Depletion-Mode GaN HEMT Q-Spoil Switches for MRI Coils

PubMed Central

Lu, Jonathan Y.; Grafendorfer, Thomas; Zhang, Tao; Vasanawala, Shreyas; Robb, Fraser; Pauly, John M.; Scott, Greig C.

2017-01-01

Q-spoiling is the process of decoupling an MRI receive coil to protect the equipment and patient. Conventionally, Q-spoiling is performed using a PIN diode switch that draws significant current. In this work, a Q-spoiling technique using a depletion-mode Gallium Nitride HEMT device was developed for coil detuning at both 1.5 T and 3 T MRI. The circuits with conventional PIN diode Q-spoiling and the GaN HEMT device were implemented on surface coils. SNR was measured and compared for all surfaces coils. At both 1.5 T and 3 T, comparable SNR was achieved for all coils with the proposed technique and conventional Q-spoiling. The GaN HEMT device has significantly reduced the required power for Q-spoiling. The GaN HEMT device also provides useful safety features by detuning the coil when unpowered. PMID:27362895

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

PubMed

Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

2016-11-01

To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative ( q )-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q -EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q -EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. © 2016 Associated Professional Sleep Societies, LLC.

Structural Analysis of Cubane-Type Iron Clusters

PubMed Central

Tan, Lay Ling; Holm, R. H.; Lee, Sonny C.

2013-01-01

The generalized cluster type [M4(μ3-Q)4Ln]x contains the cubane-type [M4Q4]z core unit that can approach, but typically deviates from, perfect Td symmetry. The geometric properties of this structure have been analyzed with reference to Td symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M4, Q4) and the total [M4Q4] core (as a tetracapped M4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe4Q4] (Q = S2−, Se2−, Te2−, [NPR3]−, [NR]2−) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information. PMID:24072952

Structural Analysis of Cubane-Type Iron Clusters.

PubMed

Tan, Lay Ling; Holm, R H; Lee, Sonny C

2013-07-13

The generalized cluster type [M 4 (μ 3 -Q) 4 L n ] x contains the cubane-type [M 4 Q 4 ] z core unit that can approach, but typically deviates from, perfect T d symmetry. The geometric properties of this structure have been analyzed with reference to T d symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M 4 , Q 4 ) and the total [M 4 Q 4 ] core (as a tetracapped M 4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe 4 Q 4 ] (Q = S 2- , Se 2- , Te 2- , [NPR 3 ] - , [NR] 2- ) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information.

High-Q enhancement of attractive and repulsive optical forces between coupled whispering-gallery- mode resonators.

PubMed

Povinelli, Michelle; Johnson, Steven; Lonèar, Marko; Ibanescu, Mihai; Smythe, Elizabeth; Capasso, Federico; Joannopoulos, J

2005-10-03

We have calculated the optically-induced force between coupled high-Q whispering gallery modes of microsphere resonators. Attractive and repulsive forces are found, depending whether the bi-sphere mode is symmetric or antisymmetric. The magnitude of the force is linearly proportional to the total power in the spheres and consequently linearly enhanced by Q. Forces on the order of 100 nN are found for Q=108, large enough to cause displacements in the range of 1mum when the sphere is attached to a fiber stem with spring constant 0.004 N/m.

High-Q BBO whispering gallery mode resonators

NASA Astrophysics Data System (ADS)

Lin, Guoping; Fürst, Josef U.; Strekalov, Dmitry V.; Grudinin, Ivan S.; Yu, Nan

2013-02-01

We report an investigation on optical whispering gallery mode (WGM) resonators made from non z-cut beta barium borate (BBO) crystals. We first fabricated high quality (Q) factor WGM resonators made of an angle-cut BBO crystal. Q factors of 1×108 level have been demonstrated at various wavelengths including UV. They led to new upper bounds for the absorption coefficients of BBO at 1560 nm, 980 nm and 370 nm. We observed only one set of ordinarily polarized WGMs with polarization rotating along the resonator circumference. We also fabricated xy-cut BBO WGM resonators, in which the optic axis is parallel to the resonator plane. In that case, two WGM families with different polarization exist, one with constant the other with oscillatory phase velocity. This enables a novel way of broadband phase matching in WGM resonators with cyclic gain. We experimentally demonstrated efficient second harmonic generation (SHG) to a wide harmonic wavelength range from 780 nm at near infrared to 317 nm in UV. It is also the first reported direct UV SHG in a high-Q WGM resonator. This work lays a foundation for further investigations of WGM properties of non-z cut birefringent resonators and their applications in nonlinear optics.

Q-plates as higher order polarization controllers for orbital angular momentum modes of fiber.

PubMed

Gregg, P; Mirhosseini, M; Rubano, A; Marrucci, L; Karimi, E; Boyd, R W; Ramachandran, S

2015-04-15

We demonstrate that a |q|=1/2 plate, in conjunction with appropriate polarization optics, can selectively and switchably excite all linear combinations of the first radial mode order |l|=1 orbital angular momentum (OAM) fiber modes. This enables full mapping of free-space polarization states onto fiber vector modes, including the radially (TM) and azimuthally polarized (TE) modes. The setup requires few optical components and can yield mode purities as high as ∼30  dB. Additionally, just as a conventional fiber polarization controller creates arbitrary elliptical polarization states to counteract fiber birefringence and yield desired polarizations at the output of a single-mode fiber, q-plates disentangle degenerate state mixing effects between fiber OAM states to yield pure states, even after long-length fiber propagation. We thus demonstrate the ability to switch dynamically, potentially at ∼GHz rates, between OAM modes, or create desired linear combinations of them. We envision applications in fiber-based lasers employing vector or OAM mode outputs, as well as communications networking schemes exploiting spatial modes for higher dimensional encoding.

Variance-Based Cluster Selection Criteria in a K-Means Framework for One-Mode Dissimilarity Data.

PubMed

Vera, J Fernando; Macías, Rodrigo

2017-06-01

One of the main problems in cluster analysis is that of determining the number of groups in the data. In general, the approach taken depends on the cluster method used. For K-means, some of the most widely employed criteria are formulated in terms of the decomposition of the total point scatter, regarding a two-mode data set of N points in p dimensions, which are optimally arranged into K classes. This paper addresses the formulation of criteria to determine the number of clusters, in the general situation in which the available information for clustering is a one-mode [Formula: see text] dissimilarity matrix describing the objects. In this framework, p and the coordinates of points are usually unknown, and the application of criteria originally formulated for two-mode data sets is dependent on their possible reformulation in the one-mode situation. The decomposition of the variability of the clustered objects is proposed in terms of the corresponding block-shaped partition of the dissimilarity matrix. Within-block and between-block dispersion values for the partitioned dissimilarity matrix are derived, and variance-based criteria are subsequently formulated in order to determine the number of groups in the data. A Monte Carlo experiment was carried out to study the performance of the proposed criteria. For simulated clustered points in p dimensions, greater efficiency in recovering the number of clusters is obtained when the criteria are calculated from the related Euclidean distances instead of the known two-mode data set, in general, for unequal-sized clusters and for low dimensionality situations. For simulated dissimilarity data sets, the proposed criteria always outperform the results obtained when these criteria are calculated from their original formulation, using dissimilarities instead of distances.

A cluster analysis method for identification of subpopulations of cells in flow cytometric list-mode arrays

NASA Technical Reports Server (NTRS)

Li, Z. K.

1985-01-01

A specialized program was developed for flow cytometric list-mode data using an heirarchical tree method for identifying and enumerating individual subpopulations, the method of principal components for a two-dimensional display of 6-parameter data array, and a standard sorting algorithm for characterizing subpopulations. The program was tested against a published data set subjected to cluster analysis and experimental data sets from controlled flow cytometry experiments using a Coulter Electronics EPICS V Cell Sorter. A version of the program in compiled BASIC is usable on a 16-bit microcomputer with the MS-DOS operating system. It is specialized for 6 parameters and up to 20,000 cells. Its two-dimensional display of Euclidean distances reveals clusters clearly, as does its 1-dimensional display. The identified subpopulations can, in suitable experiments, be related to functional subpopulations of cells.

Weakly damped modes in star clusters and galaxies

NASA Technical Reports Server (NTRS)

Weinberg, Martin D.

1994-01-01

A perturber may excite a coherent mode in a star cluster or galaxy. If the stellar system is stable, it is commonly assumed that such a mode will be strongly damped and therefore of little practical consequence other than redistributing momentum and energy deposited by the perturber. This paper demonstrates that this assumption is false; weakly damped modes exist and may persist long enough to have observable consequences. To do this, a method for investigating the dispersion relation for spherical stellar systems and for locating weakly damped modes in particular is developed and applied to King models of varying concentration. This leads to a following remarkable result: King models exhibit very weakly damped m = 1 modes over a wide range of concentration (0.67 less than or equal to c less than or equal to 1.5 have been examined). The predicted damping time is tens of hundreds of crossing times. This mode causes the peak density to shift from and slowly revolve about the initial center. The existence of the mode is supported by n-body simulation. Higher order modes and possible astronomical consequences are discussed. Weakly damped modes, for example, may provide a neutral explanation for observed discrepancies between density and kinematic centers in galaxies, off-center nuclei, the location of velocity cusps due to massive black holes, and both m = 1 and barlike disturbances of disks enbedded in massive halos or spheroids. Gravitational shocking may excite the m = 1 mode in globular clusters, which could modify their subsequent evolution and displace the positions of exotic remnants.

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

PubMed

Tang, Ping-Han; Wu, Ten-Ming; Yen, Tsung-Wen; Lai, S K; Hsu, P J

2011-09-07

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat. © 2011 American Institute of Physics

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability

PubMed Central

Miller, Christopher B.; Bartlett, Delwyn J.; Mullins, Anna E.; Dodds, Kirsty L.; Gordon, Christopher J.; Kyle, Simon D.; Kim, Jong Won; D'Rozario, Angela L.; Lee, Rico S.C.; Comas, Maria; Marshall, Nathaniel S.; Yee, Brendon J.; Espie, Colin A.; Grunstein, Ronald R.

2016-01-01

Study Objectives: To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Methods: Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. Results: From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q-EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Conclusions: Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Clinical Trial Registration: Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. Citation: Miller CB, Bartlett DJ, Mullins AE, Dodds KL, Gordon CJ, Kyle SD, Kim JW, D'Rozario AL, Lee RS, Comas

Default mode network connectivity and reciprocal social behavior in 22q11.2 deletion syndrome

PubMed Central

Schreiner, Matthew J.; Karlsgodt, Katherine H.; Uddin, Lucina Q.; Chow, Carolyn; Congdon, Eliza; Jalbrzikowski, Maria

2014-01-01

22q11.2 deletion syndrome (22q11DS) is a genetic mutation associated with disorders of cortical connectivity and social dysfunction. However, little is known about the functional connectivity (FC) of the resting brain in 22q11DS and its relationship with social behavior. A seed-based analysis of resting-state functional magnetic resonance imaging data was used to investigate FC associated with the posterior cingulate cortex (PCC), in (26) youth with 22qDS and (51) demographically matched controls. Subsequently, the relationship between PCC connectivity and Social Responsiveness Scale (SRS) scores was examined in 22q11DS participants. Relative to 22q11DS participants, controls showed significantly stronger FC between the PCC and other default mode network (DMN) nodes, including the precuneus, precentral gyrus and left frontal pole. 22q11DS patients did not show age-associated FC changes observed in typically developing controls. Increased connectivity between PCC, medial prefrontal regions and the anterior cingulate cortex, was associated with lower SRS scores (i.e. improved social competence) in 22q11DS. DMN integrity may play a key role in social information processing. We observed disrupted DMN connectivity in 22q11DS, paralleling reports from idiopathic autism and schizophrenia. Increased strength of long-range DMN connectivity was associated with improved social functioning in 22q11DS. These findings support a ‘developmental-disconnection’ hypothesis of symptom development in this disorder. PMID:23912681

4 × 20 Gbit/s mode division multiplexing over free space using vector modes and a q-plate mode (de)multiplexer

NASA Astrophysics Data System (ADS)

Milione, Giovanni; Lavery, Martin P. J.; Huang, Hao; Ren, Yongxiong; Xie, Guodong; Nguyen, Thien An; Karimi, Ebrahim; Marrucci, Lorenzo; Nolan, Daniel A.; Alfano, Robert R.; Willner, Alan E.

2015-05-01

Vector modes are spatial modes that have spatially inhomogeneous states of polarization, such as, radial and azimuthal polarization. They can produce smaller spot sizes and stronger longitudinal polarization components upon focusing. As a result, they are used for many applications, including optical trapping and nanoscale imaging. In this work, vector modes are used to increase the information capacity of free space optical communication via the method of optical communication referred to as mode division multiplexing. A mode (de)multiplexer for vector modes based on a liquid crystal technology referred to as a q-plate is introduced. As a proof of principle, using the mode (de)multiplexer four vector modes each carrying a 20 Gbit/s quadrature phase shift keying signal on a single wavelength channel (~1550nm), comprising an aggregate 80 Gbit/s, were transmitted ~1m over the lab table with <-16.4 dB (<2%) mode crosstalk. Bit error rates for all vector modes were measured at the forward error correction threshold with power penalties < 3.41dB.

Structure of picosecond pulses of a Q-switched and mode-locked diode-pumped Nd:YAG laser

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

Donin, V I; Yakovin, D V; Gribanov, A V

2015-12-31

The pulse duration of a diode-pumped Nd:YAG laser, in which Q-switching with mode-locking (QML regime) is achieved using a spherical mirror and a travelling-wave acousto-optic modulator, is directly measured with a streak camera. It is found that the picosecond pulses can have a non-single-pulse structure, which is explained by excitation of several competing transverse modes in the Q-switching regime with a pulse repetition rate of 1 kHz. In the case of cw mode-locking (without Q-switching), a new (auto-QML) regime is observed, in which the pulse train repetition rate is determined by the frequency of the relaxation oscillations of the lasermore » field while the train contains single picosecond pulses. (control of laser radiation parameters)« less

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

All-optical Photonic Oscillator with High-Q Whispering Gallery Mode Resonators

NASA Technical Reports Server (NTRS)

Savchenkov, Anatoliy A.; Matsko, Andrey B.; Strekalov, Dmitry; Mohageg, Makan; Iltchenko, Vladimir S.; Maleki, Lute

2004-01-01

We demonstrated low threshold optical photonic hyper-parametric oscillator in a high-Q 10(exp 10) CaF2 whispering gallery mode resonator which generates stable 8.5 GHz signal. The oscillations result from the resonantly enhanced four wave mixing occurring due to Kerr nonlinearity of the material.

Switching between the mode-locking and Q-switching modes in two-section QW lasers upon a change in the absorber properties due to the Stark effect

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

Gadzhiyev, I. M., E-mail: idris.intop@mail.ru; Buyalo, M. S.; Gubenko, A. E.

2016-06-15

The passive Q-switching and mode-locking modes are implemented in two-section lasers with three quantum wells. It is demonstrated that raising the reverse bias on the absorbing section changes its spectral and dynamic properties and, accordingly, leads to a change from the Q-switching mode to mode-locking. The pulse-repetition frequency in the mode-locking mode is 75 GHz, with the product of the pulse duration by the spectrum bandwidth being 0.49, which is close to the theoretical limit. It is shown that, in structures with three quantum wells, strong absorption at the lasing wavelength gives rise to a photocurrent across a section ofmore » the saturable absorber, which is sufficient for compensation of the applied bias.« less

Application of the CC(P;Q) Hierarchy of Coupled-Cluster Methods to the Beryllium Dimer.

PubMed

Magoulas, Ilias; Bauman, Nicholas P; Shen, Jun; Piecuch, Piotr

2018-02-08

The performance of coupled-cluster approaches with higher-than-doubly excited clusters, including the CCSD(T), CCSD(2) T , CR-CC(2,3), CCSD(TQ), and CR-CC(2,4) corrections to CCSD, the active-space CCSDt, CCSDtq, and CCSDTq methods, and the CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) corrections to CCSDt, CCSDtq, and CCSDTq resulting from the CC(P;Q) formalism, in reproducing the CCSDT and CCSDTQ potential energy curves and vibrational term values characterizing Be 2 in its electronic ground state is assessed. The correlation-consistent aug-cc-pVnZ and aug-cc-pCVnZ (n = T and Q) basis sets are employed. Among the CCSD-based corrections, the completely renormalized CR-CC(2,3) and CR-CC(2,4) approaches perform the best. The CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) methods, especially CC(t;3) and CC(q;4), outperform other employed approaches in reproducing the CCSDT and CCSDTQ data. Composite schemes combining the all-electron CCSDT calculations extrapolated to the complete basis set limit with the frozen-core CC(q;4) and CCSDTQ computations using the aug-cc-pVTZ basis to account for connected quadruple excitations reproduce the latest experimental vibrational spectrum of Be 2 to within 4-5 cm -1 , when the vibrational spacings are examined, with typical errors being below 1-2 cm -1 . The resulting binding energies and equilibrium bond lengths agree with their experimentally derived counterparts to within ∼10 cm -1 and 0.01 Å.

A Cr4+:YAG passively Q-switched Nd:YVO4 microchip laser for controllable high-order Hermite-Gaussian modes

NASA Astrophysics Data System (ADS)

Dong, Jun; He, Yu; Bai, Sheng-Chuang; Ueda, Ken-ichi; Kaminskii, Alexander A.

2016-09-01

A nanosecond, high peak power, passively Q-switched laser for controllable Hermite-Gaussian (HG) modes has been achieved by manipulating the saturated inversion population inside the gain medium. The stable HG modes are generated in a Cr4+:YAG passively Q-switched Nd:YVO4 microchip laser by applying a tilted pump beam. The asymmetrical saturated inversion population distribution inside the Nd:YVO4 crystal for desirable HG modes is manipulated by choosing the proper pump beam diameter and varying pump power. A HG9,8 mode passively Q-switched Nd:YVO4 microchip laser with average output power of 265 mW has been obtained. Laser pulses with a pulse width of 7.3 ns and peak power of over 1.7 kW working at 21 kHz have been generated in the passively Q-switched Nd:YVO4 microchip laser.

Analysis of digital images into energy-angular momentum modes.

PubMed

Vicent, Luis Edgar; Wolf, Kurt Bernardo

2011-05-01

The measurement of continuous wave fields by a digital (pixellated) screen of sensors can be used to assess the quality of a beam by finding its formant modes. A generic continuous field F(x, y) sampled at an N × N Cartesian grid of point sensors on a plane yields a matrix of values F(q(x), q(y)), where (q(x), q(y)) are integer coordinates. When the approximate rotational symmetry of the input field is important, one may use the sampled Laguerre-Gauss functions, with radial and angular modes (n, m), to analyze them into their corresponding coefficients F(n, m) of energy and angular momentum (E-AM). The sampled E-AM modes span an N²-dimensional space, but are not orthogonal--except for parity. In this paper, we propose the properly orthonormal "Laguerre-Kravchuk" discrete functions Λ(n, m)(q(x), q(y)) as a convenient basis to analyze the sampled beams into their E-AM polar modes, and with them synthesize the input image exactly.

Graphene oxide based reflective saturable absorber for Q-switched and mode-locked YVO4/Nd:YVO4/YVO4 laser

NASA Astrophysics Data System (ADS)

Zhang, Gang; Wang, Yonggang; Chen, Zhendong; Jiao, Zhiyong

2018-05-01

A reflective graphene oxide saturable absorber is fabricated and used in a Q-switched and mode-locked YVO4/Nd:YVO4/YVO4 laser. Stable Q-switched and mode-locked pulses with a repetition rate of 8 MHz can be obtained at a pump power of 9 W by using an X-type resonator. Pulses obtained in an X-type resonator possess higher stability, output power, and repetition rate, compared with those in a Z-type resonator. The pulse width and the repetition rate of the Q-switched envelop in an X-type resonator are superior to those in the reported Q-switched and mode-locked lasers with graphene oxide.

Cavity length dependence of mode beating in passively Q-switched Nd-solid state lasers

NASA Astrophysics Data System (ADS)

Zameroski, Nathan D.; Wanke, Michael; Bossert, David

2013-03-01

The temporal intensity profile of pulse(s) from passively Q-switched and passively Q-switched mode locked (QSML) solid-state lasers is known to be dependent on cavity length. In this work, the pulse width, modulation depth, and beat frequencies of a Nd:Cr:GSGG laser using a Cr+4:YAG passive Q-switch are investigated as function cavity length. Measured temporal widths are linearly correlated with cavity length but generally 3-5 ns larger than theoretical predictions. Some cavity lengths exhibit pulse profiles with no modulation while other lengths exhibit complete amplitude modulation. The observed beat frequencies at certain cavity lengths cannot be accounted for with passively QSML models in which the pulse train repetition rate is τRT-1, τRT= round-trip time. They can be explained, however, by including coupled cavity mode-locking effects. A theoretical model developed for a two section coupled cavity semiconductor laser is adapted to a solid-state laser to interpret measured beat frequencies. We also numerically evaluate the temporal criterion required to achieve temporally smooth Q-switched pulses, versus cavity length and pump rate. We show that in flash lamp pumped systems, the difference in buildup time between longitudinal modes is largely dependent on the pump rate. In applications where short pulse delay is important, the pumping rate may limit the ability to achieve temporally smooth pulses in passively Q-switched lasers. Simulations support trends in experimental data. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Continuous Variable Cluster State Generation over the Optical Spatial Mode Comb

DOE PAGES

Pooser, Raphael C.; Jing, Jietai

2014-10-20

One way quantum computing uses single qubit projective measurements performed on a cluster state (a highly entangled state of multiple qubits) in order to enact quantum gates. The model is promising due to its potential scalability; the cluster state may be produced at the beginning of the computation and operated on over time. Continuous variables (CV) offer another potential benefit in the form of deterministic entanglement generation. This determinism can lead to robust cluster states and scalable quantum computation. Recent demonstrations of CV cluster states have made great strides on the path to scalability utilizing either time or frequency multiplexingmore » in optical parametric oscillators (OPO) both above and below threshold. The techniques relied on a combination of entangling operators and beam splitter transformations. Here we show that an analogous transformation exists for amplifiers with Gaussian inputs states operating on multiple spatial modes. By judicious selection of local oscillators (LOs), the spatial mode distribution is analogous to the optical frequency comb consisting of axial modes in an OPO cavity. We outline an experimental system that generates cluster states across the spatial frequency comb which can also scale the amount of quantum noise reduction to potentially larger than in other systems.« less

Q-switched and mode-locked Er{sup 3+}-doped fibre laser using a single-multi-single fibre filter and piezoelectric

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

Ji Wang; Yunjun Zhang; Aotuo Dong

2014-04-28

The active Q-switched and passive mode-locked Er{sup 3+}-doped all-fibre laser is presented. The fibre laser centre wavelength is located at 1563 nm and determined by the homemade singlemulti- single (SMS) in-line fibre filter. The laser spectrum width is nearly 0.1 nm. The active Q-switched mechanism relies on the polarisation state control using a piezoelectric to press a segment of passive fibre on the circular cavity. The nonlinear polarisation rotation technology is used to realise the passive self-started modelocked operation. In the passive mode-locked regimes, the output average power is 2.1 mW, repetition frequency is 11.96 MHz, and single pulse energymore » is 0.18 nJ. With the 100-Hz Q-switched regimes running, the output average power is 1.5 mW. The total Q-switched pulse width is 15 μs, and every Q-switched pulse is made up by several tens of mode-locked peak pulses. The calculated output pulse energy of the Q-switched fibre laser is about 15 μJ, and the energy of every mode-locked pulse is about 64–68 nJ during a Q-switched pulse taking into account the power fraction propagating between pulses. (lasers)« less

WS₂ as a saturable absorber for ultrafast photonic applications of mode-locked and Q-switched lasers.

PubMed

Wu, Kan; Zhang, Xiaoyan; Wang, Jun; Li, Xing; Chen, Jianping

2015-05-04

Two-dimensional (2D) nanomaterials, especially the transition metal sulfide semiconductors, have drawn great interests due to their potential applications in viable photonic and optoelectronic devices. In this work, 2D tungsten disulfide (WS2) based saturable absorber (SA) for ultrafast photonic applications was demonstrated. WS2 nanosheets were prepared using liquid-phase exfoliation method and embedded in polyvinyl alcohol (PVA) thin film for the practical usage. Saturable absorption was discovered in the WS2-PVA SA at the telecommunication wavelength near 1550 nm. By incorporating WS2-PVA SA into a fiber laser cavity, both stable mode locking operation and Q-switching operation were achieved. In the mode locking operation, the laser obtained femtosecond output pulse width and high spectral purity in the radio frequency spectrum. In the Q-switching operation, the laser had tunable repetition rate and output pulse energy of a few tens of nano joule. Our findings suggest that few-layer WS2 nanosheets embedded in PVA thin film are promising nonlinear optical materials for ultrafast photonic applications as a mode locker or Q-switcher.

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

PubMed

Kopelman, Naama M; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A; Mayrose, Itay

2015-09-01

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. © 2015 John Wiley & Sons Ltd.

Passive Q switching and mode-locking of Er:glass lasers using VO2 mirrors

NASA Astrophysics Data System (ADS)

Pollack, S. A.; Chang, D. B.; Chudnovky, F. A.; Khakhaev, I. A.

1995-09-01

Passive Q switching of an Er:glass laser with the pulse width varying between 14 and 80 ns has been demonstrated, using three resonator vanadium-dioxide-coated (VO2) mirror samples with temperature-dependent reflectivity and differing in the reflectivity contrast. The reflectivity changes because of a phase transition from a semiconductor to a metallic state. Broad band operating characteristics of VO2 mirrors provide Q switching over a wide range of wavelengths. In addition, mode-locked pulses with much shorter time scales have been observed, due to exciton formation and recombination. A simple criterion is derived for the allowable ambient temperatures at which the Q switching operates effectively. A simple relation has also been found relating the duration of the Q-switched pulse to the contrast in reflectivities of the two mirror phases.

Multi-operational tuneable Q-switched mode-locking Er fibre laser

NASA Astrophysics Data System (ADS)

Qamar, F. Z.

2018-01-01

A wavelength-spacing tuneable, Q-switched mode-locking (QML) erbium-doped fibre laser based on non-linear polarization rotation controlled by four waveplates and a cube polarizer is proposed. A mode-locked pulse train using two quarter-wave plates and a half-wave plate (HWP) is obtained first, and then an extra HWP is inserted into the cavity to produce different operation regimes. The evolutions of temporal and spectral dynamics with different orientation angles of the extra HWP are investigated. A fully modulated stable QML pulse train is observed experimentally. This is, to the author’s best knowledge, the first experimental work reporting QML operation without adding an extra saturable absorber inside the laser cavity. Multi-wavelength pulse laser operation, multi-pulse train continuous-wave mode-locking operation and pulse-splitting operations are also reported at certain HWP angles. The observed operational dynamics are interpreted as a mutual interaction of dispersion, non-linear effect and insertion loss. This work provides a new mechanism for fabricating cheap tuneable multi-wavelength lasers with QML pulses.

Synchronizable Q-switched, mode-locked, and cavity-dumped ruby laser for plasma diagnostics

NASA Astrophysics Data System (ADS)

Houtman, H.; Meyer, J.

1985-06-01

We report on the design and operation of an optimized version of a Q-switched, mode-locked, and cavity-dumped ruby-laser oscillator. The modulator window is much narrower than that assumed in conventional active mode-lock theory, and is shown to yield much shorter pulses than the latter in cases where the number of round trips is restricted. To allow a high-power pulse (≊1 GW) to evolve in the oscillator, and to allow simple synchronization to a (˜100 ns fixed delay) CO2 laser, a limit of 23 round trips was chosen, but similar limits may be imposed by lasers having short-gain duration as in an excimer laser. Details are given on the single spark gap switching element and Pockels cells, with an analysis of their expected switching speeds, in order to establish the effectiveness of the modulator, as compared to conventional sinusoidally driven active mode lockers. Single pulses of 50-70 mJ are reliably cavity-dumped after only 100-ns delay (23 round trips) with pulse length adjustable from 50-100 ps with ±5-ps stability. Relative timing between the main (CO2) and probe (ruby) pulses allows a measurement accuracy of ±50 ps to be attained.

Synchronizable Q-switched, mode-locked, and cavity-dumped ruby laser for plasma diagnostics

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

Houtman, H.; Meyer, J.

We report on the design and operation of an optimized version of a Q-switched, mode-locked, and cavity-dumped ruby-laser oscillator. The modulator window is much narrower than that assumed in conventional active mode-lock theory, and is shown to yield much shorter pulses than the latter in cases where the number of round trips is restricted. To allow a high-power pulse (roughly-equal1 GW) to evolve in the oscillator, and to allow simple synchronization to a (approx.100 ns fixed delay) CO/sub 2/ laser, a limit of 23 round trips was chosen, but similar limits may be imposed by lasers having short-gain duration asmore » in an excimer laser. Details are given on the single spark gap switching element and Pockels cells, with an analysis of their expected switching speeds, in order to establish the effectiveness of the modulator, as compared to conventional sinusoidally driven active mode lockers. Single pulses of 50--70 mJ are reliably cavity-dumped after only 100-ns delay (23 round trips) with pulse length adjustable from 50--100 ps with +- 5-ps stability. Relative timing between the main (CO/sub 2/) and probe (ruby) pulses allows a measurement accuracy of +- 50 ps to be attained.« less

Growth mode and structures of magnetic Mn clusters on graphene

DOE PAGES

Liu, Xiaojie; Wang, Cai-Zhuang

2016-06-22

We present a systematic study of Mn clusters on graphene by first-principles calculations. We show that the growth of Mn on graphene follows a three-dimensional (3D) mode. Both adsorption and attachment energies show that (Mn) 3 and (Mn) 6 on graphene are energetically favorable in the size range (Mn) 1-7. Moreover, larger formation energy for Mn cluster on graphene implies the incoming Mn atoms are likely to nucleate and grow into bigger and bigger Mn clusters on graphene. The magnetic moments of (Mn) 1,5,7 on graphene are enhanced by 11%, 186%, and 26% from their values at free-standing clusters, respectively.more » By contrast, the net magnetic moment of (Mn) 2,3,4,6 on graphene is reduced from that of the corresponding free-standing clusters. The origin of the magnetic moment changes can be attributed to the charge transfer within the Mn clusters and between the clusters and graphene upon adsorption.« less

Diode-end-pumped single-longitudinal-mode passively Q-switched Nd:GGG laser

NASA Astrophysics Data System (ADS)

Xue, Feng; Zhang, Sasa; Cong, Zhenhua; Huang, Qingjie; Guan, Chen; Wu, Qianwen; Chen, Hui; Bai, Fen; Liu, Zhaojun

2018-03-01

Diode-end-pumped passively Q-switched Nd:GGG laser in a ring cavity at 1062 nm was demonstrated. Single-longitudinal-mode laser linewidth less than 0.5 pm was accomplished by unidirectional operation. The maximum output pulse energy was 437 µJ and the pulse width was 43 ns when Cr4+:YAG with an initial transmission of 61% was used.

Analysis of autism susceptibility gene loci on chromosomes 1p, 4p, 6q, 7q, 13q, 15q, 16p, 17q, 19q and 22q in Finnish multiplex families.

PubMed

Auranen, M; Nieminen, T; Majuri, S; Vanhala, R; Peltonen, L; Järvelä, I

2000-05-01

The role of genetic factors in the etiology of the autistic spectrum of disorders has clearly been demonstrated. Ten chromosomal regions, on chromosomes 1p, 4p, 6q, 7q, 13q, 15q, 16p, 17q, 19q and 22q have potentially been linked to autism.1-8 We have analyzed these chromosomal regions in a total of 17 multiplex families with autism originating from the isolated Finnish population by pairwise linkage analysis and sib-pair analysis. Mild evidence for putative contribution was found only with the 1p chromosomal region in the susceptibility to autism. Our data suggest that additional gene loci exist for autism which will be detectable in and even restricted to the isolated Finnish population.

Single Longitudinal Mode, High Repetition Rate, Q-switched Ho:YLF Laser for Remote Sensing

NASA Technical Reports Server (NTRS)

Bai, Yingxin; Yu, Jirong; Petzar, Paul; Petros, M.; Chen, Songsheng; Trieu, Bo; Lee, Nyung; Singh, U.

2009-01-01

Ho:YLF/LuLiF lasers have specific applications for remote sensing such as wind-speed measurement and carbon dioxide (CO2) concentration measurement in the atmosphere because the operating wavelength (around 2 m) is located in the eye-safe range and can be tuned to the characteristic lines of CO2 absorption and there is strong backward scattering signal from aerosol (Mie scattering). Experimentally, a diode pumped Ho:Tm:YLF laser has been successfully used as the transmitter of coherent differential absorption lidar for the measurement of with a repetition rate of 5 Hz and pulse energy of 75 mJ [1]. For highly precise CO2 measurements with coherent detection technique, a laser with high repetition rate is required to averaging out the speckle effect [2]. In addition, laser efficiency is critically important for the air/space borne lidar applications, because of the limited power supply. A diode pumped Ho:Tm:YLF laser is difficult to efficiently operate in high repetition rate due to the large heat loading and up-conversion. However, a Tm:fiber laser pumped Ho:YLF laser with low heat loading can be operated at high repetition rates efficiently [3]. No matter whether wind-speed or carbon dioxide (CO2) concentration measurement is the goal, a Ho:YLF/LuLiF laser as the transmitter should operate in a single longitudinal mode. Injection seeding is a valid technique for a Q-switched laser to obtain single longitudinal mode operation. In this paper, we will report the new results for a single longitudinal mode, high repetition rate, Q-switched Ho:YLF laser. In order to avoid spectral hole burning and make injection seeding easier, a four mirror ring cavity is designed for single longitudinal mode, high repetition rate Q-switched Ho:YLF laser. The ramp-fire technique is chosen for injection seeding.

Multi-mode clustering model for hierarchical wireless sensor networks

NASA Astrophysics Data System (ADS)

Hu, Xiangdong; Li, Yongfu; Xu, Huifen

2017-03-01

The topology management, i.e., clusters maintenance, of wireless sensor networks (WSNs) is still a challenge due to its numerous nodes, diverse application scenarios and limited resources as well as complex dynamics. To address this issue, a multi-mode clustering model (M2 CM) is proposed to maintain the clusters for hierarchical WSNs in this study. In particular, unlike the traditional time-trigger model based on the whole-network and periodic style, the M2 CM is proposed based on the local and event-trigger operations. In addition, an adaptive local maintenance algorithm is designed for the broken clusters in the WSNs using the spatial-temporal demand changes accordingly. Numerical experiments are performed using the NS2 network simulation platform. Results validate the effectiveness of the proposed model with respect to the network maintenance costs, node energy consumption and transmitted data as well as the network lifetime.

Collective Modes of Dust Helical Clusters

NASA Astrophysics Data System (ADS)

Tsytovich, V. N.; Gousein-Zade, N. G.; Morfill, G. E.

2005-10-01

The helical structures are the simplest 3D crystal-like cylindrical structures with radius R being a system of 2D clusters equally separated along the cylindrical axis with a relative rotation on constant angle φ0. For mean free path for grain charging much larger than the separation of the grains, the total energy of grain interaction is a sum of all pair grain interactions. The helical structures have been found experimentally for ions in laser traps in cylindrical gas discharges at very low temperatures (in both case as ``warms''). The equilibrium criterion and the criteria of stability including the absence of saddle points show that in the plane ρ, φ the bifurcation points are often present with new branches appearing (stable and unstable). Numerical MD simulations show that for cylindrical symmetry any random distributions of grains is developing into helical structures. The theory of collective modes of helical structures is developed for arbitrary grain interactions. The dispersion relation for frequencies of the collective modes for different branches of helical structures is derived and solved numerically for interaction including different type of screened grain potentials including the grain attraction. The dispersion relation in the first Brillouin zone for the square of the frequency ω2 is shown to be a be-cubic equation and gives the square of frequency ω2 > 0 for stable modes and the square of the growth rates for the unstable modes ω2 < 0. Modes for helical structures in parabolic external confining potential well perpendicular to cylindrical axis are found. Stabile self-confined structures without external confinement are discovered in presence of both non-collective and collective grain attractions.

Photonic crystal nanofiber air-mode cavity with high Q-factor and high sensitivity for refractive index sensing

NASA Astrophysics Data System (ADS)

Ma, Xiaoxue; Chen, Xin; Nie, Hongrui; Yang, Daquan

2018-01-01

Recently, due to its superior characteristics and simple manufacture, such as small size, low loss, high sensitivity and convenience to couple, the optical fiber sensor has become one of the most promising sensors. In order to achieve the most effective realization of light propagation by changing the structure of sensors, FOM(S •Q/λres) ,which is determined by two significant variables Q-factor and sensitivity, as a trade-off parameter should be optimized to a high value. In typical sensors, a high Q can be achieved by confining the optical field in the high refractive index dielectric region to make an interaction between analytes and evanescent field of the resonant mode. However, the ignored sensitivity is relatively low with a high Q achieved, which means that the resonant wavelength shift changes non-obviously when the refractive index increases. Meanwhile, the sensitivity also leads to a less desirable FOM. Therefore, a gradient structure, which can enhance the performance of sensors by achieving high Q and high sensitivity, has been developed by Kim et al. later. Here, by introducing parabolic-tapered structure, the light field localized overlaps strongly and sufficiently with analytes. And based on a one-dimensional photonic-crystal nanofiber air-mode cavity, a creative optical fiber sensor is proposed by combining good stability and transmission characteristics of fiber and strengths of tapered structure, realizing excellent FOM {4.7 x 105 with high Q-factors (Q{106) and high sensitivities (<700 nm/RIU).

Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas.

PubMed

Vékony, Hedy; Röser, Kerstin; Löning, Thomas; Ylstra, Bauke; Meijer, Gerrit A; van Wieringen, Wessel N; van de Wiel, Mark A; Carvalho, Beatriz; Kok, Klaas; Leemans, C René; van der Waal, Isaäc; Bloemena, Elisabeth

2009-02-01

Salivary gland myoepithelial tumors are relatively uncommon tumors with an unpredictable clinical course. More knowledge about their genetic profiles is necessary to identify novel predictors of disease. In this study, we subjected 27 primary tumors (15 myoepitheliomas and 12 myoepithelial carcinomas) to genome-wide microarray-based comparative genomic hybridization (array CGH). We set out to delineate known chromosomal aberrations in more detail and to unravel chromosomal differences between benign myoepitheliomas and myoepithelial carcinomas. Patterns of DNA copy number aberrations were analyzed by unsupervised hierarchical cluster analysis. Both benign and malignant tumors revealed a limited amount of chromosomal alterations (median of 5 and 7.5, respectively). In both tumor groups, high frequency gains (> or =20%) were found mainly at loci of growth factors and growth factor receptors (e.g., PDGF, FGF(R)s, and EGFR). In myoepitheliomas, high frequency losses (> or =20%) were detected at regions of proto-cadherins. Cluster analysis of the array CGH data identified three clusters. Differential copy numbers on chromosome arm 8q and chromosome 17 set the clusters apart. Cluster 1 contained a mixture of the two phenotypes (n = 10), cluster 2 included mostly benign tumors (n = 10), and cluster 3 only contained carcinomas (n = 7). Supervised analysis between malignant and benign tumors revealed a 36 Mbp-region at 8q being more frequently gained in malignant tumors (P = 0.007, FDR = 0.05). This is the first study investigating genomic differences between benign and malignant myoepithelial tumors of the salivary glands at a genomic level. Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas.

Triply heavy Q Q Q ¯ q ¯ tetraquark states

NASA Astrophysics Data System (ADS)

Jiang, Jin-Feng; Chen, Wei; Zhu, Shi-Lin

2017-11-01

Within the framework of QCD sum rules, we have investigated the tetraquark states with three heavy quarks. We systematically construct the interpolating currents for the possible c c c ¯ q ¯ , c c b ¯q ¯, b c b ¯q ¯, b b b ¯q ¯ tetraquark states with quantum numbers JP=0+ and JP=1+. Using these interpolating currents, we have calculated the two-point correlation functions and extracted the mass spectra for the above tetraquark states. We also discuss the decay patterns of these tetraquarks, and notice that the c c c ¯q ¯, c c b ¯q ¯, b c b ¯q ¯ may decay quickly with a narrow width due to their mass spectra. The b b b ¯q ¯ tetraquarks are expected to be very narrow resonances since their OZI (Okubo-Zweig-Iizuka)-allowed decay modes are kinematically forbidden. These states may be searched for in the final states with a B meson plus a light meson or photon.

Enhanced reproducibility of L-mode plasma discharges via physics-model-based q-profile feedback control in DIII-D

NASA Astrophysics Data System (ADS)

Schuster, E.; Wehner, W. P.; Barton, J. E.; Boyer, M. D.; Luce, T. C.; Ferron, J. R.; Holcomb, C. T.; Walker, M. L.; Humphreys, D. A.; Solomon, W. M.; Penaflor, B. G.; Johnson, R. D.

2017-11-01

Recent experiments on DIII-D demonstrate the potential of physics-model-based q-profile control to improve reproducibility of plasma discharges. A combined feedforward  +  feedback control scheme is employed to optimize the current ramp-up phase by consistently achieving target q profiles (Target 1: q_min=1.3, q95=4.4 ; Target 2: q_min=1.65, q95=5.0 ; Target 3: q_min=2.1, q95=6.2 ) at prescribed times during the plasma formation phase (Target 1: t=1.5 s; Target 2: t=1.3 s; Target 3: t=1.0 s). At the core of the control scheme is a nonlinear, first-principles-driven, physics-based, control-oriented model of the plasma dynamics valid for low confinement (L-mode) scenarios. To prevent undesired L-H transitions, a constraint on the maximum allowable total auxiliary power is imposed in addition to the maximum powers for the individual heating and current-drive sources. Experimental results are presented to demonstrate the effectiveness of the combined feedforward  +  feedback control scheme to consistently achieve the desired target profiles at the predefined times. These results also show how the addition of feedback control significantly improves upon the feedforward-only control solution by reducing the matching error and also how the feedback controller is able to reduce the matching error as the constraint on the maximum allowable total auxiliary power is relaxed while keeping the plasma in L-mode.

Pulse-coupled mixed-mode oscillators: Cluster states and extreme noise sensitivity

NASA Astrophysics Data System (ADS)

Karamchandani, Avinash J.; Graham, James N.; Riecke, Hermann

2018-04-01

Motivated by rhythms in the olfactory system of the brain, we investigate the synchronization of all-to-all pulse-coupled neuronal oscillators exhibiting various types of mixed-mode oscillations (MMOs) composed of sub-threshold oscillations (STOs) and action potentials ("spikes"). We focus particularly on the impact of the delay in the interaction. In the weak-coupling regime, we reduce the system to a Kuramoto-type equation with non-sinusoidal phase coupling and the associated Fokker-Planck equation. Its linear stability analysis identifies the appearance of various cluster states. Their type depends sensitively on the delay and the width of the pulses. Interestingly, long delays do not imply slow population rhythms, and the number of emerging clusters only loosely depends on the number of STOs. Direct simulations of the oscillator equations reveal that for quantitative agreement of the weak-coupling theory the coupling strength and the noise have to be extremely small. Even moderate noise leads to significant skipping of STO cycles, which can enhance the diffusion coefficient in the Fokker-Planck equation by two orders of magnitude. Introducing an effective diffusion coefficient extends the range of agreement significantly. Numerical simulations of the Fokker-Planck equation reveal bistability and solutions with oscillatory order parameters that result from nonlinear mode interactions. These are confirmed in simulations of the full spiking model.

Multiparameter bifurcations and mixed-mode oscillations in Q-switched CO2 lasers.

PubMed

Doedel, Eusebius J; Pando L, Carlos L

2014-05-01

We study the origin of mixed-mode oscillations and related bifurcations in a fully molecular laser model that describes CO2 monomode lasers with a slow saturable absorber. Our study indicates that the presence of isolas of periodic mixed-mode oscillations, as the pump parameter and the cavity-frequency detuning change, is inherent to Q-switched CO2 monomode lasers. We compare this model, known as the dual four-level model, to the more conventional 3:2 model and to a CO2 laser model for fast saturable absorbers. In these models, we find similarities as well as qualitative differences, such as the different nature of the homoclinic tangency to a relevant unstable periodic orbit, where the Gavrilov-Shilnikov theory and its extensions may hold. We also show that there are isolas of periodic mixed-mode oscillations in a model for CO2 lasers with modulated losses, as the pump parameter varies. The coarse-grained bifurcation diagrams of the periodic mixed-mode oscillations in these models suggest that these oscillations belong to similar classes.

Transcriptional analysis of exopolysaccharides biosynthesis gene clusters in Lactobacillus plantarum.

PubMed

Vastano, Valeria; Perrone, Filomena; Marasco, Rosangela; Sacco, Margherita; Muscariello, Lidia

2016-04-01

Exopolysaccharides (EPS) from lactic acid bacteria contribute to specific rheology and texture of fermented milk products and find applications also in non-dairy foods and in therapeutics. Recently, four clusters of genes (cps) associated with surface polysaccharide production have been identified in Lactobacillus plantarum WCFS1, a probiotic and food-associated lactobacillus. These clusters are involved in cell surface architecture and probably in release and/or exposure of immunomodulating bacterial molecules. Here we show a transcriptional analysis of these clusters. Indeed, RT-PCR experiments revealed that the cps loci are organized in five operons. Moreover, by reverse transcription-qPCR analysis performed on L. plantarum WCFS1 (wild type) and WCFS1-2 (ΔccpA), we demonstrated that expression of three cps clusters is under the control of the global regulator CcpA. These results, together with the identification of putative CcpA target sequences (catabolite responsive element CRE) in the regulatory region of four out of five transcriptional units, strongly suggest for the first time a role of the master regulator CcpA in EPS gene transcription among lactobacilli.

Enhanced reproducibility of L-mode plasma discharges via physics-model-based q-profile feedback control in DIII-D

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

Schuster, Eugenio J.; Wehner, William P.; Barton, Joseph E.

Recent experiments on DIII-D demonstrate the potential of physics-model-based q-profile control to improve reproducibility of plasma discharges. A combined feed forward + feedback control scheme is employed to optimize the current ramp-up phase by consistently achieving target q profiles (Target 1: q min = 1.3,q 95 = 4:4; Target 2: q min = 1.65,q 95 = 5.0; Target 3: q min = 2.1,q 95 = 6:2) at prescribed times during the plasma formation phase (Target 1: t = 1.5 s; Target 2: t = 1:3 s; Target 3: t = 1.0 s). At the core of the control scheme ismore » a nonlinear, first-principles-driven, physics-based, control-oriented model of the plasma dynamics valid for low confinement (L-mode) scenarios. To prevent undesired L-H transitions, a constraint on the maximum allowable total auxiliary power is imposed in addition to the maximum powers for the individual heating and current-drive sources. Experimental results are presented to demonstrate the effectiveness of the combined feed forward + feedback control scheme to consistently achieve the desired target profiles at the predefined times. Here, these results also show how the addition of feedback control significantly improves upon the feed forward only control solution by reducing the matching error and also how the feedback controller is able to reduce the matching error as the constraint on the maximum allowable total auxiliary power is relaxed while keeping the plasma in L-mode.« less

Enhanced reproducibility of L-mode plasma discharges via physics-model-based q-profile feedback control in DIII-D

DOE PAGES

Schuster, Eugenio J.; Wehner, William P.; Barton, Joseph E.; ...

2017-08-09

Recent experiments on DIII-D demonstrate the potential of physics-model-based q-profile control to improve reproducibility of plasma discharges. A combined feed forward + feedback control scheme is employed to optimize the current ramp-up phase by consistently achieving target q profiles (Target 1: q min = 1.3,q 95 = 4:4; Target 2: q min = 1.65,q 95 = 5.0; Target 3: q min = 2.1,q 95 = 6:2) at prescribed times during the plasma formation phase (Target 1: t = 1.5 s; Target 2: t = 1:3 s; Target 3: t = 1.0 s). At the core of the control scheme ismore » a nonlinear, first-principles-driven, physics-based, control-oriented model of the plasma dynamics valid for low confinement (L-mode) scenarios. To prevent undesired L-H transitions, a constraint on the maximum allowable total auxiliary power is imposed in addition to the maximum powers for the individual heating and current-drive sources. Experimental results are presented to demonstrate the effectiveness of the combined feed forward + feedback control scheme to consistently achieve the desired target profiles at the predefined times. Here, these results also show how the addition of feedback control significantly improves upon the feed forward only control solution by reducing the matching error and also how the feedback controller is able to reduce the matching error as the constraint on the maximum allowable total auxiliary power is relaxed while keeping the plasma in L-mode.« less

[Visual field progression in glaucoma: cluster analysis].

PubMed

Bresson-Dumont, H; Hatton, J; Foucher, J; Fonteneau, M

2012-11-01

Visual field progression analysis is one of the key points in glaucoma monitoring, but distinction between true progression and random fluctuation is sometimes difficult. There are several different algorithms but no real consensus for detecting visual field progression. The trend analysis of global indices (MD, sLV) may miss localized deficits or be affected by media opacities. Conversely, point-by-point analysis makes progression difficult to differentiate from physiological variability, particularly when the sensitivity of a point is already low. The goal of our study was to analyse visual field progression with the EyeSuite™ Octopus Perimetry Clusters algorithm in patients with no significant changes in global indices or worsening of the analysis of pointwise linear regression. We analyzed the visual fields of 162 eyes (100 patients - 58 women, 42 men, average age 66.8 ± 10.91) with ocular hypertension or glaucoma. For inclusion, at least six reliable visual fields per eye were required, and the trend analysis (EyeSuite™ Perimetry) of visual field global indices (MD and SLV), could show no significant progression. The analysis of changes in cluster mode was then performed. In a second step, eyes with statistically significant worsening of at least one of their clusters were analyzed point-by-point with the Octopus Field Analysis (OFA). Fifty four eyes (33.33%) had a significant worsening in some clusters, while their global indices remained stable over time. In this group of patients, more advanced glaucoma was present than in stable group (MD 6.41 dB vs. 2.87); 64.82% (35/54) of those eyes in which the clusters progressed, however, had no statistically significant change in the trend analysis by pointwise linear regression. Most software algorithms for analyzing visual field progression are essentially trend analyses of global indices, or point-by-point linear regression. This study shows the potential role of analysis by clusters trend. However, for best

Dynamical modeling and experiment for an intra-cavity optical parametric oscillator pumped by a Q-switched self-mode-locking laser

NASA Astrophysics Data System (ADS)

Wang, Jing; Liu, Nianqiao; Song, Peng; Zhang, Haikun

2016-11-01

The rate-equation-based model for the Q-switched mode-locking (QML) intra-cavity OPO (IOPO) is developed, which includes the behavior of the fundamental laser. The intensity fluctuation mechanism of the fundamental laser is first introduced into the dynamics of a mode-locking OPO. In the derived model, the OPO nonlinear conversion is considered as a loss for the fundamental laser and thus the QML signal profile originates from the QML fundamental laser. The rate equations are solved by a digital computer for the case of an IOPO pumped by an electro-optic (EO) Q-switched self-mode-locking fundamental laser. The simulated results for the temporal shape with 20 kHz EO repetition and 11.25 W pump power, the signal average power, the Q-switched pulsewidth and the Q-switched pulse energy are obtained from the rate equations. The signal trace and output power from an EO QML Nd3+: GdVO4/KTA IOPO are experimentally measured. The theoretical values from the rate equations agree with the experimental results well. The developed model explains the behavior, which is helpful to system optimization.

Orbit Clustering Based on Transfer Cost

NASA Technical Reports Server (NTRS)

Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.

2013-01-01

We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.

Test of the FDTD accuracy in the analysis of the scattering resonances associated with high-Q whispering-gallery modes of a circular cylinder.

PubMed

Boriskin, Artem V; Boriskina, Svetlana V; Rolland, Anthony; Sauleau, Ronan; Nosich, Alexander I

2008-05-01

Our objective is the assessment of the accuracy of a conventional finite-difference time-domain (FDTD) code in the computation of the near- and far-field scattering characteristics of a circular dielectric cylinder. We excite the cylinder with an electric or magnetic line current and demonstrate the failure of the two-dimensional FDTD algorithm to accurately characterize the emission rate and the field patterns near high-Q whispering-gallery-mode resonances. This is proven by comparison with the exact series solutions. The computational errors in the emission rate are then studied at the resonances still detectable with FDTD, i.e., having Q-factors up to 10(3).

A high repetition rate passively Q-switched microchip laser for controllable transverse laser modes

NASA Astrophysics Data System (ADS)

Dong, Jun; Bai, Sheng-Chuang; Liu, Sheng-Hui; Ueda, Ken-Ichi; Kaminskii, Alexander A.

2016-05-01

A Cr4+:YAG passively Q-switched Nd:YVO4 microchip laser for versatile controllable transverse laser modes has been demonstrated by adjusting the position of the Nd:YVO4 crystal along the tilted pump beam direction. The pump beam diameter-dependent asymmetric saturated inversion population inside the Nd:YVO4 crystal governs the oscillation of various Laguerre-Gaussian, Ince-Gaussian and Hermite-Gaussian modes. Controllable transverse laser modes with repetition rates over 25 kHz and up to 183 kHz, depending on the position of the Nd:YVO4 crystal, have been achieved. The controllable transverse laser beams with a nanosecond pulse width and peak power over hundreds of watts have been obtained for potential applications in optical trapping and quantum computation.

New localization mechanism and Hodge duality for q -form field

NASA Astrophysics Data System (ADS)

Fu, Chun-E.; Liu, Yu-Xiao; Guo, Heng; Zhang, Sheng-Li

2016-03-01

In this paper, we investigate the problem of localization and the Hodge duality for a q -form field on a p -brane with codimension one. By a general Kaluza-Klein (KK) decomposition without gauge fixing, we obtain two Schrödinger-like equations for two types of KK modes of the bulk q -form field, which determine the localization and mass spectra of these KK modes. It is found that there are two types of zero modes (the 0-level modes): a q -form zero mode and a (q -1 )-form one, which cannot be localized on the brane at the same time. For the n -level KK modes, there are two interacting KK modes, a massive q -form KK mode and a massless (q -1 )-form one. By analyzing gauge invariance of the effective action and choosing a gauge condition, the n -level massive q -form KK mode decouples from the n -level massless (q -1 )-form one. It is also found that the Hodge duality in the bulk naturally becomes two dualities on the brane. The first one is the Hodge duality between a q -form zero mode and a (p -q -1 )-form one, or between a (q -1 )-form zero mode and a (p -q )-form one. The second duality is between two group KK modes: one is an n -level massive q -form KK mode with mass mn and an n -level massless (q -1 )-form mode; another is an n -level (p -q )-form one with the same mass mn and an n -level massless (p -q -1 )-form mode. Because of the dualities, the effective field theories on the brane for the KK modes of the two dual bulk form fields are physically equivalent.

Passively Q-switched and mode-locked dual-wavelength Nd:GGG laser with Cr4+:YAG as a saturable absorber

NASA Astrophysics Data System (ADS)

Chu, Hongwei; Zhao, Shengzhi; Li, Yufei; Yang, Kejian; Li, Guiqiu; Li, Dechun; Zhao, Jia; Qiao, Wenchao; Li, Tao; Feng, Chuansheng; Zhang, Haijuan

2014-03-01

By using neodymium-doped gadolinium gallium garnet (Nd:GGG) as a laser medium, a simultaneously passively Q-switched and mode-locked (QML) dual-wavelength laser with Cr4+:YAG as a saturable absorber is presented. The laser simultaneously oscillated at 1061 nm and 1063 nm, corresponding to a frequency difference of 0.53 THz. QML pulses with nearly 100% modulation depth were observed. The mode-locked pulse duration underneath the Q-switched envelope was estimated to be about 908 ps. The experimental results indicated that the dual-wavelength QML Nd:GGG laser can be an excellent candidate for the generation of THz waves.

A dual-mode highly efficient class-E stimulator controlled by a low-Q class-E power amplifier through duty cycle.

PubMed

Chiu, Hung-Wei; Lu, Chien-Chi; Chuang, Jia-min; Lin, Wei-Tso; Lin, Chii-Wann; Kao, Ming-Chien; Lin, Mu-Lien

2013-06-01

This paper presents the design flow of two high-efficiency class-E amplifiers for the implantable electrical stimulation system. The implantable stimulator is a high-Q class-E driver that delivers a sine-wave pulsed radiofrequency (PRF) stimulation, which was verified to have a superior efficacy in pain relief to a square wave. The proposed duty-cycle-controlled class-E PRF driver designed with a high-Q factor has two operational modes that are able to achieve 100% DC-AC conversion, and involves only one switched series inductor and an unchanged parallel capacitor. The measured output amplitude under low-voltage (LV) mode using a 22% duty cycle was 0.98 V with 91% efficiency, and under high-voltage (HV) mode using a 47% duty cycle was 2.95 V with 92% efficiency. These modes were inductively controlled by a duty-cycle detector, which can detect the duty-cycle modulated signal generated from the external complementary low-Q class-E power amplifier (PA). The design methodology of the low-Q inductive interface for a non-50% duty cycle is presented. The experimental results exhibits that the 1.5-V PA that consumes DC power of 14.21 mW was able to deliver a 2.9-V sine wave to a 500 Ω load. The optimal 60% drain efficiency of the system from the PA to the load was obtained at a 10-mm coupling distance.

Nano- and picosecond 3 μm Er: YSGG lasers using InAs as passive Q-switchers and mode-lockers

NASA Astrophysics Data System (ADS)

Vodopyanov, K. L.; Lukashev, A. V.; Phillips, C. C.

1993-01-01

Recent results are reported using ultra-thin molecular beam epitaxy (MBE)-grown InAs epilayers on GaAs substrates as passive shutters for 3 μm Er: YSGG lasers ( λ = 2.8 μm). The laser photon energy is 27% higher than the InAs bandgap at 300 K and bleaching occurs due to a band filling effect with a fast recovery time of < 100 ps. Depending on the resonator geometry two modes of operation can be achieved: Q-switched with pulse duration of 35 ns and 5-6 mJ energy (TEM 00 mode) and a Q-switched/mode-locked regime with an output in the form of a train of 30 pulses separated by a 4.3 ns interval, 0.25 mJ energy per spike and 30-50 ps pulse duration in a TEM 00-mode. The latter are the shortest pulses obtained with this lasing medium to date.

Optimal mode transformations for linear-optical cluster-state generation

DOE PAGES

Uskov, Dmitry B.; Lougovski, Pavel; Alsing, Paul M.; ...

2015-06-15

In this paper, we analyze the generation of linear-optical cluster states (LOCSs) via sequential addition of one and two qubits. Existing approaches employ the stochastic linear-optical two-qubit controlled-Z (CZ) gate with success rate of 1/9 per operation. The question of optimality of the CZ gate with respect to LOCS generation has remained open. We report that there are alternative schemes to the CZ gate that are exponentially more efficient and show that sequential LOCS growth is indeed globally optimal. We find that the optimal cluster growth operation is a state transformation on a subspace of the full Hilbert space. Finally,more » we show that the maximal success rate of postselected entangling n photonic qubits or m Bell pairs into a cluster is (1/2) n-1 and (1/4) m-1, respectively, with no ancilla photons, and we give an explicit optical description of the optimal mode transformations.« less

[Principal component analysis and cluster analysis of inorganic elements in sea cucumber Apostichopus japonicus].

PubMed

Liu, Xiao-Fang; Xue, Chang-Hu; Wang, Yu-Ming; Li, Zhao-Jie; Xue, Yong; Xu, Jie

2011-11-01

The present study is to investigate the feasibility of multi-elements analysis in determination of the geographical origin of sea cucumber Apostichopus japonicus, and to make choice of the effective tracers in sea cucumber Apostichopus japonicus geographical origin assessment. The content of the elements such as Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Hg and Pb in sea cucumber Apostichopus japonicus samples from seven places of geographical origin were determined by means of ICP-MS. The results were used for the development of elements database. Cluster analysis(CA) and principal component analysis (PCA) were applied to differentiate the sea cucumber Apostichopus japonicus geographical origin. Three principal components which accounted for over 89% of the total variance were extracted from the standardized data. The results of Q-type cluster analysis showed that the 26 samples could be clustered reasonably into five groups, the classification results were significantly associated with the marine distribution of the sea cucumber Apostichopus japonicus samples. The CA and PCA were the effective methods for elements analysis of sea cucumber Apostichopus japonicus samples. The content of the mineral elements in sea cucumber Apostichopus japonicus samples was good chemical descriptors for differentiating their geographical origins.

Hazards/Failure Modes and Effects Analysis MK 1 MOD 0 LSO-HUD Console System.

DTIC Science & Technology

1980-03-24

AsI~f~ ! 127 = 3gc Z Isre -0 -q ~sI I I 𔃻~~~ ~ _ _ 3_______ II! -0udC Z Z’ P4 12 d-U * ~s ’:i~i42 S- 60 -, Uh ~ U3l I OM -C ~ . - U 4~ dcd 8U-q Ali...8 VI SCOPE AND METHODOLOGY OF ANALYSIS ........ 1O FIGURE 1: H/ FMEA /(SSA) WORK SHEET FORMAT ........... 14 APPENDIX A: HAZARD/FAILURE MODES AND...EFFECTS ANALYSIS (H/ FMEA ) -- WORK SHEETS ......... 15(A-O) TABLE: SUBSYSTEM: UNIT I Heads-Up Display Console .............. 17(A-1) UNIT 2 Auxiliary

Myeloid- and lymphoid-specific breakpoint cluster regions in chromosome band 13q14 in acute leukemia.

PubMed

Coignet, L J; Lima, C S; Min, T; Streubel, B; Swansbury, J; Telford, N; Swanton, S; Bowen, A; Nagai, M; Catovsky, D; Fonatsch, C; Dyer, M J

1999-07-01

Abnormalities of chromosome band 13q14 occur in hematologic malignancies of all lineages and at all stages of differentiation. Unlike other chromosomal translocations, which are usually specific for a given lineage, the chromosomal translocation t(12;13)(p12;q14) has been observed in both B-cell and T-cell precursor acute lymphoblastic leukemia (BCP-, TCP-ALL), in differentiated and undifferentiated acute myeloblastic leukemia (AML), and in chronic myeloid leukemia (CML) at progression to blast crisis. The nature of these translocations and their pathologic consequences remain unknown. To begin to define the gene(s) involved on chromosome 13, we have performed fluorescence in situ hybridization (FISH) using a panel of YACs from the region, on a series of 10 cases of acute leukemia with t(12;13)(p12;q14) and 1 case each with "variant" translocations including t(12;13)(q21;q14), t(10;13)(q24;q14) and t(9;13)(p21;q14). In 8/13 cases/cell lines, the 13q14 break fell within a single 1.4 Mb CEPH MegaYAC. This YAC fell immediately telomeric of the forkhead (FKHR) gene, which is disrupted in the t(2;13)(q35;q14) seen in pediatric alveolar rhabdomyosarcoma. Seven of the 8 cases with breaks in this YAC were AML. In 4/13 cases, the 13q14 break fell within a 1.7-Mb YAC located about 3 Mb telomeric of the retinoblastoma (RB1) gene: all 4 cases were ALL. One case of myelodysplastic syndrome exhibited a break within 13q12, adjacent to the BRCA2 gene. These data indicate the presence of myeloid- and lymphoid-specific breakpoint cluster regions within chromosome band 13q14 in acute leukemia.

Analysis of nonreciprocal noise based on mode splitting in a high-Q optical microresonator

NASA Astrophysics Data System (ADS)

Yang, Zhaohua; Xiao, Yarong; Huo, Jiayan; Shao, Hui

2018-01-01

The whispering gallery mode optical microresonator offers a high quality factor, which enables it to act as the core component of a high sensitivity resonator optic gyro; however, nonreciprocal noise limits its precision. Considering the Sagnac effect, i.e. mode splitting in high-quality optical micro-resonators, we derive the explicit expression for the angular velocity versus the splitting amount, and verify the sensing mechanism by simulation using finite element method. Remarkably, the accuracy of the angular velocity measurement in the whispering gallery mode optical microresonator with a quality factor of 108 is 106 °/s. We obtain the optimal coupling position of the novel angular velocity sensing system by detecting the output transmittance spectra of different vertical coupling distances and axial coupling positions. In addition, the reason for the nonreciprocal phenomenon is determined by theoretical analysis of the evanescent distribution of a tapered fiber. These results will provide an effective method and a theoretical basis for suppression of the nonreciprocal noise.

Investigations of Q-switching and mode locking in diode-pumped Nd:YVO4 laser with passive saturable absorbers

NASA Astrophysics Data System (ADS)

Kwiatkowski, Jacek; Jabczynski, Jan K.; Zendzian, Waldemar

2005-03-01

The saturable absorbers (Cr4+:YAG, GaAs and LiF crystals for 1064-nm wavelength, V3+:YAG crystals for 1340-nm respectively) were examined as passive Mode Lockers and Q-switches in diode pumped Nd:YVO4 lasers in the Z-type resonators. In each case, partially modulated long trains of QML pulses were observed. As a rule, envelopes with about 1 μs duration and more than 50% depth of modulation were observed. For stabilization of the mode locking trains nonlinear crystals (KTP or LBO) as negative feedback elements were inserted. The fully modulated QML trains for intracavity II harmonic conversion at 670-nm wavelength in V3+:YAG Q-switched Nd:YVO4 laser with LBO crystal were demonstrated.

A Cluster Analysis of Personality Style in Adults with ADHD

ERIC Educational Resources Information Center

Robin, Arthur L.; Tzelepis, Angela; Bedway, Marquita

2008-01-01

Objective: The purpose of this study was to use hierarchical linear cluster analysis to examine the normative personality styles of adults with ADHD. Method: A total of 311 adults with ADHD completed the Millon Index of Personality Styles, which consists of 24 scales assessing motivating aims, cognitive modes, and interpersonal behaviors. Results:…

Discrimination and identification of Q-markers based on 'Spider-web' mode for quality control of traditional Chinese medicine.

PubMed

Jiang, Zhenzuo; Yang, Jing; Wang, Yuefei

2017-12-28

The safety and effectiveness of traditional Chinese medicine (TCM) in clinical practice is directly related to the quality of TCM. And, the quality control of TCM is a pivotal issue to the quality of TCM, but also an obstacle impeding the modernization of TCM. The purpose of this work is to compile and develop a strategy based on discrimination and identification of quality markers (Q-markers) for quality control of TCM. Mainly established by seven variables derived from four dimensions including content, stability, pharmacokinetics and pharmacology, the 'Spider-web' mode was undertaken to assess the Q-marker property of candidate compounds originated from TCM by taking regression area (A) and coefficient variation (CV) of the tested compounds into account. The importance index (ImI), ImI = A × 1/CV, was suggested to focus Q-markers. The compounds with larger regression area (A) and less coefficient variation (CV) are preferentially adopted as Q-markers, which should possess the satisfactory properties of content, stability, pharmacokinetics and pharmacological activity. To the contrary, the compounds are excluded on the grounds of the unsatisfactory Q-markers' property, less regression area (A) and larger coefficient variation (CV), which cannot represent the quality of TCM. The 'Spider-web' mode can filter out the redundant constituents and focus on the key indexes of quality control - Q-markers. The screened Q-markers possess the optimal integrated properties of content, stability, pharmacokinetics and pharmacology among the numerous and complicated ingredients of TCM, which can comprehensively characterize inherent quality of TCM. In summary, the novel strategy established in this work provides a valuable perspective for the quality control of TCM. Copyright © 2017 Elsevier GmbH. All rights reserved.

Cluster Correspondence Analysis.

PubMed

van de Velden, M; D'Enza, A Iodice; Palumbo, F

2017-03-01

A method is proposed that combines dimension reduction and cluster analysis for categorical data by simultaneously assigning individuals to clusters and optimal scaling values to categories in such a way that a single between variance maximization objective is achieved. In a unified framework, a brief review of alternative methods is provided and we show that the proposed method is equivalent to GROUPALS applied to categorical data. Performance of the methods is appraised by means of a simulation study. The results of the joint dimension reduction and clustering methods are compared with the so-called tandem approach, a sequential analysis of dimension reduction followed by cluster analysis. The tandem approach is conjectured to perform worse when variables are added that are unrelated to the cluster structure. Our simulation study confirms this conjecture. Moreover, the results of the simulation study indicate that the proposed method also consistently outperforms alternative joint dimension reduction and clustering methods.

Treatment of Melasma with the Photoacoustic Twin Pulse Mode of Low-Fluence 1,064 nm Q-Switched Nd:YAG Laser.

PubMed

Kim, Jee Young; Choi, Misoo; Nam, Chan Hee; Kim, Ji Seok; Kim, Myung Hwa; Park, Byung Cheol; Hong, Seung Phil

2016-06-01

Low-fluence 1,064 nm Q-switched Nd:YAG laser has been widely used for the treatment of melasma. Although new Q-switched Nd:YAG lasers with photoacoustic twin pulse (PTP) mode have been recently developed for high-efficiency, there is limited information available for the new technique. This study was designed to investigate the efficacy and adverse effects after few sessions of repeated low fluence 1,064 nm Q-switched Nd:YAG laser treatment with PTP mode in Asian women with melasma. Twenty-two Korean women were treated with a total of five sessions of low-fluence PTP mode Nd:YAG laser treatment (Pastelle®) at 2 weeks interval. Responses to treatments were evaluated by using Melasma Area and Severity Index (MASI) scoring, colorimeter measurement, and the investigators' and patients' overall assessments. Adverse events were recorded at each visit. Investigators' and patients' overall assessment showed that 'significantly improved' was assessed by 13 (59.1%) and 19 of 22 patients (86.4%), respectively. MASI scores were significantly reduced by 20.4%. The lightness, measured by using a colorimeter, was significantly increased by 1.3 point. Notable adverse events were not observed. After 5 sessions of laser therapy alone, about 60% of the subjects showed significant improvement. Few sessions of repeated laser toning treatment using the PTP mode is a safe and effective way to treat facial melasma.

Nonlinear MHD simulations of QH-mode DIII-D plasmas and implications for ITER high Q scenarios

NASA Astrophysics Data System (ADS)

Liu, F.; Huijsmans, G. T. A.; Loarte, A.; Garofalo, A. M.; Solomon, W. M.; Hoelzl, M.; Nkonga, B.; Pamela, S.; Becoulet, M.; Orain, F.; Van Vugt, D.

2018-01-01

In nonlinear MHD simulations of DIII-D QH-mode plasmas it has been found that low n kink/peeling modes (KPMs) are unstable and grow to a saturated kink-peeling mode. The features of the dominant saturated KPMs, which are localised toroidally by nonlinear coupling of harmonics, such as mode frequencies, density fluctuations and their effect on pedestal particle and energy transport, are in good agreement with the observations of the edge harmonic oscillation typically present in DIII-D QH-mode experiments. The nonlinear evolution of MHD modes including both kink-peeling modes and ballooning modes, is investigated through MHD simulations by varying the pedestal current and pressure relative to the initial conditions of DIII-D QH-mode plasma. The edge current and pressure at the pedestal are key parameters for the plasma either saturating to a QH-mode regime or a ballooning mode dominant regime. The influence of E × B flow and its shear on the QH-mode plasma has been investigated. E × B flow shear has a strong stabilisation effect on the medium to high-n modes but is destabilising for the n = 2 mode. The QH-mode extrapolation results of an ITER Q = 10 plasma show that the pedestal currents are large enough to destabilise n = 1-5 KPMs, leading to a stationary saturated kink-peeling mode.

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III.

PubMed

Ohad, S; Block, C; Kravitz, V; Farber, A; Pilo, S; Breuer, R; Rorman, E

2014-05-01

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material. The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05). The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity. The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention. © 2014 The Society for Applied Microbiology.

Method for exploratory cluster analysis and visualisation of single-trial ERP ensembles.

PubMed

Williams, N J; Nasuto, S J; Saddy, J D

2015-07-30

The validity of ensemble averaging on event-related potential (ERP) data has been questioned, due to its assumption that the ERP is identical across trials. Thus, there is a need for preliminary testing for cluster structure in the data. We propose a complete pipeline for the cluster analysis of ERP data. To increase the signal-to-noise (SNR) ratio of the raw single-trials, we used a denoising method based on Empirical Mode Decomposition (EMD). Next, we used a bootstrap-based method to determine the number of clusters, through a measure called the Stability Index (SI). We then used a clustering algorithm based on a Genetic Algorithm (GA) to define initial cluster centroids for subsequent k-means clustering. Finally, we visualised the clustering results through a scheme based on Principal Component Analysis (PCA). After validating the pipeline on simulated data, we tested it on data from two experiments - a P300 speller paradigm on a single subject and a language processing study on 25 subjects. Results revealed evidence for the existence of 6 clusters in one experimental condition from the language processing study. Further, a two-way chi-square test revealed an influence of subject on cluster membership. Our analysis operates on denoised single-trials, the number of clusters are determined in a principled manner and the results are presented through an intuitive visualisation. Given the cluster structure in some experimental conditions, we suggest application of cluster analysis as a preliminary step before ensemble averaging. Copyright © 2015 Elsevier B.V. All rights reserved.

Resonant Mode Interaction in Rayleigh-Benard Convection: Hexagon Case

NASA Astrophysics Data System (ADS)

Moroz, Vadim

2002-11-01

Resonant interaction of the "main" convection mode (q) with the first harmonic (q=sqrt(3)*q) is studied in the regime where both modes are (close to being) linearly unstable. The bifurcations and the resulting family of solutions are classified using symmetry group analysis; dependence of coefficients in amplitude equations on the fluid properties is analyzed. Main focus is made on the bifurcation from hex pattern with wavevector q*sqrt(3) to hex pattern q. Particular experimental conditions under which the bifurcation could be observed (as well as existence of other instabilities which could preempt it) are stated. Helpful discussions with Prof. Hermann Riecke are gladly acknowledged.

Linearly polarized pumped passively Q-switched Nd:YVO4 microchip laser for Ince-Gaussian laser modes with controllable orientations

NASA Astrophysics Data System (ADS)

He, Hong-Sen; Zhang, Ming-Ming; Dong, Jun; Ueda, Ken-Ichi

2016-12-01

A tilted, linearly polarized laser diode end-pumped Cr4+:YAG passively Q-switched a-cut Nd:YVO4 microchip laser for generating numerous Ince-Gaussian (IG) laser modes with controllable orientations has been demonstrated by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The same IG laser mode with different orientations has been achieved with the same absorbed pump power in a passively Q-switched Nd:YVO4 microchip laser under linearly polarized pumping when the incident pump power and the crystalline orientation of an a-cut Nd:YVO4 crystal are both properly selected. The significant improvement of pulsed laser performance of controllable IG modes has been achieved by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The maximum pulse energy is obtained along the a-axis of an a-cut Nd:YVO4 crystal and the highest peak power is achieved along the c-axis of an a-cut Nd:YVO4 crystal, respectively, which has potential applications on quantum computation and optical manipulation. The generation of controllable IG laser modes in microchip lasers under linearly polarized pumping provides a convenient and universal way to control IG laser mode numbers with anisotropic crystal as a gain medium.

Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

PubMed

Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

2016-07-14

In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

[Optimization of cluster analysis based on drug resistance profiles of MRSA isolates].

PubMed

Tani, Hiroya; Kishi, Takahiko; Gotoh, Minehiro; Yamagishi, Yuka; Mikamo, Hiroshige

2015-12-01

We examined 402 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from clinical specimens in our hospital between November 19, 2010 and December 27, 2011 to evaluate the similarity between cluster analysis of drug susceptibility tests and pulsed-field gel electrophoresis (PFGE). The results showed that the 402 strains tested were classified into 27 PFGE patterns (151 subtypes of patterns). Cluster analyses of drug susceptibility tests with the cut-off distance yielding a similar classification capability showed favorable results--when the MIC method was used, and minimum inhibitory concentration (MIC) values were used directly in the method, the level of agreement with PFGE was 74.2% when 15 drugs were tested. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) method was effective when the cut-off distance was 16. Using the SIR method in which susceptible (S), intermediate (I), and resistant (R) were coded as 0, 2, and 3, respectively, according to the Clinical and Laboratory Standards Institute (CLSI) criteria, the level of agreement with PFGE was 75.9% when the number of drugs tested was 17, the method used for clustering was the UPGMA, and the cut-off distance was 3.6. In addition, to assess the reproducibility of the results, 10 strains were randomly sampled from the overall test and subjected to cluster analysis. This was repeated 100 times under the same conditions. The results indicated good reproducibility of the results, with the level of agreement with PFGE showing a mean of 82.0%, standard deviation of 12.1%, and mode of 90.0% for the MIC method and a mean of 80.0%, standard deviation of 13.4%, and mode of 90.0% for the SIR method. In summary, cluster analysis for drug susceptibility tests is useful for the epidemiological analysis of MRSA.

Treatment of Melasma with the Photoacoustic Twin Pulse Mode of Low-Fluence 1,064 nm Q-Switched Nd:YAG Laser

PubMed Central

Kim, Jee Young; Choi, Misoo; Nam, Chan Hee; Kim, Ji Seok; Kim, Myung Hwa; Park, Byung Cheol

2016-01-01

Background Low-fluence 1,064 nm Q-switched Nd:YAG laser has been widely used for the treatment of melasma. Although new Q-switched Nd:YAG lasers with photoacoustic twin pulse (PTP) mode have been recently developed for high-efficiency, there is limited information available for the new technique. Objective This study was designed to investigate the efficacy and adverse effects after few sessions of repeated low fluence 1,064 nm Q-switched Nd:YAG laser treatment with PTP mode in Asian women with melasma. Methods Twenty-two Korean women were treated with a total of five sessions of low-fluence PTP mode Nd:YAG laser treatment (Pastelle®) at 2 weeks interval. Responses to treatments were evaluated by using Melasma Area and Severity Index (MASI) scoring, colorimeter measurement, and the investigators' and patients' overall assessments. Adverse events were recorded at each visit. Results Investigators' and patients' overall assessment showed that 'significantly improved' was assessed by 13 (59.1%) and 19 of 22 patients (86.4%), respectively. MASI scores were significantly reduced by 20.4%. The lightness, measured by using a colorimeter, was significantly increased by 1.3 point. Notable adverse events were not observed. Conclusion After 5 sessions of laser therapy alone, about 60% of the subjects showed significant improvement. Few sessions of repeated laser toning treatment using the PTP mode is a safe and effective way to treat facial melasma. PMID:27274626

The tracking analysis in the Q-weak experiment

NASA Astrophysics Data System (ADS)

Pan, J.; Androic, D.; Armstrong, D. S.; Asaturyan, A.; Averett, T.; Balewski, J.; Beaufait, J.; Beminiwattha, R. S.; Benesch, J.; Benmokhtar, F.; Birchall, J.; Carlini, R. D.; Cates, G. D.; Cornejo, J. C.; Covrig, S.; Dalton, M. M.; Davis, C. A.; Deconinck, W.; Diefenbach, J.; Dowd, J. F.; Dunne, J. A.; Dutta, D.; Duvall, W. S.; Elaasar, M.; Falk, W. R.; Finn, J. M.; Forest, T.; Gaskell, D.; Gericke, M. T. W.; Grames, J.; Gray, V. M.; Grimm, K.; Guo, F.; Hoskins, J. R.; Johnston, K.; Jones, D.; Jones, M.; Jones, R.; Kargiantoulakis, M.; King, P. M.; Korkmaz, E.; Kowalski, S.; Leacock, J.; Leckey, J.; Lee, A. R.; Lee, J. H.; Lee, L.; MacEwan, S.; Mack, D.; Magee, J. A.; Mahurin, R.; Mammei, J.; Martin, J. W.; McHugh, M. J.; Meekins, D.; Mei, J.; Michaels, R.; Micherdzinska, A.; Mkrtchyan, A.; Mkrtchyan, H.; Morgan, N.; Myers, K. E.; Narayan, A.; Ndukum, L. Z.; Nelyubin, V.; Nuruzzaman; van Oers, W. T. H.; Opper, A. K.; Page, S. A.; Pan, J.; Paschke, K. D.; Phillips, S. K.; Pitt, M. L.; Poelker, M.; Rajotte, J. F.; Ramsay, W. D.; Roche, J.; Sawatzky, B.; Seva, T.; Shabestari, M. H.; Silwal, R.; Simicevic, N.; Smith, G. R.; Solvignon, P.; Spayde, D. T.; Subedi, A.; Subedi, R.; Suleiman, R.; Tadevosyan, V.; Tobias, W. A.; Tvaskis, V.; Waidyawansa, B.; Wang, P.; Wells, S. P.; Wood, S. A.; Yang, S.; Young, R. D.; Zhamkochyan, S.

2016-12-01

The Q-weak experiment at Jefferson Laboratory measured the parity violating asymmetry ( A P V ) in elastic electron-proton scattering at small momentum transfer squared ( Q 2=0.025 ( G e V/ c)2), with the aim of extracting the proton's weak charge ({Q^p_W}) to an accuracy of 5 %. As one of the major uncertainty contribution sources to {Q^p_W}, Q 2 needs to be determined to ˜1 % so as to reach the proposed experimental precision. For this purpose, two sets of high resolution tracking chambers were employed in the experiment, to measure tracks before and after the magnetic spectrometer. Data collected by the tracking system were then reconstructed with dedicated software into individual electron trajectories for experimental kinematics determination. The Q-weak kinematics and the analysis scheme for tracking data are briefly described here. The sources that contribute to the uncertainty of Q 2 are discussed, and the current analysis status is reported.

The tracking analysis in the Q-weak experiment

DOE PAGES

Pan, J.; Androic, D.; Armstrong, D. S.; ...

2016-11-21

Here, the Q-weak experiment at Jefferson Laboratory measured the parity violating asymmetry (Amore » $$_{PV}$$ ) in elastic electron-proton scattering at small momentum transfer squared (Q$$^{2}$$=0.025 (G e V/c)$$^{2}$$), with the aim of extracting the proton’s weak charge ( $${Q^p_W}$$ ) to an accuracy of 5 %. As one of the major uncertainty contribution sources to $${Q^p_W}$$ , Q$$^{2}$$ needs to be determined to ~1 % so as to reach the proposed experimental precision. For this purpose, two sets of high resolution tracking chambers were employed in the experiment, to measure tracks before and after the magnetic spectrometer. Data collected by the tracking system were then reconstructed with dedicated software into individual electron trajectories for experimental kinematics determination. The Q-weak kinematics and the analysis scheme for tracking data are briefly described here. The sources that contribute to the uncertainty of Q$$^{2}$$ are discussed, and the current analysis status is reported.« less

Analysis of correlated mutations in HIV-1 protease using spectral clustering.

PubMed

Liu, Ying; Eyal, Eran; Bahar, Ivet

2008-05-15

The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies against HIV. Resistance is usually imparted by a cooperative mechanism that can be elucidated by a covariance analysis of sequence data. Identification of such correlated substitutions of amino acids may be obscured by evolutionary noise. HIV-1 protease sequences from patients subjected to different specific treatments (set 1), and from untreated patients (set 2) were subjected to sequence covariance analysis by evaluating the mutual information (MI) between all residue pairs. Spectral clustering of the resulting covariance matrices disclosed two distinctive clusters of correlated residues: the first, observed in set 1 but absent in set 2, contained residues involved in MDR acquisition; and the second, included those residues differentiated in the various HIV-1 protease subtypes, shortly referred to as the phylogenetic cluster. The MDR cluster occupies sites close to the central symmetry axis of the enzyme, which overlap with the global hinge region identified from coarse-grained normal-mode analysis of the enzyme structure. The phylogenetic cluster, on the other hand, occupies solvent-exposed and highly mobile regions. This study demonstrates (i) the possibility of distinguishing between the correlated substitutions resulting from neutral mutations and those induced by MDR upon appropriate clustering analysis of sequence covariance data and (ii) a connection between global dynamics and functional substitution of amino acids.

Comprehensive cluster analysis with Transitivity Clustering.

PubMed

Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

2011-03-01

Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

Pulsed-laser excitation of acoustic modes in open high-Q photoacoustic resonators for trace gas monitoring: results for C2H4

NASA Astrophysics Data System (ADS)

Brand, Christian; Winkler, Andreas; Hess, Peter; Miklós, András; Bozóki, Zoltán; Sneider, János

1995-06-01

The pulsed excitation of acoustic resonances was studied with a continuously monitoring photoacoustic detector system. Acoustic waves were generated in C2H4/N 2 gas mixtures by light absorption of the pulses from a transversely excited atmospheric CO2 laser. The photoacoustic part consisted of high-Q cylindrical resonators (Q factor 820 for the first radial mode in N2) and two adjoining variable acoustic filter systems. The time-resolved signal was Fourier transformed to a frequency spectrum of high resolution. For the first radial mode a Lorentzian profile was fitted to the measured data. The outside noise suppression and the signal-to-noise ratio were investigated in a normal laboratory environment in the flow-through mode. The acoustic and electric filter system combined with the

[Cluster analysis in biomedical researches].

PubMed

Akopov, A S; Moskovtsev, A A; Dolenko, S A; Savina, G D

2013-01-01

Cluster analysis is one of the most popular methods for the analysis of multi-parameter data. The cluster analysis reveals the internal structure of the data, group the separate observations on the degree of their similarity. The review provides a definition of the basic concepts of cluster analysis, and discusses the most popular clustering algorithms: k-means, hierarchical algorithms, Kohonen networks algorithms. Examples are the use of these algorithms in biomedical research.

Trapped fast particle destabilization of internal kink mode for the locally flattened q-profile with an inflection point

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

Wang, Xian-Qu; Zhang, Rui-Bin; Meng, Guo

2016-07-15

The destabilization of ideal internal kink modes by trapped fast particles in tokamak plasmas with a “shoulder”-like equilibrium current is investigated. It is found that energetic particle branch of the mode is unstable with the driving of fast-particle precession drifts and corresponds to a precessional fishbone. The mode with a low stability threshold is also more easily excited than the conventional precessional fishbone. This is different from earlier studies for the same equilibrium in which the magnetohydrodynamic (MHD) branch of the mode is stable. Furthermore, the stability and characteristic frequency of the mode are analyzed by solving the dispersion relationmore » and comparing with the conventional fishbone. The results suggest that an equilibrium with a locally flattened q-profile, may be modified by localized current drive (or bootstrap current, etc.), is prone to the onset of the precessional fishbone branch of the mode.« less

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

Dielectric spectroscopy of the SmQ* phase

NASA Astrophysics Data System (ADS)

Perkowski, P.; Bubnov, A.; Piecek, W.; Ogrodnik, K.; Hamplová, V.; Kašpar, M.

2011-11-01

Liquid crystal possessing two biphenyl moieties in the molecular core and lateral chlorine substitution far from the chiral chain has been studied by dielectric spectroscopy. On cooling from the isotropic phase, the material possesses the frustrated smectic Q* (SmQ*) and SmCA* phases. It has been confirmed by dielectric spectroscopy that the SmQ* phase can be related to the SmCA* anti-ferroelectric phase. However, only one relaxation process has been observed in the SmQ* phase, while in the SmCA*, two relaxations are clearly detectable. It seems that the mode found in the SmQ* can be connected with high-frequency anti-phase mode observed in the SmCA* phase. Its relaxation frequency is similar to PH relaxation frequency, but is weaker. The same relaxation has been observed even a few degrees above the SmQ*-Iso phase transition. Another explanation for the mode detected in SmQ* and isotropic phases can be molecular motions around short molecular axis.

Discrete-Time Deterministic $Q$ -Learning: A Novel Convergence Analysis.

PubMed

Wei, Qinglai; Lewis, Frank L; Sun, Qiuye; Yan, Pengfei; Song, Ruizhuo

2017-05-01

In this paper, a novel discrete-time deterministic Q -learning algorithm is developed. In each iteration of the developed Q -learning algorithm, the iterative Q function is updated for all the state and control spaces, instead of updating for a single state and a single control in traditional Q -learning algorithm. A new convergence criterion is established to guarantee that the iterative Q function converges to the optimum, where the convergence criterion of the learning rates for traditional Q -learning algorithms is simplified. During the convergence analysis, the upper and lower bounds of the iterative Q function are analyzed to obtain the convergence criterion, instead of analyzing the iterative Q function itself. For convenience of analysis, the convergence properties for undiscounted case of the deterministic Q -learning algorithm are first developed. Then, considering the discounted factor, the convergence criterion for the discounted case is established. Neural networks are used to approximate the iterative Q function and compute the iterative control law, respectively, for facilitating the implementation of the deterministic Q -learning algorithm. Finally, simulation results and comparisons are given to illustrate the performance of the developed algorithm.

Application of cluster analysis to geochemical compositional data for identifying ore-related geochemical anomalies

NASA Astrophysics Data System (ADS)

Zhou, Shuguang; Zhou, Kefa; Wang, Jinlin; Yang, Genfang; Wang, Shanshan

2017-12-01

Cluster analysis is a well-known technique that is used to analyze various types of data. In this study, cluster analysis is applied to geochemical data that describe 1444 stream sediment samples collected in northwestern Xinjiang with a sample spacing of approximately 2 km. Three algorithms (the hierarchical, k-means, and fuzzy c-means algorithms) and six data transformation methods (the z-score standardization, ZST; the logarithmic transformation, LT; the additive log-ratio transformation, ALT; the centered log-ratio transformation, CLT; the isometric log-ratio transformation, ILT; and no transformation, NT) are compared in terms of their effects on the cluster analysis of the geochemical compositional data. The study shows that, on the one hand, the ZST does not affect the results of column- or variable-based (R-type) cluster analysis, whereas the other methods, including the LT, the ALT, and the CLT, have substantial effects on the results. On the other hand, the results of the row- or observation-based (Q-type) cluster analysis obtained from the geochemical data after applying NT and the ZST are relatively poor. However, we derive some improved results from the geochemical data after applying the CLT, the ILT, the LT, and the ALT. Moreover, the k-means and fuzzy c-means clustering algorithms are more reliable than the hierarchical algorithm when they are used to cluster the geochemical data. We apply cluster analysis to the geochemical data to explore for Au deposits within the study area, and we obtain a good correlation between the results retrieved by combining the CLT or the ILT with the k-means or fuzzy c-means algorithms and the potential zones of Au mineralization. Therefore, we suggest that the combination of the CLT or the ILT with the k-means or fuzzy c-means algorithms is an effective tool to identify potential zones of mineralization from geochemical data.

Molecular analysis of Hb Q-H disease and Hb Q-Hb E in a Singaporean family.

PubMed

Tan, J; Tay, J S; Wong, Y C; Kham, S K; Bte Abd Aziz, N; Teo, S H; Wong, H B

1995-01-01

Hb Q (alpha 74Asp-His) results from a mutation in the alpha-gene such that abnormal alpha Q-chains are synthesized. The alpha Q-chains combine with the normal Beta A-chains to form abnormal Hb alpha 2Q beta 2A (Hb Q). Hb Q-H disease is rare, and has been reported only in the Chinese. We report here a Chinese family, were the mother diagnosed with Hb Q-H disease and the father with Hb E heterozygosity and a child with Hb Q-E-thalassemia. Thalassemia screening of the mother's blood revealed a Hb level of 6.8g/dl with low MCV and MCH. Her blood film was indicative of thalassemia. Cellulose acetate electrophoresis showed Hb H and Hb Q with the absence of Hb A. Globin chain biosynthesis was carried out and alpha Q- and beta-chains were detected. Normal alpha- chains were absent. Digestion of the mother's DNA with Bam HI and Bgl II followed by hybridization with the 1.5 kb alpha-Pst probe showed a two alpha-gene deletion on one chromosome and the -alpha Q chain mutant with the -alpha 4.2 defect on the other chromosome. DNA amplification studies indicated the two-gene deletion to be of the -SEA/ defect. The patient was concluded to possess Hb Q-H disease (--SEA/-alpha 4.2Q). Cellulose acetate electrophoresis of the father's blood showed the presence of Hb A, F and E. Molecular analysis of the father's DNA confirmed an intact set of alpha-genes (alpha alpha/alpha alpha). Globin chain biosynthesis of fetal blood of their child showed gamma, beta A, beta E, alpha A and alpha Q-chains. Molecular analysis of the child's DNA showed one alpha-gene deletion, thus giving a genotype of alpha alpha/-alpha 4.2Q beta beta E.

Evolutionary history of linked D4Z4 and Beta satellite clusters at the FSHD locus (4q35).

PubMed

Giussani, Marta; Cardone, Maria Francesca; Bodega, Beatrice; Ginelli, Enrico; Meneveri, Raffaella

2012-11-01

We performed a detailed genomic investigation of the chimpanzee locus syntenic to human chromosome 4q35.2, associated to the facioscapulohumeral dystrophy. Two contigs of approximately 150 kb and 200 kb were derived from PTR chromosomes 4q35 and 3p12, respectively: both regions showed a very similar sequence organization, including D4Z4 and Beta satellite linked clusters. Starting from these findings, we derived a hypothetical evolutionary history of human 4q35, 10q26 and 3p12 chromosome regions focusing on the D4Z4-Beta satellite linked organization. The D4Z4 unit showed an open reading frame (DUX4) at both PTR 4q35 and 3p12 regions; furthermore some subregions of the Beta satellite unit showed a high degree of conservation between chimpanzee and humans. In conclusion, this paper provides evidence that at the 4q subtelomere the linkage between D4Z4 and Beta satellite arrays is a feature that appeared late during evolution and is conserved between chimpanzee and humans. Copyright © 2012 Elsevier Inc. All rights reserved.

Evolutionary history of linked D4Z4 and Beta satellite clusters at the FSHD locus (4q35)☆

PubMed Central

Giussani, Marta; Cardone, Maria Francesca; Bodega, Beatrice; Ginelli, Enrico; Meneveri, Raffaella

2012-01-01

We performed a detailed genomic investigation of the chimpanzee locus syntenic to human chromosome 4q35.2, associated to the facioscapulohumeral dystrophy. Two contigs of approximately 150 kb and 200 kb were derived from PTR chromosomes 4q35 and 3p12, respectively: both regions showed a very similar sequence organization, including D4Z4 and Beta satellite linked clusters. Starting from these findings, we derived a hypothetical evolutionary history of human 4q35, 10q26 and 3p12 chromosome regions focusing on the D4Z4–Beta satellite linked organization. The D4Z4 unit showed an open reading frame (DUX4) at both PTR 4q35 and 3p12 regions; furthermore some subregions of the Beta satellite unit showed a high degree of conservation between chimpanzee and humans. In conclusion, this paper provides evidence that at the 4q subtelomere the linkage between D4Z4 and Beta satellite arrays is a feature that appeared late during evolution and is conserved between chimpanzee and humans. PMID:22824653

Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase.

PubMed

Chen, Qi; Cheng, Xiaolin; Wei, Dongqing; Xu, Qin

2015-03-01

Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.

Generating high-peak-power structured lights in selectively pumped passively Q-switched lasers with astigmatic mode transformations

NASA Astrophysics Data System (ADS)

Chang, C. C.; Hsieh, Y. H.; Lee, C. Y.; Sung, C. L.; Tuan, P. H.; Tung, J. C.; Liang, H. C.; Chen, Y. F.

2017-12-01

Various high-order Hermite-Gaussian (HG) modes with high repetition rates and high peak powers are systematically generated by designing the cavity configuration to satisfy the criterion of the passive Q-switching. For the HG m,0 modes with the order m  =  1-9, the pulse repetition rate can exceed 100 kHz with peak power higher than 0.3 kW. For the HG m,m modes with the order m  =  1-10, the pulse repetition rate can be up to 37 kHz with peak power higher than 0.35 kW. Furthermore, the high-order HG beams is transformed by using an astigmatic mode converter to generate various structured lights with optical vortices. Experimental patterns of the transformed high-order HG beams in the propagation are theoretically analyzed and the phase structures are numerically manifested.

Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.

PubMed

Nurmi, Erika L; Dowd, Michael; Tadevosyan-Leyfer, Ovsanna; Haines, Jonathan L; Folstein, Susan E; Sutcliffe, James S

2003-07-01

Autism displays a remarkably high heritability but a complex genetic etiology. One approach to identifying susceptibility loci under these conditions is to define more homogeneous subsets of families on the basis of genetically relevant phenotypic or biological characteristics that vary from case to case. The authors performed a principal components analysis, using items from the Autism Diagnostic Interview, which resulted in six clusters of variables, five of which showed significant sib-sib correlation. The utility of these phenotypic subsets was tested in an exploratory genetic analysis of the autism candidate region on chromosome 15q11-q13. When the Collaborative Linkage Study of Autism sample was divided, on the basis of mean proband score for the "savant skills" cluster, the heterogeneity logarithm of the odds under a recessive model at D15S511, within the GABRB3 gene, increased from 0.6 to 2.6 in the subset of families in which probands had greater savant skills. These data are consistent with the genetic contribution of a 15q locus to autism susceptibility in a subset of affected individuals exhibiting savant skills. Similar types of skills have been noted in individuals with Prader-Willi syndrome, which results from deletions of this chromosomal region.

Q-Type Factor Analysis of Healthy Aged Men.

ERIC Educational Resources Information Center

Kleban, Morton H.

Q-type factor analysis was used to re-analyze baseline data collected in 1957, on 47 men aged 65-91. Q-type analysis is the use of factor methods to study persons rather than tests. Although 550 variables were originally studied involving psychiatry, medicine, cerebral metabolism and chemistry, personality, audiometry, dichotic and diotic memory,…

Higher Order Mode Analysis of the SNS Superconducting Linac

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

M. Doleans; D. Jeon; S. Kim

2001-06-01

Higher order modes (HOM's) of monopoles, dipoles, quadrupoles and sextupoles in {beta} = 0.61 and {beta} = 0.81 6-cell superconducting (SC) cavities for the Spallation Neutron Source (SNS) project, have been found up to about 3 GHz and their properties such as R/Q, trapping possibility, etc have been figured out in concerning with the manufacturing imperfection. Main issues of HOM's are beam instabilities (published separately) and HOM induced power especially from TM monopoles. The time structure of SNS beam has three different time scales of pulses, which are micro-pulse, midi-pulse and macropulse. Each time structure will generate resonances. When amore » mode is near these resonance frequencies, the induced voltage could be large and accordingly the resulting HOM power, too. In order to understand the effects from such a complex beam time structure on the mode excitation and resulting HOM power, analytic expressions are developed. With these analytic expressions, the induced HOM voltage and HOM power were calculated by assuming external Q for each HOM.« less

Characterization of distinct Arctic aerosol accumulation modes and their sources

NASA Astrophysics Data System (ADS)

Lange, R.; Dall'Osto, M.; Skov, H.; Nøjgaard, J. K.; Nielsen, I. E.; Beddows, D. C. S.; Simo, R.; Harrison, R. M.; Massling, A.

2018-06-01

In this work we use cluster analysis of long term particle size distribution data to expand an array of different shorter term atmospheric measurements, thereby gaining insights into longer term patterns and properties of Arctic aerosol. Measurements of aerosol number size distributions (9-915 nm) were conducted at Villum Research Station (VRS), Station Nord in North Greenland during a 5 year record (2012-2016). Alongside this, measurements of aerosol composition, meteorological parameters, gaseous compounds and cloud condensation nuclei (CCN) activity were performed during different shorter occasions. K-means clustering analysis of particle number size distributions on daily basis identified several clusters. Clusters of accumulation mode aerosols (main size modes > 100 nm) accounted for 56% of the total aerosol during the sampling period (89-91% during February-April, 1-3% during June-August). By association to chemical composition, cloud condensation nuclei properties, and meteorological variables, three typical accumulation mode aerosol clusters were identified: Haze (32% of the time), Bimodal (14%) and Aged (6%). In brief: (1) Haze accumulation mode aerosol shows a single mode at 150 nm, peaking in February-April, with highest loadings of sulfate and black carbon concentrations. (2) Accumulation mode Bimodal aerosol shows two modes, at 38 nm and 150 nm, peaking in June-August, with the highest ratio of organics to sulfate concentrations. (3) Aged accumulation mode aerosol shows a single mode at 213 nm, peaking in September-October and is associated with cloudy and humid weather conditions during autumn. The three aerosol clusters were considered alongside CCN concentrations. We suggest that organic compounds, that are likely marine biogenic in nature, greatly influence the Bimodal cluster and contribute significantly to its CCN activity. This stresses the importance of better characterizing the marine ecosystem and the aerosol-mediated climate effects in the

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.

PubMed

Wang, Jianxin; Zhong, Jiancheng; Chen, Gang; Li, Min; Wu, Fang-xiang; Pan, Yi

2015-01-01

Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

q-bosons and the q-analogue quantized field

NASA Technical Reports Server (NTRS)

Nelson, Charles A.

1995-01-01

The q-analogue coherent states are used to identify physical signatures for the presence of a 1-analogue quantized radiation field in the q-CS classical limits where the absolute value of z is large. In this quantum-optics-like limit, the fractional uncertainties of most physical quantities (momentum, position, amplitude, phase) which characterize the quantum field are O(1). They only vanish as O(1/absolute value of z) when q = 1. However, for the number operator, N, and the N-Hamiltonian for a free q-boson gas, H(sub N) = h(omega)(N + 1/2), the fractional uncertainties do still approach zero. A signature for q-boson counting statistics is that (Delta N)(exp 2)/ (N) approaches 0 as the absolute value of z approaches infinity. Except for its O(1) fractional uncertainty, the q-generalization of the Hermitian phase operator of Pegg and Barnett, phi(sub q), still exhibits normal classical behavior. The standard number-phase uncertainty-relation, Delta(N) Delta phi(sub q) = 1/2, and the approximate commutation relation, (N, phi(sub q)) = i, still hold for the single-mode q-analogue quantized field. So, N and phi(sub q) are almost canonically conjugate operators in the q-CS classical limit. The q-analogue CS's minimize this uncertainty relation for moderate (absolute value of z)(exp 2).

Seismic facies analysis based on self-organizing map and empirical mode decomposition

NASA Astrophysics Data System (ADS)

Du, Hao-kun; Cao, Jun-xing; Xue, Ya-juan; Wang, Xing-jian

2015-01-01

Seismic facies analysis plays an important role in seismic interpretation and reservoir model building by offering an effective way to identify the changes in geofacies inter wells. The selections of input seismic attributes and their time window have an obvious effect on the validity of classification and require iterative experimentation and prior knowledge. In general, it is sensitive to noise when waveform serves as the input data to cluster analysis, especially with a narrow window. To conquer this limitation, the Empirical Mode Decomposition (EMD) method is introduced into waveform classification based on SOM. We first de-noise the seismic data using EMD and then cluster the data using 1D grid SOM. The main advantages of this method are resolution enhancement and noise reduction. 3D seismic data from the western Sichuan basin, China, are collected for validation. The application results show that seismic facies analysis can be improved and better help the interpretation. The powerful tolerance for noise makes the proposed method to be a better seismic facies analysis tool than classical 1D grid SOM method, especially for waveform cluster with a narrow window.

Theoretical and experimental analysis of injection seeding a Q-switched alexandrite laser

NASA Technical Reports Server (NTRS)

Prasad, C. R.; Lee, H. S.; Glesne, T. R.; Monosmith, B.; Schwemmer, G. K.

1991-01-01

Injection seeding is a method for achieving linewidths of less than 500 MHz in the output of broadband, tunable, solid state lasers. Dye lasers, CW and pulsed diode lasers, and other solid state lasers have been used as injection seeders. By optimizing the fundamental laser parameters of pump energy, Q-switched pulse build-up time, injection seed power and mode matching, one can achieve significant improvements in the spectral purity of the Q-switched output. These parameters are incorporated into a simple model for analyzing spectral purity and pulse build-up processes in a Q-switched, injection-seeded laser. Experiments to optimize the relevant parameters of an alexandrite laser show good agreement.

Analysis of lamprey clustered Fox genes: insight into Fox gene evolution and expression in vertebrates.

PubMed

Wotton, Karl R; Shimeld, Sebastian M

2011-12-01

In the human genome, members of the FoxC, FoxF, FoxL1, and FoxQ1 gene families are found in two paralagous clusters. One cluster contains the genes FOXQ1, FOXF2, FOXC1 and the second consists of FOXF1, FOXC2, and FOXL1. In jawed vertebrates these genes are known to be expressed in different pharyngeal tissues and all, except FoxQ1, are involved in patterning the early embryonic mesoderm. We have previously traced the evolution of this cluster in the bony vertebrates, and the gene content is identical in the dogfish, a member of the most basally branching lineage of the jawed vertebrates. Here we extend these analyses to jawless vertebrates. Using genomic searches and molecular approaches we have identified homologues of these genes from lampreys. We identify two FoxC genes, two FoxF genes, two FoxQ1 genes and single FoxL1 gene. We examine the embryonic expression of one predominantly mesodermally expressed gene family, FoxC, and the endodermally expressed member of the cluster, FoxQ1. We identified FoxQ1 transcripts in the pharyngeal endoderm, while the two FoxC genes are differentially expressed in the pharyngeal mesenchyme and ectoderm. Furthermore we identify conserved expression of lamprey FoxC genes in the paraxial and intermediate mesoderms. We interpret our results through a chordate-wide comparison of expression patterns and discuss gene content in the context of theories on the evolution of the vertebrate genome. 2011 Elsevier B.V. All rights reserved.

Statistical analysis of m/ n = 2/1 locked and quasi-stationary modes with rotating precursors at DIII-D

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

Sweeney, Ryan Myles; Choi, W.; La Haye, R. J.

A database has been developed to study the evolution, the nonlinear effects on equilibria, and the disruptivity of locked and quasi-stationary modes with poloidal and toroidal mode numbers m = 2 and n = 1 at DIII-D. The analysis of 22500 discharges shows that more than 18% of disruptions are due to locked or quasi-stationary modes with rotating precursors (not including born locked modes). A parameter formulated by the plasma internal inductance l i divided by the safety factor at 95% of the poloidal flux, q 95, is found to exhibit predictive capability over whether a locked mode will cause a disruption or not, and does so up to hundreds of milliseconds before the disruption. Within 20 ms of the disruption, the shortest distance between the island separatrix and the unperturbed last closed flux surface, referred to as d edge, performs comparably tomore » $${{l}_{i}}/{{q}_{95}}$$ in its ability to discriminate disruptive locked modes. Out of all parameters considered, d edge also correlates best with the duration of the locked mode. Disruptivity following a m/n = 2/1 locked mode as a function of the normalized beta, $${{\\beta}_{\\text{N}}}$$ , is observed to peak at an intermediate value, and decrease for high values. The decrease is attributed to the correlation between $${{\\beta}_{\\text{N}}}$$ and q 95 in the DIII-D operational space. Within 50 ms of a locked mode disruption, average behavior includes exponential growth of the n = 1 perturbed field, which might be due to the 2/1 locked mode. Surprisingly, even assuming the aforementioned 2/1 growth, disruptivity following a locked mode shows little dependence on island width up to 20 ms before the disruption. Separately, greater deceleration of the rotating precursor is observed when the wall torque is large. At locking, modes are often observed to align at a particular phase, which is likely related to a residual error field. Timescales associated with the mode evolution are also studied and dictate the

Statistical analysis of m/ n = 2/1 locked and quasi-stationary modes with rotating precursors at DIII-D

DOE PAGES

Sweeney, Ryan Myles; Choi, W.; La Haye, R. J.; ...

2016-11-01

A database has been developed to study the evolution, the nonlinear effects on equilibria, and the disruptivity of locked and quasi-stationary modes with poloidal and toroidal mode numbers m = 2 and n = 1 at DIII-D. The analysis of 22500 discharges shows that more than 18% of disruptions are due to locked or quasi-stationary modes with rotating precursors (not including born locked modes). A parameter formulated by the plasma internal inductance l i divided by the safety factor at 95% of the poloidal flux, q 95, is found to exhibit predictive capability over whether a locked mode will cause a disruption or not, and does so up to hundreds of milliseconds before the disruption. Within 20 ms of the disruption, the shortest distance between the island separatrix and the unperturbed last closed flux surface, referred to as d edge, performs comparably tomore » $${{l}_{i}}/{{q}_{95}}$$ in its ability to discriminate disruptive locked modes. Out of all parameters considered, d edge also correlates best with the duration of the locked mode. Disruptivity following a m/n = 2/1 locked mode as a function of the normalized beta, $${{\\beta}_{\\text{N}}}$$ , is observed to peak at an intermediate value, and decrease for high values. The decrease is attributed to the correlation between $${{\\beta}_{\\text{N}}}$$ and q 95 in the DIII-D operational space. Within 50 ms of a locked mode disruption, average behavior includes exponential growth of the n = 1 perturbed field, which might be due to the 2/1 locked mode. Surprisingly, even assuming the aforementioned 2/1 growth, disruptivity following a locked mode shows little dependence on island width up to 20 ms before the disruption. Separately, greater deceleration of the rotating precursor is observed when the wall torque is large. At locking, modes are often observed to align at a particular phase, which is likely related to a residual error field. Timescales associated with the mode evolution are also studied and dictate the

Invited Article: Generation of one-million-mode continuous-variable cluster state by unlimited time-domain multiplexing

NASA Astrophysics Data System (ADS)

Yoshikawa, Jun-ichi; Yokoyama, Shota; Kaji, Toshiyuki; Sornphiphatphong, Chanond; Shiozawa, Yu; Makino, Kenzo; Furusawa, Akira

2016-09-01

In recent quantum optical continuous-variable experiments, the number of fully inseparable light modes has drastically increased by introducing a multiplexing scheme either in the time domain or in the frequency domain. Here, modifying the time-domain multiplexing experiment reported in the work of Yokoyama et al. [Nat. Photonics 7, 982 (2013)], we demonstrate the successive generation of fully inseparable light modes for more than one million modes. The resulting multi-mode state is useful as a dual-rail continuous variable cluster state. We circumvent the previous problem of optical phase drifts, which has limited the number of fully inseparable light modes to around ten thousands, by continuous feedback control of the optical system.

Changing cluster composition in cluster randomised controlled trials: design and analysis considerations

PubMed Central

2014-01-01

Background There are many methodological challenges in the conduct and analysis of cluster randomised controlled trials, but one that has received little attention is that of post-randomisation changes to cluster composition. To illustrate this, we focus on the issue of cluster merging, considering the impact on the design, analysis and interpretation of trial outcomes. Methods We explored the effects of merging clusters on study power using standard methods of power calculation. We assessed the potential impacts on study findings of both homogeneous cluster merges (involving clusters randomised to the same arm of a trial) and heterogeneous merges (involving clusters randomised to different arms of a trial) by simulation. To determine the impact on bias and precision of treatment effect estimates, we applied standard methods of analysis to different populations under analysis. Results Cluster merging produced a systematic reduction in study power. This effect depended on the number of merges and was most pronounced when variability in cluster size was at its greatest. Simulations demonstrate that the impact on analysis was minimal when cluster merges were homogeneous, with impact on study power being balanced by a change in observed intracluster correlation coefficient (ICC). We found a decrease in study power when cluster merges were heterogeneous, and the estimate of treatment effect was attenuated. Conclusions Examples of cluster merges found in previously published reports of cluster randomised trials were typically homogeneous rather than heterogeneous. Simulations demonstrated that trial findings in such cases would be unbiased. However, simulations also showed that any heterogeneous cluster merges would introduce bias that would be hard to quantify, as well as having negative impacts on the precision of estimates obtained. Further methodological development is warranted to better determine how to analyse such trials appropriately. Interim recommendations

Mixture modelling for cluster analysis.

PubMed

McLachlan, G J; Chang, S U

2004-10-01

Cluster analysis via a finite mixture model approach is considered. With this approach to clustering, the data can be partitioned into a specified number of clusters g by first fitting a mixture model with g components. An outright clustering of the data is then obtained by assigning an observation to the component to which it has the highest estimated posterior probability of belonging; that is, the ith cluster consists of those observations assigned to the ith component (i = 1,..., g). The focus is on the use of mixtures of normal components for the cluster analysis of data that can be regarded as being continuous. But attention is also given to the case of mixed data, where the observations consist of both continuous and discrete variables.

Error minimization algorithm for comparative quantitative PCR analysis: Q-Anal.

PubMed

OConnor, William; Runquist, Elizabeth A

2008-07-01

Current methods for comparative quantitative polymerase chain reaction (qPCR) analysis, the threshold and extrapolation methods, either make assumptions about PCR efficiency that require an arbitrary threshold selection process or extrapolate to estimate relative levels of messenger RNA (mRNA) transcripts. Here we describe an algorithm, Q-Anal, that blends elements from current methods to by-pass assumptions regarding PCR efficiency and improve the threshold selection process to minimize error in comparative qPCR analysis. This algorithm uses iterative linear regression to identify the exponential phase for both target and reference amplicons and then selects, by minimizing linear regression error, a fluorescence threshold where efficiencies for both amplicons have been defined. From this defined fluorescence threshold, cycle time (Ct) and the error for both amplicons are calculated and used to determine the expression ratio. Ratios in complementary DNA (cDNA) dilution assays from qPCR data were analyzed by the Q-Anal method and compared with the threshold method and an extrapolation method. Dilution ratios determined by the Q-Anal and threshold methods were 86 to 118% of the expected cDNA ratios, but relative errors for the Q-Anal method were 4 to 10% in comparison with 4 to 34% for the threshold method. In contrast, ratios determined by an extrapolation method were 32 to 242% of the expected cDNA ratios, with relative errors of 67 to 193%. Q-Anal will be a valuable and quick method for minimizing error in comparative qPCR analysis.

Fano q-reversal in topological insulator Bi 2Se 3

DOE PAGES

S. V. Dordevic; Petrovic, C.; Foster, G. M.; ...

2016-03-22

Here, we studied the magneto-optical response of a canonical topological insulator Bi 2Se 3 with the goal of addressing a controversial issue of electron–phonon coupling. Magnetic-field induced modifications of reflectance are very pronounced in the infrared part of the spectrum, indicating strong electron–phonon coupling. This coupling causes an asymmetric line-shape of the 60 cm –1 phonon mode, and is analyzed within the Fano formalism. The analysis reveals that the Fano asymmetry parameter ( q) changes sign when the cyclotron resonance is degenerate with the phonon mode. To the best of our knowledge this is the first example of magnetic fieldmore » driven q-reversal.« less

Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome.

PubMed

Duker, Angela L; Ballif, Blake C; Bawle, Erawati V; Person, Richard E; Mahadevan, Sangeetha; Alliman, Sarah; Thompson, Regina; Traylor, Ryan; Bejjani, Bassem A; Shaffer, Lisa G; Rosenfeld, Jill A; Lamb, Allen N; Sahoo, Trilochan

2010-11-01

Prader-Willi syndrome (PWS) is a neurobehavioral disorder manifested by infantile hypotonia and feeding difficulties in infancy, followed by morbid obesity secondary to hyperphagia. It is caused by deficiency of paternally expressed transcript(s) within the human chromosome region 15q11.2. PWS patients harboring balanced chromosomal translocations with breakpoints within small nuclear ribonucleoprotein polypeptide N (SNRPN) have provided indirect evidence for a role for the imprinted C/D box containing small nucleolar RNA (snoRNA) genes encoded downstream of SNRPN. In addition, recently published data provide strong evidence in support of a role for the snoRNA SNORD116 cluster (HBII-85) in PWS etiology. In this study, we performed detailed phenotypic, cytogenetic, and molecular analyses including chromosome analysis, array comparative genomic hybridization (array CGH), expression studies, and single-nucleotide polymorphism (SNP) genotyping for parent-of-origin determination of the 15q11.2 microdeletion on an 11-year-old child expressing the major components of the PWS phenotype. This child had an ∼236.29 kb microdeletion at 15q11.2 within the larger Prader-Willi/Angelman syndrome critical region that included the SNORD116 cluster of snoRNAs. Analysis of SNP genotypes in proband and mother provided evidence in support of the deletion being on the paternal chromosome 15. This child also met most of the major PWS diagnostic criteria including infantile hypotonia, early-onset morbid obesity, and hypogonadism. Identification and characterization of this case provide unequivocal evidence for a critical role for the SNORD116 snoRNA molecules in PWS pathogenesis. Array CGH testing for genomic copy-number changes in cases with complex phenotypes is proving to be invaluable in detecting novel alterations and enabling better genotype-phenotype correlations.

Light scattering Q-space analysis of irregularly shaped particles

NASA Astrophysics Data System (ADS)

Heinson, Yuli W.; Maughan, Justin B.; Heinson, William R.; Chakrabarti, Amitabha; Sorensen, Christopher M.

2016-01-01

We report Q-space analysis of light scattering phase function data for irregularly shaped dust particles and of theoretical model output to describe them. This analysis involves plotting the scattered intensity versus the magnitude of the scattering wave vector q = (4π/λ)sin(θ/2), where λ is the optical wavelength and θ is the scattering angle, on a double-logarithmic plot. In q-space all the particle shapes studied display a scattering pattern which includes a q-independent forward scattering regime; a crossover, Guinier regime when q is near the inverse size; a power law regime; and an enhanced backscattering regime. Power law exponents show a quasi-universal functionality with the internal coupling parameter ρ'. The absolute value of the exponents start from 4 when ρ' < 1, the diffraction limit, and decreases as ρ' increases until a constant 1.75 ± 0.25 when ρ' ≳ 10. The diffraction limit exponent implies that despite their irregular structures, all the particles studied have mass and surface scaling dimensions of Dm = 3 and Ds = 2, respectively. This is different from fractal aggregates that have a power law equal to the fractal dimension Df because Df = Dm = Ds < 3. Spheres have Dm = 3 and Ds = 2 but do not show a single power law nor the same functionality with ρ'. The results presented here imply that Q-space analysis can differentiate between spheres and these two types of irregularly shaped particles. Furthermore, they are applicable to analysis of the contribution of aerosol radiative forcing to climate change and of aerosol remote sensing data.

The non-resonant kink modes triggering strong sawtooth-like crashes in the EAST tokamak

NASA Astrophysics Data System (ADS)

Li, Erzhong; Igochine, V.; Dumbrajs, O.; Xu, L.; Chen, K.; Shi, T.; Hu, L.

2014-12-01

Evolution of the safety factor (q) profile during L-H transitions in the Experimental Advanced Superconducting Tokamak (EAST) was accompanied by strong core crashes prior to regular sawtooth behavior. These crashes appeared in the absence of q = 1 (q is the safety factor) rational surface inside the plasma. Analysis indicates that the m/n = 2/1 tearing mode is destabilized and phase-locked with the m/n = 1/1 non-resonant kink mode (the q = 1 rational surface is absent) due to the self-consistent evolution of plasma profiles as the L-H transition occurs (m and n are the poloidal and toroidal mode numbers, respectively). The growing m/n = 1/1 mode destabilizes the m/n = 2/2 kink mode which eventually triggers the strong crash due to an anomalous heat conductivity, as predicted by the transport model of stochastic magnetic fields using experimental parameters. It is also shown that the magnetic topology changes with the amplitude of m/n = 2/2 mode and the value of center safety factor in a reasonable range.

Optimal sensitivity for molecular recognition MAC-mode AFM

PubMed

Schindler; Badt; Hinterdorfer; Kienberger; Raab; Wielert-Badt; Pastushenko

2000-02-01

Molecular recognition force microscopy (MRFM) using the magnetic AC mode (MAC mode) atomic force microscope (AFM) was recently investigated to locate and probe recognition sites. A flexible crosslinker carrying a ligand is bound to the tip for the molecular recognition of receptors on the surface of a sample. In this report, the driving frequency is calculated which optimizes the sensitivity (S). The sensitivity of MRFM is defined as the relative change of the magnetically excited cantilever deflection amplitude arising from a crosslinker/antibody/antigen connection that is characterized by a very small force constant. The sensitivity is calculated in a damped oscillator model with a certain value of quality factor Q, which, together with load, defines the frequency response (unloaded oscillator shows resonance at Q > 0.707). If Q < 1, the greatest value of S corresponds to zero driving frequency omega (measured in units of eigenfrequency). Therefore, for Q < 1, MAC-mode has no advantage in comparison with DC-mode. Two additional extremes are found at omegaL = (1 - 1/Q)(1/2) and omegaR = (1 + 1/Q)(1/2), with corresponding sensitivities S(L) = Q2/(2Q - 1), S(R) = Q2/(2Q + 1). The L-extreme exists only for Q > 1, and then S(L) > S(R), i.e. the L-extreme is the main one. For Q > 1, S(L) > 1, and for Q > 2.41, S(R) > 1. These are the critical Q-values, above which selecting driving frequency equal to sigmaL or sigmaR brings advantage to MAC mode vs. DC mode. Satisfactory quality of the oscillator model is demonstrated by comparison of some results with those calculated within the classical description of cantilevers.

UPLC-Q-TOF-MS analysis of non-volatile migrants from new active packaging materials.

PubMed

Aznar, M; Rodriguez-Lafuente, A; Alfaro, P; Nerin, C

2012-10-01

Ultra-performance liquid chromatography (UPLC) coupled to mass spectrometry (MS) is a useful tool in the analysis of non-volatile compounds, and the use of a quadrupole-time-of-flight (Q-TOF) mass analyzer allows a high sensitivity and accuracy when acquiring full fragment mode, providing a high assurance of correct identification of unknown compounds. In this work, UPLC-Q-TOF-MS technology has been applied to the analysis of non-volatile migrants from new active packaging materials. The materials tested were based on polypropylene (PP), ethylene-vinyl alcohol copolymer (EVOH), and poly(ethylene terephthalate) (PET). The active packaging materials studied were one PP film containing a natural antioxidant, and two PP/EVOH films, two PET/EVOH films and one coextruded PP/EVOH/PP film containing natural antimicrobials. The chemical structure of several compounds was unequivocally identified. The analysis revealed the migration of some of the active substances used in the manufacture of active packaging, such as caffeine (0.07 ± 0.01 μg/g), carvacrol (0.31 ± 0.03 μg/g) and citral (0.20 ± 0.01 μg/g). Unintentionally added substances were also found, such as citral reaction compounds, or citral impurities present in the raw materials.

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments.

PubMed

Ganger, Michael T; Dietz, Geoffrey D; Ewing, Sarah J

2017-12-01

qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the statistical analysis of qPCR data are needed. Here we develop a mathematical model, termed the Common Base Method, for analysis of qPCR data based on threshold cycle values (C q ) and efficiencies of reactions (E). The Common Base Method keeps all calculations in the logscale as long as possible by working with log 10 (E) ∙ C q , which we call the efficiency-weighted C q value; subsequent statistical analyses are then applied in the logscale. We show how efficiency-weighted C q values may be analyzed using a simple paired or unpaired experimental design and develop blocking methods to help reduce unexplained variation. The Common Base Method has several advantages. It allows for the incorporation of well-specific efficiencies and multiple reference genes. The method does not necessitate the pairing of samples that must be performed using traditional analysis methods in order to calculate relative expression ratios. Our method is also simple enough to be implemented in any spreadsheet or statistical software without additional scripts or proprietary components.

High-Q terahertz Fano resonance with extraordinary transmission in concentric ring apertures.

PubMed

Shu, Jie; Gao, Weilu; Reichel, Kimberly; Nickel, Daniel; Dominguez, Jason; Brener, Igal; Mittleman, Daniel M; Xu, Qianfan

2014-02-24

We experimentally demonstrate a polarization-independent terahertz Fano resonance with extraordinary transmission when light passes through two concentric subwavelength ring apertures in the metal film. The Fano resonance is enabled by the coupling between a high-Q dark mode and a low-Q bright mode. We find the Q factor of the dark mode ranges from 23 to 40, which is 3~6 times higher than Q of bright mode. We show the Fano resonance can be tuned by varying the geometry and dimension of the structures. We also demonstrate a polarization dependent Fano resonance in a modified structure of concentric ring apertures.

TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

NASA Astrophysics Data System (ADS)

Jang, Inae; Lee, Sun Young; Hwangbo, Song; Kang, Dukjin; Lee, Hookeun; Kim, Hugh I.; Moon, Bongjin; Oh, Han Bin

2017-01-01

The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research.

A VLT/MUSE galaxy survey towards QSO Q1410: looking for a WHIM traced by BLAs in inter-cluster filaments

NASA Astrophysics Data System (ADS)

Pessa, Ismael; Tejos, Nicolas; Barrientos, L. Felipe; Werk, Jessica; Bielby, Richard; Padilla, Nelson; Morris, Simon L.; Prochaska, J. Xavier; Lopez, Sebastian; Hummels, Cameron

2018-07-01

Cosmological simulations predict that a significant fraction of the low-z baryon budget resides in large-scale filaments in the form of a diffuse plasma at temperatures T ˜ 105 - 107 K. However, direct observation of this so-called warm-hot intergalactic medium (WHIM) has been elusive. In the Λcold dark matter paradigm, galaxy clusters correspond to the nodes of the cosmic web at the intersection of several large-scale filamentary threads. In previous work, we used HST/COS data to conduct the first survey of broad H I Lyα absorbers (BLAs) potentially produced by WHIM in inter-cluster filaments. We targeted a single QSO, namely Q1410, whose sightline intersects seven independent inter-cluster axes at impact parameters <3 Mpc (comoving), and found a tentative excess of a factor of ˜4 with respect to the field. Here, we further investigate the origin of these BLAs by performing a blind galaxy survey within the Q1410 field using VLT/MUSE. We identified 77 sources and obtained the redshifts for 52 of them. Out of the total sample of seven BLAs in inter-cluster axes, we found three without any galaxy counterpart to stringent luminosity limits (˜4 × 108 L⊙ ˜0.01 L*), providing further evidence that these BLAs may represent genuine WHIM detections. We combined this sample with other suitable BLAs from the literature and inferred the corresponding baryon mean density for these filaments in the range Ω ^fil_bar= 0.02-0.04. Our rough estimates are consistent with the predictions from numerical simulations but still subject to large systematic uncertainties, mostly from the adopted geometry, ionization corrections, and density profile.

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets.

PubMed

Hill, Katherine E; Kelly, Andrew D; Kuijjer, Marieke L; Barry, William; Rattani, Ahmed; Garbutt, Cassandra C; Kissick, Haydn; Janeway, Katherine; Perez-Atayde, Antonio; Goldsmith, Jeffrey; Gebhardt, Mark C; Arredouani, Mohamed S; Cote, Greg; Hornicek, Francis; Choy, Edwin; Duan, Zhenfeng; Quackenbush, John; Haibe-Kains, Benjamin; Spentzos, Dimitrios

2017-05-15

A microRNA (miRNA) collection on the imprinted 14q32 MEG3 region has been associated with outcome in osteosarcoma. We assessed the clinical utility of this miRNA set and their association with methylation status. We integrated coding and non-coding RNA data from three independent annotated clinical osteosarcoma cohorts (n = 65, n = 27, and n = 25) and miRNA and methylation data from one in vitro (19 cell lines) and one clinical (NCI Therapeutically Applicable Research to Generate Effective Treatments (TARGET) osteosarcoma dataset, n = 80) dataset. We used time-dependent receiver operating characteristic (tdROC) analysis to evaluate the clinical value of candidate miRNA profiles and machine learning approaches to compare the coding and non-coding transcriptional programs of high- and low-risk osteosarcoma tumors and high- versus low-aggressiveness cell lines. In the cell line and TARGET datasets, we also studied the methylation patterns of the MEG3 imprinting control region on 14q32 and their association with miRNA expression and tumor aggressiveness. In the tdROC analysis, miRNA sets on 14q32 showed strong discriminatory power for recurrence and survival in the three clinical datasets. High- or low-risk tumor classification was robust to using different microRNA sets or classification methods. Machine learning approaches showed that genome-wide miRNA profiles and miRNA regulatory networks were quite different between the two outcome groups and mRNA profiles categorized the samples in a manner concordant with the miRNAs, suggesting potential molecular subtypes. Further, miRNA expression patterns were reproducible in comparing high-aggressiveness versus low-aggressiveness cell lines. Methylation patterns in the MEG3 differentially methylated region (DMR) also distinguished high-aggressiveness from low-aggressiveness cell lines and were associated with expression of several 14q32 miRNAs in both the cell lines and the large TARGET clinical dataset

Cluster analysis in phenotyping a Portuguese population.

PubMed

Loureiro, C C; Sa-Couto, P; Todo-Bom, A; Bousquet, J

2015-09-03

Unbiased cluster analysis using clinical parameters has identified asthma phenotypes. Adding inflammatory biomarkers to this analysis provided a better insight into the disease mechanisms. This approach has not yet been applied to asthmatic Portuguese patients. To identify phenotypes of asthma using cluster analysis in a Portuguese asthmatic population treated in secondary medical care. Consecutive patients with asthma were recruited from the outpatient clinic. Patients were optimally treated according to GINA guidelines and enrolled in the study. Procedures were performed according to a standard evaluation of asthma. Phenotypes were identified by cluster analysis using Ward's clustering method. Of the 72 patients enrolled, 57 had full data and were included for cluster analysis. Distribution was set in 5 clusters described as follows: cluster (C) 1, early onset mild allergic asthma; C2, moderate allergic asthma, with long evolution, female prevalence and mixed inflammation; C3, allergic brittle asthma in young females with early disease onset and no evidence of inflammation; C4, severe asthma in obese females with late disease onset, highly symptomatic despite low Th2 inflammation; C5, severe asthma with chronic airflow obstruction, late disease onset and eosinophilic inflammation. In our study population, the identified clusters were mainly coincident with other larger-scale cluster analysis. Variables such as age at disease onset, obesity, lung function, FeNO (Th2 biomarker) and disease severity were important for cluster distinction. Copyright © 2015. Published by Elsevier España, S.L.U.

Guidelines for Using the "Q" Test in Meta-Analysis

ERIC Educational Resources Information Center

Maeda, Yukiko; Harwell, Michael R.

2016-01-01

The "Q" test is regularly used in meta-analysis to examine variation in effect sizes. However, the assumptions of "Q" are unlikely to be satisfied in practice prompting methodological researchers to conduct computer simulation studies examining its statistical properties. Narrative summaries of this literature are available but…

Data depth based clustering analysis

DOE PAGES

Jeong, Myeong -Hun; Cai, Yaping; Sullivan, Clair J.; ...

2016-01-01

Here, this paper proposes a new algorithm for identifying patterns within data, based on data depth. Such a clustering analysis has an enormous potential to discover previously unknown insights from existing data sets. Many clustering algorithms already exist for this purpose. However, most algorithms are not affine invariant. Therefore, they must operate with different parameters after the data sets are rotated, scaled, or translated. Further, most clustering algorithms, based on Euclidean distance, can be sensitive to noises because they have no global perspective. Parameter selection also significantly affects the clustering results of each algorithm. Unlike many existing clustering algorithms, themore » proposed algorithm, called data depth based clustering analysis (DBCA), is able to detect coherent clusters after the data sets are affine transformed without changing a parameter. It is also robust to noises because using data depth can measure centrality and outlyingness of the underlying data. Further, it can generate relatively stable clusters by varying the parameter. The experimental comparison with the leading state-of-the-art alternatives demonstrates that the proposed algorithm outperforms DBSCAN and HDBSCAN in terms of affine invariance, and exceeds or matches the ro-bustness to noises of DBSCAN or HDBSCAN. The robust-ness to parameter selection is also demonstrated through the case study of clustering twitter data.« less

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

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

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

DOE PAGES

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.; ...

2017-04-24

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

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

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

Autism and 15q11-q13 disorders: behavioral, genetic, and pathophysiological issues.

PubMed

Dykens, Elisabeth M; Sutcliffe, James S; Levitt, Pat

2004-01-01

New insights into biological factors that underlie autism may be gained by comparing autism to other neurodevelopmental disorders that have autistic features and relatively well-delineated genetic etiologies or neurobiological findings. This review moves beyond global diagnoses of autism and instead uses an endophenotypic approach to compare specific clusters of autistic symptomatology to features of chromosome 15q11-q13 disorders. Paternally or maternally derived deficiencies of 15q11-q13 result in Prader-Willi or Angelman syndromes, and we first use a global approach to review potential autism susceptibility genes in the 15q11-q13 region. We then use a more trait-based approach to suggest possible ties between specific phenotypic characteristics of autism and Prader-Willi syndrome, namely savant-like skills. We conclude with insights from pathophysiological studies that implicate altered development of specific neuron types and circuits in the cerebral cortex as part of the pathophysiological processes associated with autism and mental retardation. Copyright 2004 Wiley-Liss, Inc.

Analysis of FOXF1 and the FOX gene cluster in patients with VACTERL association

PubMed Central

Agochukwu, Nneamaka B.; Pineda-Alvarez, Daniel E.; Keaton, Amelia A.; Warren-Mora, Nicole; Raam, Manu S.; Kamat, Aparna; Chandrasekharappa, Settara C.; Solomon, Benjamin D.

2011-01-01

VACTERL association, a relatively common condition with an incidence of approximately 1 in 20,000 – 35,000 births, is a non-random association of birth defects that includes vertebral defects (V), anal atresia (A), cardiac defects (C), tracheo-esophageal fistula (TE), renal anomalies (R) and limb malformations (L). Although the etiology is unknown in the majority of patients, there is evidence that it is causally heterogeneous. Several studies have shown evidence for inheritance in VACTERL, implying a role for genetic loci. Recently, patients with component features of VACTERL and a lethal developmental pulmonary disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), were found to harbor deletions or mutations affecting FOXF1 and the FOX gene cluster on chromosome 16q24. We investigated this gene through direct sequencing and high-density SNP microarray in 12 patients with VACTERL association but without ACD/MPV. Our mutational analysis of FOXF1 showed normal sequences and no genomic imbalances affecting the FOX gene cluster on chromosome 16q24 in the studied patients. Possible explanations for these results include the etiologic and clinical heterogeneity of VACTERL association, the possibility that mutations affecting this gene may occur only in more severely affected individuals, and insufficient study sample size. PMID:21315191

Polymorphisms and linkage analysis for ICAM-1 and the selectin gene cluster

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

Vora, D.K.; Rosenbloom, C.L.; Cottingham, R.W.

1994-06-01

Genetic polymorphisms in leukocyte and endothelial cell adhesion molecules may be important variables with regard to susceptibility to multifactorial disease processes that include an inflammatory component. For this reason, polymorphisms were sought for intercellular adhesion molecule-1 (ICAM-1; gene symbol ICAM1) and for the three genes in the selectin cluster, P-selectin, L-selectin, and E-selectin (gene symbols SELP, SELL, and SELE, respectively). Two amino acid polymorphisms were identified for ICAM-1; Gly or Arg at codon 241 and Lys or Glu at codon 469. Dinucleotide repeat polymorphisms were identified in the 3{prime}-untranslated region for ICAM-1 and in intron 9 for P-selectin. Restriction fragmentmore » length polymorphisms were found using cDNAs for each of the three selectin genes as probes; E-selectin with BglII, P-selectin with ScaI, and L-selectin with HincII. Linkage analysis was performed for the selectin gene cluster and for ICAM-1 using the CEPH families; ICAM-1 is very tightly linked to the LDL receptor on chromosome 19, and the selectin cluster is linked to markers at chromosome 1q23. 41 refs., 2 tabs.« less

Bearing performance degradation assessment based on a combination of empirical mode decomposition and k-medoids clustering

NASA Astrophysics Data System (ADS)

Rai, Akhand; Upadhyay, S. H.

2017-09-01

Bearing is the most critical component in rotating machinery since it is more susceptible to failure. The monitoring of degradation in bearings becomes of great concern for averting the sudden machinery breakdown. In this study, a novel method for bearing performance degradation assessment (PDA) based on an amalgamation of empirical mode decomposition (EMD) and k-medoids clustering is encouraged. The fault features are extracted from the bearing signals using the EMD process. The extracted features are then subjected to k-medoids based clustering for obtaining the normal state and failure state cluster centres. A confidence value (CV) curve based on dissimilarity of the test data object to the normal state is obtained and employed as the degradation indicator for assessing the health of bearings. The proposed outlook is applied on the vibration signals collected in run-to-failure tests of bearings to assess its effectiveness in bearing PDA. To validate the superiority of the suggested approach, it is compared with commonly used time-domain features RMS and kurtosis, well-known fault diagnosis method envelope analysis (EA) and existing PDA classifiers i.e. self-organizing maps (SOM) and Fuzzy c-means (FCM). The results demonstrate that the recommended method outperforms the time-domain features, SOM and FCM based PDA in detecting the early stage degradation more precisely. Moreover, EA can be used as an accompanying method to confirm the early stage defect detected by the proposed bearing PDA approach. The study shows the potential application of k-medoids clustering as an effective tool for PDA of bearings.

First principles study of vibrational dynamics of ceria-titania hybrid clusters

NASA Astrophysics Data System (ADS)

Majid, Abdul; Bibi, Maryam

2017-04-01

Density functional theory based calculations were performed to study vibrational properties of ceria, titania, and ceria-titania hybrid clusters. The findings revealed the dominance of vibrations related to oxygen when compared to those of metallic atoms in the clusters. In case of hybrid cluster, the softening of normal modes related to exterior oxygen atoms in ceria and softening/hardening of high/low frequency modes related to titania dimmers are observed. The results calculated for monomers conform to symmetry predictions according to which three IR and three Raman active modes were detected for TiO2, whereas two IR active and one Raman active modes were observed for CeO2. The comparative analysis indicates that the hybrid cluster CeTiO4 contains simultaneous vibrational fingerprints of the component dimmers. The symmetry, nature of vibrations, IR and Raman activity, intensities, and atomic involvement in different modes of the clusters are described in detail. The study points to engineering of CeTiO4 to tailor its properties for technological visible region applications in photocatalytic and electrochemical devices.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

Genomewide Linkage Scan for Split–Hand/Foot Malformation with Long-Bone Deficiency in a Large Arab Family Identifies Two Novel Susceptibility Loci on Chromosomes 1q42.2-q43 and 6q14.1

PubMed Central

Naveed, Mohammed; Nath, Swapan K.; Gaines, Mathew; Al-Ali, Mahmoud T.; Al-Khaja, Najib; Hutchings, David; Golla, Jeffrey; Deutsch, Samuel; Bottani, Armand; Antonarakis, Stylianos E.; Ratnamala, Uppala; Radhakrishna, Uppala

2007-01-01

Split–hand/foot malformation with long-bone deficiency (SHFLD) is a rare, severe limb deformity characterized by tibia aplasia with or without split-hand/split-foot deformity. Identification of genetic susceptibility loci for SHFLD has been unsuccessful because of its rare incidence, variable phenotypic expression and associated anomalies, and uncertain inheritance pattern. SHFLD is usually inherited as an autosomal dominant trait with reduced penetrance, although recessive inheritance has also been postulated. We conducted a genomewide linkage analysis, using a 10K SNP array in a large consanguineous family (UR078) from the United Arab Emirates (UAE) who had disease transmission consistent with an autosomal dominant inheritance pattern. The study identified two novel SHFLD susceptibility loci at 1q42.2-q43 (nonparametric linkage [NPL] 9.8, P=.000065) and 6q14.1 (NPL 7.12, P=.000897). These results were also supported by multipoint parametric linkage analysis. Maximum multipoint LOD scores of 3.20 and 3.78 were detected for genomic locations 1q42.2-43 and 6q14.1, respectively, with the use of an autosomal dominant mode of inheritance with reduced penetrance. Haplotype analysis with informative crossovers enabled mapping of the SHFLD loci to a region of ∼18.38 cM (8.4 Mb) between single-nucleotide polymorphisms rs1124110 and rs535043 on 1q42.2-q43 and to a region of ∼1.96 cM (4.1 Mb) between rs623155 and rs1547251 on 6q14.1. The study identified two novel loci for the SHFLD phenotype in this UAE family. PMID:17160898

Magnetohydrodynamic modes analysis and control of Fusion Advanced Studies Torus high-current scenarios

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

Villone, F.; Mastrostefano, S.; Calabrò, G.

2014-08-15

One of the main FAST (Fusion Advanced Studies Torus) goals is to have a flexible experiment capable to test tools and scenarios for safe and reliable tokamak operation, in order to support ITER and help the final DEMO design. In particular, in this paper, we focus on operation close to a possible border of stability related to low-q operation. To this purpose, a new FAST scenario has then been designed at I{sub p} = 10 MA, B{sub T} = 8.5 T, q{sub 95} ≈ 2.3. Transport simulations, carried out by using the code JETTO and the first principle transport model GLF23, indicate that, under these conditions, FASTmore » could achieve an equivalent Q ≈ 3.5. FAST will be equipped with a set of internal active coils for feedback control, which will produce magnetic perturbation with toroidal number n = 1 or n = 2. Magnetohydrodynamic (MHD) mode analysis and feedback control simulations performed with the codes MARS, MARS-F, CarMa (both assuming the presence of a perfect conductive wall and using the exact 3D resistive wall structure) show the possibility of the FAST conductive structures to stabilize n = 1 ideal modes. This leaves therefore room for active mitigation of the resistive mode (down to a characteristic time of 1 ms) for safety purposes, i.e., to avoid dangerous MHD-driven plasma disruption, when working close to the machine limits and magnetic and kinetic energy density not far from reactor values.« less

Molecular cytogenetic analysis of de novo dup(5)(q35.2q35.3) and review of the literature of pure partial trisomy 5q.

PubMed

Chen, Chih-Ping; Lin, Shuan-Pei; Lin, Chyi-Chyang; Chen, Yann-Jang; Chern, Schu-Rern; Li, Yueh-Chun; Hsieh, Lie-Jiau; Lee, Chen-Chi; Pan, Chen-Wen; Wang, Wayseen

2006-07-15

An 11-year-old girl presented with the phenotype of microcephaly, moderate mental retardation, motor retardation, short stature, strabismus, brachydactyly, and facial dysmorphism. She had undergone surgery for inguinal hernias. Detailed examinations of the heart and other internal organs revealed normal findings. Her karyotype was 46,XX,dup(5)(q35.2q35.3) de novo. Molecular cytogenetic analysis showed a paternally derived 5q35.2 --> q35.3 direct duplication and led to a correlation between the particular genotype and phenotype. This is the first description of a direct duplication of 5q35.2 --> q35.3. Our case represents the smallest distal duplication of chromosome 5q that is not associated with congenital heart defects. Our case also represents the smallest distal duplication of chromosome 5q that is associated with short stature and microcephaly. Mutations or deletions of the NSD1 gene, mapped to 5q35.2 --> q35.3, has been known to cause Sotos syndrome with cerebral gigantism, macrocephaly, advanced bone age and overgrowth. Our case provides evidence that the gene dosage effect of the NSD1 gene causes a reversed phenotype of microcephaly and short stature. Copyright 2006 Wiley-Liss, Inc.

Long-lived Eccentric modes in Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Lee, Wing-Kit; Dempsey, Adam M.; Lithwick, Yoram

2018-04-01

A theory is developed to understand global eccentric modes that are slowly precessing in protoplanetary disks. Using the typical self-similar density profiles, we found that these modes are trapped in the disk and are not sensitive to the uncertain boundary condition at the disk edge. This is contrary to common wisdom that the modes can only exist in disks with very sharp outer edge. Because of their discrete spectrum, once excited, a perturbed disk can stay eccentric for a long time until the mode is viscously damped. The physics behind the mode trapping depends ultimately on the relative importance of gas pressure and self-gravity, which is characterized by g = 1/ (Q h), where h is the disk aspect ratio and Q is the Toomre stability parameter. A very low mass disk (g ≪ 1) is pressure-dominated and supports pressure modes, in which the eccentricity is highest at the disk edge. The modes are trapped by a turning point due to the density drop in the outer disk. For a more massive disk with g of order of unity (Q~1/h~10-100), prograde modes are supported. Unlike the pressure modes, these modes are trapped by Q-barriers and result in a bump in the radial eccentricity profile. As the mode trapping is a generic phenomenon for typical disk profiles, the free linear eccentric modes are likely to be present in protoplanetary disks with a wide range of disk mass.

Correlation of shallow marine, deep marine, and coastal terrestrial records of central California: asynchronous responses to paleoceanographic and paleoclimatic change during the past 19,000 years

NASA Astrophysics Data System (ADS)

McGann, M.

2016-12-01

Benthic and planktic foraminiferal census data combined with pollen data acquired from the continental margin off central California (core S3-15G, 3491 m depth from the western levy of the Monterey Fan; 36°23.53'N, 123°20.52'W) provide a unique opportunity to document concurrent paleoceanographic and paleoclimatic changes in the region during the late Quaternary. Radiocarbon dates and the ratio of the planktic foraminiferal species Neogloboquardrina pachyderma (Ehrenberg) to Neogloboquardrina incompta (Cifelli) provide a good age-depth model for the last 19,000 years. Q-mode cluster analysis of the benthic foraminifera grouped the fauna into two clusters reflecting faunal adaptation to changing climatic conditions during the Pleistocene and Holocene, whereas the R-mode cluster analysis identified glacial (Uvigerina senticosa and Globobulimina auriculata) and interglacial (Melonis pompilioides and Gyroidina planulata) faunas. A slight increase in oxygen concentration in the deep sea across the Pleistocene-Holocene transition is suggested by a reduction in abundance of G. auriculata and increased frequency of M. pompilioides. Q-mode cluster analysis of the planktic foraminifera indicates a change in the surface water from a glacial subpolar fauna in the Pleistocene to a transitional fauna in the Holocene. The pollen flora separated into three clusters by Q-mode cluster analysis, two of Pleistocene age (glacial and transitional) and one in the Holocene (interglacial), reflecting adaptation of the flora in the California Coast Ranges of central California to the warmer climate in the Holocene. Decoupling is evident between the benthic foraminiferal, planktic foraminiferal, and terrestrial floral responses to changing oceanographic and climatic conditions. The floral response leads the surface-dwelling planktic fauna by several millennia, and is followed by the deep-dwelling benthic fauna a millennium later.

Self-accommodation of B19' martensite in Ti-Ni shape memory alloys. Part III. Analysis of habit plane variant clusters by the geometrically nonlinear theory

NASA Astrophysics Data System (ADS)

Inamura, T.; Nishiura, T.; Kawano, H.; Hosoda, H.; Nishida, M.

2012-06-01

Competition between the invariant plane (IP) condition at the habit plane, the twin orientation relation (OR) and the kinematic compatibility (KC) at the junction plane (JP) of self-accommodated B19‧ martensite in Ti-Ni was investigated via the geometrically nonlinear theory to understand the habit plane variant (HPV) clusters presented in Parts I and II of this work. As the IP condition cannot be satisfied simultaneously with KC, an additional rotation Q is necessary to form compatible JPs for all HPV pairs. The rotation J necessary to form the exact twin OR between the major correspondence variants (CVs) in each HPV was also examined. The observed HPV cluster was not the cluster with the smallest Q but the one satisfying Q = J with a { ? 1}B19‧ type I twin at JP. Both Q and J are crucial to understanding the various HPV clusters in realistic transformations. Finally, a scheme for the ideal HPV cluster composed of six HPVs is also proposed.

Absorption band Q model for the Earth

NASA Technical Reports Server (NTRS)

Anderson, D. L.; Given, J. W.

1981-01-01

Attenuation in solids and liquids, as measured by the quality factor Q, is typically frequency dependent. In seismology, however, Q is usually assumed to be independent of frequency. Body wave, surface wave, and normal mode data are used to place constraints on the frequency dependence of Q in the mantle. Specific features of the absorption band model are: low-Q in the seismic band at both the top and the base of the mantle, low-Q for long-period body waves in the outer core, an inner core Q sub s that increases with period, and low Q sub p/Q sub s at short periods in the middle mantle.

Pulmonary manifestations of Q fever: analysis of 38 patients.

PubMed

Kelm, Diana J; White, Darin B; Fadel, Hind J; Ryu, Jay H; Maldonado, Fabien; Baqir, Misbah

2017-10-01

Lung involvement in both acute and chronic Q fever is not well described with only a few reported cases of pseudotumor or pulmonary fibrosis in chronic Q fever. The aim of this study was to better understand the pulmonary manifestations of Q fever. We conducted a retrospective cohort study of patients with diagnosis of Q fever at Mayo Clinic Rochester. A total of 69 patients were initially identified between 2001 and 2014. Thirty-eight patients were included in this study as 3 were pediatric patients, 20 did not meet serologic criteria for Q fever, and 8 did not have imaging available at time of initial diagnosis. Descriptive analysis was conducted using JMP software. The median age was 57 years [interquartile range (IQR) 43, 62], 84% from the Midwest, and 13% worked in an occupation involving animals. The most common presentation was fevers (61%). Respiratory symptoms, such as cough, were noted in only 4 patients (11%). Twelve patients (29%) had abnormal imaging studies attributed to Q fever. Three patients (25%) with acute Q fever had findings of consolidation, lymphadenopathy, pleural effusions, and nonspecific pulmonary nodules. Radiographic findings of chronic Q fever were seen in 9 patients (75%) and included consolidation, ground-glass opacities, pleural effusions, lymphadenopathy, pulmonary edema, and lung pseudotumor. Our results demonstrate that pulmonary manifestations are uncommon in Q fever but include cough and consolidation for acute Q fever and radiographic findings of pulmonary edema with pleural effusions, consolidation, and pseudotumor in those with chronic Q fever.

Urinary metabolomic profiling in rats exposed to dietary di(2-ethylhexyl) phthalate (DEHP) using ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UPLC/Q-TOF-MS).

PubMed

Dong, Xinwen; Zhang, Yunbo; Dong, Jin; Zhao, Yue; Guo, Jipeng; Wang, Zhanju; Liu, Mingqi; Na, Xiaolin; Wang, Cheng

2017-07-01

Di(2-ethylhexyl) phthalate (DEHP) is an omnipresent environmental chemical with widespread nonoccupational human exposure through multiple ways. Although considerable efforts have been invested to investigate mechanisms of DEHP toxicity, the key metabolic biomarkers of DEHP toxicity remain to be identified. The aim of this study was to assess the urinary metabonomics of dietary DEHP in rats using the technique of ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UPLC/Q-TOF-MS). Fourteen female Wistar rats were divided into two groups and given increasing dietary doses of DEHP for 30 consecutive days. The urinary metabolite profile was studied using ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry. Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) enabled clusters to be clearly separated. Eleven principal urinary metabolites were identified as contributing to the clusters. The clusters in the positive electrospray ionization (ESI) mode were xanthurenic acid, kynurenic acid, nonate, N6-methyladenosine, and L-isoleucyl-L-proline. The clusters in the negative ESI mode were hippuric acid, tetrahydrocortisol, citric acid, phenylpropionylglycine, cPA(18:2(9Z, 12Z)/0:0), and LysoPC(14:1(9Z)). The urinary metabonomic changes indicated that exposure to dietary DEHP can affect energy-related metabolism, liver and renal function, fatty acid metabolism, and cause DNA damage in rats. The findings of this study on the urinary metabolites and metabolic pathways of DEHP may form the basis for future studies on the mechanisms of toxicity of this commonly found environmental chemical.

Passively synchronized Q-switched and mode-locked dual-band Tm3+:ZBLAN fiber lasers using a common graphene saturable absorber

NASA Astrophysics Data System (ADS)

Jia, Chenglai; Shastri, Bhavin J.; Abdukerim, Nurmemet; Rochette, Martin; Prucnal, Paul R.; Saad, Mohammed; Chen, Lawrence R.

2016-11-01

Dual-band fiber lasers are emerging as a promising technology to penetrate new industrial and medical applications from their dual-band properties, in addition to providing compactness and environmental robustness from the waveguide structure. Here, we demonstrate the use of a common graphene saturable absorber and a single gain medium (Tm3+:ZBLAN fiber) to implement (1) a dual-band fiber ring laser with synchronized Q-switched pulses at wavelengths of 1480 nm and 1840 nm, and (2) a dual-band fiber linear laser with synchronized mode-locked pulses at wavelengths of 1480 nm and 1845 nm. Q-switched operation at 1480 nm and 1840 nm is achieved with a synchronized repetition rate from 20 kHz to 40.5 kHz. For synchronous mode-locked operation, pulses with full-width at half maximum durations of 610 fs and 1.68 ps at wavelengths of 1480 nm and 1845 nm, respectively, are obtained at a repetition rate of 12.3 MHz. These dual-band pulsed sources with an ultra-broadband wavelength separation of ~360 nm will add new capabilities in applications including optical sensing, spectroscopy, and communications.

Passively synchronized Q-switched and mode-locked dual-band Tm3+:ZBLAN fiber lasers using a common graphene saturable absorber.

PubMed

Jia, Chenglai; Shastri, Bhavin J; Abdukerim, Nurmemet; Rochette, Martin; Prucnal, Paul R; Saad, Mohammed; Chen, Lawrence R

2016-11-02

Dual-band fiber lasers are emerging as a promising technology to penetrate new industrial and medical applications from their dual-band properties, in addition to providing compactness and environmental robustness from the waveguide structure. Here, we demonstrate the use of a common graphene saturable absorber and a single gain medium (Tm 3+ :ZBLAN fiber) to implement (1) a dual-band fiber ring laser with synchronized Q-switched pulses at wavelengths of 1480 nm and 1840 nm, and (2) a dual-band fiber linear laser with synchronized mode-locked pulses at wavelengths of 1480 nm and 1845 nm. Q-switched operation at 1480 nm and 1840 nm is achieved with a synchronized repetition rate from 20 kHz to 40.5 kHz. For synchronous mode-locked operation, pulses with full-width at half maximum durations of 610 fs and 1.68 ps at wavelengths of 1480 nm and 1845 nm, respectively, are obtained at a repetition rate of 12.3 MHz. These dual-band pulsed sources with an ultra-broadband wavelength separation of ~360 nm will add new capabilities in applications including optical sensing, spectroscopy, and communications.

Mode-splitting for refractive index sensing in fluorescent whispering gallery mode resonators with broken symmetry

NASA Astrophysics Data System (ADS)

Kang, Yvonne Q.; François, Alexandre; Riesen, Nicolas; Monro, Tanya M.

2018-02-01

Whispering Gallery Mode (WGM) biosensors have been widely exploited over the past decade, owing to their unprecedented detection limits and label free capability. WGM based sensing mechanisms, such as resonance frequency shift, linewidth broadening, and splitting of the two counter-propagating WGMs, have been extensively researched and applied for bio-chemical sensing. However, the mode-splitting of the originally degenerate WGMs from different equatorial planes on a fluorescent microsphere has not been fully investigated. In this work, we break the symmetry of the surrounding environment outside the microsphere by partially embedding the sphere into a high-refractive-index medium (i.e. glue), to lift the degeneracy of the modes from different WGM planes. The split-modes from multiple planes of the fluorescent microsphere are indiscriminately collected. It is found that the effective quality factor Q of the WGMs increases non-conventionally as the Refractive Index (RI) of the probing liquid increases up to the point where it is equal to that of the glue. This presents a new methodology for quantifying changes in the probing environment based on the Q spoiling of the resonances as determined by the RI difference between the environment and that of the reference glue. Furthermore, we find that this sensing platform opens the door to simple self-referenced sensing techniques based on the analysis of the spectral positions of subsets of the split modes.

2Q NMR of 2H2O ordering at solid interfaces

NASA Astrophysics Data System (ADS)

Krivokhizhina, Tatiana V.; Wittebort, R. J.

2014-06-01

Solvent ordering at an interface can be studied by multiple-quantum NMR. Quantitative studies of 2H2O ordering require clean double-quantum (2Q) filtration and an analysis of 2Q buildup curves that accounts for relaxation and, if randomly oriented samples are used, the distribution of residual couplings. A pulse sequence with absorption mode detection is extended for separating coherences by order and measuring relaxation times such as the 2Q filtered T2. Coherence separation is used to verify 2Q filtration and the 2Q filtered T2 is required to extract the coupling from the 2Q buildup curve when it is unresolved. With our analysis, the coupling extracted from the buildup curve in 2H2O hydrated collagen was equivalent to the resolved coupling measured in the usual 1D experiment and the 2Q to 1Q signal ratio was in accord with theory. Application to buildup curves from 2H2O hydrated elastin, which has an unresolved coupling, revealed a large increase in the 2Q signal upon mechanical stretch that is due to an increase in the ordered water fraction while changes in the residual coupling and T2 are small.

Noise-driven switching and chaotic itinerancy among dynamic states in a three-mode intracavity second-harmonic generation laser operating on a Λ transition

NASA Astrophysics Data System (ADS)

Otsuka, Kenju; Ohtomo, Takayuki; Maniwa, Tsuyoshi; Kawasaki, Hazumi; Ko, Jing-Yuan

2003-09-01

We studied the antiphase self-pulsation in a globally coupled three-mode laser operating in different optical spectrum configurations. We observed locking of modal pulsation frequencies, quasiperiodicity, clustering behaviors, and chaos, resulting from the nonlinear interaction among modes. The robustness of [p:q:r] three-frequency locking states and quasiperiodic oscillations against residual noise has been examined by using joint time-frequency analysis of long-term experimental time series. Two sharply antithetical types of switching behaviors among different dynamic states were observed during temporal evolutions; noise-driven switching and self-induced switching, which manifests itself in chaotic itinerancy. The modal interplay behind observed behaviors was studied by using the statistical dynamic quantity of the information circulation. Well-organized information flows among modes, which correspond to the number of degeneracies of modal pulsation frequencies, were found to be established in accordance with the inherent antiphase dynamics. Observed locking behaviors, quasiperiodic motions, and chaotic itinerancy were reproduced by numerical simulation of the model equations.

Cluster size resolving analysis of CH3F-(ortho-H2)n in solid para-hydrogen using FTIR absorption spectroscopy at 3 μm region.

PubMed

Miyamoto, Yuki; Momose, Takamasa; Kanamori, Hideto

2012-11-21

Infrared absorption spectra of methyl fluoride with ortho-hydrogen (ortho-H(2)) clusters in a solid para-hydrogen (para-H(2)) crystal at 3.6 K were studied in the C-H stretching fundamental region (~3000 cm(-1)) using an FTIR spectrometer. As shown previously, the ν(3) C-F stretching fundamental band of CH(3)F-(ortho-H(2))(n) (n = 0, 1, 2, ...) clusters at 1040 cm(-1) shows a series of n discrete absorption lines, which correspond to different-sized clusters. We observed three unresolved broad peaks in the C-H stretching region and applied this cluster model to them assuming the same intensity distribution function as the ν(3) band. A fitting analysis successfully gave us the linewidth and lineshift of the components in each vibrational band. It was found that the separately determined linewidth, matrix shift of the band origin, and cluster shift are dependent on the vibrational mode. From the transition intensities of the monomer component derived from the fitting analysis, we discuss the mixing ratio of the vibrational modes due to Fermi resonance.

Phonon-roton modes of liquid 4He beyond the roton in MCM-41

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

Azuah, Richard T; Omar Diallo, Souleymane; Adams, Mark A.

2013-01-01

We present neutron scattering measurements of the phonon-roton (P-R) mode of superfluid 4He confined in 47 A MCM-41 at T = 0.5 K at wave vectors, Q, beyond the roton wave vector (QR = 1.92 A-1). Measurements beyond the roton require access to high wave vectors (up to Q = 4 A-1) with excellent energy resolution and high statistical precision. The present results show for the first time that at T = 0.5 K the P-R mode in MCM-41 extends out to wave-vector Q 3.6 A-1 with the same energy and zero width (within precision) as observed in bulk superfluidmore » 4He. Layer modes in the roton region are also observed. Specifically, the P-R mode energy, !Q, increases with Q for Q > QR and reaches a plateau at a maximum energy !Q = 2 where is the roton energy, = 0.74 0.01 meV in MCM-41. This upper limit means the P-R mode decays to two rotons when its energy exceeds 2 . It also means that the P-R mode does not decay to two layers modes. If the P-R could decay to two layer modes, !Q would plateau at a lower energy, !Q = 2 L where L = 0.60 meV is the energy of the roton like minimum of the layer mode. The observation of the P-R mode with energy up to 2 shows that the P-R mode and the layer modes are independent modes with apparently little interaction between them.« less

Highly efficient, versatile, self-Q-switched, high-repetition-rate microchip laser generating Ince-Gaussian modes for optical trapping

NASA Astrophysics Data System (ADS)

Dong, Jun; He, Yu; Zhou, Xiao; Bai, Shengchuang

2016-03-01

Lasers operating in the Ince-Gaussian (IG) mode have potential applications for optical manipulation of microparticles and formation of optical vortices, as well as for optical trapping and optical tweezers. Versatile, self-Q-switched, high-peak-power, high-repetition-rate Cr, Nd:YAG microchip lasers operating in the IG mode are implemented under tilted, tightly focused laser-diode pumping. An average output power of over 2 W is obtained at an absorbed pump power of 6.4 W. The highest optical-to-optical efficiency of 33.2% is achieved at an absorbed pump power of 3.9 W. Laser pulses with a pulse energy of 7.5 μJ, pulse width of 3.5 ns and peak power of over 2 kW are obtained. A repetition rate up to 335 kHz is reached at an absorbed pump power of 5.8 W. Highly efficient, versatile, IG-mode lasers with a high repetition rate and a high peak power ensure a better flexibility in particle manipulation and optical trapping.

Highly efficient, versatile, self-Q-switched, high-repetition-rate microchip laser generating Ince–Gaussian modes for optical trapping

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

Jun Dong; Yu He; Xiao Zhou

2016-03-31

Lasers operating in the Ince-Gaussian (IG) mode have potential applications for optical manipulation of microparticles and formation of optical vortices, as well as for optical trapping and optical tweezers. Versatile, self-Q-switched, high-peak-power, high-repetition-rate Cr, Nd:YAG microchip lasers operating in the IG mode are implemented under tilted, tightly focused laser-diode pumping. An average output power of over 2 W is obtained at an absorbed pump power of 6.4 W. The highest optical-to-optical efficiency of 33.2% is achieved at an absorbed pump power of 3.9 W. Laser pulses with a pulse energy of 7.5 μJ, pulse width of 3.5 ns and peakmore » power of over 2 kW are obtained. A repetition rate up to 335 kHz is reached at an absorbed pump power of 5.8 W. Highly efficient, versatile, IG-mode lasers with a high repetition rate and a high peak power ensure a better flexibility in particle manipulation and optical trapping. (control of laser radiation parameters)« less

2q37 Deletion syndrome confirmed by high-resolution cytogenetic analysis

PubMed Central

Cho, Eun-Kyung; Kim, Jinsup; Yang, Aram; Jin, Dong-Kyu

2017-01-01

Chromosome 2q37 deletion syndrome is a rare chromosomal disorder characterized by mild to moderate developmental delay, brachydactyly of the third to fifth digits or toes, short stature, obesity, hypotonia, a characteristic facial appearance, and autism spectrum disorder. Here, we report on a patient with 2q37 deletion presenting with dilated cardiomyopathy (DCMP). Congenital heart malformations have been noted in up to 20% of patients with 2q37 deletions. However, DCMP has not been reported in 2q37 deletion patients previously. The patient exhibited the characteristic facial appearance (a flat nasal bridge, deep-set eyes, arched eyebrows, and a thin upper lip), developmental delay, mild mental retardation, peripheral nerve palsy, and Albright hereditary osteodystrophy (AHO)-like phenotypes (short stature and brachydactyly). Conventional chromosomal analysis results were normal; however, microarray-based comparative genomic hybridization revealed terminal deletion at 2q37.1q37.3. In addition, the patient was confirmed to have partial growth hormone (GH) deficiency and had shown a significant increase in growth rate after substitutive GH therapy. Chromosome 2q37 deletion syndrome should be considered in the differential diagnosis of patients presenting with AHO features, especially in the presence of facial dysmorphism. When patients are suspected of having a 2q37 deletion, high-resolution cytogenetic analysis is recommended. PMID:28690993

De novo direct duplication of chromosome segment 22q11.2-q13.1

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

Fujimoto, Atsuko; Lin, Ming S.

Lindsay et al. [1995] reported a case of de novo duplication of the segment 22q11-q12. Molecular cytogenetics studies showed that the segment includes the regions responsible for the {open_quotes}cat eye,{close_quotes} DiGeorge, and velo-cardio-facial syndrome, and extends distal to the breakpoint cluster region. The phenotype was milder than that of complete trisomy 22 and der(22)t(11;22) (q23;q11) syndrome and was similar in type and severity to that of {open_quotes}cat eye{close_quotes} syndrome (CES). They suggested that trisomy of gene(s) responsible for the CES might have a predominant phenotypic effect over other genes present in the region duplicated in their patient. 3 refs., 2more » figs.« less

Using Cluster Analysis to Examine Husband-Wife Decision Making

ERIC Educational Resources Information Center

Bonds-Raacke, Jennifer M.

2006-01-01

Cluster analysis has a rich history in many disciplines and although cluster analysis has been used in clinical psychology to identify types of disorders, its use in other areas of psychology has been less popular. The purpose of the current experiments was to use cluster analysis to investigate husband-wife decision making. Cluster analysis was…

DICON: interactive visual analysis of multidimensional clusters.

PubMed

Cao, Nan; Gotz, David; Sun, Jimeng; Qu, Huamin

2011-12-01

Clustering as a fundamental data analysis technique has been widely used in many analytic applications. However, it is often difficult for users to understand and evaluate multidimensional clustering results, especially the quality of clusters and their semantics. For large and complex data, high-level statistical information about the clusters is often needed for users to evaluate cluster quality while a detailed display of multidimensional attributes of the data is necessary to understand the meaning of clusters. In this paper, we introduce DICON, an icon-based cluster visualization that embeds statistical information into a multi-attribute display to facilitate cluster interpretation, evaluation, and comparison. We design a treemap-like icon to represent a multidimensional cluster, and the quality of the cluster can be conveniently evaluated with the embedded statistical information. We further develop a novel layout algorithm which can generate similar icons for similar clusters, making comparisons of clusters easier. User interaction and clutter reduction are integrated into the system to help users more effectively analyze and refine clustering results for large datasets. We demonstrate the power of DICON through a user study and a case study in the healthcare domain. Our evaluation shows the benefits of the technique, especially in support of complex multidimensional cluster analysis. © 2011 IEEE

Are clusters of dietary patterns and cluster membership stable over time? Results of a longitudinal cluster analysis study.

PubMed

Walthouwer, Michel Jean Louis; Oenema, Anke; Soetens, Katja; Lechner, Lilian; de Vries, Hein

2014-11-01

Developing nutrition education interventions based on clusters of dietary patterns can only be done adequately when it is clear if distinctive clusters of dietary patterns can be derived and reproduced over time, if cluster membership is stable, and if it is predictable which type of people belong to a certain cluster. Hence, this study aimed to: (1) identify clusters of dietary patterns among Dutch adults, (2) test the reproducibility of these clusters and stability of cluster membership over time, and (3) identify sociodemographic predictors of cluster membership and cluster transition. This study had a longitudinal design with online measurements at baseline (N=483) and 6 months follow-up (N=379). Dietary intake was assessed with a validated food frequency questionnaire. A hierarchical cluster analysis was performed, followed by a K-means cluster analysis. Multinomial logistic regression analyses were conducted to identify the sociodemographic predictors of cluster membership and cluster transition. At baseline and follow-up, a comparable three-cluster solution was derived, distinguishing a healthy, moderately healthy, and unhealthy dietary pattern. Male and lower educated participants were significantly more likely to have a less healthy dietary pattern. Further, 251 (66.2%) participants remained in the same cluster, 45 (11.9%) participants changed to an unhealthier cluster, and 83 (21.9%) participants shifted to a healthier cluster. Men and people living alone were significantly more likely to shift toward a less healthy dietary pattern. Distinctive clusters of dietary patterns can be derived. Yet, cluster membership is unstable and only few sociodemographic factors were associated with cluster membership and cluster transition. These findings imply that clusters based on dietary intake may not be suitable as a basis for nutrition education interventions. Copyright © 2014 Elsevier Ltd. All rights reserved.

The simultaneous generation of soliton bunches and Q-switched-like pulses in a partially mode-locked fiber laser with a graphene saturable absorber

NASA Astrophysics Data System (ADS)

Wang, Zhenhong; Wang, Zhi; Liu, Yan-ge; He, Ruijing; Wang, Guangdou; Yang, Guang; Han, Simeng

2018-05-01

We experimentally report the coexistence of soliton bunches and Q-switched-like pulses in a partially mode-locked fiber laser with a microfiber-based graphene saturable absorber. The soliton bunches, like isolated spikes with extreme amplitude and ultrashort duration, randomly generate in the background of the Q-switched-like pulses. The soliton bunches have some pulse envelopes in which pulses operate at a fundamental repetition rate in the temporal domain. Further investigation shows that the composite pulses are highly correlated with the noise-like pulses. Our work can make a further contribution to enrich the understanding of the nonlinear dynamics in fiber lasers.

CLUMP-3D: Three-dimensional Shape and Structure of 20 CLASH Galaxy Clusters from Combined Weak and Strong Lensing

NASA Astrophysics Data System (ADS)

Chiu, I.-Non; Umetsu, Keiichi; Sereno, Mauro; Ettori, Stefano; Meneghetti, Massimo; Merten, Julian; Sayers, Jack; Zitrin, Adi

2018-06-01

We perform a three-dimensional triaxial analysis of 16 X-ray regular and 4 high-magnification galaxy clusters selected from the CLASH survey by combining two-dimensional weak-lensing and central strong-lensing constraints. In a Bayesian framework, we constrain the intrinsic structure and geometry of each individual cluster assuming a triaxial Navarro–Frenk–White halo with arbitrary orientations, characterized by the mass {M}200{{c}}, halo concentration {c}200{{c}}, and triaxial axis ratios ({q}{{a}}≤slant {q}{{b}}), and investigate scaling relations between these halo structural parameters. From triaxial modeling of the X-ray-selected subsample, we find that the halo concentration decreases with increasing cluster mass, with a mean concentration of {c}200{{c}}=4.82+/- 0.30 at the pivot mass {M}200{{c}}={10}15{M}ȯ {h}-1. This is consistent with the result from spherical modeling, {c}200{{c}}=4.51+/- 0.14. Independently of the priors, the minor-to-major axis ratio {q}{{a}} of our full sample exhibits a clear deviation from the spherical configuration ({q}{{a}}=0.52+/- 0.04 at {10}15{M}ȯ {h}-1 with uniform priors), with a weak dependence on the cluster mass. Combining all 20 clusters, we obtain a joint ensemble constraint on the minor-to-major axis ratio of {q}{{a}}={0.652}-0.078+0.162 and a lower bound on the intermediate-to-major axis ratio of {q}{{b}}> 0.63 at the 2σ level from an analysis with uniform priors. Assuming priors on the axis ratios derived from numerical simulations, we constrain the degree of triaxiality for the full sample to be { \\mathcal T }=0.79+/- 0.03 at {10}15{M}ȯ {h}-1, indicating a preference for a prolate geometry of cluster halos. We find no statistical evidence for an orientation bias ({f}geo}=0.93+/- 0.07), which is insensitive to the priors and in agreement with the theoretical expectation for the CLASH clusters.

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

PubMed

Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

2017-08-31

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

Variable Screening for Cluster Analysis.

ERIC Educational Resources Information Center

Donoghue, John R.

Inclusion of irrelevant variables in a cluster analysis adversely affects subgroup recovery. This paper examines using moment-based statistics to screen variables; only variables that pass the screening are then used in clustering. Normal mixtures are analytically shown often to possess negative kurtosis. Two related measures, "m" and…

Using Facet Clusters to Map Learner Modes of Reasoning

NASA Astrophysics Data System (ADS)

Vokos, Stamatis; DeWater, L. S.; Seeley, L.; Kraus, P.

2006-12-01

The Department of Physics and the School of Education at Seattle Pacific University, together with FACET Innovations, LLC, are beginning the second year of a five-year NSF TPC project, Improving the Effectiveness of Teacher Diagnostic Skills and Tools. We are working in partnership with school districts in Washington State to use formative assessment as a means to helping teachers and precollege students deepen their understanding of foundational topics in physical science. We utilize a theoretical framework of knowledge-in-pieces to identify and categorize widespread productive and unproductive modes of reasoning in the topical areas of Properties of Matter, Heat and Temperature, and Physical and Chemical Changes. In this talk, we describe the development and iterative refinement of certain facet clusters of student ideas, as well as the usefulness and limitations of such a mapping scheme. * Supported in part by NSF grant #ESI-0455796, The Boeing Corporation, and the SPU Science Initiative.

Somatotyping using 3D anthropometry: a cluster analysis.

PubMed

Olds, Tim; Daniell, Nathan; Petkov, John; David Stewart, Arthur

2013-01-01

Somatotyping is the quantification of human body shape, independent of body size. Hitherto, somatotyping (including the most popular method, the Heath-Carter system) has been based on subjective visual ratings, sometimes supported by surface anthropometry. This study used data derived from three-dimensional (3D) whole-body scans as inputs for cluster analysis to objectively derive clusters of similar body shapes. Twenty-nine dimensions normalised for body size were measured on a purposive sample of 301 adults aged 17-56 years who had been scanned using a Vitus Smart laser scanner. K-means Cluster Analysis with v-fold cross-validation was used to determine shape clusters. Three male and three female clusters emerged, and were visualised using those scans closest to the cluster centroid and a caricature defined by doubling the difference between the average scan and the cluster centroid. The male clusters were decidedly endomorphic (high fatness), ectomorphic (high linearity), and endo-mesomorphic (a mixture of fatness and muscularity). The female clusters were clearly endomorphic, ectomorphic, and the ecto-mesomorphic (a mixture of linearity and muscularity). An objective shape quantification procedure combining 3D scanning and cluster analysis yielded shape clusters strikingly similar to traditional somatotyping.

Molecular analysis of SCARECROW genes expressed in white lupin cluster roots

PubMed Central

Sbabou, Laila; Bucciarelli, Bruna; Miller, Susan; Liu, Junqi; Berhada, Fatiha; Filali-Maltouf, Abdelkarim; Allan, Deborah; Vance, Carroll

2010-01-01

The Scarecrow (SCR) transcription factor plays a crucial role in root cell radial patterning and is required for maintenance of the quiescent centre and differentiation of the endodermis. In response to phosphorus (P) deficiency, white lupin (Lupinus albus L.) root surface area increases some 50-fold to 70-fold due to the development of cluster (proteoid) roots. Previously it was reported that SCR-like expressed sequence tags (ESTs) were expressed during early cluster root development. Here the cloning of two white lupin SCR genes, LaSCR1 and LaSCR2, is reported. The predicted amino acid sequences of both LaSCR gene products are highly similar to AtSCR and contain C-terminal conserved GRAS family domains. LaSCR1 and LaSCR2 transcript accumulation localized to the endodermis of both normal and cluster roots as shown by in situ hybridization and gene promoter::reporter staining. Transcript analysis as evaluated by quantitative real-time-PCR (qRT-PCR) and RNA gel hybridization indicated that the two LaSCR genes are expressed predominantly in roots. Expression of LaSCR genes was not directly responsive to the P status of the plant but was a function of cluster root development. Suppression of LaSCR1 in transformed roots of lupin and Medicago via RNAi (RNA interference) delivered through Agrobacterium rhizogenes resulted in decreased root numbers, reflecting the potential role of LaSCR1 in maintaining root growth in these species. The results suggest that the functional orthologues of AtSCR have been characterized. PMID:20167612

A Millimeter Wave BPF using WG Mode High Permittivity Dielectric Resonators

NASA Astrophysics Data System (ADS)

Sato, Yosuke; Kogami, Yoshinori; Tomabechi, Yoshiro; Matsumura, Kazuhito

In this paper, a design technique of whispering gallery mode high Q value dielectric disk resonators for a millimeter-wave bandpass filter is described. To minimize the resonator size, some high permittivity materials are used. In this resonator design, unloaded Q value of an interested mode and the higher order modes are calculated and then optimum resonator size for the WG mode dielectric filter is determined. For a designed resonator, the higher order modes are hardly excited while the Q value of the fundamental mode can be maximized. Finally, some 3stage BPFs are constructed at 60GHz by using these designed resonators.

Failure mode analysis to predict product reliability.

NASA Technical Reports Server (NTRS)

Zemanick, P. P.

1972-01-01

The failure mode analysis (FMA) is described as a design tool to predict and improve product reliability. The objectives of the failure mode analysis are presented as they influence component design, configuration selection, the product test program, the quality assurance plan, and engineering analysis priorities. The detailed mechanics of performing a failure mode analysis are discussed, including one suggested format. Some practical difficulties of implementation are indicated, drawn from experience with preparing FMAs on the nuclear rocket engine program.

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks

PubMed Central

Li, Min; Li, Dongyan; Tang, Yu; Wang, Jianxin

2017-01-01

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster. PMID:28858211

Metabolic Clustering Analysis as a Strategy for Compound Selection in the Drug Discovery Pipeline for Leishmaniasis.

PubMed

Armitage, Emily G; Godzien, Joanna; Peña, Imanol; López-Gonzálvez, Ángeles; Angulo, Santiago; Gradillas, Ana; Alonso-Herranz, Vanesa; Martín, Julio; Fiandor, Jose M; Barrett, Michael P; Gabarro, Raquel; Barbas, Coral

2018-05-18

A lack of viable hits, increasing resistance, and limited knowledge on mode of action is hindering drug discovery for many diseases. To optimize prioritization and accelerate the discovery process, a strategy to cluster compounds based on more than chemical structure is required. We show the power of metabolomics in comparing effects on metabolism of 28 different candidate treatments for Leishmaniasis (25 from the GSK Leishmania box, two analogues of Leishmania box series, and amphotericin B as a gold standard treatment), tested in the axenic amastigote form of Leishmania donovani. Capillary electrophoresis-mass spectrometry was applied to identify the metabolic profile of Leishmania donovani, and principal components analysis was used to cluster compounds on potential mode of action, offering a medium throughput screening approach in drug selection/prioritization. The comprehensive and sensitive nature of the data has also made detailed effects of each compound obtainable, providing a resource to assist in further mechanistic studies and prioritization of these compounds for the development of new antileishmanial drugs.

Genomic Anatomy of a Premier Major Histocompatibility Complex Paralogous Region on Chromosome 1q21–q22

PubMed Central

Shiina, Takashi; Ando, Asako; Suto, Yumiko; Kasai, Fumio; Shigenari, Atsuko; Takishima, Nobusada; Kikkawa, Eri; Iwata, Kyoko; Kuwano, Yuko; Kitamura, Yuka; Matsuzawa, Yumiko; Sano, Kazumi; Nogami, Masahiro; Kawata, Hisako; Li, Suyun; Fukuzumi, Yasuhito; Yamazaki, Masaaki; Tashiro, Hiroyuki; Tamiya, Gen; Kohda, Atsushi; Okumura, Katsuzumi; Ikemura, Toshimichi; Soeda, Eiichi; Mizuki, Nobuhisa; Kimura, Minoru; Bahram, Seiamak; Inoko, Hidetoshi

2001-01-01

Human chromosomes 1q21–q25, 6p21.3–22.2, 9q33–q34, and 19p13.1–p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21–25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCERIA belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21–q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, IFI-16, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides. [The nucleotide sequence data reported in this paper have been submitted to the DDBJ, EMBL, and GenBank databases under

Biological and clinical characterization of recurrent 14q deletions in CLL and other mature B-cell neoplasms.

PubMed

Reindl, Lena; Bacher, Ulrike; Dicker, Frank; Alpermann, Tamara; Kern, Wolfgang; Schnittger, Susanne; Haferlach, Torsten; Haferlach, Claudia

2010-10-01

14q-deletions have been repeatedly described in mature B-cell neoplasms, but not yet characterized in a larger cohort. Based on chromosome banding analysis, the present study identified 47 del(14q) cases in 3054 mature B-cell neoplasms (1·5%) (chronic lymphocytic leukaemia [CLL]: 1·9%; CLL/prolymphocytic leukaemia [PL]: 9·0%; others: 0·2%). Interphase fluorescence in situ hybridization was performed with probes for 14q22.1, 14q24.1, 14q32.33, and IGH@ (14q32.3). The del(14q) had heterogeneous size but showed a breakpoint cluster at the centromeric site in 14q24.1 (62% of cases). At the telomeric side, the most frequent breakpoint was within the IGH@ locus (14q32.3) between IGH@ 3'-flanking and IGHV (IgVH) probes (45%). In 16 cases (34%), breakpoints occurred within 14q24.1 and 14q32.3. Eighty-one percent of del(14q) cases showed 1-3 additional cytogenetic alterations (in 45%, +12), and 56% were IGHV-unmutated. In all cases (16/16) with breakpoints in 14q24.1 and 14q32.3, a B-CLL immunophenotype was found. Clinical follow-up in 32 del(14q) patients was compared to 383 CLL and CLL/PL patients without del(14q). While 3-year-overall survival did not differ significantly, time to treatment was significantly shorter in the del(14q) cohort (21·0 months vs. 80·1 months, P = 0·015). In conclusion, the del(14q) is a rare recurrent alteration in diverse mature B-cell neoplasms, shows variable size but distinct clustering of breakpoints, and is associated with short time to treatment. © 2010 Blackwell Publishing Ltd.

From virtual clustering analysis to self-consistent clustering analysis: a mathematical study

NASA Astrophysics Data System (ADS)

Tang, Shaoqiang; Zhang, Lei; Liu, Wing Kam

2018-03-01

In this paper, we propose a new homogenization algorithm, virtual clustering analysis (VCA), as well as provide a mathematical framework for the recently proposed self-consistent clustering analysis (SCA) (Liu et al. in Comput Methods Appl Mech Eng 306:319-341, 2016). In the mathematical theory, we clarify the key assumptions and ideas of VCA and SCA, and derive the continuous and discrete Lippmann-Schwinger equations. Based on a key postulation of "once response similarly, always response similarly", clustering is performed in an offline stage by machine learning techniques (k-means and SOM), and facilitates substantial reduction of computational complexity in an online predictive stage. The clear mathematical setup allows for the first time a convergence study of clustering refinement in one space dimension. Convergence is proved rigorously, and found to be of second order from numerical investigations. Furthermore, we propose to suitably enlarge the domain in VCA, such that the boundary terms may be neglected in the Lippmann-Schwinger equation, by virtue of the Saint-Venant's principle. In contrast, they were not obtained in the original SCA paper, and we discover these terms may well be responsible for the numerical dependency on the choice of reference material property. Since VCA enhances the accuracy by overcoming the modeling error, and reduce the numerical cost by avoiding an outer loop iteration for attaining the material property consistency in SCA, its efficiency is expected even higher than the recently proposed SCA algorithm.

Minimal disease detection of B-cell lymphoproliferative disorders by flow cytometry: multidimensional cluster analysis.

PubMed

Duque, Ricardo E

2012-04-01

Flow cytometric analysis of cell suspensions involves the sequential 'registration' of intrinsic and extrinsic parameters of thousands of cells in list mode files. Thus, it is almost irresistible to describe phenomena in numerical terms or by 'ratios' that have the appearance of 'accuracy' due to the presence of numbers obtained from thousands of cells. The concepts involved in the detection and characterization of B cell lymphoproliferative processes are revisited in this paper by identifying parameters that, when analyzed appropriately, are both necessary and sufficient. The neoplastic process (cluster) can be visualized easily because the parameters that distinguish it form a cluster in multidimensional space that is unique and distinguishable from neighboring clusters that are not of diagnostic interest but serve to provide a background. For B cell neoplasia it is operationally necessary to identify the multidimensional space occupied by a cluster whose kappa:lambda ratio is 100:0 or 0:100. Thus, the concept of kappa:lambda ratio is without meaning and would not detect B cell neoplasia in an unacceptably high number of cases.

Failure Mode, Effects, and Criticality Analysis (FMECA)

DTIC Science & Technology

1993-04-01

Preliminary Failure Modes, Effects and Criticality Analysis (FMECA) of the Brayton Isotope Power System Ground Demonstration System, Report No. TID 27301...No. TID/SNA - 3015, Aeroject Nuclear Systems Co., Sacramento, California: 1970. 95. Taylor , J.R. A Formalization of Failure Mode Analysis of Control...Roskilde, Denmark: 1973. 96. Taylor , J.R. A Semi-Automatic Method for Oualitative Failure Mode Analysis. Report No. RISO-M-1707. Available from a

Ultrasonic attenuation - Q measurements on 70215,29. [lunar rock

NASA Technical Reports Server (NTRS)

Warren, N.; Trice, R.; Stephens, J.

1974-01-01

Ultrasonic attenuation measurements have been made on an aluminum alloy, obsidian, and rock samples including lunar sample 70215,29. The measurement technique is based on a combination of the pulse transmission method and the forced resonance method. The technique is designed to explore the problem of defining experimentally, the Q of a medium or sample in which mode conversion may occur. If modes are coupled, the measured attenuation is strongly dependent on individual modes of vibration, and a range of Q-factors may be measured over various resonances or from various portions of a transient signal. On 70215,29, measurements were made over a period of a month while the sample outgassed in hard varuum. During this period, the highest measured Q of this sample increased from a few hundred into the range of 1000-1300.

A survey of tools for the analysis of quantitative PCR (qPCR) data.

PubMed

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

Two novel translocation breakpoints upstream of SOX9 define borders of the proximal and distal breakpoint cluster region in campomelic dysplasia.

PubMed

Leipoldt, M; Erdel, M; Bien-Willner, G A; Smyk, M; Theurl, M; Yatsenko, S A; Lupski, J R; Lane, A H; Shanske, A L; Stankiewicz, P; Scherer, G

2007-01-01

The semilethal skeletal malformation syndrome campomelic dysplasia (CD) with or without XY sex reversal is caused by mutations within the SOX9 gene on 17q24.3 or by chromosomal aberrations (translocations, inversions or deletions) with breakpoints outside the SOX9 coding region. The previously published CD translocation breakpoints upstream of SOX9 fall into two clusters: a proximal cluster with breakpoints between 50-300 kb and a distal cluster with breakpoints between 899-932 kb. Here, we present clinical, cytogenetic and molecular data from two novel CD translocation cases. Case 1 with karyotype 46,XY,t(1;17)(q42.1;q24.3) has characteristic symptoms of CD, including mild tibial bowing, cryptorchidism and hypospadias. By standard fluorescence in situ hybridization (FISH) and by high-resolution fiber FISH, the 17q breakpoint was mapped 375 kb from SOX9, defining the centromeric border of the proximal breakpoint cluster region. Case 2 with karyotype 46,X,t(Y;17)(q11.2;q24.3) has the acampomelic form of CD and complete XY sex reversal. By FISH and somatic cell hybrid analysis, the 17q breakpoint was mapped 789 kb from SOX9, defining the telomeric border of the distal breakpoint cluster region. We discuss the structure of the 1 Mb cis-control region upstream of SOX9 and the correlation between the position of the 14 mapped translocation breakpoints with respect to disease severity and XY sex reversal.

Q-controlled amplitude modulation atomic force microscopy in liquids: An analysis

NASA Astrophysics Data System (ADS)

Hölscher, H.; Schwarz, U. D.

2006-08-01

An analysis of amplitude modulation atomic force microscopy in liquids is presented with respect to the application of the Q-Control technique. The equation of motion is solved by numerical and analytic methods with and without Q-Control in the presence of a simple model interaction force adequate for many liquid environments. In addition, the authors give an explicit analytical formula for the tip-sample indentation showing that higher Q factors reduce the tip-sample force. It is found that Q-Control suppresses unwanted deformations of the sample surface, leading to the enhanced image quality reported in several experimental studies.

The <q>ABC modelq>: a non-hydrostatic toy model for use in convective-scale data assimilation investigations

NASA Astrophysics Data System (ADS)

Petrie, Ruth Elizabeth; Bannister, Ross Noel; Priestley Cullen, Michael John

2017-12-01

In developing methods for convective-scale data assimilation (DA), it is necessary to consider the full range of motions governed by the compressible Navier-Stokes equations (including non-hydrostatic and ageostrophic flow). These equations describe motion on a wide range of timescales with non-linear coupling. For the purpose of developing new DA techniques that suit the convective-scale problem, it is helpful to use so-called <q>toy modelsq> that are easy to run and contain the same types of motion as the full equation set. Such a model needs to permit hydrostatic and geostrophic balance at large scales but allow imbalance at small scales, and in particular, it needs to exhibit intermittent convection-like behaviour. Existing <q>toy modelsq> are not always sufficient for investigating these issues. A simplified system of intermediate complexity derived from the Euler equations is presented, which supports dispersive gravity and acoustic modes. In this system, the separation of timescales can be greatly reduced by changing the physical parameters. Unlike in existing toy models, this allows the acoustic modes to be treated explicitly and hence inexpensively. In addition, the non-linear coupling induced by the equation of state is simplified. This means that the gravity and acoustic modes are less coupled than in conventional models. A vertical slice formulation is used which contains only dry dynamics. The model is shown to give physically reasonable results, and convective behaviour is generated by localised compressible effects. This model provides an affordable and flexible framework within which some of the complex issues of convective-scale DA can later be investigated. The model is called the <q>ABC modelq> after the three tunable parameters introduced: A (the pure gravity wave frequency), B (the modulation of the divergent term in the continuity equation), and C (defining the compressibility).

Analysis of the convective evaporation of nondilute clusters of drops

NASA Technical Reports Server (NTRS)

Bellan, J.; Harstad, K.

1987-01-01

The penetration distance of an outer flow into a drop cluster volume is the critical, evaporation mode-controlling parameter in the present model for nondilute drop clusters' convective evaporation. The model is found to perform well for such low penetration distances as those obtained for dense clusters in hot environments and low relative velocities between the outer gases and the cluster. For large penetration distances, however, the predictive power of the model deteriorates; in addition, the evaporation time is found to be a weak function of the initial relative velocity and a strong function of the initial drop temperature. The results generally show that the interior drop temperature was transient throughout the drop lifetime, although temperature nonuniformities persisted up to the first third of the total evaporation time at most.

Investigating Subtypes of Child Development: A Comparison of Cluster Analysis and Latent Class Cluster Analysis in Typology Creation

ERIC Educational Resources Information Center

DiStefano, Christine; Kamphaus, R. W.

2006-01-01

Two classification methods, latent class cluster analysis and cluster analysis, are used to identify groups of child behavioral adjustment underlying a sample of elementary school children aged 6 to 11 years. Behavioral rating information across 14 subscales was obtained from classroom teachers and used as input for analyses. Both the procedures…

Time-frequency analysis : mathematical analysis of the empirical mode decomposition.

DOT National Transportation Integrated Search

2009-01-01

Invented over 10 years ago, empirical mode : decomposition (EMD) provides a nonlinear : time-frequency analysis with the ability to successfully : analyze nonstationary signals. Mathematical : Analysis of the Empirical Mode Decomposition : is a...

Genome-wide linkage meta-analysis identifies susceptibility loci at 2q34 and 13q31.3 for genetic generalized epilepsies.

PubMed

Leu, Costin; de Kovel, Carolien G F; Zara, Federico; Striano, Pasquale; Pezzella, Marianna; Robbiano, Angela; Bianchi, Amedeo; Bisulli, Francesca; Coppola, Antonietta; Giallonardo, Anna Teresa; Beccaria, Francesca; Trenité, Dorothée Kasteleijn-Nolst; Lindhout, Dick; Gaus, Verena; Schmitz, Bettina; Janz, Dieter; Weber, Yvonne G; Becker, Felicitas; Lerche, Holger; Kleefuss-Lie, Ailing A; Hallman, Kerstin; Kunz, Wolfram S; Elger, Christian E; Muhle, Hiltrud; Stephani, Ulrich; Møller, Rikke S; Hjalgrim, Helle; Mullen, Saul; Scheffer, Ingrid E; Berkovic, Samuel F; Everett, Kate V; Gardiner, Mark R; Marini, Carla; Guerrini, Renzo; Lehesjoki, Anna-Elina; Siren, Auli; Nabbout, Rima; Baulac, Stephanie; Leguern, Eric; Serratosa, Jose M; Rosenow, Felix; Feucht, Martha; Unterberger, Iris; Covanis, Athanasios; Suls, Arvid; Weckhuysen, Sarah; Kaneva, Radka; Caglayan, Hande; Turkdogan, Dilsad; Baykan, Betul; Bebek, Nerses; Ozbek, Ugur; Hempelmann, Anne; Schulz, Herbert; Rüschendorf, Franz; Trucks, Holger; Nürnberg, Peter; Avanzini, Giuliano; Koeleman, Bobby P C; Sander, Thomas

2012-02-01

Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% with heritability estimates of 80%. A considerable proportion of families with siblings affected by GGEs presumably display an oligogenic inheritance. The present genome-wide linkage meta-analysis aimed to map: (1) susceptibility loci shared by a broad spectrum of GGEs, and (2) seizure type-related genetic factors preferentially predisposing to either typical absence or myoclonic seizures, respectively. Meta-analysis of three genome-wide linkage datasets was carried out in 379 GGE-multiplex families of European ancestry including 982 relatives with GGEs. To dissect out seizure type-related susceptibility genes, two family subgroups were stratified comprising 235 families with predominantly genetic absence epilepsies (GAEs) and 118 families with an aggregation of juvenile myoclonic epilepsy (JME). To map shared and seizure type-related susceptibility loci, both nonparametric loci (NPL) and parametric linkage analyses were performed for a broad trait model (GGEs) in the entire set of GGE-multiplex families and a narrow trait model (typical absence or myoclonic seizures) in the subgroups of JME and GAE families. For the entire set of 379 GGE-multiplex families, linkage analysis revealed six loci achieving suggestive evidence for linkage at 1p36.22, 3p14.2, 5q34, 13q12.12, 13q31.3, and 19q13.42. The linkage finding at 5q34 was consistently supported by both NPL and parametric linkage results across all three family groups. A genome-wide significant nonparametric logarithm of odds score of 3.43 was obtained at 2q34 in 118 JME families. Significant parametric linkage to 13q31.3 was found in 235 GAE families assuming recessive inheritance (heterogeneity logarithm of odds = 5.02). Our linkage results support an oligogenic predisposition of familial GGE syndromes. The genetic risk factor at 5q34 confers risk to a broad spectrum of familial GGE syndromes, whereas susceptibility loci at 2q34 and 13q31

A hybrid monkey search algorithm for clustering analysis.

PubMed

Chen, Xin; Zhou, Yongquan; Luo, Qifang

2014-01-01

Clustering is a popular data analysis and data mining technique. The k-means clustering algorithm is one of the most commonly used methods. However, it highly depends on the initial solution and is easy to fall into local optimum solution. In view of the disadvantages of the k-means method, this paper proposed a hybrid monkey algorithm based on search operator of artificial bee colony algorithm for clustering analysis and experiment on synthetic and real life datasets to show that the algorithm has a good performance than that of the basic monkey algorithm for clustering analysis.

Inversion of chromosome 7q22 and q36 as a sole abnormality presenting in myelodysplastic syndrome: a case report.

PubMed

Kaneko, Hiroto; Shimura, Kazuho; Kuwahara, Saeko; Ohshiro, Muneo; Tsutsumi, Yasuhiko; Iwai, Toshiki; Horiike, Shigeo; Yokota, Shouhei; Ohkawara, Yasuo; Taniwaki, Masafumi

2014-08-05

Deletions of chromosome 7 are often detected in myelodysplastic syndrome. The most commonly deleted segments are clustered at band 7q22. A critical gene is therefore suggested to be located in this region. We report a patient with myelodysplastic syndrome whose marrow cells carried an inversion of 7q22 and q36 as a sole karyotypic abnormality. How this extremely rare chromosomal aberration contributes to the pathogenesis of myelodysplastic syndrome should be clarified by accumulating clinical data of such cases. A 74-year-old Japanese man presented with pancytopenia incidentally detected by routine medical check-up. His complete blood cell counts revealed that his white blood cells had decreased to 2100/mm3, neutrophils 940/mm3, red blood cells 320×104/mm3, hemoglobin 11.1g/dL, hematocrit 33.1%, and platelets 12.6×104/mm3. Bone marrow examination showed normal cellularity with nucleated cells of 9.4×104/mm3. The proportion of blasts was 4%. A morphological examination showed only basophilic stippling of erythroblasts which was seen as dysplasia. According to World Health Organization classification, the diagnosis was myelodysplastic syndrome-u. Karyotypic analysis showed 46,XY,inv(7)(q22q36) in all of 20 metaphases examined. Additional analysis revealed the karyotype of his lymphocytes was 46,XY. He is asymptomatic and cytopenia has slowly progressed. To the best of our knowledge, this karyotype from a clinical sample of de novo malignancies has never been documented although the identical karyotype from secondary myelodysplastic syndrome was reported. Despite the extremely low frequency, inversion of 7q22 appears to play a crucial role for myelodysplastic syndrome in this patient.

Time-varying q-deformed dark energy interacts with dark matter

NASA Astrophysics Data System (ADS)

Dil, Emre; Kolay, Erdinç

We propose a new model for studying the dark constituents of the universe by regarding the dark energy as a q-deformed scalar field interacting with the dark matter, in the framework of standard general relativity. Here we assume that the number of particles in each mode of the q-deformed scalar field varies in time by the particle creation and annihilation. We first describe the q-deformed scalar field dark energy quantum-field theoretically, then construct the action and the dynamical structure of these interacting dark sectors, in order to study the dynamics of the model. We perform the phase space analysis of the model to confirm and interpret our proposal by searching the stable attractor solutions implying the late-time accelerating phase of the universe. We then obtain the result that when interaction and equation-of-state parameter of the dark matter evolve from the present day values into a particular value, the dark energy turns out to be a q-deformed scalar field.

Applications of cluster analysis to satellite soundings

NASA Technical Reports Server (NTRS)

Munteanu, M. J.; Jakubowicz, O.; Kalnay, E.; Piraino, P.

1984-01-01

The advantages of the use of cluster analysis in the improvement of satellite temperature retrievals were evaluated since the use of natural clusters, which are associated with atmospheric temperature soundings characteristic of different types of air masses, has the potential for improving stratified regression schemes in comparison with currently used methods which stratify soundings based on latitude, season, and land/ocean. The method of discriminatory analysis was used. The correct cluster of temperature profiles from satellite measurements was located in 85% of the cases. Considerable improvement was observed at all mandatory levels using regression retrievals derived in the clusters of temperature (weighted and nonweighted) in comparison with the control experiment and with the regression retrievals derived in the clusters of brightness temperatures of 3 MSU and 5 IR channels.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway

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

Guntaka, Naga Sandhya; Healy, Alan R.; Crawford, Jason M.

Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0more » Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.« less

Preventing Raman Lasing in High-Q WGM Resonators

NASA Technical Reports Server (NTRS)

Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry; Maleki, Lute

2007-01-01

A generic design has been conceived to suppress the Raman effect in whispering- gallery-mode (WGM) optical resonators that have high values of the resonance quality factor (Q). Although it is possible to exploit the Raman effect (even striving to maximize the Raman gain to obtain Raman lasing), the present innovation is intended to satisfy a need that arises in applications in which the Raman effect inhibits the realization of the full potential of WGM resonators as frequency-selection components. Heretofore, in such applications, it has been necessary to operate high-Q WGM resonators at unattractively low power levels to prevent Raman lasing. (The Raman-lasing thresholds of WGM optical resonators are very low and are approximately proportional to Q(sup -2)). Heretofore, two ways of preventing Raman lasting at high power levels have been known, but both entail significant disadvantages: A resonator can be designed so that the optical field is spread over a relatively large mode volume to bring the power density below the threshold. For any given combination of Q and power level, there is certain mode volume wherein Raman lasing does not start. Unfortunately, a resonator that has a large mode volume also has a high spectral density, which is undesirable in a typical photonic application. A resonator can be cooled to the temperature of liquid helium, where the Raman spectrum is narrower and, therefore, the Raman gain is lower. However, liquid-helium cooling is inconvenient. The present design overcomes these disadvantages, making it possible to operate a low-spectral-density (even a single-mode) WGM resonator at a relatively high power level at room temperature, without risk of Raman lasing.

Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

PubMed

Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

2013-12-30

Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

Observation of Q-switching and mode-locking in two-section InAs/InP (100) quantum dot lasers around 1.55 mum.

PubMed

Heck, Martijn J R; Bente, Erwin A J M; Smalbrugge, Barry; Oei, Yok-Siang; Smit, Meint K; Anantathanasarn, Sanguan; Nötzel, Richard

2007-12-10

First observation of passive mode-locking in two-section quantum-dot lasers operating at wavelengths around 1.55 mum is reported. Pulse generation at 4.6 GHz from a 9 mm long device is verified by background-free autocorrelation, RF-spectra and real-time oscilloscope traces. The output pulses are stretched in time and heavily up-chirped with a value of 20 ps/nm, contrary to what is normally observed in passively mode-locked semiconductor lasers. The complete output spectrum is shown to be coherent over 10 nm. From a 7 mm long device Q-switching is observed over a large operating regime. The lasers have been realized using a fabrication technology that is compatible with further photonic integration. This makes the laser a promising candidate for e.g. a mode-comb generator in a complex photonic chip.

Cluster analysis of multiple planetary flow regimes

NASA Technical Reports Server (NTRS)

Mo, Kingtse; Ghil, Michael

1987-01-01

A modified cluster analysis method was developed to identify spatial patterns of planetary flow regimes, and to study transitions between them. This method was applied first to a simple deterministic model and second to Northern Hemisphere (NH) 500 mb data. The dynamical model is governed by the fully-nonlinear, equivalent-barotropic vorticity equation on the sphere. Clusters of point in the model's phase space are associated with either a few persistent or with many transient events. Two stationary clusters have patterns similar to unstable stationary model solutions, zonal, or blocked. Transient clusters of wave trains serve as way stations between the stationary ones. For the NH data, cluster analysis was performed in the subspace of the first seven empirical orthogonal functions (EOFs). Stationary clusters are found in the low-frequency band of more than 10 days, and transient clusters in the bandpass frequency window between 2.5 and 6 days. In the low-frequency band three pairs of clusters determine, respectively, EOFs 1, 2, and 3. They exhibit well-known regional features, such as blocking, the Pacific/North American (PNA) pattern and wave trains. Both model and low-pass data show strong bimodality. Clusters in the bandpass window show wave-train patterns in the two jet exit regions. They are related, as in the model, to transitions between stationary clusters.

Maternal uniparental disomy of chromosome 14 in a boy with t(14q14q) associated with a paternal t(13q14q)

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

Tomkins, D.J.; Waye, J.S.; Whelan, D.T.

An 11-year-old boy was referred for chromosomal analysis because of precocious development and behavioral problems suggestive of the fragile X syndrome. The cytogenetic fragile X studies were normal, but a routine GTG-banded karyotype revealed an abnormal male karyotype with a Robertsonian translocation between the two chromosome 14`s: 46,XY,t(14q14q). Paternal karyotyping revealed another abnormal karyotype: 46,XY,t(13q14q). A brother had the same karyotype as the father; the mother was deceased. In order to determine if the apparently balanced t(14q14q) in the proband might be the cause of the clinical findings, molecular analysis of the origin of the chromosome 14`s was initiated. Southernmore » blotting and hybridization with D4S13 showed that the proband had two copies of one maternal allele which was shared by his brother. The brother`s second allele corresponded to one of the paternal alleles; the proband had no alleles from the father. Analysis of four other VNTRs demonstrated the probability of paternity to be greater than 99%. Thus, the t(14q14q) was most likely composed of two maternal chromosome 14`s. Further characterization of the t(14q14q) by dinucleotide repeat polymorphic markers is in progress to determine whether it has arisen from maternal isodisomy or heterodisomy. Several cases of uniparental disomy for chromosome 14 have been reported recently. Paternal disomy appears to be associated with more severe congenital anomalies and mental retardation, whereas maternal disomy may be associated with premature puberty and minimal intellectual impairment. The origin of the t(14q14q) in the present case may be related to the paternal translocation, as the segregation of the t(13q14q) in meiosis could lead to sperm that are nullisomic for chromosome 14.« less

Cluster analysis of multiple planetary flow regimes

NASA Technical Reports Server (NTRS)

Mo, Kingtse; Ghil, Michael

1988-01-01

A modified cluster analysis method developed for the classification of quasi-stationary events into a few planetary flow regimes and for the examination of transitions between these regimes is described. The method was applied first to a simple deterministic model and then to a 500-mbar data set for Northern Hemisphere (NH), for which cluster analysis was carried out in the subspace of the first seven empirical orthogonal functions (EOFs). Stationary clusters were found in the low-frequency band of more than 10 days, while transient clusters were found in the band-pass frequency window between 2.5 and 6 days. In the low-frequency band, three pairs of clusters determined EOFs 1, 2, and 3, respectively; they exhibited well-known regional features, such as blocking, the Pacific/North American pattern, and wave trains. Both model and low-pass data exhibited strong bimodality.

Cluster Analysis to Identify Possible Subgroups in Tinnitus Patients.

PubMed

van den Berge, Minke J C; Free, Rolien H; Arnold, Rosemarie; de Kleine, Emile; Hofman, Rutger; van Dijk, J Marc C; van Dijk, Pim

2017-01-01

In tinnitus treatment, there is a tendency to shift from a "one size fits all" to a more individual, patient-tailored approach. Insight in the heterogeneity of the tinnitus spectrum might improve the management of tinnitus patients in terms of choice of treatment and identification of patients with severe mental distress. The goal of this study was to identify subgroups in a large group of tinnitus patients. Data were collected from patients with severe tinnitus complaints visiting our tertiary referral tinnitus care group at the University Medical Center Groningen. Patient-reported and physician-reported variables were collected during their visit to our clinic. Cluster analyses were used to characterize subgroups. For the selection of the right variables to enter in the cluster analysis, two approaches were used: (1) variable reduction with principle component analysis and (2) variable selection based on expert opinion. Various variables of 1,783 tinnitus patients were included in the analyses. Cluster analysis (1) included 976 patients and resulted in a four-cluster solution. The effect of external influences was the most discriminative between the groups, or clusters, of patients. The "silhouette measure" of the cluster outcome was low (0.2), indicating a "no substantial" cluster structure. Cluster analysis (2) included 761 patients and resulted in a three-cluster solution, comparable to the first analysis. Again, a "no substantial" cluster structure was found (0.2). Two cluster analyses on a large database of tinnitus patients revealed that clusters of patients are mostly formed by a different response of external influences on their disease. However, both cluster outcomes based on this dataset showed a poor stability, suggesting that our tinnitus population comprises a continuum rather than a number of clearly defined subgroups.

Open-flavor charm and bottom s q q ¯ Q ¯ and q q q ¯ Q ¯ tetraquark states

NASA Astrophysics Data System (ADS)

Chen, Wei; Chen, Hua-Xing; Liu, Xiang; Steele, T. G.; Zhu, Shi-Lin

2017-06-01

We provide comprehensive investigations for the mass spectrum of exotic open-flavor charmed/bottom s q q ¯ c ¯ , q q q ¯ c ¯ , s q q ¯ b ¯ , q q q ¯ b ¯ tetraquark states with various spin-parity assignments JP=0+,1+,2+ and 0- , 1- in the framework of QCD sum rules. In the diquark configuration, we construct the diquark-antidiquark interpolating tetraquark currents using the color-antisymmetric scalar and axial-vector diquark fields. The stable mass sum rules are established in reasonable parameter working ranges, which are used to give reliable mass predictions for these tetraquark states. We obtain the mass spectra for the open-flavor charmed/bottom s q q ¯c ¯, q q q ¯c ¯, s q q ¯b ¯, q q q ¯b ¯ tetraquark states with various spin-parity quantum numbers. In addition, we suggest searching for exotic doubly-charged tetraquarks, such as [s d ][u ¯ c ¯ ]→Ds(*)-π- in future experiments at facilities such as BESIII, BelleII, PANDA, LHCb, and CMS, etc.

High-Q/V Monolithic Diamond Microdisks Fabricated with Quasi-isotropic Etching.

PubMed

Khanaliloo, Behzad; Mitchell, Matthew; Hryciw, Aaron C; Barclay, Paul E

2015-08-12

Optical microcavities enhance light-matter interactions and are essential for many experiments in solid state quantum optics, optomechanics, and nonlinear optics. Single crystal diamond microcavities are particularly sought after for applications involving diamond quantum emitters, such as nitrogen vacancy centers, and for experiments that benefit from diamond's excellent optical and mechanical properties. Light-matter coupling rates in experiments involving microcavities typically scale with Q/V, where Q and V are the microcavity quality-factor and mode-volume, respectively. Here we demonstrate that microdisk whispering gallery mode cavities with high Q/V can be fabricated directly from bulk single crystal diamond. By using a quasi-isotropic oxygen plasma to etch along diamond crystal planes and undercut passivated diamond structures, we create monolithic diamond microdisks. Fiber taper based measurements show that these devices support TE- and TM-like optical modes with Q > 1.1 × 10(5) and V < 11(λ/n) (3) at a wavelength of 1.5 μm.

The external kink mode in diverted tokamaks

DOE PAGES

Turnbull, Alan D.; Hanson, Jeremy M.; Turco, Francesca; ...

2016-06-16

Here, an explanation is provided for the disruptive instability in diverted tokamaks when the safety factor at the 95% poloidal flux surface, q 95, is driven below 2.0. The instability is a resistive kink counterpart to the current-driven ideal mode that traditionally explained the corresponding disruption in limited cross-sections when q edge, the safety factor at the outermost closed flux surface, lies just below a rational value. Experimentally, external kink modes are observed in limiter configurations as the current in a tokamak is ramped up and q edge decreases through successive rational surfaces. For q edge < 2, the instabilitymore » is always encountered and is highly disruptive. However, diverted plasmas, in which q edge is formally infinite in the magnetohydrodynamic (MHD) model, have presented a longstanding difficulty since the theory would predict stability, yet, the disruptive limit occurs in practice when q 95, reaches 2. It is shown from numerical calculations that a resistive kink mode is linearly destabilized by the rapidly increasing resistivity at the plasma edge when q 95 < 2, but q edge >> 2. The resistive kink behaves much like the ideal kink with predominantly kink or interchange parity and no real sign of a tearing component. However, the growth rates scale with a fractional power of the resistivity near the q = 2 surface. The results have a direct bearing on the conventional edge cutoff procedures used in most ideal MHD codes, as well as implications for ITER and for future reactor options.« less

Clustering Categorical Data Using Community Detection Techniques

PubMed Central

2017-01-01

With the advent of the k-modes algorithm, the toolbox for clustering categorical data has an efficient tool that scales linearly in the number of data items. However, random initialization of cluster centers in k-modes makes it hard to reach a good clustering without resorting to many trials. Recently proposed methods for better initialization are deterministic and reduce the clustering cost considerably. A variety of initialization methods differ in how the heuristics chooses the set of initial centers. In this paper, we address the clustering problem for categorical data from the perspective of community detection. Instead of initializing k modes and running several iterations, our scheme, CD-Clustering, builds an unweighted graph and detects highly cohesive groups of nodes using a fast community detection technique. The top-k detected communities by size will define the k modes. Evaluation on ten real categorical datasets shows that our method outperforms the existing initialization methods for k-modes in terms of accuracy, precision, and recall in most of the cases. PMID:29430249

Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED)

PubMed Central

Simpson, Susan G.; Pietrabissa, Giada; Rossi, Alessandro; Seychell, Tahnee; Manzoni, Gian Mauro; Munro, Calum; Nesci, Julian B.; Castelnuovo, Gianluca

2018-01-01

Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED) in a disordered eating population. Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q) completed the 190-item adapted version of the Schema Mode Inventory (SMI). The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA) and internal consistency (Cronbach's α). Multivariate Analyses of Covariance (MANCOVA) was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables. Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population. Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population. PMID:29740379

Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED).

PubMed

Simpson, Susan G; Pietrabissa, Giada; Rossi, Alessandro; Seychell, Tahnee; Manzoni, Gian Mauro; Munro, Calum; Nesci, Julian B; Castelnuovo, Gianluca

2018-01-01

Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED) in a disordered eating population. Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q) completed the 190-item adapted version of the Schema Mode Inventory (SMI). The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA) and internal consistency (Cronbach's α). Multivariate Analyses of Covariance (MANCOVA) was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables. Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population. Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population.

Quantized mode of a leaky cavity

NASA Astrophysics Data System (ADS)

Dutra, S. M.; Nienhuis, G.

2000-12-01

We use Thomson's classical concept of mode of a leaky cavity to develop a quantum theory of cavity damping. This theory generalizes the conventional system-reservoir theory of high-Q cavity damping to arbitrary Q. The small system now consists of damped oscillators corresponding to the natural modes of the leaky cavity rather than undamped oscillators associated with the normal modes of a fictitious perfect cavity. The formalism unifies semiclassical Fox-Li modes and the normal modes traditionally used for quantization. It also lays the foundations for a full quantum description of excess noise. The connection with Siegman's semiclassical work is straightforward. In a wider context, this theory constitutes a radical departure from present models of dissipation in quantum mechanics: unlike conventional models, system and reservoir operators no longer commute with each other. This noncommutability is an unavoidable consequence of having to use natural cavity modes rather than normal modes of a fictitious perfect cavity.

Transient analysis mode participation for modal survey target mode selection using MSC/NASTRAN DMAP

NASA Technical Reports Server (NTRS)

Barnett, Alan R.; Ibrahim, Omar M.; Sullivan, Timothy L.; Goodnight, Thomas W.

1994-01-01

Many methods have been developed to aid analysts in identifying component modes which contribute significantly to component responses. These modes, typically targeted for dynamic model correlation via a modal survey, are known as target modes. Most methods used to identify target modes are based on component global dynamic behavior. It is sometimes unclear if these methods identify all modes contributing to responses important to the analyst. These responses are usually those in areas of hardware design concerns. One method used to check the completeness of target mode sets and identify modes contributing significantly to important component responses is mode participation. With this method, the participation of component modes in dynamic responses is quantified. Those modes which have high participation are likely modal survey target modes. Mode participation is most beneficial when it is used with responses from analyses simulating actual flight events. For spacecraft, these responses are generated via a structural dynamic coupled loads analysis. Using MSC/NASTRAN DMAP, a method has been developed for calculating mode participation based on transient coupled loads analysis results. The algorithm has been implemented to be compatible with an existing coupled loads methodology and has been used successfully to develop a set of modal survey target modes.

The study of the plasmon modes of square atomic clusters based on the eigen-oscillation equation of charge under the free-electron gas model

NASA Astrophysics Data System (ADS)

Xue, Hong-Jie; Wu, Reng-Lai; Hu, Cheng-Xi; Zhang, Ming

2018-04-01

In atomic clusters, plasmon modes are generally gained by the resonant responses for external fields. However, these resonant methods still carry some defects: some plasmon modes may not have been found as that may not have been excited by the external fields. Recently, by employing the extended Hubbard model to describe electron systems of atomic clusters, we have presented the eigen-oscillation equation of charge to study plasmon modes. In this work, based on the free-electron gas model, we further explore the eigen-equation method. Under different external electric fields, some of the plasmon mode spectrums with obvious differences are found, which display the defects of the resonant methods. All the plasmon modes obtained by the resonant methods are predicted by the eigen-equation method. This effectively shows that the eigen-equation method is feasible and reliable in the process of finding plasmon. In addition, various kinds of plasmons are displayed by charge distributions, and the evolution features of plasmon with system parameters are gained by the energy absorption spectrum.

Simultaneous Analysis of Iridoid Glycosides and Anthraquinones in Morinda officinalis Using UPLC-QqQ-MS/MS and UPLC-Q/TOF-MSE.

PubMed

Zhao, Xiangsheng; Wei, Jianhe; Yang, Meihua

2018-05-03

Morinda officinalis is an important herbal medicine and functional food, and its main constituents include anthraquinone and iridoid glycosides. Quantification of the main compounds is a necessary step to understand the quality and therapeutic properties of M. officinalis , but this has not yet been performed based on liquid chromatography/tandem mass spectrometry (LC-MS/MS). Analytes were extracted from M. officinalis by reflux method. Ultrahigh-performance liquid chromatography coupled with a triple quadrupole mass spectrometry (UPLC-QqQ-MS) using multiple reaction monitoring (MRM) mode was applied for quantification. Fragmentation pathways of deacetyl asperulosidic acid and rubiadin were investigated based on UPLC with quadrupole time-of-flight tandem mass spectrometry (Q/TOF-MS) in the MS E centroid mode. The method showed a good linearity over a wide concentration range (R² ≥ 0.9930). The limits of quantification of six compounds ranged from 2.6 to 27.57 ng/mL. The intra- and inter-day precisions of the investigated components exhibited an RSD within 4.5% with mean recovery rates of 95.32⁻99.86%. Contents of selected compounds in M. officinalis varied significantly depending on region. The fragmentation pathway of deacetyl asperulosidic and rubiadin was proposed. A selective and sensitive method was developed for determining six target compounds in M. officinalis by UPLC-MS/MS. Furthermore, the proposed method will be helpful for quality control and identification main compounds of M. officinalis .

Coupling of small, low-loss hexapole mode with photonic crystal slab waveguide mode.

PubMed

Kim, Guk-Hyun; Lee, Yong-Hee; Shinya, Akihiko; Notomi, Masaya

2004-12-27

Coupling characteristics between the single-cell hexapole mode and the triangular-lattice photonic crystal slab waveguide mode is studied by the finite-difference time-domain method. The single-cell hexapole mode has a high quality factor (Q) of 3.3Chi106 and a small modal volume of 1.18(lambda/n)3. Based on the symmetry, three representative types of coupling geometries (shoulder-couple, butt-couple and side-couple structures) are selected and tested. The coupling efficiency shows strong dependence on the transverse overlap of the cavity mode and the waveguide mode over the region of the waveguide. The shoulder-couple structure shows best coupling characteristics among three tested structures. For example, two shouldercouple waveguides and a hexapole cavity result in a high performance resonant-tunneling-filter with Q of 9.7Chi105 and transmittance of 0.48. In the side-couple structure, the coupling strength is much weaker than that of the shoulder-couple structure because of the poor spatial overlap between the mode profiles. In the direct-couple structure, the energy transfer from the cavity to the waveguide is prohibited because of the symmetry mismatch and no coupling is observed.

Relaxation mode analysis of a peptide system: comparison with principal component analysis.

PubMed

Mitsutake, Ayori; Iijima, Hiromitsu; Takano, Hiroshi

2011-10-28

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.

An actively Q-switched fiber laser with cylindrical vector beam generation

NASA Astrophysics Data System (ADS)

Zhang, Jiaojiao; Zhang, Zuxing; Cai, Yu; Wan, Hongdan; Wang, Zhiqiang; Zhang, Lin

2018-03-01

We demonstrate an actively Q-switched fiber laser with cylindrical vector beam (CVB) emission using a few-mode fiber Bragg grating as the mode selection component and an acousto-optic modulator to achieve Q-switching. To the best of our knowledge, this is the first such demonstration. Using a linear cavity configuration, an actively Q-switched CVB with a pulse width of about 64 ns, a pulse energy of 4.25 µJ and a repetition rate of 20 kHz has been obtained. Moreover, by tuning the polarization controllers radially and azimuthally, polarized Q-switched beams can be excited separately with a polarization purity of  >94.5%. This compact Q-switched fiber laser with ns CVB pulse output could find potential applications in the field of material processing, nonlinear optics and so on.

Effects of inspired CO2, hyperventilation, and time on VA/Q inequality in the dog

NASA Technical Reports Server (NTRS)

Tsukimoto, K.; Arcos, J. P.; Schaffartzik, W.; Wagner, P. D.; West, J. B.

1992-01-01

In a recent study by Tsukimoto et al. (J. Appl. Physiol. 68: 2488-2493, 1990), CO2 inhalation appeared to reduce the size of the high ventilation-perfusion ratio (VA/Q) mode commonly observed in anesthetized mechanically air-ventilated dogs. In that study, large tidal volumes (VT) were used during CO2 inhalation to preserve normocapnia. To separate the influences of CO2 and high VT on the VA/Q distribution in the present study, we examined the effect of inspired CO2 on the high VA/Q mode using eight mechanically ventilated dogs (4 given CO2, 4 controls). The VA/Q distribution was measured first with normal VT and then with increased VT. In the CO2 group at high VT, data were collected before, during, and after CO2 inhalation. With normal VT, there was no difference in the size of the high VA/Q mode between groups [10.5 +/- 3.5% (SE) of ventilation in the CO2 group, 11.8 +/- 5.2% in the control group]. Unexpectedly, the size of the high VA/Q mode decreased similarly in both groups over time, independently of the inspired PCO2, at a rate similar to the fall in cardiac output over time. The reduction in the high VA/Q mode together with a simultaneous increase in alveolar dead space (estimated by the difference between inert gas dead space and Fowler dead space) suggests that poorly perfused high VA/Q areas became unperfused over time. A possible mechanism is that elevated alveolar pressure and decreased cardiac output eliminate blood flow from corner vessels in nondependent high VA/Q regions.

Extending the Functionality of Behavioural Change-Point Analysis with k-Means Clustering: A Case Study with the Little Penguin (Eudyptula minor)

PubMed Central

Zhang, Jingjing; Dennis, Todd E.

2015-01-01

We present a simple framework for classifying mutually exclusive behavioural states within the geospatial lifelines of animals. This method involves use of three sequentially applied statistical procedures: (1) behavioural change point analysis to partition movement trajectories into discrete bouts of same-state behaviours, based on abrupt changes in the spatio-temporal autocorrelation structure of movement parameters; (2) hierarchical multivariate cluster analysis to determine the number of different behavioural states; and (3) k-means clustering to classify inferred bouts of same-state location observations into behavioural modes. We demonstrate application of the method by analysing synthetic trajectories of known ‘artificial behaviours’ comprised of different correlated random walks, as well as real foraging trajectories of little penguins (Eudyptula minor) obtained by global-positioning-system telemetry. Our results show that the modelling procedure correctly classified 92.5% of all individual location observations in the synthetic trajectories, demonstrating reasonable ability to successfully discriminate behavioural modes. Most individual little penguins were found to exhibit three unique behavioural states (resting, commuting/active searching, area-restricted foraging), with variation in the timing and locations of observations apparently related to ambient light, bathymetry, and proximity to coastlines and river mouths. Addition of k-means clustering extends the utility of behavioural change point analysis, by providing a simple means through which the behaviours inferred for the location observations comprising individual movement trajectories can be objectively classified. PMID:25922935

Extending the Functionality of Behavioural Change-Point Analysis with k-Means Clustering: A Case Study with the Little Penguin (Eudyptula minor).

PubMed

Zhang, Jingjing; O'Reilly, Kathleen M; Perry, George L W; Taylor, Graeme A; Dennis, Todd E

2015-01-01

We present a simple framework for classifying mutually exclusive behavioural states within the geospatial lifelines of animals. This method involves use of three sequentially applied statistical procedures: (1) behavioural change point analysis to partition movement trajectories into discrete bouts of same-state behaviours, based on abrupt changes in the spatio-temporal autocorrelation structure of movement parameters; (2) hierarchical multivariate cluster analysis to determine the number of different behavioural states; and (3) k-means clustering to classify inferred bouts of same-state location observations into behavioural modes. We demonstrate application of the method by analysing synthetic trajectories of known 'artificial behaviours' comprised of different correlated random walks, as well as real foraging trajectories of little penguins (Eudyptula minor) obtained by global-positioning-system telemetry. Our results show that the modelling procedure correctly classified 92.5% of all individual location observations in the synthetic trajectories, demonstrating reasonable ability to successfully discriminate behavioural modes. Most individual little penguins were found to exhibit three unique behavioural states (resting, commuting/active searching, area-restricted foraging), with variation in the timing and locations of observations apparently related to ambient light, bathymetry, and proximity to coastlines and river mouths. Addition of k-means clustering extends the utility of behavioural change point analysis, by providing a simple means through which the behaviours inferred for the location observations comprising individual movement trajectories can be objectively classified.

Nursing home care quality: a cluster analysis.

PubMed

Grøndahl, Vigdis Abrahamsen; Fagerli, Liv Berit

2017-02-13

Purpose The purpose of this paper is to explore potential differences in how nursing home residents rate care quality and to explore cluster characteristics. Design/methodology/approach A cross-sectional design was used, with one questionnaire including questions from quality from patients' perspective and Big Five personality traits, together with questions related to socio-demographic aspects and health condition. Residents ( n=103) from four Norwegian nursing homes participated (74.1 per cent response rate). Hierarchical cluster analysis identified clusters with respect to care quality perceptions. χ 2 tests and one-way between-groups ANOVA were performed to characterise the clusters ( p<0.05). Findings Two clusters were identified; Cluster 1 residents (28.2 per cent) had the best care quality perceptions and Cluster 2 (67.0 per cent) had the worst perceptions. The clusters were statistically significant and characterised by personal-related conditions: gender, psychological well-being, preferences, admission, satisfaction with staying in the nursing home, emotional stability and agreeableness, and by external objective care conditions: healthcare personnel and registered nurses. Research limitations/implications Residents assessed as having no cognitive impairments were included, thus excluding the largest group. By choosing questionnaire design and structured interviews, the number able to participate may increase. Practical implications Findings may provide healthcare personnel and managers with increased knowledge on which to develop strategies to improve specific care quality perceptions. Originality/value Cluster analysis can be an effective tool for differentiating between nursing homes residents' care quality perceptions.

Globular cluster x-ray sources

PubMed Central

Pooley, David

2010-01-01

Globular clusters and x-ray astronomy have a long and fruitful history. Uhuru and OSO-7 revealed highly luminous (> 1036 ergs-1) x-ray sources in globular clusters, and Einstein and ROSAT revealed a larger population of low-luminosity (< 1033 ergs-1) x-ray sources. It was realized early on that the high-luminosity sources were low-mass x-ray binaries in outburst and that they were orders of magnitude more abundant per unit mass in globular clusters than in the rest of the galaxy. However, the low-luminosity sources proved difficult to classify. Many ideas were put forth—low-mass x-ray binaries in quiescence (qLMXBs), cataclysmic variables (CVs), active main-sequence binaries (ABs), and millisecond pulsars (MSPs)—but secure identifications were scarce. In ROSAT observations of 55 clusters, about 25 low-luminosity sources were found. Chandra has now observed over 80 Galactic globular clusters, and these observations have revealed over 1,500 x-ray sources. The superb angular resolution has allowed for many counterpart identifications, providing clues to the nature of this population. It is a heterogeneous mix of qLMXBs, CVs, ABs, and MSPs, and it has been shown that the qLMXBs and CVs are both, in part, overabundant like the luminous LMXBs. The number of x-ray sources in a cluster correlates very well with its encounter frequency. This points to dynamical formation scenarios for the x-ray sources and shows them to be excellent tracers of the complicated internal dynamics. The relation between the encounter frequency and the number of x-ray sources has been used to suggest that we have misunderstood the dynamical states of globular clusters. PMID:20404204

Localization of the Netherton Syndrome Gene to Chromosome 5q32, by Linkage Analysis and Homozygosity Mapping

PubMed Central

Chavanas, Stéphane; Garner, Chad; Bodemer, Christine; Ali, Mohsin; Teillac, Dominique Hamel-; Wilkinson, John; Bonafé, Jean-Louis; Paradisi, Mauro; Kelsell, David P.; Ansai, Shin-ichi; Mitsuhashi, Yoshihiko; Larrègue, Marc; Leigh, Irene M.; Harper, John I.; Taïeb, Alain; Prost, Yves de; Cardon, Lon R.; Hovnanian, Alain

2000-01-01

Netherton syndrome (NS [MIM 256500]) is a rare and severe autosomal recessive disorder characterized by congenital ichthyosis, a specific hair-shaft defect (trichorrhexis invaginata), and atopic manifestations. Infants with this syndrome often fail to thrive; life-threatening complications result in high postnatal mortality. We report the assignment of the NS gene to chromosome 5q32, by linkage analysis and homozygosity mapping in 20 families affected with NS. Significant evidence for linkage (maximum multipoint LOD score 10.11) between markers D5S2017 and D5S413 was obtained, with no evidence for locus heterogeneity. Analysis of critical recombinants mapped the NS locus between markers D5S463 and D5S2013, within an <3.5-cM genetic interval. The NS locus is telomeric to the cytokine gene cluster in 5q31. The five known genes encoding casein kinase Iα, the α subunit of retinal rod cGMP phosphodiesterase, the regulator of mitotic-spindle assembly, adrenergic receptor β2, and the diastrophic dysplasia sulfate–transporter gene, as well as the 38 expressed-sequence tags mapped within the critical region, are not obvious candidates. Our study is the first step toward the positional cloning of the NS gene. This finding promises a better understanding of the molecular mechanisms that control epidermal differentiation and immunity. PMID:10712206

Interactive multi-mode blade impact analysis

NASA Technical Reports Server (NTRS)

Alexander, A.; Cornell, R. W.

1978-01-01

The theoretical methodology used in developing an analysis for the response of turbine engine fan blades subjected to soft-body (bird) impacts is reported, and the computer program developed using this methodology as its basis is described. This computer program is an outgrowth of two programs that were previously developed for the purpose of studying problems of a similar nature (a 3-mode beam impact analysis and a multi-mode beam impact analysis). The present program utilizes an improved missile model that is interactively coupled with blade motion which is more consistent with actual observations. It takes into account local deformation at the impact area, blade camber effects, and the spreading of the impacted missile mass on the blade surface. In addition, it accommodates plate-type mode shapes. The analysis capability in this computer program represents a significant improvement in the development of the methodology for evaluating potential fan blade materials and designs with regard to foreign object impact resistance.

Analysis of non-steroidal anti-inflammatory drugs in milk using QuEChERS and liquid chromatography coupled to mass spectrometry: triple quadrupole versus Q-Orbitrap mass analyzers.

PubMed

Rúbies, Antoni; Guo, Lili; Centrich, Francesc; Granados, Mercè

2016-08-01

We developed a Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) method for the high throughput determination of 10 non-steroidal anti-inflammatory drugs (NSAIDs) in milk samples using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) with a triple quadrupole (QqQ) instrument and an electrospray ionization (ESI) source. The new extraction procedure is highly efficient, and we obtained absolute recoveries in the range 78.1-97.1 % for the extraction and clean-up steps. Chromatographic separation is performed in the gradient mode with a biphenyl column and acidic mobile phases consisting of water and acetonitrile containing formic acid. The chromatographic run time was about 12 min, and NSAID peaks showed a good symmetry factor. For MS/MS detection, we used multiple reaction monitoring (MRM) mode, using ESI in both positive and negative modes. Our method has been validated in compliance with the European Commission Decision 657/2002/EC, and we obtained very satisfactory results in inter-laboratory testing. Furthermore, we explored the use of a hybrid high resolution mass spectrometer, combining a quadrupole and an Orbitrap mass analyzer, for high resolution (HR) MS/MS detection of NSAIDs. We achieved lower NSAID quantification limits with Q-Orbitrap high resolution mass spectrometry (HRMS/MS) detection than those achieved with the QqQ instrument; however, its main feature is its very high selectivity, which makes HRMS/MS particularly suitable for confirmatory analysis.

IM and Q-D Rules: An Analysis by French Club MURAT

DTIC Science & Technology

1996-08-01

and Q-D Rules: An Analysis by French Club Murat 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...IM(1) AND Q-D RULES: AN ANALYSIS BY FRENCH CLUB MURAT by Jean ISLER (2) - Jean G. GOLIGER (3) - Daniel BOCHAND (4) Georges QUEROL (5) - Louis PICARD...6) and Joël FERRON (7) CLUB MURAT - BP 129 78 148 VELIZY CEDEX - FRANCE Tel : (33) - (1) 39.46.15.50 Fax : (33) - (1) 39.46.15.38 ABSTRACT The

Progress in understanding the enhanced pedestal H-mode in NSTX

DOE PAGES

Gerhardt, S. P.; Canik, J. M.; Maingi, R.; ...

2014-08-01

The paper describes the enhanced pedestal (EP) H-mode observed in the National Spherical Torus Experiment (NSTX). The defining characteristics of EP H-mode are given, namely i)transition after the L- to H-mode transition, ii) region of very steep ion temperature gradient, and iii) associated region of strong rotational shear. A newly observed long-pulse EP H-mode example shows quiescent behavior for as long as the heating and current drive sources are maintained. Cases are shown where the region of steep ion temperature gradient is located at the very edge, and cases where it is shifted up to 10 cm inward from themore » plasma edge; these cases are united by a common dependence of the ion temperature gradient on the toroidal rotation frequency shear. EP H-mode examples have been observed across a wide range of q95 and pedestal collisionality. No strong changes in the fluctuation amplitudes have been observed following the eP H-mode transition, and transport analysis indicates that the ion t hermal transport is comparable to or less than anticipated from a simple neoclassical transport model. Cases are shown where EP H-modes were reliably generated, through these low-q95 examples were difficult to sustain. A case where an externally triggered ELM precipitates the transition to EP H-mode is also shown, though an initial experiment designed to trigger EP-H-modes in this fashion was successful.« less

A framework for graph-based synthesis, analysis, and visualization of HPC cluster job data.

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

Mayo, Jackson R.; Kegelmeyer, W. Philip, Jr.; Wong, Matthew H.

The monitoring and system analysis of high performance computing (HPC) clusters is of increasing importance to the HPC community. Analysis of HPC job data can be used to characterize system usage and diagnose and examine failure modes and their effects. This analysis is not straightforward, however, due to the complex relationships that exist between jobs. These relationships are based on a number of factors, including shared compute nodes between jobs, proximity of jobs in time, etc. Graph-based techniques represent an approach that is particularly well suited to this problem, and provide an effective technique for discovering important relationships in jobmore » queuing and execution data. The efficacy of these techniques is rooted in the use of a semantic graph as a knowledge representation tool. In a semantic graph job data, represented in a combination of numerical and textual forms, can be flexibly processed into edges, with corresponding weights, expressing relationships between jobs, nodes, users, and other relevant entities. This graph-based representation permits formal manipulation by a number of analysis algorithms. This report presents a methodology and software implementation that leverages semantic graph-based techniques for the system-level monitoring and analysis of HPC clusters based on job queuing and execution data. Ontology development and graph synthesis is discussed with respect to the domain of HPC job data. The framework developed automates the synthesis of graphs from a database of job information. It also provides a front end, enabling visualization of the synthesized graphs. Additionally, an analysis engine is incorporated that provides performance analysis, graph-based clustering, and failure prediction capabilities for HPC systems.« less

Failure Mode and Effects Analysis (FMEA) Introductory Overview

DTIC Science & Technology

2012-06-14

Failure Mode and Effects Analysis ( FMEA ) Introductory Overview TARDEC Systems Engineering Risk Management Team POC: Kadry Rizk or Gregor Ratajczak...2. REPORT TYPE Briefing Charts 3. DATES COVERED 01-05-2012 to 23-05-2012 4. TITLE AND SUBTITLE Failure Mode and Effects Analysis ( FMEA ) 5a...18 WELCOME Welcome to “An introductory overview of Failure Mode and Effects Analysis ( FMEA )”, A brief concerning the use and benefits of FMEA

Evolutionary analysis of groundwater flow: Application of multivariate statistical analysis to hydrochemical data in the Densu Basin, Ghana

NASA Astrophysics Data System (ADS)

Yidana, Sandow Mark; Bawoyobie, Patrick; Sakyi, Patrick; Fynn, Obed Fiifi

2018-02-01

An evolutionary trend has been postulated through the analysis of hydrochemical data of a crystalline rock aquifer system in the Densu Basin, Southern Ghana. Hydrochemcial data from 63 groundwater samples, taken from two main groundwater outlets (Boreholes and hand dug wells) were used to postulate an evolutionary theory for the basin. Sequential factor and hierarchical cluster analysis were used to disintegrate the data into three factors and five clusters (spatial associations). These were used to characterize the controls on groundwater hydrochemistry and its evolution in the terrain. The dissolution of soluble salts and cation exchange processes are the dominant processes controlling groundwater hydrochemistry in the terrain. The trend of evolution of this set of processes follows the pattern of groundwater flow predicted by a calibrated transient groundwater model in the area. The data suggest that anthropogenic activities represent the second most important process in the hydrochemistry. Silicate mineral weathering is the third most important set of processes. Groundwater associations resulting from Q-mode hierarchical cluster analysis indicate an evolutionary pattern consistent with the general groundwater flow pattern in the basin. These key findings are at variance with results of previous investigations and indicate that when carefully done, groundwater hydrochemical data can be very useful for conceptualizing groundwater flow in basins.

New determinations of Q quality factors and eigenfrequencies for the whole set of singlets of the Earth's normal modes 0S 0, 0S 2, 0S 3 and 2S 1 using superconducting gravimeter data from the GGP network

NASA Astrophysics Data System (ADS)

Roult, Geneviève; Rosat, Séverine; Clévédé, Eric; Millot-Langet, Raphaële; Hinderer, Jacques

2006-01-01

We present new modal Q measurements of the 0S 0 and 0S 2 modes, and first modal frequencies and Q measurements of 2S 1 and 0S 3 modes. The high quality of the GGP (Global Geodynamics Project) superconducting gravimeters (SGs) contributes to the clear observation of seismic normal modes at frequencies lower than 1 mHz and offers a good opportunity for studying the behaviour of these modes. The interest of scientists in the gravest normal modes is due to the fact that they do contribute to a better knowledge of the density profile in the Earth, helping to constrain Earth's models. These modes have been clearly identified after some large recent events recorded with superconducting gravimeters, particularly well-suited for low-frequency investigations. The Ms = 8.1 (Mw = 8.4) Peruvian earthquake of June 2001 and the Ms = 9.0 (Mw = 9.3) Sumatra-Andaman earthquake of December 2004 provide us with individual spectra which exhibit a clear splitting of the spheroidal modes 0S 2, 0S 3 and 2S 1, and a clear identification of each of the individual singlets, with a resolution never obtained from broad-band seismometers records. The Q quality factors have been determined from the apparent decrease of the amplitude of each singlet with time, according to a well-suited technique [Roult, G., Clévédé, E., 2000. New refinements in attenuation measurements from free-oscillation and surface-wave observations. Phys. Earth Planet. Inter. 121, 1-37]. The results are compared to the theoretical frequencies and Q quality factors computed for the PREM and 1066A models, taking into account both rotation and ellipticity effects of the Earth. The two observed datasets (frequencies and Q quality factors) exhibit a splitting on the observed values different from the predicted one. That seems to point out that some parameters as density or attenuation values used in the theoretical models do not explain the observations. A new dataset of frequencies and Q quality factors of the whole set of

Analytical performance of the various acquisition modes in Orbitrap MS and MS/MS.

PubMed

Kaufmann, Anton

2018-04-30

Quadrupole Orbitrap instruments (Q Orbitrap) permit high-resolution mass spectrometry (HRMS)-based full scan acquisitions and have a number of acquisition modes where the quadrupole isolates a particular mass range prior to a possible fragmentation and HRMS-based acquisition. Selecting the proper acquisition mode(s) is essential if trace analytes are to be quantified in complex matrix extracts. Depending on the particular requirements, such as sensitivity, selectivity of detection, linear dynamic range, and speed of analysis, different acquisition modes may have to be chosen. This is particularly important in the field of multi-residue analysis (e.g., pesticides or veterinary drugs in food samples) where a large number of analytes within a complex matrix have to be detected and reliably quantified. Meeting the specific detection and quantification performance criteria for every targeted compound may be challenging. It is the aim of this paper to describe the strengths and the limitations of the currently available Q Orbitrap acquisition modes. In addition, the incorporation of targeted acquisitions between full scan experiments is discussed. This approach is intended to integrate compounds that require an additional degree of sensitivity or selectivity into multi-residue methods. This article is protected by copyright. All rights reserved.

Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale

PubMed Central

Kobourov, Stephen; Gallant, Mike; Börner, Katy

2016-01-01

Overview Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms—Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. Cluster Quality Metrics We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Network Clustering Algorithms Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large

Siblings with opposite chromosome constitutions, dup(2q)/del(7q) and del(2q)/dup(7q).

PubMed

Shim, Sung Han; Shim, Jae Sun; Min, Kyunghoon; Lee, Hee Song; Park, Ji Eun; Park, Sang Hee; Hwang, Euna; Kim, Minyoung

2014-01-15

Chromosome 7q36 microdeletion syndrome is a rare genomic disorder characterized by underdevelopment of the brain, microcephaly, anomalies of the sex organs, and language problems. Developmental delay, intellectual disability, autistic spectrum disorders, BDMR syndrome, and unusual facial morphology are the key features of the chromosome 2q37 microdeletion syndrome. A genetic screening for two brothers with global developmental delay using high-resolution chromosomal analysis and subtelomeric multiplex ligation-dependent probe amplification revealed subtelomeric rearrangements on the same sites of 2q37.2 and 7q35, with reversed deletion and duplication. Both of them showed dysmorphic facial features, severe disability of physical and intellectual development, and abnormal genitalia with differential abnormalities in their phenotypes. The family did not have abnormal genetic phenotypes. According to the genetic analysis of their parents, adjacent-1 segregation from their mother's was suggested as a mechanism of their gene mutation. By comparing the phenotypes of our patients with previous reports on similar patients, we tried to obtain the information of related genes and their chromosomal locations. © 2013.

Constraining AGN triggering mechanisms through the clustering analysis of active black holes

NASA Astrophysics Data System (ADS)

Gatti, M.; Shankar, F.; Bouillot, V.; Menci, N.; Lamastra, A.; Hirschmann, M.; Fiore, F.

2016-02-01

The triggering mechanisms for active galactic nuclei (AGN) are still debated. Some of the most popular ones include galaxy interactions (IT) and disc instabilities (DIs). Using an advanced semi-analytic model (SAM) of galaxy formation, coupled to accurate halo occupation distribution modelling, we investigate the imprint left by each separate triggering process on the clustering strength of AGN at small and large scales. Our main results are as follows: (I) DIs, irrespective of their exact implementation in the SAM, tend to fall short in triggering AGN activity in galaxies at the centre of haloes with Mh > 1013.5 h-1 M⊙. On the contrary, the IT scenario predicts abundance of active central galaxies that generally agrees well with observations at every halo mass. (II) The relative number of satellite AGN in DIs at intermediate-to-low luminosities is always significantly higher than in IT models, especially in groups and clusters. The low AGN satellite fraction predicted for the IT scenario might suggest that different feeding modes could simultaneously contribute to the triggering of satellite AGN. (III) Both scenarios are quite degenerate in matching large-scale clustering measurements, suggesting that the sole average bias might not be an effective observational constraint. (IV) Our analysis suggests the presence of both a mild luminosity and a more consistent redshift dependence in the AGN clustering, with AGN inhabiting progressively less massive dark matter haloes as the redshift increases. We also discuss the impact of different observational selection cuts in measuring AGN clustering, including possible discrepancies between optical and X-ray surveys.

Data Analysis of Sequences and qPCR for Microbial Communities during Algal Blooms

EPA Pesticide Factsheets

A training opportunity is open to a highly microbial-research-motivated student to conduct sequence analysis, explore novel genes and metabolic pathways, validate resultant findings using qPCR/RT-qPCR and summarize the findings

The combination of high Q factor and chirality in twin cavities and microcavity chain

PubMed Central

Song, Qinghai; Zhang, Nan; Zhai, Huilin; Liu, Shuai; Gu, Zhiyuan; Wang, Kaiyang; Sun, Shang; Chen, Zhiwei; Li, Meng; Xiao, Shumin

2014-01-01

Chirality in microcavities has recently shown its bright future in optical sensing and microsized coherent light sources. The key parameters for such applications are the high quality (Q) factor and large chirality. However, the previous reported chiral resonances are either low Q modes or require very special cavity designs. Here we demonstrate a novel, robust, and general mechanism to obtain the chirality in circular cavity. By placing a circular cavity and a spiral cavity in proximity, we show that ultra-high Q factor, large chirality, and unidirectional output can be obtained simultaneously. The highest Q factors of the non-orthogonal mode pairs are almost the same as the ones in circular cavity. And the co-propagating directions of the non-orthogonal mode pairs can be reversed by tuning the mode coupling. This new mechanism for the combination of high Q factor and large chirality is found to be very robust to cavity size, refractive index, and the shape deformation, showing very nice fabrication tolerance. And it can be further extended to microcavity chain and microcavity plane. We believe that our research will shed light on the practical applications of chirality and microcavities. PMID:25262881

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil, E-mail: Anil.Shukla@pnnl.gov; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N{sub 2}). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi){sub n}Li{sup +}, (HCOOLi){sub n}Li{sub m}{sup m+}, (HCOOLi){sub n}HCOO{sup −}, and (HCOOLi){sub n}(HCOO){sub m}{sup m−}. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi){sub 3}Li{sup +} being the most abundant and stable cluster ion. Fragmentations ofmore » singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi){sub 2}) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi){sub 3}Li{sup +} as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Viscous instabilities in the q-vortex at large swirl numbers

NASA Astrophysics Data System (ADS)

Fabre, David; Jacquin, Laurent

2002-11-01

This comunication deals with the temporal stability of the q-vortex trailing line vortex model. We describe a family of viscous instabilities existing in a range of parameters which is usually assumed to be stable, namely large swirl parameters (q>1.5) and large Reynolds numbers. These instabilities affect negative azimuthal wavenumbers (m < 0) and take the form of centre-modes (i.e. with a structure concentrated along the vortex centerline). They are related to a family of viscous modes described by Stewartson, Ng & Brown (1988) in swirling Poiseuille flow, and are the temporal counterparts of weakly amplified spatial modes recently computed by Olendraru & Sellier (2002). These instabilities are studied numerically using an original and highly accurate Chebyshev collocation method, which allows a mapping of the unstable regions up to Rey 10^6 and q 7. Our results indicate that in the limit of very large Reynolds numbers, trailing vortices are affected by this kind of instabilities whatever the value of the swirl number.

The smart cluster method. Adaptive earthquake cluster identification and analysis in strong seismic regions

NASA Astrophysics Data System (ADS)

Schaefer, Andreas M.; Daniell, James E.; Wenzel, Friedemann

2017-07-01

Earthquake clustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation for probabilistic seismic hazard assessment. This study introduces the Smart Cluster Method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal cluster identification. It utilises the magnitude-dependent spatio-temporal earthquake density to adjust the search properties, subsequently analyses the identified clusters to determine directional variation and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010-2011 Darfield-Christchurch sequence, a reclassification procedure is applied to disassemble subsequent ruptures using near-field searches, nearest neighbour classification and temporal splitting. The method is capable of identifying and classifying earthquake clusters in space and time. It has been tested and validated using earthquake data from California and New Zealand. A total of more than 1500 clusters have been found in both regions since 1980 with M m i n = 2.0. Utilising the knowledge of cluster classification, the method has been adjusted to provide an earthquake declustering algorithm, which has been compared to existing methods. Its performance is comparable to established methodologies. The analysis of earthquake clustering statistics lead to various new and updated correlation functions, e.g. for ratios between mainshock and strongest aftershock and general aftershock activity metrics.

Functional Principal Component Analysis and Randomized Sparse Clustering Algorithm for Medical Image Analysis

PubMed Central

Lin, Nan; Jiang, Junhai; Guo, Shicheng; Xiong, Momiao

2015-01-01

Due to the advancement in sensor technology, the growing large medical image data have the ability to visualize the anatomical changes in biological tissues. As a consequence, the medical images have the potential to enhance the diagnosis of disease, the prediction of clinical outcomes and the characterization of disease progression. But in the meantime, the growing data dimensions pose great methodological and computational challenges for the representation and selection of features in image cluster analysis. To address these challenges, we first extend the functional principal component analysis (FPCA) from one dimension to two dimensions to fully capture the space variation of image the signals. The image signals contain a large number of redundant features which provide no additional information for clustering analysis. The widely used methods for removing the irrelevant features are sparse clustering algorithms using a lasso-type penalty to select the features. However, the accuracy of clustering using a lasso-type penalty depends on the selection of the penalty parameters and the threshold value. In practice, they are difficult to determine. Recently, randomized algorithms have received a great deal of attentions in big data analysis. This paper presents a randomized algorithm for accurate feature selection in image clustering analysis. The proposed method is applied to both the liver and kidney cancer histology image data from the TCGA database. The results demonstrate that the randomized feature selection method coupled with functional principal component analysis substantially outperforms the current sparse clustering algorithms in image cluster analysis. PMID:26196383

Simultaneous Two-Way Clustering of Multiple Correspondence Analysis

ERIC Educational Resources Information Center

Hwang, Heungsun; Dillon, William R.

2010-01-01

A 2-way clustering approach to multiple correspondence analysis is proposed to account for cluster-level heterogeneity of both respondents and variable categories in multivariate categorical data. Specifically, in the proposed method, multiple correspondence analysis is combined with k-means in a unified framework in which "k"-means is…

The applicability and effectiveness of cluster analysis

NASA Technical Reports Server (NTRS)

Ingram, D. S.; Actkinson, A. L.

1973-01-01

An insight into the characteristics which determine the performance of a clustering algorithm is presented. In order for the techniques which are examined to accurately cluster data, two conditions must be simultaneously satisfied. First the data must have a particular structure, and second the parameters chosen for the clustering algorithm must be correct. By examining the structure of the data from the Cl flight line, it is clear that no single set of parameters can be used to accurately cluster all the different crops. The effectiveness of either a noniterative or iterative clustering algorithm to accurately cluster data representative of the Cl flight line is questionable. Thus extensive a prior knowledge is required in order to use cluster analysis in its present form for applications like assisting in the definition of field boundaries and evaluating the homogeneity of a field. New or modified techniques are necessary for clustering to be a reliable tool.

CometQ: An automated tool for the detection and quantification of DNA damage using comet assay image analysis.

PubMed

Ganapathy, Sreelatha; Muraleedharan, Aparna; Sathidevi, Puthumangalathu Savithri; Chand, Parkash; Rajkumar, Ravi Philip

2016-09-01

DNA damage analysis plays an important role in determining the approaches for treatment and prevention of various diseases like cancer, schizophrenia and other heritable diseases. Comet assay is a sensitive and versatile method for DNA damage analysis. The main objective of this work is to implement a fully automated tool for the detection and quantification of DNA damage by analysing comet assay images. The comet assay image analysis consists of four stages: (1) classifier (2) comet segmentation (3) comet partitioning and (4) comet quantification. Main features of the proposed software are the design and development of four comet segmentation methods, and the automatic routing of the input comet assay image to the most suitable one among these methods depending on the type of the image (silver stained or fluorescent stained) as well as the level of DNA damage (heavily damaged or lightly/moderately damaged). A classifier stage, based on support vector machine (SVM) is designed and implemented at the front end, to categorise the input image into one of the above four groups to ensure proper routing. Comet segmentation is followed by comet partitioning which is implemented using a novel technique coined as modified fuzzy clustering. Comet parameters are calculated in the comet quantification stage and are saved in an excel file. Our dataset consists of 600 silver stained images obtained from 40 Schizophrenia patients with different levels of severity, admitted to a tertiary hospital in South India and 56 fluorescent stained images obtained from different internet sources. The performance of "CometQ", the proposed standalone application for automated analysis of comet assay images, is evaluated by a clinical expert and is also compared with that of a most recent and related software-OpenComet. CometQ gave 90.26% positive predictive value (PPV) and 93.34% sensitivity which are much higher than those of OpenComet, especially in the case of silver stained images. The

Ten years of Nd:YAG Q-switched/mode-locked ophthalmic laser system clinical treatment

NASA Astrophysics Data System (ADS)

Jelinkova, Helena; Pasta, Jiri; Hamal, Karel; Cech, Miroslav; Prochazka, Ivan

1999-06-01

Plasma breakdown generated by high power lasers is used in ophthalmic microsurgery for perforation of the various membranes. We report on ten years of clinical experiences with the ophthalmic Nd:YAG laser system operating alternatively in both Q-switched or mode-locked regimes. This option gives the surgeon a possibility to compare the effect of treatments with nanosecond or picosecond pulses. The pulse duration in the picosecond regime is 25 ps, the length of a nanosecond pulse is 4 ns and the energy is variable up to 70 mJ. In the ten year period the laser system was used for more than 10 000 treatments. From the results is possible to conclude that in clinical practice the picosecond pulses are better for the posterior capsule opacification treatment and that there are not retinal complications. The nanosecond pulses are useful for iridectomies. Our constructed Nd:YAG laser system provides the surgeons with the possibility to use different photodisruptive regimes for special indications, which can be very useful for the ophthalmologists.

Failure-Modes-And-Effects Analysis Of Software Logic

NASA Technical Reports Server (NTRS)

Garcia, Danny; Hartline, Thomas; Minor, Terry; Statum, David; Vice, David

1996-01-01

Rigorous analysis applied early in design effort. Method of identifying potential inadequacies and modes and effects of failures caused by inadequacies (failure-modes-and-effects analysis or "FMEA" for short) devised for application to software logic.

Cross-scale analysis of cluster correspondence using different operational neighborhoods

NASA Astrophysics Data System (ADS)

Lu, Yongmei; Thill, Jean-Claude

2008-09-01

Cluster correspondence analysis examines the spatial autocorrelation of multi-location events at the local scale. This paper argues that patterns of cluster correspondence are highly sensitive to the definition of operational neighborhoods that form the spatial units of analysis. A subset of multi-location events is examined for cluster correspondence if they are associated with the same operational neighborhood. This paper discusses the construction of operational neighborhoods for cluster correspondence analysis based on the spatial properties of the underlying zoning system and the scales at which the zones are aggregated into neighborhoods. Impacts of this construction on the degree of cluster correspondence are also analyzed. Empirical analyses of cluster correspondence between paired vehicle theft and recovery locations are conducted on different zoning methods and across a series of geographic scales and the dynamics of cluster correspondence patterns are discussed.

pcr: an R package for quality assessment, analysis and testing of qPCR data

PubMed Central

Ahmed, Mahmoud

2018-01-01

Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest. Results Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable. Conclusion The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way. PMID:29576953

Allergen Sensitization Pattern by Sex: A Cluster Analysis in Korea.

PubMed

Ohn, Jungyoon; Paik, Seung Hwan; Doh, Eun Jin; Park, Hyun-Sun; Yoon, Hyun-Sun; Cho, Soyun

2017-12-01

Allergens tend to sensitize simultaneously. Etiology of this phenomenon has been suggested to be allergen cross-reactivity or concurrent exposure. However, little is known about specific allergen sensitization patterns. To investigate the allergen sensitization characteristics according to gender. Multiple allergen simultaneous test (MAST) is widely used as a screening tool for detecting allergen sensitization in dermatologic clinics. We retrospectively reviewed the medical records of patients with MAST results between 2008 and 2014 in our Department of Dermatology. A cluster analysis was performed to elucidate the allergen-specific immunoglobulin (Ig)E cluster pattern. The results of MAST (39 allergen-specific IgEs) from 4,360 cases were analyzed. By cluster analysis, 39items were grouped into 8 clusters. Each cluster had characteristic features. When compared with female, the male group tended to be sensitized more frequently to all tested allergens, except for fungus allergens cluster. The cluster and comparative analysis results demonstrate that the allergen sensitization is clustered, manifesting allergen similarity or co-exposure. Only the fungus cluster allergens tend to sensitize female group more frequently than male group.

High resolution chromosome 3p, 8p, 9q and 22q allelotyping analysis in the pathogenesis of gallbladder carcinoma

PubMed Central

Wistuba, I I; Maitra, A; Carrasco, R; Tang, M; Troncoso, P; Minna, J D; Gazdar, A F

2002-01-01

Our recent genome-wide allelotyping analysis of gallbladder carcinoma identified 3p, 8p, 9q and 22q as chromosomal regions with frequent loss of heterozygosity. The present study was undertaken to more precisely identify the presence and location of regions of frequent allele loss involving those chromosomes in gallbladder carcinoma. Microdissected tissue from 24 gallbladder carcinoma were analysed for PCR-based loss of heterozygosity using 81 microsatellite markers spanning chromosome 3p (n=26), 8p (n=14), 9q (n=29) and 22q (n=12) regions. We also studied the role of those allele losses in gallbladder carcinoma pathogenesis by examining 45 microdissected normal and dysplastic gallbladder epithelia accompanying gallbladder carcinoma, using 17 microsatellite markers. Overall frequencies of loss of heterozygosity at 3p (100%), 8p (100%), 9q (88%), and 22q (92%) sites were very high in gallbladder carcinoma, and we identified 13 distinct regions undergoing frequent loss of heterozygosity in tumours. Allele losses were frequently detected in normal and dysplastic gallbladder epithelia. There was a progressive increase of the overall loss of heterozygosity frequency with increasing severity of histopathological changes. Allele losses were not random and followed a sequence. This study refines several distinct chromosome 3p, 8p, 9q and 22q regions undergoing frequent allele loss in gallbladder carcinoma that will aid in the positional identification of tumour suppressor genes involved in gallbladder carcinoma pathogenesis. British Journal of Cancer (2002) 87, 432–440. doi:10.1038/sj.bjc.6600490 www.bjcancer.com © 2002 Cancer Research UK PMID:12177780

A random Q-switched fiber laser

PubMed Central

Tang, Yulong; Xu, Jianqiu

2015-01-01

Extensive studies have been performed on random lasers in which multiple-scattering feedback is used to generate coherent emission. Q-switching and mode-locking are well-known routes for achieving high peak power output in conventional lasers. However, in random lasers, the ubiquitous random cavities that are formed by multiple scattering inhibit energy storage, making Q-switching impossible. In this paper, widespread Rayleigh scattering arising from the intrinsic micro-scale refractive-index irregularities of fiber cores is used to form random cavities along the fiber. The Q-factor of the cavity is rapidly increased by stimulated Brillouin scattering just after the spontaneous emission is enhanced by random cavity resonances, resulting in random Q-switched pulses with high brightness and high peak power. This report is the first observation of high-brightness random Q-switched laser emission and is expected to stimulate new areas of scientific research and applications, including encryption, remote three-dimensional random imaging and the simulation of stellar lasing. PMID:25797520

Hierarchical Aligned Cluster Analysis for Temporal Clustering of Human Motion.

PubMed

Zhou, Feng; De la Torre, Fernando; Hodgins, Jessica K

2013-03-01

Temporal segmentation of human motion into plausible motion primitives is central to understanding and building computational models of human motion. Several issues contribute to the challenge of discovering motion primitives: the exponential nature of all possible movement combinations, the variability in the temporal scale of human actions, and the complexity of representing articulated motion. We pose the problem of learning motion primitives as one of temporal clustering, and derive an unsupervised hierarchical bottom-up framework called hierarchical aligned cluster analysis (HACA). HACA finds a partition of a given multidimensional time series into m disjoint segments such that each segment belongs to one of k clusters. HACA combines kernel k-means with the generalized dynamic time alignment kernel to cluster time series data. Moreover, it provides a natural framework to find a low-dimensional embedding for time series. HACA is efficiently optimized with a coordinate descent strategy and dynamic programming. Experimental results on motion capture and video data demonstrate the effectiveness of HACA for segmenting complex motions and as a visualization tool. We also compare the performance of HACA to state-of-the-art algorithms for temporal clustering on data of a honey bee dance. The HACA code is available online.

Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale.

PubMed

Emmons, Scott; Kobourov, Stephen; Gallant, Mike; Börner, Katy

2016-01-01

Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms-Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large graphs with well-defined clusters.

Assessment of cluster yield components by image analysis.

PubMed

Diago, Maria P; Tardaguila, Javier; Aleixos, Nuria; Millan, Borja; Prats-Montalban, Jose M; Cubero, Sergio; Blasco, Jose

2015-04-01

Berry weight, berry number and cluster weight are key parameters for yield estimation for wine and tablegrape industry. Current yield prediction methods are destructive, labour-demanding and time-consuming. In this work, a new methodology, based on image analysis was developed to determine cluster yield components in a fast and inexpensive way. Clusters of seven different red varieties of grapevine (Vitis vinifera L.) were photographed under laboratory conditions and their cluster yield components manually determined after image acquisition. Two algorithms based on the Canny and the logarithmic image processing approaches were tested to find the contours of the berries in the images prior to berry detection performed by means of the Hough Transform. Results were obtained in two ways: by analysing either a single image of the cluster or using four images per cluster from different orientations. The best results (R(2) between 69% and 95% in berry detection and between 65% and 97% in cluster weight estimation) were achieved using four images and the Canny algorithm. The model's capability based on image analysis to predict berry weight was 84%. The new and low-cost methodology presented here enabled the assessment of cluster yield components, saving time and providing inexpensive information in comparison with current manual methods. © 2014 Society of Chemical Industry.

SU(p,q) coherent states and a Gaussian de Finetti theorem

NASA Astrophysics Data System (ADS)

Leverrier, Anthony

2018-04-01

We prove a generalization of the quantum de Finetti theorem when the local space is an infinite-dimensional Fock space. In particular, instead of considering the action of the permutation group on n copies of that space, we consider the action of the unitary group U(n) on the creation operators of the n modes and define a natural generalization of the symmetric subspace as the space of states invariant under unitaries in U(n). Our first result is a complete characterization of this subspace, which turns out to be spanned by a family of generalized coherent states related to the special unitary group SU(p, q) of signature (p, q). More precisely, this construction yields a unitary representation of the noncompact simple real Lie group SU(p, q). We therefore find a dual unitary representation of the pair of groups U(n) and SU(p, q) on an n(p + q)-mode Fock space. The (Gaussian) SU(p, q) coherent states resolve the identity on the symmetric subspace, which implies a Gaussian de Finetti theorem stating that tracing over a few modes of a unitary-invariant state yields a state close to a mixture of Gaussian states. As an application of this de Finetti theorem, we show that the n × n upper-left submatrix of an n × n Haar-invariant unitary matrix is close in total variation distance to a matrix of independent normal variables if n3 = O(m).

Edge Stability and Performance of the ELM-Free Quiescent H-Mode and the Quiescent Double Barrier Mode on DIII-D

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

West, W P; Burrell, K H; Casper, T A

2004-12-03

The quiescent H (QH) mode, an edge localized mode (ELM)-free, high-confinement mode, combines well with an internal transport barrier to form quiescent double barrier (QDB) stationary state, high performance plasmas. The QH-mode edge pedestal pressure is similar to that seen in ELMing phases of the same discharge, with similar global energy confinement. The pedestal density in early ELMing phases of strongly pumped counter injection discharges drops and a transition to QH-mode occurs, leading to lower calculated edge bootstrap current. Plasmas current ramp experiment and ELITE code modeling of edge stability suggest that QH-modes lie near an edge current stability boundary.more » At high triangularity, QH-mode discharges operate at higher pedestal density and pressure, and have achieved ITER level values of {beta}{sub PED} and {nu}*. The QDB achieves performance of {alpha}{sub N}H{sub 89} {approx} 7 in quasi-stationary conditions for a duration of 10 tE, limited by hardware. Recently we demonstrated stationary state QDB discharges with little change in kinetic and q profiles (q{sub 0} > 1) for 2 s, comparable to ELMing ''hybrid scenarios'', yet without the debilitating effects of ELMs. Plasma profile control tools, including electron cyclotron heating and current drive and neutral beam heating, have been demonstrated to control simultaneously the q profile development, the density peaking, impurity accumulation and plasma beta.« less

Advanced analysis of forest fire clustering

NASA Astrophysics Data System (ADS)

Kanevski, Mikhail; Pereira, Mario; Golay, Jean

2017-04-01

Analysis of point pattern clustering is an important topic in spatial statistics and for many applications: biodiversity, epidemiology, natural hazards, geomarketing, etc. There are several fundamental approaches used to quantify spatial data clustering using topological, statistical and fractal measures. In the present research, the recently introduced multi-point Morisita index (mMI) is applied to study the spatial clustering of forest fires in Portugal. The data set consists of more than 30000 fire events covering the time period from 1975 to 2013. The distribution of forest fires is very complex and highly variable in space. mMI is a multi-point extension of the classical two-point Morisita index. In essence, mMI is estimated by covering the region under study by a grid and by computing how many times more likely it is that m points selected at random will be from the same grid cell than it would be in the case of a complete random Poisson process. By changing the number of grid cells (size of the grid cells), mMI characterizes the scaling properties of spatial clustering. From mMI, the data intrinsic dimension (fractal dimension) of the point distribution can be estimated as well. In this study, the mMI of forest fires is compared with the mMI of random patterns (RPs) generated within the validity domain defined as the forest area of Portugal. It turns out that the forest fires are highly clustered inside the validity domain in comparison with the RPs. Moreover, they demonstrate different scaling properties at different spatial scales. The results obtained from the mMI analysis are also compared with those of fractal measures of clustering - box counting and sand box counting approaches. REFERENCES Golay J., Kanevski M., Vega Orozco C., Leuenberger M., 2014: The multipoint Morisita index for the analysis of spatial patterns. Physica A, 406, 191-202. Golay J., Kanevski M. 2015: A new estimator of intrinsic dimension based on the multipoint Morisita index

RCLUS, a new program for clustering associated species: A demonstration using a Mojave Desert plant community dataset

Treesearch

Stewart C. Sanderson; Jeffrey E. Ott; E. Durant McArthur; Kimball T. Harper

2006-01-01

This paper presents a new clustering program named RCLUS that was developed for species (R-mode) analysis of plant community data. RCLUS identifies clusters of co-occurring species that meet a user-specified cutoff level of positive association with each other. The "strict affinity" clustering algorithm in RCLUS builds clusters of species whose pairwise...

Experimental study of electro-optical Q-switched pulsed Nd:YAG laser

NASA Astrophysics Data System (ADS)

A, Maleki; M Kavosh, Tehrani; H, Saghafifar; M, H. Moghtader Dindarlu

2016-03-01

We report the specification of a compact and stable side diode-pumped Q-switched pulsed Nd:YAG laser. We experimentally study and compare the performance of the pulsed Nd:YAG laser in the free-running and Q-switched modes at different pulse repetition rates from 1 Hz to 100 Hz. The laser output energy is stabilized by using a special configuration of the optical resonator. In this laser, an unsymmetrical concave-concave resonator is used and this structure helps the mode volume to be nearly fixed when the pulse repetition rate is increased. According to the experimental results in the Q-switched operation, the laser output energy is nearly constant around 70 mJ with an FWHM pulse width of 7 ns at 100 Hz. The optical-to-optical conversion efficiency in the Q-switched regime is 17.5%.

Influence of Aromatic Molecules on the Structure and Spectroscopy of Water Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Walsh, Patrick S.; Zwier, Timothy S.

2016-06-01

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-(water)_n, 1-2-diphenoxyethane-(water)_n, and tricyclophane-(water)_n clusters. The IR spectra are modeled with a local mode Hamiltonian that was originally formulated for the analysis of benzene-(water)_n clusters with up to seven waters. The model accounts for stretch-bend Fermi coupling, which can complicate the IR spectra in the 3150-3300 cm-1 region. When the water clusters interact with each of the solutes, the hydrogen bond lengths between the water molecules change in a characteristic way, reflecting the strength of the solute-water interaction. These structural effects are also reflected spectroscopically in the shifts of the local mode OH stretch frequencies. When diphenoxyethane is the solute, the water clusters distort more significantly than when bound to benzene. Tricyclophane's structure provides an aromatic-rich binding pocket for the water clusters. The local mode model is used to extract Hamiltonians for individual water molecules. These monomer Hamiltonians divide into groups based on their local H-bonding architecture, allowing for further classification of the wide variety of water environments encountered in this study.

Distinguishing Functional DNA Words; A Method for Measuring Clustering Levels

NASA Astrophysics Data System (ADS)

Moghaddasi, Hanieh; Khalifeh, Khosrow; Darooneh, Amir Hossein

2017-01-01

Functional DNA sub-sequences and genome elements are spatially clustered through the genome just as keywords in literary texts. Therefore, some of the methods for ranking words in texts can also be used to compare different DNA sub-sequences. In analogy with the literary texts, here we claim that the distribution of distances between the successive sub-sequences (words) is q-exponential which is the distribution function in non-extensive statistical mechanics. Thus the q-parameter can be used as a measure of words clustering levels. Here, we analyzed the distribution of distances between consecutive occurrences of 16 possible dinucleotides in human chromosomes to obtain their corresponding q-parameters. We found that CG as a biologically important two-letter word concerning its methylation, has the highest clustering level. This finding shows the predicting ability of the method in biology. We also proposed that chromosome 18 with the largest value of q-parameter for promoters of genes is more sensitive to dietary and lifestyle. We extended our study to compare the genome of some selected organisms and concluded that the clustering level of CGs increases in higher evolutionary organisms compared to lower ones.

Tungsten disulphide based all fiber Q-switching cylindrical-vector beam generation

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

Lin, J.; Yan, K.; Zhou, Y.

2015-11-09

We proposed and demonstrated an all fiber passively Q-switching laser to generate cylindrical-vector beam, a two dimensional material, tungsten disulphide (WS{sub 2}), was adopted as a saturable absorber inside the laser cavity, while a few-mode fiber Bragg grating was used as a transverse mode-selective output coupler. The repetition rate of the Q-switching output pulses can be varied from 80 kHz to 120 kHz with a shortest duration of 958 ns. Attributed to the high damage threshold and polarization insensitivity of the WS{sub 2} based saturable absorber, the radially polarized beam and azimuthally polarized beam can be easily generated in the Q-switching fiber laser.

Cluster and constraint analysis in tetrahedron packings

NASA Astrophysics Data System (ADS)

Jin, Weiwei; Lu, Peng; Liu, Lufeng; Li, Shuixiang

2015-04-01

The disordered packings of tetrahedra often show no obvious macroscopic orientational or positional order for a wide range of packing densities, and it has been found that the local order in particle clusters is the main order form of tetrahedron packings. Therefore, a cluster analysis is carried out to investigate the local structures and properties of tetrahedron packings in this work. We obtain a cluster distribution of differently sized clusters, and peaks are observed at two special clusters, i.e., dimer and wagon wheel. We then calculate the amounts of dimers and wagon wheels, which are observed to have linear or approximate linear correlations with packing density. Following our previous work, the amount of particles participating in dimers is used as an order metric to evaluate the order degree of the hierarchical packing structure of tetrahedra, and an order map is consequently depicted. Furthermore, a constraint analysis is performed to determine the isostatic or hyperstatic region in the order map. We employ a Monte Carlo algorithm to test jamming and then suggest a new maximally random jammed packing of hard tetrahedra from the order map with a packing density of 0.6337.

Initial conditions of formation of starburst clusters: constraints from stellar dynamics

NASA Astrophysics Data System (ADS)

Banerjee, Sambaran

2017-03-01

How starburst clusters form out of molecular clouds is still an open question. In this article, I highlight some of the key constraints in this regard, that one can get from the dynamical evolutionary properties of dense stellar systems. I particularly focus on secular expansion of massive star clusters and hierarchical merging of sub-clusters, and discuss their implications vis-á-vis the observed properties of young massive clusters. The analysis suggests that residual gas expulsion is necessary for shaping these clusters as we see them today, irrespective of their monolithic or hierarchical mode of formation.

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

NASA Astrophysics Data System (ADS)

Vogt, Dominik Walter; Leonhardt, Rainer

2018-05-01

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

All fiber passively Q-switched laser

DOEpatents

Soh, Daniel B. S.; Bisson, Scott E

2015-05-12

Embodiments relate to an all fiber passively Q-switched laser. The laser includes a large core doped gain fiber having a first end. The large core doped gain fiber has a first core diameter. The laser includes a doped single mode fiber (saturable absorber) having a second core diameter that is smaller than the first core diameter. The laser includes a mode transformer positioned between a second end of the large core doped gain fiber and a first end of the single mode fiber. The mode transformer has a core diameter that transitions from the first core diameter to the second core diameter and filters out light modes not supported by the doped single mode fiber. The laser includes a laser cavity formed between a first reflector positioned adjacent the large core doped gain fiber and a second reflector positioned adjacent the doped single mode fiber.

Further Development of Rotating Rake Mode Measurement Data Analysis

NASA Technical Reports Server (NTRS)

Dahl, Milo D.; Hixon, Ray; Sutliff, Daniel L.

2013-01-01

The Rotating Rake mode measurement system was designed to measure acoustic duct modes generated by a fan stage. After analysis of the measured data, the mode amplitudes and phases were quantified. For low-speed fans within axisymmetric ducts, mode power levels computed from rotating rake measured data would agree with the far-field power levels on a tone by tone basis. However, this agreement required that the sound from the noise sources within the duct propagated outward from the duct exit without reflection at the exit and previous studies suggested conditions could exist where significant reflections could occur. To directly measure the modes propagating in both directions within a duct, a second rake was mounted to the rotating system with an offset in both the axial and the azimuthal directions. The rotating rake data analysis technique was extended to include the data measured by the second rake. The analysis resulted in a set of circumferential mode levels at each of the two rake microphone locations. Radial basis functions were then least-squares fit to this data to obtain the radial mode amplitudes for the modes propagating in both directions within the duct. The fit equations were also modified to allow evanescent mode amplitudes to be computed. This extension of the rotating rake data analysis technique was tested using simulated data, numerical code produced data, and preliminary in-duct measured data.

ICAP - An Interactive Cluster Analysis Procedure for analyzing remotely sensed data

NASA Technical Reports Server (NTRS)

Wharton, S. W.; Turner, B. J.

1981-01-01

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. ICAP differs from conventional clustering algorithms by allowing the analyst to optimize the cluster configuration by inspection, rather than by manipulating process parameters. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters, and the analyst, who can evaluate and elect to modify the cluster structure. Clusters can be deleted, or lumped together pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The principal advantage of this approach is that it allows prior information (when available) to be used directly in the analysis, since the analyst interacts with ICAP in a straightforward manner, using basic terms with which he is more likely to be familiar. Results from testing ICAP showed that an informed use of ICAP can improve classification, as compared to an existing cluster analysis procedure.

Mode selection in square resonator microlasers for widely tunable single mode lasing.

PubMed

Tang, Ming-Ying; Sui, Shao-Shuai; Yang, Yue-De; Xiao, Jin-Long; Du, Yun; Huang, Yong-Zhen

2015-10-19

Mode selection in square resonator semiconductor microlasers is demonstrated by adjusting the width of the output waveguide coupled to the midpoint of one side. The simulation and experimental results reveal that widely tunable single mode lasing can be realized in square resonator microlasers. Through adjusting the width of the output waveguide, the mode interval of the high-Q modes can reach four times of the longitudinal mode interval. Therefore, mode hopping can be efficiently avoided and the lasing wavelength can be tuned continuously by tuning the injection current. For a 17.8-μm-side-length square microlaser with a 1.4-μm-width output waveguide, mode-hopping-free single-mode operation is achieved with a continuous tuning range of 9.2 nm. As a result, the control of the lasing mode is realized for the square microlasers.

Regional localization of the human integrin {beta}{sub 6} gene (ITGB6) to chromosome 2q24-q31

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

Fernandez-Ruiz, E.; Sanchez-Madrid, F.

The heterodimer {alpha}{sub v}{beta}{sub 6} acts as a fibronectin receptor for human carcinoma cells. The authors report here the regional localization of the {beta}{sub 6} gene to 2q24-q31 by fluorescence in situ hybridization coupled with GTG-banding. This gene is located close to the region to which genes coding for the {alpha} subunits of the integrins VLA-4 and vitronectin receptor (ITGA4 and ITGAV, respectively) have been previously mapped (2q31-q32). These data suggest a proximal position of the integrin {beta}{sub 6} locus (ITGB6) on this integrin gene cluster. Futhermore, double-labeling in situ hybridization experiments performed with {alpha}{sub 4} and {alpha}{sub v} probesmore » indicated a telomeric position of ITGAV with respect to ITGA4. 22 refs., 2 figs.« less

Strong evidences for a nonextensive behavior of the rotation period in open clusters

NASA Astrophysics Data System (ADS)

de Freitas, D. B.; Nepomuceno, M. M. F.; Soares, B. B.; Silva, J. R. P.

2014-11-01

Time-dependent nonextensivity in a stellar astrophysical scenario combines nonextensive entropic indices qK derived from the modified Kawaler's parametrization, and q, obtained from rotational velocity distribution. These q's are related through a heuristic single relation given by q≈ q0(1-Δ t/qK) , where t is the cluster age. In a nonextensive scenario, these indices are quantities that measure the degree of nonextensivity present in the system. Recent studies reveal that the index q is correlated to the formation rate of high-energy tails present in the distribution of rotation velocity. On the other hand, the index qK is determined by the stellar rotation-age relationship. This depends on the magnetic-field configuration through the expression qK=1+4aN/3 , where a and N denote the saturation level of the star magnetic field and its topology, respectively. In the present study, we show that the connection q-qK is also consistent with 548 rotation period data for single main-sequence stars in 11 open clusters aged less than 1 Gyr. The value of qK ˜ 2.5 from our unsaturated model shows that the mean magnetic-field topology of these stars is slightly more complex than a purely radial field. Our results also suggest that stellar rotational braking behavior affects the degree of anti-correlation between q and cluster age t. Finally, we suggest that stellar magnetic braking can be scaled by the entropic index q.

Clustering analysis strategies for electron energy loss spectroscopy (EELS).

PubMed

Torruella, Pau; Estrader, Marta; López-Ortega, Alberto; Baró, Maria Dolors; Varela, Maria; Peiró, Francesca; Estradé, Sònia

2018-02-01

In this work, the use of cluster analysis algorithms, widely applied in the field of big data, is proposed to explore and analyze electron energy loss spectroscopy (EELS) data sets. Three different data clustering approaches have been tested both with simulated and experimental data from Fe 3 O 4 /Mn 3 O 4 core/shell nanoparticles. The first method consists on applying data clustering directly to the acquired spectra. A second approach is to analyze spectral variance with principal component analysis (PCA) within a given data cluster. Lastly, data clustering on PCA score maps is discussed. The advantages and requirements of each approach are studied. Results demonstrate how clustering is able to recover compositional and oxidation state information from EELS data with minimal user input, giving great prospects for its usage in EEL spectroscopy. Copyright © 2017 Elsevier B.V. All rights reserved.

Galaxy Clusters

NASA Astrophysics Data System (ADS)

Miller, Christopher J. Miller

2012-03-01

of galaxy clusters will be at locations of the peaks in the true underlying (mostly) dark matter density field. Kaiser (1984) [19] called this the high-peak model, which we demonstrate in Figure 16.1. We show a two-dimensional representation of a density field created by summing plane-waves with a predetermined power and with random wave-vector directions. In the left panel, we plot only the largest modes, where we see the density peaks (black) and valleys (white) in the combined field. In the right panel, we allow for smaller modes. You can see that the highest density peaks in the left panel contain smaller-scale, but still high-density peaks. These are the locations of future galaxy clusters. The bottom panel shows just these cluster-scale peaks. As you can see, the peaks themselves are clustered, and instead of just one large high-density peak in the original density field (see the left panel), the smaller modes show that six peaks are "born" within the broader, underlying large-scale density modes. This exemplifies the "bias" or amplified structure that is traced by galaxy clusters [19]. Clusters are rare, easy to find, and their member galaxies provide good distance estimates. In combination with their amplified clustering signal described above, galaxy clusters are considered an efficient and precise tracer of the large-scale matter density field in the Universe. Galaxy clusters can also be used to measure the baryon content of the Universe [43]. They can be used to identify gravitational lenses [38] and map the distribution of matter in clusters. The number and spatial distribution of galaxy clusters can be used to constrain cosmological parameters, like the fraction of the energy density in the Universe due to matter (Omega_matter) or the variation in the density field on fixed physical scales (sigma_8) [26,33]. The individual clusters act as “Island Universes” and as such are laboratories here we can study the evolution of the properties of the cluster

An effective fuzzy kernel clustering analysis approach for gene expression data.

PubMed

Sun, Lin; Xu, Jiucheng; Yin, Jiaojiao

2015-01-01

Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms.

Atlas-Guided Cluster Analysis of Large Tractography Datasets

PubMed Central

Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

2013-01-01

Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment. PMID:24386292

Atlas-guided cluster analysis of large tractography datasets.

PubMed

Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

2013-01-01

Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment.

Analysis of E. rutaecarpa Alkaloids Constituents In Vitro and In Vivo by UPLC-Q-TOF-MS Combined with Diagnostic Fragment

PubMed Central

Yang, Shenshen; Tian, Meng; Yuan, Lei; Deng, Haoyue; Wang, Lei; Li, Aizhu; Hou, Zhiguo; Li, Yubo

2016-01-01

Evodia rutaecarpa (Juss.) Benth. (Rutaceae) dried ripe fruit is used for dispelling colds, soothing liver, and analgesia. Pharmacological research has proved that alkaloids are the main active ingredients of E. rutaecarpa. This study aimed to rapidly classify and identify the alkaloids constituents of E. rutaecarpa by using UPLC-Q-TOF-MS coupled with diagnostic fragments. Furthermore, the effects of the material base of E. rutaecarpa bioactive ingredients in vivo were examined such that the transitional components in the blood of rats intragastrically given E. rutaecarpa were analyzed and identified. In this study, the type of alcohol extraction of E. rutaecarpa and the corresponding blood sample were used for the analysis by UPLC-Q-TOF-MS in positive ion mode. After reviewing much of the literature and collected information on the fragments, we obtained some diagnostic fragments of the alkaloids. Combining the diagnostic fragments with the technology of UPLC-Q-TOF-MS, we identified the compounds of E. rutaecarpa and blood samples and compared the ion fragment information with that of the alkaloids in E. rutaecarpa. A total of 17 alkaloids components and 6 blood components were identified. The proposed method was rapid, accurate, and sensitive. Therefore, this technique can reliably and practically analyze the chemical constituents in traditional Chinese medicine (TCM). PMID:27446630

Coupling analysis of high Q resonators in add-drop configuration through cavity ringdown spectroscopy

NASA Astrophysics Data System (ADS)

Frigenti, G.; Arjmand, M.; Barucci, A.; Baldini, F.; Berneschi, S.; Farnesi, D.; Gianfreda, M.; Pelli, S.; Soria, S.; Aray, A.; Dumeige, Y.; Féron, P.; Nunzi Conti, G.

2018-06-01

An original method able to fully characterize high-Q resonators in an add-drop configuration has been implemented. The method is based on the study of two cavity ringdown (CRD) signals, which are produced at the transmission and drop ports by wavelength sweeping a resonance in a time interval comparable with the photon cavity lifetime. All the resonator parameters can be assessed with a single set of simultaneous measurements. We first developed a model describing the two CRD output signals and a fitting program able to deduce the key parameters from the measured profiles. We successfully validated the model with an experiment based on a fiber ring resonator of known characteristics. Finally, we characterized a high-Q, home-made, MgF2 whispering gallery mode disk resonator in the add-drop configuration, assessing its intrinsic and coupling parameters.

Bi-Directional Ion Emission from Massive Gold Cluster Impacts on Nanometric Carbon Foils.

PubMed

Debord, J Daniel; Della-Negra, Serge; Fernandez-Lima, Francisco A; Verkhoturov, Stanislav V; Schweikert, Emile A

2012-04-12

Carbon cluster emission from thin carbon foils (5-40 nm) impacted by individual Au(n) (+q) cluster projectiles (95-125 qkeV, n/q = 3-200) reveals features regarding the energy deposition, projectile range, and projectile fate in matter as a function of the projectile characteristics. For the first time, the secondary ion emission from thin foils has been monitored simultaneously in both forward and backward emission directions. The projectile range and depth of emission were examined as a function of projectile size, energy, and target thickness. A key finding is that the massive cluster impact develops very differently from that of a small polyatomic projectile. The range of the 125 qkeV Au(100q) (+q) (q ≈ 4) projectile is estimated to be 20 nm (well beyond the range of an equal velocity Au(+)) and projectile disintegration occurs at the exit of even a 5 nm thick foil.

Mode coupling in hybrid square-rectangular lasers for single mode operation

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

Ma, Xiu-Wen; Huang, Yong-Zhen, E-mail: yzhuang@semi.ac.cn; Yang, Yue-De

Mode coupling between a square microcavity and a Fabry-Pérot (FP) cavity is proposed and demonstrated for realizing single mode lasers. The modulations of the mode Q factor as simulation results are observed and single mode operation is obtained with a side mode suppression ratio of 46 dB and a single mode fiber coupling loss of 3.2 dB for an AlGaInAs/InP hybrid laser as a 300-μm-length and 1.5-μm-wide FP cavity connected to a vertex of a 10-μm-side square microcavity. Furthermore, tunable single mode operation is demonstrated with a continuous wavelength tuning range over 10 nm. The simple hybrid structure may shed light on practicalmore » applications of whispering-gallery mode microcavities in large-scale photonic integrated circuits and optical communication and interconnection.« less

Effects of Group Size and Lack of Sphericity on the Recovery of Clusters in K-Means Cluster Analysis

ERIC Educational Resources Information Center

de Craen, Saskia; Commandeur, Jacques J. F.; Frank, Laurence E.; Heiser, Willem J.

2006-01-01

K-means cluster analysis is known for its tendency to produce spherical and equally sized clusters. To assess the magnitude of these effects, a simulation study was conducted, in which populations were created with varying departures from sphericity and group sizes. An analysis of the recovery of clusters in the samples taken from these…

Space-Time Analysis of Testicular Cancer Clusters Using Residential Histories: A Case-Control Study in Denmark

PubMed Central

Sloan, Chantel D.; Nordsborg, Rikke B.; Jacquez, Geoffrey M.; Raaschou-Nielsen, Ole; Meliker, Jaymie R.

2015-01-01

Though the etiology is largely unknown, testicular cancer incidence has seen recent significant increases in northern Europe and throughout many Western regions. The most common cancer in males under age 40, age period cohort models have posited exposures in the in utero environment or in early childhood as possible causes of increased risk of testicular cancer. Some of these factors may be tied to geography through being associated with behavioral, cultural, sociodemographic or built environment characteristics. If so, this could result in detectable geographic clusters of cases that could lead to hypotheses regarding environmental targets for intervention. Given a latency period between exposure to an environmental carcinogen and testicular cancer diagnosis, mobility histories are beneficial for spatial cluster analyses. Nearest-neighbor based Q-statistics allow for the incorporation of changes in residency in spatial disease cluster detection. Using these methods, a space-time cluster analysis was conducted on a population-wide case-control population selected from the Danish Cancer Registry with mobility histories since 1971 extracted from the Danish Civil Registration System. Cases (N=3297) were diagnosed between 1991 and 2003, and two sets of controls (N=3297 for each set) matched on sex and date of birth were included in the study. We also examined spatial patterns in maternal residential history for those cases and controls born in 1971 or later (N= 589 case-control pairs). Several small clusters were detected when aligning individuals by year prior to diagnosis, age at diagnosis and calendar year of diagnosis. However, the largest of these clusters contained only 2 statistically significant individuals at their center, and were not replicated in SaTScan spatial-only analyses which are less susceptible to multiple testing bias. We found little evidence of local clusters in residential histories of testicular cancer cases in this Danish population. PMID

Space-time analysis of testicular cancer clusters using residential histories: a case-control study in Denmark.

PubMed

Sloan, Chantel D; Nordsborg, Rikke B; Jacquez, Geoffrey M; Raaschou-Nielsen, Ole; Meliker, Jaymie R

2015-01-01

Though the etiology is largely unknown, testicular cancer incidence has seen recent significant increases in northern Europe and throughout many Western regions. The most common cancer in males under age 40, age period cohort models have posited exposures in the in utero environment or in early childhood as possible causes of increased risk of testicular cancer. Some of these factors may be tied to geography through being associated with behavioral, cultural, sociodemographic or built environment characteristics. If so, this could result in detectable geographic clusters of cases that could lead to hypotheses regarding environmental targets for intervention. Given a latency period between exposure to an environmental carcinogen and testicular cancer diagnosis, mobility histories are beneficial for spatial cluster analyses. Nearest-neighbor based Q-statistics allow for the incorporation of changes in residency in spatial disease cluster detection. Using these methods, a space-time cluster analysis was conducted on a population-wide case-control population selected from the Danish Cancer Registry with mobility histories since 1971 extracted from the Danish Civil Registration System. Cases (N=3297) were diagnosed between 1991 and 2003, and two sets of controls (N=3297 for each set) matched on sex and date of birth were included in the study. We also examined spatial patterns in maternal residential history for those cases and controls born in 1971 or later (N= 589 case-control pairs). Several small clusters were detected when aligning individuals by year prior to diagnosis, age at diagnosis and calendar year of diagnosis. However, the largest of these clusters contained only 2 statistically significant individuals at their center, and were not replicated in SaTScan spatial-only analyses which are less susceptible to multiple testing bias. We found little evidence of local clusters in residential histories of testicular cancer cases in this Danish population.

Sigma model Q-balls and Q-stars

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

Verbin, Y.

2007-10-15

A new kind of Q-balls is found: Q-balls in a nonlinear sigma model. Their main properties are presented together with those of their self-gravitating generalization, sigma model Q-stars. A simple special limit of solutions which are bound by gravity alone ('sigma stars') is also discussed briefly. The analysis is based on calculating the mass, global U(1) charge and binding energy for families of solutions parametrized by the central value of the scalar field. Two kinds (differing by the potential term) of the new sigma model Q-balls and Q-stars are analyzed. They are found to share some characteristics while differing inmore » other respects like their properties for weak central scalar fields which depend strongly on the form of the potential term. They are also compared with their ordinary counterparts and although similar in some respects, significant differences are found like the existence of an upper bound on the central scalar field. A special subset of the sigma model Q-stars contains those which do not possess a flat space limit. Their relation with sigma star solutions is discussed.« less

Two-Way Regularized Fuzzy Clustering of Multiple Correspondence Analysis.

PubMed

Kim, Sunmee; Choi, Ji Yeh; Hwang, Heungsun

2017-01-01

Multiple correspondence analysis (MCA) is a useful tool for investigating the interrelationships among dummy-coded categorical variables. MCA has been combined with clustering methods to examine whether there exist heterogeneous subclusters of a population, which exhibit cluster-level heterogeneity. These combined approaches aim to classify either observations only (one-way clustering of MCA) or both observations and variable categories (two-way clustering of MCA). The latter approach is favored because its solutions are easier to interpret by providing explicitly which subgroup of observations is associated with which subset of variable categories. Nonetheless, the two-way approach has been built on hard classification that assumes observations and/or variable categories to belong to only one cluster. To relax this assumption, we propose two-way fuzzy clustering of MCA. Specifically, we combine MCA with fuzzy k-means simultaneously to classify a subgroup of observations and a subset of variable categories into a common cluster, while allowing both observations and variable categories to belong partially to multiple clusters. Importantly, we adopt regularized fuzzy k-means, thereby enabling us to decide the degree of fuzziness in cluster memberships automatically. We evaluate the performance of the proposed approach through the analysis of simulated and real data, in comparison with existing two-way clustering approaches.

Spectral properties of Langmuir and beam-mode waves observed inside terrestrial foreshock by Cluster spacecraf

NASA Astrophysics Data System (ADS)

Pisa, D.; Soucek, J.; Santolik, O.

2016-12-01

Electrostatic plasma waves are commonly observed in the upstream regions of planetary shocks. Solar wind electrons accelerated at the shock front are reflected back into the solar wind and form electron beams. The electron distribution becomes unstable and electrostatic waves are generated inside the foreshock region. The processes of generation and evolution of electrostatic waves significantly depend on the solar wind plasma conditions and generally exhibit complex behavior. Langmuir waves can be identified as intense narrowband emission at the local plasma frequency and weaker broadband beam-mode waves below and above the plasma frequency deeper in the downstream region. We present a long-term survey of Langmuir and beam-mode waves in the vicinity of the plasma frequency observed upstream of the terrestrial bow shock by the Cluster spacecraft. Using solar wind data and bow shock positions from OMNI, as well as in-situ measurements of interplanetary magnetic field, we have mapped all available spacecraft positions into foreshock coordinates. For a study of plasma waves, we have used spectra and local plasma frequencies obtained from a passive and active mode of the WHISPER instrument. We show a spatial distribution of wave frequencies and spectral widths as a function of foreshock positions and solar wind conditions.

Phenotypes Determined by Cluster Analysis in Moderate to Severe Bronchial Asthma.

PubMed

Youroukova, Vania M; Dimitrova, Denitsa G; Valerieva, Anna D; Lesichkova, Spaska S; Velikova, Tsvetelina V; Ivanova-Todorova, Ekaterina I; Tumangelova-Yuzeir, Kalina D

2017-06-01

Bronchial asthma is a heterogeneous disease that includes various subtypes. They may share similar clinical characteristics, but probably have different pathological mechanisms. To identify phenotypes using cluster analysis in moderate to severe bronchial asthma and to compare differences in clinical, physiological, immunological and inflammatory data between the clusters. Forty adult patients with moderate to severe bronchial asthma out of exacerbation were included. All underwent clinical assessment, anthropometric measurements, skin prick testing, standard spirometry and measurement fraction of exhaled nitric oxide. Blood eosinophilic count, serum total IgE and periostin levels were determined. Two-step cluster approach, hierarchical clustering method and k-mean analysis were used for identification of the clusters. We have identified four clusters. Cluster 1 (n=14) - late-onset, non-atopic asthma with impaired lung function, Cluster 2 (n=13) - late-onset, atopic asthma, Cluster 3 (n=6) - late-onset, aspirin sensitivity, eosinophilic asthma, and Cluster 4 (n=7) - early-onset, atopic asthma. Our study is the first in Bulgaria in which cluster analysis is applied to asthmatic patients. We identified four clusters. The variables with greatest force for differentiation in our study were: age of asthma onset, duration of diseases, atopy, smoking, blood eosinophils, nonsteroidal anti-inflammatory drugs hypersensitivity, baseline FEV1/FVC and symptoms severity. Our results support the concept of heterogeneity of bronchial asthma and demonstrate that cluster analysis can be an useful tool for phenotyping of disease and personalized approach to the treatment of patients.

The JCMT Gould Belt Survey: Dense Core Clusters in Orion B

NASA Astrophysics Data System (ADS)

Kirk, H.; Johnstone, D.; Di Francesco, J.; Lane, J.; Buckle, J.; Berry, D. S.; Broekhoven-Fiene, H.; Currie, M. J.; Fich, M.; Hatchell, J.; Jenness, T.; Mottram, J. C.; Nutter, D.; Pattle, K.; Pineda, J. E.; Quinn, C.; Salji, C.; Tisi, S.; Hogerheijde, M. R.; Ward-Thompson, D.; The JCMT Gould Belt Survey Team

2016-04-01

The James Clerk Maxwell Telescope Gould Belt Legacy Survey obtained SCUBA-2 observations of dense cores within three sub-regions of Orion B: LDN 1622, NGC 2023/2024, and NGC 2068/2071, all of which contain clusters of cores. We present an analysis of the clustering properties of these cores, including the two-point correlation function and Cartwright’s Q parameter. We identify individual clusters of dense cores across all three regions using a minimal spanning tree technique, and find that in each cluster, the most massive cores tend to be centrally located. We also apply the independent M-Σ technique and find a strong correlation between core mass and the local surface density of cores. These two lines of evidence jointly suggest that some amount of mass segregation in clusters has happened already at the dense core stage.

Neuropsychological Endophenotype Approach to Genome-wide Linkage Analysis Identifies Susceptibility Loci for ADHD on 2q21.1 and 13q12.11

PubMed Central

Rommelse, Nanda N.J.; Arias-Vásquez, Alejandro; Altink, Marieke E.; Buschgens, Cathelijne J.M.; Fliers, Ellen; Asherson, Philip; Faraone, Stephen V.; Buitelaar, Jan K.; Sergeant, Joseph A.; Oosterlaan, Jaap; Franke, Barbara

2008-01-01

ADHD linkage findings have not all been consistently replicated, suggesting that other approaches to linkage analysis in ADHD might be necessary, such as the use of (quantitative) endophenotypes (heritable traits associated with an increased risk for ADHD). Genome-wide linkage analyses were performed in the Dutch subsample of the International Multi-Center ADHD Genetics (IMAGE) study comprising 238 DSM-IV combined-type ADHD probands and their 112 affected and 195 nonaffected siblings. Eight candidate neuropsychological ADHD endophenotypes with heritabilities > 0.2 were used as quantitative traits. In addition, an overall component score of neuropsychological functioning was used. A total of 5407 autosomal single-nucleotide polymorphisms (SNPs) were used to run multipoint regression-based linkage analyses. Two significant genome-wide linkage signals were found, one for Motor Timing on chromosome 2q21.1 (LOD score: 3.944) and one for Digit Span on 13q12.11 (LOD score: 3.959). Ten suggestive linkage signals were found (LOD scores ≥ 2) on chromosomes 2p, 2q, 3p, 4q, 8q, 12p, 12q, 14q, and 17q. The suggestive linkage signal for the component score that was found at 2q14.3 (LOD score: 2.878) overlapped with the region significantly linked to Motor Timing. Endophenotype approaches may increase power to detect susceptibility loci in ADHD and possibly in other complex disorders. PMID:18599010

Evolutions of fluctuation modes and inner structures of global stock markets

NASA Astrophysics Data System (ADS)

Yan, Yan; Wang, Lei; Liu, Maoxin; Chen, Xiaosong

2016-09-01

The paper uses empirical data, including 42 globally main stock indices in the period 1996-2014, to systematically study the evolution of fluctuation modes and inner structures of global stock markets. The data are large in scale considering both time and space. A covariance matrix-based principle fluctuation mode analysis (PFMA) is used to explore the properties of the global stock markets. It has been ignored by previous studies that covariance matrix is more suitable than the correlation matrix to be the basis of PFMA. It is found that the principle fluctuation modes of global stock markets are in the same directions, and global stock markets are divided into three clusters, which are found to be closely related to the countries’ locations with exceptions of China, Russia and Czech Republic. A time-stable correlation network constructing method is proposed to solve the problem of high-level statistical uncertainty when the estimated periods are very short, and the complex dynamic network (CDN) is constructed to investigate the evolution of inner structures. The results show when the clusters emerge and how long the clusters exist. When the 2008 financial crisis broke out, the indices form one cluster. After these crises, only the European cluster still exists. These findings complement the previous studies, and can help investors and regulators to understand the global stock markets.

Raman investigation of ro-vibrational modes of interstitial H2 in Si

NASA Astrophysics Data System (ADS)

Koch, S. G.; Lavrov, E. V.; Weber, J.

2012-08-01

A Raman scattering study of ro-vibrational transitions Q(J) of the interstitial H2 in Si is presented. It is shown that the Q(2) mode of para hydrogen is coupled to the TAX phonon of Si. The mode appears in the spectra at temperatures above 200 K. The results presented also suggest that the Q(3) transition of ortho hydrogen is resonantly coupled to the OΓ phonon.

Phonon self-energy corrections to non-zero wavevector phonon modes in single-layer graphene

NASA Astrophysics Data System (ADS)

Araujo, Paulo; Mafra, Daniela; Sato, Kentaro; Saito, Richiiro; Kong, Jing; Dresselhaus, Mildred

2012-02-01

Phonon self-energy corrections have mostly been studied theoretically and experimentally for phonon modes with zone-center (q = 0) wave-vectors. Here, gate-modulated Raman scattering is used to study phonons of a single layer of graphene (1LG) in the frequency range from 2350 to 2750 cm-1, which shows the G* and the G'-band features originating from a double-resonant Raman process with q 0. The observed phonon renormalization effects are different from what is observed for the zone-center q = 0 case. To explain our experimental findings, we explored the phonon self-energy for the phonons with non-zero wave-vectors (q 0) in 1LG in which the frequencies and decay widths are expected to behave oppositely to the behavior observed in the corresponding zone-center q = 0 processes. Within this framework, we resolve the identification of the phonon modes contributing to the G* Raman feature at 2450 cm-1 to include the iTO+LA combination modes with q 0 and the 2iTO overtone modes with q = 0, showing both to be associated with wave-vectors near the high symmetry point K in the Brillouin zone.

Isolation of Notl sites from chromosome 22q11

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

Ten Hoeve, J.; Groffen, J.; Heisterkamp, N.

1993-12-01

Chromosome 22q11 contains a large number of interesting loci, including genes associated with cancer and developmental defects. The region is also the site of the lambda immunoglobulin variable and constants regions and the BCR, [gamma]-glutamyl transpeptidase, and GGT-like activity multigene families. Because of the complexities associated with mapping highly related gene families, the authors have examined the utility of mapping large areas of DNA using a defined approach. A total of 21 complete NotI sites from band q11 were cloned and ordered into six noncontiguous clusters of sites using a combination of somatic cell hybrid panels, NotI jumping and linkingmore » libraries, and fluorescence in situ hybridization. The largest cluster spanned an estimated 2 Mb of NotI fragments, the smallest 115 kb. Approximately 3.5 Mb of band q11 could be examined for rearrangements in NotI restriction enzyme fragments. A number of conserved sequences, two genes, and a minimum of two families of related sequences were identified adjacent to NotI sites. 51 refs., 5 figs., 4 tabs.« less

White-Light Whispering-Gallery-Mode Optical Resonators

NASA Technical Reports Server (NTRS)

Matsko, Andrey; Savchenkov, Anatoliy; Maleki, Lute

2006-01-01

Whispering-gallery-mode (WGM) optical resonators can be designed to exhibit continuous spectra over wide wavelength bands (in effect, white-light spectra), with ultrahigh values of the resonance quality factor (Q) that are nearly independent of frequency. White-light WGM resonators have potential as superior alternatives to (1) larger, conventional optical resonators in ring-down spectroscopy, and (2) optical-resonator/electro-optical-modulator structures used in coupling of microwave and optical signals in atomic clocks. In these and other potential applications, the use of white-light WGM resonators makes it possible to relax the requirement of high-frequency stability of lasers, thereby enabling the use of cheaper lasers. In designing a white-light WGM resonator, one exploits the fact that the density of the mode spectrum increases predictably with the thickness of the resonator disk. By making the resonator disk sufficiently thick, one can make the frequency differences between adjacent modes significantly less than the spectral width of a single mode, so that the spectral peaks of adjacent modes overlap, making the resonator spectrum essentially continuous. Moreover, inasmuch as the Q values of the various modes are determined primarily by surface Rayleigh scattering that does not depend on mode numbers, all the modes have nearly equal Q. By use of a proper coupling technique, one can ensure excitation of a majority of the modes. For an experimental demonstration of a white-light WGM resonator, a resonator disk 0.5-mm thick and 5 mm in diameter was made from CaF2. The shape of the resonator and the fiberoptic coupling arrangement were as shown in Figure 1. The resonator was excited with laser light having a wavelength of 1,320 nm and a spectral width of 4 kHz. The coupling efficiency exceeded 80 percent at any frequency to which the laser could be set in its tuning range, which was >100-GHz wide. The resonator response was characterized by means of ring

High-Q silica zipper cavity for optical radiation pressure driven MOMS switch

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

Tetsumoto, Tomohiro; Tanabe, Takasumi, E-mail: takasumi@elec.keio.ac.jp

2014-07-15

We design a silica zipper cavity that has high optical and mechanical Q (quality factor) values and demonstrate numerically the feasibility of a radiation pressure driven micro opto-mechanical system (MOMS) directional switch. The silica zipper cavity has an optical Q of 4.0 × 10{sup 4} and an effective mode volume V{sub mode} of 0.67λ{sup 3} when the gap between two cavities is 34 nm. The mechanical Q (Q{sub m}) is determined by thermo-elastic damping and is 2.0 × 10{sup 6} in a vacuum at room temperature. The opto-mechanical coupling rate g{sub OM} is as high as 100 GHz/nm, which allowsmore » us to move the directional cavity-waveguide system and switch 1550-nm light with 770-nm light by controlling the radiation pressure.« less

Bi-Directional Ion Emission from Massive Gold Cluster Impacts on Nanometric Carbon Foils

PubMed Central

DeBord, J. Daniel; Della-Negra, Serge; Fernandez-Lima, Francisco A.; Verkhoturov, Stanislav V.; Schweikert, Emile A.

2012-01-01

Carbon cluster emission from thin carbon foils (5–40 nm) impacted by individual Aun+q cluster projectiles (95–125 qkeV, n/q = 3–200) reveals features regarding the energy deposition, projectile range, and projectile fate in matter as a function of the projectile characteristics. For the first time, the secondary ion emission from thin foils has been monitored simultaneously in both forward and backward emission directions. The projectile range and depth of emission were examined as a function of projectile size, energy, and target thickness. A key finding is that the massive cluster impact develops very differently from that of a small polyatomic projectile. The range of the 125 qkeV Au100q+q (q ≈ 4) projectile is estimated to be 20 nm (well beyond the range of an equal velocity Au+) and projectile disintegration occurs at the exit of even a 5 nm thick foil. PMID:22888385

Intracellular flow cytometry may be combined with good quality and high sensitivity RT-qPCR analysis.

PubMed

Sandstedt, Mikael; Jonsson, Marianne; Asp, Julia; Dellgren, Göran; Lindahl, Anders; Jeppsson, Anders; Sandstedt, Joakim

2015-12-01

Flow cytometry (FCM) has become a well-established method for analysis of both intracellular and cell-surface proteins, while quantitative RT-PCR (RT-qPCR) is used to determine gene expression with high sensitivity and specificity. Combining these two methods would be of great value. The effects of intracellular staining on RNA integrity and RT-qPCR sensitivity and quality have not, however, been fully examined. We, therefore, intended to assess these effects further. Cells from the human lung cancer cell line A549 were fixed, permeabilized and sorted by FCM. Sorted cells were analyzed using RT-qPCR. RNA integrity was determined by RNA quality indicator analysis. A549 cells were then mixed with cells of the mouse cardiomyocyte cell line HL-1. A549 cells were identified by the cell surface marker ABCG2, while HL-1 cells were identified by intracellular cTnT. Cells were sorted and analyzed by RT-qPCR. Finally, cell cultures from human atrial biopsies were used to evaluate the effects of fixation and permeabilization on RT-qPCR analysis of nonimmortalized cells stored prior to analysis by FCM. A large amount of RNA could be extracted even when cells had been fixed and permeabilized. Permeabilization resulted in increased RNA degradation and a moderate decrease in RT-qPCR sensitivity. Gene expression levels were also affected to a moderate extent. Sorted populations from the mixed A549 and HL-1 cell samples showed gene expression patterns that corresponded to FCM data. When samples were stored before FCM sorting, the RT-qPCR analysis could still be performed with high sensitivity and quality. In summary, our results show that intracellular FCM may be performed with only minor impairment of the RT-qPCR sensitivity and quality when analyzing sorted cells; however, these effects should be considered when comparing RT-qPCR data of not fixed samples with those of fixed and permeabilized samples. © 2015 International Society for Advancement of Cytometry.

Q methodology in health economics.

PubMed

Baker, Rachel; Thompson, Carl; Mannion, Russell

2006-01-01

The recognition that health economists need to understand the meaning of data if they are to adequately understand research findings which challenge conventional economic theory has led to the growth of qualitative modes of enquiry in health economics. The use of qualitative methods of exploration and description alongside quantitative techniques gives rise to a number of epistemological, ontological and methodological challenges: difficulties in accounting for subjectivity in choices, the need for rigour and transparency in method, and problems of disciplinary acceptability to health economists. Q methodology is introduced as a means of overcoming some of these challenges. We argue that Q offers a means of exploring subjectivity, beliefs and values while retaining the transparency, rigour and mathematical underpinnings of quantitative techniques. The various stages of Q methodological enquiry are outlined alongside potential areas of application in health economics, before discussing the strengths and limitations of the approach. We conclude that Q methodology is a useful addition to economists' methodological armoury and one that merits further consideration and evaluation in the study of health services.

Cluster analysis for determining distribution center location

NASA Astrophysics Data System (ADS)

Lestari Widaningrum, Dyah; Andika, Aditya; Murphiyanto, Richard Dimas Julian

2017-12-01

Determination of distribution facilities is highly important to survive in the high level of competition in today’s business world. Companies can operate multiple distribution centers to mitigate supply chain risk. Thus, new problems arise, namely how many and where the facilities should be provided. This study examines a fast-food restaurant brand, which located in the Greater Jakarta. This brand is included in the category of top 5 fast food restaurant chain based on retail sales. There were three stages in this study, compiling spatial data, cluster analysis, and network analysis. Cluster analysis results are used to consider the location of the additional distribution center. Network analysis results show a more efficient process referring to a shorter distance to the distribution process.

De novo tandem duplication of chromosome segement 22q11-q12: Clinical, cytogenetic, and molecular characterization

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

Lindsay, E.A.; Shaffer, L.G.; Carrozzo, R.

We report on a case of duplication of the segment 22q11-q12 due to a de novo duplication. Molecular cytogenetics studies demonstrated this to be a tandem duplication, flanked proximally by the marker D22Z4, a centromeric alpha satellite DNA repeat, and distally by D22S260, an anonymous DNA marker proximal to the Ewing sarcoma breakpoint. The segment includes the regions responsible for the {open_quotes}cat-eye{close_quotes}, Di George, and velo-cardio-facial syndromes and extends distal to the breakpoint cluster region (BCR). The clinical picture is dominated by the cardiac defects and includes findings reminiscent of {open_quotes}cat-eye{close_quotes} syndrome. These findings reinforce the hypothesis that the proximalmore » 22q region contains dosage-sensitive genes involved in development. 20 refs., 3 figs.« less

Injection-seeded operation of a Q-switched Cr,Tm,Ho:YAG laser

NASA Technical Reports Server (NTRS)

Henderson, Sammy W.; Hale, Charley P.; Magee, James R.

1991-01-01

Single-frequency Tm,Ho:YAG lasers operating near 2 microns are attractive sources for several applications including eye-safe laser radar (lidar) and pumping of AgGaSe2 parametric oscillators for efficient generation of longer wavelengths. As part of a program to develop a coherent lidar system using Tm,Ho:YAG lasers, a diode laser-pumped tunable CW single-longitudinal-mode (SLM) Cr:Tm:Ho:YAG laser and a flashlamp-pumped single-transverse-mode Q-switched Cr,Tm,Ho:YAG laser were developed. The CW laser was used to injection-seed the flashlamp-pumped laser, resulting in SLM Q-switched output. Operational characteristics of the CW and Q-switched lasers and injection-seeding results are reported.

Mandibulofacial Dysostosis in a Patient with a de novo 2;17 Translocation that Disrupts the HOXD Gene Cluster

PubMed Central

Stevenson, David A.; Bleyl, Steven B.; Maxwell, Teresa; Brothman, Arthur R.; South, Sarah T.

2011-01-01

Treacher Collins syndrome is the prototypical mandibulofacial dysostosis syndrome, but other mandibulofacial dysostosis syndromes have been described. We report an infant with mandibulofacial dysostosis and an apparently balanced de novo 2;17 translocation. She presented with severe lower eyelid colobomas requiring skin grafting, malar and mandibular hypoplasia, bilateral microtia with external auditory canal atreasia, dysplastic ossicles, hearing loss, bilateral choanal stenosis, cleft palate without cleft lip, several oral frenula of the upper lip/gum, and micrognathia requiring tracheostomy. Her limbs were normal. Chromosome analysis at the 600-band level showed a 46,XX,t(2;17)(q24.3;q23) karyotype. Sequencing of the entire TCOF1 coding region did not show evidence of a sequence variation. High-resolution genomic microarray analysis did not identify a cryptic imbalance. FISH mapping refined the breakpoints to 2q31.1 and 17q24.3–25.1 and showed the 2q31.1 breakpoint likely affects the HOXD gene cluster. Several atypical findings and lack of an identifiable TCOF1 mutation suggest that this child has a provisionally unique mandibulofacial dysostosis syndrome. The apparently balanced de novo translocation provides candidate loci for atypical and TCOF1 mutation negative cases of Treacher Collins syndrome. Based on the agreement of our findings with one previous case of mandibulofacial dysostosis with a 2q31.1 transocation, we hypothesize that misexpression of genes in the HOXD gene cluster produced the described phenotype in this patient. PMID:17431905

Mandibulofacial dysostosis in a patient with a de novo 2;17 translocation that disrupts the HOXD gene cluster.

PubMed

Stevenson, David A; Bleyl, Steven B; Maxwell, Teresa; Brothman, Arthur R; South, Sarah T

2007-05-15

Treacher Collins syndrome (TCS) is the prototypical mandibulofacial dysostosis syndrome, but other mandibulofacial dysostosis syndromes have been described. We report an infant with mandibulofacial dysostosis and an apparently balanced de novo 2;17 translocation. She presented with severe lower eyelid colobomas requiring skin grafting, malar and mandibular hypoplasia, bilateral microtia with external auditory canal atreasia, dysplastic ossicles, hearing loss, bilateral choanal stenosis, cleft palate without cleft lip, several oral frenula of the upper lip/gum, and micrognathia requiring tracheostomy. Her limbs were normal. Chromosome analysis at the 600-band level showed a 46,XX,t(2;17)(q24.3;q23) karyotype. Sequencing of the entire TCOF1 coding region did not show evidence of a sequence variation. High-resolution genomic microarray analysis did not identify a cryptic imbalance. FISH mapping refined the breakpoints to 2q31.1 and 17q24.3-25.1 and showed the 2q31.1 breakpoint likely affects the HOXD gene cluster. Several atypical findings and lack of an identifiable TCOF1 mutation suggest that this child has a provisionally unique mandibulofacial dysostosis syndrome. The apparently balanced de novo translocation provides candidate loci for atypical and TCOF1 mutation negative cases of TCS. Based on the agreement of our findings with one previous case of mandibulofacial dysostosis with a 2q31.1 transocation, we hypothesize that misexpression of genes in the HOXD gene cluster produced the described phenotype in this patient.

Interstitial duplication 8q22-q24: Report of a case proven by FISH with mapped cosmid probes

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

Wakui, Keiko; Ohashi, Hirofumi; Yamagishi, Akira

We report on a 6-month-old malformed female infant with a de novo interstitial duplication of an 8q22-q24 segment. She had an excess dark-band on the 8q distal region by GTG-banded chromosome analysis, which was likely to be 8q23. We performed FISH analysis using cosmid probes mapped to 8q23 and proved that the patient had an 8q duplication including the 8q23 region. 20 refs., 2 figs., 1 tab.

Using cluster analysis for medical resource decision making.

PubMed

Dilts, D; Khamalah, J; Plotkin, A

1995-01-01

Escalating costs of health care delivery have in the recent past often made the health care industry investigate, adapt, and apply those management techniques relating to budgeting, resource control, and forecasting that have long been used in the manufacturing sector. A strategy that has contributed much in this direction is the definition and classification of a hospital's output into "products" or groups of patients that impose similar resource or cost demands on the hospital. Existing classification schemes have frequently employed cluster analysis in generating these groupings. Unfortunately, the myriad articles and books on clustering and classification contain few formalized selection methodologies for choosing a technique for solving a particular problem, hence they often leave the novice investigator at a loss. This paper reviews the literature on clustering, particularly as it has been applied in the medical resource-utilization domain, addresses the critical choices facing an investigator in the medical field using cluster analysis, and offers suggestions (using the example of clustering low-vision patients) for how such choices can be made.

Cluster Analysis of Minnesota School Districts. A Research Report.

ERIC Educational Resources Information Center

Cleary, James

The term "cluster analysis" refers to a set of statistical methods that classify entities with similar profiles of scores on a number of measured dimensions, in order to create empirically based typologies. A 1980 Minnesota House Research Report employed cluster analysis to categorize school districts according to their relative mixtures…

Clinical Characteristics of Exacerbation-Prone Adult Asthmatics Identified by Cluster Analysis.

PubMed

Kim, Mi Ae; Shin, Seung Woo; Park, Jong Sook; Uh, Soo Taek; Chang, Hun Soo; Bae, Da Jeong; Cho, You Sook; Park, Hae Sim; Yoon, Ho Joo; Choi, Byoung Whui; Kim, Yong Hoon; Park, Choon Sik

2017-11-01

Asthma is a heterogeneous disease characterized by various types of airway inflammation and obstruction. Therefore, it is classified into several subphenotypes, such as early-onset atopic, obese non-eosinophilic, benign, and eosinophilic asthma, using cluster analysis. A number of asthmatics frequently experience exacerbation over a long-term follow-up period, but the exacerbation-prone subphenotype has rarely been evaluated by cluster analysis. This prompted us to identify clusters reflecting asthma exacerbation. A uniform cluster analysis method was applied to 259 adult asthmatics who were regularly followed-up for over 1 year using 12 variables, selected on the basis of their contribution to asthma phenotypes. After clustering, clinical profiles and exacerbation rates during follow-up were compared among the clusters. Four subphenotypes were identified: cluster 1 was comprised of patients with early-onset atopic asthma with preserved lung function, cluster 2 late-onset non-atopic asthma with impaired lung function, cluster 3 early-onset atopic asthma with severely impaired lung function, and cluster 4 late-onset non-atopic asthma with well-preserved lung function. The patients in clusters 2 and 3 were identified as exacerbation-prone asthmatics, showing a higher risk of asthma exacerbation. Two different phenotypes of exacerbation-prone asthma were identified among Korean asthmatics using cluster analysis; both were characterized by impaired lung function, but the age at asthma onset and atopic status were different between the two. Copyright © 2017 The Korean Academy of Asthma, Allergy and Clinical Immunology · The Korean Academy of Pediatric Allergy and Respiratory Disease

Asteroid clusters similar to asteroid pairs

NASA Astrophysics Data System (ADS)

Pravec, Petr; Vokrouhlicky, David; Fatka, Petr; Kusnirák, Peter; Hornoch, Kamil; Galád, Adrián

2016-10-01

We study five small, tight and young clusters of asteroids. They are placed around following largest (primary) bodies: (11842) Kap'bos, (14627) Emilkowalski, (16598) 1992 YC2, (21509) Lucascavin and (39991) 1998 HR37. Each cluster has 2-4 secondaries that are tightly clustered around the primary body, with distance in the 5-dimensional space of mean orbital elements mostly within 10 m/s, and always < 23 m/s. Backward orbital integrations indicate that they formed between 105 and 106 yr ago. In the P1-q space, where P1 is the primary's spin period and q = Σ Mj/M1 is the total secondary-to-primary mass ratio, the clusters lie in the same range as asteroid pairs formed by rotational fission. We have extended the model of a proto-system separation after rotational fission by Pravec et al. (2010) for application to systems with more than one secondary and found a perfect match for the five tight clusters. We find these clusters to be similar to asteroid pairs and we suggest that they are "extended pairs", having 2-4 escaped secondaries rather than just one secondary as in the case of an asteroid pair. We compare them to six young mini-families (1270) Datura, (2384) Schulhof, (3152) Jones, (6825) Irvine, (10321) Rampo and (20674) 1999 VT1. These mini-families have similar ages, but they have a higher number of members and/or they show a significantly larger spread in the mean orbital elements (dmean on an order of tens m/s) than the five tight clusters. In the P1-q space, all but one of the mini-families lie in the same range as asteroid pairs and the tight clusters; the exception is the mini-family of (3152) Jones which appears to be a collisional family. A possibility that the other five mini-families were also formed by rotational fission as we suggest for the tight clusters ("extended asteroid pairs") is being explored.Reference:Pravec, P., et al. Formation of asteroid pairs by rotational fission. Nature 466, 1085-1088.

Geographic atrophy phenotype identification by cluster analysis.

PubMed

Monés, Jordi; Biarnés, Marc

2018-03-01

To identify ocular phenotypes in patients with geographic atrophy secondary to age-related macular degeneration (GA) using a data-driven cluster analysis. This was a retrospective analysis of data from a prospective, natural history study of patients with GA who were followed for ≥6 months. Cluster analysis was used to identify subgroups within the population based on the presence of several phenotypic features: soft drusen, reticular pseudodrusen (RPD), primary foveal atrophy, increased fundus autofluorescence (FAF), greyish FAF appearance and subfoveal choroidal thickness (SFCT). A comparison of features between the subgroups was conducted, and a qualitative description of the new phenotypes was proposed. The atrophy growth rate between phenotypes was then compared. Data were analysed from 77 eyes of 77 patients with GA. Cluster analysis identified three groups: phenotype 1 was characterised by high soft drusen load, foveal atrophy and slow growth; phenotype 3 showed high RPD load, extrafoveal and greyish FAF appearance and thin SFCT; the characteristics of phenotype 2 were midway between phenotypes 1 and 3. Phenotypes differed in all measured features (p≤0.013), with decreases in the presence of soft drusen, foveal atrophy and SFCT seen from phenotypes 1 to 3 and corresponding increases in high RPD load, high FAF and greyish FAF appearance. Atrophy growth rate differed between phenotypes 1, 2 and 3 (0.63, 1.91 and 1.73 mm 2 /year, respectively, p=0.0005). Cluster analysis identified three distinct phenotypes in GA. One of them showed a particularly slow growth pattern. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Obstructive Sleep Apnea: A Cluster Analysis at Time of Diagnosis

PubMed Central

Grillet, Yves; Richard, Philippe; Stach, Bruno; Vivodtzev, Isabelle; Timsit, Jean-Francois; Lévy, Patrick; Tamisier, Renaud; Pépin, Jean-Louis

2016-01-01

Background The classification of obstructive sleep apnea is on the basis of sleep study criteria that may not adequately capture disease heterogeneity. Improved phenotyping may improve prognosis prediction and help select therapeutic strategies. Objectives: This study used cluster analysis to investigate the clinical clusters of obstructive sleep apnea. Methods An ascending hierarchical cluster analysis was performed on baseline symptoms, physical examination, risk factor exposure and co-morbidities from 18,263 participants in the OSFP (French national registry of sleep apnea). The probability for criteria to be associated with a given cluster was assessed using odds ratios, determined by univariate logistic regression. Results: Six clusters were identified, in which patients varied considerably in age, sex, symptoms, obesity, co-morbidities and environmental risk factors. The main significant differences between clusters were minimally symptomatic versus sleepy obstructive sleep apnea patients, lean versus obese, and among obese patients different combinations of co-morbidities and environmental risk factors. Conclusions Our cluster analysis identified six distinct clusters of obstructive sleep apnea. Our findings underscore the high degree of heterogeneity that exists within obstructive sleep apnea patients regarding clinical presentation, risk factors and consequences. This may help in both research and clinical practice for validating new prevention programs, in diagnosis and in decisions regarding therapeutic strategies. PMID:27314230

Modeling of process parameters for enhanced production of coenzyme Q10 from Rhodotorula glutinis.

PubMed

Balakumaran, Palanisamy Athiyaman; Meenakshisundaram, Sankaranarayanan

2015-01-01

Coenzyme Q10 (CoQ10) plays an indispensable role in ATP generation through oxidative phosphorylation and helps in scavenging superoxides generated during electron transfer reactions. It finds extensive applications specifically related to oxidative damage and metabolic dysfunctions. This article reports the use of a statistical approach to optimize the concentration of key variables for the enhanced production of CoQ10 by Rhodotorula glutinis in a lab-scale fermenter. The culture conditions that promote optimum growth and CoQ10 production were optimized and the interaction of significant variables para-hydroxybenzoic acid (PHB, 819.34 mg/L) and soybean oil (7.78% [v/v]) was studied using response surface methodology (RSM). CoQ10 production increased considerably from 10 mg/L (in control) to 39.2 mg/L in batch mode with RSM-optimized precursor concentration. In the fed-batch mode, PHB and soybean oil feeding strategy enhanced CoQ10 production to 78.2 mg/L.

High-power actively Q-switched single-mode 1342 nm Nd:YVO₄ ring laser, injection-locked by a cw single-frequency microchip laser.

PubMed

Koch, Peter; Bartschke, Juergen; L'huillier, Johannes A

2015-11-30

In this paper we report on the realization of a single-mode Q-switched Nd:YVO₄ ring laser at 1342 nm. Unidirectional and single-mode operation of the ring laser is achieved by injection-locking with a continuous wave Nd:YVO₄ microchip laser, emitting a single-frequency power of up to 40 mW. The ring laser provides a single-mode power of 13.9 W at 10 kHz pulse repetition frequency with a pulse duration of 18.2 ns and an excellent beam quality (M² < 1.05). By frequency doubling of the fundamental 1342 nm laser, a power of 8.7 W at 671 nm with a pulse duration of 14.8 ns and a beam propagation factor of M² < 1.1 is obtained. The 671 nm radiation features a long-term spectral width of 75 MHz.

Cluster analysis of the hot subdwarfs in the PG survey

NASA Technical Reports Server (NTRS)

Thejll, Peter; Charache, Darryl; Shipman, Harry L.

1989-01-01

Application of cluster analysis to the hot subdwarfs in the Palomar Green (PG) survey of faint blue high-Galactic-latitude objects is assessed, with emphasis on data noise and the number of clusters to subdivide the data into. The data used in the study are presented, and cluster analysis, using the CLUSTAN program, is applied to it. Distances are calculated using the Euclidean formula, and clustering is done by Ward's method. The results are discussed, and five groups representing natural divisions of the subdwarfs in the PG survey are presented.

Factor Analysis and Counseling Research

ERIC Educational Resources Information Center

Weiss, David J.

1970-01-01

Topics discussed include factor analysis versus cluster analysis, analysis of Q correlation matrices, ipsativity and factor analysis, and tests for the significance of a correlation matrix prior to application of factor analytic techniques. Techniques for factor extraction discussed include principal components, canonical factor analysis, alpha…

A Survey of Popular R Packages for Cluster Analysis

ERIC Educational Resources Information Center

Flynt, Abby; Dean, Nema

2016-01-01

Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring data sets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans, and hclust functions; the mclust library; the poLCA…

Cluster Analysis in Nursing Research: An Introduction, Historical Perspective, and Future Directions.

PubMed

Dunn, Heather; Quinn, Laurie; Corbridge, Susan J; Eldeirawi, Kamal; Kapella, Mary; Collins, Eileen G

2017-05-01

The use of cluster analysis in the nursing literature is limited to the creation of classifications of homogeneous groups and the discovery of new relationships. As such, it is important to provide clarity regarding its use and potential. The purpose of this article is to provide an introduction to distance-based, partitioning-based, and model-based cluster analysis methods commonly utilized in the nursing literature, provide a brief historical overview on the use of cluster analysis in nursing literature, and provide suggestions for future research. An electronic search included three bibliographic databases, PubMed, CINAHL and Web of Science. Key terms were cluster analysis and nursing. The use of cluster analysis in the nursing literature is increasing and expanding. The increased use of cluster analysis in the nursing literature is positioning this statistical method to result in insights that have the potential to change clinical practice.

Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in Autism Spectrum Disorder Brazilian Individuals with and without Epilepsy

PubMed Central

Moreira, Danielle P.; Griesi-Oliveira, Karina; Bossolani-Martins, Ana L.; Lourenço, Naila C. V.; Takahashi, Vanessa N. O.; da Rocha, Kátia M.; Moreira, Eloisa S.; Vadasz, Estevão; Meira, Joanna Goes Castro; Bertola, Debora; Halloran, Eoghan O’; Magalhães, Tiago R.; Fett-Conte, Agnes C.; Passos-Bueno, Maria Rita

2014-01-01

Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy. PMID:25255310

Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in autism spectrum disorder Brazilian individuals with and without epilepsy.

PubMed

Moreira, Danielle P; Griesi-Oliveira, Karina; Bossolani-Martins, Ana L; Lourenço, Naila C V; Takahashi, Vanessa N O; da Rocha, Kátia M; Moreira, Eloisa S; Vadasz, Estevão; Meira, Joanna Goes Castro; Bertola, Debora; O'Halloran, Eoghan; Magalhães, Tiago R; Fett-Conte, Agnes C; Passos-Bueno, Maria Rita

2014-01-01

Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy.

Analysis of ehealth search perspectives among female college students in the health professions using Q methodology.

PubMed

Stellefson, Michael; Hanik, Bruce; Chaney, J Don; Tennant, Bethany

2012-04-27

The current "Millennial Generation" of college students majoring in the health professions has unprecedented access to the Internet. Although some research has been initiated among medical professionals to investigate the cognitive basis for health information searches on the Internet, little is known about Internet search practices among health and medical professional students. To systematically identify health professional college student perspectives of personal eHealth search practices. Q methodology was used to examine subjective perspectives regarding personal eHealth search practices among allied health students majoring in a health education degree program. Thirteen (n = 13) undergraduate students were interviewed about their attitudes and experiences conducting eHealth searches. From the interviews, 36 statements were used in a structured ranking task to identify clusters and determine which specific perceptions of eHealth search practices discriminated students into different groups. Scores on an objective measure of eHealth literacy were used to help categorize participant perspectives. Q-technique factor analysis of the rankings identified 3 clusters of respondents with differing views on eHealth searches that generally coincided with participants' objective eHealth literacy scores. The proficient resourceful students (pattern/structure coefficient range 0.56-0.80) described themselves as using multiple resources to obtain eHealth information, as opposed to simply relying on Internet search engines. The intermediate reluctant students (pattern/structure coefficient range 0.75-0.90) reported engaging only Internet search engines to locate eHealth information, citing undeveloped evaluation skills when considering sources of information located on the Internet. Both groups of advanced students reported not knowing how to use Boolean operators to conduct Internet health searches. The basic hubristic students (pattern/structure coefficient range 0

[Study of the clinical phenotype of symptomatic chronic airways disease by hierarchical cluster analysis and two-step cluster analyses].

PubMed

Ning, P; Guo, Y F; Sun, T Y; Zhang, H S; Chai, D; Li, X M

2016-09-01

To study the distinct clinical phenotype of chronic airway diseases by hierarchical cluster analysis and two-step cluster analysis. A population sample of adult patients in Donghuamen community, Dongcheng district and Qinghe community, Haidian district, Beijing from April 2012 to January 2015, who had wheeze within the last 12 months, underwent detailed investigation, including a clinical questionnaire, pulmonary function tests, total serum IgE levels, blood eosinophil level and a peak flow diary. Nine variables were chosen as evaluating parameters, including pre-salbutamol forced expired volume in one second(FEV1)/forced vital capacity(FVC) ratio, pre-salbutamol FEV1, percentage of post-salbutamol change in FEV1, residual capacity, diffusing capacity of the lung for carbon monoxide/alveolar volume adjusted for haemoglobin level, peak expiratory flow(PEF) variability, serum IgE level, cumulative tobacco cigarette consumption (pack-years) and respiratory symptoms (cough and expectoration). Subjects' different clinical phenotype by hierarchical cluster analysis and two-step cluster analysis was identified. (1) Four clusters were identified by hierarchical cluster analysis. Cluster 1 was chronic bronchitis in smokers with normal pulmonary function. Cluster 2 was chronic bronchitis or mild chronic obstructive pulmonary disease (COPD) patients with mild airflow limitation. Cluster 3 included COPD patients with heavy smoking, poor quality of life and severe airflow limitation. Cluster 4 recognized atopic patients with mild airflow limitation, elevated serum IgE and clinical features of asthma. Significant differences were revealed regarding pre-salbutamol FEV1/FVC%, pre-salbutamol FEV1% pred, post-salbutamol change in FEV1%, maximal mid-expiratory flow curve(MMEF)% pred, carbon monoxide diffusing capacity per liter of alveolar(DLCO)/(VA)% pred, residual volume(RV)% pred, total serum IgE level, smoking history (pack-years), St.George's respiratory questionnaire

Analysis of parasitic oscillations in 42 GHz gyrotron beam tunnel

NASA Astrophysics Data System (ADS)

Kumar, N.; Singh, U.; Singh, T. P.; Sinha, A. K.

2011-02-01

Parasitic oscillation excitation analysis has been carried out for the 42 GHz gyrotron beam tunnel. This article presents a systematic approach for the analysis of parasitic oscillation excitation. The electron trajectory code EGUN has been used for the estimation of the electron beam parameters in the beam tunnel. The electromagnetic simulation code CST-MS has been used for the eigenmode and Q value analysis. The analysis of the parasitic oscillations has been performed for the symmetric TE modes and the first three cavity side copper rings. Four different approaches- the Q value study, the mode maxima-electron beam radius mismatching, the electron cyclotron frequency-mode excitation frequency mismatching and the backward wave interaction analysis- have been used for the parasitic oscillation analysis.

P/Q-type calcium channel modulators

PubMed Central

Nimmrich, V; Gross, G

2012-01-01

P/Q-type calcium channels are high-voltage-gated calcium channels contributing to vesicle release at synaptic terminals. A number of neurological diseases have been attributed to malfunctioning of P/Q channels, including ataxia, migraine and Alzheimer's disease. To date, only two specific P/Q-type blockers are known: both are peptides deriving from the spider venom of Agelenopsis aperta, ω-agatoxins. Other peptidic calcium channel blockers with activity at P/Q channels are available, albeit with less selectivity. A number of low molecular weight compounds modulate P/Q-type currents with different characteristics, and some exhibit a peculiar bidirectional pattern of modulation. Interestingly, there are a number of therapeutics in clinical use, which also show P/Q channel activity. Because selectivity as well as the exact mode of action is different between all P/Q-type channel modulators, the interpretation of clinical and experimental data is complicated and needs a comprehensive understanding of their target profile. The situation is further complicated by the fact that information on potency varies vastly in the literature, which may be the result of different experimental systems, conditions or the splice variants of the P/Q channel. This review attempts to provide a comprehensive overview of the compounds available that affect the P/Q-type channel and should help with the interpretation of results of in vitro experiments and animal models. It also aims to explain some clinical observations by implementing current knowledge about P/Q channel modulation of therapeutically used non-selective drugs. Chances and challenges of the development of P/Q channel-selective molecules are discussed. PMID:22670568

Correlation of vibrational modes and DX-like centers in GaN : O

NASA Astrophysics Data System (ADS)

Wetzel, C.; , J. W. Ager, III; Topf, M.; Meyer, B. K.; Amano, H.; Akasaki, I.

1999-12-01

Vibrational modes in O-doped GaN have been observed at 544 cm-1 in Raman spectroscopy. Under perturbation of large hydrostatic pressure the mode appears as a set of three different lines Q1⋯3 whose relative intensities change by pressure. A switching between the modes occurs near 10 and 20 GPa and is found to correlate with the electron capture process to the DX-like state of O. We employ a simple oscillator model to predict the vibrational frequencies of ON. A localization energy of 23 cm-1 with respect to the optical phonon band is predicted. This is in reasonable agreement with the observed vibrational frequencies. Therefore, we assign the Q modes to the local vibration of O on N site in GaN. Modes Q1⋯3 are tentatively assigned to three different charge states of the O defect center.

Non-linear clustering in the cold plus hot dark matter model

NASA Astrophysics Data System (ADS)

Bonometto, Silvio A.; Borgani, Stefano; Ghigna, Sebastiano; Klypin, Anatoly; Primack, Joel R.

1995-03-01

The main aim of this work is to find out if hierarchical scaling, observed in galaxy clustering, can be dynamically explained by studying N-body simulations. Previous analyses of dark matter (DM) particle distributions indicated heavy distortions with respect to the hierarchical pattern. Here, we shall describe how such distortions are to be interpreted and why they can be fully reconciled with the observed galaxy clustering. This aim is achieved by using high-resolution (512^3 grid-points) particle-mesh (PM) N-body simulations to follow the development of non-linear clustering in a Omega=1 universe, dominated either by cold dark matter (CDM) or by a mixture of cold+hot dark matter (CHDM) with Omega_cold=0.6, and Omega_hot=0.3 and Omega_baryon=0.1 a simulation box of side 100 Mpc (h=0.5) is used. We analyse two CHDM realizations with biasing factor b=1.5 (COBE normalization), starting from different initial random numbers, and compare them with CDM simulations with b=1 (COBE-compatible) and b=1.5. We evaluate high-order correlation functions and the void probability function (VPF). Correlation functions are obtained from both counts in cells and counts of neighbours. The analysis is carried out for DM particles and for galaxies identified as massive haloes of the evolved density field. We confirm that clustering of DM particles systematically exhibits deviations from hierarchical scaling, although the deviation increases somewhat in redshift space. Deviations from the hierarchical scaling of DM particles are found to be related to the spectrum shape, in a way that indicates that such distortions arise from finite sampling effects. We identify galaxy positions in the simulations and show that, quite differently from the DM particle background, galaxies follow hierarchical scaling (S_q=xi_q/& xgr^q-1_2=consta nt) far more closely, with reduced skewness and kurtosis coefficients S_3~2.5 and S_4~7.5, in general agreement with observational results. Unlike DM, the

Ordered-subsets linkage analysis detects novel Alzheimer disease loci on chromosomes 2q34 and 15q22.

PubMed

Scott, William K; Hauser, Elizabeth R; Schmechel, Donald E; Welsh-Bohmer, Kathleen A; Small, Gary W; Roses, Allen D; Saunders, Ann M; Gilbert, John R; Vance, Jeffery M; Haines, Jonathan L; Pericak-Vance, Margaret A

2003-11-01

Alzheimer disease (AD) is a complex disorder characterized by a wide range, within and between families, of ages at onset of symptoms. Consideration of age at onset as a covariate in genetic-linkage studies may reduce genetic heterogeneity and increase statistical power. Ordered-subsets analysis includes continuous covariates in linkage analysis by rank ordering families by a covariate and summing LOD scores to find a subset giving a significantly increased LOD score relative to the overall sample. We have analyzed data from 336 markers in 437 multiplex (>/=2 sampled individuals with AD) families included in a recent genomic screen for AD loci. To identify genetic heterogeneity by age at onset, families were ordered by increasing and decreasing mean and minimum ages at onset. Chromosomewide significance of increases in the LOD score in subsets relative to the overall sample was assessed by permutation. A statistically significant increase in the nonparametric multipoint LOD score was observed on chromosome 2q34, with a peak LOD score of 3.2 at D2S2944 (P=.008) in 31 families with a minimum age at onset between 50 and 60 years. The LOD score in the chromosome 9p region previously linked to AD increased to 4.6 at D9S741 (P=.01) in 334 families with minimum age at onset between 60 and 75 years. LOD scores were also significantly increased on chromosome 15q22: a peak LOD score of 2.8 (P=.0004) was detected at D15S1507 (60 cM) in 38 families with minimum age at onset >/=79 years, and a peak LOD score of 3.1 (P=.0006) was obtained at D15S153 (62 cM) in 43 families with mean age at onset >80 years. Thirty-one families were contained in both 15q22 subsets, indicating that these results are likely detecting the same locus. There is little overlap in these subsets, underscoring the utility of age at onset as a marker of genetic heterogeneity. These results indicate that linkage to chromosome 9p is strongest in late-onset AD and that regions on chromosome 2q34 and 15q22 are

Differences in Pedaling Technique in Cycling: A Cluster Analysis.

PubMed

Lanferdini, Fábio J; Bini, Rodrigo R; Figueiredo, Pedro; Diefenthaeler, Fernando; Mota, Carlos B; Arndt, Anton; Vaz, Marco A

2016-10-01

To employ cluster analysis to assess if cyclists would opt for different strategies in terms of neuromuscular patterns when pedaling at the power output of their second ventilatory threshold (PO VT2 ) compared with cycling at their maximal power output (PO MAX ). Twenty athletes performed an incremental cycling test to determine their power output (PO MAX and PO VT2 ; first session), and pedal forces, muscle activation, muscle-tendon unit length, and vastus lateralis architecture (fascicle length, pennation angle, and muscle thickness) were recorded (second session) in PO MAX and PO VT2 . Athletes were assigned to 2 clusters based on the behavior of outcome variables at PO VT2 and PO MAX using cluster analysis. Clusters 1 (n = 14) and 2 (n = 6) showed similar power output and oxygen uptake. Cluster 1 presented larger increases in pedal force and knee power than cluster 2, without differences for the index of effectiveness. Cluster 1 presented less variation in knee angle, muscle-tendon unit length, pennation angle, and tendon length than cluster 2. However, clusters 1 and 2 showed similar muscle thickness, fascicle length, and muscle activation. When cycling at PO VT2 vs PO MAX , cyclists could opt for keeping a constant knee power and pedal-force production, associated with an increase in tendon excursion and a constant fascicle length. Increases in power output lead to greater variations in knee angle, muscle-tendon unit length, tendon length, and pennation angle of vastus lateralis for a similar knee-extensor activation and smaller pedal-force changes in cyclists from cluster 2 than in cluster 1.

Heterogeneous Tensor Decomposition for Clustering via Manifold Optimization.

PubMed

Sun, Yanfeng; Gao, Junbin; Hong, Xia; Mishra, Bamdev; Yin, Baocai

2016-03-01

Tensor clustering is an important tool that exploits intrinsically rich structures in real-world multiarray or Tensor datasets. Often in dealing with those datasets, standard practice is to use subspace clustering that is based on vectorizing multiarray data. However, vectorization of tensorial data does not exploit complete structure information. In this paper, we propose a subspace clustering algorithm without adopting any vectorization process. Our approach is based on a novel heterogeneous Tucker decomposition model taking into account cluster membership information. We propose a new clustering algorithm that alternates between different modes of the proposed heterogeneous tensor model. All but the last mode have closed-form updates. Updating the last mode reduces to optimizing over the multinomial manifold for which we investigate second order Riemannian geometry and propose a trust-region algorithm. Numerical experiments show that our proposed algorithm compete effectively with state-of-the-art clustering algorithms that are based on tensor factorization.

Network Analysis Tools: from biological networks to clusters and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

Performance analysis of clustering techniques over microarray data: A case study

NASA Astrophysics Data System (ADS)

Dash, Rasmita; Misra, Bijan Bihari

2018-03-01

Handling big data is one of the major issues in the field of statistical data analysis. In such investigation cluster analysis plays a vital role to deal with the large scale data. There are many clustering techniques with different cluster analysis approach. But which approach suits a particular dataset is difficult to predict. To deal with this problem a grading approach is introduced over many clustering techniques to identify a stable technique. But the grading approach depends on the characteristic of dataset as well as on the validity indices. So a two stage grading approach is implemented. In this study the grading approach is implemented over five clustering techniques like hybrid swarm based clustering (HSC), k-means, partitioning around medoids (PAM), vector quantization (VQ) and agglomerative nesting (AGNES). The experimentation is conducted over five microarray datasets with seven validity indices. The finding of grading approach that a cluster technique is significant is also established by Nemenyi post-hoc hypothetical test.

Seismic imaging of Q structures by a trans-dimensional coda-wave analysis

NASA Astrophysics Data System (ADS)

Takahashi, Tsutomu

2017-04-01

Wave scattering and intrinsic attenuation are important processes to describe incoherent and complex wave trains of high frequency seismic wave (>1Hz). The multiple lapse time window analysis (MLTWA) has been used to estimate scattering and intrinsic Q values by assuming constant Q in a study area (e.g., Hoshiba 1993). This study generalizes this MLTWA to estimate lateral variations of Q values under the Bayesian framework in dimension variable space. Study area is partitioned into small areas by means of the Voronoi tessellation. Scattering and intrinsic Q in each small area are constant. We define a misfit function for spatiotemporal variations of wave energy as with the original MLTWA, and maximize the posterior probability with changing not only Q values but the number and spatial layout of the Voronoi cells. This maximization is conducted by means of the reversible jump Markov chain Monte Carlo (rjMCMC) (Green 1995) since the number of unknown parameters (i.e., dimension of posterior probability) is variable. After a convergence to the maximum posterior, we estimate Q structures from the ensemble averages of MCMC samples around the maximum posterior probability. Synthetic tests showed stable reconstructions of input structures with reasonable error distributions. We applied this method for seismic waveform data recorded by ocean bottom seismograms at the outer-rise area off Tohoku, and estimated Q values at 4-8Hz, 8-16Hz and 16-32Hz. Intrinsic Q are nearly constant at all frequency bands, and scattering Q shows two distinct strong scattering regions at petit spot area and high seismicity area. These strong scattering are probably related to magma inclusions and fractured structure, respectively. Difference between these two areas becomes clear at high frequencies. It means that scale dependences of inhomogeneities or smaller scale inhomogeneity is important to discuss medium property and origins of structural variations. While the generalized MLTWA is based on

OMERACT-based fibromyalgia symptom subgroups: an exploratory cluster analysis.

PubMed

Vincent, Ann; Hoskin, Tanya L; Whipple, Mary O; Clauw, Daniel J; Barton, Debra L; Benzo, Roberto P; Williams, David A

2014-10-16

The aim of this study was to identify subsets of patients with fibromyalgia with similar symptom profiles using the Outcome Measures in Rheumatology (OMERACT) core symptom domains. Female patients with a diagnosis of fibromyalgia and currently meeting fibromyalgia research survey criteria completed the Brief Pain Inventory, the 30-item Profile of Mood States, the Medical Outcomes Sleep Scale, the Multidimensional Fatigue Inventory, the Multiple Ability Self-Report Questionnaire, the Fibromyalgia Impact Questionnaire-Revised (FIQ-R) and the Short Form-36 between 1 June 2011 and 31 October 2011. Hierarchical agglomerative clustering was used to identify subgroups of patients with similar symptom profiles. To validate the results from this sample, hierarchical agglomerative clustering was repeated in an external sample of female patients with fibromyalgia with similar inclusion criteria. A total of 581 females with a mean age of 55.1 (range, 20.1 to 90.2) years were included. A four-cluster solution best fit the data, and each clustering variable differed significantly (P <0.0001) among the four clusters. The four clusters divided the sample into severity levels: Cluster 1 reflects the lowest average levels across all symptoms, and cluster 4 reflects the highest average levels. Clusters 2 and 3 capture moderate symptoms levels. Clusters 2 and 3 differed mainly in profiles of anxiety and depression, with Cluster 2 having lower levels of depression and anxiety than Cluster 3, despite higher levels of pain. The results of the cluster analysis of the external sample (n = 478) looked very similar to those found in the original cluster analysis, except for a slight difference in sleep problems. This was despite having patients in the validation sample who were significantly younger (P <0.0001) and had more severe symptoms (higher FIQ-R total scores (P = 0.0004)). In our study, we incorporated core OMERACT symptom domains, which allowed for clustering based on a

Cluster analysis of Southeastern U.S. climate stations

NASA Astrophysics Data System (ADS)

Stooksbury, D. E.; Michaels, P. J.

1991-09-01

A two-step cluster analysis of 449 Southeastern climate stations is used to objectively determine general climate clusters (groups of climate stations) for eight southeastern states. The purpose is objectively to define regions of climatic homogeneity that should perform more robustly in subsequent climatic impact models. This type of analysis has been successfully used in many related climate research problems including the determination of corn/climate districts in Iowa (Ortiz-Valdez, 1985) and the classification of synoptic climate types (Davis, 1988). These general climate clusters may be more appropriate for climate research than the standard climate divisions (CD) groupings of climate stations, which are modifications of the agro-economic United States Department of Agriculture crop reporting districts. Unlike the CD's, these objectively determined climate clusters are not restricted by state borders and thus have reduced multicollinearity which makes them more appropriate for the study of the impact of climate and climatic change.

Modest validity and fair reproducibility of dietary patterns derived by cluster analysis.

PubMed

Funtikova, Anna N; Benítez-Arciniega, Alejandra A; Fitó, Montserrat; Schröder, Helmut

2015-03-01

Cluster analysis is widely used to analyze dietary patterns. We aimed to analyze the validity and reproducibility of the dietary patterns defined by cluster analysis derived from a food frequency questionnaire (FFQ). We hypothesized that the dietary patterns derived by cluster analysis have fair to modest reproducibility and validity. Dietary data were collected from 107 individuals from population-based survey, by an FFQ at baseline (FFQ1) and after 1 year (FFQ2), and by twelve 24-hour dietary recalls (24-HDR). Repeatability and validity were measured by comparing clusters obtained by the FFQ1 and FFQ2 and by the FFQ2 and 24-HDR (reference method), respectively. Cluster analysis identified a "fruits & vegetables" and a "meat" pattern in each dietary data source. Cluster membership was concordant for 66.7% of participants in FFQ1 and FFQ2 (reproducibility), and for 67.0% in FFQ2 and 24-HDR (validity). Spearman correlation analysis showed reasonable reproducibility, especially in the "fruits & vegetables" pattern, and lower validity also especially in the "fruits & vegetables" pattern. κ statistic revealed a fair validity and reproducibility of clusters. Our findings indicate a reasonable reproducibility and fair to modest validity of dietary patterns derived by cluster analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The

The Psychology of Yoga Practitioners: A Cluster Analysis.

PubMed

Genovese, Jeremy E C; Fondran, Kristine M

2017-11-01

Yoga practitioners (N = 261) completed the revised Expression of Spirituality Inventory (ESI) and the Multidimensional Body-Self Relations Questionnaire. Cluster analysis revealed three clusters: Cluster A scored high on all four spiritual constructs. They had high positive evaluations of their appearance, but a lower orientation towards their appearance. They tended to have a high evaluation of their fitness and health, and higher body satisfaction. Cluster B showed lower scores on the spiritual constructs. Like Cluster A, members of Cluster B tended to show high positive evaluations of appearance and fitness. They also had higher body satisfaction. Members of Cluster B had a higher fitness orientation and a higher appearance orientation than members of Cluster A. Members of Cluster C had low scores for all spiritual constructs. They had a low evaluation of, and unhappiness with, their appearance. They were unhappy with the size and appearance of their bodies. They tended to see themselves as overweight. There was a significant difference in years of practice between the three groups (Kruskall -Wallis, p = .0041). Members of Cluster A have the most years of yoga experience and members of Cluster B have more yoga experience than members of Cluster C. These results suggest the possible existence of a developmental trajectory for yoga practitioners. Such a developmental sequence may have important implications for yoga practice and instruction.

The Psychology of Yoga Practitioners: A Cluster Analysis.

PubMed

Genovese, Jeremy E C; Fondran, Kristine M

2017-03-30

Yoga practitioners (N = 261) completed the revised Expression of Spirituality Inventory (ESI) and the Multidimensional Body-Self Relations Questionnaire. Cluster analysis revealed three clusters: Cluster A scored high on all four spiritual constructs. They had high positive evaluations of their appearance, but a lower orientation towards their appearance. They tended to have a high evaluation of their fitness and health, and higher body satisfaction. Cluster B showed lower scores on the spiritual constructs. Like Cluster A, members of Cluster B tended to show high positive evaluations of appearance and fitness. They also had higher body satisfaction. Members of Cluster B had a higher fitness orientation and a higher appearance orientation than members of Cluster A. Members of Cluster C had low scores for all spiritual constructs. They had a low evaluation of, and unhappiness with, their appearance. They were unhappy with the size and appearance of their bodies. They tended to see themselves as overweight. There was a significant difference in years of practice between the three groups (Kruskall-Wallis, p = .0041). Members of Cluster A have the most years of yoga experience and members of Cluster B have more yoga experience than members of Cluster C. These results suggest the possible existence of a developmental trajectory for yoga practitioners. Such a developmental sequence may have important implications for yoga practice and instruction.

A streamlined failure mode and effects analysis

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

Ford, Eric C., E-mail: eford@uw.edu; Smith, Koren; Terezakis, Stephanie

Purpose: Explore the feasibility and impact of a streamlined failure mode and effects analysis (FMEA) using a structured process that is designed to minimize staff effort. Methods: FMEA for the external beam process was conducted at an affiliate radiation oncology center that treats approximately 60 patients per day. A structured FMEA process was developed which included clearly defined roles and goals for each phase. A core group of seven people was identified and a facilitator was chosen to lead the effort. Failure modes were identified and scored according to the FMEA formalism. A risk priority number,RPN, was calculated and usedmore » to rank failure modes. Failure modes with RPN > 150 received safety improvement interventions. Staff effort was carefully tracked throughout the project. Results: Fifty-two failure modes were identified, 22 collected during meetings, and 30 from take-home worksheets. The four top-ranked failure modes were: delay in film check, missing pacemaker protocol/consent, critical structures not contoured, and pregnant patient simulated without the team's knowledge of the pregnancy. These four failure modes hadRPN > 150 and received safety interventions. The FMEA was completed in one month in four 1-h meetings. A total of 55 staff hours were required and, additionally, 20 h by the facilitator. Conclusions: Streamlined FMEA provides a means of accomplishing a relatively large-scale analysis with modest effort. One potential value of FMEA is that it potentially provides a means of measuring the impact of quality improvement efforts through a reduction in risk scores. Future study of this possibility is needed.« less

A streamlined failure mode and effects analysis.

PubMed

Ford, Eric C; Smith, Koren; Terezakis, Stephanie; Croog, Victoria; Gollamudi, Smitha; Gage, Irene; Keck, Jordie; DeWeese, Theodore; Sibley, Greg

2014-06-01

Explore the feasibility and impact of a streamlined failure mode and effects analysis (FMEA) using a structured process that is designed to minimize staff effort. FMEA for the external beam process was conducted at an affiliate radiation oncology center that treats approximately 60 patients per day. A structured FMEA process was developed which included clearly defined roles and goals for each phase. A core group of seven people was identified and a facilitator was chosen to lead the effort. Failure modes were identified and scored according to the FMEA formalism. A risk priority number,RPN, was calculated and used to rank failure modes. Failure modes with RPN > 150 received safety improvement interventions. Staff effort was carefully tracked throughout the project. Fifty-two failure modes were identified, 22 collected during meetings, and 30 from take-home worksheets. The four top-ranked failure modes were: delay in film check, missing pacemaker protocol/consent, critical structures not contoured, and pregnant patient simulated without the team's knowledge of the pregnancy. These four failure modes had RPN > 150 and received safety interventions. The FMEA was completed in one month in four 1-h meetings. A total of 55 staff hours were required and, additionally, 20 h by the facilitator. Streamlined FMEA provides a means of accomplishing a relatively large-scale analysis with modest effort. One potential value of FMEA is that it potentially provides a means of measuring the impact of quality improvement efforts through a reduction in risk scores. Future study of this possibility is needed.

Graph analysis of cell clusters forming vascular networks

NASA Astrophysics Data System (ADS)

Alves, A. P.; Mesquita, O. N.; Gómez-Gardeñes, J.; Agero, U.

2018-03-01

This manuscript describes the experimental observation of vasculogenesis in chick embryos by means of network analysis. The formation of the vascular network was observed in the area opaca of embryos from 40 to 55 h of development. In the area opaca endothelial cell clusters self-organize as a primitive and approximately regular network of capillaries. The process was observed by bright-field microscopy in control embryos and in embryos treated with Bevacizumab (Avastin), an antibody that inhibits the signalling of the vascular endothelial growth factor (VEGF). The sequence of images of the vascular growth were thresholded, and used to quantify the forming network in control and Avastin-treated embryos. This characterization is made by measuring vessels density, number of cell clusters and the largest cluster density. From the original images, the topology of the vascular network was extracted and characterized by means of the usual network metrics such as: the degree distribution, average clustering coefficient, average short path length and assortativity, among others. This analysis allows to monitor how the largest connected cluster of the vascular network evolves in time and provides with quantitative evidence of the disruptive effects that Avastin has on the tree structure of vascular networks.

Cluster analysis and prediction of treatment outcomes for chronic rhinosinusitis.

PubMed

Soler, Zachary M; Hyer, J Madison; Rudmik, Luke; Ramakrishnan, Viswanathan; Smith, Timothy L; Schlosser, Rodney J

2016-04-01

Current clinical classifications of chronic rhinosinusitis (CRS) have weak prognostic utility regarding treatment outcomes. Simplified discriminant analysis based on unsupervised clustering has identified novel phenotypic subgroups of CRS, but prognostic utility is unknown. We sought to determine whether discriminant analysis allows prognostication in patients choosing surgery versus continued medical management. A multi-institutional prospective study of patients with CRS in whom initial medical therapy failed who then self-selected continued medical management or surgical treatment was used to separate patients into 5 clusters based on a previously described discriminant analysis using total Sino-Nasal Outcome Test-22 (SNOT-22) score, age, and missed productivity. Patients completed the SNOT-22 at baseline and for 18 months of follow-up. Baseline demographic and objective measures included olfactory testing, computed tomography, and endoscopy scoring. SNOT-22 outcomes for surgical versus continued medical treatment were compared across clusters. Data were available on 690 patients. Baseline differences in demographics, comorbidities, objective disease measures, and patient-reported outcomes were similar to previous clustering reports. Three of 5 clusters identified by means of discriminant analysis had improved SNOT-22 outcomes with surgical intervention when compared with continued medical management (surgery was a mean of 21.2 points better across these 3 clusters at 6 months, P < .05). These differences were sustained at 18 months of follow-up. Two of 5 clusters had similar outcomes when comparing surgery with continued medical management. A simplified discriminant analysis based on 3 common clinical variables is able to cluster patients and provide prognostic information regarding surgical treatment versus continued medical management in patients with CRS. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All

Q3DG: A computer program for strain-energy-release rates for delamination growth in composite laminates

NASA Technical Reports Server (NTRS)

Raju, I. S.

1986-01-01

The Q3DG is a computer program developed to perform a quasi-three-dimensional stress analysis for composite laminates which may contain delaminations. The laminates may be subjected to mechanical, thermal, and hygroscopic loads. The program uses the finite element method and models the laminates with eight-noded parabolic isoparametric elements. The program computes the strain-energy-release components and the total strain-energy release in all three modes for delamination growth. A rectangular mesh and data file generator, DATGEN, is included. The DATGEN program can be executed interactively and is user friendly. The documentation includes sections dealing with the Q3D analysis theory, derivation of element stiffness matrices and consistent load vectors for the parabolic element. Several sample problems with the input for Q3DG and output from the program are included. The capabilities of the DATGEN program are illustrated with examples of interactive sessions. A microfiche of all the examples is included. The Q3DG and DATGEN programs have been implemented on CYBER 170 class computers. Q3DG and DATGEN were developed at the Langley Research Center during the early eighties and documented in 1984 to 1985.

On the tunability of quality-factor for optical Tamm plasmon modes

NASA Astrophysics Data System (ADS)

Kumar, Samir; Das, Ritwick

2017-09-01

We present a comprehensive investigation to ascertain the impact of gold and silver films on modifying the quality-factor (Q-factor) of optical Tamm-plasmon (OTP) resonance in a metal-distributed Bragg reflector (M-DBR) geometry. Here, OTP mode is excited using direct incidence of white-light-source at normal incidence as well as oblique incidence on M-DBR geometry. The lifetime of OTP in gold and silver deposited films on DBR mirror was determined from OTP resonance linewidth. The lifetime and the Q-factor of OTP modes are found to depend on DBR bilayers, metal film thickness as well as on different plasmon active metals. This finding would facilitate tuning the Q-factor and consequently, the lifetime of OTP modes for various applications in all-optical switches and modulators. In addition, we discuss the spectral characteristics of OTP modes excited using normal and oblique incident of source.

Experimental Analysis of Dampened Breathing Mode Oscillation on Hall Thruster Performance

DTIC Science & Technology

2013-03-01

38 4.5 Analysis of Discharge RMS Effect on Breathing Mode Amplitude...20 xii EXPERIMENTAL ANALYSIS OF DAMPENED BREATHING MODE OSCILLATION ON HALL EFFECT THRUSTER...the large error in the data presented above prevents many conclusions from being drawn. 4.5 Analysis of Discharge RMS Effect on Breathing Mode

Plasmon transmutation: inducing new modes in nanoclusters by adding dielectric nanoparticles.

PubMed

Wen, Fangfang; Ye, Jian; Liu, Na; Van Dorpe, Pol; Nordlander, Peter; Halas, Naomi J

2012-09-12

Planar clusters of coupled plasmonic nanoparticles support nanoscale electromagnetic "hot spots" and coherent effects, such as Fano resonances, with unique near and far field signatures, currently of prime interest for sensing applications. Here we show that plasmonic cluster properties can be substantially modified by the addition of individual, discrete dielectric nanoparticles at specific locations on the cluster, introducing new plasmon modes, or transmuting existing plasmon modes to new ones, in the resulting metallodielectric nanocomplex. Depositing a single carbon nanoparticle in the junction between a pair of adjacent nanodisks induces a metal-dielectric-metal quadrupolar plasmon mode. In a ten-membered cluster, placement of several carbon nanoparticles in junctions between multiple adjacent nanoparticles introduces a collective magnetic plasmon mode into the Fano dip, giving rise to an additional subradiant mode in the metallodielectric nanocluster response. These examples illustrate that adding dielectric nanoparticles to metallic nanoclusters expands the number and types of plasmon modes supported by these new mixed-media nanoscale assemblies.

Systematization of actinides using cluster analysis

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

Kopyrin, A.A.; Terent`eva, T.N.; Khramov, N.N.

1994-11-01

A representation of the actinides in multidimensional property space is proposed for systematization of these elements using cluster analysis. Literature data for their atomic properties are used. Owing to the wide variation of published ionization potentials, medians are used to estimate them. Vertical dendograms are used for classification on the basis of distances between the actinides in atomic-property space. The properties of actinium and lawrencium are furthest removed from the main group. Thorium and mendelevium exhibit individualized properties. A cluster based on the einsteinium-fermium pair is joined by californium.

Linkage analysis of the Fanconi anemia gene FACC with chromosome 9q markers

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

Auerbach, A.D.; Shin, H.T.; Kaporis, A.G.

1994-09-01

Fanconi anemia (FA) is a genetically heterogeneous syndrome, with at least four different complementation groups as determined by cell fusion studies. The gene for complementation group C, FACC, has been cloned and mapped to chromosome 9q22.3 by in situ hybridization, while linkage analysis has supported the placement of another gene on chromosome 20q. We have analyzed five microsatellite markers and one RFLP on chromosome 9q in a panel of FA families from the International Fanconi Anemia Registry (IFAR) in order to place FACC on the genetic map. Polymorphisms were typed in 308 individuals from 51 families. FACC is tightly linkedmore » to both D9S151 [{Theta}{sub max}=0.025, Z{sub max}=7.75] and to D9S196 [{Theta}{sub max}=0.041, Z{sub max}=7.89]; multipoint analysis is in progress. We are currently screening a YAC clone that contains the entire FACC gene for additional microsatellite markers suitable for haplotype analysis of FA families.« less

[Rapid analysis on phenolic compounds in Rheum palmatum based on UPLC-Q-TOF/MSE combined with diagnostic ions filter].

PubMed

Wang, Qing; Lu, Zhi-Wei; Liu, Yue-Hong; Wang, Ming-Ling; Fu, Shuang; Zhang, Qing-Qing; Zhao, Hui-Zhen; Zhang, Zhi-Xin; Xie, Zi-Ye; Huang, Zheng-Hai; Yu, Hong-Hong; Zhou, Wen-Juan; Gao, Xiao-Yan

2017-05-01

Diagnostic ions filter method was used to rapidly detect and identify the phenolic compounds in Rheum palmatum based on ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MSE). The representative authentic standards of phenolic compounds, including gallic acid, (+)-catechin, (－)-epicatechin, (－)-epicatechin-3-O-gallate and procyanidin B2, were subjected to analysis by UPLC-Q-TOF/MSE system with negative ion mode. Fragmentation patterns of each standard were summarized based on assigned fragment ions. The prominent product ions were selected as diagnostic ions. Subsequently, diagnostic ions filter was employed to rapidly recognize analogous skeletons. Combined with retention time, accurate mass, characteristic fragments and previous literature data, the structures of the filtered compounds were identified or tentatively characterized. A total 63 phenolic compounds (36 phenolic acid derivatives, 8 flavonoid derivatives and 19 tennis derivatives) in R. palmatum were identified, including 6 potential new compounds. The method of diagnostic ions filter could rapidly detect and identify phenolic compounds in R. palmatum This study provides a method for rapid detection of phenolic compounds in R. palmatum and is expected to complete the material basis of rhubarb. Copyright© by the Chinese Pharmaceutical Association.

A Multivariate Analysis of Galaxy Cluster Properties

NASA Astrophysics Data System (ADS)

Ogle, P. M.; Djorgovski, S.

1993-05-01

We have assembled from the literature a data base on on 394 clusters of galaxies, with up to 16 parameters per cluster. They include optical and x-ray luminosities, x-ray temperatures, galaxy velocity dispersions, central galaxy and particle densities, optical and x-ray core radii and ellipticities, etc. In addition, derived quantities, such as the mass-to-light ratios and x-ray gas masses are included. Doubtful measurements have been identified, and deleted from the data base. Our goal is to explore the correlations between these parameters, and interpret them in the framework of our understanding of evolution of clusters and large-scale structure, such as the Gott-Rees scaling hierarchy. Among the simple, monovariate correlations we found, the most significant include those between the optical and x-ray luminosities, x-ray temperatures, cluster velocity dispersions, and central galaxy densities, in various mutual combinations. While some of these correlations have been discussed previously in the literature, generally smaller samples of objects have been used. We will also present the results of a multivariate statistical analysis of the data, including a principal component analysis (PCA). Such an approach has not been used previously for studies of cluster properties, even though it is much more powerful and complete than the simple monovariate techniques which are commonly employed. The observed correlations may lead to powerful constraints for theoretical models of formation and evolution of galaxy clusters. P.M.O. was supported by a Caltech graduate fellowship. S.D. acknowledges a partial support from the NASA contract NAS5-31348 and the NSF PYI award AST-9157412.

Logistics Enterprise Evaluation Model Based On Fuzzy Clustering Analysis

NASA Astrophysics Data System (ADS)

Fu, Pei-hua; Yin, Hong-bo

In this thesis, we introduced an evaluation model based on fuzzy cluster algorithm of logistics enterprises. First of all,we present the evaluation index system which contains basic information, management level, technical strength, transport capacity,informatization level, market competition and customer service. We decided the index weight according to the grades, and evaluated integrate ability of the logistics enterprises using fuzzy cluster analysis method. In this thesis, we introduced the system evaluation module and cluster analysis module in detail and described how we achieved these two modules. At last, we gave the result of the system.

Topic modeling for cluster analysis of large biological and medical datasets

PubMed Central

2014-01-01

Background The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. Results In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Conclusion Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than

Topic modeling for cluster analysis of large biological and medical datasets.

PubMed

Zhao, Weizhong; Zou, Wen; Chen, James J

2014-01-01

The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than traditional methods, suggesting

A high-quality factor of 267 000 micromechanical silicon resonator utilizing TED-free torsional vibration mode

NASA Astrophysics Data System (ADS)

Nakamura, K.; Naito, Y.; Onishi, K.; Kawakatsu, H.

2012-12-01

In industrial applications of a micromechanical silicon resonator as a physical sensor, a high-quality factor Q and a low-temperature coefficient of Q (TCQ) are required for high sensitivity in a wide temperature range. Although the newly developed thin film encapsulation technique enables a beam to operate with low viscous damping in a vacuum cavity, the Q of a flexural vibration mode is limited by thermo-elastic damping (TED). We proposed a torsional beam resonator which features both a high Q and a low TCQ because theoretically the torsional vibration mode does not suffer from TED. From experiments, Q of 267 000 and TCQ of 1.4 for the 20 MHz torsional vibration mode were observed which were superior to those of the flexural mode. The pressure of the residual gas in the cavity of only 20 pl volume, which is one of the energy loss factors limiting the Q, was successfully estimated to be 1-14 Pa. Finally, the possibilities of improving the Q and the difference of the measured TCQ from a theoretical value were discussed.

Optimization study for metabolomics analysis of human sweat by liquid chromatography-tandem mass spectrometry in high resolution mode.

PubMed

Calderón-Santiago, M; Priego-Capote, F; Jurado-Gámez, B; Luque de Castro, M D

2014-03-14

Sweat has recently gained popularity as a potential tool for diagnostics and biomarker monitoring as it is a non-invasive biofluid the composition of which could be modified by certain pathologies, as is the case with cystic fibrosis, which increases chloride levels in sweat. The aim of the present study was to develop an analytical method for analysis of human sweat by liquid chromatography-mass spectrometry (LC-Q-TOF MS/MS) in high resolution mode. Thus, different sample preparation strategies and different chromatographic modes (HILIC and C18 reverse modes) were compared to check their effect on the profile of sweat metabolites. Forty-one compounds were identified by the MS/MS information obtained with a mass tolerance window below 4 ppm. Amino acids, dicarboxylic acids and other interesting metabolites such as inosine, choline, uric acid and tyramine were identified. Among the tested protocols, direct analysis after dilution was a suited option to obtain a representative snapshot of sweat metabolome. In addition, sample clean up by C18 SpinColumn SPE cartridges improved the sensitivity of most identified compounds and reduced the number of interferents. As most of the identified metabolites are involved in key biochemical pathways, this study opens new possibilities to the use of sweat as a source of metabolite biomarkers of specific disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiscale visual quality assessment for cluster analysis with self-organizing maps

NASA Astrophysics Data System (ADS)

Bernard, Jürgen; von Landesberger, Tatiana; Bremm, Sebastian; Schreck, Tobias

2011-01-01

Cluster analysis is an important data mining technique for analyzing large amounts of data, reducing many objects to a limited number of clusters. Cluster visualization techniques aim at supporting the user in better understanding the characteristics and relationships among the found clusters. While promising approaches to visual cluster analysis already exist, these usually fall short of incorporating the quality of the obtained clustering results. However, due to the nature of the clustering process, quality plays an important aspect, as for most practical data sets, typically many different clusterings are possible. Being aware of clustering quality is important to judge the expressiveness of a given cluster visualization, or to adjust the clustering process with refined parameters, among others. In this work, we present an encompassing suite of visual tools for quality assessment of an important visual cluster algorithm, namely, the Self-Organizing Map (SOM) technique. We define, measure, and visualize the notion of SOM cluster quality along a hierarchy of cluster abstractions. The quality abstractions range from simple scalar-valued quality scores up to the structural comparison of a given SOM clustering with output of additional supportive clustering methods. The suite of methods allows the user to assess the SOM quality on the appropriate abstraction level, and arrive at improved clustering results. We implement our tools in an integrated system, apply it on experimental data sets, and show its applicability.

Time-Frequency Analysis of the Dispersion of Lamb Modes

NASA Technical Reports Server (NTRS)

Prosser, W. H.; Seale, Michael D.; Smith, Barry T.

1999-01-01

Accurate knowledge of the velocity dispersion of Lamb modes is important for ultrasonic nondestructive evaluation methods used in detecting and locating flaws in thin plates and in determining their elastic stiffness coefficients. Lamb mode dispersion is also important in the acoustic emission technique for accurately triangulating the location of emissions in thin plates. In this research, the ability to characterize Lamb mode dispersion through a time-frequency analysis (the pseudo Wigner-Ville distribution) was demonstrated. A major advantage of time-frequency methods is the ability to analyze acoustic signals containing multiple propagation modes, which overlap and superimpose in the time domain signal. By combining time-frequency analysis with a broadband acoustic excitation source, the dispersion of multiple Lamb modes over a wide frequency range can be determined from as little as a single measurement. In addition, the technique provides a direct measurement of the group velocity dispersion. The technique was first demonstrated in the analysis of a simulated waveform in an aluminum plate in which the Lamb mode dispersion was well known. Portions of the dispersion curves of the A(sub 0), A(sub 1), S(sub 0), and S(sub 2)Lamb modes were obtained from this one waveform. The technique was also applied for the analysis of experimental waveforms from a unidirectional graphite/epoxy composite plate. Measurements were made both along, and perpendicular to the fiber direction. In this case, the signals contained only the lowest order symmetric and antisymmetric modes. A least squares fit of the results from several source to detector distances was used. Theoretical dispersion curves were calculated and are shown to be in good agreement with experimental results.

Time-Frequency Analysis of the Dispersion of Lamb Modes

NASA Technical Reports Server (NTRS)

Prosser, W. H.; Seale, Michael D.; Smith, Barry T.

1999-01-01

Accurate knowledge of the velocity dispersion of Lamb modes is important for ultrasonic nondestructive evaluation methods used in detecting and locating flaws in thin plates and in determining their elastic stiffness coefficients. Lamb mode dispersion is also important in the acoustic emission technique for accurately triangulating the location of emissions in thin plates. In this research, the ability to characterize Lamb mode dispersion through a time-frequency analysis (the pseudo-Wigner-Ville distribution) was demonstrated. A major advantage of time-frequency methods is the ability to analyze acoustic signals containing multiple propagation modes, which overlap and superimpose in the time domain signal. By combining time-frequency analysis with a broadband acoustic excitation source, the dispersion of multiple Lamb modes over a wide frequency range can be determined from as little as a single measurement. In addition, the technique provides a direct measurement of the group velocity dispersion. The technique was first demonstrated in the analysis of a simulated waveform in an aluminum plate in which the Lamb mode dispersion was well known. Portions of the dispersion curves of the AO, A I , So, and S2 Lamb modes were obtained from this one waveform. The technique was also applied for the analysis of experimental waveforms from a unidirectional graphite/epoxy composite plate. Measurements were made both along and perpendicular to the fiber direction. In this case, the signals contained only the lowest order symmetric and antisymmetric modes. A least squares fit of the results from several source to detector distances was used. Theoretical dispersion curves were calculated and are shown to be in good agreement with experimental results.

Q-switched Nd:YAG optical vortex lasers.

PubMed

Kim, D J; Kim, J W; Clarkson, W A

2013-12-02

Q-switched operation of a high-quality Nd:YAG optical vortex laser with the first order Laguerre-Gaussian mode and well-determined helical wavefronts using a fiber-based pump beam conditioning scheme is reported. A simple two-mirror resonator incorporating an acousto-optic Q-switch was employed, along with an etalon and a Brewster plate to enforce the particular helicity of the output. The laser yielded Q-switched pulses with ~250 μJ pulse energy and ~33 ns pulse duration (FWHM) at a 0.1 kHz repetition rate for 5.1 W of absorbed pump power. The handedness of the helical wavefronts was preserved regardless of the repetition rates. The prospects of further power scaling and improved laser performance are discussed.

Anharmonic vibrational spectra and mode-mode couplings analysis of 2-aminopyridine

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Bhat, Sheeraz Ahmad; Ahmad, Shabbir

2018-01-01

Vibrational spectra of 2-aminopyridine (2AP) have been analyzed using the vibrational self-consistence field theory (VSCF), correlated corrected vibrational self-consistence field theory (CC-VSCF) and vibrational perturbation theory (VPT2) at B3LYP/6-311G(d,p) framework. The mode-mode couplings affect the vibrational frequencies and intensities. The coupling integrals between pairs of normal modes have been obtained on the basis of quartic force field (2MR-QFF) approximation. The overtone and combination bands are also assigned in the FTIR spectrum with the help of anharmonic calculation at VPT2 method. A statistical analysis of deviations shows that estimated anharmonic frequencies are closer to the experiment over harmonic approximation. Furthermore, the anharmonic correction has also been carried out for the dimeric structure of 2AP. The fundamental vibration bands have been assigned on the basis of potential energy distribution (PED) and visual look over the animated modes. Other important molecular properties such as frontier molecular orbitals and molecular electrostatics potential mapping have also been analyzed.