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

PubMed

Clarke, Shannon M; Henry, Hannah M; Dodds, Ken G; Jowett, Timothy W D; Manley, Tim R; Anderson, Rayna M; McEwan, John C

2014-01-01

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

Reachability in K 3,3-Free Graphs and K 5-Free Graphs Is in Unambiguous Log-Space

NASA Astrophysics Data System (ADS)

Thierauf, Thomas; Wagner, Fabian

We show that the reachability problem for directed graphs that are either K 3,3-free or K 5-free is in unambiguous log-space, UL ∩ coUL. This significantly extends the result of Bourke, Tewari, and Vinodchandran that the reachability problem for directed planar graphs is in UL ∩ coUL.

Interferometer for the measurement of plasma density

DOEpatents

Jacobson, Abram R.

1980-01-01

An interferometer which combines the advantages of a coupled cavity interferometer requiring alignment of only one light beam, and a quadrature interferometer which has the ability to track multi-fringe phase excursions unambiguously. The device utilizes a Bragg cell for generating a signal which is electronically analyzed to unambiguously determine phase modulation which is proportional to the path integral of the plasma density.

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

Houtz, Robert, L.

This project focused on a molecular and biochemical characterization of the protein methyltransferases responsible for methylation of the LS and SS in Rubisco, and the associated functional consequences accompanying these modifications. Our results provided some of the most informative structural and mechanistic understandings of SET domain protein methyltransferases. These results also positioned us to provide the first unambiguous assignment of the kinetic reaction mechanism for SET-domain protein methyltransferases, and to design and engineer an alternative substrate for Rubisco LSMT, enabling substrate specificity and functional significance studies. We demonstrated that the minimal substrate recognized by Rubisco LSMT is free lysine asmore » well as monomethyllysine, an observation corroborated both by structural analyses as well as enzymatic activity and subsequent product distribution analyses. Ternary complexes between Rubisco LSMT and free lysine compared to complexes with monomethyllysine demonstrated that the structural basis for multiple methyl group additions is a consequence of hydrogen-bond driven spatial shifts in the amino group of Lys-14, which maintains the direct in-line geometry necessary for SN2 nucleophilic attack. The structural observations are also consistent with the previous proposal that the multiplicity of methyl group additions takes place through a processive mechanism, with successive methyl group additions to an enzyme protein complex which does not disassociate prior to the formation of trimethyllysine. This mechanism has important implications, since the regulation of gene expression by SET domain histone methyltransferases is not only dependent on site-specific lysine methylation, but also the degree of methylation. We examined the kinetic reaction mechanism for three different types of SET domain protein methyltransferases, each under conditions supporting mono-, di-, or trimethyllysine formation corroborated by product analyses. Additionally, the tight initial binding of Rubisco LSMT to Rubisco also allowed us to design a novel immobilized complex between Rubisco and Rubisco LSMT, which allowed for an unambiguous demonstration of the requirement for trimethyllysine formation prior to disassociation of the Rubisco LSMT:Rubisco complex, and therefore proof of the processive mechanism for methyl group transfer. These kinetic studies also demonstrated that an important factor has been overlooked in all kinetic analyses of SET domain protein methyltransferases reported to date. This factor is the influence of the low turnover number for SET domain protein methyltransferases and how, relative to the time-frame of kinetic enzyme assays, this can generate changes in kinetic profiles shifting reciprocal plot patterns from random/ordered bi-bi to the real kinetic reaction mechanism plots of ping-pong. Although the ternary complexes of Rubisco LSMT with S-Adenosylhomocysteine and lysine and monomethyllysine were informative in regard to reaction mechanism, they were not helpful in identifying the mechanism used by Rubisco LSMT for determining substrate specificity. We were unsuccessful at obtaining ternary complexes of Rubisco LSMT with bound synthetic polypeptide substrates, as has been reported for several histone methyltransferases. However, we were able to model a polypeptide sequence corresponding to the N-terminal region of the LS of Rubisco into the apparent substrate binding cleft in Rubisco LSMT. Knowledge of the determinants of polypeptide substrate specificity are important for identifying possible alternate substrates, as well as the possibility of generating more desirable substrates amenable to site-directed mutagenesis experiments unlike Rubisco. We determined that Rubisco LSMT is capable of methylating synthetic polypeptide mimics of the N-terminal region of the LS, both free as well as conjugated to keyhole limpet hemacyanin, but with considerable less efficiency than intact holoenzyme.« less

The Empathy Project: Using a Project-Based Learning Assignment to Increase First-Year College Students' Comfort with Interdisciplinarity

ERIC Educational Resources Information Center

Hutchison, Micol

2016-01-01

Empathy and interdisciplinarity are both concepts that are current and relevant--across professions, in research, and in academia. This paper describes a large, interdisciplinary, project-based assignment, the Empathy Project, which allows students to delve into and increase comfort and skill with interdisciplinary thinking and collaborative…

41 CFR 302-9.143 - When I am authorized to transport a POV, may I have the manufacturer or the manufacturer's agent...

Code of Federal Regulations, 2011 CFR

2011-07-01

... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... Transportation Pov Transportation at Time of Assignment § 302-9.143 When I am authorized to transport a POV, may... post of duty. POV Transportation Subsequent to the Time of Assignment ...

41 CFR 302-9.143 - When I am authorized to transport a POV, may I have the manufacturer or the manufacturer's agent...

Code of Federal Regulations, 2010 CFR

2010-07-01

... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... Transportation Pov Transportation at Time of Assignment § 302-9.143 When I am authorized to transport a POV, may... post of duty. POV Transportation Subsequent to the Time of Assignment ...

A Creative Approach to the Research Paper: Combining Creative Writing with Academic Research

ERIC Educational Resources Information Center

Blue, Tim

2006-01-01

This article describes a combination of a research essay and a creative writing assignment that encourages rigorous academic research while allowing students to get "outside the box" of traditional academic research papers. This assignment has five steps. The first two steps offer the chance to introduce academic research along with summary and…

Identifying and Remediating Student Misconceptions in Introductory Biology via Writing-to-Learn Assignments and Peer Review

ERIC Educational Resources Information Center

Halim, Audrey S.; Finkenstaedt-Quinn, Solaire A.; Olsen, Laura J.; Gere, Anne Ruggles; Shultz, Ginger V.

2018-01-01

Student misconceptions are an obstacle in science, technology, engineering, and mathematics courses and unless remediated may continue causing difficulties in learning as students advance in their studies. Writing-to-learn assignments (WTL) are characterized by their ability to promote in-depth conceptual learning by allowing students to explore…

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.

PubMed

O'Dell, William B; Bodenheimer, Annette M; Meilleur, Flora

2016-07-15

Neutron protein crystallography is a powerful tool for investigating protein chemistry because it directly locates hydrogen atom positions in a protein structure. The visibility of hydrogen and deuterium atoms arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction at resolutions typical of protein crystals. Neutrons have the additional benefit to structural biology of not inducing radiation damage in protein crystals. The same crystal could be measured multiple times for parametric studies. Here, we review the basic principles of neutron protein crystallography. The information that can be gained from a neutron structure is presented in balance with practical considerations. Methods to produce isotopically-substituted proteins and to grow large crystals are provided in the context of neutron structures reported in the literature. Available instruments for data collection and software for data processing and structure refinement are described along with technique-specific strategies including joint X-ray/neutron structure refinement. Examples are given to illustrate, ultimately, the unique scientific value of neutron protein crystal structures. Copyright © 2015 Elsevier Inc. All rights reserved.

Nematicity in FeSe single crystals probed by pump-probe spectroscopy

NASA Astrophysics Data System (ADS)

Luo, C. W.; Cheng, P. C.; Wu, K. H.; Juang, J. Y.; Wang, S.-H.; Chiang, J.-C.; Lin, J.-Y.; Chareev, D. A.; Volkova, O. S.; Vasiliev, A. N.

The anisotropic quasiparticle dynamics in FeSe single crystals have been studied by polarized pump-probe spectroscopy. Two distinguishable relaxation components were unambiguously observed in transient reflectivity changes (ΔR / R) . The orientation-dependent fast component with the timescale of 0.1-1.5 ps associated with the electronic structure clearly shows two-fold symmetry, which further reveals the gap opening along ky below the temperature of structure phase transition (Ts) and the electronic nematicity can persist up to 200 K. For the slow component with the timescale of 8-25 ps, it is assigned to the energy relaxation through spin sub-system and also shows a two-fold symmetry below Ts. However, this two-fold symmetry is dramatically weakened above Ts and surprisingly persists up to at least 200 K. Consequently, the high-temperature nematic fluctuations in FeSe may be driven by the order parameters which associated with both charge (orbital) and spin sub-systems. This project is financially sponsored by the MOST, Taiwan, (Grants No. 103-2923-M-009-001-MY3) and the MOE-ATU plan at NCTU.

Peniciadametizine A, a Dithiodiketopiperazine with a Unique Spiro[furan-2,7'-pyrazino[1,2-b][1,2]oxazine] Skeleton, and a Related Analogue, Peniciadametizine B, from the Marine Sponge-Derived Fungus Penicillium adametzioides.

PubMed

Liu, Yang; Mándi, Attila; Li, Xiao-Ming; Meng, Ling-Hong; Kurtán, Tibor; Wang, Bin-Gui

2015-06-05

Peniciadametizine A (1); a new dithiodiketopiperazine derivative possessing a unique spiro[furan-2,7'-pyrazino[1,2-b][1,2]oxazine] skeleton, together with a highly oxygenated new analogue, peniciadametizine B (2); as well as two known compounds, brasiliamide A (3); and viridicatumtoxin (4), were isolated and identified from Penicillium adametzioides AS-53, a fungus obtained from an unidentified marine sponge. The unambiguous assignment of the relative and absolute configuration for the spiro center C-2 of compound 1 was solved by the combination of NMR and ECD measurements with Density-Functional Theory (DFT) conformational analysis and Time-Dependent Density-Functional Theory-Electronic Circular Dichroism (TDDFT-ECD) calculations. The spiro[furan-2,7'-pyrazino[1,2-b][1,2]oxazine] skeleton of 1 has not been reported yet among natural products and the biosynthetic pathway for 1 and 2 was discussed. Compounds 1 and 2 showed inhibitory activity against the pathogenic fungus Alternaria brassicae.

Validity, Reliability, and the Questionable Role of Psychometrics in Plastic Surgery

PubMed Central

2014-01-01

Summary: This report examines the meaning of validity and reliability and the role of psychometrics in plastic surgery. Study titles increasingly include the word “valid” to support the authors’ claims. Studies by other investigators may be labeled “not validated.” Validity simply refers to the ability of a device to measure what it intends to measure. Validity is not an intrinsic test property. It is a relative term most credibly assigned by the independent user. Similarly, the word “reliable” is subject to interpretation. In psychometrics, its meaning is synonymous with “reproducible.” The definitions of valid and reliable are analogous to accuracy and precision. Reliability (both the reliability of the data and the consistency of measurements) is a prerequisite for validity. Outcome measures in plastic surgery are intended to be surveys, not tests. The role of psychometric modeling in plastic surgery is unclear, and this discipline introduces difficult jargon that can discourage investigators. Standard statistical tests suffice. The unambiguous term “reproducible” is preferred when discussing data consistency. Study design and methodology are essential considerations when assessing a study’s validity. PMID:25289354

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

PubMed Central

Hare, Patrick M.; Middleton, Chris T.; Mertel, Kristin I.

2008-01-01

Vibrational spectra of the lowest energy triplet states of thymine and its 2’-deoxyribonucleoside, thymidine, are reported for the first time. Time-resolved infrared (TRIR) difference spectra were recorded over seven decades of time from 300 fs – 3 µs using femtosecond and nanosecond pump-probe techniques. The carbonyl stretch bands in the triplet state are seen at 1603 and ~1700 cm−1 in room-temperature acetonitrile-d3 solution. These bands and additional ones observed between 1300 and 1450 cm−1 are quenched by dissolved oxygen on a nanosecond time scale. Density-functional calculations accurately predict the difference spectrum between triplet and singlet IR absorption cross sections, confirming the peak assignments and elucidating the nature of the vibrational modes. In the triplet state, the C4=O carbonyl exhibits substantial single-bond character, explaining the large (~70 cm−1) red shift in this vibration, relative to the singlet ground state. Femtosecond TRIR measurements unambiguously demonstrate that the triplet state is fully formed within the first 10 ps after excitation, ruling out a relaxed 1nπ* state as the triplet precursor. PMID:19936322

Peak picking NMR spectral data using non-negative matrix factorization.

PubMed

Tikole, Suhas; Jaravine, Victor; Rogov, Vladimir; Dötsch, Volker; Güntert, Peter

2014-02-11

Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap.

Chirality recognition in the glycidol···propylene oxide complex: a rotational spectroscopic study.

PubMed

Thomas, Javix; Sunahori, Fumie X; Borho, Nicole; Xu, Yunjie

2011-04-11

Chirality recognition in the hydrogen-bonded glycidol···propylene oxide complex has been studied by using rotational spectroscopy and ab initio calculations. An extensive conformational search has been performed for this binary adduct at the MP2/6-311++G(d,p) level of theory and a total of 28 homo- and heterochiral conformers were identified. The eight binary conformers, built of the two dominant glycidol monomeric conformers, g-G+ and g+G-, were predicted to be the most stable ones. Jet-cooled rotational spectra of six out of the eight conformers were observed and unambiguously assigned for the first time. The experimental stability ordering has been obtained and compared with the ab initio predictions. The relative stability of the two dominant glycidol monomeric conformers is reversed in some cases when binding to propylene oxide. The contributions of monomeric energy, deformation energy, and binary intermolecular interaction energy to the relative stability of the binary conformers are discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and tunneling dynamics in a model system of peptide co-solvents: rotational spectroscopy of the 2,2,2-trifluoroethanol⋯water complex.

PubMed

Thomas, Javix; Xu, Yunjie

2014-06-21

The hydrogen-bonding topology and tunneling dynamics of the binary adduct, 2,2,2-trifluoroethanol (TFE)⋯water, were investigated using chirped pulse and cavity based Fourier transform microwave spectroscopy with the aid of high level ab initio calculations. Rotational spectra of the most stable binary TFE⋯water conformer and five of its deuterium isotopologues were assigned. A strong preference for the insertion binding topology where water is inserted into the existing intramolecular hydrogen-bonded ring of TFE was observed. Tunneling splittings were detected in all of the measured rotational transitions of TFE⋯water. Based on the relative intensity of the two tunneling components and additional isotopic data, the splitting can be unambiguously attributed to the tunneling motion of the water subunit, i.e., the interchange of the bonded and nonbonded hydrogen atoms of water. The absence of any other splitting in the rotational transitions of all isotopologues observed indicates that the tunneling between g+ and g- TFE is quenched in the TFE⋯H2O complex.

Density functional theory and chromium: Insights from the dimers

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

Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael

2015-03-28

The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences betweenmore » functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.« less

On the formation of niacin (vitamin B3) and pyridine carboxylic acids in interstellar model ices

NASA Astrophysics Data System (ADS)

McMurtry, Brandon M.; Turner, Andrew M.; Saito, Sean E. J.; Kaiser, Ralf I.

2016-06-01

The formation of pyridine carboxylic acids in interstellar ice grains was simulated by electron exposures of binary pyridine (C5H5N)-carbon dioxide (CO2) ice mixtures at 10 K under contamination-free ultrahigh vacuum conditions. Chemical processing of the pristine ice and subsequent warm-up phase was monitored on line and in situ via Fourier transform infrared spectroscopy to probe for the formation of new radiation induced species. In the infrared spectra of the irradiated ice, bands assigned to nicotinic acid (niacin; vitamin B3; m-C5H4NCOOH) along with 2,3-, 2,5-, 3,4-, and 3,5-pyridine dicarboxylic acid (C5H3N(COOH)2) were unambiguously identified along with the hydroxycarbonyl (HOCO) radical. Our study suggests that the reactive pathway responsible for pyridine carboxylic acids formation involves a HOCO intermediate, which forms through the reaction of suprathermal hydrogen ejected from pyridine with carbon dioxide. The newly formed pyridinyl radical may then undergo radical-radical recombination with a hydroxycarbonyl radical to form a pyridine carboxylic acid.

Rovibronically Selected and Resolved Laser Photoionization and Photoelectron Studies of Transition Metal Carbides, Nitrides, and Oxides.

NASA Astrophysics Data System (ADS)

Luo, Zhihong; Chang, Yih-Chung; Huang, Huang; Ng, Cheuk-Yiu

2014-06-01

Transition metal (M) carbides, nitrides, and oxides (MX, X = C, N, and O) are important molecules in astrophysics, catalysis, and organometallic chemistry. The measurements of the ionization energies (IEs), bond energies, and spectroscopic constants for MX/MX+ in the gas phase by high-resolution photoelectron methods represent challenging but profitable approaches to gain fundamental understandings of the electronic structures and bonding properties of these compounds and their cations. We have developed a two-color laser excitation scheme for high-resolution pulse field ionization photoelectron (PFI-PE) measurements of MX species. By exciting the neutral MX species to a single rovibronic state using a visible laser prior to photoionization by a UV laser, we have obtained fully rotational resolved PFI-PE spectra for TiC+, TiO+, VCH+, VN+, CoC+, ZrO+, and NbC+. The unambiguous rotational assignments of these spectra have provided highly accurate IE values for TiC, TiO, VCH, VN, CoC, ZrO, and NbC, and spectroscopic constants for their cations.

Optical Characterization of Lead Monoxide Films Grown by Laser-Assisted Deposition

NASA Astrophysics Data System (ADS)

Baleva, M.; Tuncheva, V.

1994-05-01

The Raman spectra of PbO films, grown by laser-assisted deposition (LAD) at different substrate temperatures are investigated. The spectra of the films, deposited on amorphous, single crystal quartz and polycrystal PbTe substrates, are compared with the Raman spectra of tetragonal and orthorhombic powder samples. The phonon frequencies determined in our experiment with powder samples coincide fairly well with those obtained by Adams and Stevens, J. Chem. Soc., Dalton Trans., 1096 (1977). Thus the Raman spectra of the powder samples presented in this paper can be considered as unambiguous characteristics of the two different PbO crystal phases. It was concluded that the Raman scattering may serve as a tool for identification of PbO films and their crystal modifications. On the basis of this investigation it was concluded that the film structure changes from orthorhombic to tetragonal with increased substrate temperature, and that the nature of the substrate influences the crystal structure of the films. On the basis of the Raman spectra of the β-PbO films with prevailing (001) orientation of crystallization, an assignment of the modes is proposed.

A wavelet analysis for the X-ray absorption spectra of molecules

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

Penfold, T. J.; Ecole polytechnique Federale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BCH, CH-1015 Lausanne; SwissFEL, Paul Scherrer Inst, CH-5232 Villigen

2013-01-07

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rheniummore » diimine complex, [ReX(CO){sub 3}(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.« less

Identification of a highly sulfated fucoidan from sea cucumber Pearsonothuria graeffei with well-repeated tetrasaccharides units.

PubMed

Hu, Yaqin; Li, Shan; Li, Junhui; Ye, Xingqian; Ding, Tian; Liu, Donghong; Chen, Jianchu; Ge, Zhiwei; Chen, Shiguo

2015-12-10

Sea cucumber fucoidan is a major bioactive component of sea cucumber. The structures of fucoidans have significant influences on their biological activities. The present study clarified the delicate structure of a fucoidan from Pearsonothuria graeffei. Fucoidan was obtained after papain digestion and purified by ion chromatography. The carbohydrate sequence of fucoidan was firstly determined by negative-ion electrospray tandem mass spectrometry (ES-MS) with collision-induced dissociation of the oligosaccharide fragments, which were obtained by mild acid hydrolysis, and completed by NMR for assignment of the anomeric conformation. It was unambiguously identified as a tetrasaccharide repeating unit with a backbone of [ → 3Fuc (2S, 4S) α1 → 3Fucα1→ 3Fuc (4S) α1 → 3Fuc#7 × 10#]n. The glycosidic bonds between the non-sulfated and 2,4-O-disulfated fucose residues were selectively cleaved, and highly ordered oligosaccharide fragments with a tetrasaccharide repeating unit were obtained. The highly 4-O- and 2, 4-di-O-sulfated polysaccharide deserves further developments for Pharmacia use. Copyright © 2015 Elsevier Ltd. All rights reserved.

The BG21 isoform of Golli myelin basic protein is intrinsically disordered with a highly flexible amino-terminal domain.

PubMed

Ahmed, Mumdooh A M; Bamm, Vladimir V; Harauz, George; Ladizhansky, Vladimir

2007-08-28

The genes of the oligodendrocyte lineage (Golli) encode a family of developmentally regulated isoforms of myelin basic protein. The "classic" MBP isoforms arise from transcription start site 3, whereas Golli-specific isoforms arise from transcription start site 1, and comprise both Golli-specific and classic MBP sequences. The Golli isoform BG21 has been suggested to play roles in myelination and T cell activation pathways. It is an intrinsically disordered protein, thereby presenting a large effective surface area for interaction with other proteins such as Golli-interacting protein. We have used multidimensional heteronuclear NMR spectroscopy to achieve sequence-specific resonance assignments of the recombinant murine BG21 in physiologically relevant buffer, to analyze its secondary structure using chemical shift indexing (CSI), and to investigate its backbone dynamics using 15N spin relaxation measurements. We have assigned 184 out of 199 residues unambiguously. The CSI analysis revealed little ordered secondary structure under these conditions, with only some small fragments having a slight tendency toward alpha-helicity, which may represent putative recognition motifs. The 15N relaxation and NOE measurements confirmed the general behavior of the protein as an extended polypeptide chain, with the N-terminal Golli-specific portion (residues S5-T69) being exceptionally flexible, even in comparison to other intrinsically disordered proteins that have been studied this way. The high degree of flexibility of this N-terminal region may be to provide additional plasticity, or conformational adaptability, in protein-protein interactions. Another highly mobile segment, A126-S127-G128-G129, may function as a hinge.

Global Analysis of a-, b-, and c-Type Transitions Involving Tunneling Components of K= 0 and 1 States of the Methanol Dimer

NASA Astrophysics Data System (ADS)

Lugez, C. L.; Lovas, F. J.; Hougen, J. T.; Ohashi, N.

1999-03-01

Spectral data onK= 0 and 1 levels of the methanol dimer available from previous and present Fourier transform microwave measurements have been interpreted globally, using a group-theoretically derived effective Hamiltonian and corresponding tunneling matrix elements to describe the splittings arising from a large number of tunneling motions. In the present work, 302 new measurements (40K= 1-1 and 262K= 1-0 transitions) were added to the previous data set to give a total of 584 assigned transitions withJ≤ 6. As a result of the rather completeK= 0, 1 data set forJ≤ 4, the lone-pair exchange tunneling splittings were obtained experimentally. Matrix element expansions inJ(J+ 1) used in the previousK= 0 formalism were modified to apply toK> 0, essentially by making a number of real coefficients complex, as required by the generalized internal-axis-method tunneling formalism. To reduce the number of adjustable parameters to an acceptable level in both theK= 0 andK= 1 effective Hamiltonians (used in separateK= 0 andK= 1 least-squares fits), a rather large number of assumptions concerning probably negligible parameters had to be made. The present fitting results should thus be considered as providing assurance of the group-theoretical line assignments as well as a nearly quantitative global interpretation of the tunneling splittings, even though they do not yet unambiguously determine the relative contributions from all 25 group-theoretically inequivalent tunneling motions in this complex, nor do they permit quantitative extrapolation to higherKlevels.

Parallel universes of Black Six biology.

PubMed

Kraev, Alexander

2014-07-19

Creation of lethal and synthetic lethal mutations in an experimental organism is a cornerstone of genetic dissection of gene function, and is related to the concept of an essential gene. Common inbred mouse strains carry background mutations, which can act as genetic modifiers, interfering with the assignment of gene essentiality. The inbred strain C57BL/6J, commonly known as "Black Six", stands out, as it carries a spontaneous homozygous deletion in the nicotinamide nucleotide transhydrogenase (Nnt) gene [GenBank: AH009385.2], resulting in impairment of steroidogenic mitochondria of the adrenal gland, and a multitude of indirect modifier effects, coming from alteration of glucocorticoid-regulated processes. Over time, the popular strain has been used, by means of gene targeting technology, to assign "essential" and "redundant" qualifiers to numerous genes, thus creating an internally consistent "parallel universe" of knowledge. It is unrealistic to suggest phasing-out of this strain, given the scope of shared resources built around it, however, continuing on the road of "strain-unawareness" will result in profound waste of effort, particularly where translational research is concerned. The review analyzes the historical roots of this phenomenon and proposes that building of "parallel universes" should be urgently made visible to a critical reader by obligatory use of unambiguous and persistent tags in publications and databases, such as hypertext links, pointing to a vendor's strain description web page, or to a digital object identifier (d.o.i.) of the original publication, so that any research done exclusively in C57BL/6J, could be easily identified. This article was reviewed by Dr. Neil Smalheiser and Dr. Miguel Andrade-Navarro.

Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment.

PubMed

Zhang, Bochao; Meng, Wenzhao; Prak, Eline T Luning; Hershberg, Uri

2015-12-01

Immune repertoires are collections of lymphocytes that express diverse antigen receptor gene rearrangements consisting of Variable (V), (Diversity (D) in the case of heavy chains) and Joining (J) gene segments. Clonally related cells typically share the same germline gene segments and have highly similar junctional sequences within their third complementarity determining regions. Identifying clonal relatedness of sequences is a key step in the analysis of immune repertoires. The V gene is the most important for clone identification because it has the longest sequence and the greatest number of sequence variants. However, accurate identification of a clone's germline V gene source is challenging because there is a high degree of similarity between different germline V genes. This difficulty is compounded in antibodies, which can undergo somatic hypermutation. Furthermore, high-throughput sequencing experiments often generate partial sequences and have significant error rates. To address these issues, we describe a novel method to estimate which germline V genes (or alleles) cannot be discriminated under different conditions (read lengths, sequencing errors or somatic hypermutation frequencies). Starting with any set of germline V genes, this method measures their similarity using different sequencing lengths and calculates their likelihood of unambiguous assignment under different levels of mutation. Hence, one can identify, under different experimental and biological conditions, the germline V genes (or alleles) that cannot be uniquely identified and bundle them together into groups of specific V genes with highly similar sequences. Copyright © 2015 Elsevier B.V. All rights reserved.

41 CFR 302-3.223 - What happens if I violate my new service agreement under a tour renewal assignment?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 41 Public Contracts and Property Management 4 2012-07-01 2012-07-01 false What happens if I... Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Tour Renewal Agreement § 302-3...

41 CFR 302-3.223 - What happens if I violate my new service agreement under a tour renewal assignment?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 4 2010-07-01 2010-07-01 false What happens if I... Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Tour Renewal Agreement § 302-3...

41 CFR 302-3.223 - What happens if I violate my new service agreement under a tour renewal assignment?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true What happens if I violate... Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Tour Renewal Agreement § 302-3...

41 CFR 302-3.223 - What happens if I violate my new service agreement under a tour renewal assignment?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false What happens if I... Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Tour Renewal Agreement § 302-3...

41 CFR 302-3.223 - What happens if I violate my new service agreement under a tour renewal assignment?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 41 Public Contracts and Property Management 4 2011-07-01 2011-07-01 false What happens if I... Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES RELOCATION ALLOWANCES 3-RELOCATION ALLOWANCE BY SPECIFIC TYPE Types of Transfers Overseas Tour Renewal Agreement § 302-3...

A proactive password checker

NASA Technical Reports Server (NTRS)

Bishop, Matt

1990-01-01

Password selection has long been a difficult issue; traditionally, passwords are either assigned by the computer or chosen by the user. When the computer does the assignment, the passwords are often hard to remember; when the user makes the selection, the passwords are often easy to guess. This paper describes a technique, and a mechanism, to allow users to select passwords which to them are easy to remember but to others would be very difficult to guess. The technique is site, user, and group compatible, and allows rapid changing of constraints imposed upon the password. Although experience with this technique is limited, it appears to have much promise.

Dual-wavelength digital holographic imaging with phase background subtraction

NASA Astrophysics Data System (ADS)

Khmaladze, Alexander; Matz, Rebecca L.; Jasensky, Joshua; Seeley, Emily; Holl, Mark M. Banaszak; Chen, Zhan

2012-05-01

Three-dimensional digital holographic microscopic phase imaging of objects that are thicker than the wavelength of the imaging light is ambiguous and results in phase wrapping. In recent years, several unwrapping methods that employed two or more wavelengths were introduced. These methods compare the phase information obtained from each of the wavelengths and extend the range of unambiguous height measurements. A straightforward dual-wavelength phase imaging method is presented which allows for a flexible tradeoff between the maximum height of the sample and the amount of noise the method can tolerate. For highly accurate phase measurements, phase unwrapping of objects with heights higher than the beat (synthetic) wavelength (i.e. the product of the original two wavelengths divided by their difference), can be achieved. Consequently, three-dimensional measurements of a wide variety of biological systems and microstructures become technically feasible. Additionally, an effective method of removing phase background curvature based on slowly varying polynomial fitting is proposed. This method allows accurate volume measurements of several small objects with the same image frame.

Development and application of a method for ivory dating by analyzing radioisotopes to distinguish legal from illegal ivory.

PubMed

Schmidberger, Andreas; Durner, Bernhard; Gehrmeyer, David; Schupfner, Robert

2018-06-19

The age determination of elephant ivory provides necessary and crucial information for all criminal prosecution authorities enforcing the Convention on International Trade in Endangered Species of Wild Fauna and Flora. The knowledge of the age of ivory allows to distinguish between pre-convention, hence legal material and ivory deriving from recent, illegal poaching incidents. The commonly applied method to determine the age of ivory is radiocarbon dating in the form of bomb pulse dating, which however will fade out soon. This work provides an enhancement of the radiocarbon dating method by supplementary determination of the isotope profile of 90-Sr and the two thorium isotopes 228-Th and 232-Th. This combined analysis allows for a precise and unambiguous age determination of ivory. We provided calibration curves for all involved radionuclides by analyzing ivory samples with known age and investigated a new method for the extraction of strontium from ivory. Copyright © 2018 Elsevier B.V. All rights reserved.

Designing Mixed Detergent Micelles for Uniform Neutron Contrast

DOE PAGES

Oliver, Ryan C.; Pingali, Sai Venkatesh; Urban, Volker S.

2017-09-29

Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) performed at the neutron contrast match point of detergent molecules allows observing the scattering signal from membrane proteins unobstructed by contributions from the detergent. However, we show here that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal at the average detergent contrast match point interferes with interpreting structural datamore » of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. Here, we present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell, and allows the micelle scattering to be fully contrast matched to unambiguously resolve membrane protein structure using solution SANS.« less

Rear surface light emission measurements from laser-produced shock waves in clear and Al-coated polystyrene targets

NASA Astrophysics Data System (ADS)

McLean, E. A.; Deniz, A. V.; Schmitt, A. J.; Stamper, J. A.; Obenschain, S. P.; Lehecka, T.; Mostovych, A. N.; Seely, J.

1999-08-01

The Nike KrF laser, with its very uniform focal distributions, has been used at intensities near 10 14 W/cm 2 to launch shock waves in polystyrene targets. The rear surface visible light emission differed between clear polystyrene (CH) targets and targets with a thin (125 nm) Al coating on the rear side. The uncoated CH targets showed a relatively slowly rising emission followed by a sudden fall when the shock emerges, while the Al-coated targets showed a rapid rise in emission when the shock emerges followed by a slower fall, allowing an unambiguous determination of the time the shock arrived at the rear surface. A half-aluminized target allowed us to observe this difference in a single shot. The brightness temperature of both the aluminized targets and the non-aluminized targets was slightly below but close to rear surface temperature predictions of a hydrodynamic code. A discussion of preheat effects is given.

Designing Mixed Detergent Micelles for Uniform Neutron Contrast

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

Oliver, Ryan C.; Pingali, Sai Venkatesh; Urban, Volker S.

Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) performed at the neutron contrast match point of detergent molecules allows observing the scattering signal from membrane proteins unobstructed by contributions from the detergent. However, we show here that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal at the average detergent contrast match point interferes with interpreting structural datamore » of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. Here, we present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell, and allows the micelle scattering to be fully contrast matched to unambiguously resolve membrane protein structure using solution SANS.« less

High-resolution infrared spectrum of triacetylene: The ν5 state revisited and new vibrational states

NASA Astrophysics Data System (ADS)

Doney, K. D.; Zhao, D.; Linnartz, H.

2015-10-01

New data are presented that follow from a high-resolution survey, from 3302 to 3352 cm-1, through expanding acetylene plasma, and covering the Csbnd H asymmetric (ν5) fundamental band of triacetylene (HC6H). Absorption signals are recorded using continuous wave cavity ring-down spectroscopy (cw-CRDS). A detailed analysis of the resulting spectra allows revisiting the molecular parameters of the ν5 fundamental band in terms of interactions with a perturbing state, which is observed for the first time. Moreover, four fully resolved hot bands (501 1011, 501 1111, 501 1311, and 101 801 1110), with band origins at 3328.5829(2), 3328.9994(2), 3328.2137(2) and 3310.8104(2) cm-1, respectively, are reported for the first time. These involve low lying bending vibrations that have been studied previously, which guarantees unambiguous identifications. Combining available data allows to derive accurate molecular parameters, both for the ground state as well as the excited states involved in the bands.

41 CFR 302-9.100 - Who is eligible for transportation of a POV to a post of duty?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY 9-ALLOWANCES... transfer to the post of duty, or a new appointee or student trainee assigned to the post of duty. ...

An iterative algorithm for calculating stylus radius unambiguously

NASA Astrophysics Data System (ADS)

Vorburger, T. V.; Zheng, A.; Renegar, T. B.; Song, J.-F.; Ma, L.

2011-08-01

The stylus radius is an important specification for stylus instruments and is commonly provided by instrument manufacturers. However, it is difficult to measure the stylus radius unambiguously. Accurate profiles of the stylus tip may be obtained by profiling over an object sharper than itself, such as a razor blade. However, the stylus profile thus obtained is a partial arc, and unless the shape of the stylus tip is a perfect sphere or circle, the effective value of the radius depends on the length of the tip profile over which the radius is determined. We have developed an iterative, least squares algorithm aimed to determine the effective least squares stylus radius unambiguously. So far, the algorithm converges to reasonable results for the least squares stylus radius. We suggest that the algorithm be considered for adoption in documentary standards describing the properties of stylus instruments.

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.

PubMed

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

2017-02-01

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H δ21 and H ε21 , respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

41 CFR 302-9.175 - When I am authorized to transport a POV, including a replacement POV, to my post of duty...

Code of Federal Regulations, 2012 CFR

2012-07-01

... transport a POV, including a replacement POV, to my post of duty subsequent to the time of my assignment to... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... OWNED VEHICLE Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.175 When I...

41 CFR 302-9.175 - When I am authorized to transport a POV, including a replacement POV, to my post of duty...

Code of Federal Regulations, 2010 CFR

2010-07-01

... transport a POV, including a replacement POV, to my post of duty subsequent to the time of my assignment to... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.175 When I am authorized to...

41 CFR 302-9.175 - When I am authorized to transport a POV, including a replacement POV, to my post of duty...

Code of Federal Regulations, 2014 CFR

2014-07-01

... transport a POV, including a replacement POV, to my post of duty subsequent to the time of my assignment to... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... OWNED VEHICLE Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.175 When I...

41 CFR 302-9.175 - When I am authorized to transport a POV, including a replacement POV, to my post of duty...

Code of Federal Regulations, 2013 CFR

2013-07-01

... transport a POV, including a replacement POV, to my post of duty subsequent to the time of my assignment to... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... OWNED VEHICLE Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.175 When I...

41 CFR 302-9.175 - When I am authorized to transport a POV, including a replacement POV, to my post of duty...

Code of Federal Regulations, 2011 CFR

2011-07-01

... transport a POV, including a replacement POV, to my post of duty subsequent to the time of my assignment to... and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND... Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.175 When I am authorized to...

Dynamic Spectrum Management for Military Wireless Networks

DTIC Science & Technology

2010-09-01

auctions, and protocols and etiquettes . Command and control assignments are provided by the regulatory agency by reviewing specific licensing...devices and amateur licensees do not have specific frequency assignments. The Protocols and Etiquettes methods allow these devices to operate within a...with Collision Avoidance (CSMA/CA) a protocol . Etiquettes are rules that are followed without explicit interaction between devices. Simple etiquettes

Helicons in uniform fields. II. Poynting vector and angular momenta

NASA Astrophysics Data System (ADS)

Stenzel, R. L.; Urrutia, J. M.

2018-03-01

The orbital and spin angular momenta of helicon modes have been determined quantitatively from laboratory experiments. The current density is obtained unambiguously from three dimensional magnetic field measurements. The only approximation made is to obtain the electric field from Hall Ohm's law which is usually the case for low frequency whistler modes. This allows the evaluation of the Poynting vector from which the angular momentum is obtained. Comparing two helicon modes (m = 0 and m = 1), one can separate the contribution of angular momentum of a rotating and non-rotating wave field. The orbital angular momentum is important to assess the wave-particle interaction by the transverse Doppler shift of rotating waves which has not been considered so far.

Importance of Requirements Analysis & Traceability to Improve Software Quality and Reduce Cost and Risk

NASA Technical Reports Server (NTRS)

Kapoor, Manju M.; Mehta, Manju

2010-01-01

The goal of this paper is to emphasize the importance of developing complete and unambiguous requirements early in the project cycle (prior to Preliminary Design Phase). Having a complete set of requirements early in the project cycle allows sufficient time to generate a traceability matrix. Requirements traceability and analysis are the key elements in improving verification and validation process, and thus overall software quality. Traceability can be most beneficial when the system changes. If changes are made to high-level requirements it implies that low-level requirements need to be modified. Traceability ensures that requirements are appropriately and efficiently verified at various levels whereas analysis ensures that a rightly interpreted set of requirements is produced.

Magnetooptics of Exciton Rydberg States in a Monolayer Semiconductor

NASA Astrophysics Data System (ADS)

Stier, A. V.; Wilson, N. P.; Velizhanin, K. A.; Kono, J.; Xu, X.; Crooker, S. A.

2018-02-01

We report 65 T magnetoabsorption spectroscopy of exciton Rydberg states in the archetypal monolayer semiconductor WSe2 . The strongly field-dependent and distinct energy shifts of the 2 s , 3 s , and 4 s excited neutral excitons permits their unambiguous identification and allows for quantitative comparison with leading theoretical models. Both the sizes (via low-field diamagnetic shifts) and the energies of the n s exciton states agree remarkably well with detailed numerical simulations using the nonhydrogenic screened Keldysh potential for 2D semiconductors. Moreover, at the highest magnetic fields, the nearly linear diamagnetic shifts of the weakly bound 3 s and 4 s excitons provide a direct experimental measure of the exciton's reduced mass mr=0.20 ±0.01 m0.

Supercritical fluid extraction and direct fluid injection mass spectrometry for the determination of trichothecene mycotoxins in wheat samples

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

Kalinoski, H.T.; Udseth, H.R.; Wright, B.W.

1986-10-01

The application of on-line supercritical fluid extraction with chemical ionization mass spectrometry and collision induced dissociation tandem mass spectrometry for the rapid identification of parts-per-million levels of several trichothecene mycotoxins is demonstrated. Supercritical carbon dioxide is shown to allow identification of mycotoxins with minimum sample handling in complex natural matrices (e.g., wheat). Tandem mass spectrometry techniques are employed for unambiguous identification of compounds of varying polarity, and false positives from isobaric compounds are avoided. Capillary column supercritical fluid chromatography-mass spectrometry of a supercritical fluid extract of the same sample was also performed and detection limits in the parts-per-billion range appearmore » feasible.« less

Mission and science activity scheduling language

NASA Technical Reports Server (NTRS)

Hull, Larry G.

1993-01-01

To support the distributed and complex operational scheduling required for future National Aeronautics and Space Administration (NASA) missions, a formal, textual language, the Scheduling Applications Interface Language (SAIL), has been developed. Increased geographic dispersion of investigators is leading to distributed mission and science activity planning, scheduling, and operations. SAIL is an innovation which supports the effective and efficient communication of scheduling information among physically dispersed applications in distributed scheduling environments. SAIL offers a clear, concise, unambiguous expression of scheduling information in a readable, hardware independent format. The language concept, syntax, and semantics incorporate language features found useful during five years of research and prototyping with scheduling languages in physically distributed environments. SAIL allows concise specification of mission and science activity plans in a format which promotes repetition and reuse.

Determination of hyperfine-induced transition rates from observations of a planetary nebula.

PubMed

Brage, Tomas; Judge, Philip G; Proffitt, Charles R

2002-12-31

Observations of the planetary nebula NGC3918 made with the STIS instrument on the Hubble Space Telescope reveal the first unambiguous detection of a hyperfine-induced transition 2s2p 3P(o)(0)-->2s2 1S0 in the berylliumlike emission line spectrum of N IV at 1487.89 A. A nebular model allows us to confirm a transition rate of 4x10(-4) sec(-1)+/-33% for this line. The measurement represents the first independent confirmation of the transition rate of hyperfine-induced lines in low ionization stages, and it provides support for the techniques used to compute these transitions for the determination of very low densities and isotope ratios.

Software development without languages

NASA Technical Reports Server (NTRS)

Osborne, Haywood S.

1988-01-01

Automatic programming generally involves the construction of a formal specification; i.e., one which allows unambiguous interpretation by tools for the subsequent production of the corresponding software. Previous practical efforts in this direction have focused on the serious problems of: (1) designing the optimum specification language; and (2) mapping (translating or compiling) from this specification language to the program itself. The approach proposed bypasses the above problems. It postulates that the specification proper should be an intermediate form, with the sole function of containing information sufficient to facilitate construction of programs and also of matching documentation. Thus, the means of forming the intermediary becomes a human factors task rather than a linguistic one; human users will read documents generated from the specification, rather than the specification itself.

Scaling laws from geomagnetic time series

USGS Publications Warehouse

Voros, Z.; Kovacs, P.; Juhasz, A.; Kormendi, A.; Green, A.W.

1998-01-01

The notion of extended self-similarity (ESS) is applied here for the X - component time series of geomagnetic field fluctuations. Plotting nth order structure functions against the fourth order structure function we show that low-frequency geomagnetic fluctuations up to the order n = 10 follow the same scaling laws as MHD fluctuations in solar wind, however, for higher frequencies (f > l/5[h]) a clear departure from the expected universality is observed for n > 6. ESS does not allow to make an unambiguous statement about the non triviality of scaling laws in "geomagnetic" turbulence. However, we suggest to use higher order moments as promising diagnostic tools for mapping the contributions of various remote magnetospheric sources to local observatory data. Copyright 1998 by the American Geophysical Union.

DNA Barcodes for Forensically Important Fly Species in Brazil.

PubMed

Koroiva, Ricardo; de Souza, Mirian S; Roque, Fabio de Oliveira; Pepinelli, Mateus

2018-04-07

Here, we analyze 248 DNA barcode sequences of 35 fly species of forensic importance in Brazil. DNA barcoding can be effectively used for specimen identification of these species, allowing the unambiguous identification of 31 species, an overall success rate of 88%. Our results show a high rate of success for molecular identification using DNA barcoding sequences and open new perspectives for immature species identification, a subject on which limited forensic investigations exist in Tropical regions. We also address the implications of building a robust forensic DNA barcode database. A geographic bias is recognized for the COI dataset available for forensically important fly species in Brazil, with concentration of sequences from specimens collected mainly in sites located in the Cerrado, Mata Atlântica, and Pampa biomes.

Inclusive reconstruction of hadron resonances in elementary and heavy-ion collisions with HADES

NASA Astrophysics Data System (ADS)

Kornakov, Georgy

2016-11-01

The unambiguous identification of hadron modifications in hot and dense QCD matter is one of the important goals in nuclear physics. In the regime of 1 - 2 GeV kinetic energy per nucleon, HADES has measured rare and penetrating probes in elementary and heavy-ion collisions. The main creation mechanism of mesons is the excitation and decay of baryonic resonances throughout the fireball evolution. The reconstruction of shortlived (≈ 1 fm/c) resonance states through their decay products is notoriously difficult. We have developed a new iterative algorithm, which builds the best hypothesis of signal and background by distortion of individual particle properties. This allows to extract signals with signal-to-background ratios of <1%.

The multiple personalities of Watson and Crick strands.

PubMed

Cartwright, Reed A; Graur, Dan

2011-02-08

In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

PubMed Central

Grobei, Monica A.; Qeli, Ermir; Brunner, Erich; Rehrauer, Hubert; Zhang, Runxuan; Roschitzki, Bernd; Basler, Konrad; Ahrens, Christian H.; Grossniklaus, Ueli

2009-01-01

Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch requires relevant proteins to be stored in the mature pollen, where they have to retain functionality in a desiccated environment. Using a shotgun proteomics approach, we unambiguously identified ∼3500 proteins in Arabidopsis pollen, including 537 proteins that were not identified in genetic or transcriptomic studies. To generate this comprehensive reference data set, which extends the previously reported pollen proteome by a factor of 13, we developed a novel deterministic peptide classification scheme for protein inference. This generally applicable approach considers the gene model–protein sequence–protein accession relationships. It allowed us to classify and eliminate ambiguities inherently associated with any shotgun proteomics data set, to report a conservative list of protein identifications, and to seamlessly integrate data from previous transcriptomics studies. Manual validation of proteins unambiguously identified by a single, information-rich peptide enabled us to significantly reduce the false discovery rate, while keeping valuable identifications of shorter and lower abundant proteins. Bioinformatic analyses revealed a higher stability of pollen proteins compared to those of other tissues and implied a protein family of previously unknown function in vesicle trafficking. Interestingly, the pollen proteome is most similar to that of seeds, indicating physiological similarities between these developmentally distinct tissues. PMID:19546170

Linking Nuclear Reactions and Nuclear Structure on the Way to the Drip Line

NASA Astrophysics Data System (ADS)

Dickhoff, Willem

2012-10-01

The present understanding of the role of short- and long-range physics in determining proton properties near the Fermi energy for stable closed-shell nuclei has relied on data from the (e,e'p) reaction. Hadronic tools to extract such spectroscopic information have been hampered by the lack of a consistent reaction description that provides unambiguous and undisputed results. The dispersive optical model (DOM), originally conceived by Claude Mahaux, provides a unified description of both elastic nucleon scattering and structure information related to single-particle properties below the Fermi energy. The DOM provides the starting point to provide a framework in which nuclear reactions and structure data can be analyzed consistently to provide unambiguous spectroscopic information including its asymmetry dependence. Recent extensions of this approach include the treatment of non-locality to describe experimental data like the nuclear charge density based on information of the spectral density below the Fermi energy, the application of the DOM ingredients to the description of transfer reactions, a comparison of the microscopic content of the nucleon self-energy based on Faddeev-RPA calculations emphasizing long-range correlations with DOM potentials, and a study of the relation between a self-energy which includes the effect of short-range correlations with DOM potentials. The most recent Dom implementation currently in progress abandons the constraint of local potentials completely to allow an accurate description of various properties of the nuclear ground state.

Fourier Transform Microwave Spectroscopy of Multiconformational Molecules and Van Der Waals Complexes.

NASA Astrophysics Data System (ADS)

Hight Walker, Angela Renee

1995-01-01

With the use of a Fourier transform microwave (FTM) spectrometer, structural determinations of two types of species; multiconformational molecules and van der Waals complexes, have been performed. Presented in this thesis are three sections summarizing this research effort. The first section contains a detailed explanation of the FTM instrument. In Section II, the study of three multiconformational molecules is presented as two chapters. Finally, three chapters in Section III outline the work still in progress on many van der Waals complexes. Section I was written to be a "manual" for the FTM spectrometer and to aid new additions to the group in their understanding of the instrument. An instruction guide is necessary for home-built instruments such as this one due to their unique design and application. Vital techniques and theories are discussed and machine operation is outlined. A brief explanation of general microwave spectroscopy as performed on an FTM spectrometer is also given. Section II is composed of two chapters pertaining to multiconformational molecules. In Chapter 2, a complete structural analysis of dipropyl ether is reported. The only conformer assigned had C_{rm s} symmetry. Many transitions are yet unassigned. Chapter 3 summarizes an investigation of two nitrosamines; methyl ethyl and methyl propyl nitrosamine. Only one conformer was observed for methyl ethyl nitrosamine, but two were assigned to methyl propyl nitrosamine. Nuclear hyperfine structure and internal methyl rotation complicated the spectra. The final section, Section III, contains the ongoing progress on weakly bound van der Waals complexes. The analysis of the OCS--HBr complex identified the structure as quasi-linear with large amplitude bending motions. Five separate isotopomers were assigned. Transitions originating from the HBr--DBr complex were measured and presented in Chapter 5. Although early in the analysis, the structure was determined to be bent and deuterium bonded. The final chapter of this section is meant to be a permanent record of transition frequencies whose molecular carrier is still in question. Two different groups of transitions from two different samples are listed. Further work is needed to unambiguously assign the frequencies with a carrier and quantum numbers, however the complexes (H_2 O)--(HCl)_2 and NO--H _2O are considered possible suspects.

Alleviating inequality in climate policy costs: an integrated perspective on mitigation, damage and adaptation

NASA Astrophysics Data System (ADS)

De Cian, E.; Hof, A. F.; Marangoni, G.; Tavoni, M.; van Vuuren, D. P.

2016-07-01

Equity considerations play an important role in international climate negotiations. While policy analysis has often focused on equity as it relates to mitigation costs, there are large regional differences in adaptation costs and the level of residual damage. This paper illustrates the relevance of including adaptation and residual damage in equity considerations by determining how the allocation of emission allowances would change to counteract regional differences in total climate costs, defined as the costs of mitigation, adaptation, and residual damage. We compare emission levels resulting from a global carbon tax with two allocations of emission allowances under a global cap-and-trade system: one equating mitigation costs and one equating total climate costs as share of GDP. To account for uncertainties in both mitigation and adaptation, we use a model-comparison approach employing two alternative modeling frameworks with different damage, adaptation cost, and mitigation cost estimates, and look at two different climate goals. Despite the identified model uncertainties, we derive unambiguous results on the change in emission allowance allocation that could lessen the unequal distribution of adaptation costs and residual damages through the financial transfers associated with emission trading.

Diversity and Variability of Geoporphyrins and Chlorins During Cretaceous Oceanic Anoxic Event II.

NASA Astrophysics Data System (ADS)

Junium, C. K.; Mawson, D. H.; Arthur, M. A.; Keely, B. J.

2005-12-01

Geoporphyrins and chlorins are biomarkers that result from the transformation of tetrapyrroles including chlorophylls, bacteriochlorophylls and haems. The transformation reactions are initiated in the water column and sediments during early diagenesis and are dependent on a range of variables including, but not limited to water column redox state, burial conditions, and time. Geoporphyrins and chlorins can retain structural characteristics that allow unambiguous assignment of precursor structures and source organisms making their utility in paleoenvironmental studies extraordinary where such information is preserved. Black shales from Oceanic Anoxic Event II (OAE II, Cenomanian-Turonian Boundary) of ODP Leg 207 present a unique opportunity for investigating the variations in the tetrapyrrole record in very well preserved sediments across a globally significant biogeochemcal event. Identification and structural assignment of tetrapyrroles in this study were achieved by a combination of high-performance-liquid-chromatography (HPLC)/diode-array-detection (DAD) and liquid chromatography-mass spectrometry (LC-MSn) on acetone extracts. Stratigraphic variations in geoporphyrin compounds occur through OAE II. The relative proportions of metallated vs. free-base (metal free) porphyrins vary throughout the sequence, favoring free-base porphyrins during the height of the anoxic event. The greater proportion of free-base porphyrins associated with more extensive reducing conditions is consistent with metal ion limitation during euxinia. For example, vanadyl porphyrins become much less abundant during the peak of the event suggesting that the oceanic inventory of V was sequestered in black shales and unavailable. Preliminary characterization of the tetrapyrroles through OAE II of ODP Leg 207, Demerara Rise, reveals a wide range of geoporphyrins and chlorins. Notably, positive identification of chlorins, the geologically unstable intermediates between highly reactive chlorophylls and the more stable geoporphyrins, predates the previous oldest described sedimentary occurrence by more than 70 Ma (Miocene, Vena del Gesso). Presence of chlorins implies exceptional preservation associated with strongly reducing conditions that existed during OAE II at Demerara Rise and the excellent condition of the recovered core material. Chlorins attributed to green sulfur bacteria, on the basis of specific mass-spectral characteristics 43 and 57, confirm the presence of anaerobic photoautotrophs and periods of photic-zone euxinia at Demerara Rise during the mid-Cretaceous. Unusually high abundances of the C33 bicyclo-alkanoporphyrin were also observed. The C33 bicyclo-alkanoporphyrin is possibly derived from rearrangement of chlorophyll a and suggests that a high proportion of the extractable geoporphyrins were derived from cyanobacteria and calcareous nannoplankton.

Rotationally resolved state-to-state photoionization and the photoelectron study of vanadium monocarbide and its cations (VC/VC(+)).

PubMed

Chang, Yih Chung; Luo, Zhihong; Pan, Yi; Zhang, Zheng; Song, Ying-Nan; Kuang, Sophie Yajin; Yin, Qing Zhu; Lau, Kai-Chung; Ng, C Y

2015-04-21

By employing two-color visible (VIS)-ultraviolet (UV) laser photoionization and pulsed field ionization-photoelectron (PFI-PE) techniques, we have obtained highly rotationally resolved photoelectron spectra for vanadium monocarbide cations (VC(+)). The state-to-state VIS-UV-PFI-PE spectra thus obtained allow unambiguous assignments for the photoionization rotational transitions, resulting in a highly precise value for the adiabatic ionization energy (IE) of vanadium monocarbide (VC), IE(VC) = 57512.0 ± 0.8 cm(-1) (7.13058 ± 0.00010 eV), which is defined as the energy of the VC(+)(X(3)Δ1; v(+) = 0; J(+) = 1) ← VC(X(2)Δ3/2; v'' = 0; J'' = 3/2) photoionization transition. The spectroscopic constants for VC(+)(X(3)Δ1) determined in the present study include the harmonic vibrational frequency ωe(+) = 896.4 ± 0.8 cm(-1), the anharmonicity constant ωe(+)xe(+) = 5.7 ± 0.8 cm(-1), the rotational constants Be(+) = 0.6338 ± 0.0025 cm(-1) and αe(+) = 0.0033 ± 0.0007 cm(-1), the equilibrium bond length re(+) = 1.6549 ± 0.0003 Å, and the spin-orbit coupling constant A = 75.2 ± 0.8 cm(-1) for VC(+)(X(3)Δ1,2,3). These highly precise energetic and spectroscopic data are used to benchmark state-of-the-art CCSDTQ/CBS calculations. In general, good agreement is found between the theoretical predictions and experimental results. The theoretical calculations yield the values, IE(VC) = 7.126 eV; the 0 K bond dissociation energies: D0(V-C) = 4.023 eV and D0(V(+)-C) = 3.663 eV; and heats of formation: ΔH°(f0)(VC) = 835.2, ΔH°(f298)(VC) = 840.4, ΔH°(f0)(VC(+)) = 1522.8, and ΔH°(f298)(VC(+)) = 1528.0 kJ mol(-1).

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

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

Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H– 29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H– 29Si HETCOR and dipolar 2D 1H– 1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Insteadmore » the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H– 29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1H and 29Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.« less

Semantic integration of gene expression analysis tools and data sources using software connectors

PubMed Central

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data. PMID:24341380

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

DOE PAGES

Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.; ...

2017-11-22

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H– 29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H– 29Si HETCOR and dipolar 2D 1H– 1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Insteadmore » the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H– 29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1H and 29Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.« less

The Melting Point of Palladium Using Miniature Fixed Points of Different Ceramic Materials: Part II—Analysis of Melting Curves and Long-Term Investigation

NASA Astrophysics Data System (ADS)

Edler, F.; Huang, K.

2016-12-01

Fifteen miniature fixed-point cells made of three different ceramic crucible materials (Al2O3, ZrO2, and Al2O3(86 %)+ZrO2(14 %)) were filled with pure palladium and used to calibrate type B thermocouples (Pt30 %Rh/Pt6 %Rh). A critical point by using miniature fixed points with small amounts of fixed-point material is the analysis of the melting curves, which are characterized by significant slopes during the melting process compared to flat melting plateaus obtainable using conventional fixed-point cells. The method of the extrapolated starting point temperature using straight line approximation of the melting plateau was applied to analyze the melting curves. This method allowed an unambiguous determination of an electromotive force (emf) assignable as melting temperature. The strict consideration of two constraints resulted in a unique, repeatable and objective method to determine the emf at the melting temperature within an uncertainty of about 0.1 μ V. The lifetime and long-term stability of the miniature fixed points was investigated by performing more than 100 melt/freeze cycles for each crucible of the different ceramic materials. No failure of the crucibles occurred indicating an excellent mechanical stability of the investigated miniature cells. The consequent limitation of heating rates to values below {± }3.5 K min^{-1} above 1100° C and the carefully and completely filled crucibles (the liquid palladium occupies the whole volume of the crucible) are the reasons for successfully preventing the crucibles from breaking. The thermal stability of the melting temperature of palladium was excellent when using the crucibles made of Al2O3(86 %)+ZrO2(14 %) and ZrO2. Emf drifts over the total duration of the long-term investigation were below a temperature equivalent of about 0.1 K-0.2 K.

Induced in-source fragmentation pattern of certain novel (1Z,2E)-N-(aryl)propanehydrazonoyl chlorides by electrospray mass spectrometry (ESI-MS/MS)

PubMed Central

2013-01-01

Background Collision induced dissociation (CID) in the triple quadrupole mass spectrometer system (QQQ) typically yields more abundant fragment ions than those produced with resonance excitation in the presence of helium gas in the ion trap mass spectrometer system (IT). Detailed product ion spectra can be obtained from one stage MS2 scan using the QQQ. In contrast, generating the same number of fragment ions in the ion trap requires multiple stages of fragmentation (MSn) using CID via in-trap resonance excitation with the associated time penalties and drop in sensitivity. Results The use of in-source fragmentation with electrospray ionization (ESI) followed by product ion scan (MS2) in a triple quadrupole mass spectrometer system, was demonstrated. This process enhances the qualitative power of tandem mass spectrometry to simulate the MS3 of ion trap for a comprehensive study of fragmentation mechanisms. A five pharmacologically significant (1Z, 2E)-N-arylpropanehydrazonoyl chlorides (3a-e) were chosen as model compounds for this study. In this work, detailed fragmentation pathways were elucidated by further dissociation of each fragment ion in the ion spectrum, essentially, by incorporating fragmentor voltage induced dissociation (in-source fragmentation) and isolation of fragments in a quadrupole cell Q1. Subsequently, CID occurs in cell, Q2, and fragment ions are analyzed in Q3 operated in product ion mode this process can be referred to as pseudo-MS3 scan mode. Conclusions This approach allowed unambiguous assignment of all fragment ions using tandem mass spectrometer and provided adequate sensitivity and selectivity. It is beneficial for structure determination of unknown trace components. The data presented in this paper provide useful information on the effect of different substituents on the ionization/fragmentation processes and can be used in the characterization of this important class of compounds. PMID:23351484

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

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

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

DOE PAGES

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma; ...

2018-02-15

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Density of states and dynamical crossover in a dense fluid revealed by exponential mode analysis of the velocity autocorrelation function

NASA Astrophysics Data System (ADS)

Bellissima, S.; Neumann, M.; Guarini, E.; Bafile, U.; Barocchi, F.

2017-01-01

Extending a preceding study of the velocity autocorrelation function (VAF) in a simulated Lennard-Jones fluid [Phys. Rev. E 92, 042166 (2015), 10.1103/PhysRevE.92.042166] to cover higher-density and lower-temperature states, we show that the recently demonstrated multiexponential expansion method allows for a full account and understanding of the basic dynamical processes encompassed by a fundamental quantity as the VAF. In particular, besides obtaining evidence of a persisting long-time tail, we assign specific and unambiguous physical meanings to groups of exponential modes related to the longitudinal and transverse collective dynamics, respectively. We have made this possible by consistently introducing the interpretation of the VAF frequency spectrum as a global density of states in fluids, generalizing a solid-state concept, and by giving to specific spectral components, obtained through the VAF exponential expansion, the corresponding meaning of partial densities of states relative to specific dynamical processes. The clear identification of a high-frequency oscillation of the VAF with the near-top excitation frequency in the dispersion curve of acoustic waves is a neat example of the power of the method. As for the transverse mode contribution, its analysis turns out to be particularly important, because the multiexponential expansion reveals a transition marking the onset of propagating excitations when the density is increased beyond a threshold value. While this finding agrees with the recent literature debating the issue of dynamical crossover boundaries, such as the one identified with the Frenkel line, we can add detailed information on the modes involved in this specific process in the domains of both time and frequency. This will help obtain a still missing full account of transverse dynamics, in both its nonpropagating and propagating aspects which are linked through dynamical transitions depending on both the thermodynamic states and the excitation wave vectors.

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

PubMed Central

Kilian, Norbert; Henning, Tilo; Plitzner, Patrick; Müller, Andreas; Güntsch, Anton; Stöver, Ben C.; Müller, Kai F.; Berendsohn, Walter G.; Borsch, Thomas

2015-01-01

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work. Database URL: http://campanula.e-taxonomy.net/ PMID:26424081

Semantic integration of gene expression analysis tools and data sources using software connectors.

PubMed

Miyazaki, Flávia A; Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

2013-10-25

The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Megahertz-Rate Semi-Device-Independent Quantum Random Number Generators Based on Unambiguous State Discrimination

NASA Astrophysics Data System (ADS)

Brask, Jonatan Bohr; Martin, Anthony; Esposito, William; Houlmann, Raphael; Bowles, Joseph; Zbinden, Hugo; Brunner, Nicolas

2017-05-01

An approach to quantum random number generation based on unambiguous quantum state discrimination is developed. We consider a prepare-and-measure protocol, where two nonorthogonal quantum states can be prepared, and a measurement device aims at unambiguously discriminating between them. Because the states are nonorthogonal, this necessarily leads to a minimal rate of inconclusive events whose occurrence must be genuinely random and which provide the randomness source that we exploit. Our protocol is semi-device-independent in the sense that the output entropy can be lower bounded based on experimental data and a few general assumptions about the setup alone. It is also practically relevant, which we demonstrate by realizing a simple optical implementation, achieving rates of 16.5 Mbits /s . Combining ease of implementation, a high rate, and a real-time entropy estimation, our protocol represents a promising approach intermediate between fully device-independent protocols and commercial quantum random number generators.

Modification site localization scoring integrated into a search engine.

PubMed

Baker, Peter R; Trinidad, Jonathan C; Chalkley, Robert J

2011-07-01

Large proteomic data sets identifying hundreds or thousands of modified peptides are becoming increasingly common in the literature. Several methods for assessing the reliability of peptide identifications both at the individual peptide or data set level have become established. However, tools for measuring the confidence of modification site assignments are sparse and are not often employed. A few tools for estimating phosphorylation site assignment reliabilities have been developed, but these are not integral to a search engine, so require a particular search engine output for a second step of processing. They may also require use of a particular fragmentation method and are mostly only applicable for phosphorylation analysis, rather than post-translational modifications analysis in general. In this study, we present the performance of site assignment scoring that is directly integrated into the search engine Protein Prospector, which allows site assignment reliability to be automatically reported for all modifications present in an identified peptide. It clearly indicates when a site assignment is ambiguous (and if so, between which residues), and reports an assignment score that can be translated into a reliability measure for individual site assignments.

38 CFR 36.4322 - Loan termination.

Code of Federal Regulations, 2010 CFR

2010-07-01

... allowable time and method for foreclosure, the Secretary shall review allowances for time and method in... well as State statutory requirements. The Secretary will review such timeframes annually and, as the... scheduled or anticipated date of the liquidation sale, the holder must request that VA assign an appraiser...

41 CFR 302-9.174 - What is the “authorized point of origin” when I transport a POV, including a replacement POV, to...

Code of Federal Regulations, 2012 CFR

2012-07-01

... the time of my assignment to that post of duty? 302-9.174 Section 302-9.174 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF... Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.174 What is the “authorized point...

41 CFR 302-9.174 - What is the “authorized point of origin” when I transport a POV, including a replacement POV, to...

Code of Federal Regulations, 2013 CFR

2013-07-01

... the time of my assignment to that post of duty? 302-9.174 Section 302-9.174 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF... Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.174 What is the “authorized point...

41 CFR 302-9.174 - What is the “authorized point of origin” when I transport a POV, including a replacement POV, to...

Code of Federal Regulations, 2010 CFR

2010-07-01

... the time of my assignment to that post of duty? 302-9.174 Section 302-9.174 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF... Pov Transportation Subsequent to the Time of Assignment § 302-9.174 What is the “authorized point of...

41 CFR 302-9.174 - What is the “authorized point of origin” when I transport a POV, including a replacement POV, to...

Code of Federal Regulations, 2014 CFR

2014-07-01

... the time of my assignment to that post of duty? 302-9.174 Section 302-9.174 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF... Transportation Pov Transportation Subsequent to the Time of Assignment § 302-9.174 What is the “authorized point...

41 CFR 302-9.174 - What is the “authorized point of origin” when I transport a POV, including a replacement POV, to...

Code of Federal Regulations, 2011 CFR

2011-07-01

... the time of my assignment to that post of duty? 302-9.174 Section 302-9.174 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF... Pov Transportation Subsequent to the Time of Assignment § 302-9.174 What is the “authorized point of...

Towards Automated Structure-Based NMR Resonance Assignment

NASA Astrophysics Data System (ADS)

Jang, Richard; Gao, Xin; Li, Ming

We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

Calibrated peer review assignments for the earth sciences

USGS Publications Warehouse

Rudd, J.A.; Wang, V.Z.; Cervato, C.; Ridky, R.W.

2009-01-01

Calibrated Peer Review ??? (CPR), a web-based instructional tool developed as part of the National Science Foundation reform initiatives in undergraduate science education, allows instructors to incorporate multiple writing assignments in large courses without overwhelming the instructor. This study reports successful implementation of CPR in a large, introductory geology course and student learning of geoscience content. For each CPR assignment in this study, students studied web-based and paper resources, wrote an essay, and reviewed seven essays (three from the instructor, three from peers, and their own) on the topic. Although many students expressed negative attitudes and concerns, particularly about the peer review process of this innovative instructional approach, they also recognized the learning potential of completing CPR assignments. Comparing instruction on earthquakes and plate boundaries using a CPR assignment vs. an instructional video lecture and homework essay with extensive instructor feedback, students mastered more content via CPR instruction.

An assigned responsibility system for robotic teleoperation control.

PubMed

Small, Nicolas; Lee, Kevin; Mann, Graham

2018-01-01

This paper proposes an architecture that explores a gap in the spectrum of existing strategies for robot control mode switching in adjustable autonomy. In situations where the environment is reasonably known and/or predictable, pre-planning these control changes could relieve robot operators of the additional task of deciding when and how to switch. Such a strategy provides a clear division of labour between the automation and the human operator(s) before the job even begins, allowing for individual responsibilities to be known ahead of time, limiting confusion and allowing rest breaks to be planned. Assigned Responsibility is a new form of adjustable autonomy-based teleoperation that allows the selective inclusion of automated control elements at key stages of a robot operation plan's execution. Progression through these stages is controlled by automatic goal accomplishment tracking. An implementation is evaluated through engineering tests and a usability study, demonstrating the viability of this approach and offering insight into its potential applications.

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

PubMed Central

Dröge, J.; Gregor, I.; McHardy, A. C.

2015-01-01

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

Experimental optimal maximum-confidence discrimination and optimal unambiguous discrimination of two mixed single-photon states

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

Steudle, Gesine A.; Knauer, Sebastian; Herzog, Ulrike

2011-05-15

We present an experimental implementation of optimum measurements for quantum state discrimination. Optimum maximum-confidence discrimination and optimum unambiguous discrimination of two mixed single-photon polarization states were performed. For the latter the states of rank 2 in a four-dimensional Hilbert space are prepared using both path and polarization encoding. Linear optics and single photons from a true single-photon source based on a semiconductor quantum dot are utilized.

Multiple priming of lexically ambiguous and unambiguous targets in the cerebral hemispheres: the coarse coding hypothesis revisited

PubMed Central

Kandhadai, Padmapriya; Federmeier, Kara D.

2009-01-01

The coarse coding hypothesis (Jung-Beeman 2005) postulates that the cerebral hemispheres differ in their breadth of semantic activation, with the left hemisphere (LH) activating a narrow, focused semantic field and the right (RH) weakly activating a broader semantic field. In support of coarse coding, studies (e.g., Faust and Lavidor 2003) investigating priming for multiple senses of a lexically ambiguous word have reported a RH benefit. However, studies of mediated priming (Livesay and Burgess 2003; Richards and Chiarello 1995) have failed to find a RH advantage for processing distantly-linked, unambiguous words. To address this debate, the present study made use of a multiple priming paradigm (Balota and Paul, 1996) in which two primes either converged onto the single meaning of an unambiguous, lexically-associated target (LION-STRIPES-TIGER) or diverged onto different meanings of an ambiguous target (KIDNEY-PIANO-ORGAN). In two experiments, participants either made lexical decisions to targets (Experiment 1) or made a semantic relatedness judgment between primes and targets (Experiment 2). In both tasks, for both ambiguous and unambiguous triplets we found equivalent priming strengths and patterns across the two visual fields, counter to the predictions of the coarse coding hypothesis. Priming patterns further suggested that both hemispheres made use of lexical level representations in the lexical decision task and semantic representations in the semantic judgment task. PMID:17459344

75 FR 9763 - Relief for U.S. Military and Civilian Personnel Who Are Assigned Outside the United States in...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... take a practical test after passing a knowledge test. For example, 14 CFR 61.39(a)(1) gives a person 24... operations. SFAR 100-2 also continues to allow FSDOs to accept expired airman written test reports for certain practical tests from U.S. personnel who are assigned outside the United States in support of U.S...

Single-Sex Schools, Student Achievement, and Course Selection: Evidence from Rule-Based Student Assignments in Trinidad and Tobago. NBER Working Paper No. 16817

ERIC Educational Resources Information Center

Jackson, C. Kirabo

2011-01-01

Existing studies on single-sex schooling suffer from biases due to student selection to schools and single-sex schools being better in unmeasured ways. In Trinidad and Tobago students are assigned to secondary schools based on an algorithm allowing one to address self-selection bias and cleanly estimate an upper-bound single-sex school effect. The…

To mind the mind: An event-related potential study of word class and semantic ambiguity

PubMed Central

Lee, Chia-lin; Federmeier, Kara D.

2009-01-01

The goal of this study was to jointly examine the effects of word class, word class ambiguity, and semantic ambiguity on the brain response to words in syntactically specified contexts. Four types of words were used: (1) word class ambiguous words with a high degree of semantic ambiguity (e.g., ‘duck’); (2) word class ambiguous words with little or no semantic ambiguity (e.g., ‘vote’); (3) word class unambiguous nouns (e.g., ‘sofa’); and (4) word class unambiguous verbs (e.g., ‘eat’). These words were embedded in minimal phrases that explicitly specified their word class: “the” for nouns (and ambiguous words used as nouns) and “to” for verbs (and ambiguous words used as verbs). Our results replicate the basic word class effects found in prior work (Federmeier, K.D., Segal, J.B., Lombrozo, T., Kutas, M., 2000. Brain responses to nouns, verbs and class ambiguous words in context. Brain, 123 (12), 2552–2566), including an enhanced N400 (250–450ms) to nouns compared with verbs and an enhanced frontal positivity (300–700 ms) to unambiguous verbs in relation to unambiguous nouns. A sustained frontal negativity (250–900 ms) that was previously linked to word class ambiguity also appeared in this study but was specific to word class ambiguous items that also had a high level of semantic ambiguity; word class ambiguous items without semantic ambiguity, in contrast, were more positive than class unambiguous words in the early part of this time window (250–500 ms). Thus, this frontal negative effect seems to be driven by the need to resolve the semantic ambiguity that is sometimes associated with different grammatical uses of a word class ambiguous homograph rather than by the class ambiguity per se. PMID:16516169

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

PubMed Central

Chesters, Douglas

2017-01-01

Abstract Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. PMID:27798407

High field 27Al MAS NMR and TPD studies of active sites in ethanol dehydration using thermally treated transitional aluminas as catalysts

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

Hu, Jian Zhi; Xu, Suochang; Kwak, Ja Hun

Gamma-, sigma- and theta-Al2O3 are well known metastable “transitional” alumina structural polymorphs. Upon heating, Al2O3 transitions to the so-called and Al2O3 polymorphs and finally forms the thermally stable Al2O3. The poorly developed crystallinity and co-existence of the , , and Al2O3 prior to forming all Al2O3, making it difficult to characterize the structures as well as to quantify the various phases of the transition alumina. As a result, there are significant controversies in the literatures. In this work, a detailed NMR analysis was carried out at high magnetic field on three special aluminum oxide samples where the, , , Al2O3more » phases are made dominant, respectively, by controlling the synthesis conditions. The goal is to simplify, including making unambiguous, spectral assignments in 27Al MAS NMR spectra of transition alumina that have not yet been commonly agreed previously. Specifically, quantitative 1D 27Al MAS NMR was used to quantify the ratios of the different alumina structural units, 2D MQMAS 27Al MAS was used for obtaining the highest spectral resolution to guide the analysis of the 1D spectrum, and a saturation pulse sequence was integrated into the 1D NMR to select the amorphous structures, including obtain spectra where the penta-coordinate sites are observed with enhanced relative intensity. Collectively, this study uniquely assigns Al-peaks (both octahedral and tetrahedral) to the Al2O3 and the Al2O3 phases and offers a new way of understanding, including quantifying, the different structural units and sites in transition alumina samples.« less

Conversion of 3-imidazoline-3-oxide nitroxyl radicals into nitronylnitroxyl radicals

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

Grigor'ev, I.A.; Shchukin, G.I.; Khramtsov, V.V.

1986-04-20

Continuing the studies of the effect of the pH of the medium on the EPR spectra of nitroxyl radicals (NR) containing acid-base functional groups at a distance of 2-3 sigma-bonds from the radical center, they have examined the EPR spectra of NR, which contain OH groups in the 2-position of the heterocycle. It is assumed that deprotonation of the OH group is accompanied by changes in the hfc constant a/sub N//sup 1/ and the g-factor. At pH values greater than or equal to 12, however, the EPR spectra of aqueous solutions of radicals undergo irreversible changes from a triplet tomore » a more complex multiplet, similar to the spectra of nitronylnitroxyl radicals. The EPR spectra of these solutions remain unchanged over periods of several days. The spectra have a quintet structure, with further splitting into four or three components. When similar experiments are carried out in D/sub 2/O, the additional hfs disappear as a result of deuterium exchange in the CH/sub 2/ and CH/sub 3/ groups of the radicals. A simulation of the EPR spectra was carried out, assuming splitting into two N nuclei (a/sub N//sup 1/ and a/sub N//sup 3/), with three or two equivalent H. This resulted in complete agreement between the calculated and experimental spectra. In order to assign the nitrogen hfc constants, they synthesized radicals containing the N/sup 15/ isotope in the 3-position of the imidazole ring. Comparison of the results of simulations of the EPR spectra enabled unambiguous assignments of the hfc constants a/sub N//sup 1/ and a/sub N//sup 3/ to be made.« less

Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus group A.

PubMed

Kreis, U C; Varma, V; Pinto, B M

1995-06-01

This paper describes the use of a protocol for conformational analysis of oligosaccharide structures related to the cell-wall polysaccharide of Streptococcus group A. The polysaccharide features a branched structure with an L-rhamnopyranose (Rhap) backbone consisting of alternating alpha-(1-->2) and alpha-(1-->3) links and D-N-acetylglucosamine (GlcpNAc) residues beta-(1-->3)-connected to alternating rhamnose rings: [formula: see text] Oligomers consisting of three to six residues have been synthesized and nuclear magnetic resonance (NMR) assignments have been made. The protocol for conformational analysis of the solution structure of these oligosaccharides involves experimental and theoretical methods. Two-dimensional NMR spectroscopy methods (TOCSY, ROESY and NOESY) are utilized to obtain chemical shift data and proton-proton distances. These distances are used as constraints in 100 ps molecular dynamics simulations in water using QUANTA and CHARMm. In addition, the dynamics simulations are performed without constraints. ROE build-up curves are computed from the averaged structures of the molecular dynamics simulations using the CROSREL program and compared with the experimental curves. Thus, a refinement of the initial structure may be obtained. The alpha-(1-->2) and the beta-(1-->3) links are unambiguously defined by the observed ROE cross peaks between the A-B',A'-B and C-B,C'-B' residues, respectively. The branch-point of the trisaccharide CBA' is conformationally well-defined. Assignment of the conformation of the B-A linkage (alpha-(1-->3)) was problematic due to TOCSY relay, but could be solved by NOESY and T-ROESY techniques. A conformational model for the polysaccharide is proposed.

Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance.

PubMed

Sugiki, Toshihiko; Furuita, Kyoko; Fujiwara, Toshimichi; Kojima, Chojiro

2018-06-20

Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15 N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13 C atoms experience less isotope scrambling than the main-chain 15 N atoms do. However, little is known about the side-chain 13 C atoms. Here, the 13 C scrambling profiles of the Cα and side-chain carbons were investigated for 15 N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13 Cα and 13 C side-chain labeling than in 15 N labeling. We utilized this reduced scrambling-prone character of 13 C as a simple and efficient method for amino acid selective 13 C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13 C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1 H- 15 N heteronuclear single-quantum coherence signals of the 15 N scrambling-prone amino acid were also easily filtered using 15 N-{ 13 Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.

Assignment of the zinc ligands in RsrA, a redox-sensing ZAS protein from Streptomyces coelicolor.

PubMed

Zdanowski, Konrad; Doughty, Phillip; Jakimowicz, Piotr; O'Hara, Liisa; Buttner, Mark J; Paget, Mark S B; Kleanthous, Colin

2006-07-11

ZAS proteins are widespread bacterial zinc-containing anti-sigma factors that regulate the activity of sigma factors in response to diverse cues. One of the best characterized ZAS proteins is RsrA from Streptomyces coelicolor, which responds to disulfide stress. Zn-RsrA binds and represses the transcriptional activity of sigmaR in the reducing environment of the cytoplasm but undergoes reversible, intramolecular disulfide bond formation during oxidative stress. This expels the single metal ion and causes dramatic structural changes in RsrA that result in its dissociation from sigmaR, leaving the sigma factor free to activate the transcription of antioxidant genes. We showed recently that Zn2+ serves a critical role in modulating the redox activity of RsrA thiols but uncertainty remains as to how the metal ion is coordinated in RsrA and related ZAS proteins. Using a combination of random and site-specific mutagenesis with zinc K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy, we have assigned unambiguously the metal ligands in RsrA, thereby distinguishing between the different ligation models that have been proposed. The data show that the zinc site in RsrA is comprised of Cys11, His37, Cys41, and Cys44. Three of these residues are part of a conserved ZAS-specific sequence motif (H37xxxC41xxC44), with the fourth ligand, Cys11, found in a subset of ZAS proteins. Cys11 and Cys44 form the trigger disulfide in RsrA, explaining why the metal ion is expelled during oxidation. We discuss these data in the context of redox sensing by RsrA and the sensory mechanisms of other ZAS proteins.

Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry.

PubMed

Loquais, Yohan; Gloaguen, Eric; Habka, Sana; Vaquero-Vara, Vanesa; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

2015-06-11

The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

41 CFR 302-1.1 - Who is eligible for relocation expense allowances under this chapter?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 1-GENERAL RULES Applicability... Postal Service to an agency as defined in 5 U.S.C. 5721; (d) An employee performing travel in accordance... to the same or different Government agency. (f) A student trainee assigned to any position upon...

14 CFR 1261.104 - Allowable claims.

Code of Federal Regulations, 2010 CFR

2010-01-01

... that were assigned to the claimant or provided by the United States; (ii) Quarters outside the 50... or provided by the United States, except when the claimant is a civilian employee who is a local... office or employment. (5) Enemy action or public service. Claims may be allowed for damage to, or loss of...

Lunar occultations for gamma-ray source measurements

NASA Technical Reports Server (NTRS)

Koch, David G.; Hughes, E. B.; Nolan, Patrick L.

1990-01-01

The unambiguous association of discrete gamma-ray sources with objects radiating at other wavelengths, the separation of discrete sources from the extended emission within the Galaxy, the mapping of gamma-ray emission from nearby galaxies and the measurement of structure within a discrete source cannot presently be accomplished at gamma-ray energies. In the past, the detection processes used in high-energy gamma-ray astronomy have not allowed for good angular resolution. This problem can be overcome by placing gamma-ray detectors on the moon and using the horizon as an occulting edge to achieve arcsec resolution. For purposes of discussion, this concept is examined for gamma rays above 100 MeV for which pair production dominates the detection process and locally-generated nuclear gamma rays do not contribute to the background.

Light baryon spectroscopy

NASA Astrophysics Data System (ADS)

Crede, Volker

2013-03-01

The spectrum of excited baryons serves as an excellent probe of quantum chromodynamics (QCD). In particular, highly-excited baryon resonances are sensitive to the details of quark confinement which is only poorly understood within QCD. Facilities worldwide such as Jefferson Lab, ELSA, and MAMI, which study the systematics of hadron spectra in photo- and electroproduction experiments, have accumulated a large amount of data in recent years including unpolarized cross section and polarization data for a large variety of meson-production reactions. These are important steps toward complete experiments that will allow us to unambiguously determine the scattering amplitude in the underlying reactions and to identify the broad and overlapping baryon resonance contributions. Several new nucleon resonances have been proposed and changes to the baryon listing in the 2012 Review of Particle Physics reflect the progress in the field.

Migration of tungsten dust in tokamaks: role of dust-wall collisions

NASA Astrophysics Data System (ADS)

Ratynskaia, S.; Vignitchouk, L.; Tolias, P.; Bykov, I.; Bergsåker, H.; Litnovsky, A.; den Harder, N.; Lazzaro, E.

2013-12-01

The modelling of a controlled tungsten dust injection experiment in TEXTOR by the dust dynamics code MIGRAINe is reported. The code, in addition to the standard dust-plasma interaction processes, also encompasses major mechanical aspects of dust-surface collisions. The use of analytical expressions for the restitution coefficients as functions of the dust radius and impact velocity allows us to account for the sticking and rebound phenomena that define which parts of the dust size distribution can migrate efficiently. The experiment provided unambiguous evidence of long-distance dust migration; artificially introduced tungsten dust particles were collected 120° toroidally away from the injection point, but also a selectivity in the permissible size of transported grains was observed. The main experimental results are reproduced by modelling.

Analysis of tamoxifen-DNA adducts in endometrial explants by MS and 32P-postlabeling.

PubMed

Beland, Frederick A; Churchwell, Mona I; Hewer, Alan; Phillips, David H; Gamboa da Costa, Gonçalo; Marques, M Matilde

2004-07-23

The nonsteroidal antiestrogen tamoxifen increases the risk of endometrial cancer; however, the mechanism for the induction of these tumors is not known. Recently, Sharma et al. [Biochem. Biophys. Res. Commun. 307 (2003) 157], using high performance liquid chromatography (HPLC) with online postcolumn photochemical activation and fluorescence detection, reported the presence of (E)-alpha-(deoxyguanosin- N2-yl)tamoxifen in DNA from human endometrial explants incubated with tamoxifen. Inasmuch as the methodology used by these investigators does not allow unambiguous characterization of tamoxifen-DNA adducts, we have used two additional techniques (HPLC coupled with electrospray ionization tandem mass spectrometry and 32P-postlabeling analyses) to assay for the presence of tamoxifen-DNA adducts in the human endometrial explant DNA. Tamoxifen-DNA adducts were not detected by either method.

Chirality, Metallicity, and Transition Dependent Asymmetries in Resonance Raman Excitation Profiles of Chirality-Enriched Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Doorn, Stephen; Duque, Juan; Telg, Hagen; Haroz, Erik; Tu, Xiaomin; Zheng, Ming

2014-03-01

Access to carbon nanotube samples enriched in single chiralities allows the observation of new photophysical behaviors obscured or difficult to demonstrate in mixed-chirality ensembles. Recent examples include the observation of strongly asymmetric G-band excitation profiles resulting from non-Condon effects1 and the unambiguous demonstration of Raman interference effects.2 We present here our most recent results demonstrating the generality of the non-Condon behavior to include metallic species (specifically several armchair chiralities). Additionally, the Eii dependence in non-Condon behavior with excitations from E11 thru E44 for both RBM and G modes will be discussed. 1. J.G. Duque, et. al., ACS Nano, 5, 5233 (2011). 2. J.G. Duque, et. al., Phys. Rev. Lett. 108, 117404 (2012).

Mercury radar imaging: evidence for polar ice.

PubMed

Slade, M A; Butler, B J; Muhleman, D O

1992-10-23

The first unambiguous full-disk radar mapping of Mercury at 3.5-centimeter wavelength, with the Goldstone 70-meter antenna transmitting and 26 antennas of the Very Large Array receiving, has provided evidence for the presence of polar ice. The radar experiments, conducted on 8 and 23 August 1991, were designed to image the half of Mercury not photographed by Mariner 10. The orbital geometry allowed viewing beyond the north pole of Mercury; a highly reflective region was clearly visible on the north pole during both experiments. This polar region has areas in which the circular polarization ratio (pt) was 1.0 to 1.4; values < approximately 0.1 are typical for terrestrial planets. Such high values of have hitherto been observed in radar observations only from icy regions of Mars and icy outer planet satellites.

Discriminating the effects of collapse models from environmental diffusion with levitated nanospheres

NASA Astrophysics Data System (ADS)

Li, Jie; Zippilli, Stefano; Zhang, Jing; Vitali, David

2016-05-01

Collapse models postulate the existence of intrinsic noise which modifies quantum mechanics and is responsible for the emergence of macroscopic classicality. Assessing the validity of these models is extremely challenging because it is nontrivial to discriminate unambiguously their presence in experiments where other hardly controllable sources of noise compete to the overall decoherence. Here we provide a simple procedure that is able to probe the hypothetical presence of the collapse noise with a levitated nanosphere in a Fabry-Pérot cavity. We show that the stationary state of the system is particularly sensitive, under specific experimental conditions, to the interplay between the trapping frequency, the cavity size, and the momentum diffusion induced by the collapse models, allowing one to detect them even in the presence of standard environmental noises.

GLYDE-II: The GLYcan data exchange format

PubMed Central

Ranzinger, Rene; Kochut, Krys J.; Miller, John A.; Eavenson, Matthew; Lütteke, Thomas; York, William S.

2017-01-01

Summary The GLYcan Data Exchange (GLYDE) standard has been developed for the representation of the chemical structures of monosaccharides, glycans and glycoconjugates using a connection table formalism formatted in XML. This format allows structures, including those that do not exist in any database, to be unambiguously represented and shared by diverse computational tools. GLYDE implements a partonomy model based on human language along with rules that provide consistent structural representations, including a robust namespace for specifying monosaccharides. This approach facilitates the reuse of data processing software at the level of granularity that is most appropriate for extraction of the desired information. GLYDE-II has already been used as a key element of several glycoinformatics tools. The philosophical and technical underpinnings of GLYDE-II and recent implementation of its enhanced features are described. PMID:28955652

Development and optimization of an analytical system for volatile organic compound analysis coming from the heating of interstellar/cometary ice analogues.

PubMed

Abou Mrad, Ninette; Duvernay, Fabrice; Theulé, Patrice; Chiavassa, Thierry; Danger, Grégoire

2014-08-19

This contribution presents an original analytical system for studying volatile organic compounds (VOC) coming from the heating and/or irradiation of interstellar/cometary ice analogues (VAHIIA system) through laboratory experiments. The VAHIIA system brings solutions to three analytical constraints regarding chromatography analysis: the low desorption kinetics of VOC (many hours) in the vacuum chamber during laboratory experiments, the low pressure under which they sublime (10(-9) mbar), and the presence of water in ice analogues. The VAHIIA system which we developed, calibrated, and optimized is composed of two units. The first is a preconcentration unit providing the VOC recovery. This unit is based on a cryogenic trapping which allows VOC preconcentration and provides an adequate pressure allowing their subsequent transfer to an injection unit. The latter is a gaseous injection unit allowing the direct injection into the GC-MS of the VOC previously transferred from the preconcentration unit. The feasibility of the online transfer through this interface is demonstrated. Nanomoles of VOC can be detected with the VAHIIA system, and the variability in replicate measurements is lower than 13%. The advantages of the GC-MS in comparison to infrared spectroscopy are pointed out, the GC-MS allowing an unambiguous identification of compounds coming from complex mixtures. Beyond the application to astrophysical subjects, these analytical developments can be used for all systems requiring vacuum/cryogenic environments.

Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state.

PubMed

Malik, Nikita; Kumar, Ashutosh

2016-09-01

NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled (13)C,(15)N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

Visual word ambiguity.

PubMed

van Gemert, Jan C; Veenman, Cor J; Smeulders, Arnold W M; Geusebroek, Jan-Mark

2010-07-01

This paper studies automatic image classification by modeling soft assignment in the popular codebook model. The codebook model describes an image as a bag of discrete visual words selected from a vocabulary, where the frequency distributions of visual words in an image allow classification. One inherent component of the codebook model is the assignment of discrete visual words to continuous image features. Despite the clear mismatch of this hard assignment with the nature of continuous features, the approach has been successfully applied for some years. In this paper, we investigate four types of soft assignment of visual words to image features. We demonstrate that explicitly modeling visual word assignment ambiguity improves classification performance compared to the hard assignment of the traditional codebook model. The traditional codebook model is compared against our method for five well-known data sets: 15 natural scenes, Caltech-101, Caltech-256, and Pascal VOC 2007/2008. We demonstrate that large codebook vocabulary sizes completely deteriorate the performance of the traditional model, whereas the proposed model performs consistently. Moreover, we show that our method profits in high-dimensional feature spaces and reaps higher benefits when increasing the number of image categories.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Application of Two-Sided Matching to Internal Labor of the Hellenic Navy

DTIC Science & Technology

2012-03-01

were developed, leading to the introduction of various choice programs that allow parents to pick schools for their children within or outside...any nature (i.e., military) plays a crucial role towards the direction of efficiency and effectiveness. A well-designed assignment process is a handy...v ABSTRACT The assignment process in an organization of any nature (i.e., military) plays a crucial role towards the direction of efficiency and

Measurement of the W boson polarization in top decay at CDF at √(s)=1.8 TeV

NASA Astrophysics Data System (ADS)

Acosta, D.; Affolder, T.; Albrow, M. G.; Ambrose, D.; Amidei, D.; Anikeev, K.; Antos, J.; Apollinari, G.; Arisawa, T.; Artikov, A.; Ashmanskas, W.; Azfar, F.; Azzi-Bacchetta, P.; Bacchetta, N.; Bachacou, H.; Badgett, W.; Barbaro-Galtieri, A.; Barnes, V. E.; Barnett, B. A.; Baroiant, S.; Barone, M.; Bauer, G.; Bedeschi, F.; Behari, S.; Belforte, S.; Bell, W. H.; Bellettini, G.; Bellinger, J.; Benjamin, D.; Beretvas, A.; Bhatti, A.; Binkley, M.; Bisello, D.; Bishai, M.; Blair, R. E.; Blocker, C.; Bloom, K.; Blumenfeld, B.; Bocci, A.; Bodek, A.; Bolla, G.; Bolshov, A.; Bortoletto, D.; Boudreau, J.; Bromberg, C.; Brubaker, E.; Budagov, J.; Budd, H. S.; Burkett, K.; Busetto, G.; Byrum, K. L.; Cabrera, S.; Campbell, M.; Carithers, W.; Carlsmith, D.; Castro, A.; Cauz, D.; Cerri, A.; Cerrito, L.; Chapman, J.; Chen, C.; Chen, Y. C.; Chertok, M.; Chiarelli, G.; Chlachidze, G.; Chlebana, F.; Chu, M. L.; Chung, J. Y.; Chung, W.-H.; Chung, Y. S.; Ciobanu, C. I.; Clark, A. G.; Coca, M.; Connolly, A.; Convery, M.; Conway, J.; Cordelli, M.; Cranshaw, J.; Culbertson, R.; Dagenhart, D.; D'Auria, S.; de Barbaro, P.; Cecco, S. De; dell'Agnello, S.; dell'Orso, M.; Demers, S.; Demortier, L.; Deninno, M.; Pedis, D. De; Derwent, P. F.; Dionisi, C.; Dittmann, J. R.; Dominguez, A.; Donati, S.; D'Onofrio, M.; Dorigo, T.; Eddy, N.; Erbacher, R.; Errede, D.; Errede, S.; Eusebi, R.; Farrington, S.; Feild, R. G.; Fernandez, J. P.; Ferretti, C.; Field, R. D.; Fiori, I.; Flaugher, B.; Flores-Castillo, L. R.; Foster, G. W.; Franklin, M.; Friedman, J.; Furic, I.; Gallinaro, M.; Garcia-Sciveres, , M.; Garfinkel, A. F.; Gay, C.; Gerdes, D. W.; Gerstein, E.; Giagu, S.; Giannetti, P.; Giolo, K.; Giordani, M.; Giromini, P.; Glagolev, V.; Glenzinski, D.; Gold, M.; Goldschmidt, N.; Goldstein, J.; Gomez, G.; Goncharov, M.; Gorelov, I.; Goshaw, A. T.; Gotra, Y.; Goulianos, K.; Gresele, A.; Grosso-Pilcher, C.; Guenther, M.; da Costa, J. Guimaraes; Haber, C.; Hahn, S. R.; Halkiadakis, E.; Handler, R.; Happacher, F.; Hara, K.; Harris, R. M.; Hartmann, F.; Hatakeyama, K.; Hauser, J.; Heinrich, J.; Hennecke, M.; Herndon, M.; Hill, C.; Hocker, A.; Hoffman, K. D.; Hou, S.; Huffman, B. T.; Hughes, R.; Huston, J.; Incandela, J.; Introzzi, G.; Iori, M.; Issever, C.; Ivanov, A.; Iwata, Y.; Iyutin, B.; James, E.; Jones, M.; Kamon, T.; Kang, J.; Unel, M. Karagoz; Kartal, S.; Kasha, H.; Kato, Y.; Kennedy, R. D.; Kephart, R.; Kilminster, B.; Kim, D. H.; Kim, H. S.; Kim, M. J.; Kim, S. B.; Kim, S. H.; Kim, T. H.; Kim, Y. K.; Kirby, M.; Kirsch, L.; Klimenko, S.; Koehn, P.; Kondo, K.; Konigsberg, J.; Korn, A.; Korytov, A.; Kroll, J.; Kruse, M.; Krutelyov, V.; Kuhlmann, S. E.; Kuznetsova, N.; Laasanen, A. T.; Lami, S.; Lammel, S.; Lancaster, J.; Lancaster, M.; Lander, R.; Lannon, K.; Lath, A.; Latino, G.; Lecompte, T.; Le, Y.; Lee, J.; Lee, S. W.; Leonardo, N.; Leone, S.; Lewis, J. D.; Li, K.; Lin, C. S.; Lindgren, M.; Liss, T. M.; Litvintsev, D. O.; Liu, T.; Lockyer, N. S.; Loginov, A.; Loreti, M.; Lucchesi, D.; Lukens, P.; Lyons, L.; Lys, J.; Madrak, R.; Maeshima, K.; Maksimovic, P.; Malferrari, L.; Manca, G.; Mangano, M.; Mariotti, M.; Martin, A.; Martin, M.; Martin, V.; Martínez, M.; Mazzanti, P.; McFarland, K. S.; McIntyre, P.; Menguzzato, M.; Menzione, A.; Merkel, P.; Mesropian, C.; Meyer, A.; Miao, T.; Miller, J. S.; Miller, R.; Miscetti, S.; Mitselmakher, G.; Moggi, N.; Moore, R.; Moulik, T.; Mukherjee, A.; Mulhearn, M.; Muller, T.; Munar, A.; Murat, P.; Nachtman, J.; Nahn, S.; Nakano, I.; Napora, R.; Nelson, C.; Nelson, T.; Neu, C.; Neubauer, M. S.; Newman-Holmes, C.; Niell, F.; Nigmanov, T.; Nodulman, L.; Oh, S. H.; Oh, Y. D.; Ohsugi, T.; Okusawa, T.; Orejudos, W.; Pagliarone, C.; Palmonari, F.; Paoletti, R.; Papadimitriou, V.; Patrick, J.; Pauletta, G.; Paulini, M.; Pauly, T.; Paus, C.; Pellett, D.; Penzo, A.; Phillips, T. J.; Piacentino, G.; Piedra, J.; Pitts, K. T.; Pompoš, A.; Pondrom, L.; Pope, G.; Poukhov, O.; Pratt, T.; Prokoshin, F.; Proudfoot, J.; Ptohos, F.; Punzi, G.; Rademacker, J.; Rakitine, A.; Ratnikov, F.; Ray, H.; Reichold, A.; Renton, P.; Rescigno, M.; Rimondi, F.; Ristori, L.; Robertson, W. J.; Rodrigo, T.; Rolli, S.; Rosenson, L.; Roser, R.; Rossin, R.; Rott, C.; Roy, A.; Ruiz, A.; Ryan, D.; Safonov, A.; Denis, R. St.; Sakumoto, W. K.; Saltzberg, D.; Sanchez, C.; Sansoni, A.; Santi, L.; Sarkar, S.; Savard, P.; Savoy-Navarro, A.; Schlabach, P.; Schmidt, E. E.; Schmidt, M. P.; Schmitt, M.; Scodellaro, L.; Scribano, A.; Sedov, A.; Seidel, S.; Seiya, Y.; Semenov, A.; Semeria, F.; Shapiro, M. D.; Shepard, P. F.; Shibayama, T.; Shimojima, M.; Shochet, M.; Sidoti, A.; Sill, A.; Sinervo, P.; Slaughter, A. J.; Sliwa, K.; Snider, F. D.; Snihur, R.; Spezziga, M.; Spiegel, L.; Spinella, F.; Spiropulu, M.; Stefanini, A.; Strologas, J.; Stuart, D.; Sukhanov, A.; Sumorok, K.; Suzuki, T.; Takashima, R.; Takikawa, K.; Tanaka, M.; Tecchio, M.; Teng, P. K.; Terashi, K.; Tesarek, R. J.; Tether, S.; Thom, J.; Thompson, A. S.; Thomson, E.; Tipton, P.; Tkaczyk, S.; Toback, D.; Tollefson, K.; Tonelli, D.; Tönnesmann, M.; Toyoda, H.; Trischuk, W.; Tseng, J.; Tsybychev, D.; Turini, N.; Ukegawa, F.; Unverhau, T.; Vaiciulis, T.; Varganov, A.; Vataga, E.; Vejcik, S.; Velev, G.; Veramendi, G.; Vidal, R.; Vila, I.; Vilar, R.; Volobouev, I.; von der Mey, M.; Wagner, R. G.; Wagner, R. L.; Wagner, W.; Wan, Z.; Wang, C.; Wang, M. J.; Wang, S. M.; Ward, B.; Waschke, S.; Waters, D.; Watts, T.; Weber, M.; Wester, W. C.; Whitehouse, B.; Wicklund, A. B.; Wicklund, E.; Williams, H. H.; Wilson, P.; Winer, B. L.; Wolbers, S.; Wolter, M.; Worm, S.; Wu, X.; Würthwein, F.; Yang, U. K.; Yao, W.; Yeh, G. P.; Yi, K.; Yoh, J.; Yoshida, T.; Yu, I.; Yu, S.; Yun, J. C.; Zanello, L.; Zanetti, A.; Zetti, F.; Zucchelli, S.

2005-02-01

The polarization of the W boson in t→Wb decay is unambiguously predicted by the standard model of electroweak interactions and is a powerful test of our understanding of the tbW vertex. We measure this polarization from the invariant mass of the b quark from t→Wb and the lepton from W→lν whose momenta measure the W decay angle and direction of motion, respectively. In this paper we present a measurement of the decay rate (fV+A) of the W produced from the decay of the top quark in the hypothesis of V+A structure of the tWb vertex. We find no evidence for the nonstandard V+A vertex and set a limit on fV+A < 0.80 at 95% confidence level. By combining this result with a complementary observable in the same data, we assign a limit on fV+A < 0.61 at 95% CL. This corresponds to a constraint on the right-handed helicity component of the W polarization of f+<0.18 at 95% CL. This limit is the first significant direct constraint on fV+A in top decay.

Profiling analysis of low molecular weight heparins by multiple heart-cutting two dimensional chromatography with quadruple time-of-flight mass spectrometry.

PubMed

Ouyang, Yilan; Zeng, Yangyang; Rong, Yinxiu; Song, Yue; Shi, Lv; Chen, Bo; Yang, Xinlei; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-09-01

Low molecular weight heparins (LMWHs) are polydisperse and microheterogenous mixtures of polysaccharides used as anticoagulant drugs. Profiling analysis is important for obtaining deeper insights into the structure of LMWHs. Previous oligosaccharide mapping methods are relatively low resolution and are unable to show an entire picture of the structural complexity of LMWHs. In the current study a profiling method was developed relying on multiple heart-cutting, two-dimensional, ultrahigh performance liquid chromatography with quadruple time-of-flight mass spectrometry. This represents an efficient, automated, and robust approach for profiling LMWHs. Using size-exclusion chromatography and ion-pairing reversed-phase chromatography in a two-dimensional separation, LMW components of different sizes and LMW components of the same size but with different charges and polarities can be resolved, providing a more complete picture of a LMWH. Structural information on each component was then obtained with quadrupole time-of-flight mass spectrometry. More than 80 and 120 oligosaccharides were observed and unambiguously assigned from the LMWHs, nadroparin and enoxaparin, respectively. This method might be useful for quality control of LMWHs and as a powerful tool for heparin-related glycomics.

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

NASA Astrophysics Data System (ADS)

Hare, Patrick M.; Middleton, Chris T.; Mertel, Kristin I.; Herbert, John M.; Kohler, Bern

2008-05-01

Vibrational spectra of the lowest energy triplet states of thymine and its 2'-deoxyribonucleoside, thymidine, are reported for the first time. Time-resolved infrared (TRIR) difference spectra were recorded over seven decades of time from 300 fs to 3 μs using femtosecond and nanosecond pump-probe techniques. The carbonyl stretch bands in the triplet state are seen at 1603 and ˜1700 cm -1 in room-temperature acetonitrile- d3 solution. These bands and additional ones observed between 1300 and 1450 cm -1 are quenched by dissolved oxygen on a nanosecond time scale. Density-functional calculations accurately predict the difference spectrum between triplet and singlet IR absorption cross sections, confirming the peak assignments and elucidating the nature of the vibrational modes. In the triplet state, the C4 dbnd O carbonyl exhibits substantial single-bond character, explaining the large (˜70 cm -1) red shift in this vibration, relative to the singlet ground state. Femtosecond TRIR measurements unambiguously demonstrate that the triplet state is fully formed within the first 10 ps after excitation, ruling out a relaxed 1nπ ∗ state as the triplet precursor.

Anatomical Distribution of Lipids in Human Brain Cortex by Imaging Mass Spectrometry

NASA Astrophysics Data System (ADS)

Veloso, Antonio; Astigarraga, Egoitz; Barreda-Gómez, Gabriel; Manuel, Iván; Ferrer, Isidro; Teresa Giralt, María; Ochoa, Begoña; Fresnedo, Olatz; Rodríguez-Puertas, Rafael; Fernández, José A.

2011-02-01

Molecular mass images of tissues will be biased if differences in the physicochemical properties of the microenvironment affect the intensity of the spectra. To address this issue, we have performed—by means of MALDI-TOF mass spectrometry—imaging on slices and lipidomic analysis in extracts of frontal cortex, both from the same postmortem tissue samples of human brain. An external calibration was used to achieve a mass accuracy of 10 ppm (1 σ) in the spectra of the extracts, although the final assignment was based on a comparison with previously reported species. The spectra recorded directly from tissue slices (imaging) show excellent s/n ratios, almost comparable to those obtained from the extracts. In addition, they retain the information about the anatomical distribution of the molecular species present in autopsied frozen tissue. Further comparison between the spectra from lipid extracts devoid of proteins and those recorded directly from the tissue unambiguously show that the differences in lipid composition between gray and white matter observed in the mass images are not an artifact due to microenvironmental influences of each anatomical area on the signal intensity, but real variations in the lipid composition.

Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides.

PubMed

Armstrong, Geoffrey S; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2005-03-01

Four-dimensional nuclear magnetic resonance spectroscopy with high resolution of signals in the indirect dimensions is reported as an implementation of the filter diagonalization method (FDM). Using an oligosaccharide derivatized with 13C-labeled acetyl isotags, a four-dimensional constant-time pulse sequence was tailored for conjoint use with the FDM. Results demonstrate that high resolution in all dimensions can be achieved using a relatively short experimental time period (19 h), even though the spectrum is highly congested in the direct and all three indirect dimensions. The combined use of isotags, constant-time pulse sequences, and FDM permits rapid isolation of sugar ring proton spin systems in multiple dimensions and enables all endocyclic J-couplings to be simply measured, the key goal to assigning sugar stereochemistry and anomeric configuration. A general method for rapid, unambiguous elucidation of spin systems in oligosaccharides has been a long-sought goal of carbohydrate NMR, and isotags combined with the FDM now enable this to be easily performed. Additional general advantages of the FDM program for generating high-resolution 2D slices in any dimension from a 4D spectrum are emphasized.

Determination of astaxanthin and astaxanthin esters in the microalgae Haematococcus pluvialis by LC-(APCI)MS and characterization of predominant carotenoid isomers by NMR spectroscopy.

PubMed

Holtin, Karsten; Kuehnle, Maximilian; Rehbein, Jens; Schuler, Paul; Nicholson, Graeme; Albert, Klaus

2009-11-01

The oily product ZANTHIN consists of natural astaxanthin, which is manufactured from the microalgae Haematococcus pluvialis by supercritical CO(2) extraction. An HPLC method was developed to separate all of the components of the complex astaxanthin extract using a C(30) column. The separation resulted in different isomers of astaxanthin accompanied by two other carotenoids. The main component consisted of astaxanthin singly esterified with several different fatty acids. C18:3, C18:2, C18:1 and C16:0 were identified as the most commonly occurring fatty acids. Doubly esterified astaxanthin was also found, although in lower concentrations compared to singly esterified astaxanthin. After performing a detailed fatty acid analysis by GC-MS, the peaks from the extract were assigned via HPLC-MS. A trans to cis transmutation of the all-trans compound was performed by thermal treatment in order to obtain an enrichment of cis isomers as the basis for unambiguous identification via NMR experiments. The all-trans as well as the 9- and 13-cis isomers of astaxanthin were characterized in detail by UV/Vis, (1)H, and (1)H,(1)H COSY NMR spectroscopy.

Peak picking NMR spectral data using non-negative matrix factorization

PubMed Central

2014-01-01

Background Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. Results To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Conclusions Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap. PMID:24511909

A rigorous detection of interstellar CH3NCO: An important missing species in astrochemical networks.

PubMed

Cernicharo, J; Kisiel, Z; Tercero, B; Kolesniková, L; Medvedev, I R; López, A; Fortman, S; Winnewisser, M; de Lucia, F C; Alonso, J L; Guillemin, J-C

2016-03-01

The recent analysis of the composition of the frozen surface of comet 67P/Churyumov-Gerasimenko has revealed a significant number of complex organic molecules. Methyl isocyanate (CH 3 NCO) is one of the more abundant species detected on the comet surface. In this work we report extensive characterization of its rotational spectrum resulting in a list of 1269 confidently assigned laboratory lines and its detection in space towards the Orion clouds where 399 lines of the molecule have been unambiguously identified. We find that the limited mm-wave laboratory data reported prior to our work require some revision. The abundance of CH 3 NCO in Orion is only a factor of ten below those of HNCO and CH 3 CN. Unlike the molecular abundances in the coma of comets, which correlate with those of warm molecular clouds, molecular abundances in the gas phase in Orion are only weakly correlated with those measured on the comet surface. We also compare our abundances with those derived recently for this molecule towards Sgr B2 (Halfen et al. 2015). A more accurate abundance of CH 3 NCO is provided for this cloud based on our extensive laboratory work.

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.

PubMed Central

On, Stephen L. W.; Miller, William G.; Houf, Kurt; Fox, James G.; Vandamme, Peter

2017-01-01

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended. PMID:29034857

Evidence for trivial Berry phase and absence of chiral anomaly in semimetal NbP

NASA Astrophysics Data System (ADS)

Sudesh; Kumar, Pawan; Neha, Prakriti; Das, Tanmoy; Patnaik, Satyabrata

2017-04-01

The discovery of Weyl semimetals (WSM) has brought forth the condensed matter realization of Weyl fermions, which were previously theorized as low energy excitations in high energy particle physics. Recently, transition metal mono-pnictides are under intense investigation for understanding properties of inversion-symmetry broken Weyl semimetals. Non-trivial Berry phase and chirality are important markers for characterizing topological aspects of Weyl semimetals. Most recently, theoretical calculations predict strong influence of the position of Weyl nodes with respect to Fermi surface and weak disorder that can drive WSMs into chirally symmetric Dirac semimetals. Using magneto-transport measurements in single crystals of WSM NbP, we observe an exceptionally large magnetoresistance at low temperature, which is non-saturating and linear at high fields. The origin of linear transverse magnetoresistance is assigned to charge carrier mobility fluctuations. Negative longitudinal magnetoresistance is not seen, suggesting lack of well-defined chiral anomaly in NbP. Unambiguous Shubnikov-de Haas oscillations are observed at low temperatures that are correlated to a trivial Berry phase corresponding to Fermi surface extrema at 30.5 Tesla. Our results are important towards identifying topological characteristics of Weyl semimetals and their experimental manifestations in the presence of weak disorder.

Paternity and gregariousness in the sex-changing sessile marine gastropod Crepidula convexa: comparison with other protandrous Crepidula species.

PubMed

Le Cam, Sabrina; Riquet, Florentine; Pechenik, Jan A; Viard, Frédérique

2014-01-01

In sex-changing animals with internal fertilization, gregarious behavior may increase mating opportunities and the frequency of multiple paternity, thus increasing maternal reproductive success. Crepidula convexa is a direct-developing protandrous gastropod characterized by only modest gregarious behavior compared with previously studied members of the genus: females are frequently found isolated. Using 6 microsatellite markers, we analyzed paternity profiles in 10 broods (25 embryos per mother). The number of assigned fathers varied among families from 1 to 4 fathers per brood. Interestingly, polyandry was not detected in solitary females but only in females grouped with conspecific individuals. Overall, we found an average of 1.8 fathers per brood, but this increased to 2.6 fathers per brood when considering only the nonisolated females. Among 18 unambiguously identified fathers, only 5 were collected in our samples, suggesting substantial male mobility. Comparison with previous paternity analyses in Crepidula fornicata and Crepidula coquimbensis revealed that polyandry appears as a common trait of these sex-changing gastropods despite their different grouping behaviors and life histories. As expected, the level of polyandry was nevertheless lower in the modestly gregarious C. convexa.

Heterogeneity analysis in 40 X-linked retinitis pigmentosa families

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

Teague, P.W.; Aldred, M.A.; Dempster, M.

1994-07-01

Analysis of genetic heterogeneity in 40 kindreds with X-linked retinitis pigmentosa (XLRP), with 20 polymorphic markers, showed that significant heterogeneity is present (P=.001) and that 56% of kindreds are of RP3 type and that 26% are of RP2 type. The location of the RP3 locus was found to be 0.4 cM distal to OTC in the Xp21.1 region, and that of the RP2 locus was 6.5 cM proximal to DXS7 in Xp11.2-p11.3. Bayesian probabilities of linkage to RP2, RP3, or to neither locus were calculated. This showed that 20 of 40 kindreds could be assigned to one or the othermore » locus, with a probability >.70 (14 kindreds with RP3 and 6 kindreds with RP2 disease). A further three kindreds were found to be unlinked to either locus, with a probability >.8. The remaining 17 kindreds could not be classified unambiguously. This highlights the difficulty of classifying families in the presence of genetic heterogeneity, where two loci are separated by an estimated 16 cM. 34 refs., 1 fig., 4 tabs.« less

Direct measurement of the spin gap in a quasi-one-dimensional clinopyroxene: NaTiSi 2 O 6

DOE PAGES

Silverstein, Harlyn J.; Smith, Alison E.; Mauws, Cole; ...

2014-10-13

True inorganic Spin-Peierls materials are extremely rare, but NaTiSi 2O 6 was at one time considered an ideal candidate due to it having well separated chains of edge-sharing TiO 6 octahedra. At low temperatures, this material undergoes a phase transition from C2/c to Pmore » $$\\bar{1}$$ symmetry, where Ti 3+-Ti 3+ dimers begin to form within the chains. However, it was quickly realized with magnetic susceptibility that simple spin fluctuations do not progress to the point of enabling such a transition. Since then, considerable experimental and theoretical endeavours have been taken to find the true ground state of this system and explain how it manifests. Here, we employ the use of x-ray diffraction, neutron spectroscopy, and magnetic susceptibility to directly and simultaneously measure the symmetry loss, spin singlet-triplet gap, and phonon modes. Lastly, we observed a gap of 53(3) meV, fit to the magnetic susceptibility, and compared to previous theoretical models to unambiguously assign NaTiSi 2O 6 as having an orbital-assisted Peierls ground state.« less

Controlled flexibility in technical editing - The levels-of-edit concept at JPL

NASA Technical Reports Server (NTRS)

Buehler, M. F.

1977-01-01

The levels-of-edit concept, which can be used to specify the amount of editorial effort involved in the preparation of a manuscript for publication, is discussed. Nine types of editing are identified and described. These include coordination edit (preparing estimates, gathering cost data, monitoring production processes), policy edit, integrity edit (making sure that parts of a publication match in a physical or numerical sense), screening edit (ensuring that the quality of camera-ready copy is sufficient for external publication), copy clarification edit, format edit, mechanical style edit, language edit, and substantive edit (reviewing the manuscript for content coherence, emphasis, subordination and parallelism). These functions are grouped into five levels of edit. An edit-level number is assigned to each manuscript, providing a quantitative and qualitative indicator of the editing to be done which is clearly understood by authors, managers, and editors alike. In addition, clear boundaries are drawn between normal and extraordinary editing tasks. Individual organizations will group various edits in different ways to reflect their needs and priorities; the essential element of the system is unambiguous definition and coding of the types and amount of work to be done.

Lithologies contributing to the clast population in Apollo 17 LKFM basaltic impact melts

NASA Technical Reports Server (NTRS)

Norman, Marc D.; Taylor, G. Jeffrey; Spudis, Paul; Ryder, Graham

1992-01-01

LKFM basaltic impact melts are abundant among Apollo lunar samples, especially those from Apollo 15, 16, and 17. They are generally basaltic in composition, but are found exclusively as impact melts. They seem to be related to basins and so could represent the composition of the lower lunar crust. They contain lithic clasts that cannot be mixed in any proportion to produce the composition of the melt matrix; components rich in transition elements (Ti, Cr, Sc) and REE are not considered. To search for the mysterious cryptic component, we previously investigated the mineral clast population in two Apollo 14 LKFM basaltic impact melts, 15445 and 15455. The cryptic component was not present in the mineral clast assemblage of these breccias either, but some olivine and pyroxene grains appeared to be from lithologies not represented among identified igneous rocks from the lunar highlands. In addition, none of the mineral clasts could be unambiguously assigned to a ferroan anorthosite source. We have now extended this study to Apollo 17, starting with two LKFM impact melt breccias (76295 and 76315) from the Apollo 17 station 6 boulder. The results from the study are presented.

A rigorous detection of interstellar CH3NCO: An important missing species in astrochemical networks⋆,⋆⋆

PubMed Central

Cernicharo, J.; Kisiel, Z.; Tercero, B.; Kolesniková, L.; Medvedev, I.R.; López, A.; Fortman, S.; Winnewisser, M.; de Lucia, F. C.; Alonso, J. L.; Guillemin, J.-C.

2016-01-01

The recent analysis of the composition of the frozen surface of comet 67P/Churyumov-Gerasimenko has revealed a significant number of complex organic molecules. Methyl isocyanate (CH3NCO) is one of the more abundant species detected on the comet surface. In this work we report extensive characterization of its rotational spectrum resulting in a list of 1269 confidently assigned laboratory lines and its detection in space towards the Orion clouds where 399 lines of the molecule have been unambiguously identified. We find that the limited mm-wave laboratory data reported prior to our work require some revision. The abundance of CH3NCO in Orion is only a factor of ten below those of HNCO and CH3CN. Unlike the molecular abundances in the coma of comets, which correlate with those of warm molecular clouds, molecular abundances in the gas phase in Orion are only weakly correlated with those measured on the comet surface. We also compare our abundances with those derived recently for this molecule towards Sgr B2 (Halfen et al. 2015). A more accurate abundance of CH3NCO is provided for this cloud based on our extensive laboratory work. PMID:27274565

Long-Lived Photoinduced Charge Separation in a Trinuclear Iron-μ 3 -oxo-based Metal–Organic Framework

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

Hanna, Lauren; Kucheryavy, Pavel; Liu, Cunming

2017-06-14

The presence of long-lived charge-separated excited states in metal-organic frameworks (MOFs) can enhance their photocatalytic activity by decreasing the probability that photogenerated electrons and holes recombine before accessing adsorbed reactants. Detecting these charge separated states via optical transient absorption, however, can be challenging when they lack definitive optical signatures. Here, we investigate the long-lived excited state of a MOF with such vague optical properties, MIL-100(Fe), comprised of Fe3-μ3-oxo clusters and trimesic acid linkers using Fe K-edge X-ray transient absorption (XTA) spectroscopy, to unambiguously determine its ligand-to-metal charge transfer character. Spectra measured at time delays up to 3.6 μs confirm themore » long lived nature of the charge separated excited state. Several trinuclear iron μ3- oxo carboxylate complexes, which model the trinuclear cores of the MOF structure, are measured for comparison using both steady state XAS and XTA to further support this assignment and corresponding decay time. The MOF is prepared as a colloidal nanoparticle suspension for these measurements so both its fabrication and particle size analysis are presented, as well.« less

Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

PubMed Central

Ribardo, Deborah A.; Brennan, Caitlin A.; Ruby, Edward G.; Jensen, Grant J.; Hendrixson, David R.

2016-01-01

Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes. PMID:26976588