Neon diffusion kinetics and implications for cosmogenic neon paleothermometry in feldspars

DOE PAGES

Tremblay, Marissa M.; Shuster, David L.; Balco, Greg; ...

2017-02-20

Observations of cosmogenic neon concentrations in feldspars can potentially be used to constrain the surface exposure duration or surface temperature history of geologic samples. The applicability of cosmogenic neon to either application depends on the temperature-dependent diffusivity of neon isotopes. Here in this work, we investigate the kinetics of neon diffusion in feldspars of different compositions and geologic origins through stepwise degassing experiments on single, proton-irradiated crystals. To understand the potential causes of complex diffusion behavior that is sometimes manifest as nonlinearity in Arrhenius plots, we compare our results to argon stepwise degassing experiments previously conducted on the same feldspars.more » Many of the feldspars we studied exhibit linear Arrhenius behavior for neon whereas argon degassing from the same feldspars did not. This suggests that nonlinear behavior in argon experiments is an artifact of structural changes during laboratory heating. However, other feldspars that we examined exhibit nonlinear Arrhenius behavior for neon diffusion at temperatures far below any known structural changes, which suggests that some preexisting material property is responsible for the complex behavior. In general, neon diffusion kinetics vary widely across the different feldspars studied, with estimated activation energies (E a) ranging from 83.3 to 110.7 kJ/mol and apparent pre-exponential factors (D 0) spanning three orders of magnitude from 2.4 ×10 -3 to 8.9 × 10 -1 cm 2 s -1. Finally, as a consequence of this variability, the ability to reconstruct temperatures or exposure durations from cosmogenic neon abundances will depend on both the specific feldspar and the surface temperature conditions at the geologic site of interest.« less

Neon diffusion kinetics and implications for cosmogenic neon paleothermometry in feldspars

NASA Astrophysics Data System (ADS)

Tremblay, Marissa M.; Shuster, David L.; Balco, Greg; Cassata, William S.

2017-05-01

Observations of cosmogenic neon concentrations in feldspars can potentially be used to constrain the surface exposure duration or surface temperature history of geologic samples. The applicability of cosmogenic neon to either application depends on the temperature-dependent diffusivity of neon isotopes. In this work, we investigate the kinetics of neon diffusion in feldspars of different compositions and geologic origins through stepwise degassing experiments on single, proton-irradiated crystals. To understand the potential causes of complex diffusion behavior that is sometimes manifest as nonlinearity in Arrhenius plots, we compare our results to argon stepwise degassing experiments previously conducted on the same feldspars. Many of the feldspars we studied exhibit linear Arrhenius behavior for neon whereas argon degassing from the same feldspars did not. This suggests that nonlinear behavior in argon experiments is an artifact of structural changes during laboratory heating. However, other feldspars that we examined exhibit nonlinear Arrhenius behavior for neon diffusion at temperatures far below any known structural changes, which suggests that some preexisting material property is responsible for the complex behavior. In general, neon diffusion kinetics vary widely across the different feldspars studied, with estimated activation energies (Ea) ranging from 83.3 to 110.7 kJ/mol and apparent pre-exponential factors (D0) spanning three orders of magnitude from 2.4 × 10-3 to 8.9 × 10-1 cm2 s-1. As a consequence of this variability, the ability to reconstruct temperatures or exposure durations from cosmogenic neon abundances will depend on both the specific feldspar and the surface temperature conditions at the geologic site of interest.

Optimization of mNeonGreen for Homo sapiens increases its fluorescent intensity in mammalian cells.

PubMed

Tanida-Miyake, Emiko; Koike, Masato; Uchiyama, Yasuo; Tanida, Isei

2018-01-01

Green fluorescent protein (GFP) is tremendously useful for investigating many cellular and intracellular events. The monomeric GFP mNeonGreen is about 3- to 5-times brighter than GFP and monomeric enhanced GFP and shows high photostability. The maturation half-time of mNeonGreen is about 3-fold faster than that of monomeric enhanced GFP. However, the cDNA sequence encoding mNeonGreen contains some codons that are rarely used in Homo sapiens. For better expression of mNeonGreen in human cells, we synthesized a human-optimized cDNA encoding mNeonGreen and generated an expression plasmid for humanized mNeonGreen under the control of the cytomegalovirus promoter. The resultant plasmid was introduced into HEK293 cells. The fluorescent intensity of humanized mNeonGreen was about 1.4-fold higher than that of the original mNeonGreen. The humanized mNeonGreen with a mitochondria-targeting signal showed mitochondrial distribution of mNeonGreen. We further generated an expression vector of humanized mNeonGreen with 3xFLAG tags at its carboxyl terminus as these tags are useful for immunological analyses. The 3xFLAG-tagged mNeonGreen was recognized well with an anti-FLAG-M2 antibody. These plasmids for the expression of humanized mNeonGreen and mNeonGreen-3xFLAG are useful tools for biological studies in mammalian cells using mNeonGreen.

Ionization Potentials for Isoelectronic Series.

ERIC Educational Resources Information Center

Agmon, Noam

1988-01-01

Presents a quantitative treatment of ionization potentials of isoelectronic atoms. By looking at the single-electron view of calculating the total energy of an atom, trends in the screening and effective quantum number parameters are examined. Approaches the question of determining electron affinities. (CW)

X-ray Emission Line Anisotropy Effects on the Isoelectronic Temperature Measurement Method

NASA Astrophysics Data System (ADS)

Liedahl, Duane; Barrios, Maria; Brown, Greg; Foord, Mark; Gray, William; Hansen, Stephanie; Heeter, Robert; Jarrott, Leonard; Mauche, Christopher; Moody, John; Schneider, Marilyn; Widmann, Klaus

2016-10-01

Measurements of the ratio of analogous emission lines from isoelectronic ions of two elements form the basis of the isoelectronic method of inferring electron temperatures in laser-produced plasmas, with the expectation that atomic modeling errors cancel to first order. Helium-like ions are a common choice in many experiments. Obtaining sufficiently bright signals often requires sample sizes with non-trivial line optical depths. For lines with small destruction probabilities per scatter, such as the 1s2p-1s2 He-like resonance line, repeated scattering can cause a marked angular dependence in the escaping radiation. Isoelectronic lines from near-Z equimolar dopants have similar optical depths and similar angular variations, which leads to a near angular-invariance for their line ratios. Using Monte Carlo simulations, we show that possible ambiguities associated with anisotropy in deriving electron temperatures from X-ray line ratios are minimized by exploiting this isoelectronic invariance.

High pressure neon arc lamp

DOEpatents

Sze, Robert C.; Bigio, Irving J.

2003-07-15

A high pressure neon arc lamp and method of using the same for photodynamic therapies is provided. The high pressure neon arc lamp includes a housing that encloses a quantity of neon gas pressurized to about 500 Torr to about 22,000 Torr. At each end of the housing the lamp is connected by electrodes and wires to a pulse generator. The pulse generator generates an initial pulse voltage to breakdown the impedance of the neon gas. Then the pulse generator delivers a current through the neon gas to create an electrical arc that emits light having wavelengths from about 620 nanometers to about 645 nanometers. A method for activating a photosensitizer is provided. Initially, a photosensitizer is administered to a patient and allowed time to be absorbed into target cells. Then the high pressure neon arc lamp is used to illuminate the target cells with red light having wavelengths from about 620 nanometers to about 645 nanometers. The red light activates the photosensitizers to start a chain reaction that may involve oxygen free radicals to destroy the target cells. In this manner, a high pressure neon arc lamp that is inexpensive and efficiently generates red light useful in photodynamic therapy is provided.

Biexciton emission from single isoelectronic traps formed by nitrogen-nitrogen pairs in GaAs

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

Takamiya, Kengo; Fukushima, Toshiyuki; Yagi, Shuhei

2013-12-04

We have studied photoluminescence (PL) from individual isoelectronic traps formed by nitrogen-nitrogen (NN) pairs in GaAs. Sharp emission lines due to exciton and biexciton were observed from individual isoelectronic traps in nitrogen atomic-layer doped (ALD) GaAs. The binding energy of biexciton bound to individual isoelectronic traps was approximately 8 meV. Both the exciton and biexciton luminescence lines show completely random polarization and no fine-structure splitting. These results are desirable to the application to the quantum cryptography used in the field of quantum information technology.

Theoretical studies of massive stars. I - Evolution of a 15-solar-mass star from the zero-age main sequence to neon ignition

NASA Technical Reports Server (NTRS)

Endal, A. S.

1975-01-01

The evolution of a star with mass 15 times that of the sun from the zero-age main sequence to neon ignition has been computed by the Henyey method. The hydrogen-rich envelope and all shell sources were explicitly included in the models. An algorithm has been developed for approximating the results of carbon burning, including the branching ratio for the C-12 + C-12 reaction and taking some secondary reactions into account. Penetration of the convective envelope into the core is found to be unimportant during the stages covered by the models. Energy transfer from the carbon-burning shell to the core by degenerate electron conduction becomes important after the core carbon-burning stage. Neon ignition will occur in a semidegenerate core and will lead to a mild 'flash.' Detailed numerical results are given in an appendix. Continuation of the calculations into later stages and variations with the total mass of the star will be discussed in later papers.

The neon gas field ion source—a first characterization of neon nanomachining properties

NASA Astrophysics Data System (ADS)

Livengood, Richard H.; Tan, Shida; Hallstein, Roy; Notte, John; McVey, Shawn; Faridur Rahman, F. H. M.

2011-07-01

At the Charged Particle Optics Conference (CPO7) in 2006, a novel trimer based helium gas field ion source (GFIS) was introduced for use in a new helium ion microscope (HIM), demonstrating the novel source performance attributes and unique imaging applications of the HIM (Hill et al., 2008 [1]; Livengood et al., 2008 [2]). Since that time there have been numerous enhancements to the HIM source and platform demonstrating resolution scaling into the sub 0.5 nm regime (Scipioni et al., 2009 [3]; Pickard et al., 2010 [4]). At this Charged Particle Optics Conference (CPO8) we will be introducing a neon version of the trimer-GFIS co-developed by Carl Zeiss SMT and Intel Corporation. The neon source was developed as a possible supplement to the gallium liquid metal ion source (LMIS) used today in most focused ion beam (FIB) systems (Abramo et al., 1994 [5]; Young et al.,1998 [6]). The neon GFIS source has low energy spread (∼1 eV) and a small virtual source size (sub-nanometer), similar to that of the helium GFIS. However neon does differ from the helium GFIS in two significant ways: neon ions have high sputtering yields (e.g. 1 Si atom per incident ion at 20 keV); and have relatively shallow implant depth (e.g. 46 nm in silicon at 20 keV). Both of these are limiting factors for helium in many nanomachining applications. In this paper we will present both simulation and experimental results of the neon GFIS used for imaging and nanomachining applications.

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

PubMed

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

NEON Citizen Science: Planning and Prototyping

NASA Astrophysics Data System (ADS)

Newman, S. J.; Henderson, S.; Gardiner, L. S.; Ward, D.; Gram, W.

2011-12-01

The National Ecological Observatory Network (NEON) will be a national resource for ecological research and education. NEON citizen science projects are being designed to increase awareness and educate citizen scientists about the impacts of climate change, land-use change, and invasive species on continental-scale ecological processes as well as expand NEON data collection capacity by enabling laypersons to collect geographically distributed data. The citizen science area of the NEON web portal will enable citizen scientists to collect, contribute, interpret, and visualize scientific data, as well as access training modules, collection protocols and targeted learning experiences related to citizen science project topics. For NEON, citizen science projects are a means for interested people to interact with and contribute to NEON science. Investigations at vast spatial and temporal scales often require rapid acquisition of large amounts of data from a geographically distributed population of "human sensors." As a continental-scale ecological observatory, NEON is uniquely positioned to develop strategies to effectively integrate data collected by non-scientists into scientific databases. Ultimately, we plan to work collaboratively to transform the practice of science to include "citizens" or non-scientists in the process. Doing science is not limited to scientists, and breaking down the barriers between scientists and citizens will help people better understand the power of using science in their own decision making. In preparation for fully developing the NEON citizen science program, we are partnering with Project BudBurst (PBB), a citizen science project focused on monitoring plant phenology. The educational goals of PBB are to: (1) increase awareness of climate change, (2) educate citizen scientists about the impacts of climate change on plants and the environment, and (3) increase science literacy by engaging participants in the scientific process. Phenology was

Calculation of levels, transition rates, and lifetimes for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII

NASA Astrophysics Data System (ADS)

Wang, K.; Chen, Z. B.; Chen, C. Y.; Yan, J.; Dang, W.; Zhao, X. H.; Yang, X.

2017-09-01

Multi-configuration Dirac-Fock (MCDF) calculations of energy levels, wavelengths, oscillator strengths, lifetimes, and electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2), magnetic quadrupole (M2) transition rates are reported for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII. Results are presented among the 86 levels of the 4s2 4p3, 4 s 4p4, 4p5, 4s2 4p2 4 d, and 4 s 4p3 4 d configurations in each ion. The relativistic atomic structure package GRASP2K is adopted for the calculations, in which the contributions from the correlations within the n ≤ 7 complexes, Breit interaction (BI) and quantum electrodynamics (QED) effects are taking into account. The many-body perturbation theory (MBPT) method is also employed as an independent calculation for comparison purposes, taking W XLII as an example. Calculated results are compared with data from other calculations and the observed values from the Atomic Spectra Database (ASD) of the National Institute of Standards and Technology (NIST). Good agreements are obtained. i.e, the accuracy of our energy levels is assessed to be better than 0.6%. These accurate theoretical data should be useful for diagnostics of hot plasmas in fusion devices.

K-Shell Photoabsorption and Photoionisation of Trace Elements I. Isoelectronic Sequences With Electron Number 3< or = N < or = 11

NASA Technical Reports Server (NTRS)

Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Witthoeft, M. C.; Kallman, T. R.

2016-01-01

Context. With the recent launching of the Hitomi X-ray space observatory, K lines and edges of chemical elements with low cosmic abundances, namely F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn, can be resolved and used to determine important properties of supernova remnants, galaxy clusters and accreting black holes and neutron stars.Aims. The second stage of the present ongoing project involves the computation of the accurate photoabsorption and photoionisation cross sections required to interpret the X-ray spectra of such trace elements.Methods. Depending on target complexity and computer tractability, ground-state cross sections are computed either with the close-coupling Breit-Pauli R-matrix method or with the autostructure atomic structure code in the isolated-resonance approximation. The intermediate-coupling scheme is used whenever possible. In order to determine a realistic K-edge behaviour for each species, both radiative and Auger dampings are taken into account, the latter being included in the R-matrix formalism by means of an optical potential.Results. Photoabsorption and total and partial photoionisation cross sections are reported for isoelectronic sequences with electron numbers 3< or = N< or = 11. The Na sequence (N=11) is used to estimate the contributions from configurations with a 2s hole (i.e. [2s]) and those containing 3d orbitals, which will be crucial when considering sequences with N 11.Conclusions. It is found that the [2s/u] configurations must be included in the target representations of species with N> 11 as they contribute significantly to the monotonic background of the cross section between the L and K edges. Configurations with 3d orbitals are important in rendering an accurate L edge, but they can be practically neglected in the K-edge region.

Energy levels, lifetimes, and transition rates for the selenium isoelectronic sequence Pd XIII-Te XIX, Xe XXI-Nd XXVII, W XLI

NASA Astrophysics Data System (ADS)

Wang, K.; Yang, X.; Chen, Z. B.; Si, R.; Chen, C. Y.; Yan, J.; Zhao, X. H.; Dang, W.

2017-09-01

Energy levels, wavelengths, lifetimes, oscillator strengths, and electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2), magnetic quadrupole (M2) transition rates among the 46 fine structure levels belonging to the ([ Ar ] 3d10) 4s2 4p4, ([ Ar ] 3d10) 4s2 4p3 4 d, and ([ Ar ] 3d10) 4 s 4p5 configurations for the selenium isoelectronic sequence Pd XIII-Te XIX, Xe XXI-Nd XXVII, W XLI are reported. These data are determined in the multi-configuration Dirac-Fock (MCDF) approach, in which relativistic effects, main electron correlations within the n = 7 complex, Breit interaction (BI), and quantum electrodynamic (QED) corrections are included. The many-body perturbation theory (MBPT) method is also employed as an independent calculation to confirm the present accuracy, taking W XLI as an example. Comparisons and analysis are made between the present results and available experimental and theoretical ones, and good agreements are obtained. These accurate data are expected to be useful in nuclear fusion research and astrophysical applications.

Spectroscopic Study of Neon Z-Pinch Plasma for Sodium-Neon Photopumping Experiments

DTIC Science & Technology

1992-01-06

enhancement of the 11-A radiation from the n=4 level of neon when the sodium pump was present. For the 25-GV pump power, theoretical calculations predict...when the neon plasma is photopumped. Extensive theoretical analysis has been devoted to establishing the appropriate conditions for these plasmas. 5 ,44...producing thermonuclear neutrons. 63-65 Extensive theoretical modeling of the stability of these plasmas has guided this work.66 An imploding-liner Z

Solar helium and neon in the Earth

NASA Technical Reports Server (NTRS)

Honda, M.; Mcdougall, I.; Patterson, D. B.

1994-01-01

Neon isotopic compositions in mantle-derived samples commonly are enriched in (20)Ne and (21)Ne relative to (22)Ne compared with atmospheric neon ((20)Ne/(22)Ne and (21)Ne/(22)Ne ratios in atmospheric neon are 9.8 and 0.029, respectively), together with significant primordial (3)He. Such results have been obtained on MORB's, intraplate plume-related oceanic island basalts, backarc basin basalts, mantle xenoliths, ancient diamonds and CO2 well gases (e.g., 1 - 8). The highest (20)Ne/(22)Ne ratio observed in MORB glasses (= 13.6 plus or minus 1.3 is close to the solar value (= 13.6, as observed in solar wind). In order to explain the enrichment of (20)Ne and (21)Ne relative to atmospheric neon for samples derived from the mantle, it is necessary to postulate the presence of at least two distinct non-atmospheric components. The two most likely candidates are solar and nucleogenic ((20)Ne/(22)Ne solar = 13.6 (21)Ne/(22)Ne solar = 0.032, (20)Ne/(22)Ne nucleogenic = 2.5 and (21)Ne/(22)Ne nucleogenic = 32). This is because solar neon is the only known component with a (20)Ne/(22)Ne ratio greater than both the atmospheric value and that observed in samples derived from the mantle. Nucleogenic neon is well known to elevate (21)Ne/(22)Ne ratios. Neon isotopic signatures observed in mantle-derived samples can be accounted for by mixing of the three neon end members: solar, nucleogenic and atmospheric.

NEON Airborne Remote Sensing of Terrestrial Ecosystems

NASA Astrophysics Data System (ADS)

Kampe, T. U.; Leisso, N.; Krause, K.; Karpowicz, B. M.

2012-12-01

The National Ecological Observatory Network (NEON) is the continental-scale research platform that will collect information on ecosystems across the United States to advance our understanding and ability to forecast environmental change at the continental scale. One of NEON's observing systems, the Airborne Observation Platform (AOP), will fly an instrument suite consisting of a high-fidelity visible-to-shortwave infrared imaging spectrometer, a full waveform small footprint LiDAR, and a high-resolution digital camera on a low-altitude aircraft platform. NEON AOP is focused on acquiring data on several terrestrial Essential Climate Variables including bioclimate, biodiversity, biogeochemistry, and land use products. These variables are collected throughout a network of 60 sites across the Continental United States, Alaska, Hawaii and Puerto Rico via ground-based and airborne measurements. Airborne remote sensing plays a critical role by providing measurements at the scale of individual shrubs and larger plants over hundreds of square kilometers. The NEON AOP plays the role of bridging the spatial scales from that of individual organisms and stands to the scale of satellite-based remote sensing. NEON is building 3 airborne systems to facilitate the routine coverage of NEON sites and provide the capacity to respond to investigator requests for specific projects. The first NEON imaging spectrometer, a next-generation VSWIR instrument, was recently delivered to NEON by JPL. This instrument has been integrated with a small-footprint waveform LiDAR on the first NEON airborne platform (AOP-1). A series of AOP-1 test flights were conducted during the first year of NEON's construction phase. The goal of these flights was to test out instrument functionality and performance, exercise remote sensing collection protocols, and provide provisional data for algorithm and data product validation. These test flights focused the following questions: What is the optimal remote

Increasing the sensitivity of LXe TPCs to dark matter by doping with helium or neon

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

Lippincott, W. Hugh; Alexander, Thomas R.; Hime, Andrew

Next generation liquid xenon TPCs are poised to increase our sensitivity to dark matter by two orders of magnitude over a wide range of possible dark matter candidates. This proceedings describes an idea to expand the reach and flexibility of such detectors even further, by adding helium and neon to the xenon to enable searches for very light dark matter and combining high and low Z targets in the same detector. Adding helium or neon to LXe-TPCs has many advantages. First, the helium or neon target benefits from the excellent self-shielding provided by a large liquid xenon detector. Second, themore » same instrumentation, PMTs, and data acquisition can be used. Third, light nuclei are more robust to the systematic uncertainties that affect light WIMP searches. Fourth, helium and neon recoils will likely produce larger signals in liquid xenon than xenon recoils, achieving lower energy thresholds, and further increasing the sensitivity to light WIMPs. Finally, by adding He/Ne in sequence after a Xe-only run, the source of any observed signal can be isolated.« less

Increasing the sensitivity of LXe TPCs to dark matter by doping with helium or neon

DOE PAGES

Lippincott, W. Hugh; Alexander, Thomas R.; Hime, Andrew

2017-02-03

Next generation liquid xenon TPCs are poised to increase our sensitivity to dark matter by two orders of magnitude over a wide range of possible dark matter candidates. This proceedings describes an idea to expand the reach and flexibility of such detectors even further, by adding helium and neon to the xenon to enable searches for very light dark matter and combining high and low Z targets in the same detector. Adding helium or neon to LXe-TPCs has many advantages. First, the helium or neon target benefits from the excellent self-shielding provided by a large liquid xenon detector. Second, themore » same instrumentation, PMTs, and data acquisition can be used. Third, light nuclei are more robust to the systematic uncertainties that affect light WIMP searches. Fourth, helium and neon recoils will likely produce larger signals in liquid xenon than xenon recoils, achieving lower energy thresholds, and further increasing the sensitivity to light WIMPs. Finally, by adding He/Ne in sequence after a Xe-only run, the source of any observed signal can be isolated.« less

Hydrodynamic models for novae with ejecta rich in oxygen, neon and magnesium

NASA Technical Reports Server (NTRS)

Starrfield, S.; Sparks, W. M.; Truran, J. W.

1985-01-01

The characteristics of a new class of novae are identified and explained. This class consists of those objects that have been observed to eject material rich in oxygen, neon, magnesium, and aluminum at high velocities. We propose that for this class of novae the outburst is occurring not on a carbon-oxygen white dwarf but on an oxygen-neon-magnesium white dwarf which has evolved from a star which had a main sequence mass of approx. 8 solar masses to approx. 12 solar masses. An outburst was simulated by evolving 1.25 solar mass white dwarfs accreting hydrogen rich material at various rates. The effective enrichment of the envelope by ONeMg material from the core is simulated by enhancing oxygen in the accreted layers. The resulting evolutionary sequences can eject the entire accreted envelope plus core material at high velocities. They can also become super-Eddington at maximum bolometric luminosity. The expected frequency of such events (approx. 1/4) is in good agreement with the observed numbers of these novae.

NEON Citizen Science: Planning and Prototyping (Invited)

NASA Astrophysics Data System (ADS)

Gram, W.

2010-12-01

The National Ecological Observatory Network (NEON) will be a national resource for ecological research and education. NEON citizen science projects are being designed to increase awareness and educate citizen scientists about the impacts of climate change, land-use change, and invasive species on continental-scale ecological processes as well as expand NEON data collection capacity by enabling laypersons to collect geographically distributed data. The citizen science area of the NEON web portal will enable citizen scientists to collect, contribute, interpret, and visualize scientific data, as well as access training modules, collection protocols and targeted learning experiences related to citizen science project topics. For NEON, citizen science projects are a means for interested people to interact with and contribute to NEON science. Investigations at vast spatial and temporal scales often require rapid acquisition of large amounts of data from a geographically distributed population of “human sensors.” As a continental-scale ecological observatory, NEON is uniquely positioned to develop strategies to effectively integrate data collected by non-scientists into scientific databases. Ultimately, we plan to work collaboratively to transform the practice of science to include “citizens” or non-scientists in the process. Doing science is not limited to scientists, and breaking down the barriers between scientists and citizens will help people better understand the power of using science in their own decision making. In preparation for fully developing the NEON citizen science program, we are partnering with Project BudBurst (PBB), a citizen science project focused on monitoring plant phenology. The educational goals of PBB are to: (1) increase awareness of climate change, (2) educate citizen scientists about the impacts of climate change on plants and the environment, and (3) increase science literacy by engaging participants in the scientific process

The Helium Atom and Isoelectronic Ions in Two Dimensions

ERIC Educational Resources Information Center

Patil, S. H.

2008-01-01

The energy levels of the helium atom and isoelectronic ions in two dimensions are considered. The difficulties encountered in the analytical evaluation of the perturbative and variational expressions for the ground state, promote an interesting factorization of the inter-electronic interaction, leading to simple expressions for the energy. This…

Study of the 4p2, 5p2 and 5s5f excited configurations of the Zn and Cd isoelectronic sequences, using relativistic and non-relativistic semiempirical approaches

NASA Astrophysics Data System (ADS)

Di Rocco, Héctor O.; Raineri, Mónica; Reyna-Almandos, Jorge G.

2016-11-01

The consistency of the energy levels published for configurations 4p2, 5p2 and 5s5f belonging to Zn and Cd isoelectronic sequences is studied. Different semiempirical approaches considering the linearity of the Slater integrals for large Zc, the smoothness of the sF screening parameters, the energy values in terms of Z (or Zc), and the differences of the Ecalc - Eexp values are used, where Ecalc values are energies calculated with a Hartree-Hock method with relativistic corrections and superposition of configurations (HFR-SOC), and Eexp are the experimental values. For the np2 configurations both LS and relativistic jj expressions are considered. Configuration 5s5f is also analyzed taking into account the Landé's interval rule.

Binary collision model for neon Auger spectra from neon ion bombardment of the aluminum surface

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1986-01-01

A model is developed to account for the angle-resolved Auger spectra from neon ion bombardment of the aluminum surface recently obtained by Pepper and Aron. The neon is assumed to be excited in a single asymmetric neon-aluminum-collision and scattered back into the vacuum where it emits an Auger electron. The velocity of the Auger electron acquires a Doppler shift by virtue of the emission from a moving source. The dependence of the Auger peak shape and energy on the incident ion energy, angle of incidence and on the angle of Auger electron emission with respect to the surface is presented. Satisfactory agreement with the angle resolved experimental observations is obtained. The dependence of the angle-integrated Auger yield on the incident ion energy and angle of incidence is also obtained and shown to be in satisfactory agreement with available experimental evidence.

The energy dependence of the neon-22 excess in the cosmic radiation

NASA Technical Reports Server (NTRS)

Herrstroem, N. Y.; Lund, N.

1985-01-01

It has been recognized now for some time that the heavy neon isotope, neon-22, is overabundant by a factor of 3 to 4 with respect to neon-22 in the cosmic ray source compared to the ratio of these isotopes in the Solar System. In view of the otherwise remarkable similarity of the chemical composition of the cosmic ray source and the composition of the Solar Energetic Particles, the anomaly regarding the neon isotopes is so much more striking. The observed excess of neon-22 is too large to be explained as a result of the chemical evolution of the Galaxy since the formation of the Solar System. Further information on the origin of the neon-22 excess may come from a comparison of the energy spectra of the two neon isotopes. If the cosmic radiation in the solar neighborhood is a mixture of material from several sources, one of which has an excess of neon-22, then the source energy spectra of neon-20 and neon-22 may differ significantly.

Complete quantum control of exciton qubits bound to isoelectronic centres.

PubMed

Éthier-Majcher, G; St-Jean, P; Boso, G; Tosi, A; Klem, J F; Francoeur, S

2014-05-30

In recent years, impressive demonstrations related to quantum information processing have been realized. The scalability of quantum interactions between arbitrary qubits within an array remains however a significant hurdle to the practical realization of a quantum computer. Among the proposed ideas to achieve fully scalable quantum processing, the use of photons is appealing because they can mediate long-range quantum interactions and could serve as buses to build quantum networks. Quantum dots or nitrogen-vacancy centres in diamond can be coupled to light, but the former system lacks optical homogeneity while the latter suffers from a low dipole moment, rendering their large-scale interconnection challenging. Here, through the complete quantum control of exciton qubits, we demonstrate that nitrogen isoelectronic centres in GaAs combine both the uniformity and predictability of atomic defects and the dipole moment of semiconductor quantum dots. This establishes isoelectronic centres as a promising platform for quantum information processing.

Neon reduction program on Cymer ArF light sources

NASA Astrophysics Data System (ADS)

Kanawade, Dinesh; Roman, Yzzer; Cacouris, Ted; Thornes, Josh; O'Brien, Kevin

2016-03-01

In response to significant neon supply constraints, Cymer has responded with a multi-part plan to support its customers. Cymer's primary objective is to ensure that reliable system performance is maintained while minimizing gas consumption. Gas algorithms were optimized to ensure stable performance across all operating conditions. The Cymer neon support plan contains four elements: 1. Gas reduction program to reduce neon by >50% while maintaining existing performance levels and availability; 2. short-term containment solutions for immediate relief. 3. qualification of additional gas suppliers; and 4. long-term recycling/reclaim opportunity. The Cymer neon reduction program has shown excellent results as demonstrated through the comparison on standard gas use versus the new >50% reduced neon performance for ArF immersion light sources. Testing included stressful conditions such as repetition rate, duty cycle and energy target changes. No performance degradation has been observed over typical gas lives.

Laser gain on 3p-3d and 3s-3p transitions and X-ray line ratios for the nitrogen isoelectronic sequence

NASA Technical Reports Server (NTRS)

Feldman, U.; Seely, J. F.; Bhatia, A. K.

1989-01-01

Results are presented on calculations of the 72 levels belonging to the 2s(2)2p(3), 2s2p(4), 2p(5), 2s(2)2p(2)3s, 2s(2)2p(2)3p, and 2s(2)2p(2)3d configurations of the N I isoelectronic sequence for the ions Ar XII, Ti XVI, Fe XX, Zn XXIV, and Kr XXX, for electron densities up to 10 to the 24th/cu cm. It was found that large population inversions and gain occur between levels in the 2s(2)2p(2)3p configuration and levels in the 2s(2)2p(2)3d configuration that cannot decay to the ground configuration by an electric dipole transition. For increasing electron densities, the intensities of the X-ray transitions from the 2s(2)2p(2)3p configuration to the ground configuration decrease relative to the transitions from the 2s(2)2p(2)3s and 2s(2)2p(2)3d configurations to the ground configuration. The density dependence of these X-ray line ratios is presented.

ASA's Chandra Neon Discovery Solves Solar Paradox

NASA Astrophysics Data System (ADS)

2005-07-01

NASA's Chandra X-ray Observatory survey of nearby sun-like stars suggests there is nearly three times more neon in the sun and local universe than previously believed. If true, this would solve a critical problem with understanding how the sun works. "We use the sun to test how well we understand stars and, to some extent, the rest of the universe," said Jeremy Drake of the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass. "But in order to understand the sun, we need to know exactly what it is made of," he added. It is not well known how much neon the sun contains. This is critical information for creating theoretical models of the sun. Neon atoms, along with carbon, oxygen and nitrogen, play an important role in how quickly energy flows from nuclear reactions in the sun's core to its edge, where it then radiates into space. Chandra X-ray Spectrum of II Pegasi Chandra X-ray Spectrum of II Pegasi The rate of this energy flow determines the location and size of a crucial stellar region called the convection zone. The zone extends from near the sun's surface inward approximately 125,000 miles. The zone is where the gas undergoes a rolling, convective motion much like the unstable air in a thunderstorm. "This turbulent gas has an extremely important job, because nearly all of the energy emitted at the surface of the sun is transported there by convection," Drake said. The accepted amount of neon in the sun has led to a paradox. The predicted location and size of the solar convection zone disagree with those deduced from solar oscillations. Solar oscillations is a technique astronomers previously relied on to probe the sun's interior. Several scientists have noted the problem could be fixed if the abundance of neon is in fact about three times larger than currently accepted. Attempts to measure the precise amount of neon in the Sun have been frustrated by a quirk of nature; neon atoms in the Sun give off no signatures in visible light. However, in a gas

Studies of Ionic Photoionization Using Relativistic Random Phase Approximation and Relativistic Multichannel Quantum Defect Theory

NASA Astrophysics Data System (ADS)

Haque, Ghousia Nasreen

The absorption of electromagnetic radiation by positive ions is one of the fundamental processes of nature which occurs in every intensely hot environment. Due to the difficulties in producing sufficient densities of ions in a laboratory, there are very few measurements of ionic photoabsorption parameters. On the theoretical side, some calculations have been made of a few major photoionization parameters, but generally speaking, most of the work done so far has employed rather simple single particle models and any theoretical work which has adequately taken into account intricate atomic many-body and relativistic effects is only scanty. In the present work, several complex aspects of atomic/ionic photoabsorption parameters have been studied. Non -resonant photoionization in neon and argon isonuclear as well as isoelectronic sequences has been studied using a very sophisticated technique, namely the relativistic random phase approximation (RRPA). This technique takes into account relativistic effects as well as an important class of major many-body effects on the same footing. The present calculations confirmed that gross features of photoionization parameters calculated using simpler models were not an artifact of the simple model. Also, the present RRPA calculations on K^+ ion and neutral Ar brought out the relative importance of various many-body effects such the inter-channel coupling. Inter-channel coupling between discrete bound state photoexcitation channels from an inner atomic/ionic level and photoionization continuum channels from an outer atomic/ionic level leads to the phenomena of autoionization resonances in the photoionization process. These resonances lead to very complex effects in the atomic/ionic photoabsorption spectra. These resonances have been calculated and studied in the present work in the neon and magnesium isoelectronic sequences using the relativistic multi-channel quantum defect theory (RMQDT) within the framework of the RRPA. The

Demonstrating Fluorescence with Neon Paper and Plastic

ERIC Educational Resources Information Center

Birriel, Jennifer J.; Roe, Clarissa

2015-01-01

Several papers in this journal have dealt with the fluorescence in orange neon plastic, olive oil, and soda. In each case, the fluorescent emission was excited by either green or violet-blue laser light. In this paper, we examine the fluorescent emission spectra of so-called neon colored papers and plastic clipboards available in department and…

Fractionation of terrestrial neon by hydrodynamic hydrogen escape from ancient steam atmospheres

NASA Technical Reports Server (NTRS)

Zahnle, K.

1991-01-01

Atmospheric neon is isotopically heavier than mantle neon. By contrast, nonradiogenic mantle Ar, Kr, and Xe are not known to differ from the atmosphere. These observations are most easily explained by selective neon loss to space; however, neon is much too massive to escape from the modern atmosphere. Steam atmospheres are a likely, if intermittent, feature of the accreting Earth. They occur because, on average, the energy liberated during accretion places Earth above the runaway greenhouse threshold, so that liquid water is not stable at the surface. It is found that steam atmospheres should have lasted some ten to fifty million years. Hydrogen escape would have been vigorous, but abundant heavy constituents would have been retained. There is no lack of plausible candidates; CO2, N2, or CO could all suffice. Neon can escape because it is less massive than any of the likely pollutants. Neon fractionation would have been a natural byproduct. Assuming that the initial Ne-20/Ne-22 ratio was solar, it was found that it would have taken some ten million years to effect the observed neon fractionation in a 30 bar steam atmosphere fouled with 10 bars of CO. Thicker atmospheres would have taken longer; less CO, shorter. This mechanism for fractionating neon has about the right level of efficiency. Because the lighter isotope escapes much more readily, total neon loss is pretty minimal; less than half of the initial neon endowment escapes.

Neon in ultrashort and intense x-rays from free electron lasers

NASA Astrophysics Data System (ADS)

Buth, Christian; Beerwerth, Randolf; Obaid, Razib; Berrah, Nora; Cederbaum, Lorenz S.; Fritzsche, Stephan

2018-03-01

We theoretically examine neon atoms in ultrashort and intense x-rays from free electron lasers and compare our results with data from experiments conducted at the Linac Coherent Light Source. For this purpose, we treat in detail the electronic structure in all possible nonrelativistic cationic configurations using a relativistic multiconfiguration approach. The interaction with the x-rays is described in rate-equation approximation. To understand the mechanisms of the interaction, a path analysis is devised which allows us to investigate what sequences of photoionization and decay processes lead to a specific configuration and with what probability. Thereby, we uncover a connection to the mathematics of graph theory and formal languages. In detail, we study the ion yields and find that plain rate equations do not provide a satisfactory description. We need to extend the rate equations for neon to incorporate double Auger decay of a K-shell vacancy and photoionization shake off for neutral neon. Shake off is included for valence and core ionization; the former has hitherto been overlooked but has important consequences for the ion yields from an x-ray energy below the core ionization threshold. Furthermore, we predict the photon yields from XUV and x-ray fluorescence these allow one insights into the configurations populated by the interaction with the x-rays. Finally, we discover that inaccuracies in those Auger decay widths employed in previous studies have only a minor influence on ion and photon yields.

Neon as a Buffer Gas for a Mercury-Ion Clock

NASA Technical Reports Server (NTRS)

Prestage, John; Chung, Sang

2008-01-01

A developmental miniature mercury-ion clock has stability comparable to that of a hydrogen-maser clock. The ion-handling components are housed in a sealed vacuum tube, wherein a getter pump is used to maintain the partial vacuum, and the evacuated tube is backfilled with mercury vapor in a buffer gas. Neon was determined to be the best choice for the buffer gas: The pressure-induced frequency pulling by neon was found to be only about two-fifths of that of helium. Furthermore, because neon diffuses through solids much more slowly than does helium, the operational lifetime of a tube backfilled with neon could be considerably longer than that of a tube backfilled with helium.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

The First NEON School in La Silla

NASA Astrophysics Data System (ADS)

Dennefeld, M.; Melo, C.; Selman, F.

2016-06-01

The NEON Observing Schools have long provided PhD students with practical experience in the preparation, execution and reduction of astronomical observations, primarily at northern observatories. The NEON School was held in Chile for the first time, with observations being conducted at La Silla. The school was attended by 20 students, all from South America, and observations were performed with two telescopes, including the New Technology Telescope. A brief description of the school is presented and the observing projects and their results are described.

NEON terrestrial field observations: designing continental scale, standardized sampling

Treesearch

R. H. Kao; C.M. Gibson; R. E. Gallery; C. L. Meier; D. T. Barnett; K. M. Docherty; K. K. Blevins; P. D. Travers; E. Azuaje; Y. P. Springer; K. M. Thibault; V. J. McKenzie; M. Keller; L. F. Alves; E. L. S. Hinckley; J. Parnell; D. Schimel

2012-01-01

Rapid changes in climate and land use and the resulting shifts in species distributions and ecosystem functions have motivated the development of the National Ecological Observatory Network (NEON). Integrating across spatial scales from ground sampling to remote sensing, NEON will provide data for users to address ecological responses to changes in climate, land use,...

The NEON Aquatic Network: Expanding the Availability of Biogeochemical Data

NASA Astrophysics Data System (ADS)

Vance, J. M.; Bohall, C.; Fitzgerald, M.; Utz, R.; Parker, S. M.; Roehm, C. L.; Goodman, K. J.; McLaughlin, B.

2013-12-01

Aquatic ecosystems are facing unprecedented pressure from climate change and land-use practices. Invasive species, whether plant, animal, insect or microbe present additional threat to aquatic ecosystem services. There are significant scientific challenges to understanding how these forces will interact to affect aquatic ecosystems, as the flow of energy and materials in the environment is driven by multivariate and non-linear biogeochemical cycles. The National Ecological Observatory Network (NEON) will collect and provide observational data across multiple scales. Sites were selected to maximize representation of major North American ecosystems using a multivariate geographic clustering method that partitioned the continental US, AK, HI, and Puerto Rico into 20 eco-climatic domains. The NEON data collection systems and methods are designed to yield standardized, near real-time data subjected to rigorous quality controls prior to public dissemination through an online data portal. NEON will collect data for 30 years to facilitate spatial-temporal analysis of environmental responses and drivers of ecosystem change, ranging from local through continental scales. Here we present the NEON Aquatic Network, a multi-parameter network consisting of a combination of in situ sensor and observational data. This network will provide data to examine biogeochemical, biological, hydrologic and geomorphic metrics at 36 sites, which are a combination of small 1st/2nd order wadeable streams, large rivers and lakes. A typical NEON Aquatic site will host up to two in-stream sensor sets designed to collect near-continuous water quality data (e.g. pH/ORP, temperature, conductivity, dissolved oxygen, CDOM) along with up to 8 shallow groundwater monitoring wells (level, temp., cond.), and a local meteorological station (e.g. 2D wind speed, PAR, barometric pressure, temperature, net radiation). These coupled sensor suites will be complemented by observational data (e.g. water

Fragmentation dynamics of ionized neon trimer inside helium nanodroplets: a theoretical study.

PubMed

Bonhommeau, David; Viel, Alexandra; Halberstadt, Nadine

2004-06-22

We report a theoretical study of the fragmentation dynamics of Ne(3) (+) inside helium nanodroplets, following vertical ionization of the neutral neon trimer. The motion of the neon atoms is treated classically, while transitions between the electronic states of the ionic cluster are treated quantum mechanically. A diatomics-in-molecules description of the potential energy surfaces is used, in a minimal basis set consisting of three effective p orbitals on each neon atom for the missing electron. The helium environment is modeled by a friction force acting on the neon atoms when their speed exceeds the Landau velocity. A reasonable range of values for the corresponding friction coefficient is obtained by comparison with existing experimental measurements. (c) 2004 American Institute of Physics.

Energy-transfer processes in neon-hydrogen mixtures excited by electron beams

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

Morozov, A.; Kruecken, R.; Ulrich, A.

2005-12-15

Energy- and charge-transfer processes in neon-hydrogen mixtures (500-1400 hPa neon and 0.001-3 hPa hydrogen partial pressures) excited by a pulsed low-energy ({approx}10 keV) electron beam were investigated using time-resolved spectroscopy. Time spectra of the hydrogen Lyman-{alpha} line, neon excimer emission (second continuum), and neon atomic lines (3p-3s transitions) were recorded. The time-integrated intensity of the Lyman-{alpha} emission was measured for the same range of gas mixtures. It is shown that direct energy transfer from Ne{sub 2}* excimers and neon atoms in the four lowest excited states as well as recombination of H{sub 3}{sup +} ions are the main channels populatingmore » atomic hydrogen in the n=2 state. A rate constant of (4.2{+-}1.4)x10{sup -11} cm{sup 3} s{sup -1} was obtained for the charge transfer from Ne{sub 2}{sup +} ions to molecular hydrogen. A lower limit for the depopulation rate constant of Ne{sub 2}* excimers by molecular hydrogen (combination of energy transfer and ionization) was found to be 1.0x10{sup -10} cm{sup 3} s{sup -1}.« less

The First Four Year's of Orthoimages from NEON's Airborne Observation Platform

NASA Astrophysics Data System (ADS)

Adler, J.; Gallery, W. O.

2016-12-01

The National Ecological Observatory Network (NEON), funded by the National Science Foundation (NSF), has been collecting orthorectified images in conjunction with lidar and spectrometer data for the past four years. The NEON project breaks up the United States into 20 regional areas from Puerto Rico to the North Slope of Alaska, with each region (Domain) typically having three specific sites of interest. Each site spans between 100km2 - 720km2 in area. Currently there are over 125,000 orthorectified images online from 6 Domains for the public and scientific community to freely download. These images are expected to assist researchers in many areas including vegetation cover, dominant vegetation type, and environmental change detection. In 2016 the NEON Airborne Observation Platform (AOP) group has collected digital imagery at 8.5 cm resolution over approximately 30 sites, for a total of 60,000 orthoimages. This presentation details the current status of the surveys conducted to date, and describes the scientific details of how NEON publishes Level 1 and Level 3 products. In particular, the onboard lidar system's contribution to the orthorectification process is outlined, in addition to the routines utilized for correcting white balance and exposure. Additionally, key flight parameters needed to produce NEON's complementary data of multi-sensor (camera/lidar/spectrometer) instruments are discussed. Problems with validating the orthoimages with the coarser resolution lidar system are addressed, to include the utilization of ground-truth locations. Lastly, methods to access NEON's publically available 10cm resolution orthoimages (in both individual image format, and in 1km by 1km tiles) are presented. A brief overview of the 2017 field season's nine new sites completes the presentation.

NEON Data Products: Supporting the Validation of GCOS Essential Climate Variables

NASA Astrophysics Data System (ADS)

Petroy, S. B.; Fox, A. M.; Metzger, S.; Thorpe, A.; Meier, C. L.

2014-12-01

The National Ecological Observatory Network (NEON) is a continental-scale ecological observation platform designed to collect and disseminate data that contributes to understanding and forecasting the impacts of climate change, land use change, and invasive species on ecology. NEON will collect in-situ and airborne data over 60 sites across the US, including Alaska, Hawaii, and Puerto Rico. The NEON Biomass, Productivity, and Biogeochemistry protocols currently direct the collection of samples from distributed, gradient, and tower plots at each site, with sampling occurring either multiple times during the growing season, annually, or on three- or five-year centers (e.g. for coarse woody debris). These data are processed into a series of field-derived data products (e.g. Biogeochemistry, LAI, above ground Biomass, etc.), and when combined with the NEON airborne hyperspectral and LiDAR imagery, are used support validation efforts of algorithms for deriving vegetation characteristics from the airborne data. Sites are further characterized using airborne data combined with in-situ tower measurements, to create additional data products of interest to the GCOS community, such as Albedo and fPAR. Presented here are a summary of tower/field/airborne sampling and observation protocols and examples of provisional datasets collected at NEON sites that may be used to support the ongoing validation of GCOS Essential Climate Variables.

Suppression of Defects and Deep Levels Using Isoelectronic Tungsten Substitution in Monolayer MoSe 2

DOE PAGES

Li, Xufan; Puretzky, Alexander A.; Sang, Xiahan; ...

2017-05-18

Chemical vapor deposition (CVD) is one of the most promising, scalable synthetic techniques to enable large-area synthesis of two-dimensional (2D) transition metal dichalcogenides (TMDs) for the realization of next generation optoelectronic devices. However, defects formed during the CVD growth process currently limit the quality and electronic properties of 2D TMDs. Effective synthesis and processing strategies to suppress defects and enhance the quality of 2D TMDs are urgently needed. In this work, isoelectrnic doping to produce stable alloy is presented as a new strategy to suppress defects and enhance photoluminescence (PL) in CVD-grown TMD monolayers. The random, isoelectronic substitution of Wmore » atoms for Mo atoms in CVD-grown monolayers of Mo 1-xW xSe 2 (02 monolayers. The resultant decrease in defect-medicated non-radiative recombination in the Mo 0.82W 0.18Se 2 monolayers yielded ~10 times more intense PL and extended the carrier lifetime by a factor of 3 compared to pristine CVD-grown MoSe 2 monolayers grown under similar conditions. Low temperatures (4 125 K) PL from defect-related localized states confirms theoretical predictions that isoelectronic W alloying should suppress deep levels in MoSe 2, showing that the defect levels in Mo 1-xW xSe 2 monolayers are higher in energy and quenched more quickly than in MoSe 2. Isoelectronic substitution therefore appears to be a promising synthetic method to control the heterogeneity of 2D TMDs to realize the scalable production of high performance optoelectronic and electronic devices.« less

Suppression of Defects and Deep Levels Using Isoelectronic Tungsten Substitution in Monolayer MoSe 2

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

Li, Xufan; Puretzky, Alexander A.; Sang, Xiahan

Chemical vapor deposition (CVD) is one of the most promising, scalable synthetic techniques to enable large-area synthesis of two-dimensional (2D) transition metal dichalcogenides (TMDs) for the realization of next generation optoelectronic devices. However, defects formed during the CVD growth process currently limit the quality and electronic properties of 2D TMDs. Effective synthesis and processing strategies to suppress defects and enhance the quality of 2D TMDs are urgently needed. In this work, isoelectrnic doping to produce stable alloy is presented as a new strategy to suppress defects and enhance photoluminescence (PL) in CVD-grown TMD monolayers. The random, isoelectronic substitution of Wmore » atoms for Mo atoms in CVD-grown monolayers of Mo 1-xW xSe 2 (02 monolayers. The resultant decrease in defect-medicated non-radiative recombination in the Mo 0.82W 0.18Se 2 monolayers yielded ~10 times more intense PL and extended the carrier lifetime by a factor of 3 compared to pristine CVD-grown MoSe 2 monolayers grown under similar conditions. Low temperatures (4 125 K) PL from defect-related localized states confirms theoretical predictions that isoelectronic W alloying should suppress deep levels in MoSe 2, showing that the defect levels in Mo 1-xW xSe 2 monolayers are higher in energy and quenched more quickly than in MoSe 2. Isoelectronic substitution therefore appears to be a promising synthetic method to control the heterogeneity of 2D TMDs to realize the scalable production of high performance optoelectronic and electronic devices.« less

Isoelectronic substitutions and aluminium alloying in the Ta-Nb-Hf-Zr-Ti high-entropy alloy superconductor

NASA Astrophysics Data System (ADS)

von Rohr, Fabian O.; Cava, Robert J.

2018-03-01

High-entropy alloys (HEAs) are a new class of materials constructed from multiple principal elements statistically arranged on simple crystallographic lattices. Due to the large amount of disorder present, they are excellent model systems for investigating the properties of materials intermediate between crystalline and amorphous states. Here we report the effects of systematic isoelectronic replacements, using Mo-Y, Mo-Sc, and Cr-Sc mixtures, for the valence electron count 4 and 5 elements in the body-centered cubic (BCC) Ta-Nb-Zr-Hf-Ti high-entropy alloy (HEA) superconductor. We find that the superconducting transition temperature Tc strongly depends on the elemental makeup of the alloy, and not exclusively its electron count. The replacement of niobium or tantalum by an isoelectronic mixture lowers the transition temperature by more than 60%, while the isoelectronic replacement of hafnium, zirconium, or titanium has a limited impact on Tc. We further explore the alloying of aluminium into the nearly optimal electron count [TaNb] 0.67(ZrHfTi) 0.33 HEA superconductor. The electron count dependence of the superconducting Tc for (HEA)Al x is found to be more crystallinelike than for the [TaNb] 1 -x(ZrHfTi) x HEA solid solution. For an aluminum content of x =0.4 the high-entropy stabilization of the simple BCC lattice breaks down. This material crystallizes in the tetragonal β -uranium structure type and superconductivity is not observed above 1.8 K.

E+ Transition in GaAs1-xNx and GaAs1-xBix Due to Isoelectronic-Impurity-Induced Perturbation of the Conduction Band

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

Fluegel, B.; Mascarenhas, A.; Ptak, A. J.

2007-01-01

An above-band-gap transition E{sub +} is experimentally observed in the dilute GaAs{sub 1-x}Bi{sub x} alloy. Precise measurements at very low dilutions are made of the above-band-gap transition E{sub +} that is observed in GaAs{sub 1-x}N{sub x}, making it possible to compare the behavior of the different isoelectronic traps Bi and N in the common host GaAs with respect to their perturbation to the host electronic structure. We suggest that the origin of the E{sub +} level observed in GaAs is not the isolated isoelectronic impurity level N{sub x}, as is presumed in the band-anticrossing model, but rather the isoelectronic-impurity-induced perturbationmore » of the conduction band L{sub 6}{sup c}.« less

Triple Photoionization of Neon and Argon Near Threshold

NASA Astrophysics Data System (ADS)

Bluett, Jaques B.; Lukić, Dragan; Sellin, Ivan A.; Whitfield, Scott B.; Wehlitz, Ralf

2003-05-01

The threshold behavior of the triple ionization cross-section of neon and argon was investigated using monochromatized synchrotron radiation and ion time-of-flight spectrometry. The Ne^3+ and Ar^3+ cross-sections are found to follow the Wannier power law(G.H. Wannier, Phys. Rev. 90), 817 (1953). consistent with a Wannier exponent of 2.162 predicted by theory. This is also consistent with the findings of Samson and Angel(J.A.R. Samson and G.C. Angel, Phys. Lett. 61), 1584 (1988). for the case of Ne. In the case of argon we find a much shorter range of validity than for neon.

Using NEON Data to Test and Refine Conceptual and Numerical Models of Soil Biogeochemical and Microbial Dynamics

NASA Astrophysics Data System (ADS)

Weintraub, S. R.; Stanish, L.; Ayers, E.

2017-12-01

Recent conceptual and numerical models have proposed new mechanisms that underpin key biogeochemical phenomena, including soil organic matter storage and ecosystem response to nitrogen deposition. These models seek to explicitly capture the ecological links among biota, especially microbes, and their physical and chemical environment to represent belowground pools and fluxes and how they respond to perturbation. While these models put forth exciting new concepts, their broad predictive abilities are unclear as some have been developed and tested against only small or regional datasets. The National Ecological Observatory Network (NEON) presents new opportunities to test and validate these models with multi-site data that span wide climatic, edaphic, and ecological gradients. NEON is measuring surface soil biogeochemical pools and fluxes along with diversity, abundance, and functional potential of soil microbiota at 47 sites distributed across the United States. This includes co-located measurements of soil carbon and nitrogen concentrations and stable isotopes, net nitrogen mineralization and nitrification rates, soil moisture, pH, microbial biomass, and community composition via 16S and ITS rRNA sequencing and shotgun metagenomic analyses. Early NEON data demonstrates that these wide edaphic and climatic gradients are related to changes in microbial community structure and functional potential, as well as element pools and process rates. Going forward, NEON's suite of standardized soil data has the potential to advance our understanding of soil communities and processes by allowing us to test the predictions of new soil biogeochemical frameworks and models. Here, we highlight several recently developed models that are ripe for this kind of data validation, and discuss key insights that may result. Further, we explore synergies with other networks, such as (i)LTER and (i)CZO, which may increase our ability to advance the frontiers of soil biogeochemical modeling.

Monte Carlo simulations of nanoscale focused neon ion beam sputtering.

PubMed

Timilsina, Rajendra; Rack, Philip D

2013-12-13

A Monte Carlo simulation is developed to model the physical sputtering of aluminum and tungsten emulating nanoscale focused helium and neon ion beam etching from the gas field ion microscope. Neon beams with different beam energies (0.5-30 keV) and a constant beam diameter (Gaussian with full-width-at-half-maximum of 1 nm) were simulated to elucidate the nanostructure evolution during the physical sputtering of nanoscale high aspect ratio features. The aspect ratio and sputter yield vary with the ion species and beam energy for a constant beam diameter and are related to the distribution of the nuclear energy loss. Neon ions have a larger sputter yield than the helium ions due to their larger mass and consequently larger nuclear energy loss relative to helium. Quantitative information such as the sputtering yields, the energy-dependent aspect ratios and resolution-limiting effects are discussed.

Neon isotopes show that Earth was accreted from irradiated material

NASA Astrophysics Data System (ADS)

Moreira, M. A.

2015-12-01

Since the 1980s, the notion that the Earth's mantle has a "solar" isotopic signature for neon has been favoured. Indeed, the 20Ne/22Ne ratio is above 12.5 in the mantle sources of OIB and MORB, close to the solar composition (13.4 for the Sun or 13.8 for the solar wind) and different from both atmospheric and chondritic compositions (Phase Q, Neon A). The most well accepted process invoked to explain this observed solar composition in the mantle is dissolution into a magma ocean of solar gases captured by gravity around the proto-Earth. However, Earth was accreted after gas from the proto-planetary disk had evaporated, suggesting that Earth itself could not have captured such a solar primordial atmosphere. Only planetary embryos were formed when the gas was still present in the disk. However, these planetary embryos with the mass of Mars are not massive enough to capture a solar dense atmosphere able to incorporate enough neon into the mantle. New estimates of the neon isotopic compositions of both the Earth's mantle and of the implanted solar wind into grains suggest that the origin of the neon on Earth is related to solar wind irradiation on μm grains before planetary accretion started and not dissolution. Although incorporation of solar ions by this process is only significant for very volatiles (depleted) elements, the irradiation by x-rays has important consequences for the bulk chemistry of irradiated grains as it has been demonstrated that it produces depletion in Mg and Si, relatively to O (e.g Bradley et al., 1994), a pattern also observed for the Bulk silicate Earth. References Bradley, J. (1994). "Chemically Anomalous, Preaccretionally irradiated Grains in Interplanetary fust from Comets." Science 265: 925-929.

Transition rate diagrams and excitation of titanium in a glow discharge in argon and neon

NASA Astrophysics Data System (ADS)

Weiss, Zdeněk; Steers, Edward B. M.; Pickering, Juliet C.

2018-06-01

Emission spectra of titanium in a Grimm-type glow discharge in argon and neon were studied using the formalism of transition rate diagrams. Ti I spectra in argon and neon discharges are similar, without signs of selective excitation, and populations of Ti I levels exhibit a decreasing trend as function of energy, except for some scatter. A major excitation process of Ti II in argon discharge is charge transfer from argon ions to neutral titanium. In neon discharge, a strong selective excitation was observed of Ti II levels at ≈13.3-13.4 eV relative to the Ti I ground state. It was attributed to charge transfer from doubly charged titanium ions to neutral titanium, while the Ti++ ions are produced by charge transfer and ionization of neutral titanium by neon ions. Cascade excitation is important for Ti II levels up to an energy of ≈13 eV relative to the Ti I ground state, both in argon and neon discharges.

Study of reverse Brayton cryocooler with Helium-Neon mixture for HTS cable

NASA Astrophysics Data System (ADS)

Dhillon, A. K.; Ghosh, P.

2017-12-01

As observed in the earlier studies, helium is more efficient than neon as a refrigerant in a reverse Brayton cryocooler (RBC) from the thermodynamic point of view. However, the lower molecular weight of helium leads to higher refrigerant inventory as compared to neon. Thus, helium is suitable to realize the high thermodynamic efficiency of RBC whereas neon is appropriate for the compactness of the RBC. A binary mixture of helium and neon can be used to achieve high thermodynamic efficiency in the compact reverse Brayton cycle (RBC) based cryocooler. In this paper, an attempt has been made to analyze the thermodynamic performance of the RBC with a binary mixture of helium and neon as the working fluid to provide 1 kW cooling load for high temperature superconductor (HTS) power cables working with a temperature range of 50 K to 70 K. The basic RBC is simulated using Aspen HYSYS V8.6®, a commercial process simulator. Sizing of each component based on the optimized process parameters for each refrigerant is performed based on a computer code developed using Engineering Equation Solver (EES-V9.1). The recommendation is provided for the optimum mixture composition of the refrigerant based on the trade-off factors like thermodynamic efficiency such as the exergy efficiency and equipment considerations. The outcome of this study may be useful for recommending a suitable refrigerant for the RBC operating at a temperature level of 50 K to 70 K.

Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules

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

Al-Hamdani, Yasmine S.; Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ; Alfè, Dario

2016-04-21

Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparingmore » the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed.« less

Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules

NASA Astrophysics Data System (ADS)

Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

2016-04-01

Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed.

Method and apparatus for cooling high temperature superconductors with neon-nitrogen mixtures

DOEpatents

Laverman, Royce J.; Lai, Ban-Yen

1993-01-01

Apparatus and methods for cooling high temperature superconducting materials (HTSC) to superconductive temperatures within the range of 27.degree. K. to 77.degree. K. using a mixed refrigerant consisting of liquefied neon and nitrogen containing up to about ten mole percent neon by contacting and surrounding the HTSC material with the mixed refrigerant so that free convection or forced flow convection heat transfer can be effected.

Helium and Neon in the Accreted Ice of the Subglacial Antarctic Lake Vostok

NASA Astrophysics Data System (ADS)

Jean-Baptiste, P.; Fourré, E.; Petit, J. R.; Lipenkov, V.; Bulat, S.; Chetverikov, Y.; Raynaud, D.

2018-05-01

We analyzed helium and neon in 24 samples from between 3,607 and 3,767 m (i.e., down to 2 m above the lake-ice interface) of the accreted ice frozen to the ceiling of Lake Vostok. Within uncertainties, the neon budget of the lake is balanced, the neon supplied to the lake by the melting of glacier ice being compensated by the neon exported by lake ice. The helium concentration in the lake is about 12 times more than in the glacier ice, with a measured 3He/4He ratio of 0.12 ± 0.01 Ra. This shows that Lake Vostok's waters are enriched by a terrigenic helium source. The 3He/4He isotope ratio of this helium source was determined. Its radiogenic value (0.057 × Ra) is typical of an old continental province, ruling out any magmatic activity associated with the tectonic structure of the lake. It corresponds to a low geothermal heat flow estimated at 51 mW/m2.

Improved discovery of NEON data and samples though vocabularies, workflows, and web tools

NASA Astrophysics Data System (ADS)

Laney, C. M.; Elmendorf, S.; Flagg, C.; Harris, T.; Lunch, C. K.; Gulbransen, T.

2017-12-01

The National Ecological Observatory Network (NEON) is a continental-scale ecological observation facility sponsored by the National Science Foundation and operated by Battelle. NEON supports research on the impacts of invasive species, land use change, and environmental change on natural resources and ecosystems by gathering and disseminating a full suite of observational, instrumented, and airborne datasets from field sites across the U.S. NEON also collects thousands of samples from soil, water, and organisms every year, and partners with numerous institutions to analyze and archive samples. We have developed numerous new technologies to support processing and discovery of this highly diverse collection of data. These technologies include applications for data collection and sample management, processing pipelines specific to each collection system (field observations, installed sensors, and airborne instruments), and publication pipelines. NEON data and metadata are discoverable and downloadable via both a public API and data portal. We solicit continued engagement and advice from the informatics and environmental research communities, particularly in the areas of data versioning, usability, and visualization.

Boiling incipience and convective boiling of neon and nitrogen

NASA Technical Reports Server (NTRS)

Papell, S. S.; Hendricks, R. C.

1977-01-01

Forced convection and subcooled boiling heat transfer data for liquid nitrogen and liquid neon were obtained in support of a design study for a 30 tesla cryomagnet cooled by forced convection of liquid neon. The cryogen data obtained over a range of system pressures, fluid flow rates, and applied heat fluxes were used to develop correlations for predicting boiling incipience and convective boiling heat transfer coefficients in uniformly heated flow channels. The accuracy of the correlating equations was then evaluated. A technique was also developed to calculate the position of boiling incipience in a uniformly heated flow channel. Comparisons made with the experimental data showed a prediction accuracy of + or - 15 percent.

Diffusion of neon in white dwarf stars.

PubMed

Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

2010-12-01

Sedimentation of the neutron rich isotope 22Ne may be an important source of gravitational energy during the cooling of white dwarf stars. This depends on the diffusion constant for 22Ne in strongly coupled plasma mixtures. We calculate self-diffusion constants D(i) from molecular dynamics simulations of carbon, oxygen, and neon mixtures. We find that D(i) in a mixture does not differ greatly from earlier one component plasma results. For strong coupling (coulomb parameter Γ> few), D(i) has a modest dependence on the charge Z(i) of the ion species, D(i)∝Z(i)(-2/3). However, D(i) depends more strongly on Z(i) for weak coupling (smaller Γ). We conclude that the self-diffusion constant D(Ne) for 22Ne in carbon, oxygen, and neon plasma mixtures is accurately known so that uncertainties in D(Ne) should be unimportant for simulations of white dwarf cooling.

NEON's Mobile Deployment Platform: A Resource for Community Research

NASA Astrophysics Data System (ADS)

Sanclements, M.

2017-12-01

Here we provide an update on construction of the five NEON Mobile Deployment Platforms (MDPs) as well as a description of the infrastructure and sensors available to researchers in the near future. Additionally, we include information (i.e. timelines and procedures) on requesting MDPs for PI led projects. The MDPs will provide the means to observe stochastic or spatially important events, gradients, or quantities that cannot be reliably observed using fixed location sampling (e.g. fires and floods). Due to the transient temporal and spatial nature of such events, the MDPs are designed to accommodate rapid deployment for time periods up to 1 year. Broadly, the MDPs are comprised of infrastructure and instrumentation capable of functioning individually or in conjunction with one another to support observations of ecological change, as well as education, training and outreach. More specifically, the MDPs include the capability to make tower based measures of ecosystem exchange, radiation, and precipitation in conjunction with baseline soils data such as CO2 flux, and soil temperature and moisture. An aquatics module is also available with the MDP to facilitate research integrating terrestrial and aquatic processes. Ultimately, the NEON MDPs provide a tool for linking PI led research to the continental scale data sets collected by NEON.

An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion.

PubMed

Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D; Nam, Wonwoo

2014-02-18

Reaction of a nonheme iron(III)-peroxo complex, [Fe(III)(14-TMC)(O2)](+), with NO(+), a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2˙(-)) + NO], affords an iron(IV)-oxo complex, [Fe(IV)(14-TMC)(O)](2+), and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [Fe(III)(14-TMC)(NO3)(F)](+).

Polarizability of Helium, Neon, and Argon: New Perspectives for Gas Metrology

NASA Astrophysics Data System (ADS)

Gaiser, Christof; Fellmuth, Bernd

2018-03-01

With dielectric-constant gas thermometry, the molar polarizability of helium, neon, and argon has been determined with relative standard uncertainties of about 2 parts per million. A series of isotherms measured with the three noble gases and two different experimental setups led to this unprecedented level of uncertainty. These data are crucial for scientists in the field of gas metrology, working on pressure and temperature standards. Furthermore, with the new benchmark values for neon and argon, theoretical calculations, today about 3 orders of magnitude larger in uncertainty, can be checked and improved.

Polarizability of Helium, Neon, and Argon: New Perspectives for Gas Metrology.

PubMed

Gaiser, Christof; Fellmuth, Bernd

2018-03-23

With dielectric-constant gas thermometry, the molar polarizability of helium, neon, and argon has been determined with relative standard uncertainties of about 2 parts per million. A series of isotherms measured with the three noble gases and two different experimental setups led to this unprecedented level of uncertainty. These data are crucial for scientists in the field of gas metrology, working on pressure and temperature standards. Furthermore, with the new benchmark values for neon and argon, theoretical calculations, today about 3 orders of magnitude larger in uncertainty, can be checked and improved.

Laser optogalvanic wavelength calibration with a commercial hollow cathode iron - neon discharge lamp

NASA Technical Reports Server (NTRS)

Zhu, Xinming; Nur, Abdullahi H.; Misra, Prabhakar

1994-01-01

351 optogalvanic transitions have been observed in the 337 - 598 nm wavelength region using an iron - neon hollow cathode discharge lamp and a pulsed tunable dye laser. 223 of these have been identified as transitions associated with neon energy levels. These optogalvanic transitions have allowed, in conjunction with interference fringes recorded concomitantly with an etalon, the calibration of the dye laser wavelength with 0.3/cm accuracy.

Study of tunneling transport in Si-based tunnel field-effect transistors with ON current enhancement utilizing isoelectronic trap

NASA Astrophysics Data System (ADS)

Mori, Takahiro; Morita, Yukinori; Miyata, Noriyuki; Migita, Shinji; Fukuda, Koichi; Mizubayashi, Wataru; Masahara, Meishoku; Yasuda, Tetsuji; Ota, Hiroyuki

2015-02-01

The temperature dependence of the tunneling transport characteristics of Si diodes with an isoelectronic impurity has been investigated in order to clarify the mechanism of the ON-current enhancement in Si-based tunnel field-effect transistors (TFETs) utilizing an isoelectronic trap (IET). The Al-N complex impurity was utilized for IET formation. We observed three types of tunneling current components in the diodes: indirect band-to-band tunneling (BTBT), trap-assisted tunneling (TAT), and thermally inactive tunneling. The indirect BTBT and TAT current components can be distinguished with the plot described in this paper. The thermally inactive tunneling current probably originated from tunneling consisting of two paths: tunneling between the valence band and the IET trap and tunneling between the IET trap and the conduction band. The probability of thermally inactive tunneling with the Al-N IET state is higher than the others. Utilization of the thermally inactive tunneling current has a significant effect in enhancing the driving current of Si-based TFETs.

An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion†

PubMed Central

Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D.; Nam, Wonwoo

2014-01-01

Reaction of a nonheme iron(III)-peroxo complex, [FeIII(14-TMC)(O2)]+, with NO+, a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2•−) + NO], affords an iron(IV)-oxo complex, [FeIV(14-TMC)(O)]2+, and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [FeIII(14-TMC)(NO3)(F)]+. PMID:24394960

A strategy to sample nutrient dynamics across the terrestrial-aquatic interface at NEON sites

NASA Astrophysics Data System (ADS)

Hinckley, E. S.; Goodman, K. J.; Roehm, C. L.; Meier, C. L.; Luo, H.; Ayres, E.; Parnell, J.; Krause, K.; Fox, A. M.; SanClements, M.; Fitzgerald, M.; Barnett, D.; Loescher, H. W.; Schimel, D.

2012-12-01

The construction of the National Ecological Observatory Network (NEON) across the U.S. creates the opportunity for researchers to investigate biogeochemical transformations and transfers across ecosystems at local-to-continental scales. Here, we examine a subset of NEON sites where atmospheric, terrestrial, and aquatic observations will be collected for 30 years. These sites are located across a range of hydrological regimes, including flashy rain-driven, shallow sub-surface (perched, pipe-flow, etc), and deep groundwater, which likely affect the chemical forms and quantities of reactive elements that are retained and/or mobilized across landscapes. We present a novel spatial and temporal sampling design that enables researchers to evaluate long-term trends in carbon, nitrogen, and phosphorus biogeochemical cycles under these different hydrological regimes. This design focuses on inputs to the terrestrial system (atmospheric deposition, bulk precipitation), transfers (soil-water and groundwater sources/chemistry), and outputs (surface water, and evapotranspiration). We discuss both data that will be collected as part of the current NEON design, as well as how the research community can supplement the NEON design through collaborative efforts, such as providing additional datasets, including soil biogeochemical processes and trace gas emissions, and developing collaborative research networks. Current engagement with the research community working at the terrestrial-aquatic interface is critical to NEON's success as we begin construction, to ensure that high-quality, standardized and useful data are not only made available, but inspire further, cutting-edge research.

Coherence parameter measurements for neon and hydrogen

NASA Astrophysics Data System (ADS)

Wright, Robert; Hargreaves, Leigh; Khakoo, Murtadha; Zatsarinny, Oleg; Bartschat, Klaus; Stauffer, Al

2015-09-01

We present recent coherence parameter measurements for excitation of neon and hydrogen by 50 eV electrons. The measurements were made using a crossed electron/gas beam spectrometer, featuring a hemispherically selected electron energy analyzer for detecting scattered electrons and double-reflection VUV polarization analyzer to register fluorescence photons. Time-coincidence counting methods on the electron and photon signals were employed to determine Stokes Parameters at each scattering angle, with data measured at angles between 20 - 115 degrees. The data are compared with calculated results using the B-Spline R-Matrix (BSR) and Relativistic Distorted Wave (RDW) approaches. Measurements were made of both the linear (Plin and γ) and circular (Lperp) parameters for the lowest lying excited states in these two targets. We particularly focus on results in the Lperp parameter, which shows unusual behavior in these particular targets, including strong sign changes implying reversal of the angular momentum transfer. In the case of neon, the unusual behavior is well captured by the BSR, but not by other models.

Liquid neon heat transfer as applied to a 30 tesla cryomagnet

NASA Technical Reports Server (NTRS)

Papell, S. S.; Hendricks, R. C.

1975-01-01

A 30-tesla magnet design is studied which calls for forced convection liquid neon heat transfer in small coolant channels. The design also requires suppressing boiling by subjecting the fluid to high pressures through use of magnet coils enclosed in a pressure vessel which is maintained at the critical pressure of liquid neon. This high pressure reduces the possibility of the system flow instabilities which may occur at low pressures. The forced convection heat transfer data presented were obtained by using a blowdown technique to force the fluid to flow vertically through a resistance heated, instrumented tube.

NEON: Transforming Environmental Data into Free, Open Information

NASA Astrophysics Data System (ADS)

Wee, B.

2010-12-01

The National Ecological Observatory Network (NEON) will collect data across the United States on the impacts of climate change, land use change and invasive species on natural resources and biodiversity. NEON is a project of the U.S. National Science Foundation (NSF), with many other U.S. agencies and NGOs cooperating. The Observatory’s construction plans call for 60 sites distributed across 20 ecoclimatic Domains. Data will be collected from strategically selected sites within each Domain and synthesized into information products that can be used to describe changes in the nation’s ecosystem through space and time. Sites are arrayed across different land-use types in order to understand large-scale environmental drivers affect biodiversity, ecohydrology, biogeochemistry, and disease ecology across the US continent. NEON is an instrument that listens to the pulse of the US continental ecosystem: infrastructure deployed at these sites will collect an average of over 500 primary measurements at each site, including annual high-resolution airborne LiDAR and hyperspectral data. These primary measurements will be transformed by a state-of-the-art cyberinfrastruture into over 100 higher-order data products. All measurements, data products, algorithms used to compute the data products, and protocols used to collect the primary measurements will be freely available to the public and assessable over the internet. The information products, including selected socio-economic datasets from cooperating Federal agencies, will be served in standard formats, grid-sizes, and geographical projections. This type of information is anticipated to have a wide range of uses, including ecological forecasting, education, public engagement, socio-economic analyses, decision support for climate-change adaptation and mitigation, resource management, and environmental risk management. Open data, interoperability, an open and integrated observation infrastructure, public engagement, and a

NEON, Establishing a Standardized Network for Groundwater Observations

NASA Astrophysics Data System (ADS)

Fitzgerald, M.; Schroeter, N.; Goodman, K. J.; Roehm, C. L.

2013-12-01

The National Ecological Observatory Network (NEON) is establishing a standardized set of data collection systems comprised of in-situ sensors and observational sampling to obtain data fundamental to the analysis of environmental change at a continental scale. NEON will be collecting aquatic, terrestrial, and atmospheric data using Observatory-wide standardized designs and methods via a systems engineering approach. This approach ensures a wealth of high quality data, data algorithms, and models that will be freely accessible to all communities such as academic researchers, policy makers, and the general public. The project is established to provide 30 years of data which will enable prediction and forecasting of drivers and responses of ecological change at scales ranging from localized responses through regional gradients and up to the continental scale. The Observatory is a distributed system of sites spread across the United States, including Alaska, Hawaii, and Puerto Rico, which is subdivided into 20 statistically unique domains, based on a set of 18 ecologically important parameters. Each domain contains at least one core aquatic and terrestrial site which are located in unmanaged lands, and up to 2 additional sites selected to study domain specific questions such as nitrogen deposition gradients and responses of land use change activities on the ecosystem. Here, we present the development of NEON's groundwater observation well network design and the timing strategy for sampling groundwater chemistry. Shallow well networks, up to 100 feet in depth, will be installed at NEON aquatic sites and will allow for observation of localized ecohydrologic site conditions, by providing basic spatio-temporal near-real time data on groundwater parameters (level, temperature, conductivity) collected from in situ high-resolution instrumentation positioned in each well; and biannual sampling of geochemical and nutrient (N and P) concentrations in a subset of wells for each

NEON AND OXYGEN ABUNDANCES AND ABUNDANCE RATIO IN THE SOLAR CORONA

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

Landi, E.; Testa, P., E-mail: elandi@umich.edu

2015-02-20

In this work we determine the Ne/O abundance ratio from Solar and Heliospheric Observatory (SOHO)/Solar Ultraviolet Measurement of Emitted Radiation (SUMER) off-disk observations of quiescent streamers over the 1996-2008 period. We find that the Ne/O ratio is approximately constant over solar cycle 23 from 1996 to 2005, at a value of 0.099 ± 0.017; this value is lower than the transition region determinations from the quiet Sun used to infer the neon photospheric abundance from the oxygen photospheric abundance. Also, the Ne/O ratio we determined from SUMER is in excellent agreement with in situ determinations from ACE/SWICS. In 2005-2008, the Ne/O abundancemore » ratio increased with time and reached 0.25 ± 0.05, following the same trend found in the slowest wind analyzed by ACE/SWICS. Further, we measure the absolute abundance in the corona for both oxygen and neon from the data set of 1996 November 22, obtaining A {sub o} = 8.99 ± 0.04 and A {sub Ne} = 7.92 ± 0.03, and we find that both elements are affected by the first ionization potential (FIP) effect, with oxygen being enhanced by a factor of 1.4-2.1 over its photospheric abundance, and neon being changed by a factor of 0.75-1.20. We conclude that the Ne/O ratio is not constant in the solar atmosphere, both in time and at different heights, and that it cannot be reliably used to infer the neon abundance in the photosphere. Also, we argue that the FIP effect was less effective during the minimum of solar cycle 24, and that the Ne/O = 0.25 ± 0.05 value measured at that time is closer to the true photospheric value, leading to a neon photospheric abundance larger than assumed by ≈40%. We discuss the implications of these results for the solar abundance problem, for the FIP effect, and for the identification of the source regions of the solar wind.« less

NEON: High Frequency Monitoring Network for Watershed-Scale Processes and Aquatic Ecology

NASA Astrophysics Data System (ADS)

Vance, J. M.; Fitzgerald, M.; Parker, S. M.; Roehm, C. L.; Goodman, K. J.; Bohall, C.; Utz, R.

2014-12-01

Networked high frequency hydrologic and water quality measurements needed to investigate physical and biogeochemical processes at the watershed scale and create robust models are limited and lacking standardization. Determining the drivers and mechanisms of ecological changes in aquatic systems in response to natural and anthropogenic pressures is challenging due to the large amounts of terrestrial, aquatic, atmospheric, biological, chemical, and physical data it requires at varied spatiotemporal scales. The National Ecological Observatory Network (NEON) is a continental-scale infrastructure project designed to provide data to address the impacts of climate change, land-use, and invasive species on ecosystem structure and function. Using a combination of standardized continuous in situ measurements and observational sampling, the NEON Aquatic array will produce over 200 data products across its spatially-distributed field sites for 30 years to facilitate spatiotemporal analysis of the drivers of ecosystem change. Three NEON sites in Alabama were chosen to address linkages between watershed-scale processes and ecosystem changes along an eco-hydrological gradient within the Tombigbee River Basin. The NEON Aquatic design, once deployed, will include continuous measurements of surface water physical, chemical, and biological parameters, groundwater level, temperature and conductivity and local meteorology. Observational sampling will include bathymetry, water chemistry and isotopes, and a suite of organismal sampling from microbes to macroinvertebrates to vertebrates. NEON deployed a buoy to measure the temperature profile of the Black Warrior River from July - November, 2013 to determine the spatiotemporal variability across the water column from a daily to seasonal scale. In July 2014 a series of water quality profiles were performed to assess the contribution of physical and biogeochemical drivers over a diurnal cycle. Additional river transects were performed

The relative abundance of neon and magnesium in the solar corona

NASA Technical Reports Server (NTRS)

Rugge, H. R.; Walker, A. B. C., Jr.

1976-01-01

A technique is proposed for specifically determining the relative solar coronal abundance of neon and magnesium. The relative abundance is calculated directly from the relative intensity of the resonance lines of Ne X (12.134A) and Mg XI (9.169A) without the need for the development of a detailed model of the thermal structure of the corona. Moderate resolution Bragg crystal spectrometer results from the OVI-10 satellite were used to determine a coronal neon to magnesium relative abundance of 1.47 + or - 0.38. The application of this technique to a recent higher resolution rocket observation gave an abundance ratio of approximately 0.93 + or - 0.15.

Design study of steady-state 30-tesla liquid-neon-cooled magnet

NASA Technical Reports Server (NTRS)

Prok, G. M.; Brown, G. V.

1976-01-01

A design for a 30-tesla, liquid-neon-cooled magnet was reported which is capable of continuous operation. Cooled by nonboiling, forced-convection heat transfer to liquid neon flowing at 2.8 cu m/min in a closed, pressurized heat-transfer loop and structurally supported by a tapered structural ribbon, the tape-wound coils with a high-purity-aluminum conductor will produce over 30 teslas for 1 minute at 850 kilowatts. The magnet will have an inside diameter of 7.5 centimeters and an outside diameter of 54 centimeters. The minimum current density at design field will be 15.7 kA/sq cm.

Coherent production of ρ - mesons in charged current antineutrino-neon interactions in BEBC

NASA Astrophysics Data System (ADS)

Marage, P.; Aderholz, M.; Allport, P.; Armenise, N.; Baton, J. P.; Berggren, M.; Bertrand, D.; Brisson, V.; Bullock, F. W.; Burkot, W.; Calicchio, M.; Clayton, E. F.; Coghen, T.; Cooper-Sarkar, A. M.; Erriquez, O.; Fitch, P. J.; Guy, J.; Hamisi, F.; Hulth, P. O.; Jones, G. T.; Kasper, P.; Katz, U. F.; Klein, H.; Matsinos, E.; Middleton, R. P.; Miller, D. B.; Mobayyen, M. M.; Morrison, D. R. O.; Neveu, M.; O'Neale, S. W.; Parker, M. A.; Petiau, P.; Sacton, J.; Sansum, R. A.; Schmitz, N.; Simopoulou, E.; Vallée, C.; Varvell, K.; Vayaki, A.; Venus, W.; Wachsmuth, H.; Wells, J.; Wittek, W.

1987-09-01

Coherent production of ρ - mesons in charged current antineutrino interactions on neon nuclei is studied in the BEBC bubble chamber exposed to the CERN SPS wide band beam. The cross section is measured to be (95±25)·10-40 cm2 per neon nucleus, averaged over the beam energy spectrum. The distributions of kinematical variables and the absolute value of the cross section are in agreement with theoretical predictions based on the CVC hypothesis and the vector meson dominance model.

Boiling incipience and convective boiling of neon and nitrogen

NASA Technical Reports Server (NTRS)

Papell, S. S.; Hendricks, R. C.

1977-01-01

Forced convection and subcooled boiling heat transfer data for liquid nitrogen and liquid neon were obtained in support of a design study for a 30 tesla cryomagnet cooled by forced convection of liquid neon. This design precludes nucleate boiling in the flow channels as they are too small to handle vapor flow. Consequently, it was necessary to determine boiling incipience under the operating conditions of the magnet system. The cryogen data obtained over a range of system pressures, fluid flow rates, and applied heat fluxes were used to develop correlations for predicting boiling incipience and convective boiling heat transfer coefficients in uniformly heated flow channels. The accuracy of the correlating equations was then evaluated. A technique was also developed to calculate the position of boiling incipience in a uniformly heated flow channel. Comparisons made with the experimental data showed a prediction accuracy of plus or minus 15 percent

LCLS in—photon out: fluorescence measurement of neon using soft x-rays

DOE PAGES

Obaid, Razib; Buth, Christian; Dakovski, Georgi L.; ...

2018-01-09

Here, we measured the fluorescence photon yield of neon upon soft x-ray ionization (~1200 eV) from the x-ray free-electron laser at Linac Coherent Light Source, and demonstrated the usage of a grazing incidence spectrometer with a variable line spacing grating to perform x-ray fluorescence spectroscopy on a gas phase system. Our measurements also allowed us to estimate the focal size of the beam from the theoretical description developed, in terms of the rate equation approximation accounting for photoionization shake off of neutral neon and double auger decay of single core holes.

LCLS in—photon out: fluorescence measurement of neon using soft x-rays

NASA Astrophysics Data System (ADS)

Obaid, Razib; Buth, Christian; Dakovski, Georgi L.; Beerwerth, Randolf; Holmes, Michael; Aldrich, Jeff; Lin, Ming-Fu; Minitti, Michael; Osipov, Timur; Schlotter, William; Cederbaum, Lorenz S.; Fritzsche, Stephan; Berrah, Nora

2018-02-01

We measured the fluorescence photon yield of neon upon soft x-ray ionization (∼1200 eV) from the x-ray free-electron laser at Linac Coherent Light Source, and demonstrated the usage of a grazing incidence spectrometer with a variable line spacing grating to perform x-ray fluorescence spectroscopy on a gas phase system. Our measurements also allowed us to estimate the focal size of the beam from the theoretical description developed, in terms of the rate equation approximation accounting for photoionization shake off of neutral neon and double auger decay of single core holes.

NEON: Contributing continental-scale long-term environmental data for the benefit of society

NASA Astrophysics Data System (ADS)

Wee, B.; Aulenbach, S.

2011-12-01

The National Ecological Observatory Network (NEON) is a NSF funded national investment in physical and information infrastructure. Large-scale environmental changes pose challenges that straddle environmental, economic, and social boundaries. As we develop climate adaptation strategies at the Federal, state, local, and tribal levels, accessible and usable data are essential for implementing actions that are informed by the best available information. NEON's goal is to enable understanding and forecasting of the impacts of climate change, land use change and invasive species on continental-scale ecology by providing physical and information infrastructure. The NEON framework will take standardized, long-term, coordinated measurements of related environmental variables at each of its 62 sites across the nation. These observations, collected by automated instruments, field crews, and airborne instruments, will be processed into more than 700 data products that are provided freely over the web to support research, education, and environmental management. NEON is envisioned to be an integral component of an interoperable ecosystem of credible data and information sources. Other members of this information ecosystem include Federal, commercial, and non-profit entities. NEON is actively involved with the interoperability community via forums like the Foundation for Earth Science Information Partners and the USGS Community for Data Integration in a collective effort to identify the technical standards, best practices, and organizational principles that enable the emergence of such an information ecosystem. These forums have proven to be effective innovation engines for the experimentation of new techniques that evolve into emergent standards. These standards are, for the most part, discipline agnostic. It is becoming increasingly evident that we need to include socio-economic and public health data sources in interoperability initiatives, because the dynamics of coupled

Isoelectronic tungsten doping in monolayer MoSe 2 for carrier type modulation

DOE PAGES

Li, Xufan; Lin, Ming -Wei; Basile, Leonardo; ...

2016-07-06

Doping and alloying are effective ways to engineer the band structure and modulate the optoelectronic functionality of monolayer transition metal dichalcogenides (TMDs). In this work, we explore the synthesis and electronic properties of monolayer Mo 1-xW xSe 2 (0 < x < 0.18) alloys with almost 100% alloying degree. The isoelectronic substitutional doping of tungsten for molybdenum in the monolayer MoSe 2 is shown to suppress its intrinsically n-type conduction behavior, with p-type conduction gradually emerging to become dominant with increasing W concentration in the alloys. Atomic resolution Z-contrast electron microscopy show that W is shown to substitute directly formore » Mo without the introduction of noticeable vacancy or interstitial defects, however with randomly-distributed W-rich regions ~2 nm in diameter. Scanning tunneling microscopy/spectroscopy measurements reveal that these W-rich regions exhibit a local band structure with the valence band maximum (VBM) closer to the Fermi level as compared with the Mo-rich regions in the monolayer Mo 1-xW xSe 2 crystal. These localized upshifts of the VBM in the local band structure appear responsible for the overall p-type behavior observed for the monolayer Mo 1-xW xSe 2 crystals. Stacked monolayers of n-type MoSe 2 and p-type Mo 1-xW xSe 2 were demonstrated to form atomically thin, vertically stacked p n homojunctions with gate-tunable characteristics, which appear useful for future optoelectronic applications. Lastly, these results indicate that alloying with isoelectronic dopant atoms appears to be an effective and advantageous alternate strategy to doping or alloying with electron donors or acceptors in two-dimensional TMDs.« less

EXPANDING THE CATALOG: CONSIDERING THE IMPORTANCE OF CARBON, MAGNESIUM, AND NEON IN THE EVOLUTION OF STARS AND HABITABLE ZONES

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

Truitt, Amanda; Young, Patrick A.

Building on previous work, we have expanded our catalog of evolutionary models for stars with variable composition; here we present models for stars of mass 0.5–1.2 M {sub ⊙}, at scaled metallicities of 0.1–1.5 Z {sub ⊙}, and specific C/Fe, Mg/Fe, and Ne/Fe values of 0.58–1.72 C/Fe{sub ⊙}, 0.54–1.84 Mg/Fe{sub ⊙}, and 0.5–2.0 Ne/Fe{sub ⊙}, respectively. We include a spread in abundance values for carbon and magnesium based on observations of their variability in nearby stars; we choose an arbitrary spread in neon abundance values commensurate with the range seen in other low Z elements due to the difficult naturemore » of obtaining precise measurements of neon abundances in stars. As indicated by the results of Truitt et al., it is essential that we understand how differences in individual elemental abundances, and not just the total scaled metallicity, can measurably impact a star’s evolutionary lifetime and other physical characteristics. In that work, we found that oxygen abundances significantly impacted the stellar evolution; carbon, magnesium, and neon are potentially important elements to individually consider due to their relatively high (but also variable) abundances in stars. We present 528 new stellar main-sequence models, and we calculate the time-dependent evolution of the associated habitable zone boundaries for each based on mass, temperature, and luminosity. We also reintroduce the 2 Gyr “Continuously Habitable Zone” (CHZ{sub 2}) as a useful tool to help gauge the habitability potential for a given planetary system.« less

Surface-subsurface flow modeling: an example of large-scale research at the new NEON user facility

NASA Astrophysics Data System (ADS)

Powell, H.; McKnight, D. M.

2009-12-01

Climate change is predicted to alter surface-subsurface interactions in freshwater ecosystems. These interactions are hypothesized to control nutrient release at diel and seasonal time scales, which may then exert control over epilithic algal growth rates. The mechanisms underlying shifts in complex physical-chemical-biological patterns can be elucidated by long-term observations at sites that span hydrologic and climate gradients across the continent. Development of the National Ecological Observatory Network (NEON) will provide researchers the opportunity to investigate continental-scale patterns by combining investigator-driven measurements with Observatory data. NEON is a national-scale research platform for analyzing and understanding the impacts of climate change, land-use change, and invasive species on ecology. NEON features sensor networks and experiments, linked by advanced cyberinfrastructure to record and archive ecological data for at least 30 years. NEON partitions the United States into 20 ecoclimatic domains. Each domain hosts one fully instrumented Core Aquatic site in a wildland area and one Relocatable site, which aims to capture ecologically significant gradients (e.g. landuse, nitrogen deposition, urbanization). In the current definition of NEON there are 36 Aquatic sites: 30 streams/rivers and 6 ponds/lakes. Each site includes automated, in-situ sensors for groundwater elevation and temperature; stream flow (discharge and stage); pond water elevation; atmospheric chemistry (Tair, barometric pressure, PAR, radiation); and surface water chemistry (DO, Twater, conductivity, pH, turbidity, cDOM, nutrients). Groundwater and surface water sites shall be regularly sampled for selected chemical and isotopic parameters. The hydrologic and geochemical monitoring design provides basic information on water and chemical fluxes in streams and ponds and between groundwater and surface water, which is intended to support investigator-driven modeling studies

Development of a turbine-compressor for 10 kW class neon turbo-Brayton refrigerator

NASA Astrophysics Data System (ADS)

Hirai, Hirokazu; Hirokawa, Masaki; Yoshida, Shigeru; Sano, Tomonobu; Ozaki, Shinsuke

2014-01-01

We are developing 10 kW class turbo-Brayton refrigerator whose working fluid is neon gas. Its high pressure value is 1 MPa and its low pressure value is 0.5 MPa. The refrigerator consists of two turbine-compressors and a heat exchanger. The turbine-compressor has a turbo-expander on one side of its shaft and a turbo-compressor on the other side of the shaft. Two turbo-compressors are connected in series and two turbo-expanders are set in parallel. So, all amount of neon gas is compressed by two stages and each half a mount of neon gas is expanded by one stage. Two turbinecompressors are the same machines and development cost and time are minimized. In this stage, we made one prototype turbine-compressor and installed it in a performance test facility. This paper shows details of the turbine-compressor and refrigerator cooling power simulation results.

NEON's eddy-covariance: interoperable flux data products, software and services for you, now

NASA Astrophysics Data System (ADS)

Metzger, S.; Desai, A. R.; Durden, D.; Hartmann, J.; Li, J.; Luo, H.; Durden, N. P.; Sachs, T.; Serafimovich, A.; Sturtevant, C.; Xu, K.

2017-12-01

Networks of eddy-covariance (EC) towers such as AmeriFlux, ICOS and NEON are vital for providing the necessary distributed observations to address interactions at the soil-vegetation-atmosphere interface. NEON, close to full operation with 47 tower sites, will represent the largest single-provider EC network globally. Its standardized observation and data processing suite is designed specifically for inter-site comparability and analysis of feedbacks across multiple spatial and temporal scales. Furthermore, NEON coordinates EC with rich contextual observations such as airborne remote sensing and in-situ sampling bouts. In January 2018 NEON enters its operational phase, and EC data products, software and services become fully available to the science community at large. These resources strive to incorporate lessons-learned through collaborations with AmeriFlux, ICOS, LTER and others, to suggest novel systemic solutions, and to synergize ongoing research efforts across science communities. Here, we present an overview of the ongoing product release, alongside efforts to integrate and collaborate with existing infrastructures, networks and communities. Near-real-time heat, water and carbon cycle observations in "basic" and "expanded", self-describing HDF5 formats become accessible from the NEON Data Portal, including an Application Program Interface. Subsequently, they are ingested into the AmeriFlux processing pipeline, together with inclusion in FLUXNET globally harmonized data releases. Software for reproducible, extensible and portable data analysis and science operations management also becomes available. This includes the eddy4R family of R-packages underlying the data product generation, together with the ability to directly participate in open development via GitHub version control and DockerHub image hosting. In addition, templates for science operations management include a web-based field maintenance application and a graphical user interface to simplify

Atomic kinetics of a neon photoionized plasma experiment at Z

NASA Astrophysics Data System (ADS)

Mayes, D. C.; Mancini, R. C.; Schoenfeld, R. P.; Bailey, J. E.; Loisel, G. P.; Rochau, G. A.; ZAPP Collaboration

2017-10-01

We discuss an experimental effort to study the atomic kinetics in neon photoionized plasmas via K-shell line absorption spectroscopy. The experiment employs the intense x-ray flux emitted at the collapse of a Z-pinch to heat and backlight a photoionized plasma contained within a cm-scale gas cell placed at various distances from the Z-pinch and filled with neon gas pressures in the range from 3.5 to 120 Torr. The experimental platform affords an order of magnitude range in the ionization parameter characterizing the photoionized plasma from about 5 to 80 erg*cm/s. Thus, the experiment allows for the study of trends in ionization distribution as a function of the ionization parameter. An x-ray crystal spectrometer capable of collecting both time-integrated and time-gated data is used to collect absorption spectra. The spectra show line absorption by several ionization stages of neon, including Be-, Li-, He-, and H-like ions. Analysis of these spectra yields ion areal-densities and charge state distributions, which can be compared with results from atomic kinetics codes. In addition, the electron temperature is extracted from level population ratios of nearby energy levels in Li- and Be-like ions, which can be used to test heating models of photoionized plasmas. This work was sponsored in part by DOE Office of Science Grant DE-SC0014451, and the Z Facility Fundamental Science Program of SNL.

Simulations of Neon Pellets for Plasma Disruption Mitigation in Tokamaks

NASA Astrophysics Data System (ADS)

Bosviel, Nicolas; Samulyak, Roman; Parks, Paul

2017-10-01

Numerical studies of the ablation of neon pellets in tokamaks in the plasma disruption mitigation parameter space have been performed using a time-dependent pellet ablation model based on the front tracking code FronTier-MHD. The main features of the model include the explicit tracking of the solid pellet/ablated gas interface, a self-consistent evolving potential distribution in the ablation cloud, JxB forces, atomic processes, and an improved electrical conductivity model. The equation of state model accounts for atomic processes in the ablation cloud as well as deviations from the ideal gas law in the dense, cold layers of neon gas near the pellet surface. Simulations predict processes in the ablation cloud and pellet ablation rates and address the sensitivity of pellet ablation processes to details of physics models, in particular the equation of state.

Molecular Iodine Fluorescence Using a Green Helium-Neon Laser

ERIC Educational Resources Information Center

Williamson, J. Charles

2011-01-01

Excitation of molecular iodine vapor with a green (543.4 nm) helium-neon laser produces a fluorescence spectrum that is well suited for the upper-level undergraduate physical chemistry laboratory. Application of standard evaluation techniques to the spectrum yields ground electronic-state molecular parameters in good agreement with literature…

Trapping hydrogen atoms from a neon-gas matrix: a theoretical simulation.

PubMed

Bovino, S; Zhang, P; Kharchenko, V; Dalgarno, A

2009-08-07

Hydrogen is of critical importance in atomic and molecular physics and the development of a simple and efficient technique for trapping cold and ultracold hydrogen atoms would be a significant advance. In this study we simulate a recently proposed trap-loading mechanism for trapping hydrogen atoms released from a neon matrix. Accurate ab initio quantum calculations are reported of the neon-hydrogen interaction potential and the energy- and angular-dependent elastic scattering cross sections that control the energy transfer of initially cold atoms are obtained. They are then used to construct the Boltzmann kinetic equation, describing the energy relaxation process. Numerical solutions of the Boltzmann equation predict the time evolution of the hydrogen energy distribution function. Based on the simulations we discuss the prospects of the technique.

Helium and neon isotopes in the mantle: constraints on the origin of volatiles on Earth

NASA Astrophysics Data System (ADS)

Moreira, M. A.

2005-12-01

It is now obvious that the mantle neon is solar-like. The possibility that the origin of this solar flavor is due to incorporation of irradiated parent bodies during accretion (e.g. gas rich meteorites) has been evoked by Trieloff and collaborators. The main argument is the fact there are no precise 20Ne/22Ne measured ratios above 13 in oceanic basalts, whereas the solar wind has a 20Ne/22Ne of 13.8 and the "neon B" neon shows a ratio of 12.6-12.8. The second argument for an irradiated origin is the air-like 38Ar/36Ar in mantle-derived samples (the "neon B" argon is close to air), distinct from the solar argon. Here we present another argument for an irradiated origin of the rare gases in the Earth. The global correlation in oceanic basalts (MORB and OIB) between 4He/3He and 21Ne/22Ne (corrected for air contamination) gives a mixing hyperbolae with a r parameter (r=(3He/22Ne)MORB/(3He/22Ne)PM) close to 10. It is now clear that 3He/22Ne ratio in the MORB source is around 7, giving for the primitive mantle (PM) a 3He/22Ne of 0.7. The solar 3He/22Ne ratio is estimated at 5-6 whereas the gas rich meteorites show a ratio of 0.3. Therefore, the global correlation in oceanic basalts between the helium and neon isotopic ratios suggests that (some) parent bodies of the Earth were gas rich meteorites, irradiated by an energetic solar wind during the planetary accretion.

NEON: the first continental-scale ecological observatory with airborne remote sensing of vegetation canopy biochemistry and structure

Treesearch

Thomas U. Kampe; Brian R. Johnson; Michele Kuester; Michael Keller

2010-01-01

The National Ecological Observatory Network (NEON) is an ecological observation platform for discovering, understanding and forecasting the impacts of climate change, land use change, and invasive species on continental-scale ecology. NEON will operate for 30 years and gather long-term data on ecological response changes and on feedbacks with the geosphere, hydrosphere...

Current Status and Future Plans of the NEON Airborne Observation Platform (AOP): Data Products, Observatory Requirements and Opportunities for the Community

NASA Astrophysics Data System (ADS)

Petroy, S. B.; Leisso, N.; Goulden, T.; Gulbransen, T.

2016-12-01

The National Ecological Observatory Network (NEON) is a continental-scale ecological observation platform designed to collect and disseminate data that contributes to understanding and forecasting the impacts of climate change, land use change, and invasive species on ecology. NEON will collect in-situ and airborne data over 81 sites across the US, including Alaska, Hawaii, and Puerto Rico. The Airborne Observation Platform (AOP) group within the NEON project operates a payload suite that includes a waveform LiDAR, imaging spectrometer (NIS) and high resolution RGB camera. Data from this sensor suite will be collected annually over each site and processed into a set of standard data products, generally following the processing levels used by NASA (Level 1 through Level 3). We will present a summary of the first operational flight campaign (2016), where AOP flew 42 of the 81 planned NEON sites, our operational plans for 2017, and how we will ramp up to full operations by 2018. We will also describe the final set of AOP data products to be delivered as part of NEON construction and those field (observational) data products collected concurrently on the ground, that may be used to support validation efforts of algorithms for deriving vegetation characteristics from airborne data (e.g. Plant foliar physical/chemical properties, Digital Hemispherical Photos, Plant Diversity, etc.). Opportunities for future enhancements to data products or algorithms will be facilitated via NEON's cyberinfrastructure, which is designed to support wrapping/integration of externally-developed code. And finally, we will present NEON's plans for the third AOP Sensor Suite as an assignable asset and the intent of NSF to provide research opportunities to the community for developing higher level AOP data products that were removed from the NEON project in 2015.

Noble Gas-Uranium Coordination and Intersystem Crossing for the CUO(Ne)x(Ng)n (Ng = Ar, Kr, Xe) Complexes in Solid Neon

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

Andrews, Lester; Liang, Binyong; Li, Jun

2004-02-15

Atomic uranium excited by laser ablation reacts with CO in excess neon to produce the novel CUO molecule, which forms weak complexes CUO(Ne)m with neon and stronger complexes CUO(Ne)x(Ng)n (Ng = Ar, Kr, Xe) when the heavier noble gas atoms are present. The heavier CUO(Ne)m-1(Ng) complexes are identified through the effects of CO isotopic and Ng substitution on the neon matrix infrared spectra and by comparison to DFT frequency calculations on model complexes CUO(Ng) (Ng = Ne, Ar, Kr, Xe). The U-C and U-O stretching frequencies of CUO(Ne)m-1(Ng) complexes are slightly red shifted from 1047 and 872 cm-1 frequencies formore » the 1Sigma+ CUO ground state neon complex, which identifies singlet ground state CUO(Ne)m-1(Ng) complexes in solid neon. The next singlet CUO(Ne)x(Ng)2 complexes in excess neon follow in like manner. However, stretching modes and the isotopic shifts of the higher CUO(Ne)x(Ng)n complex approach those of the pure argon matrix CUO(Ar)n complex, which characterizes triple t ground state complexes by comparison to DFT frequency calculations.« less

Testing of a Neon Loop Heat Pipe for Large Area Cryocooling

NASA Technical Reports Server (NTRS)

Ku, Jentung; Robinson, Franklin Lee

2014-01-01

Cryocooling of large areas such as optics, detector arrays, and cryogenic propellant tanks is required for future NASA missions. A cryogenic loop heat pipe (CLHP) can provide a closed-loop cooling system for this purpose and has many advantages over other devices in terms of reduced mass, reduced vibration, high reliability, and long life. A neon CLHP was tested extensively in a thermal vacuum chamber using a cryopump as the heat sink to characterize its transient and steady performance and verify its ability to cool large areas or components. Tests conducted included loop cool-down from the ambient temperature, startup, power cycle, heat removal capability, loop capillary limit and recovery from a dry-out, low power operation, and long duration steady state operation. The neon CLHP demonstrated robust operation. The loop could be cooled from the ambient temperature to subcritical temperatures very effectively, and could start successfully by applying power to both the pump and evaporator without any pre-conditioning. It could adapt to changes in the pump power andor evaporator power, and reach a new steady state very quickly. The evaporator could remove heat loads between 0.25W and 4W. When the pump capillary limit was exceeded, the loop could resume its normal function by reducing the pump power. Steady state operations were demonstrated for up to 6 hours. The ability of the neon loop to cool large areas was therefore successfully verified.

Retention of neon in graphite after ion beam implantation or exposures to the scrape-off layer plasma in the TEXTOR tokamak

NASA Astrophysics Data System (ADS)

Kim, Y. M.; Philipps, V.; Rubel, M.; Vietzke, E.; Pospieszczyk, A.; Unterberg, B.; Jaspers, R.

2002-01-01

The interaction of neon ions with graphite was investigated for targets either irradiated with ion beams (2-10 keV range) or exposed to the scrape-off layer plasma in the TEXTOR tokamak during discharges with neon edge cooling. The emphasis was on the influence of the target temperature (300-1200 K) and the implantation dose on the neon retention and reemission. The influence of deuterium impact on the retention of neon implanted into graphite has also been addressed. In ion beam experiments saturation is observed above a certain ion dose with a saturation level, which decreases with increasing target temperature. The temperature dependence of the thermal desorption corresponds to an apparent binding energy of about 2.06 eV. The retention of neon (CNe/CC) decreases with increasing ion energy with values from 0.55 to 0.15 following irradiation with 2 and 10 keV ions, respectively. The reemission yield during the irradiation increases with target temperature and above 1200 K all impinging ions are reemitted instantaneously. The retention densities measured using the sniffer probe at the TEXTOR tokamak are less than 1% of the total neon fluence and are over one order of magnitude smaller than those observed in ion beam experiments. The results are discussed in terms of different process decisive for ion deposition and release under the two experimental conditions.

Optimizing Sampling Efficiency for Biomass Estimation Across NEON Domains

NASA Astrophysics Data System (ADS)

Abercrombie, H. H.; Meier, C. L.; Spencer, J. J.

2013-12-01

Over the course of 30 years, the National Ecological Observatory Network (NEON) will measure plant biomass and productivity across the U.S. to enable an understanding of terrestrial carbon cycle responses to ecosystem change drivers. Over the next several years, prior to operational sampling at a site, NEON will complete construction and characterization phases during which a limited amount of sampling will be done at each site to inform sampling designs, and guide standardization of data collection across all sites. Sampling biomass in 60+ sites distributed among 20 different eco-climatic domains poses major logistical and budgetary challenges. Traditional biomass sampling methods such as clip harvesting and direct measurements of Leaf Area Index (LAI) involve collecting and processing plant samples, and are time and labor intensive. Possible alternatives include using indirect sampling methods for estimating LAI such as digital hemispherical photography (DHP) or using a LI-COR 2200 Plant Canopy Analyzer. These LAI estimations can then be used as a proxy for biomass. The biomass estimates calculated can then inform the clip harvest sampling design during NEON operations, optimizing both sample size and number so that standardized uncertainty limits can be achieved with a minimum amount of sampling effort. In 2011, LAI and clip harvest data were collected from co-located sampling points at the Central Plains Experimental Range located in northern Colorado, a short grass steppe ecosystem that is the NEON Domain 10 core site. LAI was measured with a LI-COR 2200 Plant Canopy Analyzer. The layout of the sampling design included four, 300 meter transects, with clip harvests plots spaced every 50m, and LAI sub-transects spaced every 10m. LAI was measured at four points along 6m sub-transects running perpendicular to the 300m transect. Clip harvest plots were co-located 4m from corresponding LAI transects, and had dimensions of 0.1m by 2m. We conducted regression analyses

Correlated helium, neon, and melt production on the super-fast spreading East Pacific Rise near 17°S

NASA Astrophysics Data System (ADS)

Kurz, Mark D.; Moreira, Manuel; Curtice, Joshua; Lott, Dempsey E.; Mahoney, John J.; Sinton, John M.

2005-03-01

We report new helium and neon isotopic compositions in dredged basalt glasses from the superfast spreading East Pacific Rise (EPR) between 13° and 23°S. The 3He/ 4He ratios vary from 8.0 to 11.0 times the atmospheric value (Ra) [ 4He/ 3He between 65,700 and 90,300], with the least radiogenic values in samples from near 16.75°S. Atmospheric contamination corrections on neon isotopes are made using step heating and extrapolated 21Ne/ 22Ne ratios (to a solar 20Ne/ 22Ne value of 13.8). The lowest corrected 21Ne/ 22Ne ratios are found near 16.75°S, and are consistent with the helium isotopes in suggesting a less degassed mantle source. The EPR at 17°S is unusual in displaying such isotopic anomalies in the absence of any known hotspot. The minima in 4He/ 3He and 21Ne/ 22Ne correspond to extremes in Sr, Nd and Pb isotope ratios, but the length scale of the helium and neon anomalies are shorter along-axis than the peaks for the other isotopic ratios. The minimum in 4He/ 3He is observed from 16° to 18°S (a distance of ˜220 km), whereas the elevated Sr and Pb values, and lower 143Nd/ 144Nd, are observed between 16° and 20.7°S (a distance of ˜500 km); neon isotope anomalies are observed on an intermediate length scale along-axis. Unradiogenic helium and neon values correlate with low mantle Bouguer anomalies, and maxima in the axial cross-sectional area, all of which are attributed to higher melt production near 17°S. A conceptual model that fits the observations includes melting of an entrained heterogeneity beneath the EPR at 17 °S. The relationship between helium and neon isotopes and along-axis geophysical characteristics (and by inference melt distribution) is probably related to the extreme incompatibility of helium and neon. High concentrations of 3He and 21Ne (extrap) are found in the glasses near 17°S, which is consistent with higher noble gas concentrations in the anomalous mantle.

NEON's Mobile Deployment Platform: A research tool for integrating ecological processes across scales

NASA Astrophysics Data System (ADS)

Sanclements, M.

2016-12-01

Here we provide an update on construction of the five NEON Mobile Deployment Platforms (MDPs) as well as a description of the infrastructure and sensors available to researchers in the near future. Additionally, we include information (i.e. timelines and procedures) on requesting MDPs for PI led projects. The MDPs will provide the means to observe stochastic or spatially important events, gradients, or quantities that cannot be reliably observed using fixed location sampling (e.g. fires and floods). Due to the transient temporal and spatial nature of such events, the MDPs are designed to accommodate rapid deployment for time periods up to 1 year. Broadly, the MDPs are comprised of infrastructure and instrumentation capable of functioning individually or in conjunction with one another to support observations of ecological change, as well as education, training and outreach. More specifically, the MDPs include the capability to make tower based measures of ecosystem exchange, radiation, and precipitation in conjunction with baseline soils data such as CO2 flux, and soil temperature and moisture. An aquatics module is also available with the MDP to facilitate research integrating terrestrial and aquatic processes. Ultimately, the NEON MDPs provides a tool for linking PI led research to the continental scale data sets collected by NEON.

Angle-resolved Auger electron spectra induced by neon ion impact on aluminum

NASA Technical Reports Server (NTRS)

Pepper, S. V.; Aron, P. R.

1986-01-01

Auger electron emission from aluminum bombarded with 1 to 5 keV neon ions was studied by angle-resolved electron spectroscopy. The position and shape of the spectral features depended on the incident ion energy, angle of ion incidence, and electron take-off angle with respect to the aluminum surface. These spectral dependencies were interpreted in terms of the Doppler shift given to the Auger electron velocity by the excited atom ejected into the vacuum. For oblique ion incidence it is concluded that a flux of high energy atoms are ejected in a direction close to the projection of the ion beam on the target surface. In addition, a new spectral feature was found and identified as due to Auger emission from excited neon in the aluminum matrix.

Atlas of the Spectrum of a Platinum/Neon Hollow-Cathode Lamp in the Region 1130-4330 Å

National Institute of Standards and Technology Data Gateway

SRD 112 Atlas of the Spectrum of a Platinum/Neon Hollow-Cathode Lamp in the Region 1130-4330 Å (Web, free access)   Atlas of the Spectrum of a Platinum/Neon Hollow-Cathode Lamp in the Region 1130-4330 Å contains wavelengths and intensities for about 5600 lines in the region 4330 Å. An atlas plot of the spectrum is given, with the spectral lines marked and their intensities, wavelengths, and classifications listed.

Solving the Schroedinger equation for helium atom and its isoelectronic ions with the free iterative complement interaction (ICI) method

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

Nakashima, Hiroyuki; Nakatsuji, Hiroshi

2007-12-14

The Schroedinger equation was solved very accurately for helium atom and its isoelectronic ions (Z=1-10) with the free iterative complement interaction (ICI) method followed by the variational principle. We obtained highly accurate wave functions and energies of helium atom and its isoelectronic ions. For helium, the calculated energy was -2.903 724 377 034 119 598 311 159 245 194 404 446 696 905 37 a.u., correct over 40 digit accuracy, and for H{sup -}, it was -0.527 751 016 544 377 196 590 814 566 747 511 383 045 02 a.u. These results prove numerically that with the free ICImore » method, we can calculate the solutions of the Schroedinger equation as accurately as one desires. We examined several types of scaling function g and initial function {psi}{sub 0} of the free ICI method. The performance was good when logarithm functions were used in the initial function because the logarithm function is physically essential for three-particle collision area. The best performance was obtained when we introduce a new logarithm function containing not only r{sub 1} and r{sub 2} but also r{sub 12} in the same logarithm function.« less

Insight into the isoelectronic character of azomethines and vinylenes using representative models: a spectroscopic and electrochemical study.

PubMed

Bolduc, Andréanne; Al Ouahabi, Abelaziz; Mallet, Charlotte; Skene, W G

2013-09-20

A series of azomethine and vinylene dyad and triad analogues were prepared. Their absorbance, fluorescence, and redox properties were examined experimentally and theoretically using density functional theory (DFT) calculations. These measurements were done to determine the effect of the heteroatom of the azomethine relative to its all-carbon counterpart and to assess the isoelectronic character of the two bonds. The orientation of the azomethine was found to have little effect on the absorbance, fluorescence, and electrochemical properties. In contrast, the spectral and electrochemical properties were highly contingent on the electronic groups and degree of conjugation. The spectral properties could be tuned 200 nm across the visible region. More importantly, the heteroatom in the conjugated bond was found to give rise to only a 20 nm bathochromic shift in the absorbance and fluorescence spectra. The fluorescence quantum yield (ΦFl) of the vinylene derivatives varied between 5% and 20% with fluorescence quenching occurring by photoisomerization from the E to Z isomers. In contrast, the fluorescence of the analogous azomethine derivatives was completely quenched. The collective spectroscopic and electrochemical ab initio DFT data additionally confirmed that the azomethine and its analogous vinylene are isoelectronic. It was also found that a conjugated thiophene vinylene dyad with primary amines in the α,α'-positions could be prepared and isolated. The compound was stable under aerobic conditions providing electron withdrawing (either ester or nitrile) groups were located in the adjacent positions.

Translating the Science of Measuring Ecosystems at a National Scale: NEON's Online Learning Portal

NASA Astrophysics Data System (ADS)

Wasser, L. A.

2015-12-01

"Big Data" are becoming increasingly common in many fields. The National Ecological Observatory Network (NEON) will collect data over the 30 years, using consistent, standardized methods across the United States. These freely available new data provide an opportunity for increased understanding of continental- and global scale processes such as changes in vegetation structure and condition, biodiversity and landuse. However, while "big data" are becoming more accessible and available, working with big data is challenging. New and potentially unfamiliar data types and associated processing methods, required to work with a growing diversity of available data take time and resources to learn. Analysis of these big datasets may further present a challenge given large file sizes, and uncertainty regarding best methods to properly statistically summarize and analyze results. Finally, resources that support learning these concepts and approaches, are distributed widely across multiple online spaces and may take time to find. This presentation will overview the development of NEON's collaborative University-focused online education portal. It will also cover content testing, community feedback and results from workshops using online content. Portal content is hosted in github to facilitate community input, accessibility version control. Content includes 1) videos and supporting graphics that explain key concepts related to NEON and related big spatio-temporal and 2) data tutorials that include subsets of spatio-temporal data that can be used to learn key big data skills in a self-paced approach, or that can be used as a teaching tool in the classroom or in a workshop. All resources utilize free and open data processing, visualization and analysis tools, techniques and scripts. All NEON materials are being developed in collaboration with the scientific community and are being tested via in-person workshops. Visit the portal online: www.neondataskills.org.

Application and Analysis of the Isoelectronic Line Ratio Temperature Diagnostic in a Planar Ablating-Plasma Experiment at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Epstein, R.; Rosenberg, M. J.; Solodov, A. A.; Myatt, J. F.; Regan, S. P.; Seka, W.; Hohenberger, M.; Barrios, M. A.; Moody, J. D.

2015-11-01

The Mn/Co isoelectronic emission-line ratio from a microdot source in planar CH foil targets was measured to infer the electron temperature (Te) in the ablating plasma during two-plasmon-decay experiments at the National Ignition Facility (NIF). We examine the systematic uncertainty in the Te estimate based on the temperature and density sensitivities of the line ratio in conjunction with plausible density constraints, and its contribution to the total Te estimate uncertainty. The potential advantages of alternative microdot elements (e.g., Ti/Cr and Sc/V) are considered. The microdot mass was selected to provide ample line strength while minimizing the effect of self-absorption on the line emission, which is of particular concern, given the narrow linewidths of mid- Z emitters at subcritical electron densities. Atomic line-formation theory and detailed atomic-radiative simulations show that the straight forward interpretation of the isoelectronic ratio solely in terms of its temperature independence remains valid with lines of moderate optical thickness (up to ~ 10) at line center. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Translating the Science of Measuring Ecosystems at a National Scale: Developing NEON's Online Learning Portal

NASA Astrophysics Data System (ADS)

Wasser, L. A.; Gram, W.; Goehring, L.

2014-12-01

"Big Data" are becoming increasingly common in many fields. The National Ecological Observatory Network (NEON) will be collecting data over the 30 years, using consistent, standardized methods across the United States. These freely available new data provide an opportunity for increased understanding of continental- and global scale processes such as changes in vegetation structure and condition, biodiversity and landuse. However, while "big data" are becoming more accessible and available, integrating big data into the university courses is challenging. New and potentially unfamiliar data types and associated processing methods, required to work with a growing diversity of available data, may warrant time and resources that present a barrier to classroom integration. Analysis of these big datasets may further present a challenge given large file sizes, and uncertainty regarding best methods to properly statistically summarize and analyze results. Finally, teaching resources, in the form of demonstrative illustrations, and other supporting media that might help teach key data concepts, take time to find and more time to develop. Available resources are often spread widely across multi-online spaces. This presentation will overview the development of NEON's collaborative University-focused online education portal. Portal content will include 1) videos and supporting graphics that explain key concepts related to NEON data products including collection methods, key metadata to consider and consideration of potential error and uncertainty surrounding data analysis; and 2) packaged "lab" activities that include supporting data to be used in an ecology, biology or earth science classroom. To facilitate broad use in classrooms, lab activities will take advantage of freely and commonly available processing tools, techniques and scripts. All NEON materials are being developed in collaboration with existing labs and organizations.

MiniCLEAN-360: A liquid argon/neon dark matter detector

NASA Astrophysics Data System (ADS)

Rielage, Keith; DEAP/CLEAN Collaboration

2008-11-01

MiniCLEAN-360 utilizes 360 kg of liquid argon to detect the nuclear recoil from WIMP dark matter with a projected cross-section sensitivity of 10-45 cm2. To reach this planned sensitivity, a unique modular design is being developed with a spherical geometry to maximize light collection using PMTs. Pulse shape discrimination techniques separate nuclear recoil signal from the electron recoil backgrounds resulting from the beta decay of 39Ar and Compton scattering of gamma rays. The design allows for the replacement of the target material with liquid neon to examine any signal and backgrounds with a different sensitivity. It also provides research and development for a larger scale low energy solar neutrino experiment using neon (CLEAN: Cryogenic Low Energy Astrophysics with Noble gases) that plans to measure the pp-solar neutrino flux to 1%. Particular attention is being paid to mitigating the background from contamination of surfaces by radon daughters during assembly. The engineering design, radon mitigation plan, and various testing setups are presented. MiniCLEAN-360 anticipates the start of data collection in mid-2009 at SNOLAB in Sudbury, Ontario, Canada.

Modeling the gain of inner-shell X-ray laser transitions in neon, argon, and copper driven by X-ray free electron laser radiation using photo-ionization and photo-excitation processes

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

Nilsen, Joseph

2015-12-16

Using an X-ray free electron laser (XFEL) at 960 eV to photo-ionize the 1s electron in neutral neon followed by lasing on the 2p-1s transition in singly-ionized neon, an inner-shell X-ray laser was demonstrated at 849 eV in singly-ionized neon gas several years ago. It took decades to demonstrate this scheme, because it required a very strong X-ray source that could photo-ionize the 1s (K shell) electron in neon on a timescale comparable to the intrinsic Auger lifetime in neon of 2 fs. In this paper, we model the neon inner shell X-ray laser under similar conditions to those usedmore » in the XFEL experiments at the SLAC Linac Coherent Light Source (LCLS), and show how we can improve the efficiency of the neon laser and reduce the drive requirements by tuning the XFEL to the 1s-3p transition in neutral neon in order to create gain on the 2p-1s line in neutral neon. We also show how the XFEL could be used to photo-ionize L-shell electrons to drive gain on n = 3–2 transitions in singly-ionized Ar and Cu plasmas. Furthermore, these bright, coherent, and monochromatic X-ray lasers may prove very useful for doing high-resolution spectroscopy and for studying non-linear process in the X-ray regime.« less

Effects of anode geometry on forward wide-angle neon ion emissions in 3.5 kJ plasma focus device by novel mega-size panorama polycarbonate image detectors

NASA Astrophysics Data System (ADS)

Sohrabi, M.; Soltani, Z.; Sarlak, Z.

2018-03-01

Forward wide-angle neon ion emissions in a 3.5 kJ plasma focus device (PFD) were studied using 5 different anode top geometries; hollow-end cylinder, solid triangle, solid hemisphere, hollow-end cone and flat-end cone. Position-sensitive mega-size panorama polycarbonate ion image detectors (MS-PCID) developed by dual-cell circular mega-size electrochemical etching (MS-ECE) systems were applied for processesing wide-angle neon ion images on MS-PCIDs exposed on the PFD cylinder top base under a single pinch shot. The images can be simply observed, analyzed and relatively quantified in terms of ion emission angular distributions even by the unaided eyes. By analysis of the forward neon ion emission images, the ion emission yields, ion emission angular distributions, iso-fluence ion contours and solid angles of ion emissions in 4π PFD space were determined. The neon ion emission yields on the PFD cylinder top base are in an increasing order ~2.1×109, ~2.2 ×109, ~2.8×109, ~2.9×109, and ~3.5×109 neon ions/shot for the 5 stated anode top geometries respectively. The panorama neon ion images as diagnosed even by the unaided eyes demonstrate the lowest and highest ion yields from the hollow-end cylinder and flat-end cone anode tops respectively. Relative dynamic qualitative neon ion spectrometry was made by the unaided eyes demonstrating relative neon ion energy as they appear. The study also demonstrates the unique power of the MS-PCID/MS-ECE imaging system as an advanced state-of-the-art ion imaging method for wide-angle dynamic parametric studies in PFD space and other ion study applications.

Data Collection, Access and Presentation Technologies in the National Ecological Observatory (NEON) Design (Invited)

NASA Astrophysics Data System (ADS)

Aulenbach, S. M.; Berukoff, S. J.

2010-12-01

The National Ecological Observatory Network (NEON) will collect data across the United States on the impacts of climate change, land use change and invasive species on ecosystem functions and biodiversity. In-situ sampling and distributed sensor networks, linked by an advanced cyberinfrastructure, will collect site-based data on a variety of organisms, soils, aquatic systems, atmosphere and climate. Targeted airborne remote sensing observations made by NEON as well as geographical data sets and satellite resources produced by Federal agencies will provide data at regional and national scales. The resulting data streams, collected over a 30-year period, will be synthesized into fully traceable information products that are freely and openly accessible to all users. We provide an overview of several collection, access and presentation technologies evaluated for use by observatory systems throughout the data product life cycle. Specifically, we discuss smart phone applications for citizen scientists as well as the use of handheld devices for sample collection and reporting from the field. Protocols for storing, queuing, and retrieving data from observatory sites located throughout the nation are highlighted as are the application of standards throughout the pipelined production of data products. We discuss the automated incorporation of provenance information and digital object identifiers for published data products. The use of widgets and personalized user portals for the discovery and dissemination of NEON data products are also presented.

A study of the EMC effect using neutrino and antineutrino interactions in neon and deuterium

NASA Astrophysics Data System (ADS)

Guy, J.; Saitta, B.; van Apeldoorn, G.; Allport, P.; Angelini, C.; Armenise, N.; Baldini, A.; Berggren, M.; Bertrand, D.; Bobisut, F.; Brisson, V.; Bullock, F.; Calicchio, M.; Capiluppi, P.; Cirio, R.; Clayton, E. F.; Coghen, T.; Cooper-Sarkar, A. M.; Erriquez, O.; Faccini-Turluer, M. L.; Fitch, P.; Frodesen, A. G.; Gerbier, G.; Giacomelli, G.; Hulth, P. O.; Jones, G. T.; Jongejans, B.; Kasper, P.; Klein, H.; Mandrioli, G.; Marage, P.; Marzari-Chiesa, A.; Middleton, R. P.; Miller, D. B.; Morrison, D. R. O.; Mobayyen, M. M.; O'Neale, S. W.; Neveu, M.; Parker, M. A.; Petiau, P.; Romero, A.; Rossi, A. M.; Sacton, J.; Sansum, A.; Sconza, A.; Simopoulou, E.; Schmitz, N.; Tenner, A.; Vallee, C.; van Eijndhoven, N.; Varvell, K.; Vayaki, A.; Venus, W.; Vignaud, D.; Wachsmuth, H.; Wittek, W.

1987-09-01

Nearly 40000 neutrino and antineutrino interactions in BEBC are compared to measure the differences between neon and deuterium in the quark and antiquark distributions and in the nucleon structure functions. The ratio of Ne to D cross sections indicates some decrease between x˜0.2 and x˜0.6. The y distributions show there is no significant increase in the neon sea, but prefer a small decrease. Taken altogether, the x and y distributions and the measured total cross-sections indicate some change in the shape of the valence distributions. No significant dependence on A is observed for either the shape of the sea or the ratio of longitudinal to transverse cross-sections.

Light-curve Analysis of Neon Novae

NASA Astrophysics Data System (ADS)

Hachisu, Izumi; Kato, Mariko

2016-01-01

We analyzed light curves of five neon novae, QU Vul, V351 Pup, V382 Vel, V693 CrA, and V1974 Cyg, and determined their white dwarf (WD) masses and distance moduli on the basis of theoretical light curves composed of free-free and photospheric emission. For QU Vul, we obtained a distance of d ˜ 2.4 kpc, reddening of E(B - V) ˜ 0.55, and WD mass of MWD = 0.82-0.96 {M}⊙ . This suggests that an oxygen-neon WD lost a mass of more than ˜ 0.1 {M}⊙ since its birth. For V351 Pup, we obtained d˜ 5.5 {{kpc}}, E(B-V)˜ 0.45, and {M}{{WD}}=0.98-1.1 {M}⊙ . For V382 Vel, we obtained d˜ 1.6 {{kpc}}, E(B-V)˜ 0.15, and {M}{{WD}}=1.13-1.28 {M}⊙ . For V693 CrA, we obtained d˜ 7.1 {{kpc}}, E(B-V)˜ 0.05, and {M}{{WD}}=1.15-1.25 {M}⊙ . For V1974 Cyg, we obtained d˜ 1.8 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.95-1.1 {M}⊙ . For comparison, we added the carbon-oxygen nova V1668 Cyg to our analysis and obtained d˜ 5.4 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.98-1.1 {M}⊙ . In QU Vul, photospheric emission contributes 0.4-0.8 mag at most to the optical light curve compared with free-free emission only. In V351 Pup and V1974 Cyg, photospheric emission contributes very little (0.2-0.4 mag at most) to the optical light curve. In V382 Vel and V693 CrA, free-free emission dominates the continuum spectra, and photospheric emission does not contribute to the optical magnitudes. We also discuss the maximum magnitude versus rate of decline relation for these novae based on the universal decline law.

Calibration and Data Efforts of the National Ecological Observatory Network (NEON) Airborne Observation Platform during its Engineering Development Phase

NASA Astrophysics Data System (ADS)

Adler, J.; Goulden, T.; Kampe, T. U.; Leisso, N.; Musinsky, J.

2014-12-01

The National Ecological Observatory Network (NEON) has collected airborne photographic, lidar, and imaging spectrometer data in 5 of 20 unique ecological climate regions (domains) within the United States. As part of its mission to detect and forecast ecological change at continental scales over multiple decades, NEON Airborne Observation Platform (AOP) will aerially survey the entire network of 60 core and re-locatable terrestrial sites annually, each of which are a minimum of 10km-by-10km in extent. The current effort encompasses three years of AOP engineering test flights; in 2017 NEON will transition to full operational status in all 20 domains. To date the total airborne data collected spans 34 Terabytes, and three of the five sampled domain's L1 data are publically available upon request. The large volume of current data, and the expected data collection over the remaining 15 domains, is challenging NEON's data distribution plans, backup capability, and data discovery processes. To provide the public with the highest quality data, calibration and validation efforts of the camera, lidar, and spectrometer L0 data are implemented to produce L1 datasets. Where available, the collected airborne measurements are validated against ground reference points and surfaces and adjusted for instrumentation and atmospheric effects. The imaging spectrometer data is spectrally and radiometrically corrected using NIST-traceable procedures. This presentation highlights three years of flight operation experiences including:1) Lessons learned on payload re-configuration, data extraction, data distribution, permitting requirements, flight planning, and operational procedures2) Lidar validation through control data comparisons collected at the Boulder Municipal Airport (KBDU), the site of NEON's new hangar facility3) Spectrometer calibration efforts, to include both the laboratory and ground observations

Study of adsorption of Neon on open Carbon nanohorns aggregates

NASA Astrophysics Data System (ADS)

Ziegler, Carl Andrew

Adsorption isotherms can be used to determine surface area of a substrate and the heat released when adsorption occurs. Our measurements are done determining the equilibrium pressures corresponding to a given amount of gas adsorbed on a substrate at constant temperature. The adsorption studies were done on aggregates of open dahlia-like carbon nanohorns. The nanohorns were oxidized for 9 hours at 550 °C to open them up and render their interior space accessible for adsorption. Volumetric adsorption measurements of Ne were performed at twelve different temperatures between 19 K and 48 K. The isotherms showed two substeps. The first substep corresponds to adsorption on the high energy binding sites in the interior of the nanohorns, near the tip. The second substep corresponds to low energy binding sites both on the outside of the nanotubes and inside the nanotube away from the tip. The isosteric heat measurements obtained from the isotherm data also shows these two distinct substeps. The effective surface area of the open nanotubes was determined from the isotherms using the point-B method. The isosteric heat and surface area data for neon on open nanohorns were compared to two similar experiments of neon adsorbed on aggregates of closed nanohorns.

Correlating the optical properties of WS2 monolayers grown by CVD with isoelectronic Mo doping level(Conference Presentation)

NASA Astrophysics Data System (ADS)

Wang, Kai; Cross, Nick; Boulesbaa, Abdelaziz; Pudasaini, Pushpa R.; Tian, Mengkun; Mahjouri-Samani, Masoud; Oxley, Mark P.; Rouleau, Christopher M.; Puretzky, Alexander A.; Rack, Philip D.; Xiao, Kai; Yoon, Mina; Eres, Gyula; Duscher, Gerd; Geohegan, David B.

2017-02-01

Incorporating dopants in monolayer transition metal dichalcogenides (TMD) can enable manipulations of their electrical and optical properties. Previous attempts in amphoteric doping in monolayer TMDs have proven to be challenging. Here we report the incorporation of molybdenum (Mo) atoms in monolayer WS2 during growth by chemical vapor deposition, and correlate the distribution of Mo atoms with the optical properties including photoluminescence and ultrafast transient absorption dynamics. Dark field scanning transmission electron microscopy imaging quantified the isoelectronic doping of Mo in WS2 and revealed its gradual distribution along a triangular WS2 monolayer crystal, increasing from 0% at the edge to 2% in the center of the triangular WS2 triangular crystals. This agrees well with the Raman spectra data that showed two obvious modes between 360 cm-1 and 400 cm-1 that corresponded to MoS2 in the center. This in-plane gradual distribution of Mo in WS2 was found to account for the spatial variations in photoluminescence intensity and emission energy. Transition absorption spectroscopy further indicated that the incorporation of Mo in WS2 regulate the amplitude ratio of XA and XB of WS2. The effect of Mo incorporation on the electronic structure of WS2 was further elucidated by density functional theory. Finally, we compared the electrical properties of Mo incorporated and pristine WS2 monolayers by fabricating field-effect transistors. The isoelectronic doping of Mo in WS2 provides an alternative approach to engineer the bandgap and also enriches our understanding the influence of the doping on the excitonic dynamics.

Process and device integration for silicon tunnel FETs utilizing isoelectronic trap technology to enhance the ON current

NASA Astrophysics Data System (ADS)

Mori, Takahiro; Asai, Hidehiro; Fukuda, Koichi; Matsukawa, Takashi

2018-04-01

A tunnel FET (TFET) is a candidate replacement for conventional MOSFETs to realize low-power LSI. The most significant issue with the practical application of TFETs concerns their low tunneling current. Si is an indirect-gap material with a low band-to-band tunneling probability and is not favored for the channel. However, a new technology has recently been proposed to enhance the tunneling current in Si-TFETs by utilizing isoelectronic trap (IET) technology. IET technology provides an innovative approach to realizing low-power LSI with TFETs. In this paper, state-of-the-art research on Si-TFETs with IET technology from the viewpoint of process and device integration is reviewed.

Analysis of trace impurities in neon by a customized gas chromatography.

PubMed

Yin, Min Kyo; Lim, Jeong Sik; Moon, Dong Min; Lee, Gae Ho; Lee, Jeongsoon

2016-09-09

Excimer lasers, widely used in the semiconductor industry, are crucial for analyzing the purity of premix laser gases for the purpose of controlling stable laser output power. In this study, we designed a system for analyzing impurities in pure neon (Ne) base gas by customized GC. Impurities in pure neon (H2 and He), which cannot be analyzed at the sub-μmol/mol level using commercial GC detectors, were analyzed by a customized pulsed-discharge Ne ionization detector (PDNeD) and a pressurized injection thermal conductivity detector using Ne as the carrier gas (Pres. Inj. Ne-TCD). From the results, trace species in Ne were identified with the following detection limits: H2, 0.378μmol/mol; O2, 0.119μmol/mol; CH4, 0.880μmol/mol; CO, 0.263μmol/mol; CO2, 0.162μmol/mol (PDNeD); and He, 0.190μmol/mol (Pres. Inj. Ne-TCD). This PDNeD and pressurized injection Ne-TCD technique thus developed permit the quantification of trace impurities present in high-purity Ne. Copyright © 2016. Published by Elsevier B.V.

Magneto-optical properties and recombination dynamics of isoelectronic bound excitons in ZnO

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

Chen, S. L.; Chen, W. M.; Buyanova, I. A.

2014-02-21

Magneto-optical and time-resolved photoluminescence (PL) spectroscopies are employed to evaluate electronic structure of a bound exciton (BX) responsible for the 3.364 eV line (labeled as I{sub 1}{sup *}) in bulk ZnO. From time-resolved PL spectroscopy, I{sub 1}{sup *} is concluded to originate from the exciton ground state. Based on performed magneto-PL studies, the g-factors of the involved electron and hole are determined as being g{sub e} = 1.98 and g{sub h}{sup ∥}(g{sub h}{sup ⊥}) = 1.2(1.62), respectively. These values are nearly identical to the reported g-factors for the I{sup *} line in ZnO (Phys. Rev. B 86, 235205 (2012)), which proves thatmore » I{sub 1}{sup *} should have a similar origin as I{sup *} and should arise from an exciton bound to an isoelectronic center with a hole-attractive potential.« less

Quantum coherent control of the photoelectron angular distribution in bichromatic-field ionization of atomic neon

NASA Astrophysics Data System (ADS)

Gryzlova, E. V.; Grum-Grzhimailo, A. N.; Staroselskaya, E. I.; Douguet, N.; Bartschat, K.

2018-01-01

We investigate the coherent control of the photoelectron angular distribution in bichromatic atomic ionization. Neon is selected as target since it is one of the most popular systems in current gas-phase experiments with free-electron lasers (FELSs). In particular, we tackle practical questions, such as the role of the fine-structure splitting, the pulse length, and the intensity. Time-dependent and stationary perturbation theory are employed, and we also solve the time-dependent Schrödinger equation in a single-active electron model. We consider neon ionized by a FEL pulse whose fundamental frequency is in resonance with either 2 p -3 s or 2 p -4 s excitation. The contribution of the nonresonant two-photon process and its potential constructive or destructive role for quantum coherent control is investigated.

Theoretical Investigation of Methane Hydroxylation over Isoelectronic [FeO]2+- and [MnO]+-Exchanged Zeolites Activated by N2O.

PubMed

Mahyuddin, M Haris; Shiota, Yoshihito; Staykov, Aleksandar; Yoshizawa, Kazunari

2017-09-05

While the most likely structure of the active site in iron-containing zeolites has been recently identified as [FeO] 2+ (Snyder et al. Nature 2016, 536, 317-321), the mechanism for the direct conversion of methane to methanol over this active species is still debatable between the direct-radical-rebound or nonradical (concerted) mechanism. Using density functional theory on periodic systems, we calculated the two reaction mechanisms over two d 4 isoelectronic systems, [FeO] 2+ and [MnO] + zeolites. We found that [FeO] 2+ zeolites favor the direct-radical-rebound mechanism with low CH 4 activation energies, while [MnO] + zeolites prefer the nonradical mechanism with higher CH 4 activation energies. These contrasts, despite their isoelectronic structures, are mainly due to the differences in the metal coordination number and O α (oxo) spin density. Moreover, molecular orbital analyses suggest that the zeolite steric hindrance further degrades the reactivity of [MnO] + zeolites toward methane. Two types of zeolite frameworks, i.e., medium-pore ZSM-5 (MFI framework) and small-pore SSZ-39 (AEI framework) zeolites, were evaluated, but no significant differences in the reactivity were found. The rate-determining reaction step is found to be methanol desorption instead of methane activation. Careful examination of the most stable sites hosting the active species and calculation for N 2 O decomposition over [Fe] 2+ -MFI and -AEI zeolites were also performed.

Atomic kinetics of a neon photoionized plasma experiment at Z

NASA Astrophysics Data System (ADS)

Mayes, Daniel C.; Mancini, Roberto; Bailey, James E.; Loisel, Guillaume; Rochau, Gregory; ZAPP Collaboration

2018-06-01

We discuss an experimental effort to study the atomic kinetics in astrophysically relevant photoionized plasmas via K-shell line absorption spectroscopy. The experiment employs the intense x-ray flux emitted at the collapse of a Z-pinch to heat and backlight a photoionized plasma contained within a cm-scale gas cell placed at a variable distance from the Z-pinch and filled with neon gas pressures in the range from 3.5 to 30 Torr. The experimental platform affords an order of magnitude range in the ionization parameter characterizing the photoionized plasma at the peak of the x-ray drive from about 5 to 80 erg*cm/s. Thus, the experiment allows for the study of trends in ionization distribution as a function of the ionization parameter. An x-ray crystal spectrometer capable of time-integrated and/or time-gated configurations is used to collect absorption spectra. The spectra show line absorption by several ionization stages of neon, including Be-, Li-, He-, and H-like ions. Analysis of these spectra yields ion areal densities and charge state distributions, which can be compared with simulation results from atomic kinetics codes. In addition, the electron temperature is extracted from level population ratios of nearby energy levels in Li- and Be-like ions, which can be used to test heating models of photoionized plasmas.

Divergent electronic structures of isoelectronic metalloclusters: tungsten(II) halides and rhenium(III) chalcogenide halides.

PubMed

Gray, Thomas G

2009-03-02

Same but different: DFT calculations on hexanuclear tungsten(II) halide clusters [W(6)X(8)X'(6)](2-) (X, X'=Cl, Br, I) indicate a breakdown in the isoelectronic analogy between themselves and the isostructural rhenium(III) chalcogenide clusters [Re(6)S(8)X(6)](4-) (see figure).The hexanuclear tungsten(II) halide clusters and the sulfido-halide clusters of rhenium(III) are subsets of a broad system of 24-electron metal-metal bonded assemblies that share a common structure. Tungsten(II) halide clusters and rhenium(III) sulfide clusters luminesce from triplet excited states upon ultraviolet or visible excitation; emission from both cluster series has been extensively characterized elsewhere. Reported here are density-functional theory studies of the nine permutations of [W(6)X(8)X'(6)](2-) (X, X'=Cl, Br, I). Ground-state properties including geometries, harmonic vibrational frequencies, and orbital energy-level diagrams, have been calculated. Comparison is made to the sulfide clusters of rhenium(III), of which [Re(6)S(8)Cl(6)](4-) is representative. [W(6)X(8)X'(6)](2-) and [Re(6)S(8)Cl(6)](4-) possess disparate electronic structures owing to the greater covalency of the metal-sulfur bond and hence of the [Re(6)S(8)](2+) core. Low-lying virtual orbitals are raised in energy in [Re(6)S(8)Cl(6)](4-) with the result that the LUMO+7 (or LUMO+8 in some cases) of tungsten(II) halide clusters is the LUMO of [Re(6)S(8)Cl(6)](4-) species. An inversion of the HOMO and HOMO-1 between the two cluster series also occurs. Time-dependent density-functional calculations using asymptotically correct functionals do not recapture the experimentally observed periodic trend in [W(6)X(14)](2-) luminescence (E(em) increasing in the order [W(6)Cl(14)](2-) < [W(6)Br(14)](2-) < [W(6)I(14)](2-)), predicting instead that emission energies decrease with incorporation of the heavier halides. This circumstance is either a gross failure of the time-dependent formalism of DFT or it indicates extensive

Mixed refrigerant cycle with neon, hydrogen, and helium for cooling sc power transmission lines

NASA Astrophysics Data System (ADS)

Kloeppel, S.; Dittmar, N.; Haberstroh, Ch; Quack, H.

2017-02-01

The use of superconductors in very long power transmission lines requires a reliable and effective cooling. Since the use of cryocoolers does not appear feasible for very long distances, a cryogenic refrigeration cycle needs to be developed. For cooling superconducting cables based on MgB2 (T c = 39 K), liquid hydrogen (LH2) is the obvious cooling agent. For recooling LH2, one would need a refrigeration cycle providing temperatures at around 20 K. For this purpose, one could propose the use of a helium refrigeration cycle. But the very low molecular weight of helium restricts the use of turbo compressors, which limits the overall efficiency. In order to increase the molecular weight of the refrigerant a mixture of cryogens could be used, allowing the use of a turbo compressor. Temperatures below the triple point of neon are achieved by phase separation. This paper presents a possible layout of a refrigeration cycle utilizing a three component mixture of neon, hydrogen, and helium.

Positive column of a glow discharge in neon with charged dust grains (a review)

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

Polyakov, D. N., E-mail: cryolab@ihed.ras.ru; Shumova, V. V.; Vasilyak, L. M.

The effect of charged micron-size dust grains (microparticles) on the electric parameters of the positive column of a low-pressure dc glow discharge in neon has been studied experimentally and numerically. Numerical analysis is carried out in the diffusion-drift approximation with allowance for the interaction of dust grains with metastable neon atoms. In a discharge with a dust grain cloud, the longitudinal electric field increases. As the number density of dust grains in an axisymmetric cylindrical dust cloud rises, the growth of the electric field saturates. It is shown that the contribution of metastable atoms to ionization is higher in amore » discharge with dust grains, in spite of the quenching of metastable atoms on dust grains. The processes of charging of dust grains and the dust cloud are considered. As the number density of dust grains rises, their charge decreases, while the space charge of the dust cloud increases. The results obtained can be used in plasma technologies involving microparticles.« less

Spin exchange optical pumping of neon and its applications

NASA Astrophysics Data System (ADS)

Ghosh, Rajat K.

Hyperpolarized noble gases are used in a variety of applications including medical diagnostic lung imaging, tests of fundamental symmetries, spin filters, atomic gyroscopes, and atomic magnetometers. Typically 3He is utilized because large 3He polarizations on the order of 80% can be achieved. This is accomplished by optically pumping an alkali vapour which polarizes a noble gas nucleus via spin exchange optical pumping. One hyperpolarized noble gas application of particular importance is the K-3He co-magnetometer. Here, the alkali atoms optically pump a diamagnetic noble gas. The magnetic holding field for the alkali and noble gas is reduced until both species are brought into hybrid magnetic resonance. The co-magnetometer exhibits many useful attributes which make it ideal for tests of fundamental physics, such as insensitivity to magnetic fields. The co-magnetometer would demonstrate increased sensitivity by replacing 3He with polarized 21Ne gas. Tests of CPT violation using co-magnetometers would be greatly improved if one utilizes polarized 21Ne gas. The sensitivity of the nuclear spin gyroscope is inversely proportional to the gyromagnetic ratio of the noble gas. Switching to neon would instigate an order of magnitude gain in sensitivity over 3He. In order to realize these applications the interaction parameters of 21Ne with alkali metals must be measured. The spin-exchange cross section sigmase, and magnetic field enhancement factor kappa0 are unknown, and have only been theoretically calculated. There are no quantitative predictions of the neon-neon quadrupolar relaxation rate Gammaquad. In this thesis I test the application of a K-3He co-magnetometer as a navigational gyroscope. I discuss the advantages of switching the buffer gas to 21Ne. I discuss the feasibility of utilizing polarized 21Ne for operation in a co-magnetometer, and construct a prototype 21Ne co-magnetometer. I investigate polarizing 21Ne with optical pumping via spin exchange collisions

Polarization correlation study of the electron-impact excitation of neon and argon

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

Khakoo, M.A.; McConkey, J.W.

1986-08-11

The recent development of a circular polarization analyzer for the vacuum ultraviolet spectral region has enabled a Stokes parameter analysis to be carried out for the excitation of neon and argon by 80-eV incident electrons. The results show that the transfer of angular momentum to the atom is positive and is in fact surprisingly ''heliumlike.'' Small deviations from total coherence were observed and are discussed.

Fragmentation dynamics of ionized neon clusters (Ne(n), n=3-14) embedded in helium nanodroplets.

PubMed

Bonhommeau, David; Halberstadt, Nadine; Viel, Alexandra

2006-01-14

We report a theoretical study of the nonadiabatic fragmentation dynamics of ionized neon clusters embedded in helium nanodroplets for cluster sizes up to n=14 atoms. The dynamics of the neon atoms is modeled using the molecular dynamics with quantum transitions method of Tully [J. Chem. Phys. 93, 1061 (1990)] with the nuclei treated classically and transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole interactions are added. The effect of the spin-orbit interaction is also discussed. The helium environment is modeled by a friction force acting on charged atoms whose speed exceeds the critical Landau velocity. The dependence of the fragment size distribution on the friction strength and on the initial nanodroplet size is investigated. By comparing with the available experimental data obtained for Ne3+ and Ne4+, a reasonable value for the friction coefficient, the only parameter of the model, is deduced. This value is then used to predict the effect of the helium environment on the dissociation dynamics of larger neon clusters, n=5-14. The results show stabilization of larger fragments than in the gas phase, but fragmentation is not completely caged. In addition, two types of dynamics are characterized for Ne4+: fast and explosive, therefore leaving no time for friction to cool down the process when dynamics starts on one of the highest electronic states, and slower, therefore leading to some stabilization by helium when it starts on one of the lowest electronic states.

Effect of helium-neon laser on fast excitatory postsynaptic potential of neurons in the isolated rat superior cervical ganglia

NASA Astrophysics Data System (ADS)

Mo, Hua; He, Ping; Mo, Ning

2004-08-01

The aim of this study is to further measure the effect of 632.8-nm helium-neon laser on fast excitatory postsynaptic potential (f-EPSP) of postganglionic neurons in isolated rat superior cervical ganglia by means of intracellular recording techniques. The neurons with f-EPSP were irradiated by different power densities (1-5 mW/cm2) laser. Irradiated by the 2-mW/cm2 laser, the amplitude of the f-EPSP could augment (P<0.05, paired t test) and even cause action potential at the end of the first 1-2 minutes, the f-EPSP could descend and last for 3-8 minutes. But the amplitude of the f-EPSP of neurons irradiated by the 5-mW/cm2 laser could depress for the irradiating periods. The results show that: 1) the variation of the amplitude of f-EPSP caused by laser is power density-dependent and time-dependent; 2) there exist the second-order phases in the interaction of the helium-neon laser with neurons. These findings may provide certain evidence in explanation of the mechanisms of clinical helium-neon laser therapy.

The Biological Effectiveness of Four Energies of Neon Ions for the Induction of Chromosome Damage in Human Lymphocytes

NASA Technical Reports Server (NTRS)

George, Kerry; Hada, Megumi; Cucinotta, F. A.

2011-01-01

Chromosomal aberrations were measured in human peripheral blood lymphocytes after in vitro exposure to neon ions at energies of 64, 89, 142, or 267. The corresponding LET values for these energies of neon ranged from 38-103 keV/micrometers and doses delivered were in the 10 to 80 cGy range. Chromosome exchanges were assessed in metaphase and G2 phase cells at first division after exposure using fluorescence in situ hybridization (FISH) with whole chromosome probes and dose response curves were generated for different types of chromosomal exchanges. The yields of total chromosome exchanges were similar for the 64, 89, and 142 MeV exposures, whereas the 267 MeV/u neon with LET of 38 keV/micrometers produced about half as many exchanges per unit dose. The induction of complex type chromosome exchanges (exchanges involving three or more breaks and two or more chromosomes) showed a clear LET dependence for all energies. The ratio of simple to complex type exchanges increased with LET from 18 to 51%. The relative biological effectiveness (RBE) was estimated from the initial slope of the dose response curve for chromosome damage with respect to gamma-rays. The RBE(sub max) values for total chromosome exchanges for the 64 MeV/u was around 30.

Combined sample collection and gas extraction for the measurement of helium isotopes and neon in natural waters

NASA Astrophysics Data System (ADS)

Roether, Wolfgang; Vogt, Martin; Vogel, Sandra; Sültenfuß, Jürgen

2013-06-01

We present a new method to obtain samples for the measurement of helium isotopes and neon in water, to replace the classical sampling procedure using clamped-off Cu tubing containers that we have been using so far. The new method saves the gas extraction step prior to admission to the mass spectrometer, which the classical method requires. Water is drawn into evacuated glass ampoules with subsequent flame sealing. Approximately 50% headspace is left, from which admission into the mass spectrometer occurs without further treatment. Extensive testing has shown that, with due care and with small corrections applied, the samples represent the gas concentrations in the water within ±0.07% (95% confidence level; ±0.05% with special handling). Fast evacuation is achieved by pumping on a small charge of water placed in the ampoule. The new method was successfully tested at sea in comparison with Cu-tubing sampling. We found that the ampoule samples were superior in data precision and that a lower percentage of samples were lost prior to measurement. Further measurements revealed agreement between the two methods in helium, 3He and neon within ±0.1%. The new method facilitates the dealing with large sample sets and minimizes the delay between sampling and measurement. The method is applicable also for gases other than helium and neon.

A Quantitative Approach for Collocating NEON's Sensor-Based Ecological Measurements and in-situ Field Sampling and Observations

NASA Astrophysics Data System (ADS)

Zulueta, R. C.; Metzger, S.; Ayres, E.; Luo, H.; Meier, C. L.; Barnett, D.; Sanclements, M.; Elmendorf, S.

2013-12-01

The National Ecological Observatory Network (NEON) is a continental-scale research platform currently in development to assess the causes of ecological change and biological responses to change across a projected 30-year timeframe. A suite of standardized sensor-based measurements (i.e., Terrestrial Instrument System (TIS) measurements) and in-situ field sampling and observations (i.e., Terrestrial Observation System (TOS) activities) will be conducted across 20 ecoclimatic domains in the U.S. where NEON is establishing 60 terrestrial research sites. NEON's TIS measurements and TOS activities are designed to observe the temporal and spatial dynamics of key drivers and ecological processes and responses to change within each of the 60 terrestrial research sites. The TIS measurements are non-destructive and designed to provide in-situ, continuous, and areally integrated observations of the surrounding ecosystem and environment, while TOS sampling and observation activities are designed to encompass a hierarchy of measurable biological states and processes including diversity, abundance, phenology, demography, infectious disease prevalence, ecohydrology, and biogeochemistry. To establish valid relationships between these drivers and site-specific responses, two contradicting requirements must be fulfilled: (i) both types of observations shall be representative of the same ecosystem, and (ii) they shall not significantly influence one another. Here we outline the theoretical background and algorithmic process for determining areas of mutual representativeness and exclusion around NEON's TIS measurements and develop a procedure which quantitatively optimizes this trade-off through: (i) quantifying the source area distributions of TIS measurements, (ii) determining the ratio of user-defined impact threshold to effective impact area for different TOS activities, and (iii) determining the range of feasible distances between TIS locations and TOS activities. This approach

The solar wind neon abundance observed with ACE/SWICS and ULYSSES/SWICS

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

Shearer, Paul; Raines, Jim M.; Lepri, Susan T.

Using in situ ion spectrometry data from ACE/SWICS, we determine the solar wind Ne/O elemental abundance ratio and examine its dependence on wind speed and evolution with the solar cycle. We find that Ne/O is inversely correlated with wind speed, is nearly constant in the fast wind, and correlates strongly with solar activity in the slow wind. In fast wind streams with speeds above 600 km s{sup –1}, we find Ne/O = 0.10 ± 0.02, in good agreement with the extensive polar observations by Ulysses/SWICS. In slow wind streams with speeds below 400 km s{sup –1}, Ne/O ranges from amore » low of 0.12 ± 0.02 at solar maximum to a high of 0.17 ± 0.03 at solar minimum. These measurements place new and significant empirical constraints on the fractionation mechanisms governing solar wind composition and have implications for the coronal and photospheric abundances of neon and oxygen. The results are made possible by a new data analysis method that robustly identifies rare elements in the measured ion spectra. The method is also applied to Ulysses/SWICS data, which confirms the ACE observations and extends our view of solar wind neon into the three-dimensional heliosphere.« less

Double ionization of neon in elliptically polarized femtosecond laser fields

NASA Astrophysics Data System (ADS)

Kang, HuiPeng; Henrichs, Kevin; Wang, YanLan; Hao, XiaoLei; Eckart, Sebastian; Kunitski, Maksim; Schöffler, Markus; Jahnke, Till; Liu, XiaoJun; Dörner, Reinhard

2018-06-01

We present a joint experimental and theoretical investigation of the correlated electron momentum spectra from strong-field double ionization of neon induced by elliptically polarized laser pulses. A significant asymmetry of the electron momentum distributions along the major polarization axis is reported. This asymmetry depends sensitively on the laser ellipticity. Using a three-dimensional semiclassical model, we attribute this asymmetry pattern to the ellipticity-dependent probability distributions of recollision time. Our work demonstrates that, by simply varying the ellipticity, the correlated electron emission can be two-dimensionally controlled and the recolliding electron trajectories can be steered on a subcycle time scale.

Experimental study of the effects of helium-neon laser radiation on repair of injured tendon

NASA Astrophysics Data System (ADS)

Xu, Yong-Qing; Li, Zhu-Yi; Weng, Long-Jiang; An, Mei; Li, Kai-Yun; Chen, Shao-Rong; Wang, Jian-Xin; Lu, Yu

1993-03-01

Despite extensive research into the biology of tendon healing, predictably restoring normal function to a digit after a flexor tendon laceration remains one of the most difficult problems facing the hand surgeon. The challenge of simultaneously achieving tendon healing while minimizing the peritendinous scar formation, which limits tendon gliding, has captured the attention of investigators for many years. It has been said that low-power density helium-neon laser radiation had effects on anti-inflammation, detumescence, progressive wound healing, and reducing intestinal adhesions. This experimental study aims at whether helium-neon laser can reduce injured tendon adhesions and improve functional recovery of the injured tendon. Fifty white Leghorn hens were used. Ten were randomly assigned as a normal control group, the other forty were used in the operation. After anesthetizing them with Amytal, a half of the profundus tendons of the second and third foretoes on both sides of the feet were cut. Postoperatively, the hens moved freely in the cages. One side of the toes operated on were randomly chosen as a treatment group, the other side served as an untreated control group. The injured tendon toes in the treatment group were irradiated for twenty minutes daily with a fiber light needle of helium-neon laser therapeutic apparatus (wavelength, 6328 angstroms) at a constant power density of 12.74 mW/cm2, the first exposure taking place 24 hours after the operation. The longest course of treatment was 3 weeks. The control group was not irradiated. At 3 days, 1, 2, 3, and 5 weeks after surgery, 8 hens were sacrificed and their tendons were examined. The experimental results: (1) active, passive flexion and tendon gliding functional recovery were significantly better in the treatment group (p < 0.01); (2) width and thickness of the tendon at the cut site were significantly smaller in the treatment group (p < 0.01); (3) degrees of tendon adhesions were significantly lighter

Integrating continental-scale ecological data into university courses: Developing NEON's Online Learning Portal

NASA Astrophysics Data System (ADS)

Wasser, L. A.; Gram, W.; Lunch, C. K.; Petroy, S. B.; Elmendorf, S.

2013-12-01

'Big Data' are becoming increasingly common in many fields. The National Ecological Observatory Network (NEON) will be collecting data over the 30 years, using consistent, standardized methods across the United States. Similar efforts are underway in other parts of the globe (e.g. Australia's Terrestrial Ecosystem Research Network, TERN). These freely available new data provide an opportunity for increased understanding of continental- and global scale processes such as changes in vegetation structure and condition, biodiversity and landuse. However, while 'big data' are becoming more accessible and available, integrating big data into the university courses is challenging. New and potentially unfamiliar data types and associated processing methods, required to work with a growing diversity of available data, may warrant time and resources that present a barrier to classroom integration. Analysis of these big datasets may further present a challenge given large file sizes, and uncertainty regarding best methods to properly statistically summarize and analyze results. Finally, teaching resources, in the form of demonstrative illustrations, and other supporting media that might help teach key data concepts, take time to find and more time to develop. Available resources are often spread widely across multi-online spaces. This presentation will overview the development of NEON's collaborative University-focused online education portal. Portal content will include 1) interactive, online multi-media content that explains key concepts related to NEON's data products including collection methods, key metadata to consider and consideration of potential error and uncertainty surrounding data analysis; and 2) packaged 'lab' activities that include supporting data to be used in an ecology, biology or earth science classroom. To facilitate broad use in classrooms, lab activities will take advantage of freely and commonly available processing tools, techniques and scripts. All

DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. II. Probing individual notI fragments by hybridization.

PubMed

Löbrich, M; Rydberg, B; Cooper, P K

1994-08-01

The initial yields of DNA double-strand breaks induced by energetic heavy ions (425 MeV/u neon and 250, 400 and 600 MeV/u iron) in comparison to X rays were measured in normal human diploid fibroblast cells within three small areas of the genome, defined by NotI fragments of 3.2, 2.0 and 1.2 Mbp. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated cells, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with probes recognizing single-copy sequences within the three NotI fragments. The gradual disappearance of the full-size NotI fragment with dose and the appearance of a smear of broken DNA molecules are quantified. Assuming Poisson statistics for the number of double-strand breaks induced per NotI fragment of known size, absolute yields of DNA double-strand breaks were calculated and determined to be linear with dose in all cases, with the neon ion (LET 32 keV/microns) producing 4.4 x 10(-3) breaks/Mbp/Gy and all three iron-ion beams (LETs from 190 to 350 keV/microns) producing 2.8 x 10(-3) breaks/Mbp/Gy, giving RBE values for production of double-strand breaks of 0.76 for neon and 0.48 for iron in comparison to our previously determined X-ray induction rate of 5.8 x 10(-3) breaks/Mbp/Gy. These RBE values are in good agreement with results of measurements over the whole genome as reported in the accompanying paper (B. Rydberg, M. Löbrich and P. Cooper, Radiat. Res. 139, 133-141, 1994). The distribution of broken DNA molecules was similar for the various radiations, supporting a random distribution of double-strand breaks induced by the heavy ions over Mbp distances; however, correlated breaks (clusters) over much smaller distances are not ruled out. Reconstitution of the 3.2 Mbp NotI fragment was studied during postirradiation incubation of the cells as a measure of rejoining of correct DNA ends. The proportion of breaks repaired decreased with increasing LET.

Observation of coherent diffractive charged current interactions of antineutrinos on neon nuclei

NASA Astrophysics Data System (ADS)

Marage, P.; Aderholz, M.; Armenise, N.; Azemoon, T.; Barnham, K. W. J.; Bartley, J. H.; Baton, J. P.; Bertrand, D.; Brisson, V.; Bullock, F. W.; Calicchio, M.; Cooper, A. M.; Chwastowski, J.; Clayton, E. F.; Coghen, T.; Erriquez, O.; Fitch, P. J.; Gerbier, G.; Guy, J.; Hulth, P. O.; Jones, G. T.; Kasper, P.; Kochowski, C.; Leighton-Davies, S.; Middleton, R. P.; Mobayyen, M. M.; Morrison, D. R. O.; Neveu, M.; Nuzzo, S.; O'Neale, S. W.; Parker, M. A.; Petiau, P.; Ruggieri, F.; Sacton, J.; Sansum, R. A.; Simopoulou, E.; Talebzadeh, M.; Vallee, C.; Varvell, K.; Vayaki, A.; Venus, W.; Wells, J.; Wernhard, K. L.; Wittek, W.; Zevgolatakos, E.; WA59 Collaboration

1984-05-01

First observation is reported of semi-inclusive coherent diffractive charged current interactions of antineutrinos on neon nuclei. A sharp peaking towards zero is observed in the | t| distribution of interactions for which the final state charge is 0 and from which only one negative hadron is emitted, unaccompanied by any evidence of nuclear fragmentation or reinteraction. This peak is correlated with high momentum of the outgoing charged hadron and with small values of Q2 and x.

Transformational principles for NEON sampling of mammalian parasites and pathogens: a response to Springer et al. (2016)

USDA-ARS?s Scientific Manuscript database

The National Environmental Observatory Network (NEON) has recently released a series of protocols presented with apparently broad community support for studies of small mammals and parasites. Sampling designs were outlined outlined, collectively aimed at understanding how changing environmental cond...

The perception of subjective contours and neon color spreading figures in young infants.

PubMed

Kavsek, Michael

2009-02-01

The goal of the present habituation-dishabituation study was to explore sensitivity to subjective contours and neon color spreading patterns in infants. The first experiment was a replication of earlier investigations that showed evidence that even young infants are capable of perceiving subjective contours. Participants 4 months of age were habituated to a subjective Kanizsa square and were tested afterward for their ability to differentiate between the subjective square and a nonsubjective pattern that was constructed by rotating some of the inducing elements. Data analysis indicated a significant preference for the nonsubjective pattern. A control condition ensured that this result was not generated by the difference in figural symmetry or by the local differences between the test displays. In the second experiment, infant perception of a neon color spreading display was analyzed. Again, 4-month-old infants could discriminate between the illusory figure and a nonillusory pattern. Furthermore, infants in a control group did not respond to the difference in symmetry and the local differences between two nonillusory targets. Overall, the results show that young infants respond to illusory figures that are generated by either implicit T-junctions (Experiment 1) or implicit X-junctions (Experiment 2). The findings are interpreted against the background of the neurophysiological model proposed by Grossberg and Mingolla (1985).

Noble gases in diamonds - Occurrences of solarlike helium and neon

NASA Technical Reports Server (NTRS)

Honda, M.; Reynolds, J. H.; Roedder, E.; Epstein, S.

1987-01-01

Seventeen diamond samples from diverse locations were analyzed for the contents of He, Ar, Kr, and Xe, and of their isotopes, using a Reynolds (1956) type glass mass spectrometer. The results disclosed a large spread in the He-3/He-4 ratios, ranging from values below atmospheric to close to the solar ratio. In particular, solarlike He-3/He-4 ratios were seen for an Australian colorless diamond composite and an Arkansas diamond, which also displayed solarlike neon isotopic ratios. Wide variation was also observed in the He-4/Ar-40 ratios, suggesting a complex history for the source regions and the diamond crystallization processes.

Relation between the Z-1 type expansion of the total energy of isoelectronic atoms and the many-electron theory on the electron correlation by Sinanoǧlu

NASA Astrophysics Data System (ADS)

Anno, Tosinobu; Teruya, Hirohide

1987-07-01

By applying the economical formula for the total energies of isoelectronic atoms presented by the present authors [J. Chem. Phys. 84, 6895 (1986)] to both the nonrelativistic exact energy and the Hartree-Fock energy, an expression of the Z-1 expansion type for the correlation energy is obtained for isoelectronic series involving the first-row atoms. Based upon the expression obtained, the following conclusions are derived on the relation between the Z-1 type expansion theory and Sinanoǧlu's many-electron theory (MET): (i) the Z2 term has nothing to do with the electron correlation; (ii) the term proportional to Z represents the internal correlation energy Eint in MET, at least when Z is large in comparison with the number of electrons N; (iii) the constant term in the Z-1 type expansion is the limiting value of the sum of the semi-internal and the all-external correlation energy (EF+Eu) when Z→∞ and its values for the ground-state atoms show a systematic trend when plotted against N; (iv) the sum of the Z-1 and the higher order terms in Z-1 represents the Z dependence of EF+Eu, although its small amount is attributable to a part of Eint when Z-N≲1.

NEON's Mobile Deployment Platform: A Resource for Community Research

NASA Astrophysics Data System (ADS)

Sanclements, M.

2015-12-01

Here we provide an update on construction and validation of the NEON Mobile Deployment Platforms (MDPs) as well as a description of the infrastructure and sensors available to researchers in the future. The MDPs will provide the means to observe stochastic or spatially important events, gradients, or quantities that cannot be reliably observed using fixed location sampling (e.g. fires and floods). Due to the transient temporal and spatial nature of such events, the MDPs will be designed to accommodate rapid deployment for time periods up to ~ 1 year. Broadly, the MDPs will be comprised of infrastructure and instrumentation capable of functioning individually or in conjunction with one another to support observations of ecological change, as well as education, training and outreach.

Direct measurement of neon production rates by (α,n) reactions in minerals

NASA Astrophysics Data System (ADS)

Cox, Stephen E.; Farley, Kenneth A.; Cherniak, Daniele J.

2015-01-01

The production of nucleogenic neon from alpha particle capture by 18O and 19F offers a potential chronometer sensitive to temperatures higher than the more widely used (U-Th)/He chronometer. The accuracy depends on the cross sections and the calculated stopping power for alpha particles in the mineral being studied. Published 18O(α,n)21Ne production rates are in poor agreement and were calculated from contradictory cross sections, and therefore demand experimental verification. Similarly, the stopping powers for alpha particles are calculated from SRIM (Stopping Range of Ions in Matter software) based on a limited experimental dataset. To address these issues we used a particle accelerator to implant alpha particles at precisely known energies into slabs of synthetic quartz (SiO2) and barium tungstate (BaWO4) to measure 21Ne production from capture by 18O. Within experimental uncertainties the observed 21Ne production rates compare favorably to our predictions using published cross sections and stopping powers, indicating that ages calculated using these quantities are accurate at the ∼3% level. In addition, we measured the 22Ne/21Ne ratio and (U-Th)/He and (U-Th)/Ne ages of Durango fluorapatite, which is an important model system for this work because it contains both oxygen and fluorine. Finally, we present 21Ne/4He production rate ratios for a variety of minerals of geochemical interest along with software for calculating neon production rates and (U-Th)/Ne ages.

On the Noble-Gas Induced Intersystem Crossing for the CUO Molecule: Experimental and Theoretical investigations of CUO(Ng)n (Ng = Ar, Kr, Xe; n = 1, 2, 3, 4) Complexes in Solid Neon

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

Liang, Binyong; Andrews, Lester S.; Li, Jun

2004-02-09

Uranium atoms excited by laser ablation react with CO in excess neon to produce the novel CUO molecule, which forms distinct Ng complexes (Ng = Ar, Kr, Xe) when the heavier noble gases are added. The CUO(Ng) complexes are identified through CO isotopic and Ng substitution on the neon matrix infrared spectra and by comparison to DFT frequency calculations. The U-C and U-O stretching frequencies of CUO(Ng) complexes are slightly red shifted from frequencies for the 1S+ CUO ground state, which identifies singlet ground state CUO(Ng) complexes. In solid neon the CUO molecule is also a complex CUO(Ne)n, and themore » CUO(Ne)n-1(Ng) complexes are likewise specified. The next singlet CUO(Ne)x(Ng)2 complexes in excess neon follow in like manner. However, the higher CUO(Ne)x(Ng)n complex (n = 3, 4) stretching modes approach pure argon matrix CUO(Ar)n values and isotopic behavior, which are characterized as triplet ground state complexes by DFT frequency calculations. This work suggests that the singlet-triplet crossing occurs with 3 Ar, 3 Kr or 4 Xe and a balance of Ne atoms coordinated to CUO in the neon matrix host.« less

Water depth measurement using an airborne pulsed neon laser system

NASA Technical Reports Server (NTRS)

Hoge, F. E.; Swift, R. N.; Frederick, E. B.

1980-01-01

The paper presents the water depth measurement using an airborne pulsed neon laser system. The results of initial base-line field test results of NASA airborne oceanographic lidar in the bathymetry mode are given, with water-truth measurements of depth and beam attenuation coefficients by boat taken at the same time as overflights to aid in determining the system's operational performance. The nadir-angle tests and field-of-view data are presented; this laser bathymetry system is an improvement over prior models in that (1) the surface-to-bottom pulse waveform is digitally recorded on magnetic tape, and (2) wide-swath mapping data may be routinely acquired using a 30 deg full-angle conical scanner.

Sub-cooled liquid nitrogen cryogenic system with neon turbo-refrigerator for HTS power equipment

NASA Astrophysics Data System (ADS)

Yoshida, S.; Hirai, H.; Nara, N.; Ozaki, S.; Hirokawa, M.; Eguchi, T.; Hayashi, H.; Iwakuma, M.; Shiohara, Y.

2014-01-01

We developed a prototype sub-cooled liquid nitrogen (LN) circulation system for HTS power equipment. The system consists of a neon turbo-Brayton refrigerator with a LN sub-cooler and LN circulation pump unit. The neon refrigerator has more than 2 kW cooling power at 65 K. The LN sub-cooler is a plate-fin type heat exchanger and is installed in a refrigerator cold box. In order to carry out the system performance tests, a dummy cryostat having an electric heater was set instead of a HTS power equipment. Sub-cooled LN is delivered into the sub-cooler by the LN circulation pump and cooled within it. After the sub-cooler, sub-cooled LN goes out from the cold box to the dummy cryostat, and comes back to the pump unit. The system can control an outlet sub-cooled LN temperature by adjusting refrigerator cooling power. The refrigerator cooling power is automatically controlled by the turbo-compressor rotational speed. In the performance tests, we increased an electric heater power from 200 W to 1300 W abruptly. We confirmed the temperature fluctuation was about ±1 K. We show the cryogenic system details and performance test results in this paper.

Computation of the properties of liquid neon, methane, and gas helium at low temperature by the Feynman-Hibbs approach.

PubMed

Tchouar, N; Ould-Kaddour, F; Levesque, D

2004-10-15

The properties of liquid methane, liquid neon, and gas helium are calculated at low temperatures over a large range of pressure from the classical molecular-dynamics simulations. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach. The equations of state, diffusion, and shear viscosity coefficients are determined for neon at 45 K, helium at 80 K, and methane at 110 K. A comparison is made with the existing experimental data and for thermodynamical quantities, with results computed from quantum numerical simulations when they are available. The theoretical variation of the viscosity coefficient with pressure is in good agreement with the experimental data when the quantum corrections are taken into account, thus reducing considerably the 60% discrepancy between the simulations and experiments in the absence of these corrections.

Source of Volatiles in Earth's Deep Mantle from Neon Isotope Systematics in the South Atlantic

NASA Astrophysics Data System (ADS)

Williams, C. D.; Mukhopadhyay, S.

2016-12-01

The noble gases play an important role in understanding Earth's accretion and subsequent evolution. Neon isotopes in particular have the potential to distinguish between distinct sources of Earth's volatiles e.g., acquisition of nebular gas, solar wind implanted materials or chondritic meteorites and their components. The neon isotopic composition of the deep mantle remains subject to debate with the majority of mantle-derived basalts displaying maximum 20Ne/22Ne ratios less than 12.5, similar to values determined for the convective mantle (20Ne/22Ne = 12.49 +/- 0.04; [1]). These values are also much lower than those of solar wind (20Ne/22Ne = 13.8; [2,3]) and estimates of the nebular gas (20Ne/22Ne = 13.4; [4]) but comparable to solar wind implanted meteoritic materials (20Ne/22Ne = 12.5-12.7; [5]). Here we determine the neon isotopic composition of mantle-derived materials from the south Atlantic. These samples display strong linear correlations in 20Ne/22Ne-21Ne/22Ne space with maximum 20Ne/22Ne ratios that are resolvable from and higher than materials derived from the convecting mantle as well as models of solar wind implantation. These results supplement a growing database of mantle materials characterized by 20Ne/22Ne ratios greater than 12.5, challenging the notion that the entire mantle acquired volatiles from solar wind implanted meteoritic materials. In this presentation we will explore alternative origins for these volatiles and provide testable predictions for each scenario. [1] G. Holland, C.J. Ballentine.. Nature 441 (2006), 186-191. [2] A. Gimberg et al. GCA 72 (2008), 626-645. [3] V.S. Heber et al. GCA 73 (2009), 7414-7432. [4] V. S. Heber et al. ApJ 759 (2012), 121. [5] R. Wieler in: D. Porcelli, C.J. Ballentine, R. Wieler (Eds.), Reviews in Mineralogy and Geochemistry 47 (2002), 21-70.

Influence of dust particles on the neon spectral line intensities at the uniform positive column of dc discharge at the space apparatus “Plasma Kristall-4”

NASA Astrophysics Data System (ADS)

Usachev, A. D.; Zobnin, A. V.; Shonenkov, A. V.; Lipaev, A. M.; Molotkov, V. I.; Petrov, O. F.; Fortov, V. E.; Pustyl'nik, M. Y.; Fink, M. A.; Thoma, M. A.; Thomas, H. M.; Padalka, G. I.

2018-01-01

Influence of the elongated dust cloud on the intensities of different neon spectral lines in visible and near ir spectral ranges in the uniform positive column has been experimentally investigated using the Russian-European space apparatus “Plasma Kristall-4” (SA PK-4) on board of the International Space Station (ISS). The investigation was performed in the low pressure (0.5 mbar) direct current (dc, 1 mA) gas discharge in neon. Microgravity allowed us to perform experiments with a large dust cloud in the steady-state regime. To avoid the dust cloud drift in the dc electric field a switching dc polarity discharge mode has been applied. During the experiment a dust cloud of 9 mm in diameter in the discharge tube of 30 mm in diameter with the length of about 100 mm has been observed in the steady-state regime. In this regard, the intensities of neon spectral lines corresponding to 3p → 3s electronic transitions have increased by a factor of 1.4 times, while the intensities of neon spectral lines corresponding to 3d → 3p electronic transitions have increased by a factor of 1.6 times. The observed phenomenon is explained on the basis of the Schottky approach by a self-consistent rising dc electric field in the dusty plasma cloud resulting in an increase of the electron temperature.

Graphene engineering by neon ion beams

DOE PAGES

Iberi, Vighter; Ievlev, Anton V.; Vlassiouk, Ivan; ...

2016-02-18

Achieving the ultimate limits of materials and device performance necessitates the engineering of matter with atomic, molecular, and mesoscale fidelity. While common for organic and macromolecular chemistry, these capabilities are virtually absent for 2D materials. In contrast to the undesired effect of ion implantation from focused ion beam (FIB) lithography with gallium ions, and proximity effects in standard e-beam lithography techniques, the shorter mean free path and interaction volumes of helium and neon ions offer a new route for clean, resist free nanofabrication. Furthermore, with the advent of scanning helium ion microscopy, maskless He + and Ne + beam lithographymore » of graphene based nanoelectronics is coming to the forefront. Here, we will discuss the use of energetic Ne ions in engineering graphene devices and explore the mechanical, electromechanical and chemical properties of the ion-milled devices using scanning probe microscopy (SPM). By using SPM-based techniques such as band excitation (BE) force modulation microscopy, Kelvin probe force microscopy (KPFM) and Raman spectroscopy, we demonstrate that the mechanical, electrical and optical properties of the exact same devices can be quantitatively extracted. Additionally, the effect of defects inherent in ion beam direct-write lithography, on the overall performance of the fabricated devices is elucidated.« less

Zero-field splitting in the isoelectronic aqueous Gd(III) and Eu(II) complexes from a first principles analysis

NASA Astrophysics Data System (ADS)

Khan, S.; Peters, V.; Kowalewski, J.; Odelius, M.

2018-03-01

The zero-field splitting (ZFS) of the ground state octet in aqueous Eu(II) and Gd(III) solutions was investigated through multi- configurational quantum chemical calculations and ab initio molecular dynamics (AIMD) simulations. Investigation of the ZFS of the lanthanide ions is essential to understand the electron spin dynamics and nuclear spin relaxation around paramagnetic ions and consequently the mechanisms underlying applications like magnetic resonance imaging. We found by comparing clusters at identical geometries but different metallic centres that there is not a simple relationship for their ZFS, in spite of the complexes being isoelectronic - each containing 7 unpaired f electrons. Through sampling it was established that inclusion of the first hydration shell has a dominant (over 90 %) influence on the ZFS. Extended sampling of aqueous Gd(III) showed that the 2 nd order spin Hamiltonian formalism is valid and that the rhombic ZFS component is decisive.

Abundance ratios of oxygen, neon, and magnesium in solar active regions and flares: The FIP effect

NASA Technical Reports Server (NTRS)

Widing, K. G.; Feldman, U.

1995-01-01

Relative abundances of oxygen, neon, and magnesium have been derived for a sample of nine solar active regions, flares, and an erupting prominance by combining plots of the ion differential emission measures. The observations were photographed in the 300-600 A range by the Naval Research Laboratory (NRL) spectroheliograph on Skylab. Methods for deriving the Mg/Ne abundance ratio-which measures the separation between the low- first ionization potential (FIP) and high-FIP abundnace plateaus-have been described in previous papers. In this paper we describe the spectroscopic methods for deriving the O/Ne abundance ratio, which gives the ratio between two high-FIP elements. The plot of the O/Ne ratio versus the Mg/Ne ratio in the sample of nine Skylab events is shown. The variation in the Mg/Ne ratio by a factor of 6 is associated with a much smaller range in the O/Ne ratio. This is broadly consistent with the presence of the standard FIP pattern of abundances in the outer atmosphere of the Sun. However, a real change in the relative abundances of oxygen and neon by a factor of 1.5 cannot be excluded.

Mechanism of variable structural colour in the neon tetra: quantitative evaluation of the Venetian blind model.

PubMed

Yoshioka, S; Matsuhana, B; Tanaka, S; Inouye, Y; Oshima, N; Kinoshita, S

2011-01-06

The structural colour of the neon tetra is distinguishable from those of, e.g., butterfly wings and bird feathers, because it can change in response to the light intensity of the surrounding environment. This fact clearly indicates the variability of the colour-producing microstructures. It has been known that an iridophore of the neon tetra contains a few stacks of periodically arranged light-reflecting platelets, which can cause multilayer optical interference phenomena. As a mechanism of the colour variability, the Venetian blind model has been proposed, in which the light-reflecting platelets are assumed to be tilted during colour change, resulting in a variation in the spacing between the platelets. In order to quantitatively evaluate the validity of this model, we have performed a detailed optical study of a single stack of platelets inside an iridophore. In particular, we have prepared a new optical system that can simultaneously measure both the spectrum and direction of the reflected light, which are expected to be closely related to each other in the Venetian blind model. The experimental results and detailed analysis are found to quantitatively verify the model.

Triple point temperature of neon isotopes: Dependence on nitrogen impurity and sealed-cell model

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

Pavese, F.; Steur, P. P. M.; Giraudi, D.

2013-09-11

This paper illustrates a study conducted at INRIM, to further check how some quantities influence the value of the triple point temperature of the neon high-purity isotopes {sup 20}Ne and {sup 22}Ne. The influence of nitrogen as a chemical impurity in neon is critical with regard to the present best total uncertainty achieved in the measurement of these triple points, but only one determination is available in the literature. Checks are reported, performed on two different samples of {sup 22}Ne known to contain a N{sub 2} amount of 157⋅10{sup −6}, using two different models of sealed cells. The model ofmore » the cell can, in principle, have some effects on the shape of the melting plateau or on the triple point temperature observed for the sample sealed in it. This can be due to cell thermal parameters, or because the INRIM cell element mod. c contains many copper wires closely packed, which can, in principle, constrain the interface and induce a premelting-like effect. The reported results on a cell mod. Bter show no evident effect from the cell model and provide a value for the effect of N{sub 2} in Ne liquidus point of 8.6(1.9) μK ppm N{sub 2}{sup −1}, only slightly different from the literature datum.« less

Electrical and optical characteristics of atmospheric pressure plasma needle jet driven by neon trasformer

NASA Astrophysics Data System (ADS)

Elfa, Rizan Rizon; Ahmad, Mohd Khairul; Soon, Chin Fhong; Sahdan, Mohd Zainizan; Lias, Jais; Mamat, Mohamad Hafiz; Rusop, Mohamad; Nayan, Nafarizal

2017-09-01

The atmospheric pressure plasma needle jet driven by double sinusoidal waveform of neon transformer is reported in this paper. The commercial neon transformer produces about 5 kV of peak sinusoidal voltages and 35 kHz of frequency. Argon gas has been used as discharge gas for this system since the discharge was easily developed rather than using helium gas. In addition, argon gas is three times cheaper than helium gas. The electrical property of the argon discharge has been analyzed in details by measuring its voltage, current and power during the discharge process. Interestingly, it has been found that the total power on the inner needle electrode was slightly lower than that of outer electrode. This may be due to the polarization charges that occurred at inner needle electrode. Then, further investigation to understand the discharge properties was carried out using optical emission spectroscopy (OES) analysis. During OES measurements, two positions of plasma discharge are measured by aligning the quartz optical lens and spectrometer fiber. The OH emission intensity was found higher than that of N2 at the plasma orifice. However, OH emission intensity was lower at 1.5 cm distance from orifice which may be due to penning ionization effect. These results and understanding are essential for surface modification and biomedical applications of atmospheric pressure plasma needle jet.

Effect of post-implantation annealing on Al-N isoelectronic trap formation in silicon: Al-N pair formation and defect recovery mechanisms

NASA Astrophysics Data System (ADS)

Mori, Takahiro; Morita, Yukinori; Matsukawa, Takashi

2018-05-01

The effect of post-implantation annealing (PIA) on Al-N isoelectronic trap (IET) formation in silicon has been experimentally investigated to discuss the Al-N IET formation and implantation-induced defect recovery mechanisms. We performed a photoluminescence study, which indicated that self-interstitial clusters and accompanying vacancies are generated in the ion implantation process. It is supposed that Al and N atoms move to the vacancy sites and form stable Al-N pairs in the PIA process. Furthermore, the PIA process recovers self-interstitial clusters while transforming their atomic configuration. The critical temperature for the formation/dissociation of Al-N pairs was found to be 450 °C, with which we describe the process integration for devices utilizing Al-N IET technology.

Coherent production of single pions and ρ mesons in charged-current interactions of neutrinos and antineutrinos on neon nuclei at the Fermilab Tevatron

NASA Astrophysics Data System (ADS)

Willocq, S.; Aderholz, M.; Akbari, H.; Allport, P. P.; Badyal, S. K.; Ballagh, H. C.; Barth, M.; Bingham, H. H.; Brucker, E. B.; Burnstein, R. A.; Cence, R. J.; Chatterjee, T. K.; Clayton, E. F.; Corrigan, G.; de Prospo, D.; Devanand; de Wolf, E.; Faulkner, P. J.; Foeth, H.; Fretter, W. B.; Gupta, V. K.; Hanlon, J.; Harigel, G.; Harris, F. A.; Jacques, P.; Jain, V.; Jones, G. T.; Jones, M. D.; Kafka, T.; Kalelkar, M.; Kohli, J. M.; Koller, E. L.; Krawiec, R. J.; Lauko, M.; Lys, J. E.; Marage, P.; Milburn, R. H.; Mittra, I. S.; Mobayyen, M. M.; Moreels, J.; Morrison, D. R.; Myatt, G.; Nailor, P.; Naon, R.; Napier, A.; Passmore, D.; Peters, M. W.; Peterson, V. Z.; Plano, R.; Rao, N. K.; Rubin, H. A.; Sacton, J.; Sambyal, S. S.; Schmitz, N.; Schneps, J.; Singh, J. B.; Singh, S.; Smart, W.; Stamer, P.; Varvell, K. E.; Verluyten, L.; Wachsmuth, H.; Wainstein, S.; Yost, G. P.

1993-04-01

The coherent production of π and ρ mesons in νμ(ν¯μ)-neon charged-current interactions has been studied using the Fermilab 15-foot bubble chamber filled with a heavy Ne-H2 mix and exposed to the Teva- tron quadrupole triplet (anti)neutrino beam. The νμ (ν¯μ) beam had an average energy of 80 GeV (70 GeV). From a sample corresponding to approximately 28 000 charged-current interactions, net signals of (53+/-9) μ+/-π-/+ coherent events and (19+/-7) μ+/-π-/+π0 coherent events are extracted. For E>10 GeV, the coherent pion production cross section is determined to be (3.2+/-0.7)×10-38 cm2 per neon nucleus whereas the coherent ρ production cross section is (2.1+/-0.8)×10-38 cm2 per neon nucleus. These cross sections and the kinematical characteristics of the coherent events at ||t||<0.1 GeV2 are found to be in general agreement with the predictions of a model based on the hadron dominance and, in the pion case, on the partially conserved axial-vector current hypothesis. Also discussed is the coherent production of systems consisting of three pions.

Comparative effects of 60Co gamma-rays and neon and helium ions on cycle duration and division probability of EMT 6 cells. A time-lapse cinematography study.

PubMed

Collyn-d'Hooghe, M; Hemon, D; Gilet, R; Curtis, S B; Valleron, A J; Malaise, E P

1981-03-01

Exponentially growing cultures of EMT 6 cells were irradiated in vitro with neon ions, helium ions or 60Co gamma-rays. Time-lapse cinematography allowed the determination, for individual cells, of cycle duration, success of the mitotic division and the age of the cell at the moment of irradiation. Irradiation induced a significant mitotic delay increasing proportionally with the delivered dose. Using mitotic delay as an endpoint, the r.b.e. for neon ions with respect to 60Co gamma-rays was 3.3 +/- 0.2 while for helium ions it was 1.2 +/- 0.1. Mitotic delay was greatest in those cells that had progressed furthest in their cycle at the time of irradiation. No significant mitotic delay was observed in the post-irradiation generation. Division probability was significantly reduced by irradiation both in the irradiated and in the post-irradiated generation. The reduction in division probability obtained with 3 Gy of neon ions was similar to that obtained after irradiation with 6 Gy of helium ions or 60Co gamma-rays.

Multiple ionization of neon by soft x-rays at ultrahigh intensity

NASA Astrophysics Data System (ADS)

Guichard, R.; Richter, M.; Rost, J.-M.; Saalmann, U.; Sorokin, A. A.; Tiedtke, K.

2013-08-01

At the free-electron laser FLASH, multiple ionization of neon atoms was quantitatively investigated at photon energies of 93.0 and 90.5 eV. For ion charge states up to 6+, we compare the respective absolute photoionization yields with results from a minimal model and an elaborate description including standard sequential and direct photoionization channels. Both approaches are based on rate equations and take into account a Gaussian spatial intensity distribution of the laser beam. From the comparison we conclude that photoionization up to a charge of 5+ can be described by the minimal model which we interpret as sequential photoionization assisted by electron shake-up processes. For higher charges, the experimental ionization yields systematically exceed the elaborate rate-based prediction.

Measurement of total cross sections for neutrino and antineutrino charged-current interactions in hydrogen and neon

NASA Astrophysics Data System (ADS)

Aderholz, M.; Corrigan, G.; Hoffmann, E.; Jones, G. T.; Jones, R. W. L.; Kennedy, B. W.; Miller, D. B.; Mobayyen, M. M.; Morrison, D. R. O.; Myatt, G.; Radojicic, D.; Schmid, P.; Schmitz, N.; Shotton, P. N.; Towers, S. J.; Wittek, W.; Barnham, K. W. J.; Baton, J. P.; Berggren, M.; Bertrand, D.; Bullock, F. W.; Calicchio, M.; Clayton, E. F.; Coghen, T.; Cooper-Sarkar, A. M.; Erriquez, O.; Fitch, P. J.; Fogli-Muciaccia, M. T.; Guy, J. G.; Hamisi, F.; Hulth, P. O.; Kasper, P.; Klein, H.; Lagraa, M.; Marage, P.; Middleton, R. P.; O'Neale, S. W.; Parker, M. A.; Sacton, J.; Sansum, R. A.; Simopoulou, E.; Vallée, C.; Varvell, K.; Vayaki, A.; Venus, W.; Wachmuth, H.; Wells, J.

1986-06-01

BEBC filled in turn with hydrogen, and with a neon-hydrogen mixture, was exposed to the CERN SPS wide band neutrino and antineutrino beams. The ratios of the charged-current cross sections per nucleon, σ(νH2)/σ(νNe) and σ(νH2)/σ(νNe), between 20 and 300 GeV were found to be 0.656 +/- 0.020 and 1.425 +/- 0.052, respectively. Multiplying these ratios by the revised cross sections in neon, σ(νNe)/E = (0.723 +/- 0.038) × 10-38 cm2/GeV per nucleon and σ(νNe)/E = (0.351 +/- 0.019) × 10-38 cm2/GeV per nucleon, and their ratio, σ(νNe)/σ(νNe) = 0.485 +/- 0.020,, yields values for the total charged-current cross sections on protons, σ(νp)/E and σ(νp)/E, of (0.474 +/- 0.029) × 10-38 cm2/GeV and (0.500 +/- 0.032) × 10-38 cm2/GeV. respectively, and a value for the ratio σ(νp)/σ(νp) of 1.053 +/- 0.066. Present address: University of Glasgow, Glasgow G12 8QQ, UK.

Neon turbo-Brayton cycle refrigerator for HTS power machines

NASA Astrophysics Data System (ADS)

Hirai, Hirokazu; Hirokawa, M.; Yoshida, Shigeru; Nara, N.; Ozaki, S.; Hayashi, H.; Okamoto, H.; Shiohara, Y.

2012-06-01

We developed a prototype turbo-Brayton refrigerator whose working fluid is neon gas. The refrigerator is designed for a HTS (High Temperature Superconducting) power transformer and its cooling power is more than 2 kW at 65 K. The refrigerator has a turboexpander and a turbo-compressor, which utilize magnetic bearings. These rotational machines have no rubbing parts and no oil-components. Those make a long maintenance interval of the refrigerator. The refrigerator is very compact because our newly developed turbo-compressor is volumetrically smaller than a displacement type compressor in same operating specification. Another feature of the refrigerator is a wide range operation capability for various heat-loads. Cooling power is controlled by the input-power of the turbo-compressor instead of the conventional method of using an electric heater. The rotational speed of the compressor motor is adjusted by an inverter. This system is expected to be more efficient. We show design details, specification and cooling test results of the new refrigerator in this paper.

Electronic Absorption Spectra of Mass-Selected Hydrocarbon Cations in Solid Neon: C_nH_4+ (n=5-8,10,12)

NASA Astrophysics Data System (ADS)

Nagy, A.; Fulara, J.; Garkusha, I.; Maier, J. P.

2011-05-01

Small, unsaturated hydrocarbons, C_nH_m (n,m≤6), play an important role in astrochemical models as they have been detected in various space objects such as the interstellar medium or envelopes of carbon-rich stars. Although identification of most of these species was based on rotational studies, they are candidate carriers of the infamous diffuse interstellar bands. It has been proposed that corresponding cationic species formed upon UV radiation may also be of astrophysical relevance; therefore, their optical spectra need to be determined. In this contribution, electronic absorption spectra of mass-selected C_nH_4+ (n=5-8,10,12) ions trapped in neon matrices are presented. The cations were produced in a hot-cathode discharge source, guided through a series of electrostatic lenses, mass filtered and co-deposited with excess of neon onto a rhodium-coated sapphire plate held at 6 K. In the same experiments, neutral species were generated from the cations by a photobleaching procedure.

The development of the simultaneous GC method of helium, argon and neon measurements for the groundwater dating.

NASA Astrophysics Data System (ADS)

Najman, Joanna; Śliwka, Ireneusz

2014-05-01

In this work we present a chromatographic method for simultaneous analysis of helium, neon and argon in groundwater from one water sample. The concentration of helium in groundwater may be a good environmental tracer for groundwater dating. Proper use of environmental tracers in hydrogeology for dating purpose, requires the knowledge of recharge temperature of the system and the so-called "Excess air". "Excess air" allows for the necessary correction of measured concentration of helium in water. Both parameters can be determined by measuring the concentration of argon and neon in groundwater. In the Department of Physicochemistry of Ecosystems from the Institute of Nuclear Physics Polish Academy of Sciences the chromatographic method for the simultaneous analysis of He, Ar and Ne from one groundwater sample for dating purposes was developed. Water samples are taken to the stainless steel vessels with a capacity of 2900 cc. Gases are extracted from water by headspace method (HS). Helium, neon and argon are analyzed on two gas chromatographs equipped with capillary and packed columns and three thermo-conductive detectors (TCD). The chromatographic method was applied to groundwater dating from areas of Podhalańska Basin, Kraków and Żarnowiec. The levels of detection LOD for each measurement systems for the tested compounds are: 1,9•10-8 cm3STP/cm3 for Ne, 3,1•10-6 cm3STP/cm3 for Ar and 1,2•10-8 cm3STP/cm3 for He. Work performed within the strategic research project "Technologies supporting the development of safe nuclear power" financed by the National Centre for Research and Development (NCBiR). Research Task "Development of methods to assure nuclear safety and radiation protection for current and future needs of nuclear power plants", contract No. SP/J/6/143339/11. This work was also supported by grant No. N N525 3488 38 from the Polish National Science Centre.

Observations and simulations of nova Vul 1984 no. 2: A nova with ejecta rich in oxygen, neon, and magnesium

NASA Technical Reports Server (NTRS)

Starrfield, S.; Sonneborn, G.; Stryker, L. L.; Sparks, Warren M.; Truran, James W.; Ferland, Gary; Wagner, R. M.; Gallagher, J. S.; Wade, R.; Williams, R. E.

1988-01-01

Nova Vul 1984 no. 2 was observed with IUE from Dec. 1984 through Nov. 1987. The spectra are characterized by strong lines from Mg, Ne, C, Si, O, N, and other elements. Data obtained in the ultraviolet, infrared, and optical show that this nova is ejecting material rich in oxygen, neon, and magnesium.

Elastic and Inelastic Scattering of Neutrons from Neon and Argon: Impact on Neutrinoless Double-Beta Decay and Dark Matter Experimental Programs

NASA Astrophysics Data System (ADS)

MacMullin, Sean Patrick

In underground physics experiments, such as neutrinoless double-beta decay and dark matter searches, fast neutrons may be the dominant and potentially irreducible source of background. Experimental data for the elastic and inelastic scattering cross sections of neutrons from argon and neon, which are target and shielding materials of interest to the dark matter and neutrinoless double-beta decay communities, were previously unavailable. Unmeasured neutron scattering cross sections are often accounted for incorrectly in Monte-Carlo simulations. Elastic scattering cross sections were measured at the Triangle Universities Nuclear Laboratory (TUNL) using the neutron time-of-flight technique. Angular distributions for neon were measured at 5.0 and 8.0 MeV. One full angular distribution was measured for argon at 6.0 MeV. The cross-section data were compared to calculations using a global optical model. Data were also fit using the spherical optical model. These model fits were used to predict the elastic scattering cross section at unmeasured energies and also provide a benchmark where the global optical models are not well constrained. Partial gamma-ray production cross sections for (n,xngamma ) reactions in natural argon and neon were measured using the broad spectrum neutron beam at the Los Alamos Neutron Science Center (LANSCE). Neutron energies were determined using time of flight and resulting gamma rays from neutron-induced reactions were detected using the GErmanium Array for Neutron Induced Excitations (GEANIE). Partial gamma-ray production cross sections for six transitions in 40Ar, two transitions in 39Ar and the first excited state transitions is 20Ne and 22Ne were measured from threshold to a neutron energy where the gamma-ray yield dropped below the detection sensitivity. Measured (n,xngamma) cross sections were compared with calculations using the TALYS and CoH3 nuclear reaction codes. These new measurements will help to identify potential backgrounds in

Atmospheric pressure plasma jet's characterization and surface wettability driven by neon transformer

NASA Astrophysics Data System (ADS)

Elfa, R. R.; Nafarizal, N.; Ahmad, M. K.; Sahdan, M. Z.; Soon, C. F.

2017-03-01

Atmospheric pressure plasma driven by Neon transformer power supply argon is presented in this paper. Atmospheric pressure plasma system has attracted researcher interest over low pressure plasma as it provides a flexibility process, cost-efficient, portable device and vacuum-free device. Besides, another golden key of this system is the wide promising application in the field of work cover from industrial and engineering to medical. However, there are still numbers of fundamental investigation that are necessary such as device configuration, gas configuration and its effect. Dielectric barrier discharge which is also known as atmospheric pressure plasma discharge is created when there is gas ionization process occur which enhance the movement of atom and electron and provide energetic particles. These energetic particles can provide modification and cleaning property to the sample surface due to the bombardment of the high reactive ion and radicals to the sample surface. In order to develop atmospheric pressure plasma discharge, a high voltage and high frequency power supply is needed. In this work, we used a neon transformer power supply as the power supply. The flow of the Ar is feed into 10 mm cylinder quartz tube with different treatment time in order to investigate the effect of the plasma discharge. The analysis of each treatment time is presented by optical emission spectroscopy (OES) and water contact angle (WCA) measurement. The increase of gas treatment time shows increases intensity of reactive Ar and reduces the angle of water droplets in water contact angle. Treatment time of 20 s microslide glass surface shows that the plasma needle discharges have modified the sample surface from hydrophilic surface to superhydrophilic surface. Thus, this leads to another interesting application in reducing sample surface adhesion to optimize productivity in the industry of paintings, semiconductor and more.

Enhancing continental-scale understanding of agriculture: Integrating the National Ecological Observatory Network (NEON) with existing research networks to address global change.

NASA Astrophysics Data System (ADS)

Kelly, G.

2015-12-01

Over the past decade, there has been a resurgence of interest in the sustainability of the world's food system and its contributions to feeding the world's population as well as to ensuring environmental sustainability of the planet. The elements of this grand challenge are by now well known. Analysis of agricultural sustainability is made more challenging by the fact that the local responses to these global drivers of change are extremely variable in space and time due to the biophysical and geopolitical heterogeneity across the United States, and the world. Utilizing research networks allows the scientific community to leverage existing knowledge, models and data to develop a framework for understanding the interplay between global change drivers, regional, and continental sustainability of US agriculture. For example, well-established instrumented and calibrated research networks will allow for the examination of the potential tradeoffs between: 1) crop production, 2) land use and carbon emissions and sequestration, 3) groundwater depletion, and 4) nitrogen dynamics. NEON represents a major investment in scientific infrastructure in support of ecological research at a continental scale and is intended to address multiple ecological grand challenges. NEON will collect data from automated sensors and sample organisms and ecological variables in 20 eco-climatic domains. We will provide examples of how NEON's full potential can be realized when these data are combined with long term experimental results and other sensor networks [e.g., Ameriflux, Fluxnet, the Long-term Ecological Research Program (LTER), the Long-term Agroecosystem Research Network (LTAR)], Critical Zone Observatory (CZO).

Spin alignment of ρ0 mesons produced in antineutrino and neutrino neon charged-current interactions

NASA Astrophysics Data System (ADS)

Wittek, W.; Guy, J.; Adeholz, M.; Allport, P.; Baton, J. P.; Berggren, M.; Bertrand, D.; Brisson, V.; Bullock, F. W.; Burkot, W.; Calicchio, M.; Clayton, E. F.; Coghen, T.; Cooper-Sarkar, A. M.; Erriquez, O.; Fitch, P. J.; Fogli-Muciaccia, M. T.; Hulth, P. O.; Jones, G. T.; Kasper, P.; Klein, H.; Marage, P.; Middleton, R. P.; Miller, D. B.; Mobayyen, M. M.; Morrison, D. R. O.; Neveu, M.; O'Neale, S. W.; Parker, M. A.; Petiau, P.; Sacton, J.; Sansum, R. A.; Schmitz, N.; Simopoulou, E.; Vallee, C.; Varvell, K.; Vayaki, A.; Venus, W.; Wachsmuth, H.; Wells, J.

1987-03-01

In a bubble chamber experiment with BEBC the spin alignment parameter η=1/2 (2ϱ00 - ϱ11 - ϱ-1-1) is measured for ϱ0 mesons produced in deep inelastic charged-current antineutrino and neutrono interactions on neon. In the current fragmentation region η is found to be ηv=0.48+/-0.27 (stat.)+/-0.15 (syst.) for vNe and ηv=0.12+/-0.20 (stat.)+/-0.10 (syst.) for vNe interactions Present address: University College London, London WC1E 6BT, UK.

Heterodyne detection at 300 GHz using neon indicator lamp glow discharge detector.

PubMed

Aharon Akram, Avihai; Rozban, Daniel; Kopeika, Natan S; Abramovich, Amir

2013-06-10

A miniature neon indicator lamp, also known as a glow discharge detector (GDD), costing about 50 cents, was found to be an excellent room temperature terahertz radiation detector. Proof-of-concept 300 GHz heterodyne detection using GDD is demonstrated in this paper. Furthermore, a comparison to direct detection was carried out as well. Previous results with the GDD at 10 GHz showed 40 times better sensitivity using heterodyne detection compared to direct detection. Preliminary results at 300 GHz showed better sensitivity by a factor of 20 with only 56 μW local-oscillator power using heterodyne compared to direct detection. The higher the local-oscillator power (P(lo)), the better the sensitivity of the detector. Further improvement can be achieved by employing better quasi-optical design.

Low-Loss Superconducting Nanowire Circuits Using a Neon Focused Ion Beam

NASA Astrophysics Data System (ADS)

Burnett, J.; Sagar, J.; Kennedy, O. W.; Warburton, P. A.; Fenton, J. C.

2017-07-01

We present low-temperature measurements of low-loss superconducting nanowire-embedded resonators in the low-power limit relevant for quantum circuits. The superconducting resonators are embedded with superconducting nanowires with widths down to 20 nm using a neon focused ion beam. In the low-power limit, we demonstrate an internal quality factor up to 3.9 ×105 at 300 mK [implying a two-level-system-limited quality factor up to 2 ×105 at 10 mK], not only significantly higher than in similar devices but also matching the state of the art of conventional Josephson-junction-embedded resonators. We also show a high sensitivity of the nanowire to stray infrared photons, which is controllable by suitable precautions to minimize stray photons in the sample environment. Our results suggest that there are excellent prospects for superconducting-nanowire-based quantum circuits.

Strange particle production in ν and overlineν neon interactions

NASA Astrophysics Data System (ADS)

Bosetti, P.; Fritze, P.; Grässler, H.; Schulte, R.; Schultze, K.; Geich-Gimbel, C.; Glimpf, W.; Nellen, B.; Wünsch, B.; Grant, A.; Hulth, P. O.; Klein, H.; Morrison, D. R. O.; Pape, L.; Wachsmuth, H.; Mermikides, M.; Simopoulou, E.; Vayaki, A.; Butterworth, I.; Chima, J. S.; Clayton, E.; Iaselli, G.; Mobayyen, M. M.; Petrides, A.; Albajar, C.; Wells, J.; Bloch, M.; Bolognese, T.; Velasco, J.; Aachen-Bonn-CERN-Demokritos Athens-I. C. London-Oxford-Saclay Collaboration

1982-12-01

The inclusive production of K 0's and Λ's has been investigated in neutrino and antineutrino interactions in BEBC, filled with a neon-hydrogen mixture. The inclusive rates for the 3083 (1022) ν ( overlineν) induced charged current events are (23.0 ± 1.7)% ((21.9 ± 2.8)%) for K 0's and (5.7 ± 0.7)% ((6.5 ± 1.2)%) for Λ's. The general behaviour of the K 0's and Λ's is found to be similar to that in νp interactions and π+p interactions at lower < W>. In the hadronic c.m.s. K 0's are produced mostly forwards, Λ's predominantly in the backward hemisphere. The data indicate that K 0's produced in overlineν interactions on average carry a larger fraction of the total available momentum than those in ν induced reactions. The dependences of the average transverse momentum on the variables Q2, W2 and Bjorken x are presented.

Spatial distribution of fluorescent light emitted from neon and nitrogen excited by low energy electron beams

NASA Astrophysics Data System (ADS)

Morozov, A.; Krücken, R.; Ulrich, A.; Wieser, J.

2006-11-01

Side-view intensity profiles of fluorescent light were measured for neon and nitrogen excited with 12keV electron beams at gas pressures from 250to1400hPa. The intensity profiles were compared with theoretical profiles calculated using the CASINO program which performs Monte Carlo simulations of electron scattering. It was assumed that the spatial distribution of fluorescent intensity is directly proportional to the spatial distribution of energy loss by primary electrons. The comparison shows good correlation of experimental data and the results of numeric simulations.

Proton-proton correlations at small relative momentum in neon-nucleus collisions at E/A=400 and 800 MeV

NASA Technical Reports Server (NTRS)

Dupieux, P.; Alard, J. P.; Augerat, J.; Babinet, R.; Bastid, N.; Brochard, F.; Charmensat, P.; De Marco, N.; Fanet, H.; Fodor, Z.;

Comparative study of elastic electron collisions on the isoelectronic SiN{sub 2}, SiCO, and CSiO radicals

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

Fujimoto, M. M.; Michelin, S. E.; Mazon, K. T.

2007-07-15

We report a theoretical study of elastic electron collisions on three isoelectronic free radicals, namely, SiNN, SiCO, and CSiO. More specifically, differential, integral, and momentum-transfer cross sections are calculated and reported in the (1-100) eV energy range. Calculations are performed at the static-exchange-polarization-absorption level of approximation. A combination of the iterative Schwinger variational method and the distorted-wave approximation is used to solve the scattering equations. Our study reveals that the calculated cross sections for the e{sup -}-SiNN and e{sup -}-SiCO collisions are very similar even at incident energies as low as 3 eV. Strong isomeric effects are also observed inmore » the calculated cross sections for e{sup -}-CSiO and e{sup -}-SiCO collisions, particularly at incident energies below 20 eV. It is believed that the position of the silicon atom being at the center or extremity of the molecules may exert important influence on the calculated cross sections.« less

Detecting trends in regional ecosystem functioning: the importance of field data for calibrating and validating NEON airborne remote sensing instruments and science data products

NASA Astrophysics Data System (ADS)

McCorkel, J.; Kuester, M. A.; Johnson, B. R.; Krause, K.; Kampe, T. U.; Moore, D. J.

2011-12-01

The National Ecological Observatory Network (NEON) is a research facility under development by the National Science Foundation to improve our understanding of and ability to forecast the impacts of climate change, land-use change, and invasive species on ecology. The infrastructure, designed to operate over 30 years or more, includes site-based flux tower and field measurements, coordinated with airborne remote sensing observations to observe key ecological processes over a broad range of temporal and spatial scales. NEON airborne data on vegetation biochemical, biophysical, and structural properties and on land use and land cover will be captured at 1 to 2 meter resolution by an imaging spectrometer, a small-footprint waveform-LiDAR and a high-resolution digital camera. Annual coverage of the 60 NEON sites and capacity to support directed research flights or respond to unexpected events will require three airborne observation platforms (AOP). The integration of field and airborne data with satellite observations and other national geospatial data for analysis, monitoring and input to ecosystem models will extend NEON observations to regions across the United States not directly sampled by the observatory. The different spatial scales and measurement methods make quantitative comparisons between remote sensing and field data, typically collected over small sample plots (e.g. < 0.2 ha), difficult. New approaches to developing temporal and spatial scaling relationships between these data are necessary to enable validation of airborne and satellite remote sensing data and for incorporation of these data into continental or global scale ecological models. In addition to consideration of the methods used to collect ground-based measurements, careful calibration of the remote sensing instrumentation and an assessment of the accuracy of algorithms used to derive higher-level science data products are needed. Furthermore, long-term consistency of the data collected by all

Wavelengths and intensities of a platinum/neon hollow cathode lamp in the region 1100-4000 A

NASA Technical Reports Server (NTRS)

Reader, Joseph; Acquista, Nicolo; Sansonetti, Craig J.; Sansonetti, Jean E.

1990-01-01

The spectrum of a platinum hollow cathode lamp containing neon carrier gas was recorded photographically and photoelectrically with a 10.7 m normal-incidence vacuum spectrograph. Wavelengths and intensities were determined for about 3000 lines in the region 1100-4000 A. The uncertainty of the measured wavelengths is estimated to be + or - 0.0020 A. Ritz-type wavelengths are given for about 550 classified lines of Pt II with uncertainites varying from + or - 0.0004 A to + or - 0.0025 A. The uncertainty of the relative intensities is estimated to be about 20 percent.

Electrical Versus Optical: Comparing Methods for Detecting Terahertz Radiation Using Neon Lamps

NASA Astrophysics Data System (ADS)

Slocombe, L. L.; Lewis, R. A.

2018-05-01

Terahertz radiation impinging on a lit neon tube causes additional ionization of the encapsulated gas. As a result, the electrical current flowing between the electrodes increases and the glow discharge in the tube brightens. These dual phenomena suggest two distinct modes of terahertz sensing. The electrical mode simply involves measuring the electrical current. The optical mode involves monitoring the brightness of the weakly ionized plasma glow discharge. Here, we directly compare the two detection modes under identical experimental conditions. We measure 0.1-THz radiation modulated at frequencies in the range 0.1-10 kHz, for lamp currents in the range 1-10 mA. We find that electrical detection provides a superior signal-to-noise ratio while optical detection has a faster response. Either method serves as the basis of a compact, robust, and inexpensive room-temperature detector of terahertz radiation.

High-pressure versus isoelectronic doping effect on the honeycomb iridate Na2IrO3

NASA Astrophysics Data System (ADS)

Hermann, V.; Ebad-Allah, J.; Freund, F.; Pietsch, I. M.; Jesche, A.; Tsirlin, A. A.; Deisenhofer, J.; Hanfland, M.; Gegenwart, P.; Kuntscher, C. A.

2017-11-01

We study the effect of isoelectronic doping and external pressure in tuning the ground state of the honeycomb iridate Na2IrO3 by combining optical spectroscopy with synchrotron x-ray diffraction measurements on single crystals. The obtained optical conductivity of Na2IrO3 is discussed in terms of a Mott-insulating picture versus the formation of quasimolecular orbitals and in terms of Kitaev interactions. With increasing Li content x , (Na1 -xLix )2IrO3 moves deeper into the Mott-insulating regime, and there are indications that up to a doping level of 24% the compound comes closer to the Kitaev limit. The optical conductivity spectrum of single-crystalline α -Li2IrO3 does not follow the trends observed for the series up to x =0.24 . There are strong indications that α -Li2IrO3 is not as close to the Kitaev limit as Na2IrO3 and lies closer to the quasimolecular orbital picture instead. Except for the pressure-induced hardening of the phonon modes, the optical properties of Na2IrO3 seem to be robust against external pressure. Possible explanations of the unexpected evolution of the optical conductivity with isolectronic doping and the drastic change between x =0.24 and x =1 are given by comparing the pressure-induced changes of lattice parameters and the optical conductivity with the corresponding changes induced by doping.

Liquid neon heat transfer as applied to a 30 tesla cryomagnet

NASA Technical Reports Server (NTRS)

Papell, S. S.; Hendricks, R. C.

1975-01-01

Since superconducting magnets cooled by liquid helium are limited to magnetic fields of about 18 teslas, the design of a 30 tesla cryomagnet necessitates forced convection liquid neon heat transfer in small coolant channels. As these channels are too small to handle the vapor flow if the coolant were to boil, the design philosophy calls for suppressing boiling by subjecting the fluid to high pressures. Forced convection heat transfer data are obtained by using a blowdown technique to force the fluid vertically through a resistance-heated instrumented tube. The data are obtained at inlet temperatures between 28 and 34 K and system pressures between 28 to 29 bars. Data correlation is limited to a very narrow range of test conditions, since the tests were designed to simulate the heat transfer characteristics in the coolant channels of the 30 tesla cryomagnet concerned. The results can therefore be applied directly to the design of the magnet system.-

Production of stable, non-thermal atmospheric pressure rf capacitive plasmas using gases other than helium or neon

DOEpatents

Park, Jaeyoung; Henins, Ivars

2005-06-21

The present invention enables the production of stable, steady state, non-thermal atmospheric pressure rf capacitive .alpha.-mode plasmas using gases other than helium and neon. In particular, the current invention generates and maintains stable, steady-state, non-thermal atmospheric pressure rf .alpha.-mode plasmas using pure argon or argon with reactive gas mixtures, pure oxygen or air. By replacing rare and expensive helium with more readily available gases, this invention makes it more economical to use atmospheric pressure rf .alpha.-mode plasmas for various materials processing applications.

Facing the Challenges of Accessing, Managing, and Integrating Large Observational Datasets in Ecology: Enabling and Enriching the Use of NEON's Observational Data

NASA Astrophysics Data System (ADS)

Thibault, K. M.

2013-12-01

As the construction of NEON and its transition to operations progresses, more and more data will become available to the scientific community, both from NEON directly and from the concomitant growth of existing data repositories. Many of these datasets include ecological observations of a diversity of taxa in both aquatic and terrestrial environments. Although observational data have been collected and used throughout the history of organismal biology, the field has not yet fully developed a culture of data management, documentation, standardization, sharing and discoverability to facilitate the integration and synthesis of datasets. Moreover, the tools required to accomplish these goals, namely database design, implementation, and management, and automation and parallelization of analytical tasks through computational techniques, have not historically been included in biology curricula, at either the undergraduate or graduate levels. To ensure the success of data-generating projects like NEON in advancing organismal ecology and to increase transparency and reproducibility of scientific analyses, an acceleration of the cultural shift to open science practices, the development and adoption of data standards, such as the DarwinCore standard for taxonomic data, and increased training in computational approaches for biologists need to be realized. Here I highlight several initiatives that are intended to increase access to and discoverability of publicly available datasets and equip biologists and other scientists with the skills that are need to manage, integrate, and analyze data from multiple large-scale projects. The EcoData Retriever (ecodataretriever.org) is a tool that downloads publicly available datasets, re-formats the data into an efficient relational database structure, and then automatically imports the data tables onto a user's local drive into the database tool of the user's choice. The automation of these tasks results in nearly instantaneous execution

Improved Simulations of Astrophysical Plasmas: Computation of New Dielectronic Recombination Data

NASA Technical Reports Server (NTRS)

Gorczyca, T. W.; Korista, K. T.; Zatsarinny, O.; Badnell, N. R.; Savin, D. W.

2002-01-01

Here we recap the works of two posters presented at the 2002 NASA Laboratory Astrophysics Workshop. The first was Shortcomings of the R-Matrix Method for Treating Dielectronic Recombination. The second was Computation of Dielectronic Recombination Data for the Oxygen-Like Isoelectronic Sequence.

Pediatric diabetes consortium type 1 diabetes new onset (NeOn) study: Factors associated with HbA1c levels one year after diagnosis

USDA-ARS?s Scientific Manuscript database

To identify determinants of hemoglobin A1c (HbA1c) levels 1 yr after the diagnosis of type 1 diabetes (T1D) in participants in the Pediatric Diabetes Consortium (PDC) T1D New Onset (NeOn) Study. Diabetes-specific as well as socioeconomic factors during the first year following diagnosis were analyze...

RADIATION CHEMISTRY OF HIGH ENERGY CARBON, NEON AND ARGON IONS: INTEGRAL YIELDS FROM FERROUS SULFATE SOLUTIONS

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

Christman, E.A.; Appleby, A.; Jayko, M.

1980-07-01

Chemical yields of Fe{sup 3+} have been measured from FeSO{sub 4} solutions irradiated in the presence and absence of oxygen with carbon, neon, and argon ions from the Berkeley Bevalac facility. G(Fe{sup 3+}) decreases with increasing beam penetration and with increasing atomic number of the incident ion. The results are compared with current theoretical expectations of the behavior of these particles in an aqueous absorber. The chemical yields are consistently higher than theoretically predicted, by amounts varying from <6.2% (carbon ions) to <13.2% (argon ions). The additional yields are possibly attributable to fragmentation of the primary particle beams.

Feasibility of line-ratio spectroscopy on helium and neon as edge diagnostic tool for Wendelstein 7-X

DOE PAGES

Barbui, T.; Krychowiak, M.; König, R.; ...

2016-09-27

A beam emission spectroscopy system on thermal helium (He) and neon (Ne) has been set up at Wendelstein 7-X to measure edge electron temperature and density profiles utilizing the line-ratio technique or its extension by the analysis of absolutely calibrated line emissions. The setup for a first systematic test of these techniques of quantitative atomic spectroscopy in the limiter startup phase (OP1.1) is reported together with first measured profiles. Lastly, this setup and the first results are an important test for developing the technique for the upcoming high density, low temperature island divertor regime.

Correlated multielectron dynamics in mid-infrared laser pulse interactions with neon atoms.

PubMed

Tang, Qingbin; Huang, Cheng; Zhou, Yueming; Lu, Peixiang

2013-09-09

The multielectron dynamics in nonsequential triple ionization (NSTI) of neon atoms driven by mid-infrared (MIR) laser pulses is investigated with the three-dimensional classical ensemble model. In consistent with the experimental result, our numerical result shows that in the MIR regime, the triply charged ion longitudinal momentum spectrum exhibits a pronounced double-hump structure at low laser intensity. Back analysis reveals that as the intensity increases, the responsible triple ionization channels transform from direct (e, 3e) channel to the various mixed channels. This transformation of the NSTI channels leads to the results that the shape of ion momentum spectra becomes narrow and the distinct maxima shift towards low momenta with the increase of the laser intensity. By tracing the triply ionized trajectories, the various ionization channels at different laser intensities are clearly identified and these results provide an insight into the complex dynamics of the correlated three electrons in NSTI.

Elemental Abundances in NGC 3516

NASA Technical Reports Server (NTRS)

Turner, T. J.; Kraemer, S. B.; Mushotzky, R. F.; George, I. M.; Gabel, J. R.

2003-01-01

We present Reflection Grating Spectrometer data from an XMM-Newton observation of the Seyfert 1 galaxy NGC 3516, taken while the continuum source was in an extremely low flux state. This observation offers a rare opportunity for a detailed study of emission from a Seyfert 1 galaxy as these are usually dominated by high nuclear continuum levels and heavy absorption. The spectrum shows numerous narrow emission lines (FWHM approximately less than 1300 kilometers per second) in the 0.3 - 2 keV range, including the H-like lines of C, N, and O and the He-like lines of N, O and Ne. The emission-line ratios and the narrow width of the radiative recombination continuum of CVI indicate that the gas is photoionized and of fairly low temperature (kT approximately less than 0.01 keV). The availability of emission lines from different elements for two iso-electronic sequences allows us to constrain the element abundances. These data show that the N lines are far stronger than would be expected from gas of solar abundances. Based on our photoionization models we find that nitrogen is overabundant in the central regions of the galaxy, compared to carbon, oxygen and neon by at least a factor of 2.5. We suggest that this is the result of secondary production of nitrogen in intermediate mass stars, and indicative of the history of star formation in NGC 3516.

A DFT investigation on geometry and chemical bonding of isoelectronic Si8N6V-, Si8N6Cr, and Si8N6Mn+ clusters

NASA Astrophysics Data System (ADS)

Tam, Nguyen Minh; Pham, Hung Tan; Cuong, Ngo Tuan; Tung, Nguyen Thanh

2017-10-01

The geometric feature and chemical bonding of isoelectronic systems Si8N6Mq (M = V, Cr, Mn and q = -1, 0, 1, respectively) are investigated by means of density-functional-theory calculations. The encapsulated form is found for all ground-state structures, where the metal atom locates at the central site of the hollow Si8N6 cage. The Si8N6 cage is established by adding two Si atoms to a distorted Si6N6 prism, which is a combination of Si4N2 and Si2N4 strings. Chemical bonding of Si8N6Mq systems is explored by using the electron localization indicator and theory of atom in molecule, revealing the vital role of metal center in stabilizing the clusters.

Isoelectronic Manganese and Iron Hydrogenation/Dehydrogenation Catalysts: Similarities and Divergences.

PubMed

Gorgas, Nikolaus; Kirchner, Karl

2018-06-19

Sustainable processes that utilize nontoxic, readily available, and inexpensive starting materials for organic synthesis constitute a major objective in modern chemical research. In this context, it is highly important to perform reactions under catalytic conditions and to replace precious metal catalysts by earth-abundant nonprecious metal catalysts. In particular, iron and manganese are promising candidates, as these are among the most abundant metals in the earth's crust, are inexpensive, and exhibit a low environmental impact. As far as chemical processes are concerned, hydrogenations and acceptorless alcohol dehydrogenation (AAD), sometimes in conjunction with hydrogen autotransfer reactions, are becoming important areas of research. While the first is a very important synthetic process representing a highly atom-efficient and clean methodology, AAD is an oxidant-free, environmentally benign reaction where carbonyl compounds together with dihydrogen as a valuable product and/or reactant (autotransfer) and water are formed. Carbonyl compounds, typically generated in situ, can be converted into other useful organic materials such as amines, imines, or heterocycles. In 2016 several groups, including ours, discovered for the first time the potential of hydride biscarbonyl Mn(I) complexes bearing strongly bound PNP pincer ligands or related tridentate ligands as highly effective and versatile catalysts for hydrogenation, transfer hydrogenation, and dehydrogenation reactions. These complexes are isoelectronic analogues of the respective hydride monocarbonyl Fe(II) PNP compounds and display similar reactivities but also quite divergent behavior depending on the coligands. Moreover, manganese compounds show improved long-term stability and high robustness toward harsh reaction conditions. In light of these recent achievements, this Account contrasts Mn(I) and Fe(II) PNP pincer catalysts, highlighting specific features that are connected to particular structural and

A density difference based analysis of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Grabowski, Ireneusz; Teale, Andrew M.; Fabiano, Eduardo; Śmiga, Szymon; Buksztel, Adam; Della Sala, Fabio

2014-03-01

We present a density difference based analysis for a range of orbital-dependent Kohn-Sham functionals. Results for atoms, some members of the neon isoelectronic series and small molecules are reported and compared with ab initio wave function calculations. Particular attention is paid to the quality of approximations to the exchange-only optimised effective potential (OEP) approach: we consider both the localised Hartree-Fock as well as the Krieger-Li-Iafrate methods. Analysis of density differences at the exchange-only level reveals the impact of the approximations on the resulting electronic densities. These differences are further quantified in terms of the ground state energies, frontier orbital energy differences and highest occupied orbital energies obtained. At the correlated level, an OEP approach based on a perturbative second-order correlation energy expression is shown to deliver results comparable with those from traditional wave function approaches, making it suitable for use as a benchmark against which to compare standard density functional approximations.

Analysis of Optogalvanic Transients at 621.7 nm, 633.4 nm and 640.2 nm of Neon in a Discharge Plasma Fitted with a Monte Carlo Mathematical Model.

NASA Astrophysics Data System (ADS)

Ogungbemi, Kayode; Han, Xianming; Blosser, Micheal; Misra, Prabhakar; LASER Spectroscopy Group Collaboration

2014-03-01

Optogalvanic transitions have been recorded and fitted for 1s5 - 2p7\\ (621.7 nm), 1s5 - 2p8 (633.4 nm) and 1s5 - 2p9 (640.2 nm) transitions of neon in a Fe-Ne hollow cathode plasma discharge as a function of current (2-19 mA) and time evolution (0-50 microsec). The optogalvanic waveforms have been fitted to a Monte carlo mathematical model. The variation in the excited population of neon is governed by the rate of collision of the atoms involving the common metastable state (1s5) for the three transitions investigated. The concomitant changes in amplitudes and intensities of the optogalvanic signal waveforms associated with these transitions have been studied rigorously and the fitted parameters obtained using the Monte Carlo algorithm to help better understand the physics of the hollow cathode discharge. Thanks to Laser Spectroscopy group in Physics and Astronomy Dept. Howard University Washington DC.

The watercolor illusion and neon color spreading: a unified analysis of new cases and neural mechanisms

NASA Astrophysics Data System (ADS)

Pinna, Baingio; Grossberg, Stephen

2005-10-01

Coloration and figural properties of neon color spreading and the watercolor illusion are studied using phenomenal and psychophysical observations. Coloration properties of both effects can be reduced to a common limiting condition, a nearby color transition called the two-dot limiting case, which clarifies their perceptual similarities and dissimilarities. The results are explained by the FACADE neural model of biological vision. The model proposes how local properties of color transitions activate spatial competition among nearby perceptual boundaries, with boundaries of lower-contrast edges weakened by competition more than boundaries of higher-contrast edges. This asymmetry induces spreading of more color across these boundaries than conversely. The model also predicts how depth and figure-ground effects are generated in these illusions.

Challenges and Opportunities to Developing Synergies Among Diverse Environmental Observatories: FSML, NEON, and GLEON

NASA Astrophysics Data System (ADS)

Williamson, C. E.; Weathers, K. C.; Knoll, L. B.; Brentrup, J.

2012-12-01

Recent rapid advances in sensor technology and cyberinfrastructure have enabled the development of numerous environmental observatories ranging from local networks at field stations and marine laboratories (FSML) to continental scale observatories such as the National Ecological Observatory Network (NEON) to global scale observatories such as the Global Lake Ecological Observatory Network (GLEON). While divergent goals underlie the initial development of these observatories, and they are often designed to serve different communities, many opportunities for synergies exist. In addition, the use of existing infrastructure may enhance the cost-effectiveness of building and maintaining large scale observatories. For example, FSMLs are established facilities with the staff and infrastructure to host sensor nodes of larger networks. Many field stations have existing staff and long-term databases as well as smaller sensor networks that are the product of a single or small group of investigators with a unique data management system embedded in a local or regional community. These field station based facilities and data are a potentially untapped gold mine for larger continental and global scale observatories; common ecological and environmental challenges centered on understanding the impacts of changing climate, land use, and invasive species often underlie these efforts. The purpose of this talk is to stimulate a dialog on the challenges of merging efforts across these different spatial and temporal scales, as well as addressing how to develop synergies among observatory networks with divergent roots and philosophical approaches. For example, FSMLs have existing long-term databases and facilities, while NEON has sparse past data but a well-developed template and closely coordinated team working in a coherent format across a continental scale. GLEON on the other hand is a grass-roots network of experts in science, information technology, and engineering with a common goal

Mobilities of ground-state and metastable O/+/, O2/+/, O/2+/, and O2/2+/ ions in helium and neon

NASA Astrophysics Data System (ADS)

Johnsen, R.; Biondi, M. A.; Hayashi, M.

1982-09-01

The ionic mobilities of O(+), O2(+), O(2+), and O2(2+) in helium and neon have been measured using a selected-ion drift apparatus (SIDA). It is found that the mobilities of both O(+) and O2(+) ions in the metastable states (2D or 4Pi u) are measurably smaller than those of the same ions carried out by using known, state-selective ion-molecule reactions. A similar mobility differentiation of ground-state and metastable ions was not observed for the O(2+) and O2(2+) ions.

Effects of ionizing radiation on the light sensing elements of the retina. [Structural and physiological effects of carbon, helium, and neon ions on rods and cones of salamanders and mice

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

Malachowski, M.J.

1978-07-01

This investigation was undertaken to quantitate possible morphological and physiological effects of particles of high linear energy transfer on the retina, in comparison with x-ray effects. The particles used were accelerated atomic nuclei of helium, carbon, and neon at kinetic energies of several hundred MeV/nucleon. For morphological studies, scanning and transmission electron microscopy and light microscopy were used. Physiological studies consisted of autoradiographic data of the rate of incorporation of labeled protein in the structures (opsin) of the outer segment of visual cells. Structural changes were found in the nuclei, as well as the inner and outer segments of visualmore » cells, rods and cones. At a low dose of 10 rad, x rays and helium had no statistically significant morphological effects, but carbon and neon beams did cause significant degeneration of individual cells, pointing to the existence of a linear dose--effect relationship. At high doses of several hundred rads, a Pathologic Index determined the relative biological effectiveness of neon against alpha particles to have a value of greater than 6. The severity of effects per particle increased with atomic number. Labeling studies demonstrated a decreased rate of incorporation of labeled proteins in the structural organization of the outer segments of visual rods. The rate of self-renewal of visual rod discs was punctuated by irradiation and the structures themselves were depleted of amino acids. A model of rod discs (metabolic and catabolic) was postulated for correlated early and late effects to high and low doses.« less

Detection of Nitrogen and Neon in the X-ray Spectrum of GP Com with XMM/Newton

NASA Technical Reports Server (NTRS)

Strohmayer, Tod E.

2004-01-01

We report on X-ray spectroscopic observations with XMM/Newton of the ultra-compact, double white dwarf binary, GP Com. With the Reflection Grating Spectrometers (RGS) we detect the L(alpha) and L(beta) lines of hydrogen-like nitrogen (N VII) and neon (Ne X), as well as the helium-like triplets (N VI and Ne IX) of these same elements. All the emission lines are unresolved. These are the first detections of X-ray emission lines from a double-degenerate, AM CVn system. We detect the resonance (r) and intercombination (i) lines of the N VI triplet, but not the forbidden (f) line. The implied line ratios for N VI, R = f/i less than 0.3, and G = (f + i ) / r approx. = 1, combined with the strong resonance line are consistent with a dense, collision-dominated plasma. Both the RGS and EPIC/MOS spectra are well fit by emission horn an optically thin thermal plasma with an emission measure (EM) is a member of (kT/6.5 keV)(sup 0.8) (model cevmkl in XSPEC). Helium, nitrogen, oxygen and neon are required to adequately model the spectrum, however, the inclusion of sulphur and iron further improves the fit, suggesting these elements may also be present at low abundance. We confirm in the X-rays the under- abundance of both carbon and oxygen relative to nitrogen, first deduced from optical spectroscopy by Marsh et al. The average X-ray luminosity of approx. = 3 x 10(exp 30) ergs/s implies a mass accretion rate dot-m approx. = 9 x 10(exp -13) solar mass/yr. The implied temperature and density of the emitting plasma, combined with the presence of narrow emission lines and the low dot-m value, are consistent with production of the X-ray emission in an optically thin boundary layer just above the surface of the white dwarf.

[Functional state of various physiological systems of the human body during respiration of neon-oxygen mixture at depth up to 400 meters].

PubMed

Poleshuk, I P; Genin, A M; Unku, R D; Mikhnenko, A E; Sementsov, V N; Suvorov, A V

1991-01-01

Hyperbaric neon-oxygen mixture has been studied for the effect of its high density under pressure of 41 ata on basic physiological functions of human organism. Typical changes of the cardiorespiratory system and tissue respiration parameters are revealed. Changes in physical working capacity are shown. Exposure to gaseous medium of high pressure and density is accompanied by the development of some compensatory-adaptive reactions. The possibility to perform mid-hard physical work is attained with overstrain of respiration and circulation function.

VizieR Online Data Catalog: Silicon isoelectronic sequence data (Jonsson+, 2016)

NASA Astrophysics Data System (ADS)

Jonsson, P.; Radziute, L.; Gaigalas, G.; Godefroid, M. R.; Marques, J. P.; Brage, T.; Froese Fischer, C.; Grant, I. P.

2015-11-01

Calculations were performed for the five states belonging to the 3s23p2 even configuration and the 22 states belonging to the 3s3p3 and 3s23p3d odd configurations. The calculations were made by parity, meaning that the even and odd states were determined in separate calculations in the EOL scheme. (3 data files).

Thermodynamic design of hydrogen liquefaction systems with helium or neon Brayton refrigerator

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung; Ryu, Ki Nam; Baik, Jong Hoon

2018-04-01

A thermodynamic study is carried out for the design of hydrogen liquefaction systems with helium (He) or neon (Ne) Brayton refrigerator. This effort is motivated by our immediate goal to develop a small-capacity (100 L/h) liquefier for domestic use in Korea. Eight different cycles are proposed and their thermodynamic performance is investigated in comparison with the existing liquefaction systems. The proposed cycles include the standard and modified versions of He Brayton refrigerators whose lowest temperature is below 20 K. The Brayton refrigerator is in direct thermal contact with the hydrogen flow at atmospheric pressure from ambient-temperature gas to cryogenic liquid. The Linde-Hampson system pre-cooled by a Ne Brayton refrigerator is also considered. Full cycle analysis is performed with the real properties of fluids to estimate the figure of merit (FOM) under an optimized operation condition. It is concluded that He Brayton refrigerators are feasible for this small-scale liquefaction, because a reasonably high efficiency can be achieved with simple and safe (low-pressure) operation. The complete cycles with He Brayton refrigerator are presented for the development of a prototype, including the ortho-to-para conversion.

NEON AND CNO ABUNDANCES FOR EXTREME HELIUM STARS-A NON-LTE ANALYSIS

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

Pandey, Gajendra; Lambert, David L., E-mail: pandey@iiap.res.in, E-mail: dll@astro.as.utexas.edu

A non-LTE (NLTE) abundance analysis was carried out for three extreme helium stars (EHes): BD+10{sup 0} 2179, BD-9{sup 0} 4395, and LS IV+6{sup 0} 002, from their optical spectra with NLTE model atmospheres. NLTE TLUSTY model atmospheres were computed with H, He, C, N, O, and Ne treated in NLTE. Model atmosphere parameters were chosen from consideration of fits to observed He I line profiles and ionization equilibria of C and N ions. The program SYNSPEC was then used to determine the NLTE abundances for Ne as well as H, He, C, N, and O. LTE neon abundances from Nemore » I lines in the EHes: LSE 78, V1920 Cyg, HD 124448, and PV Tel, are derived from published models and an estimate of the NLTE correction applied to obtain the NLTE Ne abundance. We show that the derived abundances of these key elements, including Ne, are well matched with semi-quantitative predictions for the EHe resulting from a cold merger (i.e., no nucleosynthesis during the merger) of an He white dwarf with a C-O white dwarf.« less

Molecular simulation of the thermodynamic, structural, and vapor-liquid equilibrium properties of neon

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Frascoli, Federico; Sadus, Richard J.

2016-09-01

The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point. Lustig's thermodynamic approach is formally extended for temperature-dependent intermolecular potentials. Quantum effects are incorporated using the Feynman-Hibbs quantum correction, which results in significant improvement in the accuracy of predicted thermodynamic properties. The new Feynman-Hibbs version of the Hellmann-Bich-Vogel potential predicts the isochoric heat capacity to an accuracy of 1.4% over the entire range of liquid densities. It also predicts other thermodynamic properties more accurately than alternative intermolecular potentials.

Operational Prediction of the Habitat Suitability Index (HSI) Distribution for Neon Flying Squid in Central North Pacific by Using FORA Dataset and a New Data Assimilation System SKUIDS

NASA Astrophysics Data System (ADS)

Igarashi, H.; Ishikawa, Y.; Wakamatsu, T.; Tanaka, Y.; Nishikawa, S.; Nishikawa, H.; Kamachi, M.; Kuragano, T.; Takatsuki, Y.; Fujii, Y.; Usui, N.; Toyoda, T.; Hirose, N.; Sakai, M.; Saitoh, S. I.; Imamura, Y.

2016-02-01

The neon flying squid (Ommastrephes bartramii) has a wide-spread distribution in subtropical and temperate waters in the North Pacific, which plays an important role in the pelagic ecosystem and is one of the major targets in Japanese squid fisheries. The main fishing areas for Japanese commercial vessels are located in the central North Pacific (35-45N, around the date line) in summer. In this study, we have developed several kinds of habitat suitability index (HSI) models of the neon flying squid for investigating the relationship between its potential habitat and the ocean state variations in the target area. For developing HSI models, we have used a new ocean reanalysis dataset FORA (4-dimensional variational Ocean Re-Analysis) produced by JAMSTEC/CEIST and MRI-JMA. The horizontal resolution is 0.1*0.1 degree of latitude and longitude with 54 vertical levels, which can provide realistic fields of 3-dimensional ocean circulation and environmental structures including meso-scale eddies. In addition, we have developed a new 4D-VAR (4-dimensional variational) ocean data assimilation system for predicting ocean environmental changes in the main fishing grounds. We call this system "SKUIDS" (Scalable Kit of Under-sea Information Delivery System). By using these prediction fields of temperature, salinity, sea surface height, horizontal current velocity, we produced daily HSI maps of the neon flying squid, and provided them to the Japanese commercial vessels in operation. Squid fishermen can access the web site for delivering the information of ocean environments in the fishing ground by using Inmarsat satellite communication on board, and show the predicted fields of subsurface temperatures and HSI. Here, we present the details of SKUIDS and the web-delivery system for squid fishery, and some preliminary results of the operational prediction.

Vibrational investigations of CO2-H2O, CO2-(H2O)2, and (CO2)2-H2O complexes isolated in solid neon.

PubMed

Soulard, P; Tremblay, B

2015-12-14

The van der Waals complex of H2O with CO2 has attracted considerable theoretical interest as a typical example of a weak binding complex with a dissociation energy less than 3 kcal/mol. Up to now, experimental vibrational data are sparse. We have studied by FTIR the complexes involving CO2 and water molecules in solid neon. Many new absorption bands close to the well known monomers fundamentals give evidence for at least three (CO2)n-(H2O)m complexes, noted n:m. Concentration effects combined with a detailed vibrational analysis allow for the identification of sixteen, twelve, and five transitions for the 1:1, 1:2, and 2:1 complexes, respectively. Careful examination of the far infrared spectral region allows the assignment of several 1:1 and 1:2 intermolecular modes, confirmed by the observation of combinations of intra + intermolecular transitions, and anharmonic coupling constants have been derived. Our results demonstrate the high sensibility of the solid neon isolation to investigate the hydrogen-bonded complexes in contrast with the gas phase experiments for which two quanta transitions cannot be easily observed.

Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon.

PubMed

Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei

2016-07-11

A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coherent production of π+ and π- mesons by charged-current interactions of neutrinos and antineutrinos on neon nuclei at the Fermilab Tevatron

NASA Astrophysics Data System (ADS)

Aderholz, M.; Aggarwal, M. M.; Akbari, H.; Allport, P. P.; Baba, P. V.; Badyal, S. K.; Barth, M.; Baton, J. P.; Bingham, H. H.; Brucker, E. B.; Burnstein, R. A.; Campbell, R. C.; Cence, R.; Chatterjee, T. K.; Clayton, E. F.; Corrigan, G.; Coutures, C.; de Prospo, D.; Devanand; de Wolf, E.; Faulkner, P. J.; Fretter, W. B.; Gupta, V. K.; Guy, J.; Hanlon, J.; Harigel, G.; Harris, F.; Jabiol, M. A.; Jacques, P.; Jain, V.; Jones, G. T.; Jones, M. D.; Jones, R. W.; Kafka, T.; Kalelkar, M.; Kasper, P.; Kasper, P.; Kaul, G. L.; Kaur, M.; Kohli, J. M.; Koller, E. L.; Krawiec, R. J.; Lauko, M.; Lys, J.; Mann, W. A.; Marage, P.; Milburn, R. H.; Miller, D. B.; Mittra, I. S.; Mobayyen, M. M.; Moreels, J.; Morrison, D. R.; Myatt, G.; Nailor, P.; Naon, R.; Napier, A.; Neveu, M.; Passmore, D.; Peters, M. W.; Peterson, V. Z.; Plano, R.; Rao, N. K.; Rubin, H. A.; Sacton, J.; Saitta, B.; Schmid, P.; Schmitz, N.; Schneps, J.; Sekulin, R.; Sewell, S.; Singh, J. B.; Sood, P. M.; Smart, W.; Stamer, P.; Varvell, K. E.; Venus, W.; Verluyten, L.; Voyvodic, L.; Wachsmuth, H.; Wainstein, S.; Willocq, S.; Wittek, W.; Yost (E632 Collaboration), G. P.

1989-11-01

Coherent single-pion production on neon nuclei is studied using the Fermilab 15-ft bubble chamber filled with a heavy Ne-H2 mixture and exposed to the Tevatron neutrino beam. In the neutrino energy range 40-300 GeV, the net signal is 20+/-6 events, giving a corrected rate per charged-current event of (0.26+/-0.10)%. The cross section and kinematic distributions agree with the predictions of a model based on partial conservation of axial-vector current and meson dominance.

How Does the Ionic Liquid Organizational Landscape Change when Nonpolar Cationic Alkyl Groups Are Replaced by Polar Isoelectronic Diethers?

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

Kashyap, Hemant K.; Santos, Cherry S.; Daly, Ryan P.

2012-12-21

The X-ray scattering experiments and molecular dynamics simulations have been performed to investigate the structure of four room temperature ionic liquids (ILs) comprising the bis(trifluoromethylsulfonyl)amide (NTf 2 –) anion paired with the triethyloctylammonium (N 2228 +) and triethyloctylphosphonium (P 2228 +) cations and their isoelectronic diether analogs, the (2-ethoxyethoxy)ethyltriethylammonium (N 222(2O2O2) +) and (2-ethoxyethoxy)ethyltriethylphosphonium (P 222(2O2O2) +) cations. Agreement between simulations and experiments is good and permits a clear interpretation of the important topological differences between these systems. The first sharp diffraction peak (or prepeak) in the structure function S(q) that is present in the case of the liquids containingmore » the alkyl-substituted cations is absent in the case of the diether substituted analogs. Using different theoretical partitioning schemes for the X-ray structure function, we show that the prepeak present in the alkyl-substituted ILs arises from polarity alternations between charged groups and nonpolar alkyl tails. In the case of the diether substituted ILs, we find considerable curling of tails. Anions can be found with high probability in two different environments: close to the cationic nitrogen (phosphorus) and also close to the two ether groups. Moreover, for the two diether systems, anions are found in locations from which they are excluded in the alkyl-substituted systems. This removes the longer range (polar/nonpolar) pattern of alternation that gives rise to the prepeak in alkyl-substituted systems.« less

Stereo-selectivity of human serum albumin to enantiomeric and isoelectronic pollutants dissected by spectroscopy, calorimetry and bioinformatics.

PubMed

Ahmad, Ejaz; Rabbani, Gulam; Zaidi, Nida; Singh, Saurabh; Rehan, Mohd; Khan, Mohd Moin; Rahman, Shah Kamranur; Quadri, Zainuddin; Shadab, Mohd; Ashraf, Mohd Tashfeen; Subbarao, Naidu; Bhat, Rajiv; Khan, Rizwan Hasan

2011-01-01

1-naphthol (1N), 2-naphthol (2N) and 8-quinolinol (8H) are general water pollutants. 1N and 2N are the configurational enantiomers and 8H is isoelectronic to 1N and 2N. These pollutants when ingested are transported in the blood by proteins like human serum albumin (HSA). Binding of these pollutants to HSA has been explored to elucidate the specific selectivity of molecular recognition by this multiligand binding protein. The association constants (K(b)) of these pollutants to HSA were moderate (10(4)-10(5) M(-1)). The proximity of the ligands to HSA is also revealed by their average binding distance, r, which is estimated to be in the range of 4.39-5.37 nm. The binding free energy (ΔG) in each case remains effectively the same for each site because of enthalpy-entropy compensation (EEC). The difference observed between ΔC(p) (exp) and ΔC(p) (calc) are suggested to be caused by binding-induced flexibility changes in the HSA. Efforts are also made to elaborate the differences observed in binding isotherms obtained through multiple approaches of calorimetry, spectroscopy and bioinformatics. We suggest that difference in dissociation constants of pollutants by calorimetry, spectroscopic and computational approaches could correspond to occurrence of different set of populations of pollutants having different molecular characteristics in ground state and excited state. Furthermore, our observation of enhanced binding of pollutants (2N and 8H) in the presence of hemin signifies that ligands like hemin may enhance the storage period of these pollutants in blood that may even facilitate the ill effects of these pollutants.

CALCULATIONS WITH SPECTROSCOPIC ACCURACY: ENERGIES AND TRANSITION RATES IN THE NITROGEN ISOELECTRONIC SEQUENCE FROM Ar XII TO Zn XXIV

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

Wang, K.; Dang, W.; Si, R.

2016-03-15

Combined relativistic configuration interaction and many-body perturbation calculations are performed for the 359 fine-structure levels of the 2s{sup 2} 2p{sup 3}, 2 s2p{sup 4}, 2p{sup 5}, 2s{sup 2} 2p{sup 2} 3l, 2 s2p{sup 3} 3l, 2p{sup 4} 3l, and 2s{sup 2} 2p{sup 2} 4l configurations in N-like ions from Ar xii to Zn xxiv. Complete and consistent data sets of energies, wavelengths, radiative rates, oscillator strengths, and line strengths for all possible electric dipole, magnetic dipole, electric quadrupole, and magnetic quadrupole transitions among the 359 levels are given for each ion. The present work significantly increases the amount of accuratemore » data for ions in the nitrogen-like sequence, and the accuracy of the energy levels is high enough to enable the identification and interpretation of observed spectra involving the n = 3, 4 levels, for which experimental values are largely scarce. Meanwhile, the results should be of great help for modeling and diagnosing astrophysical and fusion plasmas.« less

[The treatment of suppurative and atonic wounds with the CO2 laser and the helium-neon laser].

PubMed

Poleganova, I U; Iarŭmov, N; Popadiĭn, N

1991-01-01

The doctrine on wounds is the most important and current one in general surgery and reflects the level and development of medicine. Each surgeon should be well acquainted with all processes and stages of wound healing, because treatment of a suppurative wound requires keen knowledge and art. The basic principle of the local treatment of a septic wound is the thorough knowledge on the objective criteria underlying the course of the wound process and on the etiopathogenetic therapy. Laser therapy of wounds accomplishes adequate necrotomy, acts aseptically on the wound surfaces, inhibits the wound microbial flora and stimulates the regeneration processes. The authors record their experience in CO2 laser and helium-neon treatment of 120 patients with suppurative, atonic and decubital wounds over the period 1984-1990.

Single- and double-core-hole ion emission spectroscopy of transient neon plasmas produced by ultraintense x-ray laser pulses

NASA Astrophysics Data System (ADS)

Gao, Cheng; Zeng, Jiaolong; Yuan, Jianmin

2016-02-01

Single-core-hole (SCH) and double-core-hole (DCH) spectroscopy is investigated systematically for neon gas in the interaction with ultraintense x-ray pulses with photon energy from 937 eV to 2000 eV. A time-dependent rate equation, implemented in detailed level accounting approximation, is utilized to study the dynamical evolution of the level population and emission properties of the laser-produced highly transient plasmas. The plasma-density effects on level populations and charge-state distribution are demonstrated with an x-ray photon energy of 2000 eV. It is shown that atomic number density of relevant experiment is about 1 × 1018 cm-3, which is comparable to a recent experiment. At this density, we systematically investigate the emissivity of the transient neon plasmas. For laser photon energy in the range 937-1360 eV, resonant absorptions (RA) of 1s\\to {np} (n≥slant 2) transitions play important roles in time evolution of the population and DCH emission spectroscopy. The RA effects are illustrated in detail for an x-ray pulse of 944 eV photon energy, which creates the 1s\\to 2p RA from the SCH states (1s2{s}22{p}4, 1s2s2p5, and 1s2p6) of Ne3+. After averaging over the space and time distribution of x-ray pulse, DCH emission spectroscopy is studied at x-ray photon energies of 937, 944, 955, 968, 980, and 990 eV, where there exist 1s\\to 2p resonances from SCH states of Ne2+-Ne7+. The processes with producing DCH states are discussed. For x-ray photon energy larger than 1360 eV, no RA exist and transient plasmas show different features in the DCH spectroscopy.

Design and experimental investigation of a neon cryogenic loop heat pipe

NASA Astrophysics Data System (ADS)

He, Jiang; Guo, Yuandong; Zhang, Hongxing; Miao, Jianyin; Wang, Lu; Lin, Guiping

2017-11-01

Next generation space infrared sensor and detector have pressing requirement for cryogenic heat transport technology in the temperature range of 30-40 K. Cryogenic loop heat pipe (CLHP) has excellent thermal performance and particular characteristics such as high flexibility transport lines and no moving parts, thus it is regarded as an ideal thermal control solution. A neon CLHP referring to infrared point-to-point heat transfer element in future space application has been designed and experimented. And it could realize supercritical startup successfully. Experimental results show that the supercritical startup were realized successfully at cases of 1.5 W secondary evaporator power, but the startup was failed when 0.5 and 1 W heat load applied to secondary evaporator. The maximum heat transport capability of primary evaporator is between 4.5 and 5 W with proper auxiliary heat load. Before startup, even the heat sink temperature decreased to 35 K, the primary evaporator can still maintain at almost 290 K; and the primary evaporator temperature increased at once when the powers were cut off, which indicated the CLHP has a perfect function of thermal switch. The CLHP could adapt to sudden changes of the primary evaporator power, and reach a new steady-state quickly. Besides, some failure phenomena were observed during the test, which indicated that proper secondary evaporator power and heat sink temperature play important roles on the normal operation.

Solar flare neon and solar cosmic ray fluxes in the past using gas-rich meteorites

NASA Technical Reports Server (NTRS)

Nautiyal, C. M.; Rao, M. N.

1986-01-01

Methods were developed earlier to deduce the composition of solar flare neon and to determine the solar cosmic ray proton fluxes in the past using etched lunar samples and at present, these techniques are extended to gas rich meteorites. By considering high temperature Ne data points for Pantar, Fayetteville and other gas rich meteorites and by applying the three component Ne-decomposition methods, the solar cosmic ray and galactic cosmic ray produced spallation Ne components from the trapped SF-Ne was resolved. Using appropiate SCR and GCR production rates, in the case of Pantar, for example, a GCR exposure age of 2 m.y. was estimated for Pantar-Dark while Pantar-Light yielded a GCR age of approx. 3 m.y. However the SCR exposure age of Pantar-Dark is two orders of magnitude higher than the average surface exposure ages of lunar soils. The possibility of higher proton fluxes in the past is discussed.

Note: Simple 100 Hz N2 laser with longitudinal discharge tube and high-voltage power supply using neon sign transformer.

PubMed

Uno, K; Jitsuno, T

2017-12-01

We developed a longitudinally excited N 2 laser with a simple driver circuit and a simple power supply. The N 2 laser consisted of a 20 cm-long glass tube with an inner diameter of 2.5 mm, a normal stable resonator formed by flat mirrors, a variable transformer, a neon sign transformer, a spark gap, and a 200 pF capacitance. The N 2 laser produced a laser pulse with an energy of 379 nJ and a pulse width of 7.5 ns at a repetition rate of 100 Hz. The laser beam was circular and had a Gaussian profile with a correlation factor of 0.992 93.

Measurements of n-p correlations in the reaction of relativistic neon with uranium

NASA Technical Reports Server (NTRS)

Frankel, K.; Schimmerling, W.; Rasmussen, J. O.; Crowe, K. M.; Bistirlich, J.; Bowman, H.; Hashimoto, O.; Murphy, D. L.; Ridout, J.; Sullivan, J. P.;

Effects of autoionising states on the single and double ionisation yields of neon with soft X-ray fields. JMO Series: Attosecond and Strong Field Science

NASA Astrophysics Data System (ADS)

Middleton, D. P. W.; Nikolopoulos, L. A. A.

2012-11-01

In this work, single and double ionisation yields of neon under extreme ultraviolet free-electron laser (FEL) radiation tuned in the vicinity of the autoionising states (AIS) of Ne+ were studied. Density matrix equations were developed and were used to calculate the dependence of the branching ratios of singly and doubly ionised neon on the field intensity and its duration. In addition, in response to a recent experiment [M. Martins et al., Phys. Rev. A 2011, 80, 023411], a quantitative analysis was undertaken in order to reproduce the magnitude of the branching ratios by varying the FEL photon frequency in the range 41.0-42.0 eV in accordance with the experimental report. While the reported variations of the species' branching ratios as a function of the FEL field's photon energy were found, their magnitude and shape differ. In general, the branching ratios are found to be heavily dependent on the given combination of the peak intensity and the pulse duration. Furthermore, the FEL's stochastic fluctuation has been modelled by solving the average density matrix equations and it was found that stochastic effects should also affect branching ratios, mainly due to the increase in the effective bandwidth of the pulse in comparison with the AIS's decay ionisation width. Our calculations suggest that field fluctuations generally diminish the resonance features of the branching ratios.

Structural and electronic properties of the V-V compounds isoelectronic to GaN and isostructural to gray arsenic

NASA Astrophysics Data System (ADS)

Yang, Zhao; Han, Dan; Chen, Guohong; Chen, Shiyou

2018-03-01

The III-V binary compound semiconductors such as GaN, GaP, InN and InP have extensive applications in various optoelectronic, microwave and power-electronic devices. Using first-principles calculation, we systematically studied the structural and electronic properties of the V-V binary compounds (BiN, BiP, SbN and SbP) that are isoelectronic to GaN, GaP, InN and InP if Bi and Sb are in the +3 valence state. Interestingly, we found that the ground-state structures of BiP, SbN and SbP have the R-3m symmetry and are isostructural to the layered structure of gray arsenic, whereas BiN prefers a different ground-state structure with the C2 symmetry. Electronic structure calculations showed that the bulk BiN is a narrow bandgap semiconductor for its bandgap is about 0.2 eV. In contrast, BiP, SbN and SbP are metallic. The layered ground-state structure of the V-V binary compounds motivates us to study the electronic properties of their few-layer structures. As the structure becomes monolayer, their bandgaps increase significantly and are all in the range from about 1 eV to 1.7 eV, which are comparative to the bandgap of the monolayer gray arsenic. The monolayer BiP, SbN and SbP have indirect bandgaps, and they show a semiconductor-metal transition as the number of layers increase. Interestingly, the monolayer BiP has the largest splitting (350 meV) of the CBM valley, and thus may have potential application in novel spintronics and valleytronics devices.

Energy, fine structure, hyperfine structure, and radiative transition rates of the high-lying multi-excited states for B-like neon

NASA Astrophysics Data System (ADS)

Zhang, Chun Mei; Chen, Chao; Sun, Yan; Gou, Bing Cong; Shao, Bin

2015-04-01

The Rayleigh-Ritz variational method with multiconfiguration interaction wave functions is used to obtain the energies of high-lying multi-excited quartet states 1 s 22 s2 pnl and 1 s 22 p 2 nl 4Pe,o ( n ≥ 2) in B-like neon, including the mass polarization and relativistic corrections. The fine structure and hyperfine structure of the excited quartet states for this system are investigated. Configuration structures of the high-lying multi-excited series are further identified by relativistic corrections and fine structure splittings. The transition rates and wavelengths are also calculated. Calculated wavelengths include the quantum electrodynamic effects. The results are compared with other theoretical and experimental data in the literature.

GASP: A computer code for calculating the thermodynamic and transport properties for ten fluids: Parahydrogen, helium, neon, methane, nitrogen, carbon monoxide, oxygen, fluorine, argon, and carbon dioxide. [enthalpy, entropy, thermal conductivity, and specific heat

NASA Technical Reports Server (NTRS)

Hendricks, R. C.; Baron, A. K.; Peller, I. C.

1975-01-01

A FORTRAN IV subprogram called GASP is discussed which calculates the thermodynamic and transport properties for 10 pure fluids: parahydrogen, helium, neon, methane, nitrogen, carbon monoxide, oxygen, fluorine, argon, and carbon dioxide. The pressure range is generally from 0.1 to 400 atmospheres (to 100 atm for helium and to 1000 atm for hydrogen). The temperature ranges are from the triple point to 300 K for neon; to 500 K for carbon monoxide, oxygen, and fluorine; to 600 K for methane and nitrogen; to 1000 K for argon and carbon dioxide; to 2000 K for hydrogen; and from 6 to 500 K for helium. GASP accepts any two of pressure, temperature and density as input conditions along with pressure, and either entropy or enthalpy. The properties available in any combination as output include temperature, density, pressure, entropy, enthalpy, specific heats, sonic velocity, viscosity, thermal conductivity, and surface tension. The subprogram design is modular so that the user can choose only those subroutines necessary to the calculations.

Specific features of a single-pulse sliding discharge in neon near the threshold for spark breakdown

NASA Astrophysics Data System (ADS)

Trusov, K. K.

2017-08-01

Experimental data on the spatial structure of a single-pulse sliding discharge in neon at voltages below, equal to, and above the threshold for spark breakdown are discussed. The experiments were carried at gas pressures of 30 and 100 kPa and different polarities of the discharge voltage. Photographs of the plasma structure in two discharge chambers with different dimensions of the discharge zone and different thicknesses of an alumina dielectric plate on the surface of which the discharge develops are inspected. Common features of the prebreakdown discharge and its specific features depending on the voltage polarity and gas pressure are analyzed. It is shown that, at voltages below the threshold for spark breakdown, a low-current glow discharge with cathode and anode spots develops in the electrode gap. Above the breakdown threshold, regardless of the voltage polarity, spark channels directed from the cathode to the anode develop against the background of a low-current discharge.

Attosecond transient absorption probing of electronic superpositions of bound states in neon. Detection of quantum beats

DOE PAGES

Beck, Annelise R; Bernhardt, Birgitta; Warrick, Erika R.; ...

2014-11-07

Electronic wavepackets composed of multiple bound excited states of atomic neon lying between 19.6 and 21.5 eV are launched using an isolated attosecond pulse. Individual quantum beats of the wavepacket are detected by perturbing the induced polarization of the medium with a time-delayed few-femtosecond near-infrared (NIR) pulse via coupling the individual states to multiple neighboring levels. All of the initially excited states are monitored simultaneously in the attosecond transient absorption spectrum, revealing Lorentzian to Fano lineshape spectral changes as well as quantum beats. The most prominent beating of the several that were observed was in the spin–orbit split 3d absorptionmore » features, which has a 40 femtosecond period that corresponds to the spin–orbit splitting of 0.1 eV. The few-level models and multilevel calculations confirm that the observed magnitude of oscillation depends strongly on the spectral bandwidth and tuning of the NIR pulse and on the location of possible coupling states.« less

Transitions of the type 2s-2p in fluorinelike and oxygenlike As, Se, Br, and Rb

NASA Technical Reports Server (NTRS)

Feldman, U.; Seely, J. F.; Behring, W. E.; Richardson, M. C.; Goldsmith, S.

1985-01-01

Transitions of the type 2s-2p in the F I and O I isoelectronic sequences of arsenic, selenium, bromine, and rubidium have been identified in spectra from laser-produced plasmas. Wavelengths in the range 50 to 90 A were measured to an accuracy of 0.01 A or better. The wavelengths of the magnetic-dipole transitions within the ground configurations are predicted.

Study on a neon cryogenic oscillating heat pipe with long heat transport distance

NASA Astrophysics Data System (ADS)

Liang, Qing; Li, Yi; Wang, Qiuliang

2018-06-01

An experimental study is carried out to study the heat transfer characteristics of a cryogenic oscillating heat pipe (OHP) with long heat transport distance. The OHP is made up of a capillary tube with an inner diameter of 1.0 mm and an outer diameter of 2.0 mm. The working fluid is neon, and the length of the adiabatic section is 480 mm. Tests are performed with the different heat inputs, liquid filling ratios and condenser temperature. For the cryogenic OHP with a liquid filling ratio of 30.7% at the condenser temperature of 28 K, the effective thermal conductivity is 3466-30,854 W/m K, and the maximum transfer power is 35.60 W. With the increment of the heat input, the effective thermal conductivity of the cryogenic OHP increases at the liquid filling ratios of 30.7% and 38.5%, while it first increases and then decreases at the liquid filling ratios of 15.2% and 23.3%. Moreover, the effective thermal conductivity increases with decreasing liquid filling ratio at the small heat input, and the maximum transfer power first increases and then decreases with increasing liquid filling ratio. Finally, it is found that the thermal performance of the cryogenic OHP can be improved by increasing the condenser temperature.

Semiempirical Theories of the Affinities of Negative Atomic Ions

NASA Technical Reports Server (NTRS)

Edie, John W.

1961-01-01

The determination of the electron affinities of negative atomic ions by means of direct experimental investigation is limited. To supplement the meager experimental results, several semiempirical theories have been advanced. One commonly used technique involves extrapolating the electron affinities along the isoelectronic sequences, The most recent of these extrapolations Is studied by extending the method to Include one more member of the isoelectronic sequence, When the results show that this extension does not increase the accuracy of the calculations, several possible explanations for this situation are explored. A different approach to the problem is suggested by the regularities appearing in the electron affinities. Noting that the regular linear pattern that exists for the ionization potentials of the p electrons as a function of Z, repeats itself for different degrees of ionization q, the slopes and intercepts of these curves are extrapolated to the case of the negative Ion. The method is placed on a theoretical basis by calculating the Slater parameters as functions of q and n, the number of equivalent p-electrons. These functions are no more than quadratic in q and n. The electron affinities are calculated by extending the linear relations that exist for the neutral atoms and positive ions to the negative ions. The extrapolated. slopes are apparently correct, but the intercepts must be slightly altered to agree with experiment. For this purpose one or two experimental affinities (depending on the extrapolation method) are used in each of the two short periods. The two extrapolation methods used are: (A) an isoelectronic sequence extrapolation of the linear pattern as such; (B) the same extrapolation of a linearization of this pattern (configuration centers) combined with an extrapolation of the other terms of the ground configurations. The latter method Is preferable, since it requires only experimental point for each period. The results agree within

Transition-matrix theory for two-photon ionization of rare-gas atoms and isoelectronic ions with application to argon

NASA Astrophysics Data System (ADS)

Starace, Anthony F.; Jiang, Tsin-Fu

1987-08-01

A transition-matrix theory for two-photon ionization processes in rare-gas atoms or isoelectronic ions is presented. Uncoupled ordinary differential equations are obtained for the radial functions needed to calculate the two-photon transition amplitude. The implications of these equations are discussed in detail. In particular, the role of correlations involving virtually excited electron pairs, which are known to be essential to the description of single-photon processes, is examined for multiphoton ionization processes. Additionally, electron scattering interactions between two electron-hole pairs are introduced into our transition amplitude in the boson approximation since these have been found important in two-photon ionization of xenon by L'Huillier and Wendin [J. Phys. B 20, L37 (1987)]. Application of our theory is made to two-photon ionization of the 3p subshell of argon below the one-photon ionization threshold. Our results are compared to previous calculations of McGuire [Phys. Rev. A 24, 835 (1981)], of Moccia, Rahman, and Rizzo [J. Phys. B 16, 2737 (1983)], and of Pindzola and Kelly [Phys. Rev. A 11, 1543 (1975)]. Results are presented for both circularly and linearly polarized photons. Among our findings are, firstly, that the electron scattering interactions, which have not been included in previous calculations for argon, produce a substantial reduction in the two-photon single-ionization cross section below the one-photon ionization threshold, which is in agreement with findings of L'Huillier and Wendin for xenon. Secondly, we find that de-excitation of virtually excited electron pairs by absorption of a photon is important for describing the interaction of the atom with the photon field, as in the case of single-photon ionization processes, but that further excitation of virtually excited electron pairs by the photon field has completely negligible effects, indicating a major simplification of the theory for higher-order absorption processes.

Relationship between cardiovascular system response and adrenocortical glucocorticoid function on exposure to diffuse, low-intensity helium-neon laser emission

NASA Astrophysics Data System (ADS)

Ushkova, I. N.; Pokrovskaya, L. A.; Stepanov, G. S.; Suvorov, I. M.; Kogan, M. Y.; Grishina, Y. F.

1984-06-01

The effect of light from a low intensity helium neon laser on the formation of a series of adaptive processes in the body is investigated. The study is carried out on 32 chinchilla rabbits, weighing from two to two point five kilograms. The right eyes of the creatures were subjected to diffuse laser radiation, for 30 days, 14 minutes per day, under conditions of low illumination. Controls are rabbits under the same conditions, but not exposed to laser radiation. In order to isolate the early glucocorticoid response to the treatment, the hydrocortisone content of the blood is determined which permitted judgment on presence of a functional cumulation effect. The body developed an adaptive/compensatory reaction to the laser radiation so that hydrocortisone levels and the system's hemodynamics and nervous system returned to normal.

NEON non-specialist use case; science data reuse in a classroom

NASA Astrophysics Data System (ADS)

Fox, P. A.; Wee, B.; West, P.; Wilson, J.; Wang, H.; Zednik, S.

2012-12-01

We present our experience in bringing science data into the undergraduate classroom. In particular we have worked with scientists associated with the NSF-funded NEON (neoninc.org) project. We have developed a non-specialist use case aimed at undergraduate education. This exercise was developed to give the teacher/professor/facilitator the means to create a lesson plan that will allow students the opportunity to work with large, spatially diverse data sets on water quality and other ecological parameters of streams in the United States. The stream parameters investigated here are total nitrogen, total phosphorus and a macro invertebrate index for the 10 EPA regions in the contiguous US. Instructors would use this lesson as an opportunity to discuss the concept of "ecosystem health," a controversial topic in science but with intuitive resonance among the general public. However, current research data is highly specialized, lacking understandable, or all together lacking, metadata. This metadata is highly specialized, understandable by only the science specialist, or domain expert. Also, the data and metadata is difficult to locate by a non-specialist. The scientist knows where to find the data, how to collect the data, and can understand the structure of the data and what the data means. The meaning, the knowledge, the understanding is in the minds of the scientist. Thus, specific accommodation of the semantics for non-specialists is required. We include a current description of the activity and its outcomes and discuss the effectiveness of our semantic web development methodology in developing this non-specialist use case.

Formation of Exotic Networks of Water Clusters in Helium Droplets Facilitated by the Presence of Neon Atoms

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

Douberly, Gary E.; Miller, Roger E.; Xantheas, Sotiris S.

Water clusters are formed in helium droplets via the sequential capture of monomers. One or two neon atoms are added to each droplet prior to the addition of water. The infrared spectrum of the droplet ensemble reveals several signatures of polar, water tetramer clusters having dipole moments between 2D and 3D. Comparison with ab initio computations supports the assignment of the cluster networks to noncyclic “3+1” clusters, which are ~5.3 kcal/mol less stable than the global minimum nonpolar cyclic tetramer. The (H2O)3Ne + H2O ring insertion barrier is sufficiently large, such that evaporative helium cooling is capable of kinetically quenchingmore » the nonequilibrium tetramer system prior to its rearrangement to the lower energy cyclic species. To this end, the reported process results in the formation of exotic water cluster networks that are either higher in energy than the most stable gas-phase analogs or not even stable in the gas phase.« less

The mechanism of color change in the neon tetra fish: a light-induced tunable photonic crystal array.

PubMed

Gur, Dvir; Palmer, Benjamin A; Leshem, Ben; Oron, Dan; Fratzl, Peter; Weiner, Steve; Addadi, Lia

2015-10-12

The fresh water fish neon tetra has the ability to change the structural color of its lateral stripe in response to a change in the light conditions, from blue-green in the light-adapted state to indigo in the dark-adapted state. The colors are produced by constructive interference of light reflected from stacks of intracellular guanine crystals, forming tunable photonic crystal arrays. We have used micro X-ray diffraction to track in time distinct diffraction spots corresponding to individual crystal arrays within a single cell during the color change. We demonstrate that reversible variations in crystal tilt within individual arrays are responsible for the light-induced color variations. These results settle a long-standing debate between the two proposed models, the "Venetian blinds" model and the "accordion" model. The insight gained from this biogenic light-induced photonic tunable system may provide inspiration for the design of artificial optical tunable systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Connoted hazard and perceived importance of fluorescent, neon, and standard safety colors.

PubMed

Zielinska, O A; Mayhorn, C B; Wogalter, M S

2017-11-01

The perceived hazard and rated importance of standard safety, fluorescent, and neon colors are investigated. Colors are used in warnings to enhance hazard communication. Red has consistently been rated as the highest in perceived hazard. Orange, yellow, and black are the next highest in connoted hazard; however, there is discrepancy in their ordering. Safety standards, such as ANSI Z535.1, also list colors to convey important information, but little research has examined the perceived importance of colors. In addition to standard safety colors, fluorescent colors are more commonly used in warnings. Understanding hazard and importance perceptions of standard safety and fluorescent colors is necessary to create effective warnings. Ninety participants rated and ranked a total of 33 colors on both perceived hazard and perceived importance. Rated highest were the safety red colors from the American National Standard Institute (ANSI), International Organization for Standardization (ISO), and Federal Highway Administration (FHWA) together with three fluorescent colors (orange, yellow, and yellow-green) from 3 M on both dimensions. Rankings were similar to ratings except that fluorescent orange was the highest on perceived hazard, while fluorescent orange and safety red from the ANSI were ranked as the highest in perceived importance. Fluorescent colors convey hazard and importance levels as high as the standard safety red colors. Implications for conveying hazard and importance in warnings through color are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electron energy distribution function in the positive column of a neon glow discharge using the black wall approximation

NASA Astrophysics Data System (ADS)

Al-Hawat, Sh; Naddaf, M.

2005-04-01

The electron energy distribution function (EEDF) was determined from the second derivative of the I-V Langmuir probe characteristics and, thereafter, theoretically calculated by solving the plasma kinetic equation, using the black wall (BW) approximation, in the positive column of a neon glow discharge. The pressure has been varied from 0.5 to 4 Torr and the current from 10 to 30 mA. The measured electron temperature, density and electric field strength were used as input data for solving the kinetic equation. Comparisons were made between the EEDFs obtained from experiment, the BW approach, the Maxwellian distribution and the Rutcher solution of the kinetic equation in the elastic energy range. The best conditions for the BW approach are found to be under the discharge conditions: current density jd = 4.45 mA cm-2 and normalized electric field strength E/p = 1.88 V cm-1 Torr-1.

Atlas of the spectrum of a platinum/neon hollow-cathode reference lamp in the region 1130-4330 A

NASA Technical Reports Server (NTRS)

Sansonetti, Jean E.; Reader, Joseph; Sansonetti, Craig J.; Acquista, Nicolo

1992-01-01

The spectrum of a platinum hollow-cathode lamp containing neon carrier gas was recorded photographically and photoelectrically with a 10.7 m normal-incidence vacuum spectrograph. Wavelengths and intensities were determined for about 5600 lines in the region 1130-4330 A. An atlas of the spectrum is given, with the spectral lines marked and their intensities, wavelengths, and classifications listed. Lines of impurity species are also identified. The uncertainty of the photographically measured wavelengths is estimated to be +/- 0.0020 A. The uncertainty of lines measured in the photoelectric scans is 0.01 A for wavelengths shorter than 2030 A and 0.02 A for longer wavelengths. Ritz-type wavelengths are given for many of the classified lines of Pt II with uncertainties varying from +/- 0.0004 to +/- 0.0025 A. The uncertainty of the relative intensities is estimated to be about 20 percent.

Comparisons of laboratory wavelength measurements with theoretical calculations for neon-like through lithium-like argon, sulfur, and silicon

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

Lepson, J K; Beiersdorfer, P; Behar, E

Atomic structure codes have a difficult time accurately calculating the wavelengths of many-electron ions without the benefit of laboratory measurements. This is especially true for wavelengths of lines in the extreme ultraviolet and soft x-ray regions. We are using the low-energy capability of the Livermore electron beam ion traps to compile a comprehensive catalog of astrophysically relevant emission lines in support of satellite x-ray observations. Our database includes wavelength measurements, relative intensities, and line assignments, and is compared to a full set of calculations using the Hebrew University - Lawrence Livermore Atomic Code (HULLAC). Mean deviation of HULLAC calculations frommore » our measured wavelength values is highest for L-shell transitions of neon-like ions and lowest for lithium-like ions, ranging from a mean deviation of over 0.5 {angstrom} for Si V to 12 m{angstrom} in Ar XVI.« less

Low-energy helium-neon laser irradiation and the tensile strength of incisional wounds in the rat.

PubMed

Broadley, C; Broadley, K N; Disimone, G; Riensch, L; Davidson, J M

1995-01-01

Low-level laser energy has been reported to modulate the wound healing process in some but not all studies. To examine this hypothesis, we investigated incisional wounds made on the dorsal pelt of rats for changes in the healing produced by low-level irradiation with a helium-neon laser. The incisions were made with a scalpel and closed with sutures. The rats were irradiated daily for 12 days with four levels of laser light (0.0, 0.47, 0.93, and 1.73 J/cm(2)). Analysis of wound tensile strength indicated a possible strengthening of fresh wounds at the highest levels of irradiation (1.73 J/cm(2)). No change was observed in the tensile strength of formalin-fixed wounds. The distribution of measured tensile strengths did not follow normal statistics; instead they showed a platykurtic distribution. Using resampling statistics, where no assumption is made as to the nature of the distribution, we found that the results were contrary to other studies: no biostimulatory effect was seen.

Effect of helium-neon laser irradiation on hair follicle growth cycle of Swiss albino mice.

PubMed

Shukla, S; Sahu, K; Verma, Y; Rao, K D; Dube, A; Gupta, P K

2010-01-01

We report the results of a study carried out to investigate the effect of helium-neon (He-Ne) laser (632.8 nm) irradiation on the hair follicle growth cycle of testosterone-treated and untreated mice. Both histology and optical coherence tomography (OCT) were used for the measurement of hair follicle length and the relative percentage of hair follicles in different growth phases. A positive correlation (R = 0.96) was observed for the lengths of hair follicles measured by both methods. Further, the ratios of the lengths of hair follicles in the anagen and catagen phases obtained by both methods were nearly the same. However, the length of the hair follicles measured by both methods differed by a factor of 1.6, with histology showing smaller lengths. He-Ne laser irradiation (at approximately 1 J/cm(2)) of the skin of both the control and the testosterone-treated mice was observed to lead to a significant increase (p < 0.05) in % anagen, indicating stimulation of hair growth. The study also demonstrates that OCT can be used to monitor the hair follicle growth cycle, and thus hair follicle disorders or treatment efficacy during alopecia. (c) 2009 S. Karger AG, Basel.

Forbidden transition probabilities for ground terms of ions with p or p5 configurations. [for solar atmosphere

NASA Technical Reports Server (NTRS)

Kastner, S. O.

1976-01-01

Forbidden transition probabilities are given for ground term transitions of ions in the isoelectronic sequences with outer configurations 2s2 2p (B I), 2p5 (F I), 3s2 3p (Al I), and 3p5 (Cl I). Tables give, for each ion, the ground term interval, the associated wavelength, the quadrupole radial integral, the electric quadrupole transition probability, and the magnetic dipole transition probability. Coronal lines due to some of these ions have been observed, while others are yet to be observed. The tales for the Al I and Cl I sequences include elements up to germanium.

A VP26-mNeonGreen Capsid Fusion HSV-2 Mutant Reactivates from Viral Latency in the Guinea Pig Genital Model with Normal Kinetics

PubMed Central

Pieknik, Julianna R.; Tang, Shuang

2018-01-01

Fluorescent herpes simplex viruses (HSV) are invaluable tools for localizing virus in cells, permitting visualization of capsid trafficking and enhancing neuroanatomical research. Fluorescent viruses can also be used to study virus kinetics and reactivation in vivo. Such studies would be facilitated by fluorescent herpes simplex virus recombinants that exhibit wild-type kinetics of replication and reactivation and that are genetically stable. We engineered an HSV-2 strain expressing the fluorescent mNeonGreen protein as a fusion with the VP26 capsid protein. This virus has normal replication and in vivo recurrence phenotypes, providing an essential improved tool for further study of HSV-2 infection. PMID:29738431

Polarizabilities of highly ionized atoms

NASA Technical Reports Server (NTRS)

Kastner, S. O.; Wolf, M. L.

1979-01-01

An extrapolation method based on a screening approximation, applied to available initial values of polarizability for low stages of ionization, is used to obtain dipole and quadrupole polarizabilities for more highly ionized members of many isoelectronic sequences. It is suggested that the derived screening constants x sub L and limiting ratios F sub L may have significant physical meaning, especially the latter which may have an interpretation in terms of hydrogenic polarizabilities.

Assessing Soil Organic C Stability at the Continental Scale: An Analysis of Soil C and Radiocarbon Profiles Across the NEON Sites

NASA Astrophysics Data System (ADS)

Heckman, K. A.; Gallo, A.; Hatten, J. A.; Swanston, C.; McKnight, D. M.; Strahm, B. D.; Sanclements, M.

2017-12-01

Soil carbon stocks have become recognized as increasingly important in the context of climate change and global C cycle modeling. As modelers seek to identify key parameters affecting the size and stability of belowground C stocks, attention has been drawn to the mineral matrix and the soil physiochemical factors influenced by it. Though clay content has often been utilized as a convenient and key explanatory variable for soil C dynamics, its utility has recently come under scrutiny as new paradigms of soil organic matter stabilization have been developed. We utilized soil cores from a range of National Ecological Observatory Network (NEON) experimental plots to examine the influence of physicochemical parameters on soil C stocks and turnover, and their relative importance in comparison to climatic variables. Soils were cored at NEON sites, sampled by genetic horizon, and density separated into light fractions (particulate organics neither occluded within aggregates nor associated with mineral surfaces), occluded fractions (particulate organics occluded within aggregates), and heavy fractions (organics associated with mineral surfaces). Bulk soils and density fractions were measured for % C and radiocarbon abundance (as a measure of C stability). Carbon and radiocarbon abundances were examined among fractions and in the context of climatic variables (temperature, precipitation, elevation) and soil physiochemical variables (% clay and pH). No direct relationships between temperature and soil C or radiocarbon abundances were found. As a whole, soil radiocarbon abundance in density fractions decreased in the order of light>heavy>occluded, highlighting the importance of both surface sorption and aggregation to the preservation of organics. Radiocarbon abundance was correlated with pH, with variance also grouping by dominate vegetation type. Soil order was also identified as an important proxy variable for C and radiocarbon abundance. Preliminary results suggest that

Single and double core-hole ion emission spectroscopy of transient neon plasmas produced by ultraintense x-ray laser pulses

NASA Astrophysics Data System (ADS)

Gao, Cheng; Zeng, Jiaolong; Yuan, Jianmin

2016-05-01

Single core-hole (SCH) and double core-hole (DCH) spectroscopy is investigated systematically for neon gas in the interaction with ultraintense x-ray pulses with photon energy from 937 eV to 2000 eV. A time-dependent rate equation, implemented in the detailed level accounting approximation, is utilized to study the dynamical evolution of the level population and emission properties of the laser-produced highly transient plasmas. The plasma density effects on level populations are demonstrated with an x-ray photon energy of 2000 eV. For laser photon energy in the range of 937 - 1360 eV, resonant absorptions (RA) of 1s-np (n> = 2) transitions play important roles in time evolution of the population and DCH emission spectroscopy. For x-ray photon energy larger than 1360 eV, no RA exist and transient plasmas show different features in the DCH spectroscopy.

Rapid evaluation for dielectronic recombination rate coefficients of the H-like isoelectronic sequence.

NASA Astrophysics Data System (ADS)

Teng, H.; Xu, Z.

1996-09-01

The authors present a set of accurate formulae for the rapid calculation of dielectronic recombination rate coefficients of H-like ions from Ne (Z = 10) to Ni (Z = 29) with an electron temperature range from 0.6 to 10 keV. This set of formulae are obtained by fitting directly the dielectronic recombination rate coefficients calculated on the basis of the intermediate - coupling multi - configuration Hartree-Fock model made by Karim and Bhalla (1988). The dielectronic recombination rate coefficients from these formulae are in close agreement with the original results of Karim et al. The errors are generally less than 0.1%. The results are also compared with the ones obtained by a set of new rate formulae developed by Hahn. These formulae can be used for generating dielectronic recombination rate coefficients of some H-like ions where the explicit calculations are unavailable. The detailed results are tabulated and discussed.

Phase space theory of evaporation in neon clusters: the role of quantum effects.

PubMed

Calvo, F; Parneix, P

2009-12-31

Unimolecular evaporation of neon clusters containing between 14 and 148 atoms is theoretically investigated in the framework of phase space theory. Quantum effects are incorporated in the vibrational densities of states, which include both zero-point and anharmonic contributions, and in the possible tunneling through the centrifugal barrier. The evaporation rates, kinetic energy released, and product angular momentum are calculated as a function of excess energy or temperature in the parent cluster and compared to the classical results. Quantum fluctuations are found to generally increase both the kinetic energy released and the angular momentum of the product, but the effects on the rate constants depend nontrivially on the excess energy. These results are interpreted as due to the very few vibrational states available in the product cluster when described quantum mechanically. Because delocalization also leads to much narrower thermal energy distributions, the variations of evaporation observables as a function of canonical temperature appear much less marked than in the microcanonical ensemble. While quantum effects tend to smooth the caloric curve in the product cluster, the melting phase change clearly keeps a signature on these observables. The microcanonical temperature extracted from fitting the kinetic energy released distribution using an improved Arrhenius form further suggests a backbending in the quantum Ne(13) cluster that is absent in the classical system. Finally, in contrast to delocalization effects, quantum tunneling through the centrifugal barrier does not play any appreciable role on the evaporation kinetics of these rather heavy clusters.

A remarkable case of rhabdomyolysis associated with ingestion of energy drink 'neon volt'.

PubMed

Iyer, Praneet S; Yelisetti, Rishitha; Miriyala, Varun; Siddiqui, Waqas; Kaji, Anand

2016-01-01

Rhabdomyolysis is defined as a syndrome characterized by muscle necrosis and the release of intracellular muscle constituents into the circulation. We present a case of a 35-year-old male who exercised for 2 h after ingesting energy drink and subsequently presented with rhabdomyolysis. After excluding common and uncommon causes of rhabdomyolysis, we reached the conclusion that the likely cause was the ingestion of energy drink 'NEON VOLT' in a setting of mild dehydration. Increasing physical activity and intense exercise is becoming a trend in many countries, due to its many health-related benefits such as prevention of obesity. This renewed focus toward optimal fitness has spawned many supplements that aid in improvement of the performance, muscle growth, and recovery. Energy drinks predominantly contain caffeine that is often combined with other supplements to form what manufacturers have termed an 'energy blend'. Studies have shown that excessive caffeine intake from energy drinks can cause arrhythmias, hypertension, dehydration, sleeplessness, nervousness, and in rare instances, rhabdomyolysis. As per Drug Abuse Warning Network report, there is a sharp increase in the number of emergency department visits involving energy drinks from 1,128 visits in 2005 to 16,053 and 13,114 visits in 2008 and 2009, respectively. Due to emergence of energy drink abuse as a national health problem, Food and Drug Administration has launched a dietary supplement adverse event reporting system for surveillance of any adverse events linked to these agents.

R-matrix calculations for electron-impact excitation of C(+), N(2+), and O(3+) including fine structure

NASA Technical Reports Server (NTRS)

Luo, D.; Pradhan, A. K.

1990-01-01

The new R-matrix package for comprehensive close-coupling calculations for electron scattering with the first three ions in the boron isoelectronic sequence, the astrophysically significant C(+), N(2+), and O(3+), is presented. The collision strengths are calculated in the LS coupling approximation, as well as in pair-coupling scheme, for the transitions among the fine-structure sublevels. Calculations are carried out at a large number of energies in order to study the detailed effects of autoionizing resonances.

Determination of 2p Excitation Transfer Rate Coefficient in Neon Gas Discharges

NASA Astrophysics Data System (ADS)

Smith, D. J.; Stewart, R. S.

2001-10-01

We will discuss our theoretical modelling and application of an array of four complementary optical diagnostic techniques for low-temperature plasmas. These are cw laser collisionally-induced fluorescence (LCIF), cw optogalvanic effect (OGE), optical emission spectroscopy (OES) and optical absorption spectroscopy (OAS). We will briefly present an overview of our investigation of neon positive column plasmas for reduced axial electric fields ranging from 3x10-17 Vcm2 to 2x10-16 Vcm2 (3-20 Td), detailing our determination of five sets of important collisional rate coefficients involving the fifteen lowest levels, the 1S0 ground state and the 1s and 2p excited states (in Paschen notation), hence information on several energy regions of the electron distribution function (EDF). The discussion will be extended to show the new results obtained from analysis of the argon positive column over similar reduced fields. Future work includes application of our multi-diagnostic technique to more complex systems, including the addition of molecules for EDF determination. array of four complementary optical diagnostic techniques OGE LCIF determination of five sets of important collisional rate coefficients

Boron, bismuth co-doping of gallium arsenide and other compounds for photonic and heterojunction bipolar transistor devices

DOEpatents

Mascarenhas, Angelo

2015-07-07

Isoelectronic co-doping of semiconductor compounds and alloys with acceptors and deep donors is sued to decrease bandgap, to increase concentration of the dopant constituents in the resulting alloys, and to increase carrier mobilities lifetimes. For example, Group III-V compounds and alloys, such as GaAs and GaP, are isoelectronically co-doped with, for example, B and Bi, to customize solar cells, and other semiconductor devices. Isoelectronically co-doped Group II-VI compounds and alloys are also included.

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

Mascarenhas, Angelo

Isoelectronic co-doping of semiconductor compounds and alloys with acceptors and deep donors is used to decrease bandgap, to increase concentration of the dopant constituents in the resulting alloys, and to increase carrier mobilities lifetimes. For example, Group III-V compounds and alloys, such as GaAs and GaP, are isoelectronically co-doped with, for example, B and Bi, to customize solar cells, and other semiconductor devices. Isoelectronically co-doped Group II-VI compounds and alloys are also included.

Coherent control schemes for the photoionization of neon and helium in the Extreme Ultraviolet spectral region.

PubMed

Giannessi, Luca; Allaria, Enrico; Prince, Kevin C; Callegari, Carlo; Sansone, Giuseppe; Ueda, Kiyoshi; Morishita, Toru; Liu, Chien Nan; Grum-Grzhimailo, Alexei N; Gryzlova, Elena V; Douguet, Nicolas; Bartschat, Klaus

2018-05-17

The seeded Free-Electron Laser (FEL) FERMI is the first source of short-wavelength light possessing the full coherence of optical lasers, together with the extreme power available from FELs. FERMI provides longitudinally coherent radiation in the Extreme Ultraviolet and soft x-ray spectral regions, and therefore opens up wide new fields of investigation in physics. We first propose experiments exploiting this property to provide coherent control of the photoionization of neon and helium, carry out numerical calculations to find optimum experimental parameters, and then describe how these experiments may be realized. The approach uses bichromatic illumination of a target and measurement of the products of the interaction, analogous to previous Brumer-Shapiro-type experiments in the optical spectral range. We describe operational schemes for the FERMI FEL, and simulate the conditions necessary to produce light at the fundamental and second or third harmonic frequencies, and to control the phase with respect to the fundamental. We conclude that a quantitative description of the phenomena is extremely challenging for present state-of-the-art theoretical and computational methods, and further development is necessary. Furthermore, the intensity available may already be excessive for the experiments proposed on helium. Perspectives for further development are discussed.

Electron-spin-resonance studies of 12CH3F + , 13CH3F + , and 12CH2DF + in neon matrices at 4 K: Comparison with theoretical calculations

NASA Astrophysics Data System (ADS)

Knight, Lon B., Jr.; Gregory, Brian W.; Hill, Devon W.; Arrington, C. A.; Momose, Takamasa; Shida, Tadamasa

1991-01-01

Various isotopic forms of the methyl fluoride cation 12CH3F+, 13CH3F+, and 12CH2DF+ have been generated by photoionization at 16.8 eV and separately by electron bombardment at 50 eV. The first electron-spin-resonance (ESR) results are reported for this radical cation which was isolated in neon matrices at 4 K. The measured A tensors or nuclear hyperfine parameters were compared with the results obtained from various computational approaches. Surprising observations were the large amounts of spin density on the methyl group, especially the hydrogen atoms, and the extreme differences in the deuterated spectra compared to the nondeuterated case. The presence of a single D atom apparently acts to prevent dynamic Jahn-Teller averaging which makes the methyl hydrogens equivalent on the ESR time scale. Such a dramatic Jahn-Teller effect has been previously observed for the similar methane cations CH+4 and CH2D+2. The magnetic parameters for CH2DF+ in neon at 4 K are gX=2.0032(5), gY=2.0106(8), and gZ=2.0120(5); for H: AX = 483(1), AY=476(1), and AZ=483(1) MHz; for D: ‖AX‖=5.0(3), ‖AY‖<3, and ‖AZ‖=7.1(3) MHz; for 19F : AX=965(1), AY=-130(2), and AZ=-166(1) MHz. For CH3F+, the g tensor and 19F A tensor were similar to those above but the H atoms were equivalent with values of AX=317(1), AY=323(2), and AZ=312 MHz.

Reduction of ion transport and turbulence via dilution with nitrogen and neon injection in C-Mod deuterium plasmas

NASA Astrophysics Data System (ADS)

Porkolab, M.; Ennever, P.; Baek, S. G.; Creely, A. J.; Edlund, E. M.; Hughes, J.; Rice, J. E.; Rost, J. C.; White, A. E.; Reinke, M. L.; Staebler, G.; Candy, J.; Alcator C-Mod Team

2016-10-01

Recent experiments on C-Mod ohmic plasmas and gyrokinetic studies indicated that dilution of deuterium plasmas by injection of nitrogen decreased the ion diffusivity and may also alter the direction of intrinsic toroidal rotation. Simulations with TGLF and GYRO showed that dilution of deuterium ions in low density (LOC) plasmas increased the critical ion temperature gradient, while in high density (SOC) plasmas it decreased the stiffness. The density fluctuation spectrum measured in low q95 plasmas with Phase Contrast Imaging (PCI), and corroborated with spatially localized reflectometer measurements show a reduction of turbulence near r/a = 0.8 with kρs <= 1, in agreement with modeling predictions in this region where the ion turbulence is well above marginal stability. Measurements also indicate that reversal of the toroidal rotation direction near the SOC-LOC transition may depend on ion collisionality rather than that of electrons. New experiments with neon seeding, which may be more relevant to ITER than with nitrogen seeding, show similar results. The impact of dilution on Te turbulence as measured with CECE diagnostic will also be presented. Supported by US DOE Awards DE-FG02-94-ER54235 and DE-FC02-99-ER54512.

Spectroscopy and atomic physics of highly ionized Cr, Fe, and Ni for tokamak plasmas

NASA Technical Reports Server (NTRS)

Feldman, U.; Doschek, G. A.; Cheng, C.-C.; Bhatia, A. K.

1980-01-01

The paper considers the spectroscopy and atomic physics for some highly ionized Cr, Fe, and Ni ions produced in tokamak plasmas. Forbidden and intersystem wavelengths for Cr and Ni ions are extrapolated and interpolated using the known wavelengths for Fe lines identified in solar-flare plasmas. Tables of transition probabilities for the B I, C I, N I, O I, and F I isoelectronic sequences are presented, and collision strengths and transition probabilities for Cr, Fe, and Ni ions of the Be I sequence are given. Similarities of tokamak and solar spectra are discussed, and it is shown how the atomic data presented may be used to determine ion abundances and electron densities in low-density plasmas.

Electron impact excitation of highly charged sodium-like ions

NASA Technical Reports Server (NTRS)

Blaha, M.; Davis, J.

1978-01-01

Optical transition probabilities and electron collision strengths for Ca X, Fe XVI, Zn XX, Kr XXVI and Mo XXXII are calculated for transitions between n equal to 3 and n equal to 4 levels. The calculations neglect relativistic effects on the radial functions. A semi-empirical approach provides wave functions of the excited states; a distorted wave function without exchange is employed to obtain the excitation cross sections. The density dependence of the relative intensities of certain emission lines in the sodium isoelectronic sequence is also discussed.

Electron spin resonance study of atomic hydrogen stabilized in solid neon below 1 K

NASA Astrophysics Data System (ADS)

Sheludiakov, S.; Ahokas, J.; Järvinen, J.; Lehtonen, L.; Vasiliev, S.; Dmitriev, Yu. A.; Lee, D. M.; Khmelenko, V. V.

2018-03-01

We report on an electron spin resonance study of atomic hydrogen stabilized in solid Ne matrices carried out at a high field of 4.6 T and temperatures below 1 K . The films of Ne, slowly deposited on the substrate at a temperature of ˜1 K , exhibited a high degree of porosity. We found that H atoms may be trapped in two different substitutional positions in the Ne lattice as well as inside clusters of pure molecular H2 in the pores of the Ne film. The latter type of atoms was very unstable against recombination at temperatures 0.3-0.6 K . Based on the observed nearly instant decays after rapid small increases of temperature, we evaluate the lower limit of the recombination rate constant kr≥5 ×10-20cm3s-1 at 0.6 K , five orders of magnitude larger than that previously found in the thin films of pure H2 at the same temperature. Such behavior assumes a very high mobility of atoms and may indicate a solid-to-liquid transition for H2 clusters of certain sizes, similar to that observed in experiments with H2 clusters inside helium droplets [Phys. Rev. Lett. 101, 205301 (2008), 10.1103/PhysRevLett.101.205301]. We found that the efficiency of dissociation of H2 in neon films is enhanced by two orders of magnitude compared to that in pure H2 as a result of the strong action of secondary electrons.

Numerical investigation of depth profiling capabilities of helium and neon ions in ion microscopy

PubMed Central

Rzeznik, Lukasz; Wirtz, Tom

2016-01-01

The analysis of polymers by secondary ion mass spectrometry (SIMS) has been a topic of interest for many years. In recent years, the primary ion species evolved from heavy monatomic ions to cluster and massive cluster primary ions in order to preserve a maximum of organic information. The progress in less-damaging sputtering goes along with a loss in lateral resolution for 2D and 3D imaging. By contrast the development of a mass spectrometer as an add-on tool for the helium ion microscope (HIM), which uses finely focussed He+ or Ne+ beams, allows for the analysis of secondary ions and small secondary cluster ions with unprecedented lateral resolution. Irradiation induced damage and depth profiling capabilities obtained with these light rare gas species have been far less investigated than ion species used classically in SIMS. In this paper we simulated the sputtering of multi-layered polymer samples using the BCA (binary collision approximation) code SD_TRIM_SP to study preferential sputtering and atomic mixing in such samples up to a fluence of 1018 ions/cm2. Results show that helium primary ions are completely inappropriate for depth profiling applications with this kind of sample materials while results for neon are similar to argon. The latter is commonly used as primary ion species in SIMS. For the two heavier species, layers separated by 10 nm can be distinguished for impact energies of a few keV. These results are encouraging for 3D imaging applications where lateral and depth information are of importance. PMID:28144525

Clinical outcomes in youth beyond the first year of type 1 diabetes: Results of the Pediatric Diabetes Consortium (PDC) type 1 diabetes new onset (NeOn) study.

PubMed

Cengiz, Eda; Cheng, Peiyao; Ruedy, Katrina J; Kollman, Craig; Tamborlane, William V; Klingensmith, Georgeanna J; Gal, Robin L; Silverstein, Janet; Lee, Joyce; Redondo, Maria J; Beck, Roy W

2017-11-01

Current data are limited on the course of type 1 diabetes (T1D) in children and adolescents through the first few years of diabetes. The Pediatric Diabetes Consortium T1D new onset (NeOn) Study was undertaken to prospectively assess natural history and clinical outcomes in children treated at 7 US diabetes centers from the time of diagnosis. This paper describes clinical outcomes in the T1D NeOn cohort during the first 3 years postdiagnosis. A total of 1048 participants (mean age 9.2 years, 49% female, 65% non-Hispanic White) were enrolled between July 2009 and April 2011. Mean glycated hemoglobin (HbA1c) (±SD) was 7.2% (55 mmol/mol) at 3 months, followed by a progressive rise to 8.4% (68 mmol/mol) at 36 months postdiagnosis, with only 30% of participants achieving target HbA1c<7.5% (58 mmol/mol). The percentage of participants in partial remission estimated by insulin dose adjusted HbA1c [HbA1c % + (4×insulin dose unit/kg/24 h)] ≤9 sharply declined from 23% at 12 months to 7% at 36 months. The percentage of participants developing diabetic ketoacidosis (DKA) was 1% in the first year after diagnosis, increasing to 6% in years 2 and 3. These results demonstrate the gradual decline in glycemic control due to waning residual endogenous insulin secretion with increasing duration of T1D in children and adolescents. These data indicate the need to translate recent advances in automated insulin delivery, new insulin analogs, and adjunctive pharmacologic agents into novel treatment strategies to maintain optimal glycemic control even early in the course of T1D. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Production of 21Ne in depth-profiled olivine from a 54 Ma basalt sequence, Eastern Highlands (37° S), Australia

NASA Astrophysics Data System (ADS)

Matchan, Erin L.; Honda, Masahiko; Barrows, Timothy T.; Phillips, David; Chivas, Allan R.; Fifield, L. Keith; Fabel, Derek

2018-01-01

In this study we investigate the cosmogenic neon component in olivine samples from a vertical profile in order to quantify muogenic 21Ne production in this mineral. Samples were collected from an 11 m thick Eocene basalt profile in the Eastern Highlands of southeastern Australia. An eruption age of 54.15 ± 0.36 Ma (2σ) was determined from 40Ar/39Ar step-heating experiments (n = 6) on three whole-rock samples. A 36Cl profile on the section indicated an apparent steady state erosion rate of 4.7 ± 0.5 m Ma-1. The eruption age was used to calculate in situ produced radiogenic 4He and nucleogenic 3He and 21Ne concentrations in olivine. Olivine mineral separates (n = 4), extracted from the upper two metres of the studied profile, reveal cosmogenic 21Ne concentrations that attenuate exponentially with depth. However, olivine (Fo68) extracted from below 2 m does not contain discernible 21Ne aside from magmatic and nucleogenic components, with the exception of one sample that apparently contained equal proportions of nucleogenic and muogenic neon. Modelling results suggest a muogenic neon sea-level high-latitude production rate of 0.02 ± 0.04 to 0.9 ± 1.3 atoms g-1 a-1 (1σ), or <2.5% of spallogenic cosmogenic 21Ne production at Earth's surface. These data support a key implicit assumption in the literature that accumulation of muogenic 21Ne in olivine in surface samples is likely to be negligible/minimal compared to spallogenic 21Ne.

Observing single FoF1-ATP synthase at work using an improved fluorescent protein mNeonGreen as FRET donor

NASA Astrophysics Data System (ADS)

Heitkamp, Thomas; Deckers-Hebestreit, Gabriele; Börsch, Michael

2016-02-01

Adenosine triphosphate (ATP) is the universal chemical energy currency for cellular activities provided mainly by the membrane enzyme FoF1-ATP synthase in bacteria, chloroplasts and mitochondria. Synthesis of ATP is accompanied by subunit rotation within the enzyme. Over the past 15 years we have developed a variety of single-molecule FRET (smFRET) experiments to monitor catalytic action of individual bacterial enzymes in vitro. By specifically labeling rotating and static subunits within a single enzyme we were able to observe three-stepped rotation in the F1 motor, ten-stepped rotation in the Fo motor and transient elastic deformation of the connected rotor subunits. However, the spatial and temporal resolution of motor activities measured by smFRET were limited by the photophysics of the FRET fluorophores. Here we evaluate the novel FRET donor mNeonGreen as a fusion to FoF1-ATP synthase and compare it to the previously used fluorophore EGFP. Topics of this manuscript are the biochemical purification procedures and the activity measurements of the fully functional mutant enzyme.

Laser-produced spectra and QED effects for Fe-, Co-, Cu-, and Zn-like ions of Au, Pb, Bi, Th, and U

NASA Technical Reports Server (NTRS)

Seely, J. F.; Ekberg, J. O.; Brown, C. M.; Feldman, U.; Behring, W. E.

1986-01-01

Spectra of very highly charged ions of Au, Pb, Bi, Th, and U have been observed in laser-produced plasmas generated by the OMEGA laser. Line identifications in the region 9-110 A were made for ions in the Fe, Co, Cu, and Zn isoelectronic sequences. Comparison of the measured wavelengths of the Cu-like ions with values calculated with and without QED corrections shows that the inclusion of QED corrections greatly improves the accuracy of the calculated 4s-4p wavelengths. However, significant differences between the observed and calculated values remain.

Spectrum lines of highly ionized zinc, germanium, selenium, zirconium, molybdenum, and silver injected into Princeton Large Torus and Tokamak Fusion Test Reactor tokamak discharges

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

Hinnov, E.; Boody, F.; Cohen, S.

1986-10-01

Measured wavelengths of a number of highly ionized atoms are reported. These include the 3s/sup 2/3p--3s3p/sup 2/ and 3s/sup 2/3p--3s/sup 2/3d transitions in the aluminum isoelectronic sequence of Zn XVIII, Ge XX, Se XXII, Zr XXVIII, Mo XXX, and Ag XXXV; several transitions in the n = 2 shell of Zn XXII, Zn XXIII, and Zn XXIV; and the resonance and intercombination lines of Ag XXXVI--Ag XXXVII and of Ge XXIX--Ge XXX.

New Boron Analogues of Pyrophosphates and Deoxynucleoside Boranophosphates

PubMed Central

Vyakaranam, Kamesh; Rana, Geeta; Spielvogel, Bernard F.

2001-01-01

Tetraethyldicyanoborane pyrophosphate (2) and 3'-(diethylphosphite-cyanoborano)-5'-dimethoxytrityl.N4-benzoyl-deoxycytidine (3) have been synthesized in 70% and 76% yields, respectively. The compatibility of the substituted boranophosphates with common protecting groups is hereby demonstrated. Boron containing biologically active compounds, such as nucleosides and nucleotides 1-6 and amino acids 7-9 are important due to their potential therapeutic activity, research and diagnostic applications. Many boron containing compounds have shown promising activity as anticancer, 10. 11. 12 antiinflammatory,13 and antiosteoporotic 13agents. Oligonucleotdes in which a non-bridging oxygen atom is replaced by a borane(BH3) group are a very important class of modified nucleic acids. 1. 3. 14-16 The BH3 group is isoelectronic with oxygen in natural oligonucleotides and isoelectronic and isostructural with the oligonucleotide methyl phosphonates, which are nuclease resistant. On the other hand, the α-borano triphosphates are good substrates for DNA polymerases and incorporation of boranophosphates into DNA causes an increase in the resistance to exo- and endonucleases 2. 17a as compared to non-modified DNA. There are also notable applications of the α-borano triphosphates in PCR sequencing 17a and nucleic acid detection 17b. PMID:18475988

The fragmentation of 670A MeV neon-20 as a function of depth in water. I. Experiment

NASA Technical Reports Server (NTRS)

Schimmerling, W.; Miller, J.; Wong, M.; Rapkin, M.; Howard, J.; Spieler, H. G.; Jarret, B. V.

1989-01-01

We present the final analysis of an experiment to study the interaction of a beam of 670A MeV neon ions incident on a water column set to different thicknesses. The atomic number Z (and, in some cases, the isotopic mass A) of primary beam particles and of the products of nuclear interactions emerging from the water column close to the central axis of the beam was obtained for nuclei between Be (Z = 4) and Ne (Z = 10) using a time-of-flight telescope to measure the velocity and a set of silicon detectors to measure the energy loss of each particle. The fluence of particles of a given charge was obtained and normalized to the incident beam intensity. Corrections were made for accidental coincidences between multiple particles triggering the TOF telescope and for interactions in the detector. The background due to beam particles interacting in beam line elements upstream of the detector was calculated. Sources of experimental artifacts and background in particle identification experiments designed to characterize heavy ion beams for radiobiological research are summarized, and some of the difficulties inherent in this work are discussed. Complete tables of absolutely normalized fluence spectra as a function of LET are included for reference purposes.

The sequence of sequencers: The history of sequencing DNA

PubMed Central

Heather, James M.; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

Optical magnetic resonances induced by the interference of reactive components in the near radiation-field zone of atoms in a glow discharge of a mixture of even neon isotopes

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

Saprykin, E. G., E-mail: Saprykin@gorodok.net

2016-02-15

Four types of anomalous optical magnetic resonances shifted with respect to the zero magnetic field and with different shapes are found in radiation of a glow discharge in a mixture of even neon isotopes placed in a swept longitudinal magnetic field. This testifies to the manifestation of collective processes of synchronous light emission by oscillators belonging to isotopically different spatially separated atoms in discharge plasma. The origin of resonances is associated with nonstationary interference of reactive fields in the near radiation-field zones of emission of atoms, averaged over the lifetime of the fields (interference), while different types of resonances aremore » associated with different methods of synchronization of the phases of the fields.« less

The sequence of sequencers: The history of sequencing DNA.

PubMed

Heather, James M; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Characteristic of lipids and fatty acid compositions of the neon flying squid, Ommastrephes bartramii.

PubMed

Saito, Hiroaki; Ishikawa, Satoru

2012-01-01

The lipids and fatty acids of the neon flying squid (Ommastrephes bartramii) were an-alyzed to clarify its lipid physiology and health benefit as marine food. Triacylglycerols were the only major component in the digestive gland (liver). In all other organs (mantle, arm, integument, and ovary), sterols and phospholipids were the major components with noticeable levels of ceramide aminoethyl phosphonate and sphingomyelin. The significant levels of sphingolipids suggest the O. bartramii lipids is a useful source for cosmetics. Although the lipid content between the liver and all other tissues markedly differed from each other, the same nine dominant fatty acids in the triacylglycerols were found in all organs; 14:0, 16:0, 18:0, 18:1n-9, 20:1n-9, 20:1n-11, 22:1n-11, 20:5n-3 (icosapentaenoic acid, EPA), and 22:6n-3 (docosahexaenoic acid, DHA). Unusually high 20:1n-11 levels in the O. bartramii triacylglycerols were probably characteristic for western Pacific animal depot lipids, compared with non-detectable levels of 20:1n-11 reported in other marine animals. O. bartramii concurrently has high levels of DHA in their triacylglycerols. The major fatty acids in the phospholipids were 16:0, 18:0, 20:1n-9, EPA, and DHA without 20:1n-11. Markedly high levels of both EPA and DHA were observed in phosphatidylethanolamine, while only DHA was found as the major one in phosphatidylcholine. In particular, high levels of DHA were found both in its depot triacylglycerols and tissue phospholipids in all organs of O. bartramii, similar to that in highly migratory fishes. The high DHA levels in all its organs suggest that O. bartramii lipids is a healthy marine source for DHA supplements.

Intercomparison of Remotely Sensed Vegetation Indices, Ground Spectroscopy, and Foliar Chemistry Data from NEON

NASA Astrophysics Data System (ADS)

Hulslander, D.; Warren, J. N.; Weintraub, S. R.

2017-12-01

Hyperspectral imaging systems can be used to produce spectral reflectance curves giving rich information about composition, relative abundances of materials, mixes and combinations. Indices based on just a few spectral bands have been used for over 40 years to study vegetation health, mineral abundance, and more. These indices are much simpler to visualize and use than a full hyperspectral data set which may contain over 400 bands. Yet historically, it has been difficult to directly relate remotely sensed spectral indices to quantitative biophysical properties significant to forest ecology such as canopy nitrogen, lignin, and chlorophyll. This linkage is a critical piece in enabling the detection of high value ecological information, usually only available from labor-intensive canopy foliar chemistry sampling, to the geographic and temporal coverage available via remote sensing. Previous studies have shown some promising results linking ground-based data and remotely sensed indices, but are consistently limited in time, geographic extent, and land cover type. Moreover, previous studies are often focused on tuning linkage algorithms for the purpose of achieving good results for only one study site or one type of vegetation, precluding development of more generalized algorithms. The National Ecological Observatory Network (NEON) is a unique system of 47 terrestrial sites covering all of the major eco-climatic domains of the US, including AK, HI, and Puerto Rico. These sites are regularly monitored and sampled using uniform instrumentation and protocols, including both foliar chemistry sampling and remote sensing flights for high resolution hyperspectral, LiDAR, and digital camera data acquisition. In this study we compare the results of foliar chemistry analysis to the remote sensing vegetation indices and investigate possible sources for variance and difference through the use of the larger hyperspectral dataset as well as ground based spectrometer measurements of

Effect of resistivity profile on current decay time of initial phase of current quench in neon-gas-puff inducing disruptions of JT-60U

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

Kawakami, S.; Ohno, N.; Shibata, Y.

2013-11-15

According to an early work [Y. Shibata et al., Nucl. Fusion 50, 025015 (2010)] on the behavior of the plasma current decay in the JT-60U disruptive discharges caused by the radiative collapse with a massive neon-gas-puff, the increase of the internal inductance mainly determined the current decay time of plasma current during the initial phase of current quench. To investigate what determines the increase of the internal inductance, we focus attention on the relationship between the electron temperature (or the resistivity) profile and the time evolution of the current density profile and carry out numerical calculations. As a result, wemore » find the reason of the increase of the internal inductance: The current density profile at the start of the current quench is broader than an expected current density profile in the steady state, which is determined by the temperature (or resistivity) profile. The current density profile evolves into peaked one and the internal inductance is increasing.« less

GASP - THERMODYNAMIC AND TRANSPORT PROPERTIES OF HELIUM, METHANE, NEON, NITROGEN, CARBON MONOXIDE, CARBON DIOXIDE, OXYGEN, AND ARGON

NASA Technical Reports Server (NTRS)

Hendricks, R. C.

1994-01-01

A computer program, GASP, has been written to calculate the thermodynamic and transport properties of argon, carbon dioxide, carbon monoxide, fluorine, methane, neon, nitrogen, and oxygen. GASP accepts any two of pressure, temperature, or density as input. In addition, entropy and enthalpy are possible inputs. Outputs are temperature, density, pressure, entropy, enthalpy, specific heats, expansion coefficient, sonic velocity, viscosity, thermal conductivity, and surface tension. A special technique is provided to estimate the thermal conductivity near the thermodynamic critical point. GASP is a group of FORTRAN subroutines. The user typically would write a main program that invoked GASP to provide only the described outputs. Subroutines are structured so that the user may call only those subroutines needed for his particular calculations. Allowable pressures range from 0.l atmosphere to 100 to l,000 atmospheres, depending on the fluid. Similarly, allowable pressures range from the triple point of each substance to 300 degrees K to 2000 degrees K, depending on the substance. The GASP package was developed to be used with heat transfer and fluid flow applications. It is particularly useful in applications of cryogenic fluids. Some problems associated with the liquefication, storage, and gasification of liquefied natural gas and liquefied petroleum gas can also be studied using GASP. This program is written in FORTRAN IV for batch execution and is available for implementation on IBM 7000 series computers. GASP was developed in 1971.

Relative populations of excited levels within the ground configuration of Si-like Cu, Zn, Ge and Se ions

NASA Technical Reports Server (NTRS)

Datla, R. U.; Roberts, J. R.; Bhatia, A. K.

1991-01-01

Populations of 3p2 1D2, 3P1, 3P2 levels in Si-like Cu, Zn, Ge, and Se ions have been deduced from the measurements of absolute intensities of magnetic dipole transitions within the 3s2 3p2 ground configuration. The measured population ratios are compared with theoretical calculations based on the distorted-wave approximation for the electron collisions and a semiclassical approximation for the proton collisions. The observed deviation from the statistical distribution for the excited-level populations within the ground configuration along the silicon isoelectronic sequence is in agreement with theoretical prediction.

Identification and Lagrangian analysis of oceanographic structures favorable for fishery of neon flying squid ( Ommastrephes bartramii) in the South Kuril area

NASA Astrophysics Data System (ADS)

Budyansky, M. V.; Prants, S. V.; Samko, E. V.; Uleysky, M. Yu.

2017-09-01

Based on the AVISO velocity field, we compute daily synoptic Lagrangian maps in the South Kuril area for the fishery seasons of 1998, 1999, and 2001-2005 from available catching data on neon flying squid (NFS). With the help of drift maps for artificial particles, we found that the majority of NFS fishing grounds featuring maximum catches are situated near large-scale Lagrangian intrusions: tongues of water penetrating the surrounding water of other Lagrangian properties. It is shown that the NFS catch locations tend to accumulate at places where waters with different magnitudes of certain Lagrangian indicators converge, mix, and produce filaments, swirls, and tendrils typical of chaotic advection. Potential NFS fishing grounds are mainly located near (1) Lagrangian intrusions of the Subarctic front, (2) intrusions of Okhotsk Sea and Oyashio waters around mesoscale anticyclones east of Hokkaido with subsequent penetration of catch locations inside eddies and (3) intrusions of subtropical waters into the central part of the South Kuril area due to interaction with eddies of different size and polarity. Possible reasons for increased biological production and fishery in the vicinity of Lagrangian intrusions are discussed.

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

PubMed Central

Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

2000-01-01

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

Resonance lines and energy levels of Cs III, Ba IV, and La V

NASA Technical Reports Server (NTRS)

Epstein, G. L.; Reader, J.

1976-01-01

Spectra of Cs III, Ba IV, and La V were photographed in a low-voltage sliding spark on a 10.7 m normal-incidence vacuum spectrograph. These ions are isoelectronic with neutral iodine and display a halogen-like energy level structure. Detailed isoelectronic comparisons, level transition diagrams, and tabular data on the transitions of the ions and percentage compositions of Cs III configurations are presented.

Structure and magnetic properties of an unprecedented syn-anti μ-nitrito-1κO:2κO' bridged Mn(III)-salen complex and its isoelectronic and isostructural formate analogue.

PubMed

Kar, Paramita; Biswas, Rituparna; Drew, Michael G B; Ida, Yumi; Ishida, Takayuki; Ghosh, Ashutosh

2011-04-07

The preparation, crystal structures and magnetic properties of two new isoelectronic and isomorphous formate- and nitrite-bridged 1D chains of Mn(III)-salen complexes, [Mn(salen)(HCOO)](n) (1) and [Mn(salen)(NO(2))](n) (2), where salen is the dianion of N,N'-bis(salicylidene)-1,2-diaminoethane, are presented. The structures show that the salen ligand coordinates to the four equatorial sites of the metal ion and the formate or nitrite ions coordinate to the axial positions to bridge the Mn(III)-salen units through a syn-antiμ-1κO:2κO' coordination mode. Such a bridging mode is unprecedented in Mn(III) for formate and in any transition metal ion for nitrite. Variable-temperature magnetic susceptibility measurements of complexes 1 and 2 indicate the presence of ferromagnetic exchange interactions with J values of 0.0607 cm(-1) (for 1) and 0.0883 cm(-1) (for 2). The ac measurements indicate negligible frequency dependence for 1 whereas compound 2 exhibits a decrease of χ(ac)' and a concomitant increase of χ(ac)'' on elevating frequency around 2 K. This finding is an indication of slow magnetization reversal characteristic of single-chain magnets or spin-glasses. The μ-nitrito-1κO:2κO' bridge seems to be a potentially superior magnetic coupler to the formate bridge for the construction of single-molecule/-chain magnets as its coupling constant is greater and the χ(ac)' and χ(ac)'' show frequency dependence. © The Royal Society of Chemistry 2011

High-power helium-neon laser irradiation inhibits the growth of traumatic scars in vitro and in vivo.

PubMed

Shu, Bin; Ni, Guo-Xin; Zhang, Lian-Yang; Li, Xiang-Ping; Jiang, Wan-Ling; Zhang, Li-Qun

2013-05-01

This study explored the inhibitory effect of the high-power helium-neon (He-Ne) laser on the growth of scars post trauma. For the in vitro study, human wound fibroblasts were exposed to the high-power He-Ne laser for 30 min, once per day with different power densities (10, 50, 100, and 150 mW/cm(2)). After 3 days of repeated irradiation with the He-Ne laser, fibroblast proliferation and collagen synthesis were evaluated. For in vivo evaluation, a wounded animal model of hypertrophic scar formation was established. At postoperative day 21, the high-power He-Ne laser irradiation (output power 120 mW, 6 mm in diameter, 30 min each session, every other day) was performed on 20 scars. At postoperative day 35, the hydroxyproline content, apoptosis rate, PCNA protein expression and FADD mRNA level were assessed. The in vitro study showed that the irradiation group that received the power densities of 100 and 150 mW/cm(2) showed decreases in the cell proliferation index, increases in the percentage of cells in the G0/G1 phase, and decreases in collagen synthesis and type I procollagen gene expression. In the in vivo animal studies, regions exposed to He-Ne irradiation showed a significant decrease in scar thickness as well as decreases in hydroxyproline levels and PCNA protein expression. Results from the in vitro and in vivo studies suggest that repeated irradiation with a He-Ne laser at certain power densities inhibits fibroblast proliferation and collagen synthesis, thereby inhibits the growth of hypertrophic scars.

Effects of Penning reactions and excitation rate on the pulsed transverse-discharge neon laser for photodynamic therapy

NASA Astrophysics Data System (ADS)

Yang, C.-H.; Itoh, K.; Tomita, H.; Obara, M.

1995-07-01

Theoretical analysis of the output performance of a transverse discharge pumped neon Penning laser (585.3 nm) using a mixture of Ne/H2 is described. The validity of the kinetic model is confirmed by comparing the results to the experimental discharge and laser performance. It is theoretically shown that the optimum mixing ratio of the Ne/H2 mixture is 1:2.5, and the optimum operating pressure is about 56 Torr. The model also predicts that the intrinsic efficiency reaches a peak of 8.5×10-6 at an excitation rate of 0.5 MW/cm3 under the optimum mixing ratio and operating pressure conditions. At excitation rates in excess of 0.5 MW/cm3 the laser output power is slowly increasing and then saturates due to electron collisional quenching of the upper laser level. The laser power extraction is increased by laser injection seeding in order to rapidly build up the lasing. The improved intrinsic efficiency is about two times higher than without the injection seeding. The improved specific laser output is 8 W/cm3, therefore, a discharge volume of 125 cm3 will be able to generate the peak laser power reaching 1 kW. This power value is sufficient to obtain the same treatment effect as the gold vapor laser used in photodynamic therapy. Moreover, by fitting this model to the experimental results of the laser output energy with a Ne/D2 mixture, it is shown that the Penning ionization rate constant of H2 is larger than that of D2.

Electron spin resonance investigations of /sup 11/B/sup 12/C, /sup 11/B/sup 13/C, and /sup 10/B/sup 12/C in neon, argon, and krypton matrices at 4 K: Comparison with theoretical results

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

Knight L.B. Jr.; Cobranchi, S.T.; Petty, J.T.

1989-01-15

The first spectroscopic study of the diatomic radical BC is reported which confirms previous theoretical predictions of a /sup 4/summation/sup -/ electronic ground state. The nuclear hyperfine interactions (A tensors) obtained for /sup 11/B, /sup 10/B, and /sup 13/C from the electron spin resonance (ESR) measurements are compared with extensive ab initio CI calculations. The BC molecule is one of the first examples of a small high spin radical for such an in-depth experimental--theoretical comparison. The electronic structure of BC obtained from an analysis of the nuclear hyperfine interaction (hfi) is compared to that obtained from a Mulliken-type population analysismore » conducted on a CI wave function which yields A/sub iso/ and A/sub dip/ results in good agreement with the observed values. The BC radical was generated by the laser vaporization of a boron--carbon mixture and trapped in neon, argon, and krypton matrices at 4 K for a complete ESR characterization. The magnetic parameters (MHz) obtained for /sup 11/B/sup 13/C in solid neon are: g/sub parallel/ = 2.0015(3); g/sub perpendicular/ = 2.0020(3); D(zfs) = 1701(2); /sup 11/B: chemically bondA/sub parallel/chemically bond = 100(1); chemically bondA/sub perpendicular/chemically bond = 79(1); /sup 13/C: chemically bondA/sub parallel/chemically bond = 5(2) and chemically bondA/sub perpendicular/chemically bond = 15(1). Based on comparison with the theoretical results, the most likely choice of signs is that all A values are positive.« less

Modeling the heating and atomic kinetics of a photoionized neon plasma experiment

NASA Astrophysics Data System (ADS)

Lockard, Tom E.

that the computed plasma heating compares well with experimental observation when the effects of the windows, hydrodynamics, and non-equilbirium neon emissivity and opacity are employed. The atomic kinetics shows significant time-dependent effects because the timescale of the x-ray drive is too short compared to that of the photoionization process. These modeling and simulation results are important to test theory and modeling assumptions and approximations, and also to provide guidance on data interpretation and analysis.

Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions (11BO; X2Sigma+)

DTIC Science & Technology

2015-04-15

Reaction products of isoelectronic boron monoxide (BO), cyano (CN), ethynyl (CCH), and silicon nitride (SiN) radicals with acetylene and ethylene. 3.10...Isoelectronicity in the Reactions of the Cyano (CN), Boron Monoxide (BO), Silicon Nitride (SiN), and Ethynyl (C2H) Radicals with Unsaturated Hydrocarbons...AFRL-OSR-VA-TR-2015-0111 Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions Ralf Kaiser UNIVERSITY OF HAWAII SYSTEMS HONOLULU

Optical transitions in highly charged californium ions with high sensitivity to variation of the fine-structure constant.

PubMed

Berengut, J C; Dzuba, V A; Flambaum, V V; Ong, A

2012-08-17

We study electronic transitions in highly charged Cf ions that are within the frequency range of optical lasers and have very high sensitivity to potential variations in the fine-structure constant, α. The transitions are in the optical range despite the large ionization energies because they lie on the level crossing of the 5f and 6p valence orbitals in the thallium isoelectronic sequence. Cf(16+) is a particularly rich ion, having several narrow lines with properties that minimize certain systematic effects. Cf(16+) has very large nuclear charge and large ionization energy, resulting in the largest α sensitivity seen in atomic systems. The lines include positive and negative shifters.

Semiempirical studies of atomic structure. Progress report, 1 July 1984-1 January 1985

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

Curtis, L.J.

1985-01-01

Through the acquisition and systematization of empirical data, remarkably precise methods for predicting excitation energies, transition wavelengths, transition probabilities, level lifetimes, ionization potentials, core polarizabilities, and core penetrabilities have been and are being developed and applied. Although the data base for heavy, highly ionized atoms is still sparse, much new information has become available since this program was begun in 1980. The purpose of the project is to perform needed measurements and to utilize the available data through parametrized extrapolations and interpolations along isoelectronic, homologous, and Rydberg sequences to provide predictions for large classes of quantities with a precision thatmore » is sharpened by subsequent measurements.« less

Fundamental Bounds for Sequence Reconstruction from Nanopore Sequencers.

PubMed

Magner, Abram; Duda, Jarosław; Szpankowski, Wojciech; Grama, Ananth

2016-06-01

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to accurately reconstruct the true sequence with high probability? Our results provide a number of important insights: (i) the probability of accurate reconstruction of a sequence from a single sample in the presence of indel errors tends quickly (i.e., exponentially) to zero as the length of the sequence increases; and (ii) replicated extrusion is an effective technique for accurate reconstruction. We show that for typical distributions of indel errors, the required number of replicas is a slow function (polylogarithmic) of sequence length - implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Moreover, we show that in certain cases, the required number of replicas can be related to information-theoretic parameters of the indel error distributions.

Identifying Pelagic Habitat Hotspots of Neon Flying Squid in the Temperate Waters of the Central North Pacific.

PubMed

Alabia, Irene D; Saitoh, Sei-Ichi; Mugo, Robinson; Igarashi, Hiromichi; Ishikawa, Yoichi; Usui, Norihisa; Kamachi, Masafumi; Awaji, Toshiyuki; Seito, Masaki

2015-01-01

We identified the pelagic habitat hotspots of the neon flying squid (Ommastrephes bartramii) in the central North Pacific from May to July and characterized the spatial patterns of squid aggregations in relation to oceanographic features such as mesoscale oceanic eddies and the Transition Zone Chlorophyll-a Front (TZCF). The data used for the habitat model construction and analyses were squid fishery information, remotely-sensed and numerical model-derived environmental data from May to July 1999-2010. Squid habitat hotspots were deduced from the monthly Maximum Entropy (MaxEnt) models and were identified as regions of persistent high suitable habitat across the 12-year period. The distribution of predicted squid habitat hotspots in central North Pacific revealed interesting spatial and temporal patterns likely linked with the presence and dynamics of oceanographic features in squid's putative foraging grounds from late spring to summer. From May to June, the inferred patches of squid habitat hotspots developed within the Kuroshio-Oyashio transition zone (KOTZ; 37-40°N) and further expanded north towards the subarctic frontal zone (SAFZ; 40-44°N) in July. The squid habitat hotspots within the KOTZ and areas west of the dateline (160°W-180°) were likely influenced and associated with the highly dynamic and transient oceanic eddies and could possibly account for lower squid suitable habitat persistence obtained from these regions. However, predicted squid habitat hotspots located in regions east of the dateline (180°-160°W) from June to July, showed predominantly higher squid habitat persistence presumably due to their proximity to the mean position of the seasonally-shifting TZCF and consequent utilization of the highly productive waters of the SAFZ.

Universal sequence map (USM) of arbitrary discrete sequences

PubMed Central

2002-01-01

Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM), is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR). The latter enables the representation of 4 unit type sequences (like DNA) as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules. PMID:11895567

Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

PubMed

Deroost, Natacha; Coomans, Daphné

2018-02-01

We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

Contamination of sequence databases with adaptor sequences

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

Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable ofmore » transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.« less

A new observational approach to investigate the heliospheric interstellar wind interface - The study of extreme and far ultraviolet resonantly scattered solar radiation from neon, oxygen, carbon and nitrogen

NASA Technical Reports Server (NTRS)

Bowyer, Stuart; Fahr, Hans J.

1990-01-01

One of the outstanding uncertainties in the understanding of the heliosphere concerns the character of the interaction between the outflowing solar wind and the interstellar medium. A new possibility for obtaining information on this topic is suggested. The cosmically abundant elements neon, oxygen, carbon, and nitrogen will be affected differently at their interface passage depending upon the character of this region. Consequently, the distribution of these atoms and their ions will vary within the inner heliosphere. The study of resonantly scattered solar radiation from these species will then provide information on the nature of the interface. A preliminary evaluation of this approach has been carried out, and the results are encouraging. The relevant lines to be studied are in the extreme and far ulraviolet. The existing data in these bands are reviewed; unfortunately, past instrumentation has had insufficient resolution and sensitivity to provide useful information. The capabilities of future approved missions with capabilities in this area are evaluated.

Method to amplify variable sequences without imposing primer sequences

DOEpatents

Bradbury, Andrew M.; Zeytun, Ahmet

2006-11-14

The present invention provides methods of amplifying target sequences without including regions flanking the target sequence in the amplified product or imposing amplification primer sequences on the amplified product. Also provided are methods of preparing a library from such amplified target sequences.

Identifying Pelagic Habitat Hotspots of Neon Flying Squid in the Temperate Waters of the Central North Pacific

PubMed Central

Alabia, Irene D.; Saitoh, Sei-Ichi; Mugo, Robinson; Igarashi, Hiromichi; Ishikawa, Yoichi; Usui, Norihisa; Kamachi, Masafumi; Awaji, Toshiyuki; Seito, Masaki

2015-01-01

We identified the pelagic habitat hotspots of the neon flying squid (Ommastrephes bartramii) in the central North Pacific from May to July and characterized the spatial patterns of squid aggregations in relation to oceanographic features such as mesoscale oceanic eddies and the Transition Zone Chlorophyll-a Front (TZCF). The data used for the habitat model construction and analyses were squid fishery information, remotely-sensed and numerical model-derived environmental data from May to July 1999–2010. Squid habitat hotspots were deduced from the monthly Maximum Entropy (MaxEnt) models and were identified as regions of persistent high suitable habitat across the 12-year period. The distribution of predicted squid habitat hotspots in central North Pacific revealed interesting spatial and temporal patterns likely linked with the presence and dynamics of oceanographic features in squid’s putative foraging grounds from late spring to summer. From May to June, the inferred patches of squid habitat hotspots developed within the Kuroshio-Oyashio transition zone (KOTZ; 37–40°N) and further expanded north towards the subarctic frontal zone (SAFZ; 40–44°N) in July. The squid habitat hotspots within the KOTZ and areas west of the dateline (160°W-180°) were likely influenced and associated with the highly dynamic and transient oceanic eddies and could possibly account for lower squid suitable habitat persistence obtained from these regions. However, predicted squid habitat hotspots located in regions east of the dateline (180°-160°W) from June to July, showed predominantly higher squid habitat persistence presumably due to their proximity to the mean position of the seasonally-shifting TZCF and consequent utilization of the highly productive waters of the SAFZ. PMID:26571118

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

NASA Astrophysics Data System (ADS)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

Measurement of emission cross sections for n = 3 → 2 transitions in Neon-like Fe XVII and Ni XIX ions

NASA Astrophysics Data System (ADS)

Lockard, Tom; Brown, Gregory V.; Hell, Natalie; Scofield, J. H.; Beiersdorfer, Peter; Porter, Frederick Scott; Kilbourne, Caroline; Kelley, Richard L.; Leutenegger, Maurice A.; Betancourt-Martinez, Gabriele

2018-06-01

The absolute excitation cross sections of the strong 1s2 2s2 2p51/2 3d3/2 1P1 → 1s2 2s2 2p6 1S0 and 1s2 2s2 2p53/2 3d5/2 3D1 → 1s2 2s2 2p6 1S0 strong resonance and intercombination lines, commonly known as 3C and 3D, have been measured in neon-like Fe16+ and Ni18+. These measurements were carried out at the Lawrence Livermore National Laboratory's EBIT-I electron beam ion trap facility using the EBIT Calorimeter Spectrometer (ECS) quantum microcalorimeter and a flat crystal spectrometer. The absolute excitation cross sections were determined by normalizing the measured spectrum to the X-ray emission from radiative recombination. The direct excitation lines 3C and 3D and radiative recombination (RR) lines were measured simultaneously using the ECS. By normalizing the measured RR flux to their theoretical cross sections, the emission from lines 3C and 3D was made absolute. Using simultaneous measurements from the higher resolution flat crystal spectrometer, it was possible to check for potential blends from lower charge states. Results of our measurements including comparison to theory, will be presented.This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Multimodal sequence learning.

PubMed

Kemény, Ferenc; Meier, Beat

2016-02-01

While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

Sequence verification of synthetic DNA by assembly of sequencing reads

PubMed Central

Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, João C.; Tyler, Brett M.; Peccoud, Jean

2013-01-01

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org. PMID:23042248

An Array of Layers in Silicon Sulfides: Chain-like and Ground State Structures

NASA Astrophysics Data System (ADS)

Alonso-Lanza, Tomás; Ayuela, Andrés; Aguilera-Granja, Faustino

While much is known about isoelectronic materials related to carbon nanostructures, such as boron nitride layers and nanotubes, rather less is known about equivalent silicon based materials. Following the recent discovery of phosphorene, we here discuss isoelectronic silicon monosulfide monolayers. We describe a set of anisotropic ground state structures that clearly have a high stability with respect to the near isotropic silicon monosulfide monolayers. The source of the layer anisotropy is related to the presence of Si-S double chains linked by some Si-Si covalent bonds, which lie at the core of the increased stability, together with a remarkable spd hybridization on Si. The involvement of d orbitals brings more variety to silicon-sulfide based nanostructures that are isoelectronic to phosphorene, which could be relevant for future applications, adding extra degrees of freedom. Spanish Ministry of Economy and Competitiveness MINECO, Basque Government (ETORTEK Program 2014), University of the Basque Country (GrantGrant No. IT-366-07) and MPC Material Physics Center - San Sebastián.

Multilocus sequence typing of total-genome-sequenced bacteria.

PubMed

Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

2012-04-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Low-level laser therapy with helium-neon laser improved viability of osteoporotic bone marrow-derived mesenchymal stem cells from ovariectomy-induced osteoporotic rats

NASA Astrophysics Data System (ADS)

Fallahnezhad, Somaye; Piryaei, Abbas; Tabeie, Faraj; Nazarian, Hamid; Darbandi, Hasan; Amini, Abdoldllah; Mostafavinia, Ataroalsadat; Ghorishi, Seyed Kamran; Jalalifirouzkouhi, Ali; Bayat, Mohammad

2016-09-01

The purpose of this study was to evaluate the influences of helium-neon (He-Ne) and infrared (IR) lasers on the viability and proliferation rate of healthy and ovariectomy-induced osteoporotic (OVX) bone marrow mesenchymal stem cells (BMMSCs) in vitro. MSCs harvested from the BM of healthy and OVX rats were culture expanded. He-Ne and IR lasers were applied three times at energy densities of 0.6, 1.2, and 2.4 J/cm2 for BMMSCs. BMMSCs viability and proliferation rate were evaluated by MTT assay on days 2, 4, 6, 14, and 21. The results showed that healthy BMMSCs responded optimally to 0.6 J/cm2 using an IR laser after three times of laser radiation. Moreover, it was found that OVX-BMMSCs responded optimally to 0.6 J/cm2 with He-Ne laser and one-time laser radiation. It is concluded that the low-level laser therapy (LLLT) effect depends on the physiological state of the BMMSCs, type of the laser, wavelength, and number of laser sessions. The biostimulation efficiency of LLLT also depends on the delivered energy density. LLLT can enhance the viability and proliferation rate of healthy and especially osteoporotic autologous BMMSCs, which could be very useful in regenerative medicine.

Atomic Data and Spectral Line Intensities for Be-like Ions

NASA Technical Reports Server (NTRS)

Bhatia, Anand; Landi, E.

2008-01-01

Atomic data and collision rates are needed to model the spectrum of optically thin astrophysical sources. Recent observations from solar instrumentation such as SOH0 and Hinode have revealed the presence of hosts of lines emitted by high-energy configurations from ions belonging to the Be-like to the 0-like isoelectronic sequences. Data for such configurations are often unavailable in the literature. We have started a program to calculate the atomic parameters and rates for the high-energy configurations of Be-like ions of the type ls2.21.nl' where n=3,4,5. We report on the results of this project and on the diagnostic application of the predicted spectral lines.

Double photoionization of Be-like (Be-F5+) ions

NASA Astrophysics Data System (ADS)

Abdel Naby, Shahin; Pindzola, Michael; Colgan, James

2015-04-01

The time-dependent close-coupling method is used to study the single photon double ionization of Be-like (Be - F5+) ions. Energy and angle differential cross sections are calculated to fully investigate the correlated motion of the two photoelectrons. Symmetric and antisymmetric amplitudes are presented along the isoelectronic sequence for different energy sharing of the emitted electrons. Our total double photoionization cross sections are in good agreement with available theoretical results and experimental measurements along the Be-like ions. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California and the National Institute for Computational Sciences in Knoxville, Tennessee.

Reactions of vanadium dioxide molecules with acetylene: infrared spectra of VO2(η(2)-C2H2)(x) (x = 1, 2) and OV(OH)CCH in solid neon.

PubMed

Zhou, Xiaojie; Chen, Mohua; Zhou, Mingfei

2013-07-03

Reactions of vanadium dioxide molecules with acetylene have been studied by matrix isolation infrared spectroscopy. Reaction intermediates and products are identified on the basis of isotopic substitutions as well as density functional frequency calculations. Ground state vanadium dioxide molecule reacts with acetylene in forming the side-on-bonded VO2(η(2)-C2H2) and VO2(η(2)-C2H2)2 complexes spontaneously on annealing in solid neon. The VO2(η(2)-C2H2) complex is characterized to have a (2)B2 ground state with C2v symmetry, whereas the VO2(η(2)-C2H2)2 complex has a (2)A ground state with C2 symmetry. The VO2(η(2)-C2H2) and VO2(η(2)-C2H2)2 complexes are photosensitive. The VO2(η(2)-C2H2) complex rearranges to the OV(OH)CCH molecule upon UV-vis light excitation.

Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences

PubMed Central

Gibbs, Mark J; Armstrong, John S; Gibbs, Adrian J

2005-01-01

Background Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, in traditional taxonomy, specimens are usually identified by 'dichotomous keys' that use combinations of characters shared by different members of the target set. Using one specific character for each target is the least efficient strategy for identification. Using combinations of shared bisectionally-distributed characters is much more efficient, and this strategy is most efficient when they separate the targets in a progressively binary way. Results We have developed a practical method for finding minimal sets of sub-sequences that identify individual sequences, and could be targeted by combinations of probes, so that the efficient strategy of traditional taxonomic identification could be used in DNA diagnosis. The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters. We found that 201 distinct cytochrome oxidase subunit-1 (CO1) genes from moths (Lepidoptera) were distinguished using only 15 sub-sequences 20 nucleotides long, whereas only 8–10 sub-sequences 6–10 nucleotides long were required to distinguish the CO1 genes of 92 species from the 9 largest orders of insects. Conclusion The presence/absence of sub-sequences in a set of gene sequences can be used like the questions in a traditional dichotomous taxonomic key; hybridisation probes complementary to such sub-sequences should provide a very efficient means for identifying individual species, subtypes or genotypes. Sequence diversity and sub-sequence length are the major factors that determine the numbers of distinguishing sub-sequences in any set of sequences. PMID:15817134

Isoelectronic bound-exciton photoluminescence in strained beryllium-doped Si0.92Ge0.08 epilayers and Si0.92Ge0.08/Si superlattices at ambient and elevated hydrostatic pressure

NASA Astrophysics Data System (ADS)

Kim, Sangsig; Chang, Ganlin; Herman, Irving P.; Bevk, Joze; Moore, Karen L.; Hall, Dennis G.

1997-03-01

Photoluminescence (PL) from a beryllium-doped Si0.92Ge0.08 epilayer and three different beryllium-doped Si0.92Ge0.08/Si superlattices (SL's) commensurately grown on Si(100) substrates is examined at 9 K at ambient pressure and, for the epilayer and one SL, as a function of hydrostatic pressure. In each structure, excitons bind to the isoelectronic Be pairs in the strained Si0.92Ge0.08 layers. The zero-phonon PL peaks of the epilayer and the in situ doped 50-Å Si0.92Ge0.08/100-Å Si SL shift linearly with pressure toward lower energy at the rate of 0.68+/-0.03 and 0.97+/-0.03 meV/kbar, respectively, which are near the 0.77-meV/kbar value for Si:Be. The PL energies at ambient and elevated pressure are analyzed by accounting for strain, quantum confinement, and exciton binding. A modified Hopfield-Thomas-Lynch model is used to model exciton binding to the Be pairs. This model, in which potential wells bind electrons to a site (that then trap holes), predicts a distribution of electron binding energies when an inhomogeneous distribution of potential-well depths is used. This accounts for the large PL linewidth and the decrease of linewidth with increasing pressure, among other observations. In SL's, the exciton binding energy is shown to depend on the width of the wells as well as the spatial distribution of Be dopants in the superlattice. Also, at and above 58 kbar a very unusual peak is observed in one of the SL's, which is associated with a free-exciton peak in Si, that shifts very fast with pressure (-6.02+/-0.03 meV/kbar).

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.

Science sequence design

NASA Technical Reports Server (NTRS)

Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

1973-01-01

The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

PubMed Central

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R. Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M.; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi. PMID:21949797

Forbidden line emission from highly ionized atoms in tokamak plasmas

NASA Technical Reports Server (NTRS)

Feldman, U.; Doschek, G. A.; Bhatia, A. K.

1982-01-01

Considerable interest in the observation of forbidden spectral lines from highly ionized atoms in tokamak plasmas is related to the significance of such observations for plasma diagnostic applications. Atomic data for the elements Ti Cr, Mn, Fe, Ni, and Kr have been published by Feldman et al. (1980) and Bhatia et al. (1980). The present investigation is concerned with collisional excitation rate coefficients and radiative decay rates, which are interpolated for ions of elements between calcium, and krypton and for levels of the 2s2 2pk, 2s 2p(k+1), and 2p(k+2) configurations, and for the O I, N I, C I, B I, and Be I isoelectronic sequences. The provided interpolated atomic data can be employed to calculate level populations and relative line intensities for ions of the considered sequences, taking into account levels of the stated configurations. Important plasma diagnostic information provided by the forbidden lines includes the ion temperature

On the local relaxation of solid neon upon Rydberg excitation of a NO impurity: the role of the NO(A)-Ne interaction potential and zero-point quantum delocalization.

PubMed

Pajón-Suárez, Pedro; Rojas-Lorenzo, Germán A; Rubayo-Soneira, Jesús; Hernández-Lamoneda, Ramón; Larrégaray, Pascal

2009-12-31

The local relaxation of solid neon subsequent to the impulsive excitation of the NO chromophore to its A(3s sigma) Ryberg state is investigated using molecular dynamics simulations. This study makes use of empirical NO(X,A)-Ne isotropic pair potentials as well as a recently developed ab initio triatomic potential energy surface for the excited state. The role of these interaction potentials is analyzed, including many-body effects. In particular, empirical potentials, designed to reproduce correctly both the NO X-A steady-state absorption and emission bands, are shown to lead to a good description of the subpicosecond relaxation dynamics. The 600 fs expansion of the electronic bubble fairly agrees with experimental data. This relatively long time scale with respect to solid Argon, which was previously attributed to the range of the NO(A)-Ne interaction, is presumably related to the quantum nature of the medium. The time-resolved local relaxation of the Ne solid is understandably intermediate between that of classical solids (e.g., Ar) and that of quantum solids (e.g., H(2)).

Pulse sequence programming in a dynamic visual environment: SequenceTree.

PubMed

Magland, Jeremy F; Li, Cheng; Langham, Michael C; Wehrli, Felix W

2016-01-01

To describe SequenceTree, an open source, integrated software environment for implementing MRI pulse sequences and, ideally, exporting them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for programmers and nonprogrammers alike. The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically, allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally, other types of scanners will be supported in the future. SequenceTree has been used for 8 years in our laboratory and elsewhere and has contributed to more than 50 peer-reviewed publications in areas such as cardiovascular imaging, solid state and nonproton NMR, MR elastography, and high-resolution structural imaging. SequenceTree is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal both for advanced users and users with limited programming experience. © 2015 Wiley Periodicals, Inc.

[Complete genome sequencing and sequence analysis of BCG Tice].

PubMed

Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

2012-10-04

The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

PubMed Central

Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abu-Duhier, Faisel M.; Al-Yamani, Essam J.; Al-Busadah, Khalid A.; Al-Arawi, Mohammed S.; Al-Khider, Ali Y.; Al-Muhaimeed, Abdullah N.; Al-Qahtani, Fahad H.; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Al-Harthi, Amer S.; Akdemir, Kadir C.; Otu, Hasan H.

2010-01-01

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and ∼40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism. PMID:20502665

Sequence to Sequence - Video to Text

DTIC Science & Technology

2015-12-11

Saenko, and S. Guadarrama. Generating natural-language video descriptions using text - mined knowledge. In AAAI, July 2013. 2 [20] P. Kuznetsova, V...Sequence to Sequence – Video to Text Subhashini Venugopalan1 Marcus Rohrbach2,4 Jeff Donahue2 Raymond Mooney1 Trevor Darrell2 Kate Saenko3...1. Introduction Describing visual content with natural language text has recently received increased interest, especially describing images with a

Feedback shift register sequences versus uniformly distributed random sequences for correlation chromatography

NASA Technical Reports Server (NTRS)

Kaljurand, M.; Valentin, J. R.; Shao, M.

1996-01-01

Two alternative input sequences are commonly employed in correlation chromatography (CC). They are sequences derived according to the algorithm of the feedback shift register (i.e., pseudo random binary sequences (PRBS)) and sequences derived by using the uniform random binary sequences (URBS). These two sequences are compared. By applying the "cleaning" data processing technique to the correlograms that result from these sequences, we show that when the PRBS is used the S/N of the correlogram is much higher than the one resulting from using URBS.

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

PubMed Central

2014-01-01

Background We introduce Sequence Bundles--a novel data visualisation method for representing multiple sequence alignments (MSAs). We identify and address key limitations of the existing bioinformatics data visualisation methods (i.e. the Sequence Logo) by enabling Sequence Bundles to give salient visual expression to sequence motifs and other data features, which would otherwise remain hidden. Methods For the development of Sequence Bundles we employed research-led information design methodologies. Sequences are encoded as uninterrupted, semi-opaque lines plotted on a 2-dimensional reconfigurable grid. Each line represents a single sequence. The thickness and opacity of the stack at each residue in each position indicates the level of conservation and the lines' curved paths expose patterns in correlation and functionality. Several MSAs can be visualised in a composite image. The Sequence Bundles method is designed to favour a tangible, continuous and intuitive display of information. Results We have developed a software demonstration application for generating a Sequence Bundles visualisation of MSAs provided for the BioVis 2013 redesign contest. A subsequent exploration of the visualised line patterns allowed for the discovery of a number of interesting features in the dataset. Reported features include the extreme conservation of sequences displaying a specific residue and bifurcations of the consensus sequence. Conclusions Sequence Bundles is a novel method for visualisation of MSAs and the discovery of sequence motifs. It can aid in generating new insight and hypothesis making. Sequence Bundles is well disposed for future implementation as an interactive visual analytics software, which can complement existing visualisation tools. PMID:25237395

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

PubMed Central

de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments.

PubMed

Sakai, Ryo; Aerts, Jan

2014-01-01

The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study. Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization. The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.

Systematization of experimental data on the spectra of 3s--3p and 3p--3d transitions of Ar IX (436--861 A)

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

Kramida, A.E.

1985-04-01

The article correlates and systematizes published data on the wavelengths of lines in the spectra of argon obtained by various authors by the so-called beam-foil method. The energies of the levels are compared with the results of an extrapolation along an isoelectronic sequence, and the lifetimes of the levels are compared with theoretical calculations. The energies of all 26 energy levels of the 2p/sup 5/3s, 3p and 3d configurations of Ar IX are determined and refined. Forty-five transitions between these configurations in the 436--861 A region are identified. The identifications are supported by combinations according to the Ritz principle andmore » by a semiempirical calculation of the energies of the levels.« less

Resonance and intercombination lines in Mg-like ions of atomic numbers Z = 13 – 92

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

Santana, Juan A.; Trabert, Elmar

2015-02-05

While prominent lines of various Na-like ions have been measured with an accuracy of better than 100 ppm and corroborate equally accurate calculations, there have been remarkably large discrepancies between calculations for Mg-like ions of high atomic number. We present ab initio calculations using the multireference Moller-Plesset approach for Mg-like ions of atomic numbers Z = 13-92 and compare the results with other calculations of this isoelectronic sequence as well as with experimental data. Our results come very close to experiment (typically 100 ppm) over a wide range. Furthermore, data at high values of Z are sparse, which calls formore » further accurate measurements in this range where relativistic and QED effects are large.« less

Elemental Abundances of Blue Compact Dwarfs from Mid-Infrared Spectroscopy with Spitzer

NASA Astrophysics Data System (ADS)

Wu, Yanling; Bernard-Salas, J.; Charmandaris, V.; Lebouteiller, V.; Hao, Lei; Brandl, B. R.; Houck, J. R.

2008-01-01

We present a study of elemental abundances in a sample of 13 blue compact dwarf (BCD) galaxies, using the ~10-37 μm high-resolution spectra obtained with Spitzer IRS. We derive the abundances of neon and sulfur for our sample using the infrared fine-structure lines probing regions which may be obscured by dust in the optical and compare our results with similar infrared studies of starburst galaxies from ISO. We find a good correlation between the neon and sulfur abundances, although sulfur is underabundant relative to neon with respect to the solar value. A comparison of the elemental abundances (neon and sulfur) measured from the infrared data with those derived from the optical (neon, sulfur, and oxygen) studies reveals a good overall agreement for sulfur, while the infrared-derived neon abundances are slightly higher than the optical values. This indicates either that the metallicities of dust-enshrouded regions in BCDs are similar to the optically accessible regions, or that if they are different they do not contribute substantially to the total infrared emission of the host galaxy.

Interannual and seasonal variability of winter-spring cohort of neon flying squid abundance in the Northwest Pacific Ocean during 1995-2011

NASA Astrophysics Data System (ADS)

Yu, Wei; Chen, Xinjun; Yi, Qian

2016-06-01

The neon flying squid, Ommastrephes bartramii, is a species of economically important cephalopod in the Northwest Pacific Ocean. Its short lifespan increases the susceptibility of the distribution and abundance to the direct impact of the environmental conditions. Based on the generalized linear model (GLM) and generalized additive model (GAM), the commercial fishery data from the Chinese squid-jigging fleets during 1995 to 2011 were used to examine the interannual and seasonal variability in the abundance of O. bartramii, and to evaluate the influences of variables on the abundance (catch per unit effort, CPUE). The results from GLM suggested that year, month, latitude, sea surface temperature (SST), mixed layer depth (MLD), and the interaction term ( SST×MLD) were significant factors. The optimal model based on GAM included all the six significant variables and could explain 42.43% of the variance in nominal CPUE. The importance of the six variables was ranked by decreasing magnitude: year, month, latitude, SST, MLD and SST×MLD. The squid was mainly distributed in the waters between 40°N and 44°N in the Northwest Pacific Ocean. The optimal ranges of SST and MLD were from 14 to 20°C and from 10 to 30 m, respectively. The squid abundance greatly fluctuated from 1995 to 2011. The CPUE was low during 1995-2002 and high during 2003-2008. Furthermore, the squid abundance was typically high in August. The interannual and seasonal variabilities in the squid abundance were associated with the variations of marine environmental conditions and the life history characteristics of squid.

Planetary Nebula Abundances and Morphology: Probing the Chemical Evolution of the Milky Way

NASA Astrophysics Data System (ADS)

Stanghellini, Letizia; Guerrero, Martín Antonio; Cunha, Katia; Manchado, Arturo; Villaver, Eva

2006-11-01

This paper presents a homogeneous study of abundances in a sample of 79 northern Galactic planetary nebulae (PNe) whose morphological classes have been uniformly determined. Ionic abundances and plasma diagnostics were derived from selected optical line strengths in the literature, and elemental abundances were estimated with the ionization correction factor developed by Kingsbourgh & Barlow in 1994. We compare the elemental abundances to the final yields obtained from stellar evolution models of low- and intermediate-mass stars, and we confirm that most bipolar PNe have high nitrogen and helium abundance and are the likely progeny of stars with main-sequence mass greater than 3 Msolar. We derive =0.27 and discuss the implication of such a high ratio in connection with the solar neon abundance. We determine the Galactic gradients of oxygen and neon and found Δlog(O/H)/ΔR=-0.01 dex kpc-1 and Δlog(Ne/H)/ΔR=-0.01 dex kpc-1. These flat PN gradients are irreconcilable with Galactic metallicity gradients flattening with time.

MRO Sequence Checking Tool

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat

2008-01-01

The MRO Sequence Checking Tool program, mro_check, automates significant portions of the MRO (Mars Reconnaissance Orbiter) sequence checking procedure. Though MRO has similar checks to the ODY s (Mars Odyssey) Mega Check tool, the checks needed for MRO are unique to the MRO spacecraft. The MRO sequence checking tool automates the majority of the sequence validation procedure and check lists that are used to validate the sequences generated by MRO MPST (mission planning and sequencing team). The tool performs more than 50 different checks on the sequence. The automation varies from summarizing data about the sequence needed for visual verification of the sequence, to performing automated checks on the sequence and providing a report for each step. To allow for the addition of new checks as needed, this tool is built in a modular fashion.

Megabase sequencing of human genome by ordered-shotgun-sequencing (OSS) strategy

NASA Astrophysics Data System (ADS)

Chen, Ellson Y.

1997-05-01

So far we have used OSS strategy to sequence over 2 megabases DNA in large-insert clones from regions of human X chromosomes with different characteristic levels of GC content. The method starts by randomly fragmenting a BAC, YAC or PAC to 8-12 kb pieces and subcloning those into lambda phage. Insert-ends of these clones are sequenced and overlapped to create a partial map. Complete sequencing is then done on a minimal tiling path of selected subclones, recursively focusing on those at the edges of contigs to facilitate mergers of clones across the entire target. To reduce manual labor, PCR processes have been adapted to prepare sequencing templates throughout the entire operation. The streamlined process can thus lend itself to further automation. The OSS approach is suitable for large- scale genomic sequencing, providing considerable flexibility in the choice of subclones or regions for more or less intensive sequencing. For example, subclones containing contaminating host cell DNA or cloning vector can be recognized and ignored with minimal sequencing effort; regions overlapping a neighboring clone already sequenced need not be redone; and segments containing tandem repeats or long repetitive sequences can be spotted early on and targeted for additional attention.

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference

Coordinate cytokine regulatory sequences

DOEpatents

Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

2005-05-10

The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing.

PubMed

Zhang, Suhua; Niu, Yong; Bian, Yingnan; Dong, Rixia; Liu, Xiling; Bao, Yun; Jin, Chao; Zheng, Hancheng; Li, Chengtao

2018-05-01

STRs vary not only in the length of the repeat units and the number of repeats but also in the region with which they conform to an incremental repeat pattern. Massively parallel sequencing (MPS) offers new possibilities in the analysis of STRs since they can simultaneously sequence multiple targets in a single reaction and capture potential internal sequence variations. Here, we sequenced 34 STRs applied in the forensic community of China with a custom-designed panel. MPS performance were evaluated from sequencing reads analysis, concordance study and sensitivity testing. High coverage sequencing data were obtained to determine the constitute ratios and heterozygous balance. No actual inconsistent genotypes were observed between capillary electrophoresis (CE) and MPS, demonstrating the reliability of the panel and the MPS technology. With the sequencing data from the 200 investigated individuals, 346 and 418 alleles were obtained via CE and MPS technologies at the 34 STRs, indicating MPS technology provides higher discrimination than CE detection. The whole study demonstrated that STR genotyping with the custom panel and MPS technology has the potential not only to reveal length and sequence variations but also to satisfy the demands of high throughput and high multiplexing with acceptable sensitivity.

Theoretical energies for the n = 1 and 2 states of the helium isoelectronic sequence up to Z = 100

NASA Technical Reports Server (NTRS)

Drake, G. W.

1988-01-01

The unified method described previously for combining high-precision nonrelativistic variational calculations with relativistic and quantum electrodynamic corrections is applied to the 1s2 1S0, 1s2s 1S0, 1s2s 1S0, 1s2s 3S1, 1s2p 1P1, and 1s2p 3P(0.1,2) states of helium-like ions. Detailed tabulations are presented for all ions in the range Z = 2-100 and are compared with a wide range of experimental data up to (Kr-34)+. The results for (U-90)+ significantly alter the recent Lamb shift measurement of Munger and Gould (1986) from 70.4 + or - 8.3 to 71.0 + or - 8.3 eV, in comparison with a revised theoretical value of 74.3 + or - 0.4 eV. The improved agreement is due to the inclusion of higher order two-electron corrections in the present work.

What A Long Strange Trip It's Been: Lessons Learned From NASA EOS, LTER, NEON, CZO And On To The Future With Sustainable Research Networks

NASA Astrophysics Data System (ADS)

Williams, M. W.

2014-12-01

The traditional, small-scale, incremental approach to environmental science is changing as researchers embrace a more integrated and multi-disciplinary approach to understanding how our natural systems work today and how they may respond in the future to forcings such as climate change. In situ networks are evolving in response to these challenges so as to provide the appropriate measurements to develop high-resolution spatial and temporal data sets across a wide range of platforms from microbial measurements to remote sensing. These large programs provide a unique set of challenges when compared to more traditional programs. Here I provide insights learned from my participation in a number of large programs, including NASA EOS, LTER, CZO, NEON, and WSC and how those experiences in environmental science can help us move forward towards more applied applications of environmental science, including sustainability initiatives. I'll chat about the importance of managerial and management skills, which most of us scientists prefer to avoid. I'll also chat about making decisions about what long-term measurements to make and when to stop. Data management is still the weakest part of environmental networks; what needs to be done. We have learned that these networks provide an important knowledge base that can lead to informed decisions leading to environmental, energy, social and cultural sustainability.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Pulse Sequence Programming in a Dynamic Visual Environment: SequenceTree

PubMed Central

Magland, Jeremy F.; Li, Cheng; Langham, Michael C.; Wehrli, Felix W.

2015-01-01

Purpose To describe SequenceTree (ST), an open source. integrated software environment for implementing MRI pulse sequences, and ideally exported them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for non-programmers and programmers alike. Methods The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally other types of scanners will be supported in the future. Results The software has been used for eight years in the authors’ laboratory and elsewhere and has been utilized in more than fifty peer-reviewed publications in areas such as cardiovascular imaging, solid state and non-proton NMR, MR elastography, and high resolution structural imaging. Conclusion ST is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal for both advanced users and those with limited programming experience. PMID:25754837

Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence

PubMed Central

Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E.

2016-01-01

It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

PubMed

Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

2016-01-01

It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

PubMed

Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

2017-10-01

Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

PubMed

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-05-01

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

PubMed Central

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-01-01

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

What are Whole Exome Sequencing and Whole Genome Sequencing?

MedlinePlus

... the future. For more information about DNA sequencing technologies and their use: Genetics Home Reference discusses whether ... University in St. Louis describes the different sequencing technologies and what the new technologies have meant for ...

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Collisional-radiative calculations for the J = 0-1 lasing line of neon-like germanium under anisotropic excitation conditions

NASA Astrophysics Data System (ADS)

Bentotoche, M. S.; Inal, M. K.; Benmouna, M.

2018-02-01

A new asymmetry parameter characterizing the differences between the polarized π and σ gain components of the soft-x-ray J = 0-1 lasing line of neon-like ions is calculated in the case of Ge22+ assuming an electron distribution which is a weighted sum of an isotropic Maxwellian and a monoenergetic beam. Using a quasi steady-state collisional-radiative model, we determine in the weak amplification regime the relative populations of the upper M = 0 and lower M=0,+/- 1 magnetic sublevels of the lasing line as a function of electron density from 1020 to 2× {10}21 cm-3. This model includes inelastic and elastic collisional transitions, as well as spontaneous radiative decay between all the 337 M-sublevels arising from the 75 lowest-lying Ge22+ J-levels. The computations were performed for a temperature {T}{{e}} of the Maxwellian component between 1.2× {10}6 and 8× {10}6 K, a kinetic energy E 0 and a fraction f of the beam component in the ranges 1.5{--}20 {keV} and 0.1 % {--}10 % , respectively. The basic atomic data, such as level energies, radiative decay probabilities and inelastic collision strengths, were calculated with the flexible atomic code. However, some modifications of this code were made to get the collision strengths for transitions between M-sublevels due to impact with isotropic electrons as well as due to impact with an electron beam in the case of de-excitation. We find that the newly introduced asymmetry parameter may become significant under certain conditions of electron distribution corresponding to relatively low {T}{{e}} (1.2× {10}6{--}2.5× {10}6 K) and E 0 (3-6 keV). The results reported here may be useful in the evaluation of the polarization degree of the J = 0-1 x-ray laser output from a germanium plasma in the presence of fast directional electrons.

Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

PubMed

Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

2016-09-01

Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

Biological sequence compression algorithms.

PubMed

Matsumoto, T; Sadakane, K; Imai, H

2000-01-01

Today, more and more DNA sequences are becoming available. The information about DNA sequences are stored in molecular biology databases. The size and importance of these databases will be bigger and bigger in the future, therefore this information must be stored or communicated efficiently. Furthermore, sequence compression can be used to define similarities between biological sequences. The standard compression algorithms such as gzip or compress cannot compress DNA sequences, but only expand them in size. On the other hand, CTW (Context Tree Weighting Method) can compress DNA sequences less than two bits per symbol. These algorithms do not use special structures of biological sequences. Two characteristic structures of DNA sequences are known. One is called palindromes or reverse complements and the other structure is approximate repeats. Several specific algorithms for DNA sequences that use these structures can compress them less than two bits per symbol. In this paper, we improve the CTW so that characteristic structures of DNA sequences are available. Before encoding the next symbol, the algorithm searches an approximate repeat and palindrome using hash and dynamic programming. If there is a palindrome or an approximate repeat with enough length then our algorithm represents it with length and distance. By using this preprocessing, a new program achieves a little higher compression ratio than that of existing DNA-oriented compression algorithms. We also describe new compression algorithm for protein sequences.

Bellerophon: A program to detect chimeric sequences in multiple sequence alignments

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

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2003-12-23

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Long sequence correlation coprocessor

NASA Astrophysics Data System (ADS)

Gage, Douglas W.

1994-09-01

A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

Nonparametric Combinatorial Sequence Models

NASA Astrophysics Data System (ADS)

Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

Next-Generation Sequencing Platforms

NASA Astrophysics Data System (ADS)

Mardis, Elaine R.

2013-06-01

Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

Sequence information signal processor

DOEpatents

Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

1999-01-01

An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

PubMed

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Dna Sequencing

DOEpatents

Tabor, Stanley; Richardson, Charles C.

1995-04-25

A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

PubMed Central

Laehnemann, David; Borkhardt, Arndt

2016-01-01

Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies. Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing, Illumina sequencing by synthesis, Ion Torrent semiconductor sequencing, Pacific Biosciences single-molecule real-time sequencing and Oxford Nanopore sequencing. There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the parameters they determine from them and the data structures and algorithms they use. We highlight the assumptions they make and for which data types these hold, providing guidance which tools to consider for benchmarking with regard to the data properties. While no benchmarking results are included here, such specific benchmarks would greatly inform tool choices and future software development. The development of stand-alone error correctors, as well as single nucleotide variant and haplotype callers, could also benefit from using more of the knowledge about error profiles and from (re)combining ideas from the existing approaches presented here. PMID:26026159

Use of the Minion nanopore sequencer for rapid sequencing of avian influenza virus isolates

USDA-ARS?s Scientific Manuscript database

A relatively new sequencing technology, the MinION nanopore sequencer, provides a platform that is smaller, faster, and cheaper than existing Next Generation Sequence (NGS) technologies. The MinION sequences of individual strands of DNA and can produce millions of sequencing reads. The cost of the s...

Design and prototype fabrication of a 30 tesla cryogenic magnet

NASA Technical Reports Server (NTRS)

Prok, G. M.; Swanson, M. C.; Brown, G. V.

1977-01-01

A liquid neon cooled magnet was designed to produce 30 teslas in steady operation. To ensure the correctness of the heat transfer relationships used, supercritical neon heat transfer tests were made. Other tests made before the final design included tests on the effect of the magnetic field on pump motors, tensile shear tests on the cryogenic adhesives, and simulated flow studies for the coolant. The magnet will consist of two pairs of coils, cooled by forced convection of supercritical neon. Heat from the supercritical neon will be rejected through heat exchangers which are made of roll bonded copper panels and are submerged in a pool of saturated liquid neon. A partial mock up coil was wound to identify the tooling required to wind the magnet. This was followed by winding a prototype pair of coils. The prototype winding established procedures for fabricating the final magnet and revealed slight changes needed in the final design.

Design and prototype fabrication of a 30 tesla cryogenic magnet

NASA Technical Reports Server (NTRS)

Prok, G. M.; Swanson, M. C.; Brown, G. V.

1977-01-01

A liquid-neon-cooled magnet has been designed to produce 30 teslas in steady operation. Its feasibility was established by a previously reported parametric study. To ensure the correctness of the heat transfer relationships used, supercritical neon heat transfer tests were made. Other tests made before the final design included tests on the effect of the magnetic field on pump motors; tensile-shear tests on the cryogenic adhesives; and simulated flow studies for the coolant. The magnet will be made of two pairs of coils, cooled by forced convection of supercritical neon. Heat from the supercritical neon will be rejected through heat exchangers which are made of roll-bonded copper panels and are submerged in a pool of saturated liquid neon. A partial mock-up coil was wound to identify the tooling required to wind the magnet. This was followed by winding a prototype pair of coils. The prototype winding established procedures for fabricating the final magnet and revealed slight changes needed in the final design.

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models

PubMed Central

2017-01-01

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder–decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis. PMID:29104927

S -matrix calculations of energy levels of sodiumlike ions

DOE PAGES

Sapirstein, J.; Cheng, K. T.

2015-06-24

A recent S -matrix-based QED calculation of energy levels of the lithium isoelectronic sequence is extended to the general case of a valence electron outside an arbitrary filled core. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and an unusual feature of the two-photon exchange contribution involving autoionizing states is discussed. Here, the method is illustrated with a calculation of the energy levels of sodiumlike ions, with results for 3s 1/2, 3p 1/2, and 3p 3/2 energies tabulated for the range Z = 30 – 100 . Comparison with experimentmore » and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed.« less

Future collaborations between NEON and the U.S. EPA: linking molecular genomics for bioassessment with national ecological data sets

EPA Science Inventory

Molecular taxonomic techniques such as DNA barcoding offer interesting new capabilities for studying community biodiversity for applications like biological monitoring. Beyond DNA barcoding, new DNA sequencing technologies (i.e. Next-Generation Sequencing) present even greater po...

A versatile laboratory cryogenic plant

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

Dobrov, V.M.; Marevichev, I.P.; Petrova, Y.B.

1983-07-01

The Institute of Theoretical and Experimental physics has designed a versatile cryogenic plant (VCP) which can liquefy helium, hydrogen, neon, and can extract neon from a gaseous neon-helium mixture. It can also be used as a refrigerator for cryostating external objects. The versatile cryogenic plant is schematicized and the refrigerating capacity and VCP control panel are detailed. Characteristic features which distinguish the VCP from other plants are specified. The processes involved in the liquefaction of helium, hydrogen, or neon, and the cryostating and cooling of an external object are explained. The use of the plant showed it to be economic,more » reliable, and convenient to operate.« less

Unlocking hidden genomic sequence

PubMed Central

Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

2004-01-01

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

Chromosome specific repetitive DNA sequences

DOEpatents

Moyzis, Robert K.; Meyne, Julianne

1991-01-01

A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

Targeted therapy according to next generation sequencing-based panel sequencing.

PubMed

Saito, Motonobu; Momma, Tomoyuki; Kono, Koji

2018-04-17

Targeted therapy against actionable gene mutations shows a significantly higher response rate as well as longer survival compared to conventional chemotherapy, and has become a standard therapy for many cancers. Recent progress in next-generation sequencing (NGS) has enabled to identify huge number of genetic aberrations. Based on sequencing results, patients recommend to undergo targeted therapy or immunotherapy. In cases where there are no available approved drugs for the genetic mutations detected in the patients, it is recommended to be facilitate the registration for the clinical trials. For that purpose, a NGS-based sequencing panel that can simultaneously target multiple genes in a single investigation has been used in daily clinical practice. To date, various types of sequencing panels have been developed to investigate genetic aberrations with tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics. Because sequencing panels are efficient and cost-effective, they are quickly being adopted outside the lab, in hospitals and clinics, in order to identify personal targeted therapy for individual cancer patients.

Regulatory sequence analysis tools.

PubMed

van Helden, Jacques

2003-07-01

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

PubMed Central

Matochko, Wadim L.; Derda, Ratmir

2013-01-01

Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N × 1 frequency vector n = ||ni||, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N × N matrix and a stochastic sampling operator (S a). The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of S a and use them to define the sequencing operator (S e q). Sequencing without any bias and errors is S e q = S a IN, where IN is a N × N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (C E N), which describes elimination or statistically significant downsampling, of specific reads during the sequencing process. PMID:24416071

Children's discrimination of vowel sequences

NASA Astrophysics Data System (ADS)

Coady, Jeffry A.; Kluender, Keith R.; Evans, Julia

2003-10-01

Children's ability to discriminate sequences of steady-state vowels was investigated. Vowels (as in ``beet,'' ``bat,'' ``bought,'' and ``boot'') were synthesized at durations of 40, 80, 160, 320, 640, and 1280 ms. Four different vowel sequences were created by concatenating different orders of vowels for each duration, separated by 10-ms intervening silence. Thus, sequences differed in vowel order and duration (rate). Sequences were 12 s in duration, with amplitude ramped linearly over the first and last 2 s. Sequence pairs included both same (identical sequences) and different trials (sequences with vowels in different orders). Sequences with vowel of equal duration were presented on individual trials. Children aged 7;0 to 10;6 listened to pairs of sequences (with 100 ms between sequences) and responded whether sequences sounded the same or different. Results indicate that children are best able to discriminate sequences of intermediate-duration vowels, typical of conversational speaking rate. Children were less accurate with both shorter and longer vowels. Results are discussed in terms of auditory processing (shortest vowels) and memory (longest vowels). [Research supported by NIDCD DC-05263, DC-04072, and DC-005650.

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

PubMed Central

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

Research Program on Factors Affecting the Brightness of AC Plasma Panels.

DTIC Science & Technology

1983-06-01

representing the second excited electronic con - figuration in neon. In an effort to devise means to improve the brightness and/or efficiency of neon filled...obtained from several panels was found to be very good (Ref. 6), a factor providing important support for the validity of the kinetic modeling pro - cedures...pressure neon Penning mixtures for I conditions typical of plasma panel displays [II]. Their work has pro - vied valuable insight regarding the electrical

Long-range barcode labeling-sequencing

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

Chen, Feng; Zhang, Tao; Singh, Kanwar K.

Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

PubMed

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2004-09-22

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

BAC sequencing using pooled methods.

PubMed

Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

2015-01-01

Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Study of the stability of beam characteristics of the neon-like Zn X-ray laser using a half cavity

NASA Astrophysics Data System (ADS)

Präg, A. R.; Mocek, T.; Kozlová, M.; Rus, B.; Jamelot, G.; Ros, D.

2003-01-01

At the Prague Asterix Laser System Center (PALS) the Asterix iodine laser delivering up to 700 J/0.5 ns is used as a pump source for X-ray laser experiments and applications. The prepulse technique was applied which is known to improve the neon-like X-ray laser output at the J = 0 {-} 1 transition dramatically. Since Zn slab targets were used the operating wavelength was 21.2 nm. A prepulse having up to 20 J precedes the main pulse by 10 ns. The main beam and the prepulse beam are focussed by two different optical systems separately and their foci are superimposed at the target surface. By implementing a half-cavity set-up for double-pass amplification using a Mo/Si multilayer mirror which can be used for more than 100 shots the X-ray laser output was more than 10 times stronger than at the single pass in a 30 mm long plasma. Double-pass amplification was observed to be most efficient when the pump pulse duration was at least 150 ps longer than the round trip time (≈ 260 ps) in the half-cavity. Under this fundamental condition the X-ray laser reached saturation in the double-pass regime containing approx. 4 mJ energy which has been proved to be enough for future applications. In this contribution, the X-ray laser features like divergence in two dimensions, the beam quality (symmetry), the pointing angle and the integrated intensity giving an estimation of the output energy are investigated over 110 shots. To characterize the stability of the X-ray laser the shot distribution, the mean value and the standard deviation for these parameters are evaluated. For 18 shots in a series what was achievable during one day the corresponding values are given, and a statistical analysis carrying out a chi-squared test characterize the Zn X-ray laser as a robust tool suitable for applications. In the future it is planned to allocate X-ray laser beam time to external research groups.

Canopy structural complexity as a continental predictor of primary production: Using NEON to transform understanding of forest structure-function

NASA Astrophysics Data System (ADS)

Atkins, J. W.; Fahey, R. T.; Gough, C. M.; Hardiman, B. S.

2016-12-01

Ecosystem structure-function relationships represent a long-standing research area for ecosystem science. Relationships between canopy structural complexity (CSC) and net primary productivity (NPP), have been characterized for a limited number of sites, yet whether these relationships are conserved across eco-climatic boundaries remains unknown. We hypothesize an underlying mechanistic basis for global NPP-CSC linkages to include improved resource-use efficiency as CSC increases, examined here by correlating CSC with measures of light-use efficiency and nitrogen-use efficiency. Here we present a broad, continental scale analysis of CSC-NPP linkages. We are using multiple NEON sites coupled with other sites across a diverse array of temperate forest types spanning six eco-climatic domains of the continental United States to examine CSC-NPP relationships. Portable canopy LiDAR (PCL) data were used to calculate a suite of CSC metrics at the plot-level within each site. Ongoing work compares CSC to co-located measurements of wood net primary production estimated from the incremental change in woody biomass calculated using tree allometries. Results to date show CSC is highly variable across forest sites and may provide additional explanatory power for predicting NPP that is independent of other commonly used forest structural attributes such as leaf area index. CSC metrics such as rugosity vary widely across sites—ranging from high values (30 - 35) in complex canopies such as the Great Smoky Mountains to low values in open, savanna systems like North-Central Florida (< 0.5 - 2). NPP, and light- and nitrogen-use calculations are underway and will be paired with site-level CSC, with the expectation that CSC, resource-use efficiency, and NPP are positively correlated. Advancing understanding of how and why CSC affects forest NPP across a broad spatial dimension could transform mechanistic understanding of ecosystem structure-carbon cycling relationships, and greatly

Effect of Atmospheric-Pressure Plasma Jet of Neon on 7-Acetoxy-6-(2,3-Dibromopropyl)-4,8-Dimethylcoumarin Molecule

NASA Astrophysics Data System (ADS)

Tanışlı, Murat; Taşal, Erol

2017-06-01

Atmospheric-pressure low-temperature plasma jets and their applications are a topic of great interest in the fields of physics, technology, and medicine. In this study, the used self-made plasma jet is based on a dielectric barrier discharge (DBD) in neon (Ne) with typical processing parameters, such as frequency in the kHz range and voltage in the kV range. The plasma is characterized by optical emission spectroscopy (OES). These types of plasma can be used in various applications such as surface modification, inactivation of microorganisms, and chemical decomposition. This study is concerned with the Fourier transform infrared spectrum (FT-IR) and ultraviolet-visible (UV-vis) absorption spectroscopy of the large 7-acetoxy-6-(2,3-dibromopropyl)-4,8-dimethylcoumarin molecule (abbreviated as 7AC) dissolved in ethanol and methanol solvents and their modification after atmospheric-pressure plasma treatment (APPT) with the DBD. The research is motivated by the significance of this molecule in different fields of application. Also the changes in the structure are recorded. After APPT, the peak corresponding to the carbonyl bond at a wavenumber of 1715 cm-1 disappears in the IR spectrum of the ethanol solution, and when splitting at a wavenumber of 1405 cm-1 is observed, the peak at 1224 cm-1 is found to disappear after plasma is applied. It is seen new peaks at frequencies of 432 and 655 cm-1 are formed. When the same situation is analyzed for the 7AC molecule dissolved in methanol, a new peak is observed at 1634 cm-1. The intensities of the peaks at 3433 and 2075 cm-1 also increase and there is a large change in the wavenumber at 600 cm-1. In the UV spectra, a significant increase in the absorbance of the 7AC molecule dissolved in ethanol is observed after APPT, whereas a small decrease in the absorbance of the 7AC molecule dissolved in methanol is obtained. Owing to the lack of symmetry, many normal bands of vibrations are mixed.

Fishing ground distribution of neon flying squid ( Ommastrephes bartramii) in relation to oceanographic conditions in the Northwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Yu, Wei; Chen, Xinjun; Yi, Qian

2017-12-01

Neon flying squid, Ommastrephes bartramii, is a squid species of the North Pacific Ocean, which plays an important economical role in the international fishery. Logbook data for Chinese squid-jigging fishery over 2004-2011 were used to evaluate the relationship between the fishing grounds of the squid and the convergent frontal areas, which were defined by the contour lines of specific sea surface temperature (SST) and chlorophyll- a (Chl- a) concentration. Our results indicate that the SST in the range of 15 to 19°C and the Chl- a concentration in the range of 0.1 to 0.4 mg m-3 are the favorable conditions for the aggregation of the squid. Additionally, we deduced that the SST at 17.5°C and the Chl- a concentration at 0.25 mg m-3 are the optimal environmental conditions for the aggregation of O. bartramii. In August, the annual CPUE is positively correlated with the proportion of the fishing grounds with favorable SST and Chl- a concentration, as well as the combination of the two variables, implying that the abundance of the squid annually is largely depending on the presence of the favorable environmental conditions for fishery in August. Minor spatial difference between mean latitudinal location of the 17.5°C SST and 0.25 mg m-3 Chl- a fronts can increase the CPUEs of O. bartramii. Furthermore, the monthly latitudinal gravity centers of the CPUE closely followed the mean latitudinal position of the contour lines of the 17.5°C SST and the 0.25 mg m-3 Chl- a concentration. Our findings suggest the convergent oceanographic features (fronts) play significant roles in regulating the distribution and abundance of the western stock of the winter-spring cohort of O. bartramii, which can help people to improve their ability to discover the O. bartramii fishing grounds with higher productivity.

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

PubMed Central

Martin, Andrew C. R.

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

PubMed

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Sequence repeats and protein structure

NASA Astrophysics Data System (ADS)

Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

2012-11-01

Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

PubMed

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

PubMed Central

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

PubMed Central

Johnson, Sarah S.; Zaikova, Elena; Goerlitz, David S.; Bai, Yu; Tighe, Scott W.

2017-01-01

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions. PMID:28337073

Contributions from associative and explicit sequence knowledge to the execution of discrete keying sequences.

PubMed

Verwey, Willem B

2015-05-01

Research has provided many indications that highly practiced 6-key sequences are carried out in a chunking mode in which key-specific stimuli past the first are largely ignored. When in such sequences a deviating stimulus occasionally occurs at an unpredictable location, participants fall back to responding to individual stimuli (Verwey & Abrahamse, 2012). The observation that in such a situation execution still benefits from prior practice has been attributed to the possibility to operate in an associative mode. To better understand the contribution to the execution of keying sequences of motor chunks, associative sequence knowledge and also of explicit sequence knowledge, the present study tested three alternative accounts for the earlier finding of an execution rate increase at the end of 6-key sequences performed in the associative mode. The results provide evidence that the earlier observed execution rate increase can be attributed to the use of explicit sequence knowledge. In the present experiment this benefit was limited to sequences that are executed at the moderately fast rates of the associative mode, and occurred at both the earlier and final elements of the sequences. Copyright © 2015 Elsevier B.V. All rights reserved.

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

PubMed Central

Shiroguchi, Katsuyuki; Jia, Tony Z.; Sims, Peter A.; Xie, X. Sunney

2012-01-01

RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. We optimized the barcodes to be unambiguously identifiable, even in the presence of multiple sequencing errors. This method allows counting with single-copy resolution despite sequence-dependent bias and PCR-amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of Escherichia coli with more accurate and reproducible quantification than conventional RNA-Seq. PMID:22232676

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

PubMed

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

Making sense of deep sequencing

PubMed Central

Goldman, D.; Domschke, K.

2016-01-01

This review, the first of an occasional series, tries to make sense of the concepts and uses of deep sequencing of polynucleic acids (DNA and RNA). Deep sequencing, synonymous with next-generation sequencing, high-throughput sequencing and massively parallel sequencing, includes whole genome sequencing but is more often and diversely applied to specific parts of the genome captured in different ways, for example the highly expressed portion of the genome known as the exome and portions of the genome that are epigenetically marked either by DNA methylation, the binding of proteins including histones, or that are in different configurations and thus more or less accessible to enzymes that cleave DNA. Deep sequencing of RNA (RNASeq) reverse-transcribed to complementary DNA is invaluable for measuring RNA expression and detecting changes in RNA structure. Important concepts in deep sequencing include the length and depth of sequence reads, mapping and assembly of reads, sequencing error, haplotypes, and the propensity of deep sequencing, as with other types of ‘big data’, to generate large numbers of errors, requiring monitoring for methodologic biases and strategies for replication and validation. Deep sequencing yields a unique genetic fingerprint that can be used to identify a person, and a trove of predictors of genetic medical diseases. Deep sequencing to identify epigenetic events including changes in DNA methylation and RNA expression can reveal the history and impact of environmental exposures. Because of the power of sequencing to identify and deliver biomedically significant information about a person and their blood relatives, it creates ethical dilemmas and practical challenges in research and clinical care, for example the decision and procedures to report incidental findings that will increasingly and frequently be discovered. PMID:24925306

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

NASA Astrophysics Data System (ADS)

Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

MSLICE Sequencing

NASA Technical Reports Server (NTRS)

Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

2011-01-01

MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

Statistical properties of filtered pseudorandom digital sequences formed from the sum of maximum-length sequences

NASA Technical Reports Server (NTRS)

Wallace, G. R.; Weathers, G. D.; Graf, E. R.

1973-01-01

The statistics of filtered pseudorandom digital sequences called hybrid-sum sequences, formed from the modulo-two sum of several maximum-length sequences, are analyzed. The results indicate that a relation exists between the statistics of the filtered sequence and the characteristic polynomials of the component maximum length sequences. An analysis procedure is developed for identifying a large group of sequences with good statistical properties for applications requiring the generation of analog pseudorandom noise. By use of the analysis approach, the filtering process is approximated by the convolution of the sequence with a sum of unit step functions. A parameter reflecting the overall statistical properties of filtered pseudorandom sequences is derived. This parameter is called the statistical quality factor. A computer algorithm to calculate the statistical quality factor for the filtered sequences is presented, and the results for two examples of sequence combinations are included. The analysis reveals that the statistics of the signals generated with the hybrid-sum generator are potentially superior to the statistics of signals generated with maximum-length generators. Furthermore, fewer calculations are required to evaluate the statistics of a large group of hybrid-sum generators than are required to evaluate the statistics of the same size group of approximately equivalent maximum-length sequences.

Program for Editing Spacecraft Command Sequences

NASA Technical Reports Server (NTRS)

Gladden, Roy; Waggoner, Bruce; Kordon, Mark; Hashemi, Mahnaz; Hanks, David; Salcedo, Jose

2006-01-01

Sequence Translator, Editor, and Expander Resource (STEER) is a computer program that facilitates construction of sequences and blocks of sequences (hereafter denoted generally as sequence products) for commanding a spacecraft. STEER also provides mechanisms for translating among various sequence product types and quickly expanding activities of a given sequence in chronological order for review and analysis of the sequence. To date, construction of sequence products has generally been done by use of such clumsy mechanisms as text-editor programs, translating among sequence product types has been challenging, and expanding sequences to time-ordered lists has involved arduous processes of converting sequence products to "real" sequences and running them through Class-A software (defined, loosely, as flight and ground software critical to a spacecraft mission). Also, heretofore, generating sequence products in standard formats has been troublesome because precise formatting and syntax are required. STEER alleviates these issues by providing a graphical user interface containing intuitive fields in which the user can enter the necessary information. The STEER expansion function provides a "quick and dirty" means of seeing how a sequence and sequence block would expand into a chronological list, without need to use of Class-A software.

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

PubMed Central

2012-01-01

Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

X-Ray Laser Program Report for FY 1989

DTIC Science & Technology

1990-05-24

theoretical photopumped x-ray laser program also involves the use of a neon lasant plasma. However, that is the only similarity to the Na/Ne scheme described...K-shell neon Z pinch photons of energy hv > 900 eV, photoionize inner K-shell electrons from the neutral neon, leading to Auger decay from Ne II to...is generated by electrons which are produced in the photoionization of Ne I. For example, ionization by the Ly-a line produces 150-eV photoelectrons

Multiplexed fragaria chloroplast genome sequencing

Treesearch

W. Njuguna; A. Liston; R. Cronn; N.V. Bassil

2010-01-01

A method to sequence multiple chloroplast genomes using ultra high throughput sequencing technologies was recently described. Complete chloroplast genome sequences can resolve phylogenetic relationships at low taxonomic levels and identify informative point mutations and indels. The objective of this research was to sequence multiple Fragaria...

A vision for ubiquitous sequencing

PubMed Central

Erlich, Yaniv

2015-01-01

Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

Automatic Command Sequence Generation

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

2007-01-01

Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the

Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

ERIC Educational Resources Information Center

Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

2016-01-01

How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

Career Academy Course Sequences.

ERIC Educational Resources Information Center

Markham, Thom; Lenz, Robert

This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

Large-Scale Concatenation cDNA Sequencing

PubMed Central

Yu, Wei; Andersson, Björn; Worley, Kim C.; Muzny, Donna M.; Ding, Yan; Liu, Wen; Ricafrente, Jennifer Y.; Wentland, Meredith A.; Lennon, Greg; Gibbs, Richard A.

1997-01-01

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching. [All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.] PMID:9110174

Kilo-sequencing: an ordered strategy for rapid DNA sequence data acquisition.

PubMed Central

Barnes, W M; Bevan, M

1983-01-01

A strategy for rapid DNA sequence acquisition in an ordered, nonrandom manner, while retaining all of the conveniences of the dideoxy method with M13 transducing phage DNA template, is described. Target DNA 3 to 14 kb in size can be stably carried by our M13 vectors. Suitable targets are stretches of DNA which lack an enzyme recognition site which is unique on our cloning vectors and adjacent to the sequencing primer; current sites that are so useful when lacking are Pst, Xba, HindIII, BglII, EcoRI. By an in vitro procedure, we cut RF DNA once randomly and once specifically, to create thousands of deletions which start at the unique restriction site adjacent to the dideoxy sequencing primer and extend various distances across the target DNA. Phage carrying a desired size of deletions, whose DNA as template will give rise to DNA sequence data in a desired location along the target DNA, may be purified by electrophoresis alive on agarose gels. Phage running in the same location on the agarose gel thus conveniently give rise to nucleotide sequence data from the same kilobase of target DNA. Images PMID:6298723

Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

NASA Technical Reports Server (NTRS)

Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

2016-01-01

On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken).

PubMed

Valenzuela-González, Fabiola; Martínez-Porchas, Marcel; Villalpando-Canchola, Enrique; Vargas-Albores, Francisco

2016-03-01

Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated when using Kraken. Kraken cumulates the information of both sequence senses, providing additional elements for the classification. In conclusion, the results demonstrate that Kraken is an excellent choice for use in the taxonomic assignment of sequences obtained by Sanger sequencing or based on third generation sequencing, of which the main goal is to generate larger sequences. Copyright © 2016 Elsevier B.V. All rights reserved.

The (CH2)2O-H2O hydrogen bonded complex. Ab Initio calculations and Fourier transform infrared spectroscopy from neon matrix and a new supersonic jet experiment coupled to the infrared AILES beamline of synchrotron SOLEIL.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Tremblay, B; Madebène, B; Alikhani, M E; Georges, R; Moudens, A; Goubet, M; Huet, T R; Pirali, O; Roy, P

2011-03-31

A series of hydrogen bonded complexes involving oxirane and water molecules have been studied. In this paper we report on the vibrational study of the oxirane-water complex (CH(2))(2)O-H(2)O. Neon matrix experiments and ab initio anharmonic vibrational calculations have been performed, providing a consistent set of vibrational frequencies and anharmonic coupling constants. The implementation of a new large flow supersonic jet coupled to the Bruker IFS 125 HR spectrometer at the infrared AILES beamline of the French synchrotron SOLEIL (Jet-AILES) enabled us to record first jet-cooled Fourier transform infrared spectra of oxirane-water complexes at different resolutions down to 0.2 cm(-1). Rovibrational parameters and a lower bound of the predissociation lifetime of 25 ps for the v(OH)(b) = 1 state have been derived from the rovibrational analysis of the ν(OH)(b) band contour recorded at respective rotational temperatures of 12 K (Jet-AILES) and 35 K (LADIR jet).

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

PubMed Central

Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M.; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

2016-01-01

Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

Detection of spatial hot spots and variation for the neon flying squid Ommastrephes bartramii resources in the northwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Feng, Yongjiu; Chen, Xinjun; Liu, Yan

2017-07-01

With the increasing effects of global climate change and fishing activities, the spatial distribution of the neon flying squid ( Ommastrephes bartramii) is changing in the traditional fishing ground of 150°-160°E and 38°-45°N in the northwest Pacific Ocean. This research aims to identify the spatial hot and cold spots (i.e. spatial clusters) of O. bartramii to reveal its spatial structure using commercial fishery data from 2007 to 2010 collected by Chinese mainland squid-jigging fleets. A relatively strongly-clustered distribution for O. bartramii was observed using an exploratory spatial data analysis (ESDA) method. The results show two hot spots and one cold spot in 2007 while only one hot and one cold spots were identified each year from 2008 to 2010. The hot and cold spots in 2007 occupied 8.2% and 5.6% of the study area, respectively; these percentages for hot and cold spot areas were 5.8% and 3.1% in 2008, 10.2% and 2.9% in 2009, and 16.4% and 11.9% in 2010, respectively. Nearly half (>45%) of the squid from 2007 to 2009 reported by Chinese fleets were caught in hot spot areas while this percentage reached its peak at 68.8% in 2010, indicating that the hot spot areas are central fishing grounds. A further change analysis shows the area centered at 156°E/43.5°N was persistent as a hot spot over the whole period from 2007 to 2010. Furthermore, the hot spots were mainly identified in areas with sea surface temperature (SST) in the range of 15-20°C around warm Kuroshio Currents as well as with the chlorophyll- a (chl- a) concentration above 0.3 mg/m3. The outcome of this research improves our understanding of spatiotemporal hotspots and its variation for O. bartramii and is useful for sustainable exploitation, assessment, and management of this squid.

Variability of Suitable Habitat of Western Winter-Spring Cohort for Neon Flying Squid in the Northwest Pacific under Anomalous Environments.

PubMed

Yu, Wei; Chen, Xinjun; Yi, Qian; Chen, Yong; Zhang, Yang

2015-01-01

We developed a habitat suitability index (HSI) model to evaluate the variability of suitable habitat for neon flying squid (Ommastrephes bartramii) under anomalous environments in the Northwest Pacific Ocean. Commercial fisheries data from the Chinese squid-jigging vessels on the traditional fishing ground bounded by 35°-45°N and 150°-175°E from July to November during 1998-2009 were used for analyses, as well as the environmental variables including sea surface temperature (SST), chlorophyll-a (Chl-a) concentration, sea surface height anomaly (SSHA) and sea surface salinity (SSS). Two empirical HSI models (arithmetic mean model, AMM; geometric mean model, GMM) were established according to the frequency distribution of fishing efforts. The AMM model was found to perform better than the GMM model. The AMM-based HSI model was further validated by the fishery and environmental data in 2010. The predicted HSI values in 1998 (high catch), 2008 (average catch) and 2009 (low catch) indicated that the squid habitat quality was strongly associated with the ENSO-induced variability in the oceanic conditions on the fishing ground. The La Niña events in 1998 tended to yield warm SST and favorable range of Chl-a concentration and SSHA, resulting in high-quality habitats for O. bartramii. While the fishing ground in the El Niño year of 2009 experienced anomalous cool waters and unfavorable range of Chl-a concentration and SSHA, leading to relatively low-quality squid habitats. Our findings suggest that the La Niña event in 1998 tended to result in more favorable habitats for O. bartramii in the Northwest Pacific with the gravity centers of fishing efforts falling within the defined suitable habitat and yielding high squid catch; whereas the El Niño event in 2009 yielded less favorable habitat areas with the fishing effort distribution mismatching the suitable habitat and a dramatic decline of the catch of O. bartramii. This study might provide some potentially valuable

DNA Sequencing by Capillary Electrophoresis

PubMed Central

Karger, Barry L.; Guttman, Andras

2009-01-01

Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

Sequence search on a supercomputer.

PubMed

Gotoh, O; Tagashira, Y

1986-01-10

A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.

Spectroscopic characterization of C7H3(+) and C7H3˙: electronic absorption and fluorescence in 6 K neon matrices.

PubMed

Chakraborty, Arghya; Fulara, Jan; Dietsche, Rainer; Maier, John P

2014-04-21

Mass selective deposition of C7H3(+) (m/z = 87) into solid neon reveals the 1(1)A1←X(1)A1 electronic absorption system of hepta-1,2,3,4,5,6-heptahexaenylium cation B(+) [H2CCCCCCCH](+) with an origin band at 441.3 nm, 1(1)A'←X(1)A' transition of 2,4-pentadiynylium,1-ethynyl cation C(+) [HCCCHCCCCH](+) starting at 414.6 nm and the 1(1)A1←X(1)A1 one of cyclopropenylium,1,3-butadiynyl cation A(+) [HCCCCC<(CH=CH)](+) with an onset at 322.2 nm. Vibrationally resolved fluorescence was observed for isomer B(+) upon laser excitation of the absorption bands in the 1(1)A1←X(1)A1 transition. After neutralization of the cations in the matrix five absorption systems of the C7H3 neutral radicals starting at 530.3, 479.4, 482.3, 325.0 and 302.5 nm were detected. These were identified as the 1(2)A'←X(2)A' and 2(2)A'←X(2)A' electronic transitions of 2-(buta-1,3-diynyl)cycloprop-2yl-1-1ylidene E˙ [HCCCCC<(C=CH2)]˙, 1(2)B1←X(2)B1 of 1,2,3,4,5,6-heptahexaenyl B˙ [H2CCCCCCCH]˙, 3(2)B1←X(2)B1 of 3-buta-1,3-diynyl-cyclopropenyl A˙ [HCCCCC<(CH=CH)]˙ and 2(2)B1←X(2)A2 transition of 1,2-divinylidene-cyclopropanyl radical F˙ [HCC-cyc-(CCHC)-CCH]˙, respectively. The assignment is based on calculated vertical excitation energies using the CASPT2 method. Comparison of the calculated harmonic vibrational frequencies with those inferred from the spectra supports the assignment.

HIV Sequence Compendium 2015

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

Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian

This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database ismore » still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.« less

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

PubMed Central

2014-01-01

Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

GuiTope: an application for mapping random-sequence peptides to protein sequences.

PubMed

Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

2012-01-03

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

Targeted sequencing of plant genomes

Treesearch

Mark D. Huynh

2014-01-01

Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

Southeast Ecological Observatory Network (SEEON) Workshop on Ecological Sensors and Information Technology. Report on Second SEEON Workshop

NASA Technical Reports Server (NTRS)

Jones, Lori N.; Binford, Michael; Hinkle, Ross C.

2004-01-01

A fundamental goal of the new National Science Foundation (NSF) initiative National Ecological Observatory Network (NEON) is to provide timely and broad access to the ecological data collected at NEON sites. Information management and data collection will be critical components to achieving this goal and a successful NEON implementation. The Southeast Ecological Observatory Network (SEEON) working group recognized the importance of information management and sensor technology in its first planning workshop and recommended that interested parties in the region come together to discuss these subjects in the context of the needs and capabilities of a southeast regional ecological observatory network. In February 2004, 28 participants from 14 organizations including academic institutions, state and federal agencies, private and non-profit entities convened at the Space Life Sciences Laboratory (SLSL) at the Kennedy Space Center, Florida for two days of presentations and discussions on ecological sensors and information management. Some of the participants were previously involved in the first SEEON workshop or other meetings concerned with NEON, but many were somewhat new to the NEON community. Each day focused on a different technical component, i.e. ecological sensors the first day and cyber-infrastructure the second day, and were structured in a similar manner. The mornings were devoted to presentations by experts to help stimulate discussions on aspects of the focal topic held in the afternoon. The formal and informal discussions held during the workshop succeeded in validating some concerns and needs identified in the first SEEON workshop, but also served to bring to light other questions or issues that will need to be addressed as the NEON planning and design stages move forward. While the expansion of the SEEON community meant that some of the presentation and discussion time was needed to help bring the newcomers up to speed on the goals, objectives and current

Chandra Finds Oxygen and Neon Ring in Ashes of Exploded Star

NASA Astrophysics Data System (ADS)

2000-01-01

NASA's Chandra X-ray Observatory has revealed an expanding ring-like structure of oxygen and neon that was hurled into space by the explosion of a massive star. The image of E0102-72 provides unprecedented details about the creation and dispersal of heavy elements necessary to form planets like Earth. The results were reported by Professor Claude Canizares of the Massachusetts Institute of Technology (MIT), Cambridge, at the 195th national meeting of the American Astronomical Society in Atlanta, Ga. Drs. Kathryn Flanagan, David Davis, and John Houck of MIT collaborated with Canizares in this investigation. E0102-72 is the remnant of a supernova explosion located in our neighbor galaxy, the Small Magellanic Cloud, nearly 200,000 light years away. It was created by the explosion of a star that was more than ten times as massive as our Sun. We are seeing the aftermath of the explosion a thousand or more years after the outburst. Shock waves are heating gas to temperatures of nearly 10 million degrees, so it glows with X-rays that are detected by Chandra's instruments. By using the High Energy Transmission Grating Spectrometer (HETG), astronomers were able to pinpoint the distribution of each chemical element individually and measure the velocities of different parts of the expanding ring. They also show the shock wave in a kind of "freeze-frame," revealing the progressive heating of the stellar matter as it plows into the surrounding gas. This is the first time such detailed X-ray information has ever been obtained for a supernova remnant, and should provide critical clues to the nature of supernovas. The grating spectrometer, which was built by an MIT team led by Canizares, spreads the X-rays according to their wavelength, giving distinct images of the object at specific wavelengths characteristic of each chemical element. Small wavelength shifts caused by the Doppler effect are used to measure the expansion velocities of each element independently. "We've been

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

PubMed

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

Pairwise Sequence Alignment Library

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

Jeff Daily, PNNL

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, amore » novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination.

PubMed

Savidor, Alon; Barzilay, Rotem; Elinger, Dalia; Yarden, Yosef; Lindzen, Moshit; Gabashvili, Alexandra; Adiv Tal, Ophir; Levin, Yishai

2017-06-01

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

PubMed

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

"First generation" automated DNA sequencing technology.

PubMed

Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

2011-10-01

Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

The recurrence sequences via Sylvester matrices

NASA Astrophysics Data System (ADS)

Karaduman, Erdal; Deveci, Ömür

2017-07-01

In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

Chip-based sequencing nucleic acids

DOEpatents

Beer, Neil Reginald

2014-08-26

A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

Reversible second-order conditional sequences in incidental sequence learning tasks.

PubMed

Pasquali, Antoine; Cleeremans, Axel; Gaillard, Vinciane

2018-06-01

In sequence learning tasks, participants' sensitivity to the sequential structure of a series of events often overshoots their ability to express relevant knowledge intentionally, as in generation tasks that require participants to produce either the next element of a sequence (inclusion) or a different element (exclusion). Comparing generation performance under inclusion and exclusion conditions makes it possible to assess the respective influences of conscious and unconscious learning. Recently, two main concerns have been expressed concerning such tasks. First, it is often difficult to design control sequences in such a way that they enable clear comparisons with the training material. Second, it is challenging to ask participants to perform appropriately under exclusion instructions, for the requirement to exclude familiar responses often leads them to adopt degenerate strategies (e.g., pushing on the same key all the time), which then need to be specifically singled out as invalid. To overcome both concerns, we introduce reversible second-order conditional (RSOC) sequences and show (a) that they elicit particularly strong transfer effects, (b) that dissociation of implicit and explicit influences becomes possible thanks to the removal of salient transitions in RSOCs, and (c) that exclusion instructions can be greatly simplified without losing sensitivity.

HIV Sequence Compendium 2010

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

Kuiken, Carla; Foley, Brian; Leitner, Thomas

This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is stillmore » increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.« less

Complete genome sequence of southern tomato virus identified from China using next generation sequencing

USDA-ARS?s Scientific Manuscript database

Complete genome sequence of a double-stranded RNA (dsRNA) virus, southern tomato virus (STV), on tomatoes in China, was elucidated using small RNAs deep sequencing. The identified STV_CN12 shares 99% sequence identity to other isolates from Mexico, France, Spain, and U.S. This is the first report ...

Nanopore sequencing in microgravity

PubMed Central

McIntyre, Alexa B R; Rizzardi, Lindsay; Yu, Angela M; Alexander, Noah; Rosen, Gail L; Botkin, Douglas J; Stahl, Sarah E; John, Kristen K; Castro-Wallace, Sarah L; McGrath, Ken; Burton, Aaron S; Feinberg, Andrew P; Mason, Christopher E

2016-01-01

Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space. PMID:28725742

Quantitative phenotyping via deep barcode sequencing.

PubMed

Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

2009-10-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

Quantitative phenotyping via deep barcode sequencing

PubMed Central

Smith, Andrew M.; Heisler, Lawrence E.; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J.; Chee, Mark; Roth, Frederick P.; Giaever, Guri; Nislow, Corey

2009-01-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or “Bar-seq,” outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that ∼20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene–environment interactions on a genome-wide scale. PMID:19622793

The advantages of SMRT sequencing.

PubMed

Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

2013-07-03

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

PubMed

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics.

PubMed

Schilmiller, Anthony L; Miner, Dennis P; Larson, Matthew; McDowell, Eric; Gang, David R; Wilkerson, Curtis; Last, Robert L

2010-07-01

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

MALDI Top-Down sequencing: calling N- and C-terminal protein sequences with high confidence and speed.

PubMed

Suckau, Detlev; Resemann, Anja

2009-12-01

The ability to match Top-Down protein sequencing (TDS) results by MALDI-TOF to protein sequences by classical protein database searching was evaluated in this work. Resulting from these analyses were the protein identity, the simultaneous assignment of the N- and C-termini and protein sequences of up to 70 residues from either terminus. In combination with de novo sequencing using the MALDI-TDS data, even fusion proteins were assigned and the detailed sequence around the fusion site was elucidated. MALDI-TDS allowed to efficiently match protein sequences quickly and to validate recombinant protein structures-in particular, protein termini-on the level of undigested proteins.

Rapid Diagnostics of Onboard Sequences

NASA Technical Reports Server (NTRS)

Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

2012-01-01

Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

78 FR 10640 - Sunshine Act Meetings; Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

... Ecological Observatory Network (NEON) Operations and Maintenance (NSB/CPP-13-3) Action Item: Authorization to... Agreements/Resolutions-- [cir] Directorate for Biological Sciences (BIO), Emerging Frontiers Office (EF): Initial Operations for the National Ecological Observatory Network (NEON) (NSB-13-7) [cir] Directorate for...

WebLogo: A Sequence Logo Generator

PubMed Central

Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc; Brenner, Steven E.

2004-01-01

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. PMID:15173120

Characterization and complete genome sequence of a panicovirus from Bermuda grass by high-throughput sequencing.

PubMed

Tahir, Muhammad N; Lockhart, Ben; Grinstead, Samuel; Mollov, Dimitre

2017-04-01

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high-throughput sequencing (HTS). The nearly full genome sequence of a panicovirus was identified from one HTS scaffold. Sanger sequencing was used to confirm the HTS results and complete the genome sequence of 4404 nt. This virus was provisionally named Bermuda grass latent virus (BGLV). Its predicted open reading frames follow the typical arrangement of the genus Panicovirus. Based on sequence comparisons and phylogenetic analyses BGLV differs from other viruses and therefore taxonomically it is a new member of the genus Panicovirus, family Tombusviridae.

Identification of Sequence Specificity of 5-Methylcytosine Oxidation by Tet1 Protein with High-Throughput Sequencing.

PubMed

Kizaki, Seiichiro; Chandran, Anandhakumar; Sugiyama, Hiroshi

2016-03-02

Tet (ten-eleven translocation) family proteins have the ability to oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC). However, the oxidation reaction of Tet is not understood completely. Evaluation of genomic-level epigenetic changes by Tet protein requires unbiased identification of the highly selective oxidation sites. In this study, we used high-throughput sequencing to investigate the sequence specificity of mC oxidation by Tet1. A 6.6×10(4) -member mC-containing random DNA-sequence library was constructed. The library was subjected to Tet-reactive pulldown followed by high-throughput sequencing. Analysis of the obtained sequence data identified the Tet1-reactive sequences. We identified mCpG as a highly reactive sequence of Tet1 protein. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; ...

2015-04-14

During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequencemore » datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.« less

Haplotype estimation using sequencing reads.

PubMed

Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan

2013-10-03

High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Theta oscillations promote temporal sequence learning.

PubMed

Crivelli-Decker, Jordan; Hsieh, Liang-Tien; Clarke, Alex; Ranganath, Charan

2018-05-17

Many theoretical models suggest that neural oscillations play a role in learning or retrieval of temporal sequences, but the extent to which oscillations support sequence representation remains unclear. To address this question, we used scalp electroencephalography (EEG) to examine oscillatory activity over learning of different object sequences. Participants made semantic decisions on each object as they were presented in a continuous stream. For three "Consistent" sequences, the order of the objects was always fixed. Activity during Consistent sequences was compared to "Random" sequences that consisted of the same objects presented in a different order on each repetition. Over the course of learning, participants made faster semantic decisions to objects in Consistent, as compared to objects in Random sequences. Thus, participants were able to use sequence knowledge to predict upcoming items in Consistent sequences. EEG analyses revealed decreased oscillatory power in the theta (4-7 Hz) band at frontal sites following decisions about objects in Consistent sequences, as compared with objects in Random sequences. The theta power difference between Consistent and Random only emerged in the second half of the task, as participants were more effectively able to predict items in Consistent sequences. Moreover, we found increases in parieto-occipital alpha (10-13 Hz) and beta (14-28 Hz) power during the pre-response period for objects in Consistent sequences, relative to objects in Random sequences. Linear mixed effects modeling revealed that single trial theta oscillations were related to reaction time for future objects in a sequence, whereas beta and alpha oscillations were only predictive of reaction time on the current trial. These results indicate that theta and alpha/beta activity preferentially relate to future and current events, respectively. More generally our findings highlight the importance of band-specific neural oscillations in the learning of

77 FR 65537 - Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-29

... DEPARTMENT OF COMMERCE Patent and Trademark Office Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures ACTION: Proposed collection; comment request... Patent applications that contain nucleotide and/or amino acid sequence disclosures must include a copy of...

Counting Patterns in Degenerated Sequences

NASA Astrophysics Data System (ADS)

Nuel, Grégory

Biological sequences like DNA or proteins, are always obtained through a sequencing process which might produce some uncertainty. As a result, such sequences are usually written in a degenerated alphabet where some symbols may correspond to several possible letters (ex: IUPAC DNA alphabet). When counting patterns in such degenerated sequences, the question that naturally arises is: how to deal with degenerated positions ? Since most (usually 99%) of the positions are not degenerated, it is considered harmless to discard the degenerated positions in order to get an observation, but the exact consequences of such a practice are unclear. In this paper, we introduce a rigorous method to take into account the uncertainty of sequencing for biological sequences (DNA, Proteins). We first introduce a Forward-Backward approach to compute the marginal distribution of the constrained sequence and use it both to perform a Expectation-Maximization estimation of parameters, as well as deriving a heterogeneous Markov distribution for the constrained sequence. This distribution is hence used along with known DFA-based pattern approaches to obtain the exact distribution of the pattern count under the constraints. As an illustration, we consider a EST dataset from the EMBL database. Despite the fact that only 1% of the positions in this dataset are degenerated, we show that not taking into account these positions might lead to erroneous observations, further proving the interest of our approach.

The EMBL nucleotide sequence database

PubMed Central

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Lombard, Vincent; Lopez, Rodrigo; Parkinson, Helen; Redaschi, Nicole; Sterk, Peter; Stoehr, Peter; Tuli, Mary Ann

2001-01-01

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:11125039

Sequencing the Connectome

PubMed Central

Zador, Anthony M.; Dubnau, Joshua; Oyibo, Hassana K.; Zhan, Huiqing; Cao, Gang; Peikon, Ian D.

2012-01-01

Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC (“barcoding of individual neuronal connections”), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale—sequencing billions of nucleotides per day is now routine—is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research. PMID:23109909

Computational analysis of sequence selection mechanisms.

PubMed

Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

2004-04-01

Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

Turtle Graphics of Morphic Sequences

NASA Astrophysics Data System (ADS)

Zantema, Hans

2016-02-01

The simplest infinite sequences that are not ultimately periodic are pure morphic sequences: fixed points of particular morphisms mapping single symbols to strings of symbols. A basic way to visualize a sequence is by a turtle curve: for every alphabet symbol fix an angle, and then consecutively for all sequence elements draw a unit segment and turn the drawing direction by the corresponding angle. This paper investigates turtle curves of pure morphic sequences. In particular, criteria are given for turtle curves being finite (consisting of finitely many segments), and for being fractal or self-similar: it contains an up-scaled copy of itself. Also space-filling turtle curves are considered, and a turtle curve that is dense in the plane. As a particular result we give an exact relationship between the Koch curve and a turtle curve for the Thue-Morse sequence, where until now for such a result only approximations were known.

Insertion Sequences

PubMed Central

Mahillon, Jacques; Chandler, Michael

1998-01-01

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-02-20

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-01-01

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Sequence Factorial and Its Applications

ERIC Educational Resources Information Center

Asiru, Muniru A.

2012-01-01

In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties…

SNMR pulse sequence phase cycling

DOEpatents

Walsh, David O; Grunewald, Elliot D

2013-11-12

Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

(Oncogenic action of ionizing radiation)

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

Not Available

1990-01-01

An extensive experiment involving approximately 400 rats exposed to the neon ion beam at the Bevalac in Berkeley, CA and to electrons is nearing completion. The carcinogenicity of energetic electrons was determined for comparison with the neon ion results. As in past reports we will describe progress in three areas corresponding to the specific aims of the proposal: (1) carcinogenesis and DNA strand breaks in rat skin following exposure by the neon ions or electrons; (2) DNA strand breaks in the epidermis as a function of radiation penetration; (3) oncogene activation in radiation-induced rat skin cancers. 72 refs., 6 tabs.

Chameleon sequences in neurodegenerative diseases.

PubMed

Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

2016-03-25

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

Chameleon sequences in neurodegenerative diseases

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

Bahramali, Golnaz; Goliaei, Bahram, E-mail: goliaei@ut.ac.ir; Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir

2016-03-25

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix tomore » coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.« less

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

Laser Optogalvanic Spectroscopy pf Neon and Argon in a Discharge Plasma and its Significance for Microgravity Combustion

NASA Technical Reports Server (NTRS)

Misra, Prabhakar; Haridass, C.; Major, H.

1999-01-01

information, such as the electron collisional ionization rate, can be extracted from the complex processes occurring within the discharge. In the optogalvanic effect (OGE), there is no problem of overlap from background emissions, and hence even weak signals can be detected with a high signal-to-noise ratio, which makes the optogalvanic effect sensitive enough to resolve vibrational changes in molecular bonds and differences in energy levels brought about by different electron spins. For calibration purposes, neon and argon gaseous discharges have been employed most extensively, because these gases are commonly used as buffer gases within hollow-cathode lamps and provide an acceptable density of calibration lines. In the present work, our main aim has been to understand the dominant physical processes responsible for the production of the OGE signal, based on the extensive time resolved optogalvanic waveforms recorded, and also to extract quantitative information on the rates of excited state collisional processes.

Rover Sequencing and Visualization Program

NASA Technical Reports Server (NTRS)

Cooper, Brian; Hartman, Frank; Maxwell, Scott; Yen, Jeng; Wright, John; Balacuit, Carlos

2005-01-01

The Rover Sequencing and Visualization Program (RSVP) is the software tool for use in the Mars Exploration Rover (MER) mission for planning rover operations and generating command sequences for accomplishing those operations. RSVP combines three-dimensional (3D) visualization for immersive exploration of the operations area, stereoscopic image display for high-resolution examination of the downlinked imagery, and a sophisticated command-sequence editing tool for analysis and completion of the sequences. RSVP is linked with actual flight-code modules for operations rehearsal to provide feedback on the expected behavior of the rover prior to committing to a particular sequence. Playback tools allow for review of both rehearsed rover behavior and downlinked results of actual rover operations. These can be displayed simultaneously for comparison of rehearsed and actual activities for verification. The primary inputs to RSVP are downlink data products from the Operations Storage Server (OSS) and activity plans generated by the science team. The activity plans are high-level goals for the next day s activities. The downlink data products include imagery, terrain models, and telemetered engineering data on rover activities and state. The Rover Sequence Editor (RoSE) component of RSVP performs activity expansion to command sequences, command creation and editing with setting of command parameters, and viewing and management of rover resources. The HyperDrive component of RSVP performs 2D and 3D visualization of the rover s environment, graphical and animated review of rover-predicted and telemetered state, and creation and editing of command sequences related to mobility and Instrument Deployment Device (IDD) operations. Additionally, RoSE and HyperDrive together evaluate command sequences for potential violations of flight and safety rules. The products of RSVP include command sequences for uplink that are stored in the Distributed Object Manager (DOM) and predicted rover

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

PubMed

Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

2018-01-01

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

Comparison of ZP3 protein sequences among vertebrate species: to obtain a consensus sequence for immunocontraception.

PubMed

Zhu, X; Naz, R K

1999-03-01

The deduced ZP3 amino acid (aa) sequences of 13 vertebrate species namely mouse, hamster, rabbit, pig, porcine, cow, dog, cat, human, bonnet, marmoset, carp, and frog were compared using the PILEUP and PRETTY alignment programs (GCG, Wisconsin, USA). The published aa sequences obtained from 13 vertebrate species indicated the overall evolutionarily conservation in the N-terminus, central region, and C-terminus of the ZP3 polypeptide. More variations of ZP3 polypeptide sequences were seen in the alignments of carp and frog from the 11 mammalian species making the leader sequence more prominent. The canonical furin proteolytic processing signal at the C-terminus was found in all the ZP3 polypeptide sequences except of carp and frog. In the central region, the ZP3 deduced aa sequences of all the 13 vertebrate species aligned well, and six relatively conserved sequences were found. There are 11 conserved cysteine residues in the central region across all species including carp and frog, indicating that these residues have longer evolutionary history. The ZP3 aa sequence similarities were examined using the GAP program (GCG). The highest aa similarities are observed between the members of the same order within the class mammalia, and also (95.4%) between pig (ungulata) and rabbit (lagomorpha). The deduced ZP3 aa sequences per se may not be enough to build a phylogenetic tree.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

Sequencing Adventure Activities: A New Perspective.

ERIC Educational Resources Information Center

Bisson, Christian

Sequencing in adventure education involves putting activities in an order appropriate to the needs of the group. Contrary to the common assumption that each adventure sequence is unique, a review of literature concerning five sequencing models reveals a certain universality. These models present sequences that move through four phases: group…

Implicit Sequence Learning in Dyslexia: A Within-Sequence Comparison of First- and Higher-Order Information

ERIC Educational Resources Information Center

Du, Wenchong; Kelly, Steve W.

2013-01-01

The present study examines implicit sequence learning in adult dyslexics with a focus on comparing sequence transitions with different statistical complexities. Learning of a 12-item deterministic sequence was assessed in 12 dyslexic and 12 non-dyslexic university students. Both groups showed equivalent standard reaction time increments when the…

Study on DNA Damage Induced by Neon Beam Irradiation in Saccharomyces Cerevisiae

NASA Astrophysics Data System (ADS)

Lu, Dong; Li, Wenjian; Wu, Xin; Wang, Jufang; Ma, Shuang; Liu, Qingfang; He, Jinyu; Jing, Xigang; Ding, Nan; Dai, Zhongying; Zhou, Jianping

2010-12-01

Yeast strain Saccharomyces cerevisiae was irradiated with different doses of 85 MeV/u 20Ne10+ to investigate DNA damage induced by heavy ion beam in eukaryotic microorganism. The survival rate, DNA double strand breaks (DSBs) and DNA polymorphic were tested after irradiation. The results showed that there were substantial differences in DNA between the control and irradiated samples. At the dose of 40 Gy, the yeast cell survival rate approached 50%, DNA double-strand breaks were barely detectable, and significant DNA polymorphism was observed. The alcohol dehydrogenase II gene was amplified and sequenced. It was observed that base changes in the mutant were mainly transversions of T→G and T→C. It can be concluded that heavy ion beam irradiation can lead to change in single gene and may be an effective way to induce mutation.

Variational Dirac-Hartree-Fock calculation of the Breit interaction

NASA Astrophysics Data System (ADS)

Goldman, S. P.

1988-04-01

The calculation of the retarded version of the Breit interaction in the context of the VDHF method is discussed. With the use of Slater-type basis functions, all the terms involved can be calculated in closed form. The results are expressed as an expansion in powers of one-electron energy differences and linear combinations of hypergeometric functions. Convergence is fast and high accuracy is obtained with a small number of terms in the expansion even for high values of the nuclear charge. An added advantage is that the lowest order cancellations occurring in the retardation terms are accounted for exactly a priori. A comparison of the number of terms in the total expansion needed for an accuracy of 12 significant digits in the total energy, as well as a comparison of the results with an without retardation and in the local potential approximation, are presented for the carbon isoelectronic sequence.

The 2017 Release Cloudy

NASA Astrophysics Data System (ADS)

Ferland, G. J.; Chatzikos, M.; Guzmán, F.; Lykins, M. L.; van Hoof, P. A. M.; Williams, R. J. R.; Abel, N. P.; Badnell, N. R.; Keenan, F. P.; Porter, R. L.; Stancil, P. C.

2017-10-01

We describe the 2017 release of the spectral synthesis code Cloudy, summarizing the many improvements to the scope and accuracy of the physics which have been made since the previous release. Exporting the atomic data into external data files has enabled many new large datasets to be incorporated into the code. The use of the complete datasets is not realistic for most calculations, so we describe the limited subset of data used by default, which predicts significantly more lines than the previous release of Cloudy. This version is nevertheless faster than the previous release, as a result of code optimizations. We give examples of the accuracy limits using small models, and the performance requirements of large complete models. We summarize several advances in the H- and He-like iso-electronic sequences and use our complete collisional-radiative models to establish the densities where the coronal and local thermodynamic equilibrium approximations work.

Manganese-Catalyzed Aminomethylation of Aromatic Compounds with Methanol as a Sustainable C1 Building Block.

PubMed

Mastalir, Matthias; Pittenauer, Ernst; Allmaier, Günter; Kirchner, Karl

2017-07-05

This study represents the first example of a manganese-catalyzed environmentally benign, practical three-component aminomethylation of activated aromatic compounds including naphtols, phenols, pyridines, indoles, carbazoles, and thiophenes in combination with amines and MeOH as a C1 source. These reactions proceed with high atom efficiency via a sequence of dehydrogenation and condensation steps which give rise to selective C-C and C-N bond formations, thereby releasing hydrogen and water. A well-defined hydride Mn(I) PNP pincer complex, recently developed in our laboratory, catalyzes this process in a very efficient way, and a total of 28 different aminomethylated products were synthesized and isolated yields of up to 91%. In a preliminary study, a related Fe(II) PNP pincer complex was shown to catalyze the methylation of 2-naphtol rather than its aminomethylation displaying again the divergent behavior of isoelectronic Mn(I) and Fe(II) PNP pincer systems.

Hylleraas-Configuration Interaction study of the 1S ground state of the negative Li ion.

PubMed

Sims, James S

2017-12-28

In a previous work Sims and Hagstrom [J. Chem. Phys. 140, 224312 (2014)] reported Hylleraas-Configuration Interaction (Hy-CI) method variational calculations for the neutral atom and positive ion 1 S ground states of the beryllium isoelectronic sequence. The Li - ion, nominally the first member of this series, has a decidedly different electronic structure. This paper reports the results of a large, comparable calculation for the Li - ground state to explore how well the Hy-CI method can represent the more diffuse L shell of Li - which is representative of the Be(2sns) excited states as well. The best non-relativistic energy obtained was -7.500 776 596 hartree, indicating that 10 - 20 nh accuracy is attainable in Hy-CI and that convergence of the r 12 r 34 double cusp is fast and that this correlation type can be accurately represented within the Hy-CI model.

Teaching Task Sequencing via Verbal Mediation.

ERIC Educational Resources Information Center

Rusch, Frank R.; And Others

1987-01-01

Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

Compressing DNA sequence databases with coil.

PubMed

White, W Timothy J; Hendy, Michael D

2008-05-20

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

Elimination sequence optimization for SPAR

NASA Technical Reports Server (NTRS)

Hogan, Harry A.

1986-01-01

SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Treesearch

Richard Cronn; Aaron Liston; Matthew Parks; David S. Gernandt; Rongkun Shen; Todd Mockler

2008-01-01

Organellar DNA sequences are widely used in evolutionary and population genetic studies; however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to...

Cerebellar activation during motor sequence learning is associated with subsequent transfer to new sequences.

PubMed

Shimizu, Renee E; Wu, Allan D; Knowlton, Barbara J

2016-12-01

Effective learning results not only in improved performance on a practiced task, but also in the ability to transfer the acquired knowledge to novel, similar tasks. Using a modified serial reaction time (RT) task, the authors examined the ability to transfer to novel sequences after practicing sequences in a repetitive order versus a nonrepeating interleaved order. Interleaved practice resulted in better performance on new sequences than repetitive practice. In a second study, participants practiced interleaved sequences in a functional MRI (fMRI) scanner and received a transfer test of novel sequences. Transfer ability was positively correlated with cerebellar blood oxygen level dependent activity during practice, indicating that greater cerebellar engagement during training resulted in better subsequent transfer performance. Interleaved practice may thus result in a more generalized representation that is robust to interference, and the degree of activation in the cerebellum may be a reflection of the instantiation and engagement of internal models. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

NEON VISUALIZATION ENVIRONMENT

DTIC Science & Technology

2017-07-28

STINFO COPY AIR FORCE RESEARCH LABORATORY INFORMATION DIRECTORATE AFRL-RI-RS-TR-2017-143  UNITED STATES AIR FORCE  ROME, NY 13441 AIR FORCE...report is available to the general public, including foreign nationals. Copies may be obtained from the Defense Technical Information Center (DTIC) (http...FOR THE CHIEF ENGINEER: / S / / S / PETER A. JEDRYSIK JULIE BRICHACEK Work Unit Manager Chief, Information Systems Division Information

Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae

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

Buchman, A.R.; Kimmerly, W.J.; Rine, J.

1988-01-01

Two DNA-binding factors from Saccharomyces cerevisiae have been characterized, GRFI (general regulatory factor I) and ABFI (ARS-binding factor I), that recognize specific sequences within diverse genetic elements. GRFI bound to sequences at the negative regulatory elements (silencers) of the silent mating type loci HML E and HMR E and to the upstream activating sequence (UAS) required for transcription of the MAT ..cap alpha.. genes. A putative conserved UAS located at genes involved in translation (RPG box) was also recognized by GRFI. In addition, GRFI bound with high affinity to sequences within the (C/sub 1-3/A)-repeat region at yeast telomeres. Binding sitesmore » for GRFI with the highest affinity appeared to be of the form 5'-(A/G)(A/C)ACCCAN NCA(T/C)(T/C)-3', where N is any nucleotide. ABFI-binding sites were located next to autonomously replicating sequences (ARSs) at controlling elements of the silent mating type loci HMR E, HMR I, and HML I and were associated with ARS1, ARS2, and the 2..mu..m plasmid ARS. Two tandem ABFI binding sites were found between the HIS3 and DED1 genes, several kilobase pairs from any ARS, indicating that ABFI-binding sites are not restricted to ARSs. The sequences recognized by AFBI showed partial dyad-symmetry and appeared to be variations of the consensus 5'-TATCATTNNNNACGA-3'. GRFI and ABFI were both abundant DNA-binding factors and did not appear to be encoded by the SIR genes, whose product are required for repression of the silent mating type loci. Together, these results indicate that both GRFI and ABFI play multiple roles within the cell.« less

Sequencing Technologies Panel at SFAF