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Sample records for unbiased moment-rate spectra

  1. UNBIASED MOMENT-RATE SPECTRA AND ABSOLUTE SITE EFFECTS IN THE KACHCHH BASIN, INDIA, FROM THE ANALYSIS OF THE AFTERSHOCKS OF THE 2001 Mw 7.6 BHUJ EARTHQUAKE

    SciTech Connect

    Malagnini, L; Bodin, P; Mayeda, K; Akinci, A

    2005-05-04

    What can be learned about absolute site effects on ground motions and about earthquake source spectra from recordings at temporary seismic stations, none of which could be considered a 'reference' (hard rock) site, for which no geotechnical information is available, in a very poorly instrumented region? This challenge motivated our current study of aftershocks of the 2001 Mw 7.6 Bhuj earthquake, in Western India. Crustal attenuation and spreading relationships based on the same data used here were determined in an earlier study. In this paper we decouple the ambiguity between absolute source radiation and site effects by first computing robust estimates of moment-rate spectra of about 200 aftershocks in each of two depth ranges. Using these new estimates of sourcespectra, and our understanding of regional wave propagation, we extract the absolute site terms of the sites of the temporary deployment. Absolute site terms (one for each component of the ground motion, for each station) are computed in an average sense, via an L{sub 1}-norm minimization, and results for each site are averaged over wide ranges of azimuths and takeoff angles. The Bhuj deployment is characterized by a variable shallow geology, mostly of soft sedimentary units. Vertical site terms in the region were observed to be almost featureless and slightly < 1.0 within wide frequency ranges. As a result, H/V spectral ratios mimic the absolute behaviors of absolute horizontal site terms, and they generally overpredict them. On the contrary, with respect to the results for sedimentary rock sites (limestone, dolomite) obtained by Malagnini et al. (2004), H/V spectral ratios in their study did not have much in common with absolute horizontal site terms. Spectral ratios between the vector sum of the computed horizontal site terms for the temporary deployment with respect to the same quantity computed at the hardest rock station available, BAC1, are seriously biased by its non-flat, non-unitary site response

  2. Covariant mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Schultz, Jussi; Toigo, Alessandro

    2016-06-01

    The connection between maximal sets of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space and finite phase-space geometries is well known. In this article, we classify MUBs according to their degree of covariance with respect to the natural symmetries of a finite phase-space, which are the group of its affine symplectic transformations. We prove that there exist maximal sets of MUBs that are covariant with respect to the full group only in odd prime-power dimensional spaces, and in this case, their equivalence class is actually unique. Despite this limitation, we show that in dimension 2r covariance can still be achieved by restricting to proper subgroups of the symplectic group, that constitute the finite analogues of the oscillator group. For these subgroups, we explicitly construct the unitary operators yielding the covariance.

  3. Variations in slow slip moment rate associated with rapid tremor reversals in Cascadia

    NASA Astrophysics Data System (ADS)

    Hawthorne, Jessica C.; Bostock, Michael G.; Royer, Alexandra A.; Thomas, Amanda M.

    2016-12-01

    During large slow slip events, tremor sometimes propagates in the reverse along-strike direction for a few hours, at speeds 10 to 40 times faster than the forward propagation. We examine the aseismic slip that underlies this rapidly propagating tremor. We use PBO (Plate Boundary Observatory) borehole strainmeter data to search for variations in the slow slip moment rate during 35 rapid tremor reversals (RTRs) that occurred beneath Vancouver Island. The strain records reveal that, on average, the strain rate increases by about 100% (±30%) during RTRs. Given the Green's functions expected for slip in the RTR locations, these strain rate increases imply 50 to 130% increases in the aseismic moment rate. The median moment released per RTR is between 8 and 21% of the daily slow slip moment, equivalent to that of a MW 5.0 to 5.1 earthquake. By combining the RTR moments with the spatial extents suggested by tremor, we estimate that a typical RTR has peak slip of roughly one-sixth of the peak slip in the main slow slip event, near-front slip rate of a few to ten times the main front slip rate, stress drop around half the main event stress drop, and strain energy release rate around one-tenth that of the main front. Our observations support a picture of RTRs as aseismic subevents with high slip rates but modest strain energy release. RTRs appear to contribute to but not dominate the overall slow slip moment, though they may accommodate most of the slip in certain locations.

  4. Clifford tori and unbiased vectors

    NASA Astrophysics Data System (ADS)

    Andersson, Ole; Bengtsson, Ingemar

    2017-02-01

    The existence problem for mutually unbiased bases is an unsolved problem in quantum information theory. A related question is whether every pair of bases admits vectors that are unbiased to both. Mathematically this translates to the question whether two Lagrangian Clifford tori intersect, and a body of results exists concerning it. These results are however rather weak from the point of view of the first problem. We make a detailed study of how the intersections behave in the simplest nontrivial case, that of complex projective 2-space (the qutrit), for which the set of pairs of Clifford tori can be usefully parametrized by the unistochastic subset of Birkhoff's polytope. Pairs that do not intersect transversally are located. Some calculations in higher dimensions are included to see which results are special to the qutrit.

  5. On the consistency of earthquake moment rates, geological fault data, and space geodetic strain: the United States

    NASA Astrophysics Data System (ADS)

    Ward, Steven N.

    1998-07-01

    New and dense space geodetic data can now map strain rates over continental-wide areas with a useful degree of precision. Stable strain indicators open the door for space geodesy to join with geology and seismology in formulating improved estimates of global earthquake recurrence. In this paper, 174 GPS/VLBI velocities map United States' strain rates of <0.03 to >30.0 × 10-8 yr-1 with regional uncertainties of 5 to 50 per cent. Kostrov's formula translates these strain values into regional geodetic moment rates. Two other moment rates M⊙seismic and M⊙geologic , extracted from historical earthquake and geological fault catalogues, contrast the geodetic rate. Because M⊙geologic , M⊙seismic and M⊙geodetic derive from different views of the earthquake engine, each illuminates different features. In California, the ratio of M⊙geodetic to M⊙geologic is 1.20. The near-unit ratio points to the completeness of the region's geological fault data and to the reliability of geodetic measurements there. In the Basin and Range, northwest and central United States, both M⊙geodetic and M⊙seismic greatly exceed M⊙geologic. Of possible causes, high incidences of understated and unrecognized faults probably drive the inconsistency. The ratio of M⊙seismic to M⊙geodetic is everywhere less than one. The ratio runs systematically from 70-80 per cent in the fastest straining regions to 2 per cent in the slowest. Although aseismic deformation may contribute to this shortfall, I argue that the existing seismic catalogues fail to reflect the long-term situation. Impelled by the systematic variation of seismic to geodetic moment rates and by the uniform strain drop observed in all earthquakes regardless of magnitude, I propose that the completeness of any seismic catalogue hinges on the product of observation duration and regional strain rate. Slowly straining regions require a proportionally longer period of observation. Characterized by this product, gamma

  6. Mutually unbiased bases and generalized Bell states

    SciTech Connect

    Klimov, Andrei B.; Sych, Denis; Sanchez-Soto, Luis L.; Leuchs, Gerd

    2009-05-15

    We employ a straightforward relation between mutually unbiased and Bell bases to extend the latter in terms of a direct construction for the former. We analyze in detail the properties of these generalized Bell states, showing that they constitute an appropriate tool for testing entanglement in bipartite multiqudit systems.

  7. Moment rate scaling for earthquakes 3.3 ≤ M ≤ 5.3 with implications for stress drop

    NASA Astrophysics Data System (ADS)

    Archuleta, Ralph J.; Ji, Chen

    2016-12-01

    We have determined a scalable apparent moment rate function (aMRF) that correctly predicts the peak ground acceleration (PGA), peak ground velocity (PGV), local magnitude, and the ratio of PGA/PGV for earthquakes 3.3 ≤ M ≤ 5.3. Using the NGA-West2 database for 3.0 ≤ M ≤ 7.7, we find a break in scaling of LogPGA and LogPGV versus M around M 5.3 with nearly linear scaling for LogPGA and LogPGV for 3.3 ≤ M ≤ 5.3. Temporal parameters tp and td—related to rise time and total duration—control the aMRF. Both scale with seismic moment. The Fourier amplitude spectrum of the aMRF has two corners between which the spectrum decays f- 1. Significant attenuation along the raypath results in a Brune-like spectrum with one corner fC. Assuming that fC ≅ 1/td, the aMRF predicts non-self-similar scaling M0∝fC3.3 and weak stress drop scaling Δσ∝M00.091. This aMRF can explain why stress drop is different from the stress parameter used to predict high-frequency ground motion.

  8. Seismic Moment Rate Function Inversions from Very Long Period Signals Associated with Strombolian Eruptions at Mount Erebus, Antarctica

    NASA Astrophysics Data System (ADS)

    Lucero, C.; Aster, R. C.; Borchers, B.; Kyle, P.

    2005-12-01

    Mount Erebus, Antarctica, shows persistent Strombolian activity, principally in the form of impulsive eruptions of simple and very large (up to 10 m diameter) gas bubbles through its long-lived phonolitic lava lake. Eruptions produce oscillatory near-field very long period (VLP; ~8-20 s period) seismic signals due to processes occurring (seconds) before, during, and (up to several minutes) following the characteristic bubble bursts that mark the onset of short period (>1 Hz) seismoacoustic signals. Coupled broadband seismoacoustic and video analysis shows that this signal is associated with three corresponding component processes: 1) the bubble ascent phase characterized by gas/lava mass transport within the conduit system that can produce a positive or negative vertical rate of momentum change, depending on the event; 2) the eruptive evisceration of the lava lake to a depth of up to 10's of m in the explosive surface decompression of the gas bubble; 3) the refilling and reestablishment gravitational equilibrium within the conduit system. We employ a new method for efficiently solving the inverse problem of finding either independent or proportional moment-tensor element rate functions using three-component near-field seismograms recorded at multiple seismic stations. The method incorporates a frequency-domain deconvolution that, in its most general formulation, solves for six independent moment rate tensor force couple time functions plus a vertical force time function. We present an efficient scheme for solving this problem using conjugate gradient methods and apply it to Erebus VLP signals from the past several years of activity.

  9. Unbiased sampling of lattice Hamilton path ensembles

    NASA Astrophysics Data System (ADS)

    Mansfield, Marc L.

    2006-10-01

    Hamilton paths, or Hamiltonian paths, are walks on a lattice which visit each site exactly once. They have been proposed as models of globular proteins and of compact polymers. A previously published algorithm [Mansfield, Macromolecules 27, 5924 (1994)] for sampling Hamilton paths on simple square and simple cubic lattices is tested for bias and for efficiency. Because the algorithm is a Metropolis Monte Carlo technique obviously satisfying detailed balance, we need only demonstrate ergodicity to ensure unbiased sampling. Two different tests for ergodicity (exact enumeration on small lattices, nonexhaustive enumeration on larger lattices) demonstrate ergodicity unequivocally for small lattices and provide strong support for ergodicity on larger lattices. Two other sampling algorithms [Ramakrishnan et al., J. Chem. Phys. 103, 7592 (1995); Lua et al., Polymer 45, 717 (2004)] are both known to produce biases on both 2×2×2 and 3×3×3 lattices, but it is shown here that the current algorithm gives unbiased sampling on these same lattices. Successive Hamilton paths are strongly correlated, so that many iterations are required between statistically independent samples. Rules for estimating the number of iterations needed to dissipate these correlations are given. However, the iteration time is so fast that the efficiency is still very good except on extremely large lattices. For example, even on lattices of total size 10×10×10 we are able to generate tens of thousands of uncorrelated Hamilton paths per hour of CPU time.

  10. Uncertainty relation based on unbiased parameter estimations

    NASA Astrophysics Data System (ADS)

    Sun, Liang-Liang; Song, Yong-Shun; Qiao, Cong-Feng; Yu, Sixia; Chen, Zeng-Bing

    2017-02-01

    Heisenberg's uncertainty relation has been extensively studied in spirit of its well-known original form, in which the inaccuracy measures used exhibit some controversial properties and don't conform with quantum metrology, where the measurement precision is well defined in terms of estimation theory. In this paper, we treat the joint measurement of incompatible observables as a parameter estimation problem, i.e., estimating the parameters characterizing the statistics of the incompatible observables. Our crucial observation is that, in a sequential measurement scenario, the bias induced by the first unbiased measurement in the subsequent measurement can be eradicated by the information acquired, allowing one to extract unbiased information of the second measurement of an incompatible observable. In terms of Fisher information we propose a kind of information comparison measure and explore various types of trade-offs between the information gains and measurement precisions, which interpret the uncertainty relation as surplus variance trade-off over individual perfect measurements instead of a constraint on extracting complete information of incompatible observables.

  11. Personalized recommendation based on unbiased consistence

    NASA Astrophysics Data System (ADS)

    Zhu, Xuzhen; Tian, Hui; Zhang, Ping; Hu, Zheng; Zhou, Tao

    2015-08-01

    Recently, in physical dynamics, mass-diffusion-based recommendation algorithms on bipartite network provide an efficient solution by automatically pushing possible relevant items to users according to their past preferences. However, traditional mass-diffusion-based algorithms just focus on unidirectional mass diffusion from objects having been collected to those which should be recommended, resulting in a biased causal similarity estimation and not-so-good performance. In this letter, we argue that in many cases, a user's interests are stable, and thus bidirectional mass diffusion abilities, no matter originated from objects having been collected or from those which should be recommended, should be consistently powerful, showing unbiased consistence. We further propose a consistence-based mass diffusion algorithm via bidirectional diffusion against biased causality, outperforming the state-of-the-art recommendation algorithms in disparate real data sets, including Netflix, MovieLens, Amazon and Rate Your Music.

  12. Decision rules for unbiased inventory estimates

    NASA Technical Reports Server (NTRS)

    Argentiero, P. D.; Koch, D.

    1979-01-01

    An efficient and accurate procedure for estimating inventories from remote sensing scenes is presented. In place of the conventional and expensive full dimensional Bayes decision rule, a one-dimensional feature extraction and classification technique was employed. It is shown that this efficient decision rule can be used to develop unbiased inventory estimates and that for large sample sizes typical of satellite derived remote sensing scenes, resulting accuracies are comparable or superior to more expensive alternative procedures. Mathematical details of the procedure are provided in the body of the report and in the appendix. Results of a numerical simulation of the technique using statistics obtained from an observed LANDSAT scene are included. The simulation demonstrates the effectiveness of the technique in computing accurate inventory estimates.

  13. Efficient and Unbiased Estimation of Population Size

    PubMed Central

    Cruz, Marcos; Gómez, Domingo; Cruz-Orive, Luis M.

    2015-01-01

    Population sizing from still aerial pictures is of wide applicability in ecological and social sciences. The problem is long standing because current automatic detection and counting algorithms are known to fail in most cases, and exhaustive manual counting is tedious, slow, difficult to verify and unfeasible for large populations. An alternative is to multiply population density with some reference area but, unfortunately, sampling details, handling of edge effects, etc., are seldom described. For the first time we address the problem using principles of geometric sampling. These principles are old and solid, but largely unknown outside the areas of three dimensional microscopy and stereology. Here we adapt them to estimate the size of any population of individuals lying on an essentially planar area, e.g. people, animals, trees on a savanna, etc. The proposed design is unbiased irrespective of population size, pattern, perspective artifacts, etc. The implementation is very simple—it is based on the random superimposition of coarse quadrat grids. Also, an objective error assessment is often lacking. For the latter purpose the quadrat counts are often assumed to be independent. We demonstrate that this approach can perform very poorly, and we propose (and check via Monte Carlo resampling) a new theoretical error prediction formula. As far as efficiency, counting about 50 (100) individuals in 20 quadrats, can yield relative standard errors of about 8% (5%) in typical cases. This fact effectively breaks the barrier hitherto imposed by the current lack of automatic face detection algorithms, because semiautomatic sampling and manual counting becomes an attractive option. PMID:26535587

  14. Entanglement patterns in mutually unbiased basis sets

    SciTech Connect

    Lawrence, Jay

    2011-08-15

    A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=p{sup N}), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (p{sup N}-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (p{sup N}-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.

  15. Building unbiased estimators from non-gaussian likelihoods with application to shear estimation

    SciTech Connect

    Madhavacheril, Mathew S.; McDonald, Patrick; Sehgal, Neelima; Slosar, Anze

    2015-01-15

    We develop a general framework for generating estimators of a given quantity which are unbiased to a given order in the difference between the true value of the underlying quantity and the fiducial position in theory space around which we expand the likelihood. We apply this formalism to rederive the optimal quadratic estimator and show how the replacement of the second derivative matrix with the Fisher matrix is a generic way of creating an unbiased estimator (assuming choice of the fiducial model is independent of data). Next we apply the approach to estimation of shear lensing, closely following the work of Bernstein and Armstrong (2014). Our first order estimator reduces to their estimator in the limit of zero shear, but it also naturally allows for the case of non-constant shear and the easy calculation of correlation functions or power spectra using standard methods. Both our first-order estimator and Bernstein and Armstrong’s estimator exhibit a bias which is quadratic in true shear. Our third-order estimator is, at least in the realm of the toy problem of Bernstein and Armstrong, unbiased to 0.1% in relative shear errors Δg/g for shears up to |g| = 0.2.

  16. Building unbiased estimators from non-gaussian likelihoods with application to shear estimation

    DOE PAGES

    Madhavacheril, Mathew S.; McDonald, Patrick; Sehgal, Neelima; ...

    2015-01-15

    We develop a general framework for generating estimators of a given quantity which are unbiased to a given order in the difference between the true value of the underlying quantity and the fiducial position in theory space around which we expand the likelihood. We apply this formalism to rederive the optimal quadratic estimator and show how the replacement of the second derivative matrix with the Fisher matrix is a generic way of creating an unbiased estimator (assuming choice of the fiducial model is independent of data). Next we apply the approach to estimation of shear lensing, closely following the workmore » of Bernstein and Armstrong (2014). Our first order estimator reduces to their estimator in the limit of zero shear, but it also naturally allows for the case of non-constant shear and the easy calculation of correlation functions or power spectra using standard methods. Both our first-order estimator and Bernstein and Armstrong’s estimator exhibit a bias which is quadratic in true shear. Our third-order estimator is, at least in the realm of the toy problem of Bernstein and Armstrong, unbiased to 0.1% in relative shear errors Δg/g for shears up to |g| = 0.2.« less

  17. Quantum process reconstruction based on mutually unbiased basis

    SciTech Connect

    Fernandez-Perez, A.; Saavedra, C.; Klimov, A. B.

    2011-05-15

    We study a quantum process reconstruction based on the use of mutually unbiased projectors (MUB projectors) as input states for a D-dimensional quantum system, with D being a power of a prime number. This approach connects the results of quantum-state tomography using mutually unbiased bases with the coefficients of a quantum process, expanded in terms of MUB projectors. We also study the performance of the reconstruction scheme against random errors when measuring probabilities at the MUB projectors.

  18. Separability criteria via sets of mutually unbiased measurements.

    PubMed

    Liu, Lu; Gao, Ting; Yan, Fengli

    2015-08-17

    Mutually unbiased measurements (MUMs) are generalized from the concept of mutually unbiased bases (MUBs) and include the complete set of MUBs as a special case, but they are superior to MUBs as they do not need to be rank one projectors. We investigate entanglement detection using sets of MUMs and derive separability criteria for multipartite qudit systems, arbitrary high-dimensional bipartite systems of a d1-dimensional subsystem and a d2-dimensional subsystem, and multipartite systems of multi-level subsystems. These criteria are of the advantages of more effective and wider application range than previous criteria. They provide experimental implementation in detecting entanglement of unknown quantum states.

  19. Unbiased Estimates of Variance Components with Bootstrap Procedures

    ERIC Educational Resources Information Center

    Brennan, Robert L.

    2007-01-01

    This article provides general procedures for obtaining unbiased estimates of variance components for any random-model balanced design under any bootstrap sampling plan, with the focus on designs of the type typically used in generalizability theory. The results reported here are particularly helpful when the bootstrap is used to estimate standard…

  20. Improving quantum state estimation with mutually unbiased bases.

    PubMed

    Adamson, R B A; Steinberg, A M

    2010-07-16

    When used in quantum state estimation, projections onto mutually unbiased bases have the ability to maximize information extraction per measurement and to minimize redundancy. We present the first experimental demonstration of quantum state tomography of two-qubit polarization states to take advantage of mutually unbiased bases. We demonstrate improved state estimation as compared to standard measurement strategies and discuss how this can be understood from the structure of the measurements we use. We experimentally compared our method to the standard state estimation method for three different states and observe that the infidelity was up to 1.84 ± 0.06 times lower by using our technique than it was by using standard state estimation methods.

  1. Unbiased estimators for spatial distribution functions of classical fluids.

    PubMed

    Adib, Artur B; Jarzynski, Christopher

    2005-01-01

    We use a statistical-mechanical identity closely related to the familiar virial theorem, to derive unbiased estimators for spatial distribution functions of classical fluids. In particular, we obtain estimators for both the fluid density rho(r) in the vicinity of a fixed solute and the pair correlation g(r) of a homogeneous classical fluid. We illustrate the utility of our estimators with numerical examples, which reveal advantages over traditional histogram-based methods of computing such distributions.

  2. Unbiased Estimation of Refractive State of Aberrated Eyes

    PubMed Central

    Martin, Jesson; Vasudevan, Balamurali; Himebaugh, Nikole; Bradley, Arthur; Thibos, Larry

    2011-01-01

    To identify unbiased methods for estimating the target vergence required to maximize visual acuity based on wavefront aberration measurements. Experiments were designed to minimize the impact of confounding factors that have hampered previous research. Objective wavefront refractions and subjective acuity refractions were obtained for the same monochromatic wavelength. Accommodation and pupil fluctuations were eliminated by cycloplegia. Unbiased subjective refractions that maximize visual acuity for high contrast letters were performed with a computer controlled forced choice staircase procedure, using 0.125 diopter steps of defocus. All experiments were performed for two pupil diameters (3mm and 6mm). As reported in the literature, subjective refractive error does not change appreciably when the pupil dilates. For 3 mm pupils most metrics yielded objective refractions that were about 0.1D more hyperopic than subjective acuity refractions. When pupil diameter increased to 6 mm, this bias changed in the myopic direction and the variability between metrics also increased. These inaccuracies were small compared to the precision of the measurements, which implies that most metrics provided unbiased estimates of refractive state for medium and large pupils. A variety of image quality metrics may be used to determine ocular refractive state for monochromatic (635nm) light, thereby achieving accurate results without the need for empirical correction factors. PMID:21777601

  3. Toward automated quantification of biological microstructures using unbiased stereology

    NASA Astrophysics Data System (ADS)

    Bonam, Om P.; Elozory, Daniel; Kramer, Kurt; Goldgof, Dmitry; Hall, Lawrence O.; Mangual, Osvaldo; Mouton, Peter R.

    2011-03-01

    Quantitative analysis of biological microstructures using unbiased stereology plays a large and growing role in bioscience research. Our aim is to add a fully automatic, high-throughput mode to a commercially available, computerized stereology device (Stereologer). The current method for estimation of first- and second order parameters of biological microstructures, requires a trained user to manually select objects of interest (cells, fibers etc.,) while stepping through the depth of a stained tissue section in fixed intervals. The proposed approach uses a combination of color and gray-level processing. Color processing is used to identify the objects of interest, by training on the images to obtain the threshold range for objects of interest. In gray-level processing, a region-growing approach was used to assign a unique identity to the objects of interest and enumerate them. This automatic approach achieved an overall object detection rate of 93.27%. Thus, these results support the view that automatic color and gray-level processing combined with unbiased sampling and assumption and model-free geometric probes can provide accurate and efficient quantification of biological objects.

  4. Unbiased water and methanol maser surveys of NGC 1333

    SciTech Connect

    Lyo, A-Ran; Kim, Jongsoo; Byun, Do-Young; Lee, Ho-Gyu

    2014-11-01

    We present the results of unbiased 22 GHz H{sub 2}O water and 44 GHz class I CH{sub 3}OH methanol maser surveys in the central 7' × 10' area of NGC 1333 and two additional mapping observations of a 22 GHz water maser in a ∼3' × 3' area of the IRAS4A region. In the 22 GHz water maser survey of NGC 1333 with a sensitivity of σ ∼ 0.3 Jy, we confirmed the detection of masers toward H{sub 2}O(B) in the region of HH 7-11 and IRAS4B. We also detected new water masers located ∼20'' away in the western direction of IRAS4B or ∼25'' away in the southern direction of IRAS4A. We could not, however, find young stellar objects or molecular outflows associated with them. They showed two different velocity components of ∼0 and ∼16 km s{sup –1}, which are blue- and redshifted relative to the adopted systemic velocity of ∼7 km s{sup –1} for NGC 1333. They also showed time variabilities in both intensity and velocity from multi-epoch observations and an anti-correlation between the intensities of the blue- and redshifted velocity components. We suggest that the unidentified power source of these masers might be found in the earliest evolutionary stage of star formation, before the onset of molecular outflows. Finding this kind of water maser is only possible through an unbiased blind survey. In the 44 GHz methanol maser survey with a sensitivity of σ ∼ 0.5 Jy, we confirmed masers toward IRAS4A2 and the eastern shock region of IRAS2A. Both sources are also detected in 95 and 132 GHz methanol maser lines. In addition, we had new detections of methanol masers at 95 and 132 GHz toward IRAS4B. In terms of the isotropic luminosity, we detected methanol maser sources brighter than ∼5 × 10{sup 25} erg s{sup –1} from our unbiased survey.

  5. Unbiased atlas formation via large deformations metric mapping.

    PubMed

    Lorenzen, Peter; Davis, Brad; Joshi, Sarang

    2005-01-01

    The construction of population atlases is a key issue in medical image analysis, and particularly in brain mapping. Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and to facilitate tissue and object segmentation via registration of anatomical labels. We formulate the unbiased atlas construction problem as a Fréchet mean estimation in the space of diffeomorphisms via large deformations metric mapping. A novel method for computing constant speed velocity fields and an analysis of atlas stability and robustness using entropy are presented. We address the question: how many images are required to build a stable brain atlas?

  6. Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

    PubMed Central

    Matranga, Christian B.; Gladden-Young, Adrianne; Qu, James; Winnicki, Sarah; Nosamiefan, Dolo; Levin, Joshua Z.; Sabeti, Pardis C.

    2016-01-01

    Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from clinical and biological sources. The method is unbiased and universal; it uses random primers for cDNA synthesis and requires no prior knowledge of the viral sequence content. Before library construction, selective RNase H-based digestion is used to deplete unwanted RNA — including poly(rA) carrier and ribosomal RNA — from the viral RNA sample. Selective depletion improves both the data quality and the number of unique reads in viral RNA sequencing libraries. Moreover, a transposase-based 'tagmentation' step is used in the protocol as it reduces overall library construction time. The protocol has enabled rapid deep sequencing of over 600 Lassa and Ebola virus samples-including collections from both blood and tissue isolates-and is broadly applicable to other microbial genomics studies. PMID:27403729

  7. Unbiased approaches to biomarker discovery in neurodegenerative diseases

    PubMed Central

    Chen-Plotkin, Alice S.

    2014-01-01

    Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, and frontotemporal dementia have several important features in common. They are progressive, they affect a relatively inaccessible organ, and we have no disease-modifying therapies for them. For these brain-based diseases, current diagnosis and evaluation of disease severity rely almost entirely on clinical examination, which may only be a rough approximation of disease state. Thus, the development of biomarkers – objective, relatively easily measured and precise indicators of pathogenic processes – could improve patient care and accelerate therapeutic discovery. Yet existing, rigorously tested neurodegenerative disease biomarkers are few, and even fewer biomarkers have translated into clinical use. To find new biomarkers for these diseases, an unbiased, high-throughput screening approach may be needed. In this review, I will describe the potential utility of such an approach to biomarker discovery, using Parkinson’s disease as a case example. PMID:25442938

  8. Galois-unitary operators that cycle mutually-unbiased bases

    NASA Astrophysics Data System (ADS)

    Dang, Hoan; Appleby, Marcus; Bengtsson, Ingemar

    2015-03-01

    Wigner's theorem states that probability-preserving transformations of quantum states must be either unitary or anti-unitary. However, if we restrict ourselves to a subspace of a Hilbert space, it is possible to generalize the notion of anti-unitaries. Such transformations were recently constructed in search of Symmetric Informationally-Complete (SIC) states. They are called Galois-unitaries (g-unitaries for short), as they are unitaries composed with Galois automorphisms of a chosen number field extension. Despite certain bizarre behaviors of theirs, we show that g-unitaries are indeed useful in the theory of Mutually-Unbiased Bases (MUBs), as they help solve the MUB-cycling problem and provide a construction of MUB-balanced states. HD was supported by the Natural Sciences and Engineering Research Council of Canada and the Vanier Canada Graduate Scholarship

  9. An analytic function approach to weak mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Olupitan, T.; Lei, C.; Vourdas, A.

    2016-08-01

    Quantum systems with variables in Z(d) are considered, and three different structures are studied. The first is weak mutually unbiased bases, for which the absolute value of the overlap of any two vectors in two different bases is 1 /√{ k } (where k | d) or 0. The second is maximal lines through the origin in the Z(d) × Z(d) phase space. The third is an analytic representation in the complex plane based on Theta functions, and their zeros. It is shown that there is a correspondence (triality) that links strongly these three apparently different structures. For simplicity, the case where d =p1 ×p2, where p1 ,p2 are odd prime numbers different from each other, is considered.

  10. Maximum likelihood: Extracting unbiased information from complex networks

    NASA Astrophysics Data System (ADS)

    Garlaschelli, Diego; Loffredo, Maria I.

    2008-07-01

    The choice of free parameters in network models is subjective, since it depends on what topological properties are being monitored. However, we show that the maximum likelihood (ML) principle indicates a unique, statistically rigorous parameter choice, associated with a well-defined topological feature. We then find that, if the ML condition is incompatible with the built-in parameter choice, network models turn out to be intrinsically ill defined or biased. To overcome this problem, we construct a class of safely unbiased models. We also propose an extension of these results that leads to the fascinating possibility to extract, only from topological data, the “hidden variables” underlying network organization, making them “no longer hidden.” We test our method on World Trade Web data, where we recover the empirical gross domestic product using only topological information.

  11. Unbiased bootstrap error estimation for linear discriminant analysis.

    PubMed

    Vu, Thang; Sima, Chao; Braga-Neto, Ulisses M; Dougherty, Edward R

    2014-12-01

    Convex bootstrap error estimation is a popular tool for classifier error estimation in gene expression studies. A basic question is how to determine the weight for the convex combination between the basic bootstrap estimator and the resubstitution estimator such that the resulting estimator is unbiased at finite sample sizes. The well-known 0.632 bootstrap error estimator uses asymptotic arguments to propose a fixed 0.632 weight, whereas the more recent 0.632+ bootstrap error estimator attempts to set the weight adaptively. In this paper, we study the finite sample problem in the case of linear discriminant analysis under Gaussian populations. We derive exact expressions for the weight that guarantee unbiasedness of the convex bootstrap error estimator in the univariate and multivariate cases, without making asymptotic simplifications. Using exact computation in the univariate case and an accurate approximation in the multivariate case, we obtain the required weight and show that it can deviate significantly from the constant 0.632 weight, depending on the sample size and Bayes error for the problem. The methodology is illustrated by application on data from a well-known cancer classification study.

  12. Unbiased methods for removing systematics from galaxy clustering measurements

    NASA Astrophysics Data System (ADS)

    Elsner, Franz; Leistedt, Boris; Peiris, Hiranya V.

    2016-02-01

    Measuring the angular clustering of galaxies as a function of redshift is a powerful method for extracting information from the three-dimensional galaxy distribution. The precision of such measurements will dramatically increase with ongoing and future wide-field galaxy surveys. However, these are also increasingly sensitive to observational and astrophysical contaminants. Here, we study the statistical properties of three methods proposed for controlling such systematics - template subtraction, basic mode projection, and extended mode projection - all of which make use of externally supplied template maps, designed to characterize and capture the spatial variations of potential systematic effects. Based on a detailed mathematical analysis, and in agreement with simulations, we find that the template subtraction method in its original formulation returns biased estimates of the galaxy angular clustering. We derive closed-form expressions that should be used to correct results for this shortcoming. Turning to the basic mode projection algorithm, we prove it to be free of any bias, whereas we conclude that results computed with extended mode projection are biased. Within a simplified setup, we derive analytical expressions for the bias and discuss the options for correcting it in more realistic configurations. Common to all three methods is an increased estimator variance induced by the cleaning process, albeit at different levels. These results enable unbiased high-precision clustering measurements in the presence of spatially varying systematics, an essential step towards realizing the full potential of current and planned galaxy surveys.

  13. Unbiased contaminant removal for 3D galaxy power spectrum measurements

    NASA Astrophysics Data System (ADS)

    Kalus, B.; Percival, W. J.; Bacon, D. J.; Samushia, L.

    2016-11-01

    We assess and develop techniques to remove contaminants when calculating the 3D galaxy power spectrum. We separate the process into three separate stages: (i) removing the contaminant signal, (ii) estimating the uncontaminated cosmological power spectrum and (iii) debiasing the resulting estimates. For (i), we show that removing the best-fitting contaminant (mode subtraction) and setting the contaminated components of the covariance to be infinite (mode deprojection) are mathematically equivalent. For (ii), performing a quadratic maximum likelihood (QML) estimate after mode deprojection gives an optimal unbiased solution, although it requires the manipulation of large N_mode^2 matrices (Nmode being the total number of modes), which is unfeasible for recent 3D galaxy surveys. Measuring a binned average of the modes for (ii) as proposed by Feldman, Kaiser & Peacock (FKP) is faster and simpler, but is sub-optimal and gives rise to a biased solution. We present a method to debias the resulting FKP measurements that does not require any large matrix calculations. We argue that the sub-optimality of the FKP estimator compared with the QML estimator, caused by contaminants, is less severe than that commonly ignored due to the survey window.

  14. Within-subject template estimation for unbiased longitudinal image analysis

    PubMed Central

    Reuter, Martin; Schmansky, Nicholas J.; Rosas, H. Diana; Fischl, Bruce

    2012-01-01

    Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to potential over-regularization. In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, within-subject template creation, for automatic surface reconstruction and segmentation of brain MRI of arbitrarily many time points. We demonstrate that it is essential to treat all input images exactly the same as removing only interpolation asymmetries is not sufficient to remove processing bias. We successfully reduce variability and avoid over-regularization by initializing the processing in each time point with common information from the subject template. The presented results show a significant increase in precision and discrimination power while preserving the ability to detect large anatomical deviations; as such they hold great potential in clinical applications, e.g. allowing for smaller sample sizes or shorter trials to establish disease specific biomarkers or to quantify drug effects. PMID:22430496

  15. An unbiased Hessian representation for Monte Carlo PDFs.

    PubMed

    Carrazza, Stefano; Forte, Stefano; Kassabov, Zahari; Latorre, José Ignacio; Rojo, Juan

    We develop a methodology for the construction of a Hessian representation of Monte Carlo sets of parton distributions, based on the use of a subset of the Monte Carlo PDF replicas as an unbiased linear basis, and of a genetic algorithm for the determination of the optimal basis. We validate the methodology by first showing that it faithfully reproduces a native Monte Carlo PDF set (NNPDF3.0), and then, that if applied to Hessian PDF set (MMHT14) which was transformed into a Monte Carlo set, it gives back the starting PDFs with minimal information loss. We then show that, when applied to a large Monte Carlo PDF set obtained as combination of several underlying sets, the methodology leads to a Hessian representation in terms of a rather smaller set of parameters (MC-H PDFs), thereby providing an alternative implementation of the recently suggested Meta-PDF idea and a Hessian version of the recently suggested PDF compression algorithm (CMC-PDFs). The mc2hessian conversion code is made publicly available together with (through LHAPDF6) a Hessian representations of the NNPDF3.0 set, and the MC-H PDF set.

  16. Unbiased determination of polarized parton distributions and their uncertainties

    NASA Astrophysics Data System (ADS)

    Ball, Richard D.; Forte, Stefano; Guffanti, Alberto; Nocera, Emanuele R.; Ridolfi, Giovanni; Rojo, Juan

    2013-09-01

    We present a determination of a set of polarized parton distributions (PDFs) of the nucleon, at next-to-leading order, from a global set of longitudinally polarized deep-inelastic scattering data: NNPDFpol1.0. The determination is based on the NNPDF methodology: a Monte Carlo approach, with neural networks used as unbiased interpolants, previously applied to the determination of unpolarized parton distributions, and designed to provide a faithful and statistically sound representation of PDF uncertainties. We present our dataset, its statistical features, and its Monte Carlo representation. We summarize the technique used to solve the polarized evolution equations and its benchmarking, and the method used to compute physical observables. We review the NNPDF methodology for parametrization and fitting of neural networks, the algorithm used to determine the optimal fit, and its adaptation to the polarized case. We finally present our set of polarized parton distributions. We discuss its statistical properties, test for its stability upon various modifications of the fitting procedure, and compare it to other recent polarized parton sets, and in particular obtain predictions for polarized first moments of PDFs based on it. We find that the uncertainties on the gluon, and to a lesser extent the strange PDF, were substantially underestimated in previous determinations.

  17. Mutually unbiased bases as minimal Clifford covariant 2-designs

    NASA Astrophysics Data System (ADS)

    Zhu, Huangjun

    2015-06-01

    Mutually unbiased bases (MUBs) are interesting for various reasons. The most attractive example of (a complete set of) MUBs is the one constructed by Ivanović as well as Wootters and Fields, which is referred to as the canonical MUB. Nevertheless, little is known about anything that is unique to this MUB. We show that the canonical MUB in any prime power dimension is uniquely determined by an extremal orbit of the (restricted) Clifford group except in dimension 3, in which case the orbit defines a special symmetric informationally complete measurement (SIC), known as the Hesse SIC. Here the extremal orbit is the orbit with the smallest number of pure states. Quite surprisingly, this characterization does not rely on any concept that is related to bases or unbiasedness. As a corollary, the canonical MUB is the unique minimal 2-design covariant with respect to the Clifford group except in dimension 3. In addition, these MUBs provide an infinite family of highly symmetric frames and positive-operator-valued measures (POVMs), which are of independent interest.

  18. Unbiased estimation of precise temporal correlations between spike trains.

    PubMed

    Stark, Eran; Abeles, Moshe

    2009-04-30

    A key issue in systems neuroscience is the contribution of precise temporal inter-neuronal interactions to information processing in the brain, and the main analytical tool used for studying pair-wise interactions is the cross-correlation histogram (CCH). Although simple to generate, a CCH is influenced by multiple factors in addition to precise temporal correlations between two spike trains, thus complicating its interpretation. A Monte-Carlo-based technique, the jittering method, has been suggested to isolate the contribution of precise temporal interactions to neural information processing. Here, we show that jittering spike trains is equivalent to convolving the CCH derived from the original trains with a finite window and using a Poisson distribution to estimate probabilities. Both procedures over-fit the original spike trains and therefore the resulting statistical tests are biased and have low power. We devise an alternative method, based on convolving the CCH with a partially hollowed window, and illustrate its utility using artificial and real spike trains. The modified convolution method is unbiased, has high power, and is computationally fast. We recommend caution in the use of the jittering method and in the interpretation of results based on it, and suggest using the modified convolution method for detecting precise temporal correlations between spike trains.

  19. X-ray Properties of an Unbiased Hard X-ray Detected Sample of AGN

    NASA Technical Reports Server (NTRS)

    Winter, Lisa M.; Mushotzky, Richard F.; Tueller, Jack; Markwardt, Craig

    2007-01-01

    The SWIFT gamma ray observatory's Burst Alert Telescope (BAT) has detected a sample of active galactic nuclei (AGN) based solely on their hard X-ray flux (14-195keV). In this paper, we present for the first time XMM-Newton X-ray spectra for 22 BAT AGXs with no previously analyzed X-ray spectra. If our sources are a representative sample of the BAT AGN, as we claim, our results present for the first time global X-ray properties of an unbiased towards absorption (n(sub H) < 3 x 10(exp 25)/sq cm), local (< z >= 0.03), AGN sample. We find 9/22 low absorption (n(sub H) < 10(exp 23)/sq cm), simple power law model sources, where 4 of these sources have a statistically significant soft component. Among these sources, we find the presence of a warm absorber statistically significant for only one Seyfert 1 source, contrasting with the ASCA results of Reynolds (1997) and George et al. (1998), who find signatures of warm absorption in half or more of their Seyfert 1 samples at similar redshifts. Additionally, the remaining sources (13122) have more complex spectra, well-fit by an absorbed power law at E > 2.0 keV. Five of the complex sources (NGC 612, ESO 362-G018, MRK 417, ESO 506-G027, and NGC 6860) are classified as Compton-thick candidates. Further, we find four more sources (SWIFT J0641.3+3257, SWIFT J0911.2+4533, SWIFT J1200.8+0650, and NGC 4992) with properties consistent with the hidden/buried AGN reported by Ueda et al. (2007). Finally, we include a comparison of the XMM EPIC spectra with available SWIFT X-ray Telescope (XRT) observations. From these comparisons, we find 6/16 sources with varying column densities, 6/16 sources with varying power law indices, and 13/16 sources with varying fluxes, over periods of hours to months. Flux and power law index are correlated for objects where both parameters vary.

  20. UNBIASED INCLINATION DISTRIBUTIONS FOR OBJECTS IN THE KUIPER BELT

    SciTech Connect

    Gulbis, A. A. S.; Elliot, J. L.; Adams, E. R.; Benecchi, S. D.; Buie, M. W.; Trilling, D. E.; Wasserman, L. H. E-mail: jle@mit.ed E-mail: lhw@lowell.ed E-mail: buie@boulder.swri.ed

    2010-08-15

    Using data from the Deep Ecliptic Survey (DES), we investigate the inclination distributions of objects in the Kuiper Belt. We present a derivation for observational bias removal and use this procedure to generate unbiased inclination distributions for Kuiper Belt objects (KBOs) of different DES dynamical classes, with respect to the Kuiper Belt plane. Consistent with previous results, we find that the inclination distribution for all DES KBOs is well fit by the sum of two Gaussians, or a Gaussian plus a generalized Lorentzian, multiplied by sin i. Approximately 80% of KBOs are in the high-inclination grouping. We find that Classical object inclinations are well fit by sin i multiplied by the sum of two Gaussians, with roughly even distribution between Gaussians of widths 2.0{sup +0.6}{sub -0.5}{sup 0} and 8.1{sup +2.6}{sub -2.1}{sup 0}. Objects in different resonances exhibit different inclination distributions. The inclinations of Scattered objects are best matched by sin i multiplied by a single Gaussian that is centered at 19.1{sup +3.9}{sub -3.6}{sup 0} with a width of 6.9{sup +4.1}{sub -2.7}{sup 0}. Centaur inclinations peak just below 20{sup 0}, with one exceptionally high-inclination object near 80{sup 0}. The currently observed inclination distribution of the Centaurs is not dissimilar to that of the Scattered Extended KBOs and Jupiter-family comets, but is significantly different from the Classical and Resonant KBOs. While the sample sizes of some dynamical classes are still small, these results should begin to serve as a critical diagnostic for models of solar system evolution.

  1. Unbiased Average Age-Appropriate Atlases for Pediatric Studies

    PubMed Central

    Fonov, Vladimir; Evans, Alan C.; Botteron, Kelly; Almli, C. Robert; McKinstry, Robert C.; Collins, D. Louis

    2010-01-01

    Spatial normalization, registration, and segmentation techniques for Magnetic Resonance Imaging (MRI) often use a target or template volume to facilitate processing, take advantage of prior information, and define a common coordinate system for analysis. In the neuroimaging literature, the MNI305 Talairach-like coordinate system is often used as a standard template. However, when studying pediatric populations, variation from the adult brain makes the MNI305 suboptimal for processing brain images of children. Morphological changes occurring during development render the use of age-appropriate templates desirable to reduce potential errors and minimize bias during processing of pediatric data. This paper presents the methods used to create unbiased, age-appropriate MRI atlas templates for pediatric studies that represent the average anatomy for the age range of 4.5–18.5 years, while maintaining a high level of anatomical detail and contrast. The creation of anatomical T1-weighted, T2-weighted, and proton density-weighted templates for specific developmentally important age-ranges, used data derived from the largest epidemiological, representative (healthy and normal) sample of the U.S. population, where each subject was carefully screened for medical and psychiatric factors and characterized using established neuropsychological and behavioral assessments. . Use of these age-specific templates was evaluated by computing average tissue maps for gray matter, white matter, and cerebrospinal fluid for each specific age range, and by conducting an exemplar voxel-wise deformation-based morphometry study using 66 young (4.5–6.9 years) participants to demonstrate the benefits of using the age-appropriate templates. The public availability of these atlases/templates will facilitate analysis of pediatric MRI data and enable comparison of results between studies in a common standardized space specific to pediatric research. PMID:20656036

  2. Unbiased statistical analysis for multi-stage proteomic search strategies.

    PubMed

    Everett, Logan J; Bierl, Charlene; Master, Stephen R

    2010-02-05

    "Multi-stage" search strategies have become widely accepted for peptide identification and are implemented in a number of available software packages. We describe limitations of these strategies for validation and decoy-based statistical analyses and demonstrate these limitations using a set of control sample spectra. We propose a solution that corrects the statistical deficiencies and describe its implementation using the open-source software X!Tandem.

  3. Inequality spectra

    NASA Astrophysics Data System (ADS)

    Eliazar, Iddo

    2017-03-01

    Inequality indices are widely applied in economics and in the social sciences as quantitative measures of the socioeconomic inequality of human societies. The application of inequality indices extends to size-distributions at large, where these indices can be used as general gauges of statistical heterogeneity. Moreover, as inequality indices are plentiful, arrays of such indices facilitate high-detail quantification of statistical heterogeneity. In this paper we elevate from arrays of inequality indices to inequality spectra: continuums of inequality indices that are parameterized by a single control parameter. We present a general methodology of constructing Lorenz-based inequality spectra, apply the general methodology to establish four sets of inequality spectra, investigate the properties of these sets, and show how these sets generalize known inequality gauges such as: the Gini index, the extended Gini index, the Rényi index, and hill curves.

  4. Spectroscopic observation of SN 2017pp by NUTS (NOT Un-biased Transient Survey)

    NASA Astrophysics Data System (ADS)

    Pastorello, A.; Elias-Rosa, N.; Benetti, S.; Cappellaro, E.; Terreran, G.; Tomasella, L.; Tronsgaard, R.

    2017-01-01

    The Nordic Optical Telescope (NOT) Unbiased Transient Survey (NUTS; ATel #8992) reports the spectroscopic classification of SN 2017pp in PGC 1378162. The candidate was discovered by F. Ciabattari, E. Mazzoni, S. Donati (ISSP; http://italiansupernovae.org).

  5. Unbiased pseudo-Cℓ power spectrum estimation with mode projection

    NASA Astrophysics Data System (ADS)

    Elsner, Franz; Leistedt, Boris; Peiris, Hiranya V.

    2017-02-01

    With the steadily improving sensitivity afforded by current and future galaxy surveys, a robust extraction of two-point correlation function measurements may become increasingly hampered by the presence of astrophysical foregrounds or observational systematics. The concept of mode projection has been introduced as a means to remove contaminants for which it is possible to construct a spatial map, reflecting the expected signal contribution. Owing to its computational efficiency compared to minimum-variance methods, the sub-optimal pseudo-Cℓ (PCL) power spectrum estimator is a popular tool for the analysis of high-resolution data sets. Here, we integrate mode projection into the framework of PCL power spectrum estimation. In contrast to results obtained with optimal estimators, we show that the uncorrected projection of template maps leads to biased power spectra. Based on analytical calculations, we find exact closed-form expressions for the expectation value of the bias and demonstrate that they can be recast in a form which allows a numerically efficient evaluation, preserving the favourable O( ℓ_{max} ^3 ) time complexity of PCL estimator algorithms. Using simulated data sets, we assess the scaling of the bias with various analysis parameters and demonstrate that it can be reliably removed. We conclude that in combination with mode projection, PCL estimators allow for a fast and robust computation of power spectra in the presence of systematic effects - properties in high demand for the analysis of ongoing and future large-scale structure surveys.

  6. A novel computational method for comparing vibrational circular dichroism spectra.

    PubMed

    Shen, Jian; Zhu, Chengyue; Reiling, Stephan; Vaz, Roy

    2010-08-01

    A novel method, SimIR/VCD, for comparing experimental and calculated VCD (vibrational circular dichroism) spectra is developed, based on newly defined spectra similarities. With computationally optimized frequency scaling and shifting, a calculated spectrum can be easily identified to match an observed spectrum, which leads to an unbiased molecular chirality assignment. The time-consuming manual band-fitting work is greatly reduced. With (1S)-(-)-alpha-pinene as an example, it demonstrates that the calculated VCD similarity is correlated with VCD spectra matching quality and has enough sensitivity to identify variations in the spectra. The study also compares spectra calculated using different DFT methods and basis sets. Using this method should facilitate the spectra matching, reduce human error and provide a confidence measure in the chiral assignment using VCD spectroscopy.

  7. Operational link between mutually unbiased bases and symmetric informationally complete positive operator-valued measures

    NASA Astrophysics Data System (ADS)

    Beneduci, Roberto; Bullock, Thomas J.; Busch, Paul; Carmeli, Claudio; Heinosaari, Teiko; Toigo, Alessandro

    2013-09-01

    We exhibit an operational connection between mutually unbiased bases and symmetric informationally complete positive operator-valued measures. Assuming that the latter exists, we show that there is a strong link between these two structures in all prime power dimensions. We also demonstrate that a similar link cannot exist in dimension 6.

  8. Reply to ''Comment on 'Mutually unbiased bases, orthogonal Latin squares, and hidden-variable models'''

    SciTech Connect

    Paterek, Tomasz; Dakic, Borivoje; Brukner, Caslav

    2011-03-15

    In this Reply to the preceding Comment by Hall and Rao [Phys. Rev. A 83, 036101 (2011)], we motivate terminology of our original paper and point out that further research is needed in order to (dis)prove the claimed link between every orthogonal Latin square of order being a power of a prime and a mutually unbiased basis.

  9. Storm Spectra

    NASA Technical Reports Server (NTRS)

    2007-01-01

    portion is defined by the day/night boundary (known as the terminator).

    These two images illustrate only a small fraction of the information contained in a single LEISA scan, highlighting just one aspect of the power of infrared spectra for atmospheric studies.

  10. Unbiased metabolite profiling by liquid chromatography-quadrupole time-of-flight mass spectrometry and multivariate data analysis for herbal authentication: classification of seven Lonicera species flower buds.

    PubMed

    Gao, Wen; Yang, Hua; Qi, Lian-Wen; Liu, E-Hu; Ren, Mei-Ting; Yan, Yu-Ting; Chen, Jun; Li, Ping

    2012-07-06

    Plant-based medicines become increasingly popular over the world. Authentication of herbal raw materials is important to ensure their safety and efficacy. Some herbs belonging to closely related species but differing in medicinal properties are difficult to be identified because of similar morphological and microscopic characteristics. Chromatographic fingerprinting is an alternative method to distinguish them. Existing approaches do not allow a comprehensive analysis for herbal authentication. We have now developed a strategy consisting of (1) full metabolic profiling of herbal medicines by rapid resolution liquid chromatography (RRLC) combined with quadrupole time-of-flight mass spectrometry (QTOF MS), (2) global analysis of non-targeted compounds by molecular feature extraction algorithm, (3) multivariate statistical analysis for classification and prediction, and (4) marker compounds characterization. This approach has provided a fast and unbiased comparative multivariate analysis of the metabolite composition of 33-batch samples covering seven Lonicera species. Individual metabolic profiles are performed at the level of molecular fragments without prior structural assignment. In the entire set, the obtained classifier for seven Lonicera species flower buds showed good prediction performance and a total of 82 statistically different components were rapidly obtained by the strategy. The elemental compositions of discriminative metabolites were characterized by the accurate mass measurement of the pseudomolecular ions and their chemical types were assigned by the MS/MS spectra. The high-resolution, comprehensive and unbiased strategy for metabolite data analysis presented here is powerful and opens the new direction of authentication in herbal analysis.

  11. Test of mutually unbiased bases for six-dimensional photonic quantum systems

    PubMed Central

    D'Ambrosio, Vincenzo; Cardano, Filippo; Karimi, Ebrahim; Nagali, Eleonora; Santamato, Enrico; Marrucci, Lorenzo; Sciarrino, Fabio

    2013-01-01

    In quantum information, complementarity of quantum mechanical observables plays a key role. The eigenstates of two complementary observables form a pair of mutually unbiased bases (MUBs). More generally, a set of MUBs consists of bases that are all pairwise unbiased. Except for specific dimensions of the Hilbert space, the maximal sets of MUBs are unknown in general. Even for a dimension as low as six, the identification of a maximal set of MUBs remains an open problem, although there is strong numerical evidence that no more than three simultaneous MUBs do exist. Here, by exploiting a newly developed holographic technique, we implement and test different sets of three MUBs for a single photon six-dimensional quantum state (a “qusix”), encoded exploiting polarization and orbital angular momentum of photons. A close agreement is observed between theory and experiments. Our results can find applications in state tomography, quantitative wave-particle duality, quantum key distribution. PMID:24067548

  12. Contextual classification of multispectral image data - An unbiased estimator for the context distribution

    NASA Technical Reports Server (NTRS)

    Tilton, J. C.; Swain, P. H.; Vardeman, S. B.

    1981-01-01

    Recent investigations have demonstrated the effectiveness of a contextual classifier that combines spatial and spectral information employing a general statistical approach. This statistical classification algorithm exploits the tendency of certain ground-cover classes to occur more frequently in some spatial contexts than in others. Indeed, a key input to this algorithm is a statistical characterization of the context: the context distribution. Here a discussion is given of an unbiased estimator of the context distribution which, besides having the advantage of statistical unbiasedness, has the additional advantage over other estimation techniques of being amenable to an adaptive implementation in which the context distribution estimate varies according to local contextual information. Results from applying the unbiased estimator to the contextual classification of three real Landsat data sets are presented and contrasted with results from noncontextual classifications and from contextual classifications utilizing other context distribution estimation techniques.

  13. Contextual classification of multispectral image data: An unbiased estimator for the context distribution

    NASA Technical Reports Server (NTRS)

    Tilton, J. C.; Swain, P. H. (Principal Investigator); Vardeman, S. B.

    1981-01-01

    A key input to a statistical classification algorithm, which exploits the tendency of certain ground cover classes to occur more frequently in some spatial context than in others, is a statistical characterization of the context: the context distribution. An unbiased estimator of the context distribution is discussed which, besides having the advantage of statistical unbiasedness, has the additional advantage over other estimation techniques of being amenable to an adaptive implementation in which the context distribution estimate varies according to local contextual information. Results from applying the unbiased estimator to the contextual classification of three real LANDSAT data sets are presented and contrasted with results from non-contextual classifications and from contextual classifications utilizing other context distribution estimation techniques.

  14. Rapid purification of quantum systems by measuring in a feedback-controlled unbiased basis

    SciTech Connect

    Combes, Joshua; Wiseman, Howard M.; Jacobs, Kurt; O'Connor, Anthony J.

    2010-08-15

    Rapid purification by feedback--specifically, reducing the mean impurity faster than by measurement alone--can be achieved by choosing the eigenbasis of the density matrix to be unbiased relative to the measurement basis. Here we further examine the protocol introduced by Combes and Jacobs [Phys. Rev. Lett. 96, 010504 (2006)] involving continuous measurement of the observable J{sub z} for a D-dimensional system. We rigorously rederive the lower bound (2/3)(D+1) on the achievable speedup factor and also an upper bound, namely D{sup 2}/2, for all feedback protocols that use measurements in unbiased bases. Finally, we extend our results to n independent measurements on a register of n qubits and derive an upper bound on the achievable speedup factor that scales linearly with n.

  15. Extending unbiased stereology of brain ultrastructure to three-dimensional volumes

    NASA Technical Reports Server (NTRS)

    Fiala, J. C.; Harris, K. M.; Koslow, S. H. (Principal Investigator)

    2001-01-01

    OBJECTIVE: Analysis of brain ultrastructure is needed to reveal how neurons communicate with one another via synapses and how disease processes alter this communication. In the past, such analyses have usually been based on single or paired sections obtained by electron microscopy. Reconstruction from multiple serial sections provides a much needed, richer representation of the three-dimensional organization of the brain. This paper introduces a new reconstruction system and new methods for analyzing in three dimensions the location and ultrastructure of neuronal components, such as synapses, which are distributed non-randomly throughout the brain. DESIGN AND MEASUREMENTS: Volumes are reconstructed by defining transformations that align the entire area of adjacent sections. Whole-field alignment requires rotation, translation, skew, scaling, and second-order nonlinear deformations. Such transformations are implemented by a linear combination of bivariate polynomials. Computer software for generating transformations based on user input is described. Stereological techniques for assessing structural distributions in reconstructed volumes are the unbiased bricking, disector, unbiased ratio, and per-length counting techniques. A new general method, the fractional counter, is also described. This unbiased technique relies on the counting of fractions of objects contained in a test volume. A volume of brain tissue from stratum radiatum of hippocampal area CA1 is reconstructed and analyzed for synaptic density to demonstrate and compare the techniques. RESULTS AND CONCLUSIONS: Reconstruction makes practicable volume-oriented analysis of ultrastructure using such techniques as the unbiased bricking and fractional counter methods. These analysis methods are less sensitive to the section-to-section variations in counts and section thickness, factors that contribute to the inaccuracy of other stereological methods. In addition, volume reconstruction facilitates visualization

  16. A Cramer-Rao Type Lower Bound for Essentially Unbiased Parameter Estimation

    DTIC Science & Technology

    1992-01-03

    should apply to the entire class of estimators with acceptably small bias. In this report a new CR-type lower bound is derived which takes into account a...unbiased CR bound. If an upper bound on the bias gradient ot tne estimator is specified, our lower bound on estimator variance can subsequently be applied ...multiple parameters. Finally, Section 8 applies the new bound to covariance estimation for a pair of HD Gaussian sequences. 2 2. PRELIMINARIES 2.1

  17. About mutually unbiased bases in even and odd prime power dimensions

    NASA Astrophysics Data System (ADS)

    Durt, Thomas

    2005-06-01

    Mutually unbiased bases generalize the X, Y and Z qubit bases. They possess numerous applications in quantum information science. It is well known that in prime power dimensions N = pm (with p prime and m a positive integer), there exists a maximal set of N + 1 mutually unbiased bases. In the present paper, we derive an explicit expression for those bases, in terms of the (operations of the) associated finite field (Galois division ring) of N elements. This expression is shown to be equivalent to the expressions previously obtained by Ivanovic (1981 J. Phys. A: Math. Gen. 14 3241) in odd prime dimensions, and Wootters and Fields (1989 Ann. Phys. 191 363) in odd prime power dimensions. In even prime power dimensions, we derive a new explicit expression for the mutually unbiased bases. The new ingredients of our approach are, basically, the following: we provide a simple expression of the generalized Pauli group in terms of the additive characters of the field, and we derive an exact groupal composition law between the elements of the commuting subsets of the generalized Pauli group, renormalized by a well-chosen phase-factor.

  18. Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations.

    PubMed

    Seligmann, Hervé

    2016-01-01

    Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.

  19. Statistical properties of Jacobian maps and the realization of unbiased large-deformation nonlinear image registration.

    PubMed

    Leow, Alex D; Yanovsky, Igor; Chiang, Ming-Chang; Lee, Agatha D; Klunder, Andrea D; Lu, Allen; Becker, James T; Davis, Simon W; Toga, Arthur W; Thompson, Paul M

    2007-06-01

    Maps of local tissue compression or expansion are often computed by comparing magnetic resonance imaging (MRI) scans using nonlinear image registration. The resulting changes are commonly analyzed using tensor-based morphometry to make inferences about anatomical differences, often based on the Jacobian map, which estimates local tissue gain or loss. Here, we provide rigorous mathematical analyses of the Jacobian maps, and use themto motivate a new numerical method to construct unbiased nonlinear image registration. First, we argue that logarithmic transformation is crucial for analyzing Jacobian values representing morphometric differences. We then examine the statistical distributions of log-Jacobian maps by defining the Kullback-Leibler (KL) distance on material density functions arising in continuum-mechanical models. With this framework, unbiased image registration can be constructed by quantifying the symmetric KL-distance between the identity map and the resulting deformation. Implementation details, addressing the proposed unbiased registration as well as the minimization of symmetric image matching functionals, are then discussed and shown to be applicable to other registration methods, such as inverse consistent registration. In the results section, we test the proposed framework, as well as present an illustrative application mapping detailed 3-D brain changes in sequential magnetic resonance imaging scans of a patient diagnosed with semantic dementia. Using permutation tests, we show that the symmetrization of image registration statistically reduces skewness in the log-Jacobian map.

  20. Spectroscopic observation of AT2016iyw and AT2016jal by NUTS (NOT Un-biased Transient Survey)

    NASA Astrophysics Data System (ADS)

    Taddia, F.; Lundqvist, P.; Ergon, M.; Kangas, T.; Mattila, S.; Kuncarayakti, H.; Harmanen, J.; Somero, A.; Reynolds, T.; Stritzinger, M.; Dong, S.; Blay, P.

    2017-01-01

    The Nordic Optical Telescope (NOT) Unbiased Transient Survey (NUTS; ATel #8992) reports the spectroscopic classification of two transients. The candidates were discovered by the ATLAS survey (Tonry et al., ATel #9685).

  1. Generalized approach for using unbiased symmetric metrics with negative values: normalized mean bias factor and normalized mean absolute error factor

    EPA Science Inventory

    Unbiased symmetric metrics provide a useful measure to quickly compare two datasets, with similar interpretations for both under and overestimations. Two examples include the normalized mean bias factor and normalized mean absolute error factor. However, the original formulations...

  2. Far-infrared observations of an unbiased sample of gamma-ray burst host galaxies

    NASA Astrophysics Data System (ADS)

    Kohn, S. A.; Michałowski, M. J.; Bourne, N.; Baes, M.; Fritz, J.; Cooray, A.; De Looze, I.; De Zotti, G.; Dannerbauer, H.; Dunne, L.; Dye, S.; Eales, S.; Furlanetto, C.; Gonzalez-Nuevo, J.; Ibar, E.; Ivison, R. J.; Maddox, S. J.; Scott, D.; Smith, D. J. B.; Smith, M. W. L.; Symeonidis, M.; Valiante, E.

    2015-04-01

    Gamma-ray bursts (GRBs) are the most energetic phenomena in the Universe; believed to result from the collapse and subsequent explosion of massive stars. Even though it has profound consequences for our understanding of their nature and selection biases, little is known about the dust properties of the galaxies hosting GRBs. We present analysis of the far-infrared properties of an unbiased sample of 20 BeppoSAX and Swift GRB host galaxies (at an average redshift of z = 3.1) located in the Herschel Astrophysical Terahertz Large Area Survey, the Herschel Virgo Cluster Survey, the Herschel Fornax Cluster Survey, the Herschel Stripe 82 Survey and the Herschel Multi-tiered Extragalactic Survey, totalling 880 deg2, or ˜3 per cent of the sky in total. Our sample selection is serendipitous, based only on whether the X-ray position of a GRB lies within a large-scale Herschel survey - therefore our sample can be considered completely unbiased. Using deep data at wavelengths of 100-500 μm, we tentatively detected 1 out of 20 GRB hosts located in these fields. We constrain their dust masses and star formation rates (SFRs), and discuss these in the context of recent measurements of submillimetre galaxies and ultraluminous infrared galaxies. The average far-infrared flux of our sample gives an upper limit on SFR of <114 M⊙ yr-1. The detection rate of GRB hosts is consistent with that predicted assuming that GRBs trace the cosmic SFR density in an unbiased way, i.e. that the fraction of GRB hosts with SFR > 500 M⊙ yr-1 is consistent with the contribution of such luminous galaxies to the cosmic star formation density.

  3. Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling

    PubMed Central

    Freyhult, Eva; Prusis, Peteris; Lapinsh, Maris; Wikberg, Jarl ES; Moulton, Vincent; Gustafsson, Mats G

    2005-01-01

    Background Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis. Results A methodology for an unbiased evaluation of the predictive power of proteochemometric models was implemented and results from applying it to two of the largest proteochemometric data sets yet reported are presented. A double cross-validation loop procedure is used to estimate the expected performance of a given design method. The unbiased performance estimates (P2) obtained for the data sets that we consider confirm that properly designed single proteochemometric models have useful predictive power, but that a standard design based on cross validation may yield models with quite limited performance. The results also show that different commercial software packages employed for the design of proteochemometric models may yield very different and therefore misleading performance estimates. In addition, the differences in the models obtained in the double CV loop indicate that detailed chemical interpretation of a single proteochemometric model is uncertain when data sets are small. Conclusion The double CV loop employed offer unbiased performance estimates about a given proteochemometric

  4. Two Types of Maximally Entangled Bases and Their Mutually Unbiased Property in Cd⊗ C^{d^' }}

    NASA Astrophysics Data System (ADS)

    Luo, Laizhen; Li, Xiaoyu; Tao, Yuanhong

    2016-12-01

    We first construct a new maximally entangled basis in bipartite systems Cd ⊗ C^{kd} (kin Z+) which is diffrent from the one in Tao et al. (Quantum Inf. Process. 14, 2291 (2015)), then we generalize such maximally entangled basis into arbitrary bipartite systems Cd ⊗ C^{d^' }}. We also study the mutual unbiased property of the two types of maximally entangled bases in bipartite systems Cd ⊗ C^{kd}. In particular, explicit examples in C2 ⊗ C4, C2 ⊗ C8 and C3 ⊗ C3 are presented.

  5. Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion.

    PubMed

    Gohlke, Holger; Hergert, Ulrike; Meyer, Tatu; Mulnaes, Daniel; Grieshaber, Manfred K; Smits, Sander H J; Schmitt, Lutz

    2013-10-28

    Opine dehydrogenases catalyze the reductive condensation of pyruvate with L-amino acids. Biochemical characterization of alanopine dehydrogenase from Arenicola marina revealed that this enzyme is highly specific for L-alanine. Unbiased molecular dynamics simulations with a homology model of alanopine dehydrogenase captured the binding of L-alanine diffusing from solvent to a putative binding region near a distinct helix-kink-helix motif. These results and sequence comparisons reveal how mutations and insertions within this motif dictate the L-amino acid specificity.

  6. Construction of An Unbiased Spatio-Temporal Atlas of the Tongue During Speech.

    PubMed

    Woo, Jonghye; Xing, Fangxu; Lee, Junghoon; Stone, Maureen; Prince, Jerry L

    2015-01-01

    Quantitative characterization and comparison of tongue motion during speech and swallowing present fundamental challenges because of striking variations in tongue structure and motion across subjects. A reliable and objective description of the dynamics tongue motion requires the consistent integration of inter-subject variability to detect the subtle changes in populations. To this end, in this work, we present an approach to constructing an unbiased spatio-temporal atlas of the tongue during speech for the first time, based on cine-MRI from twenty two normal subjects. First, we create a common spatial space using images from the reference time frame, a neutral position, in which the unbiased spatio-temporal atlas can be created. Second, we transport images from all time frames of all subjects into this common space via the single transformation. Third, we construct atlases for each time frame via groupwise diffeomorphic registration, which serves as the initial spatio-temporal atlas. Fourth, we update the spatio-temporal atlas by realigning each time sequence based on the Lipschitz norm on diffeomorphisms between each subject and the initial atlas. We evaluate and compare different configurations such as similarity measures to build the atlas. Our proposed method permits to accurately and objectively explain the main pattern of tongue surface motion.

  7. Weighted skewness and kurtosis unbiased by sample size and Gaussian uncertainties

    NASA Astrophysics Data System (ADS)

    Rimoldini, Lorenzo

    2014-07-01

    Central moments and cumulants are often employed to characterize the distribution of data. The skewness and kurtosis are particularly useful for the detection of outliers, the assessment of departures from normally distributed data, automated classification techniques and other applications. Estimators of higher order moments that are robust against outliers are more stable but might miss characteristic features of the data, as in the case of astronomical time series exhibiting brief events like stellar bursts or eclipses of binary systems, while weighting can help identify reliable measurements from uncertain or spurious outliers. Furthermore, noise is an unavoidable part of most measurements and their uncertainties need to be taken properly into account during the data analysis or biases are likely to emerge in the results, including basic descriptive statistics. This work provides unbiased estimates of the weighted skewness and kurtosis moments and cumulants, corrected for biases due to sample size and Gaussian noise, under the assumption of independent data. A comparison of biased and unbiased weighted estimators is illustrated with simulations as a function of sample size and signal-to-noise ratio, employing different data distributions and weighting schemes related to measurement uncertainties and the sampling of the signal. Detailed derivations and figures of simulation results are presented in the Appendices available online.

  8. Estimating unbiased economies of scale of HIV prevention projects: a case study of Avahan.

    PubMed

    Lépine, Aurélia; Vassall, Anna; Chandrashekar, Sudha; Blanc, Elodie; Le Nestour, Alexis

    2015-04-01

    Governments and donors are investing considerable resources on HIV prevention in order to scale up these services rapidly. Given the current economic climate, providers of HIV prevention services increasingly need to demonstrate that these investments offer good 'value for money'. One of the primary routes to achieve efficiency is to take advantage of economies of scale (a reduction in the average cost of a health service as provision scales-up), yet empirical evidence on economies of scale is scarce. Methodologically, the estimation of economies of scale is hampered by several statistical issues preventing causal inference and thus making the estimation of economies of scale complex. In order to estimate unbiased economies of scale when scaling up HIV prevention services, we apply our analysis to one of the few HIV prevention programmes globally delivered at a large scale: the Indian Avahan initiative. We costed the project by collecting data from the 138 Avahan NGOs and the supporting partners in the first four years of its scale-up, between 2004 and 2007. We develop a parsimonious empirical model and apply a system Generalized Method of Moments (GMM) and fixed-effects Instrumental Variable (IV) estimators to estimate unbiased economies of scale. At the programme level, we find that, after controlling for the endogeneity of scale, the scale-up of Avahan has generated high economies of scale. Our findings suggest that average cost reductions per person reached are achievable when scaling-up HIV prevention in low and middle income countries.

  9. Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method.

    PubMed

    Lesage, Adrien; Lelièvre, Tony; Stoltz, Gabriel; Hénin, Jérôme

    2016-12-27

    We report a theoretical description and numerical tests of the extended-system adaptive biasing force method (eABF), together with an unbiased estimator of the free energy surface from eABF dynamics. Whereas the original ABF approach uses its running estimate of the free energy gradient as the adaptive biasing force, eABF is built on the idea that the exact free energy gradient is not necessary for efficient exploration, and that it is still possible to recover the exact free energy separately with an appropriate estimator. eABF does not directly bias the collective coordinates of interest, but rather fictitious variables that are harmonically coupled to them; therefore is does not require second derivative estimates, making it easily applicable to a wider range of problems than ABF. Furthermore, the extended variables present a smoother, coarse-grain-like sampling problem on a mollified free energy surface, leading to faster exploration and convergence. We also introduce CZAR, a simple, unbiased free energy estimator from eABF trajectories. eABF/CZAR converges to the physical free energy surface faster than standard ABF for a wide range of parameters.

  10. Reactor Neutrino Spectra

    NASA Astrophysics Data System (ADS)

    Hayes, Anna C.; Vogel, Petr

    2016-10-01

    We present a review of the antineutrino spectra emitted from reactors. Knowledge of these spectra and their associated uncertainties is crucial for neutrino oscillation studies. The spectra used to date have been determined either by converting measured electron spectra to antineutrino spectra or by summing over all of the thousands of transitions that make up the spectra, using modern databases as input. The uncertainties in the subdominant corrections to β-decay plague both methods, and we provide estimates of these uncertainties. Improving on current knowledge of the antineutrino spectra from reactors will require new experiments. Such experiments would also address the so-called reactor neutrino anomaly and the possible origin of the shoulder observed in the antineutrino spectra measured in recent high-statistics reactor neutrino experiments.

  11. An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy.

    PubMed

    Harris, Alexandre M; DeGiorgio, Michael

    2017-02-09

    Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounts for related and inbred individuals in samples. Though unbiased, this estimator's variance is greater than that of the original estimator. To address this issue, we introduce a general unbiased estimator of gene diversity for samples containing related or inbred individuals, which employs the best linear unbiased estimator of allele frequencies, rather than the commonly used sample proportion. We examine the properties of this estimator, [Formula: see text] relative to alternative estimators using simulations and theoretical predictions, and show that it predominantly has the smallest mean squared error relative to others. Further, we empirically assess the performance of [Formula: see text] on a global human microsatellite dataset of 5795 individuals, from 267 populations, genotyped at 645 loci. Additionally, we show that the improved variance of [Formula: see text] leads to improved estimates of the population differentiation statistic, [Formula: see text] which employs measures of gene diversity within its calculation. Finally, we provide an R script, BestHet, to compute this estimator from genomic and pedigree data.

  12. An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy

    PubMed Central

    Harris, Alexandre M.; DeGiorgio, Michael

    2016-01-01

    Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounts for related and inbred individuals in samples. Though unbiased, this estimator’s variance is greater than that of the original estimator. To address this issue, we introduce a general unbiased estimator of gene diversity for samples containing related or inbred individuals, which employs the best linear unbiased estimator of allele frequencies, rather than the commonly used sample proportion. We examine the properties of this estimator, H∼BLUE, relative to alternative estimators using simulations and theoretical predictions, and show that it predominantly has the smallest mean squared error relative to others. Further, we empirically assess the performance of H∼BLUE on a global human microsatellite dataset of 5795 individuals, from 267 populations, genotyped at 645 loci. Additionally, we show that the improved variance of H∼BLUE leads to improved estimates of the population differentiation statistic, FST, which employs measures of gene diversity within its calculation. Finally, we provide an R script, BestHet, to compute this estimator from genomic and pedigree data. PMID:28040781

  13. Motor activity as an unbiased variable to assess anaphylaxis in allergic rats.

    PubMed

    Abril-Gil, Mar; Garcia-Just, Alba; Cambras, Trinitat; Pérez-Cano, Francisco J; Castellote, Cristina; Franch, Àngels; Castell, Margarida

    2015-10-01

    The release of mediators by mast cells triggers allergic symptoms involving various physiological systems and, in the most severe cases, the development of anaphylactic shock compromising mainly the nervous and cardiovascular systems. We aimed to establish variables to objectively study the anaphylactic response (AR) after an oral challenge in an allergy model. Brown Norway rats were immunized by intraperitoneal injection of ovalbumin with alum and toxin from Bordetella pertussis. Specific immunoglobulin (Ig) E antibodies were developed in immunized animals. Forty days after immunization, the rats were orally challenged with the allergen, and motor activity, body temperature and serum mast cell protease concentration were determined. The anaphylaxis induced a reduction in body temperature and a decrease in the number of animal movements, which was inversely correlated with serum mast cell protease release. In summary, motor activity is a reliable tool for assessing AR and also an unbiased method for screening new anti-allergic drugs.

  14. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

    NASA Astrophysics Data System (ADS)

    Procacci, Piero

    2015-04-01

    In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems.

  15. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

    SciTech Connect

    Procacci, Piero

    2015-04-21

    In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems.

  16. Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods.

    PubMed

    Mäder, Ulrike; Nicolas, Pierre; Richard, Hugues; Bessières, Philippe; Aymerich, Stéphane

    2011-02-01

    Genomic tiling array transcriptomics and RNA-seq are two powerful and rapidly developing approaches for unbiased transcriptome analysis. Providing comprehensive identification and quantification of transcripts with an unprecedented resolution, they are leading to major breakthroughs in systems biology. Here we review each step of the analysis from library preparation to the interpretation of the data, with particular attention paid to the possible sources of artifacts. Methodological requirements and statistical frameworks are often similar in both the approaches despite differences in the nature of the data. Tiling array analysis does not require rRNA depletion and benefits from a more mature computational workflow, whereas RNA-Seq has a clear lead in terms of background noise and dynamic range with a considerable potential for evolution with the improvements of sequencing technologies. Being independent of prior sequence knowledge, RNA-seq will boost metatranscriptomics and evolutionary transcriptomics applications.

  17. Construction of mutually unbiased maximally entangled bases through permutations of Hadamard matrices

    NASA Astrophysics Data System (ADS)

    xu, Dengming

    2017-03-01

    We construct mutually unbiased maximally entangled bases (MUMEBs) in bipartite system C^d⊗ C^d (d≥ 3) with d a power of a prime number. Precisely, by means of permutation matrices and Hadamard matrices, we construct 2(d-1) MUMEBs in C^d⊗ C}^d. It follows that M(d,d)≥ 2(d-1), which is twice the number given in Liu et al. (2016), where M( d, d) denotes the maximal size of all sets of MUMEBs in C^d⊗ C}^d. In addition, let q be another power of a prime number, we construct MUMEBs in C^d⊗ C^{qd} from those in C^d⊗ C^d by the use of the tensor product of unitary matrices.

  18. Unbiased reduced density matrices and electronic properties from full configuration interaction quantum Monte Carlo

    SciTech Connect

    Overy, Catherine; Blunt, N. S.; Shepherd, James J.; Booth, George H.; Cleland, Deidre; Alavi, Ali

    2014-12-28

    Properties that are necessarily formulated within pure (symmetric) expectation values are difficult to calculate for projector quantum Monte Carlo approaches, but are critical in order to compute many of the important observable properties of electronic systems. Here, we investigate an approach for the sampling of unbiased reduced density matrices within the full configuration interaction quantum Monte Carlo dynamic, which requires only small computational overheads. This is achieved via an independent replica population of walkers in the dynamic, sampled alongside the original population. The resulting reduced density matrices are free from systematic error (beyond those present via constraints on the dynamic itself) and can be used to compute a variety of expectation values and properties, with rapid convergence to an exact limit. A quasi-variational energy estimate derived from these density matrices is proposed as an accurate alternative to the projected estimator for multiconfigurational wavefunctions, while its variational property could potentially lend itself to accurate extrapolation approaches in larger systems.

  19. An unbiased X-ray sampling of stars within 25 parsecs of the sun

    NASA Technical Reports Server (NTRS)

    Johnson, H. M.

    1986-01-01

    A search of all of the Einstein Laboratory IPC and HRI fields for untargeted stars in the Woolley, et al., Catalogue of the nearby stars is reported. Optical data and IPC coordinates, flux density F sub x, and luminosity L sub x, or upper limits, are tabulated for 126 single or blended systems, and HRI results for a few of them. IPC luminosity functions are derived for the systems, for 193 individual stars in the systems (with L sub x shared equally among blended components), and for 63 individual M dwarfs. These stars have relatively large X-ray flux densities that are free of interstellar extinction, because they are nearby, but they are otherwise unbiased with respect to the X-ray properties that are found in a defined small space around the sun.

  20. An unbiased X-ray sampling of stars within 25 parsecs of the Sun

    NASA Technical Reports Server (NTRS)

    Johnson, H. M.

    1985-01-01

    A search of all of the Einstein Observatory IPC and HRI fields for untargeted stars in the Woolley, et al., Catalogue of the nearby stars is reported. Optical data and IPC coordinates, flux density F sub x, and luminosity L sub x, or upper limits, are tabulated for 126 single or blended systems, and HRI results for a few of them. IPC luminosity functions are derived for the systems, for 193 individual stars in the systems (with L sub x shared equally among blended components), and for 63 individual M dwarfs. These stars have relatively large X-ray flux densities that are free of interstellar extinction, because they are nearby, but they are otherwise unbiased with respect to the X-ray properties that are found in a defined small space around the Sun.

  1. Unbiased reduced density matrices and electronic properties from full configuration interaction quantum Monte Carlo.

    PubMed

    Overy, Catherine; Booth, George H; Blunt, N S; Shepherd, James J; Cleland, Deidre; Alavi, Ali

    2014-12-28

    Properties that are necessarily formulated within pure (symmetric) expectation values are difficult to calculate for projector quantum Monte Carlo approaches, but are critical in order to compute many of the important observable properties of electronic systems. Here, we investigate an approach for the sampling of unbiased reduced density matrices within the full configuration interaction quantum Monte Carlo dynamic, which requires only small computational overheads. This is achieved via an independent replica population of walkers in the dynamic, sampled alongside the original population. The resulting reduced density matrices are free from systematic error (beyond those present via constraints on the dynamic itself) and can be used to compute a variety of expectation values and properties, with rapid convergence to an exact limit. A quasi-variational energy estimate derived from these density matrices is proposed as an accurate alternative to the projected estimator for multiconfigurational wavefunctions, while its variational property could potentially lend itself to accurate extrapolation approaches in larger systems.

  2. Bipartite entangled stabilizer mutually unbiased bases as maximum cliques of Cayley graphs

    SciTech Connect

    Dam, Wim van; Howard, Mark

    2011-07-15

    We examine the existence and structure of particular sets of mutually unbiased bases (MUBs) in bipartite qudit systems. In contrast to well-known power-of-prime MUB constructions, we restrict ourselves to using maximally entangled stabilizer states as MUB vectors. Consequently, these bipartite entangled stabilizer MUBs (BES MUBs) provide no local information, but are sufficient and minimal for decomposing a wide variety of interesting operators including (mixtures of) Jamiolkowski states, entanglement witnesses, and more. The problem of finding such BES MUBs can be mapped, in a natural way, to that of finding maximum cliques in a family of Cayley graphs. Some relationships with known power-of-prime MUB constructions are discussed, and observables for BES MUBs are given explicitly in terms of Pauli operators.

  3. A Serendipitous, Unbiased Survey of Dying Stars in the Kepler Field

    NASA Astrophysics Data System (ADS)

    Kraemer, Kathleen

    We propose to use the Full Field Images (FFIs) from the 4-year Kepler mission, complemented by 2MASS, WISE, and Spitzer, to conduct the first accurate, unbiased census of long-period variables (LPVs) in the Galactic Disk. A fundamental question in stellar astrophysics is how stars shed the bulk of their mass as they die. Much of this mass is ejected during the LPV phase of stellar evolution. That material, enriched by the nucleosynthetic products created deep in a star's interior, is recycled into the interstellar medium (ISM) to form the next generations of stars and planets and, over time, changes the chemical composition of the Galaxy. The amplitude and period distribution of LPVs, and how long they remain in this stage, profoundly impact the type and amount of enriched material that is returned to the ISM. However, a profound impediment to our understanding of this important phase of stellar evolution is the lack of an unbiased sample for the Disk of the Milky Way. Recent variability surveys of the Magellanic Clouds and the Galactic Bulge have accurately counted LPVs in those environments as a function of luminosity, pulsation mode, and period - but no suitable comparison exists for the Galactic Disk. Current counts of Galactic LPVs are from heterogeneous compilations of countless observing programs, each with its own biases. Consequently, the impact of these populations of evolved stars on their host galaxies at solar metallicities remains unknown. Our project will use the FFIs from the Kepler archive to address this need by creating the first unbiased catalog of Disk LPVs and analyzing their properties. These images of the entire 116 square-degree field, taken at a cadence of about once every 30 days, make it possible for the first time to create an unbiased database of pulsating, dying stars on the asymptotic giant branch in the Disk. We will create an atlas of 1500+ day light curves to characterize their variability and mass-loss properties and to enable

  4. Temporal steering and security of quantum key distribution with mutually unbiased bases against individual attacks

    NASA Astrophysics Data System (ADS)

    Bartkiewicz, Karol; Černoch, Antonín; Lemr, Karel; Miranowicz, Adam; Nori, Franco

    2016-06-01

    Temporal steering, which is a temporal analog of Einstein-Podolsky-Rosen steering, refers to temporal quantum correlations between the initial and final state of a quantum system. Our analysis of temporal steering inequalities in relation to the average quantum bit error rates reveals the interplay between temporal steering and quantum cloning, which guarantees the security of quantum key distribution based on mutually unbiased bases against individual attacks. The key distributions analyzed here include the Bennett-Brassard 1984 protocol and the six-state 1998 protocol by Bruss. Moreover, we define a temporal steerable weight, which enables us to identify a kind of monogamy of temporal correlation that is essential to quantum cryptography and useful for analyzing various scenarios of quantum causality.

  5. Constructing an un-biased whole body atlas from clinical imaging data by fragment bundling.

    PubMed

    Dorfer, Matthias; Donner, René; Langs, Georg

    2013-01-01

    Atlases have a tremendous impact on the study of anatomy and function, such as in neuroimaging, or cardiac analysis. They provide a means to compare corresponding measurements across populations, or model the variability in a population. Current approaches to construct atlases rely on examples that show the same anatomical structure (e.g., the brain). If we study large heterogeneous clinical populations to capture subtle characteristics of diseases, we cannot assume consistent image acquisition any more. Instead we have to build atlases from imaging data that show only parts of the overall anatomical structure. In this paper we propose a method for the automatic contruction of an un-biased whole body atlas from so-called fragments. Experimental results indicate that the fragment based atlas improves the representation accuracy of the atlas over an initial whole body template initialization.

  6. Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

    PubMed

    Knizia, Gerald

    2013-11-12

    Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

  7. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures.

    PubMed

    Procacci, Piero

    2015-04-21

    In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems.

  8. An unbiased survey for dense cores in the Lynds 1630 molecular cloud

    NASA Technical Reports Server (NTRS)

    Lada, Elizabeth A.; Bally, John; Stark, Antony A.

    1991-01-01

    An unbiased, systematic survey for dense cores within the L1630 (Orion B) molecular cloud has been completed. This survey provides the first complete census of dense (n greater tha 10,000/cu cm) cores within a molecular cloud. To identify the dense gas, 3.6 square degrees of the L1630 cloud were surveyed in the J = 2-1 transition of CS. CS emission was detected over 10 percent of the area surveyed, and this emission is not uniformly distributed throughout the cloud but is confined to 42 dense cores. The size, shape, velocity dispersion, and mass of these cores are examined. Comparison of the mass contained within dense cores with the total gas mass within the surveyed region, estimated from CO emission, reveals that the dense cores constitute only a small fraction (not greater than 19 percent) of the total cloud mass.

  9. Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy.

    PubMed

    Mathan, Till S M; Textor, Johannes; Sköld, Annette E; Reinieren-Beeren, Inge; van Oorschot, Tom; Brüning, Mareke; Figdor, Carl G; Buschow, Sonja I; Bakdash, Ghaith; de Vries, I Jolanda M

    2017-02-08

    Effective stimulation of immune cells is crucial for the success of cancer immunotherapies. Current approaches to evaluate the efficiency of stimuli are mainly defined by known flow cytometry-based cell activation or cell maturation markers. This method however does not give a complete overview of the achieved activation state and may leave important side effects unnoticed. Here, we used an unbiased RNA sequencing (RNA-seq)-based approach to compare the capacity of four clinical-grade dendritic cell (DC) activation stimuli used to prepare DC-vaccines composed of various types of DC subsets; the already clinically applied GM-CSF and Frühsommer meningoencephalitis (FSME) prophylactic vaccine and the novel clinical grade adjuvants protamine-RNA complexes (pRNA) and CpG-P. We found that GM-CSF and pRNA had similar effects on their target cells, whereas pRNA and CpG-P induced stronger type I interferon (IFN) expression than FSME. In general, the pathways most affected by all stimuli were related to immune activity and cell migration. GM-CSF stimulation, however, also induced a significant increase of genes related to nonsense-mediated decay, indicating a possible deleterious effect of this stimulus. Taken together, the two novel stimuli appear to be promising alternatives. Our study demonstrates how RNA-seq based investigation of changes in a large number of genes and gene groups can be exploited for fast and unbiased, global evaluation of clinical-grade stimuli, as opposed to the general limited evaluation of a pre-specified set of genes, by which one might miss important biological effects that are detrimental for vaccine efficacy.

  10. An Unbiased Cell Morphology–Based Screen for New, Biologically Active Small Molecules

    PubMed Central

    Tanaka, Masahiro; Bateman, Raynard; Rauh, Daniel; Vaisberg, Eugeni; Ramachandani, Shyam; Zhang, Chao; Hansen, Kirk C; Burlingame, Alma L; Trautman, Jay K; Adams, Cynthia L

    2005-01-01

    We have implemented an unbiased cell morphology–based screen to identify small-molecule modulators of cellular processes using the Cytometrix (TM) automated imaging and analysis system. This assay format provides unbiased analysis of morphological effects induced by small molecules by capturing phenotypic readouts of most known classes of pharmacological agents and has the potential to read out pathways for which little is known. Four human-cancer cell lines and one noncancerous primary cell type were treated with 107 small molecules comprising four different protein kinase–inhibitor scaffolds. Cellular phenotypes induced by each compound were quantified by multivariate statistical analysis of the morphology, staining intensity, and spatial attributes of the cellular nuclei, microtubules, and Golgi compartments. Principal component analysis was used to identify inhibitors of cellular components not targeted by known protein kinase inhibitors. Here we focus on a hydroxyl-substituted analog (hydroxy-PP) of the known Src-family kinase inhibitor PP2 because it induced cell-specific morphological features distinct from all known kinase inhibitors in the collection. We used affinity purification to identify a target of hydroxy-PP, carbonyl reductase 1 (CBR1), a short-chain dehydrogenase-reductase. We solved the X-ray crystal structure of the CBR1/hydroxy-PP complex to 1.24 Å resolution. Structure-based design of more potent and selective CBR1 inhibitors provided probes for analyzing the biological function of CBR1 in A549 cells. These studies revealed a previously unknown function for CBR1 in serum-withdrawal-induced apoptosis. Further studies indicate CBR1 inhibitors may enhance the effectiveness of anticancer anthracyclines. Morphology-based screening of diverse cancer cell types has provided a method for discovering potent new small-molecule probes for cell biological studies and anticancer drug candidates. PMID:15799708

  11. Unbiased split variable selection for random survival forests using maximally selected rank statistics.

    PubMed

    Wright, Marvin N; Dankowski, Theresa; Ziegler, Andreas

    2017-04-15

    The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistic, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables. An alternative is to use maximally selected rank statistics for the split point selection. As in conditional inference forests, splitting variables are compared on the p-value scale. However, instead of the conditional Monte-Carlo approach used in conditional inference forests, p-value approximations are employed. We describe several p-value approximations and the implementation of the proposed random forest approach. A simulation study demonstrates that unbiased split variable selection is possible. However, there is a trade-off between unbiased split variable selection and runtime. In benchmark studies of prediction performance on simulated and real datasets, the new method performs better than random survival forests if informative dichotomous variables are combined with uninformative variables with more categories and better than conditional inference forests if non-linear covariate effects are included. In a runtime comparison, the method proves to be computationally faster than both alternatives, if a simple p-value approximation is used. Copyright © 2017 John Wiley & Sons, Ltd.

  12. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

    PubMed Central

    Gritsenko, Alexey A.; Hulsman, Marc; Reinders, Marcel J. T.; de Ridder, Dick

    2015-01-01

    Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of computational models of the process have been proposed, their application is limited by the assumptions they make. Ribosome profiling (RP), a relatively new sequencing-based technique capable of recording snapshots of the locations of actively translating ribosomes, is a promising source of information for deriving unbiased data-driven translation models. However, quantitative analysis of RP data is challenging due to high measurement variance and the inability to discriminate between the number of ribosomes measured on a gene and their speed of translation. We propose a solution in the form of a novel multi-scale interpretation of RP data that allows for deriving models with translation dynamics extracted from the snapshots. We demonstrate the usefulness of this approach by simultaneously determining for the first time per-codon translation elongation and per-gene translation initiation rates of Saccharomyces cerevisiae from RP data for two versions of the Totally Asymmetric Exclusion Process (TASEP) model of translation. We do this in an unbiased fashion, by fitting the models using only RP data with a novel optimization scheme based on Monte Carlo simulation to keep the problem tractable. The fitted models match the data significantly better than existing models and their predictions show better agreement with several independent protein abundance datasets than existing models. Results additionally indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates. PMID:26275099

  13. Testing assumptions for unbiased estimation of survival of radiomarked harlequin ducks

    USGS Publications Warehouse

    Esler, Daniel; Mulcahy, Daniel M.; Jarvis, Robert L.

    2000-01-01

    Unbiased estimates of survival based on individuals outfitted with radiotransmitters require meeting the assumptions that radios do not affect survival, and animals for which the radio signal is lost have the same survival probability as those for which fate is known. In most survival studies, researchers have made these assumptions without testing their validity. We tested these assumptions by comparing interannual recapture rates (and, by inference, survival) between radioed and unradioed adult female harlequin ducks (Histrionicus histrionicus), and for radioed females, between right-censored birds (i.e., those for which the radio signal was lost during the telemetry monitoring period) and birds with known fates. We found that recapture rates of birds equipped with implanted radiotransmitters (21.6 ± 3.0%; x̄ ± SE) were similar to unradioed birds (21.7 ± 8.6%), suggesting that radios did not affect survival. Recapture rates also were similar between right-censored (20.6 ± 5.1%) and known-fate individuals (22.1 ± 3.8%), suggesting that missing birds were not subject to differential mortality. We also determined that capture and handling resulted in short-term loss of body mass for both radioed and unradioed females and that this effect was more pronounced for radioed birds (the difference between groups was 15.4 ± 7.1 g). However, no difference existed in body mass after recapture 1 year later. Our study suggests that implanted radios are an unbiased method for estimating survival of harlequin ducks and likely other species under similar circumstances.

  14. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

    PubMed

    Gritsenko, Alexey A; Hulsman, Marc; Reinders, Marcel J T; de Ridder, Dick

    2015-08-01

    Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of computational models of the process have been proposed, their application is limited by the assumptions they make. Ribosome profiling (RP), a relatively new sequencing-based technique capable of recording snapshots of the locations of actively translating ribosomes, is a promising source of information for deriving unbiased data-driven translation models. However, quantitative analysis of RP data is challenging due to high measurement variance and the inability to discriminate between the number of ribosomes measured on a gene and their speed of translation. We propose a solution in the form of a novel multi-scale interpretation of RP data that allows for deriving models with translation dynamics extracted from the snapshots. We demonstrate the usefulness of this approach by simultaneously determining for the first time per-codon translation elongation and per-gene translation initiation rates of Saccharomyces cerevisiae from RP data for two versions of the Totally Asymmetric Exclusion Process (TASEP) model of translation. We do this in an unbiased fashion, by fitting the models using only RP data with a novel optimization scheme based on Monte Carlo simulation to keep the problem tractable. The fitted models match the data significantly better than existing models and their predictions show better agreement with several independent protein abundance datasets than existing models. Results additionally indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates.

  15. Crack spectra analysis

    SciTech Connect

    Tiernan, M.

    1980-09-01

    Crack spectra derived from velocity data have been shown to exhibit systematics which reflect microstructural and textural differences between samples (Warren and Tiernan, 1980). Further research into both properties and information content of crack spectra have yielded the following: Spectral features are reproducible even at low pressures; certain observed spectral features may correspond to non-in-situ crack populations created during sample retrieval; the functional form of a crack spectra may be diagnostic of the sample's grain texture; hysteresis is observed in crack spectra between up and down pressure runs - it may be due to friction between the faces of closed crack populations.

  16. Photographic spectra of fireballs

    NASA Astrophysics Data System (ADS)

    Borovička, J.

    2016-01-01

    Two methods of spectroscopy of meteors using image intensified video cameras and classical photographic film cameras are compared. Video cameras provide large number of low resolution spectra of meteors of normal brightness, which can be used for statistical studies. Large format film cameras have been used through the history and provide high resolution spectra, which can be used to derive temperature, density and absolute abundances of various elements in the radiating plasma. The sensitivity of films is, however, low and only spectra of bright meteors (fireballs) can be studied. Examples of photographic fireball spectra are provided.

  17. Studies of the Unbiased Fir Filter for the Time Error Model in Applications to GPS-Based Timekeeping

    DTIC Science & Technology

    2004-12-01

    TIMEKEEPING1 Yu. Shmaliy and O. Ibarra-Manzano Guanajuato University, FIMEE, Mexico E-mail: shmaliy@salamanca.ugto.mx Abstract The unbiased FIR filter...5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Guanajuato University,FIMEE, Mexico, 8. PERFORMING

  18. Block-circulant matrices with circulant blocks, Weil sums, and mutually unbiased bases. II. The prime power case

    SciTech Connect

    Combescure, Monique

    2009-03-15

    In our previous paper [Combescure, M., 'Circulant matrices, Gauss sums and the mutually unbiased bases. I. The prime number case', Cubo A Mathematical Journal (unpublished)] we have shown that the theory of circulant matrices allows to recover the result that there exists p+1 mutually unbiased bases in dimension p, p being an arbitrary prime number. Two orthonormal bases B, B{sup '} of C{sup d} are said mutually unbiased if for all b(set-membership sign)B, for all b{sup '}(set-membership sign)B{sup '} one has that |b{center_dot}b{sup '}|=1/{radical}(d) (b{center_dot}b{sup '} Hermitian scalar product in C{sup d}). In this paper we show that the theory of block-circulant matrices with circulant blocks allows to show very simply the known result that if d=p{sup n} (p a prime number and n any integer) there exists d+1 mutually unbiased bases in C{sup d}. Our result relies heavily on an idea of Klimov et al. [''Geometrical approach to the discrete Wigner function,'' J. Phys. A 39, 14471 (2006)]. As a subproduct we recover properties of quadratic Weil sums for p{>=}3, which generalizes the fact that in the prime case the quadratic Gauss sum properties follow from our results.

  19. Combination of an unbiased amplification method and a resequencing microarray for detecting and genotyping equine arteritis virus.

    PubMed

    Hans, Aymeric; Gaudaire, Delphine; Manuguerra, Jean-Claude; Leon, Albertine; Gessain, Antoine; Laugier, Claire; Berthet, Nicolas; Zientara, Stephan

    2015-01-01

    This study shows that an unbiased amplification method applied to equine arteritis virus RNA significantly improves the sensitivity of the real-time reverse transcription-quantitative PCR (RT-qPCR) recommended by the World Organization for Animal Health. Twelve viral RNAs amplified using this method were hybridized on a high-density resequencing microarray for effective viral characterization.

  20. Unbiased analysis of pancreatic cancer radiation resistance reveals cholesterol biosynthesis as a novel target for radiosensitisation

    PubMed Central

    Souchek, J J; Baine, M J; Lin, C; Rachagani, S; Gupta, S; Kaur, S; Lester, K; Zheng, D; Chen, S; Smith, L; Lazenby, A; Johansson, S L; Jain, M; Batra, S K

    2014-01-01

    Background: Despite its promise as a highly useful therapy for pancreatic cancer (PC), the addition of external beam radiation therapy to PC treatment has shown varying success in clinical trials. Understanding PC radioresistance and discovery of methods to sensitise PC to radiation will increase patient survival and improve quality of life. In this study, we identified PC radioresistance-associated pathways using global, unbiased techniques. Methods: Radioresistant cells were generated by sequential irradiation and recovery, and global genome cDNA microarray analysis was performed to identify differentially expressed genes in radiosensitive and radioresistant cells. Ingenuity pathway analysis was performed to discover cellular pathways and functions associated with differential radioresponse and identify potential small-molecule inhibitors for radiosensitisation. The expression of FDPS, one of the most differentially expressed genes, was determined in human PC tissues by IHC and the impact of its pharmacological inhibition with zoledronic acid (ZOL, Zometa) on radiosensitivity was determined by colony-forming assays. The radiosensitising effect of Zol in vivo was determined using allograft transplantation mouse model. Results: Microarray analysis indicated that 11 genes (FDPS, ACAT2, AG2, CLDN7, DHCR7, ELFN2, FASN, SC4MOL, SIX6, SLC12A2, and SQLE) were consistently associated with radioresistance in the cell lines, a majority of which are involved in cholesterol biosynthesis. We demonstrated that knockdown of farnesyl diphosphate synthase (FDPS), a branchpoint enzyme of the cholesterol synthesis pathway, radiosensitised PC cells. FDPS was significantly overexpressed in human PC tumour tissues compared with healthy pancreas samples. Also, pharmacologic inhibition of FDPS by ZOL radiosensitised PC cell lines, with a radiation enhancement ratio between 1.26 and 1.5. Further, ZOL treatment resulted in radiosensitisation of PC tumours in an allograft mouse model

  1. Identification and quantification of peptides and proteins secreted from prostate epithelial cells by unbiased liquid chromatography tandem mass spectrometry using goodness of fit and analysis of variance.

    PubMed

    Florentinus, Angelica K; Bowden, Peter; Sardana, Girish; Diamandis, Eleftherios P; Marshall, John G

    2012-02-02

    The proteins secreted by prostate cancer cells (PC3(AR)6) were separated by strong anion exchange chromatography, digested with trypsin and analyzed by unbiased liquid chromatography tandem mass spectrometry with an ion trap. The spectra were matched to peptides within proteins using a goodness of fit algorithm that showed a low false positive rate. The parent ions for MS/MS were randomly and independently sampled from a log-normal population and therefore could be analyzed by ANOVA. Normal distribution analysis confirmed that the parent and fragment ion intensity distributions were sampled over 99.9% of their range that was above the background noise. Arranging the ion intensity data with the identified peptide and protein sequences in structured query language (SQL) permitted the quantification of ion intensity across treatments, proteins and peptides. The intensity of 101,905 fragment ions from 1421 peptide precursors of 583 peptides from 233 proteins separated over 11 sample treatments were computed together in one ANOVA model using the statistical analysis system (SAS) prior to Tukey-Kramer honestly significant difference (HSD) testing. Thus complex mixtures of proteins were identified and quantified with a high degree of confidence using an ion trap without isotopic labels, multivariate analysis or comparing chromatographic retention times.

  2. Orientation decoding in human visual cortex: new insights from an unbiased perspective.

    PubMed

    Carlson, Thomas A

    2014-06-11

    The development of multivariate pattern analysis or brain "decoding" methods has substantially altered the field of fMRI research. Although these methods are highly sensitive to whether or not decodable information exists, the information they discover and make use of for decoding is often concealed within complex patterns of activation. This opacity of interpretation is embodied in influential studies showing that the orientation of visual gratings can be decoded from brain activity in human visual cortex with fMRI. Although these studies provided a compelling demonstration of the power of these methods, their findings were somewhat mysterious as the scanning resolution was insufficient to resolve orientation columns, i.e., orientation information should not have been accessible. Two theories have been put forth to account for this result, the hyperacuity account and the biased map account, both of which assume that small biases in fMRI voxels are the source of decodable information. In the present study, we use Hubel and Wiesel's (1972) classic ice-cube model of visual cortex to show that the orientation of gratings can be decoded from an unbiased representation. In our analysis, we identify patterns of activity elicited by the edges of the stimulus as the source of the decodable information. Furthermore, these activation patterns masquerade as a radial bias, a key element of the biased map account. This classic model thus sheds new light on the mystery behind orientation decoding by unveiling a new source of decodable information.

  3. Iron-based magnetic superhalogens with pseudohalogens as ligands: An unbiased structure search.

    PubMed

    Ping Ding, Li; Shao, Peng; Lu, Cheng; Hui Zhang, Fang; Wang, Li Ya

    2017-03-22

    We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands. The magnetic moment of Fe atom is almost entirly maintained when it is decorated with various ligands except for neutral and anionic (Li2H3)4. Moreover, the current work is also extended to the salt moieties formed by hyperhalogen/superhalogen anion and Na(+) ion. It is found that these salts against dissociation into Na + FeL4 are thermodynamic stable except for Na[Fe(OH)4]. These results provides a wealth of electronic structure information about FeL4 magnetic superhalogens and offer insights into the synthesis mechanisms.

  4. Multifractals embedded in short time series: An unbiased estimation of probability moment

    NASA Astrophysics Data System (ADS)

    Qiu, Lu; Yang, Tianguang; Yin, Yanhua; Gu, Changgui; Yang, Huijie

    2016-12-01

    An exact estimation of probability moments is the base for several essential concepts, such as the multifractals, the Tsallis entropy, and the transfer entropy. By means of approximation theory we propose a new method called factorial-moment-based estimation of probability moments. Theoretical prediction and computational results show that it can provide us an unbiased estimation of the probability moments of continuous order. Calculations on probability redistribution model verify that it can extract exactly multifractal behaviors from several hundred recordings. Its powerfulness in monitoring evolution of scaling behaviors is exemplified by two empirical cases, i.e., the gait time series for fast, normal, and slow trials of a healthy volunteer, and the closing price series for Shanghai stock market. By using short time series with several hundred lengths, a comparison with the well-established tools displays significant advantages of its performance over the other methods. The factorial-moment-based estimation can evaluate correctly the scaling behaviors in a scale range about three generations wider than the multifractal detrended fluctuation analysis and the basic estimation. The estimation of partition function given by the wavelet transform modulus maxima has unacceptable fluctuations. Besides the scaling invariance focused in the present paper, the proposed factorial moment of continuous order can find its various uses, such as finding nonextensive behaviors of a complex system and reconstructing the causality relationship network between elements of a complex system.

  5. The role of fire in UK peatland and moorland management: the need for informed, unbiased debate.

    PubMed

    Davies, G Matt; Kettridge, Nicholas; Stoof, Cathelijne R; Gray, Alan; Ascoli, Davide; Fernandes, Paulo M; Marrs, Rob; Allen, Katherine A; Doerr, Stefan H; Clay, Gareth D; McMorrow, Julia; Vandvik, Vigdis

    2016-06-05

    Fire has been used for centuries to generate and manage some of the UK's cultural landscapes. Despite its complex role in the ecology of UK peatlands and moorlands, there has been a trend of simplifying the narrative around burning to present it as an only ecologically damaging practice. That fire modifies peatland characteristics at a range of scales is clearly understood. Whether these changes are perceived as positive or negative depends upon how trade-offs are made between ecosystem services and the spatial and temporal scales of concern. Here we explore the complex interactions and trade-offs in peatland fire management, evaluating the benefits and costs of managed fire as they are currently understood. We highlight the need for (i) distinguishing between the impacts of fires occurring with differing severity and frequency, and (ii) improved characterization of ecosystem health that incorporates the response and recovery of peatlands to fire. We also explore how recent research has been contextualized within both scientific publications and the wider media and how this can influence non-specialist perceptions. We emphasize the need for an informed, unbiased debate on fire as an ecological management tool that is separated from other aspects of moorland management and from political and economic opinions.This article is part of the themed issue 'The interaction of fire and mankind'.

  6. Time-Dependent Tree-Structured Survival Analysis with Unbiased Variable Selection through Permutation Tests

    PubMed Central

    Wallace, M. L.

    2014-01-01

    Incorporating time-dependent covariates into tree-structured survival analysis (TSSA) may result in more accurate prognostic models than if only baseline values are used. Available time-dependent TSSA methods exhaustively test every binary split on every covariate; however, this approach may result in selection bias towards covariates with more observed values. We present a method that uses unbiased significance levels from newly proposed permutation tests to select the time-dependent or baseline covariate with the strongest relationship with the survival outcome. The specific splitting value is identified using only the selected covariate. Simulation results show that the proposed time-dependent TSSA method produces tree models of equal or greater accuracy as compared to baseline TSSA models, even with high censoring rates and large within-subject variability in the time-dependent covariate. To illustrate, the proposed method is applied to data from a cohort of bipolar youth to identify subgroups at risk for self-injurious behavior. PMID:25043382

  7. The role of fire in UK peatland and moorland management: the need for informed, unbiased debate

    PubMed Central

    Davies, G. Matt; Kettridge, Nicholas; Stoof, Cathelijne R.; Gray, Alan; Ascoli, Davide; Fernandes, Paulo M.; Marrs, Rob; Clay, Gareth D.; McMorrow, Julia; Vandvik, Vigdis

    2016-01-01

    Fire has been used for centuries to generate and manage some of the UK's cultural landscapes. Despite its complex role in the ecology of UK peatlands and moorlands, there has been a trend of simplifying the narrative around burning to present it as an only ecologically damaging practice. That fire modifies peatland characteristics at a range of scales is clearly understood. Whether these changes are perceived as positive or negative depends upon how trade-offs are made between ecosystem services and the spatial and temporal scales of concern. Here we explore the complex interactions and trade-offs in peatland fire management, evaluating the benefits and costs of managed fire as they are currently understood. We highlight the need for (i) distinguishing between the impacts of fires occurring with differing severity and frequency, and (ii) improved characterization of ecosystem health that incorporates the response and recovery of peatlands to fire. We also explore how recent research has been contextualized within both scientific publications and the wider media and how this can influence non-specialist perceptions. We emphasize the need for an informed, unbiased debate on fire as an ecological management tool that is separated from other aspects of moorland management and from political and economic opinions. This article is part of the themed issue ‘The interaction of fire and mankind’. PMID:27216512

  8. An unbiased risk estimator for image denoising in the presence of mixed poisson-gaussian noise.

    PubMed

    Le Montagner, Yoann; Angelini, Elsa D; Olivo-Marin, Jean-Christophe

    2014-03-01

    The behavior and performance of denoising algorithms are governed by one or several parameters, whose optimal settings depend on the content of the processed image and the characteristics of the noise, and are generally designed to minimize the mean squared error (MSE) between the denoised image returned by the algorithm and a virtual ground truth. In this paper, we introduce a new Poisson-Gaussian unbiased risk estimator (PG-URE) of the MSE applicable to a mixed Poisson-Gaussian noise model that unifies the widely used Gaussian and Poisson noise models in fluorescence bioimaging applications. We propose a stochastic methodology to evaluate this estimator in the case when little is known about the internal machinery of the considered denoising algorithm, and we analyze both theoretically and empirically the characteristics of the PG-URE estimator. Finally, we evaluate the PG-URE-driven parametrization for three standard denoising algorithms, with and without variance stabilizing transforms, and different characteristics of the Poisson-Gaussian noise mixture.

  9. An unbiased expression screen for synaptogenic proteins identifies the LRRTM protein family as synaptic organizers.

    PubMed

    Linhoff, Michael W; Laurén, Juha; Cassidy, Robert M; Dobie, Frederick A; Takahashi, Hideto; Nygaard, Haakon B; Airaksinen, Matti S; Strittmatter, Stephen M; Craig, Ann Marie

    2009-03-12

    Delineating the molecular basis of synapse development is crucial for understanding brain function. Cocultures of neurons with transfected fibroblasts have demonstrated the synapse-promoting activity of candidate molecules. Here, we performed an unbiased expression screen for synaptogenic proteins in the coculture assay using custom-made cDNA libraries. Reisolation of NGL-3/LRRC4B and neuroligin-2 accounts for a minority of positive clones, indicating that current understanding of mammalian synaptogenic proteins is incomplete. We identify LRRTM1 as a transmembrane protein that induces presynaptic differentiation in contacting axons. All four LRRTM family members exhibit synaptogenic activity, LRRTMs localize to excitatory synapses, and artificially induced clustering of LRRTMs mediates postsynaptic differentiation. We generate LRRTM1(-/-) mice and reveal altered distribution of the vesicular glutamate transporter VGLUT1, confirming an in vivo synaptic function. These results suggest a prevalence of LRR domain proteins in trans-synaptic signaling and provide a cellular basis for the reported linkage of LRRTM1 to handedness and schizophrenia.

  10. Hetero-type dual photoanodes for unbiased solar water splitting with extended light harvesting.

    PubMed

    Kim, Jin Hyun; Jang, Ji-Wook; Jo, Yim Hyun; Abdi, Fatwa F; Lee, Young Hye; van de Krol, Roel; Lee, Jae Sung

    2016-12-14

    Metal oxide semiconductors are promising photoelectrode materials for solar water splitting due to their robustness in aqueous solutions and low cost. Yet, their solar-to-hydrogen conversion efficiencies are still not high enough for practical applications. Here we present a strategy to enhance the efficiency of metal oxides, hetero-type dual photoelectrodes, in which two photoanodes of different bandgaps are connected in parallel for extended light harvesting. Thus, a photoelectrochemical device made of modified BiVO4 and α-Fe2O3 as dual photoanodes utilizes visible light up to 610 nm for water splitting, and shows stable photocurrents of 7.0±0.2 mA cm(-2) at 1.23 VRHE under 1 sun irradiation. A tandem cell composed with the dual photoanodes-silicon solar cell demonstrates unbiased water splitting efficiency of 7.7%. These results and concept represent a significant step forward en route to the goal of >10% efficiency required for practical solar hydrogen production.

  11. Predicting hybrid performance in rice using genomic best linear unbiased prediction.

    PubMed

    Xu, Shizhong; Zhu, Dan; Zhang, Qifa

    2014-08-26

    Genomic selection is an upgrading form of marker-assisted selection for quantitative traits, and it differs from the traditional marker-assisted selection in that markers in the entire genome are used to predict genetic values and the QTL detection step is skipped. Genomic selection holds the promise to be more efficient than the traditional marker-assisted selection for traits controlled by polygenes. Genomic selection for pure breed improvement is based on marker information and thus leads to cost-saving due to early selection before phenotypes are measured. When applied to hybrid breeding, genomic selection is anticipated to be even more efficient because genotypes of hybrids are predetermined by their inbred parents. Hybrid breeding has been an important tool to increase crop productivity. Here we proposed and applied an advanced method to predict hybrid performance, in which a subset of all potential hybrids is used as a training sample to predict trait values of all potential hybrids. The method is called genomic best linear unbiased prediction. The technology applied to hybrids is called genomic hybrid breeding. We used 278 randomly selected hybrids derived from 210 recombinant inbred lines of rice as a training sample and predicted all 21,945 potential hybrids. The average yield of top 100 selection shows a 16% increase compared with the average yield of all potential hybrids. The new strategy of marker-guided prediction of hybrid yields serves as a proof of concept for a new technology that may potentially revolutionize hybrid breeding.

  12. Unbiased Discovery of Glypican as a Novel Receptor for LRRTM4 in Regulating Excitatory Synapse Development

    PubMed Central

    de Wit, Joris; O’Sullivan, Matthew L.; Savas, Jeffrey N.; Condomitti, Giuseppe; Caccese, Max C.; Vennekens, Kristel M.; Yates, John R.; Ghosh, Anirvan

    2014-01-01

    SUMMARY Leucine-rich repeat (LRR) proteins have recently been identified as important regulators of synapse development and function, but for many LRR proteins the ligand-receptor interactions are not known. Here we identify the heparan sulfate (HS) proteoglycan glypican as a novel receptor for LRRTM4 using an unbiased proteomics-based approach. Glypican binds LRRTM4, but not LRRTM2, in a HS-dependent manner. Glypican 4 (GPC4) and LRRTM4 localize to the pre- and postsynaptic membranes of excitatory synapses, respectively. Consistent with a trans-synaptic interaction, LRRTM4 triggers GPC4 clustering in contacting axons and GPC4 induces clustering of LRRTM4 in contacting dendrites in a HS-dependent manner. LRRTM4 positively regulates excitatory synapse development in cultured neurons and in vivo, and the synaptogenic activity of LRRTM4 requires the presence of HS on the neuronal surface. Our results identify glypican as a novel LRRTM4 receptor and indicate that a trans-synaptic glypican-LRRTM4 interaction regulates excitatory synapse development. PMID:23911103

  13. Iron-based magnetic superhalogens with pseudohalogens as ligands: An unbiased structure search

    PubMed Central

    Ping Ding, Li; Shao, Peng; Lu, Cheng; Hui Zhang, Fang; Wang, Li Ya

    2017-01-01

    We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands. The magnetic moment of Fe atom is almost entirly maintained when it is decorated with various ligands except for neutral and anionic (Li2H3)4. Moreover, the current work is also extended to the salt moieties formed by hyperhalogen/superhalogen anion and Na+ ion. It is found that these salts against dissociation into Na + FeL4 are thermodynamic stable except for Na[Fe(OH)4]. These results provides a wealth of electronic structure information about FeL4 magnetic superhalogens and offer insights into the synthesis mechanisms. PMID:28327547

  14. Proteomics in Parkinson's disease: An unbiased approach towards peripheral biomarkers and new therapies.

    PubMed

    Alberio, Tiziana; Fasano, Mauro

    2011-12-20

    Parkinson's disease is the most common neurodegenerative movement disorder, affecting about 6 million people worldwide with a slow progression of the symptoms. Its prevalence is expected to double in the most populated areas within the next two decades, according to increasing aged population. Consequently, Parkinson's disease is a socio-economic trouble and a major challenge for the public health system. Parkinson's disease treatment is merely symptomatic, as clinical symptoms appear when about 70% of the involved neurons are lost and potential disease-modifying/neuroprotective therapies would have no effect. In turn, the availability of an objective measure that allows early diagnosis would strongly impact on the costs that biotech- and pharma-companies will sustain in order to develop disease-modifying therapies. The establishment of suitable models to investigate the mechanisms of Parkinson's disease progression and, on the other hand, the discovery and validation of selective and specific molecular biomarkers for early and differential diagnosis are indeed two important goals for a better management of the disease. In this review, we focus on cellular and animal models of Parkinson's disease by describing their advantages and limitations as useful tools to identify pathogenetic pathways that deserve further exploitation. In parallel, we discuss how proteomics may provide a potent tool to observe altered pathways in models or altered biomarkers in patients with an unbiased, hypothesis-free approach.

  15. The First Unbiased Radio Emission Line Survey of the Protoplanetary Disk Orbiting Lkca 15

    NASA Astrophysics Data System (ADS)

    Punzi, Kristina Marie; Kastner, Joel H.; Hily-Blant, Pierre; Forveille, Thierry; Sacco, G. G.

    2014-06-01

    We have conducted the first comprehensive mm-wave molecular emission line survey of the circumstellar disk orbiting the nearby, pre-main sequence (T Tauri) star LkCa 15 (D = 140 pc). The outer disk is chemically rich, with numerous previous detections of molecular emission lines revealing a significant gas mass. The disk around this young (˜3-5 Myr), actively accreting solar analog likely hosts a young protoplanet (LkCa 15b) within its central cavity. Hence, LkCa 15 is an excellent target for an unbiased radio spectroscopic survey intended to produce a full census of the detectable molecular species within an evolved, protoplanetary disk. Our survey of LkCa 15 was conducted with the Institute de Radioastronomie Millimétrique (IRAM) 30 meter telescope over the 1.1-1.4 mm wavelength range. The survey includes detections of the three most abundant CO isotopologues (12CO, 13CO, and C18O) which facilitate estimates of the spatially integrated CO emission line optical depths, and complete coverage of the hyperfine line complexes of CN and C2H that provide diagnostics of excitation and opacity for these species. This work demonstrates the value of comprehensive single-dish line surveys in guiding future high resolution interferometric imaging by ALMA of protoplanetary disks orbiting T Tauri stars.

  16. Estimating time-correlation functions by sampling and unbiasing dynamically activated events.

    PubMed

    Athènes, Manuel; Marinica, Mihai-Cosmin; Jourdan, Thomas

    2012-11-21

    Transition path sampling is a rare-event method that estimates state-to-state time-correlation functions in many-body systems from samples of short trajectories. In this framework, it is proposed to bias the importance function using the lowest Jacobian eigenvalue moduli along the dynamical trajectory. A lowest eigenvalue modulus is related to the lowest eigenvalue of the Hessian matrix and is evaluated here using the Lanczos algorithm as in activation-relaxation techniques. This results in favoring the sampling of activated trajectories and enhancing the occurrence of the rare reactive trajectories of interest, those corresponding to transitions between locally stable states. Estimating the time-correlation functions involves unbiasing the sample of simulated trajectories which is done using the multi-state Bennett acceptance ratio (MBAR) method. To assess the performance of our procedure, we compute the time-correlation function associated with the migration of a vacancy in α-iron. The derivative of the estimated time-correlation function yields a migration rate in agreement with the one given by transition state theory. Besides, we show that the information relative to rejected trajectories can be recycled within MBAR, resulting in a substantial speed-up. Unlike original transition path-sampling, our approach does not require computing the reversible work to confine the trajectory endpoints to a reactive state.

  17. An unbiased index to quantify participant’s phenotypic contribution to an open-access cohort

    PubMed Central

    Chan, Yingleong; Tung, Michael; Garruss, Alexander S.; Zaranek, Sarah W.; Chan, Ying Kai; Lunshof, Jeantine E.; Zaranek, Alexander W.; Ball, Madeleine P.; Chou, Michael F.; Lim, Elaine T.; Church, George M.

    2017-01-01

    The Personal Genome Project (PGP) is an effort to enroll many participants to create an open-access repository of genome, health and trait data for research. However, PGP participants are not enrolled for studying any specific traits and participants choose the phenotypes to disclose. To measure the extent and willingness and to encourage and guide participants to contribute phenotypes, we developed an algorithm to score and rank the phenotypes and participants of the PGP. The scoring algorithm calculates the participation index (P-index) for every participant, where 0 indicates no reported phenotypes and 100 indicate complete phenotype reporting. We calculated the P-index for all 5,015 participants in the PGP and they ranged from 0 to 96.7. We found that participants mainly have either high scores (P-index > 90, 29.5%) or low scores (P-index < 10, 57.8%). While, there are significantly more males than female participants (1,793 versus 1,271), females tend to have on average higher P-indexes (P = 0.015). We also reported the P-indexes of participants based on demographics and states like Missouri and Massachusetts have better P-indexes than states like Utah and Minnesota. The P-index can therefore be used as an unbiased way to measure and rank participant’s phenotypic contribution towards the PGP. PMID:28387241

  18. Unbiased identification of protein-bait interactions using biochemical enrichment and quantitative proteomics.

    PubMed

    Ong, Shao-En

    2010-03-01

    The use of recombinant proteins, antibodies, small molecules, or nucleic acids as affinity reagents is a simple yet powerful strategy to study the protein-bait interactions that drive biological processes. However, such experiments are often analyzed by Western blotting, limiting the ability to detect novel protein interactors. Unbiased protein identification by mass spectrometry (MS) extends these experiments beyond the study of pairwise interactions, allowing analyses of whole networks of protein-bait interactions. With the latest advances in MS, it is not uncommon to identify thousands of proteins from complex mixtures. Paradoxically, the improved sensitivity of proteomic analyses can make it more difficult to distinguish bait-specific interactions from the large background of identified proteins. In quantitative proteomics, MS signals from protein populations labeled with stable isotopes such as (13)C and (15)N can be identified and quantified relative to unlabeled counterparts. Using quantitative proteomics to compare biochemical enrichments with the bait of interest against those obtained with control baits allows sensitive detection and discrimination of specific protein-bait interactions among the large number of nonspecific interactions with beads. Ad hoc optimization of enrichment conditions is minimized, and mild purification conditions preserve secondary or high-order protein-protein interactions. The combination of biochemical enrichment and quantitative proteomics allows rapid characterization of molecular baits with their interacting proteins, providing tremendous insight into their biological mechanisms of action.

  19. Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

    PubMed Central

    Donovan, Rory M.; Tapia, Jose-Juan; Sullivan, Devin P.; Faeder, James R.; Murphy, Robert F.; Dittrich, Markus; Zuckerman, Daniel M.

    2016-01-01

    The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation—by orders of magnitude for some observables. PMID:26845334

  20. Unbiased simultaneous estimation of soil hydraulic properties and dynamic nonequilibrium parameters from transient outflow experiments

    NASA Astrophysics Data System (ADS)

    Iden, S. C.; Diamantopoulos, E.; Durner, W.

    2012-04-01

    Simulation of variably saturated water flow in soils requires accurate knowledge of soil hydraulic properties. Transient flow experiments like the multistep outflow and evaporation methods are now routinely applied to determine soil hydraulic parameters by inverse modelling. Recent experimental evidence suggests that the water content dynamics during such flow experiments is subject to dynamic non-equilibrium. The extent to which this affects the accuracy of determining the equilibrium soil hydraulic properties is still unknown. Conversely, any bias in the equilibrium soil hydraulic properties caused by an inappropriate parameterization must be expected to lead to biased estimates of the parameters describing the hydraulic non-equilibrium. We coupled a dual porosity non-equilibrium model which combines the Richards equation and the Ross and Smettem approach for non-equilibrium with a free-form inversion algorithm. The free-form method has been shown before to guarantee an unbiased estimation of soil hydraulic properties. The freeform non-equilibrium estimation method was applied to data from various multistep outflow experiments. The results confirm that errors in the parameterization of the soil hydraulic properties cause biased estimates of non-equilibrium parameters. Such bias can be minimized or even eliminated with the free-form approach.

  1. Iron-based magnetic superhalogens with pseudohalogens as ligands: An unbiased structure search

    NASA Astrophysics Data System (ADS)

    Ping Ding, Li; Shao, Peng; Lu, Cheng; Hui Zhang, Fang; Wang, Li Ya

    2017-03-01

    We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands. The magnetic moment of Fe atom is almost entirly maintained when it is decorated with various ligands except for neutral and anionic (Li2H3)4. Moreover, the current work is also extended to the salt moieties formed by hyperhalogen/superhalogen anion and Na+ ion. It is found that these salts against dissociation into Na + FeL4 are thermodynamic stable except for Na[Fe(OH)4]. These results provides a wealth of electronic structure information about FeL4 magnetic superhalogens and offer insights into the synthesis mechanisms.

  2. Unraveling cognitive traits using the Morris water maze unbiased strategy classification (MUST-C) algorithm.

    PubMed

    Illouz, Tomer; Madar, Ravit; Louzon, Yoram; Griffioen, Kathleen J; Okun, Eitan

    2016-02-01

    The assessment of spatial cognitive learning in rodents is a central approach in neuroscience, as it enables one to assess and quantify the effects of treatments and genetic manipulations from a broad perspective. Although the Morris water maze (MWM) is a well-validated paradigm for testing spatial learning abilities, manual categorization of performance in the MWM into behavioral strategies is subject to individual interpretation, and thus to biases. Here we offer a support vector machine (SVM) - based, automated, MWM unbiased strategy classification (MUST-C) algorithm, as well as a cognitive score scale. This model was examined and validated by analyzing data obtained from five MWM experiments with changing platform sizes, revealing a limitation in the spatial capacity of the hippocampus. We have further employed this algorithm to extract novel mechanistic insights on the impact of members of the Toll-like receptor pathway on cognitive spatial learning and memory. The MUST-C algorithm can greatly benefit MWM users as it provides a standardized method of strategy classification as well as a cognitive scoring scale, which cannot be derived from typical analysis of MWM data.

  3. Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression

    PubMed Central

    Laimighofer, Michael; Krumsiek, Jan; Theis, Fabian J.

    2016-01-01

    Abstract With widespread availability of omics profiling techniques, the analysis and interpretation of high-dimensional omics data, for example, for biomarkers, is becoming an increasingly important part of clinical medicine because such datasets constitute a promising resource for predicting survival outcomes. However, early experience has shown that biomarkers often generalize poorly. Thus, it is crucial that models are not overfitted and give accurate results with new data. In addition, reliable detection of multivariate biomarkers with high predictive power (feature selection) is of particular interest in clinical settings. We present an approach that addresses both aspects in high-dimensional survival models. Within a nested cross-validation (CV), we fit a survival model, evaluate a dataset in an unbiased fashion, and select features with the best predictive power by applying a weighted combination of CV runs. We evaluate our approach using simulated toy data, as well as three breast cancer datasets, to predict the survival of breast cancer patients after treatment. In all datasets, we achieve more reliable estimation of predictive power for unseen cases and better predictive performance compared to the standard CoxLasso model. Taken together, we present a comprehensive and flexible framework for survival models, including performance estimation, final feature selection, and final model construction. The proposed algorithm is implemented in an open source R package (SurvRank) available on CRAN. PMID:26894327

  4. Unbiased discovery of glypican as a receptor for LRRTM4 in regulating excitatory synapse development.

    PubMed

    de Wit, Joris; O'Sullivan, Matthew L; Savas, Jeffrey N; Condomitti, Giuseppe; Caccese, Max C; Vennekens, Kristel M; Yates, John R; Ghosh, Anirvan

    2013-08-21

    Leucine-rich repeat (LRR) proteins have recently been identified as important regulators of synapse development and function, but for many LRR proteins the ligand-receptor interactions are not known. Here we identify the heparan sulfate (HS) proteoglycan glypican as a receptor for LRRTM4 using an unbiased proteomics-based approach. Glypican binds LRRTM4, but not LRRTM2, in an HS-dependent manner. Glypican 4 (GPC4) and LRRTM4 localize to the pre- and postsynaptic membranes of excitatory synapses, respectively. Consistent with a trans-synaptic interaction, LRRTM4 triggers GPC4 clustering in contacting axons and GPC4 induces clustering of LRRTM4 in contacting dendrites in an HS-dependent manner. LRRTM4 positively regulates excitatory synapse development in cultured neurons and in vivo, and the synaptogenic activity of LRRTM4 requires the presence of HS on the neuronal surface. Our results identify glypican as an LRRTM4 receptor and indicate that a trans-synaptic glypican-LRRTM4 interaction regulates excitatory synapse development.

  5. A wide range of activity duration cutoffs provided unbiased estimates of exposure to computer use.

    PubMed

    Chang, Che-Hsu; Johnson, Peter W; Dennerlein, Jack T

    2008-12-01

    Integrative computer usage monitors have become widely used in epidemiologic studies to investigate the exposure-response relationship of computer-related musculoskeletal disorders. These software programs typically estimate the exposure duration of computer use by summing precisely recorded durations of input device activities and durations of inactivity periods shorter than a predetermined activity duration cutoff value, usually 30 or 60 sec. The goal of this study was to systematically compare the validity of a wide range of cutoff values. Computer use activity of 20 office workers was observed for 4 consecutive hours using both a video camera and a usage monitor. Video recordings from the camera were analyzed using specific observational criteria to determine computer use duration. This observed duration then served as the reference and was compared with 238 estimates of computer use duration calculated from the usage monitor data using activity duration cutoffs ranging from 3 to 240 sec in 1-sec increments. Estimates calculated with cutoffs ranging from 28 to 60 sec were highly correlated with the observed duration (Spearman's correlation 0.87 to 0.92) and had nearly ideal linear relationships with the observed duration (slopes and r-squares close to one, and intercepts close to zero). For the same range of cutoff values, when the observed and estimated durations were compared for dichotomous exposure classification across participants, minimal exposure misclassification was observed. It is concluded that activity duration cutoffs ranging from 28 to 60 sec provided unbiased estimates of computer use duration.

  6. Lily Pad Spectra

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The color image on the lower left from the panoramic camera on the Mars Exploration Rover Opportunity shows the 'Lily Pad' bounce-mark area at Meridiani Planum, Mars. This image was acquired on the 3rd sol, or martian day, of Opportunity's mission (Jan.26, 2004). The upper left image is a monochrome (single filter) image from the rover's panoramic camera, showing regions from which spectra were extracted from the 'Lily Pad' area. As noted by the line graph on the right, the green spectra is from the undisturbed surface and the red spectra is from the airbag bounce mark.

  7. Statistical Properties of Maximum Likelihood Estimators of Power Law Spectra Information

    NASA Technical Reports Server (NTRS)

    Howell, L. W., Jr.

    2003-01-01

    A simple power law model consisting of a single spectral index, sigma(sub 2), is believed to be an adequate description of the galactic cosmic-ray (GCR) proton flux at energies below 10(exp 13) eV, with a transition at the knee energy, E(sub k), to a steeper spectral index sigma(sub 2) greater than sigma(sub 1) above E(sub k). The maximum likelihood (ML) procedure was developed for estimating the single parameter sigma(sub 1) of a simple power law energy spectrum and generalized to estimate the three spectral parameters of the broken power law energy spectrum from simulated detector responses and real cosmic-ray data. The statistical properties of the ML estimator were investigated and shown to have the three desirable properties: (Pl) consistency (asymptotically unbiased), (P2) efficiency (asymptotically attains the Cramer-Rao minimum variance bound), and (P3) asymptotically normally distributed, under a wide range of potential detector response functions. Attainment of these properties necessarily implies that the ML estimation procedure provides the best unbiased estimator possible. While simulation studies can easily determine if a given estimation procedure provides an unbiased estimate of the spectra information, and whether or not the estimator is approximately normally distributed, attainment of the Cramer-Rao bound (CRB) can only be ascertained by calculating the CRB for an assumed energy spectrum- detector response function combination, which can be quite formidable in practice. However, the effort in calculating the CRB is very worthwhile because it provides the necessary means to compare the efficiency of competing estimation techniques and, furthermore, provides a stopping rule in the search for the best unbiased estimator. Consequently, the CRB for both the simple and broken power law energy spectra are derived herein and the conditions under which they are stained in practice are investigated.

  8. Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing

    PubMed Central

    Logue, Kyle; Keven, John Bosco; Cannon, Matthew V.; Reimer, Lisa; Siba, Peter; Walker, Edward D.; Zimmerman, Peter A.; Serre, David

    2016-01-01

    Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s. l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources. PMID:26963245

  9. A Practical Methodology to Measure Unbiased Gas Chromatographic Retention Factor vs. Temperature Relationships

    PubMed Central

    Peng, Baijie; Kuo, Mei-Yi; Yang, Panhia; Hewitt, Joshua T.; Boswell, Paul G.

    2014-01-01

    Compound identification continues to be a major challenge. Gas chromatography-mass spectrometry (GC-MS) is a primary tool used for this purpose, but the GC retention information it provides is underutilized because existing retention databases are experimentally restrictive and unreliable. A methodology called “retention projection” has the potential to overcome these limitations, but it requires the retention factor (k) vs. T relationship of a compound to calculate its retention time. Direct methods of measuring k vs. T relationships from a series of isothermal runs are tedious and time-consuming. Instead, a series of temperature programs can be used to quickly measure the k vs. T relationships, but they are generally not as accurate when measured this way because they are strongly biased by non-ideal behavior of the GC system in each of the runs. In this work, we overcome that problem by using the retention times of 25 n-alkanes to back-calculate the effective temperature profile and hold-up time vs. T profiles produced in each of six temperature programs. When the profiles were measured this way and taken into account, the k vs. T relationships measured from each of two different GC-MS instruments were nearly as accurate as the ones measured isothermally, showing less than 2-fold more error. Furthermore, temperature-programmed retention times calculated in five other labs from the new k vs. T relationships had the same distribution of error as when they were calculated from k vs. T relationships measured isothermally. Free software was developed to make the methodology easy to use. The new methodology potentially provides a relatively fast and easy way to measure unbiased k vs. T relationships. PMID:25496658

  10. Bayesian Network Inference Enables Unbiased Phenotypic Anchoring of Transcriptomic Responses to Cigarette Smoke in Humans.

    PubMed

    Jennen, Danyel G J; van Leeuwen, Danitsja M; Hendrickx, Diana M; Gottschalk, Ralph W H; van Delft, Joost H M; Kleinjans, Jos C S

    2015-10-19

    Microarray-based transcriptomic analysis has been demonstrated to hold the opportunity to study the effects of human exposure to, e.g., chemical carcinogens at the whole genome level, thus yielding broad-ranging molecular information on possible carcinogenic effects. Since genes do not operate individually but rather through concerted interactions, analyzing and visualizing networks of genes should provide important mechanistic information, especially upon connecting them to functional parameters, such as those derived from measurements of biomarkers for exposure and carcinogenic risk. Conventional methods such as hierarchical clustering and correlation analyses are frequently used to address these complex interactions but are limited as they do not provide directional causal dependence relationships. Therefore, our aim was to apply Bayesian network inference with the purpose of phenotypic anchoring of modified gene expressions. We investigated a use case on transcriptomic responses to cigarette smoking in humans, in association with plasma cotinine levels as biomarkers of exposure and aromatic DNA-adducts in blood cells as biomarkers of carcinogenic risk. Many of the genes that appear in the Bayesian networks surrounding plasma cotinine, and to a lesser extent around aromatic DNA-adducts, hold biologically relevant functions in inducing severe adverse effects of smoking. In conclusion, this study shows that Bayesian network inference enables unbiased phenotypic anchoring of transcriptomics responses. Furthermore, in all inferred Bayesian networks several dependencies are found which point to known but also to new relationships between the expression of specific genes, cigarette smoke exposure, DNA damaging-effects, and smoking-related diseases, in particular associated with apoptosis, DNA repair, and tumor suppression, as well as with autoimmunity.

  11. Testcross additive and dominance effects in best linear unbiased prediction of maize single-cross performance.

    PubMed

    Bernardo, R

    1996-11-01

    Best linear unbiased prediction (BLUP) has been found to be useful in maize (Zea mays L.) breeding. The advantage of including both testcross additive and dominance effects (Intralocus Model) in BLUP, rather than only testcross additive effects (Additive Model), has not been clearly demonstrated. The objective of this study was to compare the usefulness of Intralocus and Additive Models for BLUP of maize single-cross performance. Multilocation data from 1990 to 1995 were obtained from the hybrid testing program of Limagrain Genetics. Grain yield, moisture, stalk lodging, and root lodging of untested single crosses were predicted from (1) the performance of tested single crosses and (2) known genetic relationships among the parental inbreds. Correlations between predicted and observed performance were obtained with a delete-one cross-validation procedure. For the Intralocus Model, the correlations ranged from 0.50 to 0.66 for yield, 0.88 to 0.94 for moisture, 0.47 to 0.69 for stalk lodging, and 0.31 to 0.45 for root lodging. The BLUP procedure was consistently more effective with the Intralocus Model than with the Additive Model. When the Additive Model was used instead of the Intralocus Model, the reductions in the correlation were largest for root lodging (0.06-0.35), smallest for moisture (0.00-0.02), and intermediate for yield (0.02-0.06) and stalk lodging (0.02-0.08). The ratio of dominance variance (v D) to total genetic variance (v G) was highest for root lodging (0.47) and lowest for moisture (0.10). The Additive Model may be used if prior information indicates that VD for a given trait has little contribution to VG. Otherwise, the continued use of the Intralocus Model for BLUP of single-cross performance is recommended.

  12. Best linear unbiased prediction and optimum allocation of test resources in maize breeding with doubled haploids.

    PubMed

    Mi, Xuefei; Wegenast, Thilo; Utz, H Friedrich; Dhillon, Baldev S; Melchinger, Albrecht E

    2011-06-01

    With best linear unbiased prediction (BLUP), information from genetically related candidates is combined to obtain more precise estimates of genotypic values of test candidates and thereby increase progress from selection. We developed and applied theory and Monte Carlo simulations implementing BLUP in 2 two-stage maize breeding schemes and various selection strategies. Our objectives were to (1) derive analytical solutions of the mixed model equations under two breeding schemes, (2) determine the optimum allocation of test resources with BLUP under different assumptions regarding the variance component ratios for grain yield in maize, (3) compare the progress from selection using BLUP and conventional phenotypic selection based on mean performance solely of the candidates, and (4) analyze the potential of BLUP for further improving the progress from selection. The breeding schemes involved selection for testcross performance either of DH lines at both stages (DHTC) or of S(1) families at the first stage and DH lines at the second stage (S(1)TC-DHTC). Our analytical solutions allowed much faster calculations of the optimum allocations and superseded matrix inversions to solve the mixed model equations. Compared to conventional phenotypic selection, the progress from selection was slightly higher with BLUP for both optimization criteria, namely the selection gain and the probability to select the best genotypes. The optimum allocation of test resources in S(1)TC-DHTC involved ≥ 10 test locations at both stages, a low number of crosses (≤ 6) each with 100-300 S(1) families at the first stage, and 500-1,000 DH lines at the second stage. In breeding scheme DHTC, the optimum number of test candidates at the first stage was 5-10 times larger, whereas the number of test locations at the first stage and the number of test candidates at the second stage were strongly reduced compared to S(1)TC-DHTC.

  13. Metabolic profiling in Caenorhabditis elegans provides an unbiased approach to investigations of dosage dependent lead toxicity.

    PubMed

    Sudama, Gita; Zhang, John; Isbister, Jenefir; Willett, James D

    2013-02-01

    The nematode, Caenorhabditis elegans (CE), serves as a model system in which to explore the impact of particularly low-levels of lead [250, 500, 1000 and 2000 parts per million (ppm) (1.4 × 10(-6) M to 1.1 × 10(-5) M/nematode)] on specific metabolic pathways and processes. Chromatographic profiles of redox active metabolites are captured through application of high performance liquid chromatography coupled to electrochemical detection (Coularray/HPLC). Principal Component Analysis (PCA: unbiased cluster analysis) and the application of a slicing program, located significant areas of difference occurring within the 2.8-4.58 min section of the chromatograms. It is within this region of the data profiles that known components of the purine pathway reside. Two analytes of unknown structure were detected at 3.5 and 4 min respectively. Alterations in levels of the purine, tryptophan and tyrosine pathway intermediates measured in response to differing concentrations of lead acetate indicate that the effect of lead on these pathways is not linear, yet the ratio of the pathway precursors, tryptophan and tyrosine remains relatively constant. The application of the above combined analytical approaches enhances the value of data generated. Exposure of CE to very low levels of lead produced significant alterations in profiles of electrochemically active compounds. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0438-0) contains supplementary material, which is available to authorized users.

  14. Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing.

    PubMed

    Logue, Kyle; Keven, John Bosco; Cannon, Matthew V; Reimer, Lisa; Siba, Peter; Walker, Edward D; Zimmerman, Peter A; Serre, David

    2016-03-01

    Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s. l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources.

  15. A novel unbiased counting method for the quantification of synapses in the mouse brain

    PubMed Central

    Reichmann, Florian; Painsipp, Evelin; Holzer, Peter; Kummer, Daniel; Bock, Elisabeth; Leitinger, Gerd

    2015-01-01

    Background The numerical density of synapses and their ultrastructural features are best assessed with electron microscopy. Counting is done within counting frames placed on a pair of sections (disector technique). But this requires that the thin sections are taken from comparable brain regions and the disectors are placed in a uniform random fashion. Small brain areas like the polymorph layer of the mouse dentate gyrus are difficult to encounter, and manually moving the microscope stage for placing the micrographs seems arbitrary. New method Here the polymorph layer was approximated with 20 μm thin, Nissl-stained vibratome sections. The subsequent vibratome section was processed for electron microscopy and serially thin sectioned. The microscope stage was moved using a random number generator, placing at least 20 disectors onto a pair of sections. The numerical synapse density, the numerical density of dense-core vesicles, and other ultrastructural features were compared between mice that had been kept in an enriched environment and mice kept under standard housing conditions. Results Environmental enrichment significantly decreased the numerical density of dense-core vesicles and synaptic cleft widths within the polymorph layer, associated with behavioral improvement in the Morris water maze, a hippocampus-dependent task of spatial learning and memory. Comparison with existing methods This procedure was easy to handle and enabled us to produce thin sections in small, defined brain areas. Furthermore, placing the disectors with random numbers excluded observer bias. Conclusions Our procedure provides an uncomplicated way of assessing numerical densities in small brain areas in an unbiased manner. PMID:25445248

  16. Unbiased estimation of chloroplast number in mesophyll cells: advantage of a genuine three-dimensional approach

    PubMed Central

    Kubínová, Zuzana

    2014-01-01

    Chloroplast number per cell is a frequently examined quantitative anatomical parameter, often estimated by counting chloroplast profiles in two-dimensional (2D) sections of mesophyll cells. However, a mesophyll cell is a three-dimensional (3D) structure and this has to be taken into account when quantifying its internal structure. We compared 2D and 3D approaches to chloroplast counting from different points of view: (i) in practical measurements of mesophyll cells of Norway spruce needles, (ii) in a 3D model of a mesophyll cell with chloroplasts, and (iii) using a theoretical analysis. We applied, for the first time, the stereological method of an optical disector based on counting chloroplasts in stacks of spruce needle optical cross-sections acquired by confocal laser-scanning microscopy. This estimate was compared with counting chloroplast profiles in 2D sections from the same stacks of sections. Comparing practical measurements of mesophyll cells, calculations performed in a 3D model of a cell with chloroplasts as well as a theoretical analysis showed that the 2D approach yielded biased results, while the underestimation could be up to 10-fold. We proved that the frequently used method for counting chloroplasts in a mesophyll cell by counting their profiles in 2D sections did not give correct results. We concluded that the present disector method can be efficiently used for unbiased estimation of chloroplast number per mesophyll cell. This should be the method of choice, especially in coniferous needles and leaves with mesophyll cells with lignified cell walls where maceration methods are difficult or impossible to use. PMID:24336344

  17. Unbiased Review of Digital Diagnostic Images in Practice: Informatics Prototype and Pilot Study

    PubMed Central

    Fotenos, Anthony F.; Safdar, Nabile M.; Nagy, Paul G.; Mezrich, Reuben; Lewin, Jonathan S.

    2013-01-01

    care, despite integration of these records within production electronic workflow systems. Conclusion Information technology can facilitate the design of unbiased methods involving professional review of digital diagnostic images. PMID:23103185

  18. An unbiased approach to identifying tau kinases that phosphorylate tau at sites associated with Alzheimer disease.

    PubMed

    Cavallini, Annalisa; Brewerton, Suzanne; Bell, Amanda; Sargent, Samantha; Glover, Sarah; Hardy, Clare; Moore, Roger; Calley, John; Ramachandran, Devaki; Poidinger, Michael; Karran, Eric; Davies, Peter; Hutton, Michael; Szekeres, Philip; Bose, Suchira

    2013-08-09

    Neurofibrillary tangles, one of the hallmarks of Alzheimer disease (AD), are composed of paired helical filaments of abnormally hyperphosphorylated tau. The accumulation of these proteinaceous aggregates in AD correlates with synaptic loss and severity of dementia. Identifying the kinases involved in the pathological phosphorylation of tau may identify novel targets for AD. We used an unbiased approach to study the effect of 352 human kinases on their ability to phosphorylate tau at epitopes associated with AD. The kinases were overexpressed together with the longest form of human tau in human neuroblastoma cells. Levels of total and phosphorylated tau (epitopes Ser(P)-202, Thr(P)-231, Ser(P)-235, and Ser(P)-396/404) were measured in cell lysates using AlphaScreen assays. GSK3α, GSK3β, and MAPK13 were found to be the most active tau kinases, phosphorylating tau at all four epitopes. We further dissected the effects of GSK3α and GSK3β using pharmacological and genetic tools in hTau primary cortical neurons. Pathway analysis of the kinases identified in the screen suggested mechanisms for regulation of total tau levels and tau phosphorylation; for example, kinases that affect total tau levels do so by inhibition or activation of translation. A network fishing approach with the kinase hits identified other key molecules putatively involved in tau phosphorylation pathways, including the G-protein signaling through the Ras family of GTPases (MAPK family) pathway. The findings identify novel tau kinases and novel pathways that may be relevant for AD and other tauopathies.

  19. A/T/N: An unbiased descriptive classification scheme for Alzheimer disease biomarkers

    PubMed Central

    Bennett, David A.; Blennow, Kaj; Carrillo, Maria C.; Feldman, Howard H.; Frisoni, Giovanni B.; Hampel, Harald; Jagust, William J.; Johnson, Keith A.; Knopman, David S.; Petersen, Ronald C.; Scheltens, Philip; Sperling, Reisa A.; Dubois, Bruno

    2016-01-01

    Biomarkers have become an essential component of Alzheimer disease (AD) research and because of the pervasiveness of AD pathology in the elderly, the same biomarkers are used in cognitive aging research. A number of current issues suggest that an unbiased descriptive classification scheme for these biomarkers would be useful. We propose the “A/T/N” system in which 7 major AD biomarkers are divided into 3 binary categories based on the nature of the pathophysiology that each measures. “A” refers to the value of a β-amyloid biomarker (amyloid PET or CSF Aβ42); “T,” the value of a tau biomarker (CSF phospho tau, or tau PET); and “N,” biomarkers of neurodegeneration or neuronal injury ([18F]-fluorodeoxyglucose–PET, structural MRI, or CSF total tau). Each biomarker category is rated as positive or negative. An individual score might appear as A+/T+/N−, or A+/T−/N−, etc. The A/T/N system includes the new modality tau PET. It is agnostic to the temporal ordering of mechanisms underlying AD pathogenesis. It includes all individuals in any population regardless of the mix of biomarker findings and therefore is suited to population studies of cognitive aging. It does not specify disease labels and thus is not a diagnostic classification system. It is a descriptive system for categorizing multidomain biomarker findings at the individual person level in a format that is easy to understand and use. Given the present lack of consensus among AD specialists on terminology across the clinically normal to dementia spectrum, a biomarker classification scheme will have broadest acceptance if it is independent from any one clinically defined diagnostic scheme. PMID:27371494

  20. Unbiased feature selection through successive elimination of poor performers for EEG classification

    NASA Astrophysics Data System (ADS)

    Siddiqui, Khalid J.

    1996-04-01

    Electroencephalogram (EEG) pattern recognition problem is considered as a composite of three subproblems: feature extraction, feature selection, and pattern classification. Focusing particularly on the feature selection issue, each subproblem is reviewed briefly and a new method for feature selection is proposed. The method suggests that first one shall extract as much information (features) as conveniently possible in several pattern information domains and then apply the proposed unbiased successive feature elimination process to remove redundant and poor features. From this set select a significantly smaller, yet useful, feature subset that enhances the performance of the classifier. The successive feature elimination process is formally described. The method is successfully applied to an EEG signal classification problem. The features selected by the algorithm are used to classify three signal classes. The classes identified were eye artifacts, muscle artifacts, and clean (subject in stationary state). Two hundred samples for each of the three classes were selected and the data set was arbitrarily divided into two subsets: design subset, and testing subset. A proximity index classifier using Mahalanobis distance as the proximity criterion was developed using the smaller feature subset. The system was trained on the design set. The recognition performance on the design set was 92.33%. The recognition performance on the testing set was 88.67% by successfully identifying the samples in eye-blinks, muscle response, and clean classes, respectively, with 80%, 97%, and 89%. This performance is very encouraging. In addition, the method is computationally inexpensive and particularly useful for large data set problems. The method further reduces the need for a careful feature determination problem that a system designer usually encounters during the initial design phase of a pattern classifier.

  1. UNBIASED CORRECTION RELATIONS FOR GALAXY CLUSTER PROPERTIES DERIVED FROM CHANDRA AND XMM-NEWTON

    SciTech Connect

    Zhao, Hai-Hui; Li, Cheng-Kui; Chen, Yong; Jia, Shu-Mei; Song, Li-Ming

    2015-01-20

    We use a sample of 62 clusters of galaxies to investigate the discrepancies between the gas temperature and total mass within r {sub 500} from XMM-Newton and Chandra data. Comparisons of the properties show that (1) both the de-projected and projected temperatures determined by Chandra are higher than those of XMM-Newton and there is a good linear relationship for the de-projected temperatures: T {sub Chandra} = 1.25 × T {sub XMM}–0.13. (2) The Chandra mass is much higher than the XMM-Newton mass with a bias of 0.15 and our mass relation is log{sub 10} M {sub Chandra} = 1.02 × log{sub 10} M {sub XMM}+0.15. To explore the reasons for the discrepancy in mass, we recalculate the Chandra mass (expressed as M{sub Ch}{sup mo/d}) by modifying its temperature with the de-projected temperature relation. The results show that M{sub Ch}{sup mo/d} is closer to the XMM-Newton mass with the bias reducing to 0.02. Moreover, M{sub Ch}{sup mo/d} are corrected with the r {sub 500} measured by XMM-Newton and the intrinsic scatter is significantly improved with the value reducing from 0.20 to 0.12. These mean that the temperature bias may be the main factor causing the mass bias. Finally, we find that M{sub Ch}{sup mo/d} is consistent with the corresponding XMM-Newton mass derived directly from our mass relation at a given Chandra mass. Thus, the de-projected temperature and mass relations can provide unbiased corrections for galaxy cluster properties derived from Chandra and XMM-Newton.

  2. An Example of an Improvable Rao–Blackwell Improvement, Inefficient Maximum Likelihood Estimator, and Unbiased Generalized Bayes Estimator

    PubMed Central

    Galili, Tal; Meilijson, Isaac

    2016-01-01

    The Rao–Blackwell theorem offers a procedure for converting a crude unbiased estimator of a parameter θ into a “better” one, in fact unique and optimal if the improvement is based on a minimal sufficient statistic that is complete. In contrast, behind every minimal sufficient statistic that is not complete, there is an improvable Rao–Blackwell improvement. This is illustrated via a simple example based on the uniform distribution, in which a rather natural Rao–Blackwell improvement is uniformly improvable. Furthermore, in this example the maximum likelihood estimator is inefficient, and an unbiased generalized Bayes estimator performs exceptionally well. Counterexamples of this sort can be useful didactic tools for explaining the true nature of a methodology and possible consequences when some of the assumptions are violated. [Received December 2014. Revised September 2015.] PMID:27499547

  3. An Example of an Improvable Rao-Blackwell Improvement, Inefficient Maximum Likelihood Estimator, and Unbiased Generalized Bayes Estimator.

    PubMed

    Galili, Tal; Meilijson, Isaac

    2016-01-02

    The Rao-Blackwell theorem offers a procedure for converting a crude unbiased estimator of a parameter θ into a "better" one, in fact unique and optimal if the improvement is based on a minimal sufficient statistic that is complete. In contrast, behind every minimal sufficient statistic that is not complete, there is an improvable Rao-Blackwell improvement. This is illustrated via a simple example based on the uniform distribution, in which a rather natural Rao-Blackwell improvement is uniformly improvable. Furthermore, in this example the maximum likelihood estimator is inefficient, and an unbiased generalized Bayes estimator performs exceptionally well. Counterexamples of this sort can be useful didactic tools for explaining the true nature of a methodology and possible consequences when some of the assumptions are violated. [Received December 2014. Revised September 2015.].

  4. An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs.

    PubMed

    Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon

    2014-05-27

    Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

  5. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  6. Spectra of Surface Waves

    DTIC Science & Technology

    1989-03-22

    with a wave follower during Marsen. J. Gophysical Res. 88, 9844-9849. 11. Hughes, B.A., 1978. The effects on internal waves on surface waves : 2...Spectra of Surface Waves K. Watson March 1989 JSR-88-130 Approved for public release; distribution unlimited. DTIC SELECTE JUN0 11989 0 JASONE The...Arlington, VA 22209 8503Z 11. TITLE (hlde Secvfty Cof.kaftn) SPECTRA OF SURFACE WAVES (U) 12. PERSONAL AUTHOfRS) K. Watson 13a. TYPE OF REPORT 13b. TIME

  7. THE OPTICALLY UNBIASED GAMMA-RAY BURST HOST (TOUGH) SURVEY. I. SURVEY DESIGN AND CATALOGS

    SciTech Connect

    Hjorth, Jens; Malesani, Daniele; Fynbo, Johan P. U.; Kruehler, Thomas; Milvang-Jensen, Bo; Watson, Darach; Jakobsson, Pall; Schulze, Steve; Jaunsen, Andreas O.; Gorosabel, Javier; Levan, Andrew J.; Michalowski, Michal J.; Moller, Palle; Tanvir, Nial R.

    2012-09-10

    Long-duration gamma-ray bursts (GRBs) are powerful tracers of star-forming galaxies. We have defined a homogeneous subsample of 69 Swift GRB-selected galaxies spanning a very wide redshift range. Special attention has been devoted to making the sample optically unbiased through simple and well-defined selection criteria based on the high-energy properties of the bursts and their positions on the sky. Thanks to our extensive follow-up observations, this sample has now achieved a comparatively high degree of redshift completeness, and thus provides a legacy sample, useful for statistical studies of GRBs and their host galaxies. In this paper, we present the survey design and summarize the results of our observing program conducted at the ESO Very Large Telescope (VLT) aimed at obtaining the most basic properties of galaxies in this sample, including a catalog of R and K{sub s} magnitudes and redshifts. We detect the host galaxies for 80% of the GRBs in the sample, although only 42% have K{sub s} -band detections, which confirms that GRB-selected host galaxies are generally blue. The sample is not uniformly blue, however, with two extremely red objects detected. Moreover, galaxies hosting GRBs with no optical/NIR afterglows, whose identification therefore relies on X-ray localizations, are significantly brighter and redder than those with an optical/NIR afterglow. This supports a scenario where GRBs occurring in more massive and dusty galaxies frequently suffer high optical obscuration. Our spectroscopic campaign has resulted in 77% now having redshift measurements, with a median redshift of 2.14 {+-} 0.18. TOUGH alone includes 17 detected z > 2 Swift GRB host galaxies suitable for individual and statistical studies-a substantial increase over previous samples. Seven hosts have detections of the Ly{alpha} emission line and we can exclude an early indication that Ly{alpha} emission is ubiquitous among GRB hosts, but confirm that Ly{alpha} is stronger in GRB

  8. Age-related changes in rat cerebellar basket cells: a quantitative study using unbiased stereological methods

    PubMed Central

    HENRIQUE, RUI M. F.; ROCHA, EDUARDO; REIS, ALCINDA; MARCOS, RICARDO; OLIVEIRA, MARIA H.; SILVA, MARIA W.; MONTEIRO, ROGÉRIO A. F.

    2001-01-01

    Cortical cerebellar basket cells are stable postmitotic cells; hence, they are liable to endure age-related changes. Since the cerebellum is a vital organ for the postural control, equilibrium and motor coordination, we aimed to determine the quantitative morphological changes in those interneurons with the ageing process, using unbiased techniques. Material from the cerebellar cortex (Crus I and Crus II) was collected from female rats aged 2, 6, 9, 12, 15, 18, 21 and 24 mo (5 animals per each age group), fixed by intracardiac perfusion, and processed for transmission electron microscopy, using conventional techniques. Serial semithin sections were obtained (5 blocks from each rat), enabling the determination of the number-weighted mean nuclear volume (by the nucleator method). On ultrathin sections, 25 cell profiles from each animal were photographed. The volume density of the nucleus, ground substance, mitochondria, Golgi apparatus (Golgi) and dense bodies (DB), and the mean surface density of the rough endoplasmic reticulum (RER) were determined, by point counting, using a morphometric grid. The mean total volumes of the soma and organelles and the mean total surface area of the RER [s̄N (RER)] were then calculated. The results were analysed with 1-way ANOVA; posthoc pairwise comparisons of group means were performed using the Newman-Keuls test. The relation between age and each of the parameters was studied by regression analysis. Significant age-related changes were observed for the mean volumes of the soma, ground substance, Golgi, DB, and s̄N (RER). Positive linear trends were found for the mean volumes of the ground substance, Golgi, and DB; a negative linear trend was found for the s̄N (RER). These results indicate that rat cerebellar basket cells endure important age-related changes. The significant decrease in the s̄N (RER) may be responsible for a reduction in the rate of protein synthesis. Additionally, it may be implicated in a cascade of events

  9. Unbiased isotope equilibrium factors from partial isotope exchange experiments in 3-exchange site systems

    NASA Astrophysics Data System (ADS)

    Agrinier, Pierre; Javoy, Marc

    2016-09-01

    Two methods are available in order to evaluate the equilibrium isotope fractionation factors between exchange sites or phases from partial isotope exchange experiments. The first one developed by Northrop and Clayton (1966) is designed for isotope exchanges between two exchange sites (hereafter, the N&C method), the second one from Zheng et al. (1994) is a refinement of the first one to account for a third isotope exchanging site (hereafter, the Z method). In this paper, we use a simple model of isotope kinetic exchange for a 3-exchange site system (such as hydroxysilicates where oxygen occurs as OH and non-OH groups like in muscovite, chlorite, serpentine, or water or calcite) to explore the behavior of the N&C and Z methods. We show that these two methods lead to significant biases that cannot be detected with the usual graphical tests proposed by the authors. Our model shows that biases originate because isotopes are fractionated between all these exchanging sites. Actually, we point out that the variable mobility (or exchangeability) of isotopes in and between the exchange sites only controls the amplitude of the bias, but is not essential to the production of this bias as previously suggested. Setting a priori two of the three exchange sites at isotopic equilibrium remove the bias and thus is required for future partial exchange experiments to produce accurate and unbiased extrapolated equilibrium fractionation factors. Our modeling applied to published partial oxygen isotope exchange experiments for 3-exchange site systems (the muscovite-calcite (Chacko et al., 1996), the chlorite-water (Cole and Ripley, 1998) and the serpentine-water (Saccocia et al., 2009)) shows that the extrapolated equilibrium fractionation factors (reported as 1000 ln(α)) using either the N&C or the Z methods lead to bias that may reach several δ per mil in a few cases. These problematic cases, may be because experiments were conducted at low temperature and did not reach high

  10. Probing the effects of external irradiation on low-mass protostars through unbiased line surveys

    NASA Astrophysics Data System (ADS)

    Lindberg, J. E.; Jørgensen, J. K.; Watanabe, Y.; Bisschop, S. E.; Sakai, N.; Yamamoto, S.

    2015-12-01

    Context. The envelopes of molecular gas around embedded low-mass protostars show different chemistries, which can be used to trace their formation history and physical conditions. The excitation conditions of some molecular species can also be used to trace these physical conditions, making it possible to constrain for instance sources of heating and excitation. Aims: We study the range of influence of an intermediate-mass Herbig Be protostar. We also study the effect of feedback from the environment on the chemical and physical properties of embedded protostars. Methods: We followed up on an earlier line survey of the Class 0/I source R CrA IRS7B in the 0.8 mm window with an unbiased line survey of the same source in the 1.3 mm window using the Atacama Pathfinder Experiment (APEX) telescope. We also studied the excitation of the key species H2CO, CH3OH, and c-C3H2 in a complete sample of the 18 embedded protostars in the Corona Australis star-forming region. Radiative transfer models were employed to establish abundances of the molecular species. Results: We detect line emission from 20 molecular species (32 including isotopologues) in the two surveys. The most complex species detected are CH3OH, CH3CCH, CH3CHO, and CH3CN (the latter two are only tentatively detected). CH3CN and several other complex organic molecules are significantly under-abundant in comparison with what is found towards hot corino protostars. The H2CO rotational temperatures of the sources in the region decrease with the distance to the Herbig Be star R CrA, whereas the c-C3H2 temperatures remain constant across the star-forming region. Conclusions: The high H2CO temperatures observed towards objects close to R CrA suggest that this star has a sphere of influence of several 10 000 AU in which it increases the temperature of the molecular gas to 30-50 K through irradiation. The chemistry in the IRS7B envelope differs significantly from many other embedded protostars, which could be an effect of

  11. Quantum spectra and dynamics

    NASA Astrophysics Data System (ADS)

    Arce, Julio Cesar

    This work focuses on time-dependent quantum theory and methods for the study of the spectra and dynamics of atomic and molecular systems. Specifically, we have addressed the following two problems: (1) Development of a time-dependent spectral method for the construction of spectra of simple quantum systems. This includes the calculation of eigenenergies, the construction of bound and continuum eigenfunctions, and the calculation of photo cross-sections. Computational applications include the quadrupole photoabsorption spectra and dissociation cross-sections of molecular hydrogen from various vibrational states in its ground electronic potential-energy curve. This method is seen to provide an advantageous alternative, both from the computational and conceptual point of view, to existing standard methods. (2) Explicit time-dependent formulation of photoabsorption processes -- Analytical solutions of the time-dependent Schrodinger equation are constructed and employed for the calculation of probability densities, momentum distributions, fluxes, transition rates, expectation values and correlation functions. These quantities are seen to establish the link between the dynamics and the calculated, or measured, spectra and cross-sections, and to clarify the dynamical nature of the excitation, transition and ejection processes. Numerical calculations on atomic and molecular hydrogen corroborate and complement the previous results, allowing the identification of different regimes during the photoabsorption process.

  12. Quantum Spectra and Dynamics

    NASA Astrophysics Data System (ADS)

    Arce, Julio Cesar

    1992-01-01

    This work focuses on time-dependent quantum theory and methods for the study of the spectra and dynamics of atomic and molecular systems. Specifically, we have addressed the following two problems: (i) Development of a time-dependent spectral method for the construction of spectra of simple quantum systems--This includes the calculation of eigenenergies, the construction of bound and continuum eigenfunctions, and the calculation of photo cross-sections. Computational applications include the quadrupole photoabsorption spectra and dissociation cross-sections of molecular hydrogen from various vibrational states in its ground electronic potential -energy curve. This method is seen to provide an advantageous alternative, both from the computational and conceptual point of view, to existing standard methods. (ii) Explicit time-dependent formulation of photoabsorption processes --Analytical solutions of the time-dependent Schrodinger equation are constructed and employed for the calculation of probability densities, momentum distributions, fluxes, transition rates, expectation values and correlation functions. These quantities are seen to establish the link between the dynamics and the calculated, or measured, spectra and cross-sections, and to clarify the dynamical nature of the excitation, transition and ejection processes. Numerical calculations on atomic and molecular hydrogen corroborate and complement the previous results, allowing the identification of different regimes during the photoabsorption process.

  13. Atomic Spectra Database (ASD)

    National Institute of Standards and Technology Data Gateway

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  14. Rock Outcrop Spectra

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The color image on the lower left shows a rock outcrop at Meridiani Planum, Mars. This image was taken by the panoramic camera on the Mars Exploration Rover Opportunity, looking north, and was acquired on the 4th sol, or martian day, of the rover's mission (Jan. 27, 2004). The yellow box outlines an area detailed in the top left image, which is a monochrome (single filter) image from the rover's panoramic camera. The top image uses solid colors to show several regions on or near the rock outcrop from which spectra were extracted: the dark soil above the outcrop (yellow), the distant horizon surface (aqua), a bright rock in the outcrop (green), a darker rock in the outcrop (red), and a small dark cobblestone (blue). Spectra from these regions are shown in the plot to the right.

  15. Barnacle Bill Spectra

    NASA Technical Reports Server (NTRS)

    1997-01-01

    These IMP spectra show the characteristics of the rock surface measured by the Alpha Proton X-Ray Spectrometer (blue), the soil trapped in pits on the rock surface (red), and the deposit of bright drift on the top of the rock. The area measured by the APXS has the properties expected for nearly unweathered igneous rock, and the soil trapped in the pits is intermediate to the unweathered rock and the highly weathered drift material.

  16. Generalized approach for using unbiased symmetric metrics with negative values: normalized mean bias factor and normalized mean absolute error factor

    SciTech Connect

    Gustafson, William I.; Yu, Shaocai

    2012-10-23

    Unbiased symmetric metrics provide a useful measure to quickly compare two datasets, with similar interpretations for both under and overestimations. Two examples include the normalized mean bias factor and normalized mean absolute error factor. However, the original formulations of these metrics are only valid for datasets with positive means. This paper presents a methodology to use and interpret the metrics with datasets that have negative means. The updated formulations give identical results compared to the original formulations for the case of positive means, so researchers are encouraged to use the updated formulations going forward without introducing ambiguity.

  17. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

    PubMed

    Matranga, Christian B; Andersen, Kristian G; Winnicki, Sarah; Busby, Michele; Gladden, Adrianne D; Tewhey, Ryan; Stremlau, Matthew; Berlin, Aaron; Gire, Stephen K; England, Eleina; Moses, Lina M; Mikkelsen, Tarjei S; Odia, Ikponmwonsa; Ehiane, Philomena E; Folarin, Onikepe; Goba, Augustine; Kahn, S Humarr; Grant, Donald S; Honko, Anna; Hensley, Lisa; Happi, Christian; Garry, Robert F; Malboeuf, Christine M; Birren, Bruce W; Gnirke, Andreas; Levin, Joshua Z; Sabeti, Pardis C

    2014-01-01

    We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.

  18. AGNs with composite spectra. II. Additional data

    NASA Astrophysics Data System (ADS)

    Gonçalves, A. C.; Véron-Cetty, M.-P.; Véron, P.

    1999-03-01

    In a previous paper \\cite[(Véron et al. 1997)]{ver97} we presented medium resolution (3.4 Angstroms FWHM) spectroscopic observations of 15 ``transition objects'', selected for having an ambiguous location in the \\cite[Veilleux & Osterbrock (1987)]{vei87} diagnostic diagrams, and showed that most of them were in fact ``composite'', this being due to the simultaneous presence on the slit of both a Seyfert or Liner nucleus and a H Ii region. Here, we report new spectroscopic observations of 53 emission-line galaxies with a ``transition'' spectrum, bringing up to 61 the total number of observed objects in an unbiased sample of 88 ``transition objects''. Almost all of the observed galaxies have a ``composite" nature, confirming the finding that true ``transition'' spectra may not exist at all. By eliminating ``composite objects'' from the diagnostic diagrams, a clear separation between the different classes of nuclear emission-line regions (Seyfert 2s, Liners and H Ii regions) becomes apparent; by restricting the volume occupied by the different line-emitting regions in the 3-dimensional diagnostic diagrams, we are also restricting the range of possible physical parameters in these regions. There seems to be no continuity between Seyfert 2s and Liners, the two classes occupying distinct volumes in the 3-dimensional space defined by lambda 6300/Hα ii, lambda 6583/Hα , and lambda 6300/Hα . Based on observations collected at the Observatoire de Haute-Provence (CNRS), France, and Hubble Space Telescope (HST) data obtained from the Space Telescope European Coordinating Facility (ST-ECF) archive. Tables 5 and 6 are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/Abstract.html

  19. Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

    USGS Publications Warehouse

    Ip, Hon S.; Wiley, Michael R.; Long, Renee; Gustavo, Palacios; Shearn-Bochsler, Valerie; Whitehouse, Chris A.

    2014-01-01

    Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

  20. Autocorrelation analysis for the unbiased determination of power-law exponents in single-quantum-dot blinking.

    PubMed

    Houel, Julien; Doan, Quang T; Cajgfinger, Thomas; Ledoux, Gilles; Amans, David; Aubret, Antoine; Dominjon, Agnès; Ferriol, Sylvain; Barbier, Rémi; Nasilowski, Michel; Lhuillier, Emmanuel; Dubertret, Benoît; Dujardin, Christophe; Kulzer, Florian

    2015-01-27

    We present an unbiased and robust analysis method for power-law blinking statistics in the photoluminescence of single nanoemitters, allowing us to extract both the bright- and dark-state power-law exponents from the emitters' intensity autocorrelation functions. As opposed to the widely used threshold method, our technique therefore does not require discriminating the emission levels of bright and dark states in the experimental intensity timetraces. We rely on the simultaneous recording of 450 emission timetraces of single CdSe/CdS core/shell quantum dots at a frame rate of 250 Hz with single photon sensitivity. Under these conditions, our approach can determine ON and OFF power-law exponents with a precision of 3% from a comparison to numerical simulations, even for shot-noise-dominated emission signals with an average intensity below 1 photon per frame and per quantum dot. These capabilities pave the way for the unbiased, threshold-free determination of blinking power-law exponents at the microsecond time scale.

  1. AN UNBIASED 1.3 mm EMISSION LINE SURVEY OF THE PROTOPLANETARY DISK ORBITING LkCa 15

    SciTech Connect

    Punzi, K. M.; Kastner, J. H.; Hily-Blant, P.; Forveille, T.

    2015-06-01

    The outer (>30 AU) regions of the dusty circumstellar disk orbiting the ∼2–5 Myr old, actively accreting solar analog LkCa 15 are known to be chemically rich, and the inner disk may host a young protoplanet within its central cavity. To obtain a complete census of the brightest molecular line emission emanating from the LkCa 15 disk over the 210–270 GHz (1.4–1.1 mm) range, we have conducted an unbiased radio spectroscopic survey with the Institute de Radioastronomie Millimétrique (IRAM) 30 m telescope. The survey demonstrates that in this spectral region, the most readily detectable lines are those of CO and its isotopologues {sup 13}CO and C{sup 18}O, as well as HCO{sup +}, HCN, CN, C{sub 2}H, CS, and H{sub 2}CO. All of these species had been previously detected in the LkCa 15 disk; however, the present survey includes the first complete coverage of the CN (2–1) and C{sub 2}H (3–2) hyperfine complexes. Modeling of these emission complexes indicates that the CN and C{sub 2}H either reside in the coldest regions of the disk or are subthermally excited, and that their abundances are enhanced relative to molecular clouds and young stellar object environments. These results highlight the value of unbiased single-dish line surveys in guiding future high-resolution interferometric imaging of disks.

  2. Scanning Electrochemical Microscopy of One-Dimensional Nanostructure: Effects of Nanostructure Dimensions on the Tip Feedback Current under Unbiased Conditions

    PubMed Central

    Xiong, Hui; Kim, Jiyeon; Kim, Eunkyoung; Amemiya, Shigeru

    2009-01-01

    Scanning electrochemical microscopy (SECM) is developed as a powerful approach to electrochemical characterization of individual one-dimensional (1D) nanostructures under unbiased conditions. 1D nanostructures comprise high-aspect-ratio materials with both nanoscale and macroscale dimensions such as nanowires, nanotubes, nanobelts, and nanobands. Finite element simulations demonstrate that the feedback current at a disk-shaped ultramicroelectrode tip positioned above an unbiased nanoband, as prepared on an insulating substrate, is sensitive to finite dimensions of the band, i.e., micrometer length, nanometer width, and nanometer height from the insulating surface. The electron-transfer rate of a redox mediator at the nanoband surface depends not only on the intrinsic rate but also on the open-circuit potential of the nanoband, which is determined by the dimensions of the nanoband as well as the tip inner and outer radii, and tip–substrate distance. The theoretical predictions are confirmed experimentally by employing Au nanobands as fabricated on a SiO2 surface by electron-beam lithography, thereby yielding well defined dimensions of 100 or 500 nm in width, 47 nm in height, and 50 μm in length. A 100 nm-wide nanoband can be detected by SECM imaging with ∼2 μm-diameter tips although the tip feedback current is compromised by finite electron-transfer kinetics for Ru(NH3)63+ at the nanoband surface. PMID:20160938

  3. SPECTRA. September 2011

    DTIC Science & Technology

    2011-09-01

    Transportation Services program with the Dragon capsule. (Credit: SpaceX /Chris Thompson) S p a c e c r a f t e n g in e e r in g spectra NRL...secondary payloads on board a Space Exploration Technologies ( SpaceX ), Inc., Falcon 9 launch vehicle. NRL’s nanosatellites are part of the CubeSat...Maryland. The primary payload launched aboard the SpaceX Falcon 9 was the Dragon capsule. Developed by SpaceX and sponsored by NASA’s Commercial Orbital

  4. Determinations of Photon Spectra

    DTIC Science & Technology

    1989-01-01

    COVERED O14. DATE OF REPORT (Year, Month, Day) 115. PAGE COUNT THESIS/ftFROW*W FROM TO 1989 1 54 16. SUPPLEMENTARY NOTATION A ?RQVk;U kOR 3UB LIC RELEASE...IAW AFR 190- 1 ERNEST A. HAYGOOD, 1st Lt, USAF Executive Officer, Civilian Institution ProQrams 17. COSATI CODES 18. SUBJECT TERMS (Continue on...spectra from measurements obtained with a sodium iodide counting system. A response matrix is computed by combining photon cross sections with

  5. Control spectra for Quito

    NASA Astrophysics Data System (ADS)

    Aguiar, Roberto; Rivas-Medina, Alicia; Caiza, Pablo; Quizanga, Diego

    2017-03-01

    The Metropolitan District of Quito is located on or very close to segments of reverse blind faults, Puengasí, Ilumbisí-La Bota, Carcelen-El Inca, Bellavista-Catequilla and Tangahuilla, making it one of the most seismically dangerous cities in the world. The city is divided into five areas: south, south-central, central, north-central and north. For each of the urban areas, elastic response spectra are presented in this paper, which are determined by utilizing some of the new models of the Pacific Earthquake Engineering Research Center (PEER) NGA-West2 program. These spectra are calculated considering the maximum magnitude that could be generated by the rupture of each fault segment, and taking into account the soil type that exists at different points of the city according to the Norma Ecuatoriana de la Construcción (2015). Subsequently, the recurrence period of earthquakes of high magnitude in each fault segment is determined from the physical parameters of the fault segments (size of the fault plane and slip rate) and the pattern of recurrence of type Gutenberg-Richter earthquakes with double truncation magnitude (Mmin and Mmax) is used.

  6. Theoretical Studies of Molecular Spectra

    NASA Technical Reports Server (NTRS)

    McKay, Christopher (Technical Monitor); Freedman, Richard S.

    2002-01-01

    This summary describes the research activities of the principal investigator during the reporting period. The research includes spectroscopy, management of molecular databases, and generation of spectral line profiles and opacity data. The spectroscopy research includes oxygen broadening of nitric oxide (NO), analysis of CO2 spectra, analysis of HNO3 spectra, and analysis of CO spectra.

  7. Statistical Properties of Maximum Likelihood Estimators of Power Law Spectra Information

    NASA Technical Reports Server (NTRS)

    Howell, L. W.

    2002-01-01

    A simple power law model consisting of a single spectral index, a is believed to be an adequate description of the galactic cosmic-ray (GCR) proton flux at energies below 10(exp 13) eV, with a transition at the knee energy, E(sub k), to a steeper spectral index alpha(sub 2) greater than alpha(sub 1) above E(sub k). The Maximum likelihood (ML) procedure was developed for estimating the single parameter alpha(sub 1) of a simple power law energy spectrum and generalized to estimate the three spectral parameters of the broken power law energy spectrum from simulated detector responses and real cosmic-ray data. The statistical properties of the ML estimator were investigated and shown to have the three desirable properties: (P1) consistency (asymptotically unbiased). (P2) efficiency asymptotically attains the Cramer-Rao minimum variance bound), and (P3) asymptotically normally distributed, under a wide range of potential detector response functions. Attainment of these properties necessarily implies that the ML estimation procedure provides the best unbiased estimator possible. While simulation studies can easily determine if a given estimation procedure provides an unbiased estimate of the spectra information, and whether or not the estimator is approximately normally distributed, attainment of the Cramer-Rao bound (CRB) can only he ascertained by calculating the CRB for an assumed energy spectrum-detector response function combination, which can be quite formidable in practice. However. the effort in calculating the CRB is very worthwhile because it provides the necessary means to compare the efficiency of competing estimation techniques and, furthermore, provides a stopping rule in the search for the best unbiased estimator. Consequently, the CRB for both the simple and broken power law energy spectra are derived herein and the conditions under which they are attained in practice are investigated. The ML technique is then extended to estimate spectra information from

  8. Continuum Fitting HST QSO Spectra

    NASA Technical Reports Server (NTRS)

    Tytler, David; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    The Principal Component Analysis (PCA) method which we are using to fit and describe QSO spectra relies upon the fact that QSO continuum are generally very smooth and simple except for emission and absorption lines. To see this we need high signal-to-noise (S/N) spectra of QSOs at low redshift which have relatively few absorption lines in the Lyman-a forest. We need a large number of such spectra to use as the basis set for the PCA analysis which will find the set of principal component spectra which describe the QSO family as a whole. We have found that too few HST spectra have the required S/N and hence we need to supplement them with ground based spectra of QSOs at higher redshift. We have many such spectra and we have been working to make them suitable for this analysis. We have concentrated on this topic since 12/15/01.

  9. An unbiased infrared H2 search for embedded flows from young stars in Orion A

    NASA Astrophysics Data System (ADS)

    Stanke, Thomas

    2001-04-01

    The presence of outflows, often in the form of well-collimated jets, is a phenomenon commonly associated with the birth of young stars. Emission from shock-excited molecular hydrogen at near-infrared wavelengths is one of the signposts of the presence of such an outflow, and generally can be observed even if the flow is obscured at optical wavelengths. In this thesis, I present the results of an unbiased, sensitive, wide-field search for flows from protostellar objects in the H2 v=1-0 S(1) line at a wavelength of 2.12 µm, covering a 1 square degree area of the Orion A giant molecular cloud. Further data covering a wide wavelength range are used to search for the driving sources of the flows. The aim of this work is to obtain a sample of outflows which is free from biases as far as possible, to derive the typical properties of the outflows, to search for evolutionary trends, and to examine the impact of outflows on the ambient cloud. The first result from this survey is that outflows are indeed common in star forming regions: more than 70 candidate jets are identified. Most of them have a fairly ill-defined morphology rather than a regular or symmetric structure, which is interpreted to be due to the turbulent, clumpy ambient medium into which the jets are propagating. The jets are randomly oriented. In particular, no alignment of the jets with the large scale ambient magnetic field is found, suggesting that the spin and symmetry axis in a protostellar object is determined by random, turbulent motions in the cloud. Candidate driving sources are identified for 49 jets, and their evolutionary stage and bolometric luminosity is estimated. The jet lengths and H2 luminosities evolve as a function of the age of the driving source: the jets grow quickly from zero length to a size of a few parsec and then slowly shorten again. The jets are very luminous early on and fade during the protostellar evolution. The evolution in length and H2 luminosity is attributed to an early

  10. Direct measurement of the dynamics of hole hopping in extended DNA G-tracts. An unbiased random walk.

    PubMed

    Conron, Sarah M Mickley; Thazhathveetil, Arun K; Wasielewski, Michael R; Burin, Alexander L; Lewis, Frederick D

    2010-10-20

    We report the measurement of distance- and temperature-dependent rate constants for charge separation in capped hairpins in which a stilbene hole acceptor and hole donor are separated by A(3)G(n) diblock polypurine sequences consisting of 3 adenines and 1-19 guanines. The longer diblock systems obey the simplest model for an unbiased random walk, providing a direct measurement of k(hop) = 4.3 × 10(9) s(-1) for a single reversible G-to-G hole hopping step, somewhat faster than the value of 1.2 × 10(9) s(-1) calculated for A-tract hole hopping. The temperature dependence for hopping in A(3)G(13) provides values of E(act) = 2.8 kcal/mol and A = 7 × 10(9) s(-1), consistent with a weakly activated, conformationally gated process.

  11. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

    PubMed Central

    2014-01-01

    Background Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy. Conclusions The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle

  12. Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin.

    PubMed

    Ren, Yunzhao R; Chaerkady, Raghothama; Hu, Shaohui; Wan, Jun; Qian, Jiang; Zhu, Heng; Pandey, Akhilesh; Kern, Scott E

    2012-11-02

    Although significant effort is expended on identifying transcripts/proteins that are up-regulated in cancer, there are few reports on systematic elucidation of transcriptional mechanisms underlying such druggable cancer-specific targets. The mesothelin (MSLN) gene offers a promising subject, being expressed in a restricted pattern normally, yet highly overexpressed in almost one-third of human malignancies and a target of cancer immunotherapeutic trials. CanScript, a cis promoter element, appears to control MSLN cancer-specific expression; its related genomic sequences may up-regulate other cancer markers. CanScript is a 20-nt bipartite element consisting of an SP1-like motif and a consensus MCAT sequence. The latter recruits TEAD (TEA domain) family members, which are universally expressed. Exploration of the active CanScript element, especially the proteins binding to the SP1-like motif, thus could reveal cancer-specific features having diagnostic or therapeutic interest. The efficient identification of sequence-specific DNA-binding proteins at a given locus, however, has lagged in biomarker explorations. We used two orthogonal proteomics approaches--unbiased SILAC (stable isotope labeling by amino acids in cell culture)/DNA affinity-capture/mass spectrometry survey (SD-MS) and a large transcription factor protein microarray (TFM)--and functional validation to explore systematically the CanScript interactome. SD-MS produced nine candidates, and TFM, 18. The screens agreed in confirming binding by TEAD proteins and by newly identified NAB1 and NFATc. Among other identified candidates, we found functional roles for ZNF24, NAB1 and RFX1 in MSLN expression by cancer cells. Combined interactome screens yield an efficient, reproducible, sensitive, and unbiased approach to identify sequence-specific DNA-binding proteins and other participants in disease-specific DNA elements.

  13. Toward unbiased determination of the redshift evolution of Lyman-alpha forest clouds

    NASA Technical Reports Server (NTRS)

    Lu, Limin; Zuo, Lin

    1994-01-01

    The possibility of using D(sub A), the mean depression of a quasar spectrum due to Ly-alpha forest absorption, to study the number density evolution of the Ly-alpha forest clouds is examined in some detail. Current D(sub A) measurements are made against a continuum that is a power-law extrapolation from the continuum longward of Ly-alpha emission. Compared to the line-counting approach, the D(sub A)-method has the advantage that the D(sub A) measurements are not affected by line-blending effects. However, we find using low-redshift quasar spectra obtained with the Hubble Space Telescope (HST), where the true continuum in the Ly-alpha forest can be estimated fairly reliably because of the much lower density of the Ly-alpha forest lines, that the extrapolated continuum often deviates systematically from the true continuum in the forest region. Such systematic continuum errors introduce large errors in the D(sub A) measurements. The current D(sub A) measurements may also be significantly biased by the possible presence of the Gunn-Peterson absorption. We propose a modification to the existing D(sub A)-method, namely, to measure D(sub A) against a locally established continuum in the Ly-alpha forest. Under conditions that the quasar spectrum has good resolution and S/N to allow for a reliable estimate of the local continuum in the Ly-alpha forest, the modified D(sub A) measurements should be largely free of the systematic uncertainties suffered by the existing D(sub A) measurements. We also introduce a formalism based on the work of Zuo (1993) to simplify the application of the D(sub A)-method(s) to real data. We discuss the merits and limitations of the modified D(sub A)-method, and conclude that it is a useful alternative. Our findings that the extrapolated continuum from longward of Ly-alpha emission often deviates systematically from the true continuum in the Ly-alpha forest present a major problem in the study of the Gunn-Peterson absorption.

  14. Sequencing BPS spectra

    NASA Astrophysics Data System (ADS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  15. Sequencing BPS spectra

    SciTech Connect

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-02

    In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  16. Sequencing BPS spectra

    DOE PAGES

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; ...

    2016-03-02

    In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explainmore » from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.« less

  17. Interpreting Chromosome Aberration Spectra

    NASA Technical Reports Server (NTRS)

    Levy, Dan; Reeder, Christopher; Loucas, Bradford; Hlatky, Lynn; Chen, Allen; Cornforth, Michael; Sachs, Rainer

    2007-01-01

    Ionizing radiation can damage cells by breaking both strands of DNA in multiple locations, essentially cutting chromosomes into pieces. The cell has enzymatic mechanisms to repair such breaks; however, these mechanisms are imperfect and, in an exchange process, may produce a large-scale rearrangement of the genome, called a chromosome aberration. Chromosome aberrations are important in killing cells, during carcinogenesis, in characterizing repair/misrepair pathways, in retrospective radiation biodosimetry, and in a number of other ways. DNA staining techniques such as mFISH ( multicolor fluorescent in situ hybridization) provide a means for analyzing aberration spectra by examining observed final patterns. Unfortunately, an mFISH observed final pattern often does not uniquely determine the underlying exchange process. Further, resolution limitations in the painting protocol sometimes lead to apparently incomplete final patterns. We here describe an algorithm for systematically finding exchange processes consistent with any observed final pattern. This algorithm uses aberration multigraphs, a mathematical formalism that links the various aspects of aberration formation. By applying a measure to the space of consistent multigraphs, we will show how to generate model-specific distributions of aberration processes from mFISH experimental data. The approach is implemented by software freely available over the internet. As a sample application, we apply these algorithms to an aberration data set, obtaining a distribution of exchange cycle sizes, which serves to measure aberration complexity. Estimating complexity, in turn, helps indicate how damaging the aberrations are and may facilitate identification of radiation type in retrospective biodosimetry.

  18. Laboratory simulation of dust spectra

    NASA Technical Reports Server (NTRS)

    Allamandola, L. J.; Sandford, S. A.

    1988-01-01

    Laboratory studies of the IR spectra of interstellar dust are reviewed. Studies of the absorption spectra of dense molecular clouds are discussed, including methods to produce interstellar ice analogues, simulations of astronomical spectra, and IR absorption features caused by ices. Comparisons are made between observational and experimental results of interstellar dust studies. Also, the interstellar emission features associated with dusty regions exposed to UV radiation are examined, including bands related to PAHs and PAH-related materials. It is shown that interstellar spectra are more consistant with emission from free PAHs than with emission from particles.

  19. Unbiased estimation of probability weighted moments and partial probability weighted moments from systematic and historical flood information and their application to estimating the GEV distribution

    NASA Astrophysics Data System (ADS)

    Wang, Q. J.

    1990-12-01

    Unbiased estimators of probability weighted moments (PWM) and partial probability weighted moments (PPWM) from systematic and historical flood information are derived. Applications are made to estimating parameters and quantiles of the generalized extreme value (GEV) distribution. The effect of lower bound censoring, which might be deliberately introduced in practice, is also considered.

  20. Unbiased species-level identification of clinical isolates of coagulase-negative Staphylococci: does it change the perspective on Staphylococcus lugdunensis?

    PubMed

    Elamin, Wael F; Ball, David; Millar, Michael

    2015-01-01

    Unbiased species-level identification of coagulase-negative staphylococci (CoNS) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified Staphylococcus lugdunensis to be a more commonly isolated CoNS in our laboratory than previously observed. It has also highlighted the possibility of vertical transmission.

  1. Catalogue of representative meteor spectra

    NASA Astrophysics Data System (ADS)

    Vojáček, V.; Borovička, J.; Koten, P.; Spurný, P.; Štork, R.

    2016-01-01

    We present a library of low-resolution meteor spectra that includes sporadic meteors, members of minor meteor showers, and major meteor showers. These meteors are in the magnitude range from +2 to -3, corresponding to meteoroid sizes from 1 mm to10 mm. This catalogue is available online at the CDS for those interested in video meteor spectra.

  2. Projecting Spectra for Classroom Investigations.

    ERIC Educational Resources Information Center

    Sadler, Philip

    1991-01-01

    Describes an inexpensive spectrum projector that makes high-dispersion, high-efficiency diffraction gratings using a holographic process. Discusses classroom applications such as transmission spectra, absorption spectra, reflection characteristics of materials, color mixing, florescence and phosphorescence, and break up spectral colors. (MDH)

  3. Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid

    PubMed Central

    Suarez-Ulloa, Victoria; Fernandez-Tajes, Juan; Aguiar-Pulido, Vanessa; Prego-Faraldo, M. Veronica; Florez-Barros, Fernanda; Sexto-Iglesias, Alexia; Mendez, Josefina

    2015-01-01

    Background. Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the primary cause of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom. Methods. Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellate Prorocentrum lima for 24 h). The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues. Results. Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the mussel Mytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of

  4. A Comparison of 1D and 2D (Unbiased) Experimental Methods for Measuring CSAsolarDD Cross-Correlated Relaxation

    NASA Astrophysics Data System (ADS)

    Batta, Gy.; Kövér, K. E.; Kowalewski, J.

    1999-01-01

    Conventional and enhanced 1D experiments and different NOESY experiments (the 2D unbiased method) were performed for measuring CSA/DD cross-correlated relaxation on trehalose, a compound which could be approximated as a spherical top, and on simple model compounds comprisingC3vsymmetry (CHCl3, triphenylsilane (TPSi)). The comparison gives experimental evidence for the equivalence of the methods within the limits of the two-spin approach. 1D data are evaluated with both the simple initial rate and the Redfield relaxation matrix approach. The 2D data are obtained from the so-called transfer matrix using the Perrin-Gipe eigenvalue/eigenvector method. For the improved performance of the 2D method, anX-filtered (HHH) NOESY is suggested at the natural abundance of13C (or other dilute, low γ species). Also, experimental parameters crucial for reliable CSA data are tested (e.g., the impact of insufficient relaxation delay). Error estimation is carried out for fair comparison of methods. Revised liquid state1H and13C (29Si) CSA data are presented for chloroform and TPSi.

  5. Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes

    PubMed Central

    2015-01-01

    The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data. PMID:25540822

  6. Identification of lipid-phosphatidylserine (PS) as the target of unbiasedly selected cancer specific peptide-peptoid hybrid PPS1

    PubMed Central

    Desai, Tanvi J.; Toombs, Jason E.; Minna, John D.; Brekken, Rolf A.; Udugamasooriya, Damith Gomika

    2016-01-01

    Phosphatidylserine (PS) is an anionic phospholipid maintained on the inner-leaflet of the cell membrane and is externalized in malignant cells. We previously launched a careful unbiased selection targeting biomolecules (e.g. protein, lipid or carbohydrate) distinct to cancer cells by exploiting HCC4017 lung cancer and HBEC30KT normal epithelial cells derived from the same patient, identifying HCC4017 specific peptide-peptoid hybrid PPS1. In this current study, we identified PS as the target of PPS1. We validated direct PPS1 binding to PS using ELISA-like assays, lipid dot blot and liposome based binding assays. In addition, PPS1 recognized other negatively charged and cancer specific lipids such as phosphatidic acid, phosphatidylinositol and phosphatidylglycerol. PPS1 did not bind to neutral lipids such as phosphatidylethanolamine found in cancer and phosphatidylcholine and sphingomyelin found in normal cells. Further we found that the dimeric version of PPS1 (PPS1D1) displayed strong cytotoxicity towards lung cancer cell lines that externalize PS, but not normal cells. PPS1D1 showed potent single agent anti-tumor activity and enhanced the efficacy of docetaxel in mice bearing H460 lung cancer xenografts. Since PS and anionic phospholipid externalization is common across many cancer types, PPS1 may be an alternative to overcome limitations of protein targeted agents. PMID:27120792

  7. Unbiased estimation of biomarker panel performance when combining training and testing data in a group sequential design.

    PubMed

    Tayob, Nabihah; Do, Kim-Anh; Feng, Ziding

    2016-09-01

    Motivated by an ongoing study to develop a screening test able to identify patients with undiagnosed Sjögren's Syndrome in a symptomatic population, we propose methodology to combine multiple biomarkers and evaluate their performance in a two-stage group sequential design that proceeds as follows: biomarker data is collected from first stage samples; the biomarker panel is built and evaluated; if the panel meets pre-specified performance criteria the study continues to the second stage and the remaining samples are assayed. The design allows us to conserve valuable specimens in the case of inadequate biomarker panel performance. We propose a nonparametric conditional resampling algorithm that uses all the study data to provide unbiased estimates of the biomarker combination rule and the sensitivity of the panel corresponding to specificity of 1-t on the receiver operating characteristic curve (ROC). The Copas and Corbett (2002) correction, for bias resulting from using the same data to derive the combination rule and estimate the ROC, was also evaluated and an improved version was incorporated. An extensive simulation study was conducted to evaluate finite sample performance and propose guidelines for designing studies of this type. The methods were implemented in the National Cancer Institutes Early Detection Network Urinary PCA3 Evaluation Trial.

  8. WHFAST: a fast and unbiased implementation of a symplectic Wisdom-Holman integrator for long-term gravitational simulations

    NASA Astrophysics Data System (ADS)

    Rein, Hanno; Tamayo, Daniel

    2015-09-01

    We present WHFAST, a fast and accurate implementation of a Wisdom-Holman symplectic integrator for long-term orbit integrations of planetary systems. WHFAST is significantly faster and conserves energy better than all other Wisdom-Holman integrators tested. We achieve this by significantly improving the Kepler solver and ensuring numerical stability of coordinate transformations to and from Jacobi coordinates. These refinements allow us to remove the linear secular trend in the energy error that is present in other implementations. For small enough timesteps, we achieve Brouwer's law, i.e. the energy error is dominated by an unbiased random walk due to floating-point round-off errors. We implement symplectic correctors up to order 11 that significantly reduce the energy error. We also implement a symplectic tangent map for the variational equations. This allows us to efficiently calculate two widely used chaos indicators the Lyapunov characteristic number and the Mean Exponential Growth factor of Nearby Orbits. WHFAST is freely available as a flexible C package, as a shared library, and as an easy-to-use PYTHON module.

  9. White matter microstructural characteristics in newly diagnosed Parkinson’s disease: An unbiased whole-brain study

    PubMed Central

    Wen, Ming-Ching; Heng, Hannah S. E.; Ng, Samuel Y. E.; Tan, Louis C. S.; Chan, Ling Ling; Tan, Eng King

    2016-01-01

    Parkinson’s disease (PD) is a debilitating neurodegenerative disorder. Findings on specific white matter (WM) alterations in PD have been inconsistent. We hypothesized that WM changes occur in early PD patients and unbiased whole-brain analysis may provide additional evidence of pathological WM changes in PD. In this study, we examined various indexes of WM microstructure in newly diagnosed PD patients at the whole-brain level. 64 PDs with Hoehn & Yahr stage 1 (HY1PDs), 87 PDs with Hoehn & Yahr stage 2 (HYPD2s), and 60 controls (HCs) were recruited. Tract-based spatial statistics (TBSS) and diffusion connectometry were used to identify changes of WM pathways associated with PD. There were no significant differences in axial diffusivity, but HY1PDs exhibited greater fractional anisotropy (FA) and decreased mean and radial diffusivities (MD and RD) in callosal, projection, and association fibres than HCs and HY2PDs. Motor severity was inversely correlated with FA, but positively correlated with MD and RD in PD patients. Connectometry analysis also revealed increased WM density in the aforementioned tracts in PD patients, compared with HCs. Our study reveals WM enhancement, suggesting neural compensations in early PD. Longitudinal follow-up studies are warranted to identify the trajectory of WM changes alongside the progression of PD. PMID:27762307

  10. Unbiased Identification of Blood-based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks.

    PubMed

    Sambarey, Awanti; Devaprasad, Abhinandan; Mohan, Abhilash; Ahmed, Asma; Nayak, Soumya; Swaminathan, Soumya; D'Souza, George; Jesuraj, Anto; Dhar, Chirag; Babu, Subash; Vyakarnam, Annapurna; Chandra, Nagasuma

    2017-02-01

    Efficient diagnosis of tuberculosis (TB) is met with multiple challenges, calling for a shift of focus from pathogen-centric diagnostics towards identification of host-based multi-marker signatures. Transcriptomics offer a list of differentially expressed genes, but cannot by itself identify the most influential contributors to the disease phenotype. Here, we describe a computational pipeline that adopts an unbiased approach to identify a biomarker signature. Data from RNA sequencing from whole blood samples of TB patients were integrated with a curated genome-wide molecular interaction network, from which we obtain a comprehensive perspective of variations that occur in the host due to TB. We then implement a sensitive network mining method to shortlist gene candidates that are most central to the disease alterations. We then apply a series of filters that include applicability to multiple publicly available datasets as well as additional validation on independent patient samples, and identify a signature comprising 10 genes - FCGR1A, HK3, RAB13, RBBP8, IFI44L, TIMM10, BCL6, SMARCD3, CYP4F3 and SLPI, that can discriminate between TB and healthy controls as well as distinguish TB from latent tuberculosis and HIV in most cases. The signature has the potential to serve as a diagnostic marker of TB.

  11. Peer-reviewed and unbiased research, rather than 'sound science', should be used to evaluate endocrine-disrupting chemicals.

    PubMed

    Trasande, Leonardo; Vandenberg, Laura N; Bourguignon, Jean-Pierre; Myers, John Peterson; Slama, Remy; Vom Saal, Frederick; Zoeller, Robert Thomas

    2016-11-01

    Evidence increasingly confirms that synthetic chemicals disrupt the endocrine system and contribute to disease and disability across the lifespan. Despite a United Nations Environment Programme/WHO report affirmed by over 100 countries at the Fourth International Conference on Chemicals Management, 'manufactured doubt' continues to be cast as a cloud over rigorous, peer-reviewed and independently funded scientific data. This study describes the sources of doubt and their social costs, and suggested courses of action by policymakers to prevent disease and disability. The problem is largely based on the available data, which are all too limited. Rigorous testing programmes should not simply focus on oestrogen, androgen and thyroid. Tests should have proper statistical power. 'Good laboratory practice' (GLP) hardly represents a proper or even gold standard for laboratory studies of endocrine disruption. Studies should be evaluated with regard to the contamination of negative controls, responsiveness to positive controls and dissection techniques. Flaws in many GLP studies have been identified, yet regulatory agencies rely on these flawed studies. Peer-reviewed and unbiased research, rather than 'sound science', should be used to evaluate endocrine-disrupting chemicals.

  12. Phonon spectra of alkali metals

    NASA Astrophysics Data System (ADS)

    Zeković, S.; Vukajlović, F.; Veljković, V.

    1982-10-01

    In this work we used a simple local model pseudopotential which includes screening for the phonon spectra calculations of alkali metals. The results obtained are in very good agreement with experimental data. In some branches of phonon spectra the differences between theoretical and experimental results are within 1-2%, while the maximum error is about 6%. The suggested form of the pseudopotential allows us to describe the phonon spectra of Na, K and Rb with only one, and, at the same time, a unique, parameter. In this case, the maximum disagreements from experiment are 9% for Na, 8% for K and 7% for Rb.

  13. Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

    PubMed

    Baran, Richard; Northen, Trent R

    2013-10-15

    Untargeted metabolite profiling using liquid chromatography and mass spectrometry coupled via electrospray ionization is a powerful tool for the discovery of novel natural products, metabolic capabilities, and biomarkers. However, the elucidation of the identities of uncharacterized metabolites from spectral features remains challenging. A critical step in the metabolite identification workflow is the assignment of redundant spectral features (adducts, fragments, multimers) and calculation of the underlying chemical formula. Inspection of the data by experts using computational tools solving partial problems (e.g., chemical formula calculation for individual ions) can be performed to disambiguate alternative solutions and provide reliable results. However, manual curation is tedious and not readily scalable or standardized. Here we describe an automated procedure for the robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming optimization (RAMSI). Chemical rules among related ions are expressed as linear constraints and both the spectra interpretation and chemical formula calculation are performed in a single optimization step. This approach is unbiased in that it does not require predefined sets of neutral losses and positive and negative polarity spectra can be combined in a single optimization. The procedure was evaluated with 30 experimental mass spectra and was found to effectively identify the protonated or deprotonated molecule ([M + H](+) or [M - H](-)) while being robust to the presence of background ions. RAMSI provides a much-needed standardized tool for interpreting ions for subsequent identification in untargeted metabolomics workflows.

  14. ZASPE: A Code to Measure Stellar Atmospheric Parameters and their Covariance from Spectra

    NASA Astrophysics Data System (ADS)

    Brahm, Rafael; Jordán, Andrés; Hartman, Joel; Bakos, Gaspar

    2017-01-01

    We describe the Zonal Atmospheric Stellar Parameters Estimator (ZASPE), a new algorithm, and its associated code, for determining precise stellar atmospheric parameters and their uncertainties from high resolution echelle spectra of FGK-type stars. ZASPE estimates stellar atmospheric parameters by comparing the observed spectrum against a grid of synthetic spectra only in the most sensitive spectral zones to changes in the atmospheric parameters. Realistic uncertainties in the parameters are computed from the data itself, by taking into account the systematic mismatches between the observed spectrum and the best-fit synthetic one. The covariances between the parameters are also estimated in the process. ZASPE can in principle use any pre-calculated grid of synthetic spectra but unbiased grids are required to obtain accurate parameters. We tested the performance of two existing libraries (Coelho et al. 2005; Husser et al. 2013) and we concluded that neither is suitable for computing precise atmospheric parameters. We describe a process to synthesise a new library of synthetic spectra that was found to generate consistent results when compared with parameters obtained with different methods (interferometry, asteroseismology, equivalent widths).

  15. Spectra ID of recent SN

    NASA Astrophysics Data System (ADS)

    Challis, Peter

    2013-12-01

    P. Challis, Harvard-Smithsonian Center for Astrophysics (CfA), on behalf of the CfA Supernova Group, report spectra (range 320-860 nm) of various SN obtained during Dec. 24-27 UT by P. Challis, S. Gottilla (MMTO.org), and E. Marin (MMTO.org) with the MMT 6.5-m telescope (+ Blue Channel). Cross-correlation with a library of supernova spectra using the "Supernova Identification" code (SNID; Blondin and Tonry 2007, Ap.J.

  16. Using propensity score matching to estimate an "unbiased effect-size" between women's employment and partner violence in Tanzania.

    PubMed

    Vyas, Seema; Heise, Lori

    2014-11-01

    Estimates of the effect of employment on women's risk of partner violence in cross-sectional studies are subject to potential "self-selection bias." Women's personal choice of whether to pursue employment or not may create fundamental differences between the group of women who are employed and those who are not employed that standard regression methods cannot account for even after adjusting for confounding. The aim of this study is to demonstrate the utility of propensity score matching (PSM), a technique used widely in econometrics, to address this bias in cross-sectional studies. We use PSM to estimate an unbiased effect-size of women's employment on their risk of experiencing partner violence in urban and rural Tanzania using data from the 2010 Tanzania Demographic and Health Survey (DHS). Three different measures of women's employment were analyzed: whether they had engaged in any productive work outside of the home in the past year, whether they received payment in cash for this productive work, and whether their employment was stable. Women who worked outside of the home were significantly different from those who did not. In both urban and rural Tanzania, women's risk of violence appears higher among women who worked in the past year than among those who did not, even after using PSM to account for underlying differences in these two groups of women. Being paid in cash reversed this effect in rural areas whereas stability of employment reduced this risk in urban centers. The estimated size of effect varied by type of matching estimator, but the direction of the association remained largely consistent. This study's findings suggest substantial self-selection into employment. PSM methods, by compensating for this bias, appear to be a useful tool for estimating the relationship between women's employment and partner violence in cross-sectional studies.

  17. Nanoscale Synaptic Membrane Mimetic Allows Unbiased High Throughput Screen That Targets Binding Sites for Alzheimer’s-Associated Aβ Oligomers

    PubMed Central

    Wilcox, Kyle C.; Marunde, Matthew R.; Das, Aditi; Velasco, Pauline T.; Kuhns, Benjamin D.; Marty, Michael T.; Jiang, Haoming; Luan, Chi-Hao; Sligar, Stephen G.; Klein, William L.

    2015-01-01

    Despite their value as sources of therapeutic drug targets, membrane proteomes are largely inaccessible to high-throughput screening (HTS) tools designed for soluble proteins. An important example comprises the membrane proteins that bind amyloid β oligomers (AβOs). AβOs are neurotoxic ligands thought to instigate the synapse damage that leads to Alzheimer’s dementia. At present, the identities of initial AβO binding sites are highly uncertain, largely because of extensive protein-protein interactions that occur following attachment of AβOs to surface membranes. Here, we show that AβO binding sites can be obtained in a state suitable for unbiased HTS by encapsulating the solubilized synaptic membrane proteome into nanoscale lipid bilayers (Nanodiscs). This method gives a soluble membrane protein library (SMPL)—a collection of individualized synaptic proteins in a soluble state. Proteins within SMPL Nanodiscs showed enzymatic and ligand binding activity consistent with conformational integrity. AβOs were found to bind SMPL Nanodiscs with high affinity and specificity, with binding dependent on intact synaptic membrane proteins, and selective for the higher molecular weight oligomers known to accumulate at synapses. Combining SMPL Nanodiscs with a mix-incubate-read chemiluminescence assay provided a solution-based HTS platform to discover antagonists of AβO binding. Screening a library of 2700 drug-like compounds and natural products yielded one compound that potently reduced AβO binding to SMPL Nanodiscs, synaptosomes, and synapses in nerve cell cultures. Although not a therapeutic candidate, this small molecule inhibitor of synaptic AβO binding will provide a useful experimental antagonist for future mechanistic studies of AβOs in Alzheimer’s model systems. Overall, results provide proof of concept for using SMPLs in high throughput screening for AβO binding antagonists, and illustrate in general how a SMPL Nanodisc system can facilitate drug

  18. Personalizing, not patronizing: the case for patient autonomy by unbiased presentation of management options in stage I testicular cancer.

    PubMed

    Oldenburg, J; Aparicio, J; Beyer, J; Cohn-Cedermark, G; Cullen, M; Gilligan, T; De Giorgi, U; De Santis, M; de Wit, R; Fosså, S D; Germà-Lluch, J R; Gillessen, S; Haugnes, H S; Honecker, F; Horwich, A; Lorch, A; Ondruš, D; Rosti, G; Stephenson, A J; Tandstad, T

    2015-05-01

    Testicular cancer (TC) is the most common neoplasm in males aged 15-40 years. The majority of patients have no evidence of metastases at diagnosis and thus have clinical stage I (CSI) disease [Oldenburg J, Fossa SD, Nuver J et al. Testicular seminoma and non-seminoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2013; 24(Suppl 6): vi125-vi132; de Wit R, Fizazi K. Controversies in the management of clinical stage I testis cancer. J Clin Oncol 2006; 24: 5482-5492.]. Management of CSI TC is controversial and options include surveillance and active treatment. Different forms of adjuvant therapy exist, including either one or two cycles of carboplatin chemotherapy or radiotherapy for seminoma and either one or two cycles of cisplatin-based chemotherapy or retroperitoneal lymph node dissection for non-seminoma. Long-term disease-specific survival is ∼99% with any of these approaches, including surveillance. While surveillance allows most patients to avoid additional treatment, adjuvant therapy markedly lowers the relapse rate. Weighing the net benefits of surveillance against those of adjuvant treatment depends on prioritizing competing aims such as avoiding unnecessary treatment, avoiding more burdensome treatment with salvage chemotherapy and minimizing the anxiety, stress and life disruption associated with relapse. Unbiased information about the advantages and disadvantages of surveillance and adjuvant treatment is a prerequisite for informed consent by the patient. In a clinical scenario like CSI TC, where different disease-management options produce indistinguishable long-term survival rates, patient values, priorities and preferences should be taken into account. In this review, we provide an overview about risk factors for relapse, potential benefits and harms of adjuvant chemotherapy and active surveillance and a rationale for involving patients in individualized decision making about their treatment rather than adopting

  19. Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    PubMed Central

    Hilario, Elena; Barron, Lorna; Deng, Cecilia H.; Datson, Paul M.; Davy, Marcus W.; Storey, Roy D.

    2015-01-01

    Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al. method: some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS). By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS) method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145) of BamH I sites shared with the reference genome, compared to only 14% (11,513) by stdGBS. PMID:26633193

  20. Fundamental Parameters of a Large, Unbiased Sample of Massive, Young, Embedded Star Clusters in the Milky Way

    NASA Astrophysics Data System (ADS)

    Dallilar, Yigit; Barnes, Peter; Lada, Elizabeth; Ryder, Stuart

    2015-08-01

    Massive star cluster formation in our Galaxy is still a mystery. Unlike studies on nearby star formation regions (Pleiades, Orion Nebula), there is no unbiased sample of massive young star clusters except the CHaMP survey, which is focused on the Carina Arm (Barnes et al. 2011, ApJS, 196, 12). In this project, we examine properties of young clusters identified in the CHaMP survey through infrared photometry. Near infrared (J,H,K) imaging was obtained with the Australian Astronomical Telescope and deep mid infrared (IRAC bands 1,2) imaging was obtained with the Spitzer Space Telescope during the warm mission. Photometric analysis was performed with a combination of Sextrac- tor and Psfex software. Photometric calibration for NIR data was handled exploiting 2Mass coverage for our fields. For MIR data, photometric calibration was obtained using GLIMPSE coverage for a small number of our images, then bootstrapping this to calibrate other images, since all images are obtained with the same pipeline. To identify cluster members, we provide constraints on the source classification using field AGB stars and faint background galaxies, which have similar characteristics as reddened young stellar objects. Predicted locations of these objects on color-magnitude and color-color diagrams are used as a guide, as are the stellar classification parameter from Sextractor and faint galaxy catalogs covering our fields. We also examine extinction properties towards these young clusters, exploiting well known properties of AGB star population in our fields. Combining the IR data with existing mm-wave specroscopy, we compute values for the gas to dust ratio of these young clusters using extinction properties plus differential H-K color maps and NH column density measurements, all obtained as a part of the CHaMP survey. These results help us to identify evolutionary stages of these young clusters. Eventually, we will constrain cluster properties like age, distance and metallicity with

  1. Precision medicine in the age of big data: The present and future role of large-scale unbiased sequencing in drug discovery and development.

    PubMed

    Vicini, P; Fields, O; Lai, E; Litwack, E D; Martin, A-M; Morgan, T M; Pacanowski, M A; Papaluca, M; Perez, O D; Ringel, M S; Robson, M; Sakul, H; Vockley, J; Zaks, T; Dolsten, M; Søgaard, M

    2016-02-01

    High throughput molecular and functional profiling of patients is a key driver of precision medicine. DNA and RNA characterization has been enabled at unprecedented cost and scale through rapid, disruptive progress in sequencing technology, but challenges persist in data management and interpretation. We analyze the state-of-the-art of large-scale unbiased sequencing in drug discovery and development, including technology, application, ethical, regulatory, policy and commercial considerations, and discuss issues of LUS implementation in clinical and regulatory practice.

  2. Inhibitory impact of 3'-terminal 2'-O-methylated small silencing RNA on target-primed polymerization and unbiased amplified quantification of the RNA in Arabidopsis thaliana.

    PubMed

    Chen, Feng; Fan, Chunhai; Zhao, Yongxi

    2015-09-01

    3'-terminal 2'-O-methylation has been found in several kinds of small silencing RNA, regarded as a protective mechanism against enzymatic 3' → 5' degradation and 3'-end uridylation. The influence of this modification on enzymatic polymerization, however, remains unknown. Herein, a systematic investigation is performed to explore this issue. We found these methylated small RNAs exhibited a suppression behavior in target-primed polymerization, revealing biased result for the manipulation of these small RNAs by conventional polymerization-based methodology. The related potential mechanism is investigated and discussed, which is probably ascribed to the big size of modified group and its close location to 3'-OH. Furthermore, two novel solutions each utilizing base-stacking hybridization and three-way junction structure have been proposed to realize unbiased recognition of small RNAs. On the basis of phosphorothioate against nicking, a creative amplified strategy, phosphorothioate-protected polymerization/binicking amplification, has also been developed for the unbiased quantification of methylated small RNA in Arabidopsis thaliana, demonstrating its promising potential for real sample analysis. Collectively, our studies uncover the polymerization inhibition by 3'-terminal 2'-O-methylated small RNAs with mechanistic discussion, and propose novel unbiased solutions for amplified quantification of small RNAs in real sample.

  3. Vibrational Spectra of Selected Monohalogenated Monocarboxylic Acids.

    DTIC Science & Technology

    HALOGENATED HYDROCARBONS, INFRARED SPECTRA), (*CARBOXYLIC ACIDS, *INFRARED SPECTRA), IODINE COMPOUNDS, CHLORINE COMPOUNDS, BROMINE COMPOUNDS, ACETIC ACID , ACETATES, MOLECULAR STRUCTURE, MOLECULAR ASSOCIATION

  4. Photon spectra from WIMP annihilation

    SciTech Connect

    Cembranos, J. A. R.; Cruz-Dombriz, A. de la; Dobado, A.; Maroto, A. L.; Lineros, R. A.

    2011-04-15

    If the present dark matter in the Universe annihilates into standard model particles, it must contribute to the fluxes of cosmic rays that are detected on the Earth and, in particular, to the observed gamma-ray fluxes. The magnitude of such a contribution depends on the particular dark matter candidate, but certain features of the produced photon spectra may be analyzed in a rather model-independent fashion. In this work we provide the complete photon spectra coming from WIMP annihilation into standard model particle-antiparticle pairs obtained by extensive Monte Carlo simulations. We present results for each individual annihilation channel and provide analytical fitting formulas for the different spectra for a wide range of WIMP masses.

  5. QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

    SciTech Connect

    Sanchez Almeida, J.; Morales-Luis, A. B.; Terlevich, R.; Terlevich, E.; Cid Fernandes, R. E-mail: abml@iac.es E-mail: eterlevi@inaoep.mx

    2012-09-10

    We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

  6. The structure of BPS spectra

    NASA Astrophysics Data System (ADS)

    Longhi, Pietro

    In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

  7. Metagenomic Analysis of Taxa Associated with Lutzomyia longipalpis, Vector of Visceral Leishmaniasis, Using an Unbiased High-Throughput Approach

    PubMed Central

    McCarthy, Christina B.; Diambra, Luis A.; Rivera Pomar, Rolando V.

    2011-01-01

    Background Leishmaniasis is one of the most diverse and complex of all vector-borne diseases worldwide. It is caused by parasites of the genus Leishmania, obligate intramacrophage protists characterised by diversity and complexity. Its most severe form is visceral leishmaniasis (VL), a systemic disease that is fatal if left untreated. In Latin America VL is caused by Leishmania infantum chagasi and transmitted by Lutzomyia longipalpis. This phlebotomine sandfly is only found in the New World, from Mexico to Argentina. In South America, migration and urbanisation have largely contributed to the increase of VL as a public health problem. Moreover, the first VL outbreak was recently reported in Argentina, which has already caused 7 deaths and 83 reported cases. Methodology/Principal Findings An inventory of the microbiota associated with insect vectors, especially of wild specimens, would aid in the development of novel strategies for controlling insect vectors. Given the recent VL outbreak in Argentina and the compelling need to develop appropriate control strategies, this study focused on wild male and female Lu. longipalpis from an Argentine endemic (Posadas, Misiones) and a Brazilian non-endemic (Lapinha Cave, Minas Gerais) VL location. Previous studies on wild and laboratory reared female Lu. longipalpis have described gut bacteria using standard bacteriological methods. In this study, total RNA was extracted from the insects and submitted to high-throughput pyrosequencing. The analysis revealed the presence of sequences from bacteria, fungi, protist parasites, plants and metazoans. Conclusions/Significance This is the first time an unbiased and comprehensive metagenomic approach has been used to survey taxa associated with an infectious disease vector. The identification of gregarines suggested they are a possible efficient control method under natural conditions. Ongoing studies are determining the significance of the associated taxa found in this study in a

  8. Computer Simulation of NMR Spectra.

    ERIC Educational Resources Information Center

    Ellison, A.

    1983-01-01

    Describes a PASCAL computer program which provides interactive analysis and display of high-resolution nuclear magnetic resonance (NMR) spectra from spin one-half nuclei using a hard-copy or monitor. Includes general and theoretical program descriptions, program capability, and examples of its use. (Source for program/documentation is included.)…

  9. Classical Trajectories and Quantum Spectra

    NASA Technical Reports Server (NTRS)

    Mielnik, Bogdan; Reyes, Marco A.

    1996-01-01

    A classical model of the Schrodinger's wave packet is considered. The problem of finding the energy levels corresponds to a classical manipulation game. It leads to an approximate but non-perturbative method of finding the eigenvalues, exploring the bifurcations of classical trajectories. The role of squeezing turns out decisive in the generation of the discrete spectra.

  10. Discrimination of petroleum fluorescence spectra.

    PubMed

    Stelmaszewski, Adam

    2007-01-01

    This paper presents studies of the total spectra (fluorescence-excitation matrix) of petroleum with regard to the utilization of fluorescence for determining petroleum pollutants. Thorough testing of one group, comprising almost forty lubricating oils in the form of their hexane solutions, points out their discrimination.

  11. Shape effects on asteroid spectra

    NASA Astrophysics Data System (ADS)

    Davalos, J.; Carvano, J.

    2014-07-01

    The objective of this work is to probe how the shape of a body like an asteroid could be modifying its observed spectra and the derived mineralogical interfaces based on spectral modeling. To model this effect, we construct an oblate ellipsoid with triangular facets, where each facet contributes to the overall reflectance. The synthetic spectra is generated by the isotropic multiple-scattering approximation (IMSA) reflectance model of Hapke (1993). First, we obtained optical constants by inverting the spectra of meteorites, obtained from the RELAB spectral database. These optical constants were found inverting the reflectance bidirectional equation of Hapke; this is made in two steps: (i) The first inversion is to find the single-scattering albedo π (ii) in the model of Hapke, this albedo is found under the regime of the geometric optics, where the particle size is much larger than the wavelength of the incident radiation. Here we assumed a constant value for the real part of the optical constant n=1.5. With these optical constants, we can construct synthetic spectra for any particle size. The phase function used is the double Henyey-Greenstein phase function and an accurate expression for the H-functions. We started with the ellipsoidal shape a=1.0, b=c=0.5 for two particle size 50 and 250 μ m, in this part, we found good differences in the BAR parameter between the two geometric models, this was done for 100 Eucrite meteorites spectra. In this first study, we found that the BAR parameter between the two models is bigger when the particle size increases. In the second part, we started with different ellipsoidal shapes and produced synthetic spectra for material with eucrite and diogenite composition with a phase angle of 20 degrees, incidence and emission angles of 10 degrees, and particle size at 250 μ m. All spectra was generated for four parameters of phase angle b=[0.2,0.4,0.6,0.8] taking the empirical relation between the phase constants of Hapke (2012

  12. Phobos surface spectra mineralogical modeling

    NASA Astrophysics Data System (ADS)

    Pajola, M.; Lazzarin, M.; Dalle Ore, C. M.; Cruikshank, D. P.; Roush, T. L.; Pendleton, Y.; Bertini, I.; Magrin, S.; Carli, C.; La Forgia, F.; Barbieri, C.

    2014-04-01

    A mineralogical model composed of a mixture of Tagish Lake meteorite (TL) and Pyroxene Glass (PM80) was presented in [1] to explain the surface reflectance of Phobos from 0.25 to 4.0 μm. The positive results we obtained, when comparing the OSIRIS data [2] extended in wavelength to include the [3,4] spectra, forced us to perform a wider comparison between our TL-PM80 model and the CRISM and OMEGA Phobos spectra presented in [5]. Such spectra cover three different regions of interest (ROIs) situated in the Phobos sub-Mars hemisphere: the interior of the Stickney crater, its eastern rim, and its proximity terrain southeast of the Reldresal crater. We decided to vary the percentage mixture of the components of our model (80% TL, 20% PM80), between pure TL and pure PM80, by means of the radiative transfer code based on the [6] formulation of the slab approximation. Once this spectral range was derived, see Fig. 1, we attempted to compare it with the [5] spectra between 0.4 and 2.6 μm, i.e. below the thermal emitted radiation, to see if any spectral match was possible. We observed that CRISM scaled spectra above 1.10 μm fall within pure Tagish Lake composition and the [1] model. The CRISM data below 1.10 μm present more discrepancies with our models, in particular for the Stickney's rim spectrum. Nevertheless the TL and PM80 components seem to be good mineralogical candidates on Phobos. We performed the same analysis with the OMEGA data and, again, we found out that the Stickney's rim spectrum lies out of our model range, while the two remaining spectra still lie between pure TL and 80% TL - 20% PM80, but indicating that a different, more complicated mixture is expected in order to explain properly both the spectral trend and the possible absorption bands located above 2.0 μm. Within this analysis, we point out that a big fraction of TL material (modeled pure or present with a minimum percentage of 80% mixed together with 20% PM80) seems to explain Phobos spectral

  13. Hierarchical analysis of molecular spectra

    SciTech Connect

    Davis, M.J.

    1996-03-01

    A novel representation of molecular spectra in terms of hierarchical trees has proven to be an important aid for the study of many significant problems in gas-phase chemical dynamics. Trees are generated from molecular spectra by monitoring the changes that occur in a spectrum as resolution is changed in a continuous manner. A tree defines a genealogy among all lines of a spectrum. This allows for a detailed understanding of the assignment of features of a spectrum that may be difficult to obtain any other way as well as an understanding of intramolecular energy transfer time scales, mechanisms, and pathways. The methodology has been applied to several problems: transition state spectroscopy, intramolecular energy transfer in highly excited molecules, high-resolution overtone spectroscopy, and the nature of the classical-quantum correspondence when there is classical chaos (``quantum chaos``).

  14. Eigenvectors of optimal color spectra.

    PubMed

    Flinkman, Mika; Laamanen, Hannu; Tuomela, Jukka; Vahimaa, Pasi; Hauta-Kasari, Markku

    2013-09-01

    Principal component analysis (PCA) and weighted PCA were applied to spectra of optimal colors belonging to the outer surface of the object-color solid or to so-called MacAdam limits. The correlation matrix formed from this data is a circulant matrix whose biggest eigenvalue is simple and the corresponding eigenvector is constant. All other eigenvalues are double, and the eigenvectors can be expressed with trigonometric functions. Found trigonometric functions can be used as a general basis to reconstruct all possible smooth reflectance spectra. When the spectral data are weighted with an appropriate weight function, the essential part of the color information is compressed to the first three components and the shapes of the first three eigenvectors correspond to one achromatic response function and to two chromatic response functions, the latter corresponding approximately to Munsell opponent-hue directions 9YR-9B and 2BG-2R.

  15. Accelerated Fitting of Stellar Spectra

    NASA Astrophysics Data System (ADS)

    Ting, Yuan-Sen; Conroy, Charlie; Rix, Hans-Walter

    2016-07-01

    Stellar spectra are often modeled and fitted by interpolating within a rectilinear grid of synthetic spectra to derive the stars’ labels: stellar parameters and elemental abundances. However, the number of synthetic spectra needed for a rectilinear grid grows exponentially with the label space dimensions, precluding the simultaneous and self-consistent fitting of more than a few elemental abundances. Shortcuts such as fitting subsets of labels separately can introduce unknown systematics and do not produce correct error covariances in the derived labels. In this paper we present a new approach—Convex Hull Adaptive Tessellation (chat)—which includes several new ideas for inexpensively generating a sufficient stellar synthetic library, using linear algebra and the concept of an adaptive, data-driven grid. A convex hull approximates the region where the data lie in the label space. A variety of tests with mock data sets demonstrate that chat can reduce the number of required synthetic model calculations by three orders of magnitude in an eight-dimensional label space. The reduction will be even larger for higher dimensional label spaces. In chat the computational effort increases only linearly with the number of labels that are fit simultaneously. Around each of these grid points in the label space an approximate synthetic spectrum can be generated through linear expansion using a set of “gradient spectra” that represent flux derivatives at every wavelength point with respect to all labels. These techniques provide new opportunities to fit the full stellar spectra from large surveys with 15-30 labels simultaneously.

  16. Optical Spectra of Triggered Lightning

    NASA Astrophysics Data System (ADS)

    Walker, T. D.; Biagi, C. J.; Hill, J. D.; Jordan, D. M.; Uman, M. A.; Christian, H. J., Jr.

    2009-12-01

    In August 2009, the first optical spectra of triggered lightning flashes were acquired. Data from two triggered lightning flashes were obtained at the International Center for Lightning Research and Testing in north-central Florida. The spectrometer that was used has an average dispersion of 260 Å/mm resulting in an average resolution of 5 Å when mated to a Photron (SA1.1) high-speed camera. The spectra captured with this system had a free spectral range of 3800-8000 Å. The spectra were captured at 300,000 frames per second. The spectrometer's vertical field of view was 3 m at an altitude 50 m above the launch tower, intended to view the middle of the triggering wire. Preliminary results show that the copper spectrum dominated the earliest part of the flash and copper lines persisted during the total lifetime of the detectable spectrum. Animations over the lifetime of the stroke from the initial wire illumination to multiple return strokes show the evolution of the spectrum. In addition, coordinated high speed channel base current, electric field and imagery measurements of the exploding wire, downward leaders, and return strokes were recorded. Quantitative analysis of the spectral evolution will be discussed in the context of the overall flash development.

  17. Ultraviolet Spectra of Uranian Satellites

    NASA Astrophysics Data System (ADS)

    Roush, Ted

    1996-07-01

    The ultraviolet reflectance spectra of the icy satellites ofUranus are largely unknown. We propose to use the HubbleSpace Telescope Faint Object Spectrograph in order to obtainthe first high S/N UV spectra of Ariel, Titania, and Oberon.Because of our innovative targeting approach, we have alsobeen able to include Umbriel in our observational plans.These satellites sample almost the full range of UV albedosand UV/VIS colors exhibited by the large Uranian satellites.The spectral resolution and range will overlap with earth-based telescopic and spacecraft observations of these objectsallowing for comparisons of the UV data with existing visualand near-infrared spectra of these objects. These comparisonswill ultimately provide greater constraints on the relativelylow albedo spectrally neutral non-ice component on the Uraniansatellites. The existance of UV spectral features due tospecies such as O_3, H_2O_2 or carbon-rich macromolecules(e.g. polycyclic aromatic hydrocarbons) can provide evidencefor modification of the surfaces via plasma or meteoriticbombardment, alteration by high-energy ultraviolet radiation,or accretion of particles from nearby sources such asplanetary rings or dust bands.

  18. Spectroscopic Properties of Star-Forming Host Galaxies and Type Ia Supernova Hubble Residuals in a Nearly Unbiased Sample

    SciTech Connect

    D'Andrea, Chris B.; et al.

    2011-12-20

    We examine the correlation between supernova host galaxy properties and their residuals on the Hubble diagram. We use supernovae discovered during the Sloan Digital Sky Survey II - Supernova Survey, and focus on objects at a redshift of z < 0.15, where the selection effects of the survey are known to yield a complete Type Ia supernova sample. To minimize the bias in our analysis with respect to measured host-galaxy properties, spectra were obtained for nearly all hosts, spanning a range in magnitude of -23 < M_r < -17. In contrast to previous works that use photometric estimates of host mass as a proxy for global metallicity, we analyze host-galaxy spectra to obtain gas-phase metallicities and star-formation rates from host galaxies with active star formation. From a final sample of ~ 40 emission-line galaxies, we find that light-curve corrected Type Ia supernovae are ~ 0.1 magnitudes brighter in high-metallicity hosts than in low-metallicity hosts. We also find a significant (> 3{\\sigma}) correlation between the Hubble residuals of Type Ia supernovae and the specific star-formation rate of the host galaxy. We comment on the importance of supernova/host-galaxy correlations as a source of systematic bias in future deep supernova surveys.

  19. MODELING EXTRAGALACTIC FOREGROUNDS AND SECONDARIES FOR UNBIASED ESTIMATION OF COSMOLOGICAL PARAMETERS FROM PRIMARY COSMIC MICROWAVE BACKGROUND ANISOTROPY

    SciTech Connect

    Millea, M.; Knox, L.; Dore, O.; Dudley, J.; Holder, G.; Shaw, L.; Song, Y.-S.; Zahn, O.

    2012-02-10

    Using the latest physical modeling and constrained by the most recent data, we develop a phenomenological parameterized model of the contributions to intensity and polarization maps at millimeter wavelengths from external galaxies and Sunyaev-Zeldovich effects. We find such modeling to be necessary for estimation of cosmological parameters from Planck data. For example, ignoring the clustering of the infrared background would result in a bias in n{sub s} of 7{sigma} in the context of an eight-parameter cosmological model. We show that the simultaneous marginalization over a full foreground model can eliminate such biases, while increasing the statistical uncertainty in cosmological parameters by less than 20%. The small increases in uncertainty can be significantly reduced with the inclusion of higher-resolution ground-based data. The multi-frequency analysis we employ involves modeling 46 total power spectra and marginalization over 17 foreground parameters. We show that we can also reduce the data to a best estimate of the cosmic microwave background power spectra, with just two principal components (with constrained amplitudes) describing residual foreground contamination.

  20. SPECTROSCOPIC PROPERTIES OF STAR-FORMING HOST GALAXIES AND TYPE Ia SUPERNOVA HUBBLE RESIDUALS IN A NEARLY UNBIASED SAMPLE

    SciTech Connect

    D'Andrea, Chris B.; Gupta, Ravi R.; Sako, Masao; Morris, Matt; Nichol, Robert C.; Campbell, Heather; Lampeitl, Hubert; Brown, Peter J.; Olmstead, Matthew D.; Frieman, Joshua A.; Kessler, Richard; Garnavich, Peter; Jha, Saurabh W.; Marriner, John; Schneider, Donald P.; Smith, Mathew

    2011-12-20

    We examine the correlation between supernova (SN) host-galaxy properties and their residuals in the Hubble diagram. We use SNe discovered during the Sloan Digital Sky Survey-II Supernova Survey, and focus on objects at a redshift of z < 0.15, where the selection effects of the survey are known to yield a complete Type Ia supernova (SN Ia) sample. To minimize the bias in our analysis with respect to measured host-galaxy properties, spectra were obtained for nearly all hosts, spanning a range in magnitude of -23 < M{sub r} < -17. In contrast to previous works that use photometric estimates of host mass as a proxy for global metallicity, we analyze host-galaxy spectra to obtain gas-phase metallicities and star formation rates (SFRs) from host galaxies with active star formation. From a final sample of {approx}40 emission-line galaxies, we find that light-curve-corrected SNe Ia are {approx}0.1 mag brighter in high-metallicity hosts than in low-metallicity hosts. We also find a significant (>3{sigma}) correlation between the Hubble Residuals of SNe Ia and the specific SFR of the host galaxy. We comment on the importance of SN/host-galaxy correlations as a source of systematic bias in future deep SN surveys.

  1. A novel method for diagnosis of smear-negative tuberculosis patients by combining a random unbiased Phi29 amplification with a specific real-time PCR.

    PubMed

    Pang, Yu; Lu, Jie; Yang, Jian; Wang, Yufeng; Cohen, Chad; Ni, Xin; Zhao, Yanlin

    2015-07-01

    In this study, we develop a novel method for diagnosis of smear-negative tuberculosis patients by performing a random unbiased Phi29 amplification prior to the use of a specific real-time PCR. The limit of detection (LOD) of the conventional real-time PCR was 100 colony-forming units (CFU) of MTB genome/reaction, while the REPLI real-time PCR assay could detect 0.4 CFU/reaction. In comparison with the conventional real-time PCR, REPLI real-time PCR shows better sensitivity for the detection of smear-negative tuberculosis (P = 0.015).

  2. Action spectra for photosynthetic inhibition

    NASA Technical Reports Server (NTRS)

    Caldwell, M. M.; Flint, S.; Camp, L. B.

    1981-01-01

    The ultraviolet action spectrum for photosynthesis inhibition was determined to fall between that of the general DNA action spectrum and the generalized plant action spectrum. The characteristics of this action spectrum suggest that a combination of pronounced increase in effectiveness with decreasing wavelength, substantial specificity for the UV-B waveband, and very diminished response in the UV-A waveband result in large radiation amplification factors when the action spectra are used as weighting functions. Attempted determination of dose/response relationships for leaf disc inhibition provided inconclusive data from which to deconvolute an action spectrum.

  3. Two slow meteors with spectra

    NASA Astrophysics Data System (ADS)

    Dubs, Martin; Sposetti, Stefano; Spinner, Roger; Booz, Beat

    2017-01-01

    On January 2, 2017 two peculiar meteors (M20170102_001216 and M20170102_015202) were observed by several stations in Switzerland. Both had a long duration, slow velocity, similar brightness and a very similar radiant. As they appeared in a time interval of 100 minutes, a satellite was suspected as a possible origin of these two observations. A closer inspection however showed that this interpretation was incorrect. The two objects were slow meteors. Spectra were taken from both objects, which were nearly identical. Together this points to a common origin of the two meteors.

  4. The Optical Spectra of Aerosols.

    DTIC Science & Technology

    1983-10-01

    espressione dell’ampiezza di diffusione in * avanti vengono fattorizzati. In questo modo la somma delle am- piezze di diftusione di "cluster" con...F1D-Ali35 687 THE OPTICAL SPECTRA OF REROSOLSOU) MESSINA UNIV (ITALY) i/i 1ST DI STRIJTTURA DELLA IIATERIA F BORIIHESE OCT 83 UNCLASSIFIED DRR78--85F...ELEMENT PROJECT, TASK AREA & WORK UNIT NUMBERS * Istituto di Struttura della Materia 61102A-1T161102-BH57-01 Un iversita di Messina V~nina. Ttalv St

  5. Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples

    PubMed Central

    Indenbirken, Daniela; Meyer, Thomas; Lütgehetmann, Marc; Lellek, Heinrich; Spohn, Michael; Aepfelbacher, Martin; Alawi, Malik; Grundhoff, Adam

    2015-01-01

    Unbiased nontargeted metagenomic RNA sequencing (UMERS) has the advantage to detect known as well as unknown pathogens and, thus, can significantly improve the detection of viral, bacterial, parasitic, and fungal sequences in public health settings. In particular, conventional diagnostic methods successfully identify the putative pathogenic agent in only 30% to 40% of respiratory specimens from patients with acute respiratory illness. Here, we applied UMERS to 24 diagnostic respiratory specimens (bronchoalveolar lavage [BAL] fluid, sputum samples, and a swab) from patients with seasonal influenza infection and 5 BAL fluid samples from patients with pneumonia that tested negative for influenza to validate RNA sequencing as an unbiased diagnostic tool in comparison to conventional diagnostic methods. In addition to our comparison to PCR, we evaluated the potential to retrieve comprehensive influenza virus genomic information and the capability to detect known superinfecting pathogens. Compared to quantitative real-time PCR for influenza viral sequences, UMERS detected influenza viral sequences in 18 of 24 samples. Complete influenza virus genomes could be assembled from 8 samples. Furthermore, in 3 of 24 influenza-positive samples, additional viral pathogens could be detected, and 2 of 24 samples showed a significantly increased abundance of individual bacterial species known to cause superinfections during an influenza virus infection. Thus, analysis of respiratory samples from known or suspected influenza patients by UMERS provides valuable information that is relevant for clinical investigation. PMID:25972420

  6. Unbiased photoelectrochemical water splitting in Z-scheme device using W/Mo-doped BiVO4 and Zn(x)Cd(1-x)Se.

    PubMed

    Park, Hyun S; Lee, Heung Chan; Leonard, Kevin C; Liu, Guanjie; Bard, Allen J

    2013-07-22

    Photoelectrochemical water splitting to generate H2 and O2 using only photon energy (with no added electrical energy) has been demonstrated with dual n-type-semiconductor (or Z-scheme) systems. Here we investigated two different Z-scheme systems; one is comprised of two cells with the same metal-oxide semiconductor (W- and Mo-doped bismuth vanadate), that is, Pt-W/Mo-BiVO4, and the other is comprised of the metal oxide and a chalcogenide semiconductor, that is, Pt-W/Mo-BiVO4 and Zn(0.2)Cd(0.8)Se. The redox couples utilized in these Z-scheme configurations were I(-)/IO3(-) or S(2-)/S(n)(2-), respectively. An electrochemical analysis of the system in terms of cell components is shown to illustrate the behavior of the complete photoelectrochemical Z-scheme water-splitting system. H2 gas from the unbiased photolysis of water was detected using gas chromatography-mass spectroscopy and using a membrane-electrode assembly. The electrode configuration to achieve the maximum conversion efficiency from solar energy to chemical energy with the given materials and the Z-scheme is discussed. Here, the possibilities and challenges of Z-scheme unbiased photoelectrochemical water-splitting devices and the materials to achieve practical solar-fuel generation are discussed.

  7. Method of processing positron lifetime spectra

    SciTech Connect

    Valuev, N.P.; Klimov, A.B.; Zhikharev, A.N.

    1985-05-01

    This paper describes a method for the processing of spectra of positron annihilation which permits a much more relaible determination of the lifetime during numerical processing of spectra by computer.

  8. Infrared Spectra of Polycyclic Aromatic Hydrocarbons (PAHs)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Bakes, E. L. O.

    2000-01-01

    We have computed the synthetic infrared spectra of some polycyclic aromatic hydrocarbons containing up to 54 carbon atoms. The species studied include ovalene, circumcoronene, dicoronylene, and hexabenzocoronene. We report spectra for anions, neutrals, cations, and multiply charged cations.

  9. Visible Spectra of Titanium Dioxide

    NASA Astrophysics Data System (ADS)

    Gupta, V.; Nagarajan, R.; Maier, J. P.; Zhuang, X.; Le, A.; Steimle, T. C.

    2011-05-01

    Titanium oxide (TiO) has been extensively studied spectroscopically due to its astrophysical relevance. TiO is the main opacity source in the atmospheres of cool M-type stars in the visible and near infrared. In view of the high cosmic abundance of Ti and O, titanium dioxide (TiO2) is believed to play an important role in dust formation processes from the gas-phase in circumstellar shells of oxygen-rich stars. The electronic spectra of a cold molecular beam of TiO2 have been investigated using mass-resolved resonance enhanced multi-photon ionization and laser induced fluorescence spectroscopy. TiO2 was produced by laser ablation of a pure titanium rod in the presence of a supersonic expanding mixture of approximately 5% O2 in either helium or argon. The spectra were recorded in the region 17500 cm-1 to 22500 cm-1 and the bands assigned to the A1B2 ← X1A1 transition. The origin and harmonic vibrational constants for the A1B2 state were determined to be: T000 = 17593(5) cm-1, ω1 = 876(3) cm-1, ω2 = 184(1) cm-1, and ω3 = 316(2) cm-1. Further, the dispersed fluorescence of a few bands were recorded to obtain vibrational parameters for the X1A1 state.

  10. Separation of small metabolites and lipids in spectra from biopsies by diffusion-weighted HR-MAS NMR: a feasibility study.

    PubMed

    Diserens, G; Vermathen, M; Precht, C; Broskey, N T; Boesch, C; Amati, F; Dufour, J-F; Vermathen, P

    2015-01-07

    High Resolution Magic Angle Spinning (HR-MAS) NMR allows metabolic characterization of biopsies. HR-MAS spectra from tissues of most organs show strong lipid contributions that are overlapping metabolite regions, which hamper metabolite estimation. Metabolite quantification and analysis would benefit from a separation of lipids and small metabolites. Generally, a relaxation filter is used to reduce lipid contributions. However, the strong relaxation filter required to eliminate most of the lipids also reduces the signals for small metabolites. The aim of our study was therefore to investigate different diffusion editing techniques in order to employ diffusion differences for separating lipid and small metabolite contributions in the spectra from different organs for unbiased metabonomic analysis. Thus, 1D and 2D diffusion measurements were performed, and pure lipid spectra that were obtained at strong diffusion weighting (DW) were subtracted from those obtained at low DW, which include both small metabolites and lipids. This subtraction yielded almost lipid free small metabolite spectra from muscle tissue. Further improved separation was obtained by combining a 1D diffusion sequence with a T2-filter, with the subtraction method eliminating residual lipids from the spectra. Similar results obtained for biopsies of different organs suggest that this method is applicable in various tissue types. The elimination of lipids from HR-MAS spectra and the resulting less biased assessment of small metabolites have potential to remove ambiguities in the interpretation of metabonomic results. This is demonstrated in a reproducibility study on biopsies from human muscle.

  11. Neutron and photon spectra in LINACs.

    PubMed

    Vega-Carrillo, H R; Martínez-Ovalle, S A; Lallena, A M; Mercado, G A; Benites-Rengifo, J L

    2012-12-01

    A Monte Carlo calculation, using the MCNPX code, was carried out in order to estimate the photon and neutron spectra in two locations of two linacs operating at 15 and 18 MV. Detailed models of both linac heads were used in the calculations. Spectra were estimated below the flattening filter and at the isocenter. Neutron spectra show two components due to evaporation and knock-on neutrons. Lethargy spectra under the filter were compared to the spectra calculated from the function quoted by Tosi et al. that describes reasonably well neutron spectra beyond 1 MeV, though tends to underestimate the energy region between 10(-6) and 1 MeV. Neutron and the Bremsstrahlung spectra show the same features regardless of the linac voltage.

  12. Spectra from pair-equilibrium plasmas

    NASA Technical Reports Server (NTRS)

    Zdziarski, A. A.

    1984-01-01

    A numerical model of relativistic nonmagnetized plasma with uniform temperature and electron density distributions is considered, and spectra from plasma in pair equilibrium are studied. A range of dimensionless temperature (T) greater than about 0.2 is considered. The spectra from low pair density plasmas in pair equilibrium vary from un-Comptonized bremsstrahlung spectra at Thomson cross section tau(N) much less than one to Comptonized bremsstrahlung spectra with tau(N) over one. For high pair density plasmas the spectra are flat for T greater than about one, and have broad intensity peaks at energy roughly equal to 3T for T less than one. In the latter region the total luminosity is approximately twice the annihilation luminosity. All spectra are flat in the X-ray region, in contradiction to observed AGN spectra. For dimensionless luminosity greater than about 100, the cooling time becomes shorter than the Thomson time.

  13. [Vibrational spectra of Corallium elatius].

    PubMed

    Fan, Lu-wei; Zhang, Yan; Hu, Yang

    2013-09-01

    Corallium elatius, which has unique color distribution characteristic, is the most important species of Taiwan precious corals. EPMA, XRD, FTIR and Laser Raman detective methods were used to study the chemical, mineral composition and spectra characteristics of Corallium elatius. The result of EPMA, XRD and FTIR shows the high-Mg calcite mineral componentand the stable minor chemical constituents of the samples. Meanwhile, the cell parameter indicates the lattice distortion and the preferred orientation of calcite grain caused by organic matter. The red part of the samples shows a different Raman spectrum from that of the white part, located at 1517/1128 cm(-1) and 1296/1016 cm(-1). Raman scattering measurement reveals the relationship between the organic matter and color.

  14. Power spectra of solar convection

    NASA Technical Reports Server (NTRS)

    Chou, D.-Y.; Labonte, B. J.; Braun, D. C.; Duvall, T. L., Jr.

    1991-01-01

    The properties of convective motions on the sun are studied using Kitt Peak Doppler images and power spectra of convection. The power peaks at a scale of about 29,000 km and drops off smoothly with wavenumber. There is no evidence of apparent energy excess at the scale of the mesogranulation proposed by other authors. The vertical and horizontal power for each wavenumber are obtained and used to calculate the vertical and horizontal velocities of the supergranulation. The amplitude of vertical and horizontal velocities of the supergranulation are 0.034 (+ or - 0.002) km/s and 0.38 (+ or - 0.01) km/s, respectively. The corresponding rms values are 0.024 (+ or - 0.002) km/s and 0.27 (+ or - 0.01) km/s.

  15. Reflectance spectra of primitive chondrites

    NASA Astrophysics Data System (ADS)

    Trigo-Rodríguez, J. M.; Moyano-Cambero, C. E.; Llorca, J.

    2013-05-01

    We are studying a wide sample of pristine carbonaceous chondrites from the NASA Antarctic collection in order to get clues on the physico-chemical processes occurred in the parent bodies of these meteorites. We are obtaining laboratory reflectance spectra of different groups of carbonaceous chondrites, but here we focus in CM and CI chondrites. We discuss the main spectral features that can be used to identify primitive carbonaceous asteroids by remote sensing techniques. Two different spectrometers were used covering the entire 0.3 to 30 μm electromagnetic window. Only a handful of Near Earth Objects (NEOs) exhibit bands or features clearly associated with aqueous alteration. Among them are the target asteroids of Osiris Rex and Marco Polo-R missions.

  16. Pressure spectra and cross spectra at an area contraction in a ducted combustion system

    NASA Technical Reports Server (NTRS)

    Miles, J. H.; Raftopoulos, D. D.

    1980-01-01

    Pressure spectra and cross-spectra at an area contraction in a liquid fuel, ducted, combustion noise test facility are analyzed. Measurements made over a range of air and fuel flows are discussed. Measured spectra are compared with spectra calculated using a simple analytical model.

  17. Line Coupling in Atmospheric Spectra

    NASA Technical Reports Server (NTRS)

    Tipping, R. H.

    1996-01-01

    The theoretical modeling of atmospheric spectra is important for a number of different applications: for instance, in the determination of minor atmospheric constituents such as ozone, carbon dioxide, CFC's etc.; in monitoring the temperature profile for climate studies; and in measuring the incoming and outgoing radiation to input into global climate models. In order to accomplish the above mentioned goal, one needs to know the spectral parameters characterizing the individual spectral lines (frequency, width, strength, and shape) as well as the physical parameters of the atmosphere (temperature, abundances, and pressure). When all these parameters are known, it is usually assumed that the resultant spectra and concomitant absorption coefficient can then be calculated by a superposition of individual profiles of appropriate frequency, strength and shape. However, this is not true if the lines are 'coupled'. Line coupling is a subtle effect that takes place when lines of a particular molecule overlap in frequency. In this case when the initial states and the final states of two transitions are connected by collisions, there is a quantum interference resulting in perturbed shapes. In general, this results in the narrowing of Q-branches (those in which the rotational quantum number does not change), and vibration-rotational R- and P branches (those in which the rotational quantum number changes by +/- 1), and in the spectral region beyond band heads (regions where the spectral lines pile up due to centrifugal distortion). Because these features and spectral regions are often those of interest in the determination of the abundances and pressure-temperature profiles, one must take this effect into account in atmospheric models.

  18. Mid-IR Properties of an Unbiased AGN Sample of the Local Universe. I. Emission-Line Diagnostics

    NASA Astrophysics Data System (ADS)

    Melendez, Marcio; Weaver, K.; Kraemer, S.; Mushotzky, R. F.; Tueller, J.; Markwardt, C. B.; Malumuth, E. M.; Engle, K.; Armus, L.; Berghea, C. T.; Dudik, R. P.; Winter, L. M.

    2010-01-01

    We compare mid-IR emission-lines properties, from high-resolution Spitzer IRS spectra,of a statistically-complete hard X-ray (14-195 keV) selected sample of nearby (z < 0.05) AGN detected by the Burst Alert Telescope (BAT) aboard Swift. The luminosity distribution for the mid-infrared emission-lines, [O IV] 25.89 μm, [Ne II] 12.81μm , [Ne III] 15.56 μm and [Ne V] μm, and hard X-ray show no differences between Seyfert 1 and Seyfert 2 populations, although six newly discovered BAT AGN are shown to be under-luminous in [O IV], most likely the result of dust extinction in the host galaxy. The correlations between all the mid-infrared emission lines and BAT luminosities are statistically significant. The mid-infrared emission line fluxes are highly correlated, with the worst correlations for [Ne V]-[Ne II] and [O IV]-[Ne II], as a result of enhanced [Ne II] in some sources due to nuclear stellar activity, however the tightness of these mid-infrared correlations suggests that the emission lines primarily arise in gas ionized by the AGN. We also compared the mid-IR emission-lines in the BAT AGNs with those from published studies of star-forming galaxies and LINERs. We found that [Ne III] an [O IV] lines do not unambiguously identify AGNs as stand-along diagnostics, however the BAT AGNs fall into a distinctive region when comparing the [Ne III]/[Ne II] and the [O IV]/[Ne III] quantities. While it is likely that detection of [Ne V] indicates the presence of an AGN, the [Ne V] line is weak compared to [O IV] and may not be detected in weak AGN. We suggest that a composite method using [Ne II], [Ne III], and [O IV] provides a more robust diagnostic.

  19. Unveiling the Intrinsic X-Ray Properties of Broad Absorption Line Quasars with a Relatively Unbiased Sample

    NASA Astrophysics Data System (ADS)

    Morabito, Leah K.; Dai, Xinyu; Leighly, Karen M.; Sivakoff, Gregory R.; Shankar, Francesco

    2014-05-01

    There is growing evidence of a higher intrinsic fraction of broad absorption line quasars (BALQSOs) than that obtained in optical surveys, on which most previous X-ray studies of BALQSOs have focused. Here we present Chandra observations of 18 BALQSOs at z ~ 2, selected from a near-infrared (Two Micron All Sky Survey) sample, where the BALQSO fraction is likely to be close to the intrinsic fraction. We measure photon indices using the stacked spectra of the optically faint (i - Ks >= 2.3 mag) and optically bright (i - Ks < 2.3 mag) samples to be Γ ~= 1.5-2.1. We constrain their intrinsic column density by modeling the X-ray fractional hardness ratio, finding a mean column density of 3.5 × 1022 cm-2 assuming neutral absorption. We incorporate Sloan Digital Sky Survey optical measurements (rest frame UV) to study the broadband spectral index between the X-ray and UV bands, and compare this to a large sample of normal quasars. We estimate that the optically faint BALQSOs are X-ray weaker than the optically bright ones, and the entire sample of BALQSOs are intrinsically X-ray weak when compared to normal active galactic nuclei (AGNs). Correcting for magnification of X-ray emission via gravitational lensing by the central black hole viewed at large inclination angles makes these BALQSOs even more intrinsically X-ray weak. Finally, we estimate AGN kinetic feedback efficiencies of a few percent for an X-ray wind of 0.3c in high-ionization BALQSOs. Combined with energy carried by low-ionization BALQSOs and UV winds, the total kinetic energy in BALQSOs can be sufficient to provide AGN kinetic feedback required to explain the co-evolution between black holes and host galaxies.

  20. Mid-IR Properties of an Unbiased AGN Sample of the Local Universe. 1; Emission-Line Diagnostics

    NASA Technical Reports Server (NTRS)

    Weaver, K. A.; Melendez, M.; Muhotzky, R. F.; Kraemer, S.; Engle, K.; Malumuth. E.; Tueller, J.; Markwardt, C.; Berghea, C. T.; Dudik, R. P.; Winter, L. M.; Armus, L.

    2010-01-01

    \\Ve compare mid-IR emission-lines properties, from high-resolution Spitzer IRS spectra of a statistically-complete hard X-ray (14-195 keV) selected sample of nearby (z < 0.05) AGN detected by the Burst Alert Telescope (BAT) aboard Swift. The luminosity distribution for the mid-infrared emission-lines, [O IV] 25.89 microns, [Ne II] 12.81 microns, [Ne III] 15.56 microns and [Ne V] 14.32 microns, and hard X-ray continuum show no differences between Seyfert 1 and Seyfert 2 populations, although six newly discovered BAT AGNs are shown to be under-luminous in [O IV], most likely the result of dust extinction in the host galaxy. The overall tightness of the mid-infrared correlations and BAT luminosities suggests that the emission lines primarily arise in gas ionized by the AGN. We also compared the mid-IR emission-lines in the BAT AGNs with those from published studies of star-forming galaxies and LINERs. We found that the BAT AGN fall into a distinctive region when comparing the [Ne III]/[Ne II] and the [O IV]/[Ne III] quantities. From this we found that sources that have been previously classified in the mid-infrared/optical as AGN have smaller emission line ratios than those found for the BAT AGNs, suggesting that, in our X-ray selected sample, the AGN represents the main contribution to the observed line emission. Overall, we present a different set of emission line diagnostics to distinguish between AGN and star forming galaxies that can be used as a tool to find new AGN.

  1. OVI absorbers in SDSS spectra

    NASA Astrophysics Data System (ADS)

    Frank, Stephan

    We conducted a systematic search for signatures of the Intergalactic Medium (IGM) in Quasar spectra of the Sloan Digital Sky Survey (SDSS) Data Release 3 (DR3), focusing on finding intervening absorbers via detection of their O VI doublet. We present a search algorithm, and criteria for distinguishing candidates from spurious Lyman a forest lines. In addition, we compare our findings with simulations of the Lyman a forest in order to estimate the detectability of O VI doublets over various redshift intervals. We obtain a sample of 1866 O VI doublet candidates with rest-frame equivalent width >= 0.05 λ in 855 AGN spectra (out of 3702 objects with redshifts in the range accessible for O VI detection). This sample is subdivided into 3 groups according to the likelihood of being real and the potential for follow-up observation of the candidate. The group with the cleanest and most secure candidates is comprised of 145 candidates. 69 of these reside at a velocity separation >= 5000 km/s from the QSO, and can therefore be classified tentatively as intervening absorbers. Most of these absorbers have not been picked up by earlier, automated QSO absorption line detection algorithms. This sample increases the number of known O VI absorbers at redshifts beyond z abs >= 2.7 substantially. We propose to obtain observations of some of the candidates with the best signatures for O VI doublets with high signal-to-noise and high resolution in order to better constrain the physical state of the absorbers. We then focused on a subsample of 387 AGN sightlines with an average S/N >= 5: 0, allowing for the detection of absorbers above a rest-frame equivalent width limit of W r >= 0:19 ? A for the O VI 1032 λ component. Accounting for random interlopers mimicking an O VI doublet, we derive for the first time a secure lower limit for the redshift number density DN/Dz for redshifts z abs >= 2:8. With extensive Monte Carlo simulations we quantify the losses of absorbers due to blending

  2. Nickel-Catalyzed Mizoroki–Heck Reaction of Aryl Sulfonates and Chlorides with Electronically Unbiased Terminal Olefins: High Selectivity for Branched Products**

    PubMed Central

    Tasker, Sarah Z.; Gutierrez, Alicia C.

    2014-01-01

    Achieving high selectivity in the Heck reaction of electronically unbiased alkenes has been a longstanding challenge. Using a nickel-catalyzed cationic Heck reaction, we were able to achieve excellent selectivity for branched products (≥19:1 in all cases) over a wide range of aryl electrophiles and aliphatic olefins. A bidentate ligand with a suitable bite angle and steric profile was key to obtaining high branched/linear selectivity, while the appropriate base suppressed alkene isomerization of the product. Though aryl triflates are traditionally used to access the cationic Heck pathway, we have shown that by using triethylsilyl trifluoromethanesulfonate (TESOTf), we can effect a counterion exchange of the catalytic nickel complex such that cheaper and more stable aryl chlorides, mesylates, tosylates, and sulfamates can be used to yield the same branched products with high selectivity. PMID:24402966

  3. Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents.

    PubMed

    Inui, Tomoya; Shigeta, Yasuteru; Okuno, Katsuki; Baba, Takeshi; Kishi, Ryohei; Nakano, Masayoshi

    2013-10-15

    The static second hyperpolarizability γ of the complexes composed of open-shell singlet 1,3-dipole molecule involving a boron atom and a water molecule in aqueous phase are investigated by the finite-field (FF) method combined with a standard polarized continuum model (PCM) and with a newly proposed unbiased PCM (UBPCM). On the basis of the comparison with the results calculated by the FF method using the full quantum and the quantum-mechanical/molecular-mechanical and molecular-dynamics (QM/MM-MD) treatments, the present FF-UBPCM method is demonstrated to remedy the artificial overestimation of the γ caused by standard FF-PCM calculations and to well reproduce the FF-QM/MM-MD and FF-full-QM results with much lower costs.

  4. Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease

    PubMed Central

    Beilina, Alexandria; Rudenko, Iakov N.; Kaganovich, Alice; Civiero, Laura; Chau, Hien; Kalia, Suneil K.; Kalia, Lorraine V.; Lobbestael, Evy; Chia, Ruth; Ndukwe, Kelechi; Ding, Jinhui; Nalls, Mike A.; Olszewski, Maciej; Hauser, David N.; Kumaran, Ravindran; Lozano, Andres M.; Baekelandt, Veerle; Greene, Lois E.; Taymans, Jean-Marc; Greggio, Elisa; Cookson, Mark R.; Nalls, Mike A.; Plagnol, Vincent; Martinez, Maria; Hernandez, Dena G; Sharma, Manu; Sheerin, Una-Marie; Saad, Mohamad; Simón-Sánchez, Javier; Schulte, Claudia; Lesage, Suzanne; Sveinbjörnsdóttir, Sigurlaug; Arepalli, Sampath; Barker, Roger; Ben-Shlomo, Yoav; Berendse, Henk W; Berg, Daniela; Bhatia, Kailash; de Bie, Rob M A; Biffi, Alessandro; Bloem, Bas; Bochdanovits, Zoltan; Bonin, Michael; Bras, Jose M; Brockmann, Kathrin; Brooks, Janet; Burn, David J; Charlesworth, Gavin; Chen, Honglei; Chong, Sean; Clarke, Carl E; Cookson, Mark R; Cooper, J Mark; Corvol, Jean Christophe; Counsell, Carl; Damier, Philippe; Dartigues, Jean-François; Deloukas, Panos; Deuschl, Günther; Dexter, David T; van Dijk, Karin D; Dillman, Allissa; Durif, Frank; Dürr, Alexandra; Edkins, Sarah; Evans, Jonathan R; Foltynie, Thomas; Gao, Jianjun; Gardner, Michelle; Gibbs, J Raphael; Goate, Alison; Gray, Emma; Guerreiro, Rita; Gústafsson, Ómar; Harris, Clare; van Hilten, Jacobus J; Hofman, Albert; Hollenbeck, Albert; Holton, Janice; Hu, Michele; Huang, Xuemei; Huber, Heiko; Hudson, Gavin; Hunt, Sarah E; Huttenlocher, Johanna; Illig, Thomas; München, Helmholtz Zentrum; Jónsson, Pálmi V; Lambert, Jean-Charles; Langford, Cordelia; Lees, Andrew; Lichtner, Peter; München, Helmholtz Zentrum; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw R; Morrison, Karen E; Mudanohwo, Ese; O’Sullivan, Sean S; Pearson, Justin; Perlmutter, Joel S; Pétursson, Hjörvar; Pollak, Pierre; Post, Bart; Potter, Simon; Ravina, Bernard; Revesz, Tamas; Riess, Olaf; Rivadeneira, Fernando; Rizzu, Patrizia; Ryten, Mina; Sawcer, Stephen; Schapira, Anthony; Scheffer, Hans; Shaw, Karen; Shoulson, Ira; Sidransky, Ellen; Smith, Colin; Spencer, Chris C A; Stefánsson, Hreinn; Steinberg, Stacy; Stockton, Joanna D; Strange, Amy; Talbot, Kevin; Tanner, Carlie M; Tashakkori-Ghanbaria, Avazeh; Tison, François; Trabzuni, Daniah; Traynor, Bryan J; Uitterlinden, André G; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H; Winder-Rhodes, Sophie; Stefánsson, Kári; Hardy, John; Heutink, Peter; Brice, Alexis; Gasser, Thomas; Singleton, Andrew B; Wood, Nicholas W; Chinnery, Patrick F; Arepalli, Sampath; Cookson, Mark R; Dillman, Allissa; Ferrucci, Luigi; Gibbs, J Raphael; Hernandez, Dena G; Johnson, Robert; Longo, Dan L; Majounie, Elisa; Nalls, Michael A; O’Brien, Richard; Singleton, Andrew B; Traynor, Bryan J; Troncoso, Juan; van der Brug, Marcel; Zielke, H Ronald; Zonderman, Alan B

    2014-01-01

    Mutations in leucine-rich repeat kinase 2 (LRRK2) cause inherited Parkinson disease (PD), and common variants around LRRK2 are a risk factor for sporadic PD. Using protein–protein interaction arrays, we identified BCL2-associated athanogene 5, Rab7L1 (RAB7, member RAS oncogene family-like 1), and Cyclin-G–associated kinase as binding partners of LRRK2. The latter two genes are candidate genes for risk for sporadic PD identified by genome-wide association studies. These proteins form a complex that promotes clearance of Golgi-derived vesicles through the autophagy–lysosome system both in vitro and in vivo. We propose that three different genes for PD have a common biological function. More generally, data integration from multiple unbiased screens can provide insight into human disease mechanisms. PMID:24510904

  5. Blind extraction of exoplanetary spectra

    NASA Astrophysics Data System (ADS)

    Morello, Giuseppe; Waldmann, Ingo P.; Tinetti, Giovanna

    2016-06-01

    In the last decade, remote sensing spectroscopy enabled characterization of the atmospheres of extrasolar planets. Transmission and emission spectra of tens of transiting exoplanets have been measured with multiple instruments aboard Spitzer and Hubble Space Telescopes as well as ground-based facilities, revealing the presence of atomic, ionic and molecular species in their atmospheres, and constraining their temperature and pressure profiles.Early analyses were somehow heuristic both in measuring the spectra and in their interpretation, leading to some controversies in the literature.A photometric precision of 0.01% is necessary to detect the atmospheric spectral modulations. Current observatories, except Kepler, were not designed to achieve this precision. Data reduction is necessary to minimize the effect of instrument systematics in order to achieve the target precision. In the past, parametric models have extensively been used by most teams to remove correlated noise with the aid of auxiliary information of the instrument, the so-called optical state vectors (OSVs). Such OSVs can include inter- and intra-pixel position of the star or its spectrum, instrument temperatures and inclinations, and/or other parameters. In some cases, different parameterizations led to discrepant results.We recommend the use of blind non-parametric data detrending techniques to overcome those issues. In particular, we adopt Independent Component Analysis (ICA), i.e. a blind source separation (BSS) technique to disentangle the multiple instrument systematics and astrophysical signals in transit/eclipse light curves. ICA does not require a model for the systematics, and for this reason, it can be applied to any instrument with little changes, if any. ICA-based algorithms have been applied to Spitzer/IRAC and synthetic observations in photometry (Morello et al. 2014, 2015, 2016; Morello 2015) and to Hubble/NICMOS and Spitzer/IRS in spectroscopy (Waldmann 2012, 2014, Waldmann et al. 2013

  6. Interpretation of Nitroindolinospirobenzothiopyran Vibrational Spectra

    NASA Astrophysics Data System (ADS)

    Gladkov, L. L.; Khamchukov, Yu. D.; Lyubimov, A. V.

    2016-05-01

    The structures of four possible stereoisomers of the closed form of photochromic nitroindolinospirobenzothiopyran (NISTP) {1',3'-dihydro-1',3',3'-trimethyl-6-nitrospiro[2H-1-benzothiopyran-2,2'-(2H)-indoline]} were determined by the DFT method. The geometry of the most stable isomer was defined. Nitro-substitution changes mainly the lengths of bonds formed by S and N with spiro-atom Cs. According to the calculations, the CsS bond changes most and lengthens by 0.019 Å. It is shown that the S atom has large displacement amplitudes in normal modes assigned to Raman lines at 230, 285, 360, and 575 cm-1 and weak IR bands at 467 and 577 cm-1. Oscillations involving the nitro group are very active in Raman and IR spectra. Their frequencies are slightly lower than similar frequencies of nitrobenzene and nitroindolinospirobenzopyran, indicating a higher degree of vibrational coupling of the NO2 group with the NISTP molecular skeleton.

  7. Reflectance spectra of subarctic lichens

    NASA Technical Reports Server (NTRS)

    Petzold, Donald E.; Goward, Samuel N.

    1988-01-01

    Lichens constitute a major portion of the ground cover of high latitude environments, but little has been reported concerning their in situ solar spectral reflectance properties. Knowledge of these properties is important for the interpretation of remotely sensed observations from high latitude regions, as well as in studies of high latitude ecology and energy balance climatology. The spectral reflectance of common boreal vascular plants is similar to that of vascular plants of the midlatitudes. The dominant lichens, in contrast, display variable reflectance patterns in visible wavelengths. The relative reflectance peak at 0.55 microns, common to green vegetation, is absent or indistinct in spectra of pervasive boreal forest and tundra lichens, despite the presence of chlorophyll in the inner algal cells. Lichens of the dominant genus, Cladina, display strong absorption of ultraviolet energy and short-wavelength blue light relative to their absorption in other visible wavelengths. Since the Cladinae dominate both the surface vegetation in open woodlands of the boreal forest and the low arctic tundra, their unusual spectral reflectance patterns will enable accurate monitoring of the boreal forest-tundra ecotone and detection of its vigor and movement in the future.

  8. X-ray spectra of supernova remnants

    NASA Technical Reports Server (NTRS)

    Szymkowiak, A. E.

    1985-01-01

    X-ray spectra were obtained from fields in three supernova remnants with the solid state spectrometer of the HEAO 2 satellite. These spectra, which contain lines from K-shell transitions of several abundant elements with atomic numbers between 10 and 22, were compared with various models, including some of spectra that would be produced by adiabatic phase remnants when the time-dependence of the ionization is considered.

  9. A Bayesian method for analysing relaxation spectra

    NASA Astrophysics Data System (ADS)

    Ciocci Brazzano, L.; Pellizza, L. J.; Matteo, C. L.; Sorichetti, P. A.

    2016-01-01

    The knowledge of electrical and mechanical properties of material, relies on a precise analysis of the relaxation spectra. We explore the ability of a Bayesian method to achieve an accurate estimation of spectral parameters. We implemented a parallel-tempering Markov-chain Monte Carlo algorithm and used it to fit simulated and measured spectra. An exhaustive testing of the code shows that it presents an extremely good performance, accurately fitting complex spectra under strong noise and overlapping components. We conclude that this technique is quite suitable for relaxation spectra analysis, complementing classical methods.

  10. ALIEN: A nebular spectra analysis software

    NASA Astrophysics Data System (ADS)

    Cook, R.; Vazquez, R.

    2000-11-01

    A new C-coded software, designed to analyze nebular spectra, is presented. T his software is able to read the fluxes of the most important ions directly from IRAF's output file (splot.log). Spectra can be dereddened using the Balmer lines ratio and the Seaton's extinction law. Electron temperature and density, as well as ionic abundances by number are estimated by means of numeric calculations based on the five-level atom model. The dereddened spectra and the table containing the ionic abundances can be saved in a LaTex formatted file. This software has been initially designed to work with a low dispersion spectra.

  11. Near-Infrared Spectra of Uranian Satellites

    NASA Astrophysics Data System (ADS)

    Venturini, C. C.; Lynch, D. K.; Rudy, R. J.; Mazuk, S.; Puetter, R. C.

    2001-05-01

    We present 0.8 to 2.5 micron spectra taken on June 21 & 22, 1998 UT of the Uranian satellites Miranda, Titania, Ariel, Oberon, and Umbriel. The spectra were taken using The Aerospace Corporation's Near-Infrared Imaging Spectragraph (NIRIS) on the University of California's Lick Observatory 3 meter Shane telescope. These spectra will be compared with previous work including Brown, R.H. and Cruikshank, D.P. (1983) as well as more recent spectra and analysis by Grundy, W. et al. (1999). Support for this research was provided by The Aerospace Corporation's Independent Research and Development Program.

  12. [Describing language of spectra and rough set].

    PubMed

    Qiu, Bo; Hu, Zhan-yi; Zhao, Yong-heng

    2002-06-01

    It is the traditional way to analyze spectra by experiences in astronomical field. And until now there has never been a suitable theoretical frame to describe spectra, which is may be owing to small spectra datasets that astronomers can get by low-level instruments. With the high-speed development of telescopes, especially on behalf of LAMOST, a large telescope which can collect more than 20,000 spectra in an observing night, spectra datasets are becoming larger and larger very fast. Facing these voluminous datasets, the traditional spectra-processing way simply depending on experiences becomes unfit. In this paper, we develop a brand-new language--describing language of spectra (DLS) to describe spectra of celestial bodies by defining BE (Basic element). And based on DLS, we introduce the method of RSDA (Rough set and data analysis), which is a technique of data mining. By RSDA we extract some rules of stellar spectra, and this experiment can be regarded as an application of DLS.

  13. MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition.

    PubMed

    Li, Hao; Cai, Yuping; Guo, Yuan; Chen, Fangfang; Zhu, Zheng-Jiang

    2016-09-06

    With recent advances in mass spectrometry, there is an increased interest in data-independent acquisition (DIA) techniques for metabolomics. With DIA technique, all metabolite ions are sequentially selected and isolated using a wide window to generate multiplexed MS/MS spectra. Therefore, DIA strategy enables a continuous and unbiased acquisition of all metabolites and increases the data dimensionality, but presents a challenge to data analysis due to the loss of the direct link between precursor ion and fragment ions. However, very few DIA data processing methods are developed for metabolomics application. Here, we developed a new DIA data analysis approach, namely, MetDIA, for targeted extraction of metabolites from multiplexed MS/MS spectra generated using DIA technique. MetDIA approach considers each metabolite in the spectral library as an analysis target. Ion chromatograms for each metabolite (both precursor ion and fragment ions) and MS(2) spectra are readily detected, extracted, and scored for metabolite identification, referred as metabolite-centric identification. A minimum metabolite-centric identification score responsible for 1% false positive rate of identification is determined as 0.8 using fully (13)C labeled biological extracts. Finally, the comparisons of our MetDIA method with data-dependent acquisition (DDA) method demonstrated that MetDIA could significantly detect more metabolites in biological samples, and is more accurate and sensitive for metabolite identifications. The MetDIA program and the metabolite spectral library is freely available on the Internet.

  14. Resolution enhancement in second-derivative spectra.

    PubMed

    Czarnecki, Mirosław A

    2015-01-01

    Derivative spectroscopy is a powerful tool for the resolution enhancement in infrared, near-infrared, Raman, ultraviolet-visible, nuclear magnetic resonance, electron paramagnetic resonance, and fluorescence spectroscopy. Despite its great significance in analytical chemistry, not all aspects of the applications of this method have been explored as yet. This is the first systematic study of the parameters that influence the resolution enhancement in the second derivative spectra. The derivative spectra were calculated with the Savitzky-Golay method with different window size (5, 15, 25) and polynomial order (2, 4). The results obtained in this work show that the resolution enhancement in the second derivative spectra strongly depends on the data spacing in the original spectra, window size, polynomial order, and peak profile. As shown, the resolution enhancement is related to variations in the width of the peaks upon the differentiation. The present study reveals that in order to maximize the separation of the peaks in the second derivative spectra, the original spectra should be recorded at high resolution and differentiated using a small window size and high polynomial order. However, working with the real spectra one has to compromise between the noise reduction and optimization of the resolution enhancement in the second derivative spectra.

  15. Spectra of the Jovian ring and Amalthea

    NASA Technical Reports Server (NTRS)

    Neugebauer, G.; Becklin, E. E.; Jewitt, D. C.; Danielson, G. E.; Terrile, R. J.

    1981-01-01

    Measurements made between 0.887 and 2.4 microns demonstrate that the Jovian ring and Amalthea have similar reflection spectra. The spectra, in particular the ratio of the 0.9- to 2.2-micron reflectivities, are inconsistent with those expected from water, ammonia, or methane frosts, but are consistent with reflection from large rock bodies.

  16. Blind extraction of exoplanetary spectra

    NASA Astrophysics Data System (ADS)

    Morello, Giuseppe; Waldmann, Ingo; Damiano, Mario; Tinetti, Giovanna

    2016-10-01

    In the last decade, remote sensing spectroscopy enabled characterization of the atmospheres of extrasolar planets. Transmission and emission spectra of tens of transiting exoplanets have been measured with multiple instruments aboard Spitzer and Hubble Space Telescopes as well as ground-based facilities, revealing the presence of chemical species in their atmospheres, and constraining their temperature and pressure profiles.Early analyses were somehow heuristic, leading to some controversies in the literature.A photometric precision of 0.01% is necessary to detect the atmospheric spectral modulations. Current observatories, except Kepler, were not designed to achieve this precision. Data reduction is necessary to minimize the effect of instrument systematics in order to achieve the target precision. In the past, parametric models have extensively been used by most teams to remove correlated noise with the aid of auxiliary information of the instrument, the so-called optical state vectors (OSVs). Such OSVs can include inter- and intra-pixel position of the star or its spectrum, instrument temperatures and inclinations, and/or other parameters. In some cases, different parameterizations led to discrepant results.We recommend the use of blind non-parametric data detrending techniques to overcome those issues. In particular, we adopt Independent Component Analysis (ICA), i.e. a powerful blind source separation (BSS) technique to disentangle the multiple instrument systematics and astrophysical signals in transit/eclipse light curves. ICA does not require a model for the systematics, thence it can be applied to any instrument with little changes, if any. ICA-based algorithms have been applied to Spitzer/IRAC and synthetic observations in photometry (Morello et al. 2014, 2015, 2016; Morello 2015) and to Hubble/WFC3, Hubble/NICMOS and Spitzer/IRS and Hubble/WFC3 in spectroscopy (Damiano, Morello et al., in prep., Waldmann 2012, 2014, Waldmann et al. 2013) with excellent

  17. Mid-Infrared Spectra of Mercury

    NASA Technical Reports Server (NTRS)

    Cooper, B.; Potter, A. E.; Killen, R. M.; Morgan, T. H.

    2001-01-01

    Mid-infrared (8-13 microns) spectra of radiation emitted from the surface of solar system objects can be interpreted in terms of surface composition. However, the spectral features are weak, and require exceptionally high signal-to-noise ratio spectra to detect them. Ground-based observations of spectra in this region are plagued by strong atmospheric absorptions from water and ozone. High-altitude balloon measurements that avoid atmospheric absorptions can be affected by contamination of the optics by dust. We have developed a technique to obtain mid-infrared spectra of Mercury that minimizes these problems. The resulting spectra show evidence of transparency features that can be used to qualitatively characterize the surface composition. Additional information is contained in the original extended abstract.

  18. Isotope shifts in spectra of molecular liquids

    NASA Astrophysics Data System (ADS)

    Dubrovskaya, E. V.; Kolomiitsova, T. D.; Shurukhina, A. V.; Shchepkin, D. N.

    2016-02-01

    In the IR absorption spectra of low-temperature molecular liquids, we have observed anomalously large isotope shifts of frequencies of vibrational bands that are strong in the dipole absorption. The same effect has also been observed in their Raman spectra. At the same time, in the spectra of cryosolutions, the isotope shifts of the same bands coincide with a high accuracy (±(0.1-0.5) cm-1) with the shifts that are observed in the spectra of the gas phase. The difference between the spectra of examined low-temperature systems is caused by the occurrence of resonant dipole-dipole interactions between spectrally active identical molecules. The calculation of the band contour in the spectrum of liquid freon that we have performed in this work taking into account the resonant interaction between states of simultaneous transitions in isotopically substituted molecules can explain this effect.

  19. PCA: Principal Component Analysis for spectra modeling

    NASA Astrophysics Data System (ADS)

    Hurley, Peter D.; Oliver, Seb; Farrah, Duncan; Wang, Lingyu; Efstathiou, Andreas

    2012-07-01

    The mid-infrared spectra of ultraluminous infrared galaxies (ULIRGs) contain a variety of spectral features that can be used as diagnostics to characterize the spectra. However, such diagnostics are biased by our prior prejudices on the origin of the features. Moreover, by using only part of the spectrum they do not utilize the full information content of the spectra. Blind statistical techniques such as principal component analysis (PCA) consider the whole spectrum, find correlated features and separate them out into distinct components. This code, written in IDL, classifies principal components of IRS spectra to define a new classification scheme using 5D Gaussian mixtures modelling. The five PCs and average spectra for the four classifications to classify objects are made available with the code.

  20. Handbook of Monochromatic XPS Spectra, Semiconductors

    NASA Astrophysics Data System (ADS)

    Crist, B. Vincent

    2000-10-01

    This handbook is one of three containing an invaluable collection of research grade XPS Spectra. Each handbook concentrates on a specific family of materials (the elements and their native oxides, semiconductors and polymers) and is entirely self-contained. The introductory section to each handbook includes comprehensive information about the XPS instrument used, the materials and the advanced methods used to collect the spectra. Energy resolution settings, instrument characteristics, energy referencing methods, traceability, energy scale calibration details and transmission function are all reported. Among the many valuable features included in each of these handbooks are: ? All spectra were measured by using AlK monochromatic X-rays ? All spectra were collected in a self-consistent manner to maximise data reliability and quality ? All peaks in the wide spectra are fully annotated and accompanied by detailed atom % tables that report BEs for each of the labelled peaks ? Each high-energy resolution spectrum is peak-fitted and accompanied by detailed tables containing binding energies, FWHMs and relative percentages. In this volume 'Semiconductors' are contained XPS Spectra from a wide range of semiconductive materials and related materials, a rare tool for scientists and analysts in this area. Exclusive features of this volume include: ? Binding energies are accurate to +/- 0.08eV ? Charge compensation was done with a flood-gun mesh-screen system ? Valence band spectra document the occupied density of states (DOS) and the fundamental electronic nature of the semi-conductive materials analysed ? Analyses were done: "as received", "freshly fractured in air", "ion etched" and "chemically treated" ? Alphabetically organised by chemical abbreviations for ease of locating each material This handbook is an invaluable reference for materials scientists and electrical engineers in industry, academia and government laboratories interested in the analysis of semiconductors

  1. Computer processing of tunable diode laser spectra

    NASA Technical Reports Server (NTRS)

    May, Randy D.

    1989-01-01

    A computer-controlled tunable diode laser spectrometer and spectral analysis software are described. The three-channel system records simultaneously the transmission of a subject gas, a temperature-stabilized etalon, and a calibration gas. The software routines are applied to diode laser spectra of HNO3 and NO2 to illustrate the procedures adopted for conversion of raw spectral data to useful transmission and harmonic spectra. Extraction of line positions, absorption intensities, collisional broadening coefficients, and gas concentrations from recorded spectra is also described.

  2. Analysis of atmospheric spectra for trace gases

    NASA Technical Reports Server (NTRS)

    Rinsland, Curtis P.; Seals, Robert K., Jr.; Smith, Mary Ann H.; Goldman, Aaron; Murcray, David G.; Murcray, Frank J.

    1990-01-01

    The objective is the comprehensive analysis of high resolution atmospheric spectra recorded in the middle-infrared region to obtain simultaneous measurements of coupled parameters (gas concentrations of key trace constituents, total column amounts, pressure, and temperature) in the stratosphere and upper troposphere. Solar absorption spectra recorded at 0.002 and 0.02 cm exp -1 resolutions with the University of Denver group's balloon-borne, aircraft borne, and ground-based interferometers and 0.005 to 0.01 cm exp -1 resolution solar spectra from Kitt Peak are used in the analyses.

  3. Vibrational spectra and structure of isopropylbenzene

    NASA Astrophysics Data System (ADS)

    Fishman, A. I.; Noskov, A. I.; Remizov, A. B.; Chachkov, D. V.

    2008-12-01

    Infrared spectra (4000-400 cm -1) and Raman spectra (1700-40 cm -1) of the liquid and two crystalline solids of isopropylbenzene (cumene) and isopropylbenzene-d 12 have been recorded. The spectra indicate that in the liquid and crystalline solids isopropylbenzene exists in planar conformation only (C sbnd H bond is in the plane of the benzene ring). An assignment of the observed band wave numbers both isopropylbenzene and isopropylbenzene-d 12 is discussed by comparison with normal mode wave numbers and IR intensities calculated from ab initio 6-31G (d) force fields.

  4. Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

    SciTech Connect

    Deymier, Martin J.; Claiborne, Daniel T.; Ende, Zachary; Ratner, Hannah K.; Kilembe, William; Hunter, Eric

    2014-11-15

    The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

  5. Unbiased Cell-based Screening in a Neuronal Cell Model of Batten Disease Highlights an Interaction between Ca2+ Homeostasis, Autophagy, and CLN3 Protein Function*

    PubMed Central

    Chandrachud, Uma; Walker, Mathew W.; Simas, Alexandra M.; Heetveld, Sasja; Petcherski, Anton; Klein, Madeleine; Oh, Hyejin; Wolf, Pavlina; Zhao, Wen-Ning; Norton, Stephanie; Haggarty, Stephen J.; Lloyd-Evans, Emyr; Cotman, Susan L.

    2015-01-01

    Abnormal accumulation of undigested macromolecules, often disease-specific, is a major feature of lysosomal and neurodegenerative disease and is frequently attributed to defective autophagy. The mechanistic underpinnings of the autophagy defects are the subject of intense research, which is aided by genetic disease models. To gain an improved understanding of the pathways regulating defective autophagy specifically in juvenile neuronal ceroid lipofuscinosis (JNCL or Batten disease), a neurodegenerative disease of childhood, we developed and piloted a GFP-microtubule-associated protein 1 light chain 3 (GFP-LC3) screening assay to identify, in an unbiased fashion, genotype-sensitive small molecule autophagy modifiers, employing a JNCL neuronal cell model bearing the most common disease mutation in CLN3. Thapsigargin, a sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) Ca2+ pump inhibitor, reproducibly displayed significantly more activity in the mouse JNCL cells, an effect that was also observed in human-induced pluripotent stem cell-derived JNCL neural progenitor cells. The mechanism of thapsigargin sensitivity was Ca2+-mediated, and autophagosome accumulation in JNCL cells could be reversed by Ca2+ chelation. Interrogation of intracellular Ca2+ handling highlighted alterations in endoplasmic reticulum, mitochondrial, and lysosomal Ca2+ pools and in store-operated Ca2+ uptake in JNCL cells. These results further support an important role for the CLN3 protein in intracellular Ca2+ handling and in autophagic pathway flux and establish a powerful new platform for therapeutic screening. PMID:25878248

  6. Peer-reviewed and unbiased research, rather than ‘sound science’, should be used to evaluate endocrine-disrupting chemicals

    PubMed Central

    Trasande, Leonardo; Vandenberg, Laura N; Bourguignon, Jean-Pierre; Myers, John Peterson; Slama, Remy; Saal, Frederick vom; Zoeller, Robert Thomas

    2017-01-01

    Evidence increasingly confirms that synthetic chemicals disrupt the endocrine system and contribute to disease and disability across the lifespan. Despite a United Nations Environment Programme/WHO report affirmed by over 100 countries at the Fourth International Conference on Chemicals Management, ‘manufactured doubt’ continues to be cast as a cloud over rigorous, peer-reviewed and independently funded scientific data. This study describes the sources of doubt and their social costs, and suggested courses of action by policymakers to prevent disease and disability. The problem is largely based on the available data, which are all too limited. Rigorous testing programmes should not simply focus on oestrogen, androgen and thyroid. Tests should have proper statistical power. ‘Good laboratory practice’ (GLP) hardly represents a proper or even gold standard for laboratory studies of endocrine disruption. Studies should be evaluated with regard to the contamination of negative controls, responsiveness to positive controls and dissection techniques. Flaws in many GLP studies have been identified, yet regulatory agencies rely on these flawed studies. Peer-reviewed and unbiased research, rather than ‘sound science’, should be used to evaluate endocrine-disrupting chemicals. PMID:27417427

  7. Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq).

    PubMed

    Brouwer, Rutger W W; van den Hout, Mirjam C G N; van IJcken, Wilfred F J; Soler, Eric; Stadhouders, Ralph

    2017-01-01

    The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives have contributed tremendously to the now widely accepted view that genome topology plays an important role in many major cellular processes, at a chromosome-wide scale, but certainly also at the level of individual genetic loci. A particularly popular application of 3C technology is to study transcriptional regulation, allowing researchers to draw maps of gene regulatory connections beyond the linear genome through addition of the third dimension. In this chapter, we provide a highly detailed protocol describing 3C coupled to high-throughput sequencing (referred to as 3C-Seq or more commonly 4C-Seq), allowing the unbiased interrogation of genome-wide chromatin interactions with specific genomic regions of interest. Interactions between spatially clustered DNA fragments are revealed by crosslinking the cells with formaldehyde, digesting the genome with a restriction endonuclease and performing a proximity ligation step to link interacting genomic fragments. Next, interactions with a selected DNA fragment are extracted from the 3C library through a second round of digestion and ligation followed by an inverse PCR. The generated products are immediately compatible with high-throughput sequencing, and amplicons from different PCR reactions can easily be multiplexed to dramatically increase throughput. Finally, we provide suggestions for data analysis and visualization.

  8. Transposon-mediated generation of BCR-ABL1-expressing transgenic cell lines for unbiased sensitivity testing of tyrosine kinase inhibitors

    PubMed Central

    Berkowitsch, Bettina; Koenig, Margit; Haas, Oskar A.; Hoermann, Gregor; Valent, Peter; Lion, Thomas

    2016-01-01

    Point mutations in the ABL1 kinase domain are an important mechanism of resistance to tyrosine kinase inhibitors (TKI) in BCR-ABL1-positive and, as recently shown, BCR-ABL1-like leukemias. The cell line Ba/F3 lentivirally transduced with mutant BCR-ABL1 constructs is widely used for in vitro sensitivity testing and response prediction to tyrosine kinase inhibitors. The transposon-based Sleeping Beauty system presented offers several advantages over lentiviral transduction including the absence of biosafety issues, faster generation of transgenic cell lines, and greater efficacy in introducing large gene constructs. Nevertheless, both methods can mediate multiple insertions in the genome. Here we show that multiple BCR-ABL1 insertions result in elevated IC50 levels for individual TKIs, thus overestimating the actual resistance of mutant subclones. We have therefore established flow-sorting-based fractionation of BCR-ABL1-transformed Ba/F3 cells facilitating efficient enrichment of cells carrying single-site insertions, as demonstrated by FISH-analysis. Fractions of unselected Ba/F3 cells not only showed a greater number of BCR-ABL1 hybridization signals, but also revealed higher IC50 values for the TKIs tested. The data presented highlight the need to carefully select transfected cells by flow-sorting, and to control the insertion numbers by FISH and real-time PCR to permit unbiased in vitro testing of drug resistance. PMID:27801667

  9. Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning.

    PubMed

    Deymier, Martin J; Claiborne, Daniel T; Ende, Zachary; Ratner, Hannah K; Kilembe, William; Allen, Susan; Hunter, Eric

    2014-11-01

    The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual׳s diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens.

  10. Investigation of Raman spectra of polyethylene terephthalate

    NASA Astrophysics Data System (ADS)

    Zhu, Changjun; Tong, Na; Song, Lixin; Zhang, Guoqing

    2015-08-01

    Raman spectrometry was employed to study the characteristics of Raman spectra of polyethylene terephthalate (PET), which were treated with sodium hydroxide, sulfuric acid and copper sulfate, respectively. Raman spectra under different conditions were obtained and the characteristics of the Raman spectra were analyzed. The morphology structures were observed under different conditions using Atomic Force Microscope. The results show that the spectral intensity of PET treated with sodium hydroxide is higher than that untreated between 200-1750 cm-1, while the intensity of PET treated with sodium hydroxide is lower than that untreated beyond 1750 cm-1 and the fluorescence background of Raman spectra is decreased. The spectral intensity of PET treated with sulfuric acid is remarkably reduced than that untreated, and the intensity of PET treated with copper sulphate is much higher than that untreated.

  11. Spectra: Time series power spectrum calculator

    NASA Astrophysics Data System (ADS)

    Gallardo, Tabaré

    2017-01-01

    Spectra calculates the power spectrum of a time series equally spaced or not based on the Spectral Correlation Coefficient (Ferraz-Mello 1981, Astron. Journal 86 (4), 619). It is very efficient for detection of low frequencies.

  12. Spatial evolution of ocean wave spectra

    NASA Technical Reports Server (NTRS)

    Beal, R. C.

    1981-01-01

    The spatially evolving deep water synthetic aperture radar (SAR) directional spectra of a mixed ocean wave system are compared with a comprehensive set of surface and aircraft measurements. The evolution of the SAR spectra, at least for ocean wavelengths greater than 80 m, is seen as generally consistent with the auxiliary data set in both time and space. From the spatial evolution of the angular component of the spectra, it is possible to project back to an apparent remote storm source that is also consistent with the storm location via GOES satellite imagery. The data provide compelling evidence that the spatial evolution of SAR ocean wave spectra can be a useful tool in global ocean wave monitoring and forecasting.

  13. Synthesis and Spectra of Vanadium Complexes.

    ERIC Educational Resources Information Center

    Ophardt, Charles E.; Stupgia, Sean

    1984-01-01

    Describes an experiment which illustrates simple synthetic techniques, redox principles in synthesis reactions, interpretation of visible spectra using Orgel diagrams, and the spectrochemical series. The experiment is suitable for the advanced undergraduate inorganic chemistry laboratory. (JN)

  14. An analysis of middle ultraviolet dayglow spectra

    NASA Astrophysics Data System (ADS)

    Walden, Billie S.

    1991-12-01

    Middle ultraviolet spectra from 1800 to 3400A are analyzed. These spectra were obtained from the March 1990 rocket flight of the NPS MUSTANG instrument over the altitudes 105km to 315km. The data were compared with computer generated synthetic spectra. A least squares fitting procedure was developed for this purpose. Each data point was weighted using the standard deviation of the means. Synthetic spectra were generated for the following emissions: N2 Vegard-Kaphan; N2 Lyman-Birge-Hopfield; NO gamma, delta, and epsilon; OI 2972A, OII 2470A; and NII 2143A. Altitude profiles for the emissions were obtained. Tentative identification was made of the OIII 2853A emission. A comparison of VK and LBH profiles demonstrates the process of N2 A-state quenching by atomic oxygen.

  15. [Spectra of dark green jade from Myanmar].

    PubMed

    Mao, Jian; Chai, Lin-Tao; Guo, Shou-Guo; Fan, Jian-Liang; Bao, Feng

    2013-05-01

    Chemical compositions and spectral characteristics of one type of dark green jades assumed from omphacite jadeite from Myanmar jadeite mining area were studied by X-ray powder diffraction(XRD), X-ray fluorescence spectra(XRF), Raman spectra(RM) and UV-Vis Spectroscopy, etc. Based on testing by XRD and XRF, it was shown that it belongs to iron-enriched plagioclase, including albite and anorthite. The compositions range is between Ab0.731 An0.264 Or0.004 and Ab0.693 An0.303 Or0.004. Raman spectra of samples, albite jade and anorthite were collected and analyzed. Additionally, the distributions of Si, Al in the crystal structure were also discussed. UV-Vis spectra showed that dark green hue of this mineral is associated with d--d electronic transition of Fe3+ and Cr3+.

  16. Microwave spectra of some volatile organic compounds

    NASA Technical Reports Server (NTRS)

    White, W. F.

    1975-01-01

    A computer-controlled microwave (MRR) spectrometer was used to catalog reference spectra for chemical analysis. Tables of absorption frequency, peak absorption intensity, and integrated intensity are included for 26 volatile organic compounds, all but one of which contain oxygen.

  17. Frequency Spectra of Magnetoacoustic Emission in Meteorites

    NASA Astrophysics Data System (ADS)

    Ivanchenko, S. V.; Grokhovsky, V. I.; Kolchanov, N. N.

    2016-08-01

    We analyzed the magnetoacoustic emission spectra of iron meteorites and their industrial analogs. The revealed differences in signal amplitude, position and width of the peaks are associated with the features of structure and the magnetic texture.

  18. Contribution to the study of turbulence spectra

    NASA Technical Reports Server (NTRS)

    Dumas, R.

    1979-01-01

    An apparatus suitable for turbulence measurement between ranges of 1 to 5000 cps and from 6 to 16,000 cps was developed and is described. Turbulence spectra downstream of the grills were examined with reference to their general characteristics, their LF qualities, and the effects of periodic turbulence. Medium and HF are discussed. Turbulence spectra in the boundary layers are similarly examined, with reference to their fluctuations at right angles to the wall, and to lateral fluctuations. Turbulence spectra in a boundary layer with suction to the wall is discussed. Induced turbulence, and turbulence spectra at high Reynolds numbers. Calculations are presented relating to the effect of filtering on the value of the correlations in time and space.

  19. Comparing Ultraviolet Spectra Against Calculations: First Results

    NASA Technical Reports Server (NTRS)

    Peterson, Ruth C.

    2003-01-01

    The five-year goal of this effort is to calculate high fidelity mid-UV spectra for individual stars and stellar systems for a wide range of ages, abundances, and abundance ratios. In this first year, the emphasis was placed on revising the list of atomic line parameters used to calculate mid-UV spectra. First, new identifications of atomic lines and measurements of their transition probabilities were obtained for lines of the first and second ionization stages of iron-peak elements. Second, observed mid-UV and optical spectra for standard stars were re-analyzed and compared to new calculations, to refine the determination of transition probabilities and to estimate the identity of lines still missing from the laboratory lists. As evidenced by the figures, a dramatic improvement has resulted in the reproduction of the spectra of standard stars by the calculations.

  20. POLLUX: a database of synthetic stellar spectra

    NASA Astrophysics Data System (ADS)

    Palacios, A.; Gebran, M.; Josselin, E.; Martins, F.; Plez, B.; Belmas, M.; Lèbre, A.

    2010-06-01

    Aims: Synthetic spectra are needed to determine fundamental stellar and wind parameters of all types of stars. They are also used for the construction of theoretical spectral libraries helpful for stellar population synthesis. Therefore, a database of theoretical spectra is required to allow rapid and quantitative comparisons to spectroscopic data. We provide such a database offering an unprecedented coverage of the entire Hertzsprung-Russell diagram. Methods: We present the POLLUX database of synthetic stellar spectra. For objects with Teff ≤ 6000 K, MARCS atmosphere models are computed and the program TURBOSPECTRUM provides the synthetic spectra. ATLAS12 models are computed for stars with 7000 K ≤ Teff ≤ 15 000 K. SYNSPEC gives the corresponding spectra. Finally, the code CMFGEN provides atmosphere models for the hottest stars (Teff > 25 000 K). Their spectra are computed with CMF_FLUX. Both high resolution (R > 150 000) optical spectra in the range 3000 to 12 000 Å and spectral energy distributions extending from the UV to near-IR ranges are presented. These spectra cover the HR diagram at solar metallicity. Results: We propose a wide variety of synthetic spectra for various types of stars in a format that is compliant with the Virtual Observatory standards. A user-friendly web interface allows an easy selection of spectra and data retrieval. Upcoming developments will include an extension to a large range of metallicities and to the near-IR high resolution spectra, as well as a better coverage of the HR diagram, with the inclusion of models for Wolf-Rayet stars and large datasets for cool stars. The POLLUX database is accessible at http://pollux.graal.univ-montp2.fr/ and through the Virtual Observatory. Copy of database is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb

  1. Diffuse emission and pathological Seyfert spectra

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P.

    1995-01-01

    In this annual ROSAT status report, the diffuse emission and spectra from Seyfert galaxies are examined. Three papers are presented and their contents include the soft x-ray properties and spectra of a binary millisecond pulsar, the PSPC and HRI observations of a Starburst/Seyfert 2 Galaxy, and an analysis of the possibility of x-ray luminous starbursts in the Einstein Medium Sensitivity Survey.

  2. On the Photoelectron Spectra of Li4

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1996-01-01

    The most stable structure for Li4(-) is found to be the rhombus. Electron detachment from this structure does not seem able to fully explain the photoelectron spectra. The computed results are consistent with those Rao, Jena, and Ray who have proposed that the experimental spectra consists of a superposition of detachment from the Li4(-) rhombus and tetrahedron, forming the singlet and triplet states of Li4, respectively.

  3. New atlas of IR solar spectra

    NASA Technical Reports Server (NTRS)

    Goldman, A.; Blatherwick, R. D.; Murcray, F. H.; Vanallen, J. W.; Bradford, C. M.; Cook, G. R.; Murcray, D. G.

    1980-01-01

    Over 4500 absorption lines have been marked on the spectra and the corresponding line positions tabulated. The associated absorbing telluric or solar species for more than 90% of these lines have been identified and only a fraction of the unidentified lines have peak absorptions greater than a few percent. The high resolution and the low Sun spectra greatly enhance the sensitivity limits for identification of trace constituents.

  4. Trigonometric Polynomials For Estimation Of Spectra

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles A.

    1990-01-01

    Orthogonal sets of trigonometric polynomials used as suboptimal substitutes for discrete prolate-spheroidal "windows" of Thomson method of estimation of spectra. As used here, "windows" denotes weighting functions used in sampling time series to obtain their power spectra within specified frequency bands. Simplified windows designed to require less computation than do discrete prolate-spheroidal windows, albeit at price of some loss of accuracy.

  5. Analytical calculation of two-dimensional spectra.

    PubMed

    Bell, Joshua D; Conrad, Rebecca; Siemens, Mark E

    2015-04-01

    We demonstrate an analytical calculation of two-dimensional (2D) coherent spectra of electronic or vibrational resonances. Starting with the solution to the optical Bloch equations for a two-level system in the 2D time domain, we show that a fully analytical 2D Fourier transform can be performed if the projection-slice and Fourier-shift theorems of Fourier transforms are applied. Results can be fit to experimental 2D coherent spectra of resonances with arbitrary inhomogeneity.

  6. THE SPITZER ATLAS OF STELLAR SPECTRA (SASS)

    SciTech Connect

    Ardila, David R.; Van Dyk, Schuyler D.; Makowiecki, Wojciech; Stauffer, John; Rho, Jeonghee; Fajardo-Acosta, Sergio; Hoard, D. W.; Wachter, Stefanie; Song, Inseok

    2010-12-15

    We present the Spitzer Atlas of Stellar Spectra, which includes 159 stellar spectra (5-32 {mu}m; R {approx} 100) taken with the Infrared Spectrograph on the Spitzer Space Telescope. This Atlas gathers representative spectra of a broad section of the Hertzsprung-Russell diagram, intended to serve as a general stellar spectral reference in the mid-infrared. It includes stars from all luminosity classes, as well as Wolf-Rayet (WR) objects. Furthermore, it includes some objects of intrinsic interest, such as blue stragglers and certain pulsating variables. All of the spectra have been uniformly reduced, and all are available online. For dwarfs and giants, the spectra of early-type objects are relatively featureless, characterized by the presence of hydrogen lines in A spectral types. Besides these, the most noticeable photospheric features correspond to water vapor and silicon monoxide in late-type objects and methane and ammonia features at the latest spectral types. Most supergiant spectra in the Atlas present evidence of circumstellar gas and/or dust. The sample includes five M supergiant spectra, which show strong dust excesses and in some cases polycyclic aromatic hydrocarbon features. Sequences of WR stars present the well-known pattern of lines of He I and He II, as well as forbidden lines of ionized metals. The characteristic flat-top shape of the [Ne III] line is evident even at these low spectral resolutions. Several Luminous Blue Variables and other transition stars are present in the Atlas and show very diverse spectra, dominated by circumstellar gas and dust features. We show that the [8]-[24] Spitzer colors (IRAC and MIPS) are poor predictors of spectral type for most luminosity classes.

  7. On optimization of absorption-dispersion spectra

    NASA Astrophysics Data System (ADS)

    Hawranek, J. P.; Grabska, J.; Beć, K. B.

    2016-12-01

    A modified approach to the analysis of spectra of the complex electric permittivity of liquids in the Infrared region is presented. These spectra are derived from experimental spectra of the complex refractive index. Subsequently they are used to determine important secondary quantities, e.g. spectra of complex molecular polarizabilities and an integral property - the molar vibrational polarization. The accuracy of these quantities depends essentially on the accuracy of both components of the complex electric permittivity spectrum. In the proposed procedure, the spectra of the complex electric permittivity are approximated using the Classical Damped Harmonic Oscillator (CDHO) model for the description of individual bandshapes. The CDHO model defines both the real and imaginary part of the complex permittivity. The fitting procedure includes a simultaneous optimization of both the real and imaginary parts of the complex permittivity spectrum. A comparison of absorption-only curve fitting and the novel absorption-dispersion double curve fitting is presented; advantages of the new approach in accuracy, reliability and convergence time are pointed out. Due to the complexity of the problem, the choice was restricted to non-gradient methods of optimization. The performance of several gradientless algorithms was tested. Among numerous procedures the Powell General Least Squares Method Without Derivatives was found to be the most efficient. The reliability of obtained results of the band separatiovn process was tested on several simulated spectra of increasing complexity. The applicability of the developed approach to the analysis of exemplary experimental data was evaluated and discussed.

  8. Parameterizing Stellar Spectra Using Deep Neural Networks

    NASA Astrophysics Data System (ADS)

    Li, Xiang-Ru; Pan, Ru-Yang; Duan, Fu-Qing

    2017-03-01

    Large-scale sky surveys are observing massive amounts of stellar spectra. The large number of stellar spectra makes it necessary to automatically parameterize spectral data, which in turn helps in statistically exploring properties related to the atmospheric parameters. This work focuses on designing an automatic scheme to estimate effective temperature ({T}{eff}), surface gravity ({log}g) and metallicity [Fe/H] from stellar spectra. A scheme based on three deep neural networks (DNNs) is proposed. This scheme consists of the following three procedures: first, the configuration of a DNN is initialized using a series of autoencoder neural networks; second, the DNN is fine-tuned using a gradient descent scheme; third, three atmospheric parameters {T}{eff}, {log}g and [Fe/H] are estimated using the computed DNNs. The constructed DNN is a neural network with six layers (one input layer, one output layer and four hidden layers), for which the number of nodes in the six layers are 3821, 1000, 500, 100, 30 and 1, respectively. This proposed scheme was tested on both real spectra and theoretical spectra from Kurucz’s new opacity distribution function models. Test errors are measured with mean absolute errors (MAEs). The errors on real spectra from the Sloan Digital Sky Survey (SDSS) are 0.1477, 0.0048 and 0.1129 dex for {log}g, {log}{T}{eff} and [Fe/H] (64.85 K for {T}{eff}), respectively. Regarding theoretical spectra from Kurucz’s new opacity distribution function models, the MAE of the test errors are 0.0182, 0.0011 and 0.0112 dex for {log}g, {log}{T}{eff} and [Fe/H] (14.90 K for {T}{eff}), respectively.

  9. Pebbles and PebbleJuggler: software for accurate, unbiased, and fast measurement and analysis of nanoparticle morphology from transmission electron microscopy (TEM) micrographs

    NASA Astrophysics Data System (ADS)

    Mondini, S.; Ferretti, A. M.; Puglisi, A.; Ponti, A.

    2012-08-01

    Pebbles is a user-friendly software program which implements an accurate, unbiased, and fast method to measure the morphology of a population of nanoparticles (NPs) from TEM micrographs. The morphological parameters of the projected NP shape are obtained by fitting intensity models to the TEM micrograph. Pebbles can be used either in automatic mode, where both fitting and validation are reliably carried out with minimal human intervention, and in manual mode, where the user has full control on the fitting and validation steps. Accuracy in diameter measurement has been shown to be <~1%. When operated in automatic mode, Pebbles can be very fast. The effective speed of 1 NP s-1 has been achieved in favorable cases (packed monolayer of NPs). Since Pebbles is based on a local modeling procedure, it successfully treats cases such as low contrast NPs, NPs with significant diffraction scattering, and inhomogeneous background which often make conventional thresholding procedures fail. Pebbles is accompanied by PebbleJuggler, a software program for the statistical analysis of the sets of best-fit NP models created by Pebbles. Effort has been devoted to make Pebbles and PebbleJuggler the most user-friendly and the least user-tedious we could. Pebbles and PebbleJuggler are available at http://pebbles.istm.cnr.it.Pebbles is a user-friendly software program which implements an accurate, unbiased, and fast method to measure the morphology of a population of nanoparticles (NPs) from TEM micrographs. The morphological parameters of the projected NP shape are obtained by fitting intensity models to the TEM micrograph. Pebbles can be used either in automatic mode, where both fitting and validation are reliably carried out with minimal human intervention, and in manual mode, where the user has full control on the fitting and validation steps. Accuracy in diameter measurement has been shown to be <~1%. When operated in automatic mode, Pebbles can be very fast. The effective speed of 1

  10. Higher-order septin assembly is driven by GTP-promoted conformational changes: evidence from unbiased mutational analysis in Saccharomyces cerevisiae.

    PubMed

    Weems, Andrew D; Johnson, Courtney R; Argueso, Juan Lucas; McMurray, Michael A

    2014-03-01

    Septin proteins bind GTP and heterooligomerize into filaments with conserved functions across a wide range of eukaryotes. Most septins hydrolyze GTP, altering the oligomerization interfaces; yet mutations designed to abolish nucleotide binding or hydrolysis by yeast septins perturb function only at high temperatures. Here, we apply an unbiased mutational approach to this problem. Mutations causing defects at high temperature mapped exclusively to the oligomerization interface encompassing the GTP-binding pocket, or to the pocket itself. Strikingly, cold-sensitive defects arise when certain of these same mutations are coexpressed with a wild-type allele, suggestive of a novel mode of dominance involving incompatibility between mutant and wild-type molecules at the septin-septin interfaces that mediate filament polymerization. A different cold-sensitive mutant harbors a substitution in an unstudied but highly conserved region of the septin Cdc12. A homologous domain in the small GTPase Ran allosterically regulates GTP-binding domain conformations, pointing to a possible new functional domain in some septins. Finally, we identify a mutation in septin Cdc3 that restores the high-temperature assembly competence of a mutant allele of septin Cdc10, likely by adopting a conformation more compatible with nucleotide-free Cdc10. Taken together, our findings demonstrate that GTP binding and hydrolysis promote, but are not required for, one-time events--presumably oligomerization-associated conformational changes--during assembly of the building blocks of septin filaments. Restrictive temperatures impose conformational constraints on mutant septin proteins, preventing new assembly and in certain cases destabilizing existing assemblies. These insights from yeast relate directly to disease-causing mutations in human septins.

  11. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

    PubMed

    Graf, Erin H; Simmon, Keith E; Tardif, Keith D; Hymas, Weston; Flygare, Steven; Eilbeck, Karen; Yandell, Mark; Schlaberg, Robert

    2016-04-01

    Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (n= 42) and unselected (n= 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information.

  12. THE OPTICALLY UNBIASED GRB HOST (TOUGH) SURVEY. V. VLT/X-SHOOTER EMISSION-LINE REDSHIFTS FOR SWIFT GRBs AT z {approx} 2

    SciTech Connect

    Kruehler, Thomas; Malesani, Daniele; Milvang-Jensen, Bo; Fynbo, Johan P. U.; Hjorth, Jens; Sparre, Martin; Watson, Darach J.; Jakobsson, Pall; Levan, Andrew J.; Tanvir, Nial R.

    2012-10-10

    We present simultaneous optical and near-infrared (NIR) spectroscopy of 19 Swift {gamma}-ray burst (GRB) host galaxies observed with the VLT/X-shooter with the aim of measuring their redshifts. Galaxies were selected from The Optically Unbiased GRB Host (TOUGH) survey (15 of the 19 galaxies) or because they hosted GRBs without a bright optical afterglow. Here we provide emission-line redshifts for 13 of the observed galaxies with brightnesses between F606W > 27 mag and R = 22.9 mag (median R-tilde =24.6 mag). The median redshift is z-tilde =2.1 for all hosts and z-tilde =2.3 for the TOUGH hosts. Our new data significantly improve the redshift completeness of the TOUGH survey, which now stands at 77% (53 out of 69 GRBs). They furthermore provide accurate redshifts for nine prototype dark GRBs (e.g., GRB 071021 at z = 2.452 and GRB 080207 at z = 2.086), which are exemplary of GRBs where redshifts are challenging to obtain via afterglow spectroscopy. This establishes X-shooter spectroscopy as an efficient tool for redshift determination of faint, star-forming, high-redshift galaxies such as GRB hosts. It is hence a further step toward removing the bias in GRB samples that is caused by optically dark events, and provides the basis for a better understanding of the conditions in which GRBs form. The distribution of column densities as measured from X-ray data (N{sub H,X}), for example, is closely related to the darkness of the afterglow and skewed toward low N{sub H,X} values in samples that are dominated by bursts with bright optical afterglows.

  13. Connecting GRBs and ULIRGs: A Sensitive, Unbiased Survey for Radio Emission from Gamma-Ray Burst Host Galaxies at 0 < z < 2.5

    NASA Astrophysics Data System (ADS)

    Perley, D. A.; Perley, R. A.; Hjorth, J.; Michałowski, M. J.; Cenko, S. B.; Jakobsson, P.; Krühler, T.; Levan, A. J.; Malesani, D.; Tanvir, N. R.

    2015-03-01

    Luminous infrared galaxies and submillimeter galaxies contribute significantly to stellar mass assembly and provide an important test of the connection between the gamma-ray burst (GRB) rate and that of overall cosmic star formation. We present sensitive 3 GHz radio observations using the Karl G. Jansky Very Large Array of 32 uniformly selected GRB host galaxies spanning a redshift range from 0 < z < 2.5, providing the first fully dust- and sample-unbiased measurement of the fraction of GRBs originating from the universe's most bolometrically luminous galaxies. Four galaxies are detected, with inferred radio star formation rates (SFRs) ranging between 50 and 300 M ⊙ yr-1. Three of the four detections correspond to events consistent with being optically obscured "dark" bursts. Our overall detection fraction implies that between 9% and 23% of GRBs between 0.5 < z < 2.5 occur in galaxies with S 3GHz > 10 μJy, corresponding to SFR > 50 M ⊙ yr-1 at z ~ 1 or >250 M ⊙ yr-1 at z ~ 2. Similar galaxies contribute approximately 10%-30% of all cosmic star formation, so our results are consistent with a GRB rate that is not strongly biased with respect to the total SFR of a galaxy. However, all four radio-detected hosts have stellar masses significantly lower than IR/submillimeter-selected field galaxies of similar luminosities. We suggest that the GRB rate may be suppressed in metal-rich environments but independently enhanced in intense starbursts, producing a strong efficiency dependence on mass but little net dependence on bulk galaxy SFR.

  14. Identification and biological evaluation of a novel and potent small molecule radiation sensitizer via an unbiased screen of a chemical library.

    PubMed

    Lally, Brian E; Geiger, Geoffrey A; Kridel, Steven; Arcury-Quandt, Alice E; Robbins, Michael E; Kock, Nancy D; Wheeler, Kenneth; Peddi, Prakash; Georgakilas, Alexandros; Kao, Gary D; Koumenis, Constantinos

    2007-09-15

    For patients with solid tumors, the tolerance of surrounding tissues often limits the dose of radiation that can be delivered. Thus, agents that preferentially increase the cytotoxic effects of radiation toward tumor cells would significantly alter the therapeutic ratio and improve patient survival. Using a high-throughput, unbiased screening approach, we have identified 4'-bromo-3'-nitropropiophenone (NS-123) as a radiosensitizer of human glioma cells in vitro and in vivo. NS-123 radiosensitized U251 glioma cells in a dose-dependent and time-dependent manner, with dose enhancement ratios ranging from 1.3 to 2.0. HT-29 colorectal carcinoma and A549 lung adenocarcinoma cells were also radiosensitized by NS-123 in vitro, whereas NS-123 did not increase the radiation sensitivity of normal human astrocytes or developmental abnormalities or lethality of irradiated Zebrafish embryos. In a novel xenograft model of U251 cells implanted into Zebrafish embryos, NS-123 enhanced the tumor growth-inhibitory effects of ionizing radiation (IR) with no apparent effect on embryo development. Similar results were obtained using a mouse tumor xenograft model in which NS-123 sensitized U251 tumors to IR while exhibiting no overt toxicity. In vitro pretreatment with NS-123 resulted in accumulation of unrepaired IR-induced DNA strand breaks and prolonged phosphorylation of the surrogate markers of DNA damage H2AX, ataxia telangiectasia mutated protein, DNA-dependent protein kinase, and CHK2 after IR, suggesting that NS-123 inhibits a critical step in the DNA repair pathway. These results show the potential of this cell-based, high-throughput screening method to identify novel radiosensitizers and suggest that NS-123 and similar nitrophenol compounds may be effective in antiglioma modalities.

  15. CONNECTING GRBs AND ULIRGs: A SENSITIVE, UNBIASED SURVEY FOR RADIO EMISSION FROM GAMMA-RAY BURST HOST GALAXIES AT 0 < z < 2.5

    SciTech Connect

    Perley, D. A.; Perley, R. A.; Hjorth, J.; Malesani, D.; Michałowski, M. J.; Cenko, S. B.; Krühler, T.; Levan, A. J.; Tanvir, N. R.

    2015-03-10

    Luminous infrared galaxies and submillimeter galaxies contribute significantly to stellar mass assembly and provide an important test of the connection between the gamma-ray burst (GRB) rate and that of overall cosmic star formation. We present sensitive 3 GHz radio observations using the Karl G. Jansky Very Large Array of 32 uniformly selected GRB host galaxies spanning a redshift range from 0 < z < 2.5, providing the first fully dust- and sample-unbiased measurement of the fraction of GRBs originating from the universe's most bolometrically luminous galaxies. Four galaxies are detected, with inferred radio star formation rates (SFRs) ranging between 50 and 300 M {sub ☉} yr{sup –1}. Three of the four detections correspond to events consistent with being optically obscured 'dark' bursts. Our overall detection fraction implies that between 9% and 23% of GRBs between 0.5 < z < 2.5 occur in galaxies with S {sub 3GHz} > 10 μJy, corresponding to SFR > 50 M {sub ☉} yr{sup –1} at z ∼ 1 or >250 M {sub ☉} yr{sup –1} at z ∼ 2. Similar galaxies contribute approximately 10%-30% of all cosmic star formation, so our results are consistent with a GRB rate that is not strongly biased with respect to the total SFR of a galaxy. However, all four radio-detected hosts have stellar masses significantly lower than IR/submillimeter-selected field galaxies of similar luminosities. We suggest that the GRB rate may be suppressed in metal-rich environments but independently enhanced in intense starbursts, producing a strong efficiency dependence on mass but little net dependence on bulk galaxy SFR.

  16. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel

    PubMed Central

    Graf, Erin H.; Simmon, Keith E.; Tardif, Keith D.; Hymas, Weston; Flygare, Steven; Eilbeck, Karen; Yandell, Mark

    2016-01-01

    Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (n = 42) and unselected (n = 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information. PMID:26818672

  17. Hemifield-dependent N1 and event-related theta/delta oscillations: An unbiased comparison of surface Laplacian and common EEG reference choices

    PubMed Central

    Kayser, Jürgen; Tenke, Craig E.

    2015-01-01

    Surface Laplacian methodology has been used to reduce the impact of volume conduction and arbitrary choice of EEG recording reference for the analysis of surface potentials. However, the empirical implications of employing these different transformations to the same EEG data remain obscure. This study directly compared the statistical effects of four commonly-used (nose, linked mastoids, average) or recommended (reference electrode standardization technique [REST]) references and their spherical spline current source density (CSD) transformation for a large data set stemming from a well-understood experimental manipulation. ERPs (72 sites) recorded from 130 individuals during a visual half-field paradigm with highly-controlled emotional stimuli were characterized by mid-parietooccipital N1 (125 ms peak latency) and event-related synchronization (ERS) of theta/delta (160 ms), which were most robust over the contralateral hemisphere. All five data transformations were rescaled to the same covariance and submitted to a single temporal or time-frequency PCA (Varimax) to yield simplified estimates of N1 or theta/delta ERS. Unbiased nonparametric permutation tests revealed that these hemifield-dependent asymmetries were by far most focal and prominent for CSD data, despite all transformations showing maximum effects at mid-parietooccipital sites. Employing smaller subsamples (signal-to-noise) or window-based ERP/ERS amplitudes did not affect these comparisons. Furthermore, correlations between N1 and theta/delta ERS at these sites were strongest for CSD and weakest for nose-referenced data. Contrary to the common notion that the spatial high pass filter properties of a surface Laplacian reduce important contributions of neuronal generators to the EEG signal, the present findings demonstrate that instead volume conduction inherent in surface potentials weakens the representation of neuronal activation patterns at scalp that directly reflect regional brain activity. PMID

  18. Disk-Averaged Synthetic Spectra of Mars

    NASA Astrophysics Data System (ADS)

    Tinetti, Giovanna; Meadows, Victoria S.; Crisp, David; Fong ,William; Velusamy, Thangasamy; Snively, Heather

    2005-08-01

    The principal goal of the NASA Terrestrial Planet Finder (TPF) and European Space Agency's Darwin mission concepts is to directly detect and characterize extrasolar terrestrial (Earthsized) planets. This first generation of instruments is expected to provide disk-averaged spectra with modest spectral resolution and signal-to-noise. Here we use a spatially and spectrally resolved model of a Mars-like planet to study the detectability of a planet's surface and atmospheric properties from disk-averaged spectra. We explore the detectability as a function of spectral resolution and wavelength range, for both the proposed visible coronograph (TPFC) and mid-infrared interferometer (TPF-I/Darwin) architectures. At the core of our model is a spectrum-resolving (line-by-line) atmospheric/surface radiative transfer model. This model uses observational data as input to generate a database of spatially resolved synthetic spectra for a range of illumination conditions and viewing geometries. The model was validated against spectra recorded by the Mars Global Surveyor-Thermal Emission Spectrometer and the Mariner 9-Infrared Interferometer Spectrometer. Results presented here include disk-averaged synthetic spectra, light curves, and the spectral variability at visible and mid-infrared wavelengths for Mars as a function of viewing angle, illumination, and season. We also considered the differences in the spectral appearance of an increasingly ice-covered Mars, as a function of spectral resolution, signal-to-noise and integration time for both TPF-C and TPFI/ Darwin.

  19. H. N. Russell and Atomic Spectra

    NASA Astrophysics Data System (ADS)

    Devorkin, David

    2001-04-01

    “I would rather analyze spectra than do cross-word puzzles or do almost anything else” Henry Norris Russell wrote to William F. Meggers in 1927. Meggers, chief of the spectroscopy division at the NBS, had been surprised that an astrophysicist could be so keen about the analysis of complex spectra. But Russell was a new type of astrophysicist, one who made physics the core of his research. Spectra, for Russell, held the "master key" to knowledge about the universe, and of the atom. He was first attracted by the challenge of detecting and explaining anomalies, which he hoped would lead to new knowledge about the structure of matter. Then, influenced by physicists such as Meggers, he devoted himself to filling in the picture of the structure of atoms from their characteristic spectra as completely as possible. In this talk I will review how Russell worked with Meggers and became the nucleus of an ever-widening circle of spectroscopists devoted to the analysis of complex spectra.

  20. Improving Algorithm for Automatic Spectra Processing

    NASA Astrophysics Data System (ADS)

    Rackovic, K.; Nikolic, S.; Kotrc, P.

    2009-09-01

    Testing and improving of the computer program for automatic processing (flat-fielding) of a great number of solar spectra obtained with the horizontal heliospectrograph HSFA2 has been done. This program was developed in the Astronomical Institute of Academy of Sciences of the Czech Republic in Ondřejov. An irregularity in its work has been discovered, i.e. the program didn't work for some of the spectra. To discover a cause of this error an algorithm has been developed, and a program for examination of the parallelism of reference hairs crossing the spectral slit on records of solar spectra has been made. The standard methods for data processing have been applied-calculating and analyzing higher-order moments of distribution of radiation intensity. The spectra with the disturbed parallelism of the reference hairs have been eliminated from further processing. In order to improve this algorithm of smoothing of spectra, isolation and removal of the harmonic made by a sunspot with multiple elementary transformations of ordinates (Labrouste's transformations) are planned. This project was accomplished at the first summer astronomy practice of students of the Faculty of Mathematics, University of Belgrade, Serbia in 2007 in Ondřejov.

  1. Cloud supersaturations from CCN spectra Hoppel minima

    NASA Astrophysics Data System (ADS)

    Hudson, James G.; Noble, Stephen; Tabor, Samantha

    2015-04-01

    High-resolution cloud condensation nucleus (CCN) spectral measurements in two aircraft field projects, Marine Stratus/Stratocumulus Experiment (MASE) and Ice in Clouds Experiment-Tropical (ICE-T), often showed bimodality that had previously been observed in submicrometer aerosol size distributions obtained by differential mobility analyzers. However, a great deal of spectral shape variability from very bimodal to very monomodal was observed in close proximity. Cloud supersaturation (S) estimates based on critical S, Sc, at minimal CCN concentrations between two modes (Hoppel minima) were ascertained for 63% of 325 measured spectra. These cloud S were lower than effective S (Seff) determined by comparing ambient CCN spectra with nearby cloud droplet concentrations (Nc). Averages for the polluted MASE stratus were 0.15 and 0.23% and for the cumulus clouds of ICE-T 0.44 and 1.03%. This cloud S disagreement between the two methods might in part be due to the fact that Hoppel minima include the effects of cloud processing, which push CCN spectra toward lower S. Furthermore, there is less cloud processing by the smaller cloud droplets, which might be related to smaller droplets evaporating more readily. Significantly lower concentrations within the more bimodal spectra compared with the monomodal spectra indicated active physical processes: Brownian capture of interstitial CCN and droplet coalescence. Chemical cloud processing also contributed to bimodality, especially in MASE.

  2. Disk-averaged synthetic spectra of Mars

    NASA Technical Reports Server (NTRS)

    Tinetti, Giovanna; Meadows, Victoria S.; Crisp, David; Fong, William; Velusamy, Thangasamy; Snively, Heather

    2005-01-01

    The principal goal of the NASA Terrestrial Planet Finder (TPF) and European Space Agency's Darwin mission concepts is to directly detect and characterize extrasolar terrestrial (Earthsized) planets. This first generation of instruments is expected to provide disk-averaged spectra with modest spectral resolution and signal-to-noise. Here we use a spatially and spectrally resolved model of a Mars-like planet to study the detectability of a planet's surface and atmospheric properties from disk-averaged spectra. We explore the detectability as a function of spectral resolution and wavelength range, for both the proposed visible coronograph (TPFC) and mid-infrared interferometer (TPF-I/Darwin) architectures. At the core of our model is a spectrum-resolving (line-by-line) atmospheric/surface radiative transfer model. This model uses observational data as input to generate a database of spatially resolved synthetic spectra for a range of illumination conditions and viewing geometries. The model was validated against spectra recorded by the Mars Global Surveyor-Thermal Emission Spectrometer and the Mariner 9-Infrared Interferometer Spectrometer. Results presented here include disk-averaged synthetic spectra, light curves, and the spectral variability at visible and mid-infrared wavelengths for Mars as a function of viewing angle, illumination, and season. We also considered the differences in the spectral appearance of an increasingly ice-covered Mars, as a function of spectral resolution, signal-to-noise and integration time for both TPF-C and TPFI/ Darwin.

  3. Disk-averaged synthetic spectra of Mars.

    PubMed

    Tinetti, Giovanna; Meadows, Victoria S; Crisp, David; Fong, William; Velusamy, Thangasamy; Snively, Heather

    2005-08-01

    The principal goal of the NASA Terrestrial Planet Finder (TPF) and European Space Agency's Darwin mission concepts is to directly detect and characterize extrasolar terrestrial (Earthsized) planets. This first generation of instruments is expected to provide disk-averaged spectra with modest spectral resolution and signal-to-noise. Here we use a spatially and spectrally resolved model of a Mars-like planet to study the detectability of a planet's surface and atmospheric properties from disk-averaged spectra. We explore the detectability as a function of spectral resolution and wavelength range, for both the proposed visible coronograph (TPFC) and mid-infrared interferometer (TPF-I/Darwin) architectures. At the core of our model is a spectrum-resolving (line-by-line) atmospheric/surface radiative transfer model. This model uses observational data as input to generate a database of spatially resolved synthetic spectra for a range of illumination conditions and viewing geometries. The model was validated against spectra recorded by the Mars Global Surveyor-Thermal Emission Spectrometer and the Mariner 9-Infrared Interferometer Spectrometer. Results presented here include disk-averaged synthetic spectra, light curves, and the spectral variability at visible and mid-infrared wavelengths for Mars as a function of viewing angle, illumination, and season. We also considered the differences in the spectral appearance of an increasingly ice-covered Mars, as a function of spectral resolution, signal-to-noise and integration time for both TPF-C and TPFI/ Darwin.

  4. EXPLORING THE MORPHOLOGY OF RAVE STELLAR SPECTRA

    SciTech Connect

    Matijevic, G.; Zwitter, T.; Bienayme, O.; Siebert, A.; Bland-Hawthorn, J.; Boeche, C.; Grebel, E. K.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Helmi, A.; Munari, U.; Navarro, J.; Parker, Q. A.; Reid, W.; Seabroke, G.; Siviero, A.; Steinmetz, M.; Williams, M.; Watson, F. G.; and others

    2012-06-01

    The RAdial Velocity Experiment (RAVE) is a medium-resolution (R {approx} 7500) spectroscopic survey of the Milky Way that has already obtained over half a million stellar spectra. They present a randomly selected magnitude-limited sample, so it is important to use a reliable and automated classification scheme that identifies normal single stars and discovers different types of peculiar stars. To this end, we present a morphological classification of {approx}350, 000 RAVE survey stellar spectra using locally linear embedding, a dimensionality reduction method that enables representing the complex spectral morphology in a low-dimensional projected space while still preserving the properties of the local neighborhoods of spectra. We find that the majority of all spectra in the database ({approx} 90%-95%) belong to normal single stars, but there is also a significant population of several types of peculiars. Among them, the most populated groups are those of various types of spectroscopic binary and chromospherically active stars. Both of them include several thousands of spectra. Particularly the latter group offers significant further investigation opportunities since activity of stars is a known proxy of stellar ages. Applying the same classification procedure to the sample of normal single stars alone shows that the shape of the projected manifold in two-dimensional space correlates with stellar temperature, surface gravity, and metallicity.

  5. Cleaning HI Spectra Contaminated by GPS RFI

    NASA Astrophysics Data System (ADS)

    Sylvia, Kamin; Hallenbeck, Gregory L.; Undergraduate ALFALFA Team

    2016-01-01

    The NUDET systems aboard GPS satellites utilize radio waves to communicate information regarding surface nuclear events. The system tests appear in spectra as RFI (radio frequency interference) at 1381MHz, which contaminates observations of extragalactic HI (atomic hydrogen) signals at 50-150 Mpc. Test durations last roughly 20-120 seconds and can occur upwards of 30 times during a single night of observing. The disruption essentially renders the corresponding HI spectra useless.We present a method that automatically removes RFI in HI spectra caused by these tests. By capitalizing on the GPS system's short test durations and predictable frequency appearance we are able to devise a method of identifying times containing compromised data records. By reevaluating the remaining data, we are able to recover clean spectra while sacrificing little in terms of sensitivity to extragalactic signals. This method has been tested on 500+ spectra taken by the Undergraduate ALFALFA Team (UAT), in which it successfully identified and removed all sources of GPS RFI. It will also be used to eliminate RFI in the upcoming Arecibo Pisces-Perseus Supercluster Survey (APPSS).This work has been supported by NSF grant AST-1211005.

  6. Background noise spectra of global seismic stations

    SciTech Connect

    Wada, M.M.; Claassen, J.P.

    1996-08-01

    Over an extended period of time station noise spectra were collected from various sources for use in estimating the detection and location performance of global networks of seismic stations. As the database of noise spectra enlarged and duplicate entries became available, an effort was mounted to more carefully select station noise spectra while discarding others. This report discusses the methodology and criteria by which the noise spectra were selected. It also identifies and illustrates the station noise spectra which survived the selection process and which currently contribute to the modeling efforts. The resulting catalog of noise statistics not only benefits those who model network performance but also those who wish to select stations on the basis of their noise level as may occur in designing networks or in selecting seismological data for analysis on the basis of station noise level. In view of the various ways by which station noise were estimated by the different contributors, it is advisable that future efforts which predict network performance have available station noise data and spectral estimation methods which are compatible with the statistics underlying seismic noise. This appropriately requires (1) averaging noise over seasonal and/or diurnal cycles, (2) averaging noise over time intervals comparable to those employed by actual detectors, and (3) using logarithmic measures of the noise.

  7. Red spectra from white and blue noise

    PubMed Central

    Balmforth, N. J.; Provenzale, A.; Spiegel, E. A.; Martens, M.; Tresser, C.; Wu, C. W.

    1999-01-01

    The value of maps of the interval in modelling population dynamics has recently been called into question because temporal variations from such maps have blue or white power spectra, whereas many observations of real populations show time-series with red spectra. One way to deal with this discrepancy is to introduce chaotic or stochastic fluctuations in the parameters of the map. This leads to on–off intermittency and can markedly redden the spectrum produced by a model that does not by itself have a red spectrum. The parameter fluctuations need not themselves have a red spectrum in order to achieve this effect. Because the power spectrum is not invariant under a change of variable, another way to redden the spectrum is by a suitable transformation of the variables used. The question this poses is whether spectra are the best means of characterizing a fluctuating variable.

  8. Crystal field spectra of lunar pyroxenes.

    NASA Technical Reports Server (NTRS)

    Burns, R. G.; Abu-Eid, R. M.; Huggins, F. E.

    1972-01-01

    Absorption spectra in the visible and near infrared regions have been obtained for pyroxene single crystals in rocks from the Apollo 11, 12, 14, and 15 missions. The polarized spectra are compared with those obtained from terrestrial calcic clinopyroxenes, subcalcic augites, pigeonites, and orthopyroxenes. The lunar pyroxenes contain several broad, intense absorption bands in the near infrared, the positions of which are related to bulk composition, Fe(2+) site occupancy and structure type of the pyroxene. The visible spectra contain several sharp, weak peaks mainly due to spin-forbidden transitions in Fe(2+). Additional weak bands in this region in Apollo 11 pyroxenes are attributed to Ti(3+) ions. Spectral features from Fe(3+), Mn(2+), Cr(3+), and Cr(2+) were not observed.

  9. Vibrational spectra of molecular fluids in nanopores

    NASA Astrophysics Data System (ADS)

    Arakcheev, V. G.; Morozov, V. B.

    2012-12-01

    Coherent anti-Stokes Raman spectroscopy (CARS) is applied for quantitative analysis of carbon dioxide phase composition in pores of nanoporous glass samples at nearcritical temperatures. Measurements of the 1388 1/cm Q-branch were made in a wide pressure range corresponding to coexistence of gas (gas-like), adsorbed and condensed phases within pores. At temperatures several degrees below the critical value, CARS spectra behavior is easy to interpret in terms of thermodynamic model of surface adsorption and capillary condensation. It allows estimating mass fractions of different phase components. Moreover, spectra measured at near critical temperatures 30.5 and 33°C have pronounced inhomogeneous shapes and indicate the presence of condensed phase in the volume of pores. The effect obviously reflects the fluid behaviour near the critical point in nanopores. Pores with smaller radii are filled with condensed phase at lower pressures. The analysis of the CARS spectra is informative for quantitative evaluation of phase composition in nanopores.

  10. Janus Spectra in Two-Dimensional Flows

    NASA Astrophysics Data System (ADS)

    Liu, Chien-Chia; Cerbus, Rory T.; Chakraborty, Pinaki

    2016-09-01

    In large-scale atmospheric flows, soap-film flows, and other two-dimensional flows, the exponent of the turbulent energy spectra, α , may theoretically take either of two distinct values, 3 or 5 /3 , but measurements downstream of obstacles have invariably revealed α =3 . Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which α transitions from 3 to 5 /3 for the streamwise fluctuations but remains equal to 3 for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows.

  11. FAST INVERSION OF SOLAR Ca II SPECTRA

    SciTech Connect

    Beck, C.; Choudhary, D. P.; Rezaei, R.; Louis, R. E.

    2015-01-10

    We present a fast (<<1 s per profile) inversion code for solar Ca II lines. The code uses an archive of spectra that are synthesized prior to the inversion under the assumption of local thermodynamic equilibrium (LTE). We show that it can be successfully applied to spectrograph data or more sparsely sampled spectra from two-dimensional spectrometers. From a comparison to a non-LTE inversion of the same set of spectra, we derive a first-order non-LTE correction to the temperature stratifications derived in the LTE approach. The correction factor is close to unity up to log τ ∼ –3 and increases to values of 2.5 and 4 at log τ = –6 in the quiet Sun and the umbra, respectively.

  12. Molecular dynamics and spectra. II. Diatomic Raman

    NASA Astrophysics Data System (ADS)

    Berens, Peter H.; White, Steven R.; Wilson, Kent R.

    1981-07-01

    This paper and paper I in this series [P.H. Berens and K.R. Wilison, J. Chem. Phys. 74, 4872 (1981)] indicate that infrared and Raman rotational and fundamental vibrational-rotational spectra of dense systems (high pressure gases, liquids, and solids) are essentially classical, in that they can be computed and understood from a basically classical mechanical viewpoint, with some caveats for features in which anharmonicity is important, such as the detailed shape of Q branches. It is demonstrated here, using the diatomic case as an example, that ordinary, i.e., nonresonant, Raman band contours can be computed from classical mechanics plus simple quantum corrections. Classical versions of molecular dynamics, linear response theory, and ensemble averaging, followed by straightforward quantum corrections, are used to compute the pure rotational and fundamental vibration-rotational Raman band contours of N2 for the gas phase and for solutions of N2 in different densities of gas phase Ar and in liquid Ar. The evolution is seen from multiple peaked line shapes characteristic of free rotation in the gas phase to single peaks characteristic of hindered rotation in the liquid phase. Comparison is made with quantum and correspondence principle classical gas phase spectral calculations and with experimental measurements for pure N2 and N2 in liquid Ar. Three advantages are pointed out for a classical approach to infrared and Raman spectra. First, a classical approach can be used to compute the spectra of complex molecular systems, e.g., of large molecules, clusters, liquids, solutions, and solids. Second, this classical approach can be extended to compute the spectra of nonequilibrium and time-dependent systems, e.g., infrared and Raman spectra during the course of chemical reactions. Third, a classical viewpoint allows experimental infrared and Raman spectra to be understood and interpreted in terms of atomic motions with the considerable aid of classical models and of our

  13. Infrared spectra of cesium chloride aqueous solutions

    NASA Astrophysics Data System (ADS)

    Max, Jean-Joseph; Chapados, Camille

    2000-10-01

    The aqueous solutions of CsCl were studied at room temperature by infrared (IR) spectroscopy in the entire solubility range, 0-1200 g/L, using attenuated total reflection (ATR) sampling. The influence of anomalous dispersion on the IR-ATR spectra was evaluated by calculating the imaginary refractive index, k(ν), of each sample. Factor analysis (FA) was used to determine the number and abundance of species in the solutions. FA applied to both k(ν) spectra and IR-ATR spectra produced two principal spectra with a similar abundance of species. This result indicates that, even at high salt concentration, the optical effects do not influence the chemical analysis of IR-ATR spectra. The spectral modifications related to the salt concentrations are mainly first order. Second order effects were observed, but being weak, were not investigated. The two principal spectra are related to the two species present in the solution: pure water and CsCl-solvated water. From the latter, 2.8±0.4 water molecules were calculated to be associated with each close-bound Cs+/Cl- ion pair. In the case of KCl and NaCl aqueous solutions, both of which showed the same number of species, the number of water molecules associated to an ion pair was 5.0±0.4. That the latter number is different from that of CsCl indicates that the interaction between water molecules and ion pairs is different when cation Na or K in the chloride salt is replaced by Cs.

  14. Observed and theoretical spectra in the 10-100 A interval. [of solar spectra

    NASA Technical Reports Server (NTRS)

    Brown, W. A.; Bruner, M. E.; Acton, L. W.

    1988-01-01

    The soft X-ray spectra recorded in two sounding-rocket flights in 1982 and 1985 are compared with predicted spectra. The processed densitometer trace of the full spectrum is presented, together with the new spectrum from the 1985 experiment. The intensities of the lines are then compared with predictions.

  15. Experimental Constraints on Neutrino Spectra Following Fission

    NASA Astrophysics Data System (ADS)

    Napolitano, Jim; Daya Bay Collaboration

    2016-09-01

    We discuss new initiatives to constrain predictions of fission neutrino spectra from nuclear reactors. These predictions are germane to the understanding of reactor flux anomalies; are needed to reduce systematic uncertainty in neutrino oscillation spectra; and inform searches for the diffuse supernova neutrino background. The initiatives include a search for very high- Q beta decay components to the neutrino spectrum from the Daya Bay power plant; plans for a measurement of the β- spectrum from 252Cf fission products; and precision measurements of the 235U fission neutrino spectrum from PROSPECT and other very short baseline reactor experiments.

  16. A data base of geologic field spectra

    NASA Technical Reports Server (NTRS)

    Kahle, A. B.; Goetz, A. F. H.; Paley, H. N.; Alley, R. E.; Abbott, E. A.

    1981-01-01

    It is noted that field samples measured in the laboratory do not always present an accurate picture of the ground surface sensed by airborne or spaceborne instruments because of the heterogeneous nature of most surfaces and because samples are disturbed and surface characteristics changed by collection and handling. The development of new remote sensing instruments relies on the analysis of surface materials in their natural state. The existence of thousands of Portable Field Reflectance Spectrometer (PFRS) spectra has necessitated a single, all-inclusive data base that permits greatly simplified searching and sorting procedures and facilitates further statistical analyses. The data base developed at JPL for cataloging geologic field spectra is discussed.

  17. Separating Peaks in X-Ray Spectra

    NASA Technical Reports Server (NTRS)

    Nicolas, David; Taylor, Clayborne; Wade, Thomas

    1987-01-01

    Deconvolution algorithm assists in analysis of x-ray spectra from scanning electron microscopes, electron microprobe analyzers, x-ray fluorescence spectrometers, and like. New algorithm automatically deconvolves x-ray spectrum, identifies locations of spectral peaks, and selects chemical elements most likely producing peaks. Technique based on similarities between zero- and second-order terms of Taylor-series expansions of Gaussian distribution and of damped sinusoid. Principal advantage of algorithm: no requirement to adjust weighting factors or other parameters when analyzing general x-ray spectra.

  18. Vibrational spectra study on quinolones antibiotics

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Yu, Ke; Wang, Sihuan

    2006-09-01

    In order to be able to fully understand and easily identify the quilonoles, we collected IR and Raman spectra of six quinolones, and attempted to assign the attribution of the observed frequencies and their association with specific modes of vibration. According to the structure, the compounds were divided into the groups, and the similarities and differences were further studied by comparing. The result of the study shows that the frequency and intensity are comparable to the corresponding structure. The spectra not only have the commonness but also the individualities.

  19. Hadron rapidity spectra within a hybrid model

    NASA Astrophysics Data System (ADS)

    Khvorostukhin, A. S.; Toneev, V. D.

    2017-01-01

    A 2-stage hybrid model is proposed that joins the fast initial state of interaction, described by the hadron string dynamics (HSD) model, to subsequent evolution of the expanding system at the second stage, treated within ideal hydrodynamics. The developed hybrid model is assigned to describe heavy-ion collisions in the energy range of the NICA collider under construction in Dubna. Generally, the model is in reasonable agreement with the available data on proton rapidity spectra. However, reproducing proton rapidity spectra, our hybrid model cannot describe the rapidity distributions of pions. The model should be improved by taking into consideration viscosity effects at the hydrodynamical stage of system evolution.

  20. Four years of meteor spectra patrol

    NASA Technical Reports Server (NTRS)

    Harvey, G. A.

    1974-01-01

    The development of the NASA-Langley Research Center meteor spectra patrol is described in general terms. The recording of very faint meteors was made possible by three great strides in optical and photographic technology in the 1960's: (1) the availability of optical-grade fused silica at modest cost, (2) the development of large transmission gratings with high blaze efficiency, and (3) the development of a method for avoiding plate fogging due to background skylight, which consisted of using a photoelectric meteor detector which actuates the spectrograph shutter when a meteor occurs in the field. The classification scheme for meteor spectra developed by Peter M. Millman is described.

  1. Micro-Raman spectra of ugrandite garnet.

    PubMed

    Moroz, T; Ragozin, A; Salikhov, D; Belikova, G; Puchkov, V; Kagi, H

    2009-08-01

    The natural garnets from chromite ores associated with pegmatoid pyroxenites of Sangalyk area (Uchaly ore district, southern Urals, Russia) were studied by means of micro-Raman spectroscopy. The compositions of these garnets were close to ugrandite, an isomorphous intermediate group of uvarovite-grossularite-andradite, X(3)Y(2)(SiO(4))(3), X = Ca(2+), Y = Al(3+), Fe(3+), Cr(3+), according to Raman spectra and X-ray microprobe analyses. An assignment of most of the observed bands in visible and near infrared Raman spectra is reported.

  2. Micro-Raman spectra of ugrandite garnet

    NASA Astrophysics Data System (ADS)

    Moroz, T.; Ragozin, A.; Salikhov, D.; Belikova, G.; Puchkov, V.; Kagi, H.

    2009-08-01

    The natural garnets from chromite ores associated with pegmatoid pyroxenites of Sangalyk area (Uchaly ore district, southern Urals, Russia) were studied by means of micro-Raman spectroscopy. The compositions of these garnets were close to ugrandite, an isomorphous intermediate group of uvarovite-grossularite-andradite, X 3Y 2(SiO 4) 3, X = Ca 2+, Y = Al 3+, Fe 3+, Cr 3+, according to Raman spectra and X-ray microprobe analyses. An assignment of most of the observed bands in visible and near infrared Raman spectra is reported.

  3. Gravitational effects on planetary neutron flux spectra

    NASA Astrophysics Data System (ADS)

    Feldman, W. C.; Drake, D. M.; O'dell, R. D.; Brinkley, F. W.; Anderson, R. C.

    1989-01-01

    The effects of gravity on the planetary neutron flux spectra for planet Mars, and the lifetime of the neutron, were investigated using a modified one-dimensional diffusion accelerated neutral-particle transport code, coupled with a multigroup cross-section library tailored specifically for Mars. The results showed the presence of a qualitatively new feature in planetary neutron leakage spectra in the form of a component of returning neutrons with kinetic energies less than the gravitational binding energy (0.132 eV for Mars). The net effect is an enhancement in flux at the lowest energies that is largest at and above the outermost layer of planetary matter.

  4. Algorithms for classification of astronomical object spectra

    NASA Astrophysics Data System (ADS)

    Wasiewicz, P.; Szuppe, J.; Hryniewicz, K.

    2015-09-01

    Obtaining interesting celestial objects from tens of thousands or even millions of recorded optical-ultraviolet spectra depends not only on the data quality but also on the accuracy of spectra decomposition. Additionally rapidly growing data volumes demands higher computing power and/or more efficient algorithms implementations. In this paper we speed up the process of substracting iron transitions and fitting Gaussian functions to emission peaks utilising C++ and OpenCL methods together with the NOSQL database. In this paper we implemented typical astronomical methods of detecting peaks in comparison to our previous hybrid methods implemented with CUDA.

  5. Parallel Genetic Algorithm for Alpha Spectra Fitting

    NASA Astrophysics Data System (ADS)

    García-Orellana, Carlos J.; Rubio-Montero, Pilar; González-Velasco, Horacio

    2005-01-01

    We present a performance study of alpha-particle spectra fitting using parallel Genetic Algorithm (GA). The method uses a two-step approach. In the first step we run parallel GA to find an initial solution for the second step, in which we use Levenberg-Marquardt (LM) method for a precise final fit. GA is a high resources-demanding method, so we use a Beowulf cluster for parallel simulation. The relationship between simulation time (and parallel efficiency) and processors number is studied using several alpha spectra, with the aim of obtaining a method to estimate the optimal processors number that must be used in a simulation.

  6. Thermal Emission and Reflected Light Spectra of Super Earths with Flat Transmission Spectra

    NASA Astrophysics Data System (ADS)

    Morley, Caroline V.; Fortney, Jonathan J.; Marley, Mark S.; Zahnle, Kevin; Line, Michael; Kempton, Eliza; Lewis, Nikole; Cahoy, Kerri

    2015-12-01

    Planets larger than Earth and smaller than Neptune are some of the most numerous in the galaxy, but observational efforts to understand this population have proved challenging because optically thick clouds or hazes at high altitudes obscure molecular features. We present models of super Earths that include thick clouds and hazes and predict their transmission, thermal emission, and reflected light spectra. Very thick, lofted clouds of salts or sulfides in high metallicity (1000× solar) atmospheres create featureless transmission spectra in the near-infrared. Photochemical hazes with a range of particle sizes also create featureless transmission spectra at lower metallicities. Cloudy thermal emission spectra have muted features more like blackbodies, and hazy thermal emission spectra have emission features caused by an inversion layer at altitudes where the haze forms. Close analysis of reflected light from warm (˜400-800 K) planets can distinguish cloudy spectra, which have moderate albedos (0.05-0.20), from hazy models, which are very dark (0.0-0.03). Reflected light spectra of cold planets (˜200 K) accessible to a space-based visible light coronagraph will have high albedos and large molecular features that will allow them to be more easily characterized than the warmer transiting planets. We suggest a number of complementary observations to characterize this population of planets, including transmission spectra of hot (≳ 1000 K) targets, thermal emission spectra of warm targets using the James Webb Space Telescope, high spectral resolution (R ˜ 105) observations of cloudy targets, and reflected light spectral observations of directly imaged cold targets. Despite the dearth of features observed in super Earth transmission spectra to date, different observations will provide rich diagnostics of their atmospheres.

  7. THE OPTICALLY UNBIASED GRB HOST (TOUGH) SURVEY. VI. RADIO OBSERVATIONS AT z {approx}< 1 AND CONSISTENCY WITH TYPICAL STAR-FORMING GALAXIES

    SciTech Connect

    Michalowski, M. J.; Dunlop, J. S.; Kamble, A.; Kaplan, D. L.; Hjorth, J.; Malesani, D.; Fynbo, J. P. U.; Kruehler, T.; Reinfrank, R. F.; Bonavera, L.; Ibar, E.; Garrett, M. A.; Jakobsson, P.; Levan, A. J.; Massardi, M.; Pal, S.; Sollerman, J.; Tanvir, N. R.; Van der Horst, A. J.; and others

    2012-08-20

    The objective of this paper is to determine the level of obscured star formation activity and dust attenuation in a sample of gamma-ray burst (GRB) hosts, and to test the hypothesis that GRB hosts have properties consistent with those of the general star-forming galaxy populations. We present a radio continuum survey of all z < 1 GRB hosts in The Optically Unbiased GRB Host (TOUGH) sample supplemented with radio data for all (mostly pre-Swift) GRB-SN hosts discovered before 2006 October. We present new radio data for 22 objects and have obtained a detection for three of them (GRB 980425, 021211, 031203; none in the TOUGH sample), increasing the number of radio-detected GRB hosts from two to five. The star formation rate (SFR) for the GRB 021211 host of {approx}825 M{sub Sun} yr{sup -1}, the highest ever reported for a GRB host, places it in the category of ultraluminous infrared galaxies. We found that at least {approx}63% of GRB hosts have SFR < 100 M{sub Sun} yr{sup -1} and at most {approx}8% can have SFR > 500 M{sub Sun} yr{sup -1}. For the undetected hosts the mean radio flux (<35 {mu}Jy 3{sigma}) corresponds to an average SFR < 15 M{sub Sun} yr{sup -1}. Moreover, {approx}> 88% of the z {approx}< 1 GRB hosts have ultraviolet dust attenuation A{sub UV} < 6.7 mag (visual attenuation A{sub V} < 3 mag). Hence, we did not find evidence for large dust obscuration in a majority of GRB hosts. Finally, we found that the distributions of SFRs and A{sub UV} of GRB hosts are consistent with those of Lyman break galaxies, H{alpha} emitters at similar redshifts, and of galaxies from cosmological simulations. The similarity of the GRB population with other star-forming galaxies is consistent with the hypothesis that GRBs, a least at z {approx}< 1, trace a large fraction of all star formation, and are therefore less biased indicators than once thought.

  8. Unbiased millimeter-wave line surveys of TW Hya and V4046 Sgr: The enhanced C{sub 2}H and CN abundances of evolved protoplanetary disks

    SciTech Connect

    Kastner, Joel H.; Punzi, Kristina; Hily-Blant, Pierre; Forveille, Thierry

    2014-09-20

    We have conducted the first comprehensive millimeter-wave molecular emission line surveys of the evolved circumstellar disks orbiting the nearby, roughly solar-mass, pre-main-sequence (T Tauri) stars, TW Hya (D = 54 pc) and V4046 Sgr AB (D = 73 pc). Both disks are known to retain significant residual gaseous components despite the advanced ages of their host stars (∼8 Myr and ∼21 Myr, respectively). Our unbiased broadband radio spectral surveys of the TW Hya and V4046 Sgr disks were performed with the Atacama Pathfinder Experiment 12 m telescope, and are intended to yield a complete census of the bright molecular emission lines in the range 275-357 GHz (1.1-0.85 mm). We find that lines of {sup 12}CO, {sup 13}CO, HCN, CN, and C{sub 2}H, all of which lie in the higher frequency (>330 GHz) range, constitute the strongest molecular emission from both disks in the spectral region surveyed. The molecule C{sub 2}H is detected here for the first time in both disks, as is CS in the TW Hya disk. The survey results also include the first measurements of the full suite of the hyperfine transitions of CN N = 3 → 2 and C{sub 2}H N = 4 → 3 in both disks. Modeling of these CN and C{sub 2}H hyperfine complexes in the spectrum of TW Hya indicates that the emission from both species is optically thick and may originate from very cold (≲10 K) disk regions. The latter result, if confirmed, would suggest the efficient production of CN and C{sub 2}H in the outer disk and/or near the disk midplane. It furthermore appears that the fractional abundances of CN and C{sub 2}H are significantly enhanced in these evolved protoplanetary disks, relative to the fractional abundances of the same molecules in the environments of deeply embedded protostars. These results, combined with previous determinations of the enhanced abundances of other species (such as HCO{sup +}) in T Tauri star disks, underscore the importance of properly accounting for high-energy (FUV and X-ray) radiation from

  9. Fourier smoothing of digital photographic spectra

    NASA Astrophysics Data System (ADS)

    Anupama, G. C.

    1990-03-01

    Fourier methods of smoothing one-dimensional data are discussed with particular reference to digital photographic spectra. Data smoothed using lowpass filters with different cut-off frequencies are intercompared. A method to scale densities in order to remove the dependence of grain noise on density is described. Optimal filtering technique which models signal and noise in Fourier domain is also explained.

  10. Rotational and Vibrational Spectra of Molecular Clusters.

    DTIC Science & Technology

    1986-06-30

    3 I D ’- 2095 205 209 2105 i k (c),,.-..0 WavenumbersHCN/Av ixture .Pekarlbld asM -mnmr dmr 6 9014 CARS spectra ofthe v, region of HCN in...shown above, the bond stretching constants below the structure. Values shown in parentheses were held fixed. %% -.. .4 .. 0 Table 8 Sumawy of norma

  11. Laboratory millimeter and submillimeter spectra of CO/+/

    NASA Technical Reports Server (NTRS)

    Sastry, K. V. L. N.; Helminger, P.; Herbst, E.; De Lucia, F. C.

    1981-01-01

    The strong electric dipole-allowed transitions of the molecular ion CO(+) in the region 235-470 GHz have been measured in the laboratory. The laboratory spectra at 235 GHz appear to confirm the claim by Erickson et al. (1981) to have observed CO(+) in OMC-1.

  12. Principal component analysis of phenolic acid spectra

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenolic acids are common plant metabolites that exhibit bioactive properties and have applications in functional food and animal feed formulations. The ultraviolet (UV) and infrared (IR) spectra of four closely related phenolic acid structures were evaluated by principal component analysis (PCA) to...

  13. Variations on supersymmetry breaking and neutrino spectra

    SciTech Connect

    Borzumati, F.; Hamaguchi, K.; Nomura, Y.; Yanagida, T.

    2000-12-11

    The problem of generating light neutrinos within supersymmetric models is discussed. It is shown that the hierarchy of scales induced by supersymmetry breaking can give rise to suppression factors of the correct order of magnitude to produce experimentally allowed neutrino spectra.

  14. Chaotic spectra: How to extract dynamic information

    SciTech Connect

    Taylor, H.S.; Gomez Llorente, J.M.; Zakrzewski, J.; Kulander, K.C.

    1988-10-01

    Nonlinear dynamics is applied to chaotic unassignable atomic and molecular spectra with the aim of extracting detailed information about regular dynamic motions that exist over short intervals of time. It is shown how this motion can be extracted from high resolution spectra by doing low resolution studies or by Fourier transforming limited regions of the spectrum. These motions mimic those of periodic orbits (PO) and are inserts into the dominant chaotic motion. Considering these inserts and the PO as a dynamically decoupled region of space, resonant scattering theory and stabilization methods enable us to compute ladders of resonant states which interact with the chaotic quasi-continuum computed in principle from basis sets placed off the PO. The interaction of the resonances with the quasicontinuum explains the low resolution spectra seen in such experiments. It also allows one to associate low resolution features with a particular PO. The motion on the PO thereby supplies the molecular movements whose quantization causes the low resolution spectra. Characteristic properties of the periodic orbit based resonances are discussed. The method is illustrated on the photoabsorption spectrum of the hydrogen atom in a strong magnetic field and on the photodissociation spectrum of H/sub 3//sup +/. Other molecular systems which are currently under investigation using this formalism are also mentioned. 53 refs., 10 figs., 2 tabs.

  15. Correlation Functions Aid Analyses Of Spectra

    NASA Technical Reports Server (NTRS)

    Beer, Reinhard; Norton, Robert H., Jr.

    1989-01-01

    New uses found for correlation functions in analyses of spectra. In approach combining elements of both pattern-recognition and traditional spectral-analysis techniques, spectral lines identified in data appear useless at first glance because they are dominated by noise. New approach particularly useful in measurement of concentrations of rare species of molecules in atmosphere.

  16. EEG Power Spectra of Adolescent Poor Readers.

    ERIC Educational Resources Information Center

    Ackerman, Peggy T.; McPherson, W. Brian; Oglesby, D. Michael; Dykman, Roscoe A.

    1998-01-01

    Electroencephalographic power spectra were studied in two poor-reading adolescent groups (n=38), dysphonetic and phonetic. Significant Group x Hemisphere effects were found in the alpha and beta bands, with the phonetic group showing right greater than left asymmetry. Results suggest more circumscribed and mature processing in the phonetically…

  17. Discriminating Dysarthria Type from Envelope Modulation Spectra

    ERIC Educational Resources Information Center

    Liss, Julie M.; LeGendre, Sue; Lotto, Andrew J.

    2010-01-01

    Purpose: Previous research demonstrated the ability of temporally based rhythm metrics to distinguish among dysarthrias with different prosodic deficit profiles (J. M. Liss et al., 2009). The authors examined whether comparable results could be obtained by an automated analysis of speech envelope modulation spectra (EMS), which quantifies the…

  18. Prompt fission neutron spectra of actinides

    DOE PAGES

    Capote, R.; Chen, Y. -J.; Hambsch, F. -J.; ...

    2016-01-06

    Here, the energy spectrum of prompt neutrons emitted in fission (PFNS) plays a very important role in nuclear science and technology. A Coordinated Research Project (CRP) "Evaluation of Prompt Fission Neutron Spectra of Actinides" was established by the IAEA Nuclear Data Section in 2009, with the major goal to produce new PFNS evaluations with uncertainties for actinide nuclei.

  19. Spectra of Angrites and Possible Parent Bodies

    NASA Technical Reports Server (NTRS)

    Burbine, T. H.; McCoy, T. J.; Binzel, R. P.

    2001-01-01

    One meteorite class where very little progress has been made in identifying possible parent bodies is the angrites. We have obtained spectra of two new angrites (D'Orbigny and Sahara 99555). Additional information is contained in the original extended abstract.

  20. Calculated late time spectra of supernovae

    SciTech Connect

    Axelrod, T.S.

    1987-10-30

    We consider here the nebular phase spectra of supernovae whose late time luminosity is provided by the radioactive decay of /sup 56/Ni and /sup 56/Co synthesized in the explosion. A broad variety of supernovae are known or suspected to fall in this category. This includes all SNIa and SNIb, and at least some SNII, in particular SN1987a. At sufficiently late times the expanding supernova becomes basically nebular in character due to its decreasing optical depth. The spectra produced during this stage contain information on the density and abundance structure of the entire supernova, as opposed to spectra near maximum light which are affected only by the outermost layers. A numerical model for nebular spectrum formation is therefore potentially very valuable for answering currently outstanding questions about the post-explosion supernova structure. As an example, we can hope to determine the degree of mixing which occurs between the layers of the ''onion-skin'' abundance structure predicted by current one dimensional explosion calculations. In the sections which follow, such a numerical model is briefly described and then applied to SN1972e, a typical SNIa, SN1985f, an SNIb, and finally to SN1987a. In the case of SN1987a predicted spectra are presented for the wavelength range from 1 to 100 microns at a time 300 days after explosion. 18 refs., 6 figs.

  1. Astronomy Spectra Experiment for Nonscience Students.

    ERIC Educational Resources Information Center

    Kaufman, S. E.

    1982-01-01

    An experimental technique to develop inferential thinking in less scientifically-oriented community college students is described. Students activate unlabeled gas discharge tubes and identify the gases by comparing color photographs with spectrometer observations. Includes methods for taking color photographs of spectra. (SK)

  2. Students' Mental Models of Atomic Spectra

    ERIC Educational Resources Information Center

    Körhasan, Nilüfer Didis; Wang, Lu

    2016-01-01

    Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…

  3. Automatic Spike Removal Algorithm for Raman Spectra.

    PubMed

    Tian, Yao; Burch, Kenneth S

    2016-11-01

    Raman spectroscopy is a powerful technique, widely used in both academia and industry. In part, the technique's extensive use stems from its ability to uniquely identify and image various material parameters: composition, strain, temperature, lattice/excitation symmetry, and magnetism in bulk, nano, solid, and organic materials. However, in nanomaterials and samples with low thermal conductivity, these measurements require long acquisition times. On the other hand, charge-coupled device (CCD) detectors used in Raman microscopes are vulnerable to cosmic rays. As a result, many spurious spikes occur in the measured spectra, which can distort the result or require the spectra to be ignored. In this paper, we outline a new method that significantly improves upon existing algorithms for removing these spikes. Specifically, we employ wavelet transform and data clustering in a new spike-removal algorithm. This algorithm results in spike-free spectra with negligible spectral distortion. The reduced dependence on the selection of wavelets and intuitive wavelet coefficient adjustment strategy enables non-experts to employ these powerful spectra-filtering techniques.

  4. Temporal Evolution of Solar Energetic Particle Spectra

    NASA Astrophysics Data System (ADS)

    Doran, Donald J.; Dalla, Silvia

    2016-08-01

    During solar flares and coronal mass ejections, Solar Energetic Particles (SEPs) may be released into the interplanetary medium and near-Earth locations. The energy spectra of SEP events at 1 AU are typically averaged over the entire event or studied in a few snapshots. In this article we analyze the time evolution of the energy spectra of four large selected SEP events using a large number of snapshots. We use a multi-spacecraft and multi-instrument approach for the observations, obtained over a wide SEP energy range. We find large differences in the spectra at the beginning of the events as measured by different instruments. We show that over time, a wave-like structure is observed traveling through the spectra from the highest energies to the lowest energies, creating an "arch" shape that then straightens into a power law later in the event, after times on the order of 10 hours. We discuss the processes that determine SEP intensities and their role in shaping the spectral time evolution.

  5. Solar Energetic Particle Spectra Measured with PAMELA

    NASA Astrophysics Data System (ADS)

    Ryan, James; Bruno, Alessandro; Boezio, Mirko; Bravar, Ulisse; Christian, Eric; Georgia, De Nolfo; Martucci, Matteo; Merge, Matteo; Munini, Riccardo; Sparvoli, Roberta; Stochaj, Steven; Pamela Collaboration

    2017-01-01

    We have measured the event integrated spectra from several SEP events from 2006 to 2014 in the energy range starting at 80 MeV and extending well above the neutron monitor threshold. The PAMELA instrument is in a high inclination, low Earth orbit and has access to SEPs when at high geographic latitudes. This means that the spectra have been assembled from regularly spaced measurements with gaps during the course of the event. Furthermore, the field of view of PAMELA is small and during the high latitude passes it scans a wide range of asymptotic directions as the spacecraft moves. Correcting for data gaps and solid angle effects, we have compiled event-integrated intensity spectra that typically exhibit power law shapes in energy with an exponential roll over. The events analyzed include two, maybe three, GLEs. In those cases the roll over energy lies above the neutron monitor threshold (1 GV) while the others are lower. We see no qualitative difference between the spectra of GLE vs. non-GLE events. National Science Foundation, NASA, Italian Space Agency, Russian Space Agency.

  6. Mid-infrared spectra of comet nuclei

    NASA Astrophysics Data System (ADS)

    Kelley, Michael S. P.; Woodward, Charles E.; Gehrz, Robert D.; Reach, William T.; Harker, David E.

    2017-03-01

    Comet nuclei and D-type asteroids have several similarities at optical and near-IR wavelengths, including near-featureless red reflectance spectra, and low albedos. Mineral identifications based on these characteristics are fraught with degeneracies, although some general trends can be identified. In contrast, spectral emissivity features in the mid-infrared provide important compositional information that might not otherwise be achievable. Jovian Trojan D-type asteroids have emissivity features strikingly similar to comet comae, suggesting that they have the same compositions and that the surfaces of the Trojans are highly porous. However, a direct comparison between a comet and asteroid surface has not been possible due to the paucity of spectra of comet nuclei at mid-infrared wavelengths. We present 5-35 μm thermal emission spectra of comets 10P/Tempel 2, and 49P/Arend-Rigaux observed with the Infrared Spectrograph on the Spitzer Space Telescope. Our analysis reveals no evidence for a coma or tail at the time of observation, suggesting the spectra are dominated by the comet nucleus. We fit each spectrum with the near-Earth asteroid thermal model (NEATM) and find sizes in agreement with previous values. However, the NEATM beaming parameters of the nuclei, 0.74-0.83, are systematically lower than the Jupiter-family comet population mean of 1.03 ± 0.11, derived from 16- and 22-μm photometry. We suggest this may be either an artifact of the spectral reduction, or the consequence of an emissivity low near 16 μm. When the spectra are normalized by the NEATM model, a weak 10-μm silicate plateau is evident, with a shape similar to those seen in mid-infrared spectra of D-type asteroids. A silicate plateau is also evident in previously published Spitzer spectra of the nucleus of comet 9P/Tempel 1. We compare, in detail, these comet nucleus emission features to those seen in spectra of the Jovian Trojan D-types (624) Hektor, (911) Agamemnon, and (1172) Aneas, as well

  7. Raman spectra of carotenoids in natural products

    NASA Astrophysics Data System (ADS)

    Withnall, Robert; Chowdhry, Babur Z.; Silver, Jack; Edwards, Howell G. M.; de Oliveira, Luiz F. C.

    2003-08-01

    Resonance Raman spectra of naturally occurring carotenoids have been obtained from nautilus, periwinkle ( Littorina littorea) and clam shells under 514.5 nm excitation and these spectra are compared with the resonance Raman spectra obtained in situ from tomatoes, carrots, red peppers and saffron. The tomatoes, carrots and red peppers gave rise to resonance Raman spectra exhibiting a ν1 band at ca. 1520 cm -1, in keeping with its assignment to carotenoids with ca. nine conjugated carboncarbon double bonds in their main chains, whereas the resonance Raman spectrum of saffron showed a ν1 band at 1537 cm -1 which can be assigned to crocetin, having seven conjugated carboncarbon double bonds. A correlation between ν1 wavenumber location and effective conjugated chain length has been used to interpret the data obtained from the shells, and the wavenumber position (1522 cm -1) of the ν1 band of the carotenoid in the orange clam shell suggests that it contains nine conjugated double bonds in the main chain. However, the black periwinkle and nautilus shells exhibit ν1 bands at 1504 and 1496 cm -1, respectively. On the basis of the correlation between ν1 wavenumber location and effective conjugated chain length, this indicates that they contain carotenoids with longer conjugated chains, the former having ca. 11 double bonds and the latter ca. 13 or even more. Raman spectra of the nautilus, periwinkle and clam shells also exhibited a strong band at 1085 cm -1 and a doublet with components at 701 and 705 cm -1, which can be assigned to biogenic calcium carbonate in the aragonite crystallographic form.

  8. An Interactive Gallery of Planetary Nebula Spectra

    NASA Astrophysics Data System (ADS)

    Kwitter, K. B.; Henry, R. B. C.

    2002-12-01

    We have created a website containing high-quality moderate-resolution spectra of 88 planetary nebulae (PNe) from 3600 to 9600 Å, obtained at KPNO and CTIO. Spectra are displayed in a zoomable window, and there are templates available that show wavelength and ion identifications. In addition to the spectra themselves, the website also contains a brief discussion of PNe as astronomical objects and as contributors to our understanding of stellar evolution, and a table with atlas information for each object along with a link to an image. This table can be re-ordered by object name, galactic or equatorial coordinates, distance from the sun, the galactic center, or the galactic plane. We envision that this website, which concentrates a large amount of data in one place, will be of interest to a variety of users. PN researchers might need to check the spectrum of a particular object of interest; the non-specialist astronomer might simply be interested in perusing such a collection of spectra; and finally, teachers of introductory astronomy can use this database to illustrate basic principles of atomic physics and radiation. To encourage such use, we have written two simple exercises at a basic level to introduce beginning astronomy students to the wealth of information that PN spectra contain. We are grateful to Adam Wang of the Williams College OIT and to his summer student teams who worked on various apects of the implementation of this website. This work has been supported by NSF grant AST-9819123 and by Williams College and the University of Oklahoma.

  9. EMPCA and Cluster Analysis of Quasar Spectra: Construction and Application to Simulated Spectra

    NASA Astrophysics Data System (ADS)

    Marrs, Adam; Leighly, Karen; Wagner, Cassidy; Macinnis, Francis

    2017-01-01

    Quasars have complex spectra with emission lines influenced by many factors. Therefore, to fully describe the spectrum requires specification of a large number of parameters, such as line equivalent width, blueshift, and ratios. Principal Component Analysis (PCA) aims to construct eigenvectors-or principal components-from the data with the goal of finding a few key parameters that can be used to predict the rest of the spectrum fairly well. Analysis of simulated quasar spectra was used to verify and justify our modified application of PCA.We used a variant of PCA called Weighted Expectation Maximization PCA (EMPCA; Bailey 2012) along with k-means cluster analysis to analyze simulated quasar spectra. Our approach combines both analytical methods to address two known problems with classical PCA. EMPCA uses weights to account for uncertainty and missing points in the spectra. K-means groups similar spectra together to address the nonlinearity of quasar spectra, specifically variance in blueshifts and widths of the emission lines.In producing and analyzing simulations, we first tested the effects of varying equivalent widths and blueshifts on the derived principal components, and explored the differences between standard PCA and EMPCA. We also tested the effects of varying signal-to-noise ratio. Next we used the results of fits to composite quasar spectra (see accompanying poster by Wagner et al.) to construct a set of realistic simulated spectra, and subjected those spectra to the EMPCA /k-means analysis. We concluded that our approach was validated when we found that the mean spectra from our k-means clusters derived from PCA projection coefficients reproduced the trends observed in the composite spectra.Furthermore, our method needed only two eigenvectors to identify both sets of correlations used to construct the simulations, as well as indicating the linear and nonlinear segments. Comparing this to regular PCA, which can require a dozen or more components, or to

  10. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  11. Automated analysis of slitless spectra - Stars

    NASA Astrophysics Data System (ADS)

    Beauchemin, M.; Borra, E. F.; Levesque, S.

    1991-09-01

    The stellar spectral classification that can be achieved with very low-dispersion spectroscopy is examined. Several methods are applied to slitless spectra taken from the automated grens plates analysis project undertaken at Laval University. It is suggested that an accuracy in B - V of about 0.1 mag at B approximating 19 for stars bluer than B - V below 0.8 mag or better for redder stars can be obtained by probing the continuum. Results from DDO-like photometry show that grens data behave similarly to the Gunn and Stryker library of standard stars for many indices. Results of multivariate analysis are coherent with the stellar spectral classification and provide a powerful and objective means of cataloging spectra of the same spectral shape.

  12. High resolution derivative spectra in remote sensing

    NASA Technical Reports Server (NTRS)

    Demetriades-Shah, Tanvir H.; Steven, Michael D.; Clark, Jeremy A.

    1990-01-01

    The use of derivative spectra is an established technique in analytical chemistry for the elimination of background signals and for resolving overlapping spectral features. Application of this technique for tackling analogous problems such as interference from soil background reflectance in the remote sensing of vegetation or for resolving complex spectra of several target species within individual pixels in remote sensing is proposed. Methods for generating derivatives of high spectral resolution data are reviewed. Results of experiments to test the use of derivatives for monitoring chlorosis in vegetation show that derivative spectral indices are superior to conventional broad-band spectral indices such as the near-infrared/red reflectance ratio. Conventional broad-band indices are sensitive to both leaf cover as well as leaf color. New derivative spectral indices which were able to monitor chlorosis unambiguously were identified. Potential areas for the application of this technique in remote sensing are considered.

  13. Vibrational Spectra of Hydrolysed Triethoxysilane on Germania

    NASA Astrophysics Data System (ADS)

    Anabtawi, Sami; Mallik, Robert

    1996-04-01

    Hydrolysed triethoxysilane (TES) monolayers are introduced onto ultra-thin (of order 1.5 nm) and relatively hydrogern-free sputtered germania films. Two methods are used to dope the germania surface: (i) from TES vapor under a water vapor/nitrogen atmosphere, and (ii) from aqueous acidic hydrolysed TES solution. Vibrational Spectra obtained using these two methods are similar; in both cases Si-H stretching and bending modes are present at approximately 2000 - 2200, and 900 wavenumbers respectively, together with broad Si-O-Si symmetric and asymmetric stretching peaks centered at 700 and 1100 wavenumbers respectively. Only very weak features due to residual CH species are present indicating a large degree of hydrolysis in both cases. All spectra obtained closely resemble those of hydrogenated amorphous silicon monoxide films, confirming that a polysiloxane matrix is present.

  14. Cathodoluminescence spectra of gallium nitride nanorods

    PubMed Central

    2011-01-01

    Gallium nitride [GaN] nanorods grown on a Si(111) substrate at 720°C via plasma-assisted molecular beam epitaxy were studied by field-emission electron microscopy and cathodoluminescence [CL]. The surface topography and optical properties of the GaN nanorod cluster and single GaN nanorod were measured and discussed. The defect-related CL spectra of GaN nanorods and their dependence on temperature were investigated. The CL spectra along the length of the individual GaN nanorod were also studied. The results reveal that the 3.2-eV peak comes from the structural defect at the interface between the GaN nanorod and Si substrate. The surface state emission of the single GaN nanorod is stronger as the diameter of the GaN nanorod becomes smaller due to an increased surface-to-volume ratio. PMID:22168896

  15. Energy spectra in elasto-inertial turbulence

    NASA Astrophysics Data System (ADS)

    Valente, P. C.; da Silva, C. B.; Pinho, F. T.

    2016-07-01

    Direct numerical simulations of statistically steady homogeneous isotropic turbulence in viscoelastic fluids described by the FENE-P model are presented. Emphasis is given to large polymer relaxation times compared to the eddy turnover time, which is a regime recently termed elasto-inertial turbulence. In this regime the polymers are ineffective in dissipating kinetic energy but they play a lead role in transferring kinetic energy to the small solvent scales which turns out to be concomitant with the depletion of the usual non-linear energy cascade. However, we show that the non-linear interactions are still highly active, but they lead to no net downscale energy transfer because the forward and reversed energy cascades are nearly balanced. Finally, we show that the tendency for a steeper elasto-inertial power-law spectra is reversed for large polymer relaxation times and the spectra tend towards the usual k-5/3 functional form.

  16. Terahertz-sideband spectra involving Kapteyn series

    NASA Astrophysics Data System (ADS)

    Lerche, Ian; Tautz, Robert C.; Citrin, D. S.

    2009-09-01

    Kapteyn series of the second kind appear in models of even- and odd-order sideband spectra in the optical regime of a quantum system modulated by a high-frequency (e.g., terahertz) electromagnetic field (Citrin D S 1999 Phys. Rev. B 60 5659) and in certain time-periodic transport problems in superlattices (Ignatov A A and Romanov Y A 1976 Phys. Status Solidi b 73 327; Feise M W and Citrin D S 1999 Appl. Phys. Lett. 75 3536). This paper shows that both the even- and the odd-order Kapteyn series that appear can be summed in closed form, thereby allowing more transparent insight into the structural dependence of the sideband spectra and also providing an analytic control for the accuracy of numerical procedures designed to evaluate the series. The general method of analysis may also be of interest for other Kapteyn series.

  17. Analysis of spectra using correlation functions

    NASA Technical Reports Server (NTRS)

    Beer, Reinhard; Norton, Robert H.

    1988-01-01

    A novel method is presented for the quantitative analysis of spectra based on the properties of the cross correlation between a real spectrum and either a numerical synthesis or laboratory simulation. A new goodness-of-fit criterion called the heteromorphic coefficient H is proposed that has the property of being zero when a fit is achieved and varying smoothly through zero as the iteration proceeds, providing a powerful tool for automatic or near-automatic analysis. It is also shown that H can be rendered substantially noise-immune, permitting the analysis of very weak spectra well below the apparent noise level and, as a byproduct, providing Doppler shift and radial velocity information with excellent precision. The technique is in regular use in the Atmospheric Trace Molecule Spectroscopy (ATMOS) project and operates in an interactive, realtime computing environment with turn-around times of a few seconds or less.

  18. RADLite: Raytracer for infrared line spectra

    NASA Astrophysics Data System (ADS)

    Pontoppidan, Klaus; Dullemond, Kees

    2013-08-01

    RADLite is a raytracer that is optimized for producing infrared line spectra and images from axisymmetric density structures, originally developed to function on top of the dust radiative transfer code RADMC. RADLite can consistently deal with a wide range of velocity gradients, such as those typical for the inner regions of protoplanetary disks. The code is intended as a back-end for chemical and excitation codes, and can rapidly produce spectra of thousands of lines for grids of models for comparison with observations. It includes functionality for simulating telescopic images for optical/IR/midIR/farIR telescopes. It takes advantage of multi-threaded CPUs and includes an escape-probability non-LTE module.

  19. Bone densitometry using x-ray spectra.

    PubMed

    Krmar, M; Shukla, S; Ganezer, K

    2010-10-21

    In contrast to the two distinct energy regions that are involved in dual-energy x-ray absorptiometry for bone densitometry, the complete spectrum of a beam transmitted through two layers of different materials is utilized in this study to calculate the areal density of each material. Test objects constructed from aluminum and Plexiglas were used to simulate cortical bone and soft tissue, respectively. Solid-state HPGe (high-purity germanium) detectors provided high-resolution x-ray spectra over an energy range of approximately 20-80 keV. Areal densities were obtained from spectra using two methods: a system of equations for two spectral regions and a nonlinear fit of the entire spectrum. Good agreement with the known areal densities of aluminum was obtained over a wide range of PMMA thicknesses. The spectral method presented here can be used to decrease beam hardening at a small number of bodily points selected for examination.

  20. Creating semiconductor metafilms with designer absorption spectra

    PubMed Central

    Kim, Soo Jin; Fan, Pengyu; Kang, Ju-Hyung; Brongersma, Mark L.

    2015-01-01

    The optical properties of semiconductors are typically considered intrinsic and fixed. Here we leverage the rapid developments in the field of optical metamaterials to create ultrathin semiconductor metafilms with designer absorption spectra. We show how such metafilms can be constructed by placing one or more types of high-index semiconductor antennas into a dense array with subwavelength spacings. It is argued that the large absorption cross-section of semiconductor antennas and their weak near-field coupling open a unique opportunity to create strongly absorbing metafilms whose spectral absorption properties directly reflect those of the individual antennas. Using experiments and simulations, we demonstrate that near-unity absorption at one or more target wavelengths of interest can be achieved in a sub-50-nm-thick metafilm using judiciously sized and spaced Ge nanobeams. The ability to create semiconductor metafilms with custom absorption spectra opens up new design strategies for planar optoelectronic devices and solar cells. PMID:26184335

  1. Specific heat of multifractal energy spectra

    NASA Astrophysics Data System (ADS)

    da Silva, L. R.; Vallejos, R. O.; Tsallis, C.; Mendes, R. S.; Roux, S.

    2001-07-01

    Motivated by the self-similar character of energy spectra demonstrated for quasicrystals, we investigate the case of multifractal energy spectra, and compute the specific heat associated with simple archetypal forms of multifractal sets as generated by iterated maps. We considered the logistic map and the circle map at their threshold to chaos. Both examples show nontrivial structures associated with the scaling properties of their respective chaotic attractors. The specific heat displays generically log-periodic oscillations around a value that characterizes a single exponent, the ``fractal dimension,'' of the distribution of energy levels close to the minimum value set to 0. It is shown that when the fractal dimension and the frequency of log oscillations of the density of states are large, the amplitude of the resulting log oscillation in the specific heat becomes much smaller than the log-periodic oscillation measured on the density of states.

  2. Specific heat spectra for quasiperiodic ladder sequences

    NASA Astrophysics Data System (ADS)

    Moreira, D. A.; Albuquerque, E. L.; Bezerra, C. G.

    2006-12-01

    We performed a theoretical study of the specific heat C(T) as a function of the temperature for double-strand quasiperiodic sequences. To mimic DNA molecules, the sequences are made up from the nucleotides guanine G, adenine A, cytosine C and thymine T, arranged according to the Fibonacci and Rudin-Shapiro quasiperiodic sequences. The energy spectra are calculated using the two-dimensional Schrödinger equation, in a tight-binding approximation, with the on-site energy exhibiting long-range disorder and non-random hopping amplitudes. We compare the specific heat features of these quasiperiodic artificial sequences to the spectra considering a segment of the first sequenced human chromosome 22 (Ch22), a real genomic DNA sequence.

  3. Neutron Spectra in a 15 MV LINAC

    SciTech Connect

    Vega-Carrillo, H. R.; Chu, Wei-Han; Tung, Chuan-Jong; Lan, Jen-Hong

    2010-12-07

    Neutron spectra were calculated inside the treatment hall of a 15 MV LINAC, calculations were carried out using Monte Carlo methods. With a Bonner sphere spectrometer with pairs of thermoluminiscent dosimeters the neutron spectrum at 100 cm from the isocenter was measured and compared with the calculated spectrum. All the spectra in the treatment hall show the presence of evaporation and knock-on neutrons; also the room-return due to the hall features is shown. In the maze the large contribution are due to epithermal and thermal neutrons. A good agreement between the calculated and measured spectrum at 100 cm was noticed, from this comparison the differences are attributed to the water content in the concrete of the hall.

  4. Measurement and interpretation of plutonium spectra

    SciTech Connect

    Blaise, J.; Fred, M.S.; Carnall, W.T.; Crosswhite, H.M.; Crosswhite, H.

    1982-01-01

    The atomic spectroscopic data available for plutonium are among the rickest of any in the periodic system. They include high-resolution grating and Fourier-transform spectra as well as extensive Zeeman and isotope-shift studies. We summarize the present status of the term analysis and cite the configurations that have been identified. A least-squares adjustment of a parametric Hamiltonian for configurations of both Pu I and Pu II has shown that almost all of the expected low levels are now known. The use of a model Hamiltonian applicable to both lanthanide and actinide atomic species has been applied to the low configurations of Pu I and Pu II making use of trends predicted by ab initio calculations. This same model has been used to describe the energy levels of Pu/sup 3 +/ in LaCl/sub 3/, and an extension has permitted preliminary calculations of the spectra of other valence states.

  5. Model atmospheres, predicted spectra, and colors

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Theoretical models of stellar atmospheres and the process of forming a spectrum are reviewed with particular reference to the spectra of B stars. In the case of classical models the stellar atmosphere is though to consist of plane parallel layers of gas in which radiative and hydrostatic equilibrium exists. No radiative energy is lost or gained in the model atmosphere, but the detailed shape of the spectrum is changed as a result of the interactions with the ionized gas. Predicted line spectra using statistical equilibrium local thermodynamic equilibrium (LTE), and non-LTE physics are compared and the determination of abundances is discussed. The limitations of classical modeling are examined. Models developed to demonstrate what motions in the upper atmosphere will do to the spectrum and to explore the effects of using geometries different from plane parallel layer are reviewed. In particular the problem of radiative transfer is addressed.

  6. Cathodoluminescence spectra of gallium nitride nanorods.

    PubMed

    Tsai, Chia-Chang; Li, Guan-Hua; Lin, Yuan-Ting; Chang, Ching-Wen; Wadekar, Paritosh; Chen, Quark Yung-Sung; Rigutti, Lorenzo; Tchernycheva, Maria; Julien, François Henri; Tu, Li-Wei

    2011-12-14

    Gallium nitride [GaN] nanorods grown on a Si(111) substrate at 720°C via plasma-assisted molecular beam epitaxy were studied by field-emission electron microscopy and cathodoluminescence [CL]. The surface topography and optical properties of the GaN nanorod cluster and single GaN nanorod were measured and discussed. The defect-related CL spectra of GaN nanorods and their dependence on temperature were investigated. The CL spectra along the length of the individual GaN nanorod were also studied. The results reveal that the 3.2-eV peak comes from the structural defect at the interface between the GaN nanorod and Si substrate. The surface state emission of the single GaN nanorod is stronger as the diameter of the GaN nanorod becomes smaller due to an increased surface-to-volume ratio.

  7. Characteristics of magnetospheric radio noise spectra

    NASA Technical Reports Server (NTRS)

    Herman, J. R.

    1976-01-01

    Magnetospheric radio noise spectra (30 kHz to 10 MHz) taken by IMP-6 and RAE-2 exhibit time-varying characteristics which are related to spacecraft position and magnetospheric processes. In the mid-frequency range (100-1,000 kHz) intense noise peaks rise by a factor of 100 or more above background; 80% of the peak frequencies are within the band 125 kHz to 600 kHz, and the peak occurs most often (18% of the time) at 280 kHz. This intense mid-frequency noise has been detected at radial distances from 1.3 Re to 60 Re on all sides of the Earth during magnetically quiet as well as disturbed periods. Maximum occurrence of the mid-frequency noise is in the evening to midnight hours where splash-type energetic particle precipitation takes place. ""Magnetospheric lightning'' can be invoked to explain the spectral shape of the observed spectra.

  8. Knowledge Discovery in Mega-Spectra Archives

    NASA Astrophysics Data System (ADS)

    Škoda, P.; Bromová, P.; Lopatovsk'y, L.; Palička, A.; Vávzný, J.

    2015-09-01

    The recent progress of astronomical instrumentation resulted in the construction of multi-object spectrographs with hundreds to thousands of micro-slits or optical fibres allowing the acquisition of tens of thousands of spectra of celestial objects per observing night. Currently there are two spectroscopic surveys containing millions of spectra. These surveys are being processed by automatic pipelines, spectrum by spectrum, in order to estimate physical parameters of individual objects resulting in extensive catalogues, used typically to construct the better models of space-kinematic structure and evolution of the Universe or its subsystems. Such surveys are, however, very good source of homogenised, pre-processed data for application of machine learning techniques common in Astroinformatics. We present challenges of knowledge discovery in such surveys as well as practical examples of machine learning based on specific shapes of spectral features used in searching for new candidates of interesting astronomical objects, namely Be and B[e] stars and quasars.

  9. Reanalysis of Tyrannosaurus rex Mass Spectra.

    PubMed

    Bern, Marshall; Phinney, Brett S; Goldberg, David

    2009-09-01

    Asara et al. reported the detection of collagen peptides in a 68-million-year-old Tyrannosaurus rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.

  10. Dynamical analysis of highly excited molecular spectra

    SciTech Connect

    Kellman, M.E.

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  11. Ir spectra of preparations of ozonized pyrocatechin

    NASA Astrophysics Data System (ADS)

    Khovratovich, N. N.; Novikova, T. M.; Khmel'Nitskii, A. I.; Cherenkevich, S. N.; Loban, V. A.

    1998-03-01

    We investigate IR spectra of the solid phase of products obtained at different stages in the process of ozonizing aqueous solutions of pyrocatechin. We found that melanin structures are formed in the process of pyrocatechin ozonization. The existence of intra- and intermolecular interactions in the melanin preparations formed, leading to the formation of molecular associates, is shown. Thorough treatment of preparations with ozone leads to destruction of polymer systems and formation of water-soluble products of acid type.

  12. Understanding the baryon and meson spectra

    SciTech Connect

    Pennington, Michael R.

    2013-10-01

    A brief overview is given of what we know of the baryon and meson spectra, with a focus on what are the key internal degrees of freedom and how these relate to strong coupling QCD. The challenges, experimental, theoretical and phenomenological, for the future are outlined, with particular reference to a program at Jefferson Lab to extract hadronic states in which glue unambiguously contributes to their quantum numbers.

  13. Nebular spectra of pair-instability supernovae

    NASA Astrophysics Data System (ADS)

    Jerkstrand, A.; Smartt, S. J.; Heger, A.

    2016-01-01

    If very massive stars (M ≳ 100 M⊙) can form and avoid too strong mass-loss during their evolution, they are predicted to explode as pair-instability supernovae (PISNe). One critical test for candidate events is whether their nucleosynthesis yields and internal ejecta structure, being revealed through nebular-phase spectra at t ≳ 1 yr, match those of model predictions. Here, we compute theoretical spectra based on model PISN ejecta at 1-3 yr post-explosion to allow quantitative comparison with observations. The high column densities of PISNe lead to complete gamma-ray trapping for t ≳ 2 yr which, combined with fulfilled conditions of steady state, leads to bolometric supernova luminosities matching the 56Co decay. Most of the gamma-rays are absorbed by the deep-lying iron and silicon/sulphur layers. The ionization balance shows a predominantly neutral gas state, which leads to emission lines of Fe I, Si I, and S I. For low-mass PISNe, the metal core expands slowly enough to produce a forest of distinct lines, whereas high-mass PISNe expand faster and produce more featureless spectra. Line blocking is complete below ˜5000 Å for several years, and the model spectra are red. The strongest line is typically [Ca II] λλ7291, 7323, one of few lines from ionized species. We compare our models with proposed PISN candidates SN 2007bi and PTF12dam, finding discrepancies for several key observables and thus no support for a PISN interpretation. We discuss distinct spectral features predicted by the models, and the possibility of detecting pair-instability explosions among non-superluminous supernovae.

  14. Analysis of the IRAS Low Resolution Spectra

    DTIC Science & Technology

    1988-04-01

    which were previously not known. 1. RESEARCH The Infrared Astronomical Satellite , IRAS, surveyed the sky in four wavelength bands centered on 12, 25, 60...agree at 12 Am unless a linear baseline is subtracted from the usable portion of the spectrum. The IRAS science team characterized the LRS spectra...that have silicate dust grain emission features extending from about 8 -14 Am with a maximum around 10 Am are characterized as 2n where n= I to 9

  15. CUBISM: CUbe Builder for IRS Spectra Maps

    NASA Astrophysics Data System (ADS)

    Sings Irs Team; Smith, J. D.; Armus, Lee; Bot, Caroline; Buckalew, Brent; Dale, Danny; Helou, George; Jarrett, Tom; Roussel, Helene; Sheth, Kartik

    2011-11-01

    CUBISM, written in IDL, constructs spectral cubes, maps, and arbitrary aperture 1D spectral extractions from sets of mapping mode spectra taken with Spitzer's IRS spectrograph. CUBISM is optimized for non-sparse maps of extended objects, e.g. the nearby galaxy sample of SINGS, but can be used with data from any spectral mapping AOR (primarily validated for maps which are designed as suggested by the mapping HOWTO).

  16. Wavevector-Frequency Spectra of Nonhomogeneous Fields

    DTIC Science & Technology

    1987-01-22

    TITLE (Indud* Security Qasafication) WAVEVECTOR-FREQUENCY SPECTRA OF NONHOMOGENEOUS FIELDS 12. PERSONAL AUTHOR(S) Dr . Wayne A. Strawderman...SAME AS RPT. D DTIC USERS 22a. NAME OF RESPONSIBLE INDIVIDUAL Dr . Wayne A. Strawderman 21. ABSTRACT SECURITY CLASSIFICATION UNCLASSIFIED 22b.T...Program Element 62314N. The NUSC Project No. is B60010. Principal Investigator Dr . H. P. Bakewell, Jr., Code 2141. The Sponsoring Activity was the Office

  17. Simultaneous Confidence Bands for Autoregressive Spectra.

    DTIC Science & Technology

    1982-06-01

    CONFIDENCE BANDS FOR AUTOREGRESSIVE SPECTRA H. Joseph Newton Marcello Pagano Institute of Statistics Department of Biostatistics Texas A&M University...AUTHOR(4) 8. CONTRACT OR GRANT NUMIUER(a) H. Joseph Newton and Marcello Pagano ONR N00014-82-MP-2001 ARU DAAG 29-80-C-0070 0. PERFORMING ORGANIZATION NAME...Parzen (1974), Uirych and Bishop (1975), and Beamish and Priestley (1981), for example) despite 1) a continuing discussion of the problems of order

  18. Meteor spectra in the EDMOND database

    NASA Astrophysics Data System (ADS)

    Koukal, J.; Gorková, S.; Srba, J.; Ferus, M.; Civiš, S.; di Pietro, C. A.

    2015-01-01

    We present a selection of five interesting meteor spectra obtained in the years 2014 and 2015 via CCTV video systems with a holographic grating, working in CEMENT and BRAMON meteor observation networks. Based on the EDMOND multi stations video meteor trajectory data an orbital classification of these meteors was performed. Selected meteors are members of the LYR, SPE, DSA and LVI meteor streams, one meteor is classified as sporadic background (SPO). In calibrated spectra the main chemical components were identified. Meteors are chemically classified based on relative intensities of the main spectral lines (or multiplets): Mg I (2), Na I (1), and Fe I (15). Bolide EN091214 is linked with the 23rd meteorite with known orbit (informally known as "Žďár"), two fragments of the parent body were found in the Czech Republic so far (August, 2015). For this particular event a time resolved spectral observation and comparison with laboratory spectra of LL3.2 chondritic meteorite are presented.

  19. Infrared spectra of substituted polycylic aromatic hydrocarbons

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W. Jr; Hudgins, D. M.; Sandford, S. A.; Allamandola, L. J.

    1998-01-01

    Calculations are carried out using density functional theory (DFT) to determine the harmonic frequencies and intensities of 1-methylanthracene, 9-methylanthracene, 9-cyanoanthracene, 2-aminoanthracene, acridine, and their positive ions. The theoretical data are compared with matrix-isolation spectra for these species also reported in this work. The theoretical and experimental frequencies and relative intensities for the neutral species are in generally good agreement, whereas the positive ion spectra are only in qualitative agreement. Relative to anthracene, we find that substitution of a methyl or CN for a hydrogen does not significantly affect the spectrum other than to add the characteristic methyl C-H and C triple bond N stretches near 2900 and 2200 cm-1, respectively. However, addition of NH2 dramatically affects the spectrum of the neutral. Not only are the NH2 modes themselves strong, but this electron-withdrawing group induces sufficient partial charge on the ring to give the neutral molecule spectra characteristics of the anthracene cation. The sum of the absolute intensities is about four times larger for 2-aminoanthracene than those for 9-cyanoanthracene. Substituting nitrogen in the ring at the nine position (acridine) does not greatly alter the spectrum compared with anthracene.

  20. Analysis of positron lifetime spectra in polymers

    NASA Technical Reports Server (NTRS)

    Singh, Jag J.; Mall, Gerald H.; Sprinkle, Danny R.

    1988-01-01

    A new procedure for analyzing multicomponent positron lifetime spectra in polymers was developed. It requires initial estimates of the lifetimes and the intensities of various components, which are readily obtainable by a standard spectrum stripping process. These initial estimates, after convolution with the timing system resolution function, are then used as the inputs for a nonlinear least squares analysis to compute the estimates that conform to a global error minimization criterion. The convolution integral uses the full experimental resolution function, in contrast to the previous studies where analytical approximations of it were utilized. These concepts were incorporated into a generalized Computer Program for Analyzing Positron Lifetime Spectra (PAPLS) in polymers. Its validity was tested using several artificially generated data sets. These data sets were also analyzed using the widely used POSITRONFIT program. In almost all cases, the PAPLS program gives closer fit to the input values. The new procedure was applied to the analysis of several lifetime spectra measured in metal ion containing Epon-828 samples. The results are described.

  1. Janus spectra: cascades without local isotropy

    NASA Astrophysics Data System (ADS)

    Liu, Chien-Chia; Cerbus, Rory; Chakraborty, Pinaki

    2016-11-01

    Two-dimensional turbulent flows host two disparate cascades: of enstrophy and of energy. The phenomenological theory of turbulence, which provides the theoretical underpinning of these cascades, assumes local isotropy. This assumption has been amply verified via computational, experimental and field data amassed to date. Local isotropy mandates that the streamwise (u) and transverse (v) velocity fluctuations partake in the same cascade; consequently, the attendant spectral exponents (αu and αv) of the turbulent energy spectra are the same, αu =αv . Here we report experiments in soap-film flows where αu corresponds to the energy cascade, but concurrently αv corresponds to the enstrophy cascade, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Remarkably, the tools of phenomenological theory can be invoked to elucidate this manifestly anisotropic flow. Okinawa Institute of Science and Technology.

  2. IRAS Low Resolution Spectra of Asteroids

    NASA Technical Reports Server (NTRS)

    Cohen, Martin; Walker, Russell G.

    2002-01-01

    Optical/near-infrared studies of asteroids are based on reflected sunlight and surface albedo variations create broad spectral features, suggestive of families of materials. There is a significant literature on these features, but there is very little work in the thermal infrared that directly probes the materials emitting on the surfaces of asteroids. We have searched for and extracted 534 thermal spectra of 245 asteroids from the original Dutch (Groningen) archive of spectra observed by the IRAS Low Resolution Spectrometer (LRS). We find that, in general, the observed shapes of the spectral continua are inconsistent with that predicted by the standard thermal model used by IRAS. Thermal models such as proposed by Harris (1998) and Harris et al.(1998) for the near-earth asteroids with the "beaming parameter" in the range of 1.0 to 1.2 best represent the observed spectral shapes. This implies that the IRAS Minor Planet Survey (IMPS, Tedesco, 1992) and the Supplementary IMPS (SIMPS, Tedesco, et al., 2002) derived asteroid diameters are systematically underestimated, and the albedos are overestimated. We have tentatively identified several spectral features that appear to be diagnostic of at least families of materials. The variation of spectral features with taxonomic class hints that thermal infrared spectra can be a valuable tool for taxonomic classification of asteroids.

  3. Optical spectra analysis for breast cancer diagnostics

    NASA Astrophysics Data System (ADS)

    Belkov, S. A.; Kochemasov, G. G.; Lyubynskaya, T. E.; Maslov, N. V.; Nuzhny, A. S.; da Silva, L. B.; Rubenchik, A.

    2011-11-01

    Minimally invasive probe and optical biopsy system based on optical spectra recording and analysis seem to be a promising tool for early diagnostics of breast cancer. Light scattering and absorption spectra are generated continuously as far as the needle-like probe with one emitting and several collecting optical fibers penetrates through the tissues toward to the suspicious area. That allows analyzing not only the state of local site, but also the structure of tissues along the needle trace. The suggested method has the advantages of automated on-line diagnosing and minimal tissue destruction and in parallel with the conventional diagnostic procedures provides the ground for decision-making. 165 medical trials were completed in Nizhny Novgorod Regional Oncology Centre, Russia. Independent diagnoses were the results of fine biopsy and histology. Application of wavelet expansion and clasterization techniques for spectra analysis revealed several main spectral types for malignant and benign tumors. Automatic classification algorithm demonstrated specificity ˜90% and sensitivity ˜91%. Large amount of information, fuzziness in criteria and data noisiness make neural networks to be an attractive analytic tool. The model based on three-layer perceptron was tested over the sample of 29 `cancer' and 29 `non-cancer' cases and demonstrated total separation.

  4. VARIABILITY IN OPTICAL SPECTRA OF {epsilon} ORIONIS

    SciTech Connect

    Thompson, Gregory B.; Morrison, Nancy D. E-mail: nmorris@utnet.utoledo.edu

    2013-04-15

    We present the results of a time series analysis of 130 echelle spectra of {epsilon} Ori (B0 Ia), acquired over seven observing seasons between 1998 and 2006 at Ritter Observatory. The equivalent widths of H{alpha} (net) and He I {lambda}5876 were measured and radial velocities were obtained from the central absorption of He I {lambda}5876. Temporal variance spectra (TVS) revealed significant wind variability in both H{alpha} and He I {lambda}5876. The He I TVS have a double-peaked profile consistent with radial velocity oscillations. A periodicity search was carried out on the equivalent width and radial velocity data, as well as on wavelength-binned spectra. This analysis has revealed several periods in the variability with timescales of two to seven days. Many of these periods exhibit sinusoidal modulation in the associated phase diagrams. Several of these periods were present in both H{alpha} and He I, indicating a possible connection between the wind and the photosphere. Due to the harmonic nature of these periods, stellar pulsations may be the origin of some of the observed variability. Periods on the order of the rotational period were also detected in the He I line in the 1998-1999 season and in both lines during the 2004-2005 season. These periods may indicate rotational modulation due to structure in the wind.

  5. Host galaxy spectra and consequences for supernova typing from the SDSS SN survey

    SciTech Connect

    Olmstead, Matthew D.; Brown, Peter J.; Brownstein, Joel R.; Dawson, Kyle S.; Sako, Masao; Gupta, Ravi R.; Bassett, Bruce; Kunz, Martin; Bizyaev, Dmitry; Brinkmann, J.; Brewington, Howard; Ebelke, Garrett L.; Campbell, Heather; D'Andrea, Chris B.; Lampeitl, Hubert; Frieman, Joshua A.; Galbany, Lluís; Garnavich, Peter; Hlozek, Renee; Jha, Saurabh W.; and others

    2014-04-01

    We present the spectroscopy from 5254 galaxies that hosted supernovae (SNe) or other transient events in the Sloan Digital Sky Survey II (SDSS-II). Obtained during SDSS-I, SDSS-II, and the Baryon Oscillation Spectroscopic Survey, this sample represents the largest systematic, unbiased, magnitude limited spectroscopic survey of SN host galaxies. Using the host galaxy redshifts, we test the impact of photometric SN classification based on SDSS imaging data with and without using spectroscopic redshifts of the host galaxies. Following our suggested scheme, there are a total of 1166 photometrically classified SNe Ia when using a flat redshift prior and 1126 SNe Ia when the host spectroscopic redshift is assumed. For 1024 (87.8%) candidates classified as likely SNe Ia without redshift information, we find that the classification is unchanged when adding the host galaxy redshift. Using photometry from SDSS imaging data and the host galaxy spectra, we also report host galaxy properties for use in future analysis of SN astrophysics. Finally, we investigate the differences in the interpretation of the light curve properties with and without knowledge of the redshift. Without host galaxy redshifts, we find that SALT2 light curve fits are systematically biased toward lower photometric redshift estimates and redder colors in the limit of low signal-to-noise data. The general improvements in performance of the light curve fitter and the increased diversity of the host galaxy sample highlights the importance of host galaxy spectroscopy for current photometric SN surveys such as the Dark Energy Survey and future surveys such as the Large Synoptic Survey Telescope.

  6. Host Galaxy Spectra and Consequences for SN Typing from the SDSS SN Survey

    SciTech Connect

    Olmstead, Matthew D.; Brown, Peter J.; Sako, Masao; Bassett, Bruce; Bizyaev, Dmitry; Brinkmann, J.; Brownstein, Joel R.; Brewington, Howard; Campbell, Heather; D’Andrea, Chris B.; Dawson, Kyle S.; Ebelke, Garrett L.; Frieman, Joshua A.; Galbany, Lluís; Garnavich, Peter; Gupta, Ravi R.; Hlozek, Renee; Jha, Saurabh W.; Kunz, Martin; Lampeitl, Hubert; Malanushenko, Elena; Malanushenko, Viktor; Marriner, John; Miquel, Ramon; Montero-Dorta, Antonio D.; Nichol, Robert C.; Oravetz, Daniel J.; Pan, Kaike; Schneider, Donald P.; Simmons, Audrey E.; Smith, Mathew; Snedden, Stephanie A.

    2014-03-06

    We present the spectroscopy from 5254 galaxies that hosted supernovae (SNe) or other transient events in the Sloan Digital Sky Survey II (SDSS-II). Obtained during SDSS-I, SDSS-II, and the Baryon Oscillation Spectroscopic Survey (BOSS), this sample represents the largest systematic, unbiased, magnitude limited spectroscopic survey of supernova (SN) host galaxies. Using the host galaxy redshifts, we test the impact of photometric SN classification based on SDSS imaging data with and without using spectroscopic redshifts of the host galaxies. Following our suggested scheme, there are a total of 1166 photometrically classified SNe Ia when using a flat redshift prior and 1126 SNe Ia when the host spectroscopic redshift is assumed. For 1024 (87.8%) candidates classified as likely SNe Ia without redshift information, we find that the classification is unchanged when adding the host galaxy redshift. Using photometry from SDSS imaging data and the host galaxy spectra, we also report host galaxy properties for use in future nalysis of SN astrophysics. Finally, we investigate the differences in the interpretation of the light curve properties with and without knowledge of the redshift. When using the SALT2 light curve fitter, we find a 21% increase in the number of fits that converge when using the spectroscopic redshift. Without host galaxy redshifts, we find that SALT2 light curve fits are systematically biased towards lower photometric redshift estimates and redder colors in the limit of low signal-to-noise data. The general improvements in performance of the light curve fitter and the increased diversity of the host galaxy sample highlights the importance of host galaxy spectroscopy for current photometric SN surveys such as the Dark Energy Survey and future surveys such as the Large Synoptic Survey Telescope.

  7. The ALMA Protostellar Interferometric Line Survey (PILS). First results from an unbiased submillimeter wavelength line survey of the Class 0 protostellar binary IRAS 16293-2422 with ALMA

    NASA Astrophysics Data System (ADS)

    Jørgensen, J. K.; van der Wiel, M. H. D.; Coutens, A.; Lykke, J. M.; Müller, H. S. P.; van Dishoeck, E. F.; Calcutt, H.; Bjerkeli, P.; Bourke, T. L.; Drozdovskaya, M. N.; Favre, C.; Fayolle, E. C.; Garrod, R. T.; Jacobsen, S. K.; Öberg, K. I.; Persson, M. V.; Wampfler, S. F.

    2016-11-01

    Context. The inner regions of the envelopes surrounding young protostars are characterized by a complex chemistry, with prebiotic molecules present on the scales where protoplanetary disks eventually may form. The Atacama Large Millimeter/submillimeter Array (ALMA) provides an unprecedented view of these regions zooming in on solar system scales of nearby protostars and mapping the emission from rare species. Aims: The goal is to introduce a systematic survey, the Protostellar Interferometric Line Survey (PILS), of the chemical complexity of one of the nearby astrochemical templates, the Class 0 protostellar binary IRAS 16293-2422, using ALMA in order to understand the origin of the complex molecules formed in its vicinity. In addition to presenting the overall survey, the analysis in this paper focuses on new results for the prebiotic molecule glycolaldehyde, its isomers, and rarer isotopologues and other related molecules. Methods: An unbiased spectral survey of IRAS 16293-2422 covering the full frequency range from 329 to 363 GHz (0.8 mm) has been obtained with ALMA, in addition to a few targeted observations at 3.0 and 1.3 mm. The data consist of full maps of the protostellar binary system with an angular resolution of 0.5'' (60 AU diameter), a spectral resolution of 0.2 km s-1, and a sensitivity of 4-5 mJy beam-1 km s-1, which is approximately two orders of magnitude better than any previous studies. Results: More than 10 000 features are detected toward one component in the protostellar binary, corresponding to an average line density of approximately one line per 3 km s-1. Glycolaldehyde; its isomers, methyl formate and acetic acid; and its reduced alcohol, ethylene glycol, are clearly detected and their emission well-modeled with an excitation temperature of 300 K. For ethylene glycol both lowest state conformers, aGg' and gGg', are detected, the latter for the first time in the interstellar medium (ISM). The abundance of glycolaldehyde is comparable to or

  8. Near-infrared spectra of Jupiter, Saturn, and Uranus

    NASA Technical Reports Server (NTRS)

    Potter, A. E.

    1974-01-01

    Near infrared spectra of Jupiter, Saturn, and Uranus were measured at resolutions higher than previously available in the range from 6,000 to 10,750/cm. The resolution was 0.5/cm for Jupiter and Saturn, and 32/cm for Uranus. The spectra are presented both individually and as ratio spectra, in which the planetary spectra are divided by the solar spectrum. The Uranus spectrum is shown with Saturn, Jupiter, and Sun spectra reduced to the same resolution so that Uranus can be compared with the other outer planets. The high resolution Saturn, Jupiter, and Sun spectra are presented in parallel plots to simplify comparisons between them.

  9. EMPCA and Cluster Analysis of Quasar Spectra: Application to SDSS Spectra

    NASA Astrophysics Data System (ADS)

    Leighly, Karen; Marrs, Adam; Wagner, Cassidy; Macinnis, Francis

    2017-01-01

    Accurate modeling of the quasar continuum is necessary to measure and analyze absorption lines. But quasar continua, in particular the emission lines, vary from object to object. Patterns in the variations allow a spectral principal component analysis (SPCA) approach using large samples of quasar spectra, e.g., from the SDSS. Then, a small number of the derived principal component spectra can be used to reconstruct an arbitrary quasar's continuum.A problem with this approach is that the number of principal components required to model an arbitrary quasar, usually 8 to 20 in the literature, is large. One reason why so many components are required is that SPCA implicitly assumes that spectra bins are independent. Quasar emission lines are spread over a range of spectral bins, and more importantly, can sometimes be blueshifted. So while the intrinsic variability may only be a function of a few physical parameters, the nonlinearity inherent in the variations from object to object requires a large number of prinicipal components to accurately model a quasar continuum.We present a modified approach. We perform a SPCA analysis, using an expectation-maximization algorithm by Bailey et al. 2012, which takes into account uncertainties and missing data. We project the sample spectra on the resulting eignevectors to obtain the projection coefficients. Reasoning that intriniscally similar spectra will have similar projection coefficients, we perform a cluster analysis on the projection coefficients. The results are used to divide the sample into groups of similar spectra. A second PCA analysis is then performed on each group. We find that many fewer eigenspectra are required to accurately model the spectra in each group. We apply this approach to several samples of quasars from the SDSS.

  10. Host Galaxy Spectra of Stripped SN from the Palomar Transient Factory: SN Progenitor Diagnostics and the SN-GRB Connection

    NASA Astrophysics Data System (ADS)

    Modjaz, Maryam; Gal-Yam, Avishay; Arcavi, Iair

    2012-02-01

    Stripped core-collapse supernovae (Stripped SNe) are powerful cosmic engines that energize and enrich the ISM and that sometimes accompany GRBs, but the exact mass and metallicity range of their massive progenitors is not known, nor the detailed physics of the explosion. We propose to continue conducting the first uniform and statistically significant study of host galaxies of 60 stripped SNe from the same innovative, homogeneous and galaxy-unbiased survey Palomar Transient Factory in order to determine the environmental conditions that influence the various kinds of massive stellar deaths. By obtaining spectra of the immediate host environments of our sample of stripped SN, we will (1) measure local abundances in order to differentiate between the two progenitor scenarios for stripped SN and (2) derive stellar population ages, masses and star formation histories via detailed stellar population synthesis models. Moreover, we will test if natal chemical abundance has effects on basic SN characteristics, such as peak luminosity. Any observed trends will have ramifications on SN and GRB explosion models and imply important demographic SN considerations. Our dataset will provide a crucial complimentary set to host galaxy studies of long-duration GRBs and pave the way for host studies of transients and SN found via upcoming surveys such as LSST.

  11. Intrinsic Wavelength Shifts in Stellar Spectra

    NASA Astrophysics Data System (ADS)

    Dravins, D.; Lindegren, L.; Ludwig, H.-G.; Madsen, S.

    2004-12-01

    Wavelengths of stellar spectral lines do not have the precise values `naively' expected from laboratory wavelengths merely Doppler-shifted by stellar radial motion. Slight displacements may originate as convective shifts (correlated velocity and brightness patterns in the photosphere), as gravitational redshifts, or perhaps be induced by wave motions. Intrinsic lineshifts thus reveal stellar surface structure, while possible periodic changes (during a stellar activity cycle, say) need to be segregated from variability induced by orbiting exoplanets. Absolute lineshifts can now be studied also in some stars other than the Sun, thanks to astrometric determinations of stellar radial motion. Comparisons between spectroscopic apparent radial velocities and astrometrically determined radial motions reveal greater spectral blueshifts in F-type stars than in the Sun (as theoretically expected from their more vigorous convection), further increasing in A-type stars (possibly due to atmospheric shockwaves). Solar spectral atlases, and high-resolution spectra (from UVES on ESO VLT) of a dozen solar-type stars are being surveyed for `unblended' photospheric lines of most atomic species with accurate laboratory wavelengths available. One aim is to understand the ultimate information content of stellar spectra, and in what detail it will be feasible to verify models of stellar atmospheric hydrodynamics. These may predict line asymmetries (bisectors) and shifts for widely different classes of lines, but there will not result any comparison with observations if such lines do not exist in real spectra. An expected near-future development in stellar physics is spatially resolved spectroscopy across stellar disks, enabled by optical interferometry and adaptive optics on very large telescopes. Stellar surface structure manifests itself in the center-to-limb wavelength changes along a stellar diameter, and their spatially resolved time variability, diagnostics which already now can be

  12. Effect of Temperature on Jet Velocity Spectra

    NASA Technical Reports Server (NTRS)

    Bridges, James E.; Wernet, Mark P.

    2007-01-01

    Statistical jet noise prediction codes that accurately predict spectral directivity for both cold and hot jets are highly sought both in industry and academia. Their formulation, whether based upon manipulations of the Navier-Stokes equations or upon heuristic arguments, require substantial experimental observation of jet turbulence statistics. Unfortunately, the statistics of most interest involve the space-time correlation of flow quantities, especially velocity. Until the last 10 years, all turbulence statistics were made with single-point probes, such as hotwires or laser Doppler anemometry. Particle image velocimetry (PIV) brought many new insights with its ability to measure velocity fields over large regions of jets simultaneously; however, it could not measure velocity at rates higher than a few fields per second, making it unsuitable for obtaining temporal spectra and correlations. The development of time-resolved PIV, herein called TR-PIV, has removed this limitation, enabling measurement of velocity fields at high resolution in both space and time. In this paper, ground-breaking results from the application of TR-PIV to single-flow hot jets are used to explore the impact of heat on turbulent statistics of interest to jet noise models. First, a brief summary of validation studies is reported, undertaken to show that the new technique produces the same trusted results as hotwire at cold, low-speed jets. Second, velocity spectra from cold and hot jets are compared to see the effect of heat on the spectra. It is seen that heated jets possess 10 percent more turbulence intensity compared to the unheated jets with the same velocity. The spectral shapes, when normalized using Strouhal scaling, are insensitive to temperature if the stream-wise location is normalized relative to the potential core length. Similarly, second order velocity correlations, of interest in modeling of jet noise sources, are also insensitive to temperature as well.

  13. High precision radial velocities with GIANO spectra

    NASA Astrophysics Data System (ADS)

    Carleo, I.; Sanna, N.; Gratton, R.; Benatti, S.; Bonavita, M.; Oliva, E.; Origlia, L.; Desidera, S.; Claudi, R.; Sissa, E.

    2016-06-01

    Radial velocities (RV) measured from near-infrared (NIR) spectra are a potentially excellent tool to search for extrasolar planets around cool or active stars. High resolution infrared (IR) spectrographs now available are reaching the high precision of visible instruments, with a constant improvement over time. GIANO is an infrared echelle spectrograph at the Telescopio Nazionale Galileo (TNG) and it is a powerful tool to provide high resolution spectra for accurate RV measurements of exoplanets and for chemical and dynamical studies of stellar or extragalactic objects. No other high spectral resolution IR instrument has GIANO's capability to cover the entire NIR wavelength range (0.95-2.45 μm) in a single exposure. In this paper we describe the ensemble of procedures that we have developed to measure high precision RVs on GIANO spectra acquired during the Science Verification (SV) run, using the telluric lines as wavelength reference. We used the Cross Correlation Function (CCF) method to determine the velocity for both the star and the telluric lines. For this purpose, we constructed two suitable digital masks that include about 2000 stellar lines, and a similar number of telluric lines. The method is applied to various targets with different spectral type, from K2V to M8 stars. We reached different precisions mainly depending on the H-magnitudes: for H ˜ 5 we obtain an rms scatter of ˜ 10 m s-1, while for H ˜ 9 the standard deviation increases to ˜ 50 ÷ 80 m s-1. The corresponding theoretical error expectations are ˜ 4 m s-1 and 30 m s-1, respectively. Finally we provide the RVs measured with our procedure for the targets observed during GIANO Science Verification.

  14. Evolution of Fourier spectra through interplanetary shocks

    NASA Astrophysics Data System (ADS)

    Pitna, Alexander; Safrankova, Jana; Nemecek, Zdenek; Nemec, Frantisek; Goncharov, Oleksandr

    2014-05-01

    Well established nearly isothermic solar wind expansion requires an additional heating. A dissipation of large scale variations of the solar wind kinetic energy into the thermal energy via turbulence cascades is thought to be an important source of this heating, although the exact mechanism is yet to be found. For this reason, the turbulence in the solar wind is a subject of extensive theoretical and experimental studies on different time scales ranging from years to minutes. The frequency spectrum of magnetic field fluctuations can be divided into several domains differing by spectral indices - the lowest frequencies are controlled by the solar activity, MHD activity shapes the spectrum at higher (up to 0.1 Hz) frequencies, whereas the ion and electron kinetic effects dominate at the high frequency end of the spectra. Interplanetary shocks of various origins are a part of solar wind turbulence naturally occurring in the solar wind and the BMSW instrument onboard the Spektr-R spacecraft has detected tens of them in course of the 2011-2013 years. Based on its high-time resolution of the ion flux, density and velocity measurements reaching 31 ms, we study an evolution of the frequency spectra on MHD and kinetic scales across fast forward low Mach number shocks. We have found that the power of downstream fluctuations rises by an order of magnitude in a broad range of frequencies independently of its upstream value but the slope of the spectrum on the kinetic scale (≡3-8 Hz) has been found to be statistically steeper downstream than upstream of the shock. The time needed to a full relaxation to the pre-shock spectral shape is as long as several hours. A combination of the ion flux power spectra obtained by BMSW with fast magnetic field observations of other spacecraft enhances our understanding of dissipation mechanisms.

  15. Synthesized Spectra of Optically Thin Emission Lines

    NASA Astrophysics Data System (ADS)

    Olluri, K.; Gudiksen, B. V.; Hansteen, V. H.; De Pontieu, B.

    2015-03-01

    In recent years realistic 3D numerical models of the solar atmosphere have become available. The models attempt to recreate the solar atmosphere and mimic observations in the best way, in order to make it possible to couple complicated observations with physical properties such as the temperatures, densities, velocities, and magnetic fields. We here present a study of synthetic spectra created using the Bifrost code in order to assess how well they fit with previously taken solar data. A study of the synthetic intensity, nonthermal line widths, Doppler shifts, and correlations between any two of these three components of the spectra first assuming statistical equilibrium is made, followed by a report on some of the effects nonequilibrium ionization will have on the synthesized spectra. We find that the synthetic intensities compare well with the observations. The synthetic observations depend on the assumed resolution and point-spread function (PSF) of the instrument, and we find a large effect on the results, especially for intensity and nonthermal line width. The Doppler shifts produce the reported persistent redshifts for the transition region (TR) lines and blueshifts for the upper TR and corona lines. The nonthermal line widths reproduce the well-known turnoff point around (2-3) × 105 K, but with much lower values than those observed. The nonthermal line widths tend to increase with decreasing assumed instrumental resolution, also when nonequilibrium ionization is included. Correlations between the nonthermal line width of any two TR line studies as reported by Chae et al. are reproduced, while the correlations of intensity to line width are reproduced only after applying a PSF to the data. Doppler shift correlations reported by Doschek for the TR lines and correlations of Doppler shift to nonthermal line width of the Fe xii 19.5 line reported by Doschek et al. are reproduced.

  16. Ultraviolet Spectra of Normal Spiral Galaxies

    NASA Technical Reports Server (NTRS)

    Kinney, Anne

    1997-01-01

    The data related to this grant on the Ultraviolet Spectra of Normal Spiral Galaxies have been entirely reduced and analyzed. It is incorporated into templates of Spiral galaxies used in the calculation of K corrections towards the understanding of high redshift galaxies. The main paper was published in the Astrophysical Journal, August 1996, Volume 467, page 38. The data was also used in another publication, The Spectral Energy Distribution of Normal Starburst and Active Galaxies, June 1997, preprint series No. 1158. Copies of both have been attached.

  17. SIMULATION OF PARTICLE SPECTRA AT RHIC.

    SciTech Connect

    KAHANA,D.E.; KAHANA,S.H.

    2001-09-04

    A purely hadronic simulation is performed of the recently reported data from PHOBOS at energies of {radical}s = 56, 130 GeV using the relativistic heavy ion cascade LUCIFER which had previously given a good description of the NA49 inclusive spectra at {radical}s = 17.2 GeV/A. The results compare well with these early measurements at RHIC and indeed successfully predict the increase in multiplicity now seen by PHOBOS and the other RHIC detectors at the nominal maximum energy of {radical}s = 200 GeV/A, suggesting that evidence for quark-gluon matter remains elusive.

  18. Electronic absorption spectra from first principles

    NASA Astrophysics Data System (ADS)

    Hazra, Anirban

    Methods for simulating electronic absorption spectra of molecules from first principles (i.e., without any experimental input, using quantum mechanics) are developed and compared. The electronic excitation and photoelectron spectra of ethylene are simulated, using the EOM-CCSD method for the electronic structure calculations. The different approaches for simulating spectra are broadly of two types---Frank-Condon (FC) approaches and vibronic coupling approaches. For treating the vibrational motion, the former use the Born-Oppenheimer or single surface approximation while the latter do not. Moreover, in our FC approaches the vibrational Hamiltonian is additively separable along normal mode coordinates, while in vibronic approaches a model Hamiltonian (obtained from ab initio electronic structure theory) provides an intricate coupling between both normal modes and electronic states. A method called vertical FC is proposed, where in accord with the short-time picture of molecular spectroscopy, the approximate excited-state potential energy surface that is used to calculate the electronic spectrum is taken to reproduce the ab initio potential at the ground-state equilibrium geometry. The potential energy surface along normal modes may be treated either in the harmonic approximation or using the full one-dimensional potential. Systems with highly anharmonic potential surfaces can be treated and expensive geometry optimizations are not required, unlike the traditional FC approach. The ultraviolet spectrum of ethylene between 6.2 and 8.7 eV is simulated using vertical FC. While FC approaches for simulation are computationally very efficient, they are not accurate when the underlying approximations are unreasonable. Then, vibronic coupling model Hamiltonians are necessary. Since these Hamiltonians have an analytic form, they are used to map the potential energy surfaces and understand their topology. Spectra are obtained by numerical diagonalization of the Hamiltonians. The

  19. Multifractal spectra in homogeneous shear flow

    NASA Technical Reports Server (NTRS)

    Deane, A. E.; Keefe, L. R.

    1988-01-01

    Employing numerical simulations of 3-D homogeneous shear flow, the associated multifractal spectra of the energy dissipation, scalar dissipation and vorticity fields were calculated. The results for (128) cubed simulations of this flow, and those obtained in recent experiments that analyzed 1- and 2-D intersections of atmospheric and laboratory flows, are in some agreement. A two-scale Cantor set model of the energy cascade process which describes the experimental results from 1-D intersections quite well, describes the 3-D results only marginally.

  20. Applying Zeeman Doppler imaging to solar spectra

    NASA Astrophysics Data System (ADS)

    Hussain, G. A. J.; Saar, S. H.; Collier Cameron, A.

    2004-03-01

    A new generation of spectro-polarimeters with high throughput (e.g. CFHT/ESPADONS and LBT/PEPSI) is becoming available. This opportunity can be exploited using Zeeman Doppler imaging (ZDI), a technique that inverts time-series of Stokes V spectra to map stellar surface magnetic fields (Semel 1989). ZDI is assisted by ``Least squares deconvolution'' (LSD), which sums up the signal from 1000's of photospheric lines to produce a mean deconvolved profile with higher S:N (Donati & Collier Cameron 1997).

  1. Transmission spectra of sausage-like microresonators.

    PubMed

    Ye, Ming-Yong; Shen, Mei-Xia; Lin, Xiu-Min

    2015-10-05

    We experimentally develop a sausage-like microresonator (SLM) by making two microtapers on a single-mode fiber, and study whispering-gallery modes (WGMs) in SLMs with different lengths. The transmission spectra from 1530 nm to 1550 nm of several SLMs are presented and SLMs with different lengths are shown to have different transmission features. The maximal Q factor observed in the SLMs is 3.8 * 10(7). For comparison, the transmission spectrum of a fiber cylinder microresonator is given and the maximal Q factor achieved in the fiber microcylinder resonator is 1.7 * 10(7). The strain tuning of the SLM is also demonstrated.

  2. Far-infrared spectra of acetanilide revisited

    NASA Astrophysics Data System (ADS)

    Spire, A.; Barthes, M.; Kellouai, H.; De Nunzio, G.

    2000-03-01

    A new investigation of the temperature dependence of the far-infrared spectra of acetanilide and some isotopomers is presented. Four absorption bands are considered at 31, 42, 64, and 80 cm-1, and no significant change of their integrated intensity is observed when reducing the temperature. The temperature induced frequency shift values and other properties of these bands are consistent with an assignment as anharmonic lattice phonons. These results rule out the assignment of the 64, 80, and 106 cm-1 bands as normal modes of the polaronic excitation, as previously suggested.

  3. Beamstrahlung spectra in next generation linear colliders

    SciTech Connect

    Barklow, T.; Chen, P. ); Kozanecki, W. )

    1992-04-01

    For the next generation of linear colliders, the energy loss due to beamstrahlung during the collision of the e{sup +}e{sup {minus}} beams is expected to substantially influence the effective center-of-mass energy distribution of the colliding particles. In this paper, we first derive analytical formulae for the electron and photon energy spectra under multiple beamstrahlung processes, and for the e{sup +}e{sup {minus}} and {gamma}{gamma} differential luminosities. We then apply our formulation to various classes of 500 GeV e{sup +}e{sup {minus}} linear collider designs currently under study.

  4. Solar Doppler shifts - Sources of continuous spectra

    NASA Technical Reports Server (NTRS)

    Duvall, T. L., Jr.; Harvey, J. W.

    1986-01-01

    Oscillation observations can be used to study nonoscillatory solar phenomena that exhibit Doppler shifts. The paper discusses several effects of these phenomena and their associated temporal and spatial power spectra: (1) they limit the signal-to-noise ratio and sometimes detectability of oscillation modes; (2) there is the potential for better understanding and/or detection of solar phenomena; (3) large-scale convection may spatially modulate oscillation modes, leading to a continuous background spectrum; and (4) in regions of the spectrum where the resolution to separate modes is lacking one can determine upper limits for the integrated effects of modes.

  5. Methane and the Spectra of T Dwarfs

    NASA Astrophysics Data System (ADS)

    Homeier, Derek; Hauschildt, Peter H.; Allard, France

    2003-06-01

    We have updated our PHOENIX model atmospheres and theoretical spectra for ultracool dwarfs with new opacity data for methane based on line strength predictions with the STDS software. By extending the line list to rotational levels of J = 40 we can significantly improve the shape of the near-IR absorption features of CH_4, and in addition find an enhanced blanketing effect, resulting in up to 50% more flux emerging in the J band than seen in previous models, which may thus contribute to the brightening in J and blue IR colors observed in T dwarfs.

  6. Covariance Analysis of Gamma Ray Spectra

    SciTech Connect

    Trainham, R.; Tinsley, J.

    2013-01-01

    The covariance method exploits fluctuations in signals to recover information encoded in correlations which are usually lost when signal averaging occurs. In nuclear spectroscopy it can be regarded as a generalization of the coincidence technique. The method can be used to extract signal from uncorrelated noise, to separate overlapping spectral peaks, to identify escape peaks, to reconstruct spectra from Compton continua, and to generate secondary spectral fingerprints. We discuss a few statistical considerations of the covariance method and present experimental examples of its use in gamma spectroscopy.

  7. Covariance analysis of gamma ray spectra

    SciTech Connect

    Trainham, R.; Tinsley, J.

    2013-01-15

    The covariance method exploits fluctuations in signals to recover information encoded in correlations which are usually lost when signal averaging occurs. In nuclear spectroscopy it can be regarded as a generalization of the coincidence technique. The method can be used to extract signal from uncorrelated noise, to separate overlapping spectral peaks, to identify escape peaks, to reconstruct spectra from Compton continua, and to generate secondary spectral fingerprints. We discuss a few statistical considerations of the covariance method and present experimental examples of its use in gamma spectroscopy.

  8. GENERAL RELATIVISTIC EFFECTS ON NONLINEAR POWER SPECTRA

    SciTech Connect

    Jeong, Donghui; Gong, Jinn-Ouk; Noh, Hyerim; Hwang, Jai-chan E-mail: jgong@lorentz.leidenuniv.nl E-mail: jchan@knu.ac.kr

    2011-01-20

    The nonlinear nature of Einstein's equation introduces genuine relativistic higher order corrections to the usual Newtonian fluid equations describing the evolution of cosmological perturbations. We study the effect of such novel nonlinearities on the next-to-leading order matter and velocity power spectra for the case of a pressureless, irrotational fluid in a flat Friedmann background. We find that pure general relativistic corrections are negligibly small over all scales. Our result guarantees that, in the current paradigm of standard cosmology, one can safely use Newtonian cosmology even in nonlinear regimes.

  9. Classification of specialty seed meals from NIR reflectance spectra

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Near infrared reflectance spectroscopy was used to identify alternative seed meals proposed for food and feed formulations. Spectra were collected from cold pressed Camelina (Camelina sativa), Coriander (Coriandrum sativum), and Pennycress (Thlaspi arvense) meals. Additional spectra were collected ...

  10. Velocity, scalar and transfer spectra in numerical turbulence

    NASA Astrophysics Data System (ADS)

    Kerr, Robert M.

    1990-02-01

    Velocity and passive-scalar spectra for turbulent fields generated by a forced three-dimensional simulation with 128-cubed grid points and Taylor-microscale Reynolds numbers up to 83 are shown to have convective and diffusive spectral regimes. One- and three-dimensional spectra are compared with experiment and theory. If normalized by the Kolmogorov dissipation scales and scalar dissipation, velocity spectra and scalar spectra for given Prandtl numbers collapse to single curves in the dissipation regime with exponentail tails. If multiplied by k exp 5/3, the velocity spectra show an anomalously high Kolmogorov constant that is consistent with low Reynolds number experiments. When normalized by the Batchelor scales, the scalar spectra show a universal dissipation regime that is independent of Prandtl numbers from 0.1 to 1.0. The time development of velocity spectra is illustrated by energy-transfer spectra in which distinct pulses propagate to high wavenumbers.

  11. Study on Mössbauer spectra of hemoglobin in thalassemia

    NASA Astrophysics Data System (ADS)

    Xuanhui, Guo; Nanming, Zhao; Xiufang, Zhang; Naifei, Gao; Youwen, Huang; Rongxin, Wang

    1988-02-01

    The57Fe Mössbauer spectra of erythrocytes in normal subjects and nine patients of different thalassemias were studied. Together with clinical analysis, the correlation between the components in the spectra and different types of anemias was discussed.

  12. Quantum synchrotron spectra from semirelativistic electrons in teragauss magnetic fields

    NASA Technical Reports Server (NTRS)

    Brainerd, J. J.

    1987-01-01

    Synchrotron spectra are calculated from quantum electrodynamic transition rates for thermal and power-law electron distributions. It is shown that quantum effects appear in thermal spectra when the photon energy is greater than the electron temperature, and in power-law spectra when the electron energy in units of the electron rest mass times the magnetic field strength in units of the critical field strength is of order unity. These spectra are compared with spectra calculated from the ultrarelativistic approximation for synchrotron emission. It is found that the approximation for the power-law spectra is good, and the approximation for thermal spectra produces the shape of the spectrum accurately but fails to give the correct normalization. Single photon pair creation masks the quantum effects for power-law distributions, so only modifications to thermal spectra are important for gamma-ray bursts.

  13. REPS: REscaled Power Spectra for initial conditions with massive neutrinos

    NASA Astrophysics Data System (ADS)

    Zennaro, Matteo; Bel, Julien; Villaescusa-Navarro, Francisco; Carbone, Carmelita; Sefusatti, Emiliano; Guzzo, Luigi

    2016-12-01

    REPS (REscaled Power Spectra) provides accurate, one-percent level, numerical simulations of the initial conditions for massive neutrino cosmologies, rescaling the late-time linear power spectra to the simulation initial redshift.

  14. Identifying Minerals from Their Infra-red Spectra.

    ERIC Educational Resources Information Center

    Paterson, W. G.

    1986-01-01

    Describes a British secondary school's use of a spectrometer to identify minerals. Discusses the origins of mineral spectra, the preparation of the specimen, the actual spectroscopic scanning, and the interpretation of the spectra. (TW)

  15. LAMOST Observations in the Kepler Field. Analysis of the Stellar Parameters Measured with LASP Based on Low-resolution Spectra

    NASA Astrophysics Data System (ADS)

    Ren, Anbing; Fu, Jianning; De Cat, Peter; Wu, Yue; Yang, Xiaohu; Shi, Jianrong; Luo, Ali; Zhang, Haotong; Dong, Subo; Zhang, Ruyuan; Zhang, Yong; Hou, Yonghui; Wang, Yuefei; Cao, Zihuang; Du, Bing

    2016-08-01

    All 14 subfields of the Kepler field were observed at least once with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (lamost, Xinglong Observatory, China) during the 2012-2014 observation seasons. There are 88,628 reduced spectra with a signal-to-noise ratio in the g band (S/N g ) ≥ 6 after the first round (2012-2014) of observations of the lamost- Kepler project (LK-project). By adopting the upgraded version of the lamost Stellar Parameter pipeline (lasp), we have determined the atmospheric parameters ({T}{eff}, {log}g, and [Fe/H]) and heliocentric radial velocity v rad for 51,406 stars with 61,226 spectra. Compared with the atmospheric parameters derived from both high-resolution spectroscopy and asteroseismology for common stars in Huber et al., an external calibration of lasp atmospheric parameters was made, leading to the determination of the external errors for giants and dwarfs. Multiple spectroscopic observations of the same objects in the LK-project were used to estimate the internal uncertainties of the atmospheric parameters as a function of S/N g with the unbiased estimation method. The lasp atmospheric parameters were calibrated based on both the external and internal uncertainties for the giants and dwarfs. A general statistical analysis of the stellar parameters leads to the discovery of 106 candidate metal-poor stars, 9 candidate very metal-poor stars, and 18 candidate high-velocity stars. Fitting formulae were obtained segmentally for both the calibrated atmospheric parameters of the LK-project and the Kepler Input Catalog (KIC) parameters with common stars. The calibrated atmospheric parameters and radial velocities of the LK-project will be useful for studying stars in the Kepler field. ) located at the Xinglong Observatory, China.

  16. Retrieving sea-wave spectra using satellite-imagery spectra in a wide range of frequencies

    NASA Astrophysics Data System (ADS)

    Bondur, V. G.; Dulov, V. A.; Murynin, A. B.; Ignatiev, V. Yu.

    2016-11-01

    A method to register sea-wave spectra using optical aerospace imagery has been developed. The method is based on the use of retrieval operators both in areas of high and low spatial frequencies, including the areas of spectral maximum. The approach to adjust and validate the method developed using sea truth data obtained by string wave recorders has been suggested. This paper presents the results of using the suggested method to study sea-wave spectra using high-resolution satellite imagery for various water areas under different conditions of wave generation.

  17. Odor Impression Prediction from Mass Spectra.

    PubMed

    Nozaki, Yuji; Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61).

  18. Infrared Spectra of Substituted Polycyclic Aromatic Hydrocarbons

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Hudgins, Douglas M.; Sandford, Scott A.; Allamandola, Louis J.; Arnold, James O. (Technical Monitor)

    1997-01-01

    Calculations are carried out using density functional theory (DFT) to determine the harmonic frequencies and intensities of 1-methylanthracene, 9-methylanthracene, 9-cyanoanthracene, 2-aminoanthracene, acridine, and their positive ions. The theoretical data are compared with matrix-isolation spectra for these species also reported in this work. The theoretical and experimental frequencies and relative intensities for the neutral species are in generally good agreement, whereas the positive ion spectra are only in qualitative agreement. Relative to anthracene, we find that substitution of amethyl or CN for a hydrogen does not significantly affect the spectrum other than to add the characteristic methyl C-H stretch and C-N stretch (near 2200/cm), respectively. However, addition of NH2 dramatically affects the spectrum of the neutral. Not only are the NH2 modes themselves strong, but this electron withdrawing group induces sufficient partial charge on the ring to give the neutral molecule characteristics of the anthracene cation spectrum. The sum of the absolute intensities is about four times larger for 2-aminoanthracene than for 9-cyanoanthracene. Substituting nitrogen in the ring at the nine position (acridine) does not greatly alter the spectrum compared with anthracene.

  19. An atlas of selected calibrated stellar spectra

    NASA Technical Reports Server (NTRS)

    Walker, Russell G.; Cohen, Martin

    1992-01-01

    Five hundred and fifty six stars in the IRAS PSC-2 that are suitable for stellar radiometric standards and are brighter than 1 Jy at 25 microns were identified. In addition, 123 stars that meet all of our criteria for calibration standards, but which lack a luminosity class were identified. An approach to absolute stellar calibration of broadband infrared filters based upon new models of Vega and Sirius due to Kurucz (1992) is presented. A general technique used to assemble continuous wide-band calibrated infrared spectra is described and an absolutely calibrated 1-35 micron spectrum of alpha(Tau) is constructed and the method using new and carefully designed observations is independently validated. The absolute calibration of the IRAS Low Resolution Spectrometer (LRS) database is investigated by comparing the observed spectrum of alpha(Tau) with that assumed in the original LRS calibration scheme. Neglect of the SiO fundamental band in alpha(Tau) has led to the presence of a specious 'emission' feature in all LRS spectra near 8.5 microns, and to an incorrect spectral slope between 8 and 12 microns. Finally, some of the properties of asteroids that effect their utility as calibration objects for the middle and far infrared region are examined. A technique to determine, from IRAS multiwaveband observations, the basic physical parameters needed by various asteroid thermal models that minimize the number of assumptions required is developed.

  20. Reflectance Spectra of Space Debris in GEO

    NASA Astrophysics Data System (ADS)

    Schildknecht, T.; Vannanti, A.; Krag, H.; Erd, C.

    The space debris environment in the Geostationary Earth Orbit (GEO) region is mostly investigated by means of optical surveys. Such surveys revealed a considerable amount of debris in the size range of 10 centimeter to one meter. Some of these debris exhibit particularly high area-to-mass ratios as derived from the evolution of their orbits. In order to understand the nature and eventually the origin of these objects, observations allowing to derive physical characteristics like size, shape and material are required. Information on the shape and the attitude motion of a debris piece may be obtained by photometric light curves. The most promising technique to investigate the surface material properties is reflectance spectroscopy. This paper discusses preliminary results obtained from spectrometric observations of space debris in GEO. The observations were acquired at the 1-meter ESA Space Debris Telescope (ESASDT) on Tenerife with a low-resolution spectrograph in the wavelength range of 450-960 nm. The target objects were space debris of different types with brightness as small as magnitude 15. Some simple-shaped, intact "calibration objects" with known surface materials like the MSG-2 satellites were also observed. The spectra show shape variations expected to be caused by the different physical properties of the objects. The determination of the possible materials is still in a preliminary phase. Limitations of the acquisition process of the spectra and the subsequent analysis are discussed. Future steps planned for a better characterization of the debris from the observed data are briefly outlined.

  1. Spectra of {gamma} rays feeding superdeformed bands

    SciTech Connect

    Lauritsen, T.; Khoo, T.L.; Henry, R.G.

    1995-08-01

    The spectrum of {gamma}rays coincident with SD transitions contains the transitions which populate the SD band. This spectrum can provide information on the feeding mechanism and on the properties (moment of inertia, collectivity) of excited SD states. We used a model we developed to explain the feeding of SD bands, to calculate the spectrum of feeding {gamma}rays. The Monte Carlo simulations take into account the trigger conditions present in our Eurogam experiment. Both experimental and theoretical spectra contain a statistical component and a broad E2 peak (from transitions occurring between excited states in the SD well). There is good resemblance between the measured and calculated spectra although the calculated multiplicity of an E2 bump is low by {approximately}30%. Work is continuing to improve the quality of the fits, which will result in a better understanding of excited SD states. In addition, a model for the last steps, which cool the {gamma} cascade into the SD yrast line, needs to be developed. A strong M1/E2 low-energy component, which we believe is responsible for this cooling, was observed.

  2. Wave spectra from sun glint patterns

    NASA Astrophysics Data System (ADS)

    Alvarez-Borrego, Josue

    1992-12-01

    The problem of retrieving spatial information of the sea surface heights from aerial images is considered. We proceed, for simplicity, by considering a one-dimensional model of the problem. With some simplifying assumptions, we derive some analytical and numerical results that relate the autocorrelation of the surface heights and those of the sunglint patterns. We assume that the surfaces are such that they constitute approximations to Gaussian random processes. We also assume that the surfaces are illuminated by a source (the sun) of a fixed angular extent and imaged through a lens that subtends a very small solid angle. With these assumptions, we calculate their images, as they would be formed by a signal clipping detector. In order to do this, we define a `glitter function,' which operates on the slope of the surfaces. To test our predictions we have conducted a Monte Carlo type simulation. Random surfaces with two different power spectra have been generated in a computer. We find that under favorable conditions, it is possible to invert the relation numerically and estimate the surface height autocorrelation from the sunglint data. We obtain the wave spectra from the surface height autocorrelation via a Fourier transform.

  3. Odor Impression Prediction from Mass Spectra

    PubMed Central

    Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61). PMID:27326765

  4. Equilibria and absorption spectra of tryptophanase.

    PubMed

    Metzler, C M; Viswanath, R; Metzler, D E

    1991-05-25

    Tryptophanase (tryptophan: indole-lyase) from Escherichia coli has been isolated in the holoenzyme form and its absorption spectra and acid-base chemistry have been reevaluated. Apoenzyme has been prepared by dialysis against sodium phosphate and L-alanine and molar absorptivities of the coenzyme bands have been estimated by readdition of pyridoxal 5'-phosphate. The spectrophotometric titration curve, whose midpoint is at pH 7.6 in 0.1 M potassium phosphate buffers, indicates some degree of cooperativity in dissociation of a pair of protons. Resolution of the computed spectra of individual ionic forms of the enzyme with lognormal distribution curves shows that band shapes are similar to those of model Schiff bases and of aspartate aminotransferase. Using molar areas from the latter we estimated amounts of individual tautomeric species. In addition to ketoenamine and enolimine or covalent adduct the high pH form also appears to contain approximately 18% of a species with a dipolar ionic ring (protonated on the ring nitrogen and with phenolate -O-). We suggest that this may be the catalytically active form of the coenzyme in tryptophanase. The equilibrium between tryptophanase and L-alanine has also been reevaluated.

  5. Millimeter wave absorption spectra of biological samples

    SciTech Connect

    Gandhi, O.P.; Hagmann, M.J.; Hill, D.W.; Partlow, L.M.; Bush, L.

    1980-01-01

    A solid-state computer-controlled system has been used to make swept-frequency measurements of absorption of biological specimens from 26.5 to 90.0 GHz. A wide range of samples was used, including solutions of DNA and RNA, and suspensions of BHK-21/C13 cells, Candida albicans, C krusei, and Escherichia coli. Sharp spectra reported by other workers were not observed. The strong absorbance of water (10--30 dB/mm) caused the absorbance of all aqueous preparations that we examined to have a water-like dependence on frequency. Reduction of incident power (to below 1.0 microW), elimination of modulation, and control of temperature to assure cell viability were not found to significantly alter the water-dominated absorbance. Frozen samples of BHK-21/C13 cells tested at dry ice and liquid nitrogen temperatures were found to have average insertion loss reduced to 0.2 dB/cm but still showed no reproducible peaks that could be attributed to absorption spectra. It is concluded that the special resonances reported by others are likely to be in error.

  6. Rotary spectra analysis applied to static stabilometry.

    PubMed

    Chiaramello, E; Knaflitz, M; Agostini, V

    2011-01-01

    Static stabilometry is a technique aimed at quantifying postural sway during quiet standing in the upright position. Many different models and many different techniques to analyze the trajectories of the Centre of Pressure (CoP) have been proposed. Most of the parameters calculated according to these different approaches are affected by a relevant intra- and inter-subject variability or do not have a clear physiological interpretation. In this study we hypothesize that CoP trajectories have rotational characteristics, therefore we decompose them in clockwise and counter-clockwise components, using the rotary spectra analysis. Rotary spectra obtained studying a population of healthy subjects are described through the group average of spectral parameters, i.e., 95% spectral bandwidth, mean frequency, median frequency, and skewness. Results are reported for the clockwise and the counter-clockwise components and refer to the upright position maintained with eyes open or closed. This study demonstrates that the approach is feasible and that some of the spectral parameters are statistically different between the open and closed eyes conditions. More research is needed to demonstrate the clinical applicability of this approach, but results so far obtained are promising.

  7. Nuclear size effects in vibrational spectra.

    PubMed

    Almoukhalalati, Adel; Shee, Avijit; Saue, Trond

    2016-06-01

    We present a theoretical study of nuclear volume in the rovibrational spectra of diatomic molecules which is an extension of a previous study restricted to rotational spectra [Chem. Phys., 2012, 401, 103]. We provide a new derivation for the electron-nucleus electrostatic interaction energy which is basically independent of the choice of model for the nuclear charge distribution. Starting from this expression we derive expressions for the electronic, rotational and vibrational field shift parameters in terms of effective electron density and its first and second derivatives with respect to internuclear distance. The effective density is often approximated by the contact density, but we demonstrate that this leads to errors on the order of 10% and is furthermore not necessary since the contact and effective densities can be obtained at the same computational cost. We calculate the field shift parameters at the 4-component relativistic coupled-cluster singles-and-doubles level and find that our results confirm the experimental findings of Tiemann and co-workers [Chem. Phys., 1982, 68(21), 1982, Ber. Bunsenges. Phys. Chem., 1982, 86, 821], whereas we find no theoretical justification for a scaling factor introduced in later work [Chem. Phys., 1985, 93, 349]. For lead sulfide we study the effective density as a function of internuclear distance and find a minimum some 0.2 Å inside the equilibrium bond distance. We also discuss Bigeleisen-Goeppert-Mayer theory of isotope fractionation in light of our results.

  8. Serial FBG sensor network allowing overlapping spectra

    NASA Astrophysics Data System (ADS)

    Abbenseth, S.; Lochmann, S.; Ahrens, A.; Rehm, B.

    2016-05-01

    For structure or material monitoring low impact serial fiber Bragg grating (FBG) networks have attracted increasing research interest. Common sensor networks using wavelength division multiplexing (WDM) for FBG interrogation are limited in their efficiency by the spectral width of their light source, the FBG tuning range and the spectral guard bands. Overlapping spectra are strictly forbidden in this case. Applying time division multiplexing (TDM) or active resonator schemes may overcome these restrictions. However, they introduce other substantial disadvantages like signal roundtrip dependency or sophisticated control of active resonating structures. Code division multiplexing (CDM) as a means of FBG interrogation by simple autocorrelation of appropriate codes has been shown to be superior in this respect. However, it came at the cost of a second spectrometer introducing additional equalization efforts. We demonstrate a new serial FBG sensor network utilizing CDM signal processing for efficient sensor interrogation without the need of a second spectrometer and additional state of polarization (SOP) controlling components. It allows overlapping spectra even when all sensing FBGs are positioned at the same centre wavelength and it shows a high degree of insensitivity to SOP. Sequence inversed keyed (SIK) serial signal processing utilizing quasi-orthogonal balanced codes ensures simple and quick sensor interrogation with high signal-to-interference/noise ratio.

  9. Spectra and statistics in compressible isotropic turbulence

    NASA Astrophysics Data System (ADS)

    Wang, Jianchun; Gotoh, Toshiyuki; Watanabe, Takeshi

    2017-01-01

    Spectra and one-point statistics of velocity and thermodynamic variables in isotropic turbulence of compressible fluid are examined by using numerical simulations with solenoidal forcing at the turbulent Mach number Mt from 0.05 to 1.0 and at the Taylor Reynolds number Reλ from 40 to 350. The velocity field is decomposed into a solenoidal component and a compressible component in terms of the Helmholtz decomposition, and the compressible velocity component is further decomposed into a pseudosound component, namely, the hydrodynamic component associated with the incompressible field and an acoustic component associated with sound waves. It is found that the acoustic mode dominates over the pseudosound mode at turbulent Mach numbers Mt≥0.4 in our numerical simulations. At turbulent Mach numbers Mt≤0.4 , there exists a critical wave number kc beyond which the pseudosound mode dominates while the acoustic mode dominates at small wave numbers k spectra of pressure, density, and temperature exhibit a k-7 /3 scaling for Mt≤0.3 and a k-5 /3 scaling for Mt≥0.5 .

  10. High Resolution Infrared Spectra of Triacetylene

    NASA Astrophysics Data System (ADS)

    Doney, Kirstin D.; Zhao, Dongfeng; Linnartz, Harold

    2015-06-01

    Triacetylene, HC6H, is the longest poly-acetylene chain found in space, and is believed to be involved in the formation of longer chain molecules and polycyclic aromatic hydrocarbons (PAHs). However, abundances are expected to be low, and observational confirmation requires knowledge of the gas-phase spectra, which up to now has been incomplete with only the weak, low lying bending modes being known. We present new infrared (IR) spectra in the C-H stretch region obtained using ultra-sensitive and highly precise IR continuous wave cavity ring-down spectroscopy (cw-CRDS), combined with supersonic plasma expansions The talk reviews the accurate determination of the rotational constants of the asymmetric fundamental mode, νb{5}, including discussion on the perturber state, and associated hot bands. The determined molecular parameters are accurate enough to aid astronomical searches with such facilities as ALMA (Atacama Large Millimeter Array) or the upcoming JWST (James Webb Space Telecscope), which can now probe even trace molecules (abundances of ˜ 10-6 - 10-10 with respect to H2). D. Zhao, J. Guss, A. Walsh, H. Linnartz, Chem. Phys. Lett., 565, 132 (2013) K.D. Doney, D. Zhao, H. Linnartz, in preparation

  11. Discriminating Dysarthria Type From Envelope Modulation Spectra

    PubMed Central

    Liss, Julie M.; LeGendre, Sue; Lotto, Andrew J.

    2013-01-01

    Purpose Previous research demonstrated the ability of temporally based rhythm metrics to distinguish among dysarthrias with different prosodic deficit profiles (J. M. Liss et al., 2009). The authors examined whether comparable results could be obtained by an automated analysis of speech envelope modulation spectra (EMS), which quantifies the rhythmicity of speech within specified frequency bands. Method EMS was conducted on sentences produced by 43 speakers with 1 of 4 types of dysarthria and healthy controls. The EMS consisted of the spectra of the slow-rate (up to 10 Hz) amplitude modulations of the full signal and 7 octave bands ranging in center frequency from 125 to 8000 Hz. Six variables were calculated for each band relating to peak frequency and amplitude and relative energy above, below, and in the region of 4 Hz. Discriminant function analyses (DFA) determined which sets of predictor variables best discriminated between and among groups. Results Each of 6 DFAs identified 2–6 of the 48 predictor variables. These variables achieved 84%–100% classification accuracy for group membership. Conclusions Dysarthrias can be characterized by quantifiable temporal patterns in acoustic output. Because EMS analysis is automated and requires no editing or linguistic assumptions, it shows promise as a clinical and research tool. PMID:20643800

  12. Microwave Spectra of 9-FLUORENONE and Benzophenone

    NASA Astrophysics Data System (ADS)

    West, Channing; Sedo, Galen; van Wijngaarden, Jennifer

    2015-06-01

    The pure rotational spectra of 9-fluorenone (C13H8O) and benzophenone (C13H10O) were observed using chirped-pulse Fourier transform microwave spectroscopy (cp-FTMW). The 9-fluorenone spectrum was collected between 8 and 13 GHz, which allowed for the assignment of 124 rotational transitions. A separate spectrum spanning from 8 to 14 GHz was collected for benzophenone, allowing for the assignment of 133 rotational transitions. Both aromatic ketones exhibited strong b-type spectra with little to no centrifugal distortion, indicating highly rigid molecular structures. A comparison of the experimentally determined spectral constants of 9-fluorenone to those calculated using both ab initio and density functional theory strongly suggest the molecule conforms to a planar C2v symmetric geometry as expected for its polycyclic structure. Whereas, a comparison of the experimental benzophenone constants to those predicted by theory suggests a molecule with non-planar C2 symmetry, where the two phenyl groups are rotated approximately 32° out-of-plane to form a paddlewheel like geometry.

  13. Stellar parametrization from Gaia RVS spectra

    NASA Astrophysics Data System (ADS)

    Recio-Blanco, A.; de Laverny, P.; Allende Prieto, C.; Fustes, D.; Manteiga, M.; Arcay, B.; Bijaoui, A.; Dafonte, C.; Ordenovic, C.; Ordoñez Blanco, D.

    2016-01-01

    Context. Among the myriad of data collected by the ESA Gaia satellite, about 150 million spectra will be delivered by the Radial Velocity Spectrometer (RVS) for stars as faint as GRVS~ 16. A specific stellar parametrization will be performed on most of these RVS spectra, i.e. those with enough high signal-to-noise ratio (S/N), which should correspond to single stars that have a magnitude in the RVS band brighter than ~14.5. Some individual chemical abundances will also be estimated for the brightest targets. Aims: We describe the different parametrization codes that have been specifically developed or adapted for RVS spectra within the GSP-Spec working group of the analysis consortium. The tested codes are based on optimisation (FERRE and GAUGUIN), projection (MATISSE), or pattern-recognition methods (Artificial Neural Networks). We present and discuss each of their expected performances in the recovered stellar atmospheric parameters (effective temperature, surface gravity, overall metallicity) for B- to K-type stars. The performances for determining of [α/Fe] ratios are also presented for cool stars. Methods: Each code has been homogeneously tested with a large grid of RVS simulated synthetic spectra of BAFGK-spectral types (dwarfs and giants), with metallicities varying from 10-2.5 to 10+ 0.5 the solar metallicity, and taking variations of ±0.4 dex in the composition of the α-elements into consideration. The tests were performed for S/N ranging from ten to 350. Results: For all the stellar types we considered, stars brighter than GRVS~ 12.5 are very efficiently parametrized by the GSP-Spec pipeline, including reliable estimations of [α/Fe]. Typical internal errors for FGK metal-rich and metal-intermediate stars are around 40 K in Teff, 0.10 dex in log(g), 0.04 dex in [M/H], and 0.03 dex in [α/Fe] at GRVS = 10.3. They degrade to 155 K in Teff, 0.15 dex in log(g), 0.10 dex in [M/H], and 0.1 dex in [α/Fe] at GRVS~ 12. Similar accuracies in Teff and [M/H] are

  14. Spatially Resolved Mid-IR Spectra from Meteorites; Linking Composition, Crystallographic Orientation and Spectra on the Micro-Scale

    NASA Astrophysics Data System (ADS)

    Stephen, N. R.

    2016-08-01

    IR spectroscopy is used to infer composition of extraterrestrial bodies, comparing bulk spectra to databases of separate mineral phases. We extract spatially resolved meteorite-specific spectra from achondrites with respect to zonation and orientation.

  15. Mineral Spectra from Nili Fossae, Mars

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Spectra collected by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) indicate the presence of three distinct minerals. The graphed information comes from an observation of terrain in the Nili Fossae area of northern Mars. CRISM is one of six science instruments on NASA's Mars Reconnaissance Orbiter.

    Iron-magnesium smectite clay is formed through alteration of rocks by liquid water and is characterized by distinctive absorptions at 1.4, 1.9, and 2.3 micrometers due to water (H2O) and OH in the atomic structure of the mineral. Olivine is an iron magnesium silicate and primary igneous mineral, and water is not in its structure. Its spectrum is characterized by a strong and broad absorption at 1.0 micrometer due to ferrous iron (Fe2+). Carbonate is an alteration mineral identified by the distinctive paired absorptions at 2.3 and 2.5 micrometers. The precise band positions at 2.31 and 2.51 micrometers identify the carbonate at this location as magnesium carbonate. The broad 1.0 micrometer band indicates some small amount of ferrous iron is also present and the feature at 1.9 micrometers indicates the presence of water. CRISM researchers believe the magnesium carbonate found in the Nili Fossae region formed from alteration of olivine by water.

    The data come from a CRISM image catalogued as FRT00003E12. The spectra shown here are five-pixel-by-five-pixel averages of CRISM L-detector spectra taken from three different areas within the image that have then been ratioed to a five-pixel-by-five-pixel common denominator spectrum taken from a spectrally unremarkable area with no distinctive mineralogic signatures. This technique highlights the spectral contrasts between regions due to their unique mineralogy. The spectral wavelengths near 2.0 micrometers are affected by atmospheric absorptions and have been removed for clarity.

    NASA's Jet Propulsion Laboratory, a division of the California Institute of Technology, Pasadena, manages the Mars

  16. IR SPECTRA BY DFT FOR GLUCOSE AND ITS EPIMERS: A COMPARISON BETWEEN VACUUM AND SOLVATED SPECTRA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infrared spectra were calculated for the low energy geometry optimized structures of glucose and all of its epimers, at B3LYP/6-311++G** level of theory. Calculations were performed both in vacuo and using the COSMO solvation method. Frequencies, zero point energies, enthalpies, entropies, and rel...

  17. Infrared Spectra of Polycyclic Aromatic Hydrocarbons: Nitrogen Substitution

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Arnold, James O. (Technical Monitor)

    1998-01-01

    The B3LYP/4-31G approach is used to compute the harmonic frequencies of substituted naphthalene, anthracene, and their cations. The substitutions include cyano (CN), aminio (NH2), imino (NH), and replacement of a CH group by a nitrogen atom. All unique sites are considered, namely 1 and 2 for naphthalene and 1, 2, and 9 for an'tracene, except for the imino, where only 2-iminonaphthalene is studied. The IR spectra of these substituted species are compared with those of the unsubstituted molecules. The addition of a CN group does not significantly affect the spectra except to add the CN stretching frequency. Replacing a CH group by N has only a small effect on the IR spectra. The addition of the NH2 group dramatically affects the neutral spectra, giving it much of the character of the cation spectra. However, the neutral 2-irrinonaphthalene spectra looks more like that of naphthalene than like the 2-aminonaphthalene spectra.

  18. New LRS spectra for 356 bright IRAS sources

    NASA Technical Reports Server (NTRS)

    Volk, Kevin; Cohen, Martin

    1989-01-01

    The low-resolution spectra of all IRAS point sources with F(nu) (12 microns) greater than 40 Jy that were not included in the Atlas of Low-Resolution Spectra are presented. These have been classified into eight groups based upon the spectral morphology. Silicate emission spectra and red-continuum spectra associated with H II region sources form about 60 percent of this sample. All types of spectra in the LRS Atlas are represented in the sample except for emission-line sources. The sample is used to test a recent classification scheme for IRAS sources based on broadband colors. The spectra is used to test a recent classification scheme for IRAS sources based on broadband colors. The spectra are consistent with the classifications from the colors in most cases.

  19. Phonon spectra of plutonium at high temperatures

    NASA Astrophysics Data System (ADS)

    Dorado, Boris; Bottin, François; Bouchet, Johann

    2017-03-01

    Ab initio molecular dynamics calculations are used to investigate the vibrational properties of the high-temperature δ and ɛ phases of plutonium. We combine the local-density approximation (LDA)+U for strong electron correlations and the temperature-dependent effective potential method in order to calculate the phonon spectra of the two phases, as well as their dependence on temperature. Our results show that the ɛ phase can only be stabilized when temperature and correlations are simultaneously accounted for. We are also able to quantify the degree of anharmonicity of the two phases. While the δ phase is fairly harmonic up to 1000 K, we find that the ɛ phase is strongly anharmonic, which explains why this structure dominates the phase diagram at high temperature.

  20. Electron spectra from decay of fission products

    SciTech Connect

    Dickens, J K

    1982-09-01

    Electron spectra following decay of individual fission products (72 less than or equal to A less than or equal to 162) are obtained from the nuclear data given in the compilation using a listed and documented computer subroutine. Data are given for more than 500 radionuclides created during or after fission. The data include transition energies, absolute intensities, and shape parameters when known. An average beta-ray energy is given for fission products lacking experimental information on transition energies and intensities. For fission products having partial or incomplete decay information, the available data are utilized to provide best estimates of otherwise unknown decay schemes. This compilation is completely referenced and includes data available in the reviewed literature up to January 1982.

  1. Multiconfigurational Effects in Theoretical Resonance Raman Spectra

    PubMed Central

    Ma, Yingjin

    2017-01-01

    Abstract We analyze resonance Raman spectra of the nucleobase uracil in the short‐time approximation calculated with multiconfigurational methods. We discuss the importance of static electron correlation by means of density‐matrix renormalization group self‐consistent field (DMRG‐SCF) calculations. Our DMRG‐SCF results reveal that a minimal active orbital space that leads to a qualitatively correct description of the resonance Raman spectrum of uracil should encompass parts of the σ/σ* bonding/anti‐bonding orbitals of the pyrimidine ring. We trace these findings back to the considerable entanglement between the σ/σ* bonding/anti‐bonding as well as valence π/π* orbitals in the excited‐state electronic structure of uracil, which indicates non‐negligible non‐dynamical correlation effects that are less pronounced in the electronic ground state. PMID:27933695

  2. Chemical and isotopic determination from complex spectra

    SciTech Connect

    Zardecki, A.; Strittmatter, R.B.

    1995-07-01

    Challenges for proliferation detection include remote, high- sensitivity detection of chemical effluents from suspect facilities and enhanced detection sensitivity for nuclear material. Both the identification of chemical effluents with lidar and enhanced nuclear material detection from radiation sensors involve determining constituents from complex spectra. In this paper, we extend techniques used to analyze time series to the analysis of spectral data. Pattern identification methods are applied to spectral data for domains where standard matrix inversion may not be suitable because of detection statistics. We use a feed-forward, back-propagation neural network in which the nodes of the input layer are fed with the observed spectral data. The nodes of the output layer contain the identification and concentration of the isotope or chemical effluent the sensor is to identify. We will discuss the neural network architecture, together with preliminary results obtained from the training process.

  3. Terahertz absorption spectra of highly energetic chemicals

    NASA Astrophysics Data System (ADS)

    Slingerland, E. J.; Vallon, M. K.; Jahngen, E. G. E.; Giles, R. H.; Goyette, T. M.

    2010-04-01

    Research into absorption spectra is useful for detecting chemicals in the field. Each molecule absorbs a set of specific frequencies, which are dependent on the molecule's structure. While theoretical models are available for predicting the absorption frequencies of a particular molecule, experimental measurements are a more reliable method of determining a molecule's actual absorption behavior. The goal of this research is to explore chemical markers (absorption frequencies) that can be used to identify highly energetic molecules of interest to the remote sensing community. Particular attention was paid to the frequency ranges located within the terahertz transmission windows of the atmosphere. In addition, theoretical derivations, with the purpose of calculating the detection limits of such chemicals, will also be presented.

  4. Radioactive sample effects on EDXRF spectra

    SciTech Connect

    Worley, Christopher G

    2008-01-01

    Energy dispersive X-ray fluorescence (EDXRF) is a rapid, straightforward method to determine sample elemental composition. A spectrum can be collected in a few minutes or less, and elemental content can be determined easily if there is adequate energy resolution. Radioactive alpha emitters, however, emit X-rays during the alpha decay process that complicate spectral interpretation. This is particularly noticeable when using a portable instrument where the detector is located in close proximity to the instrument analysis window held against the sample. A portable EDXRF instrument was used to collect spectra from specimens containing plutonium-239 (a moderate alpha emitter) and americium-241 (a heavy alpha emitter). These specimens were then analyzed with a wavelength dispersive XRF (WDXRF) instrument to demonstrate the differences to which sample radiation-induced X-ray emission affects the detectors on these two types of XRF instruments.

  5. Evolution and infrared spectra of brown dwarfs

    NASA Technical Reports Server (NTRS)

    Lunine, Jonathan I.; Hubbard, William B.; Marley, Mark S.

    1986-01-01

    Self-consistent models are constructed for the structure, evolution, and observable properties of degenerately cooling objects, or 'brown dwarfs'. Model atmospheres composed of a range of likely gaseous and particulate opacity sources are calculated in order to provide a boundary condition for interior temperature-pressure profiles and to determine the emergent spectra for such objects. The radius derived from the interior models is combined with the emergent fluxes calculated from the atmosphere model to fit the data of McCarthy, Probst, and Low (1985) and to derive the luminosity and mass of VB 8B. The latter is found to be most probably an 0.05 solar mass object with effective temperature in the 1200-1500 K range and an atmosphere which very likely contains particulate absorbers. Key changes in chemical oxidation state and condensation of major constituents during the evolution of brown dwarfs are presented.

  6. Neural Network Solutions to Optical Absorption Spectra

    NASA Astrophysics Data System (ADS)

    Rosenbrock, Conrad

    2012-10-01

    Artificial neural networks have been effective in reducing computation time while achieving remarkable accuracy for a variety of difficult physics problems. Neural networks are trained iteratively by adjusting the size and shape of sums of non-linear functions by varying the function parameters to fit results for complex non-linear systems. For smaller structures, ab initio simulation methods can be used to determine absorption spectra under field perturbations. However, these methods are impractical for larger structures. Designing and training an artificial neural network with simulated data from time-dependent density functional theory may allow time-dependent perturbation effects to be calculated more efficiently. I investigate the design considerations and results of neural network implementations for calculating perturbation-coupled electron oscillations in small molecules.

  7. First dynamic spectra of stellar microwave flares

    NASA Technical Reports Server (NTRS)

    Bastian, T. S.; Bookbinder, J. A.

    1987-01-01

    The VLA has been used in the spectral-line mode at 1.4 GHz to obtain the first dynamic spectra of stellar sources other than the sun. Two very intense, highly circularly polarized, microwave outbursts were observed on the dMe flare star UV Cet, in addition to a slowly varying, unpolarized component. One outburst was purely left circularly polarized and showed no variations as a function of frequency across the 41 MHz band, whereas the other was as much as 70 percent right-circularly polarized and showed distinct variations with frequency. Although the slowly varying emission is probably due to incoherent gyrosynchrotron emission, the two flaring events are the result of coherent mechanisms. The coherent emission is interpreted in terms of plasma radiation and the cyclotron maser instability.

  8. Spectra of Particulate Backscattering in Natural Waters

    NASA Technical Reports Server (NTRS)

    Gordon, Howard, R.; Lewis, Marlon R.; McLean, Scott D.; Twardowski, Michael S.; Freeman, Scott A.; Voss, Kenneth J.; Boynton, Chris G.

    2009-01-01

    Hyperspectral profiles of downwelling irradiance and upwelling radiance in natural waters (oligotrophic and mesotrophic) are combined with inverse radiative transfer to obtain high resolution spectra of the absorption coefficient (a) and the backscattering coefficient (bb) of the water and its constituents. The absorption coefficient at the mesotrophic station clearly shows spectral absorption features attributable to several phytoplankton pigments (Chlorophyll a, b, c, and Carotenoids). The backscattering shows only weak spectral features and can be well represented by a power-law variation with wavelength (lambda): b(sub b) approx. Lambda(sup -n), where n is a constant between 0.4 and 1.0. However, the weak spectral features in b(sub b), suggest that it is depressed in spectral regions of strong particle absorption. The applicability of the present inverse radiative transfer algorithm, which omits the influence of Raman scattering, is limited to lambda < 490 nm in oligotrophic waters and lambda < 575 nm in mesotrophic waters.

  9. Galactic cosmic ray composition and energy spectra

    NASA Technical Reports Server (NTRS)

    Mewaldt, R. A.

    1994-01-01

    Galactic cosmic ray nuclei represent a significant risk to long-duration spaceflight outside the magnetosphere. We review briefly existing measurements of the composition and energy spectra of heavy cosmic ray nuclei, pointing out which species and energy ranges are most critical to assessing cosmic ray risks for spaceflight. Key data sets are identified and a table of cosmic ray abundances is presented for elements from H to Ni (Z = 1 to 28). Because of the 22-year nature of the solar modulation cycle, data from the approaching 1998 solar minimum is especially important to reducing uncertainties in the cosmic ray radiation hazard. It is recommended that efforts to model this hazard take advantage of approaches that have been developed to model the astrophysical aspects of cosmic rays.

  10. 3- to 13-micron spectra of Io

    NASA Technical Reports Server (NTRS)

    Noll, Keith S.; Hammel, H. B.; Young, Leslie; Joiner, Joanna; Hackwell, J.; Lynch, D. K.; Russell, R.

    1993-01-01

    The Broadband Array Spectrograph System with the NASA Infrared Telescope Facility was used to obtain 3- to 13-micron spectra of Io on June 14-16, 1991. The extinction correction and its error for each standard star (Alpha Boo, Alpha Lyr, and Mu UMa) were found individually by performing an unweighted linear fit of instrumental magnitude as a function of airmass. The model results indicate two significant trends: (1) modest differences between the two hemispheres at lower background temperatures and (2) a tendency to higher temperatures, smaller areas, and less power from the warm component at higher background temperatures with an increased contrast between the two hemispheres. The increased flux from 8 to 13 microns is due primarily to a greater area on the Loki (trailing) hemisphere for the warm component, although temperature also plays a role.

  11. UV Spectra, Bombs, and the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Judge, Philip G.

    2015-08-01

    A recent analysis of UV data from the Interface Region Imaging Spectrograph (IRIS) reports plasma “bombs” with temperatures near 8 × 104 K within the solar photosphere. This is a curious result, first because most bomb plasma pressures p (the largest reported case exceeds 103 dyn cm-2) fall well below photospheric pressures (\\gt 7× {10}3), and second, UV radiation cannot easily escape from the photosphere. In the present paper the IRIS data is independently analyzed. I find that the bombs arise from plasma originally at pressures between ≤ 80 and 800 dyne cm-2 before explosion, i.e., between ≥ 850 and 550 km above {τ }500=1. This places the phenomenon’s origin in the low-mid chromosphere or above. I suggest that bomb spectra are more compatible with Alfvénic turbulence than with bi-directional reconnection jets.

  12. On Magnetic Spectra of Earth and Mars

    NASA Technical Reports Server (NTRS)

    Voorhies, C. V.; Sabaka, T. J.; Purucker, M.

    2002-01-01

    The spectral method for distinguishing crustal from core-source magnetic fields is reexamined, modified, and applied to both a comprehensive geomagnetic field model and an altitude normalized magnetic map of Mars. The observational spectra are fairly fitted by theoretical forms expected from certain elementary classes of magnetic sources. For Earth we find fields from a core of radius 3512 +/- 64 km, in accord with the seismologic core radius of 3480 km, and a crust represented by a shell of random dipolar sources at radius 6367 +/- 14 km, near the planetary mean radius of 6371.2 km. For Mars we find no sign of a core-source field, only a field from a crust represented in same way, but at radius 3344 +/- 10 km, about 46 km below the planetary mean radius of 3389.5 km, and with sources about 9.6 +/- 3.2 times stronger.

  13. Spectra as windows into exoplanet atmospheres.

    PubMed

    Burrows, Adam S

    2014-09-02

    Understanding a planet's atmosphere is a necessary condition for understanding not only the planet itself, but also its formation, structure, evolution, and habitability. This requirement puts a premium on obtaining spectra and developing credible interpretative tools with which to retrieve vital planetary information. However, for exoplanets, these twin goals are far from being realized. In this paper, I provide a personal perspective on exoplanet theory and remote sensing via photometry and low-resolution spectroscopy. Although not a review in any sense, this paper highlights the limitations in our knowledge of compositions, thermal profiles, and the effects of stellar irradiation, focusing on, but not restricted to, transiting giant planets. I suggest that the true function of the recent past of exoplanet atmospheric research has been not to constrain planet properties for all time, but to train a new generation of scientists who, by rapid trial and error, are fast establishing a solid future foundation for a robust science of exoplanets.

  14. Towards simulation of high temperature methane spectra

    NASA Astrophysics Data System (ADS)

    Borysov, A.; Champion, J. P.; Jørgensen, U. G.; Wenger, C.

    Methane plays a central role in gas layers of temperatures up to around 3000K in a number of astrophysical objects ranging from giant planets to brown dwarfs, over proto-solar nebulae, to several classes of cool stars. In order to model and analyse these objects correctly, an accurate and complete list of spectral lines at high temperature is demanded. Predicting high temperature spectra implies, however, predicting hot bands and thus modelling highly excited vibrational states. This is a real challenge in the case of methane. We report the preliminary results of a theoretical study combining the global effective Hamiltonian approach and its computational implementation (STDS package: http://www.u-bourgogne.fr/LPUB/ shTDS.html) with semi-quantitative statistical considerations.

  15. Satellite spectra for helium-like titanium

    SciTech Connect

    Bely-Dubac, F.; Faucher, P.; Steeman-Clark, L.; Dubau, J.; Cammy-Val, C.; Bitter, M.; Hill, K.W.; von Goeler, S.

    1982-06-01

    Wavelengths and atomic parameters for both dielectronic and inner-shell satellite lines of the type ls/sup 2/ nl - 1s2l' nl, with n = 2, 3, and 4, have been calculated for Ti XX. The atomic data were calculated in a multiconfiguration intermediate coupling scheme and are compared with previous results for n = 2. The intensities of the higher n satellites are derived from these data, and thus an estimate of the contribution of the unresolved dielectronic satellites to the resonance line is obtained. Direct excitation rates are also given for the resonance, intercombination and forbidden lines for He-like titanium. Cascades and the effect of resonances for these lines are not considered in this paper. These results are used to fit an experimental soft x-ray spectrum from the PDX (Poloidal Divertor Experiment) tokamak discharge. Good agreement is obtained between computed and observed spectra.

  16. Workshop to establish databases of carbohydrate spectra

    SciTech Connect

    1995-12-31

    The workshop was organized to formulate guidelines for establishing spectral databases of complex carbohydrates. The databases will enable the scientific community to avoid the great waste of research effort and funds that frequently occurs when carbohydrate chemists are forced to duplicate the structural characterization of previously characterized complex carbohydrates. Chemists waste their effort on repetitive characterizations because in the absence of spectral databases they are unaware they are analyzing a known molecule until they have completely determined its structure. Chemists will be able to avoid much of this wasted effort when the collections of mass and of nuclear magnetic resonance (NMR) spectra initiated at the workshop are subsequently developed into searchable databases. Then scientists only need query the databases with the spectrum or with information defining the spectrum of an unidentified carbohydrate to find out if it has been previously characterized.

  17. Optical absorption spectra of dications of carotenoids

    SciTech Connect

    Jeevarajan, J.A.; Wei, C.C.; Jeevarajan, A.S.; Kispert, L.D.

    1996-04-04

    Quantitative optical absorption spectra of the cation radicals and the dications of canthaxanthin (I), {beta}carotene (II), 7`-cyano-7`-ethoxycarbonyl-7`-apo-{beta}-carotene (III), and 7`,7`-dimethyl-7`-apo-{beta}-carotene (IV) in dichloromethane solution are reported. Exclusive formation of dications occurs when the carotenoids are oxidized with ferric chloride. Addition of neutral carotenoid to the dications results in equilibrium formation of cation radicals. Oxidation with iodine in dichloromethane affords only cation radicals; electrochemical oxidation under suitable conditions yields both dications and cation radicals. Values of the optical parameters depend on the nature of the oxidative medium. The oscillator strengths calculated for gas phase cation radicals and dications of I-IV using the INDO/S method show the same trend as the experimental values. 31 refs., 4 figs., 2 tabs.

  18. X ray spectra of cataclysmic variables

    NASA Technical Reports Server (NTRS)

    Patterson, Joseph; Halpern, Jules

    1990-01-01

    X ray spectral parameters of cataclysmic variables observed with the 'Einstein' imaging proportional counter were determined by fitting an optically thin, thermal bremsstrahlung spectrum to the raw data. Most of the sources show temperatures of order a few keV, while a few sources exhibit harder spectra with temperatures in excess of 10 keV. Estimated 0.1 to 3.5 keV luminosities are generally in the range from 10(exp 30) to 10(exp 32) erg/sec. The results are consistent with the x rays originating in a disk/white dwarf boundary layer of non-magnetic systems, or in a hot, post-shock region in the accretion column of DQ Her stars, with a negligible contribution from the corona of the companion. In a few objects column densities were found that are unusually high for interstellar material. It was suggested that the absorption occurs in the system itself.

  19. HF Accelerated Electron Fluxes, Spectra, and Ionization

    NASA Astrophysics Data System (ADS)

    Carlson, Herbert C.; Jensen, Joseph B.

    2015-10-01

    Wave particle interactions, an essential aspect of laboratory, terrestrial, and astrophysical plasmas, have been studied for decades by transmitting high power HF radio waves into Earth's weakly ionized space plasma, to use it as a laboratory without walls. Application to HF electron acceleration remains an active area of research (Gurevich in Usp Fizicheskikh Nauk 177(11):1145-1177, 2007) today. HF electron acceleration studies began when plasma line observations proved (Carlson et al. in J Atmos Terr Phys 44:1089-1100, 1982) that high power HF radio wave-excited processes accelerated electrons not to ~eV, but instead to -100 times thermal energy (10 s of eV), as a consequence of inelastic collision effects on electron transport. Gurevich et al (J Atmos Terr Phys 47:1057-1070, 1985) quantified the theory of this transport effect. Merging experiment with theory in plasma physics and aeronomy, enabled prediction (Carlson in Adv Space Res 13:1015-1024, 1993) of creating artificial ionospheres once ~GW HF effective radiated power could be achieved. Eventual confirmation of this prediction (Pedersen et al. in Geophys Res Lett 36:L18107, 2009; Pedersen et al. in Geophys Res Lett 37:L02106, 2010; Blagoveshchenskaya et al. in Ann Geophys 27:131-145, 2009) sparked renewed interest in optical inversion to estimate electron spectra in terrestrial (Hysell et al. in J Geophys Res Space Phys 119:2038-2045, 2014) and planetary (Simon et al. in Ann Geophys 29:187-195, 2011) atmospheres. Here we present our unpublished optical data, which combined with our modeling, lead to conclusions that should meaningfully improve future estimates of the spectrum of HF accelerated electron fluxes. Photometric imaging data can significantly improve detection of emissions near ionization threshold, and confirm depth of penetration of accelerated electrons many km below the excitation altitude. Comparing observed to modeled emission altitude shows future experiments need electron density profiles

  20. Universality of vibrational spectra of globular proteins

    NASA Astrophysics Data System (ADS)

    Na, Hyuntae; Song, Guang; ben-Avraham, Daniel

    2016-02-01

    It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e. regardless of the protein in question, it closely follows one universal curve. The present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, goes far beyond previous claims of universality, confirming that universality holds even in the frequency range that is well above 100 cm-1 (300-4000 cm-1), where peaks and turns in the density of states are faithfully reproduced from one protein to the next. We also characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such ‘outlier’ proteins. Since the method used for the derivation of the vibrational modes (potential energy formulation, set of degrees of freedom employed, etc) has a dramatic effect on the spectral density, another significant implication of our findings is that the universality can provide an exquisite tool for assessing and improving the quality of potential functions and the quality of various models used for NMA computations. Finally, we show that the input configuration also affects the density of modes, thus emphasizing the importance of simplified potential energy formulations that are minimized at the outset. In summary, our findings call for a serious two-way dialogue between theory and experiment: experimental spectra of proteins could now guide the fine tuning of theoretical empirical potentials, and the various features and peaks observed in theoretical studies—being universal, and hence now rising in importance—would hopefully spur experimental confirmation.

  1. Spectra of small Koronis family members

    NASA Astrophysics Data System (ADS)

    Thomas, C.; Rivkin, A.; Trilling, D.; Moskovitz, N.

    2014-07-01

    The space-weathering process and its implications for the relationships between S- and Q-type asteroids and ordinary chondrite meteorites are long-standing problems in asteroid science. Although the visible and near-infrared spectra of S- and Q-type objects qualitatively show the same absorption features and quantitatively show evidence of the same minerals, the S types display increased spectral slopes and muted absorption features compared to the Q types. This spectral mismatch is consistent with the effects of the space weathering process. Binzel et al. provided the missing link between Q- and S-type bodies in near-Earth space by showing a reddening of spectral slope in objects from 0.1 to 5 km that corresponded to the transition from Q- to S-type spectra. This result implied that size, and therefore age, is related to the relationship between Q- and S-type. The existence of Q-type objects in the main belt was not confirmed until Mothe-Diniz and Nesvorny (2008) found them in young S-type clusters. To investigate the trend from Q to S in the main belt, we examined space weathering within the old main-belt Koronis family using a spectrophotometric survey (Rivkin et al. 2011, Thomas et al. 2011). Rivkin et al. (2011) identified several potential Q-type objects within the Koronis family. Our Q-type candidates were identified using broad-band spectrophotometry and could not be taxonomically classified on that basis alone. We obtained follow-up visible and near-infrared spectral observations of our potential Q-type objects, (26970) Elias, (45610) 2000 DJ_{48}, and (37411) 2001 XF_{152}, using Gemini and Magellan. We will present the results of these spectral follow-up observations. Observations of (26970) Elias demonstrate that the object is more consistent with the average Q-type spectrum than the average S-type spectrum.

  2. Polarization effects in cutaneous autofluorescent spectra

    NASA Astrophysics Data System (ADS)

    Borisova, E.; Angelova, L.; Jeliazkova, Al.; Genova, Ts.; Pavlova, E.; Troyanova, P.; Avramov, L.

    2014-05-01

    Used polarized light for fluorescence excitation one could obtain response related to the anisotropy features of extracellular matrix. The fluorophore anisotropy is attenuated during lesions' growth and level of such decrease could be correlated with the stage of tumor development. Our preliminary investigations are based on in vivo point-by-point measurements of excitation-emission matrices (EEM) from healthy volunteers skin on different ages and from different anatomical places using linear polarizer and analyzer for excitation and emission light detected. Measurements were made using spectrofluorimeter FluoroLog 3 (HORIBA Jobin Yvon, France) with fiber-optic probe in steady-state regime using excitation in the region of 280-440 nm. Three different situations were evaluated and corresponding excitation-emission matrices were developed - with parallel and perpendicular positions for linear polarizer and analyzer, and without polarization of excitation and fluorescence light detected from a forearm skin surface. The fluorescence spectra obtained reveal differences in spectral intensity, related to general attenuation, due to filtering effects of used polarizer/analyzer couple. Significant spectral shape changes were observed for the complex autofluorescence signal detected, which correlated with collagen and protein cross-links fluorescence, that could be addressed to the tissue extracellular matrix and general condition of the skin investigated, due to morphological destruction during lesions' growth. A correlation between volunteers' age and the fluorescence spectra detected was observed during our measurements. Our next step is to increase developed initial database and to evaluate all sources of intrinsic fluorescent polarization effects and found if they are significantly altered from normal skin to cancerous state of the tissue, this way to develop a non-invasive diagnostic tool for dermatological practice.

  3. Curved Radio Spectra of Weak Cluster Shocks

    NASA Astrophysics Data System (ADS)

    Kang, Hyesung; Ryu, Dongsu

    2015-08-01

    In order to understand certain observed features of arc-like giant radio relics such as the rareness, uniform surface brightness, and curved integrated spectra, we explore a diffusive shock acceleration (DSA) model for radio relics in which a spherical shock impinges on a magnetized cloud containing fossil relativistic electrons. Toward this end, we perform DSA simulations of spherical shocks with the parameters relevant for the Sausage radio relic in cluster CIZA J2242.8+5301, and calculate the ensuing radio synchrotron emission from re-accelerated electrons. Three types of fossil electron populations are considered: a delta-function like population with the shock injection momentum, a power-law distribution, and a power law with an exponential cutoff. The surface brightness profile of the radio-emitting postshock region and the volume-integrated radio spectrum are calculated and compared with observations. We find that the observed width of the Sausage relic can be explained reasonably well by shocks with speed {u}{{s}}˜ 3× {10}3 {km} {{{s}}}-1 and sonic Mach number {M}{{s}}˜ 3. These shocks produce curved radio spectra that steepen gradually over (0.1-10){ν }{br} with a break frequency {ν }{br}˜ 1 GHz if the duration of electron acceleration is ˜60-80 Myr. However, the abrupt increase in the spectral index above ˜1.5 GHz observed in the Sausage relic seems to indicate that additional physical processes, other than radiative losses, operate for electrons with {γ }{{e}}≳ {10}4.

  4. High Pressure Oxygen A-Band Spectra

    NASA Astrophysics Data System (ADS)

    Drouin, Brian; Sung, Keeyoon; Yu, Shanshan; Lunny, Elizabeth M.; Bui, Thinh Quoc; Okumura, Mitchio; Rupasinghe, Priyanka; Bray, Caitlin; Long, David A.; Hodges, Joseph; Robichaud, David; Benner, D. Chris; Devi, V. Malathy; Hoo, Jiajun

    2015-06-01

    Composition measurements from remote sensing platforms require knowledge of air mass to better than the desired precision of the composition. Oxygen spectra allow determination of air mass since the mixing ratio of oxygen is fixed. The OCO-2 mission is currently retrieving carbon dioxide concentration using the oxygen A-band for air mass normalization. The 0.25% accuracy desired for the carbon dioxide concentration has pushed the state-of-the-art for oxygen spectroscopy. To produce atmospheric pressure A-band cross-sections with this accuracy requires a sophisticated line-shape model (Galatry or Speed-Dependent) with line mixing (LM) and collision induced absorption (CIA). Models of each of these phenomena exist, but an integrated self-consistent model must be developed to ensure accuracy. This presentation will describe the ongoing effort to parameterize these phenomena on a representative data set created from complementary experimental techniques. The techniques include Fourier transform spectroscopy (FTS), photo-acoustic spectroscopy (PAS) and cavity ring-down spectroscopy (CRDS). CRDS data allow long-pathlength measurements with absolute intensities, providing lineshape information as well as LM and CIA, however the subtleties of the lineshape are diminished in the saturated line-centers. Conversely, the short paths and large dynamic range of the PAS data allow the full lineshape to be discerned, but with an arbitrary intensity axis. Finally, the FTS data provides intermediate paths and consistency across a broad pressure range. These spectra are all modeled with the Labfit software using first the spectral line database HITRAN, and then model values are adjusted and fitted for better agreement with the data.

  5. [Raman spectra of monkey cerebral cortex tissue].

    PubMed

    Zhu, Ji-chun; Guo, Jian-yu; Cai, Wei-ying; Wang, Zu-geng; Sun, Zhen-rong

    2010-01-01

    Monkey cerebral cortex, an important part in the brain to control action and thought activities, is mainly composed of grey matter and nerve cell. In the present paper, the in situ Raman spectra of the cerebral cortex of the birth, teenage and aged monkeys were achieved for the first time. The results show that the Raman spectra for the different age monkey cerebral cortex exhibit most obvious changes in the regions of 1000-1400 and 2800-3000 cm(-1). With monkey growing up, the relative intensities of the Raman bands at 1313 and 2885 cm(-1) mainly assigned to CH2 chain vibrational mode of lipid become stronger and stronger whereas the relative intensities of the Raman bands at 1338 and 2932 cm(-1) mainly assigned to CH3 chain vibrational mode of protein become weaker and weaker. In addition, the two new Raman bands at 1296 and 2850 cm(-1) are only observed in the aged monkey cerebral cortex, therefore, the two bands can be considered as a character or "marker" to differentiate the caducity degree with monkey growth In order to further explore the changes, the relative intensity ratios of the Raman band at 1313 cm(-1) to that at 1338 cm(-1) and the Raman band at 2885 cm(-1) to that at 2 932 cm(-1), I1313/I1338 and I2885/I2932, which are the lipid-to-protein ratios, are introduced to denote the degree of the lipid content. The results show that the relative intensity ratios increase significantly with monkey growth, namely, the lipid content in the cerebral cortex increases greatly with monkey growth. So, the authors can deduce that the overmuch lipid is an important cause to induce the caducity. Therefore, the results will be a powerful assistance and valuable parameter to study the order of life growth and diagnose diseases.

  6. THEORETICAL SPECTRA OF TERRESTRIAL EXOPLANET SURFACES

    SciTech Connect

    Hu Renyu; Seager, Sara; Ehlmann, Bethany L.

    2012-06-10

    We investigate spectra of airless rocky exoplanets with a theoretical framework that self-consistently treats reflection and thermal emission. We find that a silicate surface on an exoplanet is spectroscopically detectable via prominent Si-O features in the thermal emission bands of 7-13 {mu}m and 15-25 {mu}m. The variation of brightness temperature due to the silicate features can be up to 20 K for an airless Earth analog, and the silicate features are wide enough to be distinguished from atmospheric features with relatively high resolution spectra. The surface characterization thus provides a method to unambiguously identify a rocky exoplanet. Furthermore, identification of specific rocky surface types is possible with the planet's reflectance spectrum in near-infrared broad bands. A key parameter to observe is the difference between K-band and J-band geometric albedos (A{sub g}(K) - A{sub g}(J)): A{sub g}(K) - A{sub g}(J) > 0.2 indicates that more than half of the planet's surface has abundant mafic minerals, such as olivine and pyroxene, in other words primary crust from a magma ocean or high-temperature lavas; A{sub g}(K) - A{sub g}(J) < -0.09 indicates that more than half of the planet's surface is covered or partially covered by water ice or hydrated silicates, implying extant or past water on its surface. Also, surface water ice can be specifically distinguished by an H-band geometric albedo lower than the J-band geometric albedo. The surface features can be distinguished from possible atmospheric features with molecule identification of atmospheric species by transmission spectroscopy. We therefore propose that mid-infrared spectroscopy of exoplanets may detect rocky surfaces, and near-infrared spectrophotometry may identify ultramafic surfaces, hydrated surfaces, and water ice.

  7. Prediction of electroencephalographic spectra from neurophysiology

    NASA Astrophysics Data System (ADS)

    Robinson, P. A.; Rennie, C. J.; Wright, J. J.; Bahramali, H.; Gordon, E.; Rowe, D. L.

    2001-02-01

    A recent neurophysical model of propagation of electrical waves in the cortex is extended to include a physiologically motivated subcortical feedback loop via the thalamus. The electroencephalographic spectrum when the system is driven by white noise is then calculated analytically in terms of physiological parameters, including the effects of filtering of signals by the cerebrospinal fluid, skull, and scalp. The spectral power at low frequencies is found to vary as f-1 when awake and f-3 when asleep, with a breakpoint to a steeper power-law tail at frequencies above about 20 Hz in both cases; the f-1 range concurs with recent magnetoencephalographic observations of such a regime. Parameter sensitivities are explored, enabling a model with fewer free parameters to be proposed, and showing that spectra predicted for physiologically reasonable parameter values strongly resemble those observed in the laboratory. Alpha and beta peaks seen near 10 Hz and twice that frequency, respectively, in the relaxed wakeful state are generated via subcortical feedback in this model, thereby leading to predictions of their frequencies in terms of physiological parameters, and of correlations in their occurrence. Subcortical feedback is also predicted to be responsible for production of anticorrelated peaks in deep sleep states that correspond to the occurrence of theta rhythm at around half the alpha frequency and sleep spindles at 3/2 times the alpha frequency. An additional positively correlated waking peak near three times the alpha frequency is also predicted and tentatively observed, as are two new types of sleep spindle near 5/2 and 7/2 times the alpha frequency, and anticorrelated with alpha. These results provide a theoretical basis for the conventional division of EEG spectra into frequency bands, but imply that the exact bounds of these bands depend on the individual. Three types of potential instability are found: one at zero frequency, another in the theta band at around

  8. CO2 profile retrievals from TCCON spectra

    NASA Astrophysics Data System (ADS)

    Dohe, Susanne; Hase, Frank; Sepúlveda, Eliezer; García, Omaira; Wunch, Debra; Wennberg, Paul; Gómez-Peláez, Angel; Abshire, James B.; Wofsy, Steven C.; Schneider, Matthias; Blumenstock, Thomas

    2014-05-01

    The Total Carbon Column Observing Network (TCCON) is a global network of ground-based Fourier Transform Spectrometers recording direct solar spectra in the near-infrared spectral region. With stringent requirements on the instrumentation, data processing and calibration, accurate and precise column-averaged abundances of CO2, CH4, N2O, HF, CO, H2O, and HDO are retrieved being an essential contribution for the validation of satellite data (e.g. GOSAT, OCO-2) and carbon cycle research (Olsen and Randerson, 2004). However, the determined column-averaged dry air mole fraction (DMF) contains no information about the vertical CO2 profile, due to the use of a simple scaling retrieval within the common TCCON analysis, where the fitting algorithm GFIT (e.g. Yang et al., 2005) is used. In this presentation we will apply a different procedure for calculating trace gas abundances from the measured spectra, the fitting algorithm PROFFIT (Hase et. al., 2004) which has been shown to be in very good accordance with GFIT. PROFFIT additionally offers the ability to perform profile retrievals in which the pressure broadening effect of absorption lines is used to retrieve vertical gas profiles, being of great interest especially for the CO2 modelling community. A new analyzing procedure will be shown and retrieved vertical CO2 profiles of the TCCON sites Izaña (Tenerife, Canary Islands, Spain) and Lamont (Oklahoma, USA) will be presented and compared with simultaneously performed surface in-situ measurements and CO2 profiles from different aircraft campaigns. References: - Hase, F. et al., J.Q.S.R.T. 87, 25-52, 2004. - Olsen, S.C. and Randerson, J.T., J.G.Res., 109, D023012, 2004. - Yang, Z. et al., J.Q.S.R.T., 90, 309-321, 2005.

  9. Spectra of volcanic rocks glasses as analogues of Mercury surface spectra

    NASA Astrophysics Data System (ADS)

    Carli, C.; Capaccioni, F.; de Sanctis, M.; Filacchione, G.; Sgavetti, M.; di Genova, D.; Vona, A.; Visonà, D.; Ammannito, E.

    2010-12-01

    Remote-sensing studies have revealed that most of the inner planets surfaces are composed by magmatic effusive rocks as lava flows or pyroclastic deposits, that are the natural products of magma-rock dynamic systems controlled by T, P, oxygen fugacity and time. These materials generally contain a fair amount of volcanic glass, due to the magma rapid cooling once effused on the surface. The VNIR reflectance spectroscopy is one of the most relevant tools for remote-sensing studies and in the last decades gave important results identifying the presence of different Fe-Mg silicates, such as olivine and pyroxenes, on the planets surfaces. However, the mineralogical interpretation of the observed spectral features of several volcanic areas on the inner Solar System bodies is still matter of debate. In particular the presence of dark volcanic glass, which can dominate or not the rock texture, influences the spectra signatures. In fact samples with a glass-bearing groundmass have lower albedo and reduced band intensity of the spectra of samples with comparable mineral composition and intergranular texture. As a consequence, an important goal for studying the planetary crusts is to understand the spectral behavior of volcanic material, where chemical or physical parameters are different depending on geologic context and effusive processes. We present here preliminary laboratory activity to investigate VNIR reflectance spectra of several volcanic glasses. Reflectance spectra, in the wavelength range between 0.35- 2.50 μm, are measured on powders of magmatic rocks, having different composition and textures, at fine (<60 μm in diameter) and very fine (<10 μm) grain sizes. For each rock sample a corresponding “thermal shocked-sample” is produced by heating at 1300°C and P=1 atm and a glass-sample was produced by melting at 1500°C and P=1 atm, than quenching it in air. Reflectance spectra of powders of shocked and glass-samples were acquired at the same grain size, and

  10. Browsing a wealth of millimeter-wavelength doppler spectra data

    SciTech Connect

    Johnson,K.; Luke,E.; Kollias, P.; Remillard, J.; Widener, K.; Jensen, M.

    2010-03-15

    The ARM Climate Research Facility has collected an extensive archive of vertically pointing millimeter wavelength Doppler radar spectra at both 35 and 95 GHz. These data are a rich potential source of detailed microphysical and dynamical cloud and precipitation information. The recording of spectra, which is ongoing, began at the Southern Great Plains site in September of 2003, at the North Slope of Alaska site in April 2004, and at Tropical Western Pacific sites in 2006. Spectra are also being collected during ARM Mobile Facility deployments. The data’s temporal resolution is as high as two seconds, at height intervals of 45 to 90 m. However, the sheer volume of available data can be somewhat daunting to access and search for specific features of interest. Here we present a user interface for spectra browsing, which allows the user to view time-height images of radar moments, select a time or height of interest, and then “drill down” through images of spectrograms to individual Doppler spectra or time- and height-sequences of spectra. Also available are images summarizing spectral characteristics, such as number of spectral peaks, spectral shape information (skewness and kurtosis), moment uncertainty estimates, and hydrometeor vs. clutter identification as produced by the ARM MicroARSCL (Microphysical Active Remote Sensing of Clouds) value-added product. In addition to the access and visualization tools, we are developing a Doppler spectra simulator capable of generating Doppler spectra from liquid, mixed-phase, and solid cloud constituents and precipitation. The Doppler spectra simulator can be used as an interface between explicit microphysics models and Doppler spectra observations from the ARM radars. The plan is to ultimately make the spectra simulator available from within the spectra browser, allowing a user to associate observed spectra with the microphysical conditions capable of producing them.

  11. Conformal symmetry and light flavor baryon spectra

    NASA Astrophysics Data System (ADS)

    Kirchbach, M.; Compean, C. B.

    2010-08-01

    The degeneracy among parity pairs systematically observed in the N and Δ spectra is interpreted to hint on a possible conformal symmetry realization in the light flavor baryon sector in line with AdS5/CFT4. The case is made by showing that all the observed N and Δ resonances with masses below 2500 MeV distribute fairly well each over the first levels of a unitary representation of the conformal group, a representation that covers the spectrum of a quark-diquark system, placed directly on a conformally compactified Minkowski spacetime, R1⊗S3, as approached from the AdS5 cone. The free geodesic motion on the S3 manifold is described by means of the scalar conformal equation there, which is of the Klein-Gordon-type. The equation is then gauged by the curved Coulomb potential that has the form of a cotangent function. Conformal symmetry is not exact, this because the gauge potential slightly modifies the conformal centrifugal barrier of the free geodesic motion. Thanks to this, the degeneracy between P11-S11 pairs from same level is relaxed, while the remaining states belonging to same level remain practically degenerate. The model describes the correct mass ordering in the P11-S11 pairs through the spectra as a combined effect of the above conformal symmetry breaking, on the one side, and a parity change of the diquark from a scalar at low masses, to a pseudoscalar at higher masses, on the other. The quality of the wave functions is illustrated by calculations of realistic mean square charge radii and electric charge form factors on the examples of the proton, and the protonic P11(1440), and S11(1535) resonances. The scheme also allows for a prediction of the dressing function of an effective instantaneous gluon propagator from the Fourier transform of the gauge potential. We find a dressing function that is finite in the infrared and tends to zero at infinity.

  12. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  13. [Raman spectra of fossil dinosaurs from different regions].

    PubMed

    Yang, Qun; Wang, Yi-lin

    2007-12-01

    Raman microscopic spectra in the higher wave number region were obtained from 7 fossil dinosaurs specimens from different regions. The specimens of fossil dinosaurs are different parts of bone. The Raman spectra of fossil dinosaurs indicate the high similarity among peak positions of different fossil dinosaurs; but important differences exist in the spectral peak figures. In the wave number region of 1000-1800 cm(-1) the Raman spectra of the same bone part fossils from different regions are very similar, example similarities between spectra of Lufeing backbone head and Yua nmou backbone head; Lufeng limb bone and Wuding limb bone. There are relations between the same bone part spectra of different fossil dinosaurs. The characteristic does not relate to regions. Raman spectra of fossil dinosaurs cannot be used to distinguish fossil source, although the part of bone can be used as an indicator to narrow the range of possible geographical origins.

  14. Radial Distribution of Electron Spectra from High-Energy Ions

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Katz, Robert; Wilson, John W.

    1998-01-01

    The average track model describes the response of physical and biological systems using radial dose distribution as the key physical descriptor. We report on an extension of this model to describe the average distribution of electron spectra as a function of radial distance from an ion. We present calculations of these spectra for ions of identical linear energy transfer (LET), but dissimilar charge and velocity to evaluate the differences in electron spectra from these ions. To illustrate the usefulness of the radial electron spectra for describing effects that are not described by electron dose, we consider the evaluation of the indirect events in microdosimetric distributions for ions. We show that folding our average electron spectra model with experimentally determined frequency distributions for photons or electrons provides a good representation of radial event spectra from high-energy ions in 0.5-2 micrometer sites.

  15. Monte Carlo simulation of Auger-electron spectra.

    PubMed

    Grau Carles, A; Kossert, K

    2009-01-01

    A procedure to calculate the complex spectra of electron-capture nuclides which simultaneously eject several electrons and X-rays with different energies is presented. The model is applied to compute spectra of the radionuclides (125)I, (123)I and (111)In. The spectra are then compared with experimental spectra obtained by means of liquid scintillation counting. To this end, the computed spectra were transformed to allow for the nonlinear response function for a liquid scintillator, chemical quenching, as well as the Wallac-type amplifier used for the measurements. The calculated spectra are important for applications of free parameter models in liquid scintillation counting and also for studying the impact of electron-capture nuclides on DNA.

  16. Camera artifacts in IUE low-dispersion spectra

    NASA Technical Reports Server (NTRS)

    Crenshaw, D. Michael; Norman, Dara J.; Bruegman, Otto W.

    1990-01-01

    Sky-background images obtained by the International Ultraviolet Explorer (IUE) were analyzed to study artificial spectral features (camera artifacts) in low-dispersion spectra. The artifacts mimic emission features and have been present in long-exposure spectra since the launch of the IUE satellite. The camera artifacts are strong in spectra characterized by long exposure times because they scale in time-integrated flux with the background level, which increases during the exposure due to camera phosphorescence. The artifacts cannot be detected in spectra obtained from short, direct exposures of flat-field lamps or standard stars. Plots of average sky-background spectra for the three operational IUE cameras (SWP, LWP, and LWR) are given to aid scientists in the identification of artifacts in their spectra.

  17. Simulation of dielectric spectra of erythrocytes with various shapes

    NASA Astrophysics Data System (ADS)

    Asami, Koji

    2009-07-01

    Dielectric spectra of erythrocyte suspensions were numerically simulated over a frequency range from 1 kHz to 100 MHz to study the effects of erythrocyte shape on the dielectric spectra. First, a biconcave-discoid model for normal erythrocytes or discocytes was compared with an equivalent oblate spheroid model. The two models showed similar dielectric spectra to each other, suggesting that the oblate spheroid model can be approximately used for discocytes. Second, dielectric spectra were simulated for discocytes deformed by osmotic cell swelling. The deformation resulted in the increase in relaxation intensity and the sharpening of spectrum shape. Finally, dielectric spectra were simulated for echinocytes, stomatocytes and sickle cells that are induced by chemical agents and diseases. The dielectric spectra of echinocytes and stomatocytes were similar to each other, being distinguishable from that of discocytes and quite different from that of sickle cells.

  18. Principal spectra describing magnetooptic permittivity tensor in cubic crystals

    NASA Astrophysics Data System (ADS)

    Hamrlová, Jana; Legut, Dominik; Veis, Martin; Pištora, Jaromír; Hamrle, Jaroslav

    2016-12-01

    We provide unified phenomenological description of magnetooptic effects being linear and quadratic in magnetization. The description is based on few principal spectra, describing elements of permittivity tensor up to the second order in magnetization. Each permittivity tensor element for any magnetization direction and any sample surface orientation is simply determined by weighted summation of the principal spectra, where weights are given by crystallographic and magnetization orientations. The number of principal spectra depends on the symmetry of the crystal. In cubic crystals owning point symmetry we need only four principal spectra. Here, the principal spectra are expressed by ab initio calculations for bcc Fe, fcc Co and fcc Ni in optical range as well as in hard and soft x-ray energy range, i.e. at the 2p- and 3p-edges. We also express principal spectra analytically using modified Kubo formula.

  19. AIS spectra of desert shrub canopies

    NASA Technical Reports Server (NTRS)

    Murray, R.; Isaacson, D. L.; Schrumpf, B. J.; Ripple, W. J.; Lewis, A. J.

    1986-01-01

    Airborne Imaging Spectrometer (AIS) data were collected 30 August 1985 from a desert shrub community in central Oregon. Spectra from artificial targets placed on the test site and from bare soil, big sagebrush (Artemesia tridentata wyomingensis), silver sagebrush (Artemesia cana bolander), and exposed volcanic rocks were studied. Spectral data from grating position 3 (tree mode) were selected from 25 ground positions for analysis by Principal Factor Analysis (PFA). In this grating position, as many as six factors were identified as significant in contributing to spectral structure. Channels 74 through 84 (tree mode) best characterized between-class differences. Other channels were identified as nondiscriminating and as associated with such errors as excessive atmospheric absorption and grating positin changes. The test site was relatively simple with the two species (A. tridentata and A. cana) representing nearly 95% of biomass and with only two mineral backgrounds, a montmorillonitic soil and volcanic rocks. If, as in this study, six factors of spectral structure can be extracted from a single grating position from data acquired over a simple vegetation community, then AIS data must be considered rich in information-gathering potential.

  20. Derivation of Piezoelectric Losses from Admittance Spectra

    NASA Astrophysics Data System (ADS)

    Zhuang, Yuan; Ural, Seyit O.; Rajapurkar, Aditya; Tuncdemir, Safakcan; Amin, Ahmed; Uchino, Kenji

    2009-04-01

    High power density piezoelectrics are required to miniaturize devices such as ultrasonic motors, transformers, and sound projectors. The power density is limited by the heat generation in piezoelectrics, therefore, clarification of the loss mechanisms is necessary. This paper provides a methodology to determine the electromechanical losses, i.e., dielectric, elastic and piezoelectric loss factors in piezoelectrics by means of a detailed analysis of the admittance/impedance spectra. This method was applied to determine the piezoelectric losses for lead zirconate titanate ceramics and lead magnesium niobate-lead titanate single crystals. The analytical solution provides a new method for obtaining the piezoelectric loss factor, which is usually neglected in practice by transducer designers. Finite element simulation demonstrated the importance of piezoelectric losses to yield a more accurate fitting to the experimental data. A phenomenological model based on two phase-shifts and the Devonshire theory of a polarizable-deformable insulator is developed to interpret the experimentally observed magnitudes of the mechanical quality factor at resonance and anti-resonance.

  1. Spectra as windows into exoplanet atmospheres

    PubMed Central

    Burrows, Adam S.

    2014-01-01

    Understanding a planet’s atmosphere is a necessary condition for understanding not only the planet itself, but also its formation, structure, evolution, and habitability. This requirement puts a premium on obtaining spectra and developing credible interpretative tools with which to retrieve vital planetary information. However, for exoplanets, these twin goals are far from being realized. In this paper, I provide a personal perspective on exoplanet theory and remote sensing via photometry and low-resolution spectroscopy. Although not a review in any sense, this paper highlights the limitations in our knowledge of compositions, thermal profiles, and the effects of stellar irradiation, focusing on, but not restricted to, transiting giant planets. I suggest that the true function of the recent past of exoplanet atmospheric research has been not to constrain planet properties for all time, but to train a new generation of scientists who, by rapid trial and error, are fast establishing a solid future foundation for a robust science of exoplanets. PMID:24613929

  2. Shape of the A=14 {beta} spectra

    SciTech Connect

    Garcia, A.; Brown, B.A.

    1995-10-01

    The shape of allowed {Beta} spectra have a small contribution from the interference of the vector, weak-magnetism and axial GT matrix elements. According to CVC plus charge-symmetry of nuclear interactions, in a 0{sup +}{r_arrow} 1{sup +} transition like the {Beta} and {gamma} decays of the A=14 system, the weak-magnetism and electro-magnetic-Ml matrix elements should be equal. A measurement of the shape of the {sup 14}O spectrum, however, disagrees, by a factor of two with naive calculation described above. It has been speculated that because of the high supression of GT matrix element in the A=14 system, one could understand this discrepancy based on small charge-symmetry-effects. We have used shell-model wave functions adjusted to fit {sup 14}N(e,e{sup {prime}}) inelastic scattering, the width of the M1-{gamma} transition, and the {Beta} log f t`s, and show that reasonable assumptions lead to estimates that are very close to the naive CVC estimation. We propose that the {sup 14}O discrepancy is important and that new experiments should be done to measure the shape of the spectrum.

  3. Characteristics of magnetospheric radio noise spectra

    NASA Technical Reports Server (NTRS)

    Herman, J. R.

    1976-01-01

    Magnetospheric radio noise spectra (30 kHz to 10 MHz) taken by IMP-6 and RAE-2 exhibit time varying characteristics which are related to spacecraft position and magnetospheric processes. In the midfrequency range (100-1000 kHz) intense noise peaks rise a factor of 100 or more above background; 80% of the peak frequencies are within the band 125 kHz to 600 kHz, and the peak occurs most often (18% of the time) at 280 kHz. Bandwidths of the peaks range from about 100 kHz to more than 500 kHz; most often the lower cutoff is at about 100 kHz and the upper at 380 kHz for a total bandwidth of 280 kHz. This intense mid-frequency noise was detected at radial distances from 1.3 Re to 60 Re on all sides of the earth (i.e., all local times) during magnetically quiet as well as disturbed periods. Maximum occurrence of the mid-frequency noise is in the evening to midnight hours where splash-type energetic particle precipitation takes place.

  4. AB initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.

    1982-08-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.

  5. Xgremlin: Interferograms and spectra from Fourier transform spectrometers analysis

    NASA Astrophysics Data System (ADS)

    Nave, G.; Griesmann, U.; Brault, J. W.; Abrams, M. C.

    2015-11-01

    Xgremlin is a hardware and operating system independent version of the data analysis program Gremlin used for Fourier transform spectrometry. Xgremlin runs on PCs and workstations that use the X11 window system, including cygwin in Windows. It is used to Fourier transform interferograms, plot spectra, perform phase corrections, perform intensity and wavenumber calibration, and find and fit spectral lines. It can also be used to construct synthetic spectra, subtract continua, compare several different spectra, and eliminate ringing around lines.

  6. Enhancement of energy spectra through constant fraction timing method

    NASA Astrophysics Data System (ADS)

    Ermis, Elif Ebru; Celiktas, Cuneyt

    2017-02-01

    The energy spectra of 137Cs, 60Co and 14C were achieved by using the spectrometers composed of different types of detectors. In this work, constant fraction timing method was used to enhance their energy spectra. Energy resolution values of 137Cs and 60Co gamma energy spectra were improved through this timing method. In addition, electronic noise appeared in the energy spectrum of 14C was discriminated through the timing method, leading to clear beta energy spectrum.

  7. Double-Resonance Facilitated Decomposion of Emission Spectra

    NASA Astrophysics Data System (ADS)

    Kato, Ryota; Ishikawa, Haruki

    2016-06-01

    Emission spectra provide us with rich information about the excited-state processes such as proton-transfer, charge-transfer and so on. In the cases that more than one excited states are involved, emission spectra from different excited states sometimes overlap and a decomposition of the overlapped spectra is desired. One of the methods to perform a decomposition is a time-resolved fluorescence technique. It uses a difference in time evolutions of components involved. However, in the gas-phase, a concentration of the sample is frequently too small to carry out this method. On the other hand, double-resonance technique is a very powerful tool to discriminate or identify a common species in the spectra in the gas-phase. Thus, in the present study, we applied the double-resonance technique to resolve the overlapped emission spectra. When transient IR absorption spectra of the excited state are available, we can label the population of the certain species by the IR excitation with a proper selection of the IR wavenumbers. Thus, we can obtain the emission spectra of labeled species by subtracting the emission spectra with IR labeling from that without IR. In the present study, we chose the charge-transfer emission spectra of cyanophenyldisilane (CPDS) as a test system. One of us reported that two charge-transfer (CT) states are involved in the intramolecular charge-transfer (ICT) process of CPDS-water cluster and recorded the transient IR spectra. As expected, we have succeeded in resolving the CT emission spectra of CPDS-water cluster by the double resonance facilitated decomposion technique. In the present paper, we will report the details of the experimental scheme and the results of the decomposition of the emission spectra. H. Ishikawa, et al., Chem. Phys. Phys. Chem., 9, 117 (2007).

  8. Correspondence of electron spectra from photoionization and nuclear internal conversion

    SciTech Connect

    Wark, D.L.; Bartlett, R.; Bowles, T.J.; Robertson, R.G.H.; Sivia, D.S.; Trela, W.; Wilkerson, J.F. ); Brown, G.S. ); Crasemann, B.; Sorensen, S.L.; Schaphorst, S.J. ); Knapp, D.A.; Henderson, J. ); Tulkki, J.; Aberg, T. )

    1991-10-21

    Electron energy spectra have been measured that result from {ital K}-shell ionization of Kr by two different mechanisms: (1) photoionization and (2) internal conversion in the decay of the isomeric state of {sup 83}Kr. It is demonstrated experimentally that these spectra, including satellites on the low-energy side of the primary 1{ital s}-electron peak, are identical. A theoretical interpretation of the identity of the spectra is given. The spectra agree well with a relativistic many-electron calculation in which the satellites are attributed to excitation and ionization of {ital M} and {ital N} electrons during the {ital K}-ionization process.

  9. Infrared spectra of lunar soil analogs. [spectral reflectance of minerals

    NASA Technical Reports Server (NTRS)

    Aronson, J. R.

    1977-01-01

    The infrared spectra of analogs of lunar soils were investigated to further the development of methodology for interpretation of remotely measured infrared spectra of the lunar surface. The optical constants of dunite, bytownite, augite, ilmenite, and a mare glass analog were obtained. The infrared emittance spectra of powdered minerals were measured and compared with spectra calculated by the reflectance theory using a catalog of optical constants. The results indicate that the predictions of the theory closely simulate the experimental measurements if the optical constants are properly derived.

  10. Energy Spectra of Very Large Gradual Solar Particle Events

    DTIC Science & Technology

    2001-01-01

    Bastille Day event, the Fe spectrum here does not harden with increasing energy. Instead, it falls much Fig. 2. Sample heavy-ion spectra from the 1998 April... Bastille Day) event from two intervals covering 6–14 and 22–26 hours after the flare (Tylka et al. 2001). The spectra clearly evolve, with e-folding...flare component much larger than 5% is excluded by <QFe> 10 from SEPICA in the Bastille Day event. To model the Fe spectra, we first fit the spectra

  11. [Near infrared Raman spectra analysis of rhizoma dioscoreae].

    PubMed

    Lin, Wen-Shuo; Chen, Rong; Li, Yong-Zeng; Feng, Shang-Yuan; Huang, Zu-Fang; Xie, Bing-Xian

    2008-05-01

    A novel and compact near-infrared (NIR) Raman system was developed using 785 nm diode laser, volume-phase technology holographic system, and NIR intensified charge-coupled device (CCD). The Raman spectra and first derivative spectra of rhizoma dioscoreae were obtained. The Raman spectra of rhizoma dioscoreae showed three strong characteristic peaks at 477, 863 and 936 cm(-1), respectively. The major ingredients are protein, amino acid, starch, polysaccharides and so on, matching the known basic biochemical composition of rhizoma dioscoreae. In the first derivative spectra of rhizoma dioscoreae, the distinguishing characteristic peaks appeared at 467, 484, 870 and 943 cm(-1). Contrasted with rhizoma dioscoreae Raman spectra in the ranges of 600 to 800 cm(-1) and 1 000 to 1 400 cm(-1), the changes in rhizoma dioscoreae Raman first derivative spectra are represented more clearly than the rhizoma dioscoreae Raman spectra. So the rhizoma dioscoreae Raman first derivative spectra can be an accurate supplementary analysis method to the rhizoma dioscoreae Raman spectra.

  12. Vibrational Spectra and Structures of Silicon - Clusters

    NASA Astrophysics Data System (ADS)

    Presilla-Marquez, Jose-Domingo

    1992-01-01

    Fourier transform studies of silicon-carbon clusters produced by vaporizing mixtures of silicon and carbon-12 or carbon-13 and quenching the products in argon, have enabled the identification of new vibrational spectra and structures. The far infrared nu_3(b_2) fundamental has been found at 160.4 cm ^{-1} for SiC_2 . Its structure is now described as T-shaped with ionic bonding. In the case of Si_2C, a previously observed vibration at 1188.4 cm^ {-1} has been confirmed as the nu_3(b_2), antisymmetric Si -C stretching mode, and a new vibration at 839.5 cm ^{-1} has been identified as the nu_1(a_1), symmetric Si-Si stretching fundamental. The nu_2(a _1) bending mode has not been observed; however, the nu_2(a_1) + nu_3(b_2) combination band has been identified at 1354.8 cm^{-1} . The results of force constant adjustment calculations confirm the ground state geometry of Si_2 C as a floppy, bent symmetrical structure. Five out of six fundamental modes have been identified for the Si_3C cluster which is observed here for the first time: the symmetric breathing vibration, nu_1(a_1) = 658.2 cm ^{-1}; the Si_ beta-Si_alpha -Si_beta symmetric deformation vibration, nu_2(a_1) = 511.8 cm^{-1}; the Si beta-C-Si_{beta } symmetric deformation vibration, nu_3(a_1) = 309.5 cm ^{-1}; the Si_beta -C antisymmetric stretching vibration, nu_5(b_2) = 1101.4 cm ^{-1}; and the Si_ alpha-Si_beta antisymmetric stretching vibration, nu_6(b _2) = 357.6 cm^{-1} . The fundamental frequencies, relative intensities, and isotopic shifts are in excellent agreement with the results of ab initio calculations predicting a rhomboidal structure of C_{2v} symmetry for Si_3C, with carbon-silicon transannular bonding between the two equivalent Si atoms. Another new silicon-carbon cluster, rhombic Si _2C_2, has been identified and the nu_3(b_ {rm 1u}) = 982.9 and nu _4(b_{rm 2u}) = 382.2 cm^{-1} fundamentals have been assigned. These results are in excellent agreement with ab initio calculations. The first

  13. Prompt Fission Neutron Spectra of Actinides

    SciTech Connect

    Capote, R; Chen, Y J; Hambsch, F J; Kornilov, N V; Lestone, J P; Litaize, O; Morillon, B; Neudecker, D; Oberstedt, S; Ohsawa, T; Smith, D. L.

    2016-01-01

    The energy spectrum of prompt neutrons emitted in fission (PFNS) plays a very important role in nuclear science and technology. A Coordinated Research Project (CRP) “Evaluation of Prompt Fission Neutron Spectra of Actinides”was established by the IAEA Nuclear Data Section in 2009, with the major goal to produce new PFNS evaluations with uncertainties for actinide nuclei. The following technical areas were addressed: (i) experiments and uncertainty quantification (UQ): New data for neutron-induced fission of 233U, 235U, 238U, and 239Pu have been measured, and older data have been compiled and reassessed. There is evidence from the experimental work of this CRP that a very small percentage of neutrons emitted in fission are actually scission neutrons; (ii) modeling: The Los Alamos model (LAM) continues to be the workhorse for PFNS evaluations. Monte Carlo models have been developed that describe the fission phenomena microscopically, but further development is needed to produce PFNS evaluations meeting the uncertainty targets; (iii) evaluation methodologies: PFNS evaluations rely on the use of the least-squares techniques for merging experimental and model data. Considerable insight was achieved on how to deal with the problem of too small uncertainties in PFNS evaluations. The importance of considering that all experimental PFNS data are “shape” data was stressed; (iv) PFNS evaluations: New evaluations, including covariance data, were generated for major actinides including 1) non-model GMA evaluations of the 235U(nth,f), 239Pu(nth,f), and 233U(nth,f) PFNS based exclusively on experimental data (0.02 ≤ E ≤ 10 MeV), which resulted in PFNS average energies E of 2.00±0.01, 2.073±0.010, and 2.030±0.013 MeV, respectively; 2) LAM evaluations of neutron-induced fission spectra on uranium and plutonium targets with improved UQ for incident energies from thermal up to 30 MeV; and 3) Point-by-Point calculations for 232Th, 234U and 237Np targets; and (v) data

  14. Quantum confinement in metal nanofilms: Optical spectra

    NASA Astrophysics Data System (ADS)

    Khmelinskii, Igor; Makarov, Vladimir I.

    2016-05-01

    We report optical absorption and photoluminescence spectra of Au, Fe, Co and Ni polycrystalline nanofilms in the UV-vis-NIR range, featuring discrete bands resulting from transverse quantum confinement. The film thickness ranged from 1.1 to 15.6 nm, depending on the material. The films were deposited on fused silica substrates by sputtering/thermo-evaporation, with Fe, Co and Ni protected by a SiO2 film deposited on top. The results are interpreted within the particle-in-a-box model, with the box width equal to the mass thickness of the nanofilm. The transverse-quantized energy levels and transition energies scale as the inverse square of the film thickness. The calculated values of the effective electron mass are 0.93 (Au), 0.027 (Fe), 0.21 (Co) and 0.16 (Ni), in units of mo - the mass of the free electron, being independent on the film thickness. The uncertainties in the effective mass values are ca. 2.5%, determined by the film thickness calibration. The second calculated model parameter, the quantum number n of the HOMO, was thickness-independent in Au (5.00) and Fe (6.00), and increased with the film thickness in Co (from 7 to 9) and Ni (from 7 to 11). The transitions observed in the absorbance all start at the level n and correspond to Δn=+1, +2, +3, etc. The photoluminescence bands exhibit large Stokes shifts, shifting to higher energies with the increased excitation energy. The photoluminescence quantum yields grow linearly with the excitation energy, showing evidence of multiple exciton generation. A prototype Fe-SnO2 nanofilm photovoltaic cell demonstrated at least 90% quantum yield of photoelectrons at 77 K.

  15. Mutation spectra of complex environmental mixtures

    SciTech Connect

    DeMarini, D.M.

    1997-10-01

    Bioassay-directed chemical analysis of complex environmental mixtures has indicated that much of the genotoxic activity of mixtures is due to the presence of one or a few classes or chemicals within the mixture. We have extended this observation to the molecular level by using colony probe hybridization and PCR/DNA sequence analysis to determine the mutation spectra of {approximately}8,000 revertants induced by a variety of complex mixtures and their chemical fractions in TA100 and TA98 of Salmonella. For urban air, >80% of mutagenic activity was due to a base/neutral fraction that contained primarily PAHs. The mutation spectrum induced by unfractionated urban air was not significantly different from that produced by a model PAH, B(a)P. The mutation spectrum induced by organic extracts of chlorinated drinking water were similar to those produced by the chlorinated furanone MX, which accounted for {approximately}20% of the mutagenic activity of the samples. The base/neutral fraction of municipal waste incinerator emissions accounted for the primary class of mutations induced by the emissions, and a polar neutral fraction accounted for the secondary class of mutations induced by the emissions. The primary class of mutations induced by cigarette smoke condensate in TA100 (GC {yields} TA) is also the primary class of mutations in the p53 gene of lung tumors of cigarette smokers. These results confirm at the molecular level that the mutations induced by a complex mixture reflect the dominance of one or a few classes of chemicals within the mixture.

  16. FULL POLARIZATION SPECTRA OF 3C 279

    SciTech Connect

    Homan, D. C.; Lister, M. L.; Aller, H. D.; Aller, M. F.; Wardle, J. F. C. E-mail: mlister@physics.purdue.edu E-mail: mfa@umich.edu

    2009-05-01

    We report the results of parsec-scale, multifrequency Very Long Baseline Array observations of the core region of 3C 279 in Stokes I, linear polarization, and circular polarization. These full polarization spectra are modeled by radiative transfer simulations to constrain the magnetic field and particle properties of the parsec-scale jet in 3C 279. We find that the polarization properties of the core region, including the amount of linear polarization, the amount and sign of Faraday rotation, and the amount and sign of circular polarization can be explained by a consistent physical picture. The base of the jet, component D, is modeled as an inhomogeneous Blandford-Koenigl style conical jet dominated by a vector-ordered poloidal magnetic field along the jet axis, and we estimate its net magnetic flux. This poloidal field is responsible for the linear and circular polarization from this inhomogeneous component. Farther down the jet, the magnetic field in two homogeneous features is dominated by local shocks and a smaller fraction of vector-ordered poloidal field remains along the jet axis. This remaining poloidal field provides internal Faraday rotation which drives Faraday conversion of linear polarization into circular polarization from these components. In this picture, we find the jet to be kinetically dominated by protons with the radiating particles being dominated by electrons at an approximate fraction of {approx}>75%, still allowing the potential for a significant admixture of positrons. Based on the amounts of Faraday conversion deduced for the homogeneous components, we find a plausible range for the lower cutoff in the relativistic particle energy spectrum to be 5 {approx}< {gamma} {sub l} {approx}< 35. The physical picture described here is not unique if the observed Faraday rotation and depolarization occur in screens external to the jet; however, we find the joint explanation of linear and circular polarization observations from a single set of

  17. First Infrared Spectra of Nitrous Oxide Pentamer

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2012-06-01

    High resolution spectra have previously been studied for N_2O dimers (two isomers), trimers (one isomer), and tetramers (two isomers). Here, we assign two new bands to the N_2O pentamer. The bands are observed in the region of the N_2O νb{1} fundamental using a tunable laser to probe a pulsed supersonic slit jet expansion. They are centered at 2233.9 and 2236.4 wn for 14N_2O, and at 2164.4 and 2166.8 wn for 15N_2O. Attribution to the pentamer is based on comparison of the observed rotational constants with theoretical ones from calculated cluster structures based on two rather different N_2O pair potentials. The first potential function is from a recent high level ab initio study. The second potential is a relatively simple empirical one, based partly on fitting to bulk properties. The likely pentamer structure is a completely unsymmetric one. It can be visualized starting with a highly symmetric oblate tetramer which is attacked by a fifth monomer, locating itself at a favorable distance and breaking the symmetry. Interestingly, analysis of the two bands yields very similar but not quite identical ground state parameters. We believe that they are due to distinct isomers having this same basic structure but differing in the orientation direction of one N_2O monomer. [1] R. Dawes, X.-G. Wang, A.W. Jasper, and T. Carrington, Jr., {J. Chem. Phys.} {133}, 134304 (2010). [2] B. Kutcha, R.D. Etters, and R. LeSar, {J. Chem. Phys.} {97}, 5662 (1992). [3] J.N. Oliaee, M. Dehghany, N. Moazzen-Ahmadi, and A.R.W. McKellar, {J. Chem. Phys.} {134}, 074310 (2011).

  18. Hardness ratios of different neutron spectra.

    PubMed

    Tommasino, L; Tripathy, S P

    2004-01-01

    Extensive data have been gathered in the past on the response of different detectors, based on the registration of neutron-induced fissions in bismuth, gold, tantalum and thorium by the spark-replica counter and the thin film breakdown counter. These detectors make it possible to exploit the excellent characteristics of the fission reactions for the measurements of high-energy neutrons. Most of the investigations have been carried out at the quasi-monoenergetic neutron beam facility at The Svedberg Laboratory-TSL of the Uppsala University in cooperation with the Khlopin Radium Institute (KRI). The responses of different fission detectors in the neutron energy range 35-180 MeV have been evaluated: a region where the predictive power of available nuclear reaction models and codes is not reliable yet. For neutron energy >200 MeV, the fission-detector responses have been derived from the data of the proton fission cross sections. By using the ratio of the responses of these detectors, a simple and accurate way to evaluate the spectrum hardness can be obtained, thus providing a tool to obtain spectral information needed for neutron dosimetry without the need to know the entire spectrum. Extensive data have been already obtained for the high-energy neutron spectrum from the CERN concrete facility. In the present paper, the measured values of the response ratios for different fissile detectors exposed at the CERN facility are compared with those calculated for the spectra from the same facility and from different altitudes in the atmosphere, respectively.

  19. Turbulence Spectra and Eddy Diffusivity over Forests.

    NASA Astrophysics Data System (ADS)

    Lee, Xuhui

    1996-08-01

    The main objectives of this observational study are to examine the stability dependence of velocity and air temperature spectra and to employ the spectral quantities to establish relations for eddy diffusivity over forests. The datasets chosen for the analysis were collected above the Browns River forest and the Camp Borden forest over a wide range of stability conditions.Under neutral and unstable conditions the nondimensional dissipation rate of turbulent kinetic energy (TKE) over the forests is lower than that from its Monin-Obukhov similarity (MOS) function for the smooth-wall surface layer. The agreement is somewhat better under stable conditions but a large scatter is evident. When the frequency is made nondimensional by the height of the stand (h) and the longitudinal velocity at this height (uh, the Kaimal spectral model for neutral air describes the observations very well. The eddy diffusivity formulation K = c 4w/ provides a promising alternative to the MOS approach, where w is the standard deviation of the vertical velocity and TKE dissipation rate. Current datasets yield a constant of 0.43 for c for sensible heat in neutral and stable air, a value very close to that for the smooth-wall surface layer. It is postulated that c is a conservative parameter for sensible heat in the unstable air, its value probably falling between 0.41 and 0.54. In the absence of data, it is possible to estimate K from measurements of the local mean wind u and air stability. As a special case, it is shown that K = 0.27(uh/uh)w under neutral stability. This relation is then used to establish a profile model for wind speed and scalar concentration in the roughness sublayer. The analysis points out that uh and h are important scaling parameters in attempts to formulate quantitative relations for turbulence over tall vegetation.

  20. Database-Driven Analyses of Astronomical Spectra

    NASA Astrophysics Data System (ADS)

    Cami, Jan

    2012-03-01

    species to the fullerene species C60 and C70 [4]. Given the large number and variety of molecules detected in space, molecular infrared spectroscopy can be used to study pretty much any astrophysical environment that is not too energetic to dissociate the molecules. At the lowest energies, it is interesting to note that molecules such as CN have been used to measure the temperature of the Cosmic Microwave Background (see e.g., Ref. 15). The great diagnostic potential of infrared molecular spectroscopy comes at a price though. Extracting the physical parameters from the observations requires expertise in knowing how various physical processes and instrumental characteristics play together in producing the observed spectra. In addition to the astronomical aspects, this often includes interpreting and understanding the limitations of laboratory data and quantum-chemical calculations; the study of the interaction of matter with radiation at microscopic scales (called radiative transfer, akin to ray tracing) and the effects of observing (e.g., smoothing and resampling) on the resulting spectra and possible instrumental effects (e.g., fringes). All this is not trivial. To make matters worse, observational spectra often contain many components, and might include spectral contributions stemming from very different physical conditions. Fully analyzing such observations is thus a time-consuming task that requires mastery of several techniques. And with ever-increasing rates of observational data acquisition, it seems clear that in the near future, some form of automation is required to handle the data stream. It is thus appealing to consider what part of such analyses could be done without too much human intervention. Two different aspects can be separated: the first step involves simply identifying the molecular species present in the observations. Once the molecular inventory is known, we can try to extract the physical parameters from the observed spectral properties. For both