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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. This indicates that often the actual behavior of a rock outcrop is far from that of an ideal, reference site.

  2. An Application of the Coda Methodology for Moment-Rate Spectra Using Broadband Stations in Turkey

    SciTech Connect

    Eken Tuna, Kevin Mayeda, Abraham Hofstetter, Rengin Gok, Gonca Orgulu, Niyazi Turkelli

    2004-07-11

    A recently developed coda magnitude methodology was applied to selected broadband stations in Turkey for the purpose of testing the coda method in a large, laterally complex region. As found in other, albeit smaller regions, coda envelope amplitude measurements are significantly less variable than distance-corrected direct wave measurements (i.e., L{sub g} and surface waves) by roughly a factor 3-to-4. Despite strong lateral crustal heterogeneity in Turkey, they found that the region could be adequately modeled assuming a simple 1-D, radially symmetric path correction. After calibrating the stations ISP, ISKB and MALT for local and regional distances, single-station moment-magnitude estimates (M{sub W}) derived from the coda spectra were in excellent agreement with those determined from multistation waveform modeling inversions, exhibiting a data standard deviation of 0.17. Though the calibration was validated using large events, the results of the calibration will extend M{sub W} estimates to significantly smaller events which could not otherwise be waveform modeled. The successful application of the method is remarkable considering the significant lateral complexity in Turkey and the simple assumptions used in the coda method.

  3. Universal mean moment rate profiles of earthquake ruptures

    SciTech Connect

    Mehta, Amit P.; Dahmen, Karin A.; Ben-Zion, Yehuda

    2006-05-15

    Earthquake phenomenology exhibits a number of power law distributions including the Gutenberg-Richter frequency-size statistics and the Omori law for aftershock decay rates. In search for a basic model that renders correct predictions on long spatiotemporal scales, we discuss results associated with a heterogeneous fault with long-range stress-transfer interactions. To better understand earthquake dynamics we focus on faults with Gutenberg-Richter-like earthquake statistics and develop two universal scaling functions as a stronger test of the theory against observations than mere scaling exponents that have large error bars. Universal shape profiles contain crucial information on the underlying dynamics in a variety of systems. As in magnetic systems, we find that our analysis for earthquakes provides a good overall agreement between theory and observations, but with a potential discrepancy in one particular universal scaling function for moment rates. We primarily use mean field theory for the theoretical analysis, since it has been shown to be in the same universality class as the full three-dimensional version of the model (up to logarithmic corrections). The results point to the existence of deep connections between the physics of avalanches in different systems.

  4. Mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Chaturvedi, S.

    2002-08-01

    After a brief review of the notion of a full set of mutually unbiased bases in an N-dimensional Hilbert space, we summarize the work of Wootters and Fields (W K Wootters and B C Fields, Ann. Phys. 191, 363 (1989)) which gives an explicit construction for such bases for the case N=pr, where p is a prime. Further, we show how, by exploiting certain freedom in the Wootters-Fields construction, the task of explicitly writing down such bases can be simplified for the case when p is an odd prime. In particular, we express the results entirely in terms of the character vectors of the cyclic group G of order p. We also analyse the connection between mutually unbiased bases and the representations of G.

  5. Constraining the Moment Rate Budget for Continental Alaska by Combining Geologic and Earthquake Productivity Rate Data

    NASA Astrophysics Data System (ADS)

    Klein, E. C.; Kreemer, C. W.

    2011-12-01

    As part of the Global Earthquake Model (GEM) project (www.globalquakemodel.org), there is a need for geodetically constrained, high-resolution, strain rate models of plate boundary zones. These models can be used to assess the completeness of the moment rate budget implied by Quaternary faulting data bases and earthquake productivity rates, which are the typical foundations of any seismic hazard model. The ultimate goal is to create strain rate models that best satisfy the geodetic, geologic, and seismic observations simultaneously. Such models could reveal any significant discrepancy between Quaternary faulting slip rates and geodetic observations, and could constrain the maximum expected magnitude in light of a Gutenberg-Richter or Characteristic Earthquake distribution of seismicity. One limitation of kinematic models heavily reliant on geodetic data, is that they may suffer from uncertainties arising from difficult to remove postseismic and interseismic transient affects. To better understand the role of the interseismic strain field and how it relates to seismic hazard motivates the need for a longer-term kinematic estimate. We present long-term strain rate models for continental Alaska based on geologic and seismic observations. When solving for a continuous velocity gradient tensor field we use seismic and geologic data as apriori constraints on the strain rate model covariance matrix. For the a priori strain rate variances, we use Quaternary fault slip rates from Finzel et al. [2011], and for all "non-faulting" cells of our model grid we combine unit summed moment tensors with strain rates associated with the moment release rate given an area's a- and b-value and assumed maximum moment. Because the majority of the seismicity occurs in central and southern Alaska, we divide the plate boundary zone into two seismologically distinct regions and determine the Characteristic Earthquake distribution for each region separately. Using a plate velocity of 51 mm/a, a seismogenic thickness of 20 km, and a shear modulus of 30 GPa, we will show that the total moment rate for the plate boundary zone is approximately 84.8 * 1018 Nm/a and that "off-fault" seismicity accounts for about 40% of this moment rate. Given a plate velocity of 51 mm/a necessitates that the quaternary fault interfaces take up roughly 31 mm/a of slip. In addition to this preliminary result, we will show results for our preferred model, as well as the strain rate models that are based on either the geologic or seismic data alone. We will discuss the significant differences between these models in terms of using these data sets in seismic hazard modeling.

  6. Unbiased sampling of network ensembles

    NASA Astrophysics Data System (ADS)

    Squartini, Tiziano; Mastrandrea, Rossana; Garlaschelli, Diego

    2015-02-01

    Sampling random graphs with given properties is a key step in the analysis of networks, as random ensembles represent basic null models required to identify patterns such as communities and motifs. An important requirement is that the sampling process is unbiased and efficient. The main approaches are microcanonical, i.e. they sample graphs that match the enforced constraints exactly. Unfortunately, when applied to strongly heterogeneous networks (like most real-world examples), the majority of these approaches become biased and/or time-consuming. Moreover, the algorithms defined in the simplest cases, such as binary graphs with given degrees, are not easily generalizable to more complicated ensembles. Here we propose a solution to the problem via the introduction of a Maximize and Sample (Max & Sam for short) method to correctly sample ensembles of networks where the constraints are soft, i.e. realized as ensemble averages. Our method is based on exact maximum-entropy distributions and is therefore unbiased by construction, even for strongly heterogeneous networks. It is also more computationally efficient than most microcanonical alternatives. Finally, it works for both binary and weighted networks with a variety of constraints, including combined degree-strength sequences and full reciprocity structure, for which no alternative method exists. Our canonical approach can in principle be turned into an unbiased microcanonical one, via a restriction to the relevant subset. Importantly, the analysis of the fluctuations of the constraints suggests that the microcanonical and canonical versions of all the ensembles considered here are not equivalent. We show various real-world applications and provide a code implementing all our algorithms.

  7. Constructing mutually unbiased bases in dimension six

    SciTech Connect

    Brierley, Stephen; Weigert, Stefan

    2009-05-15

    The density matrix of a qudit may be reconstructed with optimal efficiency if the expectation values of a specific set of observables are known. In dimension six, the required observables only exist if it is possible to identify six mutually unbiased complex (6x6) Hadamard matrices. Prescribing a first Hadamard matrix, we construct all others mutually unbiased to it, using algebraic computations performed by a computer program. We repeat this calculation many times, sampling all known complex Hadamard matrices, and we never find more than two that are mutually unbiased. This result adds considerable support to the conjecture that no seven mutually unbiased bases exist in dimension six.

  8. Stress states and moment rates of a two-asperity fault in the presence of viscoelastic relaxation

    NASA Astrophysics Data System (ADS)

    Dragoni, M.; Lorenzano, E.

    2015-06-01

    A fault containing two asperities with different strengths is considered. The fault is embedded in a shear zone subject to a constant strain rate by the motions of adjacent tectonic plates. The fault is modelled as a discrete dynamical system where the average values of stress, friction and slip on each asperity are considered. The state of the fault is described by three variables: the slip deficits of the asperities and the viscoelastic deformation. The system has four dynamic modes, for which analytical solutions are calculated. The relationship between the state of the fault before a seismic event and the sequence of slipping modes in the event is enlightened. Since the moment rate depends on the number and sequence of slipping modes, the knowledge of the source function of an earthquake constrains the orbit of the system in the phase space. If the source functions of a larger number of consecutive earthquakes were known, the orbit could be constrained more and more and its evolution could be predicted with a smaller uncertainty. The model is applied to the 1964 Alaska earthquake, which was the effect of the failure of two asperities and for which a remarkable post-seismic relaxation has been observed in the subsequent decades. The evolution of the system after the 1964 event depends on the state from which the event was originated, that is constrained by the observed moment rate. The possible durations of the interseismic interval and the possible moment rates of the next earthquake are calculated as functions of the initial state.

  9. Mutually unbiased bases with free parameters

    NASA Astrophysics Data System (ADS)

    Goyeneche, Dardo; Gmez, Santiago

    2015-12-01

    We present a systematic method to introduce free parameters in sets of mutually unbiased bases. In particular, we demonstrate that any set of m real mutually unbiased bases existing in dimension N >2 admits the introduction of (m -1 )N /2 free parameters that cannot be absorbed by a global unitary operation. As consequence, there are m =k +1 mutually unbiased bases in every dimension N =k2 with k3/2 free parameters, where k is even. We explicitly construct the maximal set of triplets of mutually unbiased bases for two-qubit systems and triplets, quadruplets, and quintuplets of mutually unbiased bases with free parameters for three-qubit systems. Furthermore, we study the richness of the entanglement structure of such bases and provide the quantum circuits required to implement all these bases with free parameters in the laboratory. We also show that the free parameters introduced can be controlled by a single party of the system. Finally, we find the upper bound for the maximal number of real and complex mutually unbiased bases existing in every dimension. This proof is simple, short, and considers basic matrix algebra.

  10. Improving spatial resolution of the moment rate function in regions of high slip determined from finite fault inversions

    NASA Astrophysics Data System (ADS)

    Adams, M.; Ji, C.; Archuleta, R. J.

    2014-12-01

    Finite fault inversions attempt to resolve the spatial distribution of the moment rate function per unit area using seismic observations. However, the observational and synthetic limitations that exist due to the station distribution and frequency content of signals that can be modeled imply that various simplifications to the source representation need to be made in order to stabilize the inversions. These simplifications inevitably affect the final results, though it is largely unknown how serious the regularization can be. Here, we explore the effects caused by a pre-assumed slip rate function using synthetic data from the Source Inversion Validation (SIV) produced by a crack-like spontaneous dynamic rupture embedded in a layered, elastic medium. Thus we have exact Green's functions, which allow us to consider only the effects of varying the slip rate function. We study the effect of three different inverted slip rate functions: i) asymmetric cosine functions; ii) modified Yoffe functions and iii) no negative functions within given time windows. The first approach has been used routinely in finite fault inversions and the second one is characteristic of dynamic simulations. We perform the inversions using the first two cases with a simulated annealing algorithm and attempt to answer whether the ideal synthetic data can differentiate between them. The last one has the inverted slip rate function with the least a priori constraints but uses many more free parameters. It is inverted using the newly developed Projected Landweber (PL) method and we will explore its dependence on the choice of the initial model and the bandwidth of signals.

  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. Alternative unbiased consistent converted measurements for target tracking

    NASA Astrophysics Data System (ADS)

    Mo, Longbin; Song, Xiaoquan; Zhou, Yiyu; Sun, Zhongkang

    1997-06-01

    The accurate debiasing processing for the bias in the classical conversion mainly depends on the first and second statistic of the cosine of the bearing measurement errors. An unbiased conversion is presented. Some comparison between this unbiased conversion with the previously offered debiased conversion is made.

  14. A Note on the Unbiased Estimation of the Intraclass Correlation.

    ERIC Educational Resources Information Center

    Donoghue, John R.; Collins, Linda M.

    1990-01-01

    I. Olkin and J. W. Pratt (1958) derived the minimum variance unbiased estimator of intraclass correlation, but use of the estimator has been impeded by lack of a closed form solution. The unbiased estimator is reviewed, and a FORTRAN-77 subroutine (UNBIAS) is proposed to calculate the estimator. (SLD)

  15. 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

  16. Efficient and Unbiased Estimation of Population Size.

    PubMed

    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

  17. 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 Armstrongs 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 ?g/g for shears up to |g| = 0.2.

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

    DOE PAGESBeta

    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 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

  19. 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.

  20. 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.

  1. Separability criteria via sets of mutually unbiased measurements.

    PubMed

    Liu, Lu; Gao, Ting; Yan, Fengli

    2015-01-01

    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. PMID:26278628

  2. Separability criteria via sets of mutually unbiased measurements

    PubMed Central

    Liu, Lu; Gao, Ting; Yan, Fengli

    2015-01-01

    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. PMID:26278628

  3. High-dimensional inference by unbiased risk estimation

    NASA Astrophysics Data System (ADS)

    Chetelat, Didier

    This thesis derives natural and efficient solutions of three high-dimensional statistical problems by exploiting unbiased risk estimation. They exemplify a general methodology that provides attractive estimators in situations where classical theory is unsuccessful, and that could be exploited in many other problems. First, we extend the classical James-Stein shrinkage estimator to the context where the number of covariates is larger than the sample size and the covariance matrix is unknown. The construction is obtained by manipulating an unbiased risk estimator and shown to dominate in invariant squared loss the maximum likelihood estimator. The estimator is interpreted as performing shrinkage only the random subspace spanned by the sample covariance matrix. Second, we investigate the estimation of a covariance and precision matrix, and discriminant coefficients, of linearly dependent data in a normal framework. By boundingthe difference in risk over classes of interest using unbiased risk estimation, we construct interesting estimators and show domination over naive solutions. Finally, we explore the problem of estimating the noise coefficient in the spiked covariance model. By decomposing an unbiased risk estimator and minimizing its dominant part using calculus of variations, we obtain an estimator in closed form that approximates the optimal solution. Several attractive properties are proven about the proposed construction. We conclude by showing that the associated spiked covariance estimators possess excellent behavior under the Frobenius loss.

  4. 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

  5. Improving Quantum State Estimation with Mutually Unbiased Bases

    NASA Astrophysics Data System (ADS)

    Adamson, R. B. A.; Steinberg, A. M.

    2010-07-01

    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 1.840.06 times lower by using our technique than it was by using standard state estimation methods.

  6. Least-bias state estimation with incomplete unbiased measurements

    NASA Astrophysics Data System (ADS)

    Řeháček, Jaroslav; Hradil, Zdeněk; Teo, Yong Siah; Sánchez-Soto, Luis L.; Ng, Hui Khoon; Chai, Jing Hao; Englert, Berthold-Georg

    2015-11-01

    Measuring incomplete sets of mutually unbiased bases constitutes a sensible approach to the tomography of high-dimensional quantum systems. The unbiased nature of these bases optimizes the uncertainty hypervolume. However, imposing unbiasedness on the probabilities for the unmeasured bases does not generally yield the estimator with the largest von Neumann entropy, a popular figure of merit in this context. Furthermore, this imposition typically leads to mock density matrices that are not even positive definite. This provides a strong argument against perfunctory applications of linear estimation strategies. We propose to use instead the physical state estimators that maximize the Shannon entropy of the unmeasured outcomes, which quantifies our lack of knowledge fittingly and gives physically meaningful statistical predictions.

  7. 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. PMID:15638649

  8. Unbiased stereological quantification of neurons in the human spiral ganglion.

    PubMed

    Ishiyama, A; Agena, J; Lopez, I; Tang, Y

    2001-05-18

    We applied an unbiased stereological technique, the optical fractionator, on five human archival temporal bone specimens to estimate the total number of spiral ganglion neurons. Available archival human temporal bone specimen has been serially sectioned at 20 microm and every tenth section was stained. All the stained sections passing through the spiral ganglion were used for the analysis. From each section sampled, the counting areas were systematically randomly sampled within the sectional area of the spiral ganglion. The neurons within the counting areas sampled were counted with the optical disector technique. The total number of the human spiral ganglion neurons was estimated by multiplying the number of neurons counted by the reciprocal of the aggregate sampling fraction. We found an average of 41700 neurons with a coefficient of variation of 0.14, which is a significant departure from the previously published data obtained with the assumption-based methods. The mean coefficient of error for the stereological estimates of the total number of human spiral ganglion neurons was 0.078. The present report presents unbiased stereological sampling and counting strategies for the future quantitative studies on the spiral ganglion neurons. The result of the present study provides the first unbiased baseline value of the human spiral ganglion neurons. PMID:11335063

  9. Unbiased estimation of mutation rates under fluctuating final counts.

    PubMed

    Ycart, Bernard; Veziris, Nicolas

    2014-01-01

    Estimation methods for mutation rates (or probabilities) in Luria-Delbrck fluctuation analysis usually assume that the final number of cells remains constant from one culture to another. We show that this leads to systematically underestimate the mutation rate. Two levels of information on final numbers are considered: either the coefficient of variation has been independently estimated, or the final number of cells in each culture is known. In both cases, unbiased estimation methods are proposed. Their statistical properties are assessed both theoretically and through Monte-Carlo simulation. As an application, the data from two well known fluctuation analysis studies on Mycobacterium tuberculosis are reexamined. PMID:24988217

  10. Mobility of Holstein polaron at finite temperature: an unbiased approach.

    PubMed

    Mishchenko, A S; Nagaosa, N; De Filippis, G; de Candia, A; Cataudella, V

    2015-04-10

    We present the first unbiased results for the mobility μ of a one-dimensional Holstein polaron obtained by numerical analytic continuation combined with diagrammatic and worldline Monte Carlo methods in the thermodynamic limit. We have identified for the first time several distinct regimes in the λ-T plane including a band conduction region, incoherent metallic region, an activated hopping region, and a high-temperature saturation region. We observe that although mobilities and mean free paths at different values of λ differ by many orders of magnitude at small temperatures, their values at T larger than the bandwidth become very close to each other. PMID:25910142

  11. Improved correspondence for DTI population studies via unbiased atlas building.

    PubMed

    Goodlett, Casey; Davis, Brad; Jean, Remi; Gilmore, John; Gerig, Guido

    2006-01-01

    We present a method for automatically finding correspondence in Diffusion Tensor Imaging (DTI) from deformable registration to a common atlas. The registration jointly produces an average DTI atlas, which is unbiased with respect to the choice of a template image, along with diffeomorphic correspondence between each image. The registration image match metric uses a feature detector for thin fiber structures of white matter, and interpolation and averaging of diffusion tensors use the Riemannian symmetric space framework. The anatomically significant correspondence provides a basis for comparison of tensor features and fiber tract geometry in clinical studies and for building DTI population atlases. PMID:17354780

  12. 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.

  13. 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 ? ? 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 ? ? 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.

  14. 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.

  15. 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

  16. 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

  17. Neurostereology protocol for unbiased quantification of neuronal injury and neurodegeneration

    PubMed Central

    Golub, Victoria M.; Brewer, Jonathan; Wu, Xin; Kuruba, Ramkumar; Short, Jenessa; Manchi, Maunica; Swonke, Megan; Younus, Iyan; Reddy, Doodipala Samba

    2015-01-01

    Neuronal injury and neurodegeneration are the hallmark pathologies in a variety of neurological conditions such as epilepsy, stroke, traumatic brain injury, Parkinson’s disease and Alzheimer’s disease. Quantification of absolute neuron and interneuron counts in various brain regions is essential to understand the impact of neurological insults or neurodegenerative disease progression in animal models. However, conventional qualitative scoring-based protocols are superficial and less reliable for use in studies of neuroprotection evaluations. Here, we describe an optimized stereology protocol for quantification of neuronal injury and neurodegeneration by unbiased counting of neurons and interneurons. Every 20th section in each series of 20 sections was processed for NeuN(+) total neuron and parvalbumin(+) interneuron immunostaining. The sections that contain the hippocampus were then delineated into five reliably predefined subregions. Each region was separately analyzed with a microscope driven by the stereology software. Regional tissue volume was determined by using the Cavalieri estimator, as well as cell density and cell number were determined by using the optical disector and optical fractionator. This protocol yielded an estimate of 1.5 million total neurons and 0.05 million PV(+) interneurons within the rat hippocampus. The protocol has greater predictive power for absolute counts as it is based on 3D features rather than 2D images. The total neuron counts were consistent with literature values from sophisticated systems, which are more expensive than our stereology system. This unbiased stereology protocol allows for sensitive, medium-throughput counting of total neurons in any brain region, and thus provides a quantitative tool for studies of neuronal injury and neurodegeneration in a variety of acute brain injury and chronic neurological models. PMID:26582988

  18. Entropic uncertainty relations and locking: Tight bounds for mutually unbiased bases

    SciTech Connect

    Ballester, Manuel A.; Wehner, Stephanie

    2007-02-15

    We prove tight entropic uncertainty relations for a large number of mutually unbiased measurements. In particular, we show that a bound derived from the result by Maassen and Uffink [Phys. Rev. Lett. 60, 1103 (1988)] for two such measurements can in fact be tight for up to {radical}(d) measurements in mutually unbiased bases. We then show that using more mutually unbiased bases does not always lead to a better locking effect. We prove that the optimal bound for the accessible information using up to {radical}(d) specific mutually unbiased bases is log d/2, which is the same as can be achieved by using only two bases. Our result indicates that merely using mutually unbiased bases is not sufficient to achieve a strong locking effect and we need to look for additional properties.

  19. Mutually unbiased projectors and duality between lines and bases in finite quantum systems

    SciTech Connect

    Shalaby, M.; Vourdas, A.

    2013-10-15

    Quantum systems with variables in the ring Z(d) are considered, and the concepts of weak mutually unbiased bases and mutually unbiased projectors are discussed. The lines through the origin in the Z(d)Z(d) phase space, are classified into maximal lines (sets of d points), and sublines (sets of d{sub i} points where d{sub i}|d). The sublines are intersections of maximal lines. It is shown that there exists a duality between the properties of lines (resp., sublines), and the properties of weak mutually unbiased bases (resp., mutually unbiased projectors). -- Highlights: Lines in discrete phase space. Bases in finite quantum systems. Duality between bases and lines. Weak mutually unbiased bases.

  20. Unbiased, scalable sampling of protein loop conformations from probabilistic priors

    PubMed Central

    2013-01-01

    Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

  1. 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.

  2. 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 Ivanovi? 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.

  3. The Unbiased Search of Biomarkers in Neurodegenerative Diseases.

    PubMed

    Ferrara, Pascual

    2016-01-01

    A clear link exists between the extension of life expectancy throughout the world and the increased incidence of age-related neurodegenerative disorders. Diseases like Alzheimer's and Parkinson's are chronic diseases with devastating consequences for patients and their families. They also represent a major economic cost for society. Therapeutic progress has been made mainly by alleviating some of the symptoms of these diseases, but currently no cure is available. Attempts to develop new therapies have been hampered mainly because of gaps in our current knowledge about the pathogenic mechanism underlying neurodegeneration, making difficult the identification of targets for new drug development, and also because of the lack of biomarkers essential for early diagnosis, patient stratification and follow up of treatment. Taking advantage of the latest technical developments, proteomics and peptidomics based approaches are being used to identify new cellular pathophysiological pathways as well as biomarkers in biological fluids. Here we will review the results, mainly published in the last five years, of unbiased proteomics and peptidomics approaches for biomarker research using biological fluids of Alzheimer's, Parkinson's and Amyotrophic Lateral Sclerosis patients. PMID:26956112

  4. 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.

  5. 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.

  6. Quantitative and unbiased analysis of directional persistence in cell migration.

    PubMed

    Gorelik, Roman; Gautreau, Alexis

    2014-08-01

    The mechanism by which cells control directional persistence during migration is a major question. However, the common index measuring directional persistence, namely the ratio of displacement to trajectory length, is biased, particularly by cell speed. An unbiased method is to calculate direction autocorrelation as a function of time. This function depends only on the angles of the vectors tangent to the trajectory. This method has not been widely used, because it is more difficult to compute. Here we discuss biases of the classical index and introduce a custom-made open-source computer program, DiPer, which calculates direction autocorrelation. In addition, DiPer also plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time. This user-friendly program is executable through Microsoft Excel, and it generates plots of publication-level quality. The protocol takes ?15 min to complete. We have recently used DiPer to analyze cell migration of three different mammalian cell types in 2D cultures: the mammary carcinoma cell line MDA-MB-231, the motile amoeba Dictyostelium discoideum and fish-scale keratocytes. DiPer can potentially be used not only for random migration in 2D but also for directed migration and for migration in 3D (direction autocorrelation only). Moreover, it can be used for any types of tracked particles: cellular organelles, bacteria and whole organisms. PMID:25033209

  7. 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

  8. Construction of the most suitable unbiased estimate distortions of radiation processes from remote sensing data

    NASA Astrophysics Data System (ADS)

    Ayman, Iskakova

    2014-03-01

    Proposed and studied in a multivariate discrete probability model of distribution of processes distortion of radiation from remote sensing data. Introduce the concept of the most appropriate evaluation of the set of unbiased, which has good asymptotic properties.

  9. Building an unbiased sample of quiescent galaxies up to z=2.5 based on the Mg(UV) absorption index

    NASA Astrophysics Data System (ADS)

    Domnguez Snchez, H.; Eliche-Moral, M. Carmen; Prez-Gonzlez, P. G.; Esquej, P.; Alcalde-Pampliega, B.; SHARDS Team

    2015-05-01

    Samples of ``red & dead" galaxies selected through traditional color-based techniques usually suffer from contamination by strongly dust obscured sources. We are using GTC/OSIRIS data from the SHARDS project on the GOODSN field to define unbiased samples of really quiescent massive galaxies at different redshifts up to z=2.5. By measuring the Mg(UV) absorption index in the pseudo-spectra of these galaxies, we intend to determine the redshift evolution of the characteristic age of their stellar populations to shed some light into their assembly epoch.

  10. Acceleration spectra for subduction zone earthquakes

    USGS Publications Warehouse

    Boatwright, J.; Choy, G.L.

    1989-01-01

    We estimate the source spectra of shallow earthquakes from digital recordings of teleseismic P wave groups, that is, P+pP+sP, by making frequency dependent corrections for the attenuation and for the interference of the free surface. The correction for the interference of the free surface assumes that the earthquake radiates energy from a range of depths. We apply this spectral analysis to a set of 12 subduction zone earthquakes which range in size from Ms = 6.2 to 8.1, obtaining corrected P wave acceleration spectra on the frequency band from 0.01 to 2.0 Hz. Seismic moment estimates from surface waves and normal modes are used to extend these P wave spectra to the frequency band from 0.001 to 0.01 Hz. The acceleration spectra of large subduction zone earthquakes, that is, earthquakes whose seismic moments are greater than 1027 dyn cm, exhibit intermediate slopes where u(w)???w5/4 for frequencies from 0.005 to 0.05 Hz. For these earthquakes, spectral shape appears to be a discontinuous function of seismic moment. Using reasonable assumptions for the phase characteristics, we transform the spectral shape observed for large earthquakes into the time domain to fit Ekstrom's (1987) moment rate functions for the Ms=8.1 Michoacan earthquake of September 19, 1985, and the Ms=7.6 Michoacan aftershock of September 21, 1985. -from Authors

  11. A PC program for unbiased and predictive linear and quadratic discriminant analysis.

    PubMed

    Grouven, U; Bergel, F; Schultz, B; Schultz, A

    1995-07-01

    Discriminant analysis plays an important role in biological and medical research. The most popular methods of discrimination in practical applications are parametric methods like linear and quadratic discriminant analysis. However, there exist modifications of these approaches, namely unbiased and predictive discriminant analysis, which lead to reduced error rates in certain situations. In this paper a menu-driven, user-friendly PC program written in Borland Pascal 7.0 is introduced which performs unbiased and predictive linear and quadratic discriminant analysis. PMID:7497704

  12. 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.

  13. 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.

  14. Estimating Unbiased Treatment Effects in Education Using a Regression Discontinuity Design

    ERIC Educational Resources Information Center

    Smith, William C.

    2014-01-01

    The ability of regression discontinuity (RD) designs to provide an unbiased treatment effect while overcoming the ethical concerns plagued by Random Control Trials (RCTs) make it a valuable and useful approach in education evaluation. RD is the only explicitly recognized quasi-experimental approach identified by the Institute of Education

  15. A kinematically unbiased search for nearby young stars in the Northern hemisphere selected using SuperWASP rotation periods

    NASA Astrophysics Data System (ADS)

    Binks, A. S.; Jeffries, R. D.; Maxted, P. F. L.

    2015-09-01

    We present a kinematically-unbiased search to identify young, nearby low-mass members of kinematic moving groups (MGs). Objects with both rotation periods shorter than 5 d in the SuperWASP All-Sky Survey and X-ray counterparts in the ROSAT All-Sky Survey were chosen to create a catalogue of several thousand rapidly rotating, X-ray active FGK stars. These objects are expected to be either young single stars or tidally locked spectroscopic binaries. We obtained optical spectra for a sub-sample of 146 stars to determine their ages and kinematics, and in some cases repeat radial velocity measurements were used to identify binarity. 26 stars are found to have lithium abundances consistent with an age of ?200 Myr, and show no evidence for binarity and in most cases measurements of H ? and v sin i support their youthful status. Based on their youth, their radial velocities and estimates of their three-dimensional kinematics, we find 11 objects that may be members of known MGs, eight that do not appear associated with any young MG and a further seven that are close to the kinematics of the recently proposed `Octans-Near' MG, and which may be the first members of this MG found in the Northern hemisphere. The initial search mechanism was 18 per cent efficient at identifying likely-single stars younger than 200 Myr, of which 80 per cent were early-K spectral types.

  16. Rotational Spectra in HELIUM-4 Clusters and Droplets:. Size Dependence and Rotational Linewidth

    NASA Astrophysics Data System (ADS)

    Zillich, Robert E.; Whaley, K. Birgitta

    2008-06-01

    We have implemented the correlated basis function method for molecule dynamics in 4He using ground state properties obtained by unbiased diffusion Monte Carlo simulation. We have calculated rotational spectra of linear molecules solvated in superfluid 4He. We present a simple model for solvation in finite 4He droplets, that is able to explain the observed Lorentzian lineshape of CO rotation spectra by inhomogeneous broadening originating from the wide size distribution of experimentally generated droplets.

  17. Higher-dimensional orbital-angular-momentum-based quantum key distribution with mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Mafu, Mhlambululi; Dudley, Angela; Goyal, Sandeep; Giovannini, Daniel; McLaren, Melanie; Padgett, Miles J.; Konrad, Thomas; Petruccione, Francesco; Lütkenhaus, Norbert; Forbes, Andrew

    2013-09-01

    We present an experimental study of higher-dimensional quantum key distribution protocols based on mutually unbiased bases, implemented by means of photons carrying orbital angular momentum. We perform (d+1) mutually unbiased measurements in a classically simulated prepare-and-measure scheme and on a pair of entangled photons for dimensions ranging from d=2 to 5. In our analysis, we pay attention to the detection efficiency and photon pair creation probability. As security measures, we determine from experimental data the average error rate, the mutual information shared between the sender and receiver, and the secret key generation rate per photon. We demonstrate that increasing the dimension leads to an increased information capacity as well as higher key generation rates per photon. However, we find that the benefit of increasing the dimension is limited by practical implementation considerations, which in our case results in deleterious effects observed beyond a dimension of d=4.

  18. 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.

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

    SciTech Connect

    Hall, Joanne L.; Rao, Asha

    2011-03-15

    In a recent article Paterek, Dakic, and Brukner [Phys. Rev. A 79, 012109 (2009)] show an algorithm for generating mutually unbiased bases from sets of orthogonal Latin squares. They claim that this algorithm works for every set of orthogonal Latin squares. We show that the algorithm only works for particular sets of orthogonal Latin squares. Furthermore, the algorithm is a more readable version of work previously published [Phys. Rev. A 70, 062101 (2004)].

  20. 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 and modeling of structures and analysis of three-dimensional relationships such as synaptic connectivity.

  1. Increasing the security of the ping-pong protocol by using many mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Zawadzki, Piotr; Pucha?a, Zbigniew; Miszczak, Jaros?aw Adam

    2013-01-01

    In this paper we propose an extended version of the ping-pong protocol and study its security. The proposed protocol incorporates the usage of mutually unbiased bases in the control mode. We show that, by increasing the number of bases, it is possible to improve the security of this protocol. We also provide the upper bounds on eavesdropping average non-detection probability and propose a control mode modification that increases the attack detection probability.

  2. Structure of the sets of mutually unbiased bases with cyclic symmetry

    NASA Astrophysics Data System (ADS)

    Seyfarth, U.; Snchez-Soto, L. L.; Leuchs, G.

    2014-11-01

    Mutually unbiased bases that can be cyclically generated by a single unitary operator are of special interest, for they can be readily implemented in practice. We show that, for a system of qubits, finding such a generator can be cast as the problem of finding a symmetric matrix over the field {F}2 equipped with an irreducible characteristic polynomial of a given Fibonacci index. The entanglement structure of the resulting complete sets is determined by two additive matrices of the same size.

  3. An efficient and unbiased method for sensitivity analysis of stochastic reaction networks

    PubMed Central

    Gupta, Ankit; Khammash, Mustafa

    2014-01-01

    We consider the problem of estimating parameter sensitivity for Markovian models of reaction networks. Sensitivity values measure the responsiveness of an output with respect to the model parameters. They help in analysing the network, understanding its robustness properties and identifying the important reactions for a specific output. Sensitivity values are commonly estimated using methods that perform finite-difference computations along with Monte Carlo simulations of the reaction dynamics. These methods are computationally efficient and easy to implement, but they produce a biased estimate which can be unreliable for certain applications. Moreover, the size of the bias is generally unknown and hence the accuracy of these methods cannot be easily determined. There also exist unbiased schemes for sensitivity estimation but these schemes can be computationally infeasible, even for very simple networks. Our goal in this paper is to present a new method for sensitivity estimation, which combines the computational efficiency of finite-difference methods with the accuracy of unbiased schemes. Our method is easy to implement and it relies on an exact representation of parameter sensitivity that we recently proved elsewhere. Through examples, we demonstrate that the proposed method can outperform the existing methods, both biased and unbiased, in many situations. PMID:25354975

  4. Losing the rose tinted glasses: neural substrates of unbiased belief updating in depression

    PubMed Central

    Garrett, Neil; Sharot, Tali; Faulkner, Paul; Korn, Christoph W.; Roiser, Jonathan P.; Dolan, Raymond J.

    2014-01-01

    Recent evidence suggests that a state of good mental health is associated with biased processing of information that supports a positively skewed view of the future. Depression, on the other hand, is associated with unbiased processing of such information. Here, we use brain imaging in conjunction with a belief update task administered to clinically depressed patients and healthy controls to characterize brain activity that supports unbiased belief updating in clinically depressed individuals. Our results reveal that unbiased belief updating in depression is mediated by strong neural coding of estimation errors in response to both good news (in left inferior frontal gyrus and bilateral superior frontal gyrus) and bad news (in right inferior parietal lobule and right inferior frontal gyrus) regarding the future. In contrast, intact mental health was linked to a relatively attenuated neural coding of bad news about the future. These findings identify a neural substrate mediating the breakdown of biased updating in major depression disorder, which may be essential for mental health. PMID:25221492

  5. Hierarchical unbiased group-wise registration for atlas construction and population comparison

    NASA Astrophysics Data System (ADS)

    Chen, Yasheng; Shen, Dinggang; Zhu, Hongtu; An, Hongyu; Gilmore, John; Lin, Weili

    2009-02-01

    A novel hierarchical unbiased group-wise registration is developed to robustly transform each individual image towards a common space for atlas based analysis. This hierarchical group-wise registration approach consists of two main components, (1) data clustering to group similar images together and (2) unbiased group-wise registration to generate a mean image for each cluster. The mean images generated in the lower hierarchical level are regarded as the input images for the higher hierarchy. In the higher hierarchical level, these input images will be further clustered and then registered by using the same two components mentioned. This hierarchical bottom-up clustering and within-cluster group-wise registration is repeated until a final mean image for the whole population is formed. This final mean image represents the common space for all the subjects to be warped to in order for the atlas based analysis. Each individual image at the bottom of the constructed hierarchy is transformed towards the root node through concatenating all the intermediate displacement fields. In order to evaluate the performance of the proposed hierarchical registration in atlas based statistical analysis, comparisons were made with the conventional group-wise registration in detecting simulated brain atrophy as well as fractional anisotropy differences between neonates and 1-year-olds. In both cases, the proposed approach demonstrated improved sensitivity (higher t-scores) than the conventional unbiased registration approach.

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

    NASA Astrophysics Data System (ADS)

    Kohn, S. A.; Micha?owski, 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 ?m, 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.

  7. Improving Agricultural Drought Monitoring in East Africa with Unbiased Rainfall Fields and Detailed Land Surface Physics

    NASA Astrophysics Data System (ADS)

    McNally, A.; Yatheendradas, S.; Peters-Lidard, C. D.; Michaelsen, J.

    2010-12-01

    Monitoring drought is particularly challenging within rainfed agricultural and pastoral systems, where it can serve the greatest need. Such locations often have sparse or non-existent ground based measurements of precipitation, evapotranspiration (ET), and soil moisture. For more effective drought monitoring with limited hydroclimate observations, we simulate land surface states using the Community Noah Land Surface Model forced with different merged rainfall products inside a Land Information System (LIS). Using model outputs we will answer the questions: How sensitive are soil moisture and ET fields to differences in rainfall forcing and model physics? What are acceptable drought-specific tradeoffs between near-real time availability and skill of rainfall data? Preliminary results with the African Rainfall Estimation Algorithm Version 2 (RFE2.0) outperformed global products, suggesting that sub-global rainfall estimates are the way forward for regional drought monitoring. Specifically, the Noah model forced with RFE2.0 better resolved the heterogeneous patterns in crop stress than the Famine Early Warning System Network (FEWS NET) operational Water Requirement Satisfaction Index (WRSI) model. To further investigate the improvement in drought monitoring while maintaining timeliness, we unbias (using Africa specific climatology) the precipitation products from CPC Merged Analysis of Precipitation (CMAP), Tropical Rainfall Measurement Mission (TRMM), and RFE2.0. The skill (relative accuracy) and reliability (average agreement) of the unbiased rainfall are calculated against an unbiased precipitation product augmented with station data from Ethiopia and Kenya. Soil moisture and ET fields from Noah are compared to the operational FEWS NET WRSI, soil water anomaly index, and the World Food Programs Crop and Food Security Assessment Mission reports. We anticipate that the unbiased rainfall fields will improve the accuracy, spatio-temporal resolution, and heterogeneity of the ET and soil moisture estimates compared to current operational drought indicators. Ultimately, these improved information products will better inform decision makers about seasonal food production and help them assess the need for relief, potentially saving millions of lives.

  8. Cluster Recognition Program - Progress Towards an Unbiased Detection and Analysis of Clusters

    NASA Astrophysics Data System (ADS)

    Ferreira, Bruno; Lada, Elizabeth

    2005-07-01

    Having developed and tested a systematic and unbiased method of cluster detection I present, in this poster, the method and the results of this work. In order to make statistically sound affirmations on the properties of young stellar clusters one needs to study a large number of these clusters and to do so in an identical way so as to make their results suitable for comparison. The method developed had that specific goal. Furthermore, so as to not have a biased sample, we removed identification-by-eye and subtituted it with a more robust method.

  9. Unbiased Statistics of a Constraint Satisfaction Problem - a Controlled-Bias Generator

    NASA Astrophysics Data System (ADS)

    Berthier, Denis

    We show that estimating the complexity (mean and distribution) of the instances of a fixed size Constraint Satisfaction Problem (CSP) can be very hard. We deal with the main two aspects of the problem: defining a measure of complexity and generating random unbiased instances. For the first problem, we rely on a general framework and a measure of complexity we presented at CISSE08. For the generation problem, we restrict our analysis to the Sudoku example and we provide a solution that also explains why it is so difficult.

  10. Unbiased treatment effect estimates by modeling the disease process of multiple sclerosis.

    PubMed

    Healy, Brian C; Hayden, Douglas L; Sampat, Mehul P; Bakshi, Rohit; Guttmann, Charles R G

    2009-03-15

    Gadolinium-enhancing lesions in the brain are commonly used as a primary outcome measure of disease activity in phase I/II clinical trials in multiple sclerosis (MS). The advent of effective therapy and the cost of clinical trials have led some researchers to adopt a one-arm study design with selection towards patients showing MRI activity. Regression to the mean is recognized as an important consideration in these trials, but the additional confounding effect of alternating active and inactive phases of disease has not been considered. Simulated data were generated from Poisson and normal distributions to mimic outcomes from phase I/II clinical trials of patients with relapsing-remitting MS under a constant or changing disease process model. In all cases, conventional comparison of pretreatment to on-treatment measurements overestimated the treatment effect. Although correction for regression to the mean provided unbiased estimates of the treatment effect under a constant disease process model, this correction also overestimated the treatment effect when disease activity changed over time. Conversely, unbiased estimates of the treatment effect under an alternating (active/inactive) disease process were obtained by correctly accounting for regression to the mean and the disease process. The implications of these results are discussed in terms of efficacy and safety. PMID:19121526

  11. 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.

  12. 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. PMID:25779621

  13. Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis*

    PubMed Central

    Len, Ileana R.; Schwmmle, Veit; Jensen, Ole N.; Sprenger, Richard R.

    2013-01-01

    The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921

  14. An unbiased method for clustering bacterial effectors using host cellular phenotypes.

    PubMed

    Dowling, Andrea J; Hodgson, David J

    2014-02-01

    We present a novel method implementing unbiased high-content morphometric cell analysis to classify bacterial effector phenotypes. This clustering methodology represents a significant advance over more qualitative visual approaches and can also be used to classify, and therefore predict the likely function of, unknown effector genes from any microbial genome. As a proof of concept, we use this approach to investigate 23 genetic regions predicted to encode antimacrophage effectors located across the genome of the insect and human pathogen Photorhabdus asymbiotica. Statistical cluster analysis using multiple cellular measures categorized treated macrophage phenotypes into three major groups relating to their putative functionality: (i) adhesins, (ii) cytolethal toxins, and (iii) cytomodulating toxins. Further investigation into their effects on phagocytosis revealed that several effectors also modulate this function and that the nature of this modulation (increased or decreased phagocytosis) is linked to the phenotype cluster group. Categorizing potential functionalities in this way allows rapid functional follow-up of key candidates for more-directed cell biological or biochemical investigation. Such an unbiased approach to the classification of candidate effectors will be useful for describing virulence-related regions in a wide range of genomes and will be useful in assigning putative functions to the growing number of microbial genes whose function remains unclear from homology searching. PMID:24296505

  15. Unbiased constraints on the clumpiness of the Universe from standard candles

    NASA Astrophysics Data System (ADS)

    Li, Zhengxiang; Ding, Xuheng; Zhu, Zong-Hong

    2015-04-01

    We perform unbiased tests for the clumpiness of the Universe by confronting the Zel'dovich-Kantowski-Dyer-Roeder luminosity distance, which describes the effect of local inhomogeneities on the propagation of light with the observational one estimated from measurements of standard candles, i.e., type Ia supernovae (SNe Ia) and gamma-ray bursts (GRBs). Methodologically, we first determine the light-curve fitting parameters which account for distance estimation in SNe Ia observations and the luminosity/energy relations which are responsible for distance estimation of GRBs in the global fit to reconstruct the Hubble diagrams in the context of a clumpy Universe. Subsequently, these Hubble diagrams allow us to achieve unbiased constraints on the matter density parameter ?m , as well as the clumpiness parameter ? which quantifies the fraction of homogeneously distributed matter within a given light cone. At a 1 ? confidence level, the constraints are ?m=0.34 0.02 and ? =1.0 0-0.02+0.00 from the joint analysis. The results suggest that the Universe full of Friedman-Lematre-Robertson-Walker fluid is favored by observations of standard candles with very high statistical significance. On the other hand, they may also indicate that the Zel'dovich-Kantowski-Dyer-Roeder approximation is a sufficiently accurate form to describe the effects of local homogeneity on the expanding Universe.

  16. Construction of mutually unbiased bases with cyclic symmetry for qubit systems

    NASA Astrophysics Data System (ADS)

    Seyfarth, Ulrich; Ranade, Kedar S.

    2011-10-01

    For the complete estimation of arbitrary unknown quantum states by measurements, the use of mutually unbiased bases has been well established in theory and experiment for the past 20 years. However, most constructions of these bases make heavy use of abstract algebra and the mathematical theory of finite rings and fields, and no simple and generally accessible construction is available. This is particularly true in the case of a system composed of several qubits, which is arguably the most important case in quantum information science and quantum computation. In this paper, we close this gap by providing a simple and straightforward method for the construction of mutually unbiased bases in the case of a qubit register. We show that our construction is also accessible to experiments, since only Hadamard and controlled-phase gates are needed, which are available in most practical realizations of a quantum computer. Moreover, our scheme possesses the optimal scaling possible, i.e., the number of gates scales only linearly in the number of qubits.

  17. Unbiased screening of polymer libraries to define novel substrates for functional hepatocytes with inducible drug metabolism.

    PubMed

    Hay, David C; Pernagallo, Salvatore; Diaz-Mochon, Juan Jose; Medine, Claire N; Greenhough, Sebastian; Hannoun, Zara; Schrader, Joerg; Black, James R; Fletcher, Judy; Dalgetty, Donna; Thompson, Alexandra I; Newsome, Philip N; Forbes, Stuart J; Ross, James A; Bradley, Mark; Iredale, John P

    2011-03-01

    Maintaining stable differentiated somatic cell function in culture is essential to a range of biological endeavors. However, current technologies, employing, for example, primary hepatic cell culture (essential to the development of a bio-artificial liver and improved drug and toxicology testing), are limited by supply, expense, and functional instability even on biological cell culture substrata. As such, novel biologically active substrates manufacturable to GMP standards have the potential to improve cell culture-based assay applications. Currently hepatic endoderm (HE) generated from pluripotent stem cells is a genotypically diverse, cheap, and stable source of "hepatocytes"; however, HE routine applications are limited due to phenotypic instability in culture. Therefore a manufacturable subcellular matrix capable of supporting long-term differentiated cell function would represent a step forward in developing scalable and phenotypically stable hESC-derived hepatocytes. Adopting an unbiased approach we screened polymer microarrays and identified a polyurethane matrix which promoted HE viability, hepatocellular gene expression, drug-inducible metabolism, and function. Moreover, the polyurethane supported, when coated on a clinically approved bio-artificial liver matrix, long-term hepatocyte function and growth. In conclusion, our data suggest that an unbiased screening approach can identify cell culture substrate(s) that enhance the phenotypic stability of primary and stem cell-derived cell resources. PMID:21277274

  18. Phosphonic Acid Modification of GaInP2 Photocathodes Toward Unbiased Photoelectrochemical Water Splitting.

    PubMed

    MacLeod, Bradley A; Steirer, K Xerxes; Young, James L; Koldemir, Unsal; Sellinger, Alan; Turner, John A; Deutsch, Todd G; Olson, Dana C

    2015-06-01

    The p-type semiconductor GaInP2 has a nearly ideal bandgap (?1.83 eV) for hydrogen fuel generation by photoelectrochemical water splitting but is unable to drive this reaction because of misalignment of the semiconductor band edges with the water redox half reactions. Here, we show that attachment of an appropriate conjugated phosphonic acid to the GaInP2 electrode surface improves the band edge alignment, closer to the desired overlap with the water redox potentials. We demonstrate that this surface modification approach is able to adjust the energetic position of the band edges by as much as 0.8 eV, showing that it may be possible to engineer the energetics at the semiconductor/electrolyte interface to allow for unbiased water splitting with a single photoelectrode having a bandgap of less than 2 eV. PMID:25970795

  19. 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.

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

    PubMed

    Abril-Gil, Mar; Garcia-Just, Alba; Cambras, Trinitat; Prez-Cano, Francisco J; Castellote, Cristina; Franch, ngels; 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. PMID:25716015

  1. Asymptotically Unbiased Estimation of Exposure Odds Ratios in Complete Records Logistic Regression.

    PubMed

    Bartlett, Jonathan W; Harel, Ofer; Carpenter, James R

    2015-10-15

    Missing data are a commonly occurring threat to the validity and efficiency of epidemiologic studies. Perhaps the most common approach to handling missing data is to simply drop those records with 1 or more missing values, in so-called "complete records" or "complete case" analysis. In this paper, we bring together earlier-derived yet perhaps now somewhat neglected results which show that a logistic regression complete records analysis can provide asymptotically unbiased estimates of the association of an exposure of interest with an outcome, adjusted for a number of confounders, under a surprisingly wide range of missing-data assumptions. We give detailed guidance describing how the observed data can be used to judge the plausibility of these assumptions. The results mean that in large epidemiologic studies which are affected by missing data and analyzed by logistic regression, exposure associations may be estimated without bias in a number of settings where researchers might otherwise assume that bias would occur. PMID:26429998

  2. 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.

  3. FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

    NASA Astrophysics Data System (ADS)

    Min, Junhong; Vonesch, Cédric; Kirshner, Hagai; Carlini, Lina; Olivier, Nicolas; Holden, Seamus; Manley, Suliana; Ye, Jong Chul; Unser, Michael

    2014-04-01

    Super resolution microscopy such as STORM and (F)PALM is now a well known method for biological studies at the nanometer scale. However, conventional imaging schemes based on sparse activation of photo-switchable fluorescent probes have inherently slow temporal resolution which is a serious limitation when investigating live-cell dynamics. Here, we present an algorithm for high-density super-resolution microscopy which combines a sparsity-promoting formulation with a Taylor series approximation of the PSF. Our algorithm is designed to provide unbiased localization on continuous space and high recall rates for high-density imaging, and to have orders-of-magnitude shorter run times compared to previous high-density algorithms. We validated our algorithm on both simulated and experimental data, and demonstrated live-cell imaging with temporal resolution of 2.5 seconds by recovering fast ER dynamics.

  4. An unbiased estimator of peculiar velocity with Gaussian distributed errors for precision cosmology

    NASA Astrophysics Data System (ADS)

    Watkins, Richard; Feldman, Hume A.

    2015-06-01

    We introduce a new estimator of the peculiar velocity of a galaxy or group of galaxies from redshift and distance estimates. This estimator results in peculiar velocity estimates which are statistically unbiased and have Gaussian distributed errors, thus complying with the assumptions of analyses that rely on individual peculiar velocities. We apply this estimator to the SFI++ and the Cosmicflows-2 catalogues of galaxy distances and, since peculiar velocity estimates of distant galaxies are error dominated, examine their error distributions. The adoption of the new estimator significantly improves the accuracy and validity of studies of the large-scale peculiar velocity field that assume Gaussian distributed velocity errors and eliminates potential systematic biases, thus helping to bring peculiar velocity analysis into the era of precision cosmology. In addition, our method of examining the distribution of velocity errors should provide a useful check of the statistics of large peculiar velocity catalogues, particularly those that are compiled out of data from multiple sources.

  5. Nonexistence of sharply covariant mutually unbiased bases in odd prime dimensions

    NASA Astrophysics Data System (ADS)

    Zhu, Huangjun

    2015-09-01

    Mutually unbiased bases (MUB) are useful in a number of research areas. The symmetry of MUB is an elusive and interesting subject. A (complete set of) MUB in dimension d is sharply covariant if it can be generated by a group of order d (d +1 ) from a basis state. Such MUB, if they exist, would be most appealing to theoretical studies and practical applications. Unfortunately, they seem to be quite rare. Here we prove that no MUB in odd prime dimensions is sharply covariant, by virtue of clever applications of Mersenne primes, Galois fields, and Frobenius groups. This conclusion provides valuable insight about the symmetry of MUB and the geometry of quantum state space. It complements and strengthens the earlier result of the author that only two stabilizer MUB are sharply covariant. Our study leads to the conjecture that no MUB other than those in dimensions 2 and 4 is sharply covariant.

  6. Gross examination of musculoskeletal sarcomas. Estimation of tumour volume and sampling for unbiased morphometry.

    PubMed

    Jensen, O M

    1991-11-01

    A method for handling and gross examination of specimens from musculoskeletal sarcomas is described. The method, which can be modified to relate to modern, preoperative tumour imaging, allows an accurate estimation of tumour volume and a systematic random sampling for morphometry, which for instance permits the unbiased estimation of tumour necrosis, cellularity and mitotic index. Furthermore, sampling can be performed in such a way that stereological parameters (for the estimation of nuclear size and pleomorphism) based on 'vertical sections' can be measured. The method in no way prohibits routine sampling, for instance from specimen margins and specific areas of interest within the tumour, and with a little practice does not take much extra time. PMID:1958347

  7. Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages

    PubMed Central

    Chamberlain, Michael Dean; Wells, Laura A.; Lisovsky, Alexandra; Guo, Hongbo; Isserlin, Ruth; Talior-Volodarsky, Ilana; Mahou, Redouan; Emili, Andrew; Sefton, Michael V.

    2015-01-01

    An unbiased phosphoproteomic method was used to identify biomaterial-associated changes in the phosphorylation patterns of macrophage-like cells. The phosphorylation differences between differentiated THP1 (dTHP1) cells treated for 10, 20, or 30 min with a vascular regenerative methacrylic acid (MAA) copolymer or a control methyl methacrylate (MM) copolymer were determined by MS. There were 1,470 peptides (corresponding to 729 proteins) that were differentially phosphorylated in dTHP1 cells treated with the two materials with a greater cellular response to MAA treatment. In addition to identifying pathways (such as integrin signaling and cytoskeletal arrangement) that are well known to change with cell–material interaction, previously unidentified pathways, such as apoptosis and mRNA splicing, were also discovered. PMID:26261332

  8. Technical Note: Estimating unbiased transfer-function performances in spatially structured environments

    NASA Astrophysics Data System (ADS)

    Trachsel, M.; Telford, R. J.

    2015-10-01

    Conventional cross-validation schemes for assessing transfer-function performance assume that observations are independent. In spatially-structured environments this assumption is violated, resulting in over-optimistic estimates of transfer-function performance. H block cross-validation, where all samples within h km of the test samples are omitted is a method for obtaining unbiased transfer function performance estimates. In this study, we assess three methods for determining the optimal h. Using simulated data, we find that all three methods result in comparable values of h. Applying the three methods to published transfer functions, we find they yield similar values for h. Some transfer functions perform notably worse when h block cross-validation is used.

  9. Mutually unbiased bases: tomography of spin states and the star-product scheme

    NASA Astrophysics Data System (ADS)

    Filippov, S. N.; Man'ko, V. I.

    2011-02-01

    Mutually unbiased bases (MUBs) are considered within the framework of a generic star-product scheme. We rederive that a full set of MUBs is adequate for a spin tomography, i.e. knowledge of all probabilities to find a system in each MUB-state is enough for a state reconstruction. Extending the ideas of the tomographic-probability representation and the star-product scheme to MUB tomography, dequantizer and quantizer operators for MUB symbols of spin states and operators are introduced, ordinary and dual star-product kernels are found. Since MUB projectors are to obey specific rules of the star-product scheme, we reveal the Lie algebraic structure of MUB projectors and derive new relations on triple- and four-products of MUB projectors. An example of qubits is considered in detail. MUB tomography by means of the Stern-Gerlach apparatus is discussed.

  10. Autonomous navigation method based on unbiased minimum-variance estimation during Mars entry

    NASA Astrophysics Data System (ADS)

    Fu, Huimin; Yang, Yusong; Xiao, Qiang; Wu, Yunzhang; Zhang, Yongbo

    2015-03-01

    Accurate navigation systems are required for future pinpoint Mars landing missions. A radio ranging augmented inertial measurement unit (IMU) navigation system concept is considered for the guided atmospheric entry phase. The systematic errors associated to the radio ranging and inertial measurements, and the atmospheric mission uncertainties are considered to be unknown. This paper presents the extension of an unbiased minimum-variance (EUMV) filter of a radio beacon/IMU navigation system. In the presence of unknown dynamics inputs, the filter joins the system state and the unknown systematic error estimation of a stochastic nonlinear time-varying discrete system. 3-DOF simulation results show that the performances of the proposed navigation filter algorithm, 100 m estimated altitude error and 8 m/s estimated velocity error, fulfills the need of future pinpoint Mars landing missions.

  11. 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.

  12. Asymptotically Unbiased Estimation of Exposure Odds Ratios in Complete Records Logistic Regression

    PubMed Central

    Bartlett, Jonathan W.; Harel, Ofer; Carpenter, James R.

    2015-01-01

    Missing data are a commonly occurring threat to the validity and efficiency of epidemiologic studies. Perhaps the most common approach to handling missing data is to simply drop those records with 1 or more missing values, in so-called complete records or complete case analysis. In this paper, we bring together earlier-derived yet perhaps now somewhat neglected results which show that a logistic regression complete records analysis can provide asymptotically unbiased estimates of the association of an exposure of interest with an outcome, adjusted for a number of confounders, under a surprisingly wide range of missing-data assumptions. We give detailed guidance describing how the observed data can be used to judge the plausibility of these assumptions. The results mean that in large epidemiologic studies which are affected by missing data and analyzed by logistic regression, exposure associations may be estimated without bias in a number of settings where researchers might otherwise assume that bias would occur. PMID:26429998

  13. 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.

  14. Optimal and unbiased FIR filtering in discrete time state space with smoothing and predictive properties

    NASA Astrophysics Data System (ADS)

    Shmaliy, Yuriy S.; Ibarra-Manzano, Oscar

    2012-12-01

    We address p-shift finite impulse response optimal (OFIR) and unbiased (UFIR) algorithms for predictive filtering ( p > 0), filtering ( p = 0), and smoothing filtering ( p < 0) at a discrete point n over N neighboring points. The algorithms were designed for linear time-invariant state-space signal models with white Gaussian noise. The OFIR filter self-determines the initial mean square state function by solving the discrete algebraic Riccati equation. The UFIR one represented both in the batch and iterative Kalman-like forms does not require the noise covariances and initial errors. An example of applications is given for smoothing and predictive filtering of a two-state polynomial model. Based upon this example, we show that exact optimality is redundant when N ? 1 and still a nice suboptimal estimate can fairly be provided with a UFIR filter at a much lower cost.

  15. FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

    PubMed Central

    Min, Junhong; Vonesch, Cdric; Kirshner, Hagai; Carlini, Lina; Olivier, Nicolas; Holden, Seamus; Manley, Suliana; Ye, Jong Chul; Unser, Michael

    2014-01-01

    Super resolution microscopy such as STORM and (F)PALM is now a well known method for biological studies at the nanometer scale. However, conventional imaging schemes based on sparse activation of photo-switchable fluorescent probes have inherently slow temporal resolution which is a serious limitation when investigating live-cell dynamics. Here, we present an algorithm for high-density super-resolution microscopy which combines a sparsity-promoting formulation with a Taylor series approximation of the PSF. Our algorithm is designed to provide unbiased localization on continuous space and high recall rates for high-density imaging, and to have orders-of-magnitude shorter run times compared to previous high-density algorithms. We validated our algorithm on both simulated and experimental data, and demonstrated live-cell imaging with temporal resolution of 2.5 seconds by recovering fast ER dynamics. PMID:24694686

  16. 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 (?), C 1s core-level shifts, resonance substituent parameters (?R), Lewis structures, and oxidation states of transition-metal complexes. PMID:26583402

  17. 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. PMID:26275099

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

    USGS Publications Warehouse

    Esler, Daniel; Mulcahy, D.M.; Jarvis, R.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%; x?? ?? 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.

  19. An Unbiased Cell MorphologyBased Screen for New, Biologically Active Small Molecules

    PubMed Central

    2005-01-01

    We have implemented an unbiased cell morphologybased 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 kinaseinhibitor 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 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

  20. 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

  1. 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. PMID:25339390

  2. 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. Conclusions: Unbiased pathway analysis of radioresistance allowed for the discovery of novel pathways associated with resistance to ionising radiation in PC. Specifically, our analysis indicates the importance of the cholesterol synthesis pathway in PC radioresistance. Further, a novel radiosensitiser, ZOL, showed promising results and warrants further study into the universality of these findings in PC, as well as the true potential of this drug as a clinical radiosensitiser. PMID:25025965

  3. Unbiased feature selection in learning random forests for high-dimensional data.

    PubMed

    Nguyen, Thanh-Tung; Huang, Joshua Zhexue; Nguyen, Thuy Thi

    2015-01-01

    Random forests (RFs) have been widely used as a powerful classification method. However, with the randomization in both bagging samples and feature selection, the trees in the forest tend to select uninformative features for node splitting. This makes RFs have poor accuracy when working with high-dimensional data. Besides that, RFs have bias in the feature selection process where multivalued features are favored. Aiming at debiasing feature selection in RFs, we propose a new RF algorithm, called xRF, to select good features in learning RFs for high-dimensional data. We first remove the uninformative features using p-value assessment, and the subset of unbiased features is then selected based on some statistical measures. This feature subset is then partitioned into two subsets. A feature weighting sampling technique is used to sample features from these two subsets for building trees. This approach enables one to generate more accurate trees, while allowing one to reduce dimensionality and the amount of data needed for learning RFs. An extensive set of experiments has been conducted on 47 high-dimensional real-world datasets including image datasets. The experimental results have shown that RFs with the proposed approach outperformed the existing random forests in increasing the accuracy and the AUC measures. PMID:25879059

  4. Unbiased Feature Selection in Learning Random Forests for High-Dimensional Data

    PubMed Central

    Nguyen, Thanh-Tung; Huang, Joshua Zhexue; Nguyen, Thuy Thi

    2015-01-01

    Random forests (RFs) have been widely used as a powerful classification method. However, with the randomization in both bagging samples and feature selection, the trees in the forest tend to select uninformative features for node splitting. This makes RFs have poor accuracy when working with high-dimensional data. Besides that, RFs have bias in the feature selection process where multivalued features are favored. Aiming at debiasing feature selection in RFs, we propose a new RF algorithm, called xRF, to select good features in learning RFs for high-dimensional data. We first remove the uninformative features using p-value assessment, and the subset of unbiased features is then selected based on some statistical measures. This feature subset is then partitioned into two subsets. A feature weighting sampling technique is used to sample features from these two subsets for building trees. This approach enables one to generate more accurate trees, while allowing one to reduce dimensionality and the amount of data needed for learning RFs. An extensive set of experiments has been conducted on 47 high-dimensional real-world datasets including image datasets. The experimental results have shown that RFs with the proposed approach outperformed the existing random forests in increasing the accuracy and the AUC measures. PMID:25879059

  5. 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. PMID:26522398

  6. Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model.

    PubMed

    Rosta, Edina; Hummer, Gerhard

    2015-01-13

    The weighted histogram analysis method (WHAM) is widely used to obtain accurate free energies from biased molecular simulations. However, WHAM free energies can exhibit significant errors if some of the biasing windows are not fully equilibrated. To account for the lack of full equilibration, we develop the dynamic histogram analysis method (DHAM). DHAM uses a global Markov state model to obtain the free energy along the reaction coordinate. A maximum likelihood estimate of the Markov transition matrix is constructed by joint unbiasing of the transition counts from multiple umbrella-sampling simulations along discretized reaction coordinates. The free energy profile is the stationary distribution of the resulting Markov matrix. For this matrix, we derive an explicit approximation that does not require the usual iterative solution of WHAM. We apply DHAM to model systems, a chemical reaction in water treated using quantum-mechanics/molecular-mechanics (QM/MM) simulations, and the Na(+) ion passage through the membrane-embedded ion channel GLIC. We find that DHAM gives accurate free energies even in cases where WHAM fails. In addition, DHAM provides kinetic information, which we here use to assess the extent of convergence in each of the simulation windows. DHAM may also prove useful in the construction of Markov state models from biased simulations in phase-space regions with otherwise low population. PMID:26574225

  7. P7C3 and an unbiased approach to drug discovery for neurodegenerative diseases

    PubMed Central

    McKnight, Steven L.; Ready, Joseph M.

    2014-01-01

    A novel neuroprotective small molecule was discovered using a target-agnostic in vivo screen in living mice. This aminopropyl carbazole, named P7C3, is orally bioavailable, crosses the bloodbrain barrier, and is non-toxic at doses several fold higher than the efficacious dose. The potency and drug-like properties of P7C3 were optimized through a medicinal chemistry campaign, providing analogues for detailed examination. Improved versions, such as (?)-P7C3-S243 and P7C3-A20, displayed neuro-protective properties in rodent models of Parkinsons disease, amyotrophic lateral sclerosis, traumatic brain injury and age-related cognitive decline. Derivatives appended with immobilizing moieties may reveal the protein targets of the P7C3 class of neuroprotective compounds. Our results indicate that unbiased, in vivo screens might provide starting points for the development of treatments for neurodegenerative diseases as well as tools to study the biology underlying these disorders. PMID:24514864

  8. A Grand Challenge: Unbiased Phenotypic Function of Metabolites from Jaspis splendens against Parkinson's Disease.

    PubMed

    Wang, Dongdong; Feng, Yunjiang; Murtaza, Mariyam; Wood, Stephen; Mellick, George; Hooper, John N A; Quinn, Ronald J

    2016-02-26

    A grand challenge in natural product chemistry is to determine the biological effects of all natural products. A phenotypic approach is frequently used for determining the activity of a compound and its potential impact on a disease state. Chemical investigation of a specimen of Jaspis splendens collected from the Great Barrier Reef resulted in the isolation of a new pterin derivative, jaspterin (1), a new bisindole alkaloid, splendamide (2), and a new imidazole alkaloid, jaspnin A (3) TFA salt. Jaspamycin (8) and 6-bromo-1H-indole-3-carboximidamide (16) are reported for the first time as naturally occurring metabolites. Known nucleosides (4-7, 9, 10), aglycones (11-13), indole alkaloids (14, 15, 17), and jaspamide peptides (18-22) were also isolated. The structures of the three new compounds 1-3 were unambiguously elucidated based on NMR and mass spectroscopic data. Jaspnin A (3) contained a rare thiomethylated imidazolinium unit. Coupling an unbiased phenotypic assay using a human olfactory neurosphere-derived cell model of Parkinson's disease to all of the natural products from the species J. splendens allowed the phenotypic profiles of the metabolites to be investigated. PMID:26883470

  9. AN UNBIASED METHOD OF MODELING THE LOCAL PECULIAR VELOCITY FIELD WITH TYPE Ia SUPERNOVAE

    SciTech Connect

    Weyant, Anja; Wood-Vasey, Michael; Wasserman, Larry; Freeman, Peter E-mail: wmwv@pitt.edu E-mail: pfreeman@cmu.edu

    2011-05-10

    We apply statistically rigorous methods of nonparametric risk estimation to the problem of inferring the local peculiar velocity field from nearby Type Ia supernovae (SNIa). We use two nonparametric methods-weighted least squares (WLS) and coefficient unbiased (CU)-both of which employ spherical harmonics to model the field and use the estimated risk to determine at which multipole to truncate the series. We show that if the data are not drawn from a uniform distribution or if there is power beyond the maximum multipole in the regression, a bias is introduced on the coefficients using WLS. CU estimates the coefficients without this bias by including the sampling density making the coefficients more accurate but not necessarily modeling the velocity field more accurately. After applying nonparametric risk estimation to SNIa data, we find that there are not enough data at this time to measure power beyond the dipole. The WLS Local Group bulk flow is moving at 538 {+-} 86 km s{sup -1} toward (l, b) = (258 deg. {+-} 10 deg., 36 deg. {+-} 11 deg.) and the CU bulk flow is moving at 446 {+-} 101 km s{sup -1} toward (l, b) = (273 deg. {+-} 11 deg., 46 deg. {+-} 8 deg.). We find that the magnitude and direction of these measurements are in agreement with each other and previous results in the literature.

  10. Quantification of Cysteinyl-S-Nitrosylation by Fluorescence in Unbiased Proteomic Studies*

    PubMed Central

    Wiktorowicz, John E.; Stafford, Susan; Rea, Harriet; Urvil, Petri; Soman, Kizhake; Kurosky, Alexander; Perez-Polo, J. Regino; Savidge, Tor C.

    2011-01-01

    Cysteinyl-S-nitrosylation has emerged as an important post-translational modification affecting protein function in health and disease. Great emphasis has been placed on global, unbiased quantification of S-nitrosylated proteins due to physiologic and oxidative stimuli. However, current strategies have been hampered by sample loss and altered protein electrophoretic mobility. Here, we describe a novel quantitative approach that combines accurate, sensitive fluorescence modification of cysteine S-nitrosylation that leaves electrophoretic mobility unaffected (SNOFlo), and introduce unique concepts for measuring changes in S-nitrosylation status relative to protein abundance. Its efficacy in defining the functional S-nitrosoproteome is demonstrated in two diverse biological applications: an in vivo rat hypoxia-ischemia reperfusion model, and antimicrobial S-nitrosoglutathione-driven transnitrosylation of an enteric microbial pathogen. The suitability of this approach for investigating endogenous S-nitrosylation is further demonstrated using Ingenuity Pathways analysis that identified nervous system and cellular development networks as the top two networks. Functional analysis of differentially S-nitrosylated proteins indicated their involvement in apoptosis, branching morphogenesis of axons, cortical neurons, and sympathetic neurites, neurogenesis, and calcium signaling. Major abundance changes were also observed for fibrillar proteins known to be stress-responsive in neurons and glia. Thus, both examples demonstrate the techniques power in confirming the widespread involvement of S-nitrosylation in hypoxia-ischemia/reperfusion injury and in antimicrobial host responses. PMID:21615140

  11. 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

  12. Quantification of cysteinyl S-nitrosylation by fluorescence in unbiased proteomic studies.

    PubMed

    Wiktorowicz, John E; Stafford, Susan; Rea, Harriet; Urvil, Petri; Soman, Kizhake; Kurosky, Alexander; Perez-Polo, J Regino; Savidge, Tor C

    2011-06-28

    Cysteinyl S-nitrosylation has emerged as an important post-translational modification affecting protein function in health and disease. Great emphasis has been placed on global, unbiased quantification of S-nitrosylated proteins because of physiologic and oxidative stimuli. However, current strategies have been hampered by sample loss and altered protein electrophoretic mobility. Here, we describe a novel quantitative approach that uses accurate, sensitive fluorescence modification of cysteine S-nitrosylation that leaves electrophoretic mobility unaffected (SNOFlo) and introduce unique concepts for measuring changes in S-nitrosylation status relative to protein abundance. Its efficacy in defining the functional S-nitrosoproteome is demonstrated in two diverse biological applications: an in vivo rat hypoxia-ischemia/reperfusion model and antimicrobial S-nitrosoglutathione-driven transnitrosylation of an enteric microbial pathogen. The suitability of this approach for investigating endogenous S-nitrosylation is further demonstrated using Ingenuity Pathways analysis that identified nervous system and cellular development networks as the top two networks. Functional analysis of differentially S-nitrosylated proteins indicated their involvement in apoptosis, branching morphogenesis of axons, cortical neurons, and sympathetic neurites, neurogenesis, and calcium signaling. Major abundance changes were also observed for fibrillar proteins known to be stress-responsive in neurons and glia. Thus, both examples demonstrate the technique's power in confirming the widespread involvement of S-nitrosylation in hypoxia-ischemia/reperfusion injury and in antimicrobial host responses. PMID:21615140

  13. Toward Unbiased Galaxy Cluster Masses from Line-of-sight Velocity Dispersions

    NASA Astrophysics Data System (ADS)

    Saro, Alex; Mohr, Joseph J.; Bazin, Gurvan; Dolag, Klaus

    2013-07-01

    We study the use of red-sequence-selected galaxy spectroscopy for unbiased estimation of galaxy cluster masses by using a publicly available simulated galaxy catalog. We explore the impact of selection using galaxy color, projected separation from the cluster center, galaxy luminosity, and spectroscopic redshift. We identify and characterize each of the following sources of bias and scatter in velocity dispersion at fixed mass: the intrinsic properties of halos in the form of halo triaxiality, sampling noise, the presence of multiple kinematic populations within the cluster, and the effect of interlopers. We show that even in red-sequence and spectroscopically selected galaxy samples, the interloper fraction is significant, and that the variations in the interloper population from cluster to cluster provide the dominant contribution to the velocity dispersion scatter at fixed mass. We present measurements of the total scatter in dispersion at fixed mass as a function of the number of redshifts. Results indicate that improvements in scatter are modest beyond samples of ~30 redshifts per cluster. Our results show that while cluster velocity dispersions extracted from a few dozen red-sequence-selected galaxies do not provide precise masses on a single cluster basis, an ensemble of cluster velocity dispersions can be combined to produce a precise calibration of a cluster survey-mass-observable relation. Currently, disagreements in the literature on simulated subhalo velocity dispersion-mass relations place a systematic floor on velocity dispersion mass calibration at the 5% level in dispersion.

  14. Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin.

    PubMed

    Zhou, Zhongwu; Yang, Yi; Konieczny, Stephen F; Irudayaraj, Joseph M K

    2015-12-24

    An ultra fast and unbiased method that uses salicylic acid coated magnetic nanoparticles (SAMNPs) and magnetophoretic chromatography is developed to extract chromatin associated RNAs (CARs). The SAMNPs were first used for enriching cells from the cell culture media and further used for capturing chromatin after cells were lysed. The formed SAMNPs-chromatin complexes were transferred to a viscous polyethylene glycol (PEG) solution stored in a 200-?l pipette tip. Due to the difference in viscosities, a bi-layer liquid was formed inside the pipette tip. The SAMNPs-chromatin complexes were separated from the free SAMNPs and free RNA-SAMNPs complexes by applying an external magnetic field. The CARs were further extracted from the SAMNP-chromatin complexes directly. The extracted CARs were reverse transcribed as cDNA and further characterized by real-time qPCR. The total assay time taken for cell separation, chromatin purification and chromatin associated RNAs extraction can be accomplished in less than 2h. PMID:26643718

  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 Millimtrique (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. An unbiased proteomics approach to identify human cytomegalovirus RNA-associated proteins.

    PubMed

    Lenarcic, Erik M; Ziehr, Benjamin J; Moorman, Nathaniel J

    2015-07-01

    Post-transcriptional events regulate herpesvirus gene expression, yet few herpesvirus RNA-binding proteins have been identified. We used an unbiased approach coupling oligo(dT) affinity capture with proteomics to identify viral RNA-associated proteins during infection. Using this approach, we identified and confirmed changes in the abundance or activity of two host RNA-associated proteins, DHX9 and DDX3, in cells infected with human cytomegalovirus (HCMV). We also identified and confirmed previously unreported activities for the HCMV US22 and pp71 proteins as RNA-associated viral proteins and confirmed that a known viral RNA-binding protein, pTRS1, associates with RNA in infected cells. Further, we found that HCMV pp71 co-sedimented with polysomes, associated with host and viral RNAs, and stimulated the overall rate of protein synthesis. These results demonstrate that oligo(dT) affinity capture coupled with proteomics provides a rapid and straightforward means to identify RNA-associated viral proteins during infection that may participate in the post-transcriptional control of gene expression. PMID:25765003

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

    PubMed

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

    2016-02-01

    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

  18. TOWARD UNBIASED GALAXY CLUSTER MASSES FROM LINE-OF-SIGHT VELOCITY DISPERSIONS

    SciTech Connect

    Saro, Alex; Mohr, Joseph J.; Bazin, Gurvan; Dolag, Klaus

    2013-07-20

    We study the use of red-sequence-selected galaxy spectroscopy for unbiased estimation of galaxy cluster masses by using a publicly available simulated galaxy catalog. We explore the impact of selection using galaxy color, projected separation from the cluster center, galaxy luminosity, and spectroscopic redshift. We identify and characterize each of the following sources of bias and scatter in velocity dispersion at fixed mass: the intrinsic properties of halos in the form of halo triaxiality, sampling noise, the presence of multiple kinematic populations within the cluster, and the effect of interlopers. We show that even in red-sequence and spectroscopically selected galaxy samples, the interloper fraction is significant, and that the variations in the interloper population from cluster to cluster provide the dominant contribution to the velocity dispersion scatter at fixed mass. We present measurements of the total scatter in dispersion at fixed mass as a function of the number of redshifts. Results indicate that improvements in scatter are modest beyond samples of {approx}30 redshifts per cluster. Our results show that while cluster velocity dispersions extracted from a few dozen red-sequence-selected galaxies do not provide precise masses on a single cluster basis, an ensemble of cluster velocity dispersions can be combined to produce a precise calibration of a cluster survey-mass-observable relation. Currently, disagreements in the literature on simulated subhalo velocity dispersion-mass relations place a systematic floor on velocity dispersion mass calibration at the 5% level in dispersion.

  19. Unbiased Metabolomic Investigation of Alzheimer's Disease Brain Points to Dysregulation of Mitochondrial Aspartate Metabolism.

    PubMed

    Paglia, Giuseppe; Stocchero, Matteo; Cacciatore, Stefano; Lai, Steven; Angel, Peggi; Alam, Mohammad Tauqeer; Keller, Markus; Ralser, Markus; Astarita, Giuseppe

    2016-02-01

    Alzheimer's disease (AD) is the most common cause of adult dementia. Yet the complete set of molecular changes accompanying this inexorable, neurodegenerative disease remains elusive. Here we adopted an unbiased lipidomics and metabolomics approach to surveying frozen frontal cortex samples from clinically characterized AD patients (n = 21) and age-matched controls (n = 19), revealing marked molecular differences between them. Then, by means of metabolomic pathway analysis, we incorporated the novel molecular information into the known biochemical pathways and compared it with the results of a metabolomics meta-analysis of previously published AD research. We found six metabolic pathways of the central metabolism as well as glycerophospholipid metabolism predominantly altered in AD brains. Using targeted metabolomics approaches and MS imaging, we confirmed a marked dysregulation of mitochondrial aspartate metabolism. The altered metabolic pathways were further integrated with clinical data, showing various degrees of correlation with parameters of dementia and AD pathology. Our study highlights specific, altered biochemical pathways in the brains of individuals with AD compared with those of control subjects, emphasizing dysregulation of mitochondrial aspartate metabolism and supporting future venues of investigation. PMID:26717242

  20. Interscale Stein's Unbiased Risk Estimate and Intrascale Feature Patches Distance Constraint for Image Denoising

    NASA Astrophysics Data System (ADS)

    Zhang, Qieshi; Kamata, Sei-Ichiro; Ahrary, Alireza

    The influence of noise is an important problem on image acquisition and transmission stages. The traditional image denoising approaches only analyzing the pixels of local region with a moving window, which calculated by neighbor pixels to denoise. Recently, this research has been focused on the transform domain and feature space. Compare with the traditional approaches, the global multi-scale analyzing and unchangeable noise distribution is the advantage. Apparently, the estimation based methods can be used in transform domain and get better effect. This paper proposed a new approach to image denoising in orthonormal wavelet domain. In this paper, we adopt Stein's unbiased risk estimate (SURE) based method to denoise the low-frequency bands and the feature patches distance constraint (FPDC) method also be proposed to estimate the noise free bands in Wavelet domain. The key point is that how to divide the lower frequency sub-bands and the higher frequency sub-bands, and do interscale SURE and intrascale FPDC, respectively. We compared our denoising method with some well-known and new denoising algorithms, the experimental results show that the proposed method can give better performance and keep more detail information in most objective and subjective criteria than other methods.

  1. Regulation of kidney development by Shp2: an unbiased stereological analysis.

    PubMed

    David, Frank S; Cullen-McEwen, Luise; Wu, Xue Sue; Zins, Stephen R; Lin, Julie; Bertram, John F; Neel, Benjamin G

    2010-12-01

    Genes that regulate renal branching morphogenesis are likely to indirectly regulate nephron endowment, but few have been validated to do so in vivo. PTPN11, which encodes the nonreceptor protein tyrosine phosphatase Shp2, acts downstream of receptor tyrosine kinases to modulate the Ras-MAPK pathway and has been implicated in branching morphogenesis in vitro and in invertebrates, and is therefore a candidate in vivo regulator of nephron number. In this work, heterozygous null mutant Shp2(+/-) mice at postnatal days 30-35 were compared with their wild-type (WT) littermates using unbiased stereology to determine if, indeed, the former had decreased nephron number due to their 50% decrease in gene/protein dosage. Although there was a trend toward decreases in total glomerular (nephron) number and kidney volume in Shp2(+/-) mice compared with WT, neither difference was statistically significant (11310 vs. 12198 glomeruli, P = 0.22; 62.8 mm(3) vs. 66.0 mm(3) renal volume; P = 0.40). We conclude that loss of 50% gene/protein dosage of PTPN11/Shp2 is insufficient to affect glomerular (and thereby nephron) number in mouse kidneys in vivo. PMID:20734316

  2. How unbiased is non-targeted metabolomics and is targeted pathway screening the solution?

    PubMed

    Christians, Uwe; Klawitter, Jelena; Hornberger, Andrea; Klawitter, Jost

    2011-07-01

    Metabolomics is only truly unbiased if the whole metabolome is captured. Current metabolomics technologies capture only a part of the metabolome and therefore produce inherently biased results. Important factors that introduce such bias into a metabolomic analysis may include but are not limited to, timing of sample collection, the sample collection procedure, sample processing, stabilization, stability and storage, extraction procedures, dilution of sample, type and number of analytical methods used, preferences of analytical assays for metabolites with certain physico-chemical properties, ion suppression (LC-MS), derivatization (GC-MS), sensitivity of the assay, range of reliable response and the ability to allow at least for semi-quantitative comparison. Consideration of the many computational, chemometric and biostatistical steps required to link changes in metabolite patterns to metabolic pathways and the additional bias and risks that these steps entail, brings up the question of whether or not screening for changes in known metabolic pathways using a set of validated, quantitative multiplexing LC-MS assays (targeted pathway screening, TAPAS) would be a more robust and reliable approach. Instead of non-selectively screening for changes in metabolite patterns, TAPAS screens for changes in metabolic pathways. Since such assays are designed for specific groups of metabolites, TAPAS can cover a larger number of metabolic pathways including metabolites of a wide variety of physicochemical properties and concentration ranges and thus, although based on suite of targeted assays, TAPAS may ultimately be a less biased strategy than current non-targeted metabolomics technologies. PMID:21466457

  3. Unravelling the matrix effect of fresh sampled cells for in vivo unbiased FTIR determination of the absolute concentration of total lipid content of microalgae.

    PubMed

    Coat, Rmy; Montalescot, Valeria; Len, Esteban Serrano; Kucma, Delphine; Perrier, Candice; Jubeau, Sbastien; Thouand, Grald; Legrand, Jack; Pruvost, Jrmy; Gonalves, Olivier

    2014-11-01

    Over the past years, the substitution of the classical biochemical quantification techniques by Fourier transform infrared (FTIR) spectroscopy has been widely studied on microalgae because of its tremendous application potential for bioprocess monitoring. In the present work, mandatory aspects that have never been approached by FTIR end-users working onto fresh biomass were assessed. We demonstrated first that fresh cells' FTIR spectra main characteristics could be severely and unspecifically altered when the properties of the sampled biomass were not monitored. Microscopy indicated that important cell reorganization could occur when diminishing the cells density of the sample. Molecular probing approach suggested that such a modification could provoke an alteration of the hydrogen-bonding network of the sample. The sample heterogeneity was found to impact also the shape and intensity of the recorded FTIR bands, participating then to a matrix effect uncharacterized until now. In the second part of our study, we selected FTIR spectra not influenced by this matrix effect and the corresponding accurate calibration data obtained by the whole cell analytical procedure to elaborate an optimized total lipid quantification PLS-R model. Results demonstrated that our strategy could provide a small volume sampling (1mL of fresh culture), rapid (within minutes), robust (physiological condition independent), and accurate (as accurate as the reference method could be) FTIR absolute quantification method to determine the fresh microalgae intracellular total lipid content. To validate our unbiased FTIR approach, a photobioprocess monitoring pipeline was developed and allowed assessing the effect of light attenuation on total lipid production by the marine microalga Nannochloropsis oculata. PMID:24788985

  4. Unbiased and biased estimators in coded aperture imaging for far field standoff detection at low count rates.

    PubMed

    Huh, Sam S; Gunter, Donald; Chivers, Daniel; Mihailescu, Lucian; Vetter, Kai

    2013-08-01

    In general, the reconstructed image in coded aperture imaging is affected by the source configuration. Fenimore's balanced convolution method in conjunction with the uniformly redundant array can remove the interference due to the source configuration. As an extension of Fenimore's balanced convolution method, we present general conditions for designing an unbiased mean estimator for a far-field coded aperture imaging system with a random binary mask. As part of the general conditions, we propose decoding arrays whose elements are variable with respect to source directions. We also show that the unbiased mean estimator from Fenimore's balanced convolution method is a special case of the general conditions. We also present a practical example of designing restoring arrays for a coded aperture system with a random mask. PMID:23913069

  5. 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. PMID:26963245

  6. 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

  7. Unbiased and Mobile Gait Analysis Detects Motor Impairment in Parkinson's Disease

    PubMed Central

    Klucken, Jochen; Barth, Jens; Kugler, Patrick; Schlachetzki, Johannes; Henze, Thore; Marxreiter, Franz; Kohl, Zacharias; Steidl, Ralph; Hornegger, Joachim; Eskofier, Bjoern; Winkler, Juergen

    2013-01-01

    Motor impairments are the prerequisite for the diagnosis in Parkinson's disease (PD). The cardinal symptoms (bradykinesia, rigor, tremor, and postural instability) are used for disease staging and assessment of progression. They serve as primary outcome measures for clinical studies aiming at symptomatic and disease modifying interventions. One major caveat of clinical scores such as the Unified Parkinson Disease Rating Scale (UPDRS) or Hoehn&Yahr (H&Y) staging is its rater and time-of-assessment dependency. Thus, we aimed to objectively and automatically classify specific stages and motor signs in PD using a mobile, biosensor based Embedded Gait Analysis using Intelligent Technology (eGaIT). eGaIT consist of accelerometers and gyroscopes attached to shoes that record motion signals during standardized gait and leg function. From sensor signals 694 features were calculated and pattern recognition algorithms were applied to classify PD, H&Y stages, and motor signs correlating to the UPDRS-III motor score in a training cohort of 50 PD patients and 42 age matched controls. Classification results were confirmed in a second independent validation cohort (42 patients, 39 controls). eGaIT was able to successfully distinguish PD patients from controls with an overall classification rate of 81%. Classification accuracy increased with higher levels of motor impairment (91% for more severely affected patients) or more advanced stages of PD (91% for H&Y III patients compared to controls), supporting the PD-specific type of analysis by eGaIT. In addition, eGaIT was able to classify different H&Y stages, or different levels of motor impairment (UPDRS-III). In conclusion, eGaIT as an unbiased, mobile, and automated assessment tool is able to identify PD patients and characterize their motor impairment. It may serve as a complementary mean for the daily clinical workup and support therapeutic decisions throughout the course of the disease. PMID:23431395

  8. Predicting Genetic Values: A Kernel-Based Best Linear Unbiased Prediction With Genomic Data

    PubMed Central

    Ober, Ulrike; Erbe, Malena; Long, Nanye; Porcu, Emilio; Schlather, Martin; Simianer, Henner

    2011-01-01

    Genomic data provide a valuable source of information for modeling covariance structures, allowing a more accurate prediction of total genetic values (GVs). We apply the kriging concept, originally developed in the geostatistical context for predictions in the low-dimensional space, to the high-dimensional space spanned by genomic single nucleotide polymorphism (SNP) vectors and study its properties in different gene-action scenarios. Two different kriging methods [“universal kriging” (UK) and “simple kriging” (SK)] are presented. As a novelty, we suggest use of the family of Matérn covariance functions to model the covariance structure of SNP vectors. A genomic best linear unbiased prediction (GBLUP) is applied as a reference method. The three approaches are compared in a whole-genome simulation study considering additive, additive-dominance, and epistatic gene-action models. Predictive performance is measured in terms of correlation between true and predicted GVs and average true GVs of the individuals ranked best by prediction. We show that UK outperforms GBLUP in the presence of dominance and epistatic effects. In a limiting case, it is shown that the genomic covariance structure proposed by VanRaden (2008) can be considered as a covariance function with corresponding quadratic variogram. We also prove theoretically that if a specific linear relationship exists between covariance matrices for two linear mixed models, the GVs resulting from BLUP are linked by a scaling factor. Finally, the relation of kriging to other models is discussed and further options for modeling the covariance structure, which might be more appropriate in the genomic context, are suggested. PMID:21515573

  9. An Unbiased Assessment of the Role of Imprinted Genes in an Intergenerational Model of Developmental Programming

    PubMed Central

    Radford, Elizabeth J.; Isganaitis, Elvira; Jimenez-Chillaron, Josep; Schroeder, Joshua; Molla, Michael; Andrews, Simon; Didier, Nathalie; Charalambous, Marika; McEwen, Kirsten; Marazzi, Giovanna; Sassoon, David; Patti, Mary-Elizabeth; Ferguson-Smith, Anne C.

    2012-01-01

    Environmental factors during early life are critical for the later metabolic health of the individual and of future progeny. In our obesogenic environment, it is of great socioeconomic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Imprinted genes, a class of functionally mono-allelic genes critical for early growth and metabolic axis development, have been proposed to be uniquely susceptible to environmental change. Furthermore, it has also been suggested that perturbation of the epigenetic reprogramming of imprinting control regions (ICRs) may play a role in phenotypic heritability following early life insults. Alternatively, the presence of multiple layers of epigenetic regulation may in fact protect imprinted genes from such perturbation. Unbiased investigation of these alternative hypotheses requires assessment of imprinted gene expression in the context of the response of the whole transcriptome to environmental assault. We therefore analyse the role of imprinted genes in multiple tissues in two affected generations of an established murine model of the developmental origins of health and disease using microarrays and quantitative RT–PCR. We demonstrate that, despite the functional mono-allelicism of imprinted genes and their unique mechanisms of epigenetic dosage control, imprinted genes as a class are neither more susceptible nor protected from expression perturbation induced by maternal undernutrition in either the F1 or the F2 generation compared to other genes. Nor do we find any evidence that the epigenetic reprogramming of ICRs in the germline is susceptible to nutritional restriction. However, we propose that those imprinted genes that are affected may play important roles in the foetal response to undernutrition and potentially its long-term sequelae. We suggest that recently described instances of dosage regulation by relaxation of imprinting are rare and likely to be highly regulated. PMID:22511876

  10. A practical methodology to measure unbiased gas chromatographic retention factor vs. temperature relationships.

    PubMed

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

    2014-12-29

    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 the 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 two-fold more error. Furthermore, temperature-programmed retention times calculated in five other laboratories 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

  11. 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

    2013-08-01

    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. GSK3?, GSK3?, and MAPK13 were found to be the most active tau kinases, phosphorylating tau at all four epitopes. We further dissected the effects of GSK3? and GSK3? 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. PMID:23798682

  12. Unbiased estimates of long-term net survival of solid cancers in France.

    PubMed

    Jooste, Valrie; Grosclaude, Pascale; Remontet, Laurent; Launoy, Guy; Baldi, Isabelle; Molini, Florence; Arveux, Patrick; Bossard, Nadine; Bouvier, Anne-Marie; Colonna, Marc

    2013-05-15

    In cancer studies, net survival (observed if cancer was the only cause of death) is a useful indicator but survival estimation at 5 years is insufficient for planning healthcare needs. We estimated the net survivals at 5 and 10 years in a cohort of 387,961 patients who had solid tumors between 1989 and 2004 and were followed-up until January 1, 2008. The cases were actively followed-up. Net survival was estimated with the unbiased Pohar-Perme method. The standardized net survival used the international cancer survival standard weights. In men, the standardized net survivals ranged from 92% at 5 years and 89% at 10 years (testis) to 6% at 5 years and 5% at 10 years (pancreas). In women, it ranged from 91% at 5 years and 88% at 10 years (thyroid) to 10% at 5 years and 7% at 10 years (pancreas). The most frequent cancers had the highest net survivals: 84% at 5 years and 71% at 10 years for prostate and 84% at 5 years and 74% at 10 years for breast cancer. Advanced age was associated with poorer prognosis. In most cancers, the net survivals at 5 and 10 years increased over periods of diagnosis. Net cancer survival is unaffected by mortalities due to other causes. It is the only indicator suitable for comparisons between countries or periods of diagnosis within a given country. The 10-year net survival confirmed the persistent unfavorable role of age in prognosis and the general improvement of cancer management over the last decade. PMID:23001495

  13. 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.

  14. 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?m 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

  15. 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

  16. Extending our Unbiased Survey for Disks Around White Dwarfs; One Foot in Terra Incognita

    NASA Astrophysics Data System (ADS)

    Farihi, Jay; Gaensicke, Boris

    2015-10-01

    Eleven cycles of Spitzer studies have firmly linked the presence of atmospheric metals in white dwarfs to closely orbiting circumstellar dust; the result of large planetesimal disruptions in active planetary systems. These evolved stars represent a unique tool to study long term planetary system evolution in the descendants of A-type and similar stars. Yet despite 35 IRAC-detected dust disks at white dwarfs, we are still unable to determine true disk frequency as a function of post-main sequence planetary system age. In Cycle 8 we carried out the first double-blind Spitzer/HST survey of a large white dwarf sample in the cooling age range 25-100 Myr. We found a fraction of 4% have an IRAC excess, while 30% of the sample display atmospheric metals, indicating that many white dwarf dust disks are faint in the infrared, and hinting at an undiscovered disk population. Additionally, these joint observations provided the first quantitative link between circumstellar dust and atmospheric metals in an unbiased sample of stars. Here we propose to extend our work to younger (5-25 Myr) and older (100-300 Myr) cooling ages, using a sample of 106 white dwarfs selected only for temperature and brightness. As with our previous survey, the same sample of 106 stars will be searched for atmospheric metals with HST/COS in approved Cycle 22 and 23 Snapshots. These combined observations will measure true disk frequency over a range of cooling ages for the first time, and thus constrain models of post-main sequence, planetary system dynamical instabilities. Importantly, Spitzer observations are critical to determine the fraction of disks in the cooling age range 5-25 Myr, which has not been explored, and where dynamical instabilities are expected to be relatively frequent.

  17. Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA Repertoires

    PubMed Central

    Rubelt, Florian; Sievert, Volker; Knaust, Florian; Diener, Christian; Lim, Theam Soon; Skriner, Karl; Klipp, Edda; Reinhardt, Richard; Lehrach, Hans; Konthur, Zoltn

    2012-01-01

    The immune system protects us from foreign substances or pathogens by generating specific antibodies. The variety of immunoglobulin (Ig) paratopes for antigen recognition is a result of the V(D)J rearrangement mechanism, while a fast and efficient immune response is mediated by specific immunoglobulin isotypes obtained through class switch recombination (CSR). To get a better understanding on how antibody-based immune protection works and how it changes with age, the interdependency between these two parameters need to be addressed. Here, we have performed an in depth analysis of antibody repertoires of 14 healthy donors representing different gender and age groups. For this task, we developed a unique pyrosequencing approach, which is able to monitor the expression levels of all immunoglobulin V(D)J recombinations of all isotypes including subtypes in an unbiased and quantitative manner. Our results show that donors have individual immunoglobulin repertoires and cannot be clustered according to V(D)J recombination patterns, neither by age nor gender. However, after incorporating isotype-specific analysis and considering CSR information into hierarchical clustering the situation changes. For the first time the donors cluster according to age and separate into young adults and elderly donors (>50). As a direct consequence, this clustering defines the onset of immune senescence at the age of fifty and beyond. The observed age-dependent reduction of CSR ability proposes a feasible explanation why reduced efficacy of vaccination is seen in the elderly and implies that novel vaccine strategies for the elderly should include the Golden Agers. PMID:23226220

  18. Unbiased Transcriptional Comparisons of Generalist and Specialist Herbivores Feeding on Progressively Defenseless Nicotiana attenuata Plants

    PubMed Central

    Govind, Geetha; Mittapalli, Omprakash; Griebel, Thasso; Allmann, Silke; Böcker, Sebastian; Baldwin, Ian Thomas

    2010-01-01

    Background Herbivore feeding elicits dramatic increases in defenses, most of which require jasmonate (JA) signaling, and against which specialist herbivores are thought to be better adapted than generalist herbivores. Unbiased transcriptional analyses of how neonate larvae cope with these induced plant defenses are lacking. Methodology/Principal Findings We created cDNA microarrays for Manduca sexta and Heliothis virescens separately, by spotting normalized midgut-specific cDNA libraries created from larvae that fed for 24 hours on MeJA-elicited wild-type (WT) Nicotiana attenuata plants. These microarrays were hybridized with labeled probes from neonates that fed for 24 hours on WT and isogenic plants progressively silenced in JA-mediated defenses (N: nicotine; N/PI: N and trypsin protease inhibitors; JA: all JA-mediated defenses). H. virescens neonates regulated 16 times more genes than did M. sexta neonates when they fed on plants silenced in JA-mediated defenses, and for both species, the greater the number of defenses silenced in the host plant (JA > N/PI > N), the greater were the number of transcripts regulated in the larvae. M. sexta larvae tended to down-regulate while H. virescens larvae up- and down-regulated transcripts from the same functional categories of genes. M. sexta larvae regulated transcripts in a diet-specific manner, while H. virescens larvae regulated a similar suite of transcripts across all diet types. Conclusions/Significance The observations are consistent with the expectation that specialists are better adapted than generalist herbivores to the defense responses elicited in their host plants by their feeding. While M. sexta larvae appear to be better adapted to N. attenuata's defenses, some of the elicited responses remain effective defenses against both herbivore species. The regulated genes provide novel insights into larval adaptations to N. attenuata's induced defenses, and represent potential targets for plant-mediated RNAi to falsify hypotheses about the process of adaptation. PMID:20090945

  19. 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. PMID:24749745

  20. Quantum fluctuations as deviation from classical dynamics of ensemble of trajectories parameterized by unbiased hidden random variable

    NASA Astrophysics Data System (ADS)

    Budiyono, Agung

    2012-06-01

    A quantization method based on replacement of c-number by c-number parameterized by an unbiased hidden random variable is developed. In contrast to canonical quantization, the replacement has a straightforward physical interpretation as a statistical modification of classical dynamics of an ensemble of trajectories, and implies a unique operator ordering. We then apply the method to develop quantum measurement without wave function collapse and external observer a la pilot-wave theory.

  1. 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.

  2. 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.

  3. 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-selected galaxies than in flux-limited samples of Lyman break galaxies.

  4. Unbiased Estimate of Dark Energy Density from Type Ia Supernova Data

    NASA Astrophysics Data System (ADS)

    Wang, Yun; Lovelace, Geoffrey

    2001-12-01

    Type Ia supernovae (SNe Ia) are currently the best probes of the dark energy in the universe. To constrain the nature of dark energy, we assume a flat universe and that the weak energy condition is satisfied, and we allow the density of dark energy, ?X(z), to be an arbitrary function of redshift. Using simulated data from a space-based SN pencil-beam survey, we find that by optimizing the number of parameters used to parameterize the dimensionless dark energy density, f(z)=?X(z)/?X(z=0), we can obtain an unbiased estimate of both f(z) and the fractional matter density of the universe, ?m. A plausible SN pencil-beam survey (with a square degree field of view and for an observational duration of 1 yr) can yield about 2000 SNe Ia with 0<=z<=2. Such a survey in space would yield SN peak luminosities with a combined intrinsic and observational dispersion of ?(mint)=0.16 mag. We find that for such an idealized survey, ?m can be measured to 10% accuracy, and the dark energy density can be estimated to ~20% to z~1.5, and ~20%-40% to z~2, depending on the time dependence of the true dark energy density. Dark energy densities that vary more slowly can be more accurately measured. For the anticipated Supernova/Acceleration Probe (SNAP) mission, ?m can be measured to 14% accuracy, and the dark energy density can be estimated to ~20% to z~1.2. Our results suggest that SNAP may gain much sensitivity to the time dependence of the dark energy density and ?m by devoting more observational time to the central pencil-beam fields to obtain more SNe Ia at z>1.2. We use both a maximum likelihood analysis and a Monte Carlo analysis (when appropriate) to determine the errors of estimated parameters. We find that the Monte Carlo analysis gives a more accurate estimate of the dark energy density than the maximum likelihood analysis.

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

    NASA Astrophysics Data System (ADS)

    Lindberg, J. E.; Jrgensen, 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 the external irradiation from R CrA. Based on observations with the Atacama Pathfinder EXperiment (APEX) telescope. APEX is a collaboration between the Max Planck Institute for Radio Astronomy, the European Southern Observatory, and the Onsala Space Observatory.Appendices are available in electronic form at http://www.aanda.org

  6. A Novel Unbiased Proteomic Approach to Detect the Reactivity of Cerebrospinal Fluid in Neurological Diseases*

    PubMed Central

    Menon, Krishnakumar N.; Steer, David L.; Short, Martin; Petratos, Steven; Smith, Ian; Bernard, Claude C. A.

    2011-01-01

    Neurodegenerative diseases, such as multiple sclerosis represent global health issues. Accordingly, there is an urgent need to understand the pathogenesis of this and other central nervous system disorders, so that more effective therapeutics can be developed. Cerebrospinal fluid is a potential source of important reporter molecules released from various cell types as a result of central nervous system pathology. Here, we report the development of an unbiased approach for the detection of reactive cerebrospinal fluid molecules and target brain proteins from patients with multiple sclerosis. To help identify molecules that may serve as clinical biomarkers for multiple sclerosis, we have biotinylated proteins present in the cerebrospinal fluid and tested their reactivity against brain homogenate as well as myelin and myelin-axolemmal complexes. Proteins were separated by two-dimensional gel electrophoresis, blotted onto membranes and probed separately with biotinylated unprocessed cerebrospinal fluid samples. Protein spots that reacted to two or more multiple sclerosis-cerebrospinal fluids were further analyzed by matrix assisted laser desorption ionization-time-of-flight time-of-flight mass spectrometry. In addition to previously reported proteins found in multiple sclerosis cerebrospinal fluid, such as αβ crystallin, enolase, and 14–3-3-protein, we have identified several additional molecules involved in mitochondrial and energy metabolism, myelin gene expression and/or cytoskeletal organization. These include aspartate aminotransferase, cyclophilin-A, quaking protein, collapsin response mediator protein-2, ubiquitin carboxy-terminal hydrolase L1, and cofilin. To further validate these findings, the cellular expression pattern of collapsin response mediator protein-2 and ubiquitin carboxy-terminal hydrolase L1 were investigated in human chronic-active MS lesions by immunohistochemistry. The observation that in multiple sclerosis lesions phosphorylated collapsin response mediator protein-2 was increased, whereas Ubiquitin carboxy-terminal hydrolase L1 was down-regulated, not only highlights the importance of these molecules in the pathology of this disease, but also illustrates the use of our approach in attempting to decipher the complex pathological processes leading to multiple sclerosis and other neurodegenerative diseases. PMID:21421798

  7. Elevated temperature reference spectra

    SciTech Connect

    Brown, D.; Phillips, B.; Tussey, L.

    1997-12-31

    A compilation of infrared spectra at elevated temperatures is required for the accurate quantification of gas concentrations for Fourier transform infrared (FTIR) extractive sampling of stack gases and FTIR in-situ process monitoring. Analysis of high temperature gases utilizing ambient temperature reference spectra can result in significant quantification errors. The US Air Force`s Arnold Engineering Development Center (AEDC) is currently assisting the EPA in measuring reference spectra and making existing and new data available to the public through two ongoing efforts. One of these efforts is the measurement of elevated temperature infrared reference spectra of the low vapor pressure hazardous air pollutants (HAP) compounds, as well as spectral interfering compounds. The equipment and procedures used for the elevated temperature reference spectra measurements is described as well as some of the challenges encountered in these measurements. Examples of the reference spectra are also presented. To make the reference spectra developed by AEDC and other EPA programs easily accessible, AEDC has also been tasked to maintain a site on the World Wide Web containing reference spectra, reports, and software tools of interest to the optical sensing community. This web site has seen increased use during the three years that it has been in existence with users from academia, commercial, and government, both domestic and foreign. The site has undergone several improvements since inception and actively solicits inputs for further improvements from its users. A description of this web site and recent improvements and additions is given in this paper.

  8. 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.

  9. Validation of the Isotropic Fractionator: Comparison with Unbiased Stereology and DNA Extraction for Quantification of Glial Cells

    PubMed Central

    Bahney, Jami; von Bartheld, Christopher S.

    2014-01-01

    Background The “isotropic fractionator” (IF) is a novel cell counting technique that homogenizes fixed tissue, recovers cell nuclei in solution, and samples and quantifies nuclei by extrapolation. Studies using this technique indicate that the ratio of glia to neurons in the human brain is approximately 1:1 rather than the 10:1 or 50:1 ratio previously assumed. Although some results obtained with the IF have been similar to those obtained by stereology, the IF has never been calibrated or validated. It is conceivable that only a fraction of glial cell nuclei are recovered intact or recognized after the homogenization step. New Method To rule out this simple explanation for the claim of a 1:1 glia-neuron ratio, we compared cell numbers obtained from adjacent, weight-normalized samples of human and macaque monkey white matter using three techniques: the IF, unbiased stereology of histological sections in exhaustively sectioned samples, and cell numbers calculated from DNA extraction. Results and comparison of methods In primate forebrains, the IF yielded 73,000–90,000 nuclei/mg white matter, unbiased stereology yielded 75,000–92,000 nuclei/mg, with coefficients of error ranging from 0.013–0.063, while DNA extraction yielded only 4,000–23,000 nuclei/mg in fixed white matter tissues. Conclusions Since the IF revealed about 100% of the numbers produced by unbiased stereology, there is no significant underestimate of glial cells. This confirms the notion that the human brain overall contains glial cells and neurons with a ratio of about 1:1 far from the originally assumed ratio of 10:1 in favor of glial cells. PMID:24239779

  10. 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. PMID:25403361

  11. Thermodynamic analysis of spectra

    SciTech Connect

    Mitchell, G. E.; Shriner, J. F. Jr.

    2008-04-04

    Although random matrix theory had its initial application to neutron resonances, there is a relative scarcity of suitable nuclear data. The primary reason for this is the sensitivity of the standard measures used to evaluate spectra--the spectra must be essential pure (no state with a different symmetry) and complete (no states missing). Additional measures that are less sensitive to these experimental limitations are of significant value. The standard measure for long range order is the {delta}{sub 3} statistic. In the original paper that introduced this statistic, Dyson and Mehta also attempted to evaluate spectra with thermodynamic variables obtained from the circular orthogonal ensemble. We consider the thermodynamic 'internal energy' and evaluate its sensitivity to experimental limitations such as missing and spurious levels. Monte Carlo simulations suggest that the internal energy is less sensitive to mistakes than is {delta}{sub 3}, and thus the internal energy can serve as a addition to the tool kit for evaluating experimental spectra.

  12. Spectra over complex terrain

    SciTech Connect

    Panofsky, H.A.; Larko, D.; Lipschutz, R.; Stone, G.

    1981-01-01

    Spectra have been measured over land downwind of a water surface, over hilltops and escarpments, and over rolling farmland. The following hypotheses can be used to explain the differences between these spectra. (1) For wavelengths short compared to the fetch over the new terrain, spectral densities are in equilibrium with the new terrain. (2) For wavelengths long compared to this fetch, spectral densities remain unchanged if the ground is horizontal. If the flow is over a steep hill, the low-frequency structure is modified by distortion of the mean flow, with the longitudinal component losing energy relative to the lateral and vertical components. Because vertical-velocity spectra contain relatively less low-frequency energy than horizontal-velocity spectra, energetic vertical-velocity fluctuations tend to be in equilibrium with local terrain.

  13. 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, Agns; Ferriol, Sylvain; Barbier, Rmi; Nasilowski, Michel; Lhuillier, Emmanuel; Dubertret, Benot; 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. PMID:25549009

  14. 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.

  15. An Unbiased 1.3 mm Emission Line Survey of the Protoplanetary Disk Orbiting LkCa 15

    NASA Astrophysics Data System (ADS)

    Punzi, K. M.; Hily-Blant, P.; Kastner, J. H.; Sacco, G. G.; 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 Millimtrique (IRAM) 30 m telescope. The survey demonstrates that in this spectral region, the most readily detectable lines are those of CO and its isotopologues 13CO and C18O, as well as HCO+, HCN, CN, C2H, CS, and H2CO. 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 C2H (3-2) hyperfine complexes. Modeling of these emission complexes indicates that the CN and C2H 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.

  16. Nanoslit cavity plasmonic modes and built-in fields enhance the CW THz radiation in an unbiased antennaless photomixers array.

    PubMed

    Mohammad-Zamani, Mohammad Javad; Neshat, Mohammad; Moravvej-Farshi, Mohammad Kazem

    2016-01-15

    A new generation unbiased antennaless CW terahertz (THz) photomixer emitters array made of asymmetric metal-semiconductor-metal (MSM) gratings with a subwavelength pitch, operating in the optical near-field regime, is proposed. We take advantage of size effects in near-field optics and electrostatics to demonstrate the possibility of enhancing the THz power by 4 orders of magnitude, compared to a similar unbiased antennaless array of the same size that operates in the far-field regime. We show that, with the appropriate choice of grating parameters in such THz sources, the first plasmonic resonant cavity mode in the nanoslit between two adjacent MSMs can enhance the optical near-field absorption and, hence, the generation of photocarriers under the slit in the active medium. These photocarriers, on the other hand, are accelerated by the large built-in electric field sustained under the nanoslits by two dissimilar Schottky barriers to create the desired large THz power that is mainly radiated downward. The proposed structure can be tuned in a broadband frequency range of 0.1-3 THz, with output power increasing with frequency. PMID:26766729

  17. First principles calculation of electron ionization mass spectra for selected organic drug molecules.

    PubMed

    Bauer, Christoph Alexander; Grimme, Stefan

    2014-11-21

    This study presents a showcase for the novel Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) method on five FDA-approved drugs. The method allows a first-principles electronic structure-based prediction of EI mass spectra in principle for any molecule. The systems in this case study are organic substances of nominal masses between 404 and 853 atomic mass units and cover a wide range of functional groups and organic molecular structure motifs. The results demonstrate the widespread applicability of the QCEIMS method for the unbiased computation of EI mass spectra even for larger molecules. Its strengths compared to standard (static) or database driven approaches in such cases are highlighted. Weak points regarding the required computation times or the approximate character of the employed QC methods are also discussed. We propose QCEIMS as a viable and robust way of predicting EI mass spectra for sizeable organic molecules relevant to medicinal and pharmaceutical chemistry. PMID:25260171

  18. "Decoupled" Proton NMR Spectra

    NASA Astrophysics Data System (ADS)

    Woodley, M.; Freeman, R.

    High-resolution proton NMR spectra are recorded in a new form where all resonances are singlets at the chemical-shift frequencies, with no spin-spin splittings. These "decoupled" proton spectra are derived from two-dimensional J spectra after real Fourier transformation (without frequency discrimination in F1) so that each spin multiplet lies along both the 45° and the 135° diagonal, forming a pattern similar to St. Andrew's cross, with C 4 symmetry. The chemical shifts are located by searching for these centers of symmetry with a postacquisition data-processing algorithm. This is designed to facilitate the separation of overlapping and interpenetrating spin multiplets. The method is illustrated with applications to the 400 MHz high-resolution proton spectra of dehydrotestosterone and 4-androsten-3,17-dione. It is also possible to separate the spectra of components in a mixture and this is illustrated by breaking down the spectrum of an aqueous solution of D-glucose into subspectra from the α and β anomers, in order to follow the time evolution of the mutarotation.

  19. 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 m, 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 phase of strong accretion, which subsequently decreases. The shortening of the jets with time requires the presence of a continuous deceleration of the jets. A simple model of the simultaneous evolution of a protostar, its circumstellar environment, and its outflow (Smith 2000) can reproduce the measured values of H2 luminosity and driving source luminosity under the assumption of a strong accretion plus high ejection efficiency phase early in the protostellar evolution. Tatematsu et al. (1993) found 125 dense cloud cores in the survey area. The jet driving sources are found to have formed predominantly in quiet cores with a low ratio of internal kinetic energy to gravitational potential energy; these are the cores with higher masses. The cores which are associated with jets have on average larger linewidths than cores without jets. This is due to the preferred presence of jets in more massive cores, which generally have larger linewidths. There is no evidence for additional internal motions excited by the interaction of the jets with the cores. The jet H2 luminosity and the core linewidth (as predicted by theory) are related, if Class 0 and Class I jets are considered separately; the relation lies at higher values of the H2 luminosity for the Class 0 jets than for Class I jets. This also suggests a time evolution of the accretion rate, with a strong peak early on and a subsequent decay. Finally, the impact of a protostellar jet population on a molecular cloud is considered. Under the conservative assumption of strict forward momentum conservation, the jets appear to fail to provide sufficient momentum to replenish decaying turbulence on the scales of a giant molecular cloud and on the scales of molecular cloud cores. At the intermediate scales of molecular clumps with sizes of a few parsec and masses of a few hundred solar masses, the jets provide enough momentum in a short enough time to potentially replenish turbulence and thus might help to stabilize the clump against further collapse. Gasausstrmungen, oft in der Form hoch kollimierter Jets, sind ein allg

  20. 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.

  1. Quasi-linear least squares and computer code for numerical evaluation of relaxation time distribution from broadband dielectric spectra.

    PubMed

    Zasetsky, A Y; Buchner, R

    2011-01-19

    We present a new fitting procedure and computer code for numerical evaluation of dielectric relaxation time distribution functions. The technique is based on linear least squares minimization and aims primarily at the analysis of compound experimental spectra of complex dielectric permittivity. It is fast, robust, and easy to use. No prior knowledge about the number of relaxation modes, their characteristic times, relaxation strengths, or the functional form of the underlying relaxation time distribution function is required, the procedure determines these parameters instead. The method is tested by both synthetic spectra with well-defined parameters of dielectric relaxation and experimental wide-band dielectric spectra of different types. We believe that this new fitting instrument, which allows an unbiased approach to the formal description of dielectric spectra, may be of interest in many areas of dielectric spectroscopy. PMID:21406849

  2. 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 10,000years 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 populations, which is essential for an effective conservation of the bovine genetic resources. PMID:24739206

  3. 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 an arbitrary number of astrophysics data sets produced by vastly different science instruments. This theory and its successful implementation will facilitate the interpretation of spectral information from multiple astrophysics missions and thereby permit the derivation of superior spectral parameter estimates based on the combination of data sets.

  4. Mass spectra of copolymers.

    PubMed

    Montaudo, Maurizio S

    2002-01-01

    Recent and older literature (covering the last 12-13 years) in the field of mass spectra of random and block copolymers is reviewed. A detailed description is given of the information on copolymer properties that can be recovered from the analysis of the low-mass region of the spectrum (the region below 500 Da) and the high-mass region. The features of mass spectra of copolymers obtained by different synthetic routes are discussed, such as free radical, condensation, ring-chain equilibration, microbial synthesis, ring-opening, simple anionic, cationic, Ziegler-Natta, and/or metallocene catalysis, along with some random and block copolymers that occur in Nature. The emphasis is on copolymer composition and average molar mass determination, and on the benefits of coupling mass spectrometry (MS) with separation techniques such as size-exclusion chromatography (SEC) and high performance liquid chromatography (HPLC). PMID:12373747

  5. Parmeterization of spectra

    NASA Technical Reports Server (NTRS)

    Cornish, C. R.

    1983-01-01

    Following reception and analog to digital conversion (A/D) conversion, atmospheric radar backscatter echoes need to be processed so as to obtain desired information about atmospheric processes and to eliminate or minimize contaminating contributions from other sources. Various signal processing techniques have been implemented at mesosphere-stratosphere-troposphere (MST) radar facilities to estimate parameters of interest from received spectra. Such estimation techniques need to be both accurate and sufficiently efficient to be within the capabilities of the particular data-processing system. The various techniques used to parameterize the spectra of received signals are reviewed herein. Noise estimation, electromagnetic interference, data smoothing, correlation, and the Doppler effect are among the specific points addressed.

  6. Dual multifractal spectra.

    PubMed

    Roux, Stphane; Jensen, Mogens H

    2004-01-01

    The multifractal formalism characterizes the scaling properties of a physical density rho as a function of the distance L. To each singularity alpha of the field is attributed a fractal dimension for its support f(alpha). An alternative representation has been proposed by considering the distribution of distances associated to a fixed mass. Computing these spectra for a multifractal Cantor set, it is shown that these two approaches are dual to each other, and that both spectra as well as the moment scaling exponents are simply related. We apply the same inversion formalism to exponents obtained for turbulent statistics in the Gledzer-Ohkitani-Yamada shell model and observe that the same duality relation holds here. PMID:14995714

  7. 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.

  8. Martian neutron leakage spectra

    SciTech Connect

    Drake, D.M.; Feldman, W.C.; Jakosky, B.M.

    1988-06-10

    Energy spectra of Martian leakage neutrons are calculated by a high-energy nucleon-meson transport code using a Monte Carlo technique and a one-dimensional diffusion accelerated neutral-particle transport code, which solves the Boltzmann equation. Four series of calculations were made to simulate (1) a uniform surface layer containing various amounts of H/sub 2/O, (2) different burial depths of a 50% H/sub 2/O layer underneath a 1% H/sub 2/O layer, (3) changing atmospheric pressure, and (4) a thick CO/sub 2/ ice sheet overlying a ''dirty'' water ice sheet. We found that all calculated spectra at energies less than about 1000 eV could be fitted by a superposition of thermal and epithermal functions having four free parameters. Two of these parameters, the thermal and epithermal amplitudes, were found to vary systematically over ranges exceeding 1 order of magnitude and to specify uniquely the configuration in each of the series. We conclude that measurements of leakage neutron spectra should allow determination of the hydrogen content of surface layers buried to depths up to about 100 g/cm/sup 2/ and determination of the thickness of a polar dry ice cap up to thicknesses of about 250 g/cm/sup 2/. Variations of these parameters were also shown to depend on the composition of the assumed surface layers through the average atomic mass and the macroscopic scattering and absorption cross sections. copyright American Geophysical Union 1988

  9. IUE archived spectra

    NASA Technical Reports Server (NTRS)

    Sullivan, Edward C.; Bohlin, Ralph C.; Heap, Sara R.; West, Donald K.; Schmitz, Marion

    1988-01-01

    The International Ultraviolet Explorer (IUE) Satellite has been in continuous operation since January 26, 1978. To date, approximately 65,000 spectra have been stored in an archive at Goddard Space Flight Center in Greenbelt, MD. A number of procedures have been generated to facilitate access to the data in the IUE spectral archive. This document describes the procedures which include on-line quick look of the displays, search of an observation data base for selected observations, and several methods for ordering data from the archive.

  10. IUE archived spectra

    SciTech Connect

    Sullivan, E.C.; Bohlin, R.C.; Heap, S.R.; West, D.K.; Schmitz, M.

    1988-06-01

    The International Ultraviolet Explorer (IUE) Satellite has been in continuous operation since January 26, 1978. To date, approximately 65,000 spectra have been stored in an archive at Goddard Space Flight Center in Greenbelt, MD. A number of procedures have been generated to facilitate access to the data in the IUE spectral archive. This document describes the procedures which include on-line quick look of the displays, search of an observation data base for selected observations, and several methods for ordering data from the archive.

  11. Phosphorescence spectra of bacteriochlorophylls

    SciTech Connect

    Takiff, L.; Boxer, S.G.

    1988-06-22

    The authors wish to report phosphorescence spectra of the lowest triplet state of a number of bacteriochlorophylls (BChls) which provide the first accurate values for the triplet state energies of these chromophores. There have been many previous attempts to estimate the triplet state energies of bacteriochlorins motivated by the possible importance of triplet states in photosynthesis, the utility of these chromophores as sensitizers and quenchers of singlet oxygen, model studies of electron transfer, and intrinsic theoretical interest in the excited state energies of extended conjugated macrocycles.

  12. Einstein spectra of quasars

    NASA Technical Reports Server (NTRS)

    Wilkes, Belinda J.

    1988-01-01

    The results of the initial stage of the CfA survey of quasar energy distributions are reviewed. Einstein imaging proportional counter spectra of 33 quasars have been studied by fitting a single power law slope and absorption by an equivalent column density of neutral hydrogen. Comparison with the higher energy HEAO-A2 data leads to a two-component model for the X-ray spectrum. The X-ray column density is systematically lower than the 21-cm measured Galactic column density along the same line of sight.

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

    PubMed

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

    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 this tissue for future biomonitoring studies. Discussion. Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of tools for the monitoring of OA pollution. PMID:26618092

  14. 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 this tissue for future biomonitoring studies. Discussion. Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of tools for the monitoring of OA pollution. PMID:26618092

  15. Vibrational spectra of dipropylsulfoxide.

    PubMed

    Markarian, Shiraz A; Gabrielian, Liana S; Bonora, Sergio

    2007-12-31

    FTIR and Raman spectra analysis of pure dipropylsulfoxide (DPSO), binary mixtures of DPSO/CCl(4), and DPSO/water has been first performed. The complex pattern of spectra has been explained on the basis of molecular interactions between DPSO and other molecules and, in the aqueous solutions, the role of both hydrophilic and hydrophobic interactions have been discussed depending on the concentrations. The changes in the intensities and in the frequencies of DPSO bands on concentration have been considered. The curve fitting procedure has been performed for both SO and C-H stretching region, and, on the basis of deconvolution results different type of molecular interactions have been considered. Density function theory DFT/(B3LYP) method has been used to determine the optimized geometry for free DPSO and for 1 DPSO:1 water complex. On the basis of the 6-31+G(d) quality sets parameters, the DFT calculated bond parameters and harmonic vibrations are in a very good agreement with experimental data. PMID:17350885

  16. 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.

  17. 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.

  18. Testing the Pareto against the lognormal distributions with the uniformly most powerful unbiased test applied to the distribution of cities

    NASA Astrophysics Data System (ADS)

    Malevergne, Yannick; Pisarenko, Vladilen; Sornette, Didier

    2011-03-01

    Fat-tail distributions of sizes abound in natural, physical, economic, and social systems. The lognormal and the power laws have historically competed for recognition with sometimes closely related generating processes and hard-to-distinguish tail properties. This state-of-affair is illustrated with the debate between Eeckhout [Amer. Econ. Rev.SCIEAS0002-828210.1257/0002828043052303 94, 1429 (2004)] and Levy [Amer. Econ. Rev.SCIEAS0002-828210.1257/aer.99.4.1672 99, 1672 (2009)] on the validity of Zipf’s law for US city sizes. By using a uniformly most powerful unbiased (UMPU) test between the lognormal and the power-laws, we show that conclusive results can be achieved to end this debate. We advocate the UMPU test as a systematic tool to address similar controversies in the literature of many disciplines involving power laws, scaling, “fat” or “heavy” tails. In order to demonstrate that our procedure works for data sets other than the US city size distribution, we also briefly present the results obtained for the power-law tail of the distribution of personal identity (ID) losses, which constitute one of the major emergent risks at the interface between cyberspace and reality.

  19. Testing the Pareto against the lognormal distributions with the uniformly most powerful unbiased test applied to the distribution of cities.

    PubMed

    Malevergne, Yannick; Pisarenko, Vladilen; Sornette, Didier

    2011-03-01

    Fat-tail distributions of sizes abound in natural, physical, economic, and social systems. The lognormal and the power laws have historically competed for recognition with sometimes closely related generating processes and hard-to-distinguish tail properties. This state-of-affair is illustrated with the debate between Eeckhout [Amer. Econ. Rev. 94, 1429 (2004)] and Levy [Amer. Econ. Rev. 99, 1672 (2009)] on the validity of Zipf's law for US city sizes. By using a uniformly most powerful unbiased (UMPU) test between the lognormal and the power-laws, we show that conclusive results can be achieved to end this debate. We advocate the UMPU test as a systematic tool to address similar controversies in the literature of many disciplines involving power laws, scaling, "fat" or "heavy" tails. In order to demonstrate that our procedure works for data sets other than the US city size distribution, we also briefly present the results obtained for the power-law tail of the distribution of personal identity (ID) losses, which constitute one of the major emergent risks at the interface between cyberspace and reality. PMID:21517562

  20. 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

  1. Two Distinct States of the HAMP Domain from Sensory Rhodopsin Transducer Observed in Unbiased Molecular Dynamics Simulations

    PubMed Central

    Gushchin, Ivan; Gordeliy, Valentin; Grudinin, Sergei

    2013-01-01

    HAMP domain is a ubiquitous module of bacterial and archaeal two-component signaling systems. Considerable progress has been made recently in studies of its structure and conformational changes. However, the mechanism of signal transduction through the HAMP domain is not clear. It remains a question whether all the HAMPs have the same mechanism of action and what are the differences between the domains from different protein families. Here, we present the results of unbiased molecular dynamics simulations of the HAMP domain from the archaeal phototaxis signal transducer NpHtrII. Two distinct conformational states of the HAMP domain are observed, that differ in relative position of the helices AS1 and AS2. The longitudinal shift is roughly equal to a half of an α-helix turn, although sometimes it reaches one full turn. The states are closely related to the position of bulky hydrophobic aminoacids at the HAMP domain core. The observed features are in good agreement with recent experimental results and allow us to propose that the states detected in the simulations are the resting state and the signaling state of the NpHtrII HAMP domain. To the best of our knowledge, this is the first observation of the same HAMP domain in different conformations. The simulations also underline the difference between AMBER ff99-SB-ILDN and CHARMM22-CMAP forcefields, as the former favors the resting state and the latter favors the signaling state. PMID:23843970

  2. Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

    PubMed

    Franken, Holger; Mathieson, Toby; Childs, Dorothee; Sweetman, Gavain M A; Werner, Thilo; Tgel, Ina; Doce, Carola; Gade, Stephan; Bantscheff, Marcus; Drewes, Gerard; Reinhard, Friedrich B M; Huber, Wolfgang; Savitski, Mikhail M

    2015-10-01

    The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. We determined the intracellular thermal profiles for up to 7,000 proteins, and by comparing profiles derived from cultured mammalian cells in the presence or absence of a drug we showed that it was possible to identify direct and indirect targets of drugs in living cells in an unbiased manner. Here we demonstrate the complete workflow using the histone deacetylase inhibitor panobinostat. The key to this approach is the use of isobaric tandem mass tag 10-plex (TMT10) reagents to label digested protein samples corresponding to each temperature point in the melting curve so that the samples can be analyzed by multiplexed quantitative mass spectrometry. Important steps in the bioinformatic analysis include data normalization, melting curve fitting and statistical significance determination of compound concentration-dependent changes in protein stability. All analysis tools are made freely available as R and Python packages. The workflow can be completed in 2 weeks. PMID:26379230

  3. Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis

    PubMed Central

    Dai, Kaifan; He, Linling; Khan, Salar N.; O’Dell, Sijy; McKee, Krisha; Tran, Karen; Li, Yuxing; Sundling, Christopher; Morris, Charles D.; Mascola, John R.; Hedestam, Gunilla B. Karlsson

    2015-01-01

    ABSTRACT Next-generation sequencing (NGS) has been used to investigate the diversity and maturation of broadly neutralizing antibodies (bNAbs) in HIV-1-infected individuals. However, the application of NGS to the preclinical assessment of human vaccines, particularly the monitoring of vaccine-induced B-cell responses in a nonhuman primate (NHP) model, has not been reported. Here, we present a longitudinal NGS analysis of memory B-cell responses to an HIV-1 trimer vaccine in a macaque that has been extensively studied by single B-cell sorting and antibody characterization. We first established an NHP antibodyomics pipeline using the available 454 pyrosequencing data from this macaque and developed a protocol to sequence the NHP antibody repertoire in an unbiased manner. Using these methods, we then analyzed memory B-cell repertoires at four time points of NHP immunization and traced the lineages of seven CD4-binding site (CD4bs)-directed monoclonal antibodies previously isolated from this macaque. Longitudinal analysis revealed distinct patterns of B-cell lineage development in response to an HIV-1 trimer vaccine. While the temporal B-cell repertoire profiles and lineage patterns provide a baseline for comparison with forthcoming HIV-1 trimer vaccines, the newly developed NHP antibody NGS technologies and antibodyomics tools will facilitate future evaluation of human vaccine candidates. PMID:26530382

  4. Identifying New Molecules from Comparison of Herschel-HIFI Spectra with ab initio Computational Spectra

    NASA Astrophysics Data System (ADS)

    Rangwala, Naseem; Colgan, Sean; Lee, Timothy J.; Huang, Xinchuan; Fortenberry, Ryan

    2015-08-01

    We will identify new molecules in the interstellar medium (ISM) by comparing a catalog of theoretical spectra generated by the NASA Ames quantum chemistry group with astronomical line surveys from the HIFI instrument onboard the Herschel Space Observatory. HIFI has produced very high-resolution (1.1 MHz), unbiased spectral line surveys at sub-millimeter wavelengths of the Orion-KL and SgrB2(N) molecular clouds, encompassing the largest coverage (480-1907 GHz) ever towards a star-forming complex. Approximately 21000 spectral lines have been detected towards the two molecular cloud complexes, with roughly 85% identified as molecular transitions using existing laboratory databases (Crockett et al., 2014; Neil et al. 2014). A large fraction of the lines that remain unidentified most likely arise from molecules previously undetected. A large repository of reference data (line centers and relative intensities) is required to identify new molecules. For many molecules, experimental reference data do not exist. In this case, quantum chemical computations can provide alternative estimates for these parameters without some of the limitations inherent in generating experimental reference data.This project will enhance the chemical inventory for these star forming regions, allowing astrochemists to establish or confirm a variety of chemical networks, understand organic chemistry associated with star formation, and inform the studies that investigate the supply pathways of key organic molecules in Earth-like planet formation. Once new molecules are identified, we will determine their abundances relative to the other molecules in the same source and derive physical conditions in the star-forming regions. In addition, we will propose complementary observations of the newly identified molecules and related species with the Atacama Large Millimeter Array (ALMA) and the Stratospheric Observatory for Infrared Astronomy (SOFIA).

  5. TDS spectra analysis

    NASA Astrophysics Data System (ADS)

    Tomkov, E.

    1996-05-01

    Methods of TDS spectra analysis start usually from the Polanyi-Wigner desorption rate equation. The Redhead approximative solution of the equation can be rearranged into a reduced form in which it serves as an analytical expression for the desorption rate versus time or temperature. Fitting the analytical form to an experimental curve we can confirm or deny the invariability of kinetic parameters a desorption energy Ed and a preexponential factor ?l and determine their values. If the parameters depend on surface coverage ? the application of the reduced form allows us to determine their values at ??0 and ?? ?0 and estimate the dependence Ed( ?), ?(?) from a single TDS spectrum. The method proposed in this paper is valid for the first-order kinetics of desorption; for the estimation mentioned above an assumption is made that desorption sites are identical and that E d as well as ?l changes with ? monotonously.

  6. Spectra of hot stars

    NASA Astrophysics Data System (ADS)

    Hillier, D. John

    2015-08-01

    Non-LTE modeling is essential for interpreting the spectra of O stars and their decendents, and much progress has been made. The major uncertainty associated with analyzing photospheric spectra of O stars arises from issues related to microturbulence and macroturbulence. Many supergiants, for example, have microturbulent velocities that approach the sound speed, while macroturbulent velocities are often several times the sound speed. The cause of this turbulence is unknown, but may be related to pulsation, an underlying convection zone associated with the Fe opacity bump, or feedback from the stellar wind. Determining accurate abundances in O stars is hampered by the lack of lines belonging to low-z elements. Many species only have a few observable lines, and some of these are subject to complex non-LTE effects. A characteristic of massive stars is the existence of a stellar wind which is driven by radiation pressure. Radiation driving is inherently unstable, and this leads to winds with an inhomogeneous structure. Major issues that are still unresolved include: How are winds driven through the sonic point? What is the nature of the inhomogeneities, and how do the properties of these inhomogeneities change with density and velocity? How important is spatial porosity, and porosity in velocity space? What is the structure of the shocks, and in what stars do the shocks fail to cool? With Wolf-Rayet (W-R) stars the major uncertainty arises because the classic spectroscopic radius (i.e., the location where ? = 2/3) often refers to a location in the wind not necessarily the stellar radius associated with stellar evolution models. Derived radii are typically several times those predicted by stellar evolution calculations, although for strong-lined W-R stars it is possible to construct models that are consistent with evolution calculations. The driving of the winds in these stars is strongly coupled to the closeness of the stars to the Eddington limit and to their inhomogeneities, and the latter have not been derived from first principles. Theoretically, it is possible that the radii of the stars are inflated due to the Fe opacity bump.

  7. Interpreting chromosome aberration spectra.

    PubMed

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

    2007-03-01

    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. PMID:17456013

  8. 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.

  9. 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.

  10. 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 discovery for membrane protein targets. PMID:25928376

  11. Unbiased Selection of Peptide-Peptoid Hybrids Specific for Lung Cancer Compared to Normal Lung Epithelial Cells.

    PubMed

    Matharage, Jaya M; Minna, John D; Brekken, Rolf A; Udugamasooriya, D Gomika

    2015-12-18

    To develop widely applicable diagnostic and potentially therapeutic approaches overcoming protein heterogeneity in human cancer, we have developed a technology to unbiasedly select high specificity compound(s) that bind any biomolecule (e.g., proteins, lipids, carbohydrates) presented on the cancer cell surface but not on normal cells. We utilized a peptidomimetic based on-bead two-color (OBTC) combinatorial cell screen that can detect differences between two cell surfaces at high accuracy by looking for beads (where each bead in the library had one peptide-peptoid hybrid on the surface) that only bound cancer but not normal cells. We screened a library of 393?216 compounds targeting HCC4017 lung adenocarcinoma cells (labeled in red) in the presence of HBEC30KT normal bronchial epithelial cells (labeled in green) derived from the same tissue of the same patient. This screen identified a peptide-peptoid hybrid called PPS1 which displayed high specific binding for HCC4017 cancer cells over HBEC30KT cells. Specificity was validated through on-bead, ELISA-like and magnetic bead pulldown studies, while a scrambled version of PPS1 did not show any binding. Of interest, the simple dimeric version (PPS1D1) displayed cytotoxic activity on HCC4017 cells, but not on normal HBEC30KT cells. PPS1D1 also strongly accumulated in HCC4017 lung cancer xenografts in mice over control constructs. We conclude that such combinatorial screens using tumor and normal cells from the same patient have significant potential to develop new reagents for cancer biology, diagnosis, and potentially therapy. PMID:26509598

  12. 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

  13. 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 isochrone fitting routines.

  14. 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. PMID:26536838

  15. 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)

  16. 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. PMID:24032353

  17. 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 greater number of adult male and female Lu. longipalpis samples from endemic and non-endemic locations. A particular emphasis is being given to those species involved in the biological control of this vector and to the etiologic agents of animal and plant diseases. PMID:21909446

  18. Anisotropic spectra of acoustic turbulence

    SciTech Connect

    L'vov, V. S.; L'vov, Yu. V.; Pomyalov, A.

    2000-03-01

    We found universal anizopropic spectra of acoustic turbulence with the linear dispersion law {omega}(k)=ck within the framework of generalized kinetic equation which takes into account the finite time of three-wave interactions. This anisotropic spectra can assume both scale-invariant and non-scale-invariant form. The implications for the evolution of the acoustic turbulence with nonisotropic pumping are discussed. The main result of the article is that the spectra of acoustic turbulence tend to become more isotropic. (c) 2000 The American Physical Society.

  19. 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.

  20. Multifractal spectra in shear flows

    NASA Technical Reports Server (NTRS)

    Keefe, L. R.; Deane, Anil E.

    1989-01-01

    Numerical simulations of three-dimensional homogeneous shear flow and fully developed channel flow, are used to calculate the associated multifractal spectra of the energy dissipation field. Only weak parameterization of the results with the nondimensional shear is found, and this only if the flow has reached its asymptotic development state. Multifractal spectra of these flows coincide with those from experiments only at the range alpha less than 1.

  1. Infrared spectra of joint fluids

    NASA Astrophysics Data System (ADS)

    Eysel, Hans H.; Mantsch, Henry H.; Jackson, Michael

    1994-01-01

    The present study demonstrates the application of infrared spectroscopy to the diagnosis of arthritic conditions by analysis of joint fluids. The detection of carbon dioxide clathrates, their origin and the nature of the host material is discussed. The analytical sensitivity of mid IR second derivative spectra is demonstrated with the detection of the local anaesthetic lidocaine in some of the samples. Linear discriminant analysis and hierarchical clustering are successfully used to classify the spectra according to their respective clinical diagnosis.

  2. 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.

  3. 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.

  4. Complex Spectra in Fusion Plasmas

    NASA Astrophysics Data System (ADS)

    von Hellermann, M. G.; Bertschinger, G.; Biel, W.; Giroud, C.; Jaspers, R.; Jupen, C.; Marchuk, O.; O'Mullane, M.; Summers, H. P.; Whiteford, A.; Zastrow, K.-D.

    2005-01-01

    The need for quantitative evaluation of complex line emission spectra as observed in hot fusion plasmas initiated a challenging development of sophisticated interpretation tools based on integrating advanced atomic modelling with detailed treatment of the plasma environment. The successful merging of the two worlds has led to routine diagnostic procedures which have contributed enormously to the understanding of underlying plasma processes and also to a wide acceptance of spectroscopy as a reliable diagnostic method. In this paper three characteristic types of spectra of current and continuing interest are presented. The first is that of medium/heavy species with many ionisation stages revealed in survey VUV and XUV spectra. Such species occur as control gases, as wall materials, as ablated heavy species and possible as layered wall dopants for monitoring erosion. The spectra are complex with line-like and quasi-continuum regions and are amenable to advanced `pattern recognition' methods. The second type is of few electron, highly ionised systems observed as line-of-sight integrated passive emission spectra in the soft x-ray region. They are analysed successfully in terms of plasma parameters through matching of observation with predicted synthetic spectra. Examples used here include highly resolved helium-like emission spectra of argon, iron and titanium observed on the tokamaks TEXTOR and Tore Supra. The third type, and the emphasis of this work, comprises spectra linked to active beam spectroscopy, that is, charge exchange recombination spectroscopy (CXRS) and beam emission spectroscopy (BES). In this case, a complex spectrum is again composed of a (usually) dominating active spectrum and an underlying passive emission spectrum. Its analysis requires modelling of both active and passive features. Examples used here are from the CXRS diagnostic at JET and TEXTOR. They display characteristic features of the main light impurity ions (C+6, He+2, N+7, Ne+10 and Ar+18), as well as that of the bulk plasma ions, H+, D+ and T+. A main conclusion is that spectral complexity is not necessarily negative, but that `complex structures' can provide a rich source of information on the plasma and its parametersprovided it is matched with integrated analysisand that the methods can have universal applicability. In the present preparatory phase of the next generation fusion experiment ITER (International Thermonuclear Experimental Reactor) the concepts and expectations of complex spectra and integrated data analysis play an important role in the design and optimisation procedure of the ITER diagnostic assembly.

  5. The Optically Unbiased GRB Host (TOUGH) Survey. VII. The Host Galaxy Luminosity Function: Probing the Relationship between GRBs and Star Formation to Redshift ? 6

    NASA Astrophysics Data System (ADS)

    Schulze, S.; Chapman, R.; Hjorth, J.; Levan, A. J.; Jakobsson, P.; Bjrnsson, G.; Perley, D. A.; Krhler, T.; Gorosabel, J.; Tanvir, N. R.; de Ugarte Postigo, A.; Fynbo, J. P. U.; Milvang-Jensen, B.; Mller, P.; Watson, D. J.

    2015-07-01

    Gamma-ray bursts (GRBs) offer a route to characterizing star-forming galaxies and quantifying high-z star formation that is distinct from the approach of traditional galaxy surveys: GRB selection is independent of dust and probes even the faintest galaxies which can evade detection in flux-limited surveys. However, the exact relation between the GRB rate and the star formation rate (SFR) throughout all redshifts is controversial. The Optically Unbiased GRB Host (TOUGH) survey includes observations of all GRB hosts (69) in an optically unbiased sample of Swift GRBs; we utilize these to constrain the evolution of the UV GRB-host-galaxy luminosity function (LF) between z = 0 and z = 4.5, and compare this with LFs derived from both Lyman-break galaxy (LBG) surveys and simulation modeling. At all redshifts we find the GRB hosts to be most consistent with an LF derived from SFR weighted models incorporating GRB production via both metallicity-dependent and independent channels with a relatively high level of bias toward low metallicity hosts. In the range 1\\lt z\\lt 3 an SFR weighted LBG derived (i.e., non-metallicity biased) LF is also a reasonable fit to the data. Between z ? 3 and z ? 6, we observe an apparent lack of UV bright hosts in comparison with LBGs, though the significance of this shortfall is limited by nine hosts of unknown redshift.

  6. Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding.

    PubMed

    He, Linling; Sok, Devin; Azadnia, Parisa; Hsueh, Jessica; Landais, Elise; Simek, Melissa; Koff, Wayne C; Poignard, Pascal; Burton, Dennis R; Zhu, Jiang

    2014-01-01

    B-cell repertoire analysis using next-generation sequencing has become a valuable tool for interrogating the genetic record of humoral response to infection. However, key obstacles such as low throughput, short read length, high error rate, and undetermined bias of multiplex PCR method have hindered broader application of this technology. In this study, we report several technical advances in antibody repertoire sequencing. We first demonstrated the ability to sequence antibody variable domains using the Ion Torrent PGM platform. As a test case, we analyzed the PGT121 class of antibodies from IAVI donor 17, an HIV-1-infected individual. We then obtained "unbiased" antibody repertoires by sequencing the 5'-RACE PCR products of B-cell transcripts from IAVI donor 17 and two HIV-1-uninfected individuals. We also quantified the bias of previously published gene-specific primers by comparing the repertoires generated by 5'-RACE PCR and multiplex PCR. We further developed a single-molecule barcoding strategy to reduce PCR-based amplification noise. Lastly, we evaluated several new PGM technologies in the context of antibody sequencing. We expect that, based upon long-read and high-fidelity next-generation sequencing technologies, the unbiased analysis will provide a more accurate view of the overall antibody repertoire while the barcoding strategy will facilitate high-resolution analysis of individual antibody families. PMID:25345460

  7. 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

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

    PubMed

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

    2015-07-01

    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

  9. 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.

  10. Reduction of multielement mass spectra

    SciTech Connect

    Russ, G.P. III; Caffee, M.W.; Hudson, G.B.; Storch, N.A.

    1990-06-29

    Even though the spectra obtained by inductively coupled plasma source spectrometry (ICP-MS) are relatively simple, their interpretation can be complicated by the presence of molecular and isobaric interferants. To the extent that isotopic abundances are known and constant, one can treat observed spectra as sums of known components. A linear decomposition approach for determining the concentrations of the components in a spectrum and correctly propagating uncertainties is presented. This technique differs from linear regression in that an exact fit is made to a subset of isotopes and goodness-of-fit is evaluated from the deviations between the predicted and measured intensities of the other, unfit isotopes. This technique can be applied to a wide range of spectral fitting problems. In this paper, its applicability to ICP-MS spectra is used to demonstrate the use and utility of the technique. 2 refs., 9 figs.

  11. 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.

  12. Spectra of Irradiated Giant Planets

    NASA Astrophysics Data System (ADS)

    Burrows, Adam; Sudarsky, David

    2002-11-01

    As many as 101 extrasolar giant planets (EGPs) have been detected by radial-velocity techniques, but none has been detected directly by its own emission or by reflection of the light from its parent star. We review the current state-of-the-art in the theoretical modeling of the spectra of giant planets outside the solar system and the basic theory of EGP spectra and atmospheres. We are now entering a new era of planet discovery and measurement. This contribution is meant to communicate some of the excitement in the astronomical community as the hunt for these exotic and remarkable objects accelerates.

  13. Vibrational Spectra of ?-Aminobutyric Acid

    NASA Astrophysics Data System (ADS)

    Suresh, D. M.; Sajan, D.; Laladas, K. P.; Joe, I. Hubert; Jayakumar, V. S.

    2008-11-01

    The NIR-FT Raman, FT-IR spectral analysis of ?-Aminobutyric acid (GABA) a simple amino acid is carried out by density functional computations. The vibrational spectra confirm the existence of NH3+ in GABA. Hydroxyl groups H-bonded to the different extents are analysed, supported by computed results.

  14. 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.)

  15. 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.

  16. The LickX spectra

    NASA Astrophysics Data System (ADS)

    Worthey, G.; Danilet, A. B.; Faber, S. M.

    2014-01-01

    Context. Collections of stellar spectra, often called stellar libraries, are useful in a variety of applications in the field of stellar populations. Aims: This is an attempt to improve the much-used Lick library of stellar spectra by removing jitter from the wavelength scale via cross-correlation, and calling the result the LickX library. Methods: Each spectrum was cross-correlated with a template spectrum and a new wavelength solution sought. Low-order polynomials were fit to adjust the old scale to a new fit. Indices were measured, new standard star averages found, and adjusted averages derived for the program stars. Results: The greatest gains in accuracy are expected for the fainter stars and stars of extreme surface temperatures; the bright K giant standard stars in LickX have the same uncertainties as Lick. The spectra and a table of index measurements in which repeated measurements are averaged are made available electronically. Individual stellar spectra, in FITS files, and the ascii catalog of absorption feature index strengths are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/561/A36

  17. Cloud Processing of CCN Spectra

    NASA Astrophysics Data System (ADS)

    Hudson, J. G.; Noble, S. R., Jr.

    2014-12-01

    Cloud processing often makes bimodal aerosol spectra from which size at minimal concentration infers cloud effective supersaturation (Seff) (Hoppel et al. 1986). Particle hygroscopicity (?) converts this Hoppel minimum to critical S, Sc. Only lower Sc particles that produce cloud droplets are physically (coalescence) or chemically (gas-to-particle conversion) processed, which increases soluble content so that upon evaporation, these CCN have even lower Sc whereas the unactivated CCN do not change size or Sc. This results in the size gap at Seff. DRI CCN spectrometers have revealed bimodality in 6 projects for which Seff can be obtained without ?. However in 2 projects, MASE and ICE-T, simultaneous DMA measurements also provided ? by transposing DMA sizes to Sc; the ? that makes the DMA spectra agree with simultaneous CCN spectra (Fig). There was DMA-CCN agreement for 227 MASE and 50 ICE-T measurements. Since unlike Fig. a mean ? of the processed modes was greater than mean ? of the unprocessed modes, chemical processing was indicated; since most ? were lower than ammonium sulfate ? (0.61) chemical processing should move processed ? closer to 0.61. Chemical processing was also indicated in MASE by greater sulfate and nitrate concentrations for bimodal spectra and greater sulfur dioxide and ozone concentrations for monomodal spectra. MASE above cloud measurements showed higher ? and less bimodality than below cloud measurements, this is consistent with the higher above cloud NCCN, that ? is lower in pollution and for these less cloud interacted samples. Interspersed bimodal and monomodal CCN spectra under the ubiquitous MASE stratus suggested less than well-mixed boundary layers. Somewhat surprisingly there was more bimodality for the cumulus ICE-T clouds than the MASE stratus. ICE-T indicated more physical than chemical cloud processing. Cloud-processing of CCN spectra is as important as CCN sources; it alters Seff, cloud droplet concentrations, mean diameter, spectral width and albedo. These changes and the lower Hoppel minima Seff than Seff from spectral comparisons with droplet concentrations; i.e., probably due to unprocessed small droplets, could be additional or counter indirect aerosol effects.

  18. Source spectra of seismic hum

    NASA Astrophysics Data System (ADS)

    Nishida, Kiwamu

    2014-10-01

    The observation of seismic hum from 2 to 20 mHz, also known as Earth's background free oscillations, has been established. Recent observations by broad-band seismometers show simultaneous excitation of Love waves (fundamental toroidal modes) and Rayleigh waves (fundamental spheroidal modes). The excitation amplitudes above 10 mHz can be explained by random shear traction sources on Earth's surface. With estimated source distributions, the most likely excitation mechanism is a linear coupling between ocean infragravity waves and seismic surface waves through seafloor topography. Observed Love and Rayleigh wave amplitudes below 5 mHz suggest that surface pressure sources could also contribute to their excitations, although the amplitudes have large uncertainties due to the high noise levels of the horizontal components. To quantify the observation, we develop a new method for estimation of the source spectra of random tractions on Earth's surface by modelling cross-spectra between pairs of stations. The method is to calculate synthetic cross-spectra for spatially isotropic and homogeneous excitations by random shear traction and pressure sources, and invert them with the observed cross-spectra to obtain the source spectra. We applied this method to the IRIS, ORFEUS, and F-net records from 618 stations with three components of broad-band seismometers for 2004-2011. The results show the dominance of shear traction above 5 mHz, which is consistent with past studies. Below 5 mHz, however, the spectral amplitudes of the pressure sources are comparable to those of shear traction. Observed acoustic resonance between the atmosphere and the solid Earth at 3.7 and 4.4 mHz suggests that atmospheric disturbances are responsible for the surface pressure sources, although non-linear ocean wave processes are also candidates for the pressure sources. Excitation mechanisms of seismic hum should be considered as a superposition of the processes of the solid Earth, atmosphere and ocean as a coupled system.

  19. 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; Simn-Snchez, Javier; Schulte, Claudia; Lesage, Suzanne; Sveinbjrnsdttir, 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-Franois; Deloukas, Panos; Deuschl, Gnther; Dexter, David T; van Dijk, Karin D; Dillman, Allissa; Durif, Frank; Drr, Alexandra; Edkins, Sarah; Evans, Jonathan R; Foltynie, Thomas; Gao, Jianjun; Gardner, Michelle; Gibbs, J Raphael; Goate, Alison; Gray, Emma; Guerreiro, Rita; Gstafsson, mar; 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; Mnchen, Helmholtz Zentrum; Jnsson, Plmi V; Lambert, Jean-Charles; Langford, Cordelia; Lees, Andrew; Lichtner, Peter; Mnchen, Helmholtz Zentrum; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw R; Morrison, Karen E; Mudanohwo, Ese; OSullivan, Sean S; Pearson, Justin; Perlmutter, Joel S; Ptursson, Hjrvar; 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; Stefnsson, Hreinn; Steinberg, Stacy; Stockton, Joanna D; Strange, Amy; Talbot, Kevin; Tanner, Carlie M; Tashakkori-Ghanbaria, Avazeh; Tison, Franois; Trabzuni, Daniah; Traynor, Bryan J; Uitterlinden, Andr G; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H; Winder-Rhodes, Sophie; Stefnsson, Kri; 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; OBrien, 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 proteinprotein interaction arrays, we identified BCL2-associated athanogene 5, Rab7L1 (RAB7, member RAS oncogene family-like 1), and Cyclin-Gassociated 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 autophagylysosome 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

  20. 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. PMID:24323262

  1. 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``).

  2. Raman spectra in chiral superconductors

    NASA Astrophysics Data System (ADS)

    Kee, Hae-Young; Maki, K.; Chung, C. H.

    2004-08-01

    The clapping modes with angular momentum 2 are common to the spin triplet superconductors, which breaks chiral symmetry like Sr 2RuO 4[Phys. Rev. B 67 (2003) 180504] and (TMTSF) 2PF 6[Phys. Rev. Lett. 88 (2002) 017004]. These clapping modes appear as a huge resonance in B1 g and B2 g Raman spectra [Phys. Rev. B 67 (2003) 180504]. Therefore the Raman experiment will provide a unique signature of the underlying superconductors. We discuss the Raman spectra of Sr 2RuO 4 in terms of two competing models; 2-dimensional f-wave model and multi-gap model by Zhitomirsky and Rice [Phys. Rev. Lett. 87 (2001) 057001].

  3. Ultraviolet fluorescence spectra of fingerprints.

    PubMed

    Saitoh, Naoki; Akiba, Norimitsu

    2005-05-01

    We have studied inherent fluorescence spectra and imaging of fingerprints in the deep ultraviolet (UV) region with a nanosecond-pulsed Nd-YAG laser system that consists of a tunable laser, a cooled CCD camera, and a grating spectrometer. In this paper, we have studied UV fluorescence spectra of fingerprints under 266-nm illumination. Fluorescence spectra of fingerprints have two main peaks, around 330 nm (peak A) and 440 nm (peak B). At first, when a fingerprint has just been pressed, peak A is dominant. However, its intensity reduces as the total illumination time increases. On the other hand, peak B is weak at first. It appears after enough 266-nm illumination and its intensity increases as time elapses. After 3 h of illumination, peak A almost diminishes and peak B becomes dominant. By leaving the fingerprint under a fluorescent lamp in a room without laser illumination, peak A can be restored partly, while the intensity of peak B still increases. Time-resolved fluorescence spectra were also measured for these two peaks. The lifetime of each peak is 2.0 nsec (peak A) and 6.2 nsec (peak B) on average. Both peaks seem to consist of several components with different lifetimes. In the case of peak A, the 330-nm peak decays fast and a new component at 360 nm becomes dominant when the delay time exceeds 20 nsec. In the case of peak B, unlike peak A, no clear peak separation is observed, but the peak position seems to move from 440 to 460 nm when the delay time becomes larger. PMID:15870848

  4. Catalogue of representative meteor spectra

    NASA Astrophysics Data System (ADS)

    Voj?ek, V.; Borovi?ka, J.; Koten, P.; Spurn, P.; tork, R.

    2015-08-01

    Aims: 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 to 10 mm. Methods: Parallel double-station video observations allowed us to compute heliocentric orbits for all meteors. Most observations were performed during the periods of activity of major meteor showers in the years between 2006 and 2012. Spectra are classified according to relative intensities of the low-temperature emission lines of Mg, Na, and Fe. Results: Shower meteors were found to be of normal composition, except for Southern ? Aquariids and some members of the Geminid shower, neither of which have Na in the meteor spectra. Variations in Na content are typical for the Geminid shower. Three populations of Na-free mereoroids were identified. The first population are iron meteorites, which have an asteroidal-chondritic origin, but one meteoroid with low perihelion (0.11 AU) was found among the iron meteorites. The second population were Sun-approaching meteoroids in which sodium is depleted by thermal desorption. The third population were Na-free meteoroids of cometary origin. Long exposure to cosmic rays on the surface of comets in the Oort cloud and disintegration of this crust might be the origin of this population of meteoroids. Spectra (Figs. 17-30) are only, Tables 4-6 are also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/580/A67

  5. Unveiling the intrinsic X-ray properties of broad absorption line quasars with a relatively unbiased sample

    SciTech Connect

    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 K{sub s} ? 2.3 mag) and optically bright (i K{sub s} < 2.3 mag) samples to be ? ? 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 10{sup 22} cm{sup 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.

  6. 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.

  7. Prediction of earthquake response spectra

    USGS Publications Warehouse

    Joyner, W.B.; Boore, David M.

    1982-01-01

    We have developed empirical equations for predicting earthquake response spectra in terms of magnitude, distance, and site conditions, using a two-stage regression method similar to the one we used previously for peak horizontal acceleration and velocity. We analyzed horizontal pseudo-velocity response at 5 percent damping for 64 records of 12 shallow earthquakes in Western North America, including the recent Coyote Lake and Imperial Valley, California, earthquakes. We developed predictive equations for 12 different periods between 0.1 and 4.0 s, both for the larger of two horizontal components and for the random horizontal component. The resulting spectra show amplification at soil sites compared to rock sites for periods greater than or equal to 0.3 s, with maximum amplification exceeding a factor of 2 at 2.0 s. For periods less than 0.3 s there is slight deamplification at the soil sites. These results are generally consistent with those of several earlier studies. A particularly significant aspect of the predicted spectra is the change of shape with magnitude (confirming earlier results by McGuire and by Irifunac and Anderson). This result indicates that the conventional practice of scaling a constant spectral shape by peak acceleration will not give accurate answers. The Newmark and Hall method of spectral scaling, using both peak acceleration and peak velocity, largely avoids this error. Comparison of our spectra with the Nuclear Regulatory Commission's Regulatory Guide 1.60 spectrum anchored at the same value at 0.1 s shows that the Regulatory Guide 1.60 spectrum is exceeded at soil sites for a magnitude of 7.5 at all distances for periods greater than about 0.5 s. Comparison of our spectra for soil sites with the corresponding ATC-3 curve of lateral design force coefficient for the highest seismic zone indicates that the ATC-3 curve is exceeded within about 7 km of a magnitude 6.5 earthquake and within about 15 km of a magnitude 7.5 event. The amount by which it is exceeded for the 7.5 event is largest in the period range from 0.5 to 2.0 s.

  8. Planetary spectra for anisotropic scattering

    NASA Technical Reports Server (NTRS)

    Chamberlain, J. W.

    1975-01-01

    Some of the effects on planetary spectra that would be produced by departures from isotropic scattering are examined. The phase function is the simplest departure to handle analytically and the only phase function, other than the isotropic one, that can be incorporated into a Chandrasekhar first approximation. This approach has the advantage of illustrating trends resulting from anisotropies while retaining the simplicity that yields physical insight. An algebraic solution to the two sets of anisotropic H functions is developed in the appendix. It is readily adaptable to progammable desk calculators and gives emergent intensities accurate to 0.3 percent, which is sufficient even for spectroscopic analysis.

  9. 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.

  10. Satellite spectra of heliumlike nickel

    SciTech Connect

    Hsuan, H.; Bitter, M.; Hill, K.W.; von Goeler, S. Grek, B.; Johnson, D.; Johnson, L.C.; Sesnic, S.; Bhalla, C.P.; Karim, K.R.

    1987-02-01

    Spectra of heliumlike nickel, NiXXVII, have been observed from Tokamak Fusion Test Reactor (TFTR) plasmas with a high resolution crystal spectrometer. The experimental arrangement permits simultaneous observation of the heliumlike resonance line, the intercombination and forbidden lines, and all the associated satellites due to transitions 1s/sup 2/nl - 1s2l'nl'' with N greater than or equal to 2. Relative wavelengths and line intensities can thus be determined very accurately. The observed spectral data are in good agreement with results from the present Hartree-Fock-Slater atomic model calculations and predictions from the Z-expansion method.

  11. 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.

  12. QUALITY CONTROL AND EVALUATION OF MASS SPECTRA

    EPA Science Inventory

    Over 1400 electron ionization mass spectra of selected organic compounds have been measured under carefully defined conditions. In this paper, the variables such as sample purity and spectrometer calibration that are controlled are described. The quality of the resulting spectra ...

  13. Proton Chemical-Shift Spectra

    NASA Astrophysics Data System (ADS)

    Simova, Svetlana; Sengstschmid, Helmut; Freeman, Ray

    1997-01-01

    Three related methods are explored for obtaining high-resolution proton spectra without spin-spin splittings, termed "chemical-shift spectra." They are based on two-dimensionalJspectroscopy, where theF1dimension is derived by Fourier transformation of spin-echo modulation. The first technique superimposes theJspectrum on its reflection in theF1= 0 axis, creating multiplet patterns in the form of a St. Andrew's cross. The other two techniques purge certain antiphase product-operator terms, either by dispersal in an inhomogeneous effective radiofrequency field oriented at the magic angle (54.7°) or by means of azfilter. In all three cases, the two-dimensional multiplets are separated by means of a symmetry filter and their centers are taken as a measure of the respective chemical shifts. The 400 MHz proton chemical-shift spectrum of 4-androsten-3,17-dione is presented as an illustrative example. Good separation is achieved, even for interpenetrating spin multiplets with near degeneracies in their chemical shifts. Complications due to strong-coupling effects are discussed.

  14. Intensity Spectra Versus Response Spectra: Basic Concepts and Applications

    NASA Astrophysics Data System (ADS)

    Sandi, Horea; Borcia, Ioan Sorin

    2011-01-01

    This paper begins with a critical assessment of the concept of macroseismic intensity, on which traditional scales, such as MSK and EMS, are based. The main shortcoming identified is the model's failure to consider the spectral features of ground motion. This omission may lead to erroneous seismic zonation, as shown in the paper. As a result, the model is of little interest to engineers who must design and build safe structures while adopting economical solutions. The paper presents a way to radically improve this situation. The starting point for this approach was the experience of the destructive Vrancea earthquake of 1977.03.04, which made it clear that intensity appears to be different for structures having natural periods pertaining to different spectral domains. The solution proposed to the shortcomings of the traditional intensity concept is postulated on a system of analytical expressions, covering definitions of global intensities, of intensities related to oscillation frequency and of intensities related to a definite spectral band. The latter definition lies at the basis of a definition of discrete intensity spectra. Illustrative applications are presented, in relation to global intensities and to discrete intensity spectra. We then analyze an illustrative case in which the use of traditional macroseismic survey techniques led to erroneous seismic zonation. Finally, some conclusions and recommendations are presented. Based on the authors' long-term experience, we strongly recommend close interaction between seismologists and engineers in working groups and joint projects targeted on radical improvement of the basic concepts of seismic intensity and of specific analysis procedures.

  15. An RGB approach to extraordinary spectra

    NASA Astrophysics Data System (ADS)

    Grusche, Sascha; Theilmann, Florian

    2015-09-01

    After Newton had explained a series of ordinary spectra and Goethe had pointed out its complementary counterpart, Nussbaumer discovered a series of extraordinary spectra which are geometrically identical and colourwise analogous to Newtons and Goethes spectra. To understand the geometry and colours of extraordinary spectra, the wavelength composition is explored with filters and spectroscopic setups. Visualized in a dispersion diagram, the wavelength composition is interpreted in terms of additive colour mixing. Finally, all spectra are simulated as the superposition of red, green, and blue images that are shifted apart. This RGB approach makes it easy to understand the complex relationship between wavelengths and colours.

  16. Background estimation in experimental spectra

    SciTech Connect

    Fischer, R.; Hanson, K. M.; Los Alamos National Laboratory, MS P940, Los Alamos, New Mexico 87545 ; Dose, V.; Linden, W. von der

    2000-02-01

    A general probabilistic technique for estimating background contributions to measured spectra is presented. A Bayesian model is used to capture the defining characteristics of the problem, namely, that the background is smoother than the signal. The signal is allowed to have positive and/or negative components. The background is represented in terms of a cubic spline basis. A variable degree of smoothness of the background is attained by allowing the number of knots and the knot positions to be adaptively chosen on the basis of the data. The fully Bayesian approach taken provides a natural way to handle knot adaptivity and allows uncertainties in the background to be estimated. Our technique is demonstrated on a particle induced x-ray emission spectrum from a geological sample and an Auger spectrum from iron, which contains signals with both positive and negative components. (c) 2000 The American Physical Society.

  17. Graviton spectra in string cosmology

    SciTech Connect

    Galluccio, Massimo; Litterio, Marco; Occhionero, Franco

    1996-08-01

    We propose to uncover the signature of a stringy era in the primordial Universe by searching for a prominent peak in the relic graviton spectrum. This feature, which in our specific model terminates an ? increase and initiates an ??? decrease, is induced during the so far overlooked bounce of the scale factor between the collapsing deflationary era (or pre-Big Bang) and the expanding inflationary era (or post-Big Bang). We evaluate both analytically and numerically the frequency and the intensity of the peak and we show that they may likely fall in the realm of the new generation of interferometric detectors. The existence of a peak is at variance with ordinarily monotonic (either increasing or decreasing) graviton spectra of canonical cosmologies; its detection would therefore offer strong support to string cosmology.

  18. Reflectance spectra of primitive chondrites

    NASA Astrophysics Data System (ADS)

    Trigo-Rodrguez, 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 ?m 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.

  19. Schottky spectra and crystalline beams

    NASA Astrophysics Data System (ADS)

    Pestrikov, D. V.

    1996-02-01

    In this paper we revise the current dependence of the Schottky noise power of a cooled proton beam previously measured at NAP-M. More careful study of experimental data indicates a linear decrease in the inverse Schottky noise power with an increase in the beam intensity ( N). The root of this function determines a threshold current which occurs at N = N th ? 1.2 10 8 particles. The inspection of measured Schottky spectra shows that this threshold does not correspond to some collective instability of the measured harmonic of the linear beam density. The found value of Nth does not depend on the longitudinal beam temperature. For the case of NAP-M lattice, the study of the spectral properties of the Schottky noise in the crystalline string predicts the current dependence of the equilibrium momentum spread of the beam, which qualitatively agrees with that, recalculated from the NAP-M data.

  20. 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.

  1. 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.

  2. DNA polymerase-mediated synthesis of unbiased threose nucleic acid (TNA) polymers requires 7-deazaguanine to suppress G:G mispairing during TNA transcription.

    PubMed

    Dunn, Matthew R; Larsen, Andrew C; Zahurancik, Walter J; Fahmi, Nour Eddine; Meyers, Madeline; Suo, Zucai; Chaput, John C

    2015-04-01

    Threose nucleic acid (TNA) is an unnatural genetic polymer capable of undergoing Darwinian evolution to generate folded molecules with ligand-binding activity. This property, coupled with a nuclease-resistant backbone, makes TNA an attractive candidate for future applications in biotechnology. Previously, we have shown that an engineered form of the Archaean replicative DNA polymerase 9N, known commercially as Therminator DNA polymerase, can copy a three-letter genetic alphabet (A,T,C) from DNA into TNA. However, our ability to transcribe four-nucleotide libraries has been limited by chain termination events that prevent the synthesis of full-length TNA products. Here, we show that chain termination is caused by tG:dG mispairing in the enzyme active site. We demonstrate that the unnatural base analogue 7-deazaguanine (7dG) will suppress tGTP misincorporation by inhibiting the formation of Hoogsteen tG:dG base pairs. DNA templates that contain 7dG in place of natural dG residues replicate with high efficiency and >99% overall fidelity. Pre-steady-state kinetic measurements indicate that the rate of tCTP incorporation is 5-fold higher opposite 7dG than dG and only slightly lower than dCTP incorporation opposite either 7dG or dG. These results provide a chemical solution to the problem of how to synthesize large, unbiased pools of TNA molecules by polymerase-mediated synthesis. PMID:25785966

  3. Application of the ?2 principle and unbiased predictive risk estimator for determining the regularization parameter in 3-D focusing gravity inversion

    NASA Astrophysics Data System (ADS)

    Vatankhah, Saeed; Ardestani, Vahid E.; Renaut, Rosemary A.

    2015-01-01

    The ?2 principle and the unbiased predictive risk estimator are used to determine optimal regularization parameters in the context of 3-D focusing gravity inversion with the minimum support stabilizer. At each iteration of the focusing inversion the minimum support stabilizer is determined and then the fidelity term is updated using the standard form transformation. Solution of the resulting Tikhonov functional is found efficiently using the singular value decomposition of the transformed model matrix, which also provides for efficient determination of the updated regularization parameter each step. Experimental 3-D simulations using synthetic data of a dipping dike and a cube anomaly demonstrate that both parameter estimation techniques outperform the Morozov discrepancy principle for determining the regularization parameter. Smaller relative errors of the reconstructed models are obtained with fewer iterations. Data acquired over the Gotvand dam site in the south-west of Iran are used to validate use of the methods for inversion of practical data and provide good estimates of anomalous structures within the subsurface.

  4. Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices.

    PubMed

    Zhou, L; Lund, M S; Wang, Y; Su, G

    2014-08-01

    This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G-matrices) across these two breeds. Single-trait genomic best linear unbiased prediction (GBLUP) model and two-trait GBLUP model were used for single-breed and two-breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50000 SNP chip. Using the two-breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two-breed predictions. Weighting the two-breed G-matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two-breed predictions. PMID:24750283

  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

    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

    2015-06-01

    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 Ca(2+)-ATPase (SERCA) Ca(2+) 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 Ca(2+)-mediated, and autophagosome accumulation in JNCL cells could be reversed by Ca(2+) chelation. Interrogation of intracellular Ca(2+) handling highlighted alterations in endoplasmic reticulum, mitochondrial, and lysosomal Ca(2+) pools and in store-operated Ca(2+) uptake in JNCL cells. These results further support an important role for the CLN3 protein in intracellular Ca(2+) handling and in autophagic pathway flux and establish a powerful new platform for therapeutic screening. PMID:25878248

  6. The application of total vertical projections for the unbiased estimation of the length of blood vessels and other structures by magnetic resonance imaging.

    PubMed

    Roberts, N; Howard, C V; Cruz-Orive, L M; Edwards, R H

    1991-01-01

    A new stereological method has recently been developed to estimate the total length of a bounded curve in 3D from a sample of projections about a vertical axis. Unlike other methods based on serial section reconstructions, the new method is unbiased (i.e., it has zero systematic error). A basic requirement, not difficult to fulfill in many cases, is that the masking of one structure by another is not appreciable. The application of the new method to real curvilinear structures using a clinical magnetic resonance (MR) imager is illustrated. The first structure measured was a twisted water-filled glass tube of known length. The accuracy of the method was assessed: With six vertical projections, the tube length was measured to within 2% of the true value. The second example was a living bonsai tree, and the third was a clinical application of MR angiography. The possibility of applying the method to other scientific disciplines, for example, the monitoring of plant root growth, is discussed. PMID:1766316

  7. Efficient selection against categorically scored hip dysplasia in dogs is possible using best linear unbiased prediction and optimum contribution selection: a simulation study.

    PubMed

    Malm, S; Srensen, A C; Fikse, W F; Strandberg, E

    2013-04-01

    Breeding to reduce the prevalence of categorically scored hip dysplasia (HD), based on phenotypic assessment of radiographic hip status, has had limited success. The aim of this study was to evaluate two selection strategies for improved hip status: truncation selection based on phenotypic record versus best linear unbiased prediction (BLUP), using stochastic simulation and selection scenarios resembling those in real dog populations. In addition, optimum contribution selection (OCS) was evaluated. Two traits were considered: HD (as a categorical trait with five classes and a heritability of 0.45 on the liability scale) and a continuous trait (with a heritability of 0.25) intended to represent other characteristics in the breeding goal. A population structure mimicking that in real dog populations was modelled. The categorical nature of HD caused a considerably lower genetic gain compared to simulating HD as a continuous trait. Genetic gain was larger for BLUP selection than for phenotypic selection in all scenarios. However, BLUP selection resulted in higher rates of inbreeding. By applying OCS, the rate of inbreeding was lowered to about the same level as phenotypic selection but with increased genetic improvement. For efficient selection against HD, use of BLUP breeding values should be prioritized. In small populations, BLUP should be used together with OCS or similar strategy to maintain genetic variation. PMID:23496016

  8. 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 Central

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

    2014-01-01

    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 could be universally applied to the study of human viral pathogens. PMID:25243334

  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

    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.

  10. The Theory of Spectra and Atomic Constitution

    NASA Astrophysics Data System (ADS)

    Bohr, Niels

    2011-06-01

    Part I. On the Spectrum of Hydrogen: 1. Empirical spectral laws; 2. Laws of temperature radiation; 3. The nuclear theory of the atom; 4. Quantum theory of spectra; 5. Hydrogen spectrum; 6. The Pickering lines; 7. Other spectra; Part II. On the Series Spectra of the Elements; Section 1. Introduction; Section 2. General Principles of the Quantum Theory of Spectra: 8. Hydrogen spectrum; 9. The correspondence principle; 10. General spectral laws; 11. Absorption and excitation of radiation; Section 3. Development of the Quantum Theory of Spectra: 12. Effect of external forces on the hydrogen spectrum; 13. The Stark effect; 14. The Zoeman effect; 15. Central pertubations; 16. Relativity effect of hydrogen lines; 17. Theory of series spectra; 18. Correspondence principle and conservation of angular momentum; 19. The spectra of helium and lithium; 20. Complex structure of series lines; Section 4. Conclusion; Part III. The Structure of the Atom and the Physical and Chemical Properties of the Elements; Section 5. Preliminary: 21. The nuclear atom; 22. The postulates of the quantum theory; 23. Hydrogen atom; 24. Hydrogen spectrum and x-ray spectra; 25. The fine structure of the hydrogen lines; 26. Periodic table; 27. Recent atomic models; Section 6. Series Spectra and the Capture of Electrons by Atoms: 28. Arc and spark spectra; 29. Series diagram; 30. Correspondence principle; Section 7. Formation of Atoms and the Periodic Table: 31. First period. Hydrogen-helium; 32. Second period. Lithium-neon; 33. Third period. Sodium-argon; 34. Fourth period. Potassium-Krypton; 35. Fifth period. Rubidium-xenon; 36. Sixth period. Caesium-niton; 37. Seventh period; 38. Survey of the periodic table; Section 8. Reorganization of Atoms and X-Ray SPectra: 39. Absorption and emission of x-rays and correspondence principle; 40. X-ray spectra and atomic structure; 41. Classification of x-ray spectra; 42. Conclusion; Appendix.

  11. Overcoming Degeneracies in Exoplanet Spectra

    NASA Astrophysics Data System (ADS)

    Benneke, Bjrn

    2015-08-01

    Spectroscopic observations of exoplanets can provide invaluable insights into the planets compositions, their formation and evolution histories, and even their habitability. Obtaining exoplanet spectra is observationally challenging; however, and we are generally limited to relatively low signal-to-noise, low spectral resolution, disk-integrated observations , often with relatively narrow wavelength coverage. This low data situation results in strong correlations and degeneracies between the different planet and atmospheric parameters of interest. In this talk, I will present a conceptual picture of how vital information about the planet is encoded in its observable spectrum. I will then give an overview about the wide range of correlations and degeneracies relevant to todays exoplanet observations. Finally, I will demonstrate how some degeneracies can be overcome and improved constraints can be obtained by including prior knowledge of atmospheric chemistry and physics in the retrieval. I present a new atmospheric retrieval framework, SCARLET, that combines observational data and our prior (limited) knowledge of atmospheric processes in a statistical robust Bayesian framework. New results for hot Jupiters will be presented.

  12. 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.

  13. Model atmospheres and spectra of cool stars

    NASA Astrophysics Data System (ADS)

    Pavlenko, Ya. V.

    2007-10-01

    Procedure and results of computations of model atmospheres, synthetic spectra, spectral energy distributions (SEDs), and fits them to observed spectra of M- and C-giants as well giants with anomalies of abundances are discussed. Blanketing effects due to absorption of atomic and molecular lines are taken into account within the framework of opacity sampling approach. Model atmospheres and syntetic spectra are computed in LTE, the specific opacities are implemented.

  14. Infrared spectra of natural and synthetic malachites

    NASA Astrophysics Data System (ADS)

    Schuiskii, A. V.; Zorina, M. L.

    2013-09-01

    IR absorption and reflection spectra of dark and light samples of natural and synthetic malachite over 400-4000 cm-1 are studied for the purpose of improving the synthesis technique and in order to distinguish between natural malachite and malachite grown from ammonia solutions. Nitrogen was not detected in the IR spectra or in microprobe analyses of the synthetic material. The differences found in the IR spectra were insignificant and cannot be regarded as distinctive indicators of these materials.

  15. 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.

  16. 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.

  17. Superfluorescence spectra of excitons in quantum wells

    NASA Astrophysics Data System (ADS)

    Grünwald, P.; Burau, G. K. G.; Stolz, H.; Vogel, W.

    2013-11-01

    We study the fluorescence light emitted from GaAs excitons in semiconductor quantum wells. The excitons are modeled as interacting bosons. By combining quantum optical methods for the excitonic emission spectrum with many particle descriptions of the transmission through the medium, we can evaluate the spectra outside the well. Comparing with experimental spectra, we get a very good agreement. The method helps to explain the main features of the observed spectra. It is demonstrated that the observed spectra show clear evidence of superfluorescent emission.

  18. Near infrared Raman spectra of Rhizoma dioscoreae

    NASA Astrophysics Data System (ADS)

    Lin, Wenshuo; Chen, Rong; Chen, Guannan; Feng, Sangyuan; Li, Yongzeng; Huang, Zufang; Li, Yongsen

    2008-03-01

    A novel and compact near-infrared (NIR) Raman system is developed using 785-nm diode laser, volume-phase technology holographic system, and NIR intensified charge-coupled device (CCD). Raman spectra and first derivative spectra of Rhizoma Dioscoreae are obtained. Raman spectra of Rhizoma Dioscoreae showed three strong characteristic peaks at 477.4cm -1, 863.9cm -1, and 936.0cm -1. The major ingredients are protein, amino acid, starch, polysaccharides and so on, matched with the known basic biochemical composition of Rhizoma Dioscoreae. In the first derivative spectra of Rhizoma Dioscoreae, distinguishing characteristic peaks appeared at 467.674cm -1, 484.603cm -1, 870.37cm -1, 943.368cm -1. Contrasted with Rhizoma Dioscoreae Raman spectra, in 600cm -1 to 800cm -1, 1000cm -1 to 1400cm -1 regions, changes in Rhizoma Dioscoreae Raman first derivative spectra are represented more clearly than Rhizoma Dioscoreae Raman spectra. So Rhizoma Dioscoreae raman first derivative spectra can be an accurate supplementary analysis method to Rhizoma Dioscoreae Raman spectra.

  19. Modeling of asteroid spectra - M4AST

    NASA Astrophysics Data System (ADS)

    Popescu, M.; Birlan, M.; Nedelcu, D. A.

    2012-08-01

    Context. The interpretation of asteroid spectra provides the basis for determining the chemical composition and physical process that modified the surface of the asteroids. The increasing number of asteroid spectral measurements has lead to well-developed methods for analyzing asteroid spectra. There is however no centralized database for all the published data and a set of standard routines is also required. Aims: We present a public software tool that combines both data archives and analyses of asteroid spectra. Methods: Our project M4AST (Modeling for asteroids) consists of an asteroid spectral database and a set of applications for analyzing asteroid spectra. These applications cover aspects related to taxonomy, curve matching with laboratory spectra, space weathering models, and mineralogical diagnosis. Results: M4AST project is fully available via a web interface. The database contains around 2700 spectra that can be either processed in M4AST and/or downloaded. The paper presents the algorithms we developed for spectral analyses based on existing methods. The robustness of routines is proven by the solutions found for spectra of three different asteroids: (9147) Kourakuen, (99 942) Apophis, and (175 706) 1996 FG3. The available results confirm those in the literature. M4AST applications can also be used to characterize any new asteroid spectra. Conclusions: M4AST is a robust and reliable tool dedicated to asteroid spectra. M4AST is available via the web interface: http://cardamine.imcce.fr/m4ast/

  20. High Resolution Spectra of Solar Flares

    NASA Astrophysics Data System (ADS)

    Doschek, G. A.

    I discuss high-resolution solar flare spectra from the soft X-ray region through the extreme ultraviolet (EUV) wavelength regions. Spectra of solar flares at these wavelengths have been recorded since the late 1960s, beginning primarily with the NASA Orbiting Solar Observatory (OSO) series of spacecraft. Knowledge of EUV flare spectra took a quantum leap with the NASA Skylab Apollo Telescope Mount spectrographs in the early 1970s. Knowledge of the X-ray spectrum took a similar leap in the 1980s with the US Department of Defense P78-1 spacecraft, the NASA Solar Maximum Mission spacecraft (SMM), and the Japanese Hinotori spacecraft. Investigations of flare X-ray spectra continued with the BCS X-ray spectrometer experiment on the Japanese Yohkoh mission. Recently, EUV solar flare spectroscopy has been extended with the SUMER spectrometer on the ESA SOHO spacecraft. In addition to the above missions, significant contributions were made with instrumentation on a number of other spacecraft, e.g., the Soviet Intercosmos X-ray spectrometers. Our knowledge of the physical conditions in solar flares has been greatly expanded from analyses of X-ray and EUV flare spectra. I will discuss the general characteristics of the flare emission line and continuum spectra, and the physical processes that produce them. I will discuss what we have learned about solar flares from the spectra, and discuss solar flare spectra in terms of spectra expected from other astrophysical sources.

  1. Cancer net survival on registry data: use of the new unbiased Pohar-Perme estimator and magnitude of the bias with the classical methods.

    PubMed

    Roche, Laurent; Danieli, Coraline; Belot, Aurélien; Grosclaude, Pascale; Bouvier, Anne-Marie; Velten, Michel; Iwaz, Jean; Remontet, Laurent; Bossard, Nadine

    2013-05-15

    Net survival, the survival which might occur if cancer was the only cause of death, is a major epidemiological indicator required for international or temporal comparisons. Recent findings have shown that all classical methods used for routine estimation of net survival from cancer-registry data, sometimes called "relative-survival methods," provide biased estimates. Meanwhile, an unbiased estimator, the Pohar-Perme estimator (PPE), was recently proposed. Using real data, we investigated the magnitude of the errors made by four "relative-survival" methods (Ederer I, Hakulinen, Ederer II and a univariable regression model) vs. PPE as reference and examined the influence of time of follow-up, cancer prognosis, and age on the errors made. The data concerned seven cancer sites (2,51,316 cases) collected by FRANCIM cancer registries. Net survivals were estimated at 5, 10 and 15 years postdiagnosis. At 5 years, the errors were generally small. At 10 years, in good-prognosis cancers, the errors made in nonstandardized estimates with all classical methods were generally great (+2.7 to +9% points in prostate cancer) and increased in age-class estimations (vs. 5-year ones). At 15 years, in bad- or average-prognosis cancers, the errors were often substantial whatever the nature of the estimation. In good-prognosis cancers, the errors in nonstandardized estimates of all classical methods were great and sometimes very important. With all classical methods, great errors occurred in age-class estimates resulting in errors in age-standardized estimates (+0.4 to +3.2% points in breast cancer). In estimating net survival, cancer registries should abandon all classical methods and adopt the new Pohar-Perme estimator. PMID:22961565

  2. 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.; Micha?owski, M. J.; Cenko, S. B.; Jakobsson, P.; Krhler, 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 ?Jy, 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.

  3. 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.

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

    PubMed

    Kayser, Jrgen; Tenke, Craig E

    2015-09-01

    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:25562833

  5. 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. PMID:26818672

  6. An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

    PubMed Central

    Scozzari, Rosaria; Massaia, Andrea; Trombetta, Beniamino; Bellusci, Giovanna; Myres, Natalie M.; Novelletto, Andrea; Cruciani, Fulvio

    2014-01-01

    Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next-generation sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY, a large proportion of newly arisen alleles has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers. PMID:24395829

  7. Identification and Biological Evaluation of a Novel and Potent Small Molecule Radiation Sensitizer via an Unbiased Screen of a Chemical Library

    PubMed Central

    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

    2013-01-01

    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. PMID:17875720

  8. Exploiting the full potential of photometric quasar surveys: optimal power spectra through blind mitigation of systematics

    NASA Astrophysics Data System (ADS)

    Leistedt, Boris; Peiris, Hiranya V.

    2014-10-01

    We present optimal measurements of the angular power spectrum of the XDQSOz catalogue of photometric quasars from the Sloan Digital Sky Survey. These measurements rely on a quadratic maximum likelihood estimator that simultaneously measures the auto- and cross-power spectra of four redshift samples, and provides minimum-variance, unbiased estimates even at the largest angular scales. Since photometric quasars are known to be strongly affected by systematics such as spatially-varying depth and stellar contamination, we introduce a new framework of extended mode projection to robustly mitigate the impact of systematics on the power spectrum measurements. This technique involves constructing template maps of potential systematics, decorrelating them on the sky, and projecting out modes which are significantly correlated with the data. Our method is able to simultaneously process several thousands of non-linearly correlated systematics, and mode projection is performed in a blind fashion. Using our final power spectrum measurements, we find a good agreement with theoretical predictions, and no evidence for further contamination by systematics. Extended mode projection not only obviates the need for aggressive sky and quality cuts, but also provides control over the level of systematics in the measurements, enabling the search for small signals of new physics while avoiding confirmation bias.

  9. Heavy primary spectra observed by RUNJOB

    NASA Astrophysics Data System (ADS)

    Apanasenko, A. V.; Beresovskaya, V. A.; Fujii, M.; Galkin, V. I.; Hareyama, M.; Ichimura, M.; Ito, S.; Kamioka, E.; Kitami, T.; Kobayashi, T.; Kopenkin, V. V.; Kuramata, S.; Kuriyama, T.; Lapshin, V. I.; Managadze, A. K.; Matsutani, H.; Mikami, H.; Misnikova, N. P.; Mukhamedshin, R. A.; Namiki, M.; Nanjo, H.; Nazarov, S. N.; Nikolsky, S. I.; Oe, T.; Ohta, S.; Osedlo, V. I.; Oshuev, D. S.; Publichenko, P. A.; Rakobolskaya, I. V.; Roganova, T. M.; Saito, M.; Sazhina, G. P.; Semba, H.; Shabanova, Yu. N.; Shibata, T.; Sugimoto, H.; Sveshnikova, L. G.; Takahashi, K.; Tsutiya, T.; Taran, V. M.; Yajima, N.; Yamagami, T.; Yamamoto, K.; Yashin, I. V.; Zamchalova, E. A.; Zatsepin, G. T.; Zayarnaya, I. S.

    2001-08-01

    RUssian Nippon JOint Balloon (RUNJOB) has been observing the primary spectra of cosmic ray nuclei since 1995. Data from 6 out of 10 succesful flights will be used to report the spectra of heavy primaries up to iron nucleus with the energy range more than 1014 eV/particle. The details of analysis like charge and energy determinations will be also given.

  10. Faster optical-spectra recording and analysis

    NASA Technical Reports Server (NTRS)

    Richmond, R. G.

    1977-01-01

    Optical spectra are recorded and rapidly analyzed by system that links multichannel analyzer and desk-top programable calculator. Cassette-memory storage is provided. System can be programed to automate background subtraction, axis expansion, and other data-analysis techniques and can store several hundred spectra for immediate or delayed analysis and comparisons.

  11. 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.

  12. COMPUTER INTERPRETATION OF POLLUTANT MASS SPECTRA

    EPA Science Inventory

    The objective of this research was to improve systems for computer examination of the mass spectra of unknown pollutants. For this we have developed a new probability based matching (PBM) system for the retrieval of mass spectra from a large data base, and have substantially impr...

  13. 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.

  14. THE SUZAKU VIEW OF THE SWIFT/BAT ACTIVE GALACTIC NUCLEI. II. TIME VARIABILITY AND SPECTRA OF FIVE 'HIDDEN' ACTIVE GALACTIC NUCLEI

    SciTech Connect

    Winter, Lisa M.; Mushotzky, Richard F.; Terashima, Yuichi; Ueda, Yoshihiro

    2009-08-20

    The fraction of Compton-thick sources is one of the main uncertainties left in understanding the active galactic nucleus (AGN) population. The Swift Burst Alert Telescope (BAT) all-sky survey for the first time gives us an unbiased sample of AGNs for all but the most heavily absorbed sources N {sub H} > 10{sup 25} cm{sup -2}). Still, the BAT spectra (14-195 keV) are time averaged over months of observations and therefore hard to compare with softer spectra from the Swift XRT or other missions. This makes it difficult to distinguish between Compton-thin and Compton-thick models. With Suzaku, we have obtained simultaneous hard (>15 keV) and soft (0.3-10 keV) X-ray spectra for five Compton-thick candidate sources. We report on the spectra and a comparison with the BAT and earlier XMM observations. Based on both flux variability and spectral shape, we conclude that these hidden sources are not Compton thick. We also report on a possible correlation between excess variance and Swift BAT luminosity from the 16 day binned light curves, which holds true for a sample of both absorbed (four sources), unabsorbed (eight sources), and Compton-thick (Circinus) AGNs, but is weak in the 64 day binned BAT light curves.

  15. Characteristics of energetic solar flare electron spectra

    NASA Technical Reports Server (NTRS)

    Moses, Dan; Droege, Wolfgang; Meyer, Peter; Evenson, Paul

    1989-01-01

    A 55 event survey of energy spectra of 0.1-100 MeV interplanetary electrons originating from solar flares as measured by two spectrometers onboard the ISEE 3 (ICE) spacecraft for the years 1978-1982 has been completed. Spectra generated using the maximum flux of a given event in each energy channel were restricted to events with a well-defined flux rise time. Two broad groups of electron spectra are considered. In one group, the spectra are well represented by a single power law in rigidity with spectral index in the range 3-4.5. The spectra in the other group deviate from a power law in rigidity systematically in that they harden with increasing rigidity. Events with near power-law spectra are found to be correlated with long-duration soft X-ray events, whereas those with hardening spectra are correlated with short-duration events. The possible variation of acceleration and propagation processes with the properties of the flare site is discussed, using the duration of the soft X-ray flare emission as an indicator of the physical parameters of the flare site (flare volume, density, coronal height, and magnetic field geometry).

  16. 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.

  17. Simulation of x-ray fluorescence spectra

    SciTech Connect

    Collins, M.L.; Hsue, S.T.; Gunnink, R.

    1996-09-01

    A method for simulating x-ray fluorescence (XRF) spectra in hybrid densitometry is presented. This technique allows simulation of XRF spectra for solutions with arbitrary concentrations of special nuclear material and minor actinides excited by an x-ray generator. Spectra for mixed uranium and plutonium solutions with U/Pu ratios ranging from 100 to 1 have been generated. This range of ratios applies to most solutions found in plutonium reprocessing plants. XRF simulation can provide important data for estimating instrument precision, evaluating analysis techniques, and training system operators. Applications of XRF simulation in the development of the Los Alamos Hybrid K-Edge/XRF Densitometer system are described.

  18. Microscopic measurement of circular dichroism spectra.

    PubMed

    Matsugaki, Aira; Takechi, Hideaki; Monjushiro, Hideaki; Watarai, Hitoshi

    2008-02-01

    A microscope device to measure the circular dichroism (CD) spectra of a specified microscopic region of chiral samples was constructed by combining of a couple of objective lenses and a CCD camera, which was installed in a sample chamber of a commercially available CD spectropolarimeter. By using this apparatus, high quality micro-CD spectra in the 60 x 60 microm region of samples could be measured. Micro-CD spectra of thin film of chiral DNA samples on glass and a natural kidney bean leaf were measured, and the potential of the micro-CD apparatus was successfully demonstrated. PMID:18270427

  19. 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.

  20. 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 the central T Tauri star when modeling protoplanetary disk gas chemistry and physical conditions.

  1. 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.

  2. 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.

  3. Dynamic radio spectra from two fireballs

    NASA Astrophysics Data System (ADS)

    Obenberger, K. S.; Taylor, G. B.; Lin, C. S.; Dowell, J.; Schinzel, F. K.; Stovall, K.

    2015-11-01

    We present dynamic spectra from the Long Wavelength Array telescope of two large meteors (fireballs) observed to emit between 37 and 54 MHz. These spectra show the first ever recorded broadband measurements of this newly discovered VHF emission. The spectra show that the emission is smooth and steep, getting very bright at lower frequencies. We suggest that this signal is possibly emission of Langmuir waves and that these waves could be excited by a bump-on-tail instability within the trail. The spectra of one fireball display broadband temporal frequency sweeps. We suggest that these sweeps are evidence of individual expanding clumps of emitting plasma. While some of these proposed clumps may have formed at the very beginning of the fireball event, others must have formed seconds after the initial event.

  4. 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.

  5. PIA update: Correlation analyses of mass spectra

    NASA Technical Reports Server (NTRS)

    Mason, L. W.; Clark, B. C.

    1988-01-01

    The PIA instrument aboard the Giotto spacecraft (a time of flight spectrometer) has been presented elsewhere. The mass spectra used in this analysis were decoded and mass numbers assigned according to the presence of carbon and silver, using the global values for these elements in their spectral absence. The results presented here were obtained using a frequency of occurrence based on analysis which correlated how often mass numbers appear in the mass spectra and which mass numbers tend to occur together in the same spectra; no amplitude information is utilized. The data are presented as plots of mass vs coincident mass for different subsets of the PIA data set, with both axes having units of atomic mass. Frequency contours are plotted at approximately five percent contour intervals, relative to the maximum AMU occurrence in that plot. The plots presented are symmetrical about the matrix diagonal, i.e., every mass is coincident with itself in a given spectra.

  6. [Resonance raman spectra of linear polymer molecule].

    PubMed

    Zhang, Xue; Li, Shuo; Liu, Tie-Cheng; Sun, Cheng-Lin; Li, Zuo-Wei

    2014-05-01

    The present paper summarizes the characteristics of resonance Raman spectra of the linear polymer molecule, and its relations with the molecular structure, including: electronic spectra(ultraviolet-visible absorption spectrum), Raman spectra characteristics and its relations with external field; Modulation relation between the electron energy gap and CC atom vibration; Several experimental results were obtained: The UV-visible absorption spectra are red-shifted with decreasing temperature, increasing solvent density and reducing solution concentration, and because the linear polymer molecule has high structured order, decreasing pi electron energy gap; extended pi electronic delocalization, large effective conjugation length, large intensity of the Raman activity, Ramrnan spectrum are red-shifted, with large scattering cross section. "Am plitude modes" are the ideal theory models to study the linear polymer molecule. PMID:25095421

  7. 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)

  8. 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.

  9. Study on Raman spectra of synthetic celluloses

    NASA Astrophysics Data System (ADS)

    Tong, Na; Zhu, Changjun; Zhang, Yixin

    2015-02-01

    Raman spectrometry was employed to study the characteristics of Raman spectra of aliphatic polyamide fiber and 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 results show that Raman peaks beyond 1200 cm-1 appear for aliphatic polyamide fiber processed by sodium hydroxide, while the Raman peaks beyond 1000 cm-1 disappear for aliphatic polyamide fiber processed by sulfuric acid. Raman peaks beyond 1750 cm-1 decrease for polyethylene terephthalate processed by sodium hydroxide, while Raman peaks beyond 1000 cm-1 disappear, except weak peaks around 3000 cm-1 , for polyethylene terephthalate processed by sulfuric acid. The variations of the Raman spectra are primarily related to the changes of chemical bonds and molecular structures.

  10. 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.

  11. Improved peak shape fitting in alpha spectra.

    PubMed

    Pomm, S; Caro Marroyo, B

    2015-02-01

    Peak overlap is a recurrent issue in alpha-particle spectrometry, not only in routine analyses but also in the high-resolution spectra from which reference values for alpha emission probabilities are derived. In this work, improved peak shape formulae are presented for the deconvolution of alpha-particle spectra. They have been implemented as fit functions in a spreadsheet application and optimum fit parameters were searched with built-in optimisation routines. Deconvolution results are shown for a few challenging spectra with high statistical precision. The algorithm outperforms the best available routines for high-resolution spectrometry, which may facilitate a more reliable determination of alpha emission probabilities in the future. It is also applicable to alpha spectra with inferior energy resolution. PMID:25497323

  12. Phonon spectra of a Fibonacci chain

    NASA Astrophysics Data System (ADS)

    Li, Liqin; Yang, Xiangbo

    2008-08-01

    Based on more realistic physics we study the phonon spectra of the Fibonacci chain by taking into account a nonlinear resistance. It is found that the nonlinear force should be very weak and consequently, the continuity, range and gaps of the phonon spectra would be still controlled dominantly by the relative strength of spring constants and chain length. It means that even if no additional nonlinear resistance was taken into account, the conventional results of phonon spectra are exactly correct. On the other hand, in the framework of a conventional model we investigated the relationship between the biggest gaps of phonon spectra and defects of Fibonacci-like aperiodic chains. By means of numerical calculations one can obtain quantitatively the maximum of the length of a one-dimensional aperiodic chain sensitive to boundaries. This method would be useful for the calculation of quasiperiodic and aperiodic lattices.

  13. [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+. PMID:23905358

  14. Angular power spectra with finite counts

    NASA Astrophysics Data System (ADS)

    Campbell, Sheldon S.

    2015-04-01

    Angular anisotropy techniques for cosmic diffuse radiation maps are powerful probes, even for quite small data sets. A popular observable is the angular power spectrum; we present a detailed study applicable to any unbinned source skymap S(n) from which N random, independent events are observed. Its exact variance, which is due to the finite statistics, depends only on S(n) and N; we also derive an unbiased estimator of the variance from the data. First-order effects agree with previous analytic estimates. Importantly, heretofore unidentified higher order effects are found to contribute to the variance and may cause the uncertainty to be significantly larger than previous analytic estimates - potentially orders of magnitude larger. Neglect of these higher order terms, when significant, may result in a spurious detection of the power spectrum. On the other hand, this would indicate the presence of higher order spatial correlations, such as a large bispectrum, providing new clues about the sources. Numerical simulations are shown to support these conclusions. Applying the formalism to an ensemble of Gaussian-distributed skymaps, the noise-dominated part of the power-spectrum uncertainty is significantly increased at high multipoles by the new, higher order effects. This work is important for harmonic analyses of the distributions of diffuse high-energy ?-rays, neutrinos, and charged cosmic rays, as well as for populations of sparse point sources such as active galactic nuclei.

  15. 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.

  16. 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.

  17. Investigation of nonequilibrium hydroxyl emission spectra

    NASA Astrophysics Data System (ADS)

    Moskalenko, N. I.; Zaripov, A. V.; Il'in, Yu. A.

    2010-07-01

    Ultraviolet nonequilibrium OH emission spectra in flames are measured and analyzed. Spectra of nonequilibrium coefficients are recorded for an optically thin jet, and spectral absorption coefficients and electronic absorption band intensities are determined. Based on the developed mathematical radiative transfer model in a nonequilibrium radiating media, the OH contribution to radiative jet cooling is estimated, and practical applications of the nonequilibrium emission process to the development of optoelectronic systems of observation over aero carriers are considered.

  18. 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.

  19. T1 weighted brain images at 7 Tesla unbiased for Proton Density, T2* contrast and RF coil receive B1 sensitivity with simultaneous vessel visualization.

    PubMed

    Van de Moortele, Pierre-Franois; Auerbach, Edwards J; Olman, Cheryl; Yacoub, Essa; U?urbil, Kmil; Moeller, Steen

    2009-06-01

    At high magnetic field, MR images exhibit large, undesirable signal intensity variations commonly referred to as "intensity field bias". Such inhomogeneities mostly originate from heterogeneous RF coil B(1) profiles and, with no appropriate correction, are further pronounced when utilizing rooted sum of square reconstruction with receive coil arrays. These artifacts can significantly alter whole brain high resolution T(1)-weighted (T(1)w) images that are extensively utilized for clinical diagnosis, for gray/white matter segmentation as well as for coregistration with functional time series. In T(1) weighted 3D-MPRAGE sequences, it is possible to preserve a bulk amount of T(1) contrast through space by using adiabatic inversion RF pulses that are insensitive to transmit B(1) variations above a minimum threshold. However, large intensity variations persist in the images, which are significantly more difficult to address at very high field where RF coil B(1) profiles become more heterogeneous. Another characteristic of T(1)w MPRAGE sequences is their intrinsic sensitivity to Proton Density and T(2)(*) contrast, which cannot be removed with post-processing algorithms utilized to correct for receive coil sensitivity. In this paper, we demonstrate a simple technique capable of producing normalized, high resolution T(1)w 3D-MPRAGE images that are devoid of receive coil sensitivity, Proton Density and T(2)(*) contrast. These images, which are suitable for routinely obtaining whole brain tissue segmentation at 7 T, provide higher T(1) contrast specificity than standard MPRAGE acquisitions. Our results show that removing the Proton Density component can help in identifying small brain structures and that T(2)(*) induced artifacts can be removed from the images. The resulting unbiased T(1)w images can also be used to generate Maximum Intensity Projection angiograms, without additional data acquisition, that are inherently registered with T(1)w structural images. In addition, we introduce a simple technique to reduce residual signal intensity variations induced by transmit B(1) heterogeneity. Because this approach requires two 3D images, one divided with the other, head motion could create serious problems, especially at high spatial resolution. To alleviate such inter-scan motion problems, we developed a new sequence where the two contrast acquisitions are interleaved within a single scan. This interleaved approach however comes with greater risk of intra-scan motion issues because of a longer single scan time. Users can choose between these two trade offs depending on specific protocols and patient populations. We believe that the simplicity and the robustness of this double contrast based approach to address intensity field bias at high field and improve T(1) contrast specificity, together with the capability of simultaneously obtaining angiography maps, advantageously counter balance the potential drawbacks of the technique, mainly a longer acquisition time and a moderate reduction in signal to noise ratio. PMID:19233292

  20. Climatology of tropospheric vertical velocity spectra

    NASA Technical Reports Server (NTRS)

    Ecklund, W. L.; Gage, K. S.; Balsley, B. B.; Carter, D. A.

    1986-01-01

    Vertical velocity power spectra obtained from Poker Flat, Alaska; Platteville, Colorado; Rhone Delta, France; and Ponape, East Caroline Islands using 50-MHz clear-air radars with vertical beams are given. The spectra were obtained by analyzing the quietest periods from the one-minute-resolution time series for each site. The lengths of available vertical records ranged from as long as 6 months at Poker Flat to about 1 month at Platteville. The quiet-time vertical velocity spectra are shown. Spectral period ranging from 2 minutes to 4 hours is shown on the abscissa and power spectral density is given on the ordinate. The Brunt-Vaisala (B-V) periods (determined from nearby sounding balloons) are indicated. All spectra (except the one from Platteville) exhibit a peak at periods slightly longer than the B-V period, are flat at longer periods, and fall rapidly at periods less than the B-V period. This behavior is expected for a spectrum of internal waves and is very similar to what is observed in the ocean (Eriksen, 1978). The spectral amplitudes vary by only a factor of 2 or 3 about the mean, and show that under quiet conditions vertical velocity spectra from the troposphere are very similar at widely different locations.

  1. Ir Spectra of Cold Protonated Methane

    NASA Astrophysics Data System (ADS)

    Asvany, Oskar; Yamada, Koichi MT; Brnken, Sandra; Potapov, Alexey; Schlemmer, Stephan

    2015-06-01

    High-resolution infrared spectra of mass selected protonated methane, CH_5^+, have been recorded in the C-H stretching region in a 22-pole ion trap experiment at low temperatures. The frequencies of the infrared OPO system (pump and signal) have been calibrated using a NIR frequency comb. As a result the ro-vibrational IR transition frequencies of CH_5^+ could be determined to an accuracy in the MHz regime. In this contribution we discuss different techniques of laser induced reactions which enabled recording spectra at different temperatures. The spectra simplify dramatically at a nominal trap temperature of 4~K. Nevertheless an assignment of these spectra is very difficult. We apply the idea of the Rydberg-Ritz combination principle to the complex spectra of protonated methane in order to get first hints at the energy level structure of this enigmatic molecule. O. Asvany, J. Krieg, and S. Schlemmer, Frequency comb assisted mid-infrared spectroscopy of cold molecular ions, Review of Scientific Instruments, 83 (2012), 076102. O. Asvany, S. Brnken, L. Kluge, and S. Schlemmer, COLTRAP: a 22-pole ion trapping machine for spectroscopy at 4 K, Applied Physics B: Lasers and Optics, 114 (2014), 203-211

  2. 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.

  3. 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.

  4. 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.

  5. Quantitative characteristics of methane's infrared spectra

    NASA Astrophysics Data System (ADS)

    Liu, Xian-yong; Shang, Li-ping; Li, Hong-lei

    2005-01-01

    FTIR spectra have been widely used in quantitative analyses of mixed gases. Although Beer's Law regulates the relationships between absorbency and the product of concentration and path length, its deviations have been found rather complicated. Here we present the complexity of quantitative relationships between methane's infrared spectra and concentrations and resolutions. Measurements of the same methane sample's spectra under different resolutions demonstrate that both area absorbency and height absorbency vary with resolutions; spectra at lower resolution have bigger area absorbency for most of the peaks and are more likely to saturate for peaks of strong absorption. Standard methane sample of certain concentration is diluted with super pure nitrogen via mass control flowmeters and continuously passes through a 2-meter gas cell, such that the spectra of methane of different concentrations are collected. The area absorbencies of different peaks are carefully calculated via OMNIC software and results show that peaks with lower absorption are more likely to fit to linearity but more reluctant to changing concentrations. Area absorbencies are integrated through characteristic absorption regions, height absorbencies and area absorbencies are calculated at the two main absorption peaks and measurements show that approximative linearity fits all the areas and the best linearity appears at 1035.6cm-1.

  6. Spectra from nuclear-excited plasmas

    NASA Technical Reports Server (NTRS)

    De Young, R. J.; Weaver, W. R.

    1980-01-01

    The paper discusses the spectra taken from He-3(n,p)H-3 nuclear-induced plasmas under high thermal neutron flux, lasing conditions. Also, initial spectra are presented for U-235F6 generated plasmas. From an evaluation of these spectra, important atomic and molecular processes that occur in the plasma can be inferred. The spectra presented are the first to be generated by He-3 and U-235F6 nuclear reactions under high neutron flux, lasing conditions. The U-235(n,ff)FF reaction, which liberates 165 MeV of fission-fragment kinetic energy, creates plasmas that are of great interest, since at sufficiently high densities of U-235F6 the gas becomes self-critical; thus, there is no need for an external driving reactor (source of neutrons). The spectra from mixtures of He-3 and Ar, Xe, Kr, Ne, Cl2, F2 and N2 indicate little difference between high-pressure nuclear-induced plasmas and high-pressure electrically pulsed afterglow plasmas for noble-gas systems

  7. Group independent component analysis of MR spectra

    PubMed Central

    Kalyanam, Ravi; Boutte, David; Gasparovic, Chuck; Hutchison, Kent E; Calhoun, Vince D

    2013-01-01

    This study investigates the potential of independent component analysis (ICA) to provide a data-driven approach for group level analysis of magnetic resonance (MR) spectra. ICA collectively analyzes data to identify maximally independent components, each of which captures covarying resonances, including those from different metabolic sources. A comparative evaluation of the ICA approach with the more established LCModel method in analyzing two different noise-free, artifact-free, simulated data sets of known compositions is presented. The results from such ideal simulations demonstrate the ability of data-driven ICA to decompose data and accurately extract components resembling modeled basis spectra from both data sets, whereas the LCModel results suffer when the underlying model deviates from assumptions, thus highlighting the sensitivity of model-based approaches to modeling inaccuracies. Analyses with simulated data show that independent component weights are good estimates of concentrations, even of metabolites with low intensity singlet peaks, such as scyllo-inositol. ICA is also applied to single voxel spectra from 193 subjects, without correcting for baseline variations, line-width broadening or noise. The results provide evidence that, despite the presence of confounding artifacts, ICA can be used to analyze in vivo spectra and extract resonances of interest. ICA is a promising technique for decomposing MR spectral data into components resembling metabolite resonances, and therefore has the potential to provide a data-driven alternative to the use of metabolite concentrations derived from curve-fitting individual spectra in making group comparisons. PMID:23785655

  8. 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.

  9. 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.

  10. Optical High Resolution Spectra of APOGEE Stars

    NASA Astrophysics Data System (ADS)

    Feuillet, Diane; Holtzman, J. A.; Cunha, K. M.; Garcia Perez, A.; Ghezzi, L.; Hayden, M. R.; Meszaros, Sz.; Allende Prieto, C.; Shetrone, M. D.; Smith, V. V.; Zasowski, G.

    2013-01-01

    The Apache Point Observatory Galactic Evolution Experiment (APOGEE) is an SDSS-III survey that is obtaining high resolution near-IR (H band) spectra of 100,000 Milky Way stars in an effort to chemically trace formation and evolution of Galactic stellar populations. Optical echelle spectra of a small subset of survey targets have been obtained with the ARC 3.5m telescope for the purpose of 1) helping to understand and calibrate the abundance analysis of the APOGEE IR spectra, and 2) measuring abundances of elements that do not have spectral features in the APOGEE wavelength region, which will ideally include neutron capture elements. We present our current sample of ~130 (out of a projected 500) stars, which is drawn from the brightest APOGEE targets and covers a range of stellar parameters (temperature, metallicity, and surface gravity), and compare some optically derived quantities with those from the APOGEE abundance pipeline.

  11. Fast Inversion of Solar Ca II Spectra

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    We present a fast (Lt1 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 ? ~ -3 and increases to values of 2.5 and 4 at log ? = -6 in the quiet Sun and the umbra, respectively.

  12. Degradation spectra of electrons in the ionosphere

    NASA Astrophysics Data System (ADS)

    Konovalov, V. P.; Son, E. E.

    2015-11-01

    Theory and numerical simulations of degradation spectra of electrons in gases are presented. Theory is based on the power spectra of degradation charged particles as the spectra with fluxes in energy space. Numerical calculations of the electron energy distribution function have been performed for ionospheric gas mixtures constituted of molecules N2, O2 and atom O under influence of high energy electron source with detailed elementary electron collision processes with molecules and atoms being taken into consideration. The energy expenses of electrons into ionization, dissociation and excitation of various levels have been obtained so that to determine the rates of electron collision processes. The dependence of the electron energy expenses into various inelastic electronic processes upon the energy of primary electron source has been revealed. The results are presented for the rates of numerous elementary processes of electron interaction with basic ionospheric components to be suitably determined.

  13. Ultraviolet spectra and chromospheres of R stars

    NASA Technical Reports Server (NTRS)

    Eaton, J. A.; Johnson, H. R.; Obrien, G. T.; Baumert, J. H.

    1985-01-01

    Long-wavelength IUE spectra of 13 normal R stars and two hydrogen-deficient R0 supergiants were obtained. Early R stars are noted to have line spectra and levels of flux in the ultraviolet characteristic of G5-K2 III stars, whereas late R stars were observed to have colors and line spectra similar to late K and M stars, but with greatly enhanced strength of low-lying multiplets of neutral metals. Hydrogen-deficient carbon stars show readily apparent differences from the normal early R stars, reflecting their luminosity and somewhat higher temperatures. The lines of neutral metals in these stars are weakened, while those of ionized metals are strengthened.

  14. Meteor spectra in the EDMOND database

    NASA Astrophysics Data System (ADS)

    Koukal, J.; Gorkov, S.; Srba, J.; Ferus, M.; Civi, 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 "?r"), 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.

  15. Thermal radiation spectra of individual subwavelength microheaters

    NASA Astrophysics Data System (ADS)

    Au, Yat-Yin; Skulason, Helgi Skuli; Ingvarsson, Snorri; Klein, Levente J.; Hamann, Hendrik F.

    2008-08-01

    Polarization resolved spectra of infrared radiation from individual electrically driven platinum microheaters have been measured by Fourier-transform infrared spectrometry as a function of heaters width. When the heater width approaches zero, the signal with polarization parallel to the heater long axis converges to a finite value, while its perpendicularly polarized counterpart drops below our detection limit. As a result this leads to strongly polarized radiation for very narrow heaters. Further, while the parallel polarized radiation spectra appear to be insensitive to heater width variation (at least within the sensitive range of our light detector), the perpendicular polarized spectra were heavily affected. We observed a ?/2 -like resonance that we attribute to correlation of charge oscillations across the heaters width, which are possibly mediated by surface plasmons. These findings provide implications for fabrication of nanoscale electrically driven thermal antennas.

  16. 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.

  17. Cosmic ray proton spectra at low rigidities

    NASA Technical Reports Server (NTRS)

    Seo, E. S.; Ormes, J. F.; Streitmatter, R. E.; Lloyd-Evans, J.; Jones, W. V.

    1990-01-01

    The cosmic ray proton rigidity spectra have been investigated with data collected in the Low Energy Antiproton (LEAP) balloon flight experiment flown from Prince Albert, Canada in 1987. The LEAP apparatus was designed to measure antiprotons using a superconducting magnet spectrometer with ancillary scintillator, time-of-flight, and liquid Cherenkov detectors. After reaching float altitude the balloon drifted south and west to higher geomagnetic cutoffs. The effect of the changing geomagnetic cutoff on the observed spectra was observed during analysis of the proton data along the balloon trajectory. This is the first measurement of the primary and splash albedo spectra over a wide rigidity range (few hundred MV to about 100 GV) with a single instrument.

  18. 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.

  19. Proton and Helium spectra observed by RUNJOB

    NASA Astrophysics Data System (ADS)

    Apanasenko, A. V.; Beresovksaya, V. A.; Fujii, M.; Galkin, V. I.; Hareyama, M.; Ichimura, M.; Ito, S.; Kamioka, E.; Kitami, T.; Kobayashi, T.; Kopenkin, V. V.; Kuramata, S.; Kuriyama, Y.; Lapshin, V. I.; Managadze, A. K.; Matsutani, H.; Misnikova, N. P.; Muhamedshin, R. A.; Namiki, M.; Nanjo, H.; Nazarov, S. N.; Nikolsky, S. I.; Oe, T.; Ohta, S.; Osedlo, V. I.; Oshuev, D. S.; Publichenko, P. A.; Rakobolskaya, I. V.; Roganova, T. M.; Saito, M.; Sazhina, G. P.; Semba, H.; Shabanova, Yu. N.; Shibata, T.; Sugimoto, H.; Sveshnikova, L. G.; Takahashi, K.; Tsutiya, T.; Taran, V. M.; Yajima, N.; Yamagami, T.; Yamamoto, K.; Yashin, I. V.; Zamchalova, E. A.; Zatsepin, G. T.; Zayarnaya, I. S.

    2001-08-01

    We have been carrying out 10 of long duration balloon flights with emulsion chamber for observation of cosmic- ray primaries from 1995 through 1999. We report the energy spectra of proton and helium primaries basing on 45% of observed data which have been analyzed up to now. Our results cover the energy range of 10 300 TeV for proton, and 2 50 TeV/n for helium. And one proton primary with the energy larger than 1015 eV is observed. Both of proton and helium spectra can connect to indirect measurement data smoothly.

  20. 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.

  1. Interpretation of IR Spectra of Indolinospirobenzothiopyran

    NASA Astrophysics Data System (ADS)

    Gladkov, L. L.; Khamchukov, Yu. D.; Sychev, I. Yu.; Lyubimov, A. V.; Gladkova, G. A.

    2015-09-01

    The structures of four stereomers (enantiomers) of photochromic indolinospirobenzothiopyran (ISTP) in the closed form were studied by the DFT method. The most stable structure was found. IR spectra of ISTP in KBr pellets and as a film on single-crystalline KBr plates (in the region 400-4000 cm -1 ) and as a powder between polyethylene plates (100-400 cm -1 ) were measured. An interpretation of the obtained IR spectra was proposed. Specific features of normal modes of ISTP caused by the presence of the spiro center were revealed.

  2. Photon spectra from quark generation by WIMPs

    SciTech Connect

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

    2011-05-23

    If the present dark matter (DM) in the Universe annihilates into Standard Model (SM) particles, it must contribute to the gamma ray fluxes that are detected on the Earth. The magnitude of such contribution depends on the particular DM candidate, but certain features of these spectra may be analyzed in a model-independent fashion. In this work we provide the fitting formula valid for the simulated photon spectra from WIMP annihilation into light quark-anti quark (qq-bar) channels in a wide range of WIMP masses. We illustrate our results for the cc-bar channel.

  3. Energy spectra of geomagnetically trapped oxygen ions.

    PubMed

    Leicher, M; Beaujean, R; Enge, W

    1999-06-01

    In a series of COSMOS satellite flights plastic nuclear track detectors have been exposed in low-earth orbits to monitor anomalous cosmic rays (ACR) at energies below 25 MeV/nuc. The analysis of energy spectra has now been extended to energies up to 40 MeV/nuc for two exposures aboard COSMOS 2260 in 1993 and COSMOS 2311 in 1995. Our data on trapped ACR (TACR) oxygen energy spectra might indicate the influence of energy-dependent stripping probabilities and the presence of multiply charged ACR oxygen at high energies as reported by latest SAMPEX observations. PMID:12025845

  4. 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.

  5. 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. PMID:19084471

  6. Absorption spectra of photosensitized human fat tissue

    NASA Astrophysics Data System (ADS)

    Yanina, I. Yu.; Simonenko, G. V.; Kochubey, V. I.; Tuchin, V. V.

    2010-08-01

    We study experimentally the optical characteristics of adipose tissue in vitro in its dye sensitizationby indocyanin green and brilliant green. We conducted experiments on a PerkinElmer Lambda 950 spectrophotometer in the spectral range of 250-900 nm. From an analysis of the measured absorption spectra, we determine the shifts in the maximum of the absorption band for the studied photosensitizers in adipose tissue in comparison to their spectra in solutions. These shifts are explained by the bonding of photosensitizer molecules with the protein matrix of adipose tissue. We find the relative monomer and dimer concentrations of dye molecules in solutions and stained samples.

  7. Simultaneous Selective Detection of Multiple Quantum Spectra

    NASA Astrophysics Data System (ADS)

    Syvitski, R. T.; Burlinson, N.; Burnell, E. E.; Jeener, J.

    2002-04-01

    A three-dimensional multiple-quantum NMR experiment that produces individual spectra of all quantum orders is described. The separation of different quantum orders is accomplished via Fourier transformation with respect to the phase of the first two pulses of a generic three-pulse multiple-quantum sequence. This dramatically reduces the time required to obtain several selectively detected spectra and enhances the sensitivity and digital resolution from that obtained using the original two-dimensional technique. The experiment is demonstrated on the protons of para-chlorotoluene dissolved in the nematic liquid crystal Merck ZLI-1132.

  8. 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.

  9. Parallel Genetic Algorithm for Alpha Spectra Fitting

    NASA Astrophysics Data System (ADS)

    Garca-Orellana, Carlos J.; Rubio-Montero, Pilar; Gonzlez-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.

  10. Gravitational effects on planetary neutron flux spectra

    NASA Technical Reports Server (NTRS)

    Feldman, W. C.; Drake, D. M.; O'Dell, R. D.; Brinkley, F. W., Jr.; 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.

  11. What can we learn from inclusive spectra

    SciTech Connect

    Nagamiya, S.

    1981-05-01

    The present experimental status on single particle inclusive measurements is described. Then, the geometrical aspect of the collision is discussed from the data of total integrated cross sections of nuclear charge or mass. The dynamical aspect of the collision, especially that for the participating region is discussed in connection with proton spectra, composite fragment spectra, pion production, ratios of ..pi../sup -//..pi../sup +/, n/p and t//sup 3/He, and production of strange particles. The spectator physics is described from the data on projectile fragments. (GHT)

  12. On the varying slope of velocity spectra

    NASA Technical Reports Server (NTRS)

    Rottger, J.

    1986-01-01

    Spectra of zonal, meridional and vertical wind velocity, measured during a 24 hour period with the spaced-antenna technique indicate quite a variable slope as a function of height. It is found that the spectral slope (1h to 24h) of all three components correlates with the mean horizontal wind velocity. A possible conclusion is that the frequency dependence of power density of horizontal and vertical fluctuation component apparently depends on the mean wind velocity. However, the vertical spectra at periods larger than about 1 hour can also be influenced by spillover (due to finite radar antenna beam width) from the horizontal fluctuation component or by a Doppler shift.

  13. Elemental Spectra from the First ATIC Flight

    NASA Technical Reports Server (NTRS)

    Ahn, H. S.; Adams, J. H.; Bashindzhagyan, G.; Batkov, K. E.; Changv, J.; Christl, M.; Fazely, A. R.; Ganel, O.; Gunasingha, R. M.; Guzik, T. G.

    2005-01-01

    The Advanced Thin Ionization Calorimeter (ATIC) instrument is a balloon-borne experiment designed to measure the composition and energy spectra of Z = l to 26 cosmic rays over the energy range from approx. 10(exp 11) to approx. 10(exp 14) eV. The instrument consists of a silicon matrix charge detector, plastic scintillator strip hodoscopes interleaved with graphite interaction targets, and a fully active Bismuth Germanate (BGO) calorimeter. ATIC had two successful Long Duration Balloon flights launched from McMurdo Station, Antarctica in 2000 and 2002. In this paper, spectra of various elements measured during the first 16 day flight are presented.

  14. Augmentation of ENDF/B fission product gamma-ray spectra by calculated spectra

    SciTech Connect

    Katakura, J. ); England, T.R. )

    1991-11-01

    Gamma-ray spectral data of the ENDF/B-V fission product decay data file have been augmented by calculated spectra. The calculations were performed with a model using beta strength functions and cascade gamma-ray transitions. The calculated spectra were applied to individual fission product nuclides. Comparisons with several hundred measured aggregate gamma spectra after fission were performed to confirm the applicability of the calculated spectra. The augmentation was extended to a preliminary ENDF/B-VI file, and to beta spectra. Appendix C provides information on the total decay energies for individual products and some comparisons of measured and aggregate values based on the preliminary ENDF/B-VI files. 15 refs., 411 figs.

  15. 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.

  16. Unbiased Scanning Method and Data Banking Approach Using Ultra-High Performance Liquid Chromatography Coupled with High-Resolution Mass Spectrometry for Quantitative Comparison of Metabolite Exposure in Plasma across Species Analyzed at Different Dates.

    PubMed

    Gao, Hongying; Deng, Shibing; Obach, R Scott

    2015-12-01

    An unbiased scanning methodology using ultra high-performance liquid chromatography coupled with high-resolution mass spectrometry was used to bank data and plasma samples for comparing the data generated at different dates. This method was applied to bank the data generated earlier in animal samples and then to compare the exposure to metabolites in animal versus human for safety assessment. With neither authentic standards nor prior knowledge of the identities and structures of metabolites, full scans for precursor ions and all ion fragments (AIF) were employed with a generic gradient LC method to analyze plasma samples at positive and negative polarity, respectively. In a total of 22 tested drugs and metabolites, 21 analytes were detected using this unbiased scanning method except that naproxen was not detected due to low sensitivity at negative polarity and interference at positive polarity; and 4'- or 5-hydroxy diclofenac was not separated by a generic UPLC method. Statistical analysis of the peak area ratios of the analytes versus the internal standard in five repetitive analyses over approximately 1 year demonstrated that the analysis variation was significantly different from sample instability. The confidence limits for comparing the exposure using peak area ratio of metabolites in animal plasma versus human plasma measured over approximately 1 year apart were comparable to the analysis undertaken side by side on the same days. These statistical analysis results showed it was feasible to compare data generated at different dates with neither authentic standards nor prior knowledge of the analytes. PMID:26528960

  17. Determinations of photon spectra. Master's thesis

    SciTech Connect

    Wannigman, D.L.

    1989-01-01

    A method is developed to unfold photon spectra from measurements obtained with a sodium iodide counting system. A response matrix is computed by combining photon cross sections with probability distributions of path lengths for incident and internally generated photons in the energy range 0-2.8 MeV. This matrix is inverted and multiplied by a measured pulse height spectrum to obtain the photon energy distribution incident upon the detector. This deconvolution procedure provides improved information about the energy continuum of incident photons and can enhanced the identification of discrete gamma energies. Experiments were performed to verify the unfolding methodology and to evaluate the feasibility and accuracy of this technique. Measured spectra were acquired from indoor and outdoor environments and unfolded. The results show that measured spectra overestimate the number of photons below 240 keV by up to 30 %. When the total exposure was calculated directly from the measured spectra, the low energy contribution was overestimated by a factor of two. This may have implications on the interpretation and calibration of energy dependent dosimeters used for occupational and environmental monitoring.

  18. 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.

  19. CO2 retrievals from GOSAT glint spectra

    NASA Astrophysics Data System (ADS)

    Irion, F. W.; Frankenberg, C.; Natraj, V.; McDuffie, J.; O'Dell, C. W.

    2011-12-01

    Algorithms for retrieving column-averaged CO2 mixing ratio (XCO2) are being developed in preparation for the launch of the OCO-2 satellite. We describe features of the retrieval algorithm for observations made over ocean glint, and present current results for XCO2 using spectra from the Greenhouse Gases Observing Satellite (GOSAT) instrument currently in-flight.

  20. Squeezing spectra for nonlinear optical systems

    NASA Technical Reports Server (NTRS)

    Collett, M. J.; Walls, D. F.

    1985-01-01

    The squeezing spectra for the output fields of several intracavity nonlinear optical systems are obtained. It is shown that at critical points, e.g., the turning points for optical bistability, the threshold for parametric oscillation, and the self-pulsing instability in second-harmonic generation, perfect squeezing in the output field is, in principle, possible.

  1. 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

  2. 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...

  3. Analysis of COSIMA spectra: Bayesian approach

    NASA Astrophysics Data System (ADS)

    Lehto, H. J.; Zaprudin, B.; Lehto, K. M.; Lnnberg, T.; Siln, J.; Ryn, J.; Krger, H.; Hilchenbach, M.; Kissel, J.

    2015-06-01

    We describe the use of Bayesian analysis methods applied to time-of-flight secondary ion mass spectrometer (TOF-SIMS) spectra. The method is applied to the COmetary Secondary Ion Mass Analyzer (COSIMA) TOF-SIMS mass spectra where the analysis can be broken into subgroups of lines close to integer mass values. The effects of the instrumental dead time are discussed in a new way. The method finds the joint probability density functions of measured line parameters (number of lines, and their widths, peak amplitudes, integrated amplitudes and positions). In the case of two or more lines, these distributions can take complex forms. The derived line parameters can be used to further calibrate the mass scaling of TOF-SIMS and to feed the results into other analysis methods such as multivariate analyses of spectra. We intend to use the method, first as a comprehensive tool to perform quantitative analysis of spectra, and second as a fast tool for studying interesting targets for obtaining additional TOF-SIMS measurements of the sample, a property unique to COSIMA. Finally, we point out that the Bayesian method can be thought of as a means to solve inverse problems but with forward calculations, only with no iterative corrections or other manipulation of the observed data.

  4. Finding diagnostic biomarkers in proteomic spectra.

    PubMed

    Pratapa, Pallavi N; Patz, Edward F; Hartemink, Alexander J

    2006-01-01

    In seeking to find diagnostic biomarkers in proteomic spectra, two significant problems arise. First, not only is there noise in the measured intensity at each m/z value, but there is also noise in the measured m/z value itself. Second, the potential for overfitting is severe: it is easy to find features in the spectra that accurately discriminate disease states but have no biological meaning. We address these problems by developing and testing a series of steps for pre-processing proteomic spectra and extracting putatively meaningful features before presentation to feature selection and classification algorithms. These steps include an HMM-based latent spectrum extraction algorithm for fusing the information from multiple replicate spectra obtained from a single tissue sample, a simple algorithm for baseline correction based on a segmented convex hull, a peak identification and quantification algorithm, and a peak registration algorithm to align peaks from multiple tissue samples into common peak registers. We apply these steps to MALDI spectral data collected from normal and tumor lung tissue samples, and then compare the performance of feature selection with FDR followed by classification with an SVM, versus joint feature selection and classification with Bayesian sparse multinomial logistic regression (SMLR). The SMLR approach outperformed FDR+SVM, but both were effective in achieving good diagnostic accuracy with a small number of features. Some of the selected features have previously been investigated as clinical markers for lung cancer diagnosis; some of the remaining features are excellent candidates for further research. PMID:17094246

  5. Limitation of energetic ring current ion spectra

    NASA Astrophysics Data System (ADS)

    Summers, Danny; Shi, Run

    2015-09-01

    We address the problem of determining the limiting energetic ring current ion spectrum resulting from electromagnetic ion cyclotron (EMIC)-wave-ion interactions. We solve the problem in a relativistic regime, incorporating a cold background multi-ion plasma component and without assuming a predetermined form for the ion energy distribution. The limiting (Kennel-Petschek) spectrum is determined by the condition that the EMIC waves acquire a specified gain over a given convective length scale for all frequencies over which wave growth occurs. We find that the limiting ion spectrum satisfies an integral equation that must be solved numerically. However, at large particle energy E, the limiting spectrum takes the simple form J ∝ 1/E, E → ∞. Moreover, this 1/E spectral shape does not depend on the energetic ion in question nor on the background multi-ion plasma composition. We provide numerical solutions for the limiting spectra for Earth-like parameters. In addition, at four planets, Jupiter, Saturn, Uranus, and Neptune, we compare measured ion spectra with corresponding numerical limiting spectra. This paper parallels an earlier analogous study on the limitation of radiation belt electron spectra by whistler mode wave-electron interactions.

  6. Electronic excitation spectra of the Emery model

    SciTech Connect

    Unger, P.; Fulde, P. )

    1993-04-01

    We calculate the photoemission and inverse photoemission spectra of holes in copper-oxygen planes, the characteristic structural unit of high-temperature superconductors. The computations are based on the extended Hubbard or Emery model in the limit of infinitely strong Coulomb repulsion [ital U][sub [ital d

  7. 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.

  8. Raman Spectra of Gyrotropic Cadmium Diphosphide Crystals

    NASA Astrophysics Data System (ADS)

    Fekeshgazi, I. V.; Sidenko, T. S.; Czitrovszky, A.; Veresh, M.; Trukhan, V. M.; Shoukavaya, T. V.

    2015-07-01

    Samples of CdP2 single crystals oriented relative to the crystallographic axes were prepared. Their optical quality was studied using conoscopy and atomic-force microscopy. Raman spectra of CdP2 single crystals in polarized and unpolarized light in backscattering confi guration were obtained and analyzed.

  9. 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.

  10. 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.

  11. Prompt fission neutron spectra of actinides

    DOE PAGESBeta

    Capote, R.; Chen, Y. -J.; Hambsch, F. -J.; Kornilov, N. V.; Lestone, J. P.; Litaize, O.; Morillon, B.; Neudecker, D.; Oberstedt, S.; Ohsawa, T.; et al

    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.

  12. 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.

  13. LMM Auger primary excitation spectra of copper

    NASA Astrophysics Data System (ADS)

    Pauly, N.; Tougaard, S.; Yubero, F.

    2014-12-01

    The shape and intensity of measured Auger peaks are strongly affected by extrinsic excitations due to electron transport out of the surface and to intrinsic excitations induced by the sudden creation of the two static core holes. Following a method developed for XPS in a previous work [N. Pauly, S. Tougaard, F. Yubero, Surf. Sci. 620 (2014) 17], we have calculated the effective energy-differential inelastic electron scattering cross-sections, including the effects of the surface and of the two core holes, within the dielectric response theory by means of the QUEELS-XPS software (QUantitative analysis of Electron Energy Losses at Surfaces for XPS). The Auger spectra are then modeled by convoluting this energy loss cross section with the primary excitation spectrum that accounts for all effects which are part of the initial Auger process, i.e. L-S coupling and vacancy satellite effects. The shape of this primary excitation spectrum is fitted to get close agreement between the theoretical and the experimental spectra obtained from X-ray excited Auger electron spectroscopy (XAES). We have performed these calculations of XAES spectra for various LMM Auger transitions of pure Cu (L3M45M45, L3M23M45, L3M23M23 and L2M45M45 transitions). We compare the resulting primary excitation spectra with theoretical results published in the literature and obtain reasonable quantitative agreement. In particular, we extract from experimental spectra quantitative intensities due to Coster-Kronig, shake-off and shake-up processes relative to the intensity from the normal Auger process.

  14. Single molecule Raman spectra of porphycene isotopologues

    NASA Astrophysics Data System (ADS)

    Gawinkowski, Sylwester; Pszona, Maria; Gorski, Alexandr; Niedziółka-Jönsson, Joanna; Kamińska, Izabela; Nogala, Wojciech; Waluk, Jacek

    2016-02-01

    Single molecule surface-enhanced resonance Raman scattering (SERRS) spectra have been obtained for the parent porphycene (Pc-d0) and its deuterated isotopologue (Pc-d12), located on gold and silver nanoparticles. Equal populations of ``hot spots'' by the two isotopologues are observed for 1 : 1 mixtures in a higher concentration range of the single molecule regime (5 × 10-9 M). For decreasing concentrations, hot spots are preferentially populated by undeuterated molecules. This is interpreted as an indication of a lower surface diffusion coefficient of Pc-d12. The photostability of single Pc molecules placed on nanoparticles is strongly increased in comparison with polymer environments. Trans tautomeric species dominate the spectra, but the analysis of time traces reveals transient intermediates, possibly due to rare cis tautomeric forms.Single molecule surface-enhanced resonance Raman scattering (SERRS) spectra have been obtained for the parent porphycene (Pc-d0) and its deuterated isotopologue (Pc-d12), located on gold and silver nanoparticles. Equal populations of ``hot spots'' by the two isotopologues are observed for 1 : 1 mixtures in a higher concentration range of the single molecule regime (5 × 10-9 M). For decreasing concentrations, hot spots are preferentially populated by undeuterated molecules. This is interpreted as an indication of a lower surface diffusion coefficient of Pc-d12. The photostability of single Pc molecules placed on nanoparticles is strongly increased in comparison with polymer environments. Trans tautomeric species dominate the spectra, but the analysis of time traces reveals transient intermediates, possibly due to rare cis tautomeric forms. Electronic supplementary information (ESI) available: Details of estimation of the enhancement factors, additional Raman, SERS, fluorescence, and absorption spectra and maps. See DOI: 10.1039/c5nr08627b

  15. Savannah River Site disaggregated seismic spectra

    SciTech Connect

    Stephenson, D.E.

    1993-02-01

    The objective of this technical note is to characterize seismic ground motion at the Savannah River Site (SRS) by postulated earthquakes that may impact facilities at the site. This task is accomplished by reviewing the deterministic and probabilistic assessments of the seismic hazard to establish the earthquakes that control the hazard to establish the earthquakes that control the hazard at the site and then evaluate the associated seismic ground motions in terms of response spectra. For engineering design criteria of earthquake-resistant structures, response spectra serve the function of characterizing ground motions as a function of period or frequency. These motions then provide the input parameters that are used in the analysis of structural response. Because they use the maximum response, the response spectra are an inherently conservative design tool. Response spectra are described in terms of amplitude, duration, and frequency content, and these are related to source parameters, travel path, and site conditions. Studies by a number of investigators have shown by statistical analysis that for different magnitudes the response spectrum values are different for differing periods. These facts support Jennings' position that using different shapes of design spectra for earthquakes of different magnitudes and travel paths is a better practice than employing a single, general-purpose shape. All seismic ground motion characterization results indicate that the PGA is controlled by a local event with M[sub w] < 6 and R < 30km. The results also show that lower frequencies are controlled by a larger, more distant event, typically the Charleston source. The PGA of 0.2 g, based originally on the Blume study, is consistent with LLNL report UCRL-15910 (1990) and with the DOE position on LLNL/EPRI.

  16. Savannah River Site disaggregated seismic spectra

    SciTech Connect

    Stephenson, D.E.

    1993-02-01

    The objective of this technical note is to characterize seismic ground motion at the Savannah River Site (SRS) by postulated earthquakes that may impact facilities at the site. This task is accomplished by reviewing the deterministic and probabilistic assessments of the seismic hazard to establish the earthquakes that control the hazard to establish the earthquakes that control the hazard at the site and then evaluate the associated seismic ground motions in terms of response spectra. For engineering design criteria of earthquake-resistant structures, response spectra serve the function of characterizing ground motions as a function of period or frequency. These motions then provide the input parameters that are used in the analysis of structural response. Because they use the maximum response, the response spectra are an inherently conservative design tool. Response spectra are described in terms of amplitude, duration, and frequency content, and these are related to source parameters, travel path, and site conditions. Studies by a number of investigators have shown by statistical analysis that for different magnitudes the response spectrum values are different for differing periods. These facts support Jennings` position that using different shapes of design spectra for earthquakes of different magnitudes and travel paths is a better practice than employing a single, general-purpose shape. All seismic ground motion characterization results indicate that the PGA is controlled by a local event with M{sub w} < 6 and R < 30km. The results also show that lower frequencies are controlled by a larger, more distant event, typically the Charleston source. The PGA of 0.2 g, based originally on the Blume study, is consistent with LLNL report UCRL-15910 (1990) and with the DOE position on LLNL/EPRI.

  17. Improved predictions of reactor antineutrino spectra

    NASA Astrophysics Data System (ADS)

    Mueller, Th. A.; Lhuillier, D.; Fallot, M.; Letourneau, A.; Cormon, S.; Fechner, M.; Giot, L.; Lasserre, T.; Martino, J.; Mention, G.; Porta, A.; Yermia, F.

    2011-05-01

    Precise predictions of the antineutrino spectra emitted by nuclear reactors is a key ingredient in measurements of reactor neutrino oscillations as well as in recent applications to the surveillance of power plants in the context of nonproliferation of nuclear weapons. We report new calculations including the latest information from nuclear databases and a detailed error budget. The first part of this work is the so-called ab initio approach where the total antineutrino spectrum is built from the sum of all β branches of all fission products predicted by an evolution code. Systematic effects and missing information in nuclear databases lead to final relative uncertainties in the 10-20% range. A prediction of the antineutrino spectrum associated with the fission of U238 is given based on this ab initio method. For the dominant isotopes we developed a more accurate approach combining information from nuclear databases and reference electron spectra associated with the fission of U235, Pu239, and Pu241, measured at Institut Laue-Langevin (ILL) in the 1980s. We show how the anchor point of the measured total β spectra can be used to suppress the uncertainty in nuclear databases while taking advantage of all the information they contain. We provide new reference antineutrino spectra for U235, Pu239, and Pu241 isotopes in the 2-8 MeV range. While the shapes of the spectra and their uncertainties are comparable to those of the previous analysis of the ILL data, the normalization is shifted by about +3% on average. In the perspective of the reanalysis of past experiments and direct use of these results by upcoming oscillation experiments, we discuss the various sources of errors and their correlations as well as the corrections induced by off-equilibrium effects.

  18. 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.

  19. Discrimination of phytoplankton classes using characteristic spectra of 3D fluorescence spectra.

    PubMed

    Zhang, Qian-Qian; Lei, Shu-He; Wang, Xiu-Lin; Wang, Lei; Zhu, Chen-Jian

    2006-02-01

    The discrimination of phytoplankton classes using the characteristic fluorescence spectra extracted from three-dimensional fluorescence spectra was investigated. Single species cultures of 11 phytoplankton species, representing 5 major phytoplankton divisions, were used. The 3D fluorescence spectra of the cultures grown at different temperatures (20 and 15 degrees C) and illumination intensities (140, 80 and 30 microM m(-2) s(-1)) were measured and their feature extraction methods were explored. Ordering Rayleigh and Raman scattering data as zero, the obtained excitation-emission matrices were processed by both singular value decomposition (SVD) and trilinear decomposition methods. The resulting first principal component can be regarded as the characteristic spectrum of the original 3D fluorescence spectrum. The analysis shows that such characteristic spectra have a discriminatory capability. At different temperatures, the characteristic spectra of Isochrysis galbana, Platymonas helgolanidica and Skeletonema costatuma have high degrees of similarity to their own species samples, while the spectra similarities of Alexandrium tamarense, Prorocentrum dentatum, Pseudo-nitzschia pungens, Chaetoceros curvisetus, Ch. Debilis, Ch. Didymus and Synechococcus sp. are not as significant as the other three species. C. curvisetus, Ch. Debilis and Ch. Didymus, belonging to genus Chaetoceros, have identical spectra and cannot be discriminated at all. Regarding all six diatom species as one class, the average discriminant error rate is below 9%. It is worth mentioning that the diatom class can be distinguished from A. tamarense and P. dentatum, which belong to Dinophyta. PMID:16024277

  20. Discrimination of phytoplankton classes using characteristic spectra of 3D fluorescence spectra

    NASA Astrophysics Data System (ADS)

    Zhang, Qian-Qian; Lei, Shu-He; Wang, Xiu-Lin; Wang, Lei; Zhu, Chen-Jian

    2006-02-01

    The discrimination of phytoplankton classes using the characteristic fluorescence spectra extracted from three-dimensional fluorescence spectra was investigated. Single species cultures of 11 phytoplankton species, representing 5 major phytoplankton divisions, were used. The 3D fluorescence spectra of the cultures grown at different temperatures (20 and 15 °C) and illumination intensities (140, 80 and 30 μM m -2 s -1) were measured and their feature extraction methods were explored. Ordering Rayleigh and Raman scattering data as zero, the obtained excitation-emission matrices were processed by both singular value decomposition (SVD) and trilinear decomposition methods. The resulting first principal component can be regarded as the characteristic spectrum of the original 3D fluorescence spectrum. The analysis shows that such characteristic spectra have a discriminatory capability. At different temperatures, the characteristic spectra of Isochrysis galbana, Platymonas helgolanidica and Skeletonema costatuma have high degrees of similarity to their own species samples, while the spectra similarities of Alexandrium tamarense, Prorocentrum dentatum, Pseudo-nitzschia pungens, Chaetoceros curvisetus, Ch. Debilis, Ch. Didymus and Synechococcus sp. are not as significant as the other three species. C. curvisetus, Ch. Debilis and Ch. Didymus, belonging to genus Chaetoceros, have identical spectra and cannot be discriminated at all. Regarding all six diatom species as one class, the average discriminant error rate is below 9%. It is worth mentioning that the diatom class can be distinguished from A. tamarense and P. dentatum, which belong to Dinophyta.

  1. Reflectance spectra of mafic silicate-opaque assemblages with applications to meteorite spectra

    NASA Technical Reports Server (NTRS)

    Cloutis, Edward A.; Smith, Dorian G. W.; Lambert, Richard St. J.; Gaffey, Michael J.

    1990-01-01

    The addition of fine-grained magnetite to mafic silicate spectra can impart not only an overall blue slope, but also lower overall reflectance and band intensities. The reflectance spectra of the CO and CV magnetite-bearing carbonaceous chondrites are noted to exhibit many of these features; the low band depths of these meteorites suggest that an additional dark, neutral phase, such as ordered carbon, is present. Carbon + mafic silicate spectra possess a red overall slope at low amorphous carbon concentrations. The parent bodies of some of the darkest meteorites should exhibit spectral features attributable to mafic silicates.

  2. 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.

  3. Bone densitometry using x-ray spectra

    NASA Astrophysics Data System (ADS)

    Krmar, M.; Shukla, S.; Ganezer, K.

    2010-10-01

    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.

  4. Knowledge Discovery in Mega-Spectra Archives

    NASA Astrophysics Data System (ADS)

    koda, P.; Bromov, P.; Lopatovsk'y, L.; Pali?ka, A.; Vvzn, 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.

  5. Creating semiconductor metafilms with designer absorption spectra.

    PubMed

    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

  6. Raman spectra of deuteriated taurine single crystals

    NASA Astrophysics Data System (ADS)

    Souza, J. M. de; Lima, R. J. C.; Freire, P. T. C.; Sasaki, J. M.; Melo, F. E. A.; Filho, J. Mendes; Jones, Derry W.

    2005-05-01

    The polarized Raman spectra of partially deuteriated taurine [(ND 3+) 0.65(NH 3+) 0.35(CH 2) 2SO 3-] crystals from x( zz) x and x( zy) x scattering geometries of the A g and B g irreducible representations of the factor group C 2h are reported. The temperature-dependent Raman spectra of partially deuteriated taurine do not reveal any evidence of the structural phase transition undergone by normal taurine at about 250 K, but an anomaly observed in the 180 cm -1 band at 120 K implies a different dynamic for this band (which is involved in a pressure-induced phase transition) in the deuteriated crystal.

  7. Primordial power spectra from anisotropic inflation

    SciTech Connect

    Dulaney, Timothy R.; Gresham, Moira I.

    2010-05-15

    We examine cosmological perturbations in a dynamical theory of inflation in which an Abelian gauge field couples directly to the inflaton, breaking conformal invariance. When the coupling between the gauge field and the inflaton takes a specific form, inflation becomes anisotropic and anisotropy can persist throughout inflation, avoiding Wald's no-hair theorem. After discussing scenarios in which anisotropy can persist during inflation, we calculate the dominant effects of a small persistent anisotropy on the primordial gravitational wave and curvature perturbation power spectra using the ''in-in'' formalism of perturbation theory. We find that the primordial power spectra of cosmological perturbations gain significant direction dependence and that the fractional direction dependence of the tensor power spectrum is suppressed in comparison to that of the scalar power spectrum.

  8. Nuclear structure insights into reactor antineutrino spectra

    NASA Astrophysics Data System (ADS)

    Sonzogni, A. A.; Johnson, T. D.; McCutchan, E. A.

    2015-01-01

    Antineutrino spectra following the neutron induced fission of 235U ,238U ,239Pu, and 241Pu are calculated using the summation approach. While each system involves the decay of more than 800 fission products, the energy region of the spectra most relevant to neutrino oscillations and the reactor antineutrino anomaly is dominated by fewer than 20 nuclei, for which we provide a priority list to drive new measurements. The very-high-energy portion of the spectrum is mainly due to the decay of just two nuclides, 92Rb and 96Y. The integral of the signal measured by antineutrino experiments is found to have a dependence on the mass and proton numbers of the fissioning system. In addition, we observe that 70 % of the signal originates from the light fission fragment group and about 50 % from the decay of odd-Z , odd-N nuclides.

  9. Vibrational spectra of amorphous clusters: Universal aspects

    SciTech Connect

    Matharoo, Gurpreet S.; Sarkar, Subir K.; Pandey, Akhilesh

    2005-08-15

    We have performed extensive numerical computations on the vibrational spectra of isolated amorphous clusters of medium to large size and containing one or two types of atoms. The interaction potential is also varied to study possible universality. For all the potentials and cluster sizes we find that the cumulative density of states can be described very accurately by the same functional form over a large central region of the spectrum. This functional form contains only one scale of frequency. We also find that the statistical fluctuations of the spectra are described by the Gaussian orthogonal ensemble of random matrices. For the largest clusters this is tested to a very high degree of precision in the central region and to a somewhat lower degree for most of the rest of the spectrum. We put forward a conjecture regarding the domain of the space of local minima of the potential energy function where universality with respect to the density of states function may be expected.

  10. Single molecule Raman spectra of porphycene isotopologues.

    PubMed

    Gawinkowski, Sylwester; Pszona, Maria; Gorski, Alexandr; Niedzi?ka-Jnsson, Joanna; Kami?ska, Izabela; Nogala, Wojciech; Waluk, Jacek

    2016-02-14

    Single molecule surface-enhanced resonance Raman scattering (SERRS) spectra have been obtained for the parent porphycene (Pc-d0) and its deuterated isotopologue (Pc-d12), located on gold and silver nanoparticles. Equal populations of "hot spots" by the two isotopologues are observed for 1?:?1 mixtures in a higher concentration range of the single molecule regime (5 10(-9) M). For decreasing concentrations, hot spots are preferentially populated by undeuterated molecules. This is interpreted as an indication of a lower surface diffusion coefficient of Pc-d12. The photostability of single Pc molecules placed on nanoparticles is strongly increased in comparison with polymer environments. Trans tautomeric species dominate the spectra, but the analysis of time traces reveals transient intermediates, possibly due to rare cis tautomeric forms. PMID:26731569

  11. 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

  12. QSOS with IPC X-Ray Spectra

    NASA Astrophysics Data System (ADS)

    Elvis, Martin S.

    Observations with the Einstein IPC have produced a unique sample of 33 quasars with well determined soft x-ray spectra. 24 of these are bright enough to be observed with IUE. Our previous programs in years 8 and 9 have obtained spectra of many of the opticall-selected PG quasars In the IPC sample. With this proposal we aim to complete IUE coverage for the bright objects in the sample. This primarily requires observations of radio-laud quasars. The x-ray results show a clear difference In the properties of radio-loud and radio-quiet quasars. With the new data collected from this proposed program we can see if these differences extend into the neighboring ultraviolet region.

  13. 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.

  14. Inflation and alternatives with blue tensor spectra

    SciTech Connect

    Wang, Yi; Xue, Wei E-mail: wei.xue@sissa.it

    2014-10-01

    We study the tilt of the primordial gravitational waves spectrum. A hint of blue tilt is shown from analyzing the BICEP2 and POLARBEAR data. Motivated by this, we explore the possibilities of blue tensor spectra from the very early universe cosmology models, including null energy condition violating inflation, inflation with general initial conditions, and string gas cosmology, etc. For the simplest G-inflation, blue tensor spectrum also implies blue scalar spectrum. In general, the inflation models with blue tensor spectra indicate large non-Gaussianities. On the other hand, string gas cosmology predicts blue tensor spectrum with highly Gaussian fluctuations. If further experiments do confirm the blue tensor spectrum, non-Gaussianity becomes a distinguishing test between inflation and alternatives.

  15. Graph Classification Based on Optimizing Graph Spectra

    NASA Astrophysics Data System (ADS)

    Vinh, Nguyen Duy; Inokuchi, Akihiro; Washio, Takashi

    Kernel methods such as the SVM are becoming increasingly popular due to their high performance in graph classification. In this paper, we propose a novel graph kernel, called SPEC, based on graph spectra and the Interlace Theorem, as well as an algorithm, called OPTSPEC, to optimize the SPEC kernel used in an SVM for graph classification. The fundamental performance of the method is evaluated using artificial datasets, and its practicality confirmed through experiments using a real-world dataset.

  16. 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. PMID:19603827

  17. 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.

  18. Electronic spectra of astrophysically interesting cations

    SciTech Connect

    Maier, John P. Rice, Corey A. Mazzotti, Fabio J. Johnson, Anatoly

    2015-01-22

    The electronic spectra of polyacetylene cations were recorded at 20K in the laboratory in an ion trap instrument. These can then be compared with diffuse interstellar band (DIB) absorptions. Examination of recently published data shows that the attribution of a weak DIB at ?506.9 nm to diacetylene cation is not justified. Study of the higher excited electronic states of polyacetylene cations shows that their widths can still be sufficiently narrow for consideration as DIB carriers.

  19. 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.

  20. Dose spectra from energetic particles and neutrons

    NASA Astrophysics Data System (ADS)

    Schwadron, Nathan; Bancroft, Chris; Bloser, Peter; Legere, Jason; Ryan, James; Smith, Sonya; Spence, Harlan; Mazur, Joe; Zeitlin, Cary

    2013-10-01

    spectra from energetic particles and neutrons (DoSEN) are an early-stage space technology research project that combines two advanced complementary radiation detection concepts with fundamental advantages over traditional dosimetry. DoSEN measures not only the energy but also the charge distribution (including neutrons) of energetic particles that affect human (and robotic) health in a way not presently possible with current dosimeters. For heavy ions and protons, DoSEN provides a direct measurement of the lineal energy transfer (LET) spectra behind shielding material. For LET measurements, DoSEN contains stacks of thin-thick Si detectors similar in design to those used for the Cosmic Ray Telescope for the Effects of Radiation. With LET spectra, we can now directly break down the observed spectrum of radiation into its constituent heavy-ion components and through biologically based quality factors that provide not only doses and dose rates but also dose equivalents, associated rates, and even organ doses. DoSEN also measures neutrons from 10 to 100 MeV, which requires enough sensitive mass to fully absorb recoil particles that the neutrons produce. DoSEN develops the new concept of combining these independent measurements and using the coincidence of LET measurements and neutron detection to significantly reduce backgrounds in each measurement. The background suppression through the use of coincidence allows for significant reductions in size, mass, and power needed to provide measurements of dose, neutron dose, dose equivalents, LET spectra, and organ doses. Thus, we introduce the DoSEN concept: a promising low-mass instrument that detects the full spectrum of energetic particles, heavy ions, and neutrons to determine biological impact of radiation in space.

  1. 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.

  2. Optical identifications and spectra of radio sources

    NASA Astrophysics Data System (ADS)

    Afanas'ev, V. L.; Dodonov, S. N.; Moiseev, A. V.; Gorshkov, A. G.; Konnikova, V. K.; Mingaliev, M. G.

    2009-04-01

    We present classifications, optical identifications, and radio spectra for eight radio sources from three flux-density-complete samples in the following declination ranges: 4°-6° (B1950), S 3.9 > 200 mJy; 10°-12°30' (J2000), S 4.85 > 200 mJy; 74°-75° (J2000), S 4.85 > 100 mJy. For all these samples, the right ascensions are 0h-24h and the Galactic latitudes, | b| > 15°. Our optical observations at 4000-7500 ° were made with the 6-m telescope of the Special Astrophysical Observatory; we also observed at 0.97-21.7 GHz with the RATAN-600 radio telescope of the Special Astrophysical Observatory. We classify four of the objects as quasars and four as galaxies. Five of the radio sources have power-law spectra at 0.97-21.7 GHz, while two objects have flat spectra. The quasar J2358+0430 virtually did not vary during 23 years.

  3. MAGNETIC ENERGY SPECTRA IN SOLAR ACTIVE REGIONS

    SciTech Connect

    Abramenko, Valentyna; Yurchyshyn, Vasyl

    2010-09-01

    Line-of-sight magnetograms for 217 active regions (ARs) with different flare rates observed at the solar disk center from 1997 January until 2006 December are utilized to study the turbulence regime and its relationship to flare productivity. Data from the SOHO/MDI instrument recorded in the high-resolution mode and data from the BBSO magnetograph were used. The turbulence regime was probed via magnetic energy spectra and magnetic dissipation spectra. We found steeper energy spectra for ARs with higher flare productivity. We also report that both the power index, {alpha}, of the energy spectrum, E(k) {approx} k{sup -}{alpha}, and the total spectral energy, W = {integral}E(k)dk, are comparably correlated with the flare index, A, of an AR. The correlations are found to be stronger than those found between the flare index and the total unsigned flux. The flare index for an AR can be estimated based on measurements of {alpha} and W as A = 10{sup b}({alpha}W){sup c}, with b = -7.92 {+-} 0.58 and c = 1.85 {+-} 0.13. We found that the regime of the fully developed turbulence occurs in decaying ARs and in emerging ARs (at the very early stage of emergence). Well-developed ARs display underdeveloped turbulence with strong magnetic dissipation at all scales.

  4. Low Temperature Reflectance Spectra of Titan Tholins

    NASA Technical Reports Server (NTRS)

    Roush, T. L.; Dalton, J. B.; Fonda, Mark (Technical Monitor)

    2001-01-01

    Compositional interpretation of remotely obtained reflectance spectra of outer solar system surfaces is achieved by a variety of methods. These include matching spectral curves, matching spectral features, quantitative spectral interpretation, and theoretical modeling of spectra. All of these approaches rely upon laboratory measurements of one kind or another. The bulk of these laboratory measurements are obtained with the sample of interest at ambient temperatures and pressures. However, surface temperatures of planets, satellites, and asteroids in the outer solar system are significantly cooler than ambient laboratory conditions on Earth. The infrared spectra of many materials change as a function of temperature. As has been recently demonstrated it is important to assess what effects colder temperatures have on spectral properties and hence, compositional interpretations. Titan tholin is a solid residue created by energetic processing of H-, C-, and N-bearing gases. Such residues can also be created by energetic processing if the gases are condensed into ices. Titan tholin has been suggested as a coloring agent for several surfaces in the outer solar system. Here we report laboratory measurements of Titan tholin at a temperature of 100 K and compare these to measurements of the same sample near room temperature. At low temperature the absorption features beyond 1 micrometer narrow slightly. At wavelengths greater than approx. 0.8 micrometer the overall reflectance of the sample decreases slightly making the sample less red at low temperatures. We will discuss the implications of the laboratory measurements for interpretation of cold outer solar system surfaces.

  5. Analysis of COSIMA spectra: Bayesian approach

    NASA Astrophysics Data System (ADS)

    Lehto, H. J.; Zaprudin, B.; Lehto, K. M.; Lnnberg, T.; Siln, J.; Ryn, J.; Krger, H.; Hilchenbach, M.; Kissel, J.

    2014-11-01

    We describe the use of Bayesian analysis methods applied to TOF-SIMS spectra. The method finds the probability density functions of measured line parameters (number of lines, and their widths, peak amplitudes, integrated amplitudes, positions) in mass intervals over the whole spectrum. We discuss the results we can expect from this analysis. We discuss the effects the instrument dead time causes in the COSIMA TOF SIMS. We address this issue in a new way. The derived line parameters can be used to further calibrate the mass scaling of TOF-SIMS and to feed the results into other analysis methods such as multivariate analyses of spectra. We intend to use the method in two ways, first as a comprehensive tool to perform quantitative analysis of spectra, and second as a fast tool for studying interesting targets for obtaining additional TOF-SIMS measurements of the sample, a property unique for COSIMA. Finally, we point out that the Bayesian method can be thought as a means to solve inverse problems but with forward calculations only.

  6. 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.

  7. Gold Spectra Measurements from LLNL EBIT Plasmas

    NASA Astrophysics Data System (ADS)

    May, M.; Brown, G. V.; Chen, H.; Chung, H. K.; Gu, M.; Hansen, S. B.; Schneider, M. B.; Widmann, K.; Beiersdorfer, P.

    2008-11-01

    Spectra have been recorded from gold that has been injected into the Lawrence Livermore Electron Beam Ion Trap (EBIT-II). Both mono-energetic and experimentally simulated Maxwell-Boltzmann (MB) plasmas were created for these measurements. The beam plasmas had energies of 2.75, 3.0, 3.6, 4.6, 5.5, 6.0, 6.5 keV. The MB plasmas had electron temperatures of 2.0, 2.5 and 3.0 keV. M-band gold spectra (n = 4-3, 5-3, 6-3 and 7-3 transitions) were recorded between 1 - 8 keV from K-like to Kr-like ions in the x-ray. The emission of gold was recorded by crystal spectrometers and a micro-calorimeter from the Goddard Space Flight Center. A full survey of the recorded spectra will be presented along with line emission and charge state modeling from the flexible atomic code (FAC). Some comparisons with laser produced plasmas will be made. *This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  8. 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.

  9. DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA

    SciTech Connect

    Michael E. Kellman

    2005-06-17

    Spectra and internal dynamics of highly excited molecules are essential to understanding processes of fundamental importance for combustion, including intramolecular energy transfer and isomerization reactions. The goal of our program is to develop new theoretical tools to unravel information about intramolecular dynamics encoded in highly excited experimental spectra. We want to understand the formations of ''new vibrational modes'' when the ordinary normal modes picture breaks down in highly excited vibrations. We use bifurcation analysis of semiclassical versions of the effective Hamiltonians used by spectroscopists to fit complex experimental spectra. Specific molecular systems are of interest for their relevance to combustion and the availability of high-quality experimental data. Because of its immense importance in combustion, the isomerizing acetylene/vinylidene system has been the object of long-standing experimental and theoretical research. We have made significant progress in systematically understanding the bending dynamics of the acetylene system. We have begun to make progress on extending our methodology to the full bend-stretch vibrational degrees of freedom, including dynamics with multiple wells and above barrier motion, and time-dependent dynamics. For this, development of our previous methods using spectroscopic fitting Hamiltonians is needed, for example, for systems with multiple barriers.

  10. Soil emissivity and reflectance spectra measurements

    SciTech Connect

    Sobrino, Jose A.; Mattar, Cristian; Pardo, Pablo; Jimenez-Munoz, Juan C.; Hook, Simon J.; Baldridge, Alice; Ibanez, Rafael

    2009-07-01

    We present an analysis of the laboratory reflectance and emissivity spectra of 11 soil samples collected on different field campaigns carried out over a diverse suite of test sites in Europe, North Africa, and South America from 2002 to 2008. Hemispherical reflectance spectra were measured from 2.0 to 14 {mu}m with a Fourier transform infrared spectrometer, and x-ray diffraction analysis (XRD) was used to determine the mineralogical phases of the soil samples. Emissivity spectra were obtained from the hemispherical reflectance measurements using Kirchhoff's law and compared with in situ radiance measurements obtained with a CIMEL Electronique CE312-2 thermal radiometer and converted to emissivity using the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) temperature and emissivity separation algorithm. The CIMEL has five narrow bands at approximately the same positions as the ASTER. Results show a root mean square error typically below 0.015 between laboratory emissivity measurements and emissivity measurements derived from the field radiometer.

  11. 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.

  12. 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.

  13. Resonance Raman Spectra of Photodissociated Hemoglobins

    PubMed Central

    Rousseau, D. L.; Ondrias, M. R.

    1985-01-01

    Resonance Raman spectra at cryogenic temperatures of photodissociated hemoglobins and the corresponding deoxygenated preparations are compared and significant differences are found in modes with contributions from peripheral substituents of the heme as well as in the iron-histidine stretching mode. These differences in heme vibrational spectra reflect differences in the tertiary structure of the heme pocket between deoxyhemoglobin and the CO-bound form. An analysis of the effects of cooperative energy storage on the tertiary structure around the heme is made and used to interpret this resonance Raman data. The differences between the spectra of the deoxygenated preparations and the photoproducts provide evidence that a fraction of the free energy of cooperativity, ?G, is located away from the heme. These data support models for cooperativity in which the cooperative energy is distributed over many bonds or is localized in protein bonds only, such as those at the subunit interface. In addition, the local changes in amino acid positions, which must occur following the change in the state of ligand binding, may drive the changes in the structural relationships of the subunits and hence form one of the initial steps for triggering the quaternary structure transition. PMID:19431591

  14. 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.

  15. Deconvolution of spectra for intimate mixtures

    NASA Technical Reports Server (NTRS)

    Mustard, John F.; Pieters, Carle M.; Pratt, Stephen F.

    1987-01-01

    Visible to near infrared reflectance spectra of macroscopic mixtures have been shown to be linear combinations of the reflections of the pure mineral components in the mixture. However, for microscopic mixtures the mixing systematics are in general nonlinear. The systematics may be linearized by conversion of reflectance to single scattering albedo (w), where the equations which relate reflectance to w depend on the method of data collection. Several proposed mixing models may be used to estimate mineral abundances from the reflectance spectra of intimate mixtures. These models are summarized and a revised model is presented. A noniterative (linear) least squares approach was used for curve fitting and the data, measured as bi-directional reflectance with incidence and emergence angles of 30 and 0 deg were converted to w by a simplified version of Hapke's equation for bi-directional reflectance. This model was tested with two mixture series composed of 45 to 75 micron particles: an anorthite-enstatite series and an olivine-magnetite series. The data indicate that the simplified Hapke's equation may be used to convolve reflectance spectra into mineral abundances if appropriate endmembers are known or derived from other techniques. For surfaces that contain a significant component of very low albedo material, a somewhat modified version of this technique will need to be developed. Since the abundances are calculated using a noniterative approach, the application of this method is especially efficient for large spectral data sets, such as those produced by mapping spectrometers.

  16. Soft X-ray properties of Seyfert galaxies. I - Spectra

    NASA Technical Reports Server (NTRS)

    Kruper, J. S.; Canizares, C. R.; Urry, C. M.

    1990-01-01

    Results are presented from a study of soft X-ray spectra of 75 Seyfert galaxies observed by the Einstein Observatory IPC. The spectra in this sample (mostly high-luminosity Seyfert type 1s) are found to be consistent with a single power-law index alpha = 81. The AGN spectra observed with the IPC are compared with those from higher energy experiments, where AGN spectra have power law indices alpha = 0.7. It is found that the IPC spectra are systematically steeper than the HEAO 1 A-2 spectra of the same Seyfert galaxies, indicating a flattening toward higher energies.

  17. 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.

  18. 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.

  19. 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.

  20. High-energy spectra of atmospheric neutrinos

    NASA Astrophysics Data System (ADS)

    Petrova, O. N.; Sinegovskaya, T. S.; Sinegovsky, S. I.

    2012-12-01

    A calculation of the atmospheric high-energy muon neutrino spectra and zenith-angle distributions is performed for two primary spectrum parameterizations (by Gaisser and Honda and by Zatsepin and Sokolskaya) with the use of QGSJET-II-03 and SIBYLL 2.1 hadronic models. A comparison of the zenith angle-averaged muon neutrino spectrum with the data of Frejus, AMANDA-II, and IceCube40 experiments makes it clear that, even at energies above 100 TeV, the prompt neutrino contribution is not apparent because of the considerable uncertainties of the experimental data in the high-energy region.

  1. Matching the linear spectra of twinlike defects

    NASA Astrophysics Data System (ADS)

    Zhong, Yuan; Liu, Yu-Xiao

    2015-08-01

    Twinlike defects refer to topological defect solutions of some apparently different field models that share the same defect configuration and the same energy density. Usually, one can distinguish twinlike defects in terms of their linear spectra, but in some special cases twinlike defects even share the same linear spectrum. In this paper, we derive the algebraic conditions for two twinlike defects to share an identical linear spectrum from the viewpoint of the normal modes of the linear fluctuations. We also extend our discussion to braneworld models, where gravity plays an important role.

  2. Transmission spectra of sausage-like microresonators.

    PubMed

    Ye, Ming-Yong; Shen, Mei-Xia; Lin, Xiu-Min

    2015-10-01

    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. PMID:26480098

  3. 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.

  4. Glow Sticks: Spectra and Color Mixing

    NASA Astrophysics Data System (ADS)

    Birriel, Jennifer; Birriel, Ignacio

    2014-10-01

    Glow sticks are a popular Halloween staple familiar to most of our students. The production of light via a chemical reaction is called "chemiluminescence," and glow sticks are often used as demonstrations and experiments in the chemistry classroom to study reaction rates as a function of temperature.1-3 A black light can be used to illuminate glow sticks that have not been cracked or those that are "dead" in order to demonstrate fluorescence in liquid chemicals.4 In this article, we present the use of glow sticks as an inexpensive demonstration of spectra and color addition.

  5. Techniques for classifying acoustic resonant spectra

    SciTech Connect

    Roberts, R.S.; Lewis, P.S.; Chen, J.T.; Vela, O.A.

    1995-12-31

    A second-generation nondestructive evaluation (NDE) system that discriminates between different types of chemical munitions is under development. The NDE system extracts features from the acoustic spectra of known munitions, builds templates from these features, and performs classification by comparing features extracted from an unknown munition to a template library. Improvements over first-generation feature extraction template construction and classification algorithms are reported. Results are presented on the performance of the system and a large data set collected from surrogate-filled munitions.

  6. 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.

  7. 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.

  8. 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.

  9. Spectra of electron oscillations in magnetoplasmadynamic thruster

    NASA Astrophysics Data System (ADS)

    Kirdyashev, K. P.; Kubarev, Yu. V.

    2012-03-01

    The intensity and spectra of electron oscillations in magnetoplasmadynamic (MPD) thruster have been experimentally studied. Oscillatory regimes corresponding to various relations between the relative gradients of magnetic field, electron concentration, and residual gas pressure in the vacuum chamber of the experimental setup have been determined. Relationship between the regimes of excitation of electron oscillations, the formation of an azimuthal current, and a change in the plasma flow potential is revealed. Model notions about the instability of plasma flow on low- and high-frequency branches of electron oscillations are developed.

  10. Hilbert transform: Applications to atomic spectra

    NASA Astrophysics Data System (ADS)

    Whittaker, Kate A.; Keaveney, James; Hughes, Ifan G.; Adams, Charles S.

    2015-03-01

    In many areas of physics, the Kramers-Kronig relations are used to extract information about the real part of the optical response of a medium from its imaginary counterpart. In this paper we discuss an alternative but mathematically equivalent approach based on the Hilbert transform. We apply the Hilbert transform to transmission spectra to find the group and refractive indices of a Cs vapor and thereby demonstrate how the Hilbert transform allows indirect measurement of the refractive index, group index, and group delay while avoiding the use of complicated experimental setups.

  11. 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.

  12. Uncertainty Quantification on Prompt Fission Neutrons Spectra

    SciTech Connect

    Talou, P. Madland, D.G.; Kawano, T.

    2008-12-15

    Uncertainties in the evaluated prompt fission neutrons spectra present in ENDF/B-VII.0 are assessed in the framework of the Los Alamos model. The methodology used to quantify the uncertainties on an evaluated spectrum is introduced. We also briefly review the Los Alamos model and single out the parameters that have the largest influence on the calculated results. Using a Kalman filter, experimental data and uncertainties are introduced to constrain model parameters, and construct an evaluated covariance matrix for the prompt neutrons spectrum. Preliminary results are shown in the case of neutron-induced fission of {sup 235}U from thermal up to 15 MeV incident energies.

  13. Thermal Infrared Spectra of Lunar Soils

    NASA Astrophysics Data System (ADS)

    Salisbury, John W.; Basu, Abhijit; Fischer, Erich M.

    1997-11-01

    We have measured the infrared (2.08-14 μm) directional hemispherical reflectance spectra of lunar soils representing the major lithologic units so far sampled on the lunar surface, and soils of different exposure ages within those units. Such reflectance (R) spectra can be used to calculate absolute emissivity (E) using Kirchhoff's Law (E= 1 -R). The effects of exposure age vary with wavelength region. In the 2-5 μm and 8-14 μm regions, lunar soils darken with exposure age, consistent with spectral behavior in the VNIR and the dominant optical effect of increasing amounts of finely divided metallic iron in more mature soils. However, in the 5-8 μm region soils tend to show higher reflectances with greater exposure age, which suggests some unanticipated change in the optical properties of fine metallic iron at those wavelengths. The most useful spectral feature for compositional remote sensing is the Christiansen reflectance minimum (emissivity maximum), the spectral contrast of which is enhanced by the lunar environment, and the wavelength position of which can be related to composition without being much affected by exposure age. The vacuum environment at the lunar surface not only enhances the spectral contrast of the Christiansen feature, but also shifts it slightly to shorter wavelength, an effect that must be compensated for in inferring composition. By contrast with the Christiansen feature, the weak and relatively few overtone/combination tone absorption bands in the volume scattering region between 3 and 8 μm appear to be of limited usefulness. The reststrahlen bands are also very weak in absolute emissivity spectra, and are evidently not enhanced by the lunar environment in the same fashion as the Christiansen feature. Thus, they can only be used for remote sensing with measurements of extraordinarily high signal-to-noise (1000/1). However, these features, as well as the transparency feature (which is particularly prominent in spectra of feldspathic soils), do contain important mineralogical information, such as the relative abundances of plagioclase and pyroxene, and can be used for laboratory studies of lunar soils. More certain and more quantitative mineralogical analyses of lunar soils appear feasible after additional spectral analysis of soil separates, and additional mineralogical analysis of soil samples for which spectral data are available.

  14. Conductance Spectra in Graphene-Superconductor Junctions

    NASA Astrophysics Data System (ADS)

    Tian, Jie; Zhou, Shi-Ping; Deng, Zhen-Yan

    2015-01-01

    The conductance spectra of a graphene ribbon and graphene-superconductor (G-S) junctions are investigated, using the tight-binding model and non-equilibrium Green' function formalism. It is found that the quantized conductance related to graphene' edge-states is robust against perturbations in the model parameters for a graphene monolayer ribbon with the zigzag boundary. With appropriate model parameter of the spin-orbit interaction strength, a new bound state with odd-frequency symmetry is found in the G-S junction. An enhancement in the zero-energy conductance amplitude is followed.

  15. 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.

  16. 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)

  17. 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 ...

  18. Study on Mssbauer 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 Mssbauer 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.

  19. SEC Vidicon spectra of Geminid meteors, 1972

    NASA Technical Reports Server (NTRS)

    Millman, P. M.; Clifton, K. S.

    1975-01-01

    The SEC Vidicon, a low light level closed circuit television system, was used to obtain 137 spectrographic records of meteors at Mt. Hopkins, Arizona, during the Geminid meteor shower in December 1972. Seven of the best Geminid meteor spectra are studied here in detail. The near infrared, out to wavelengths near 9000 A, is recorded for the first time for Geminids. The spectra, in general, exhibit the elements previously found in photographic records of this shower but show a surprising frequency of occurrence of the forbidden green line of O I at 5577 A. This line is normally absent from meteors moving as slowly as the Geminids (36 km/sec) and its presence in these records may be due to the added sensitivity available with the SEC Vidicon. The average green line duration in Geminid meteors with a luminosity near zero absolute visual magnitude is 0.73 sec at a mean height of 95 km, 11 km lower than the green line peak in Perseid meteors of the same luminosity.

  20. 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.

  1. 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.

  2. Determination of antineutrino spectra from nuclear reactors

    SciTech Connect

    Huber, Patrick

    2011-08-15

    In this paper we study the effect of well-known higher-order corrections to the allowed {beta}-decay spectrum on the determination of antineutrino spectra resulting from the decays of fission fragments. In particular, we try to estimate the associated theory errors and find that induced currents like weak magnetism may ultimately limit our ability to improve the current accuracy and under certain circumstance could even greatly increase the theoretical errors. We also perform a critical evaluation of the errors associated with our method to extract the antineutrino spectrum using synthetic {beta} spectra. It turns out that a fit using only virtual {beta} branches with a judicious choice of the effective nuclear charge provides results with a minimal bias. We apply this method to actual data for {sup 235}U, {sup 239}Pu, and {sup 241}Pu and confirm, within errors, recent results, which indicate a net 3% upward shift in energy-averaged antineutrino fluxes. However, we also find significant shape differences which can, in principle, be tested by high-statistics antineutrino data samples.

  3. Theory of giant planet atmospheres and spectra

    NASA Astrophysics Data System (ADS)

    Burrows, Adam Seth

    2014-06-01

    Giant exoplanet atmospheres have now been studied by transit spectroscopy, spectroscopy and photometry at secondary eclipse, photometric light curves as a function of orbital phase, very high-resolution spectroscopic velocity measurements, and high-contrast imaging. Moreover, there is a correspondence between brown dwarf and giant planet atmospheres and spectra that has been profitably exploited for many years to better understand exoplanets. In this presentation, I endeavor to review the information extracted by these techniques about close-in giant exoplanet compositions and temperatures. Then, I will summarize the expected character of the spectra, light curves, and polarizations of the objects soon to be studied using high-contrast imaging by GPI, SPHERE, WFIRST-AFTA, and Subaru/HiCIAO as a function of mass, age, Keplerian elements, and birth properties (such as entropy). The goal will be to frame the theoretical discussion concerning what physical information can be gleaned in the next years about giant planet atmospheres by direct (or almost direct) imaging and characterization campaigns, and their role as stepping stones to the even more numerous sub-Neptunes, super-Earths, and Earths.

  4. Absorption Features in Soil Spectra Assessment.

    PubMed

    Vat, Radim; Kodeov, Radka; Bor?vka, Lubo; Jakk, Ond?ej; Klement, Ale; Drbek, Ond?ej

    2015-12-01

    From a wide range of techniques appropriate to relate spectra measurements with soil properties, partial least squares (PLS) regression and support vector machines (SVM) are most commonly used. This is due to their predictive power and the availability of software tools. Both represent exclusively statistically based approaches and, as such, benefit from multiple responses of soil material in the spectrum. However, physical-based approaches that focus only on a single spectral feature, such as simple linear regression using selected continuum-removed spectra values as a predictor variable, often provide accurate estimates. Furthermore, if this approach extends to multiple cases by taking into account three basic absorption feature parameters (area, width, and depth) of all occurring features as predictors and subjecting them to best subset selection, one can achieve even higher prediction accuracy compared with PLS regression. Here, we attempt to further extend this approach by adding two additional absorption feature parameters (left and right side area), as they can be important diagnostic markers, too. As a result, we achieved higher prediction accuracy compared with PLS regression and SVM for exchangeable soil pH, slightly higher or comparable for dithionite-citrate and ammonium oxalate extractable Fe and Mn forms, but slightly worse for oxidizable carbon content. Therefore, we suggest incorporating the multiple linear regression approach based on absorption feature parameters into existing working practices. PMID:26555184

  5. Biological NMR FIDs and spectra normalization

    NASA Astrophysics Data System (ADS)

    Romano, R.; Canonico, R.; Acernese, F.; Giordano, G.; Barone, F.

    2014-03-01

    There is increasing use of spectroscopic techniques, such as high-resolution NMR spectroscopy, to examine variations in cell metabolism and / or structure in response to numerous physical, chemical, and biological agents. In these types of studies, in order to obtain relative quantitative information, a comparison between signal intensities of control samples and treated or exposed ones is often conducted. The methods thus far developed for this purpose are not directly related to the overall intrinsic properties of the samples, but rather to the addition of external substances of known concentrations or to indirect measurement of internal substances. Another possibility is to estimate, by an opportune algorithm, a normalization constant which takes into consideration all cell metabolites present in the sample. Recently, a new normalization algorithm, based on Principal Component Analysis (PCA), was presented. PCA is a well-known statistical technique for analysis of large, multivariate datasets, which extracts the basic features of the data. The PRICONA (PRincipal COmponent Normalization Algorithm) algorithm use PCA in a new totally different manner: PCA is, in fact, used to normalize spectra in order to obtain quantitative information about the treatment effects. In this paper, a comparison of results obtained in the time domain, that is on NMR FIDs (Free Induction Decay) and in the frequency domain, on NMR spectra, is conducted. The comparison is useful because in NMR spectroscopy analysis in the different domain can have different advantages. The algorithm was tested by Monte Carlo simulations of NMR FIDs.

  6. Fourier transform spectra of quantum dots

    NASA Astrophysics Data System (ADS)

    Damian, V.; Ardelean, I.; Arm??elu, Anca; Apostol, D.

    2009-09-01

    Semiconductor quantum dots are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. These nanocrystals absorb light over a very broad spectral range as compared to molecular fluorophores which have very narrow excitation spectra. High-quality QDs are proper to be use in different biological and medical applications (as fluorescent labels, the cancer treatment and the drug delivery). In this article, we discuss Fourier transform visible spectroscopy of commercial quantum dots. We reveal that QDs produced by Evident Technologies when are enlightened by laser or luminescent diode light provides a spectral shift of their fluorescence spectra correlated to exciting emission wavelengths, as shown by the ARCspectroNIR Fourier Transform Spectrometer. In the final part of this paper we show an important biological application of CdSe/ZnS core-shell ODs as microbial labeling both for pure cultures of cyanobacteria (Synechocystis PCC 6803) and for mixed cultures of phototrophic and heterotrophic microorganisms.

  7. Fourier transform spectra of quantum dots

    NASA Astrophysics Data System (ADS)

    Damian, V.; Ardelean, I.; Arm??elu, Anca; Apostol, D.

    2010-05-01

    Semiconductor quantum dots are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. These nanocrystals absorb light over a very broad spectral range as compared to molecular fluorophores which have very narrow excitation spectra. High-quality QDs are proper to be use in different biological and medical applications (as fluorescent labels, the cancer treatment and the drug delivery). In this article, we discuss Fourier transform visible spectroscopy of commercial quantum dots. We reveal that QDs produced by Evident Technologies when are enlightened by laser or luminescent diode light provides a spectral shift of their fluorescence spectra correlated to exciting emission wavelengths, as shown by the ARCspectroNIR Fourier Transform Spectrometer. In the final part of this paper we show an important biological application of CdSe/ZnS core-shell ODs as microbial labeling both for pure cultures of cyanobacteria (Synechocystis PCC 6803) and for mixed cultures of phototrophic and heterotrophic microorganisms.

  8. Fully automated microcomputer calculation of vibrational spectra

    NASA Astrophysics Data System (ADS)

    Dowty, Eric

    1987-01-01

    A fully automated method for computing frequencies and atomic displacements of normal modes, giving synthetic infrared and Raman spectra, has been developed for use on small computers. No expertise in group theory or the mathematics of normal-mode calculation are required to use the computer program. The method takes full account of symmetry and is applicable to any crystal or molecule. Force constants can be specified in terms of any two-atom bonds or three-atom angles. The essential steps in the computer program are: (1) Locate all atoms in the unit cell or molecule and compute displacement vectors for each internal coordinate; (2) Convert the basis of the force constants from bonds and angles to cartesian displacements; (3) Construct the full-matrix irreducible representations of the point or factor group in question, using appropriate symmetry matrices and polynomial basis functions; (4) Derive the symmetry coordinates in terms of cartesian displacements using the projection/transfer-operator technique; (5) construct secular equations for each species with Wilson's f g method; (6) solve for frequencies and atomic motions; and (7) use simple models of infrared and Raman intensities to calculate spectra.

  9. Millimeter wave absorption spectra of biological samples.

    PubMed

    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. PMID:6169346

  10. The energy spectra of solar flare electrons

    NASA Technical Reports Server (NTRS)

    Evenson, P. A.; Hovestadt, D.; Meyer, P.; Moses, D.

    1985-01-01

    A survey of 50 electron energy spectra from .1 to 100 MeV originating from solar flares was made by the combination of data from two spectrometers onboard the International Sun Earth Explorer-3 spacecraft. The observed spectral shapes of flare events can be divided into two classes through the criteria of fit to an acceleration model. This standard two step acceleration model, which fits the spectral shape of the first class of flares, involves an impulsive step that accelerates particles up to 100 keV and a second step that further accelerates these particles up to 100 MeV by a single shock. This fit fails for the second class of flares that can be characterized as having excessively hard spectra above 1 MeV relative to the predictions of the model. Correlations with soft X-ray and meter radio observations imply that the acceleration of the high energy particles in the second class of flares is dominated by the impulsive phase of the flares.

  11. Blind Source Separation For Ion Mobility Spectra

    SciTech Connect

    Marco, S.; Pomareda, V.

    2009-05-23

    Miniaturization is a powerful trend for smart chemical instrumentation in a diversity of applications. It is know that miniaturization in IMS leads to a degradation of the system characteristics. For the present work, we are interested in signal processing solutions to mitigate limitations introduced by limited drift tube length that basically involve a loss of chemical selectivity. While blind source separation techniques (BSS) are popular in other domains, their application for smart chemical instrumentation is limited. However, in some conditions, basically linearity, BSS may fully recover the concentration time evolution and the pure spectra with few underlying hypothesis. This is extremely helpful in conditions where non-expected chemical interferents may appear, or unwanted perturbations may pollute the spectra. SIMPLISMA has been advocated by Harrington et al. in several papers. However, more modern methods of BSS for bilinear decomposition with the restriction of positiveness have appeared in the last decade. In order to explore and compare the performances of those methods a series of experiments were performed.

  12. INFRARED SPECTRA OF AMMONIA-WATER ICES

    SciTech Connect

    Zheng Weijun; Jewitt, David; Kaiser, Ralf I. E-mail: ralfk@hawaii.edu

    2009-03-15

    We conducted a systematic study of the near-IR and mid-IR spectra of ammonia-water ices at various NH{sub 3}/H{sub 2}O ratios. The differences between the spectra of amorphous and crystalline ammonia-water ices were also investigated. The 2.0 {mu}m ammonia band central wavelength is a function of the ammonia/water ratio. It shifts from 2.006 {+-} 0.003 {mu}m (4985 {+-} 5 cm{sup -1}) to 1.993 {+-} 0.003 {mu}m (5018 {+-} 5 cm{sup -1}) as the percentage of ammonia decreases from 100% to 1%. The 2.2 {mu}m ammonia band center shifts from 2.229 {+-} 0.003 {mu}m (4486 {+-} 5 cm{sup -1}) to 2.208 {+-} 0.003 {mu}m (4528 {+-} 5 cm{sup -1}) over the same range. Temperature-dependent shifts of those bands are below the uncertainty of the measurement, and therefore are not detectable. These results are important for comparison with astronomical observations as well as for estimating the concentration of ammonia in outer solar system ices.

  13. Supersymmetric mass spectra and the seesaw scale

    NASA Astrophysics Data System (ADS)

    Hirsch, M.; Reichert, L.; Porod, W.

    2011-05-01

    Supersymmetric mass spectra within two variants of the seesaw mechanism, commonly known as type-II and type-III seesaw, are calculated using full 2-loop RGEs and minimal Supergravity boundary conditions. The type-II seesaw is realized using one pair of 15 and 15 superfields, while the type-III is realized using three copies of 24 M superfields. Using published, estimated errors on SUSY mass observables attainable at the LHC and in a combined LHC+ ILC analysis, we calculate expected errors for the parameters of the models, most notably the seesaw scale. If SUSY particles are within the reach of the ILC, pure mSugra can be distinguished from mSugra plus type-II or type-III seesaw for nearly all relevant values of the seesaw scale. Even in the case when only the much less accurate LHC measurements are used, we find that indications for the seesaw can be found in favourable parts of the parameter space. Since our conclusions crucially depend on the reliability of the theoretically forecasted error bars, we discuss in some detail the accuracies which need to be achieved for the most important LHC and ILC observables before an analysis, such as the one presented here, can find any hints for type-II or type-III seesaw in SUSY spectra.

  14. 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.

  15. Atomic Spectra Bibliography Databases at NIST

    NASA Astrophysics Data System (ADS)

    Kramida, Alexander

    2008-05-01

    NIST's Atomic Spectroscopy Data Center maintains three online Bibliographic Databases (BD) containing references to papers with atomic data for controlled fusion research, modeling and diagnostics of astrophysical and terrestrial plasmas, and fundamental properties of electronic spectra of atoms and ions. The NIST Atomic Energy Levels and Spectra BD [http://physics.nist.gov/elevbib] now includes about 11500 references, mostly for years 1967--2007. The NIST Atomic Transition Probability BD, v. 8.1 [http://physics.nist.gov/fvalbib] with its 7500 references mainly covers years 1964--2007. The NIST Spectral Line Broadening BD, v. 2.0 [http://physics.nist.gov/linebrbib] has 3670 references, mostly for 1978--2006. All three databases are maintained in a unified database management system that allows us to quickly update the contents. Updates become available to users on the next day. An automated Data Entry module makes it easy to enter and categorize the data. The system allows us to keep the contents of all BDs up to date. A number of enhancements made since last year greatly increased public usability of the databases. This work is supported in part by the Office of Fusion Energy Sciences of the U.S. Department of Energy and by the National Aeronautics and Space Administration.

  16. 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

  17. Low energy particle composition. [energy spectra, particle emission - solar flares

    NASA Technical Reports Server (NTRS)

    Gloeckler, G.

    1975-01-01

    The energy spectra and composition of the steady or 'quiet-time' particle flux, whose origin is unknown was studied. Particles and photons which are associated with solar flares or active regions on the sun were also studied. Various detection techniques used to measure the composition and energy spectra of low energy particles are discussed. Graphs of elemental abundance and energy spectra are given.

  18. Spectral coordinates in spectra fitting for explicit photodynamic therapy dosimetry

    NASA Astrophysics Data System (ADS)

    Kustov, E. F.; Loschenov, M. V.; Lilge, L.

    2005-08-01

    In this work a new method for spectra fitting is presented. The method was named spectral coordinates fitting ( SCF) because the central equation system is based on spectral coordinates. The method was validated on model spectra and spectra acquired during light intensity measurements during in-vivo Photodynamic Therapy (PDT) of dogs prostates.

  19. 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 found for A-type stars, while the log(g) derivation is more accurate (errors of 0.07 and 0.12 dex at GRVS = 12.6 and 13.4, respectively). For the faintest stars, with GRVS≳ 13-14, a Teff input from the spectrophotometric-derived parameters will allow the final GSP-Spec parametrization to be improved. Conclusions: The reported results, while neglecting possible mismatches between synthetic and real spectra, show that the contribution of the RVS-based stellar parameters will be unique in the brighter part of the Gaia survey, which allows for crucial age estimations and accurate chemical abundances. This will constitute a unique and precious sample, providing many pieces of the Milky Way history puzzle with unprecedented precision and statistical relevance.

  20. Estimation of vertical sea level muon energy spectra from the latest primary cosmic ray elemental spectra

    NASA Astrophysics Data System (ADS)

    Mitra, M.; Molla, N. H.; Bhattacharyya, D. P.

    The directly measured elemental spectra of primary cosmic rays obtained from Webber et al., Seo et al., Menn et al., Ryan et al. and experiments like JACEE, CRN, SOKOL, RICH on P, He, CNO, Ne-S and Fe have been considered to estimate the vertical sea level muon energy spectra. The primary elemental energy spectra of P, He, CNO, Ne-S and Fe available from the different experimental data duly fitted by power law are given by Np(E)dE = 1.2216E-2.68 dE [cm2 .s.sr.GeV/n]-1 NHe(E)dE = 0.0424E-2.59 dE [cm2 .s.sr.GeV/n]-1 NCNO(E)dE = 0.0026E-2.57 dE[cm2 .s.sr.GeV/n]-1 NNe-S(E)dE = 0.00066E-2.57 dE [cm2 .s.sr.GeV/n]-1 NF e(E)dE = 0.0056E-2.55 dE [cm2 .s.sr.GeV/n]-1 Using the conventional superposition model the all nucleon primary cosmic ray spectrum has been derived which is of the form N(E)dE = 1.42E-2.66 dE [cm2 .s.sr.GeV/n]-1 We have considered all these spectra separately as parents of the secondary mesons and finallty the sea level muon fluxes at 00 from each species have been derived. To evaluate the meson spectra which are the initial air shower interaction products initiated by the primary nucleon air collisions, the hadronic energy moments have been calculated from the CERN LEBCEHS data for pp collisions and FNAL data for ?p collisions. Pion production by secondary pions have been taken into account and the final total muon spectrum has been derived from pp rightarrow? x, pp ? K x, ?p ? ? x channels. The Z-factors have been corrected for p-air collisions. We have adopted the constant values of ?p-air and ??-air crosssections which are 273 mb and 213 mb, respectively. The adopted inelastic cross-sections for pp and ?p interactions are 35 mb and 22 mb, respectively. The Q-G plasma correction of Z-factors have also been incorporated in the final form. The solution to the standard differential equation for mesons is considered for muon flux estimation from Ngenerations of the parent mesons. By this formulation vertical muon spectra from each element along with the total primary nucleon spectrum have been derived. We wanted to observe the different shape of the muon spectra evaluated from different elemental spectra and to make a comparative study of that. In this energy range (102 - 104 ) GeV we have observed that the majority of the total muon flux is coming from the proton spectra. The contribution from the other elemental spectra to the total muon flux is not at all comparable with that of proton spectra.

  1. 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 Reconnaissance Orbiter for the NASA Science Mission Directorate, Washington. Lockheed Martin Space Systems, Denver, is the prime contractor for the project and built the spacecraft. The Johns Hopkins University Applied Physics Laboratory led the effort to build the CRISM instrument and operates CRISM in coordination with an international team of researchers from universities, government and the private sector.

  2. Characterizing Pyroxene Cooling Rate Using Reflectance Spectra

    NASA Astrophysics Data System (ADS)

    Shank, E.; Klima, R. L.; Dyar, M. D.

    2011-12-01

    Pyroxenes are among the most common minerals in the inner solar system, and their reflectance spectra are highly diagnostic of their crystal structure and composition. Previous work has revealed that the ordering of Fe2+ and Mg between the M1 and M2 cation sites affects the relative strengths of absorption bands in the near-infrared. We have performed a series of heating experiments to help constrain the relationship between cation ordering and reflectance spectra for orthopyroxenes. For the experiments, crushed up samples of two pyroxenes (a bronzite and an orthopyroxene) were heated in an alumina capsule sealed inside an evacuated high-purity silica tube. The crushed samples consisted of grains greater than 250 ?m and were hand-picked for purity. 100 mg of the clean sample was put in the alumina capsule to go into the silica tube; beneath the capsule we placed a small piece of iron foil to buffer oxygen fugacity. We also put a small piece of the iron foil outside the seal to show the difference between the atmospheres inside and outside the tube. Subsets of each pyroxene were heated to four different temperatures: 500C, 600C, 700C and 800C and held at those temperatures for between one day to a month to ensure Mg-Fe2+ equilibration. Samples were then measured using near-infrared reflectance spectroscopy and Mossbauer spectroscopy to determine the cation ordering. Various spectra will be taken of the heated samples and compared to unheated samples to get a sense of the order/disorder. In pyroxenes, the degree of order/disorder relates to the cooling history of the mineral. Fe2+ prefers the M2 site, and Mg prefers the M1 site in the crystallographic structure, and the slower it cools, the more ordered it will be. Since Fe2+ is responsible for crystal field absorption bands, the placement of the Fe2+ in the crystal structure affects the strength and possibly the positions of the absorption bands. Many of the pyroxenes on Earth have experienced slower cooling or metamorphism, resulting in a more ordered sample. More rapid cooling, as extraterrestrial materials often experience, results in more disorder, or a random placement of Fe2+ and Mg throughout the M1 and M2 sites.

  3. Automatic one dimensional spectra extraction for Weihai fiber-fed high resolution echelle spectra

    NASA Astrophysics Data System (ADS)

    Hu, Shao Ming; Gao, Dong Yang

    2014-11-01

    One fiber-fed high resolution echelle spectrograph was built for the one meter telescope atWeihai Observatory of Shandong University. It is used for exoplanet searching by radial velocity method and for stellar spectra analysis. One dimensional spectra extraction from the raw echelle data is researched in this paper. Flat field images with different exposure times were used to trace the order position accurately. The accurate background was fitted from each CCD image and it was subtracted from the raw image to correct the background and straylight. The intensity of each order decreases towards the order margin, and the lengths of order are different between the blue and red regions. The order tracing during the data reduction was investigated in this work. Accurate flux can be obtained after considering the effects of bad pixels, the curvature of each order and so on. One Interactive Data Language program for one dimensional spectra extraction was adopted and implemented to echelle data reduction for Weihai fiber-fed high resolution echelle spectra, and the results are illustrated here. The program is efficient and accurate for echelle data reduction. It can be adopted to reduce data taken by other instruments even the spectrographs in other fields, and it is very convenient for astronomers.

  4. 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...

  5. Dynamic energy/power spectra from X-ray spectra and light curves

    NASA Astrophysics Data System (ADS)

    Ness, Jan-Uwe

    2015-09-01

    The key data product of an X-ray observation is an events table with information of calibrated position, energy, and arrival time for each individual X-ray photon. Many X-ray sources are variable and clues for origins for variations can be found in spectral changes along with light curve variations. This is commonly done by extracting spectra from certain episodes of variability such as low-states/high-states. I present a systematic approach of a dynamic X-ray spectrum, a 3-dimensional representation of wavelength/energy, time, and intensity. It is constructed from a series of spectra extracted from adjacent short time intervals, displayed as wavelength (or energy) versus time and a colour code for intensity. The same concept can be used for dynamic power spectra, displaying the evolution of periodic oscillations in an X-ray light curve. Dynamic energy/power spectra constructed from XMM-Newton and Chandra data have revealed some surprises such as short-lived emission lines during a flare, softening owed to changes in the absorption column of OI, or transient short-period oscillations in various supersoft sources. Some examples are shown to illustrate the diagnostic power of these diagrams.

  6. Improving the estimation of reactor antineutrino spectra

    NASA Astrophysics Data System (ADS)

    Kos, Marek; Asner, David; Burns, Kimberly; Greenfield, Bryce; Schram, Malachi; Orrell, John; Wood, Lynn; Vandevender, Brent; Wootan, David

    2014-03-01

    The flux of antineutrinos emanating from reactors has been used for a range of experiments studying neutrino properties. Results from these experiments are in tension with models that have mixing only among the three active neutrino flavors of the Standard Model. Knowledge of reactor antineutrino flux is based on inversion of total reactor beta spectra measured at the Institut Laue Langevin in the 1980s. Recent reanalysis of that data has resulted in a signficant 3% upward shift in the antineutrino flux with implications for the possible existence of sterile neutrinos. We explore the possibility that the present situation could be improved with a new measurement of the underlying reactor beta spectrum. Possibilities are considered to improve knowledge of the beta source by using actinide foils activated in a neutron beam tailored to the energy spectrum found in a reactor core, and magnetic beta spectroscopy with tracking to suppress backgrounds and control systematics.

  7. Spectra as windows into exoplanet atmospheres.

    PubMed

    Burrows, Adam S

    2014-09-01

    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

  8. A Study of Pioneer Venus Nightglow Spectra

    NASA Technical Reports Server (NTRS)

    Slanger, Tom G.

    1993-01-01

    The work performed during the 12-month period of this contract involved: (1) further analysis of latitudinal variations in the Venusian NO nightglow intensity from PVOUVS data; (2) corrections made to the input data for the VTGCM model, relating specifically to a factor of three increase in the three-body recombination rate coefficient of N + O; (3) consideration of limits on the rate of reaction of N-atoms with CO2; (4) consideration of the Venusian equivalent of the terrestrial hot N-atom reaction for NO production; and (5) successful location of video images of meteor trails from space, for the purpose of making a comparison with the meteor trail that we have hypothesized as an explanation of intense UV spectra observed on a particular Pioneer Venus (PV) orbit.

  9. 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.

  10. Oxidation of carbynes: Signatures in infrared spectra

    SciTech Connect

    Cinquanta, E. E-mail: p.rudolf@rug.nl; Manini, N.; Caramella, L.; Onida, G.; Ravagnan, L.; Milani, P.; Rudolf, P. E-mail: p.rudolf@rug.nl

    2014-06-28

    We report and solidly interpret the infrared spectrum of both pristine and oxidized carbynes embedded in a pure-carbon matrix. The spectra probe separately the effects of oxidation on sp- and on sp{sup 2}-hybridized carbon, and provide information on the stability of the different structures in an oxidizing atmosphere. The final products are mostly short end-oxidized carbynes anchored with a double bond to sp{sup 2} fragments, plus an oxidized sp{sup 2} amorphous matrix. Our results have important implications for the realization of carbyne-based nano-electronics devices and highlight the active participation of carbynes in astrochemical reactions where they act as carbon source for the promotion of more complex organic species.

  11. Multinuclear NMR spectra of microscopic gaseous samples

    NASA Astrophysics Data System (ADS)

    Jackowski, Karol

    2004-01-01

    Nuclear magnetic resonance (NMR) of some nuclei (e.g. 1H, 13C, 19F, 29Si and 31P) gives strong signals which allow one for analytical investigations of gaseous compounds. The other magnetic nuclei have low natural abundance or/and contain electric quadrupole moments and therefore they are less suitable for such NMR applications. In our laboratory we have developed new experimental techniques which permit us to monitor several micrograms of chemical compounds in the gas phase. For the first time we have observed 17O and 33S NMR spectra of gaseous compounds at the natural abundance as a function of density. We have also found density-dependent spin-spin coupling constants in many molecules. We could extend our gas-phase studies on molecules which exhibit strong intermolecular interactions and are liquids at room temperature. All the latter NMR experimental results obtained for gaseous mixtures are reviewed in this paper.

  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. The complex X ray spectra of AGN

    NASA Technical Reports Server (NTRS)

    Urry, C. M.; Arnaud, Keith; Edelson, R. A.; Kruper, J. S.; Mushotzky, R. F.

    1989-01-01

    X-ray spectral surveys of large samples of Seyfert galaxies are discussed. The spectral shape in the 0.1 to 20 keV energy range is considered. Two new spectral survey are undertaken, one involving 105 Imaging Proportional Counter (IPC) observations of 75 Seyfert galaxies, the other using IPC and Monitor Proportional Counter (MPC) data from 28 observations of 23 Seyfert galaxies. The X-ray spectra of active galactic nuclei (AGN) are complex, with in most cases considerable steepening at the lowest energies. At higher energies (2 to 20 keV), the existence of a universal, canonical power law is confirmed, independent of X-ray luminosity over four orders of magnitude.

  14. 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.

  15. Tunneling spectra simulation of interacting Majorana wires

    NASA Astrophysics Data System (ADS)

    Thomale, Ronny; Rachel, Stephan; Schmitteckert, Peter

    2013-10-01

    Recent tunneling experiments on InSb hybrid superconductor-semiconductor devices have provided hope for a stabilization of Majorana edge modes in a spin-orbit quantum wire subject to a magnetic field and superconducting proximity effect. Connecting the experimental scenario with a microscopic description poses challenges of a different kind, such as accounting for the effect of interactions on the tunneling properties of the wire. We develop a density matrix renormalization group (DMRG) analysis of the tunneling spectra of interacting Majorana chains, which we explicate for the Kitaev chain model. Our DMRG approach allows us to calculate the spectral function down to zero frequency, where we analyze how the Majorana zero-bias peak is affected by interactions. For topological phase transitions between the topological and trivial superconducting phase in the Majorana wire, the bulk gap closure generically affects the proximity peaks and the Majorana peak.

  16. 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 {? }500=1. This places the phenomenons origin in the low-mid chromosphere or above. I suggest that bomb spectra are more compatible with Alfvnic turbulence than with bi-directional reconnection jets.

  17. Spectra of cool stars in galaxies

    NASA Astrophysics Data System (ADS)

    Bergemann, Maria

    2015-08-01

    The best way to understand structure and evolution of galaxies is to study their stars. Cool stars are bright, span a wide range of ages and metallicities, their individual or combined spectra contain information about tens of chemical elements and thus shed light on galaxy's chemical enrichment history. I will discuss what fundamental observational data can be obtained by state-of-the-art spectroscopic analysis of cool stars, from main-sequence to massive red supergiants, and from stellar populations, such as ultra-bright RSG star clusters. I will summarise what improvements in models and observed techniques are needed to make yet another revolutinary leap in our understanding of stellar content of galaxies.

  18. Boson sampling for molecular vibronic spectra

    NASA Astrophysics Data System (ADS)

    Huh, Joonsuk; Guerreschi, Gian Giacomo; Peropadre, Borja; McClean, Jarrod R.; Aspuru-Guzik, Aln

    2015-09-01

    Controllable quantum devices open novel directions to both quantum computation and quantum simulation. Recently, a problem known as boson sampling has been shown to provide a pathway for solving a computationally intractable problem without the need for a full quantum computer, instead using a linear optics quantum set-up. In this work, we propose a modification of boson sampling for the purpose of quantum simulation. In particular, we show that, by means of squeezed states of light coupled to a boson sampling optical network, one can generate molecular vibronic spectra, a problem for which no efficient classical algorithm is currently known. We provide a general framework for carrying out these simulations via unitary quantum optical transformations and supply specific molecular examples for future experimental realization.

  19. 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.

  20. Spectra of Aurorae in Exoplanet Atmospheres

    NASA Astrophysics Data System (ADS)

    Rimmer, Paul Brandon; Helling, Christiane; Morley, Caroline; Littlefair, Stuart; Hallinan, Gregg

    2015-12-01

    Aurorae have been observed on an object at the end of the stellar main sequence, many times brighter than any produced on Earth or the solar system planets (Hallinan et al 2015). This provokes the question of whether exoplanets have aurorae, and whether their aurorae can be detected. In order to address this question, we apply an ion-neutral chemical kinetics and transport model to a model atmospheric temperature profile for a hypothetical directly imaged giant gas planet. We consider beams of 500 eV and 10 keV auroral electrons and their effect on the upper atmospheric chemistry. The chemical profiles that result from these calculations are applied to a radiative transfer model in order to predict the effect aurorae have on the optical and infrared spectra of giant gas planets. We will also comment on whether hydrogen anions would have a sufficient column to explain the Planck curve optical spectrum observed by Hallinan et al (2015).

  1. 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.

  2. Power spectra for deterministic chaotic dynamical systems

    NASA Astrophysics Data System (ADS)

    Melbourne, Ian; Gottwald, Georg A.

    2008-01-01

    We present results on the broadband nature of power spectra for large classes of discrete chaotic dynamical systems, including uniformly hyperbolic (Axiom A) diffeomorphisms and certain nonuniformly hyperbolic diffeomorphisms (such as the Hnon map). Our results also apply to noninvertible maps, including Collet-Eckmann maps. For such maps (even the nonmixing ones) and Hlder continuous observables, we prove that the power spectrum is analytic except for finitely many removable singularities, and that for typical observables the spectrum is nowhere zero. Indeed, we show that the power spectrum is bounded away from zero except for infinitely degenerate observables. For slowly mixing systems such as Pomeau-Manneville intermittency maps, where the power spectrum is at most finitely differentiable, nonvanishing of the spectrum remains valid provided the decay of correlations is summable.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Arc structure in Saturn's radio dynamic spectra

    NASA Technical Reports Server (NTRS)

    Boischot, A.; Leblanc, Y.; Lecacheux, A.; Pedersen, B. M.; Kaiser, M. L.

    1981-01-01

    It is pointed out that one of the most spectacular findings of the Voyager 1 planetary radio astronomy experiment (PRA) was the discovery of nested arc-like structures in the dynamic spectra of Jupiter's decametric emission. These arcs have curvature in either a direction towards increasing or decreasing time. Similar arc structures are also evident in Saturn kilometric radiation. These structures appear superimposed on the strong intensity modulation which is controlled by the rotation of the planet and on fast and narrow band fluctuations which give a very large variability to the PRA observations on a 6-s, 20-kHz scale. The characteristics of the arcs are examined and compared with the arc structure in Jupiter. The similarities between Saturn's and Jupiter's arc structures are found to imply that they are probably due to the same physical mechanism.

  8. 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.

  9. 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.

  10. 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.

  11. CO2 profile retrievals from TCCON spectra

    NASA Astrophysics Data System (ADS)

    Dohe, Susanne; Hase, Frank; Seplveda, Eliezer; Garca, Omaira; Wunch, Debra; Wennberg, Paul; Gmez-Pelez, 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 Izaa (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.

  12. 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.

  13. 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.

  14. Universality of vibrational spectra of globular proteins.

    PubMed

    Na, Hyuntae; Song, Guang; Ben-Avraham, Daniel

    2016-01-01

    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. PMID:26907186

  15. 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.

  16. Cooling Flow Spectra in Ginga Galaxy Clusters

    NASA Technical Reports Server (NTRS)

    White, Raymond E., III

    1997-01-01

    The primary focus of this research project has been a joint analysis of Ginga LAC and Einstein SSS X-ray spectra of the hot gas in galaxy clusters with cooling flows is reported. We studied four clusters (A496, A1795, A2142 & A2199) and found their central temperatures to be cooler than in the exterior, which is expected from their having cooling flows. More interestingly, we found central metal abundance enhancements in two of the clusters, A496 and A2142. We have been assessing whether the abundance gradients (or lack thereof) in intracluster gas is correlated with galaxy morphological gradients in the host clusters. In rich, dense galaxy clusters, elliptical and SO galaxies are generally found in the cluster cores, while spiral galaxies are found in the outskirts. If the metals observed in clusters came from proto-ellipticals and proto-S0s blowing winds, then the metal distribution in intracluster gas may still reflect the distribution of their former host galaxies. In a research project which was inspired by the success of the Ginga LAC/Einstein SSS work, we analyzed X-ray spectra from the HEAO-A2 MED and the Einstein SSS to look for temperature gradients in cluster gas. The HEAO-A2 MED was also a non-imaging detector with a large field of view compared to the SSS, so we used the differing fields of view of the two instruments to extract spatial information. We found some evidence of cool gas in the outskirts of clusters, which may indicate that the nominally isothermal mass density distributions in these clusters are steepening in the outer parts of these clusters.

  17. 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 to derive more accurate HF electron flux spectra.

  18. 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.

  19. 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.

  20. The perspectives of clinical staff and bereaved informal care-givers on the use of continuous sedation until death for cancer patients: The study protocol of the UNBIASED study

    PubMed Central

    2011-01-01

    Background A significant minority of dying people experience refractory symptoms or extreme distress unresponsive to conventional therapies. In such circumstances, sedation may be used to decrease or remove consciousness until death occurs. This practice is described in a variety of ways, including: 'palliative sedation', 'terminal sedation', 'continuous deep sedation until death', 'proportionate sedation' or 'palliative sedation to unconsciousness'. Surveys show large unexplained variation in incidence of sedation at the end of life across countries and care settings and there are ethical concerns about the use, intentions, risks and significance of the practice in palliative care. There are also questions about how to explain international variation in the use of the practice. This protocol relates to the UNBIASED study (UK Netherlands Belgium International Sedation Study), which comprises three linked studies with separate funding sources in the UK, Belgium and the Netherlands. The aims of the study are to explore decision-making surrounding the application of continuous sedation until death in contemporary clinical practice, and to understand the experiences of clinical staff and decedents' informal care-givers of the use of continuous sedation until death and their perceptions of its contribution to the dying process. The UNBIASED study is part of the European Association for Palliative Care Research Network. Methods/Design To realize the study aims, a two-phase study has been designed. The study settings include: the domestic home, hospital and expert palliative care sites. Phase 1 consists of: a) focus groups with health care staff and bereaved informal care-givers; and b) a preliminary case notes review to study the range of sedation therapy provided at the end of life to cancer patients who died within a 12 week period. Phase 2 employs qualitative methods to develop 30 patient-centred case studies in each country. These involve interviews with staff and informal care-givers closely involved in the care of cancer patients who received continuous sedation until death. Discussion To our knowledge, this is one of the few studies which seek to take a qualitative perspective on clinical decision making surrounding the use of continuous sedation until death and the only one which includes the perspectives of nurses, physicians, as well as bereaved informal care-givers. It has several potential strengths, weaknesses, opportunities and threats associated with the specific design of the study, as well as with the sensitive nature of the topic and the different frameworks for ethical review in the participating countries. PMID:21375747

  1. 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 compared with rock-powder spectra. This laboratory activity is in support of the SIMBIO-SYS/VIHI imaging spectrometer aboard the future ESA mission to Mercury and is financially supported by an ASI grant.

  2. 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.

  3. A Comparison of SIR-B Directional Ocean Wave Spectra with Aircraft Scanning Radar Spectra.

    PubMed

    Beal, R C; Monaldo, F M; Tilley, D G; Irvine, D E; Walsh, E J; Jackson, F C; Hancock, D W; Hines, D E; Swift, R N; Gonzalez, F L; Lyzenga, D R; Zambresky, L F

    1986-06-20

    Directional ocean wave spectra derived from Shuttle Imaging Radar-B (SIR-B) L-band imagery collected off the coast of southern Chile on 11 and 12 October 1984 were compared with independent spectral estimates from two airborne scanning radars. In sea states with significant wave heights ranging from 3 to 5 meters, the SIR-B-derived spectra at 18 degrees and 25 degrees off nadir yielded reasonable estimates of wavelengths, directions, and spectral shapes for all wave systems encountered, including a purely azimuth-traveling system. A SIR-B image intensity variance spectrum containing predominantly range-traveling waves closely resembles an independent aircraft estimate of the slope variance spectrum. The prediction of a U.S. Navy global spectral ocean wave model on 11 October 1984 exhibited no significant bias in dominant wave number but contained a directional bias of about 30 degrees espect to the mean of the aircraft and spacecraft estimates. PMID:17773503

  4. Spectra of volcanic rocks glasses as analogues of Mercury surface spectra

    NASA Astrophysics Data System (ADS)

    Carli, Cristian; Capaccioni, Fabrizio; de Sanctis, Maria Cristina; Filacchione, Gianrico; Sgavetti, Maria; Visonà, Dario; Nestola, Fabrizio; Ammannito, Eleonora

    2010-05-01

    Remote-sensing studies have revealed that most of the inner planets surfaces are covered by magmatic effusive rocks, that are the natural products of magma-rock dynamic systems controlled by T, P, oxygen fugacity and time, as lava flows or pyroclastic deposits. These materials generally contain a fair amount of volcanic glass, due to the magma rapid cooling once effused on the surface. Volcanic glass can dominate or not the rock texture. The VNIR reflectance spectroscopy is one of the most important methods 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. As a consequence, an important goal for studying the planetary crusts is to understand the spectral behavior of volcanic material produced by different volcanic systems, where chemical or physical parameters are different. We present here preliminary laboratory activity to investigate in the VNIR reflectance spectra the different behaviors of volcanic glasses. Reflectance spectra, in the range of wavelength between 350-2500 nm, were measured on powders of magmatic rocks, with different composition and textures, at fine (<0.06 mm) and very fine (<0.01 mm) grain sizes. For each rock sample a corresponding glass-sample was produced by melting at 1300°C and P=1atm, than quenching it in water. Reflectance spectra of powders of glass-samples were acquired at the same grain size, and compared with rock-powder spectra.

  5. Necessary conditions for a maximum likelihood estimate to become asymptotically unbiased and attain the Cramer-Rao lower bound. II. Range and depth localization of a sound source in an ocean waveguide

    NASA Astrophysics Data System (ADS)

    Thode, Aaron; Zanolin, Michele; Naftali, Eran; Ingram, Ian; Ratilal, Purnima; Makris, Nicholas C.

    2002-11-01

    Analytic expressions for the first order bias and second order covariance of a maximum-likelihood estimate (MLE) are applied to the problem of localizing an acoustic source in range and depth in a shallow water waveguide with a vertical hydrophone array. These expressions are then used to determine necessary conditions on sample size, or equivalently signal-to-noise ratio (SNR), for the localization MLE to become asymptotically unbiased and attain minimum variance as expressed by the Cramer-Rao lower bound (CRLB). These analytic expressions can be applied in a similar fashion to any ocean-acoustic inverse problem involving random data. Both deterministic and completely randomized signals embedded in independent and additive waveguide noise are investigated. As the energy ratio of received signal to additive noise (SANR) descends to the lower operational range of a typical passive localization system, source range and depth estimates exhibit significant biases and have variances that can exceed the CRLB by orders of magnitude. The spatial structure of the bias suggests that acoustic range and depth estimates tend to converge around particular range and depth cells for moderate SANR values. copyright 2002 Acoustical Society of America.

  6. Model Atmospheres and X-Ray Spectra of Bursting Neutron Stars: Hydrogen-Helium Comptonized Spectra

    NASA Astrophysics Data System (ADS)

    Madej, J.; Joss, P. C.; R?a?ska, A.

    2004-02-01

    Compton scattering plays a crucial role in determining the structure of the atmosphere of an X-ray burster and its theoretical spectrum. Our paper presents a description of the plane-parallel model atmosphere of a very hot neutron star and its theoretical flux spectrum of outgoing radiation. Our model equations take into account all bound-free and free-free monochromatic opacities relevant to hydrogen-helium chemical composition and take into account the effects of Compton scattering of radiation in thermal plasma with fully relativistic thermal velocities. We use Compton scattering terms in the equation of transfer, which precisely describe photon-electron energy and momentum exchange for photons with initial energies exceeding the electron rest mass of 511 keV. Model atmosphere equations are solved with the variable Eddington factors technique. The grid of H-He model atmospheres and flux spectra is computed on a dense mesh of 107K<=Teff<=3107K and a surface gravity of logg. In many cases, the assumed logg approached the critical gravity loggcr, i.e., the Eddington limit. We confirm that H-He spectra of X-ray bursters deviate from blackbody spectra and discuss their shapes. The table of color to effective temperature ratios shows that theoretical values of Tc/Teff do not exceed 1.9 in H-He atmospheres in hydrostatic and radiative equilibrium.

  7. 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.

  8. 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.

  9. Infrared reflectance spectra (4-12 micron) of lunar samples

    NASA Technical Reports Server (NTRS)

    Nash, Douglas B.

    1991-01-01

    Presented here are infrared reflectance spectra of a typical set of Apollo samples to illustrate spectral character in the mid-infrared (4 to 12 microns) of lunar materials and how the spectra varies among three main forms: soil, breccia, and igneous rocks. Reflectance data, to a close approximation, are the inverse of emission spectra; thus, for a given material the spectral reflectance (R) at any given wavelength is related to emission (E) by 1 - R equals E. Therefore, one can use reflectance spectra of lunar samples to predict how emission spectra of material on the lunar surface will appear to spectrometers on orbiting spacecraft or earthbound telescopes. Spectra were measured in the lab in dry air using a Fourier Transform Infrared spectrometer. Shown here is only the key portion (4 to 12 microns) of each spectrum relating to the principal spectral emission region for sunlit lunar materials and to where the most diagnostic spectral features occur.

  10. Electrical Analogues of Optical & EELS Spectra: Silicon

    NASA Astrophysics Data System (ADS)

    Smith, David Y.; Karstens, William

    2014-03-01

    We have explored an analogy between optical and electrical-circuit resonances that yields insight into single-particle and collective excitations. The analogy rests on the similarity of the differential equations for the Drude-Lorentz model of optics and the impedance of ac circuits. A parallel combination of capacitive (C) and inductive-capacitive (L-C) branches is a suitable circuit model. The L-C branches correspond to single-particle excitations. The C branch accounts for the electric-field term in the displacement, or equivalently the free-space susceptibility. Collective excitations represent combination resonances of the L-C and C branches. These excitations involve only internal mesh currents that can flow in the absence of an external (input) current. In this case, the admittance of the circuit is zero corresponding to the vanishing of the dielectric function at the plasmon resonance in optics (absent resistive losses). Circuit impedance corresponds to charged-particle energy loss. In contrast, circuit admittance (inverse impedance) corresponds to optical measurements. The interference of mesh currents in the circuit model plays the role of Coulomb screening in energy-loss spectra. Supported in part by the US Department of Energy, Office of Nuclear Physics under contract DE-AC02-06CH11357.

  11. Radio spectra of High Frequency Peakers

    NASA Astrophysics Data System (ADS)

    Dallacasa, D.; Orienti, M.

    2016-01-01

    New radio spectra of High Frequency Peakers (HFP) obtained from the Jansky Very Large Array (JVLA) show that variability is common among this class of sources. A subsample of sources have been observed with a nearly continuous spectral sampling between 1 and 10 GHz. The observed HFP sources were previously classified as F (flat), H (HFP profile with little or no flux density variability) and V (variable, but preserving a peaked spectrum). In general, sources classified as V and H show a decrease of the flux density measured in the optically thin part of the spectrum, while there is a moderate increment in the optically thick region, resulting into a progressive shift of the spectral peak to lower frequencies. This is consistent with the idea of an expanding bubble of radio plasma. The sources with an F classification instead show substantial variability, both in spectral shape and in time evolution. In these HFP sources an irregular production of energy is best observed since the radio emission is dominated by recently generated relativistic plasma, and the contribution of mini lobes, in which old plasma accumulates, is marginal if not absent at all, given the short radiative life of electrons in strong magnetic fields (tens of mG) found in these objects.

  12. A digital boxcar integrator for IMS spectra

    NASA Technical Reports Server (NTRS)

    Cohen, Martin J.; Stimac, Robert M.; Wernlund, Roger F.; Parker, Donald C.

    1995-01-01

    When trying to detect or quantify a signal at or near the limit of detectability, it is invariably embeded in the noise. This statement is true for nearly all detectors of any physical phenomena and the limit of detectability, hopefully, occurs at very low signal-to-noise levels. This is particularly true of IMS (Ion Mobility Spectrometers) spectra due to the low vapor pressure of several chemical compounds of great interest and the small currents associated with the ionic detection process. Gated Integrators and Boxcar Integrators or Averagers are designed to recover fast, repetitive analog signals. In a typical application, a time 'Gate' or 'Window' is generated, characterized by a set delay from a trigger or gate pulse and a certain width. A Gated Integrator amplifies and integrates the signal that is present during the time the gate is open, ignoring noise and interference that may be present at other times. Boxcar Integration refers to the practice of averaging the output of the Gated Integrator over many sweeps of the detector. Since any signal present during the gate will add linearly, while noise will add in a 'random walk' fashion as the square root of the number of sweeps, averaging N sweeps will improve the 'Signal-to-Noise Ratio' by a factor of the square root of N.

  13. Raman spectra of pigmented skin conditions

    NASA Astrophysics Data System (ADS)

    Bitar, Renata; Moreno, Marcelo; Oliveira, Andra; Cartaxo, Sidney; Martinho, Herculano; Esprito Santo, Ana Maria do; Santos, Ivan Dunshee; Ferreira, Lydia Massako; Martin, Airton

    2007-02-01

    Melanoma is the most aggressive skin cancer and is invariably fatal if left untreated. Melanoma removal at early stages is almost always curative and therefore early detection is essential. Removal of every pigmented lesion is unacceptable for the patient, especially in the case of multiple skin lesions or lesions localized in cosmetically important parts of the body such as the face because of risk of scarring. The development of a technique to detect these changes in a noninvasive way is therefore crucial for melanoma detection. In this study, we have used FT-Raman Spectroscopy to investigate through PCA analysis the alterations in the molecular structure of 90 skin spectra, being 30 Pigmented Nevi, 30 Primary Melanoma, and 30 Metastasis, for 6 patients. For projection of data, the scores (Principal Components) PC1 to PC3 were calculated. PC1 versus PC3 for the 800 to 1800 cm -1 spectral region. PC1 versus PC2 for the 1200 to 1400 cm -1 spectral region. In both analysis, we could differentiate the three different types of tissues.

  14. Passive ranging using atmospheric oxygen absorption spectra

    NASA Astrophysics Data System (ADS)

    Hawks, Michael R.

    The depth of absorption bands in observed spectra of distant, bright sources can be used to estimate range to the source. A novel approach is presented and demonstrated using observations of the oxygen absorption band near 762 nm. Range is estimated by comparing observed values of band-average absorption against curves derived from either historical data or model predictions. Curves are based on fitting a random band model to the data, which reduces average range error by 67% compared to the Beer's Law model used in previous work. A new modification to existing band models for long, inhomogeneous paths is presented and shown to reduces error 50% in short-range experiments. A static rocket motor test was observed using a Fourier transform spectrometer at a range of 2.8 km. The range estimated from this data was accurate to within 0.5% (14 m). Similar accuracy was also achieved at shorter ranges using a lamp as a surrogate target. Long-range performance is predicted by using FASCODE and theoretical models to extrapolate observed short-range performance. Range error of 5% or less is predicted at ranges up to 400 km for a representative target.

  15. 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

  16. Cosmological information from lensed CMB power spectra

    SciTech Connect

    Smith, Kendrick M.; Hu, Wayne; Kaplinghat, Manoj

    2006-12-15

    Gravitational lensing distorts the cosmic microwave background (CMB) temperature and polarization fields and encodes valuable information on distances and growth rates at intermediate redshifts into the lensed power spectra. The non-Gaussian band-power covariance induced by the lenses is negligible to l=2000 for all but the B polarization field where it increases the net variance by up to a factor of 10 and favors an observing strategy with 3 times more area than if it were Gaussian. To quantify the cosmological information, we introduce two lensing observables, characterizing nearly all of the information, which simplify the study of non-Gaussian impact, parameter degeneracies, dark energy models, and complementarity with other cosmological probes. Information on the intermediate-redshift parameters rapidly becomes limited by constraints on the cold dark matter density and initial amplitude of fluctuations as observations improve. Extraction of this information requires deep polarization measurements on only 5%-10% of the sky, and can improve Planck lensing constraints by a factor of {approx}2-3 on any one of the parameters with the others fixed. Sensitivity to the curvature and neutrino mass is the highest due to the high-redshift weight of CMB lensing but degeneracies between the parameters must be broken externally.

  17. FUV Spectra of Massive Hot Stars

    NASA Astrophysics Data System (ADS)

    Willis, Allan J.

    The FUSE mission will be providing high resolution FUV spectra of a large sample of OB and WR stars in the Galaxy, LMC, SMC, and other local group galaxies. The wealth of resonance lines in the FUV provide vital diagnostics of the stellar winds of such stars, covering a huge range of ionization species of common elements( eg CIII, NIII, SIV, SVI, and OVI) not accessible to IUE or the HST. Detailed analyses of these wind lines will provide quantitative measurements of the wind ionization balance, velocity laws, and mass loss rates for stars in Galaxy environments spanning a range of metallicities. The results will provide crucial tests of stellar wind driving theory (presumed to be due to radiation pressure), as well as detailed determinations of the mass loss and ISM enrichment from massive stars in different galaxies. This paper will provide an overview of the early results from FUSE in this field. This will include (i) a detailed comparison of two O7 supergiants in the LMC and SMC, (ii) the physical, chemical and mass loss properties of the WO2 star Sand~2 in the SMC, and (iii) first results on stellar wind variability in the FUV lines in O stars in Magellanic Clouds. First results indicate that major changes will be needed in our understanding of the mass loss and physical (ie. Teff, L*) properties of O-type stars.

  18. Research on fluorescence spectra of cancer blood

    NASA Astrophysics Data System (ADS)

    Liu, Kunxiang; He, Wenliang; Zhao, Wenyan; Liu, Ying

    2007-11-01

    The fluorescence spectral characteristic of tumor blood was studied by laser-induced fluorescence technology, and compared with the fluorescence spectra of the same type healthy mice blood, the differences between them are distinct. When the whole blood solutions were induced by 407nm laser, they radiate fluorescence band from 420nm to 750 nm, which spectral peak located at 620nm. In high concentration solutions (blood concentration is higher than 4%), the fluorescence intensity are lower than normal blood, but in those low concentration solutions (blood concentration is lower than 2%) the fluorescence intensity of the tumor blood are higher than the normal ones. It is analyzed that the change of the fluorescence characteristic between the tumor blood and the normal is caused by the concentration difference of the tumor identification-porphyrin. The experimental results showed that the obvious difference of the fluorescence spectral characteristic between the forepart tumor and normal blood can offer some value assistance to clinical diagnosis on cancer.

  19. Synthetic infrared spectra for correlation spectroscopy

    SciTech Connect

    Sinclair, M.B.; Butler, M.A.; Ricco, A.J.; Kravitz, S.H.; Zubrzycki, W.J.; Warren, M.E.

    1997-12-01

    As a first step toward the development of a new remote sensing technique that the authors call holographic correlation spectroscopy, they demonstrate that diffractive optics can be used to synthesize the infrared spectra of real compounds. In particular, they have designed, fabricated, and characterized a diffractive element that successfully reproduces the major features f the spectrum of gaseous HF in the region between 3,600 cm{sup {minus}1} and 4,300 cm{sup {minus}1}. The reflection-mode diffractive optic consists of 4,096 lines, each 4.5 {micro}m wide, at 16 discrete depths relative to the substrate (from 0 to 1.2 {micro}m), and was fabricated on a silicon wafer using anisotropic reactive ion-beam etching in a four-mask-level process. The authors envision the use of diffractive elements of this type to replace the cumbersome reference cells of conventional correlation spectroscopy and thereby enable a new class of compact and versatile correlation spectrometers.

  20. Inverting MRI measurements to heterogeneity spectra

    NASA Astrophysics Data System (ADS)

    Pomerantz, Andrew E.; Tilke, Peter; Song, Yi-Qiao

    2008-08-01

    Spatially resolved MRI measurements of porosity and relaxation time have been performed on a series of sandstone and carbonate rock cores in order to assess spatial heterogeneity in these samples. Geostatistical techniques such as the construction of experimental variograms provide a quantitative measure of heterogeneity, although the interpretation of standard techniques is at times ambiguous. Here, we attempt to resolve some of that ambiguity by addressing the influence of regularization (spatial averaging over the volume of a voxel) on the variogram. Modeling the influence of regularization allows measured variograms to be inverted, yielding a heterogeneity spectrum that shows the extent of spatial heterogeneity as a function of length scale. The current experiment is sensitive to heterogeneity on the 0.3-100 mm length scale, and heterogeneity spectra of carbonates are shown to vary widely from sample to sample over this range. Thus, this analysis is shown to provide a more detailed description of these porous media than the variogram or the first two moments of the porosity distribution provide. The magnetic resonance aspects of this technique are described here, while details of the geostatistical methodology are presented in a companion paper [A.E. Pomerantz, P.G. Tilke, Y.-Q. Song, Math. Geosci., submitted for publication].