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Sample records for echo sequences improves

  1. Optimized, Unequal Pulse Spacing in Multiple Echo Sequences Improves Refocusing

    CERN Document Server

    Jenista, Elizabeth; Branca, Rosa; Warren, Warren

    2009-01-01

    A recent quantum computing paper (G. S. Uhrig, Phys Rev Lett 98 100504 (2007)) analytically derived optimal pulse spacings for a multiple spin echo sequence designed to remove decoherence in a two level system coupled to a bath. The spacings in what has been called a UDD sequence differ dramatically from the conventional, equal pulse spacing of a Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo sequence. The UDD sequence was derived for a model that is unrelated to magnetic resonance, but was recently shown theoretically to be more general. Here we show that the UDD sequence has theoretical advantages for magnetic resonance imaging of structured materials such as tissue, where diffusion in compartmentalized and microstructured environments leads to fluctuating fields on a range of different timescales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T2-weighted contrast than do CPMG sequences with the same number of pulses an...

  2. Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo sequence: improvement of the image quality of oxygen-enhanced MRI

    Energy Technology Data Exchange (ETDEWEB)

    Ohno, Yoshiharu E-mail: yosirad@kobe-u.ac.jpyosirad@med.kobe-u.ac.jpyoshiharuohno@aol.com; Hatabu, Hiroto; Higashino, Takanori; Kawamitsu, Hideaki; Watanabe, Hirokazu; Takenaka, Daisuke; Cauteren, Marc van; Sugimura, Kazuro

    2004-11-01

    Purpose: The purpose of the study presented here was to determine the improvement in image quality of oxygen-enhanced magnetic resonance (MR) subtraction imaging obtained with a centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence compared with that obtained with a conventional sequentially reordered inversion recovery single-shot HASTE (s-IR-HASTE) sequence for pulmonary imaging. Materials and methods: Oxygen-enhanced MR imaging using a 1.5 T whole body scanner was performed on 12 healthy, non-smoking volunteers. Oxygen-enhanced MR images were obtained with the coronal two-dimensional (2D) c-IR-HASTE sequence and 2D s-IR-HASTE sequence combined with respiratory triggering. For a 256x256 matrix, 132 phase-encoding steps were acquired including four steps for phase correction. Inter-echo spacing for each sequence was 4.0 ms. The effective echo time (TE) for c-IR-HASTE was 4.0 ms, and 16 ms for s-IR-HASTE. The inversion time (TI) was 900 ms. To determine the improvement in oxygen-enhanced MR subtraction imaging by c-IR-HASTE, CNRs of subtraction image, overall image quality, and image degradation of the c-IR-HASTE and s-IR-HASTE techniques were statistically compared. Results: CNR, overall image quality, and image degradation of c-IR-HASTE images showed significant improvement compared to those s-IR-HASTE images (P<0.05). Conclusion: Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence enhanced the signal from the lung and improved the image quality of oxygen-enhanced MR subtraction imaging.

  3. Improved Echo cancellation in VOIP

    Directory of Open Access Journals (Sweden)

    Patrashiya Magdolina Halder

    2011-11-01

    Full Text Available VoIP (voice over internet protocol is very popular communication technology of this century and has played tremendous role in communication system. It is preferred by all because it deploys many benefits it uses Internet protocol (IP networks to deliver multimedia information such as speech over a data network. VoIP system can be configured in these connection modes respectively; PC to PC, Telephony to Telephony and PC to Telephony. Echo is very annoying problem which occurs in VoIP and echo reduces the voice quality of VoIP. It is not possible to remove echo 100% from echoed signal because if echo is tried to be eliminated completely then the attempt may distort the main signal. That is why echo cannot be eliminated echo perfectly but the echo to a tolerable range. Clipping is not a good solution to suppress echo because part of speech may erroneously removed. Besides an NLP does not respond rapidly enough and also confuses the fading of the voice level at the end of a sentence with a residual echo. This paper has proposed echo cancellation in VoIP that has been tested and verified by MATLAB. The goal was to suppress echo without clipping and distorting the main signal. By the help of MATLAB program the echo is minimized to enduring level so that the received signal seems echo free. The percentage of suppressing echo varies with the amplitude of the main signal. With regarding the amplitude variation in received (echo free signal the proposed method performs better in finding the echo free signal than the other conventional system.

  4. Echo

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Dustin Yewell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-01-25

    This document is a white paper marketing proposal for Echo™ is a data analysis platform designed for efficient, robust, and scalable creation and execution of complex workflows. Echo’s analysis management system refers to the ability to track, understand, and reproduce workflows used for arriving at results and decisions. Echo improves on traditional scripted data analysis in MATLAB, Python, R, and other languages to allow analysts to make better use of their time. Additionally, the Echo platform provides a powerful data management and curation solution allowing analysts to quickly find, access, and consume datasets. After two years of development and a first release in early 2016, Echo is now available for use with many data types in a wide range of application domains. Echo provides tools that allow users to focus on data analysis and decisions with confidence that results are reported accurately.

  5. Clinical application of gradient echo sequences with prolonged repetition times

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    Tiling, R.; Fink, U.; Deimling, M.; Bauer, W.M.; Yousry, T.; Krauss, B.

    1988-09-01

    Studies designed to optimise image contrasts of gradient echo sequences showed, that especially repetition times between 250 and 500 ms in combination with adequate echo times and flip angles provide new image contrasts. The clinical purpose of gradient echo sequences with longer TR was systematically evaluated in 450 patients. A major advantage of GE sequences was the low signal intensity of fat and bone tissue. On the other hand differnt pathologic changes showed a high signal intensity in comparison to T/sub 2/ weighted spin echo sequences as well. With the possibility of multiple slices GE sequences were of outstanding diagnostic value especially in MR of soft tissue and of the musculoskeletal system. T/sub 2/ weighted SE sequences provided no additional informations and could therefore be omitted in a great number of examinations.

  6. Inaudible functional MRI using a truly mute gradient echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Marcar, V.L. [University of Zurich, Department of Psychology, Neuropsychology, Treichlerstrasse 10, 8032 Zurich (Switzerland); Girard, F. [GE Medical Systems SA, 283, rue de la Miniere B.P. 34, 78533 Buc Cedex (France); Rinkel, Y.; Schneider, J.F.; Martin, E. [University Children' s Hospital, Neuroradiology and Magnetic Resonance, Department of Diagnostic Imaging, Steinwiesstrasse 75, 8032 Zurich (Switzerland)

    2002-11-01

    We performed functional MRI experiments using a mute version of a gradient echo sequence on adult volunteers using either a simple visual stimulus (flicker goggles: 4 subjects) or an auditory stimulus (music: 4 subjects). Because the mute sequence delivers fewer images per unit time than a fast echo planar imaging (EPI) sequence, we explored our data using a parametric ANOVA test and a non-parametric Wilcoxon-Mann-Whitney test in addition to performing a cross-correlation analysis. All three methods were in close agreement regarding the location of the BOLD contrast signal change. We demonstrated that, using appropriate statistical analysis, functional MRI using an MR sequence that is acoustically inaudible to the subject is feasible. Furthermore compared with the ''silent'' event-related procedures involving an EPI protocol, our mGE protocol compares favourably with respect to experiment time and the BOLD signal. (orig.)

  7. An Improved Susceptibility Weighted Imaging Method using Multi-Echo Acquisition

    Science.gov (United States)

    Oh, Sung Suk; Oh, Se-Hong; Nam, Yoonho; Han, Dongyeob; Stafford, Randall B.; Hwang, Jinyoung; Kim, Dong-Hyun; Park, HyunWook; Lee, Jongho

    2013-01-01

    Purpose To introduce novel acquisition and post-processing approaches for susceptibility weighted imaging (SWI) to remove background field inhomogeneity artifacts in both magnitude and phase data. Method The proposed method acquires three echoes in a 3D gradient echo (GRE) sequence, with a field compensation gradient (z-shim gradient) applied to the third echo. The artifacts in the magnitude data are compensated by signal estimation from all three echoes. The artifacts in phase signals are removed by modeling the background phase distortions using Gaussians. The method was applied in vivo and compared with conventional SWI. Results The method successfully compensates for background field inhomogeneity artifacts in magnitude and phase images, and demonstrated improved SWI images. In particular, vessels in frontal lobe, which were not observed in conventional SWI, were identified in the proposed method. Conclusion The new method improves image quality in SWI by restoring signal in the frontal and temporal regions. PMID:24105838

  8. Improved convection compensating pulsed field gradient spin-echo and stimulated-echo methods.

    Science.gov (United States)

    Sørland, G H; Seland, J G; Krane, J; Anthonsen, H W

    2000-02-01

    The need for convection compensating methods in NMR has been manifested through an increasing number of publications related to the subject over the past few years (J. Magn. Reson. 125, 372 (1997); 132, 13 (1998); 131, 126 (1998); 118, 50 (1996); 133, 379 (1998)). When performing measurements at elevated temperature, small convection currents may give rise to erroneous values of the diffusion coefficient. In work with high resolution NMR spectroscopy, the application of magnetic field gradients also introduces an eddy-current magnetic field which may result in errors in phase and baseline in the FFT-spectra. The eddy current field has been greatly suppressed by the application of bipolar magnetic field gradients. However, when introducing bipolar magnetic field gradients, the pulse sequence is lengthened significantly. This has recently been pointed out as a major drawback because of the loss of coherence and of NMR-signal due to transverse relaxation processes. Here we present modified convection compensating pulsed field gradient double spin echo and double stimulated echo sequences which suppress the eddy-current magnetic field without increasing the duration of the pulse sequences.

  9. Spin Dynamics Simulations of Multiple Echo Spacing Pulse Sequences in Grossly Inhomogeneous Fields

    Science.gov (United States)

    Heidler, R.; Bachman, H. N.; Johansen, Y.

    2008-12-01

    Pulse sequences with multiple lengths of echo spacings are used in oilfield NMR logging for diffusion-based NMR applications such as rock and fluid characterization. One specific implementation is the so-called diffusion editing sequence comprising two long echo spacings followed by a standard CPMG at a shorter echo spacing. The echoes in the CPMG portion contain signal from both the direct and stimulated echoes. Modern oilfield NMR logging tools are designed for continuous depth logging of earth formations by projecting both the static (B0) and dynamic (B1) fields into the formation. Both B0 and B1 profiles are grossly inhomogeneous which results in non-steady-state behavior in the early echoes. The spin dynamics effects present a challenge for processing the echo amplitudes to measure porosity (amplitude extrapolated to zero time) and attenuations for fluid or pore size characterization. In this work we describe a calculation of the spin dynamics of the diffusion editing sequence with two long echo spacings. The calculation takes into account full B1 and B0 field maps, and comparisons will be made for sensors and parameters typical of oilfield logging tools and environments.

  10. Feasibility of noninvasive quantitative measurements of intrarenal R(2) ' in humans using an asymmetric spin echo echo planar imaging sequence.

    Science.gov (United States)

    Zhang, Xiaodong; Zhang, Yudong; Yang, Xuedong; Wang, Xiaoying; An, Hongyu; Zhang, Jue; Fang, Jing

    2013-01-01

    The purpose of this study was to demonstrate the feasibility of an asymmetric spin echo (ASE) single-shot echo planar imaging (EPI) sequence for the noninvasive quantitative measurement of intrarenal R(2) ' in humans within 20 s. The reproducibility of R(2) ' measurements with the ASE-EPI sequence was assessed in nine healthy young subjects in repeated studies conducted over three consecutive days. Moreover, we also evaluated whether the ASE-EPI sequence-measured R(2) ' reflected the intrarenal oxygenation changes induced by furosemide in another group of normal human subjects (n = 10). Different flow attenuation gradients (b = 0, 40 and 80 s/mm(2) ) were utilized to examine the impact of the intravascular signal contribution on the estimation of intrarenal R(2) '. In the absence of flow dephasing gradients (b = 0 s/mm(2) ), the computed coefficient of variation (CV) of R(2) ' was 21.31 ± 4.52%, and the estimated R(2) ' value decreased slightly, but not statistically significantly (p > 0.05), after the administration of furosemide in the medullary region. However, CV of R(2) ' was much smaller in the presence of flow dephasing gradients (9.68 ± 3.58% with b = 40 s/mm(2) and 10.50 ± 3.62% with b = 80 s/mm(2) ). Moreover, a significant reduction in R(2) ' in the renal medulla was obtained (p R(2) ' measurements did not differ between the b = 40 s/mm(2) and b = 80 s/mm(2) scans, suggesting that small diffusion gradients were sufficient to minimize the intravascular signal contribution. In summary, we have demonstrated that renal R(2) ' can be obtained rapidly using an ASE-EPI sequence. The measurement was highly reproducible and reflected the expected intrarenal oxygenation changes induced by furosemide.

  11. Long echo time STIR sequence MRI of optic nerves in optic neuritis

    Energy Technology Data Exchange (ETDEWEB)

    Onofrj, M. [Dept. of Neurology, State Univ. of Chieti, Ospedale ex-Pediatrico (Italy); Tartaro, A. [Dept. of Radiology, State Univ. of Chieti (Italy); Thomas, A. [Dept. of Neurology, State Univ. of Chieti, Ospedale ex-Pediatrico (Italy); Gambi, D. [Dept. of Neurology, State Univ. of Chieti, Ospedale ex-Pediatrico (Italy); Fulgente, T. [Dept. of Neurology, State Univ. of Chieti, Ospedale ex-Pediatrico (Italy); Delli Pizzi, C. [Dept. of Radiology, State Univ. of Chieti (Italy); Bonomo, L. [Dept. of Radiology, State Univ. of Chieti (Italy)

    1996-01-01

    MRI of the optic nerves was obtained in 13 patients with acute optic neuritis and 13 with a previous optic neuritis (ON), assessed by clinical features, visual fields and visual evoked potentials. Results of the conventional short tau inversion recovery (STIR) sequence obtained with a short echo time (STE-STIR; 22 ms) were compared with those of a long echo time (LTE-STIR: 80 ms) sequence. The conventional STE-STIR sequence revealed lesions in the optic nerves in 78.5% of acute and 58.8% of previous ON. The LTE-STIR sequence showed abnormalities in 92.8% of acutely symptomatic nerves and 94.1% of nerves with previous ON. The optic nerve lesions appeared significantly longer with the LTE-STIR sequence than with the conventional STE-STIR sequences, in both acute and previous ON. (orig.)

  12. Phase-aligned multiple spin-echo averaging: a simple way to improve signal-to-noise ratio of in vivo mouse spinal cord diffusion tensor image.

    Science.gov (United States)

    Tu, Tsang-Wei; Budde, Matthew D; Xie, Mingqiang; Chen, Ying-Jr; Wang, Qing; Quirk, James D; Song, Sheng-Kwei

    2014-12-01

    To improve signal-noise-ratio of in vivo mouse spinal cord diffusion tensor imaging using-phase aligned multiple spin-echo technique. In vivo mouse spinal cord diffusion tensor imaging maps generated by multiple spin-echo and conventional spin-echo diffusion weighting were examined to demonstrate the efficacy of multiple spin-echo diffusion sequence to improve image quality and throughput. Effects of signal averaging using complex, magnitude and phased images from multiple spin-echo diffusion weighting were also assessed. Bayesian probability theory was used to generate phased images by moving the coherent signals to the real channel to eliminate the effect of phase variation between echoes while preserving the Gaussian noise distribution. Signal averaging of phased multiple spin-echo images potentially solves both the phase incoherence problem and the bias of the elevated Rician noise distribution in magnitude image. The proposed signal averaging with Bayesian phase-aligned multiple spin-echo images approach was compared to the conventional spin-echo data acquired with doubling the scan time. The diffusion tensor imaging parameters were compared in the mouse contusion spinal cord injury. Significance level (p-value) and effect size (Cohen's d) were reported between the control and contused spinal cord to inspect the sensitivity of each approach in detecting white matter pathology. Compared to the spin-echo image, the signal-noise-ratio increased to 1.84-fold using the phased image averaging and to 1.30-fold using magnitude image averaging in the spinal cord white matter. Multiple spin-echo phased image averaging showed improved image quality of the mouse spinal cord among the tested methods. Diffusion tensor imaging metrics obtained from multiple spin-echo phased images using three echoes and two averages closely agreed with those derived by spin-echo magnitude data with four averages (two times more in acquisition time). The phased image averaging correctly

  13. Magnetic Resonance Elastography of the Liver: Qualitative and Quantitative Comparison of Gradient Echo and Spin Echo Echoplanar Imaging Sequences.

    Science.gov (United States)

    Wagner, Mathilde; Besa, Cecilia; Bou Ayache, Jad; Yasar, Temel Kaya; Bane, Octavia; Fung, Maggie; Ehman, Richard L; Taouli, Bachir

    2016-09-01

    The aim of this study was to compare 2-dimensional (2D) gradient recalled echo (GRE) and 2D spin echo echoplanar imaging (SE-EPI) magnetic resonance elastography (MRE) sequences of the liver in terms of image quality and quantitative liver stiffness (LS) measurement. This prospective study involved 50 consecutive subjects (male/female, 33/17; mean age, 58 years) who underwent liver magnetic resonance imaging at 3.0 T including 2 MRE sequences, 2D GRE, and 2D SE-EPI (acquisition time 56 vs 16 seconds, respectively). Image quality scores were assessed by 2 independent observers based on wave propagation and organ coverage on the confidence map (range, 0-15). A third observer measured LS on stiffness maps (in kilopascal). Mean LS values, regions of interest size (based on confidence map), and image quality scores between SE-EPI and GRE-MRE were compared using paired nonparametric Wilcoxon test. Reproducibility of LS values between the 2 sequences was assessed using intraclass coefficient correlation, coefficient of variation, and Bland-Altman limits of agreement. T2* effect on image quality was assessed using partial Spearman correlation. There were 4 cases of failure with GRE-MRE and none with SE-EPI-MRE. Image quality scores and region of interest size were significantly higher using SE-EPI-MRE versus GRE-MRE (P < 0.0001 for both measurements and observers). Liver stiffness measurements were not significantly different between the 2 sequences (3.75 ± 1.87 kPa vs 3.55 ± 1.51 kPa, P = 0.062), were significantly correlated (intraclass coefficient correlation, 0.909), and had excellent reproducibility (coefficient of variation, 10.2%; bias, 0.023; Bland-Altman limits of agreement, -1.19; 1.66 kPa). Image quality scores using GRE-MRE were significantly correlated with T2* while there was no correlation for SE-EPI-MRE. Our data suggest that SE-EPI-MRE may be a better alternative to GRE-MRE. The diagnostic performance of SE-EPI-MRE for detection of liver fibrosis needs

  14. Dual-pathway multi-echo sequence for simultaneous frequency and T2 mapping

    Science.gov (United States)

    Cheng, Cheng-Chieh; Mei, Chang-Sheng; Duryea, Jeffrey; Chung, Hsiao-Wen; Chao, Tzu-Cheng; Panych, Lawrence P.; Madore, Bruno

    2016-04-01

    Purpose: To present a dual-pathway multi-echo steady state sequence and reconstruction algorithm to capture T2, T2∗ and field map information. Methods: Typically, pulse sequences based on spin echoes are needed for T2 mapping while gradient echoes are needed for field mapping, making it difficult to jointly acquire both types of information. A dual-pathway multi-echo pulse sequence is employed here to generate T2 and field maps from the same acquired data. The approach might be used, for example, to obtain both thermometry and tissue damage information during thermal therapies, or susceptibility and T2 information from a same head scan, or to generate bonus T2 maps during a knee scan. Results: Quantitative T2, T2∗ and field maps were generated in gel phantoms, ex vivo bovine muscle, and twelve volunteers. T2 results were validated against a spin-echo reference standard: A linear regression based on ROI analysis in phantoms provided close agreement (slope/R2 = 0.99/0.998). A pixel-wise in vivo Bland-Altman analysis of R2 = 1/T2 showed a bias of 0.034 Hz (about 0.3%), as averaged over four volunteers. Ex vivo results, with and without motion, suggested that tissue damage detection based on T2 rather than temperature-dose measurements might prove more robust to motion. Conclusion: T2, T2∗ and field maps were obtained simultaneously, from the same datasets, in thermometry, susceptibility-weighted imaging and knee-imaging contexts.

  15. Substitute CT generation from a single ultra short time echo MRI sequence: preliminary study

    Science.gov (United States)

    Ghose, Soumya; Dowling, Jason A.; Rai, Robba; Liney, Gary P.

    2017-04-01

    In MR guided radiation therapy planning both MR and CT images for a patient are acquired and co-registered to obtain a tissue specific HU map. Generation of the HU map directly from the MRI would eliminate the CT acquisition and may improve radiation therapy planning. In this preliminary study of substitute CT (sCT) generation, two porcine leg phantoms were scanned using a 3D ultrashort echo time (PETRA) sequence and co-registered to corresponding CT images to build tissue specific regression models. The model was created from one co-registered CT-PETRA pair to generate the sCT for the other PETRA image. An expectation maximization based clustering was performed on the co-registered PETRA image to identify the soft tissues, dense bone and air class membership probabilities. A tissue specific non linear regression model was built from one registered CT-PETRA pair dataset to predict the sCT of the second PETRA image in a two-fold cross validation schema. A complete substitute CT is generated in 3 min. The mean absolute HU error for air was 0.3 HU, bone was 95 HU, fat was 30 HU and for muscle it was 10 HU. The mean surface reconstruction error for the bone was 1.3 mm. The PETRA sequence enabled a low mean absolute surface distance for the bone and a low HU error for other classes. The sCT generated from a single PETRA sequence shows promise for the generation of fast sCT for MRI based radiation therapy planning.

  16. Magnetic resonance findings in amyotrophic lateral sclerosis using a spin echo magnetization transfer sequence: preliminary report

    Directory of Open Access Journals (Sweden)

    ROCHA ANTÔNIO JOSÉ DA

    1999-01-01

    Full Text Available We present the magnetic resonance (MR findings of five patients with amyotrophic lateral sclerosis (ALS using a spin-echo sequence with an additional magnetization transfer (MT pulse on T1-weighted images (T1 SE/MT. These findings were absent in the control group and consisted of hyperintensity of the corticospinal tract. Moreover we discuss the principles and the use of this fast but simple MR technique in the diagnosis of ALS

  17. Broadband echo sequence using a pi composite pulse for the pure NQR of a spin I = 32 powder sample

    Science.gov (United States)

    Odin

    2000-04-01

    This work presents a numerical approach to optimizing sequences with composite pulses for the pure NQR of a spin I = 32 powder sample. The calculations are based on a formalism developed in a previous paper, which allows a fast powder-averaging procedure to be implemented. The framework of the Cayley-Klein matrices to describe space rotations by 2 x 2 unitary and unimodular complex matrices is used to calculate the pulse propagators. The object of such a study is to design a high-performance echo sequence composed of a single preparation pulse and a three-pulse composite transfer pulse. We mean a sequence leading to a large excitation bandwidth with a good signal-to-noise ratio, a flat excitation profile near the irradiation frequency, and a good linearity of the phase as a function of frequency offset. Such a composite echo sequence is intended to give a better excitation profile than the classical Hahn (θ)-tau-(2θ) echo sequence. It is argued that in pure NQR of a powder sample, the sequence must be optimized as a whole since both the excitation and the reception of the signal depend on the relative orientation of the crystallites with respect to the coil axis. To our knowledge, this is the first time such a global approach is presented. An extensive numerical study of the composite echo sequence described above is performed in this article. The key of the discrimination between the sequences lies in using the first five reduced moments of the excitation profile as well as an estimator of the phase linearity. Based on such information, we suggest that the echo sequence that best fulfills our criterion is (1)(0)-tau-(0.35)(0)(2.1)(pi)(0.35)(0), the pulse angles omega(RF)t(p) being in radians. The subscripts are the relative pulse phases. We outlined the way to implement the spin echo mapping method to reconstruct large spectra with this sequence, and it is shown that it reduces the acquisition time by a factor of 1.7 if compared to the classical Hahn echo. Some

  18. Improving Multi-Beam Echo Sounder Depth Measurements

    NARCIS (Netherlands)

    Snellen, M.; Ameele, J.J.P. van den; Biersteker, R.; Simons, D.G.

    2006-01-01

    An important research question is how to adequately correct multi-beam echo sounder (MBES) bathymetric data for refraction effects. This is especially relevant for survey areas, like the Maasgeul area off the Dutch coast, where the water column properties and thus the prevailing sound speed profile

  19. Prognostic value of gradient echo T2* sequences for brain MR imaging in preterm infants

    Energy Technology Data Exchange (ETDEWEB)

    Bruine, Francisca T. de; Berg-Huysmans, Annette A. van den; Buchem, Mark A. van; Grond, Jeroen van der [Leiden University Medical Center, Department of Radiology, PO Box 9600, Leiden (Netherlands); Steggerda, Sylke J.; Leijser, Lara M.; Rijken, Monique [Leiden University Medical Center, Department of Pediatrics, subdivision of Neonatology, Leiden (Netherlands); Wezel-Meijler, Gerda van [Leiden University Medical Center, Department of Pediatrics, subdivision of Neonatology, Leiden (Netherlands); Isala Hospital, Department of Neonatology, Zwolle (Netherlands)

    2014-03-15

    Gradient echo T2*-W sequences are more sensitive than T2-W spin-echo sequences for detecting hemorrhages in the brain. The aim of this study is to correlate presence of hemosiderin deposits in the brain of very preterm infants (gestational age <32 weeks) detected by T2*-W gradient echo MRI to white matter injury and neurodevelopmental outcome at 2 years. In 101 preterm infants, presence and location of hemosiderin were assessed on T2*-W gradient echo MRI performed around term-equivalent age (range: 40-60 weeks). White matter injury was defined as the presence of >6 non-hemorrhagic punctate white matter lesions (PWML), cysts and/or ventricular dilatation. Six infants with post-hemorrhagic ventricular dilatation detected by US in the neonatal period were excluded. Infants were seen for follow-up at 2 years. Univariate and regression analysis assessed the relation between presence and location of hemosiderin, white matter injury and neurodevelopmental outcome. In 38/95 (40%) of the infants, hemosiderin was detected. Twenty percent (19/95) of the infants were lost to follow-up. There was a correlation between hemosiderin in the ventricular wall with >6 PWML (P < 0.001) and cysts (P < 0.001) at term-equivalent age, and with a lower psychomotor development index (PDI) (P=0.02) at 2 years. After correcting for known confounders (gestational age, gender, intrauterine growth retardation and white matter injury), the correlation with PDI was no longer significant. The clinical importance of detecting small hemosiderin deposits is limited as there is no independent association with neurodevelopmental outcome. (orig.)

  20. Demonstration of improved sensitivity of echo interferometers to gravitational acceleration

    CERN Document Server

    Mok, C; Carew, A; Berthiaume, R; Beattie, S; Kumarakrishnan, A

    2013-01-01

    We have developed two configurations of an echo interferometer that rely on standing wave excitation of a laser-cooled sample of rubidium atoms that measures acceleration. For a two-pulse configuration, the interferometer signal is modulated at the recoil frequency and exhibits a sinusoidal frequency chirp as a function of pulse spacing. For a three-pulse stimulated echo configuration, the signal is observed without recoil modulation and exhibits a modulation at a single frequency. The three-pulse configuration is less sensitive to effects of vibrations and magnetic field curvature leading to a longer experimental timescale. For both configurations of the atom interferometer (AI), we show that a measurement of acceleration with a statistical precision of 0.5% can be realized by analyzing the shape of the echo envelope that has a temporal duration of a few microseconds. Using the two-pulse AI, we obtain measurements of acceleration that are statistically precise to 6 parts per million (ppm) on a 25 ms timescal...

  1. Object analysis of bone marrow MR imaging using double echo STIR sequence in hematological diseases

    Energy Technology Data Exchange (ETDEWEB)

    Mizuno, Hitomi [Saitama Medical School, Moroyama (Japan)

    1995-07-01

    The bone marrow of 84 patients with hematological disorders was investigated using short inversion time inversion recovery sequence (STIR) on an 1.5 Tesla superconducting MRI system. Double echo times of 20 and 100 msec were applied to research the signal characteristics of the lesion and carry out quantitative analysis of the receiver operating characteristic curve (ROC). The hematological diseases included 19 cases of myelodysplastic syndrome (MDS), 18 of multiple myeloma (MM), 18 of chronic myelocytic leukemia (CML), 9 of aplastic anemia (AA), 8 of acute myelocytic leukemia (AML), 3 of chronic lymphocytic leukemia (CLL), 3 of myelofibrosis, and 3 others. Using STIR with double echo times, bone marrow showed high signal intensity (SI) on short TE and low SI on long TE in MDS and CML; high SI on short and long TE in myelofibrosis and CLL; high SI on short TE and high to moderately high SI on long TE in MM; and low SI on short and long TE in AA. Quantitative analysis of 33 patients showed high sensitivity and specificity in AA (81% and 94%, respectively) and moderate sensitivity and high specificity in MM (61%, 88%). CML and MDS were similar with low sensitivities (40%, 41%) and high specificities (80%, 78%). Differential diagnosis between CML and MDS was difficult using STIR with the double echo time method. (author).

  2. [Influence of the difference in start-up echo on signal intensity in the FIESTA sequence].

    Science.gov (United States)

    Naka, Takanori; Takahashi, Mitsuyuki

    2008-11-20

    The FIESTA sequence is a fast imaging method used for various parts in recent years. A constant flip angle (CFA) or linear flip angle (LFA) are used as the start-up echo in many cases. It is reported from CFA, which is the conventional method, that the T1 value and T2 value influence the speed that reaches steady state. However, there is no such report in LFA. Therefore, we examined the influence of the difference of start-up echo method upon signal intensity. In phantoms other than vegetable oil, the difference was not accepted in the change of speed that reaches steady state and the signal intensity in steady-state transit. In LFA, signal intensity of vegetable oil was clearly lower than CFA. The same result was obtained regardless of on or off resonance. From the result, it was thought that it depended on T2/T1 for the speed that reaches steady state. Moreover, the difference in resonant frequency was considered to greatly influence LFA but not CFA. That is, it was suggested by the difference in start-up echo that the signal intensity of fat changes greatly.

  3. Comparison of 2-D turbo spin echo and 3-D gradient echo sequences for the detection of the trigeminal nerve and branches anatomy

    Energy Technology Data Exchange (ETDEWEB)

    Held, P.; Fruend, R.; Seitz, J.; Nitz, W.; Haffke, T.; Hees, H

    2001-01-01

    The aim of this study was to assess the detectability of the trigeminal nerve and its branches using T1 weighted (w.) 3-D magnetization prepared rapid gradient echo (MP-RAGE), T2* w. 3D CISS and T2 w. 2-D turbo spin echo MR sequences. Thirty healthy volunteers were examined for this purpose using a 1.5 Tesla MR unit. The detectability of the trigeminal nerve and Gasser's Ganglion, i.e. structures that are surrounded by liquor was best using 3-D CISS. In the case of the ophthalmic, maxillary and mandibular nerves, the T1 w. 3-D MPRAGE was significantly better than T2* w. CISS and T2 w. 2-D turbo spin echo. The latter yielded the poorest results. We conclude that both high resolution T2* w. and T1 w. 3-D sequences are necessary in order to detect the liquor-surrounded trigeminal nerve and its soft tissue-surrounded branches. We would therefore recommend the inclusion of constructive interference in steady state (CISS) and MP-RAGE in a MR imaging protocol of the trigeminal nerve and its branches.

  4. Utility of two types of MR cisternography for patency evaluation of aqueduct and third ventriculostomy site: Three dimentsional sagittal fast spin echo sequence and steady-state coherent fast gradient echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jung Hyun; Kim, Eun Hee; Park, Jong Bin; Kim, Jae Hyoung; Choi, Byung Se; Jung, Cheol Kyu; Bae, Yun Jung; Lee, Kyung Mi [Dept. of Radiology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam (Korea, Republic of)

    2015-07-15

    We aimed to evaluate the utility of two types of MR cisternography [fast spin echo sequence and steady-state coherent gradient echo (GRE) sequence] in addition to phase contrast-cine imaging (PC-cine), for assessing patency at the aqueduct and third ventriculostomy site. 43 patients (35 patients with suspected aqueductal stenosis and 8 patients with third ventriculostomy) were retrospectively analyzed. PC-cine, 3 dimensional sagittal fast spin echo sequence [driven-equilibrium imaging (DRIVE) or volumetric isotrophic T2-weighted acquisition (T2 VISTA)] and steady-state coherent fast GRE sequence (balanced turbo field echo; bTFE) imaging were performed in all patients. The patency of the aqueduct or third ventriculostomy site was scored. Some pitfalls of each sequence were also analyzed in individual cases. 93% of all cases showed consistent scores in PC-cine, DRIVE/T2 VISTA, and bTFE imaging. DRIVE/T2 VISTA imaging provided functional information of cerebrospinal fluid flow with flow-related artifacts, while bTFE imaging allowed direct visualization of the aqueduct or ventriculostomy site. However, evaluation of anatomical structures was difficult in three cases with strong flow-related artifacts on DRIVE/T2 VISTA and in 2 cases with susceptibility artifacts on bTFE. Both DRIVE/T2 VISTA and bTFE imaging have complementary roles in evaluating the patency of the aqueduct and 3rd ventriculostomy site.

  5. Accelerated susceptibility-based positive contrast imaging of MR compatible metallic devices based on modified fast spin echo sequences

    Science.gov (United States)

    Shi, Caiyun; Xie, Guoxi; Zhang, Yongqin; Zhang, Xiaoyong; Chen, Min; Su, Shi; Dong, Ying; Liu, Xin; Ji, Jim

    2017-04-01

    This study aims to develop an accelerated susceptibility-based positive contrast MR imaging method for visualizing MR compatible metallic devices. A modified fast spin echo sequence is used to accelerate data acquisition. Each readout gradient in the modified fast spin echo is slightly shifted by a short distance T shift. Phase changes accumulated within T shift are then used to calculate the susceptibility map by using a kernel deconvolution algorithm with a regularized ℓ1 minimization. To evaluate the proposed fast spin echo method, three phantom experiments were conducted and compared to a spin echo based technique and the gold standard CT for visualizing biopsy needles and brachytherapy seeds. Compared to the spin echo based technique, the data sampling speed of the proposed method was faster by 2–4 times while still being able to accurately visualize and identify the location of the biopsy needle and brachytherapy seeds. These results were confirmed by CT images of the same devices. Results also demonstrated that the proposed fast spin echo method can achieve good visualization of the brachytherapy seeds in positive contrast and in different orientations. It is also capable of correctly differentiating brachytherapy seeds from other similar structures on conventional magnitude images.

  6. Imaging articular cartilage defects with 3D fat-suppressed echo planar imaging: comparison with conventional 3D fat-suppressed gradient echo sequence and correlation with histology.

    Science.gov (United States)

    Trattnig, S; Huber, M; Breitenseher, M J; Trnka, H J; Rand, T; Kaider, A; Helbich, T; Imhof, H; Resnick, D

    1998-01-01

    Our goal was to shorten examination time in articular cartilage imaging by use of a recently developed 3D multishot echo planar imaging (EPI) sequence with fat suppression (FS). We performed comparisons with 3D FS GE sequence using histology as the standard of reference. Twenty patients with severe gonarthrosis who were scheduled for total knee replacement underwent MRI prior to surgery. Hyaline cartilage was imaged with a 3D FS EPI and a 3D FS GE sequence. Signal intensities of articular structures were measured, and contrast-to-noise (C/N) ratios were calculated. Each knee was subdivided into 10 cartilage surfaces. From a total of 188 (3D EPI sequence) and 198 (3D GE sequence) cartilage surfaces, 73 and 79 histologic specimens could be obtained and analyzed. MR grading of cartilage lesions on both sequences was based on a five grade classification scheme and compared with histologic grading. The 3D FS EPI sequence provided a high C/N ratio between cartilage and subchondral bone similar to that of the 3D FS GE sequence. The C/N ratio between cartilage and effusion was significantly lower on the 3D EPI sequence due to higher signal intensity of fluid. MR grading of cartilage abnormalities using 3D FS EPI and 3D GE sequence correlated well with histologic grading. 3D FS EPI sequence agreed within one grade in 69 of 73 (94.5%) histologically proven cartilage lesions and 3D FS GE sequence agreed within one grade in 76 of 79 (96.2%) lesions. The gradings were identical in 38 of 73 (52.1%) and in 46 of 79 (58.3%) cases, respectively. The difference between the sensitivities was statistically not significant. The 3D FS EPI sequence is comparable with the 3D FS GE sequence in the noninvasive evaluation of advanced cartilage abnormalities but reduces scan time by a factor of 4.

  7. Improving the intensity and efficiency of compressed echo in rare-earth-ion-doped crystal

    Science.gov (United States)

    Xiu-Rong, Ma; Yu-Qing, Liang; Song, Wang; Shuang-Gen, Zhang; Yun-Long, Shan

    2016-07-01

    We investigate the intensity and efficiency of a compressed echo, which is important in arbitrary waveform generation (AWG). A new model of compressed echo is proposed based on the optical Bloch equations, which exposes much more detailed parameters than the conventional model, such as the time delay of the chirp lasers, the nature of the rare-earth-ion-doped crystal, etc. According to the novel model of compressed echo, we find that reducing the time delay of the chirp lasers and scanning the lasers around the center frequency of the inhomogeneously broadened spectrum, while utilizing a crystal with larger coherence time and excitation lifetime can improve the compressed echo’s intensity and efficiency. The theoretical analysis is validated by numerical simulations. Project supported by Special Funds for Scientific and Technological Innovation Projects in Tianjin, China (Grant No. 10FDZDGX00400) and the Tianjin Research Program of Application Foundation and Advanced Technology, China (Grant No. 15JCQNJC01100).

  8. MR cisternography using a three-dimensional half-Fourier single-shot fast spin-echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, K.; Yamakami, N.; Hachiya, J. [Department of Radiology, Kyorin University School of Medicine, Tokyo (Japan); Kassai, Y. [Toshiba Corp., Tokyo (Japan)

    1998-03-27

    Application of a three-dimensional half-fourier single-shot fast spin-echo sequence to MR cisternography is presented. This technique is capable of demonstrating normal cranial nerves. It is also useful in screening for acoustic neuroma as well as in the diagnosis of neurovascular compression. (orig.) With 3 figs., 12 refs.

  9. Single-shot echo-planar MR sequences in the diagnosis of intracranial infectious diseases

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Kazuhiro; Katase, Shichiro; Yoshino, Ayako; Yamakami, Norio; Hachiya, Junichi [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1998-06-01

    The purpose of this study was to present our preliminary experience in the application of echo-planar-imaging (EPI) MR sequences for the diagnosis of intracranial infectious diseases and to assess the value of these sequences. We reviewed single-shot EPI MR images obtained at 1.5 T in 17 patients and compared these images with conventional or fast spin-echo (SE) or fluid attenuated inversion-recovery (FLAIR) images. The clinical diagnoses for the 17 patients were meningitis (2 patients), encephalitis or meningoencephalitis (7 patients), brain abscess (5 patients), epidural empyema (2 patients) and Creutzfeldt-Jakob disease (1 patient). We obtained EPI-T{sub 2}-weighted (T{sub 2}W) images in 8 patients, EPI-FLAIR images in 13 patients and EPI-diffusion-weighted (DW) images in 14 patients. Among the 8 patients for whom EPI-T{sub 2}W imaging was performed, EPI-T{sub 2}W imaging yielded superior results compared with SE-T{sub 2}W imaging in 3 patients as a consequence of patient motion and equal results compared with SE-T{sub 2}W imaging in 5 patients. Among the 13 patients for whom EPI-FLAIR imaging was performed, the EPI-FLAIR images were superior to conventional FLAIR images in 3 unstable patients. In the remaining 10 patients for whom EPI-FLAIR imaging was performed, EPI-FLAIR images were equivalent or inferior to conventional FLAIR images. In 6 patients with encephalitis or meningoencephalitis, the encephalitic lesions showed hyperintensity in EPI-DW images to a greater extent than in images obtained with the other techniques. In 3 patients, EPI-DW images also demonstrated hyperintensity for the contents of abscesses or areas of empyema that was not seen with the other imaging techniques. The value of EPI-T{sub 2}W and EPI-FLAIR imaging is limited in uncooperative patients. EPI-DW imaging was found to be of value for the evaluation of several intracranial infectious diseases. (author)

  10. ECHO Project: a series of tools for studying and characterizing seismic sequences evolution

    Science.gov (United States)

    Falcone, Giuseppe; De Santis, Angelo; Di Giovambattista, Rita; Cianchini, Gianfranco; Murru, Maura; Calderoni, Giovanna; Lucente, Pio Francesco; De Gori, Pasquale; Frepoli, Alberto; Signanini, Patrizio; Rainone, Mario; Vessia, Giovanna

    2016-04-01

    One of the most ubiquitous problems in seismology is to discriminate between seismic sequences (a series of small-to-moderate earthquakes that culminate with a mainshock) and swarms (diffuse seismicity w/o mainshock), that can be easily done only after a certain class of earthquakes have occurred. We propose to put these phenomena under the same framework provided by the geosystemics (De Santis, 2009, 2014), where the planet Earth and its processes are seen from a holistic point of view, and the New Geophysics (Crampin et al., 2013), where fluid-saturated microcracks in almost all crustal rocks are so closely-spaced they verge on failure and hence are highly-compliant critical systems (Signanini and De Santis, 2012). In this context, nonlinear concepts typical of Chaos and Information theories are fundamental to study and characterize the various features of the series of seismic events, and, eventually, to discriminate between seismic sequences and swarms. The two theories imply the use of non-linear techniques which are innovative in seismology. The project ECHO ("Entropy and CHaOs: tools for studying and characterizing seismic sequences evolution"), a recent INGV-funded project, would aim at applying the above approaches in a more integrated way mainly to establish a suite of effective tools to disclose and characterise the principal features of the series of earthquakes which are of interest. In our view this will represent the very first step before to face the more challenging (but longer-term) problem of discriminating between the two kinds of series of seismic events. This poster will describe these kinds of preliminary activities and relative results in the framework of the project.

  11. The diagnostic value of magnetic resonance urography using a balanced turbo field echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Cifci, Egemen; Coban, Goekcen [Baskent University Faculty of Medicine, Department of Radiology, Konya (Turkey); Cicek, Tufan; Goenuelalan, Umut [Baskent University Faculty of Medicine, Department of Urology, Konya (Turkey)

    2016-12-15

    The aim of the study was to compare the inter-observer variability and the accuracy of magnetic resonance urography (MRU) using a thin sectional balanced-turbo field echo (B-TFE) sequence for detecting ureteral calculi and to determine the effect of additional factors (size, density and location of the calculus) on the sensitivity and specificity of the MRU. MRU and CT images were evaluated independently by two radiologists according to presence, density and localization of calculi. The degrees of inter-rater agreement for categorical items were evaluated by the Kappa coefficient. According to the 1st and 2nd observers, the sensitivity of MRU was 65.9 %, 71.8 % and the specificity of MRU was 95.9 %, 100 %, respectively. Inter-observer agreement was 84.6 % for stone detection. The larger size had a better effect on detectability (p < 0.05). Also, the higher density had a better impact on detectability (p < 0.05). Our study has shown that B-TFE MRU was useful to detect ureteral calculi. However, B-TFE MRU has low sensitivity and high specificity in comparison with CT images. MRU is a reasonable alternative imaging technique for follow-up periods of selective groups like patients with large urinary stones, children or pregnant patients when ionizing radiation is undesirable. (orig.)

  12. The diagnostic value of magnetic resonance urography using a balanced turbo field echo sequence.

    Science.gov (United States)

    Çifçi, Egemen; Çoban, Gökçen; Çiçek, Tufan; Gönülalan, Umut

    2016-12-01

    The aim of the study was to compare the inter-observer variability and the accuracy of magnetic resonance urography (MRU) using a thin sectional balanced-turbo field echo (B-TFE) sequence for detecting ureteral calculi and to determine the effect of additional factors (size, density and location of the calculus) on the sensitivity and specificity of the MRU. MRU and CT images were evaluated independently by two radiologists according to presence, density and localization of calculi. The degrees of inter-rater agreement for categorical items were evaluated by the Kappa coefficient. According to the 1st and 2nd observers, the sensitivity of MRU was 65.9 %, 71.8 % and the specificity of MRU was 95.9 %, 100 %, respectively. Inter-observer agreement was 84.6 % for stone detection. The larger size had a better effect on detectability (p MRU was useful to detect ureteral calculi. However, B-TFE MRU has low sensitivity and high specificity in comparison with CT images. MRU is a reasonable alternative imaging technique for follow-up periods of selective groups like patients with large urinary stones, children or pregnant patients when ionizing radiation is undesirable. • According to 1st and 2nd observers, sensitivity of MRU was 65.9 %, 71.8 %, respectively. • According to 1st and 2nd observers, MRU specificity was 95.9 %, 100 %, respectively. • Interobserver agreement was found to be over 84 % for stone detection. • B-TFE sequence provides calculus follow-up without radiation. • Larger calculi and more dense calculi individually have the better effect on detectability.

  13. An Improved Variable Structure Adaptive Filter Design and Analysis for Acoustic Echo Cancellation

    Directory of Open Access Journals (Sweden)

    A. Kar

    2015-04-01

    Full Text Available In this research an advance variable structure adaptive Multiple Sub-Filters (MSF based algorithm for single channel Acoustic Echo Cancellation (AEC is proposed and analyzed. This work suggests a new and improved direction to find the optimum tap-length of adaptive filter employed for AEC. The structure adaptation, supported by a tap-length based weight update approach helps the designed echo canceller to maintain a trade-off between the Mean Square Error (MSE and time taken to attain the steady state MSE. The work done in this paper focuses on replacing the fixed length sub-filters in existing MSF based AEC algorithms which brings refinements in terms of convergence, steady state error and tracking over the single long filter, different error and common error algorithms. A dynamic structure selective coefficient update approach to reduce the structural and computational cost of adaptive design is discussed in context with the proposed algorithm. Simulated results reveal a comparative performance analysis over proposed variable structure multiple sub-filters designs and existing fixed tap-length sub-filters based acoustic echo cancellers.

  14. Broadband Echo Sequence Using a π Composite Pulse for the Pure NQR of a Spin I = {3}/{2} Powder Sample

    Science.gov (United States)

    Odin, Christophe

    2000-04-01

    This work presents a numerical approach to optimizing sequences with composite pulses for the pure NQR of a spin I = {3}/{2} powder sample. The calculations are based on a formalism developed in a previous paper, which allows a fast powder-averaging procedure to be implemented. The framework of the Cayley-Klein matrices to describe space rotations by 2 × 2 unitary and unimodular complex matrices is used to calculate the pulse propagators. The object of such a study is to design a high-performance echo sequence composed of a single preparation pulse and a three-pulse composite transfer pulse. We mean a sequence leading to a large excitation bandwidth with a good signal-to-noise ratio, a flat excitation profile near the irradiation frequency, and a good linearity of the phase as a function of frequency offset. Such a composite echo sequence is intended to give a better excitation profile than the classical Hahn (θ)-τ-(2θ) echo sequence. It is argued that in pure NQR of a powder sample, the sequence must be optimized as a whole since both the excitation and the reception of the signal depend on the relative orientation of the crystallites with respect to the coil axis. To our knowledge, this is the first time such a global approach is presented. An extensive numerical study of the composite echo sequence described above is performed in this article. The key of the discrimination between the sequences lies in using the first five reduced moments of the excitation profile as well as an estimator of the phase linearity. Based on such information, we suggest that the echo sequence that best fulfills our criterion is (1)0-τ-(0.35)0(2.1)π(0.35)0, the pulse angles ωRFtp being in radians. The subscripts are the relative pulse phases. We outlined the way to implement the spin echo mapping method to reconstruct large spectra with this sequence, and it is shown that it reduces the acquisition time by a factor of 1.7 if compared to the classical Hahn echo. Some other

  15. Comparison of dB/dt between EPI and spin-echo pulse sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ogura, Akio [Kyoto City Hospital (Japan); Hongoh, Takaharu; Inoue, Hiroshi; Yamazaki, Masaru; Higashida, Mitsuharu

    2001-04-01

    In MR imaging, the time-varying magnetic field associated with gradients induces electric fields in the human body and may stimulate nerves and even the heart. The time rate of change in gradient magnetic fields on echo planar imaging (EPI) needs to exceed 20 mT/ms. EPI has recently become more widely used in the clinical field, and the protection of patient safety during MR scans has become an issue. However dB/dt as an index of the time-varying magnetic field is not displayed on the operating monitor. Therefore dB/dt of various scan techniques was measured using a search coil and storage oscilloscope, according to the IEC standard method. The results demonstrated that dB/dt of EPI, spin-echo, and field-echo techniques are much the same. Thus, the possibility of a risk to health resulting from EPI scanning is the same as that for other scanning techniques that use a high-performance MRI system. Therefore, even with spin-echo scanning, it is necessary to consider biological change in patients. (author)

  16. Sub-piexl methods for improving vector quality in echo PIV flow, imaging technology.

    Science.gov (United States)

    Niu, Lili; Wang, Jing; Qian, Ming; Zheng, Hairong

    2009-01-01

    Developments of many cardiovascular problems have been shown to have a close relationship with arterial flow conditions. An ultrasound-based particle image velocimetry technique(Echo PIV) was recently developed to measure multi-component velocity vectors and local shear rates in arteries and opaque fluid flows by identifying and tracking flow tracers (ultrasound contrast microbubbles) within these flow fields. To improve the measurement accuracy, sub-pixel calculation method was adopted in this paper to maximize the ultrasound RF signal and B mode image correlation accuracy and increase the image spatial resolution. This algorithm is employed in processing both computer-generated particle image patterns and the B-mode images of microbubbles in rotating flows obtained by a high frame rate (up to 1000 frames per second) ultrasound imaging system. The results show the correlation of particle patterns and individual flow vector quality are improved and the overall flow mappings are also improved significantly. This would help the Echo PIV system to provide better multi-component velocity accuracy.

  17. Evaluation of small ({<=}2 cm) dysplastic nodules and well-differentiated hepatocellular carcinomas with ferucarbotran-enhanced MRI in a 1.0-T MRI unit: Utility of T2*-weighted gradient echo sequences with an intermediate-echo time

    Energy Technology Data Exchange (ETDEWEB)

    Tonan, Tatsuyuki [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan); Fujimoto, Kiminori [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan)], E-mail: kimichan@med.kurume-u.ac.jp; Azuma, Sanae [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan); Ono, Noriyuki [Department of Internal Medicine, Chikugo City Hospital, Chikugo (Japan); Matsushita, Sunao [Department of Radiology, Chikugo City Hospital, 917-1 Izumi, Chikugo 833-0041 (Japan); Kojiro, Masamichi [Department of Pathology, Kurume University School of Medicine, Kurume (Japan); Hayabuchi, Naofumi [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan)

    2007-10-15

    Purpose: To evaluate the detectability and signal intensities of small ({<=}2 cm) dysplastic nodules (DNs) and well-differentiated hepatocellular carcinomas (w-HCCs) by T2*-weighted gradient echo (GRE) sequences using an intermediate echo-time (TE) with ferucarbotran in a 1.0-T magnetic resonance imaging (MRI) unit. Materials and methods: Pathologically confirmed DNs (n = 13) and w-HCCs (n = 31) with a median largest dimension of 1.1 cm were scanned using ferucarbotran-enhanced MRI. Conventional T2*-weighted GRE sequences (conventional-T2*-GRE: repetition time, 280 ms; echo time, 14 ms; flip angle, 60 deg.) and specific T2*-weighted GRE sequences using an intermediate-TE (specific-T2*-GRE: repetition time, 140 ms; echo time, 8 ms; flip angle, 30 deg.) were obtained before and after ferucarbotran administration. Two independent observers scored all nodules for visibility and assigned confidence level scores to their observations. To assess the effect of ferucarbotran, the tumor-liver signal contrast-to-noise ratio (tumor-liver-CNR) was also calculated for detected nodules by the same two observers with consensus. Results: There was good interobserver agreement regarding the presence of nodules for both sequence types. Qualitative and quantitative analyses indicated that specific-T2*GRE sequences were superior to conventional-T2*-GRE sequences for detecting DNs and w-HCCs with hypointense signals. The tumor-liver-CNR of DNs was significantly different between specific-T2*-GRE sequences and conventional-T2*-GRE sequences (Mann-Whitney test, P < 0.001). Both qualitative and quantitative analyses indicated that conventional-T2*-GRE sequences were superior to specific-T2*-GRE sequences for detecting w-HCCs with heterogeneous and hyperintense signals. Conclusion: Specific-T2*-GRE sequences with ferucarbotran are useful for detecting DNs and w-HCCs that produce hypointense signals on a 1.0-T MRI unit.

  18. Correction of phase errors in quantitative water-fat imaging using a monopolar time-interleaved multi-echo gradient echo sequence.

    Science.gov (United States)

    Ruschke, Stefan; Eggers, Holger; Kooijman, Hendrik; Diefenbach, Maximilian N; Baum, Thomas; Haase, Axel; Rummeny, Ernst J; Hu, Houchun H; Karampinos, Dimitrios C

    2017-09-01

    To propose a phase error correction scheme for monopolar time-interleaved multi-echo gradient echo water-fat imaging that allows accurate and robust complex-based quantification of the proton density fat fraction (PDFF). A three-step phase correction scheme is proposed to address a) a phase term induced by echo misalignments that can be measured with a reference scan using reversed readout polarity, b) a phase term induced by the concomitant gradient field that can be predicted from the gradient waveforms, and c) a phase offset between time-interleaved echo trains. Simulations were carried out to characterize the concomitant gradient field-induced PDFF bias and the performance estimating the phase offset between time-interleaved echo trains. Phantom experiments and in vivo liver and thigh imaging were performed to study the relevance of each of the three phase correction steps on PDFF accuracy and robustness. The simulation, phantom, and in vivo results showed in agreement with the theory an echo time-dependent PDFF bias introduced by the three phase error sources. The proposed phase correction scheme was found to provide accurate PDFF estimation independent of the employed echo time combination. Complex-based time-interleaved water-fat imaging was found to give accurate and robust PDFF measurements after applying the proposed phase error correction scheme. Magn Reson Med 78:984-996, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  19. Adaptive Light Modulation for Improved Resolution and Efficiency in All-Optical Pulse-Echo Ultrasound.

    Science.gov (United States)

    Alles, Erwin J; Colchester, Richard J; Desjardins, Adrien E

    2016-01-01

    In biomedical all-optical pulse-echo ultrasound systems, ultrasound is generated with the photoacoustic effect by illuminating an optically absorbing structure with a temporally modulated light source. Nanosecond range laser pulses are typically used, which can yield bandwidths exceeding 100 MHz. However, acoustical attenuation within tissue or nonuniformities in the detector or source power spectra result in energy loss at the affected frequencies and in a reduced overall system efficiency. In this work, a laser diode is used to generate linear and nonlinear chirp optical modulations that are extended to microsecond time scales, with bandwidths constrained to the system sensitivity. Compared to those obtained using a 2-ns pulsed laser, pulse-echo images of a phantom obtained using linear chirp excitation exhibit similar axial resolution (99 versus 92 μm, respectively) and signal-to-noise ratios (SNRs) (10.3 versus 9.6 dB). In addition, the axial point spread function (PSF) exhibits lower sidelobe levels in the case of chirp modulation. Using nonlinear (time-stretched) chirp excitations, where the nonlinearity is computed from measurements of the spectral sensitivity of the system, the power spectrum of the imaging system was flattened and its bandwidth broadened. Consequently, the PSF has a narrower axial extent and still lower sidelobe levels. Pulse-echo images acquired with time-stretched chirps as optical modulation have higher axial resolution (64 μm) than those obtained with linear chirps, at the expense of a lower SNR (6.8 dB). Using a linear or time-stretched chirp, the conversion efficiency from optical power to acoustical pressure improved by a factor of 70 or 61, respectively, compared to that obtained with pulsed excitation.

  20. Off-resonance effects in (14)N NQR signals from the pulsed spin-locking (PSL) and three-pulse echo sequence; a study for monoclinic TNT.

    Science.gov (United States)

    Smith, John A S; Rowe, Michael D; Althoefer, Kaspar; Peirson, Neil F; Barras, Jamie

    2015-10-01

    In NQR detection applications signal averaging by the summation of rapidly regenerated signals from multiple pulse sequences of the pulsed spin-locking (PSL) type is often used to improve sensitivity. It is important to characterise and if possible minimise PSL sequence off-resonance effects since they can make it difficult to optimise detection performance. We illustrate this with measurements of the variation of the decay time T2e and the amplitude of PSL signal trains with pulse spacing and excitation offset frequency for the 870 kHz ν+(14)N NQR line of monoclinic TNT under carefully stabilised temperature conditions. We have also carried out a similar study of signals from monoclinic TNT and 1H-1,2,3-triazole generated by a three-pulse echo sequence and the results are shown to agree well with a theoretical treatment appropriate to polycrystalline NQR samples such as TNT for which spin I=1, asymmetry parameter η≠0 and T1≫T2. Based on this theory we derive simple models for calculating TNT PSL signal trains and hence the pulse spacing and off-resonance dependence of signal amplitude and T2e which we compare to our experimental data. We discuss the influence of PSL echo summation on off-resonance effects in detected signal intensity and show how a phase-alternated multiple pulse sequence can be used in combination with the PSL sequence to eliminate variation in detection performance due to off-resonance effects.

  1. Diffusion-Weighted Imaging with Dual-Echo Echo-Planar Imaging for Better Sensitivity to Acute Stroke

    Science.gov (United States)

    Holdsworth, S.J.; Yeom, K.W.; Antonucci, M.U.; Andre, J.B.; Rosenberg, J.; Aksoy, M.; Straka, M.; Fischbein, N.J.; Bammer, R.; Moseley, M.E.; Zaharchuk, G.; Skare, S.

    2015-01-01

    BACKGROUND AND PURPOSE Parallel imaging facilitates the acquisition of echo-planar images with a reduced TE, enabling the incorporation of an additional image at a later TE. Here we investigated the use of a parallel imaging–enhanced dual-echo EPI sequence to improve lesion conspicuity in diffusion-weighted imaging. MATERIALS AND METHODS Parallel imaging–enhanced dual-echo DWI data were acquired in 50 consecutive patients suspected of stroke at 1.5T. The dual-echo acquisition included 2 EPI for 1 diffusion-preparation period (echo 1 [TE = 48 ms] and echo 2 [TE = 105 ms]). Three neuroradiologists independently reviewed the 2 echoes by using the routine DWI of our institution as a reference. Images were graded on lesion conspicuity, diagnostic confidence, and image quality. The apparent diffusion coefficient map from echo 1 was used to validate the presence of acute infarction. Relaxivity maps calculated from the 2 echoes were evaluated for potential complementary information. RESULTS Echo 1 and 2 DWIs were rated as better than the reference DWI. While echo 1 had better image quality overall, echo 2 was unanimously favored over both echo 1 and the reference DWI for its high sensitivity in detecting acute infarcts. CONCLUSIONS Parallel imaging–enhanced dual-echo diffusion-weighted EPI is a useful method for evaluating lesions with reduced diffusivity. The long TE of echo 2 produced DWIs that exhibited superior lesion conspicuity compared with images acquired at a shorter TE. Echo 1 provided higher SNR ADC maps for specificity to acute infarction. The relaxivity maps may serve to complement information regarding blood products and mineralization. PMID:24763417

  2. Differentiation between focal malignant marrow-replacing lesions and benign red marrow deposition of the spine with T2{sup *}-corrected fat-signal fraction map using a three -echo volume interpolated breath-hold gradient echo dixon sequence

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yong Pyo; Kim, Sung Jun; Chung, Tae Sub; Yoo, Yeon Hwa; Yoon, Choon Sik [Dept. of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Kanneengiesser, Stephan [MR Applications Development, Siemens AG, Healthcare Sector, Erlangen (Germany); Paek, Moon Young [Siemens Ltd., Seoul (Korea, Republic of); Song, Ho Taek; Lee, Young Han; Suh, Jin Suck [Dept. of Radiology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2014-12-15

    To assess the feasibility of T2{sup *}-corrected fat-signal fraction (FF) map by using the three-echo volume interpolated breath-hold gradient echo (VIBE) Dixon sequence to differentiate between malignant marrow-replacing lesions and benign red marrow deposition of vertebrae. We assessed 32 lesions from 32 patients who underwent magnetic resonance imaging after being referred for assessment of a known or possible vertebral marrow abnormality. The lesions were divided into 21 malignant marrow-replacing lesions and 11 benign red marrow depositions. Three sequences for the parameter measurements were obtained by using a 1.5-T MR imaging scanner as follows: three-echo VIBE Dixon sequence for FF; conventional T1-weighted imaging for the lesion-disc ratio (LDR); pre- and post-gadolinium enhanced fat-suppressed T1-weighted images for the contrast-enhancement ratio (CER). A region of interest was drawn for each lesion for parameter measurements. The areas under the curve (AUC) of the parameters and their sensitivities and specificities at the most ideal cutoff values from receiver operating characteristic curve analysis were obtained. AUC, sensitivity, and specificity were respectively compared between FF and CER. The AUCs of FF, LDR, and CER were 0.96, 0.80, and 0.72, respectively. In the comparison of diagnostic performance between the FF and CER, the FF showed a significantly larger AUC as compared to the CER (p = 0.030), although the difference of sensitivity (p = 0.157) and specificity (p = 0.157) were not significant. Fat-signal fraction measurement using T2{sup *}-corrected three-echo VIBE Dixon sequence is feasible and has a more accurate diagnostic performance, than the CER, in distinguishing benign red marrow deposition from malignant bone marrow-replacing lesions.

  3. Supraspinatus tendon tears at 3.0 T shoulder MR arthrography: diagnosis with 3D isotropic turbo spin-echo SPACE sequence versus 2D conventional sequences

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Joon-Yong; Jee, Won-Hee; Park, Michael Y.; Lee, So-Yeon [Seoul St. Mary' s Hospital, The Catholic University of Korea, Department of Radiology, Seoul (Korea, Republic of); Kim, Yang-Soo [Seoul St. Mary' s Hospital, The Catholic University of Korea, Department of Orthopedic Surgery, Seoul (Korea, Republic of)

    2012-11-15

    To assess the diagnostic performance of shoulder MR arthrography with 3D isotropic fat-suppressed (FS) turbo spin-echo sequence (TSE-SPACE) for supraspinatus tendon tears in comparison with 2D conventional sequences at 3.0 T. The study was HIPAA-compliant and approved by the institutional review board with a waiver of informed consent. Eighty-seven arthroscopically confirmed patients who underwent 3.0 T shoulder MR arthrography with 2D sequences and 3D TSE-SPACE were included in a consecutive fashion from March 2009 to February 2010. Two reviewers independently analyzed 2D sequences and 3D TSE-SPACE. Sensitivity, specificity, accuracy, and interobserver agreement ({kappa}) were compared between 2D sequences and 3D TSE-SPACE for full-thickness and partial-thickness supraspinatus tendon tears together and for partial-thickness supraspinatus tendon tears alone. There were 33 full-thickness tears and 28 partial-thickness tears of supraspinatus tendons. For full-thickness and partial-thickness supraspinatus tendon tears together, the mean sensitivity, specificity, and accuracy of both readers were 96, 92, and 94% on 2D sequences and 91, 84, and 89% on 3D TSE-SPACE. For partial-thickness supraspinatus tendon tears alone, the mean sensitivity, specificity, and accuracy were 95, 92, and 94% on 2D sequences and 84, 85, and 84% on 3D TSE-SPACE. There was no statistical difference between 2D sequences and 3D TSE-SPACE. Interobserver agreements were almost perfect on 2D conventional sequences and substantial on 3D TSE-SPACE. Compared with 2D conventional sequences, MR arthrography using 3D TSE-SPACE was comparable for diagnosing supraspinatus tendon tears despite limitations in detecting small partial-thickness tears and in discriminating between full-thickness and deep partial-thickness tears. (orig.)

  4. Semiquantitative assessment of subchondral bone marrow edema-like lesions and subchondral cysts of the knee at 3T MRI: A comparison between intermediate-weighted fat-suppressed spin echo and Dual Echo Steady State sequences

    Directory of Open Access Journals (Sweden)

    Jakicic John M

    2011-09-01

    Full Text Available Abstract Background Choice of appropriate MR pulse sequence is important for any research studies using imaging-derived data. The aim of this study was to compare semiquantitative assessment of subchondral bone marrow edema-like lesions and subchondral cysts using intermediate-weighted (IW fat-suppressed (fs spin echo and Dual Echo Steady State (DESS sequences on 3 T MRI. Methods Included were 201 subjects aged 35-65 with frequent knee pain. 3T MRI was performed with the same sequence protocol as in the Osteoarthritis Initiative (OAI. In a primary reading subchondral bone marrow edema-like lesions were assessed according to the WORMS system. Two hundred subregions with such lesions were randomly chosen. The extent of subchondral bone marrow edema-like lesions was re-evaluated separately using sagittal IW fs and DESS sequences according to WORMS. Lesion size and confidence of the differentiation between subchondral bone marrow edema-like lesions and subchondral cysts located within or adjacent to them was rated from 0 to 3. Wilcoxon signed-rank tests and chi-square statistics were used to examine differences between the two sequences. Results Of 200 subchondral bone marrow edema-like lesions detected by IW fs sequence, 93 lesions (46.5% were not depicted by the DESS sequence. The IW fs sequence depicted subchondral bone marrow edema-like lesions to a larger extent than DESS (p Conclusions In direct comparison the IW fs sequence depicts more subchondral bone marrow edema-like lesions and better demonstrate the extent of their maximum size. The DESS sequence helps in the differentiation of subchondral bone marrow edema-like lesions and subchondral cysts. The IW fs sequence should be used for determination of lesion extent whenever the size of subchondral bone marrow edema-like lesions is the focus of attention.

  5. Cartilage destruction in small joints by rheumatoid arthritis: assessment of fat-suppressed three-dimensional gradient-echo MR pulse sequences in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Uhl, M.; Allmann, K.H.; Hauer, M.P.; Langer, M. [Department of Diagnostic Radiology, University Hospital Freiburg (Germany); Ihling, C. [Department of Pathology, University Hospital Freiburg, Freiburg (Germany); Conca, W. [Department of Rheumatology, University Hospital Freiburg (Germany)

    1998-12-01

    Purpose. To assess the accuracy of different MR sequences for the detection of articular cartilage abnormalities in rheumatoid arthritis. Design and patients. Ten metacarpophalangeal joints and 10 metatarsophalangeal joints (specimens from arthritis patients undergoing ablative joint surgery) were examined with a fat-suppressed (FS) 3D FLASH, a FS 3D FISP, a FS 2D fast spin-echo T2-weighted, and a 2D FS spin-echo T1-weighted sequence. Each cartilage lesion and each cortical lesion was graded from 0 to 4 (modified Outerbridge staging system). Subsequently, the results of each sequence were compared with the macroscopic findings and statistically tested against each other. Results. The study shows that 3D gradient-echo sequences with fat suppression were best for imaging and grading of cartilage lesions in arthritis of the small joints of the hands and feet. Using 3D techniques, all grade 2, grade 3, and grade 4 lesions of cartilage or cortical bone were detected. Conclusion. FS 3D gradient-echo techniques were best for the detection and grading of hyaline cartilage and subchondral bone lesions in rheumatoid arthritis. MRI has a great potential as an objective method of evaluating cartilage damage and bone erosions in rheumatoid arthritis. (orig.) With 5 figs., 19 refs.

  6. Combining parallel detection of proton echo planar spectroscopic imaging (PEPSI) measurements with a data-consistency constraint improves SNR.

    Science.gov (United States)

    Tsai, Shang-Yueh; Hsu, Yi-Cheng; Chu, Ying-Hua; Kuo, Wen-Jui; Lin, Fa-Hsuan

    2015-12-01

    One major challenge of MRSI is the poor signal-to-noise ratio (SNR), which can be improved by using a surface coil array. Here we propose to exploit the spatial sensitivity of different channels of a coil array to enforce the k-space data consistency (DC) in order to suppress noise and consequently to improve MRSI SNR. MRSI data were collected using a proton echo planar spectroscopic imaging (PEPSI) sequence at 3 T using a 32-channel coil array and were averaged with one, two and eight measurements (avg-1, avg-2 and avg-8). The DC constraint was applied using a regularization parameter λ of 1, 2, 3, 5 or 10. Metabolite concentrations were quantified using LCModel. Our results show that the suppression of noise by applying the DC constraint to PEPSI reconstruction yields up to 32% and 27% SNR gain for avg-1 and avg-2 data with λ = 5, respectively. According to the reported Cramer-Rao lower bounds, the improvement in metabolic fitting was significant (p < 0.01) when the DC constraint was applied with λ ≥ 2. Using the DC constraint with λ = 3 or 5 can minimize both root-mean-square errors and spatial variation for all subjects using the avg-8 data set as reference values. Our results suggest that MRSI reconstructed with a DC constraint can save around 70% of scanning time to obtain images and spectra with similar SNRs using λ = 5.

  7. Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences

    Energy Technology Data Exchange (ETDEWEB)

    Altahawi, Faysal F.; Blount, Kevin J.; Omar, Imran M. [Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL (United States); Morley, Nicholas P. [Marshfield Clinic, Department of Radiology, Marshfield, WI (United States); Raithel, Esther [Siemens Healthcare GmbH, Erlangen (Germany)

    2017-01-15

    To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 x 0.5 x 3 mm{sup 3}; ∝10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci. (orig.)

  8. Comparison between gadolinium-enhanced 2D T1-weighted gradient-echo and spin-echo sequences in the detection of active multiple sclerosis lesions on 3.0T MRI

    Energy Technology Data Exchange (ETDEWEB)

    Aymerich, F.X. [Hospital Universitari Vall d' Hebron, Universitat Autonoma de Barcelona, MR Unit. Department of Radiology (IDI), Barcelona (Spain); Universitat Politecnica de Catalunya - Barcelona Tech (UPC), Department of Automatic Control (ESAII), Barcelona (Spain); Auger, C.; Alcaide-Leon, P.; Pareto, D.; Huerga, E.; Corral, J.F.; Mitjana, R.; Rovira, A. [Hospital Universitari Vall d' Hebron, Universitat Autonoma de Barcelona, MR Unit. Department of Radiology (IDI), Barcelona (Spain); Sastre-Garriga, J.; Montalban, X. [Hospital Universitari Vall d' Hebron, Universitat Autonoma de Barcelona, Centre d' Esclerosi Multiple de Catalunya (Cemcat), Department of Neurology/Neuroimmunology, Barcelona (Spain)

    2017-04-15

    To compare the sensitivity of enhancing multiple sclerosis (MS) lesions in gadolinium-enhanced 2D T1-weighted gradient-echo (GRE) and spin-echo (SE) sequences, and to assess the influence of visual conspicuity and laterality on detection of these lesions. One hundred MS patients underwent 3.0T brain MRI including gadolinium-enhanced 2D T1-weighted GRE and SE sequences. The two sets of contrast-enhanced scans were evaluated in random fashion by three experienced readers. Lesion conspicuity was assessed by the image contrast ratio (CR) and contrast-to-noise ratio (CNR). The intracranial region was divided into four quadrants and the impact of lesion location on detection was assessed in each slice. Six hundred and seven gadolinium-enhancing MS lesions were identified. GRE images were more sensitive for lesion detection (0.828) than SE images (0.767). Lesions showed a higher CR in SE than in GRE images, whereas the CNR was higher in GRE than SE. Most misclassifications occurred in the right posterior quadrant. The gadolinium-enhanced 2D T1-weighted GRE sequence at 3.0T MRI enables detection of enhancing MS lesions with higher sensitivity and better lesion conspicuity than 2D T1-weighted SE. Hence, we propose the use of gadolinium-enhanced GRE sequences rather than SE sequences for routine scanning of MS patients at 3.0T. (orig.)

  9. Magnetization transfer contrast imaging in bovine and human cortical bone applying an ultrashort echo time sequence at 3 Tesla.

    Science.gov (United States)

    Springer, Fabian; Martirosian, Petros; Machann, Jürgen; Schwenzer, Nina F; Claussen, Claus D; Schick, Fritz

    2009-05-01

    Magnetization transfer (MT) contrast imaging reveals interactions between free water molecules and macromolecules in a variety of tissues. The introduction of ultrashort echo time (UTE) sequences to clinical whole-body MR scanners expands the possibility of MT imaging to tissues with extremely fast signal decay such as cortical bone. The aim of this study was to investigate the MT effect of bovine cortical bone in vitro on a 3 Tesla whole-body MR unit. A 3D-UTE sequence with a rectangular-shaped on-resonant excitation pulse and a Gaussian-shaped off-resonant saturation pulse for MT preparation was applied. The flip angle and off-resonance frequency of the MT pulse was systematically varied. Measurements on various samples of bovine cortical bone, agar gel, aqueous manganese chloride solutions, and solid polymeric materials (polyurethane) were performed, followed by preliminary applications on human tibial bone in vivo. Direct on-resonant saturation effects of the MT prepulses were calculated numerically by means of Bloch's equations. Corrected for direct saturation effects dry and fresh bovine cortical bone showed "true" MTR values of 0.26 and 0.21, respectively. In vivo data were obtained from three healthy subjects and showed MTR values of 0.30 +/- 0.08. In vivo studies into MT of cortical bone might have the potential to give new insights in musculoskeletal pathologies.

  10. Magnetic resonance visualization of conductive structures by sequence-triggered direct currents and spin-echo phase imaging

    Energy Technology Data Exchange (ETDEWEB)

    Eibofner, Frank; Wojtczyk, Hanne; Graf, Hansjörg, E-mail: hansjoerg.graf@med.uni-tuebingen.de, E-mail: drGraf@t-online.de [Section on Experimental Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany); Clasen, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany)

    2014-06-15

    Purpose: Instrument visualization in interventional magnetic resonance imaging (MRI) is commonly performed via susceptibility artifacts. Unfortunately, this approach suffers from limited conspicuity in inhomogeneous tissue and disturbed spatial encoding. Also, susceptibility artifacts are controllable only by sequence parameters. This work presents the basics of a new visualization method overcoming such problems by applying sequence-triggered direct current (DC) pulses in spin-echo (SE) imaging. SE phase images allow for background free current path localization. Methods: Application of a sequence-triggered DC pulse in SE imaging, e.g., during a time period between radiofrequency excitation and refocusing, results in transient field inhomogeneities. Dependent on the additional z-magnetic field from the DC, a phase offset results despite the refocusing pulse. False spatial encoding is avoided by DC application during periods when read-out or slice-encoding gradients are inactive. A water phantom containing a brass conductor (water equivalent susceptibility) and a titanium needle (serving as susceptibility source) was used to demonstrate the feasibility. Artifact dependence on current strength and orientation was examined. Results: Without DC, the brass conductor was only visible due to its water displacement. The titanium needle showed typical susceptibility artifacts. Applying triggered DC pulses, the phase offset of spins near the conductor appeared. Because SE phase images are homogenous also in regions of persistent field inhomogeneities, the position of the conductor could be determined with high reliability. Artifact characteristic could be easily controlled by amperage leaving sequence parameters unchanged. For an angle of 30° between current and static field visualization was still possible. Conclusions: SE phase images display the position of a conductor carrying pulsed DC free from artifacts caused by persistent field inhomogeneities. Magnitude and phase

  11. T{sub 2}-weighted half-fourier acquired single-shot turbo-spin-echo-sequence in comparison with standard T{sub 2}-weighted fast-spin-echo-sequence for cerebral MRI. A sequence comparison; Die T{sub 2}-gewichtete Halb-Fourier Turbo-Spin-Echo-Technik mit erhoehter Echozuglaenge im Vergleich zur konventionellen T{sub 2}-gewichteten Turbo-Spin-Echo-Technik fuer die zerebrale Magnetresonanztomographie. Ein Sequenzvergleich

    Energy Technology Data Exchange (ETDEWEB)

    Hoffmann, K.T.; Hosten, N.; Ehrenstein, T.; Gutberlet, M.; Felix, R. [Humboldt-Universitaet, Berlin (Germany). Strahlenklinik und Poliklinik; Roericht, S. [Humboldt-Universitaet, Berlin (Germany). Neurologische Klinik

    2000-06-01

    Purpose: To compare a T{sub 2}-weighted half-fourier acquired single-shot turbo spin-echo (HF-TSE) sequence (HASTE-sequence) for cerebral MRI with a standard T{sub 2}-weighted fast spin-echo (TSE) sequence. Materials and Methods: Signal-to-noise (SNR) and contrast-to-noise ratios (CNR) for different cerebral structures, and intracerebral lesions as well as the detectability of intracerebral lesions depending on size and relaxation properties were evaluated on cranial MR examinations of 46 patients with both a TSE and a HF-TSE sequence. Results: SNR and CNR were found to be significantly higher with the TSE sequence for all normal structures and lesions except CSF, and lesions with short relaxation time T{sub 2} (p<0.001). The number of detected lesions larger than 10 mm was similar with both sequences. Thirty-six (TSE) and 34 (HF-TSE) hyperintense, and 7 (TSE) and 2 (HF-TSE) hyperintense lesions of at least 5 mm but less than 10 mm in size were detected. Thirty-three (TSE) and 10 (HF-TSE) hyperintense, and 2 (TSE) and no (HF-TSE) hypointense lesions smaller than 5 mm were detected. Conclusion: Due to its short acquisition time, the HF-TSE sequence is an alternative for MR examinations of non-compliant or claustrophobic patients. The low SNR and CNR relative to the TSE-technique are limiting factors as to the detectability of small lesions or lesions with low contrast to surrounding structures, with the risk of an increasing number of false negative results in lesions with short T{sub 2} relaxation time smaller than 10 mm. (orig.) [German] Zielsetzung: Bewertung der T{sub 2}-gewichteten Halb-Fourier Turbo-Spin-Echo-Technik mit erhoehter Echozuglaenge (HF-TSE) fuer die zerebrale MRT im Vergleich zur konventionellen T{sub 2}-gewichteten Turbo-Spin-Echo-Technik (TSE). Methodik: Anhand von 46 MRT-Untersuchungen wurden das Signal-zu-Rauschen- (SRV) und Kontrast-zu-Rauschen-Verhaeltnis (KRV) zerebraler Strukturen, von Liquor und zerebralen Laesionen sowie die

  12. ECHO virus

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/001340.htm ECHO virus To use the sharing features on this page, please enable JavaScript. Enteric cytopathic human orphan (ECHO) viruses are a group of viruses that lead to ...

  13. Fractional Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Siour, G; Hartmann, J -M; Faucher, O; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh

    2016-01-01

    We report the observation of fractional echoes in a double-pulse excited nonlinear system. Unlike standard echoes which appear periodically at delays which are integer multiple of the delay between the two exciting pulses, the fractional echoes appear at rational fractions of this delay. We discuss the mechanism leading to this phenomenon, and provide the first experimental demonstration of fractional echoes by measuring third harmonic generation in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses.

  14. Multi-Echo-Based Echo-Planar Spectroscopic Imaging Using a 3T MRI Scanner

    Directory of Open Access Journals (Sweden)

    Jon K. Furuyama

    2011-10-01

    Full Text Available The use of spin-echoes has been employed in an Echo-Planar Spectroscopic Imaging (EPSI sequence to collect multiple phase encoded lines within a single TR in a Multi-Echo-based Echo-Planar Spectroscopic Imaging technique (MEEPSI. Despite the T2 dependence on the amplitude of the spin-echoes, the Full Width at Half Maximum (FWHM of the derived multi-echo Point Spread Function (PSF is shown to decrease, indicating an improved overall spatial resolution without requiring any additional scan time. The improved spatial resolution is demonstrated in the one-dimensional (1D spatial profiles of the N-Acetyl Aspartate (NAA singlet along the phase encode dimension in a gray matter phantom. Although the improved spatial resolution comes at the expense of spectral resolution, it is shown in vivo that peak broadening due to T2* decay is more significant than the loss of resolution from using spin-echoes and therefore does not affect the ability to quantify metabolites using the LCModel fitting algorithm.

  15. Comparison of 3D turbo spin-echo SPACE sequences with conventional 2D MRI sequences to assess the shoulder joint

    Energy Technology Data Exchange (ETDEWEB)

    Kloth, Jost Karsten, E-mail: jost.kloth@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Winterstein, Marianne, E-mail: marianne.winterstein@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Akbar, Michael, E-mail: michael.akbar@med.uni-heidelberg.de [Orthopedic and Trauma Surgery, University Hospital Heidelberg, Schlierbacher Landstraße 200a, D-69118 Heidelberg (Germany); Meyer, Esther, E-mail: esther.meyer@siemens.com [Siemens Healthcare, Erlangen (Germany); Paul, Dominik, E-mail: dominik.paul@siemens.com [Siemens Healthcare, Erlangen (Germany); Kauczor, Haus-Ulrich, E-mail: hans-ulrich.kauczor@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Weber, Marc-André, E-mail: marcandre.weber@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany)

    2014-10-15

    Highlights: • 3D SPACE and conventional 2D TSE MRI for assessment of the shoulder joint were compared. • Concordance for most pathologys was substantial to almost perfect. • Examination time could be reduced up to 8 min (27%). • Regarding rotator cuff injuries an additional sagittal T2w TSE sequence in 3D protocol is recommended. - Abstract: Purpose: To determine the accuracy and reliability of three-dimensional (3D) T1- and proton density (PD)-weighted turbo spin-echo (TSE) sampling perfection with application-optimized contrasts using different flip-angle evolution (SPACE) compared with conventional 2D sequences in assessment of the shoulder-joint. Materials and methods: Ninety-three subjects were examined on a 3-T MRI system with both conventional 2D-TSE sequences in T1-, T2- and PD-weighting and 3D SPACE sequences in T1- and PD-weighting. All examinations were assessed independently by two reviewers for common pathologies of the shoulder-joint. Agreement between 2D- and 3D-sequences and inter-observer-agreement was evaluated using kappa-statistics. Results: Using conventional 2D TSE sequences as standard of reference, sensitivity, specificity, and accuracy values of 3D SPACE were 81.8%, 95.1%, and 93.5% for injuries of the supraspinatus-tendon (SSP), 81.3%, 93.5%, and 91.4% for the cartilage layer and 82.4%, 98.5%, and 97.5% for the long biceps tendon. Concordance between 2D and 3D was almost perfect for tendinopathies of the SSP (κ = 0.85), osteoarthritis (κ = 1), luxation of the biceps tendon (κ = 1) and adjacent bone marrow (κ = 0.92). Inter-observer-agreement was generally higher for conventional 2D TSE sequences (κ, 0.23–1.0), when compared to 3D SPACE sequences (κ, −0.33 to 1.0) except for disorders of the long biceps tendon and supraspinatus tendon rupture. Conclusion: Because of substantial and almost perfect concordance with conventional 2D TSE sequences for common shoulder pathologies, MRI examination-time can be reduced by nearly 40

  16. Assessment of cerebral venous sinus ‎thrombosis using T2*-weighted ‎gradient echo magnetic resonance ‎imaging sequences

    Directory of Open Access Journals (Sweden)

    Fatemeh Bidar

    2016-04-01

    Full Text Available Background: The purpose of this study is to demonstrate the advantages of gradient echo (GRE sequences in the detection and characterization of cerebral venous sinus thrombosis compared to conventional magnetic resonance sequences.Methods: A total of 17 patients with cerebral venous thrombosis (CVT were evaluated using different magnetic resonance imaging (MRI sequences. The MRI sequences included T1-weighted spin echo (SE imaging, -weighted turbo SE (TSE, fluid attenuated inversion recovery (FLAIR, -weighted conventional GRE, and diffusion weighted imaging (DWI. MR venography (MRV images were obtained as the golden standard.Results: Venous sinus thrombosis was best detectable in -weighted conventional GRE sequences in all patients except in one case. Venous thrombosis was undetectable in DWI. -weighted GRE sequences were superior to -weighted TSE, T1-weighted SE, and FLAIR. Enhanced MRV was successful in displaying the location of thrombosis.Conclusion: -weighted conventional GRE sequences are probably the best method for the assessment of cerebral venous sinus thrombosis. The mentioned method is non-invasive; therefore, it can be employed in the clinical evaluation of cerebral venous sinus thrombosis.

  17. Semiquantitative assessment of focal cartilage damage at 3 T MRI: A comparative study of dual echo at steady state (DESS) and intermediate-weighted (IW) fat suppressed fast spin echo sequences

    Energy Technology Data Exchange (ETDEWEB)

    Roemer, Frank W., E-mail: froemer@bu.edu [Quantitative Imaging Center (QIC), Department of Radiology, Boston University Medical Center, Boston, MA (United States); Department of Radiology, Klinikum Augsburg, Augsburg (Germany); Kwoh, C. Kent [Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine (United States); VA Pittsburgh Healthcare System (United States); Hannon, Michael J. [Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine (United States); Crema, Michel D. [Quantitative Imaging Center (QIC), Department of Radiology, Boston University Medical Center, Boston, MA (United States); Moore, Carolyn E. [Department of Nutrition and Food Sciences, Texas Woman' s University (United States); Jakicic, John M. [Department of Health and Physical Activity, University of Pittsburgh (United States); Green, Stephanie M. [Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine (United States); Guermazi, Ali [Quantitative Imaging Center (QIC), Department of Radiology, Boston University Medical Center, Boston, MA (United States)

    2011-11-15

    Purpose: The aim of the study was to compare semiquantitative assessment of focal cartilage damage using the dual echo at steady state (DESS)- and intermediate-weighted (IW) fat suppressed (fs) sequences at 3 T MRI. Methods: Included were 201 subjects aged 35-65 with frequent knee pain. MRI was performed with the same sequence protocol as in the Osteoarthritis Initiative (OAI): sagittal IW fs, triplanar DESS and coronal IW sequences. Cartilage status was scored according to the WORMS system using all five sequences. A total of 243 focal defects were detected. In an additional consensus reading, the lesions were evaluated side-by-side using only the sagittal DESS and IW fs sequences. Lesion conspicuity was graded from 0 to 3, intrachondral signal changes adjacent to the defect were recorded and the sequence that depicted the lesion with larger diameter was noted. Wilcoxon signed-rank tests, controlled for clustering by person, were used to examine differences between the sequences. Results: 37 (17.5%) of the scorable lesions were located in the medial tibio-femoral (TF), 48 (22.7%) in the lateral TF and 126 (59.7%) in the patello-femoral compartment. 82.5% were superficial and 17.5% full-thickness defects. Conspicuity was superior for the IW sequence (p < 0.001). The DESS sequence showed more associated intrachondral signal changes (p < 0.001). In 103 (48.8%) cases, the IW fs sequence depicted the lesions as being larger (p < 0.001). Conclusions: The IW fs sequence detected more and larger focal cartilage defects than the DESS. More intrachondral signal changes were observed with the DESS.

  18. Low-field MR imaging of the spine. A comparative study of a traditional and a new, completely balanced gradient-echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Drejer, J. [Dept. of Diagnostic Radiology, Herlev Hospital, Univ. Copenhagen (Denmark); Thomsen, H.S. [Dept. of Diagnostic Radiology, Herlev Hospital, Univ. Copenhagen (Denmark); Tanttu, J. [Picker Nordstar, Helsinki (Finland)

    1995-09-01

    49 patients underwent 53 examinations with both a traditional T1-weighted gradient-echo (PS) sequence and a new completely balanced steady-state 3-D (CBASS3D) sequence; 20 examinations included the cervical spine, 8 the thoracic spine and 25 the lumbar spine. All 106 examinations were reviewed twice regarding visibility of selected structures in the spinal region and diagnostic usefulness. The CBASS3D sequence delineated the medulla, nerve roots, CSF, the intervertebral discs and the posterior longitudinal ligament significantly better than the PS sequence. Disc hernia was also better visualised (p<0.01). There were significantly more artefacts on images obtained with the CBASS3D sequence, but they were usually outside the region of interest and occurred less frequently over time due to increased experience of the staff. Both reviewers found the diagnostic usefulness of CBASS3D to be superior compared to that of PS and excellent for diagnostic purposes. (orig./MG).

  19. SLAP tears: diagnosis using 3-T shoulder MR arthrography with the 3D isotropic turbo spin-echo space sequence versus conventional 2D sequences

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Joon-Yong; Jee, Won-Hee; Park, Michael Yong [The Catholic University of Korea, Department of Radiology, Seoul St. Mary' s Hospital, College of Medicine, Seoul (Korea, Republic of); Lee, So-Yeon [Sungkyunkwan University School of Medicine, Department of Radiology, Kangbuk Samsung Hospital, Seoul (Korea, Republic of); Kim, Yang-Soo [The Catholic University of Korea, Department of Orthopaedic Surgery, Seoul St. Mary' s Hospital, College of Medicine, Seoul (Korea, Republic of)

    2013-02-15

    The aim of this study was to determine the accuracy and reliability of shoulder magnetic resonance (MR) arthrography with three-dimensional (3D) isotropic intermediate-weighted turbo spin-echo (TSE) sampling perfection with application-optimised contrasts using different flip angle evolution (SPACE) in the diagnosis of superior labrum anterior-to-posterior (SLAP) lesions compared with two-dimensional (2D) TSE at 3.0 T. MR arthrograms, including 2D TSE and 3D TSE-SPACE, in 87 patients who underwent arthroscopy were retrospectively analysed by two reviewers for the presence and type of SLAP lesions. Sensitivity and specificity were compared using McNemar's test, and inter-observer agreement was calculated using Cohen's kappa. Receiver operating characteristic (ROC) curve analyses were performed. The mean sensitivity, specificity and accuracy were 90%, 85% and 86% for 2D TSE, and 81%, 86% and 85% for 3D TSE-SPACE respectively, with no statistically significant differences. Inter-observer agreements were substantial in 2D TSE ({kappa} = 0.76) and 3D TSE-SPACE ({kappa} = 0.68). The areas under the ROC curves were 0.92 for 2D TSE and 0.90 for 3D TSE-SPACE, which were not significantly different. MR arthrography with 3D TSE-SPACE showed comparable accuracy and substantial inter-observer agreement for the diagnosis of SLAP lesions circle MR arthrography is regarded as the definitive method of shoulder imaging circle Different MR sequences are evolving for SLAP lesions circle 3D TSE-SPACE demonstrated comparable overall accuracy to 2D TSE for SLAP lesions. (orig.)

  20. Graffiti echoes

    National Research Council Canada - National Science Library

    Purcell, John

    2014-01-01

      Graffiti and street art are a kind of "voice" of the city. From the street-tagged neighborhoods to the grand billboards high in the air, graffiti seems to always echo what is happening in Los Angeles...

  1. Visualization of the 12th Cranial Nerve with MRI: Value of Balanced Fast-Field Echo and 3D-Drive Sequences Among the T2 TSE Post-Contrast T1 Sequences

    OpenAIRE

    2010-01-01

    Background/Objective: Our aim was to optimize the most effective MR imaging sequence for visualization of the 12th cranial nerve (hypoglossal nerve) through its cisternal course."nPatients and Methods: We applied balanced fast-field echo (B-FFE), 3D-T2 weighted Driven Equilibrium RF Reset Pulse (DRIVE), T2 weighted 2D TSE and post-contrast T1 weighted sequences and tried to find out the best sequence for the perfect visualization of the 12th cranial nerve. One-hundred patients without an...

  2. Improved polynomial remainder sequences for Ore polynomials.

    Science.gov (United States)

    Jaroschek, Maximilian

    2013-11-01

    Polynomial remainder sequences contain the intermediate results of the Euclidean algorithm when applied to (non-)commutative polynomials. The running time of the algorithm is dependent on the size of the coefficients of the remainders. Different ways have been studied to make these as small as possible. The subresultant sequence of two polynomials is a polynomial remainder sequence in which the size of the coefficients is optimal in the generic case, but when taking the input from applications, the coefficients are often larger than necessary. We generalize two improvements of the subresultant sequence to Ore polynomials and derive a new bound for the minimal coefficient size. Our approach also yields a new proof for the results in the commutative case, providing a new point of view on the origin of the extraneous factors of the coefficients.

  3. Whole body sodium MRI at 3T using an asymmetric birdcage resonator and short echo time sequence: first images of a male volunteer

    Science.gov (United States)

    Wetterling, Friedrich; Corteville, Dominique M.; Kalayciyan, Raffi; Rennings, Andreas; Konstandin, Simon; Nagel, Armin M.; Stark, Helmut; Schad, Lothar R.

    2012-07-01

    Sodium magnetic resonance imaging (23Na MRI) is a non-invasive technique which allows spatial resolution of the tissue sodium concentration (TSC) in the human body. TSC measurements could potentially serve to monitor early treatment success of chemotherapy on patients who suffer from whole body metastases. Yet, the acquisition of whole body sodium (23Na) images has been hampered so far by the lack of large resonators and the extremely low signal-to-noise ratio (SNR) achieved with existing resonator systems. In this study, a 23Na resonator was constructed for whole body 23Na MRI at 3T comprising of a 16-leg, asymmetrical birdcage structure with 34 cm height, 47.5 cm width and 50 cm length. The resonator was driven in quadrature mode and could be used either as a transceiver resonator or, since active decoupling was included, as a transmit-only resonator in conjunction with a receive-only (RO) surface resonator. The relative B1-field profile was simulated and measured on phantoms, and 3D whole body 23Na MRI data of a healthy male volunteer were acquired in five segments with a nominal isotropic resolution of (6 × 6 × 6) mm3 and a 10 min acquisition time per scan. The measured SNR values in the 23Na-MR images varied from 9 ± 2 in calf muscle, 15 ± 2 in brain tissue, 23 ± 2 in the prostate and up to 42 ± 5 in the vertebral discs. Arms, legs, knees and hands could also be resolved with applied resonator and short time-to-echo (TE) (0.5 ms) radial sequence. Up to fivefold SNR improvement was achieved through combining the birdcage with local RO surface coil. In conclusion, 23Na MRI of the entire human body provides sub-cm spatial resolution, which allows resolution of all major human body parts with a scan time of less than 60 min.

  4. Effect of physiological heart rate variability on quantitative T2 measurement with ECG-gated Fast Spin Echo (FSE) sequence and its retrospective correction.

    Science.gov (United States)

    de Roquefeuil, Marion; Vuissoz, Pierre-André; Escanyé, Jean-Marie; Felblinger, Jacques

    2013-11-01

    Quantitative T2 measurement is applied in cardiac Magnetic Resonance Imaging (MRI) for the diagnosis and follow-up of myocardial pathologies. Standard Electrocardiogram (ECG)-gated fast spin echo pulse sequences can be used clinically for T2 assessment, with multiple breath-holds. However, heart rate is subject to physiological variability, which causes repetition time variations and affects the recovery of longitudinal magnetization between TR periods. The bias caused by heart rate variability on quantitative T2 measurements is evaluated for fast spin echo pulse sequence. Its retrospective correction based on an effective TR is proposed. Heart rate variations during breath-holds are provided by the ECG recordings from healthy volunteers. T2 measurements were performed on a phantom with known T2 values, by synchronizing the sequence with the recorded ECG. Cardiac T2 measurements were performed twice on six volunteers. The impact of T1 on T2 is also studied. Maximum error in T2 is 26% for phantoms and 18% for myocardial measurement. It is reduced by the proposed compensation method to 20% for phantoms and 10% for in vivo measurements. Only approximate knowledge of T1 is needed for T2 correction. Heart rate variability may cause a bias in T2 measurement with ECG-gated FSE. It needs to be taken into account to avoid a misleading diagnosis from the measurements. © 2013.

  5. Diagnostic performance of the three-dimensional fast spin echo-Cube sequence in comparison with a conventional imaging protocol in evaluation of the lachrymal drainage system

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jing; Chen, Lang; Wang, Qiu-Xia; Zhu, Wen-Zhen; Luo, Xin; Peng, Li [Huazhong University of Science and Technology, Department of Radiology, Tongji Hospital, Wuhan (China); Liu, Rong [Huazhong University of Science and Technology, Department of Ophthalmology, Tongji Hospital, Wuhan (China); Xiong, Wei [GE Healthcare China Wuhan Office, Wuhan (China)

    2014-10-15

    To compare the three-dimensional (3D)-fast spin-echo (FSE)-Cube with a conventional imaging protocol in evaluation of dacryostenosis. Thirty-three patients with epiphora underwent examinations using Cube magnetic resonance dacryocystography (MRD) and a conventional protocol, which included 3D fast-recovery fast spin-echo (FRFSE) MRD and two-dimensional (2D)-FSE sequences at 3.0 T. Using lachrymal endoscopic findings as the reference standard, we calculated the sensitivity and specificity of both protocols for detecting lachrymal drainage system (LDS) obstruction and their accuracies in depicting the level of obstruction. Comparable coronal and axial images were selected for bot sequences. Two neuroradiologists graded paired images for blurring, artefacts, anatomic details, and overall image quality. The two methods showed no significant difference in sensitivity (89.5 % vs. 94.7 %; p =0.674), specificity (64.3 %; p =1) or accuracy (86.8 %; p =1) in detecting or depicting LDS obstruction. Blurring and artefacts were significantly better on 2D-FSE images (p <0.01 and p <0.05, respectively). Anatomic details were significantly better on Cube reformats (p <0.001). No significant difference existed in overall image quality (p >0.05). In comparison with the conventional protocol, Cube MRD demonstrates satisfactory image quality and similar diagnostic capability for cases of possible LDS disease. (orig.)

  6. An improved pulse sequence and inversion algorithm of T2 spectrum

    Science.gov (United States)

    Ge, Xinmin; Chen, Hua; Fan, Yiren; Liu, Juntao; Cai, Jianchao; Liu, Jianyu

    2017-03-01

    The nuclear magnetic resonance transversal relaxation time is widely applied in geological prospecting, both in laboratory and downhole environments. However, current methods used for data acquisition and inversion should be reformed to characterize geological samples with complicated relaxation components and pore size distributions, such as samples of tight oil, gas shale, and carbonate. We present an improved pulse sequence to collect transversal relaxation signals based on the CPMG (Carr, Purcell, Meiboom, and Gill) pulse sequence. The echo spacing is not constant but varies in different windows, depending on prior knowledge or customer requirements. We use the entropy based truncated singular value decomposition (TSVD) to compress the ill-posed matrix and discard small singular values which cause the inversion instability. A hybrid algorithm combining the iterative TSVD and a simultaneous iterative reconstruction technique is implemented to reach the global convergence and stability of the inversion. Numerical simulations indicate that the improved pulse sequence leads to the same result as CPMG, but with lower echo numbers and computational time. The proposed method is a promising technique for geophysical prospecting and other related fields in future.

  7. Improved motor sequence retention by motionless listening.

    Science.gov (United States)

    Lahav, Amir; Katz, Tal; Chess, Roxanne; Saltzman, Elliot

    2013-05-01

    This study examined the effect of listening to a newly learned musical piece on subsequent motor retention of the piece. Thirty-six non-musicians were trained to play an unfamiliar melody on a piano keyboard. Next, they were randomly assigned to participate in three follow-up listening sessions over 1 week. Subjects who, during their listening sessions, listened to the same initial piece showed significant improvements in motor memory and retention of the piece despite the absence of physical practice. These improvements included increased pitch accuracy, time accuracy, and dynamic intensity of key pressing. Similar improvements, though to a lesser degree, were observed in subjects who, during their listening sessions, were distracted by another task. Control subjects, who after learning the piece had listened to nonmusical sounds, showed impaired motoric retention of the piece at 1 week from the initial acquisition day. These results imply that motor sequences can be established in motor memory without direct access to motor-related information. In addition, the study revealed that the listening-induced improvements did not generalize to the learning of a new musical piece composed of the same notes as the initial piece learned, limiting the effects to musical motor sequences that are already part of the individual's motor repertoire.

  8. SU-E-J-224: Using UTE and T1 Weighted Spin Echo Pulse Sequences for MR-Only Treatment Planning; Phantom Study

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H; Fatemi, A [Sunnybrook Health Sciences Centre, Toronto, Ontario (Canada); Sahgal, A [University of Toronto, Toronto, ON (Canada)

    2015-06-15

    Purpose: Investigating a new approach in MRI based treatment planning using the combination of (Ultrashort Echo Time) UTE and T1 weighted spin echo pulse sequences to delineate air, bone and water (soft tissues) in generating pseudo CT images comparable with CT. Methods: A gel phantom containing chicken bones, ping pang balls filled with distilled water and air bubbles, was made. It scanned with MRI using UTE and 2D T1W SE pulse sequences with (in plane resolution= 0.53mm, slice thickness= 2 mm) and CT with (in plane resolution= 0.5 mm and slice thickness= 0.75mm) as a ground truth for geometrical accuracy. The UTE and T1W SE images were registered with CT using mutual information registration algorithm provided by Philips Pinnacle treatment planning system. The phantom boundaries were detected using Canny edge detection algorithm for CT, and MR images. The bone, air bubbles and water in ping pong balls were segmented from CT images using threshold 300HU, - 950HU and 0HU, respectively. These tissue inserts were automatically segmented from combined UTE and T1W SE images using edge detection and relative intensity histograms of the phantom. The obtained segmentations of air, bone and water inserts were evaluated with those obtained from CT. Results: Bone and air can be clearly differentiated in UTE images comparable to CT. Combining UTE and T1W SE images successfully segmented the air, bone and water. The maximum segmentation differences from combine MRI images (UTE and T1W SE) and CT are within 1.3 mm, 1.1mm for bone, air, respectively. The geometric distortion of UTE sequence is small less than 1 pixel (0.53 mm) of MR image resolution. Conclusion: Our approach indicates that MRI can be used solely for treatment planning and its quality is comparable with CT.

  9. Improving The Accuracy Of Selection Of Bird Radar Echoes Against A Background Of Atomized Clouds And Atmospheric Inhomogeneities

    Directory of Open Access Journals (Sweden)

    Dinevich Leonid

    2015-12-01

    Full Text Available The algorithm for bird radar echo selection was developed in Israel and has been successfully used for many years to monitor birds in periods of massive intercontinental migration in order to ensure flight safety in civil and military aviation. However, it has been found that under certain meteorological conditions the bird echo selection algorithm does not filter out false signals formed by atomized clouds and atmospheric inhomogeneities. Although the algorithm is designed to identify and sift false signals, some useful echoes from smaller birds are erroneously sifted as well.

  10. Improved genome sequencing using an engineered transposase.

    Science.gov (United States)

    Kia, Amirali; Gloeckner, Christian; Osothprarop, Trina; Gormley, Niall; Bomati, Erin; Stephenson, Michelle; Goryshin, Igor; He, Molly Min

    2017-01-17

    Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias. Here we present the discovery of a mutant transposase (Tn5-059) with a lowered GC insertion bias through protein engineering. We demonstrate Tn5-059 reduces AT dropout and increases uniformity of genome coverage in both bacterial genomes and human genome. We also observe higher library diversity generated by Tn5-059 when compared to Nextera v2 for human exomes, which leads to less sequencing and lower cost per genome. In addition, when used for human exomes, Tn5-059 delivers consistent library insert size over a range of input DNA, allowing up to a tenfold variance from the 50 ng input recommendation. Enhanced DNA input tolerance of Tn5-059 can translate to flexibility and robustness of workflow. DNA input tolerance together with superior uniformity of coverage and lower AT dropouts extend the applications of transposase based library preps. We discuss possible mechanisms of improvements in Tn5-059, and potential advantages of using the new mutant in varieties of applications including microbiome sequencing and chromatin profiling.

  11. Diffusion-weighted imaging of the sellar region: A comparison study of BLADE and single-shot echo planar imaging sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yiping, Lu [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China); Hui, Liu [MR Collaboration NE Asia, Siemens Healthcare, Siemens Ltd., China, Shanghai 201318 (China); Kun, Zhou [MR PLM APPL, Siemens Shenzhen Magnetic Resonance Ltd., Shenzhen 518057 (China); Daoying, Geng, E-mail: GengdaoyingGDY@163.com [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China); Bo, Yin, E-mail: yinbo7@163.com [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China)

    2014-07-15

    Purpose: The purpose of this study is to compare BLADE diffusion-weighted imaging (DWI) with single-shot echo planar imaging (EPI) DWI on the aspects of feasibility of imaging the sellar region and image quality. Methods: A total of 3 healthy volunteers and 52 patients with suspected lesions in the sellar region were included in this prospective intra-individual study. All exams were performed at 3.0 T with a BLADE DWI sequence and a standard single-shot EP-DWI sequence. Phantom measurements were performed to measure the objective signal-to-noise ratio (SNR). Two radiologists rated the image quality according to the visualisation of the internal carotid arteries, optic chiasm, pituitary stalk, pituitary gland and lesion, and the overall image quality. One radiologist measured lesion sizes for detecting their relationship with the image score. Results: The SNR in BLADE DWI sequence showed no significant difference from the single-shot EPI sequence (P > 0.05). All of the assessed regions received higher scores in BLADE DWI images than single-shot EP-DWI.

  12. Effects of in-pulse transverse relaxation in 3D ultrashort echo time sequences: analytical derivation, comparison to numerical simulation and experimental application at 3T.

    Science.gov (United States)

    Springer, Fabian; Steidle, Günter; Martirosian, Petros; Claussen, Claus D; Schick, Fritz

    2010-09-01

    The introduction of ultrashort-echo-time-(UTE)-sequences to clinical whole-body MR scanners has opened up the field of MR characterization of materials or tissues with extremely fast signal decay. If the transverse relaxation time is in the range of the RF-pulse duration, approximation of the RF-pulse by an instantaneous rotation applied at the middle of the RF-pulse and immediately followed by free relaxation will lead to a distinctly underestimated echo signal. Thus, the regular Ernst equation is not adequate to correctly describe steady state signal under those conditions. The paper presents an analytically derived modified Ernst equation, which correctly describes in-pulse relaxation of transverse magnetization under typical conditions: The equation is valid for rectangular excitation pulses, usually applied in 3D UTE sequences. Longitudinal relaxation time of the specimen must be clearly longer than RF-pulse duration, which is fulfilled for tendons and bony structures as well as many solid materials. Under these conditions, the proposed modified Ernst equation enables adequate and relatively simple calculation of the magnetization of materials or tissues. Analytically derived data are compared to numerical results obtained by using an established Runge-Kutta-algorithm based on the Bloch equations. Validity of the new approach was also tested by systematical measurements of a solid polymeric material on a 3T whole-body MR scanner. Thus, the presented modified Ernst equation provides a suitable basis for T1 measurements, even in tissues with T2 values as short as the RF-pulse duration: independent of RF-pulse duration, the 'variable flip angle method' led to consistent results of longitudinal relaxation time T1, if the T2 relaxation time of the material of interest is known as well.

  13. Fast T2 Mapping With Improved Accuracy Using Undersampled Spin-Echo MRI and Model-Based Reconstructions With a Generating Function

    Science.gov (United States)

    Petrovic, Andreas; Uecker, Martin; Knoll, Florian; Frahm, Jens

    2015-01-01

    A model-based reconstruction technique for accelerated T2 mapping with improved accuracy is proposed using under-sampled Cartesian spin-echo magnetic resonance imaging (MRI) data. The technique employs an advanced signal model for T2 relaxation that accounts for contributions from indirect echoes in a train of multiple spin echoes. An iterative solution of the nonlinear inverse reconstruction problem directly estimates spin-density and T2 maps from undersampled raw data. The algorithm is validated for simulated data as well as phantom and human brain MRI at 3T. The performance of the advanced model is compared to conventional pixel-based fitting of echo-time images from fully sampled data. The proposed method yields more accurate T2 values than the mono-exponential model and allows for retrospective under-sampling factors of at least 6. Although limitations are observed for very long T2 relaxation times, respective reconstruction problems may be overcome by a gradient dampening approach. The analytical gradient of the utilized cost function is included as Appendix. The source code is made available to the community. PMID:24988592

  14. Fast T2 Mapping with Improved Accuracy Using Undersampled Spin-echo MRI and Model-based Reconstructions with a Generating Function

    CERN Document Server

    Sumpf, Tilman J; Uecker, Martin; Knoll, Florian; Frahm, Jens

    2014-01-01

    A model-based reconstruction technique for accelerated T2 mapping with improved accuracy is proposed using undersampled Cartesian spin-echo MRI data. The technique employs an advanced signal model for T2 relaxation that accounts for contributions from indirect echoes in a train of multiple spin echoes. An iterative solution of the nonlinear inverse reconstruction problem directly estimates spin-density and T2 maps from undersampled raw data. The algorithm is validated for simulated data as well as phantom and human brain MRI at 3 T. The performance of the advanced model is compared to conventional pixel-based fitting of echo-time images from fully sampled data. The proposed method yields more accurate T2 values than the mono-exponential model and allows for undersampling factors of at least 6. Although limitations are observed for very long T2 relaxation times, respective reconstruction problems may be overcome by a gradient dampening approach. The analytical gradient of the utilized cost function is included...

  15. Echo project

    DEFF Research Database (Denmark)

    Gfader, Verina; Carson, Rebecca; Kraus, Chris

    2016-01-01

    team to both present the printed matter in the format of running a book stall, and stage a discursive event at the Classroom. Echo reverberates some of the encounters and debates there, with new commissioned chapters propelling a ongoing correspondence across urban environs: An essay on the General...... Intellect and Financialization sets a conceptual ground for rethinking subjective freedom; an encounter with Another LA opens out a multitude of cartographies - revealing more discreet and politically dynamic movements in the urban grid; there are glimpses of Machine Project’s events, a visual story around...

  16. Echo project

    DEFF Research Database (Denmark)

    Gfader, Verina; Carson, Rebecca; Kraus, Chris

    Echo project (ed. by Verina Gfader and Ruth Höflich) is an online publication and community board that developed from a visit to the Los Angeles Art Book fair in January 2014. It was on the occasion of a prior book project, titled Prospectus, that the editorial team had been invited by the LAABF...... Intellect and Financialization sets a conceptual ground for rethinking subjective freedom; an encounter with Another LA opens out a multitude of cartographies - revealing more discreet and politically dynamic movements in the urban grid; there are glimpses of Machine Project’s events, a visual story around...

  17. Exact solution of the CPMG pulse sequence with phase variation down the echo train: application to R₂ measurements.

    Science.gov (United States)

    Bain, Alex D; Kumar Anand, Christopher; Nie, Zhenghua

    2011-04-01

    An implicit exact algebraic solution of CPMG experiments is presented and applied to fit experiments. Approximate solutions are also employed to explore oscillations and effective decay rates of CPMG experiments. The simplest algebraic approximate solution has illustrated that measured intensities will oscillate in the conventional CPMG experiments and that using even echoes can suppress errors of measurements of R₂ due to the imperfection of high-power pulses. To deal with low-power pulses with finite width, we adapt the effective field to calculate oscillations. An optimization model with the effective field approximation and dimensionless variables is proposed to quantify oscillations of measured intensities of CPMG experiments of different phases of the π pulses. We show, as was known using other methods, that repeating one group of four pulses with different phases in CPMG experiments, which we call phase variation, but others call phase alternation or phase cycling, can significantly smooth the dependence of measured intensities on frequency offset in the range of ±½γB₁. In this paper, a second-order expression with respect to the ratio of frequency offset to π-pulse amplitude is developed to describe the effective R₂ of CPMG experiments when using a group phase variation scheme. Experiments demonstrate that (1) the exact calculation of CPMG experiments can remarkably eliminate systematic errors in measured R₂s due to the effects of frequency offset, even in the absence of phase variation; (2) CPMG experiments with group phase variation can substantially remove oscillations and effects of the field inhomogeneity; (3) the second-order expression of the effective decay rate with phase variation is able to provide reliable estimates of R₂ when offsets are roughly within ±½γB₁; and, most significantly, (4) the more sophisticated optimization model using an exact solution of the discretized CPMG experiment extends, to ±γB₁, the range of

  18. Reducing motion artefacts in diffusion-weighted MRI of the brain: efficacy of navigator echo correction and pulse triggering

    Energy Technology Data Exchange (ETDEWEB)

    Dietrich, O.; Heiland, S.; Benner, T.; Sartor, K. [Dept. of Neuroradiology, University of Heidelberg Medical School, Heidelberg (Germany)

    2000-02-01

    Diffusion-weighted MRI (DWI) is extremely sensitive to motion of the object being examined. Pulse triggering and navigator echo correction are methods for reducing motion artefacts which can be combined with conventional DWI sequences. Implementation of these methods in imaging sequences with a readout of one, three, or five echoes is presented and imaging results compared in a study of five healthy volunteers. As an objective measure for motion-induced image artefacts, the ''artefacticity'' of an image is defined. Pulse triggering and navigator echo correction significantly improve image quality and provide a technique for high-quality DWI on standard imagers without improved gradient hardware. (orig.)

  19. An analysis of the uncertainty and bias in DCE-MRI measurements using the spoiled gradient-recalled echo pulse sequence

    Energy Technology Data Exchange (ETDEWEB)

    Subashi, Ergys [Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina 27710 and Medical Physics Graduate Program, Duke University Medical Center, Durham, North Carolina 27710 (United States); Choudhury, Kingshuk R. [Department of Biomedical Engineering, Duke University Medical Center, Durham, North Carolina 27710 (United States); Johnson, G. Allan, E-mail: gjohnson@duke.edu [Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina 27710 (United States); Medical Physics Graduate Program, Duke University Medical Center, Durham, North Carolina 27710 (United States); Department of Biomedical Engineering, Duke University Medical Center, Durham, North Carolina 27710 (United States); Department of Radiology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2014-03-15

    Purpose: The pharmacokinetic parameters derived from dynamic contrast-enhanced (DCE) MRI have been used in more than 100 phase I trials and investigator led studies. A comparison of the absolute values of these quantities requires an estimation of their respective probability distribution function (PDF). The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence. Methods: The variance in the SPGR signal intensity arises from quadrature detection and excitation flip angle inconsistency. The noise power was measured in 11 phantoms of contrast agent concentration in the range [0–1] mM (in steps of 0.1 mM) and in onein vivo acquisition of a tumor-bearing mouse. The distribution of the flip angle was determined in a uniform 10 mM CuSO{sub 4} phantom using the spin echo double angle method. The PDF of a wide range of T1 values measured with the varying flip angle (VFA) technique was estimated through numerical simulations of the SPGR equation. The resultant uncertainty in contrast agent concentration was incorporated in the most common model of tracer exchange kinetics and the PDF of the derived pharmacokinetic parameters was studied numerically. Results: The VFA method is an unbiased technique for measuringT1 only in the absence of bias in excitation flip angle. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted uncertainty. The uncertainty in measuring K{sup trans} with SPGR pulse sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time (T1{sub 0}). The lowest achievable bias/uncertainty in estimating this parameter is approximately 20%–70% higher than the bias/uncertainty in the measurement of the pre-injection T1 map. The fractional volume parameters derived from the extended Tofts model

  20. Intracranial cerebrospinal fluid spaces imaging using a pulse-triggered three-dimensional turbo spin echo MR sequence with variable flip-angle distribution

    Energy Technology Data Exchange (ETDEWEB)

    Hodel, Jerome [Unite Analyse et Restauration du Mouvement, UMR-CNRS, 8005 LBM ParisTech Ensam, Paris (France); University Paris Est Creteil (UPEC), Creteil (France); Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Henri Mondor, Department of Neuroradiology, Creteil (France); Hopital Henri Mondor, Creteil (France); Silvera, Jonathan [University Paris Est Creteil (UPEC), Creteil (France); Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Henri Mondor, Department of Neuroradiology, Creteil (France); Bekaert, Olivier; Decq, Philippe [Unite Analyse et Restauration du Mouvement, UMR-CNRS, 8005 LBM ParisTech Ensam, Paris (France); University Paris Est Creteil (UPEC), Creteil (France); Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Henri Mondor, Department of Neurosurgery, Creteil (France); Rahmouni, Alain [University Paris Est Creteil (UPEC), Creteil (France); Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Henri Mondor, Department of Radiology, Creteil (France); Bastuji-Garin, Sylvie [University Paris Est Creteil (UPEC), Creteil (France); Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Henri Mondor, Department of Public Health, Creteil (France); Vignaud, Alexandre [Siemens Healthcare, Saint Denis (France); Petit, Eric; Durning, Bruno [Laboratoire Images Signaux et Systemes Intelligents, UPEC, Creteil (France)

    2011-02-15

    To assess the three-dimensional turbo spin echo with variable flip-angle distribution magnetic resonance sequence (SPACE: Sampling Perfection with Application optimised Contrast using different flip-angle Evolution) for the imaging of intracranial cerebrospinal fluid (CSF) spaces. We prospectively investigated 18 healthy volunteers and 25 patients, 20 with communicating hydrocephalus (CH), five with non-communicating hydrocephalus (NCH), using the SPACE sequence at 1.5T. Volume rendering views of both intracranial and ventricular CSF were obtained for all patients and volunteers. The subarachnoid CSF distribution was qualitatively evaluated on volume rendering views using a four-point scale. The CSF volumes within total, ventricular and subarachnoid spaces were calculated as well as the ratio between ventricular and subarachnoid CSF volumes. Three different patterns of subarachnoid CSF distribution were observed. In healthy volunteers we found narrowed CSF spaces within the occipital aera. A diffuse narrowing of the subarachnoid CSF spaces was observed in patients with NCH whereas patients with CH exhibited narrowed CSF spaces within the high midline convexity. The ratios between ventricular and subarachnoid CSF volumes were significantly different among the volunteers, patients with CH and patients with NCH. The assessment of CSF spaces volume and distribution may help to characterise hydrocephalus. (orig.)

  1. Bilateral mesial temporal sclerosis: MRI with high-resolution fast spin-echo and fluid-attenuated inversion-recovery sequences

    Energy Technology Data Exchange (ETDEWEB)

    Oppenheim, C.; Dormont, D.; Lehericy, S.; Marsault, C. [Dept. of Neuroradiology, Groupe Hospitalier Pite-Salpetriere, Paris (France); Hasboun, D. [Dept. of Neuroradiology, Groupe Hospitalier Pite-Salpetriere, Paris (France)]|[Dept. of Neurology, Paris VI Univ. (France); Bazin, B.; Samson, S.; Baulac, M. [Dept. of Neurology, Paris VI Univ. (France)

    1999-07-01

    We report a retrospective analysis of MRI in 206 patients with intractable seizures and describe the findings in bilateral mesial temporal sclerosis (MTS) on fast spin-echo (FSE) and fast fluid-attenuated inversion-recovery (fFLAIR) sequences. Criteria for MTS were atrophy, signal change and loss of the digitations of the head of the hippocampus. In patients with bilateral MRI signs of MTS, correlation with clinical electro, volumetric MRI data and neuropsychological tests, when available, was performed. Bilateral MTS was observed in seven patients. Bilateral loss of the digitations and signal change of fFLAIR was seen in all seven. In three, bilateral atrophy was obvious. In two patients, mild bilateral atrophy was observed and in two others, the hippocampi were: asymmetrical, with obvious atrophy on only one side. Volumetric data confirmed bilateral symmetrical atrophy in five patients, and volumes were at the lowest of the normal range in other two. The EEG showed temporal abnormalities in all patients, unilateral in five and bilateral in two. All patients had memory impairment and neuropsychological data confirmed visual and verbal memory deficits; two patients failed the Wada test on both sides. High-resolution T2-weighted FSE and fFLAIR sequences allow diagnosis of bilateral MTS, which has important therapeutic and prognostic implications. (orig.)

  2. Contrast-enhanced MR Imaging of Metastatic Brain Tumor at 3 Tesla: Utility of T1-weighted SPACE Compared with 2D Spin Echo and 3D Gradient Echo Sequence

    National Research Council Canada - National Science Library

    KOMADA, Tomohiro; NAGANAWA, Shinji; OGAWA, Hiroshi; MATSUSHIMA, Masaya; KUBOTA, Seiji; KAWAI, Hisashi; FUKATSU, Hiroshi; IKEDA, Mitsuru; KAWAMURA, Minako; SAKURAI, Yasuo; MARUYAMA, Katsuya

    2008-01-01

    ...), and 2-dimensional T1-weighted spin echo (2D-SE) imaging at 3T. We quantitatively compared SPACE, MP-RAGE, and 2D-SE images by using signal-to-noise ratios (SNRs) for gray matter (GM) and white matter (WM...

  3. Improving riverbed sediment classification using backscatter and depth residual features of multi-beam echo-sounder systems

    NARCIS (Netherlands)

    Eleftherakis, D.; Amiri-Simkooei, A.; Snellen, M; Simons, D.G.

    2012-01-01

    Riverbed and seafloor sediment classification using acoustic remote sensing techniques is of high interest due to their high coverage capabilities at limited cost. This contribution presents the results of riverbed sediment classification using multi-beam echo-sounder data based on an empirical meth

  4. Echo-Planar Imaging-Based, J-Resolved Spectroscopic Imaging for Improved Metabolite Detection in Prostate Cancer

    Science.gov (United States)

    2016-12-01

    64 increments along the indirect spectral (t1) and 16 spatial ky dimensions. In Fig. 5A, an axial MRI of the abdomen is shown displaying the VOI...Fan X, Zamora MA, Karczmar GS. Reduction of spectral ghost artifacts in high-resolution echo-planar spectroscopic imaging of water and fat resonances

  5. Visualization of the 12th Cranial Nerve with MRI: Value of Balanced Fast-Field Echo and 3D-Drive Sequences Among the T2 TSE Post-Contrast T1 Sequences

    Directory of Open Access Journals (Sweden)

    H Aydin

    2010-10-01

    Full Text Available Background/Objective: Our aim was to optimize the most effective MR imaging sequence for visualization of the 12th cranial nerve (hypoglossal nerve through its cisternal course."nPatients and Methods: We applied balanced fast-field echo (B-FFE, 3D-T2 weighted Driven Equilibrium RF Reset Pulse (DRIVE, T2 weighted 2D TSE and post-contrast T1 weighted sequences and tried to find out the best sequence for the perfect visualization of the 12th cranial nerve. One-hundred patients without any hypoglossal nerve paralysis were examined via these sequences. Imaging analysis was graded as follows: certain visualization of nerves (score 2, partially visualized nerves (score 1, non-visualized nerves (score 0."nResults: The hypoglossal nerve was visualized exactly in only eight cases and partially depicted in only six cases with the post-contrast T1 series. In B-FFE sequence; 56% of the nerves were properly seen and 8% of the nerves were partially identified, using T2 weighted DRIVE sequences; 30% of the nerves were clearly visualized, the nerves were partially depicted in 15 patients. Regarding the T2 weighted TSE sequence, 15% of the nerves were certainly depicted and in seven patients the nerves were partially depicted."nConclusion: The most diagnostic sequence for the exact visualization of the cisternal course of hypoglossal nerve is B-FFE revealing a 64% visualization rate for the cisternal parts (112 exactly, 16 partially. T2W DRIVE sequence is shown to be more diagnostic than the T2W TSE for visualization of the cisternal part of the hypoglossal nerve.    

  6. MRI of respiratory dynamics with 2D steady-state free-precession and 2D gradient echo sequences at 1.5 and 3 Tesla: an observer preference study

    Energy Technology Data Exchange (ETDEWEB)

    Fabel, M.; Biederer, J. [University Hospital Schleswig-Holstein, Department of Diagnostic Radiology, Kiel (Germany); Wintersperger, B.J.; Dietrich, O. [University Hospital Munich, Department of Clinical Radiology, Munich (Germany); Eichinger, M.; Puderbach, M. [German Cancer Research Center, Department of Oncological Diagnostics and Therapy, Heidelberg (Germany); Fink, C.; Schoenberg, S.O. [University Hospital Heidelberg-Mannheim, Department of Clinical Radiology, Mannheim (Germany); Kauczor, H.U. [University Hospital Heidelberg, Department of Diagnostic Radiology, Heidelberg (Germany)

    2009-02-15

    To compare the image quality of dynamic lung MRI with variations of steady-state free-precession (SSFP) and gradient echo (GRE) cine techniques at 1.5 T and 3 T. Ventilated porcine lungs with simulated lesions inside a chest phantom and four healthy human subjects were assessed with SSFP (TR/TE = 2.9/1.22 ms; 3 ima/s) and GRE sequences (TR/TE=2.34/0.96 ms; 8 ima/s) as baseline at 1.5 and 3 T. Modified SSFPs were performed with nine to ten images/s (parallel imaging factors 2 and 3). Image quality for representative structures and artifacts was ranked by three observers independently. At 1.5 T, standard SSFP achieved the best image quality with superior spatial resolution and signal, but equal temporal resolution to GRE. SSFP with improved temporal resolution was ranked second best. Further acceleration (PI factor 3) was of no benefit, but increased artifacts. At 3 T, GRE outranged SSFP imaging with high lesion signal intensity, while artifacts on SSFP images increased visibly. At 1.5 T, a modified SSFP with moderate parallel imaging (PI factor 2) was considered the best compromise of temporal and spatial resolution. At 3 T, GRE sequences remain the best choice for dynamic lung MRI. (orig.)

  7. Magnetization transfer in human achilles tendon assessed by a 3D ultrashort echo time sequence. Quantitative examinations in healthy volunteers at 3T

    Energy Technology Data Exchange (ETDEWEB)

    Syha, R.; Grosse, U.; Springer, F. [Tuebingen Univ. (Germany). Diagnostic and Interventional Radiology; Tuebingen Univ. (Germany). Section on Experimental Radiology; Martirosian, P.; Schick, F. [Tuebingen Univ. (Germany). Section on Experimental Radiology; Ketelsen, D.; Claussen, C.D. [Tuebingen Univ. (Germany). Diagnostic and Interventional Radiology

    2011-11-15

    Magnetization transfer contrast (MTC) imaging provides insight into interactions between free and bounded water. Newly developed ultrashort echo time (UTE) sequences implemented on whole-body magnetic resonance (MR) scanners allow MTC imaging in tissues with extremely fast signal decay such as tendons. The aim of this study was to develop a technique for the quantification of the MT effect in healthy Achilles tendons in-vivo at 3 Tesla. 16 normal tendons of volunteers with no history of tendinopathy were examined using a 3D-UTE sequence with a rectangular on-resonant excitation pulse and a Fermi-shaped off-resonant MT preparation pulse. The frequency of the MT pulse was varied from 1 to 5 kHz. MT effects were calculated in terms of the MT ratio (MTR) between measurements without and with MT preparation. Direct saturation effects of MT preparation on the signal intensity were evaluated using numerical simulation of Bloch equations. One patient with tendinopathy was examined to exemplarily show changes of MTR under pathologic conditions. Calculation of MTR data was feasible in all examined tendons and showed a decrease from 0.53 {+-} 0.05 to 0.25 {+-} 0.03 (1 kHz to 5 kHz) for healthy volunteers. Evaluation of variation with gender and dominance of ankle revealed no significant differences (p > 0.05). In contrast, the patient with confirmed tendinopathy showed MTR values between 0.36 (1 kHz) and 0.19 (5 kHz). MT effects in human Achilles tendons can be reliably assessed in-vivo using a 3D UTE sequence at 3 T. All healthy tendons showed similar MTR values (coefficient of variation 10.0 {+-} 1.2 %). The examined patient showed a clearly different MT effect revealing a changed microstructure in the case of tendinopathy. (orig.)

  8. Increasing sensitivity of pulse EPR experiments using echo train detection schemes

    Science.gov (United States)

    Mentink-Vigier, F.; Collauto, A.; Feintuch, A.; Kaminker, I.; Tarle, V.; Goldfarb, D.

    2013-11-01

    Modern pulse EPR experiments are routinely used to study the structural features of paramagnetic centers. They are usually performed at low temperatures, where relaxation times are long and polarization is high, to achieve a sufficient Signal/Noise Ratio (SNR). However, when working with samples whose amount and/or concentration are limited, sensitivity becomes an issue and therefore measurements may require a significant accumulation time, up to 12 h or more. As the detection scheme of practically all pulse EPR sequences is based on the integration of a spin echo - either primary, stimulated or refocused - a considerable increase in SNR can be obtained by replacing the single echo detection scheme by a train of echoes. All these echoes, generated by Carr-Purcell type sequences, are integrated and summed together to improve the SNR. This scheme is commonly used in NMR and here we demonstrate its applicability to a number of frequently used pulse EPR experiments: Echo-Detected EPR, Davies and Mims ENDOR (Electron-Nuclear Double Resonance), DEER (Electron-Electron Double Resonance|) and EDNMR (Electron-Electron Double Resonance (ELDOR)-Detected NMR), which were combined with a Carr-Purcell-Meiboom-Gill (CPMG) type detection scheme at W-band. By collecting the transient signal and integrating a number of refocused echoes, this detection scheme yielded a 1.6-5 folds SNR improvement, depending on the paramagnetic center and the pulse sequence applied. This improvement is achieved while keeping the experimental time constant and it does not introduce signal distortion.

  9. Improved liver T1rho measurement precision with a breathhold black blood single shot fast spin echo acquisition: a validation study in healthy volunteers

    CERN Document Server

    Wang, Yi-Xiang; Lo, GladsG; Chan, Queenie; Yuan, Jing; Chen, Weitian

    2016-01-01

    Purpose: To explore the usability and normal T1rho value of liver parenchyma with a novel single breathhold black blood single shot fast spin echo acquisition based liver imaging sequence. Materials and Methods: In total 19 health subjects (10 males, 9 females; mean age: 37.4 yrs; range: 23-54 yrs) participated in the study. 11 subjects had liver scanned twice in the same session to access scan-rescan repeatability. 12 subjects had liver scanned twice in two sessions with 7-10 days' interval to access scan-rescan reproducibility. MR was performed with a 3.0 T scanner with dual transmitter. The MR sequence allows simultaneous acquisition of 4 spin lock times (TSLs: 0ms, 10 ms, 30 ms, 50ms) in 10 second. Inherent black blood effect of fast spin echo and double inversion recovery were utilized to achieve blood signal suppression. Results: The technique demonstrated good image quality and minimal artifacts. For liver parenchyma, Bland-Altman plot showed the scan-rescan repeatability mean difference was 0.025 ms (...

  10. Echo-Planar Imaging-Based, J-Resolved Spectroscopic Imaging for Improved Metabolite Detection in Prostate Cancer

    Science.gov (United States)

    2015-10-01

    16 July 2015, Accepted: 17 July 2015, Published online in Wiley Online Library : 7 September 2015 (wileyonlinelibrary.com) DOI: 10.1002/nbm.3373 NMR...published online at www.rsna2014.rsna.org, Abstract LL-PHE118, 2014. Accelerated echo planar J-resolved spectroscopic imaging in prostate cancer: a...than 13 min and we were able to detect and quantify several metabolites. Copyright © 2015 John Wiley & Sons, Ltd. Keywords: MRS; prostate cancer; 4D

  11. Intradiurnal fluctuations of off-resonance saturation effects in healthy human achilles tendons assessed with a 3D ultrashort echo time MRI sequence at 3 tesla

    Energy Technology Data Exchange (ETDEWEB)

    Grosse, U.; Syha, R.; Kessler, D.E.; Bongers, M.; Seith, F.; Nikolaou, K.; Springer, F. [University Hospital Tuebingen (Germany). Dept. of Diagnostic and Interventional Radiology; Partovi, S.; Robbin, M. [Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Radiology; Schick, F. [University Hospital Tuebingen (Germany). Section on Experimental Radiology

    2015-11-15

    The purpose of this study was to evaluate whether gravitational interstitial fluid accumulation in healthy subjects has an impact on off-resonance saturation ratios (OSR) or the volume of the Achilles tendon after a prolonged time of reduced levels of physical activity. 7 healthy volunteers were repeatedly investigated on 3 consecutive days on a 3 T whole body MR scanner using an ultrashort echo time (UTE) imaging sequence with a Gaussian off-resonance saturation pulse at a frequency offset of 2000 Hz to calculate OSR values. For accurate volumetric quantification of the Achilles tendon, a newly developed contour detection snake algorithm was applied on high-resolution isotropic T2-weighted SPACE sequence datasets. Single-measure intraclass correlation coefficients (ICC) were calculated to estimate test-retest reliability. For OSR and tendon volume measurements on three consecutive days, excellent reproducibility could be achieved with ICC values above 0.96 and 0.97, respectively. Comparing the results of all three days, a statistically significant mean individual percentage decrease (-4.1 ± 1.5 %; p=0.001) of calculated tendon OSR values was found for the evening measurements. No statistically significant difference between tendon volumes in the morning and the evening could be detected (p=0.589). The results of this in-vivo study demonstrate a significant influence of gravitational interstitial fluid accumulation after reduced physical activity on OSR values in the Achilles tendon, but not on tendon volume. Taken together with the demonstrated excellent reproducibility, these findings are important for future studies investigating temporal changes of the Achilles tendon microstructure.

  12. Value of Fat-Suppressed Proton-Density-Weighted Turbo Spin-Echo Sequences in Detecting Meniscal Lesions: Comparison with Arthroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, F.K.W.; Schaefer, P.J.; Brossmann, J.; Frahm, C.; Hilgert, R.E.; Heller, M.; Jahnke, T. [Univ. Hospital of Schleswig-Holstein, Kiel (Germany). Dept. of Diagnostic Radiology

    2006-07-15

    Purpose: To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging (MRI) compared to arthroscopy in the detection of meniscal lesions. Material and Methods: In a prospective study, 31 knee joints were imaged on a 1.5T MR scanner before arthroscopy using the following sequences: (a) coronal and sagittal FS-PDw TSE (TR/TE: 4009/15 ms); (b) coronal T1w SE (TR/TE: 722/20 ms), and sagittal PDw TSE (TR/TE: 3800/15 ms). Other imaging parameters were: slice thickness 3 mm, FOV 160 mm, matrix 256x256. A total of 186 meniscal regions (62 menisci; anterior horn, body, posterior horn) were evaluated. Standard of reference was arthroscopy. Sensitivity, specificity, negative predictive value (npv), positive predictive value (ppv), and accuracy were calculated. Results: Arthroscopically, meniscal lesions were detected in 55/186 segments (35 medial and 20 lateral meniscal lesions). Sensitivity, specificity, npv, ppv, and accuracy for combination of coronal and sagittal FS PDw TSE were 91.4%, 98.3%, 95%, 97%, and 93.5% for the medial meniscus, and 90%, 98.6%, 97.3%, 94.7%, and 96.8% for the lateral. The results were comparable to the combination of coronal T1w SE and sagittal PDw TSE for the medial (88.6%, 98.3%, 93.4%, 96.9%, 91.4%) and the lateral (90%, 95.9%, 97.2%, 85.7%, 92.5%) meniscus. Conclusion: FS PDw TSE-MR sequences are an excellent alternative for the detection of meniscal lesions in comparison with diagnostic arthroscopy.

  13. Detection of optic nerve atrophy following a single episode of unilateral optic neuritis by MRI using a fat-saturated short-echo fast FLAIR sequence

    Energy Technology Data Exchange (ETDEWEB)

    Hickman, S.J. [Inst. of Neurology, Univ. College London (United Kingdom); Dept. of Neuro-Ophthalmology, Moorfields Eye Hospital, London (United Kingdom); Brex, P.A.; Silver, N.C.; Barker, G.J.; Miller, D.H. [Inst. of Neurology, Univ. College London (United Kingdom); Brierley, C.M.H.; Compston, D.A.S. [Cambridge Centre for Brain Repair, Cambridge (United Kingdom); Scolding, N.J. [Inst. of Clinical Neurosciences, Frenchay Hospital, Bristol (United Kingdom); Moseley, I.F. [Lysholm Radiological Dept., National Hospital for Neurology and Neurosurgery, London (United Kingdom); Plant, G.T. [Dept. of Neuro-Ophthalmology, Moorfields Eye Hospital, London (United Kingdom)

    2001-02-01

    We describe an MRI technique for quantifying optic nerve atrophy resulting from a single episode of unilateral optic neuritis. We imaged 17 patients, with a median time since onset of optic neuritis of 21 months (range 3-81 months), using a coronal-oblique fat-saturated short-echo fast fluid-attenuated inversion-recovery (sTE fFLAIR) sequence. The mean cross-sectional area of the intraorbital portion of the optic nerves was calculated by a blinded observer from five consecutive 3 mm slices from the orbital apex forwards using a semiautomated contouring technique and compared with data from 16 controls. The mean optic nerve area was 11.2mm{sup 2} in the affected eye of the patients, 12.9mm{sup 2} in the contralateral eye (P = 0.006 compared to the affected eye) and 12.8mm{sup 2} in controls (P = 0.03 compared to the affected eyes). There was a significant negative correlation between disease duration and the size of the affected optic nerve (r = -0.59, P = 0.012). The measurement coefficient of variation was 4.8 %. The sTE fFLAIR sequence enables measurement of optic nerve area with sufficient reproducibility to show optic nerve atrophy following a single episode of unilateral optic neuritis. The correlation of increasing optic nerve atrophy with disease duration would be consistent with ongoing axonal loss in a persistently demyelinated lesion, or Wallerian degeneration following axonal damage during the acute inflammatory phase. (orig.)

  14. Subjective and objective image qualities: a comparison of sagittal T2 weighted spin-echo and turbo-spin-eco sequences in magnetic resonance imaging of the spine by use of a subjective ranking system

    Energy Technology Data Exchange (ETDEWEB)

    Goerres, G. [Institut fuer diagnostische Radiologie, Departement Radiologie, Universitaetskliniken, Kantonsspital Basel (Switzerland); Mader, I. [Radiologische Gemeinschaftspraxis Dres. Siems, Grossmann, Bayreuth (Germany); Proske, M. [Klinikum Rosenheim (Germany). Inst. fuer Diagnostische Radiologie

    1998-12-31

    We evaluated the subjective image impression of two different magnetic resonance (MR) sequences by using a subjective ranking system. This ranking system was based on 20 criteria describing several tissue characteristics such as the signal intensity of normal anatomical structures and the changes of signal intensities and shape of lesions as well as artefacts. MR of the vertebral spine was performed in 48 female and 52 male patients (mean age 44.8 years) referred consecutively for investigation of a back problem. Ninety-six pathologies were found in 82 patients. Sagittal and axial T1 weighted spin-echo before and after administration of Gadolinium (Gd-DOTA), and sagittal T2 weighted spin-echo (T2wSE) and Turbo-spin-echo (TSE) sequences were performed by means of surface coils. Using the subjective ranking system the sagittal T2wSE and sagittal TSE were compared. Both sequences were suitable for identification of normal anatomy and pathologic changes and there was no trend for increased detection of disease by one imaging sequence over the other. We found that sagittal TSE sequences can replace sagittal T2wSE sequences in spinal MR and that artefacts at the cervical and lumbar spine are less frequent using TSE, thus confirming previous studies. In this study, our ranking system reveiled, that there are differences between the subjective judgement of image qualities and objective measurement of SNR. However, this approach may not be helpful to compare two different MR sequences as it is limited to the anatomical area investigated and is time consuming. The subjective image impression, i.e. the quality of images, may not always be represented by physical parameters such as a signal-to-noise ratio (SNR), radiologists should try to define influences of image quality also by subjective parameters. (orig.)

  15. Metal artefact suppression at 3 T MRI: comparison of MAVRIC-SL with conventional fast spin echo sequences in patients with Hip joint arthroplasty

    Energy Technology Data Exchange (ETDEWEB)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M. [University of California San Francisco, Musculoskeletal Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States); Koch, Kevin M. [Medical Collage of Wisconsin, Departments of Biophysics and Radiology, Milwaukee, WI (United States)

    2015-08-15

    The aim of our study was to evaluate the clinical feasibility and diagnostic value of a new MRI metal artefact reduction pulse sequence called MAVRIC-SL in a 3 T MRI environment. Two MAVRIC-SL sequences obtained in 61 patients with symptomatic total hip replacement were compared with standard FSE-STIR sequences optimized for imaging around metal. Artefact size was measured on the slice of greatest extent. Image quality, fat saturation, image distortion, visibility of anatomical structures, and detectability of joint abnormalities were visually assessed and graded on qualitative scales. Differences between MAVRIC-SL and FSE sequences were tested with the Wilcoxon signed-rank test. MAVRIC-SL sequences at 3 T showed significantly smaller metal artefacts compared to FSE-STIR sequences (p < 0.0001). The general image quality of MAVRIC-SL sequences was reduced with regard to spatial resolution, noise and contrast (p = 0.001), and fat saturation (p < 0.0001). The reduction of artefact size and image distortion significantly improved visualization of joint anatomy (p < 0.0001) and diagnostic confidence regarding implant-associated abnormalities (p = 0.0075 to <0.0001). Although the image quality of MAVRIC-SL sequences is limited at 3 T, its clinical application is feasible and provides important additional diagnostic information for the workup of patients with symptomatic hip replacement through substantially reduced metal artefacts. (orig.)

  16. Diagnosis of nerve root compromise of the lumbar spine: Evaluation of the performance of three-dimensional isotropic T2-weighted turbo spin-echo SPACE sequence at 3T

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Jin Kyeong; Jee, Won Hee; Jung, Joon Yong; Jang, Jin Hee; Kim, Jin Sung; Kim, Young Hoon; Ha, Kee Yong [Seoul St. Mary' s Hospital, College of Medicine, The Catholic University of Korea, Seoul (Korea, Republic of)

    2017-01-15

    To explore the performance of three-dimensional (3D) isotropic T2-weighted turbo spin-echo (TSE) sampling perfection with application optimized contrasts using different flip angle evolution (SPACE) sequence on a 3T system, for the evaluation of nerve root compromise by disc herniation or stenosis from central to extraforaminal location of the lumbar spine, when used alone or in combination with conventional two-dimensional (2D) TSE sequence. Thirty-seven patients who had undergone 3T spine MRI including 2D and 3D sequences, and had subsequent spine surgery for nerve root compromise at a total of 39 nerve levels, were analyzed. A total of 78 nerve roots (48 symptomatic and 30 asymptomatic sites) were graded (0 to 3) using different MRI sets of 2D, 3D (axial plus sagittal), 3D (all planes), and combination of 2D and 3D sequences, with respect to the nerve root compromise caused by posterior disc herniations, lateral recess stenoses, neural foraminal stenoses, or extraforaminal disc herniations; grading was done independently by two readers. Diagnostic performance was compared between different imaging sets using the receiver operating characteristics (ROC) curve analysis. There were no statistically significant differences (p = 0.203 to > 0.999) in the ROC curve area between the imaging sets for both readers 1 and 2, except for combined 2D and 3D (0.843) vs. 2D (0.802) for reader 1 (p = 0.035), and combined 2D and 3D (0.820) vs. 3D including all planes (0.765) for reader 2 (p = 0.049). The performance of 3D isotropic T2-weighted TSE sequence of the lumbar spine, whether axial plus sagittal images, or all planes of images, was not significantly different from that of 2D TSE sequences, for the evaluation of nerve root compromise of the lumbar spine. Combining 2D and 3D might possibly improve the diagnostic accuracy compared with either one.

  17. Diagnosis of Nerve Root Compromise of the Lumbar Spine: Evaluation of the Performance of Three-dimensional Isotropic T2-weighted Turbo Spin-Echo SPACE Sequence at 3T

    Science.gov (United States)

    Sung, Jinkyeong; Jung, Joon-Yong; Jang, Jinhee; Kim, Jin-Sung; Kim, Young-Hoon; Ha, Kee-Yong

    2017-01-01

    Objective To explore the performance of three-dimensional (3D) isotropic T2-weighted turbo spin-echo (TSE) sampling perfection with application optimized contrasts using different flip angle evolution (SPACE) sequence on a 3T system, for the evaluation of nerve root compromise by disc herniation or stenosis from central to extraforaminal location of the lumbar spine, when used alone or in combination with conventional two-dimensional (2D) TSE sequence. Materials and Methods Thirty-seven patients who had undergone 3T spine MRI including 2D and 3D sequences, and had subsequent spine surgery for nerve root compromise at a total of 39 nerve levels, were analyzed. A total of 78 nerve roots (48 symptomatic and 30 asymptomatic sites) were graded (0 to 3) using different MRI sets of 2D, 3D (axial plus sagittal), 3D (all planes), and combination of 2D and 3D sequences, with respect to the nerve root compromise caused by posterior disc herniations, lateral recess stenoses, neural foraminal stenoses, or extraforaminal disc herniations; grading was done independently by two readers. Diagnostic performance was compared between different imaging sets using the receiver operating characteristics (ROC) curve analysis. Results There were no statistically significant differences (p = 0.203 to > 0.999) in the ROC curve area between the imaging sets for both readers 1 and 2, except for combined 2D and 3D (0.843) vs. 2D (0.802) for reader 1 (p = 0.035), and combined 2D and 3D (0.820) vs. 3D including all planes (0.765) for reader 2 (p = 0.049). Conclusion The performance of 3D isotropic T2-weighted TSE sequence of the lumbar spine, whether axial plus sagittal images, or all planes of images, was not significantly different from that of 2D TSE sequences, for the evaluation of nerve root compromise of the lumbar spine. Combining 2D and 3D might possibly improve the diagnostic accuracy compared with either one. PMID:28096733

  18. Usefulness of R2* maps generated by iterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence for cerebral artery dissection

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Ayumi; Shinohara, Yuki; Fujii, Shinya; Miyoshi, Fuminori; Kuya, Keita; Ogawa, Toshihide [Tottori University, Division of Radiology, Department of Pathophysiological, and Therapeutic Science, Faculty of Medicine, Yonago (Japan); Yamashita, Eijiro [Tottori University Hospital, Division of Clinical Radiology, Yonago (Japan)

    2015-09-15

    Acute intramural hematoma resulting from cerebral artery dissection is usually visualized as a region of intermediate signal intensity on T1-weighted images (WI). This often causes problems with distinguishing acute atheromatous lesions from surrounding parenchyma and dissection. The present study aimed to determine whether or not R2* maps generated by the iterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence (IDEAL IQ) can distinguish cerebral artery dissection more effectively than three-dimensional variable refocusing flip angle TSE T1WI (T1-CUBE) and T2*WI. We reviewed data from nine patients with arterial dissection who were assessed by MR images including R2* maps, T2*WI, T1-CUBE, and 3D time-of-flight (TOF)-MRA. We visually assessed intramural hematomas in each patient as positive (clearly visible susceptibility effect reflecting intramural hematoma as hyperintensity on R2* map and hypointensity on T2*WI), negative (absent intramural hematoma), equivocal (difficult to distinguish between intramural hematoma and other paramagnetic substances such as veins, vessel wall calcification, or hemorrhage) and not evaluable (difficult to determine intramural hematoma due to susceptibility artifacts arising from skull base). Eight of nine patients were assessed during the acute phase. Lesions in all eight patients were positive for intramural hematoma corresponding to dissection sites on R2* maps, while two lesions were positive on T2*WI and three lesions showed high-intensity on T1-CUBE reflected intramural hematoma during the acute phase. R2* maps generated using IDEAL IQ can detect acute intramural hematoma associated with cerebral artery dissection more effectively than T2*WI and earlier than T1-CUBE. (orig.)

  19. Faster pediatric 3-T abdominal magnetic resonance imaging: comparison between conventional and variable refocusing flip-angle single-shot fast spin-echo sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ruangwattanapaisarn, Nichanan [Mahidol University, Department of Diagnostic and Therapeutic Radiology, Ramathibodi Hospital, Bangkok (Thailand); Stanford University, LPCH Department of Radiology, Stanford, CA (United States); Loening, Andreas M.; Saranathan, Manojkumar; Vasanawala, Shreyas S. [Stanford University, LPCH Department of Radiology, Stanford, CA (United States); Litwiller, Daniel V. [GE Healthcare, Rochester, MN (United States)

    2015-06-15

    Single-shot fast spin echo (SSFSE) is particularly appealing in pediatric patients because of its motion robustness. However radiofrequency energy deposition at 3 tesla forces long pauses between slices, leading to longer scans, longer breath-holds and more between-slice motion. We sought to learn whether modulation of the SSFSE refocusing flip-angle train could reduce radiofrequency energy deposition without degrading image quality, thereby reducing inter-slice pauses and overall scan times. We modulated the refocusing flip-angle train for SSFSE to minimize energy deposition while minimizing blurring and motion-related signal loss. In a cohort of 50 consecutive patients (25 boys, mean age 5.5 years, range 1 month to 17 years) referred for abdominal MRI we obtained standard SSFSE and variable refocusing flip-angle (vrfSSFSE) images and recorded sequence scan times. Two readers independently scored the images in blinded, randomized order for noise, tissue contrast, sharpness, artifacts and left lobe hepatic signal uniformity on a four-point scale. The null hypothesis of no difference between SSFSE and vrfSSFSE image-quality was assessed with a Mann-Whitney U test, and the null hypothesis of no scan time difference was assessed with the paired t-test. SSFSE and vrfSSFSE mean acquisition times were 54.3 and 26.2 s, respectively (P-value <0.0001). For each reader, SSFSE and vrfSSFSE noise, tissue contrast, sharpness and artifacts were not significantly different (P-values 0.18-0.86). However, SSFSE had better left lobe hepatic signal uniformity (P < 0.01, both readers). vrfSSFSE is twice as fast as SSFSE, with equivalent image quality with the exception of left hepatic lobe signal heterogeneity. (orig.)

  20. Increased BOLD sensitivity in the orbitofrontal cortex using slice-dependent echo times at 3 T.

    Science.gov (United States)

    Domsch, Sebastian; Linke, Julia; Heiler, Patrick M; Kroll, Alexander; Flor, Herta; Wessa, Michèle; Schad, Lothar R

    2013-02-01

    Functional magnetic resonance imaging (fMRI) exploits the blood oxygenation level dependent (BOLD) effect to detect neuronal activation related to various experimental paradigms. Some of these, such as reversal learning, involve the orbitofrontal cortex and its interaction with other brain regions like the amygdala, striatum or dorsolateral prefrontal cortex. These paradigms are commonly investigated with event-related methods and gradient echo-planar imaging (EPI) with short echo time of 27 ms. However, susceptibility-induced signal losses and image distortions in the orbitofrontal cortex are still a problem for this optimized sequence as this brain region consists of several slices with different optimal echo times. An EPI sequence with slice-dependent echo times is suitable to maximize BOLD sensitivity in all slices and might thus improve signal detection in the orbitofrontal cortex. To test this hypothesis, we first optimized echo times via BOLD sensitivity simulation. Second, we measured 12 healthy volunteers using a standard EPI sequence with an echo time of 27 ms and a modified EPI sequence with echo times ranging from 22 ms to 47 ms. In the orbitofrontal cortex, the number of activated voxels increased from 87 ± 44 to 549 ± 83 and the maximal t-value increased from 4.4 ± 0.3 to 5.4 ± 0.3 when the modified EPI was used. We conclude that an EPI with slice-dependent echo times may be a valuable tool to mitigate susceptibility artifacts in event-related whole-brain fMRI studies with a focus on the orbitofrontal cortex.

  1. T2{sup *} mapping from multi-echo dixon sequence on gadoxetic acid-enhanced magnetic resonance imaging for the hepatic fat quantification: Can it be used for hepatic function assessment?

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Hyun Suk; Lee, Jeong Min; Yoon, Jeong Hee; Kang, Hyo Jin; Lee, Sang Min; Yang, Hyun Kyung; Han, Joon Koo [Dept. of Radiology, Seoul National University Hospital, Seoul (Korea, Republic of)

    2017-08-01

    To evaluate the diagnostic value of T2{sup *} mapping using 3D multi-echo Dixon gradient echo acquisition on gadoxetic acid-enhanced liver magnetic resonance imaging (MRI) as a tool to evaluate hepatic function. This retrospective study was approved by the IRB and the requirement of informed consent was waived. 242 patients who underwent liver MRIs, including 3D multi-echo Dixon fast gradient-recalled echo (GRE) sequence at 3T, before and after administration of gadoxetic acid, were included. Based on clinico-laboratory manifestation, the patients were classified as having normal liver function (NLF, n = 50), mild liver damage (MLD, n = 143), or severe liver damage (SLD, n = 30). The 3D multi-echo Dixon GRE sequence was obtained before, and 10 minutes after, gadoxetic acid administration. Pre- and post-contrast T2{sup *} values, as well as T2{sup *} reduction rates, were measured from T2{sup *} maps, and compared among the three groups. There was a significant difference in T2{sup *} reduction rates between the NLF and SLD groups (−0.2 ± 4.9% vs. 5.0 ± 6.9%, p = 0.002), and between the MLD and SLD groups (3.2 ± 6.0% vs. 5.0 ± 6.9%, p = 0.003). However, there was no significant difference in both the pre- and post-contrast T2{sup *} values among different liver function groups (p = 0.735 and 0.131, respectively). A receiver operating characteristic (ROC) curve analysis showed that the area under the ROC curve for using T2{sup *} reduction rates to differentiate the SLD group from the NLF group was 0.74 (95% confidence interval: 0.63–0.83). Incorporation of T2{sup *} mapping using 3D multi-echo Dixon GRE sequence in gadoxetic acid-enhanced liver MRI protocol may provide supplemental information for liver function deterioration in patients with SLD.

  2. Magnetic resonance urography in pediatrics: utilization of ultrafast single-shot spin echo sequences; Urografia por resonancia magnetic en pediatria: utilizacion de las secuencias ultrarrapidas single shot en eco del espin

    Energy Technology Data Exchange (ETDEWEB)

    Martin, C.; Martin, J.; Duran, C. [Unidad de Diagnostico por la Imagen de Alta Tecnologia (UDIAT). Sabadell (Spain); Rigol, S.; Rojo, J. C. [Corporacion Sanatiaria Parc Tauli. Sabadell (Spain)

    1999-07-01

    To determine the value of magnetic resonance urography (MRU) using ultrafast single-shot (SS) rapid acquisition with relaxation enhancement (RARE) and half-Fourier (HF) SS-RARE (SS-HF-RARE or HASTE) in the evaluation of congenital urinary tract anomalies in pediatric patients, and their possible application as alternatives to intravenous urography (IVU). Eighteen children (11 boys and 7 girls) aged 2 months to 15 years (mean: 5 years) with a total of 19 congenital urinary tract anomalies were studies by MU using SS-RARE and HASTE sequences in a 1 Tesla scanner. All the patients had previously been studies by ultrasound (US) and IVU. Twelve patients required anesthesia. The images were acquired by means of a HASTE sequence with multisection technique (TR, infinite; TE{sub e}f, 87 msec; echo train, 128; interval between echoes, 10.9 msec; total acquisition time, 13 sections/12 seconds), and SS-RARE (TR, infinite; TE{sub e}f, 1.100 msec; echo train, 240, and acquisition time, 7 seconds). Four radiologists evaluated the images independently; two who reviewed the IV images in consensus and two who reviewed the MRU images in consensus. The images were evaluated to assess the dilatation of the urinary tract and their utility in detecting the level and cause of the obstruction. MRU images revealed the urinary tract dilation, the level of the obstruction and the type of anomaly in 18 patients (100%), while IVU provided this information in only 10 [ sensitivity, 53%, 95% confidence interval (29%, 76%)]. The mean time required for MRU was 20 minutes (range: 7 to 30 minutes), while that of IVU was 1,242 minutes (range: 45 to 1,440 minutes). MRU using ultrafast single-short spin echo sequences is a rapid and effective technique that permits and excellent evaluation of congenital urinary tract anomalies in pediatric patients and does not require the administration of contrast media or ionizing radiation. (Author) 10 refs.

  3. T2-weighted MR imaging of liver lesions: a prospective evaluation comparing turbo spin-echo, breath-hold turbo spin-echo and half-Fourier turbo spin-echo (HASTE) sequences; Estudio de lesiones hepaticas con imagenes de resonancia magnetica potenciadas en T2: evaluacion prospectiva comparando secuencias turbo eco del espin, turbo eco del espin con respiracion sostenida y half-Fourier turbo eco del espin (HASTE)

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J.; Villajos, M.; Oses, M. J.; Veintemillas, M.; Rue, M.; Puig, J.; Sentis, M. [Fundacion Parc Tauli. Sabadell (Spain)

    2000-07-01

    To compare turbo spin-echo (TSE), breath-hold TSE and half-Fourier acquisition single-shot turbo spin-echo (HASTE) sequences quantitatively and qualitatively in T2-weighted images of liver lesions. The authors evaluated prospectively 89 liver lesions in 73 patients using a 1.0-T magnetic resonance system to compare TSE, breath-hold TSE and HASTE sequences. The quantitative parameters were: lesion-to-liver contrast and lesion-to-liver contrast-to-noise ratio. The qualitative analysis was performed by two observers in consensus who examined four parameters: respiratory artifacts, lesion edge definition, intrahepatic vessel definition and image quality. Repeated measures analysis of variance was utilized to compare the quantitative variables and Friedman's nonparametric test for the qualitative parameters. In quantitative terms, the lesion-to-liver contrast was similar in TSE and breath-hold TSE sequences (2.45{+-}1.44 versus 2.60{+-}1.66), both of which were significantly better than the HASTE sequence (1.12{+-}0.72; p<0.001). The lesion-to-liver contrast-to-noise ratio was significantly higher in the TSE sequence (62.60{+-}46.40 versus 40.22{+-}25.35 versus 50.90{+-}32.10 for TSE, breath-hold TSE and HASTE sequences, respectively; p<0.001). In the qualitative comparisons, the HASTE sequence was significantly better than the TSE and breath-hold TSE sequences (p<0.001) in terms of artifacts and definition of lesion edge and intrahepatic vessels. Image quality was also significantly greater in the HASTE sequence (p<0.001). In quantitative terms, the TSE sequence is better than the breath-hold TSE and HASTE sequences, but there are no movement artifacts in the HASTE sequence, which is also significantly superior to TSE and breath-hold TSE sequences in qualitative terms and, thus, can be employed for T2-weighted images in liver studies. (Author) 17 refs.

  4. ECHO: a reference-free short-read error correction algorithm.

    Science.gov (United States)

    Kao, Wei-Chun; Chan, Andrew H; Song, Yun S

    2011-07-01

    Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters in the assumed model and estimates error characteristics specific to each sequencing run, while maintaining a running time that is within the range of practical use. ECHO is based on a probabilistic model and is able to assign a quality score to each corrected base. Furthermore, it explicitly models heterozygosity in diploid genomes and provides a reference-free method for detecting bases that originated from heterozygous sites. On both real and simulated data, ECHO is able to improve the accuracy of previous error-correction methods by several folds to an order of magnitude, depending on the sequence coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown that using ECHO to perform error correction as a preprocessing step considerably facilitates de novo assembly, particularly in the case of low-to-moderate sequence coverage depth.

  5. Improved taboo search algorithm for designing DNA sequences

    Institute of Scientific and Technical Information of China (English)

    Kai Zhang; Jin Xu; Xiutang Geng; Jianhua Xiao; Linqiang Pan

    2008-01-01

    The design of DNA sequences is one of the most practical and important research topics in DNA computing.We adopt taboo search algorithm and improve the method for the systematic design of equal-length DNA sequences,which can satisfy certain combinatorial and thermodynamic constraints.Using taboo search algorithm,our method can avoid trapping into local optimization and can find a set of good DNA sequences satisfying required constraints.

  6. An improved high throughput sequencing method for studying oomycete communities

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Nicolaisen, Mogens

    2015-01-01

    Culture-independent studies using next generation sequencing have revolutionizedmicrobial ecology, however, oomycete ecology in soils is severely lagging behind. The aimof this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomyce...

  7. Applications of Floquet-Magnus expansion, average Hamiltonian theory and Fer expansion to study interactions in solid state NMR when irradiated with the magic-echo sequence.

    Science.gov (United States)

    Mananga, Eugene Stephane

    2013-01-01

    This work presents the possibility of applying the Floquet-Magnus expansion and the Fer expansion approaches to the most useful interactions known in solid-state nuclear magnetic resonance using the magic-echo scheme. The results of the effective Hamiltonians of these theories and average Hamiltonian theory are presented.

  8. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh

    2015-01-01

    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  9. Detection of Traumatic Bone Marrow Lesions after Knee Trauma: Comparison of ADC Maps Derived from Diffusion-weighted Imaging with Standard Fat-saturated Proton Density-weighted Turbo Spin-Echo Sequences.

    Science.gov (United States)

    Klengel, Alexis; Stumpp, Patrick; Klengel, Steffen; Böttger, Ina; Rönisch, Nadja; Kahn, Thomas

    2016-10-24

    Purpose To compare single-shot echo-planar diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps with fat-saturated (FS) proton density (PD)-weighted turbo spin-echo (TSE) imaging in the detection of bone marrow lesions (BMLs) after knee trauma. Materials and Methods Institutional review board approval was obtained from Leipzig University. Written informed consent was waived. Three radiologists retrospectively re-examined 97 consecutive patients with reported knee trauma who underwent 1.5-T magnetic resonance (MR) imaging within 90 days of knee trauma. The following sequences were used: (a) sagittal T1-weighted TSE and FS PD-weighted TSE and (b) sagittal T1-weighted TSE and single-shot echo-planar diffusion-weighted imaging-derived ADC mapping. BMLs on the lateral and medial femoral condyle, lateral and medial aspect of the tibial plateau, and patella were documented. Volumetry was performed on BMLs with a thickness of at least 15 mm (major BMLs). ADC values were measured in intact bone marrow and major BMLs. A McNemar test and t tests were used as appropriate to test for significant differences between BML number and volume at an α level of .05. Results Significantly more patients showed at least one BML on ADC maps (98%, 95 of 97 patients) than on FS PD-weighted TSE images (86%, 84 of 97 patients) (P saturation, such as the patella. (©) RSNA, 2016 Online supplemental material is available for this article.

  10. Echo Hunting

    DEFF Research Database (Denmark)

    King, Anthea L.

    of the ongoing OzDES reverberation mapping survey.AGN are highly luminous, numerous, and are present over a huge range of cosmic history.Due to this, they can be used to probe unexplored regions in the Universe's expansion historyand help constrain the properties of dark energy. To investigate the usefulness...... emission line fluxes of individual objects, in order to measure black hole masses for a broad range of AGN and constrain the radius-luminosity (R — L) relationship, which makes them viable standard candles. I investigate the expected efficiency of the OzDES reverberation mapping campaign and its possible...... an unbiased measurement of the radius-luminosity relationship for the emission lines: Hβ, Mgii, and Civ. However, enhancing thebaseline survey by either increasing the spectroscopic cadence, extending the survey season,or improving the accuracy of the emission line flux measurement will significantly...

  11. Cardiac resynchronization therapy by multipoint pacing improves response of left ventricular mechanics and fluid dynamics: a three-dimensional and particle image velocimetry echo study.

    Science.gov (United States)

    Siciliano, Mariachiara; Migliore, Federico; Badano, Luigi; Bertaglia, Emanuele; Pedrizzetti, Gianni; Cavedon, Stefano; Zorzi, Alessandro; Corrado, Domenico; Iliceto, Sabino; Muraru, Denisa

    2016-12-26

    To characterize the effect of multipoint pacing (MPP) compared to biventricular pacing (BiV) on left ventricle (LV) mechanics and intraventricular fluid dynamics by three-dimensional echocardiography (3DE) and echocardiographic particle imaging velocimetry (Echo-PIV). In 11 consecutive patients [8 men; median age 65 years (57-75)] receiving cardiac resynchronization therapy (CRT) with a quadripolar LV lead (Quartet,St.Jude Medical,Inc.), 3DE and Echo-PIV data were collected for each pacing configuration (CRT-OFF, BiV, and MPP) at follow-up after 6 months. 3DE data included LV volumes, LV ejection fraction (LVEF), strain, and systolic dyssynchrony index (SDI). Echo-PIV was used to evaluate the directional distribution of global blood flow momentum, ranging from zero, when flow force is predominantly along the base-apex direction, up to 90° when it becomes transversal. MPP resulted in significant reduction in end-diastolic and end-systolic volumes compared with both CRT-OFF (P = 0.02; P = 0.008, respectively) and BiV (P = 0.04; P = 0.03, respectively). LVEF and cardiac output were significant superior in MPP compared with CRT-OFF, but similar between MPP and BiV. Statistical significant differences when comparing global longitudinal and circumferential strain and SDI with MPP vs. CRT-OFF were observed (P = 0.008; P = 0.008; P = 0.01, respectively). There was also a trend towards improvement in strain between BiV and MPP that did not reach statistical significance. MPP reflected into a significant reduction of the deviation of global blood flow momentum compared with both CRT-OFF and BiV (P = 0.002) indicating a systematic increase of longitudinal alignment from the base-apex orientation of the haemodynamic forces. These preliminary results suggest that MPP resulted in significant improvement of LV mechanics and fluid dynamics compared with BiV. However, larger studies are needed to confirm this hypothesis. © Crown copyright 2016.

  12. Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture.

    Science.gov (United States)

    Thottathil, Gincy Paily; Jayasekaran, Kandakumar; Othman, Ahmad Sofiman

    2016-02-01

    Agricultural development in the tropics lags behind development in the temperate latitudes due to the lack of advanced technology, and various biotic and abiotic factors. To cope with the increasing demand for food and other plant-based products, improved crop varieties have to be developed. To breed improved varieties, a better understanding of crop genetics is necessary. With the advent of next-generation DNA sequencing technologies, many important crop genomes have been sequenced. Primary importance has been given to food crops, including cereals, tuber crops, vegetables, and fruits. The DNA sequence information is extremely valuable for identifying key genes controlling important agronomic traits and for identifying genetic variability among the cultivars. However, massive DNA re-sequencing and gene expression studies have to be performed to substantially improve our understanding of crop genetics. Application of the knowledge obtained from the genomes, transcriptomes, expression studies, and epigenetic studies would enable the development of improved varieties and may lead to a second green revolution. The applications of next generation DNA sequencing technologies in crop improvement, its limitations, future prospects, and the features of important crop genome projects are reviewed herein.

  13. Direct magnetic field estimation based on echo planar raw data.

    Science.gov (United States)

    Testud, Frederik; Splitthoff, Daniel Nicolas; Speck, Oliver; Hennig, Jürgen; Zaitsev, Maxim

    2010-07-01

    Gradient recalled echo echo planar imaging is widely used in functional magnetic resonance imaging. The fast data acquisition is, however, very sensitive to field inhomogeneities which manifest themselves as artifacts in the images. Typically used correction methods have the common deficit that the data for the correction are acquired only once at the beginning of the experiment, assuming the field inhomogeneity distribution B(0) does not change over the course of the experiment. In this paper, methods to extract the magnetic field distribution from the acquired k-space data or from the reconstructed phase image of a gradient echo planar sequence are compared and extended. A common derivation for the presented approaches provides a solid theoretical basis, enables a fair comparison and demonstrates the equivalence of the k-space and the image phase based approaches. The image phase analysis is extended here to calculate the local gradient in the readout direction and improvements are introduced to the echo shift analysis, referred to here as "k-space filtering analysis." The described methods are compared to experimentally acquired B(0) maps in phantoms and in vivo. The k-space filtering analysis presented in this work demonstrated to be the most sensitive method to detect field inhomogeneities.

  14. Magnetic resonance imaging of the sacroiliac joints in patients with suspected spondyloarthritis. Comparison of turbo spin-echo and gradient-echo sequences for the detection of structural alterations; MRT-Bildgebung der Sakroiliakalgelenke bei Verdacht auf Spondyloarthritis. Vergleich von Turbospinecho- und Gradientenechosequenzen zum Nachweis struktureller Veraenderungen

    Energy Technology Data Exchange (ETDEWEB)

    Dornia, C.; Hoffstetter, P. [Universitaetsklinikum Regensburg (Germany). Inst. fuer Roentgendiagnostik; Asklepios Klinikum, Bad Abbach (Germany). Inst. fuer Roentgendiagnostik; Fleck, M. [Universitaetsklinikum Regensburg (Germany). Klinik fuer Innere Medizin I; Asklepios Klinikum, Bad Abbach (Germany). Klinik fuer Rheumatologie und Klinische Immunologie; Hartung, W. [Asklepios Klinikum, Bad Abbach (Germany). Klinik fuer Rheumatologie und Klinische Immunologie; Niessen, C.; Stroszczynski, C. [Universitaetsklinikum Regensburg (Germany). Inst. fuer Roentgendiagnostik

    2015-02-15

    Magnetic resonance imaging (MRI) is the method of choice for the evaluation of spondyloarthritis (SpA). According to the guidelines of the Assessment of Spondyloarthritis International Society (ASAS) and Outcome Measures in Rheumatology (OMERACT), MRI findings in SpA of the spine and the sacroiliac joints (SIJ) are classified as inflammatory and structural alterations. Modern gradient-echo sequences (GRE) are recommended for optimized detection of structural alterations of the SIJ. We assess the benefit of GRE in the detection of structural alterations of the SIJ in comparison to conventional turbo spin-echo sequences (TSE). Retrospective study of 114 patients who received MRI of the SIJ for the evaluation of SpA. Structural alterations of the SIJ were assessed by two blinded readers separately for T1 TSE and T2{sup *} GRE. The findings were classified according to a previously published chronicity score separately for both sides and sequences. Interobserver reliability was calculated with Cohen's Kappa, and the significance of findings was assessed with the Wilcoxon test. P-values < 0.05 were required for statistical significance. 68 of 114 (60%) patients showed SpA-typical findings of the SIJ. The average chronicity score for GRE (score 3.3) was significantly higher than for TSE (score 2.6), p=0.001. The Kappa-values for the interobserver reliability were 0.86-0.90 without any statistically significant differences between both sides and sequences. Both T1 TSE and T2{sup *} GRE showed a high interobserver reliability in the detection of structural alterations in patients with SpA. However, T2{sup *} GRE detected significantly more structural alterations than T1 TSE and should be an integral part of a modern MRI protocol for the diagnostic workup of patients with suspected SpA.

  15. Characterization of gradient echo signal decays in healthy and cancerous prostate at 3T improves with a Gaussian augmentation of the mono-exponential (GAME) model.

    Science.gov (United States)

    Ciris, Pelin Aksit; Balasubramanian, Mukund; Seethamraju, Ravi T; Tokuda, Junichi; Scalera, Jonathan; Penzkofer, Tobias; Fennessy, Fiona M; Tempany-Afdhal, Clare M; Tuncali, Kemal; Mulkern, Robert V

    2016-07-01

    A biomarker of cancer aggressiveness, such as hypoxia, could substantially impact treatment decisions in the prostate, especially radiation therapy, by balancing treatment morbidity (urinary incontinence, erectile dysfunction, etc.) against mortality. R2 (*) mapping with Mono-Exponential (ME) decay modeling has shown potential for identifying areas of prostate cancer hypoxia at 1.5T. However, Gaussian deviations from ME decay have been observed in other tissues at 3T. The purpose of this study is to assess whether gradient-echo signal decays are better characterized by a standard ME decay model, or a Gaussian Augmentation of the Mono-Exponential (GAME) decay model, in the prostate at 3T. Multi-gradient-echo signals were acquired on 20 consecutive patients with a clinical suspicion of prostate cancer undergoing MR-guided prostate biopsies. Data were fitted with both ME and GAME models. The information contents of these models were compared using Akaike's information criterion (second order, AICC ), in skeletal muscle, the prostate central gland (CG), and peripheral zone (PZ) regions of interest (ROIs). The GAME model had higher information content in 30% of the prostate on average (across all patients and ROIs), covering up to 67% of cancerous PZ ROIs, and up to 100% of cancerous CG ROIs (in individual patients). The higher information content of GAME became more prominent in regions that would be assumed hypoxic using ME alone, reaching 50% of the PZ and 70% of the CG as ME R2 (*) approached 40 s(-1) . R2 (*) mapping may have important applications in MRI; however, information lost due to modeling could mask differences in parameters due to underlying tissue anatomy or physiology. The GAME model improves characterization of signal behavior in the prostate at 3T, and may increase the potential for determining correlates of fit parameters with biomarkers, for example of oxygenation status.

  16. Advanced morphological 3D magnetic resonance observation of cartilage repair tissue (MOCART) scoring using a new isotropic 3D proton-density, turbo spin echo sequence with variable flip angle distribution (PD-SPACE) compared to an isotropic 3D steady-state free precession sequence (True-FISP) and standard 2D sequences.

    Science.gov (United States)

    Welsch, Goetz H; Zak, Lukas; Mamisch, Tallal C; Paul, Dominik; Lauer, Lars; Mauerer, Andreas; Marlovits, Stefan; Trattnig, Siegfried

    2011-01-01

    To evaluate a new isotropic 3D proton-density, turbo-spin-echo sequence with variable flip-angle distribution (PD-SPACE) sequence compared to an isotropic 3D true-fast-imaging with steady-state-precession (True-FISP) sequence and 2D standard MR sequences with regard to the new 3D magnetic resonance observation of cartilage repair tissue (MOCART) score. Sixty consecutive MR scans on 37 patients (age: 32.8 ± 7.9 years) after matrix-associated autologous chondrocyte transplantation (MACT) of the knee were prospectively included. The 3D MOCART score was assessed using the standard 2D sequences and the multiplanar-reconstruction (MPR) of both isotropic sequences. Statistical, Bonferroni-corrected correlation as well as subjective quality analysis were performed. The correlation of the different sequences was significant for the variables defect fill, cartilage interface, bone interface, surface, subchondral lamina, chondral osteophytes, and effusion (Pearson coefficients 0.514-0.865). Especially between the standard sequences and the 3D True-FISP sequence, the variables structure, signal intensity, subchondral bone, and bone marrow edema revealed lower, not significant, correlation values (0.242-0.383). Subjective quality was good for all sequences (P ≥ 0.05). Artifacts were most often visible on the 3D True-FISP sequence (P < 0.05). Different isotropic sequences can be used for the 3D evaluation of cartilage repair with the benefits of isotropic 3D MRI, MPR, and a significantly reduced scan time, where the 3D PD-SPACE sequence reveals the best results. Copyright © 2010 Wiley-Liss, Inc.

  17. Echo-Planar Imaging Based J-Resolved Spectroscopic Imaging for Improved Metabolite Detection in Prostate Cancer

    Science.gov (United States)

    2013-10-01

    patients, which included a 3D water- and fat -suppressed spectroscopic acquisition. 3D MRSI parameters of the endorectal and external phased array... fat . Artif Cells Blood Substit Immobil Biotechnol. 1994;22(4): 1477–83. 12. Maio A, Rifkin MD. Magnetic resonance imaging of prostate cancer...axial MRI of the abdomen is shown displaying the VOI covering the prostate localized by the PRESS sequence and the EP-JRESI grids. The split-Bregman

  18. Reduced susceptibility effects in perfusion fMRI with single-shot spin-echo EPI acquisitions at 1.5 Tesla.

    Science.gov (United States)

    Wang, Jiongjiong; Li, Lin; Roc, Anne C; Alsop, David C; Tang, Kathy; Butler, Norman S; Schnall, Mitchell D; Detre, John A

    2004-01-01

    Arterial spin labeling (ASL) perfusion contrast is not based on susceptibility effects and can therefore be used to study brain function in regions of high static inhomogeneity. As a proof of concept, single-shot spin-echo echo-planar imaging (EPI) acquisition was carried out with a multislice continuous ASL (CASL) method at 1.5T. A bilateral finger tapping paradigm was used in the presence of an exogenously induced susceptibility artifact over left motor cortex. The spin-echo CASL technique was compared with a regular gradient-echo EPI sequence with the same slice thickness, as well as other imaging methods using thin slices and spin-echo acquisitions. The results demonstrate improved functional sensitivity and efficiency of the spin-echo CASL approach as compared with gradient-echo EPI techniques, and a trend of improved sensitivity as compared with spin-echo EPI approach in the brain regions affected by the susceptibility artifact. ASL images, either with or without subtraction of the control, provide a robust alternative to blood oxygenation level dependant (BOLD) methods for activation imaging in regions of high static field inhomogeneity.

  19. Evaluation of balanced steady-state free precession (TrueFISP) and K-space segmented gradient echo sequences for 3D coronary MR angiography with navigator gating at 3 tesla

    Energy Technology Data Exchange (ETDEWEB)

    Kaul, M.G.; Stork, A.; Bansmann, P.M.; Nolte-Ernsting, C.; Weber, C.; Adam, G. [Radiologisches Zentrum, Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Lund, G.K. [Herzzentrum, Klinik und Poliklinik fuer Kardiologie/Angiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany)

    2004-11-01

    Purpose: To test the feasibility of k-space segmented gradient-echo pulse sequences for free-breathing coronary magnetic resonance angiography (cMRA)on a clinical 3T system. Materials and Methods: T2-prepared, fat-suppressed turbo field echo (TFE, turboFLASH, SFPGR) as well as balanced TFE (b-TFE, trueFISP, FIESTA, segmented SSFP) sequences with navigator gating for prospective motion correction were applied on a 3T system equipped with a six-element phased-array cardiac coil. In 15 healthy volunteers, the right coronary artery (RCA) was examined with TFE and b-TFE sequences. Due to examination time limitations, the left coronary artery (LM/LAD) was examined exclusively with the TFE sequence in ten volunteers. Image quality was graded on a five point scale (0=not visualized to 4=excellent). The length, diameter and sharpness of the vessels and the contrast-to-noise ratios (CNR) were measured. Results: 98% of all major segments (proximal/middle/distal) of the RCA could be seen with the TFE sequence and 82% with the b-TFE sequence. The image quality for the three segments was graded higher for the TFE sequence (2.7/2.7/1.5) than for the b-TFE sequence (1.9/1.6/0.9) with P: ({<=}0.001/{<=}0.004/{<=}0.056). The kappa of the interobserver variability was 0.75 for the TFE sequence and 0.8 for the b-TFE sequence. The measured vessel lengths were longer for the TFE sequence (95{+-}22 mm) than for the b-TFE sequence (80{+-}40 mm; P{<=}0.115). No significant changes (P{<=}0.074, P{<=}0.145) in diameter and vessel sharpness of the RCAs were observed between the TFE (2.4{+-}0.3 mm, 60%{+-}5) and b-TFE sequences (2.4{+-}0.3 mm, 62%{+-}6). The CNR was higher for the TFE sequence (10.1{+-}3.4) than for the b-TFE sequence (6.6{+-}2.1; P{<=}0.014). All ten main and proximal segments of the LM/LAD, which were examined exclusively with the TFE sequence, were visible with grade 2.5 and 2.1. The middle segment was visible in seven cases with grade 1.3. In three cases, the distal

  20. Sparse adaptive filters for echo cancellation

    CERN Document Server

    Paleologu, Constantin

    2011-01-01

    Adaptive filters with a large number of coefficients are usually involved in both network and acoustic echo cancellation. Consequently, it is important to improve the convergence rate and tracking of the conventional algorithms used for these applications. This can be achieved by exploiting the sparseness character of the echo paths. Identification of sparse impulse responses was addressed mainly in the last decade with the development of the so-called ``proportionate''-type algorithms. The goal of this book is to present the most important sparse adaptive filters developed for echo cancellati

  1. MR-Imaging optimisation of the articular hip cartilage by using a T{sub 1}-weighted 3-dimensional gradient-echo sequence and the application of a hip joint traction; Magnetresonanztomographische Optimierung der Hueftknorpeldarstellung durch die Wahl einer T{sub 1}-Volumen-Gradienten-Echo-Sequenz und die Anwendung einer Hueftgelenkstraktion

    Energy Technology Data Exchange (ETDEWEB)

    Rosenberg, R. [Heidelberg Univ. (Germany). Orthopaedische Klinik und Poliklinik; Bernd, L. [Heidelberg Univ. (Germany). Orthopaedische Klinik und Poliklinik; Wrazidlo, W. [ATOS-Praxisklinik, Heidelberg (Germany). Radiologische Gemeinschaftspraxis Drs. Lederer, Schneider und Wrazidlo; Lederer, W. [ATOS-Praxisklinik, Heidelberg (Germany). Radiologische Gemeinschaftspraxis Drs. Lederer, Schneider und Wrazidlo; Schneider, S. [ATOS-Praxisklinik, Heidelberg (Germany). Radiologische Gemeinschaftspraxis Drs. Lederer, Schneider und Wrazidlo

    1995-10-01

    Images of three animal cadaver hips, 8 dissected patient femoral heads and 18 hip joints of human corpses, all either with arthrosis stage I-III or artificial cartilage defects, were compared with their corresponding anatomic sections. Additional histomorphologic examinations of the arthrotic cartilages were conducted, and MR-Imaging of 20 healthy and 21 arthrotic patient hips was performed using a specific traction method. Using a T{sub 1}-weighted 3-dimensional gradient-echo sequence and a traction of the hip joint, it was possible due to the low-signal imaging of the joint space to separate in vivo the high-signal femoral head cartilage from the high-signal acetabular cartilage. In horizontal position of the phase-encoding parameter, minimisation of the chemical-shift artifact, mainly in the ventro-lateral areas, was accomplished. MRI measurements of the articular cartilage widths showed significant correlations (p < 0.001) with the corresponding anatomic sections. At the same time the T{sub 1} 3-dimensional gradient-echo sequence of the lateral femoral head with r = 0.94 showed the lowest deviations of the measurements. It was possible with MR-Imaging to distinguish four cartilage qualities. (orig./MG) [Deutsch] Im experimentellen Teil der Studie wurden den MRT-Bildern von drei Kadavertierhueften, 8 resezierten Patientenhueftkoepfen und 18 Leichenhueftgelenken, an denen entweder artifizielle Knorpeldefekte gesetzt wurden oder die ein Koxarthrose-Stadium I-III aufwiesen, die korrespondierenden makroskopischen Kryomikrotomschnitte zugeordnet. Bei den Koxarthrosen erfolgten zusaetzliche histomorphologische Knorpeluntersuchungen. Im klinischen Teil der Studie wurden 20 gesunde und 21 arthrotische Probandenhueftgelenke mit einem speziellen Traktionsverfahren untersucht. Unter Anwendung einer T{sub 1}-Volumen-Gradienten-Echo-Sequenz und einer Traktion am zu untersuchenden Hueftgelenk konnte in vivo durch die signalarme Darstellung des Gelenkspaltes der

  2. Detection and appearance of intraparenchymal haematomas of the brain at 1.5 T with spin-echo, FLAIR and GE sequences: poor relationship to the age of the haematoma

    Energy Technology Data Exchange (ETDEWEB)

    Alemany Ripoll, M. [Department of Radiology, Uppsala University Hospital, Uppsala (Sweden); Fundacion Rioja Salud, Avda de Portugal no. 7, Logrono, La Rioja (Spain); Stenborg, A.; Terent, A. [Department of Internal Medicine, Uppsala University Hospital, Uppsala (Sweden); Sonninen, P. [Department of Radiology, Turku University Hospital, Turku (Finland); Raininko, R. [Department of Radiology, Uppsala University Hospital, Uppsala (Sweden)

    2004-06-01

    The specific appearance of blood related to time at T1- and T2-weighted spin-echo (SE) sequences is generally accepted; thus, these sequences are classically used for estimating the age of haematomas. Magnetic resonance imaging at 1.5 T, including T1- and T2-weighted SE fluid-attenuated inversion recovery (FLAIR) and T2*-weighted gradient-echo (GE) sequences, was performed on 82 intraparenchymal haematomas (IPHs) and 15 haemorrhagic infarcts (HIs) in order to analyse the appearance at different stages and with different sequences, and to investigate how reliably the age of hematomas can be estimated. The IPHs had been previously detected by CT, were spontaneous (n=72) or traumatic (n=10) in origin and were of different sizes (2 mm to 7 cm) and ages (from 7.5 h to 4 years after acute haemorrhagic event). The age of the lesion was calculated from the moment when clinical symptoms started or the traumatic event occurred. The 15 patients with HIs were patients with ischaemic stroke in whom there was either a suspicion of haemorrhagic transformation on CT, or haemorrhage was detected as an additional finding on MR performed for other indications. Patients with conditions that could affect the SI of blood, such as anticoagulant therapy or severe anaemia, were excluded. The signal intensity pattern of the lesions was analysed and related to their ages without prior knowledge of the clinical data. All lesions were detected with T2*-weighted GE. T1-weighted SE missed 13 haematomas and T2-weighted SE and FLAIR sequences missed five. Haemorrhagic transformation was missed in three infarcts by T1-, T2-weighted SE and FLAIR. The signal pattern on FLAIR was identical to that on T2-weighted SE. For all sequences, a wide variety of signal patterns, without a clear relationship to the age of the haematomas, was observed. There was a poor relationship between the real MR appearance of IPHs and the theoretical appearance on SE sequences. T2*-weighted GE was effective for detecting

  3. Improved Algorithm for Analysis of DNA Sequences Using Multiresolution Transformation

    Directory of Open Access Journals (Sweden)

    T. M. Inbamalar

    2015-01-01

    Full Text Available Bioinformatics and genomic signal processing use computational techniques to solve various biological problems. They aim to study the information allied with genetic materials such as the deoxyribonucleic acid (DNA, the ribonucleic acid (RNA, and the proteins. Fast and precise identification of the protein coding regions in DNA sequence is one of the most important tasks in analysis. Existing digital signal processing (DSP methods provide less accurate and computationally complex solution with greater background noise. Hence, improvements in accuracy, computational complexity, and reduction in background noise are essential in identification of the protein coding regions in the DNA sequences. In this paper, a new DSP based method is introduced to detect the protein coding regions in DNA sequences. Here, the DNA sequences are converted into numeric sequences using electron ion interaction potential (EIIP representation. Then discrete wavelet transformation is taken. Absolute value of the energy is found followed by proper threshold. The test is conducted using the data bases available in the National Centre for Biotechnology Information (NCBI site. The comparative analysis is done and it ensures the efficiency of the proposed system.

  4. Improved algorithm for analysis of DNA sequences using multiresolution transformation.

    Science.gov (United States)

    Inbamalar, T M; Sivakumar, R

    2015-01-01

    Bioinformatics and genomic signal processing use computational techniques to solve various biological problems. They aim to study the information allied with genetic materials such as the deoxyribonucleic acid (DNA), the ribonucleic acid (RNA), and the proteins. Fast and precise identification of the protein coding regions in DNA sequence is one of the most important tasks in analysis. Existing digital signal processing (DSP) methods provide less accurate and computationally complex solution with greater background noise. Hence, improvements in accuracy, computational complexity, and reduction in background noise are essential in identification of the protein coding regions in the DNA sequences. In this paper, a new DSP based method is introduced to detect the protein coding regions in DNA sequences. Here, the DNA sequences are converted into numeric sequences using electron ion interaction potential (EIIP) representation. Then discrete wavelet transformation is taken. Absolute value of the energy is found followed by proper threshold. The test is conducted using the data bases available in the National Centre for Biotechnology Information (NCBI) site. The comparative analysis is done and it ensures the efficiency of the proposed system.

  5. MRI of the anterior talofibular ligament, talar cartilage and os subfibulare: Comparison of isotropic resolution 3D and conventional 2D T2-weighted fast spin-echo sequences at 3.0 T

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Jisook; Cha, Jang Gyu [Soonchunhyang University Bucheon Hospital, Department of Radiology, Wonmi-gu, Bucheon-si (Korea, Republic of); Lee, Young Koo [Soonchunhyang University Bucheon Hospital, Department of Orthopedics, Wonmi-gu, Bucheon-si (Korea, Republic of); Lee, Bo Ra [Soonchunhyang University Bucheon Hospital, Department of Biomedical Statistics, Wonmi-gu, Bucheon-si (Korea, Republic of); Jeon, Chan Hong [Soonchunhyang University Bucheon Hospital, Division of Rheumatology, Department of Internal Medicine, Wonmi-gu, Bucheon-si (Korea, Republic of)

    2016-07-15

    To determine the accuracy of a three-dimensional (3D) T2-weighted fast spin-echo (FSE) magnetic resonance (MR) sequence compared with two-dimensional (2D) sequence for diagnosing anterior talofibular ligament (ATFL) tears, chondral lesion of the talus (CLT) and os subfibulare/avulsion fracture of the distal fibula (OSF). Thirty-five patients were included, who had undergone ankle MRI with 3D T2-weighted FSE and 2D T2-weighted FSE sequences, as well as subsequent ankle arthroscopy, between November 2013 and July 2014. Each MR imaging sequence was independently scored by two readers retrospectively for the presence of ATFL tears, CLT and OSF. The area under the receiver operating curve (AUC) was compared to determine the discriminatory power of the two image sequences. Interobserver agreement was expressed as unweighted kappa value. Arthroscopic findings confirmed 21 complete tears of the ATFL, 14 partial tears of the ATFL, 17 CLTs and 7 OSFs. There were no significant differences in the diagnoses of ATFL tears (p = 0.074-0.501), CLT (p = 0.090-0.450) and OSF (p = 0.317) obtained from the 2D and 3D sequences by either reader. The interobserver agreement rates between two readers using the 3D T2-weighted FSE sequence versus those obtained with the 2D sequence were substantial (κ = 0.659) versus moderate (κ = 0.553) for ATFL tears, moderate (κ = 0.499) versus substantial (κ = 0.676) for CLT and substantial (κ = 0.621) versus substantial (κ = 0.689) for OSF. Three-dimensional isotropic T2-weighted FSE MRI of the ankle resulted in no statistically significant difference in diagnostic performance compared to two-dimensional T2-weighted FSE MRI in the evaluation of ATFL tears, CLTs and OSFs. (orig.)

  6. Improving effect size estimation and statistical power with multi-echo fMRI and its impact on understanding the neural systems supporting mentalizing.

    Science.gov (United States)

    Lombardo, Michael V; Auyeung, Bonnie; Holt, Rosemary J; Waldman, Jack; Ruigrok, Amber N V; Mooney, Natasha; Bullmore, Edward T; Baron-Cohen, Simon; Kundu, Prantik

    2016-11-15

    Functional magnetic resonance imaging (fMRI) research is routinely criticized for being statistically underpowered due to characteristically small sample sizes and much larger sample sizes are being increasingly recommended. Additionally, various sources of artifact inherent in fMRI data can have detrimental impact on effect size estimates and statistical power. Here we show how specific removal of non-BOLD artifacts can improve effect size estimation and statistical power in task-fMRI contexts, with particular application to the social-cognitive domain of mentalizing/theory of mind. Non-BOLD variability identification and removal is achieved in a biophysical and statistically principled manner by combining multi-echo fMRI acquisition and independent components analysis (ME-ICA). Without smoothing, group-level effect size estimates on two different mentalizing tasks were enhanced by ME-ICA at a median rate of 24% in regions canonically associated with mentalizing, while much more substantial boosts (40-149%) were observed in non-canonical cerebellar areas. Effect size boosting occurs via reduction of non-BOLD noise at the subject-level and consequent reductions in between-subject variance at the group-level. Smoothing can attenuate ME-ICA-related effect size improvements in certain circumstances. Power simulations demonstrate that ME-ICA-related effect size enhancements enable much higher-powered studies at traditional sample sizes. Cerebellar effects observed after applying ME-ICA may be unobservable with conventional imaging at traditional sample sizes. Thus, ME-ICA allows for principled design-agnostic non-BOLD artifact removal that can substantially improve effect size estimates and statistical power in task-fMRI contexts. ME-ICA could mitigate some issues regarding statistical power in fMRI studies and enable novel discovery of aspects of brain organization that are currently under-appreciated and not well understood.

  7. Happy birthday Echo!

    CERN Multimedia

    Staff Association

    2010-01-01

    You are reading the number hundred and one (no. 101) edition of our bulletin Echo. Just over four years ago, on 27th March 2006, the first untitled edition was published (Fig. 1 on the left). The title Echo appeared on the second edition on 10th April 2006 (Fig. 1 in the centre). Today (see Fig. 1 on the right), the layout is slightly different, but the structure of each edition has remained more or less the same: an editorial informing you of the important issues, followed by articles on club life, cultural activities (exhibitions and conferences), information from GAC-EPA, and special offers for our members.     Fig. 1 : Nos. 1, 2 and 100 of our twice-monthly publication Echo Echo was created in March 2006 when, much to our regret, CERN official communication and that of your representatives were separated. November 2009 saw a return to normal practice, and since then the CERN st...

  8. Facilities | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  9. Improved nonparametric inference for multiple correlated periodic sequences

    KAUST Repository

    Sun, Ying

    2013-08-26

    This paper proposes a cross-validation method for estimating the period as well as the values of multiple correlated periodic sequences when data are observed at evenly spaced time points. The period of interest is estimated conditional on the other correlated sequences. An alternative method for period estimation based on Akaike\\'s information criterion is also discussed. The improvement of the period estimation performance is investigated both theoretically and by simulation. We apply the multivariate cross-validation method to the temperature data obtained from multiple ice cores, investigating the periodicity of the El Niño effect. Our methodology is also illustrated by estimating patients\\' cardiac cycle from different physiological signals, including arterial blood pressure, electrocardiography, and fingertip plethysmograph.

  10. Diffusion-weighted imaging in the prostate: an apparent diffusion coefficient comparison of half-Fourier acquisition single-shot turbo spin-echo and echo planar imaging.

    Science.gov (United States)

    Babourina-Brooks, Ben; Cowin, Gary J; Wang, Deming

    2012-02-01

    Prostate cancer detection using diffusion-weighted imaging is highly affected by the accuracy of the apparent diffusion coefficient (ADC) values in an image. Echo planar imaging (EPI) is a fast sequence commonly used for diffusion imaging but has inherent magnetic susceptibility and chemical shift artefacts associated. A diffusion sequence that is less affected by these artefacts is therefore advantageous. The half-Fourier acquisition single-shot turbo spin-echo (HASTE) sequence was chosen. The diffusion sequences were compared in image quality, repeatability of the ADC value and the effect on the ADC value with varied b values. Eight volunteers underwent three scans of each sequence, on a 1.5-T Siemens system, using b values of 0, 150, 300, 450, 600, 750, 900 and 1000 s/mm(2). ADC maps were created to address the reproducibility of the ADC value when using two b values compared to eight b values. The ADC value using all b values with the HASTE sequence gave the best performance in all tested categories. Both sequences gave significantly different ADC mean values for two b values compared to when using eight b values (Perror is present when using two b values. HASTE was shown to be an improvement over EPI in terms of repeatability, signal variation within a region of interest and standard deviation over the volunteer set. The improved accuracy of the ADC value in the HASTE sequence makes it potentially a more sensitive tumor detection technique.

  11. Efficacy on maximum intensity projection of contrast-enhanced 3D spin echo imaging with improved motion-sensitized driven-equilibrium preparation in the detection of brain metastases

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Yun Jung; Choi, Byung Se; Yoon, Yeon Hong; Woo, Leonard Sun; Jung, Cheol Kyu; Kim, Jae Hyoung [Dept. of Radiology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam (Korea, Republic of); Lee, Kyung Mi [Dept. of Radiology, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul (Korea, Republic of)

    2017-08-01

    To evaluate the diagnostic benefits of 5-mm maximum intensity projection of improved motion-sensitized driven-equilibrium prepared contrast-enhanced 3D T1-weighted turbo-spin echo imaging (MIP iMSDE-TSE) in the detection of brain metastases. The imaging technique was compared with 1-mm images of iMSDE-TSE (non-MIP iMSDE-TSE), 1-mm contrast-enhanced 3D T1-weighted gradient-echo imaging (non-MIP 3D-GRE), and 5-mm MIP 3D-GRE. From October 2014 to July 2015, 30 patients with 460 enhancing brain metastases (size > 3 mm, n = 150; size ≤ 3 mm, n = 310) were scanned with non-MIP iMSDE-TSE and non-MIP 3D-GRE. We then performed 5-mm MIP reconstruction of these images. Two independent neuroradiologists reviewed these four sequences. Their diagnostic performance was compared using the following parameters: sensitivity, reading time, and figure of merit (FOM) derived by jackknife alternative free-response receiver operating characteristic analysis. Interobserver agreement was also tested. The mean FOM (all lesions, 0.984; lesions ≤ 3 mm, 0.980) and sensitivity ([reader 1: all lesions, 97.3%; lesions ≤ 3 mm, 96.2%], [reader 2: all lesions, 97.0%; lesions ≤ 3 mm, 95.8%]) of MIP iMSDE-TSE was comparable to the mean FOM (0.985, 0.977) and sensitivity ([reader 1: 96.7, 99.0%], [reader 2: 97, 95.3%]) of non-MIP iMSDE-TSE, but they were superior to those of non-MIP and MIP 3D-GREs (all, p < 0.001). The reading time of MIP iMSDE-TSE (reader 1: 47.7 ± 35.9 seconds; reader 2: 44.7 ± 23.6 seconds) was significantly shorter than that of non-MIP iMSDE-TSE (reader 1: 78.8 ± 43.7 seconds, p = 0.01; reader 2: 82.9 ± 39.9 seconds, p < 0.001). Interobserver agreement was excellent (κ > 0.75) for all lesions in both sequences. MIP iMSDE-TSE showed high detectability of brain metastases. Its detectability was comparable to that of non-MIP iMSDE-TSE, but it was superior to the detectability of non-MIP/MIP 3D-GREs. With a shorter reading time, the false-positive results of MIP i

  12. Characterization of Nyquist ghost in EPI-fMRI acquisition sequences implemented on two clinical 1.5 T MR scanner systems: effect of readout bandwidth and echo spacing.

    Science.gov (United States)

    Giannelli, Marco; Diciotti, Stefano; Tessa, Carlo; Mascalchi, Mario

    2010-07-12

    In EPI-fMRI acquisitions, various readout bandwidth (BW) values are used as a function of gradients' characteristics of the MR scanner system. Echo spacing (ES) is another fundamental parameter of EPI-fMRI sequences, but the employed ES value is not usually reported in fMRI studies. Nyquist ghost is a typical EPI artifact that can degrade the overall quality of fMRI time series. In this work, the authors assessed the basic effect of BW and ES for two clinical 1.5 T MR scanner systems (scanner-A, scanner-B) on Nyquist ghost of gradient-echo EPI-fMRI sequences. BW range was: scanner-A, 1953-3906 Hz/pixel; scanner-B, 1220-2894 Hz/pixel. ES range was: scanner-A, scanner-B: 0.75-1.33 ms. The ghost-to-signal ratio of time series acquisition (GSRts) and drift of ghost-to-signal ratio (DRGSR) were measured in a water phantom. For both scanner-A (93% of variation) and scanner-B (102% of variation) the mean GSRts significantly increased with increasing BW. GSRts values of scanner-A did not significantly depended on ES. On the other hand, GSRts values of scanner-B significantly varied with ES, showing a downward trend (81% of variation) with increasing ES. In addition, a GSRts spike point at ES = 1.05 ms indicating a potential resonant effect was revealed. For both scanners, no significant effect of ES on DRGSR was revealed. DRGSR values of scanner-B did not significantly vary with BW, whereas DRGSR values of scanner-A significantly depended on BW showing an upward trend from negative to positive values with increasing BW. GSRts and DRGSR can significantly vary with BW and ES, and the specific pattern of variation may depend on gradients performances, EPI sequence calibrations and functional design of radiofrequency coil. Thus, each MR scanner system should be separately characterized. In general, the employment of low BW values seems to reduce the intensity and temporal variation of Nyquist ghost in EPI-fMRI time series. On the other hand, the use of minimum ES value might

  13. Comparison of 3D Maximum intensity projection (MIP reconstruction and 2D T2 Half-Fourier Acquisition Single-Shot Turbo Spin-Echo (HASTE sequence in magnetic resonance cholangiopancreatography

    Directory of Open Access Journals (Sweden)

    Fuad Julardžija

    2014-04-01

    Full Text Available Introduction: Magnetic resonance cholangiopancreatography (MRCP is a method that allows noninvasive visualization of pancreatobiliary tree and does not require contrast application. It is a modern method based on heavily T2-weighted imaging (hydrography, which uses bile and pancreatic secretions as a natural contrast medium. Certain weaknesses in quality of demonstration of pancreatobiliary tract can be observed in addition to its good characteristics. Our aim was to compare the 3D Maximum intensity projection (MIP reconstruction and 2D T2 Half-Fourier Acquisition Single-Shot Turbo Spin-Echo (HASTE sequence in magnetic resonance cholangiopancreatography.Methods: During the period of one year 51 patients underwent MRCP on 3T „Trio“ system. Patients of different sex and age structure were included, both outpatient and hospitalized. 3D MIP reconstruction and 2D T2 haste sequence were used according to standard scanning protocols.Results: There were 45.1% (n= 23 male and 54.9% (n=28 female patients, age range from 17 to 81 years. 2D T2 haste sequence was more susceptible to respiratory artifacts presence in 64% patients, compared to 3D MIP reconstruction with standard error (0.09, result significance indication (p=0.129 and confidence interval (0.46 to 0.81. 2D T2 haste sequences is more sensitive and superior for pancreatic duct demonstration compared to 3D MIP reconstruction with standard error (0.07, result significance indication (p=0.01 and confidence interval (0.59 to 0.87Conclusion: In order to make qualitative demonstration and analysis of hepatobiliary and pancreatic system on MR, both 2D T2 haste sequence in transversal plane and 3D MIP reconstruction are required.

  14. Contrast enhancement of intracranial lesions at 1.5 T: comparison among 2D spin echo, black-blood (BB) Cube, and BB Cube-FLAIR sequences

    Energy Technology Data Exchange (ETDEWEB)

    Im, SungWoon; Ashikaga, Ryuichiro; Yagyu, Yukinobu; Hyodo, Tomoko; Imaoka, Izumi; Kumano, Seishi; Ishii, Kazunari; Murakami, Takamichi [Kinki University Faculty of Medicine, Department of Radiology, Osaka-Sayama, Osaka (Japan); Wakayama, Tetsuya; Miyoshi, Mitsuharu [GE Healthcare Japan, MR Applications and Workflow, Asia Pacific, Hino, Tokyo (Japan)

    2015-11-15

    The purpose of this study was to investigate the usefulness of T1W black-blood Cube (BB Cube) and T1W BB Cube fluid-attenuated inversion recovery (BB Cube-FLAIR) sequences for contrast-enhanced brain imaging, by evaluating flow-related artefacts, detectability, and contrast ratio (CR) of intracranial lesions among these sequences and T1W-SE. Phantom studies were performed to determine the optimal parameters of BB Cube and BB Cube-FLAIR. A clinical study in 23 patients with intracranial lesions was performed to evaluate the usefulness of these two sequences for the diagnosis of intracranial lesions compared with the conventional 2D T1W-SE sequence. The phantom study revealed that the optimal parameters for contrast-enhanced T1W imaging were TR/TE = 500 ms/minimum in BB Cube and TR/TE/TI = 600 ms/minimum/300 ms in BB Cube-FLAIR imaging. In the clinical study, the degree of flow-related artefacts was significantly lower in BB Cube and BB Cube-FLAIR than in T1W-SE. Regarding tumour detection, BB Cube showed the best detectability; however, there were no significant differences in CR among the sequences. At 1.5 T, contrast-enhanced BB Cube was a better imaging sequence for detecting brain lesions than T1W-SE or BB Cube-FLAIR. (orig.)

  15. Echoes in Space and Time

    Science.gov (United States)

    Lin, Kang; Lu, Peifen; Ma, Junyang; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Zhang, Wenbin; Zeng, Heping; Wu, Jian; Karras, Gabriel; Siour, Guillaume; Hartmann, Jean-Michel; Faucher, Olivier; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh.

    2016-10-01

    Echo in mountains is a well-known phenomenon, where an acoustic pulse is mirrored by the rocks, often with reverberating recurrences. For spin echoes in magnetic resonance and photon echoes in atomic and molecular systems, the role of the mirror is played by a second, time-delayed pulse that is able to reverse the flow of time and recreate the original impulsive event. Recently, alignment and orientation echoes were discussed in terms of rotational-phase-space filamentation, and they were optically observed in laser-excited molecular gases. Here, we observe hitherto unreported fractional echoes of high order, spatially rotated echoes, and the counterintuitive imaginary echoes at negative times. Coincidence Coulomb explosion imaging is used for a direct spatiotemporal analysis of various molecular alignment echoes, and the implications to echo phenomena in other fields of physics are discussed.

  16. USPIO-enhanced 3D-cine self-gated cardiac MRI based on a stack-of-stars golden angle short echo time sequence: Application on mice with acute myocardial infarction.

    Science.gov (United States)

    Trotier, Aurélien J; Castets, Charles R; Lefrançois, William; Ribot, Emeline J; Franconi, Jean-Michel; Thiaudière, Eric; Miraux, Sylvain

    2016-08-01

    To develop and assess a 3D-cine self-gated method for cardiac imaging of murine models. A 3D stack-of-stars (SOS) short echo time (STE) sequence with a navigator echo was performed at 7T on healthy mice (n = 4) and mice with acute myocardial infarction (MI) (n = 4) injected with ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles. In all, 402 spokes were acquired per stack with the incremental or the golden angle method using an angle increment of (360/402)° or 222.48°, respectively. A cylindrical k-space was filled and repeated with a maximum number of repetitions (NR) of 10. 3D cine cardiac images at 156 μm resolution were reconstructed retrospectively and compared for the two methods in terms of contrast-to-noise ratio (CNR). The golden angle images were also reconstructed with NR = 10, 6, and 3, to assess cardiac functional parameters (ejection fraction, EF) on both animal models. The combination of 3D SOS-STE and USPIO injection allowed us to optimize the identification of cardiac peaks on navigator signal and generate high CNR between blood and myocardium (15.3 ± 1.0). The golden angle method resulted in a more homogeneous distribution of the spokes inside a stack (P cine images could be obtained without electrocardiogram or respiratory gating in mice. It allows precise measurement of cardiac functional parameters even on MI mice. J. Magn. Reson. Imaging 2016;44:355-365. © 2016 Wiley Periodicals, Inc.

  17. Improvement of SNR with Chaotic Spreading Sequences for CDMA

    CERN Document Server

    Umeno, K; Umeno, Ken; Kitayama, Ken-ichi

    1999-01-01

    We show that chaotic spreading sequences generated by ergodic mappings of Chebyshev orthogonal polynomials have better correlation properties for CDMA(code division multiple access) than the optimal binary sequences (Gold sequences) in the sense of ensemble average.

  18. Phylo: a citizen science approach for improving multiple sequence alignment.

    Science.gov (United States)

    Kawrykow, Alexander; Roumanis, Gary; Kam, Alfred; Kwak, Daniel; Leung, Clarence; Wu, Chu; Zarour, Eleyine; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

    2012-01-01

    Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. We introduce Phylo, a human-based computing framework applying "crowd sourcing" techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of "human-brain peta-flops" of computation that are spent every day playing games. Phylo is available at: http://phylo.cs.mcgill.ca.

  19. Phylo: a citizen science approach for improving multiple sequence alignment.

    Directory of Open Access Journals (Sweden)

    Alexander Kawrykow

    Full Text Available BACKGROUND: Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. METHODOLOGY/PRINCIPAL FINDINGS: We introduce Phylo, a human-based computing framework applying "crowd sourcing" techniques to solve the Multiple Sequence Alignment (MSA problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. CONCLUSIONS/SIGNIFICANCE: We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of "human-brain peta-flops" of computation that are spent every day playing games

  20. Experimental observation of fractional echoes

    Science.gov (United States)

    Karras, G.; Hertz, E.; Billard, F.; Lavorel, B.; Siour, G.; Hartmann, J.-M.; Faucher, O.; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh.

    2016-09-01

    We report the observation of fractional echoes in a double-pulse excited nonlinear system. Unlike standard echoes, which appear periodically at delays which are integer multiples of the delay between the two exciting pulses, the fractional echoes appear at rational fractions of this delay. We discuss the mechanism leading to this phenomenon, and provide experimental demonstration of fractional echoes by measuring third harmonic generation in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses.

  1. Visualization of the Peripheral Branches of the Mandibular Division of the Trigeminal Nerve on 3D Double-Echo Steady-State with Water Excitation Sequence

    National Research Council Canada - National Science Library

    Fujii, H; Fujita, A; Yang, A; Kanazawa, H; Buch, K; Sakai, O; Sugimoto, H

    2015-01-01

    Although visualization of the extracranial branches of the cranial nerves has improved with advances in MR imaging, only limited studies have assessed the detection of extracranial branches of the mandibular nerve (V3...

  2. Improved transfer logic of two-path algorithm for acoustic echo cancellation%基于声回波抵消两路算法的改进更新逻辑

    Institute of Scientific and Technical Information of China (English)

    王飞; 刘畅

    2012-01-01

    the two-path algorithm in the acoustic echo cancellation ia widely applied to avoid the false adaptation problem during the double-talk situation. This paper proposed an improved transfer logic for the two-path algorithm; based on the comparison of the Echo Return Los9 Enhancement (ERLE) for the fillers, the improved transfer logic decided whether to permit filter update. Furthermore, the improved transfer logic managed to detect the double-talk and avoid the false filter update, improved the convergence speed and allowed the reduction of the memory requirement and computational complexity. The simulation results show the improved performance of the proposed solution.%声回波抵消两路算法被广泛用来检测系统双向通话;基于声回波抵消两路算法,提出了一种改进的控制更新逻辑.此更新逻辑通过比较滤波器的回波返回损失(ERLE),判断是否对滤波器进行更新.此改进更新逻辑能正确检测系统双向通话,避免滤波器的错误更新,并提高两路算法的收敛速度,减小存储器资源和计算量.仿真结果证实了此更新逻辑的有效性.

  3. Evaluation of correlation property of linear-frequency-modulated signals coded by maximum-length sequences

    Science.gov (United States)

    Yamanaka, Kota; Hirata, Shinnosuke; Hachiya, Hiroyuki

    2016-07-01

    Ultrasonic distance measurement for obstacles has been recently applied in automobiles. The pulse-echo method based on the transmission of an ultrasonic pulse and time-of-flight (TOF) determination of the reflected echo is one of the typical methods of ultrasonic distance measurement. Improvement of the signal-to-noise ratio (SNR) of the echo and the avoidance of crosstalk between ultrasonic sensors in the pulse-echo method are required in automotive measurement. The SNR of the reflected echo and the resolution of the TOF are improved by the employment of pulse compression using a maximum-length sequence (M-sequence), which is one of the binary pseudorandom sequences generated from a linear feedback shift register (LFSR). Crosstalk is avoided by using transmitted signals coded by different M-sequences generated from different LFSRs. In the case of lower-order M-sequences, however, the number of measurement channels corresponding to the pattern of the LFSR is not enough. In this paper, pulse compression using linear-frequency-modulated (LFM) signals coded by M-sequences has been proposed. The coding of LFM signals by the same M-sequence can produce different transmitted signals and increase the number of measurement channels. In the proposed method, however, the truncation noise in autocorrelation functions and the interference noise in cross-correlation functions degrade the SNRs of received echoes. Therefore, autocorrelation properties and cross-correlation properties in all patterns of combinations of coded LFM signals are evaluated.

  4. Comparison of spoiled gradient echo and steady-state free-precession imaging for native myocardial T1 mapping using the slice-interleaved T1 mapping (STONE) sequence.

    Science.gov (United States)

    Jang, Jihye; Bellm, Steven; Roujol, Sébastien; Basha, Tamer A; Nezafat, Maryam; Kato, Shingo; Weingärtner, Sebastian; Nezafat, Reza

    2016-10-01

    Cardiac T1 mapping allows non-invasive imaging of interstitial diffuse fibrosis. Myocardial T1 is commonly calculated by voxel-wise fitting of the images acquired using balanced steady-state free precession (SSFP) after an inversion pulse. However, SSFP imaging is sensitive to B1 and B0 imperfection, which may result in additional artifacts. A gradient echo (GRE) imaging sequence has been used for myocardial T1 mapping; however, its use has been limited to higher magnetic field to compensate for the lower signal-to-noise ratio (SNR) of GRE versus SSFP imaging. A slice-interleaved T1 mapping (STONE) sequence with SSFP readout (STONE-SSFP) has been recently proposed for native myocardial T1 mapping, which allows longer recovery of magnetization (>8 R-R) after each inversion pulse. In this study, we hypothesize that a longer recovery allows higher SNR and enables native myocardial T1 mapping using STONE with GRE imaging readout (STONE-GRE) at 1.5T. Numerical simulations and phantom and in vivo imaging were performed to compare the performance of STONE-GRE and STONE-SSFP for native myocardial T1 mapping at 1.5T. In numerical simulations, STONE-SSFP shows sensitivity to both T2 and off resonance. Despite the insensitivity of GRE imaging to T2 , STONE-GRE remains sensitive to T2 due to the dependence of the inversion pulse performance on T2 . In the phantom study, STONE-GRE had inferior accuracy and precision and similar repeatability as compared with STONE-SSFP. In in vivo studies, STONE-GRE and STONE-SSFP had similar myocardial native T1 times, precisions, repeatabilities and subjective T1 map qualities. Despite the lower SNR of the GRE imaging readout compared with SSFP, STONE-GRE provides similar native myocardial T1 measurements, precision, repeatability, and subjective image quality when compared with STONE-SSFP at 1.5T.

  5. Echo: skin stress test

    Science.gov (United States)

    1960-01-01

    Skin Stress Test of the 12-foot satellite built as a prototype of the full-scale Echo satellite. The 12-foot diameter of the sphere was chosen because that was the ceiling height in the Langley model shop. The proposal to build the 12-foot satellite was made in November 1957. - Published in James R. Hansen, Spaceflight Revolution: NASA Langley Research Center From Sputnik to Apollo, NASA SP-4308, pp. 170-171.

  6. Spin echo in synchrotrons

    Science.gov (United States)

    Chao, Alexander W.; Courant, Ernest D.

    2007-01-01

    As a polarized beam is accelerated through a depolarization resonance, its polarization is reduced by a well-defined calculable reduction factor. When the beam subsequently crosses a second resonance, the final beam polarization is considered to be reduced by the product of the two reduction factors corresponding to the two crossings, each calculated independently of the other. This is a good approximation when the spread of spin precession frequency Δνspin of the beam (particularly due to its energy spread) is sufficiently large that the spin precession phases of individual particles smear out completely during the time τ between the two crossings. This approximate picture, however, ignores two spin dynamics effects: an interference-overlap effect and a spin echo effect. This paper is to address these two effects. The interference-overlap effect occurs when Δνspin is too small, or when τ is too short, to complete the smearing process. In this case, the two resonance crossings overlap each other, and the final polarization exhibits constructive or destructive interference patterns depending on the exact value of τ. Typically, the beam’s energy spread is large and this interference-overlap effect does not occur. To study this effect, therefore, it is necessary to reduce the beam energy spread and to consider two resonance crossings very close to each other. The other mechanism, also due to the interplay between two resonance crossings, is spin echo. It turns out that even when the precession phases appear to be completely smeared between the two crossings, there will still be a sudden and short-lived echo signal of beam polarization at a time τ after the second crossing; the magnitude of which can be as large as 57%. This echo signal exists even when the beam has a sizable energy spread and when τ is very large, and could be a sensitive (albeit challenging) way to experimentally test the intricate spin dynamics in a synchrotron. After giving an analysis

  7. Spin Echo in Synchrotrons

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Alexander W.; /SLAC; Courant, Ernest D.; /Brookhaven

    2006-12-01

    As a polarized beam is accelerated through a depolarization resonance, its polarization is reduced by a well-defined calculable reduction factor. When the beam subsequently crosses a second resonance, the final beam polarization is considered to be reduced by the product of the two reduction factors corresponding to the two crossings, each calculated independently of the other. This is a good approximation when the spread of spin precession frequency {Delta}{nu}{sub spin} of the beam (particularly due to its energy spread) is sufficiently large that the spin precession phases of individual particles smear out completely during the time {tau} between the two crossings. This approximate picture, however, ignores two spin dynamics effects: an interference effect and a spin echo effect. This paper is to address these two effects. The interference effect occurs when {Delta}{nu}{sub spin} is too small, or when {tau} is too short, to complete the smearing process. In this case, the two resonance crossings interfere with each other, and the final polarization exhibits constructive or destructive patterns depending on the exact value of {tau}. Typically, the beam's energy spread is large and this interference effect does not occur. To study this effect, therefore, it is necessary to reduce the beam energy spread and to consider two resonance crossings very close to each other. The other mechanism, also due to the interplay between two resonance crossings, is spin echo. It turns out that even when the precession phases appear to be completely smeared between the two crossings, there will still be a sudden and short-lived echo signal of beam polarization at a time {tau} after the second crossing; the magnitude of which can be as large as 57%. This echo signal exists even when the beam has a sizable energy spread and when {tau} is very large, and could be a sensitive (albeit challenging) way to experimentally test the intricate spin dynamics in a synchrotron. After giving

  8. Exome sequencing can improve diagnosis and alter patient management

    NARCIS (Netherlands)

    Dixon-Salazar, T.J.; Silhavy, J.L.; Udpa, N.; Schroth, J.; Bielas, S.; Schaffer, A.E.; Olvera, J.; Bafna, V.; Zaki, M.S.; Abdel-Salam, G.H.; Mansour, L.A.; Selim, L.; Abdel-Hadi, S.; Marzouki, N.; Ben-Omran, T.; Al-Saana, N.A.; Sonmez, F.M.; Celep, F.; Azam, M.; Hill, K.J.; Collazo, A.; Fenstermaker, A.G.; Novarino, G.; Akizu, N.; Garimella, K.V.; Sougnez, C.; Russ, C.; Gabriel, S.B.; Gleeson, J.G.

    2012-01-01

    The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing

  9. Protein sequence classification with improved extreme learning machine algorithms.

    Science.gov (United States)

    Cao, Jiuwen; Xiong, Lianglin

    2014-01-01

    Precisely classifying a protein sequence from a large biological protein sequences database plays an important role for developing competitive pharmacological products. Comparing the unseen sequence with all the identified protein sequences and returning the category index with the highest similarity scored protein, conventional methods are usually time-consuming. Therefore, it is urgent and necessary to build an efficient protein sequence classification system. In this paper, we study the performance of protein sequence classification using SLFNs. The recent efficient extreme learning machine (ELM) and its invariants are utilized as the training algorithms. The optimal pruned ELM is first employed for protein sequence classification in this paper. To further enhance the performance, the ensemble based SLFNs structure is constructed where multiple SLFNs with the same number of hidden nodes and the same activation function are used as ensembles. For each ensemble, the same training algorithm is adopted. The final category index is derived using the majority voting method. Two approaches, namely, the basic ELM and the OP-ELM, are adopted for the ensemble based SLFNs. The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center. The experimental results show the priority of the proposed algorithms.

  10. Characterization of the collagen component of cartilage repair tissue of the talus with quantitative MRI: comparison of T2 relaxation time measurements with a diffusion-weighted double-echo steady-state sequence (dwDESS)

    Energy Technology Data Exchange (ETDEWEB)

    Kretzschmar, M.; Hainc, N.; Studler, U. [University Hospital Basel, Department of Radiology, Basel (Switzerland); Bieri, O. [University Hospital Basel, Division of Radiological Physics, Basel (Switzerland); Miska, M. [University Hospital, Department of Orthopedics, Heidelberg (Germany); Wiewiorski, M.; Valderrabano, V. [University Hospital Basel, Department of Orthopedic Surgery, Basel (Switzerland)

    2015-04-01

    The purpose of this study was to characterize the collagen component of repair tissue (RT) of the talus after autologous matrix-induced chondrogenesis (AMIC) using quantitative T2 and diffusion-weighted imaging. Mean T2 values and diffusion coefficients of AMIC-RT and normal cartilage of the talus of 25 patients with posttraumatic osteochondral lesions and AMIC repair were compared in a cross-sectional design using partially spoiled steady-state free precession (pSSFP) for T2 quantification, and diffusion-weighted double-echo steady-state (dwDESS) for diffusion measurement. RT and cartilage were graded with modified Noyes and MOCART scores on morphological sequences. An association between follow-up interval and quantitative MRI measures was assessed using multivariate regression, after stratifying the cohort according to time interval between surgery and MRI. Mean T2 of the AMIC-RT and cartilage were 43.1 ms and 39.1 ms, respectively (p = 0.26). Mean diffusivity of the RT (1.76 μm{sup 2}/ms) was significantly higher compared to normal cartilage (1.46 μm{sup 2}/ms) (p = 0.0092). No correlation was found between morphological and quantitative parameters. RT diffusivity was lowest in the subgroup with follow-up >28 months (p = 0.027). Compared to T2-mapping, dwDESS demonstrated greater sensitivity in detecting differences in the collagen matrix between AMIC-RT and cartilage. Decreased diffusivity in patients with longer follow-up times may indicate an increased matrix organization of RT. (orig.)

  11. Dissecting a Light Echo

    Science.gov (United States)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for audio animation This animation illustrates how a light echo works, and how an optical illusion of material moving outward is created. A light echo occurs when a star explodes, acting like a cosmic flashbulb. The light from this explosion zips through nearby dust clumps, illuminating and heating them up slightly. This brief period of warming causes them to glow in infrared, like a chain of Christmas bulbs lighting up one by one. The animation starts by showing the explosion of a star, which results in a flash of light that moves outward in all directions. The direction of our line of sight from Earth is indicated by the blue arrow. When the light flash reaches surrounding dust, shown here as three dark clouds, the dust is heated up, creating infrared light that begins to travel toward Earth (indicated by the red arrows). Dust closest to the explosion lights up first, while the explosion's shock wave takes longer to reach more distant material. This results in light from different parts of the cloud reaching Earth at different times, creating the illusion of motion over time. As the animation shows, the inclination of the cloud toward our line of sight can result in the material seeming to move both away from and toward the central star.

  12. Stark echo modulation for quantum memories

    Science.gov (United States)

    Arcangeli, A.; Ferrier, A.; Goldner, Ph.

    2016-06-01

    Quantum memories for optical and microwave photons provide key functionalities in quantum processing and communications. Here we propose a protocol well adapted to solid-state ensemble-based memories coupled to cavities. It is called Stark echo modulation memory (SEMM) and allows large storage bandwidths and low noise. This is achieved in an echo-like sequence combined with phase shifts induced by small electric fields through the linear Stark effect. We investigated the protocol for rare-earth nuclear spins and found a high suppression of unwanted collective emissions that is compatible with single-photon-level operation. Broadband storage together with high fidelity for the Stark retrieval process is also demonstrated. SEMM could be used to store optical or microwave photons in ions and/or spins. This includes nitrogen-vacancy centers in diamond and rare-earth-doped crystals, which are among the most promising solid-state quantum memories.

  13. High-resolution MR cisternography of the cerebellopontine angle, obtained with a three-dimensional fast asymmetric spin-echo sequence in a 0.35-T open MR imaging unit.

    Science.gov (United States)

    Naganawa, S; Ito, T; Iwayama, E; Fukatsu, H; Ishigaki, T

    1999-01-01

    High-resolution MR cisternography performed with 3D fast asymmetric spin-echo imaging (3D fast spin-echo with an ultra-long echo train length and asymmetric Fourier imaging) was optimized in a 0.35-T open MR imaging unit. The 0.35- and 1.5-T images of the two volunteers and three patients with acoustic schwannomas were then compared. The optimal parameters for images obtained by 3D fast asymmetric spin-echo imaging at 0.35 T were as follows: field of view, 15 cm; matrix, 256 x 256 x 40; section thickness, 1 mm; echo train length, 76; and imaging time, 10 minutes 44 seconds. Scans obtained from both normal volunteers showed the facial, cochlear, and superior and inferior vestibular nerves separately in the internal auditory canal on both 0.35- and 1.5-T images. All three acoustic schwannomas were depicted on both 0.35- and 1.5-T images. Screening for disease at the cerebellopontine angle and in the internal auditory canal, without the administration of contrast material on a low-field open MR imaging unit and within a clinically acceptable imaging time, may be possible. Further controlled prospective studies are required, however, before implementation on a wide basis. If proved effective, this may be of particular value for reducing healthcare costs and for imaging claustrophobic and pediatric patients in an open system.

  14. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  15. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing.

    Science.gov (United States)

    Li, Kelvin; Shrivastava, Susmita; Brownley, Anushka; Katzel, Dan; Bera, Jayati; Nguyen, Anh Thu; Thovarai, Vishal; Halpin, Rebecca; Stockwell, Timothy B

    2012-11-06

    In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute's (JCVI) high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus sequence that encapsulates the allelic variation of the targeted

  16. Multiple photon-echo rephasing of coherent matter waves

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Ruizhi; Yue, Xuguang; Xu, Xia; Lu, Haichang; Zhou, Xiaoji, E-mail: xjzhou@pku.edu.cn

    2015-03-20

    We investigate the multiple photon echo processes in a Bose–Einstein condensate (BEC) with inhomogeneous momentum broadening. By applying Bragg pulses with adjusted frequency mismatch to induce multiple rephasing, the BEC satisfies the coherence condition for successive superradiance. The atomic system can be efficiently transferred to a high momentum state step by step and emits multiple photon echo signals. These echo signals as a sequence show increasing widths and descending peaks, reflecting a residual dephasing effect due to kinetic-energy phase discrepancy during the population inversions. Our work may contribute to the coherence maintenance for ultracold atomic gas in the quantum information area and the high-precision measurement of atomic momentum width. - Highlights: • A multipulse protocol to induce multiple photon echo rephasing of a BEC is proposed. • Our method is a new and efficient way to transfer the BEC to high momentum modes. • Our method can extend a BEC's coherence time. • The echo sequence is analyzed to study the residual dephasing effect. • The echo decaying is useful in high-precision measurement of BEC's momentum width.

  17. Can Computationally Designed Protein Sequences Improve Secondary Structure Prediction?

    Science.gov (United States)

    2011-01-01

    with the structural classification of proteins ( SCOP ) database of known structural domains (Kuhlman and Baker, 2000; Rohl et al., 2004). Secondary...reported in the literature. Methods In this work, the Astral SCOP 1.75 (Murzin et al., 1995; Hubbard et al., 1999) structural domain database filtered...entry matching the query test sequence can be left out. A total of 6511 SCOP 1.75 domains were used after some domains were discarded due to large

  18. Application of single-shot fast spin-echo sequence in MRimaging of normal fetus%单次激发快速自旋回波序列MR检查在正常胎儿中的应用

    Institute of Scientific and Technical Information of China (English)

    胡晓华; 罗先富; 陈娟; 傅剑雄; 王军; 吴晶涛

    2011-01-01

    Objective To investigate the ability of single-shot fast spin-echo (SSFSE) sequence in delineating the anatomic structures of fetus, and to explore the clinical value of this sequence. Methods Fourteen normal fetuses with gestational age larger than 20 weeks underwent MR imaging 1 week within ultrasonic examination. SSFSE sequence was performed at the coronal, sagittal and axial view of the fetus body and the head. The normal fetus anatomy of brain, lungs, heart, liver,spleen, gastrointestinal tract, etc. and their MR manifestations were observed. Results The main organs of fetus had developed in 20 weeks gestation. In the central nervous system, against the high signal of the ventricular system, three layers of the cerebrum were identified, including the hypointense cortical gray matter, the hyperintense white matter, and the lower-signal-intensity germinal matrix. Cortical gyri and sulci developed significantly after 30 weeks gestation. The lungs, trachea, bronchi, stomach bubble, renal collecting system and bladder showed as high signal intensities, while gastrointestinal tract displayed mixed signal, the heart, great vessels, liver, spleen and kidneys appeared as hypointensities. Conclusion SSFSE sequence MR imaging can clearly show the normal anatomy of main fetal organs.%目的 观察单次激发快速自旋回波序列(SSFSE)在胎儿解剖结构方面的显示能力,探讨其在胎儿MR检查中的临床应用价值.方法 对14胎20周以上正常胎儿行MR检查,采用SSFSE序列对胎儿头颅、躯干行轴位、冠状位、矢状位扫描,观察胎儿各系统主要器官,包括脑、肺、心脏、肝、脾、胃肠道等的解剖和MR表现.结果孕20周时,胎儿各主要器官均已发育.中枢神经系统:在SSFSE图像脑室系统高信号的衬托下,大脑三层结构清晰可辨,皮层及脑室旁生发层呈低信号,白质呈稍高信号.脑室系统呈生理性扩大状态,30周后脑沟、回形成逐渐明显;非神经系统:SSFSE图

  19. Improved definition of the mouse transcriptome via targeted RNA sequencing.

    Science.gov (United States)

    Bussotti, Giovanni; Leonardi, Tommaso; Clark, Michael B; Mercer, Tim R; Crawford, Joanna; Malquori, Lorenzo; Notredame, Cedric; Dinger, Marcel E; Mattick, John S; Enright, Anton J

    2016-05-01

    Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.

  20. An Improved Search Algorithm for Optimal Multiple-Sequence Alignment

    CERN Document Server

    Schroedl, S

    2011-01-01

    Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further. Since MSA can be cast as a classical path finding problem, it is attracting a growing number of AI researchers interested in heuristic search algorithms as a challenge with actual practical relevance. In this paper, we first review two previous, complementary lines of research. Based on Hirschbergs algorithm, Dynamic Programming needs O(kN^(k-1)) space to store both the search frontier and the nodes needed to reconstruct the solution path, for k sequences of length N. Best first search, on the other hand, has the advantage of bounding the search space that has to be explored using a heuristic. However, it is necessary to maintain all explored nodes up to the final solution in order to prevent the search from re-expanding them at hig...

  1. The impact of spin coupling signal loss on fat content characterization in multi-echo acquisitions with different echo spacing.

    Science.gov (United States)

    Nikiforaki, K; Manikis, G C; Boursianis, T; Marias, K; Karantanas, A; Maris, T G

    2017-05-01

    This study aimed to assess the effect of echo spacing in transverse magnetization (T2) signal decay of gel and fat (oil) samples. Additionally, we assess the feasibility of using spin coupling as a determinant of fat content. Phantoms of known T2 values, as well as vegetable oil phantoms, were scanned at 1.5T scanner with a multi echo FSE sequence of variable echo spacing above and below the empirical threshold of 20ms for echo train signal modulation (6.7, 13.6, 26.8, and 40ms). T2 values were calculated from monoexponential fitting of the data. Relative signal loss between the four acquisitions of different echo spacing was calculated. Agreement in the T2 values of water gel phantom was observed in all acquisitions as opposed to fat phantom (oil) samples. Relative differences in signal intensity between two successive sequences of different echo spacing on composite fat/water regions of interest was found to be linearly correlated to fat fraction of the ROI. The sample specific degree of signal loss that was observed between different fat samples (vegetable oils) can be attributed to the composition of each sample in J coupled fat components. Hence, spin coupling may be used as a determinant of fat content. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Decoherence of spin echoes

    Energy Technology Data Exchange (ETDEWEB)

    Prosen, Tomaz [Physics Department, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana (Slovenia)]. E-mail: prosen@fiz.uni-lj.si; Seligman, Thomas H. [Centro de Ciencias Fisicas, University of Mexico (UNAM), Cuernavaca (Mexico)]. E-mail: seligman@fis.unam.mx

    2002-06-07

    We define a quantity, the so-called purity fidelity, which measures the rate of dynamical irreversibility due to decoherence, observed e.g. in echo experiments, in the presence of an arbitrary small perturbation of the total (system + environment) Hamiltonian. We derive a linear response formula for the purity fidelity in terms of integrated time correlation functions of the perturbation. Our relation predicts, similar to the case of fidelity decay, that the faster the decay of purity fidelity the slower is the decay of time correlations. In particular, we find exponential decay in quantum mixing regime and faster, initially quadratic and later typically Gaussian decay in the regime of non-ergodic, e.g. integrable quantum dynamics. We illustrate our approach by an analytical calculation and numerical experiments in the Ising spin 1/2 chain kicked with tilted homogeneous magnetic field where part of the chain is interpreted as a system under observation and part as an environment. (author)

  3. A comparison of multi-echo spin-echo and triple-echo steady-state T2 mapping for in vivo evaluation of articular cartilage

    Energy Technology Data Exchange (ETDEWEB)

    Juras, Vladimir; Szomolanyi, Pavol [Medical University of Vienna, High Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Vienna (Austria); Institute of Measurement Science, Department of Imaging Methods, Bratislava (Slovakia); Bohndorf, Klaus; Kronnerwetter, Claudia; Hager, Benedikt; Zbyn, Stefan [Medical University of Vienna, High Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Vienna (Austria); Heule, Rahel; Bieri, Oliver [University of Basel Hospital, Division of Radiological Physics, Department of Radiology, Basel (Switzerland); Trattnig, Siegfried [Medical University of Vienna, High Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Vienna (Austria); Christian Doppler Laboratory for Clinical Molecular MR Imaging, Vienna (Austria); Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Austrian Cluster for Tissue Regeneration, Vienna (Austria)

    2016-06-15

    To assess the clinical relevance of T{sub 2} relaxation times, measured by 3D triple-echo steady-state (3D-TESS), in knee articular cartilage compared to conventional multi-echo spin-echo T{sub 2}-mapping. Thirteen volunteers and ten patients with focal cartilage lesions were included in this prospective study. All subjects underwent 3-Tesla MRI consisting of a multi-echo multi-slice spin-echo sequence (CPMG) as a reference method for T{sub 2} mapping, and 3D TESS with the same geometry settings, but variable acquisition times: standard (TESSs 4:35min) and quick (TESSq 2:05min). T{sub 2} values were compared in six different regions in the femoral and tibial cartilage using a Wilcoxon signed ranks test and the Pearson correlation coefficient (r). The local ethics committee approved this study, and all participants gave written informed consent. The mean quantitative T{sub 2} values measured by CPMG (mean: 46±9ms) in volunteers were significantly higher compared to those measured with TESS (mean: 31±5ms) in all regions. Both methods performed similarly in patients, but CPMG provided a slightly higher difference between lesions and native cartilage (CPMG: 90ms→61ms [31%],p=0.0125;TESS 32ms→24ms [24%],p=0.0839). 3D-TESS provides results similar to those of a conventional multi-echo spin-echo sequence with many benefits, such as shortening of total acquisition time and insensitivity to B{sub 1} and B{sub 0} changes. (orig.)

  4. 11-interval PFG pulse sequence for improved measurement of fast velocities of fluids with high diffusivity in systems with short T2∗

    Science.gov (United States)

    Boyce, C. M.; Rice, N. P.; Sederman, A. J.; Dennis, J. S.; Holland, D. J.

    2016-04-01

    Magnetic resonance (MR) was used to measure SF6 gas velocities in beds filled with particles of 1.1 mm and 0.5 mm in diameter. Four pulse sequences were tested: a traditional spin echo pulse sequence, the 9-interval and 13-interval pulse sequence of Cotts et al. (1989) and a newly developed 11-interval pulse sequence. All pulse sequences measured gas velocity accurately in the region above the particles at the highest velocities that could be achieved (up to 0.1 m s-1). The spin echo pulse sequence was unable to measure gas velocity accurately in the bed of particles, due to effects of background gradients, diffusivity and acceleration in flow around particles. The 9- and 13-interval pulse sequence measured gas velocity accurately at low flow rates through the particles (expected velocity <0.06 m s-1), but could not measure velocity accurately at higher flow rates. The newly developed 11-interval pulse sequence was more accurate than the 9- and 13-interval pulse sequences at higher flow rates, but for velocities in excess of 0.1 m s-1 the measured velocity was lower than the expected velocity. The increased accuracy arose from the smaller echo time that the new pulse sequence enabled, reducing selective attenuation of signal from faster moving nuclei.

  5. MRI of intraosseous fistulous systems and sequesters in chronic osteomyelitis with standard spin echo sequences, highly selective chemical-shift imaging, diffusion weighted imaging, and magnetization-transfer; MRT-Darstellung intraossaerer Sequester und Fistelsysteme bei chronischer Osteomyelitis durch Standardsequenzen, hochselektive Chemical-Shift-Bildgebung, Diffusionsgewichtung und Magnetisierungstransfer

    Energy Technology Data Exchange (ETDEWEB)

    Bitzer, M.; Hartmann, J.; Geist-Barth, B.; Stern, W.; Seemann, M.; Pereira, P.; Claussen, C.D. [Abteilung fuer Radiologische Diagnostik, Klinikum der Eberhart-Karls-Universitaet Tuebingen (Germany); Schick, F. [Sektion fuer Experimentelle Radiologie, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany); Krackhardt, T. [Berufsgenossenschaftliche Klinik, Tuebingen (Germany); Morgalla, M. [Chirurgische Klinik, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany)

    2002-11-01

    Purpose: To study and test the impact of modern MRI techniques in diagnostic imaging in the evaluation of intra-osseous fistulous systems and sequesters. Materials and Methods: In a prospective study, nine patients with chronic osteomyelitis of the legs were examined by MRI. Patients with clinical signs of osteomyelitis requiring surgery were included in the study. T1-weighted spin echo (SE) sequences, proton density (PD) and T2-weighted fast spin echo (FSE) sequences, water- and fat-selective FSE sequences, and diffusion weighted (DW) PSIF sequences were used preoperatively. Furthermore, magnetizing transfer (MT) with gradient echo (GRE) sequences was evaluated. Results: Water selective sequences revealed the highest sensitivity for the detection of fistulas (100%), providing the best delineation of the extent of the entire fistulous systems. Fat-selective sequences (sensitivity 55.6%) and T1-weighted sequences (sensitivity 77.8%) displayed fistulas as hypointense bands, which, however, cannot be well differentiated from cortical bone in the transcortical areas. PD and T2-weighted images were found to have a poor sensitivity (55.6% and 66.7%) for fistulas in any location. The sensitivity of water-selective sequences to demonstrate intraosseous sequesters was 100%. The sensitivity was low for the other sequences. In 4 of 5 patients with surgically proven infection, DW and MT revealed an abnormal spatial distribution, with high diffusion in the central parts of the fistulas and high MT effect peripherally surrounding a weak MT effect centrally. (orig.) [German] Zielsetzung: Die vorliegende Arbeit soll die Moeglichkeiten des Einsatzes spezieller Sequenztechniken der MRT bei der Diagnostik von intraossaeren Fisteln und Sequestern pruefen und beschreiben. Material und Methode: In einer prospektiven Studie wurden 9 Patienten mit chronischen Osteomyelitiden der unteren Extremitaeten kernspintomographisch untersucht. Die MRT-Befunde wurden qualitativ anhand der Operations

  6. Lesion discrimination in optic neuritis using high-resolution fat-suppressed fast spin-echo MRI

    Energy Technology Data Exchange (ETDEWEB)

    Gass, A. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom); Moseley, I.F. [Lysholm Department of Radiology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom)]|[Moorfields Eye Hospital, City Road, London EC 1V 2PD (United Kingdom); Barker, G.J. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom); Jones, S. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom); MacManus, D. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom); McDonald, W.I. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom)]|[Moorfields Eye Hospital, City Road, London EC 1V 2PD (United Kingdom); Miller, D.H. [NMR Research Group, Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London WC 1N 3BG (United Kingdom)

    1996-05-01

    Fast spin-echo (FSE) is a new sequence with acquisition times currently down to one-sixteenth of those obtained with conventional spin-echo sequences, which allows high-resolution (512 x 512 matrix) images to be acquired in an acceptable time. We compared the higher resolution of FSE with the medium resolution of a short inversion-time inversion-recovery (STIR) sequence in depicting the optic nerves of healthy controls and patients with optic neuritis. Optic nerve MRI examinations were performed in 18 patients with optic neuritis and 10 normal controls. Two sequences were obtained coronally: fat-suppressed FSE (FSE TR 3250 ms/TEef 68 ms, echo-train length 16, 4 excitations, 24 cm rectangular field of view, 3 mm interleaved contiguous slices, in-plane resolution 0.5 x 0.5 mm) and STIR (TR 2000 ms/TE 50 ms/TI 175 ms, in-plane resolution 0.8 x 0.8 mm, slice thickness 5 mm). FSE demonstrated much more anatomical detail than STIR, e. g. distinction of optic nerve and sheath. Lesions were seen in 20 of 21 symptomatic nerves using FSE and in 18 of 21 using STIR. Nerve swelling or partial cross-sectional lesions of the optic nerve were each seen only on FSE in 3 cases. Fat-suppressed FSE imaging of the optic nerve improves anatomical definition and increases lesion detection in optic neuritis. (orig.). With 5 figs.

  7. X-ray Echo Spectroscopy

    Science.gov (United States)

    Shvyd'ko, Yuri

    2016-02-01

    X-ray echo spectroscopy, a counterpart of neutron spin echo, is being introduced here to overcome limitations in spectral resolution and weak signals of the traditional inelastic x-ray scattering (IXS) probes. An image of a pointlike x-ray source is defocused by a dispersing system comprised of asymmetrically cut specially arranged Bragg diffracting crystals. The defocused image is refocused into a point (echo) in a time-reversal dispersing system. If the defocused beam is inelastically scattered from a sample, the echo signal acquires a spatial distribution, which is a map of the inelastic scattering spectrum. The spectral resolution of the echo spectroscopy does not rely on the monochromaticity of the x rays, ensuring strong signals along with a very high spectral resolution. Particular schemes of x-ray echo spectrometers for 0.1-0.02 meV ultrahigh-resolution IXS applications (resolving power >108 ) with broadband ≃5 - 13 meV dispersing systems are introduced featuring more than 103 signal enhancement. The technique is general, applicable in different photon frequency domains.

  8. X-ray echo spectroscopy

    CERN Document Server

    Shvyd'ko, Yuri

    2015-01-01

    X-ray echo spectroscopy, a counterpart of neutron spin-echo, is being introduced here to overcome limitations in spectral resolution and weak signals of the traditional inelastic x-ray scattering (IXS) probes. An image of a point-like x-ray source is defocused by a dispersing system comprised of asymmetrically cut specially arranged Bragg diffracting crystals. The defocused image is refocused into a point (echo) in a time-reversal dispersing system. If the defocused beam is inelastically scattered from a sample, the echo signal acquires a spatial distribution, which is a map of the inelastic scattering spectrum. The spectral resolution of the echo spectroscopy does not rely on the monochromaticity of the x-rays, ensuring strong signals along with a very high spectral resolution. Particular schemes of x-ray echo spectrometers for 0.1--0.02-meV ultra-high-resolution IXS applications (resolving power $> 10^8$) with broadband $\\simeq$~5--13~meV dispersing systems are introduced featuring more than $10^3$ signal e...

  9. X-ray Echo Spectroscopy.

    Science.gov (United States)

    Shvyd'ko, Yuri

    2016-02-26

    X-ray echo spectroscopy, a counterpart of neutron spin echo, is being introduced here to overcome limitations in spectral resolution and weak signals of the traditional inelastic x-ray scattering (IXS) probes. An image of a pointlike x-ray source is defocused by a dispersing system comprised of asymmetrically cut specially arranged Bragg diffracting crystals. The defocused image is refocused into a point (echo) in a time-reversal dispersing system. If the defocused beam is inelastically scattered from a sample, the echo signal acquires a spatial distribution, which is a map of the inelastic scattering spectrum. The spectral resolution of the echo spectroscopy does not rely on the monochromaticity of the x rays, ensuring strong signals along with a very high spectral resolution. Particular schemes of x-ray echo spectrometers for 0.1-0.02 meV ultrahigh-resolution IXS applications (resolving power >10^{8}) with broadband ≃5-13  meV dispersing systems are introduced featuring more than 10^{3} signal enhancement. The technique is general, applicable in different photon frequency domains.

  10. Echo particle image velocimetry.

    Science.gov (United States)

    DeMarchi, Nicholas; White, Christopher

    2012-12-27

    The transport of mass, momentum, and energy in fluid flows is ultimately determined by spatiotemporal distributions of the fluid velocity field.(1) Consequently, a prerequisite for understanding, predicting, and controlling fluid flows is the capability to measure the velocity field with adequate spatial and temporal resolution.(2) For velocity measurements in optically opaque fluids or through optically opaque geometries, echo particle image velocimetry (EPIV) is an attractive diagnostic technique to generate "instantaneous" two-dimensional fields of velocity.(3,4,5,6) In this paper, the operating protocol for an EPIV system built by integrating a commercial medical ultrasound machine(7) with a PC running commercial particle image velocimetry (PIV) software(8) is described, and validation measurements in Hagen-Poiseuille (i.e., laminar pipe) flow are reported. For the EPIV measurements, a phased array probe connected to the medical ultrasound machine is used to generate a two-dimensional ultrasound image by pulsing the piezoelectric probe elements at different times. Each probe element transmits an ultrasound pulse into the fluid, and tracer particles in the fluid (either naturally occurring or seeded) reflect ultrasound echoes back to the probe where they are recorded. The amplitude of the reflected ultrasound waves and their time delay relative to transmission are used to create what is known as B-mode (brightness mode) two-dimensional ultrasound images. Specifically, the time delay is used to determine the position of the scatterer in the fluid and the amplitude is used to assign intensity to the scatterer. The time required to obtain a single B-mode image, t, is determined by the time it take to pulse all the elements of the phased array probe. For acquiring multiple B-mode images, the frame rate of the system in frames per second (fps) = 1/δt. (See 9 for a review of ultrasound imaging.) For a typical EPIV experiment, the frame rate is between 20-60 fps

  11. Improved hand tracking algorithm in video sequences for intelligent rehabilitation

    Institute of Scientific and Technical Information of China (English)

    LI Ling; LUO Yuan; ZHANG Yi; ZHANG Bai-sheng

    2009-01-01

    Intelligent rehabilitation system is an active research topic. It is motivated by the increased number of limb disabled patients. Human motion tracking is the key technology of intelligent rehabilitation system, because the movement of limb disabled patients needs to be localized and learned so that any undesired motion behavior can be corrected in order to reach an expectation. This paper introduces a real-time tracking system of human hand motion, specifically intent to be used for home rehabilitation. Vision sensor (camera) is employed in this system to track the hand movement, and the improved Camshift algorithm and Kalman filter are used to implement dynamic hand tracking in the video. CAMSHIFT algorithm is able to track any kind of target colors by building a histogram distribution of the H channel in HSV color space from the region of interests selected by users at the initial stage. Kalman filter is able to predict hand location in one image frame based on its location data detected in the previous frame. The experimental results show that this system can track 2D hand motion and has acceptable accuracy by using the two algorithms properly. The new algorithm proposed in this paper can not only deal with the skin color interference problems, but also deal well with the track of complex background.

  12. Differentiation of breast cancer from fibroadenoma with dual-echo dynamic contrast-enhanced MRI.

    Directory of Open Access Journals (Sweden)

    Shiwei Wang

    Full Text Available Dynamic contrast-enhanced magnetic resonance imaging (DCE MRI of the breast is a routinely used imaging method which is highly sensitive for detecting breast malignancy. Specificity, though, remains suboptimal. Dynamic susceptibility contrast magnetic resonance imaging (DSC MRI, an alternative dynamic contrast imaging technique, evaluates perfusion-related parameters unique from DCE MRI. Previous work has shown that the combination of DSC MRI with DCE MRI can improve diagnostic specificity, though an additional administration of intravenous contrast is required. Dual-echo MRI can measure both T1W DCE MRI and T2*W DSC MRI parameters with a single contrast bolus, but has not been previously implemented in breast imaging. We have developed a dual-echo gradient-echo sequence to perform such simultaneous measurements in the breast, and use it to calculate the semi-quantitative T1W and T2*W related parameters such as peak enhancement ratio, time of maximal enhancement, regional blood flow, and regional blood volume in 20 malignant lesions and 10 benign fibroadenomas in 38 patients. Imaging parameters were compared to surgical or biopsy obtained tissue samples. Receiver operating characteristic (ROC curves and area under the ROC curves were calculated for each parameter and combination of parameters. The time of maximal enhancement derived from DCE MRI had a 90% sensitivity and 69% specificity for predicting malignancy. When combined with DSC MRI derived regional blood flow and volume parameters, sensitivity remained unchanged at 90% but specificity increased to 80%. In conclusion, we show that dual-echo MRI with a single administration of contrast agent can simultaneously measure both T1W and T2*W related perfusion and kinetic parameters in the breast and the combination of DCE MRI and DSC MRI parameters improves the diagnostic performance of breast MRI to differentiate breast cancer from benign fibroadenomas.

  13. Temperature sheets and aspect sensitive radar echoes

    Directory of Open Access Journals (Sweden)

    H. Luce

    Full Text Available here have been years of discussion and controversy about the existence of very thin and stable temperature sheets and their relationship to the VHF radar aspect sensitivity. It is only recently that very high-resolution in situ temperature observations have brought credence to the reality and ubiquity of these structures in the free atmosphere and to their contribution to radar echo enhancements along the vertical. Indeed, measurements with very high-resolution sensors are still extremely rare and rather difficult to obtain outside of the planetary boundary layer. They have only been carried out up to the lower stratosphere by Service d’A´ eronomie (CNRS, France for about 10 years. The controversy also persisted due to the volume resolution of the (Mesosphere-Stratosphere-Troposphere VHF radars which is coarse with respect to sheet thickness, although widely sufficient for meteorological or mesoscale investigations. The contribution within the range gate of many of these structures, which are advected by the wind, and decay and grow at different instants and could be distorted either by internal gravity waves or turbulence fields, could lead to radar echoes with statistical properties similar to those produced by anisotropic turbulence. Some questions thus remain regarding the manner in which temperature sheets contribute to VHF radar echoes. In particular, the zenithal and azimuthal angular dependence of the echo power may not only be produced by diffuse reflection on stable distorted or corrugated sheets, but also by extra contributions from anisotropic turbulence occurring in the stratified atmosphere. Thus, for several years, efforts have been put forth to improve the radar height resolution in order to better describe thin structures. Frequency interferometric techniques are widely used and have been recently further developed with the implementation of high-resolution data processings. We begin by reviewing briefly some characteristics

  14. Stellar Echo Imaging of Exoplanets

    Science.gov (United States)

    Mann, Chris; Lerch, Kieran; Lucente, Mark; Meza-Galvan, Jesus; Mitchell, Dan; Ruedin, Josh; Williams, Spencer; Zollars, Byron

    2016-01-01

    All stars exhibit intensity fluctuations over several timescales, from nanoseconds to years. These intensity fluctuations echo off bodies and structures in the star system. We posit that it is possible to take advantage of these echoes to detect, and possibly image, Earth-scale exoplanets. Unlike direct imaging techniques, temporal measurements do not require fringe tracking, maintaining an optically-perfect baseline, or utilizing ultra-contrast coronagraphs. Unlike transit or radial velocity techniques, stellar echo detection is not constrained to any specific orbital inclination. Current results suggest that existing and emerging technology can already enable stellar echo techniques at flare stars, such as Proxima Centauri, including detection, spectroscopic interrogation, and possibly even continent-level imaging of exoplanets in a variety of orbits. Detection of Earth-like planets around Sun-like stars appears to be extremely challenging, but cannot be fully quantified without additional data on micro- and millisecond-scale intensity fluctuations of the Sun. We consider survey missions in the mold of Kepler and place preliminary constraints on the feasibility of producing 3D tomographic maps of other structures in star systems, such as accretion disks. In this report we discuss the theory, limitations, models, and future opportunities for stellar echo imaging.

  15. Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging

    Directory of Open Access Journals (Sweden)

    Trong-Kha Truong

    2015-01-01

    Full Text Available In most diffusion tensor imaging (DTI studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR. However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact. Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2*-weighting (i.e., Type 3 artifact. These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

  16. Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging.

    Science.gov (United States)

    Truong, Trong-Kha; Song, Allen W; Chen, Nan-Kuei

    2015-01-01

    In most diffusion tensor imaging (DTI) studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI) sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR). However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact). Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact) associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2(∗) -weighting (i.e., Type 3 artifact). These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

  17. Prospective navigator-echo-based real-time triggering of fetal head movement for the reduction of artifacts

    Energy Technology Data Exchange (ETDEWEB)

    Bonel, H. [University Hospital Berne-Inselspital, Freiburgstrasse, Institute of Diagnostic, Interventional and Pediatric Radiology, Bern (Switzerland); Frei, K.A.; Raio, L.; Meyer-Wittkopf, M. [University of Berne, Women' s' Hospital, Bern (Switzerland); Remonda, L.; Wiest, R. [University of Berne, Institute of Diagnostic and Interventional Neuroradiology (DIN), Inselspital, Bern (Switzerland)

    2008-04-15

    The purpose of this study was to evaluate the neuroimaging quality and accuracy of prospective real-time navigator-echo acquisition correction versus untriggered intrauterine magnetic resonance imaging (MRI) techniques. Twenty women in whom fetal motion artifacts compromised the neuroimaging quality of fetal MRI taken during the 28.7 {+-} 4 week of pregnancy below diagnostic levels were additionally investigated using a navigator-triggered half-Fourier acquired single-shot turbo-spin echo (HASTE) sequence. Imaging quality was evaluated by two blinded readers applying a rating scale from 1 (not diagnostic) to 5 (excellent). Diagnostic criteria included depiction of the germinal matrix, grey and white matter, CSF, brain stem and cerebellum. Signal-difference-to-noise ratios (SDNRs) in the white matter and germinal zone were quantitatively evaluated. Imaging quality improved in 18/20 patients using the navigator echo technique (2.4 {+-} 0.58 vs. 3.65 {+-} 0.73 SD, p < 0.01 for all evaluation criteria). In 2/20 patients fetal movement severely impaired image quality in conventional and navigated HASTE. Navigator-echo imaging revealed additional structural brain abnormalities and confirmed diagnosis in 8/20 patients. The accuracy improved from 50% to 90%. Average SDNR increased from 0.7 {+-} 7.27 to 19.83 {+-} 15.71 (p < 0.01). Navigator-echo-based real-time triggering of fetal head movement is a reliable technique that can deliver diagnostic fetal MR image quality despite vigorous fetal movement. (orig.)

  18. SNR efficiency of combined bipolar gradient echoes: Comparison of three-dimensional FLASH, MPRAGE, and multiparameter mapping with VFA-FLASH and MP2RAGE.

    Science.gov (United States)

    Jutras, Jean-David; Wachowicz, Keith; Gilbert, Guillaume; De Zanche, Nicola

    2017-06-01

    High-bandwidth bipolar multiecho gradient echo sequences are increasingly popular in structural brain imaging because of reduced water-fat shifts, lower susceptibility effects, and improved signal-to-noise ratio (SNR) efficiency. In this study, we investigated the performance of three three-dimensional multiecho sequences (MPRAGE, MP2RAGE, and FLASH) with scan times technique with multiecho FLASH (VFA-FLASH). Multiecho sequences were optimized to yield equivalent contrast and improved SNR compared with their single-echo counterparts. Theoretical SNR gains were verified with measurements in a multilayered phantom. Robust image processing pipelines extracted PD, T1 , and T2* maps from MP2RAGE or VFA-FLASH, and the corresponding SNR was measured with varying SENSE accelerations (R = 1-5) and number of echoes (N = 1-12). All sequences were tested on four healthy volunteers. Multiecho sequences achieved SNR gains of 1.3-1.6 over single-echo sequences. MP2RAGE yielded comparable T1 -to-noise ratio to VFA-FLASH, but significantly lower SNR (sampling bandwidths. VFA-FLASH surpasses MP2RAGE in its ability to map three parameters with high SNR and 1-mm isotropic resolution in a clinically relevant scan time (∼8:30 min), whereas MP2RAGE yields lower intersubject variability in T1 . Magn Reson Med 77:2186-2202, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  19. Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

    Science.gov (United States)

    Sato, Kengo; Kuroki, Yoko; Kumita, Wakako; Fujiyama, Asao; Toyoda, Atsushi; Kawai, Jun; Iriki, Atsushi; Sasaki, Erika; Okano, Hideyuki; Sakakibara, Yasubumi

    2015-11-20

    The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis Consortium. The draft was based on whole-genome shotgun sequencing, and the current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions and supercontigs and relatively short contigs that are unmapped to chromosomes in the draft genome. We performed resequencing and assembly of the genome of common marmoset by deep sequencing with high-throughput sequencing technology. Several different sequence runs using Illumina sequencing platforms were executed, and 181 Gbp of high-quality bases including mate-pairs with long insert lengths of 3, 8, 20, and 40 Kbp were obtained, that is, approximately 60× coverage. The resequencing significantly improved the MGSAC draft genome sequence. The N50 of the contigs, which is a statistical measure used to evaluate assembly quality, doubled. As a result, 51% of the contigs (total length: 299 Mbp) that were unmapped to chromosomes in the MGSAC draft were merged with chromosomal contigs, and the improved genome sequence helped to detect 5,288 new genes that are homologous to human cDNAs and the gaps in 5,187 transcripts of the Ensembl gene annotations were completely filled.

  20. Control of spatial correlations between Rydberg excitations using rotary echo

    CERN Document Server

    Thaicharoen, N; Raithel, G

    2016-01-01

    We manipulate correlations between Rydberg excitations in cold atom samples using a rotary-echo technique. The correlations are due to interactions between the Rydberg atoms. In the rotary-echo excitation sequence, the phase of the excitation pulse is flipped at a selected time during the pulse. We measure the resultant change in the spatial pair correlation function of the excitations via direct position-sensitive atom imaging. For zero detuning of the lasers from the interaction-free Rydberg-excitation resonance, the pair-correlation value at the most likely nearest-neighbor Rydberg-atom distance is substantially enhanced when the phase is flipped at the middle of the excitation pulse. In this case, the rotary echo eliminates most uncorrelated (un-paired) atoms, leaving an abundance of correlated atom pairs at the end of the sequence. In off-resonant cases, a complementary behavior is observed. We further characterize the effect of the rotary-echo excitation sequence on the excitation-number statistics of t...

  1. Improving Auditory Sequencing Skills in the Kindergarten-Age Child through the Increased Instruction of Music.

    Science.gov (United States)

    Brandt, Millicent Hume

    A music teacher specialist at an elementary school with a typical kindergarten music program implemented a 10-week practicum intervention designed to improve the auditory sequencing skills of kindergarten children through increased instruction in music. Test scores on screening measures indicated the need to improve the children's auditory memory…

  2. Improving Auditory Sequencing Skills in the Kindergarten-Age Child through the Increased Instruction of Music.

    Science.gov (United States)

    Brandt, Millicent Hume

    A music teacher specialist at an elementary school with a typical kindergarten music program implemented a 10-week practicum intervention designed to improve the auditory sequencing skills of kindergarten children through increased instruction in music. Test scores on screening measures indicated the need to improve the children's auditory memory…

  3. In vivo evaluation of multi-echo hybrid PRF/T1 approach for temperature monitoring during breast MR-guided focused ultrasound surgery treatments.

    Science.gov (United States)

    Todd, Nick; Diakite, Mahamadou; Payne, Allison; Parker, Dennis L

    2014-09-01

    To evaluate the precision of in vivo temperature measurements in adipose and glandular breast tissue using a multi-echo hybrid PRF/T1 pulse sequence. A high-bandwidth, multi-echo hybrid PRF/T1 sequence was developed for monitoring temperature changes simultaneously in fat- and water-based tissues. The multiple echoes were combined with the optimal weightings for magnitude and phase images, allowing for precise measurement of both T1 and the proton resonance frequency (PRF) shift. The sequence was tested during in vivo imaging of 10 healthy volunteers in a breast-specific MR-guided focused ultrasound system and also during focused ultrasound heating of excised breast adipose tissue. The in vivo results indicated that the sequence can measure PRF temperatures with 1.25 × 1.25 × 3.5 mm resolution, 1.9 s temporal resolution, and 1.0°C temperature precision, and can measure T1 values with 3.75 × 3.75 × 3.5 mm resolution, 3.8 s temporal resolution, and 2.5%-4.8% precision. The excised tissue heating experiments demonstrate the sequence's ability to monitor temperature changes simultaneously in water- and fat-based tissues. The addition of a high-bandwidth, multi-echo readout to the hybrid PRF/T1 sequence improves the precision of each measurement, providing a sequence that will be beneficial to several MR-guided thermal therapies. Copyright © 2013 Wiley Periodicals, Inc.

  4. Fluid echoes in a pure electron plasma.

    Science.gov (United States)

    Yu, J H; O'Neil, T M; Driscoll, C F

    2005-01-21

    Experimental observations of diocotron wave echoes on a magnetized electron column are reported, representing Kelvin wave echoes on a rotating near-ideal fluid. The echoes occur by reversal of an inviscid wave damping process, and the phase-space mixing and unmixing are directly imaged. The basic echo characteristics agree with a simple nonlinear ballistic theory. At late times, the echo is degraded, and the maximal observed echo times agree with a theory of electron-electron collisions acting on separately evolving velocity classes.

  5. Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

    Directory of Open Access Journals (Sweden)

    Wang Yong

    2011-10-01

    Full Text Available Abstract Background With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched. Results In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology. Conclusions By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.

  6. High-resolution 3D T2-weighted fast spin echo: new applications in the orbit

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Erin M. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); Department of Radiology, Children' s Hospital of Philadelphia, 34th Street and Civic Center Boulevard, Philadelphia, PA 19104-4399 (United States); McCaffery, Sharon; O' Brien, Joan M. [Department of Ophthalmology, University of California San Francisco, San Francisco, CA (United States); Rowley, Howard A. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); University of Wisconsin Medical School, Madison, WI (United States); Fischbein, Nancy J. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); Shimikawa, Ann [General Electric Medical Systems, Milwaukee, WI (United States)

    2003-07-01

    Recent developments have made available for ophthalmologic MR imaging a very high-resolution 3D fast spin echo T2 (3D FSE T2) sequence, which runs in a standard head coil. A modification of this technique, 3D FSEz T2, uses a zero-filled slice interpolation method during post-processing to further improve spatial resolution. We describe the technique and share our early clinical observations in patients with ocular masses. Briefly, the additional information from the 3D FSEz T2 resulted in a change in diagnosis from the conventional imaging series in 11 of (41%) 27 studies, usually through the identification of previously treated retinoblastoma lesions. The new sequence significantly increased diagnostic confidence in six (38%) of the remaining 16 cases, usually through better anatomical detail and lesion conspicuity, and did not change interpretation in 10 cases. Such an approach improves diagnostic confidence and may eliminate the need for a dedicated surface coil examination. (orig.)

  7. Preprocessing of ionospheric echo Doppler spectra

    Institute of Scientific and Technical Information of China (English)

    FANG Liang; ZHAO Zhengyu; WANG Feng; SU Fanfan

    2007-01-01

    The real-time information of the distant ionosphere can be acquired by using the Wuhan ionospheric oblique backscattering sounding system(WIOBSS),which adopts a discontinuous wave mechanism.After the characteristics of the ionospheric echo Doppler spectra were analyzed,the signal preprocessing was developed in this paper,which aimed at improving the Doppler spectra.The results indicate that the preprocessing not only makes the system acquire a higher ability of target detection but also suppresses the radio frequency interference by 6-7 dB.

  8. Fast spin-echo (FSE) and gradient- and spin-echo (GRASE) in fast MRI of the pelvis.

    Science.gov (United States)

    Fellner, F; Held, P; Fellner, C; Schmitt, R; Obletter, N

    1997-01-01

    In this prospective study two different T2-weighted fast spin-echo (FSE) sequences and a gradient- and spin-echo (GRASE) sequence were compared in 20 consecutive patients undergoing clinical pelvic MR examinations. A GRASE and two FSE sequences were applied, whereby the FSE sequences differed from each other by altered echo spacings (15.0 and 22.5 ms) and T2 contrast. Quantitative image analysis included ROI evaluation of different S/N and C/N values. Visual image analysis was performed by two independent readers using a standardized score sheet for anatomic and pathologic findings. Overall image quality was significantly better in both FSE sequences. GRASE and FSE22.5 were superior in delineation of most of anatomic and pathologic structures due to intermediate to hypointense contrast behavior of pelvic fat compared to FSE15.0 in which fat was bright. Therefore, FSE15.0 was optimal for low intensity lesions. Short acquisition times of FSE and GRASE sequences allow application of two different techniques-fat hypointense respectively bright-for excellent lesion visualisation. This study demonstrates the usefulness of contrast manipulation in fast T2-weighted MRI techniques without special techniques, such as fat saturation.

  9. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features.

    Science.gov (United States)

    Dai, Qi; Wu, Li; Li, Lihua

    2011-12-01

    Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.

  10. Efficient Fast Stereo Acoustic Echo Cancellation Based on Pairwise Optimal Weight Realization Technique

    Directory of Open Access Journals (Sweden)

    Yukawa Masahiro

    2006-01-01

    Full Text Available In stereophonic acoustic echo cancellation (SAEC problem, fast and accurate tracking of echo path is strongly required for stable echo cancellation. In this paper, we propose a class of efficient fast SAEC schemes with linear computational complexity (with respect to filter length. The proposed schemes are based on pairwise optimal weight realization (POWER technique, thus realizing a "best" strategy (in the sense of pairwise and worst-case optimization to use multiple-state information obtained by preprocessing. Numerical examples demonstrate that the proposed schemes significantly improve the convergence behavior compared with conventional methods in terms of system mismatch as well as echo return loss enhancement (ERLE.

  11. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

    Directory of Open Access Journals (Sweden)

    Liang-Tsung Huang

    2015-01-01

    Full Text Available Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs. In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory. We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20 and compared it with two classic methods in CUDASW++. Further, the performance on different numbers of threads and blocks has been analyzed. The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers.

  12. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs.

    Science.gov (United States)

    Huang, Liang-Tsung; Wu, Chao-Chin; Lai, Lien-Fu; Li, Yun-Ju

    2015-01-01

    Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory. We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20) and compared it with two classic methods in CUDASW++. Further, the performance on different numbers of threads and blocks has been analyzed. The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers.

  13. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing.

    Science.gov (United States)

    Shi, Chao; Hu, Na; Huang, Hui; Gao, Ju; Zhao, You-Jie; Gao, Li-Zhi

    2012-01-01

    Chloroplast genomes supply valuable genetic information for evolutionary and functional studies in plants. The past five years have witnessed a dramatic increase in the number of completely sequenced chloroplast genomes with the application of second-generation sequencing technology in plastid genome sequencing projects. However, cost-effective high-throughput chloroplast DNA (cpDNA) extraction becomes a major bottleneck restricting the application, as conventional methods are difficult to make a balance between the quality and yield of cpDNAs. We first tested two traditional methods to isolate cpDNA from the three species, Oryza brachyantha, Leersia japonica and Prinsepia utihis. Both of them failed to obtain properly defined cpDNA bands. However, we developed a simple but efficient method based on sucrose gradients and found that the modified protocol worked efficiently to isolate the cpDNA from the same three plant species. We sequenced the isolated DNA samples with Illumina (Solexa) sequencing technology to test cpDNA purity according to aligning sequence reads to the reference chloroplast genomes, showing that the reference genome was properly covered. We show that 40-50% cpDNA purity is achieved with our method. Here we provide an improved method used to isolate cpDNA from angiosperms. The Illumina sequencing results suggest that the isolated cpDNA has reached enough yield and sufficient purity to perform subsequent genome assembly. The cpDNA isolation protocol thus will be widely applicable to the plant chloroplast genome sequencing projects.

  14. Fast spin echo vs conventional spin echo in cervical spine imaging

    Energy Technology Data Exchange (ETDEWEB)

    Gillams, A.R.; Soto, J.A.; Carter, A.P. [Department of Radiology, Boston University Medical School and Boston City Hospital Imaging Foundation, Boston, MA 02118 (United States)

    1997-10-01

    The major attraction of fast-spin-echo (FSE) imaging is reduced acquisition time; however, careful review of the literature reveals many weaknesses: phase-encoded blurring, truncation artefact, bright fat signal, reduced magnetic susceptibility and increased motion artefact. Our aim was a prospective, blinded comparison of FSE and conventional spin echo (CSE) in the cervical spine. Both sequences were performed in 43 patients (19 males and 24 females; mean age 45 years, range 15-66 years). Twenty-eight patients were studied at 1.5 T and 15 at 0.5 T. Typical sequence parameters were: at 1.5 T, TR/TE 2000/90 CSE and 3000/120 FSE, and at 0.5 T, 2200/80 CSE and 2800/120 FSE. Time saved on the FSE was used to increase the matrix and the number of acquisitions. Two neuroradiologists evaluated the images for pathology, artefacts, disc signal intensity, thecal sac compression and image quality. Ten patients had cord lesions; 2 (20%) were missed on CSE. In 4 of 10 patients with moderate/severe thecal sac compression, the degree of stenosis was apparently exaggerated on CSE. The mean degree of confidence for the CSE sequences was 1.8 and for the FSE 1.1, where 1 is optimal. For cervical spine imaging, FSE should be preferred to CSE. (orig.). With 3 figs.

  15. Dance of the Light Echoes

    Science.gov (United States)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for larger poster version This composite image from NASA's Spitzer Space Telescope shows the remnant of a star that exploded, called Cassiopeia A (center) and its surrounding 'light echoes' -- dances of light through dusty clouds, created when stars blast apart. The light echoes are colored and the surrounding clouds of dust are gray. In figure 1, dramatic changes are highlighted in phenomena referred to as light echoes (colored areas) around the Cassiopeia A supernova remnant (center). Cassiopeia A is the remnant of a once massive star that died in a violent supernova explosion. It consists of a dead star, called a neutron star, and a surrounding shell of material that was blasted off as the star died. A light echo occurs when a star explodes, acting like a cosmic flashbulb. The light from this explosion zips through nearby dust clumps, illuminating and heating them up slightly. This brief period of warming causes them to glow in infrared, like a chain of Christmas bulbs lighting up one by one. The result is an optical illusion, in which the dust appears to be flying outward at the speed of light. In figure 1, this apparent motion can be seen here by the shift in colored dust clumps Cassiopeia A is the remnant of a once massive star that died in a violent supernova explosion. It consists of a dead star, called a neutron star, and a surrounding shell of material that was blasted off as the star died. This remnant is located 11,000 light-years away in the northern constellation Cassiopeia. This composite consists of six processed images taken over a time span of three years. Dust features that have not changed over time appear gray, while those that have changed are colored blue or orange. Bluer colors represent an earlier time and redder ones, a later time. The progression of the light echo through the dust can be seen here by the shift in colored dust clumps. This light echo is the largest ever seen

  16. SIMULATION STUDY ON AIRBORNE SAR ECHO SIGNAL

    Institute of Scientific and Technical Information of China (English)

    Bao Houbing; Liu Zhao

    2004-01-01

    Through analyzing the influence on echo signal by factors of kinematical parameters of airborne SAR platform and radar antenna direction, this letter, on the basis of classical SAR echo signal analogue algorithm, puts forward certain airborne SAR echo signal analogue algorithm of distance directional frequency domain pulse coherent accumulation, and goes through simulation. The simulation results have proved the effectiveness of this algorithm.

  17. Photon echo in exciton-plasmon nanomaterials: a signature of strong coupling

    CERN Document Server

    Blake, Adam

    2016-01-01

    The results of rigorous numerical simulations of photon echoes in exciton-plasmon systems are presented. Using a self-consistent model based on coupled Maxwell-Bloch equations we investigate femtosecond time dynamics of ensembles of interacting molecules and molecular aggregates optically coupled to surface-plasmon supporting materials. It is shown that observed photon echoes under two pulse pump-probe sequence are highly dependent on various material parameters such as molecular concentration and periodicity. Simulations of photon echoes in exciton-plasmon materials reveal a unique signature of the strong exciton-plasmon coupling, namely a double-peak structure in spectra of recorded echo signals. This phenomenon is shown to be related to hybrid states (upper and lower polaritons) in exciton-plasmon systems under strong coupling conditions. It is also demonstrated that the double-peak echo is highly sensitive to mild deviations of the coupling from the resonance between molecules and plasmons making it a gre...

  18. Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

    Science.gov (United States)

    Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

    2017-07-01

    DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

  19. IMPROVING THE SKILL AND THE INTEREST OF WRITING ADVERTISEMENTS AND POSTERS THROUGH ESA SEQUENCE

    Directory of Open Access Journals (Sweden)

    Fatma Yuniarti

    2016-04-01

    Full Text Available The action reserach aims at improving the students’ writing skill especially to write advertsements and posters. Both are the short functional texts to be learned at the first semester of the ninth grade. According to the data on pre cycle, the students of class IXA Junior High School Swadhipa Natar, South Lampung got difficulties in writing advertisements and posters. A treatment was necessary to help the students overcome their problem. To consider the related literature, the writer decided to implement ESA sequence in the class. The elements of teaching in ESA Sequence are Engage (to arouse the students’ interests, Study (learn the language focus, and Activate (use the language freely and communicatively.The data were taken from the test of the linguistic competence mastery, the students writing, and the questionnaire. The result shows ESA Sequence can improve the students’ ability in writing advertisements and posters.Key words : ESA (Engange Study Activate, advertisement, poster.

  20. Examining the robustness of automated aural classification of active sonar echoes.

    Science.gov (United States)

    Murphy, Stefan M; Hines, Paul C

    2014-02-01

    Active sonar systems are used to detect underwater man-made objects of interest (targets) that are too quiet to be reliably detected with passive sonar. Performance of active sonar can be degraded by false alarms caused by echoes returned from geological seabed structures (clutter) in shallow regions. To reduce false alarms, a method of distinguishing target echoes from clutter echoes is required. Research has demonstrated that perceptual-based signal features similar to those employed in the human auditory system can be used to automatically discriminate between target and clutter echoes, thereby reducing the number of false alarms and improving sonar performance. An active sonar experiment on the Malta Plateau in the Mediterranean Sea was conducted during the Clutter07 sea trial and repeated during the Clutter09 sea trial. The dataset consists of more than 95,000 pulse-compressed echoes returned from two targets and many geological clutter objects. These echoes were processed using an automatic classifier that quantifies the timbre of each echo using a number of perceptual signal features. Using echoes from 2007, the aural classifier was trained to establish a boundary between targets and clutter in the feature space. Temporal robustness was then investigated by testing the classifier on echoes from the 2009 experiment.

  1. Nuclear quadrupole resonance echoes from hexamethylenetetramine.

    Science.gov (United States)

    Ota, Go; Itozaki, Hideo

    2006-10-01

    We investigated the echo phenomenon of nuclear quadrupole resonance (NQR) from hexamethylenetetramine (HMT). We detected the pure NQR echo signal of HMT with a short pulse interval. The intensity of the echo signal increased as the pulse interval time was decreased. We observed that a clean echo signal was generated even when the pulse interval was shorter than the decay time constant T(2)(*). Since the short interval time gives a strong echo, our result insists that shorter interval time is preferred for the NQR detection.

  2. Simultaneous perfusion and permeability measurements using combined spin- and gradient-echo MRI.

    Science.gov (United States)

    Schmiedeskamp, Heiko; Andre, Jalal B; Straka, Matus; Christen, Thomas; Nagpal, Seema; Recht, Lawrence; Thomas, Reena P; Zaharchuk, Greg; Bammer, Roland

    2013-05-01

    The purpose of this study was to estimate magnetic resonance imaging-based brain perfusion parameters from combined multiecho spin-echo and gradient-echo acquisitions, to correct them for T₁₋, T₂₋, and T₂₋*-related contrast agent (CA) extravasation effects, and to simultaneously determine vascular permeability. Perfusion data were acquired using a combined multiecho spin- and gradient-echo (SAGE) echo-planar imaging sequence, which was corrected for CA extravasation effects using pharmacokinetic modeling. The presented method was validated in simulations and brain tumor patients, and compared with uncorrected single-echo and multiecho data. In the presence of CA extravasation, uncorrected single-echo data resulted in underestimated CA concentrations, leading to underestimated single-echo cerebral blood volume (CBV) and mean transit time (MTT). In contrast, uncorrected multiecho data resulted in overestimations of CA concentrations, CBV, and MTT. The correction of CA extravasation effects resulted in CBV and MTT estimates that were more consistent with the underlying tissue characteristics. Spin-echo perfusion data showed reduced large-vessel blooming effects, facilitating better distinction between increased CBV due to active tumor progression and elevated CBV due to the presence of cortical vessels in tumor proximity. Furthermore, extracted permeability parameters were in good agreement with elevated T1-weighted postcontrast signal values.

  3. On the theory of proton solid echo in polymer melts

    CERN Document Server

    Fatkullin, N; Mattea, C; Stapf, S

    2015-01-01

    Based on a modified Anderson-Weiss approximation (N. Fatkullin, A. Gubaidullin, C. Mattea, S.Stapf, J. Chem. Phys. 137 (2012), 224907) an improved theory of proton spin solid echo in polymer melts is formulated, taking into account contribution from intermolecular magnetic dipole-dipole interactions. The solid echo build-up function defined by the relation , where , and are the respective signals arising from ( ),( ) and ( ) spin echo experiments, where is an operator rotating the spin system on the angle relatively axis , is investigated. It is shown that the intermolecular part of this function at short times , where is a characteristic time for flip-flop transitions between proton spins, contains information about the relative mean squared displacements of polymer segments at different macromolecules, opening up a new opportunity for obtaining information about polymer dynamics in the millisecond regime.

  4. Molecular echoes in space and time

    CERN Document Server

    Lin, Kang; Ma, Junyang; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Zhang, Wenbin; Zeng, Heping; Wu, Jian; Karras, Gabriel; Siour, Guillaume; Hartmann, Jean-Michel; Faucher, Olivier; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh

    2016-01-01

    Mountain echoes are a well-known phenomenon, where an impulse excitation is mirrored by the rocks to generate a replica of the original stimulus, often with reverberating recurrences. For spin echoes in magnetic resonance and photon echoes in atomic and molecular systems the role of the mirror is played by a second, time delayed pulse which is able to reverse the ow of time and recreate the original event. Recently, laser-induced rotational alignment and orientation echoes were introduced for molecular gases, and discussed in terms of rotational-phase-space filamentation. Here we present, for the first time, a direct spatiotemporal analysis of various molecular alignment echoes by means of coincidence Coulomb explosion imaging. We observe hitherto unreported spatially rotated echoes, that depend on the polarization direction of the pump pulses, and find surprising imaginary echoes at negative times.

  5. Fast Echo Canceller in IP Telephony Gateway

    Institute of Scientific and Technical Information of China (English)

    黄永峰; 李星

    2003-01-01

    The length of the echo path in the IP telephony system is very long. Generally, the echo canceller is implemented on the IP telephony gateway which needs to perform concurrently multi-channel echo cancellation and voice compression. Hence, the most key technique to design the echo canceller is to reduce greatly the computational requirement. For this reason a number of innovative features to implement a fast echo canceller are presented. The key components of this canceller include: the separation of adaptive and cancel filters, non-real-time adaptation and real-time cancellation, sharing VAD algorithms with the speech codec, the incorporation of delay indexing with zero coefficients, and windowing the adaptive filter coefficients to reduce the cost of DSP during the cancellation. Finally, the performance of the echo canceller is summarized; the results of evaluation show that the performance gains for echo cancellation are significant.

  6. Longitudinal collective echoes in coasting particle beams

    Directory of Open Access Journals (Sweden)

    Ahmed Al-Khateeb

    2003-01-01

    Full Text Available Longitudinal ballistic and collective beam echoes with diffusion effects are investigated theoretically. In the presence of the space-charge impedance, the collective echo amplitude is obtained as a closed form expression. In contrast to the ballistic case, the collective echo amplitude consists of one maximum at time t_{echo}. The echo amplitude grows up and damps down with a rate proportional to the Landau damping rate of space-charge waves. The effect of weak diffusion is found to modify the ballistic and the collective echo amplitudes in the same manner. This effect of diffusion was confirmed using a “noiseless,” grid-based simulation code. As a first application the amount of numerical diffusion in our simulation code was determined using the echo effect.

  7. Theory of quantum Loschmidt echoes

    CERN Document Server

    Prosen, T; Znidaric, M; Prosen, Tomaz; Seligman, Thomas H.; Znidaric, Marko

    2003-01-01

    In this paper we review our recent work on the theoretical approach to quantum Loschmidt echoes, i.e. various properties of the so called echo dynamics -- the composition of forward and backward time evolutions generated by two slightly different Hamiltonians, such as the state autocorrelation function (fidelity) and the purity of a reduced density matrix traced over a subsystem (purity fidelity). Our main theoretical result is a linear response formalism, expressing the fidelity and purity fidelity in terms of integrated time autocorrelation function of the generator of the perturbation. Surprisingly, this relation predicts that the decay of fidelity is the slower the faster the decay of correlations. In particular for a static (time-independent) perturbation, and for non-ergodic and non-mixing dynamics where asymptotic decay of correlations is absent, a qualitatively different and faster decay of fidelity is predicted on a time scale 1/delta as opposed to mixing dynamics where the fidelity is found to decay...

  8. Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters.

    Science.gov (United States)

    Pellow, David; Filippova, Darya; Kingsford, Carl

    2017-06-01

    Using a sequence's k-mer content rather than the full sequence directly has enabled significant performance improvements in several sequencing applications, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. As k-mer sets often reach hundreds of millions of elements, traditional data structures are often impractical for k-mer set storage, and Bloom filters (BFs) and their variants are used instead. BFs reduce the memory footprint required to store millions of k-mers while allowing for fast set containment queries, at the cost of a low false positive rate (FPR). We show that, because k-mers are derived from sequencing reads, the information about k-mer overlap in the original sequence can be used to reduce the FPR up to 30 × with little or no additional memory and with set containment queries that are only 1.3 - 1.6 times slower. Alternatively, we can leverage k-mer overlap information to store k-mer sets in about half the space while maintaining the original FPR. We consider several variants of such k-mer Bloom filters (kBFs), derive theoretical upper bounds for their FPR, and discuss their range of applications and limitations.

  9. Echo-Enabled Harmonic Generation

    Energy Technology Data Exchange (ETDEWEB)

    Stupakov, Gennady; /SLAC

    2012-06-28

    A recently proposed concept of the Echo-Enabled Harmonic Generation (EEHG) FEL uses two laser modulators in combination with two dispersion sections to generate a high-harmonic density modulation in a relativistic beam. This seeding technique holds promise of a one-stage soft x-ray FEL that radiates not only transversely but also longitudinally coherent pulses. Currently, an experimental verification of the concept is being conducted at the SLAC National Accelerator Laboratory aimed at the demonstration of the EEHG.

  10. Echo-Enabled Harmonic Generation

    Energy Technology Data Exchange (ETDEWEB)

    Stupakov, Gennady; /SLAC

    2012-06-28

    A recently proposed concept of the Echo-Enabled Harmonic Generation (EEHG) FEL uses two laser modulators in combination with two dispersion sections to generate a high-harmonic density modulation in a relativistic beam. This seeding technique holds promise of a one-stage soft x-ray FEL that radiates not only transversely but also longitudinally coherent pulses. Currently, an experimental verification of the concept is being conducted at the SLAC National Accelerator Laboratory aimed at the demonstration of the EEHG.

  11. Elasticity reconstructive imaging by means of stimulated echo MRI.

    Science.gov (United States)

    Chenevert, T L; Skovoroda, A R; O'Donnell, M; Emelianov, S Y

    1998-03-01

    A method is introduced to measure internal mechanical displacement and strain by means of MRI. Such measurements are needed to reconstruct an image of the elastic Young's modulus. A stimulated echo acquisition sequence with additional gradient pulses encodes internal displacements in response to an externally applied differential deformation. The sequence provides an accurate measure of static displacement by limiting the mechanical transitions to the mixing period of the simulated echo. Elasticity reconstruction involves definition of a region of interest having uniform Young's modulus along its boundary and subsequent solution of the discretized elasticity equilibrium equations. Data acquisition and reconstruction were performed on a urethane rubber phantom of known elastic properties and an ex vivo canine kidney phantom using elastic properties are well represented on Young's modulus images. The long-term objective of this work is to provide a means for remote palpation and elasticity quantitation in deep tissues otherwise inaccessible to manual palpation.

  12. Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast

    DEFF Research Database (Denmark)

    Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L.

    2015-01-01

    interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV...... to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could...

  13. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.

    Science.gov (United States)

    Mosher, Jennifer J; Bowman, Brett; Bernberg, Erin L; Shevchenko, Olga; Kan, Jinjun; Korlach, Jonas; Kaplan, Louis A

    2014-09-01

    Improved sequencing accuracy was obtained with 16S amplicons from environmental samples and a known pure culture when upgraded Pacific Biosciences (PacBio) hardware and enzymes were used for the single molecule, real-time (SMRT) sequencing platform. The new PacBio RS II system with P4/C2 chemistry, when used with previously constructed libraries (Mosher et al., 2013) surpassed the accuracy of Roche/454 pyrosequencing platform. With accurate read lengths of >1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing.

    Directory of Open Access Journals (Sweden)

    Chao Shi

    Full Text Available BACKGROUND: Chloroplast genomes supply valuable genetic information for evolutionary and functional studies in plants. The past five years have witnessed a dramatic increase in the number of completely sequenced chloroplast genomes with the application of second-generation sequencing technology in plastid genome sequencing projects. However, cost-effective high-throughput chloroplast DNA (cpDNA extraction becomes a major bottleneck restricting the application, as conventional methods are difficult to make a balance between the quality and yield of cpDNAs. METHODOLOGY/PRINCIPAL FINDINGS: We first tested two traditional methods to isolate cpDNA from the three species, Oryza brachyantha, Leersia japonica and Prinsepia utihis. Both of them failed to obtain properly defined cpDNA bands. However, we developed a simple but efficient method based on sucrose gradients and found that the modified protocol worked efficiently to isolate the cpDNA from the same three plant species. We sequenced the isolated DNA samples with Illumina (Solexa sequencing technology to test cpDNA purity according to aligning sequence reads to the reference chloroplast genomes, showing that the reference genome was properly covered. We show that 40-50% cpDNA purity is achieved with our method. CONCLUSION: Here we provide an improved method used to isolate cpDNA from angiosperms. The Illumina sequencing results suggest that the isolated cpDNA has reached enough yield and sufficient purity to perform subsequent genome assembly. The cpDNA isolation protocol thus will be widely applicable to the plant chloroplast genome sequencing projects.

  15. Independence of echo-threshold and echo-delay in the barn owl.

    Directory of Open Access Journals (Sweden)

    Brian S Nelson

    Full Text Available Despite their prevalence in nature, echoes are not perceived as events separate from the sounds arriving directly from an active source, until the echo's delay is long. We measured the head-saccades of barn owls and the responses of neurons in their auditory space-maps while presenting a long duration noise-burst and a simulated echo. Under this paradigm, there were two possible stimulus segments that could potentially signal the location of the echo. One was at the onset of the echo; the other, after the offset of the direct (leading sound, when only the echo was present. By lengthening the echo's duration, independently of its delay, spikes and saccades were evoked by the source of the echo even at delays that normally evoked saccades to only the direct source. An echo's location thus appears to be signaled by the neural response evoked after the offset of the direct sound.

  16. Research and development of marine radar echo simulator%船用雷达回波信号模拟器软件的研究与开发

    Institute of Scientific and Technical Information of China (English)

    齐天; 赵宇; 李燕青

    2011-01-01

    A method of the generation of a radar echo video digital sequence is proposed, which is the core of the software of Marine radar echo video signal simulator. This method generates the radar echo video digital sequence by the way of polar-coordinates scanning according to radar resolution model, radar echo signal model, sea clutter model and noise model. Marine radar echo simulator outputs radar echo video signal by downloading the digital sequence which verifies the feasibility of the method. Experimental results show the contribute to echo signal's characteristics of radar system, also contribute to the radar system parameter optimization design which provides a great value to improve the radar system performance.%提出船用雷达回波视频信号模拟器上位机软件中的核心部分,即雷达回波视频数字序列的产生方法.该方法根据雷达分辨率模型、雷达回波信号模型、海杂波和噪声模型,以极坐标扫描模拟海图的方式生成雷达回波视频数字序列.通过将算法相关模型加入到MATLAB中仿真、画图并对实验结果进行比较和分析,验证了以上述方法生成雷达回波视频数字序列是可行的.通过将数字序列下载到船用雷达回波信号模拟器板卡后输出较逼真的雷达回波视频信号,验证了船用雷达回波信号模拟器可以完成对于船用雷达回波信号的模拟.验证结果表明,船用雷达回波模拟器系统有助于雷达系统对雷达回波信号特征进行分析研究,有助于雷达后级系统设计的参数优化研究,对改善雷达系统系能具有重要的参考价值.

  17. Localization of the cortical motor area by functional magnetic resonance imaging with gradient echo and echo-planar methods, using clinical 1.5 Tesla MR imaging systems.

    Science.gov (United States)

    Nakayama, K

    1997-06-01

    Functional magnetic resonance imaging (MRI) with gradient echo and echo-planar sequences was applied to healthy volunteers and neurological patients to evaluate the feasibility of detecting and localizing the motor cortex. Time course of the change in signal intensity by an alternate repetition of motor task (squeezing hand) and rest periods was also examined. The motor cortex was localized as the area of signal increase in 88.9% of 45 healthy volunteers by gradient echo method, which mainly reflected the cortical vein, and 83.3% of 30 healthy volunteers by echo-planar method, which mainly reflected the cerebral gyrus. Among 21 volunteers who participated in the both studies, success rate in the localization for the motor cortex was 90.5% (21 volunteers) by gradient echo method and 81% (17 volunteers) by echo-planar method. It was also shown from the time course of the change in signal intensity that signal increase in the most significantly activated area generally corresponded with the periods of the motor task, and the latency between the onset of signal increase and the onset of motor task was usually about 4 seconds. In four of 6 patients with brain tumor, the motor cortex was localized, although activated areas were displaced or distorted. The results indicate that fMRI, either with gradient echo or echo-planar sequence, is a useful method for localizing the primary motor area activated during the motor task and clinically available for noninvasive evaluation of the anatomical relation between brain tumors and the motor area before surgical therapy.

  18. High temporal resolution functional MRI using parallel echo volumar imaging

    Energy Technology Data Exchange (ETDEWEB)

    Rabrait, C.; Ciuciu, P.; Ribes, A.; Poupon, C.; Dehaine-Lambertz, G.; LeBihan, D.; Lethimonnier, F. [CEA Saclay, DSV, I2BM, Neurospin, F-91191 Gif Sur Yvette (France); Le Roux, P. [GEHC, Buc (France); Dehaine-Lambertz, G. [Unite INSERM 562, Gif Sur Yvette (France)

    2008-07-01

    Purpose: To combine parallel imaging with 3D single-shot acquisition (echo volumar imaging, EVI) in order to acquire high temporal resolution volumar functional MRI (fMRI) data. Materials and Methods: An improved EVI sequence was associated with parallel acquisition and field of view reduction in order to acquire a large brain volume in 200 msec. Temporal stability and functional sensitivity were increased through optimization of all imaging parameters and Tikhonov regularization of parallel reconstruction. Two human volunteers were scanned with parallel EVI in a 1.5 T whole-body MR system, while submitted to a slow event-related auditory paradigm. Results: Thanks to parallel acquisition, the EVI volumes display a low level of geometric distortions and signal losses. After removal of low-frequency drifts and physiological artifacts,activations were detected in the temporal lobes of both volunteers and voxel-wise hemodynamic response functions (HRF) could be computed. On these HRF different habituation behaviors in response to sentence repetition could be identified. Conclusion: This work demonstrates the feasibility of high temporal resolution 3D fMRI with parallel EVI. Combined with advanced estimation tools,this acquisition method should prove useful to measure neural activity timing differences or study the nonlinearities and non-stationarities of the BOLD response. (authors)

  19. Rapid fat-suppressed isotropic steady-state free precession imaging using true 3D multiple-half-echo projection reconstruction.

    Science.gov (United States)

    Lu, Aiming; Brodsky, Ethan; Grist, Thomas M; Block, Walter F

    2005-03-01

    Three-dimensional projection reconstruction (3D PR)-based techniques are advantageous for steady-state free precession (SSFP) imaging for several reasons, including the capability to achieve short repetition times (TRs). In this paper, a multi-half-echo technique is presented that dramatically improves the data-sampling efficiency of 3D PR sequences while it retains this short-TR capability. The k-space trajectory deviations are measured quickly and corrected on a per-sample point basis. A two-pass RF cycling technique is then applied to the dual-half-echo implementation to generate fat/water-separated images. The resultant improvement in the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) was demonstrated in volunteer studies. Volumetric images with excellent spatial resolution, coverage, and contrast were obtained with high speed. The non-contrast-enhanced SSFP studies show that this technique has promising potential for MR angiography (MRA).

  20. DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2005-03-01

    Full Text Available Abstract Background We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. Results In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. Conclusion On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

  1. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  2. Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

    Science.gov (United States)

    Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

    2013-01-01

    Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

  3. Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Shunichi Kosugi

    Full Text Available Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.

  4. Locus Reference Genomic sequences: An improved basis for describing human DNA variants

    KAUST Repository

    Dalgleish, Raymond

    2010-04-15

    As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

  5. Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

    Science.gov (United States)

    Vingron, Martin

    2016-01-01

    Non-methylated islands (NMIs) of DNA are genomic regions that are important for gene regulation and development. A recent study of genome-wide non-methylation data in vertebrates by Long et al. (eLife 2013;2:e00348) has shown that many experimentally identified non-methylated regions do not overlap with classically defined CpG islands which are computationally predicted using simple DNA sequence features. This is especially true in cold-blooded vertebrates such as Danio rerio (zebrafish). In order to investigate how predictive DNA sequence is of a region’s methylation status, we applied a supervised learning approach using a spectrum kernel support vector machine, to see if a more complex model and supervised learning can be used to improve non-methylated island prediction and to understand the sequence properties of these regions. We demonstrate that DNA sequence is highly predictive of methylation status, and that in contrast to existing CpG island prediction methods our method is able to provide more useful predictions of NMIs genome-wide in all vertebrate organisms that were studied. Our results also show that in cold-blooded vertebrates (Anolis carolinensis, Xenopus tropicalis and Danio rerio) where genome-wide classical CpG island predictions consist primarily of false positives, longer primarily AT-rich DNA sequence features are able to identify these regions much more accurately. PMID:27984582

  6. Initial study of stability and repeatability of measuring R2 ' and oxygen extraction fraction values in the healthy brain with gradient-echo sampling of spin-echo sequence%梯度回波采样自旋回波序列测量脑R2'及氧摄取分数值稳定性及重复性的研究

    Institute of Scientific and Technical Information of China (English)

    惠丽红; 张晓东; 何超; 谢晟; 肖江喜; 张珏; 王霄英; 蒋学祥

    2010-01-01

    目的 通过梯度回波采样自旋回波序列(GESSE)测量脑组织R2'值与传统梯度回波序列(GRE)间接测量R2'值的方法在正常志愿者内进行比较,初步评价该序列的稳定性及重复性.方法 8名正常健康志愿者,平静状态下进行头颅单层GESSE序列和该层面T2图(T2 map)和有效横向弛豫时间图(T2*map)扫描.1 d之后,再重复进行相同层面的上述序列扫描.应用北大医院和北京大学工学院生物医学工程系共同自主开发的软件对GESSE序列原始图像进行后处理得到R2'图(R2'map)及氧摄取分数图(OEF map),将左、右大脑半球等分为前、中、后3个区域,测量该区域R2'值和OEF值;T2 map及T2*map的数据在Functool工作站上进行后处理得到自旋-自旋弛豫率图(R2 map)和表观自旋-自旋弛豫率图(R2*map),利用公式计算得到R2'值(R2'=R2*-R2,R2*=1/T2*,R2=1/T2),ROI测量方法及部位同GESSE序列.通过配对t检验比较GESSE序列及传统序列2次测得R2',初步评价该序列的稳定性,通过配对t检验比较GESSE序列前后2次扫描得到的OEF值,初步判断该序列测量OEF值的重复性.结果 GESSE序列前后2次扫描得到的R2'值分别为(4.21±0.92)、(4.45±0.94)Hz,差异无统计学意义(t=-0.83,P>0.05).前后2次传统方法得到R2'平均值分别为(7.37±1.47)、(6.42±2.33)Hz,差异有统计学意义(t=1.80,P<0.05),第1次GESSE序列和传统方法所测R2'差异有统计学意义(t=1.71,P<0.05).GESSE序列前后2次所测OEF值分别为0.327±0.036和0.336±0.035,差异无统计学意义(t=-1.48,P>0.05).结论 在正常被试者中GESSE序列测量R2'值与传统方法相比稳定性较好.GESSE序列测量的OEF值重复性较好.该技术有进一步临床应用的前景.%Objective To evaluate the stability and repeatability of gradient-echo sampling of spinecho (GESSE) sequence in measuring the R2'value in volunteers, by comparison with traditional GRE sequence (T2* map and T2 map). Methods

  7. An improved hierarchical fragile watermarking scheme using chaotic sequence sorting and subblock post-processing

    Science.gov (United States)

    Xiao, Di; Shih, Frank Y.

    2012-05-01

    The original hierarchical watermarking scheme for image tamper detection and recovery has simple computation and high performance precision which can achieve 2 × 2 subblock. However, four-scanning and blind attacks have been proposed recently on this scheme. We generalize these attacks and analyze the cause of security flaws. We think that it is promising to improve the original scheme's security and keep its merit at the same time. In order to defeat these attacks, we develop an improved method to generate a block mapping sequence by sorting the chaotic sequence and add the chaotic encryption and permutation based on the exact content of each subblock to be the post-processing of the 3-tuple watermark. Our method uses the simple watermarking scheme and satisfies the performance requirements of fragile watermarking, such as high-precision tamper detection, localization and recovery. Theoretical analysis and computer simulation demonstrate that our proposed scheme is much more secure and can overcome possible attacks.

  8. Improving High-Throughput Sequencing Approaches for Reconstructing the Evolutionary Dynamics of Upper Paleolithic Human Groups

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine

    been mainly driven by the development of High-Throughput DNA Sequencing (HTS) technologies but also by the implementation of novel molecular tools tailored to the manipulation of ultra short and damaged DNA molecules. Our ability to retrieve traces of genetic material has tremendously improved, pushing...... work on admixture events between Neanderthals and anatomically modern humans and but also suggested that the latter were organized in small family units whose members avoided inbreeding....

  9. Improvement of energy efficiency via spectrum optimization of excitation sequence for multichannel simultaneously triggered airborne sonar system.

    Science.gov (United States)

    Meng, Qing-Hao; Yao, Zhen-Jing; Peng, Han-Yang

    2009-12-01

    Both the energy efficiency and correlation characteristics are important in airborne sonar systems to realize multichannel ultrasonic transducers working together. High energy efficiency can increase echo energy and measurement range, and sharp autocorrelation and flat cross correlation can help eliminate cross-talk among multichannel transducers. This paper addresses energy efficiency optimization under the premise that cross-talk between different sonar transducers can be avoided. The nondominated sorting genetic algorithm-II is applied to optimize both the spectrum and correlation characteristics of the excitation sequence. The central idea of the spectrum optimization is to distribute most of the energy of the excitation sequence within the frequency band of the sonar transducer; thus, less energy is filtered out by the transducers. Real experiments show that a sonar system consisting of eight-channel Polaroid 600 series electrostatic transducers excited with 2 ms optimized pulse-position-modulation sequences can work together without cross-talk and can measure distances up to 650 cm with maximal 1% relative error.

  10. IMPROVING THE SKILL AND THE INTEREST OF WRITING ADVERTISEMENTS AND POSTERS THROUGH ESA SEQUENCE

    Directory of Open Access Journals (Sweden)

    author Fatma Yuniarti

    2015-01-01

    Full Text Available The action reserach aims at improving the students’ writing skill especially to write advertsements and posters. Both are the short functional texts to be learned at the second semester. According to the data on pre cycle, the students of second semester got difficulties to write advertisements and posters. A treatment was necessary to help the students overcome their problem. To consider the related literature, the writer decided to implement ESA sequence (Harmer 2001 in the class. The elements of teaching in ESA Sequence are Engage (to arouse the students’ interests, Study (learn the language focus, and Activate (use the language freely and communicatively. The data were taken from the test of the linguistic competence mastery, the students writing, and the questionnaire. The students’ linguistic competence got increased as shown by the score (58 in pre-cycle, 66 in cycle 1, and 70 in cycle 2. The students’ ability to write the short functional texts also get improved as indicated by the average score on writing tasks (53 in pre-cycle, 63 in cycle 1, 72 in cycle 2. The interest also gets better as shown by the score of the questionnaire (22,3 in pre-cycle, 33,5 in cycle 1, and 37 in cycle 2. It means ESA Sequence can improve the studets’ ability to write advertisements and posters.Key words : advertisement, ESA (Engange Study Activate, poster

  11. An SNR improvement of passive SAW tags with 5-bit Barker code sequence

    Science.gov (United States)

    Bae, Hyunchul; Kim, Jaekwon; Burm, Jinwook

    2012-07-01

    Passive surface acoustic wave (SAW) tags require a large signal-to-noise ratio (SNR) in order to increase the interrogation range. For the purpose of achieving high SNR for radio frequency identification (RFID) communication systems, Barker codes, a binary phase shift keying (BPSK) modulation technique, have been adopted in this study. Passive SAW RFID tags were designed with 5-bit Barker code sequences to generate BPSK modulated signals. Through the SNR analysis, the improvements in SNR were about 11 dB using Barker codes along with a correlator, which can be further improved by optimisation in the correlator.

  12. Is Echo a complex adaptive system?

    Science.gov (United States)

    Smith, R M; Bedau, M A

    2000-01-01

    We evaluate whether John Holland's Echo model exemplifies his theory of complex adaptive systems. After reviewing Holland's theory of complex adaptive systems and describing his Escho model, we describe and explain the characteristic evolutionary behavior observed in a series of Echo model runs. We conclude that Echo lacks the diversity of hierarchically organized aggregates that typify complex adaptive systems, and we explore possible explanations for this failure.

  13. Loschmidt echo for quantum metrology

    Science.gov (United States)

    Macrı, Tommaso; Smerzi, Augusto; Pezzè, Luca

    2016-07-01

    We propose a versatile Loschmidt echo protocol to detect and quantify multiparticle entanglement. It allows us to extract the quantum Fisher information for arbitrary pure states, and finds direct application in quantum metrology. In particular, the protocol applies to states that are generally difficult to characterize, as non-Gaussian states, and states that are not symmetric under particle exchange. We focus on atomic systems, including trapped ions, polar molecules, and Rydberg atoms, where entanglement is generated dynamically via long-range interaction, and show that the protocol is stable against experimental detection errors.

  14. A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

    Directory of Open Access Journals (Sweden)

    Pinheiro Daniel G

    2009-06-01

    Full Text Available Abstract Background High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE, Massively Parallel Signature Sequencing (MPSS or Sequencing-by-Synthesis (SBS represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/. S3T source code and datasets can also be downloaded from the aforementioned website.

  15. Improved abdominal MRI in non-breath-holding children using a radial k-space sampling technique.

    Science.gov (United States)

    Lee, Jong Hyuk; Choi, Young Hun; Cheon, Jung Eun; Lee, So Mi; Cho, Hyun Hae; Shin, Su Mi; Kim, Woo Sun; Kim, In One

    2015-06-01

    Radial k-space sampling techniques have been shown to reduce motion artifacts in adult abdominal MRI. To compare a T2-weighted radial k-space sampling MRI pulse sequence (BLADE) with standard respiratory-triggered T2-weighted turbo spin echo (TSE) in pediatric abdominal imaging. Axial BLADE and respiratory-triggered turbo spin echo sequences were performed without fat suppression in 32 abdominal MR examinations in children. We retrospectively assessed overall image quality, the presence of respiratory, peristaltic and radial artifact, and lesion conspicuity. We evaluated signal uniformity of each sequence. BLADE showed improved overall image quality (3.35 ± 0.85 vs. 2.59 ± 0.59, P sampling technique improved the quality and reduced respiratory motion artifacts in young children compared with conventional respiratory-triggered turbo spin-echo sequences.

  16. Diffusion measurement from observed transverse beam echoes

    Science.gov (United States)

    Sen, Tanaji; Fischer, Wolfram

    2017-01-01

    We study the measurement of transverse diffusion through beam echoes. We revisit earlier observations of echoes in the Relativistic Heavy Ion Collider and apply an updated theoretical model to these measurements. We consider three possible models for the diffusion coefficient and show that only one is consistent with measured echo amplitudes and pulse widths. This model allows us to parameterize the diffusion coefficients as functions of the bunch charge. We demonstrate that echoes can be used to measure diffusion much quicker than present methods and could be useful to a variety of hadron synchrotrons.

  17. A scheme for multiple sequence alignment optimization--an improvement based on family representative mechanics features.

    Science.gov (United States)

    Liu, Xin; Zhao, Ya-Pu

    2009-12-21

    As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue-residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue-residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (approximately 50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

  18. Minimum complexity echo state network.

    Science.gov (United States)

    Rodan, Ali; Tino, Peter

    2011-01-01

    Reservoir computing (RC) refers to a new class of state-space models with a fixed state transition structure (the reservoir) and an adaptable readout form the state space. The reservoir is supposed to be sufficiently complex so as to capture a large number of features of the input stream that can be exploited by the reservoir-to-output readout mapping. The field of RC has been growing rapidly with many successful applications. However, RC has been criticized for not being principled enough. Reservoir construction is largely driven by a series of randomized model-building stages, with both researchers and practitioners having to rely on a series of trials and errors. To initialize a systematic study of the field, we concentrate on one of the most popular classes of RC methods, namely echo state network, and ask: What is the minimal complexity of reservoir construction for obtaining competitive models and what is the memory capacity (MC) of such simplified reservoirs? On a number of widely used time series benchmarks of different origin and characteristics, as well as by conducting a theoretical analysis we show that a simple deterministically constructed cycle reservoir is comparable to the standard echo state network methodology. The (short-term) MC of linear cyclic reservoirs can be made arbitrarily close to the proved optimal value.

  19. How to misuse echo contrast

    Directory of Open Access Journals (Sweden)

    Missios Anna

    2009-01-01

    Full Text Available Abstract Background Primary intracardiac tumours are rare, there are however several entities that can mimic tumours. Contrast echocardiography has been suggested to aid the differentiation of various suspected masses. We present a case where transthoracic echocardiography completely misdiagnosed a left atrial mass, partly due to use of echo contrast. Case presentation An 80 year-old woman was referred for transthoracic echocardiography because of one-month duration of worsening of dyspnoea. Transthoracic echocardiography displayed a large echodense mass in the left atrium. Intravenous injection of contrast (SonoVue, Bracco Inc., It indicated contrast-enhancement of the structure, suggesting tumour. Transesophageal echocardiography revealed, however, a completely normal finding in the left atrium. Subsequent gastroscopy examination showed a hiatal hernia. Conclusion It is noteworthy that the transthoracic echocardiographic exam completely misdiagnosed what seemed like a left atrial mass, which in part was an effect of the use of echo contrast. This example highlights that liberal use of transoesophageal echocardiography is often warranted if optimal display of cardiac structures is desired.

  20. Diffusion imaging with stimulated echoes: signal models and experiment design

    CERN Document Server

    Alexander, Daniel C

    2013-01-01

    Purpose: Stimulated echo acquisition mode (STEAM) diffusion MRI can be advantageous over pulsed-gradient spin-echo (PGSE) for diffusion times that are long compared to $\\ttwo$. It is important therefore for biomedical diffusion imaging applications at 7T and above where $\\ttwo$ is short. However, imaging gradients in the STEAM sequence contribute much greater diffusion weighting than in PGSE, but are often ignored during post-processing. We demonstrate here that this can severely bias parameter estimates. Method: We present models for the STEAM signal for free and restricted diffusion that account for crusher and slice-select (butterfly) gradients to avoid such bias. The butterfly gradients also disrupt experiment design, typically by skewing gradient-vectors towards the slice direction. We propose a simple compensation to the diffusion gradient vector specified to the scanner that counterbalances the butterfly gradients to preserve the intended experiment design. Results: High-field data fixed monkey brain e...

  1. Prospects for Precise Measurements with Echo Atom Interferometry

    Directory of Open Access Journals (Sweden)

    Brynle Barrett

    2016-06-01

    Full Text Available Echo atom interferometers have emerged as interesting alternatives to Raman interferometers for the realization of precise measurements of the gravitational acceleration g and the determination of the atomic fine structure through measurements of the atomic recoil frequency ω q . Here we review the development of different configurations of echo interferometers that are best suited to achieve these goals. We describe experiments that utilize near-resonant excitation of laser-cooled rubidium atoms by a sequence of standing wave pulses to measure ω q with a statistical uncertainty of 37 parts per billion (ppb on a time scale of ∼50 ms and g with a statistical precision of 75 ppb. Related coherent transient techniques that have achieved the most statistically precise measurements of atomic g-factor ratios are also outlined. We discuss the reduction of prominent systematic effects in these experiments using off-resonant excitation by low-cost, high-power lasers.

  2. Prospects for Precise Measurements with Echo Atom Interferometry

    CERN Document Server

    Barrett, Brynle; Beica, Hermina C; Vorozcovs, Andrejs; Pouliot, Alexander; Kumarakrishnan, A

    2016-01-01

    Echo atom interferometers have emerged as interesting alternatives to Raman interferometers for the realization of precise measurements of the gravitational acceleration $g$ and the determination of the atomic fine structure through measurements of the atomic recoil frequency $\\omega_q$. Here we review the development of different configurations of echo interferometers that are best suited to achieve these goals. We describe experiments that utilize near-resonant excitation of laser-cooled rubidium atoms by a sequence of standing wave pulses to measure $\\omega_q$ with a statistical uncertainty of 37 parts per billion (ppb) on a time scale of $\\sim 50$ ms and $g$ with a statistical precision of 75 ppb. Related coherent transient techniques that have achieved the most statistically precise measurements of atomic g-factor ratios are also outlined. We discuss the reduction of prominent systematic effects in these experiments using off-resonant excitation by low-cost, high-power lasers.

  3. Improvement of sequence selectivity in triple helical recognition of RNA by phenylalanine-derived PNA.

    Science.gov (United States)

    Zengeya, Thomas; Gindin, Artem; Rozners, Eriks

    2013-01-01

    Modified peptide nucleic acids (PNA) containing one or two thymine PNA monomers derived from phenylalanine were synthesized. Triple helix formation by these modified PNAs with RNA and DNA hairpins having a variable base pair in the middle of the helix were studied using isothermal titration calorimetry and compared with triple helix formation by non-modified PNAs. While unmodified PNA had low sequence selectivity against mismatched hairpins, introduction of one or two phenylalanine-derived monomers significantly increased the mismatch discrimination and sequence selectivity of the modified PNA. Consistent with our previous observations, PNA formed more stable triple helices with RNA than with DNA. Interestingly, the phenylalanine modification further improved the preference of PNA for RNA over DNA hairpin.

  4. Subband Affine Projection Algorithm for Acoustic Echo Cancellation System

    Directory of Open Access Journals (Sweden)

    Choi Hun

    2007-01-01

    Full Text Available We present a new subband affine projection (SAP algorithm for the adaptive acoustic echo cancellation with long echo path delay. Generally, the acoustic echo canceller suffers from the long echo path and large computational complexity. To solve this problem, the proposed algorithm combines merits of the affine projection (AP algorithm and the subband filtering. Convergence speed of the proposed algorithm is improved by the signal-decorrelating property of the orthogonal subband filtering and the weight updating with the prewhitened input signal of the AP algorithm. Moreover, in the proposed algorithms, as applying the polyphase decomposition, the noble identity, and the critical decimation to subband the adaptive filter, the sufficiently decomposed SAP updates the weights of adaptive subfilters without a matrix inversion. Therefore, computational complexity of the proposed method is considerably reduced. In the SAP, the derived weight updating formula for the subband adaptive filter has a simple form as ever compared with the normalized least-mean-square (NLMS algorithm. The efficiency of the proposed algorithm for the colored signal and speech signal was evaluated experimentally.

  5. Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates.

    Science.gov (United States)

    Maningi, Nontuthuko E; Daum, Luke T; Rodriguez, John D; Mphahlele, Matsie; Peters, Remco P H; Fischer, Gerald W; Chambers, James P; Fourie, P Bernard

    2015-12-01

    The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance in Mycobacterium tuberculosis isolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising the pncA coding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolates from an archived series collected in 2001. These 88 isolates were previously Sanger sequenced, with 55 (61%) designated as carrying the wild-type pncA gene and 33 (37%) showing mutations. PZA susceptibility of the isolates was also determined using the Bactec 460 TB system and the Wayne test. In this study, isolates were recultured and susceptibility testing was performed in Bactec 960 MGIT. Concordance between NGS and MGIT results was 93% (n = 88), and concordance values between the Bactec 460, the Wayne test, or pncA gene Sanger sequencing and NGS results were 82% (n = 88), 83% (n = 88), and 89% (n = 88), respectively. NGS confirmed the majority of pncA mutations detected by Sanger sequencing but revealed several new and mixed-strain mutations that resolved discordancy in other phenotypic results. Importantly, in 53% (18/34) of these isolates, pncA mutations were located in the 151 to 360 region and warrant further exploration. In these isolates, with their known resistance to rifampin, NGS of pncA improved PZA resistance detection sensitivity to 97% and specificity to 94% using NGS as the gold standard and helped to resolve discordant results from conventional methodologies.

  6. Open-Source Sequence Clustering Methods Improve the State Of the Art.

    Science.gov (United States)

    Kopylova, Evguenia; Navas-Molina, Jose A; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J Gregory; Knight, Rob

    2016-01-01

    Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http

  7. Comparison of T{sub 2}-weighted turbo-spin echo sequence and ultra-fast HASTE sequence in the diagnosis of cervical myelopathies and spinal stenoses against static and kinematic MRT of the cervical spine; Vergleich von T{sub 2}-gewichteter Turbo-Spin-Echo- und ultraschneller, HASTE-Sequenz in der Diagnostik von zervikalen Myelopathien und Spinalstenosen mit der statischen und kinematischen MRT der Halswirbelsaeule

    Energy Technology Data Exchange (ETDEWEB)

    Muhle, C.; Metzner, J.; Brinkmann, G.; Kuehn, B.; Bischoff, L.; Hutzelmann, A.; Wesner, F.; Heller, M. [Klinik fuer Radiologische Diagnostik, Christian-Albrechts-Universitaet zu Kiel (Germany)

    1997-11-01

    Purpose: The purpose of this study was to compare HASTE-sequence with T{sub 2}-weighted TSE-sequence in the detection of cervical myelopathy and cervical spinal stenosis in kinematic MRI. Methods: 24 patients with degenerative disease of the cervical spine were studied. Images were evaluated according to the following criteria: Artifacts, delineation of the vertebra, disks and degenerative changes, grade of spinal stenosis (grade 0-3) and evaluation of the cervical spinal cord. Results: Due to image blurring and artifacts, evaluation and delineation of the cervical spine was possible in all cases in the T{sub 2}-weighted TSE-sequence, but only in 23 of 24 patients using HASTE-sequence. Differentiation between osteophytes and disks was obtained in most cases (23/24) in the T{sub 2}-weighted TSE-sequence but none in the HASTE-sequence. Cervical myelopathy was observed in 4 patients in T{sub 2}-weighted TSE images but only in two cases using HASTE-sequence. Compared to T{sub 2}-weighted TSE-sequence spinal canal stenosis was underestimated using HASTE-sequence. (orig./AJ) [Deutsch] Ziel: Beurteilung von zervikalen Myelopathien und Spinalstenosen im Vergleich von ultraschneller HASTE-Sequenz sowie T{sub 2}-TSE-Sequenz. Methode: 24 Patienten mit degenerativen Halswirbelsaeulenveraenderungen wurden untersucht. Die Aufnahmen wurden hinsichtlich der Artefaktanfaelligkeit, der Darstellung von Halswirbelkoerper, Bandscheiben und degenerativen Veraenderungen, dem Grad einer Spinalstenose (Stadium 0-3) sowie der Beurteilung des Zervikalmarks ausgewertet. Ergebnisse; Aufgrund von ausgepraegten Artefakten konnten nur 23 von 24 Untersuchungen mit der HASTE-Sequenz, hingegen alle Untersuchungen mit der T{sub 2}-TSE-Sequenz ausgewertet werden. Eine Differenzierung von osteophytaeren Randanbauten von Bandscheiben und Wirbelkoerpern war in der HASTE-Sequenz gegenueber der T{sub 2}-TSE-Sequenz nur eingeschraenkt moeglich. Eine in 4 Faellen in der T{sub 2}-TSE-Sequenz diagnostizierte

  8. Improved sequence learning with subthalamic nucleus deep brain stimulation: evidence for treatment-specific network modulation.

    Science.gov (United States)

    Mure, Hideo; Tang, Chris C; Argyelan, Miklos; Ghilardi, Maria-Felice; Kaplitt, Michael G; Dhawan, Vijay; Eidelberg, David

    2012-02-22

    We used a network approach to study the effects of anti-parkinsonian treatment on motor sequence learning in humans. Eight Parkinson's disease (PD) patients with bilateral subthalamic nucleus (STN) deep brain stimulation underwent H(2)(15)O positron emission tomography (PET) imaging to measure regional cerebral blood flow (rCBF) while they performed kinematically matched sequence learning and movement tasks at baseline and during stimulation. Network analysis revealed a significant learning-related spatial covariance pattern characterized by consistent increases in subject expression during stimulation (p = 0.008, permutation test). The network was associated with increased activity in the lateral cerebellum, dorsal premotor cortex, and parahippocampal gyrus, with covarying reductions in the supplementary motor area (SMA) and orbitofrontal cortex. Stimulation-mediated increases in network activity correlated with concurrent improvement in learning performance (p learning performance or network activity. Analysis of learning-related rCBF in network regions revealed improvement in baseline abnormalities with STN stimulation but not levodopa. These effects were most pronounced in the SMA. In this region, a consistent rCBF response to stimulation was observed across subjects and trials (p = 0.01), although the levodopa response was not significant. These findings link the cognitive treatment response in PD to changes in the activity of a specific cerebello-premotor cortical network. Selective modulation of overactive SMA-STN projection pathways may underlie the improvement in learning found with stimulation.

  9. Photon echo relaxation in molecular mixed crystals

    NARCIS (Netherlands)

    Aartsma, Thijs Jitse

    1978-01-01

    In dit proefschrift worden foton-echo experimenten beschreven, toegepast op molekulaire mengkristallen. De primaire doelstelling van het onderzoek was om met behulp van foton-echo experimenten nieuwe informatie te verkrijgen over de relaxatie processen die optreden in molekulaire mengkristallen bij

  10. Evaluation of ECHO PS Positioning System in a Porcine Model of Simulated Laparoscopic Ventral Hernia Repair.

    Science.gov (United States)

    Hanna, Erin M; Voeller, Guy R; Roth, J Scott; Scott, Jeffrey R; Gagne, Darcy H; Iannitti, David A

    2013-01-01

    Purpose. Operative efficiency improvements for laparoscopic ventral hernia repair (LVHR) have focused on reducing operative time while maintaining overall repair efficacy. Our objective was to evaluate procedure time and positioning accuracy of an inflatable mesh positioning device (Echo PS Positioning System), as compared to a standard transfascial suture technique, using a porcine model of simulated LVHR. Methods. The study population consisted of seventeen general surgeons (n = 17) that performed simulated LVHR on seventeen (n = 17) female Yorkshire pigs using two implantation techniques: (1) Ventralight ST Mesh + Echo PS Positioning System (Echo PS) and (2) Ventralight ST Mesh + transfascial sutures (TSs). Procedure time and mesh centering accuracy overtop of a simulated surgical defect were evaluated. Results. Echo PS demonstrated a 38.9% reduction in the overall procedure time, as compared to TS. During mesh preparation and positioning, Echo PS demonstrated a 60.5% reduction in procedure time (P Echo PS (16.2%), this was not significantly different than TS. Conclusions. Echo PS demonstrated a significant reduction in overall simulated LVHR procedure time, particularly during mesh preparation/positioning. These operative time savings may translate into reduced operating room costs and improved surgeon/operating room efficiency.

  11. Photon echo without a free induction decay in a double-Λ system.

    Science.gov (United States)

    Beavan, Sarah E; Ledingham, Patrick M; Longdell, Jevon J; Sellars, Matthew J

    2011-04-01

    We have characterized a novel photon-echo pulse sequence for a double-Λ-type energy level system where the input and rephasing transitions are different from the applied π pulses. We show that, despite having imperfect π-pulses associated with large coherent emission due to free induction decay (FID), the noise added in the echo mode is only 0.2 ± 0.1 photons per shot, compared to 4 × 10⁴ photons in the FID modes. Using this echo pulse sequence in the "rephased amplified spontaneous emission" (RASE) scheme [Phys. Rev. A 81, 012301 (2010)] will allow for generation of entangled photon pairs that are in different frequency, temporal, and potentially spatial modes to any bright driving fields. The coherence and efficiency properties of this sequence were characterized in a Pr(3+):Y₂SiO₅ crystal.

  12. Cryptanalysis of a novel image encryption scheme based on improved hyperchaotic sequences

    Science.gov (United States)

    Özkaynak, Fatih; Özer, Ahmet Bedri; Yavuz, Sırma

    2012-11-01

    Chaotic cryptography is a new field that has seen a significant amount of research activity during the last 20 years. Despite the many proposals that use various methods in the design of encryption algorithms, there is a definite need for a mathematically rigorous cryptanalysis of these designs. In this study, we analyze the security weaknesses of the "C. Zhu, A novel image encryption scheme based on improved hyperchaotic sequences, Optics Communications 285 (2012) 29-37". By applying chosen plaintext attacks, we show that all the secret parameters can be revealed.

  13. Theoretical description of depth pulse sequences, on and off resonance, including improvements and extensions thereof.

    Science.gov (United States)

    Bendall, M R; Pegg, D T

    1985-04-01

    A general mathematical description of depth pulse sequences in terms of rotation matrices permits a single matrix, known as a cycle matrix, to be written down for each phase-cycled pulse in the overall sequence, such that the result for the total phase-cycled sequence is the product of the individual cycle matrices. It is straightforward to include the effect of the tilted rf axis off resonance and obtain exact solutions. The two types of phase-cycled pulse used in a depth pulse scheme are 2 theta [+/- x] and 2 theta [+/- x, +/- y] and for the general off-resonance case, four of the off-diagonal elements in the 2 theta [+/- x] cycle matrix, and all of the off-diagonal elements in the 2 theta [+/- x, +/- y] cycle matrix, are zero. These simplifications enable important improvements of depth pulse schemes for the elimination of high-flux signals, the reduction of signals from sample regions experiencing pulse angles differing from 90 degrees, and the avoidance of deleterious off-resonance effects such as the production of dispersion signals. In all cases, the dependence of signal intensity off resonance can be easily and exactly calculated. There are important applications in in vivo spectroscopy.

  14. Theory of Quantum Loschmidt Echoes

    Science.gov (United States)

    Prosen, T.; Seligman, T. H.; Žnidarič, M.

    In this paper we review our recent work on the theoretical approach to quantum Loschmidt echoes, i.e., various properties of the so-called echo dynamics -- the composition of forward and backward time evolutions generated by two slightly different Hamiltonians, such as the state autocorrelation function (fidelity) and the purity of a reduced density matrix traced over a subsystem (purity fidelity). Our main theoretical result is a linear response formalism, expressing the fidelity and purity fidelity in terms of integrated time autocorrelation function of the generator of the perturbation. Surprisingly, this relation predicts that the decay of fidelity is the slower the faster the decay of correlations. In particular for a static (time-independent) perturbation, and for non-ergodic and non-mixing dynamics where asymptotic decay of correlations is absent, a qualitatively different and faster decay of fidelity is predicted on a time scale ∝ 1/δ as opposed to mixing dynamics where the fidelity is found to decay exponentially on a time-scale ∝ 1/δ2, where δ is a strength of perturbation. A detailed discussion of a semi-classical regime of small effective values of Planck constant hbar is given where classical correlation functions can be used to predict quantum fidelity decay. Note that the correct and intuitively expected classical stability behavior is recovered in the classical limit hbarto 0, as the two limits δto 0 and hbarto 0 do not commute. The theoretical results are demonstrated numerically for two models, the quantized kicked top and the multi-level Jaynes Cummings model. Our method can for example be applied to the stability analysis of quantum computation and quantum information processing.

  15. An Improved Protein Structural Prediction Method by Incorporating Both Sequence and Structure Information.

    Science.gov (United States)

    Wei, Leyi; Liao, Minghong; Gao, Xing; Zou, Quan

    2014-09-15

    Protein structural classes information is beneficial for secondary and tertiary structure prediction, protein folds prediction, and protein function analysis. Thus, predicting protein structural classes is of vital importance. In recent years, several computational methods have been developed for low-sequence-similarity (25% - 40%) protein structural classes prediction. However, the reported prediction accuracies are actually not satisfactory. Aiming to further improve the prediction accuracies, we propose three different feature extraction methods and construct a comprehensive feature set that captures both sequence and structure information. By applying a random forest (RF) classifier to the feature set, we further develop a novel method for structural classes prediction. We test the proposed method on three benchmark datasets (25PDB, 640, and 1189) with low sequence similarity, and obtain the overall prediction accuracies of 93.5%, 92.6%, and 93.4%, respectively. Compared with six competing methods, the accuracies we achieved are 3.4%, 6.2%, and 8.7% higher than that achieved by the best-performing methods, showing the superiority of our method. Moreover, due to the limitation of the size of the three benchmark datasets, we further test the proposed method on three updated large-scale datasets with different sequence similarity (40%, 30%, and 25%). The proposed method achieves above 90% accuracies for all the three datasets, consistency with the accuracies on the above three benchmark datasets. Experimental results suggest our method as an effective and promising tool for structural classes prediction. Currently, a webserver that implements the proposed method is available on http://121.192.180.204:8080/RF_PSCP/Index.html.

  16. Comparison of Quantitative Assessment of BLADE and Isotropic Three-Dimensional Fast Spin Echo Cube (3D T2 SPACE Sequences with Conventional Protocols of wrist Joint at 3 Tesla Magnetic Resonance Imaging

    Directory of Open Access Journals (Sweden)

    Naghibi

    2016-09-01

    Full Text Available Background Magnetic resonance imaging (MRI of the wrist joint is a useful method in the diagnosis of triangular fibrocartilage complex (TFCC, ligaments and tendons, peripheral nerves, cartilage and carpal tunnel syndrome. However, the evaluation of these small anatomical structures is a topic of investigation. In some instances, the diagnostic indices of MRI in tears and other lesions of cartilage and ligamentous structures are relatively low, so the protocols should be optimized. Objectives In this study, we aim to compare new MRI protocols of 3D T2SPACE, PD BLADE and T2 BLADE with the conventional protocols, including T2 FSE, PD FSE, and T1 FSE in case of signal intensity. Patients and Methods Twenty patients with a history of wrist trauma or suspected wrist lesions were referred by orthopedic hand surgeons and enrolled into the study. All the protocols were carried out on all patients and the images were assessed quantitatively by measurement of signal to noise ratio (SNR and contrast to noise ratio (CNR. Then, these parameters were compared between different protocols. SPSS ver.18 was used for the statistical analyses. Results SNR of the cartilage, TFCC on 3D T2SPACE and T1 FSE was better than other sequences (P < 0.001. SNR of the bone on PD BLADE was significantly higher (P < 0.001 than that of conventional protocols. PD BLADE images showed significantly higher bone- cartilage CNR and bone- TFCC CNR (P < 0.001 to P < 0.001. CNR of cartilage-TFCC on T1 FSE was better than other sequences, but no significant statistical differences were seen. Conclusion High-resolution MR images of the wrist using 3D T2SPACE, PD BLADE and T2 BLADE were superior to those using conventional sequences quantitatively. High-SNR and CNR MR imaging with SPACE and BLADE would be a promising method to diagnose wrist lesions.

  17. Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5'-end 16S rRNA gene sequencing.

    Science.gov (United States)

    Wang, Tao; Kong, Fanrong; Chen, Sharon; Xiao, Meng; Sorrell, Tania; Wang, Xiaoyan; Wang, Shuo; Sintchenko, Vitali

    2011-01-01

    The identification of fastidious aerobic Actinomycetes such as Gordonia, Rhodococcus, and Tsukamurella has remained a challenge leading to clinically significant misclassifications. This study is intended to examine the feasibility of partial 5'-end 16S rRNA gene sequencing for the identification of Gordonia, Rhodococcus, and Tsukamurella, and defined potential reference sequences for species from each of these genera. The 16S rRNA gene sequence based identification algorithm for species identification was used and enhanced by aligning test sequences with reference sequences from the List of Prokaryotic Names with Standing in Nomenclature. Conventional PCR based 16S rRNA gene sequencing and the alignment of the isolate 16S rRNA gene sequence with reference sequences accurately identified 100% of clinical strains of aerobic Actinomycetes. While partial 16S rRNA gene sequences of reference type strains matched with the 16S rRNA gene sequences of 19 isolates in our data set, another 13 strains demonstrated a degree of polymorphism with a 1-4 bp difference in the regions of difference. 5'-end 606 bp 16S rRNA gene sequencing, coupled with the assignment of well defined reference sequences to clinically relevant species of bacteria, can be a useful strategy for improving the identification of clinically relevant aerobic Actinomycetes.

  18. Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

    Directory of Open Access Journals (Sweden)

    Karen Massel

    2016-10-01

    Full Text Available Nitrogen (N fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and mobilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum.

  19. Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

    Science.gov (United States)

    Massel, Karen; Campbell, Bradley C.; Mace, Emma S.; Tai, Shuaishuai; Tao, Yongfu; Worland, Belinda G.; Jordan, David R.; Botella, Jose R.; Godwin, Ian D.

    2016-01-01

    Nitrogen (N) fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum) is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and utilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT) genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR) genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum. PMID:27826302

  20. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  1. Pre-ejection period by radial artery tonometry supplements echo doppler findings during biventricular pacemaker optimization

    Directory of Open Access Journals (Sweden)

    Qamruddin Salima

    2011-07-01

    Full Text Available Abstract Background Biventricular (Biv pacemaker echo optimization has been shown to improve cardiac output however is not routinely used due to its complexity. We investigated the role of a simple method involving computerized pre-ejection time (PEP assessment by radial artery tonometry in guiding Biv pacemaker optimization. Methods Blinded echo and radial artery tonometry were performed simultaneously in 37 patients, age 69.1 ± 12.8 years, left ventricular (LV ejection fraction (EF 33 ± 10%, during Biv pacemaker optimization. Effect of optimization on echo derived velocity time integral (VTI, ejection time (ET, myocardial performance index (MPI, radial artery tonometry derived PEP and echo-radial artery tonometry derived PEP/VTI and PEP/ET indices was evaluated. Results Significant improvement post optimization was achieved in LV ET (286.9 ± 37.3 to 299 ± 34.6 ms, p Conclusion An acute shortening of PEP by radial artery tonometry occurs post Biv pacemaker optimization and correlates with improvement in hemodynamics by echo Doppler and may provide a cost-efficient approach to assist with Biv pacemaker echo optimization.

  2. Severe accident improvements for Carem-25 to arrest reactor vessel meltdown sequences

    Energy Technology Data Exchange (ETDEWEB)

    Poier Baez, L.E.; Nunez Mac Leod, J.E.; Baron, J.H. [Cuyo National University, Engineering Faculty, Mendoza (Argentina)

    2001-07-01

    Given an accident sequence, that leads to sustained uncovering of the core, the progression of core damage involves several complex phenomena. The progression of these phenomena can lead to a breach of the reactor vessel followed by the discharge of molten core materials to the containment. Advanced nuclear reactor designs, such as the CAREM reactor, include several improvements related to safety issues either enhancing the passive safety functions or allowing plant operators more time to undertake different management actions against radioactive releases to the environment. In the development of the nuclear power plant CAREM, the possibility of including a passive metallic in-vessel container in its design is being considered, to arrest the reactor pressure vessel meltdown sequence during a core damaging event, and thereof prevent its failure. The paper comprises the first analyses, via numerical simulation, for the conceptual design of such a container type; furthermore, the paper addresses simulation model characteristics helping to establish geometrical dimensions, materials and container compatibility with power plant engineering features. The paper also presents the first model developed to analyze the complex relocation phenomena in the core of CAREM during a severe accident sequence caused by a loss of coolant. The PC version of MELCOR 1.8.4 code has been used to predict the transient behavior of core parameters. MELCOR is a fully integrated relatively fast running code that models the progression of accidents in light water reactor power plants. This paper presents reactor variables behavior during the first hours of the event being studied, giving preliminary conclusions about the use and capability of a metallic in-vessel core catcher. (authors)

  3. Severe accident improvements for Carem-25 to arrest reactor vessel meltdown sequences

    Energy Technology Data Exchange (ETDEWEB)

    Poier Baez, L.E.; Nunez Mac Leod, J.E.; Baron, J.H. [Cuyo National University, Engineering Faculty, Mendoza (Argentina)

    2001-07-01

    Given an accident sequence, that leads to sustained uncovering of the core, the progression of core damage involves several complex phenomena. The progression of these phenomena can lead to a breach of the reactor vessel followed by the discharge of molten core materials to the containment. Advanced nuclear reactor designs, such as the CAREM reactor, include several improvements related to safety issues either enhancing the passive safety functions or allowing plant operators more time to undertake different management actions against radioactive releases to the environment. In the development of the nuclear power plant CAREM, the possibility of including a passive metallic in-vessel container in its design is being considered, to arrest the reactor pressure vessel meltdown sequence during a core damaging event, and thereof prevent its failure. The paper comprises the first analyses, via numerical simulation, for the conceptual design of such a container type; furthermore, the paper addresses simulation model characteristics helping to establish geometrical dimensions, materials and container compatibility with power plant engineering features. The paper also presents the first model developed to analyze the complex relocation phenomena in the core of CAREM during a severe accident sequence caused by a loss of coolant. The PC version of MELCOR 1.8.4 code has been used to predict the transient behavior of core parameters. MELCOR is a fully integrated relatively fast running code that models the progression of accidents in light water reactor power plants. This paper presents reactor variables behavior during the first hours of the event being studied, giving preliminary conclusions about the use and capability of a metallic in-vessel core catcher. (authors)

  4. Improving transcriptome assembly through error correction of high-throughput sequence reads.

    Science.gov (United States)

    Macmanes, Matthew D; Eisen, Michael B

    2013-01-01

    The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.

  5. Two-dimensional Nutation Echo Nuclear Quadrupole Resonance Spectroscopy

    Science.gov (United States)

    Harbison, Gerard S.; Slokenbergs, Andris

    1990-04-01

    We discuss two new two-dimensional nuclear quadrupole resonance experiments, both based on the principle of nutation spectroscopy, which can be used to determine the asymmetry parameter, and thus the full quadrupolar tensor, of spin-3/2 nuclei at zero applied magnetic field. The first experiment is a simple nutation pulse sequence in which the first time period (t1) is the duration of the radiofrequency exciting pulse; and the second (t2) is the normal free-precession of a quadrupolar nucleus at zero-field. After double Fourier-transformation, the result is a 2 D spectrum in which the first frequency dimension is the nutation spectrum for the quadrupolar nucleus at zero-field. For polycrystalline samples this sequence generates powder lineshapes; the position of the singularities, in these lineshapes can be used to determine the asymmetry parameters η in a very straightforward manner, η has previously only been obtainable using Zeeman perturbed NQR methods. The second sequence is the same nutation experiment with a spin-echo pulse added. The virtue of this refocussing pulse is that it allows acquisition of nutation spectra from samples with arbitrary inhomogeneous linewidth; thus, asymmetry parameters can be determined even where the quadrupolar resonance is wider than the bandwidth of the spectrometer. Experimental examples of 35Cl, 81Br and 63Cu nutation and nutation-echo spectra are presented.

  6. Mono-Exponential Fitting in T2-Relaxometry: Relevance of Offset and First Echo.

    Directory of Open Access Journals (Sweden)

    David Milford

    Full Text Available T2 relaxometry has become an important tool in quantitative MRI. Little focus has been put on the effect of the refocusing flip angle upon the offset parameter, which was introduced to account for a signal floor due to noise or to long T2 components. The aim of this study was to show that B1 imperfections contribute significantly to the offset. We further introduce a simple method to reduce the systematic error in T2 by discarding the first echo and using the offset fitting approach.Signal curves of T2 relaxometry were simulated based on extended phase graph theory and evaluated for 4 different methods (inclusion and exclusion of the first echo, while fitting with and without the offset. We further performed T2 relaxometry in a phantom at 9.4T magnetic resonance imaging scanner and used the same methods for post-processing as in the extended phase graph simulated data. Single spin echo sequences were used to determine the correct T2 time.The simulation data showed that the systematic error in T2 and the offset depends on the refocusing pulse, the echo spacing and the echo train length. The systematic error could be reduced by discarding the first echo. Further reduction of the systematic T2 error was reached by using the offset as fitting parameter. The phantom experiments confirmed these findings.The fitted offset parameter in T2 relaxometry is influenced by imperfect refocusing pulses. Using the offset as a fitting parameter and discarding the first echo is a fast and easy method to minimize the error in T2, particularly for low to intermediate echo train length.

  7. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

    DEFF Research Database (Denmark)

    Li, Ying-hui; Zhao, Shan-cen; Ma, Jian-xin

    2013-01-01

    BACKGROUND:Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re......-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.RESULTS:A total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found...... that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits...

  8. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.

    Science.gov (United States)

    Varshney, Rajeev K; Song, Chi; Saxena, Rachit K; Azam, Sarwar; Yu, Sheng; Sharpe, Andrew G; Cannon, Steven; Baek, Jongmin; Rosen, Benjamin D; Tar'an, Bunyamin; Millan, Teresa; Zhang, Xudong; Ramsay, Larissa D; Iwata, Aiko; Wang, Ying; Nelson, William; Farmer, Andrew D; Gaur, Pooran M; Soderlund, Carol; Penmetsa, R Varma; Xu, Chunyan; Bharti, Arvind K; He, Weiming; Winter, Peter; Zhao, Shancen; Hane, James K; Carrasquilla-Garcia, Noelia; Condie, Janet A; Upadhyaya, Hari D; Luo, Ming-Cheng; Thudi, Mahendar; Gowda, C L L; Singh, Narendra P; Lichtenzveig, Judith; Gali, Krishna K; Rubio, Josefa; Nadarajan, N; Dolezel, Jaroslav; Bansal, Kailash C; Xu, Xun; Edwards, David; Zhang, Gengyun; Kahl, Guenter; Gil, Juan; Singh, Karam B; Datta, Swapan K; Jackson, Scott A; Wang, Jun; Cook, Douglas R

    2013-03-01

    Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

  9. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

    DEFF Research Database (Denmark)

    Otero, José Manuel; Vongsangnak, Wanwipa; Asadollahi, Mohammadali;

    2010-01-01

    BACKGROUND: The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where s...... that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at http://www.sysbio.se/cenpk.......BACKGROUND: The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where...... selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering. RESULTS: In this work we...

  10. EChO - Exoplanet Characterisation Observatory

    CERN Document Server

    Tinetti, G; Henning, T; Meyer, M; Micela, G; Ribas, I; Stam, D; Swain, M; Krause, O; Ollivier, M; Pace, E; Swinyard, B; Aylward, A; van Boekel, R; Coradini, A; Encrenaz, T; Snellen, I; Zapatero-Osorio, M R; Bouwman, J; Cho, J Y-K; Foresto, V Coudé du; Guillot, T; Lopez-Morales, M; Mueller-Wodarg, I; Palle, E; Selsis, F; Sozzetti, A; Ade, P A R; Achilleos, N; Adriani, A; Agnor, C B; Afonso, C; Prieto, C Allende; Bakos, G; Barber, R J; Barlow, M; Bernath, P; Bezard, B; Bordé, P; Brown, L R; Cassan, A; Cavarroc, C; Ciaravella, A; Cockell, C O U; Coustenis, A; Danielski, C; Decin, L; De Kok, R; Demangeon, O; Deroo, P; Doel, P; Drossart, P; Fletcher, L N; Focardi, M; Forget, F; Fossey, S; Fouqué, P; Frith, J; Galand, M; Gaulme, P; Hernández, J I González; Grasset, O; Grassi, D; Grenfell, J L; Griffin, M J; Griffith, C A; Grözinger, U; Guedel, M; Guio, P; Hainaut, O; Hargreaves, R; Hauschildt, P H; Heng, K; Heyrovsky, D; Hueso, R; Irwin, P; Kaltenegger, L; Kervella, P; Kipping, D; Koskinen, T T; Kovács, G; La Barbera, A; Lammer, H; Lellouch, E; Leto, G; Morales, M Lopez; Valverde, M A Lopez; Lopez-Puertas, M; Lovis, C; Maggio, A; Maillard, J P; Prado, J Maldonado; Marquette, J B; Martin-Torres, F J; Maxted, P; Miller, S; Molinari, S; Montes, D; Moro-Martin, A; Moses, J I; Mousis, O; Tuong, N Nguyen; Nelson, R; Orton, G S; Pantin, E; Pascale, E; Pezzuto, S; Pinfield, D; Poretti, E; Prinja, R; Prisinzano, L; Rees, J M; Reiners, A; Samuel, B; Sanchez-Lavega, A; Forcada, J Sanz; Sasselov, D; Savini, G; Sicardy, B; Smith, A; Stixrude, L; Strazzulla, G; Tennyson, J; Tessenyi, M; Vasisht, G; Vinatier, S; Viti, S; Waldmann, I; White, G J; Widemann, T; Wordsworth, R; Yelle, R; Yung, Y; Yurchenko, S N

    2011-01-01

    A dedicated mission to investigate exoplanetary atmospheres represents a major milestone in our quest to understand our place in the universe by placing our Solar System in context and by addressing the suitability of planets for the presence of life. EChO -the Exoplanet Characterisation Observatory- is a mission concept specifically geared for this purpose. EChO will provide simultaneous, multi-wavelength spectroscopic observations on a stable platform that will allow very long exposures. EChO will build on observations by Hubble, Spitzer and groundbased telescopes, which discovered the first molecules and atoms in exoplanetary atmospheres. EChO will simultaneously observe a broad enough spectral region -from the visible to the mid-IR- to constrain from one single spectrum the temperature structure of the atmosphere and the abundances of the major molecular species. The spectral range and resolution are tailored to separate bands belonging to up to 30 molecules to retrieve the composition and temperature str...

  11. Geometric spin echo under zero field

    Science.gov (United States)

    Sekiguchi, Yuhei; Komura, Yusuke; Mishima, Shota; Tanaka, Touta; Niikura, Naeko; Kosaka, Hideo

    2016-01-01

    Spin echo is a fundamental tool for quantum registers and biomedical imaging. It is believed that a strong magnetic field is needed for the spin echo to provide long memory and high resolution, since a degenerate spin cannot be controlled or addressed under a zero magnetic field. While a degenerate spin is never subject to dynamic control, it is still subject to geometric control. Here we show the spin echo of a degenerate spin subsystem, which is geometrically controlled via a mediating state split by the crystal field, in a nitrogen vacancy centre in diamond. The demonstration reveals that the degenerate spin is protected by inherent symmetry breaking called zero-field splitting. The geometric spin echo under zero field provides an ideal way to maintain the coherence without any dynamics, thus opening the way to pseudo-static quantum random access memory and non-invasive biosensors. PMID:27193936

  12. Air Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    The dashboards found on the Enforcement and Compliance History Online (ECHO) website are specialized to track both facility and agency performance as they relate to compliance with and enforcement of environmental standards under the Clean Air Act (CAA).

  13. Echo State Condition at the Critical Point

    Directory of Open Access Journals (Sweden)

    Norbert Michael Mayer

    2016-12-01

    Full Text Available Recurrent networks with transfer functions that fulfil the Lipschitz continuity with K = 1 may be echo state networks if certain limitations on the recurrent connectivity are applied. It has been shown that it is sufficient if the largest singular value of the recurrent connectivity is smaller than 1. The main achievement of this paper is a proof under which conditions the network is an echo state network even if the largest singular value is one. It turns out that in this critical case the exact shape of the transfer function plays a decisive role in determining whether the network still fulfills the echo state condition. In addition, several examples with one-neuron networks are outlined to illustrate effects of critical connectivity. Moreover, within the manuscript a mathematical definition for a critical echo state network is suggested.

  14. Time Delay Estimation Algoritms for Echo Cancellation

    Directory of Open Access Journals (Sweden)

    Kirill Sakhnov

    2011-01-01

    Full Text Available The following case study describes how to eliminate echo in a VoIP network using delay estimation algorithms. It is known that echo with long transmission delays becomes more noticeable to users. Thus, time delay estimation, as a part of echo cancellation, is an important topic during transmission of voice signals over packetswitching telecommunication systems. An echo delay problem associated with IP-based transport networks is discussed in the following text. The paper introduces the comparative study of time delay estimation algorithm, used for estimation of the true time delay between two speech signals. Experimental results of MATLab simulations that describe the performance of several methods based on cross-correlation, normalized crosscorrelation and generalized cross-correlation are also presented in the paper.

  15. Hazardous Waste Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    The dashboards found on the Enforcement and Compliance History Online (ECHO) website are specialized to track both facility and agency performance as they relate to compliance with and enforcement of environmental standards under the Resource Conservation and Recovery Act (RCRA).

  16. Enforcement and Compliance History Online (ECHO) Facilities

    Data.gov (United States)

    U.S. Environmental Protection Agency — ECHO provides integrated compliance and enforcement information for about 800,000 regulated facilities nationwide. Its features range from simple to advanced,...

  17. Water Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    The dashboards found on the Enforcement and Compliance History Online (ECHO) website are specialized to track both facility and agency performance as they relate to compliance with and enforcement of environmental standards under the Clean Water Act (CWA).

  18. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

    Directory of Open Access Journals (Sweden)

    Asadollahi Mohammad A

    2010-12-01

    Full Text Available Abstract Background The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering. Results In this work we performed whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs between Saccharomyces cerevisiae strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the Saccharomyces Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c. Considering only metabolic genes (782 of 5,596 annotated genes, a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being nonsynonymous (e.g., encoding amino acid modifications. Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (GAL1, GAL10 and ergosterol biosynthetic pathway (ERG8, ERG9. Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that

  19. Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement

    Science.gov (United States)

    Sun, Yongwei; Li, Jingying; Xia, Lanqin

    2016-01-01

    Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes’ encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT) that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired “safe” harbor in a predefined manner. The emergence of three programmable SSNs, such as zinc finger nucleases, transcriptional activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential mechanisms underlying HDR events in

  20. Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement.

    Science.gov (United States)

    Sun, Yongwei; Li, Jingying; Xia, Lanqin

    2016-01-01

    Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes' encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT) that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired "safe" harbor in a predefined manner. The emergence of three programmable SSNs, such as zinc finger nucleases, transcriptional activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential mechanisms underlying HDR events in plant

  1. Precise genome modification via sequence-specific nucleases-mediated gene targeting for crop improvement

    Directory of Open Access Journals (Sweden)

    Yongwei Sun

    2016-12-01

    Full Text Available Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks (DSBs by sequence-specific nucleases (SSNs to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ or homology-directed repair (HDR. While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes’ encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired ‘safe’ harbor in a predefined manner. The emergence of three programmable SSNs such as zinc finger nucleases (ZFNs, transcriptional activator-like effector nucleases (TALENs, and the clustered regularly interspaced short palindromic repeat (CRISPR/CRISPR-associated protein 9 (Cas9 systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential

  2. Experimental study of fast and ultrafast T2-weighted imaging sequences using AMI-25 superparamagnetic iron oxide (SPIO.

    Directory of Open Access Journals (Sweden)

    Kurokawa H

    2001-02-01

    Full Text Available The objective of this study was to evaluate fast and ultrafast T2-weighted images (T2WI, including echo planar imaging (EPI, using an AMI-25 agar phantom. Image quality for conventional spin echo (CSE and turbo spin echo (TSE was almost equivalent. In high-resolution TSE, image quality was highest due to the use of a 512 x 256 matrix. Half-Fourier single-shot turbo SE (HASTE was associated with blurring of images, and turbo-gradient SE (TGSE showed a deterioration of image quality. EPI also suffered from poor image quality because this method is very sensitive to magnetic field inhomogeneity. CSE showed good signal-to-noise ratio (S/N and contrast ratio (CR, but also required the longest imaging times. Among the TSE sequences, TSE with a short echo train length (ETL was superior in terms of S/N. The CR of EPI and fast low angle shot (FLASH images were improved in proportion to the effective echo time (TE. At present, TSE is inferior to CSE in terms of S/N and CR. However, taking into consideration scanning time, TSE with a short ETL is thought to be suitable for routine examinations. Effective TE is an important factor in gradient echo (GRE examinations.

  3. NovoPen Echo® insulin delivery device

    Directory of Open Access Journals (Sweden)

    Hyllested-Winge J

    2016-01-01

    Full Text Available Jacob Hyllested-Winge,1 Thomas Sparre,2 Line Kynemund Pedersen2 1Novo Nordisk Pharma Ltd, Tokyo, Japan; 2Novo Nordisk A/S, Søborg, Denmark Abstract: The introduction of insulin pen devices has provided easier, well-tolerated, and more convenient treatment regimens for patients with diabetes mellitus. When compared with vial and syringe regimens, insulin pens offer a greater clinical efficacy, improved quality of life, and increased dosing accuracy, particularly at low doses. The portable and discreet nature of pen devices reduces the burden on the patient, facilitates adherence, and subsequently contributes to the improvement in glycemic control. NovoPen Echo® is one of the latest members of the NovoPen® family that has been specifically designed for the pediatric population and is the first to combine half-unit increment (=0.5 U of insulin dosing with a simple memory function. The half-unit increment dosing amendments and accurate injection of 0.5 U of insulin are particularly beneficial for children (and insulin-sensitive adults/elders, who often require small insulin doses. The memory function can be used to record the time and amount of the last dose, reducing the fear of double dosing or missing a dose. The memory function also provides parents with extra confidence and security that their child is taking insulin at the correct doses and times. NovoPen Echo is a lightweight, durable insulin delivery pen; it is available in two different colors, which may help to distinguish between different types of insulin, providing more confidence for both users and caregivers. Studies have demonstrated a high level of patient satisfaction, with 80% of users preferring NovoPen Echo to other pediatric insulin pens. Keywords: NovoPen Echo®, memory function, half-unit increment dosing, adherence, children, adolescents 

  4. Air Pollutant Report | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  5. Air Pollutant Report Help | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  6. Drinking Water Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  7. Analyze Trends: State Hazardous Waste Dashboard | ECHO ...

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  8. Analyze Trends: Pesticide Dashboard | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  9. Water Pollution Search | ECHO | US EPA

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  10. Criminal Enforcement Case Report Data Dictionary | ECHO ...

    Science.gov (United States)

    ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

  11. The Rhythms of Echo. Variations on Repetition

    Directory of Open Access Journals (Sweden)

    Rosa María Aradra Sánchez

    2015-04-01

    Full Text Available This paper presents a study on the echo as metric and rhetorical procedure. It makes a brief tour through some of the poetic manifestations of echo in the Spanish literary tradition, and a brief tour through the attention that metric theory has paid to this phenomenon. Then it stops at the possibilities that rhetoric offers for its analysis from the generic approach of the discursive repetition phenomena.

  12. Short echo time proton spectroscopy of the brain in healthy volunteers using an insert gradient head coil

    DEFF Research Database (Denmark)

    Gideon, P; Danielsen, E R; Schneider, M;

    1995-01-01

    An insert gradient head coil with built-in X, Y, and Z gradients was used for localized proton spectroscopy in the brain of healthy volunteers, using short echo time stimulated echo acquisition mode (STEAM) sequences. Volume of interest size was 3.4 ml, repetition time was 6.0 s, and echo times...... were 10 and 20 ms, respectively. Good quality proton spectra with practically no eddy current artefacts were acquired allowing observation of strongly coupled compounds, and compounds with short T2 relaxation times. The gradient head coil thus permits further studies of compounds such as glutamine...

  13. Short echo time proton spectroscopy of the brain in healthy volunteers using an insert gradient head coil

    DEFF Research Database (Denmark)

    Gideon, P; Danielsen, E R; Schneider, M

    1995-01-01

    An insert gradient head coil with built-in X, Y, and Z gradients was used for localized proton spectroscopy in the brain of healthy volunteers, using short echo time stimulated echo acquisition mode (STEAM) sequences. Volume of interest size was 3.4 ml, repetition time was 6.0 s, and echo times w....../glutamate and myo-inositols. These compounds were more prominent within grey matter than within white matter. Rough estimations of metabolite concentrations using water as an internal standard were in good agreement with previous reports....

  14. MAG-PGSTE: a new STE-based PGSE NMR sequence for the determination of diffusion in magnetically inhomogeneous samples.

    Science.gov (United States)

    Zheng, Gang; Price, William S

    2008-11-01

    A new stimulated echo based pulsed gradient spin-echo sequence, MAG-PGSTE, has been developed for the determination of self-diffusion in magnetically inhomogeneous samples. The sequence was tested on two glass bead samples (i.e., 212-300 and Thesis, Universität Leipzig, 2003, P.Z. Sun, Nuclear Magnetic Resonance Microscopy and Diffusion, Ph.D. Thesis, Massachusetts Institute of Technology, 2003] sequence and Cotts 13-interval [R.M. Cotts, M.J.R. Hoch, T. Sun, J.T. Marker, Pulsed field gradient stimulated echo methods for improved NMR diffusion measurements in heterogeneous systems, J. Magn. Reson. 83 (1989) 252-266] sequence using both glass bead samples. The MAG-PGSTE and MAGSTE (or MPFG) sequences outperformed the Cotts 13-interval sequence in the measurement of diffusion coefficients; more interestingly, for the sample with higher background gradients (i.e., the sample), the MAG-PGSTE sequence provided higher signal-to-noise ratios and thus better diffusion measurements than the MAGSTE and Cotts 13-interval sequences. In addition, the MAG-PGSTE sequence provided good characterization of the surface-to-volume ratio for the glass bead samples.

  15. X-ray echo spectroscopy (Conference Presentation)

    Science.gov (United States)

    Shvyd'ko, Yuri V.

    2016-09-01

    X-ray echo spectroscopy, a counterpart of neutron spin-echo, was recently introduced [1] to overcome limitations in spectral resolution and weak signals of the traditional inelastic x-ray scattering (IXS) probes. An image of a point-like x-ray source is defocused by a dispersing system comprised of asymmetrically cut specially arranged Bragg diffracting crystals. The defocused image is refocused into a point (echo) in a time-reversal dispersing system. If the defocused beam is inelastically scattered from a sample, the echo signal acquires a spatial distribution, which is a map of the inelastic scattering spectrum. The spectral resolution of the echo spectroscopy does not rely on the monochromaticity of the x-rays, ensuring strong signals along with a very high spectral resolution. Particular schemes of x-ray echo spectrometers for 0.1-meV and 0.02-meV ultra-high-resolution IXS applications (resolving power > 10^8) with broadband 5-13 meV dispersing systems will be presented featuring more than 1000-fold signal enhancement. The technique is general, applicable in different photon frequency domains. [1.] Yu. Shvyd'ko, Phys. Rev. Lett. 116, accepted (2016), arXiv:1511.01526.

  16. On the Search for Quasar Light Echoes

    CERN Document Server

    Visbal, Eli

    2007-01-01

    The UV radiation from a quasar leaves a characteristic pattern in the distribution of ionized hydrogen throughout the surrounding space. This pattern or light echo propagates through the intergalactic medium at the speed of light, and can be observed by its imprint on the Ly-alpha forest spectra of background sources. As the echo persists after the quasar has switched off, it offers the possibility of searching for dead quasars, and constraining their luminosities and lifetimes. We outline a technique to search for and characterize these light echoes. To test the method, we create artificial Ly-alpha forest spectra from cosmological simulations at z=3, apply light echoes and search for them. We show how the simulations can also be used to quantify the significance level of any detection. We find that light echoes from the brightest quasars could be found in observational data. With absorption line spectra of 100 redshift z~3-3.5 quasars or galaxies in a 1 square degree area, we expect that ~10 echoes from qua...

  17. Echoes from a Dying Star

    Science.gov (United States)

    Kohler, Susanna

    2017-06-01

    When a passing star is torn apart by a supermassive black hole, it emits a flare of X-ray, ultraviolet, and optical light. What can we learn from the infrared echo of a violent disruption like this one?Stellar DestructionOptical (black triangles) and infrared (blue circles and red squares) observations of F010042237. Day 0 marks the day the optical emission peaked. The infrared emission rises steadily through the end of the data. [Dou et al. 2017]Tidal disruption events occur when a star passes within the tidal radius of a supermassive black hole. After tidal forces pull the star apart, much of the stellar matter falls onto the black hole, radiating briefly in X-ray, ultraviolet and optical as it accretes. This signature rise and gradual fall of emission has allowed us to detect dozens of tidal disruption events thus far.One of the recently discovered candidate events is a little puzzling. Not only does the candidate in ultraluminous infrared galaxy F010042237 have an unusual host most disruptions occur in galaxies that are no longer star-forming, in contrast to this one but its optical light curve also shows an unusually long decay time.Now mid-infrared observations of this event have beenpresented by a team of scientists led by Liming Dou (Guangzhou University and Department of Education, Guangdong Province, China), revealing why this disruption is behaving unusually.Schematic of a convex dusty ring (red bows) that absorbs UV photons and re-emits in the infrared. It simultaneously scatters UV and optical photons into our line of sight. The dashed lines illustrate the delays at lags of 60 days, 1, 2, 3, 4, and 5 years. [Adapted from Dou et al. 2017]A Dusty Solution?The optical flare from F010042237s nucleus peaked in 2010, so Dou and collaborators obtained archival mid-infrared data from the WISE and NEOWISE missions from 2010 to 2016. The data show that the galaxy is quiescent in mid-infrared in 2010 but in data from three years later, the infrared emission has

  18. Analysis of Partial Volume Effects on Arterial Input Functions Using Gradient Echo: A Simulation Study

    DEFF Research Database (Denmark)

    Kjølby, Birgitte Fuglsang; Mikkelsen, Irene Klærke; Pedersen, Michael

    2009-01-01

    perfusion metrics was investigated for the gradient echo pulse sequence at 1.5 T and 3.0 T. It is shown that the tissue contribution broadens and introduces fluctuations in the AIF. Furthermore, partial volume effects bias perfusion metrics in a nonlinear fashion, compromising quantitative perfusion...

  19. Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis

    Directory of Open Access Journals (Sweden)

    Lacombe Didier

    2011-05-01

    Full Text Available Abstract Background Usher syndrome (USH combines sensorineural deafness with blindness. It is inherited in an autosomal recessive mode. Early diagnosis is critical for adapted educational and patient management choices, and for genetic counseling. To date, nine causative genes have been identified for the three clinical subtypes (USH1, USH2 and USH3. Current diagnostic strategies make use of a genotyping microarray that is based on the previously reported mutations. The purpose of this study was to design a more accurate molecular diagnosis tool. Methods We sequenced the 366 coding exons and flanking regions of the nine known USH genes, in 54 USH patients (27 USH1, 21 USH2 and 6 USH3. Results Biallelic mutations were detected in 39 patients (72% and monoallelic mutations in an additional 10 patients (18.5%. In addition to biallelic mutations in one of the USH genes, presumably pathogenic mutations in another USH gene were detected in seven patients (13%, and another patient carried monoallelic mutations in three different USH genes. Notably, none of the USH3 patients carried detectable mutations in the only known USH3 gene, whereas they all carried mutations in USH2 genes. Most importantly, the currently used microarray would have detected only 30 of the 81 different mutations that we found, of which 39 (48% were novel. Conclusions Based on these results, complete exon sequencing of the currently known USH genes stands as a definite improvement for molecular diagnosis of this disease, which is of utmost importance in the perspective of gene therapy.

  20. Normal range of hepatic fat fraction on dual- and triple-echo fat quantification MR in children.

    Science.gov (United States)

    Shin, Hyun Joo; Kim, Hyun Gi; Kim, Myung-Joon; Koh, Hong; Kim, Ha Yan; Roh, Yun Ho; Lee, Mi-Jung

    2015-01-01

    To evaluate hepatic fat fraction on dual- and triple-echo gradient-recalled echo MRI sequences in healthy children. We retrospectively reviewed the records of children in a medical check-up clinic from May 2012 to November 2013. We excluded children with abnormal laboratory findings or those who were overweight. Hepatic fat fraction was measured on dual- and triple-echo sequences using 3T MRI. We compared fat fractions using the Wilcoxon signed rank test and the Bland-Altman 95% limits of agreement. The correlation between fat fractions and clinical and laboratory findings was evaluated using Spearman's correlation test, and the cut-off values of fat fractions for diagnosing fatty liver were obtained from reference intervals. In 54 children (M:F = 26:28; 5-15 years; mean 9 years), the dual fat fraction (0.1-8.0%; median 1.6%) was not different from the triple fat fraction (0.4-6.5%; median 2.7%) (p = 0.010). The dual- and triple-echo fat fractions showed good agreement using a Bland-Altman plot (-0.6 ± 2.8%). Eight children (14.8%) on dual-echo sequences and six (11.1%) on triple-echo sequences had greater than 5% fat fraction. From these children, six out of eight children on dual-echo sequences and four out of six children on triple-echo sequences had a 5-6% hepatic fat fraction. When using a cut-off value of a 6% fat fraction derived from a reference interval, only 3.7% of children were diagnosed with fatty liver. There was no significant correlation between clinical and laboratory findings with dual and triple-echo fat fractions. Dual fat fraction was not different from triple fat fraction. We suggest a cut-off value of a 6% fat fraction is more appropriate for diagnosing fatty liver on both dual- and triple-echo sequences in children.

  1. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

    DEFF Research Database (Denmark)

    Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.

    2016-01-01

    insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

  2. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  3. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    Directory of Open Access Journals (Sweden)

    von Reumont Björn M

    2010-03-01

    Full Text Available Abstract Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment

  4. Fast method of NMR imaging based on trains of spin echoes

    Energy Technology Data Exchange (ETDEWEB)

    Hennel, F.

    1993-12-31

    A theoretical introduction to Fourier NMR imaging and a discussion of fast methods are presented. Then an application of the method of echo-planar imaging (EPI) with spin echoes in a micro-imaging system is described together with introduced modifications of the sequence. A new technique for the measurement of flow profiles in liquids which results from a modification of x-pulsed EPI is presented. The development of new software for a NMR micro-imaging system is described, too. 51 refs, 29 refs.

  5. Expanding Health Care Access Through Education: Dissemination and Implementation of the ECHO Model.

    Science.gov (United States)

    Katzman, Joanna G; Galloway, Kevin; Olivas, Cynthia; McCoy-Stafford, Kimberly; Duhigg, Daniel; Comerci, George; Kalishman, Summers; Buckenmaier, Chester C; McGhee, Laura; Joltes, Kristin; Bradford, Andrea; Shelley, Brian; Hernandez, Jessica; Arora, Sanjeev

    2016-03-01

    Project ECHO (Extension for Community Healthcare Outcomes) is an evidence-based model that provides high-quality medical education for common and complex diseases through telementoring and comanagement of patients with primary care clinicians. In a one to many knowledge network, the ECHO model helps to bridge the gap between primary care clinicians and specialists by enhancing the knowledge, skills, confidence, and practice of primary care clinicians in their local communities. As a result, patients in rural and urban underserved areas are able to receive best practice care without long waits or having to travel long distances. The ECHO model has been replicated in 43 university hubs in the United States and five other countries. A new replication tool was developed by the Project ECHO Pain team and U.S. Army Medical Command to ensure a high-fidelity replication of the model. The adoption of the tool led to successful replication of ECHO in the Army Pain initiative. This replication tool has the potential to improve the fidelity of ECHO replication efforts around the world.

  6. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

    Science.gov (United States)

    Frank, J A; Pan, Y; Tooming-Klunderud, A; Eijsink, V G H; McHardy, A C; Nederbragt, A J; Pope, P B

    2016-05-09

    DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.

  7. Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

    Directory of Open Access Journals (Sweden)

    Dybowski J Nikolaj

    2011-11-01

    Full Text Available Abstract Background Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. Results We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. Conclusions Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.

  8. 127I NMR study of quadrupolar echoes in KI

    Science.gov (United States)

    Lee, Nelson; Sanctuary, B. C.; Halstead, T. K.

    Potassium iodide (K 121I), like KBr and many other alkali halide solids, has cubic symmetry. Distortion of this cubic symmetry in single crystals of KI creates electric field gradients of sufficient strength for the quadrupolar interactions to dominate the dynamics of the system. Simple one-, two-, and three-pulse sequences applied to such crystals permit the observation, in the time domain, of the solid- or quadrupolar-echo phenomenon for spin I = {5}/{2}( 127I) . Using the multipole approach to interpret the experimental responses of three-pulse sequences, the characteristic relaxation behavior of the first-, second-, third-, and fifth-rank zero- and multiquantum polarizations are determined. The experimental determination of distinct relaxation times for the higher rank polarizations in both KI and KBr ( I = {3}/{2}) lends credibility to the concept of the multipoles as physical quantities.

  9. Nonlinear echoes and Landau damping with insufficient regularity

    CERN Document Server

    Bedrossian, Jacob

    2016-01-01

    We prove that the theorem of Mouhot and Villani on Landau damping near equilibrium for the Vlasov-Poisson equations on $\\mathbb T \\times \\mathbb R$ cannot, in general, be extended to Sobolev spaces. This is demonstrated by constructing a sequence of homogeneous background distributions and arbitrarily small perturbations in $H^s$ which deviate arbitrarily far from free transport for long times (in a sense to be made precise). The density experiences a sequence of nonlinear oscillations that damp at a rate which is arbitrarily slow compared to the predictions of the linearized Vlasov equations. The nonlinear instability is due to the repeated re-excitation of a resonance known as a plasma echo. The results hold for a specific, small background distribution, but include both electrostatic and gravitational interactions.

  10. MRI appearances of the asymptomatic patellar tendon on gradient echo imaging

    Energy Technology Data Exchange (ETDEWEB)

    Reiff, D.B. [Dept. of Diagnostic Radiology, St. George`s Hospital, London (United Kingdom); Heenan, S.D. [Dept. of Diagnostic Radiology, St. George`s Hospital, London (United Kingdom); Heron, C.W. [Dept. of Diagnostic Radiology, St. George`s Hospital, London (United Kingdom)

    1995-02-01

    Thickening of the patellar tendon and foci of increased signal intensity have been described as characteristic features of ``jumper`s knee`` (chronic patellar tendinitis) on magnetic resonance imaging (MRI). It was our impression that such appearances may be seen in the patellar tendons of patients without symptoms referable to the anterior part of the knee when using gradient echo images. The appearances of the asymptomatic patellar tendon on three-dimensional gradient echo sequences were studied by retrospectively reviewing the images of 60 patients, none of whom had symptoms related to the anterior part of the knee. The anteroposterior width of the patellar tendon was measured at three levels (superior, middle and inferior) on the central sagittal image of a gradient echo sequence. The relative signal intensities at the same levels were recorded. In 97% of subjects the superior part of the tendon was wider than the midpoint, and in 97% the inferior part was wider than the midpoint. The range of widths was wide, and there was no significant difference between sexes. Focal increased signal intensity in the superior part was shown in 75%, and in the inferior part in 43%. The asymptomatic patellar tendon shows uniform thickness throughout most of its length, but there are focal expansions at the proximal and distal ends. It usually demonstrates low signal on MRI, but may contain foci of increased signal intensity at either or both ends when imaged on gradient-echo sequences. (orig.)

  11. Multi-shot turbo spin-echo for 3D vascular space occupancy imaging.

    Science.gov (United States)

    Cretti, Fabiola R; Summers, Paul E; Porro, Carlo A

    2013-07-01

    Vascular space occupancy (VASO) is a magnetic resonance imaging technique sensitive to cerebral blood volume, and is a potential alternative to the blood oxygenation level dependent (BOLD) sensitive technique as a basis for functional mapping of the neurovascular response to a task. Many implementations of VASO have made use of echo-planar imaging strategies that allow rapid acquisition, but risk introducing potentially confounding BOLD effects. Recently, multi-slice and 3D VASO techniques have been implemented to increase the imaging volume beyond the single slice of early reports. These techniques usually rely, however, on advanced scanner software or hardware not yet available in many centers. In the present study, we have implemented a short-echo time, multi-shot 3D Turbo Spin-Echo (TSE) VASO sequence that provided 8-slice coverage on a routine clinical scanner. The proposed VASO sequence was tested in assessing the response of the human motor cortex during a block design finger tapping task in 10 healthy subjects. Significant VASO responses, inversely correlated with the task, were found at both individual and group level. The location and extent of VASO responses were in close correspondence to those observed using a conventional BOLD acquisition in the same subjects. Although the spatial coverage and temporal resolution achieved were limited, robust and consistent VASO responses were observed. The use of a susceptibility insensitive volumetric TSE VASO sequence may have advantages in locations where conventional BOLD and echo-planar based VASO imaging is compromised.

  12. Noise reduction in multiple-echo data sets using singular value decomposition.

    Science.gov (United States)

    Bydder, Mark; Du, Jiang

    2006-09-01

    A method is described for denoising multiple-echo data sets using singular value decomposition (SVD). Images are acquired using a multiple gradient- or spin-echo sequence, and the variation of the signal with echo time (TE) in all pixels is subjected to SVD analysis to determine the components of the signal variation. The least significant components are associated with small singular values and tend to characterize the noise variation. Applying a "minimum variance" filter to the singular values suppresses the noise components in a way that optimally approximates the underlying noise-free images. The result is a reduction in noise in the individual TE images with minimal degradation of the spatial resolution and contrast. Phantom and in vivo results are presented.

  13. Transient Loschmidt echo in quenched Ising chains

    Science.gov (United States)

    Lupo, Carla; Schiró, Marco

    2016-07-01

    We study the response to sudden local perturbations of highly excited quantum Ising spin chains. The key quantity encoding this response is the overlap between time-dependent wave functions, which we write as a transient Loschmidt Echo. Its asymptotics at long time differences contain crucial information about the structure of the highly excited nonequilibrium environment induced by the quench. We compute the echo perturbatively for a weak local quench but for arbitrarily large global quench, using a cumulant expansion. Our perturbative results suggest that the echo decays exponentially, rather than power law as in the low-energy orthogonality catastrophe, a further example of quench-induced decoherence already found in the case of quenched Luttinger liquids. The emerging decoherence scale is set by the strength of the local potential and the bulk excitation energy.

  14. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

    Science.gov (United States)

    Liu, Sanzhen; Zheng, Jun; Migeon, Pierre; Ren, Jie; Hu, Ying; He, Cheng; Liu, Hongjun; Fu, Junjie; White, Frank F.; Toomajian, Christopher; Wang, Guoying

    2017-01-01

    The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement. PMID:28186206

  15. Imaging of the Achilles tendon in spondyloarthritis: a comparison of ultrasound and conventional, short and ultrashort echo time MRI with and without intravenous contrast

    Energy Technology Data Exchange (ETDEWEB)

    Hodgson, R.J.; Emery, P. [University of Leeds, Chapel Allerton Hospital, Leeds Musculoskeletal Biomedical Research Centre, Leeds (United Kingdom); Grainger, A.J.; O' Connor, P.J.; Evans, R. [Chapel Allerton Hospital, Leeds Musculoskeletal Biomedical Research Centre, Leeds (United Kingdom); Coates, L.; Marzo-Ortega, H.; Helliwell, P.; McGonagle, D. [University of Leeds, Leeds Institute for Molecular Medicine, Leeds (United Kingdom); Robson, M.D. [University of Oxford, Oxford Centre for Clinical Magnetic Resonance Research, Oxford (United Kingdom)

    2011-06-15

    To compare conventional MRI, ultrashort echo time MRI and ultrasound for assessing the extent of tendon abnormalities in spondyloarthritis. 25 patients with spondyloarthritis and Achilles symptoms were studied with MRI and ultrasound. MR images of the Achilles tendon were acquired using T1-weighted spin echo, gradient echo and ultrashort echo time (UTE) sequences with echo times (TE) between 0.07 and 16 ms, before and after intravenous contrast medium. Greyscale and power Doppler ultrasound were also performed. The craniocaudal extent of imaging abnormalities measured by a consultant musculoskeletal radiologist was compared between the different techniques. Abnormalities were most extensive on spoiled gradient echo images with TE=2 ms. Contrast enhancement after intravenous gadolinium was greatest on the UTE images (TE=0.07 ms). Fewer abnormalities were demonstrated using unenhanced UTE. Abnormalities were more extensive on MRI than ultrasound. Contrast enhancement was more extensive than power Doppler signal. 3D spoiled gradient echo images with an echo time of 2 ms demonstrate more extensive tendon abnormalities than the other techniques in spondyloarthritis. Abnormalities of vascularity are best demonstrated on enhanced ultrashort echo time images. (orig.)

  16. Improving ESL Writing Using an Online Formulaic Sequence Word-Combination Checker

    Science.gov (United States)

    Grami, G. M. A.; Alkazemi, B. Y.

    2016-01-01

    Writing correct English sentences can be challenging. Furthermore, writing correct formulaic sequences can be especially difficult because accepted combinations do not follow clear rules governing which words appear together in a sequence. One solution is to provide examples of correct usage accompanied by statistical feedback from web-based…

  17. How can dolphins recognize fish according to their echoes? A statistical analysis of fish echoes.

    Directory of Open Access Journals (Sweden)

    Yossi Yovel

    Full Text Available Echo-based object classification is a fundamental task of animals that use a biosonar system. Dolphins and porpoises should be able to rely on echoes to discriminate a predator from a prey or to select a desired prey from an undesired object. Many studies have shown that dolphins and porpoises can discriminate between objects according to their echoes. All of these studies however, used unnatural objects that can be easily characterized in human terminologies (e.g., metallic spheres, disks, cylinders. In this work, we collected real fish echoes from many angles of acquisition using a sonar system that mimics the emission properties of dolphins and porpoises. We then tested two alternative statistical approaches in classifying these echoes. Our results suggest that fish species can be classified according to echoes returning from porpoise- and dolphin-like signals. These results suggest how dolphins and porpoises can classify fish based on their echoes and provide some insight as to which features might enable the classification.

  18. Evolution of entanglement under echo dynamics

    Science.gov (United States)

    Prosen, Tomaž; Seligman, Thomas H.; Žnidarič, Marko

    2003-04-01

    Echo dynamics and fidelity are often used to discuss stability in quantum-information processing and quantum chaos. Yet fidelity yields no information about entanglement, the characteristic property of quantum mechanics. We study the evolution of entanglement in echo dynamics. We find qualitatively different behavior between integrable and chaotic systems on one hand and between random and coherent initial states for integrable systems on the other. For the latter the evolution of entanglement is given by a classical time scale. Analytic results are illustrated numerically in a Jaynes-Cummings model.

  19. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    Guang-Ming Tan; Lin Xu; Dong-Bo Bu; Sheng-Zhong Feng; Ning-Hui Sun

    2006-01-01

    MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool)toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject (database) sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory,since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability.

  20. Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

    Science.gov (United States)

    Liu, Tsunglin; Tsai, Cheng-Hung; Lee, Wen-Bin; Chiang, Jung-Hsien

    2013-01-01

    Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.

  1. Improving irrigation efficiency : the need for a relevant sequence of the management tools

    Science.gov (United States)

    Fayolle, Y.

    2009-04-01

    With 70 % of worldwide withdrawals, irrigation efficiency is a key issue in the overall problem of water resources. Management of water dedicated to agriculture should be improved to secure food production and save water to deal with increasing domestic and industrial demands. This paper is based on the results of a collaborative research project conducted in India with a local NGO (the Aga Khan Rural Support Programme, AKRSP(I)) during which GIS were tested. It is aimed at analyzing the efficiency of water usage in a water development programme conducted by the partner NGO in the semi-arid margins of Gujarat state. The analysis raises the question of the articulation of legal, institutional, economical, and technical tools to improve water efficiency. The NGO supervises the construction of surface water harvesting structures for irrigation purposes. Following a participatory approach, it creates and trains user groups to which the management of dams would then be devolved. User group membership depends on financial contribution to the building costs. A legal vacuum regarding surface water management combined with unequal investment capacities favor the concentration of water resources in the hands of a limited number of farmers. This causes low water use efficiency, irrigation choices being mostly oriented to high water consumptive crops and recipient farmers showing no interest in investing in water saving techniques. Our observations favor equality of access and paying more attention to the sequence in which management tools are articulated. On a national scale, as a prerequisite, water user rights as well as NGO's intervention legal framework should be clarified. On a project scale, before construction, information systems could help to identify all potential beneficiaries and optimize equality of access. It aims at reducing the volume of water per farmer to encourage them to irrigate low water consumptive crops and invest in water saving techniques. Depending

  2. Implementation of the ECHO(®) telementoring model for the treatment of patients with hepatitis C.

    Science.gov (United States)

    Marciano, Sebastián; Haddad, Leila; Plazzotta, Fernando; Mauro, Ezequiel; Terraza, Sergio; Arora, Sanjeev; Thornton, Karla; Ríos, Beatriz; García Dans, Carlos; Ratusnu, Natalia; Calanni, Liliana; Allevato, José; Sirotinsky, María Ester; Pedrosa, Marcos; Gadano, Adrián

    2017-04-01

    We aimed to implement the Extension for Community Healthcare Outcomes (ECHO) telementoring model for hepatitis C and to evaluate its outcomes in the health providers. Following the ECHO model, an hepatitis C teleECHO clinic was established at the Hospital Italiano in Argentina. The teleECHO clinic provides support and training to physicians from Patagonia who treat patients with hepatitis C. In order to evaluate the teleECHO clinic outcomes, physicians completed a survey focused on skills and competence in hepatitis C before and after 6 months of participating in the project. The survey consisted of 10 questions, which participants rated from 1 to 7 (1 no ability; 7 highest ability). To analyze the difference before and after participation in the project, Wilcoxon signed-rank test was used. During the first 6 months of implementation of the model, a total of 14 physicians from 12 sites in Patagonia agreed to participate in the survey. The median age of the participants was 42 years. Participants' primary specialties were Hepatology (55%), Infectious Diseases (25%), General Practice (10%), and other (10%). A significant improvement was observed in all the evaluated fields after 6 month of the participation in the teleECHO clinic, namely fibrosis staging, determining appropriate candidates for treatment, and selecting appropriate HCV treatment. In addition, their general interest in hepatitis C increased. We successfully replicated and implemented the first teleECHO clinic in Argentina. Physicians improved their ability to provide best practice care for patients with Hepatitis C. J. Med. Virol. 89:660-664, 2017. © 2016 Wiley Periodicals, Inc.

  3. Expanding access to hepatitis C virus treatment--Extension for Community Healthcare Outcomes (ECHO) project: disruptive innovation in specialty care.

    Science.gov (United States)

    Arora, Sanjeev; Kalishman, Summers; Thornton, Karla; Dion, Denise; Murata, Glen; Deming, Paulina; Parish, Brooke; Brown, John; Komaromy, Miriam; Colleran, Kathleen; Bankhurst, Arthur; Katzman, Joanna; Harkins, Michelle; Curet, Luis; Cosgrove, Ellen; Pak, Wesley

    2010-09-01

    The Extension for Community Healthcare Outcomes (ECHO) Model was developed by the University of New Mexico Health Sciences Center as a platform to deliver complex specialty medical care to underserved populations through an innovative educational model of team-based interdisciplinary development. Using state-of-the-art telehealth technology, best practice protocols, and case-based learning, ECHO trains and supports primary care providers to develop knowledge and self-efficacy on a variety of diseases. As a result, they can deliver best practice care for complex health conditions in communities where specialty care is unavailable. ECHO was first developed for the management of hepatitis C virus (HCV), optimal management of which requires consultation with multidisciplinary experts in medical specialties, mental health, and substance abuse. Few practitioners, particularly in rural and underserved areas, have the knowledge to manage its emerging treatment options, side effects, drug toxicities, and treatment-induced depression. In addition, data were obtained from observation of ECHO weekly clinics and database of ECHO clinic participation and patient presentations by clinical provider. Evaluation of the ECHO program incorporates an annual survey integrated into the ECHO annual meeting and routine surveys of community providers about workplace learning, personal and professional experiences, systems and environmental factors associated with professional practice, self-efficacy, facilitators, and barriers to ECHO. The initial survey data show a significant improvement in provider knowledge, self-efficacy, and professional satisfaction through participation in ECHO HCV clinics. Clinicians reported a moderate to major benefit from participation. We conclude that ECHO expands access to best practice care for underserved populations, builds communities of practice to enhance professional development and satisfaction of primary care clinicians, and expands sustainable

  4. The Implementation of "The n-term" Formula to Improve Student Ability in Determining the Rules of a Numeric Sequence

    Science.gov (United States)

    In'am, Akhsanul; Hajar, Siti

    2013-01-01

    A good-quality teacher may determines a good-quality learning, thus good-quality students will be the results. In order to have a good-quality learning, a lot of strategies and methods can be adopted. The objective of this research is to improve students' ability in determining the rules of a numeric sequence and analysing the effectiveness of the…

  5. Recoding method that removes inhibitory sequences and improves HIV gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Rabadan, Raul; Krasnitz, Michael; Robins, Harlan; Witten, Daniela; Levine, Arnold

    2016-08-23

    The invention relates to inhibitory nucleotide signal sequences or "INS" sequences in the genomes of lentiviruses. In particular the invention relates to the AGG motif present in all viral genomes. The AGG motif may have an inhibitory effect on a virus, for example by reducing the levels of, or maintaining low steady-state levels of, viral RNAs in host cells, and inducing and/or maintaining in viral latency. In one aspect, the invention provides vaccines that contain, or are produced from, viral nucleic acids in which the AGG sequences have been mutated. In another aspect, the invention provides methods and compositions for affecting the function of the AGG motif, and methods for identifying other INS sequences in viral genomes.

  6. Recoding method that removes inhibitory sequences and improves HIV gene expression

    Science.gov (United States)

    Rabadan, Raul; Krasnitz, Michael; Robins, Harlan; Witten, Daniela; Levine, Arnold

    2016-08-23

    The invention relates to inhibitory nucleotide signal sequences or "INS" sequences in the genomes of lentiviruses. In particular the invention relates to the AGG motif present in all viral genomes. The AGG motif may have an inhibitory effect on a virus, for example by reducing the levels of, or maintaining low steady-state levels of, viral RNAs in host cells, and inducing and/or maintaining in viral latency. In one aspect, the invention provides vaccines that contain, or are produced from, viral nucleic acids in which the AGG sequences have been mutated. In another aspect, the invention provides methods and compositions for affecting the function of the AGG motif, and methods for identifying other INS sequences in viral genomes.

  7. Finding and Improving the Key-Frames of Long Video Sequences for Face Recognition

    DEFF Research Database (Denmark)

    Nasrollahi, Kamal; Moeslund, Thomas B.

    2010-01-01

    Face recognition systems are very sensitive to the quality and resolution of their input face images. This makes such systems unreliable when working with long surveillance video sequences without employing some selection and enhancement algorithms. On the other hand, processing all the frames...... of such video sequences by any enhancement or even face recognition algorithm is demanding. Thus, there is a need for a mechanism to summarize the input video sequence to a set of key-frames and then applying an enhancement algorithm to this subset. This paper presents a system doing exactly this. The system...... uses face quality assessment to select the key-frames and a hybrid super-resolution to enhance the face image quality. The suggested system that employs a linear associator face recognizer to evaluate the enhanced results has been tested on real surveillance video sequences and the experimental results...

  8. Magnetization transfer prepared gradient echo MRI for CEST imaging.

    Directory of Open Access Journals (Sweden)

    Zhuozhi Dai

    Full Text Available Chemical exchange saturation transfer (CEST is an emerging MRI contrast mechanism that is capable of noninvasively imaging dilute CEST agents and local properties such as pH and temperature, augmenting the routine MRI methods. However, the routine CEST MRI includes a long RF saturation pulse followed by fast image readout, which is associated with high specific absorption rate and limited spatial resolution. In addition, echo planar imaging (EPI-based fast image readout is prone to image distortion, particularly severe at high field. To address these limitations, we evaluated magnetization transfer (MT prepared gradient echo (GRE MRI for CEST imaging. We proved the feasibility using numerical simulations and experiments in vitro and in vivo. Then we optimized the sequence by serially evaluating the effects of the number of saturation steps, MT saturation power (B1, GRE readout flip angle (FA, and repetition time (TR upon the CEST MRI, and further demonstrated the endogenous amide proton CEST imaging in rats brains (n = 5 that underwent permanent middle cerebral artery occlusion. The CEST images can identify ischemic lesions in the first 3 hours after occlusion. In summary, our study demonstrated that the readily available MT-prepared GRE MRI, if optimized, is CEST-sensitive and remains promising for translational CEST imaging.

  9. First Demonstration of ECHO: an External Calibrator for Hydrogen Observatories

    Science.gov (United States)

    Jacobs, Daniel C.; Burba, Jacob; Bowman, Judd D.; Neben, Abraham R.; Stinnett, Benjamin; Turner, Lauren; Johnson, Kali; Busch, Michael; Allison, Jay; Leatham, Marc; Serrano Rodriguez, Victoria; Denney, Mason; Nelson, David

    2017-03-01

    Multiple instruments are pursuing constraints on dark energy, observing reionization and opening a window on the dark ages through the detection and characterization of the 21 cm hydrogen line for redshifts ranging from ∼1 to 25. These instruments, including CHIME in the sub-meter and HERA in the meter bands, are wide-field arrays with multiple-degree beams, typically operating in transit mode. Accurate knowledge of their primary beams is critical for separation of bright foregrounds from the desired cosmological signals, but difficult to achieve through astronomical observations alone. Previous beam calibration work at low frequencies has focused on model verification and does not address the need of 21 cm experiments for routine beam mapping, to the horizon, of the as-built array. We describe the design and methodology of a drone-mounted calibrator, the External Calibrator for Hydrogen Observatories (ECHO), that aims to address this need. We report on a first set of trials to calibrate low-frequency dipoles at 137 MHz and compare ECHO measurements to an established beam-mapping system based on transmissions from the Orbcomm satellite constellation. We create beam maps of two dipoles at a 9° resolution and find sample noise ranging from 1% at the zenith to 100% in the far sidelobes. Assuming this sample noise represents the error in the measurement, the higher end of this range is not yet consistent with the desired requirement but is an improvement on Orbcomm. The overall performance of ECHO suggests that the desired precision and angular coverage is achievable in practice with modest improvements. We identify the main sources of systematic error and uncertainty in our measurements and describe the steps needed to overcome them.

  10. Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates

    OpenAIRE

    Maningi, Nontuthuko E.; Daum, Luke T.; Rodriguez, John D.; Mphahlele, Matsie; Peters, Remco P. H.; Fischer, Gerald W.; Chambers, James P.; Fourie, P. Bernard

    2015-01-01

    The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance in Mycobacterium tuberculosis isolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising the pncA coding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolat...

  11. Methods for Improving the Tractability of the Block Sequencing Problem for Open Pit Mining

    Science.gov (United States)

    2008-07-01

    21 3.1 Defining the Block Sequencing Problem . . . . . . . . . . . . . . . . . 21 3.2 Conceptual Framework ...block sequencing problem and recently more literature is appearing on this topic. Denby and Schofield (1994) use genetic algorithms to simultaneously... knapsack problems help illustrate this principle. First, examine the following problem : max 10x1 + 10x2 + 10x3 (4.9) subject to : 10x1 + 10x2 + 10x3 ≤ 25

  12. Evolution of Web Services in EOSDIS: Search and Order Metadata Registry (ECHO)

    Science.gov (United States)

    Mitchell, Andrew; Ramapriyan, Hampapuram; Lowe, Dawn

    2009-01-01

    During 2005 through 2008, NASA defined and implemented a major evolutionary change in it Earth Observing system Data and Information System (EOSDIS) to modernize its capabilities. This implementation was based on a vision for 2015 developed during 2005. The EOSDIS 2015 Vision emphasizes increased end-to-end data system efficiency and operability; increased data usability; improved support for end users; and decreased operations costs. One key feature of the Evolution plan was achieving higher operational maturity (ingest, reconciliation, search and order, performance, error handling) for the NASA s Earth Observing System Clearinghouse (ECHO). The ECHO system is an operational metadata registry through which the scientific community can easily discover and exchange NASA's Earth science data and services. ECHO contains metadata for 2,726 data collections comprising over 87 million individual data granules and 34 million browse images, consisting of NASA s EOSDIS Data Centers and the United States Geological Survey's Landsat Project holdings. ECHO is a middleware component based on a Service Oriented Architecture (SOA). The system is comprised of a set of infrastructure services that enable the fundamental SOA functions: publish, discover, and access Earth science resources. It also provides additional services such as user management, data access control, and order management. The ECHO system has a data registry and a services registry. The data registry enables organizations to publish EOS and other Earth-science related data holdings to a common metadata model. These holdings are described through metadata in terms of datasets (types of data) and granules (specific data items of those types). ECHO also supports browse images, which provide a visual representation of the data. The published metadata can be mapped to and from existing standards (e.g., FGDC, ISO 19115). With ECHO, users can find the metadata stored in the data registry and then access the data either

  13. Echo planar diffusion-weighted imaging: possibilities and considerations with 12- and 32-channel head coils.

    Science.gov (United States)

    Morelli, John N; Saettele, Megan R; Rangaswamy, Rajesh A; Vu, Lan; Gerdes, Clint M; Zhang, Wei; Ai, Fei

    2012-01-01

    Interest in clinical brain magnetic resonance imaging using 32-channel head coils for signal reception continues to increase. The present investigation assesses possibilities for improving diffusion-weighted image quality using a 32-channel in comparison to a conventional 12-channel coil. The utility of single-shot (ss) and an approach to readout-segmented (rs) echo planar imaging (EPI) are examined using both head coils. Substantial image quality improvements are found with rs-EPI. Imaging with a 32-channel head coil allows for implementation of greater parallel imaging acceleration factors or acquisition of scans at a higher resolution. Specifically, higher resolution imaging with rs-EPI can be achieved by increasing the number of readout segments without increasing echo-spacing or echo time to the degree necessary with ss-EPI - a factor resulting in increased susceptibility artifact and reduced signal-to-noise with the latter.

  14. Echo Planar Diffusion-Weighted Imaging: Possibilities and Considerations with 12- and 32-Channel Head Coils

    Directory of Open Access Journals (Sweden)

    John N Morelli

    2012-01-01

    Full Text Available Interest in clinical brain magnetic resonance imaging using 32-channel head coils for signal reception continues to increase. The present investigation assesses possibilities for improving diffusion-weighted image quality using a 32-channel in comparison to a conventional 12-channel coil. The utility of single-shot (ss and an approach to readout-segmented (rs echo planar imaging (EPI are examined using both head coils. Substantial image quality improvements are found with rs-EPI. Imaging with a 32-channel head coil allows for implementation of greater parallel imaging acceleration factors or acquisition of scans at a higher resolution. Specifically, higher resolution imaging with rs-EPI can be achieved by increasing the number of readout segments without increasing echo-spacing or echo time to the degree necessary with ss-EPI - a factor resulting in increased susceptibility artifact and reduced signal-to-noise with the latter.

  15. Asymmetric radar echo patterns from insects

    Science.gov (United States)

    Radar echoes from insects, birds, and bats in the atmosphere exhibit both symmetry and asymmetry in polarimetric patterns. Symmetry refers to similar magnitudes of polarimetric variables at opposite azimuths, and asymmetry relegates to differences in these magnitudes. Asymmetry can be due to diffe...

  16. Picosecond Photon Echoes Detected by Optical Mixing

    NARCIS (Netherlands)

    Hesselink, Wim H.; Wiersma, Douwe A.

    1978-01-01

    Picosecond photon echoes are shown to be easily detected by optical mixing. The synchronized picosecond excitation and probe pulses are generated by amplifying pulses from two dye lasers, synchronously pumped by a mode-locked argon-ion laser. The technique is used to study optical dephasing in the o

  17. Pesticide Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    The dashboards found on the Enforcement and Compliance History Online (ECHO) website are specialized to track both facility and agency performance as they relate to compliance with and enforcement of environmental standards under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA).

  18. Using mating-type gene sequences for improved phylogenetic resolution of Collectotrichum species complexes.

    Science.gov (United States)

    Du, Meizhu; Schardl, Christopher L; Nuckles, Etta M; Vaillancourt, Lisa J

    2005-01-01

    Colletotrichum species are defined primarily on the basis of host preference and morphology of the organism in planta and in culture. However the genus contains several species complexes that encompass such a broad range of morphological and pathological variation that the species name is of relatively little use either to the taxonomist or plant pathologist. Phylogenetic analyses, primarily based on variable regions of the ribosomal DNA (rDNA) sequences, have indicated that these species complexes comprise a variable number of identifiable monophyletic clades. However rDNA sequences often are insufficiently diverse to fully resolve such closely related lineages. A group of isolates representing three species complexes (C. graminicola, C. gloeosporioides and C. acutatum) were analyzed by using the high mobility group (HMG)-encoding sequence of the MAT1-2 mating type sequence, which has been shown in other fungi to be especially suitable for distinguishing relationships among closely related groups. Results were compared with those obtained from analysis of variable regions of the rDNA as well as from standard morphological classification methods. Results achieved through analysis of MAT1-2 sequences correlated well with those obtained by analysis of rDNA sequences but provided significantly better resolution among the various lineages. Morphological traits, including hyphopodia size, colony appearance, spore size, appresorial shape and size and host preference, frequently were unreliable as indicators of phylogenetic association. Spore shape and hyphopodia shape more often were useful for this purpose.

  19. Echo voltage reflected by turtle on various angles

    OpenAIRE

    Sunardi Sunardi; Anton Yudhana; Azrul Mahfurdz; Sharipah Salwa Mohamed

    2015-01-01

    This research proposes the acoustic measurement by using echo sounder for green turtle detection of 1 year, 12 and 18 years. Various positions or angles of turtles are head, tail, shell, lung, left and right side. MATLAB software and echo sounder are used to analyse the frequency and the response of the turtle as echo voltage and target strength parameter. Based on the experiment and analysis have been conducted, the bigger size of the turtle, the higher echo voltage and target strength. The ...

  20. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units.

    Science.gov (United States)

    Westcott, Sarah L; Schloss, Patrick D

    2017-01-01

    Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to 10 other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6 times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the data set. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications. IMPORTANCE The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other

  1. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

    Science.gov (United States)

    Westcott, Sarah L.

    2017-01-01

    ABSTRACT Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to 10 other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6 times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the data set. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications. IMPORTANCE The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other

  2. Preliminary Results of the Echo-Seeding Experiment ECHO-7 at SLAC

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, D.; Colby, E.; Ding, Y.; Dunning, M.; Frederico, J.; Gilevich, S.; Hast, C.; Jobe, K.; McCormick, D.; Nelson, J.; Raubenheimer, T.O.; Soong, K.; Stupakov, G.; Szalata, Z.; Walz, D.; Weathersby, S.; Woodley, M.; /SLAC; Corlett, J.; Qiang, J.; Penn, G.; Prestemon, S.; /LBL, Berkeley /LPHE, Lausanne

    2010-06-15

    ECHO-7 is a proof-of-principle echo-enabled harmonic generation FEL experiment in the Next Linear Collider Test Accelerator (NLCTA) at SLAC. The experiment aims to generate coherent radiation at 318 nm and 227 nm, which are the 5th and 7th harmonic of the infrared seed laser. In this paper we present the preliminary results from the commissioning run of the completed experimental setup which started in April 2010.

  3. Ultrasonic echo signal fetures of dissimilar material bonding joints

    Institute of Scientific and Technical Information of China (English)

    GANG Tie(刚铁); Yasuo TAKAHASHI

    2004-01-01

    An ultrasonic evaluation method of echo feature of diffusion bond joint between two dissimilar materials is presented. The echo signal was acquired by an automatic ultrasonic C-scan test system. It is found that the intensity of echo and its phase can be used to evaluate the joint quality, and interface products of dissimilar materials bonding can be evaluated by ultrasonic method.

  4. 21 CFR 892.1560 - Ultrasonic pulsed echo imaging system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Ultrasonic pulsed echo imaging system. 892.1560... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1560 Ultrasonic pulsed echo imaging system. (a) Identification. An ultrasonic pulsed echo imaging system is a device intended to project...

  5. A Low Delay and Fast Converging Improved Proportionate Algorithm for Sparse System Identification

    Directory of Open Access Journals (Sweden)

    Andy W. H. Khong

    2007-04-01

    Full Text Available A sparse system identification algorithm for network echo cancellation is presented. This new approach exploits both the fast convergence of the improved proportionate normalized least mean square (IPNLMS algorithm and the efficient implementation of the multidelay adaptive filtering (MDF algorithm inheriting the beneficial properties of both. The proposed IPMDF algorithm is evaluated using impulse responses with various degrees of sparseness. Simulation results are also presented for both speech and white Gaussian noise input sequences. It has been shown that the IPMDF algorithm outperforms the MDF and IPNLMS algorithms for both sparse and dispersive echo path impulse responses. Computational complexity of the proposed algorithm is also discussed.

  6. A Low Delay and Fast Converging Improved Proportionate Algorithm for Sparse System Identification

    Directory of Open Access Journals (Sweden)

    Benesty Jacob

    2007-01-01

    Full Text Available A sparse system identification algorithm for network echo cancellation is presented. This new approach exploits both the fast convergence of the improved proportionate normalized least mean square (IPNLMS algorithm and the efficient implementation of the multidelay adaptive filtering (MDF algorithm inheriting the beneficial properties of both. The proposed IPMDF algorithm is evaluated using impulse responses with various degrees of sparseness. Simulation results are also presented for both speech and white Gaussian noise input sequences. It has been shown that the IPMDF algorithm outperforms the MDF and IPNLMS algorithms for both sparse and dispersive echo path impulse responses. Computational complexity of the proposed algorithm is also discussed.

  7. Fat/water separation in single acquisition steady-state free precession using multiple echo radial trajectories.

    Science.gov (United States)

    Lu, Aiming; Grist, Thomas M; Block, Walter F

    2005-11-01

    Phase detection in fully refocused SSFP imaging has recently allowed fat/water separation without preparing the magnetization or using multiple acquisitions. Instead, it exploits the phase difference between fat and water at an echo time at the midpoint of the TR. To minimize the TR for improved robustness to B0 inhomogeneity, a 3D projection acquisition collecting two half echoes at the beginning and end of each excitation was previously implemented. Since echoes are not formed at the midpoint of the TR, this method still requires two passes of k-space for fat/water separation. A new method is presented to linearly combine the half echoes to separate fat and water in a single acquisition. Separation using phase detection provides superior contrast between fat and water voxels. Results from high resolution angiography and musculoskeletal studies with improved robustness to inhomogeneity and a 50% scan time reduction compared to the two pass method are presented.

  8. cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer

    Directory of Open Access Journals (Sweden)

    Jesionek-Kupnicka Dorota

    2009-08-01

    Full Text Available Abstract Background Recently published data showed discrepancies beteween P53 cDNA and DNA sequencing in glioblastomas. We hypothesised that similar discrepancies may be observed in other human cancers. Methods To this end, we analyzed 23 colorectal cancers for P53 mutations and gene expression using both DNA and cDNA sequencing, real-time PCR and immunohistochemistry. Results We found P53 gene mutations in 16 cases (15 missense and 1 nonsense. Two of the 15 cases with missense mutations showed alterations based only on cDNA, and not DNA sequencing. Moreover, in 6 of the 15 cases with a cDNA mutation those mutations were difficult to detect in the DNA sequencing, so the results of DNA analysis alone could be misinterpreted if the cDNA sequencing results had not also been available. In all those 15 cases, we observed a higher ratio of the mutated to the wild type template by cDNA analysis, but not by the DNA analysis. Interestingly, a similar overexpression of P53 mRNA was present in samples with and without P53 mutations. Conclusion In terms of colorectal cancer, those discrepancies might be explained under three conditions: 1, overexpression of mutated P53 mRNA in cancer cells as compared with normal cells; 2, a higher content of cells without P53 mutation (normal cells and cells showing K-RAS and/or APC but not P53 mutation in samples presenting P53 mutation; 3, heterozygous or hemizygous mutations of P53 gene. Additionally, for heterozygous mutations unknown mechanism(s causing selective overproduction of mutated allele should also be considered. Our data offer new clues for studying discrepancy in P53 cDNA and DNA sequencing analysis.

  9. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

    Directory of Open Access Journals (Sweden)

    B. Bennetts

    2014-09-01

    Full Text Available Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA in collaboration with the Human Genetics Society of Australasia (HGSA, and the Human Variome Project (HVP is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

  10. Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design

    Science.gov (United States)

    Pilotte, Nils; Papaiakovou, Marina; Grant, Jessica R.; Bierwert, Lou Ann; Llewellyn, Stacey; McCarthy, James S.; Williams, Steven A.

    2016-01-01

    Background The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. Methodology/Principal Findings Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. Conclusions/Significance The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other

  11. Segmental dynamics of polyethylene-alt-propylene studied by NMR spin echo techniques

    Science.gov (United States)

    Lozovoi, A.; Mattea, C.; Hofmann, M.; Saalwaechter, K.; Fatkullin, N.; Stapf, S.

    2017-06-01

    Segmental dynamics of a highly entangled melt of linear polyethylene-alt-propylene with a molecular weight of 200 kDa was studied with a novel proton nuclear magnetic resonance (NMR) approach based upon 1H → 2H isotope dilution as applied to a solid-echo build-up function ISE(t), which is constructed from the NMR spin echo signals arising from the Hahn echo (HE) and two variations of the solid-echo pulse sequence. The isotope dilution enables the separation of inter- and intramolecular contributions to this function and allows one to extract the segmental mean-squared displacements in the millisecond time range, which is hardly accessible by other experimental methods. The proposed technique in combination with time-temperature superposition yields information about segmental translation in polyethylene-alt-propylene over 6 decades in time from 10-6 s up to 1 s. The time dependence of the mean-squared displacement obtained in this time range clearly shows three regimes of power law with exponents, which are in good agreement with the tube-reptation model predictions for the Rouse model, incoherent reptation and coherent reptation regimes. The results at short times coincide with the fast-field cycling relaxometry and neutron spin echo data, yet, significantly extending the probed time range. Furthermore, the obtained data are verified as well by the use of the dipolar-correlation effect on the Hahn echo, which was developed before by the co-authors. At the same time, the amplitude ratio of the intermolecular part of the proton dynamic dipole-dipole correlation function over the intramolecular part obtained from the experimental data is not in agreement with the predictions of the tube-reptation model for the regimes of incoherent and coherent reptation.

  12. Quantification of early fatty infiltration of the rotator cuff muscles: comparison of multi-echo Dixon with single-voxel MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Agten, Christoph A.; Rosskopf, Andrea B.; Pfirrmann, Christian W.A. [Balgrist University Hospital, Radiology, Zurich (Switzerland); University of Zurich, Faculty of Medicine, Zurich (Switzerland); Gerber, Christian [Balgrist University Hospital, Orthopaedic Surgery, Zurich (Switzerland); University of Zurich, Faculty of Medicine, Zurich (Switzerland)

    2016-10-15

    To evaluate quantification of early fatty infiltration in supraspinatus muscles with magnetic resonance (MR) imaging using a T2*-corrected multi-echo 3D-gradient-echo Dixon-based sequence (multi-echo Dixon) and compare it to proton-MR-spectroscopy. Sixty subjects (mean age 46 years, 41 men) with good supraspinatus muscle quality on 1.5 T MR imaging were included. Fat percentage (FP) in the supraspinatus muscle was quantified using a multi-echo Dixon compared to single-voxel MR spectroscopy as reference standard. In 18 subjects the multi-echo Dixon was repeated to assess test-retest reliability. Measurements based on multi-echo Dixon were performed by two independent readers by placing regions-of-interest (ROIs) in the supraspinatus muscle corresponding to the MR-spectroscopy voxel. Intraclass and concordance correlation coefficients (ICC/CCC) were used for statistical analysis. Test-retest reliability was substantial for reader 1 (ICC = 0.757) and almost perfect for reader 2 (ICC = 0.873). Inter-reader reliability for multi-echo Dixon was almost perfect (ICC = 0.893, P <.0005). Mean FP in all 60 subjects with multi-echo Dixon was 3.5 ± 1.6 for reader 1, 3.7 ± 1.8 for reader 2, and 2.8 ± 1.4 with MR spectroscopy. Correlation between multi-echo Dixon and MR spectroscopy was moderate (CCC = 0.641). The multi-echo Dixon sequence is a reliable method and comparable to MR-spectroscopy for quantification of low levels of fatty infiltration in the supraspinatus muscle. (orig.)

  13. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

    Science.gov (United States)

    Cotton is the world’s most important natural textile fibre and a significant oilseed crop. Upland cotton (Gossypium hirsutum L.), an allotetraploid derived from A- and D-genome progenitors, accounts for >95% of world production. Here, we sequenced and assembled 88% of the 2.5-gigabase genome of the ...

  14. Increased sequence diversity coverage improves detection of HIV-Specific T cell responses

    DEFF Research Database (Denmark)

    Frahm, N.; Kaufmann, D.E.; Yusim, K.

    2007-01-01

    The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss res...

  15. Increased sequence diversity coverage improves detection of HIV-Specific T cell responses

    DEFF Research Database (Denmark)

    Frahm, N.; Kaufmann, D.E.; Yusim, K.

    2007-01-01

    The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss res...

  16. Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing

    NARCIS (Netherlands)

    van Heesch, Sebastiaan; Kloosterman, Wigard P.; Lansu, Nico; Ruzius, Frans-Paul; Levandowsky, Elizabeth; Lee, Clarence C.; Zhou, Shiguo; Goldstein, Steve; Schwartz, David C.; Harkins, Timothy T.; Guryev, Victor; Cuppen, Edwin

    2013-01-01

    Background: Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. Results: Here, we systematically assessed the utility

  17. Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples.

    Science.gov (United States)

    Uyaguari-Diaz, Miguel I; Slobodan, Jared R; Nesbitt, Matthew J; Croxen, Matthew A; Isaac-Renton, Judith; Prystajecky, Natalie A; Tang, Patrick

    2015-04-17

    Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads.

  18. Comparison of Diversity of Type IIb Supernovae with Asymmetry in Cassiopeia A Using Light Echoes

    CERN Document Server

    Finn, Kieran; Modjaz, Maryam; Liu, Yu-Qian; Rest, Armin

    2016-01-01

    We compare the diversity of spectral line velocities in a large sample of type IIb supernovae (SNe IIb) with the expected asphericity in the explosion, as measured from the light echoes of Cassiopeia A (Cas A), which was a historical galactic SN IIb. We revisit the results of Rest et al. (2011a), who used light echoes to observe Cas A from multiple lines of sight and hence determine its asphericity, as seen in the velocity of three spectral lines (He I $\\lambda$5876, H$\\alpha$ and the Ca II NIR triplet). We confirm and improve on this measurement by reproducing the effect of the light echoes in the spectra of several extragalactic SNe IIb found in the literature as well as a new SN IIb template recently created by Liu et al. (2015), and comparing these to the observed light echo spectra of Cas A, including their associated uncertainties. In order to quantify the accuracy of this comparison we smooth the light echo spectra of Cas A using Gaussian processes and we use a Monte Carlo method to measure the absorpt...

  19. Physical understanding of an echo-Doppler test with voice-induced vibration

    CERN Document Server

    D'Alessandro, Alessio; Minetti, Giuseppe; Rosso, Franco; Villa, Alessandro

    2008-01-01

    The physical understanding of a method of detecting mammalian cancer via vocalization during a normal echo-Doppler test is provided. The backscattered ultrasound frequency in the case of a vocal humming resonating in the chest wall is computed: the overall effect is that the signal/noise ratio could be easily improved at no cost. Clinical results are to appear separately elsewhere.

  20. Light-echo spectroscopy of historic Supernovae

    Science.gov (United States)

    Krause, Oliver

    Young Galactic supernova remnants are unique laboratories for supernova physics. Due to their proximity they provide us with the most detailed view of the outcome of a supernova. However, the exact spectroscopic types of their original explosions have been undetermined so far -hindering to link the wealth of multi-wavelength knowledge about their remnants with the diverse population of supernovae. Light echoes, reflektions of the brilliant supernova burst of light by interstellar dust, provide a unique opportunity to reobserve today -with powerful scientific instruments of the 21st century -historic supernova exlosions even after hundreds of years and to conclude on their nature. We report on optical light-echo spectroscopy of two famous Galactic supernovae: Tycho Brahe's SN 1572 and the supernova that created the Cassiopeia A remnant around the year 1680. These observations finally recovered the missing spectroscopic classifications and provide new constraints on explosion models for future studies.

  1. Workshop on neutron spin-echo

    Energy Technology Data Exchange (ETDEWEB)

    Aynajian, P.; Habicht, K.; Keller, Th.; Keimer, B.; Mezei, F.; Monkenbusch, M.; Allgaier, J.; Richter, D.; Fetters, L.J.; Muller, K.; Kreiling, S.; Dehnicke, K.; Greiner, A.; Ehlers, G.; Arbe, A.; Colmenero, J.; Richter, D.; Farago, B.; Monkenbusch, M.; Ohl, M.; Butzek, M.; Kozielewski, T.; Monkenbusch, M.; Richter, D.; Pappas, C.; Hillier, A.; Manuel, P.; Cywinski, R.; Bentley, P.; Alba, M.; Mezei, F.; Campbell, I.A.; Zimmermann, U.; Ellis, J.; Jobic, H.; Pickup, R.M.; Pappas, C.; Farago, B.; Cywinski, R.; Haussler, W.; Holderer, O.; Frielinghaus, H.; Byelov, D.; Monkenbusch, M.; Allgaier, J.; Richter, D.; Egger, H.; Hellweg, Th.; Malikova, N.; Cadene, A.; Marry, V.; Dubois, E.; Turq, P.; Gardner, J.S.; Ehlers, G.; Bramwell, St.S.; Grigoriev, S.; Kraan, W.; Rekveldt, T.; Bouwman, W.; Van Dijk, N.; Falus, P.; Vorobiev, A.; Major, J.; Felcher, G.P.; Te-velthuis, S.; Dosch, H.; Vorobiev, A.; Dridi, M.H.; Major, J.; Dosch, H.; Falus, P.; Felcher, G.P.; Te Velthuis, S.G.E.; Bleuel, M.; Broell, M.; Lang, E.; Littrell, K.; Gahler, R.; Lal, J.; Lauter, H.; Toperverg, B.; Lauter, V.; Jernenkov, M.; Stueber, S.; Enderle, M.; Janoschek, M.; Keller, Th.; Klimko, S.; Boeni, P.; Nagao, M.; Yamada, N.; Kawabata, Y.; Seto, H.; Takeda, T.; Yoshizawa, H.; Yoshida, K.; Yamaguchi, T.; Bellissent-Funel, M.C.; Longeville, St

    2005-07-01

    This document gathers the abstracts of most papers presented at the workshop. Neutron spin-echo (NSE) spectroscopy is a well established technique with a growing expert user community, the aim of the meeting was to discuss the latest achievements in neutron spin-echo science and instrumentation. One of the applications presented is the investigation on the microscopic scale of the dynamics of water in montmorillonite clays with Na{sup +} and Cs{sup +} ions in monolayer and bilayer states. The NSE technique has been used in the normal and resonance modes. NSE results show consistently slower dynamics (higher relaxation times) than both time-of-flight technique (TOF) and classical molecular dynamics simulations (MD). In the present TOF and NSE experiments, anisotropy of the water motion in the interlayer is almost impossible to detect, due to the use of powder samples and insufficient resolution. (A.C.)

  2. Wind Shear Target Echo Modeling and Simulation

    Directory of Open Access Journals (Sweden)

    Xiaoyang Liu

    2015-01-01

    Full Text Available Wind shear is a dangerous atmospheric phenomenon in aviation. Wind shear is defined as a sudden change of speed or direction of the wind. In order to analyze the influence of wind shear on the efficiency of the airplane, this paper proposes a mathematical model of point target rain echo and weather target signal echo based on Doppler effect. The wind field model is developed in this paper, and the antenna model is also studied by using Bessel function. The spectrum distribution of symmetric and asymmetric wind fields is researched by using the mathematical model proposed in this paper. The simulation results are in accordance with radial velocity component, and the simulation results also confirm the correctness of the established model of antenna.

  3. Quantum Reversibility: Is there an Echo?

    CERN Document Server

    Hiller, M; Cohen, D; Geisel, T; Hiller, Moritz; Kottos, Tsampikos; Cohen, Doron; Geisel, Theo

    2004-01-01

    We study the possibility to undo the quantum mechanical evolution in a time reversal experiment. The naive expectation, as reflected in the common terminology ("Loschmidt echo"), is that maximum compensation results if the reversed dynamics extends to the same time as the forward evolution. We challenge this belief, and demonstrate that the time $t_r$ for maximum return probability is in general shorter. We find that $t_r$ depends on $lambda = eps_evol/eps_prep$, being the ratio of the error in setting the parameters (fields) for the time reversed evolution to the perturbation which is involved in the preparation process. Our results should be observable in spin-echo experiments where the dynamical irreversibility of quantum phases is measured.

  4. Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals

    Directory of Open Access Journals (Sweden)

    John P. Wares

    2014-09-01

    Full Text Available There are well-known difficulties in using the cytochrome oxidase I (COI mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.

  5. Improvement of sequence selectivity in triple helical recognition of RNA by phenylalanine-derived PNA

    OpenAIRE

    Zengeya, Thomas; Gindin, Artem; Rozners, Eriks

    2013-01-01

    Modified peptide nucleic acids (PNA) containing one or two thymine PNA monomers derived from phenylalanine were synthesized. Triple helix formation by these modified PNAs with RNA and DNA hairpins having a variable base pair in the middle of the helix were studied using isothermal titration calorimetry and compared with triple helix formation by non-modified PNAs. While unmodified PNA had low sequence selectivity against mismatched hairpins, introduction of one or two phenylalanine-derived mo...

  6. Eldor spin echoes and slow motions

    Science.gov (United States)

    Hornak, Joseph P.; Freed, Jack H.

    1983-10-01

    It is shown how an ELDOR technique based upon spin echoes and rapid stepping of the magnetic field may be employed to measure rotational correlation times, τ R for very slow motions. Experiments on PD-Tempone in 85% glycerol/ D 2O at low temperatures led to τ R values of 10 -4 to 10 -5 s obtained with a simple analysis of the data.

  7. Spin-echo spectroscopy with ultracold neutrons

    CERN Document Server

    Afach, S; Ban, G; Bison, G; Bodek, K; Chowdhuri, Z; Daum, M; Fertl, M; Franke, B; Griffith, W C; Grujić, Z D; Harris, P G; Heil, W; Hélaine, V; Kasprzak, M; Kermaidic, Y; Kirch, K; Knowles, P; Koch, H -C; Komposch, S; Kozela, A; Krempel, J; Lauss, B; Lefort, T; Lemière, Y; Mtchedlishvili, A; Musgrave, M; Naviliat-Cunic, O; Pendlebury, J M; Piegsa, F M; Pignol, G; Plonka-Spehr, C; Prashanth, P N; Quéméner, G; Rawlik, M; Rebreyend, D; Ries, D; Roccia, S; Rozpedzik, D; Schmidt-Wellenburg, P; Severijns, N; Thorne, J A; Weis, A; Wursten, E; Wyszynski, G; Zejma, J; Zenner, J; Zsigmond, G

    2015-01-01

    We describe a spin-echo method for ultracold neutrons (UCNs) confined in a precession chamber and exposed to a |B_0 | = 1uT magnetic field. We demonstrate a gravity-dependent spin dephasing by applying small vertical magnetic field gradients. The method gives access to the energy spectrum of stored UCNs, which can be crucial for the assessment of systematic effects in precision experiments such as searches for an electric dipole moment of the neutron.

  8. Quantification of hepatic iron concentration in chronic viral hepatitis: usefulness of T2-weighted single-shot spin-echo echo-planar MR imaging.

    Directory of Open Access Journals (Sweden)

    Tatsuyuki Tonan

    Full Text Available OBJECTIVE: To investigate the usefulness of single-shot spin-echo echo-planar imaging (SSEPI sequence for quantifying mild degree of hepatic iron stores in patients with viral hepatitis. METHODS: This retrospective study included 34 patients with chronic viral hepatitis/cirrhosis who had undergone histological investigation and magnetic resonance imaging with T2-weighted gradient-recalled echo sequence (T2-GRE and diffusion-weighted SSEPI sequence with b-factors of 0 s/mm(2 (T2-EPI, 500 s/mm(2 (DW-EPI-500, and 1000 s/mm(2 (DW-EPI-1000. The correlation between the liver-to-muscle signal intensity ratio, which was generated by regions of interest placed in the liver and paraspinous muscles of each sequence image, and the hepatic iron concentration (µmol/g dry liver, which was assessed by spectrophotometry, was analyzed by linear regression using a spline model. Akaike information criterion (AIC was used to select the optimal model. RESULTS: Mean ± standard deviation of the hepatic iron concentration quantified by spectrophotometry was 24.6 ± 16.4 (range, 5.5 to 83.2 µmol/g dry liver. DW-EPI correlated more closely with hepatic iron concentration than T2-GRE (R square values: 0.75 for T2-EPI, 0.69 for DW-EPI-500, 0.62 for DW-EPI-1000, and 0.61 for T2-GRE, respectively, all P<0.0001. Using the AIC, the regression model for T2-EPI generated by spline model was optimal because of lowest cross validation error. CONCLUSION: T2-EPI was sensitive to hepatic iron, and might be a more useful sequence for quantifying mild degree of hepatic iron stores in patients with chronic viral hepatitis.

  9. Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas.

    Science.gov (United States)

    Taylor, D Lee; McCormick, Melissa K

    2008-01-01

    Despite advances owing to molecular approaches, several hurdles still obstruct the identification of fungi forming orchid mycorrhizas. The Tulasnellaceae exhibit accelerated evolution of the nuclear ribosomal operon, causing most standard primers to fail in polymerase chain reaction (PCR) trials. Insufficient sequences are available from well characterized isolates and fruitbodies. Lastly, taxon-specific PCR primers are needed in order to explore the ecology of the fungi outside of the orchid root. Here, progress in overcoming these hurdles is reported. Broad-spectrum basidiomycete internal transcribed spacer (ITS) primers that do not exclude most known Tulasnellaceae are presented. blast searches and empirical PCR tests support their wide utility within the Basidiomycota. Taxon-specific ITS primers are presented targeted to orchid-associated Tulasnella, and a core component of the Thelephora-Tomentella complex. The efficiency and selectivity of these primer sets are again supported by blast searches and empirical tests. Lastly, ITS DNA sequences are presented from several strains of Epulorhiza, Ceratorhiza, Ceratobasidium, Sistotrema, Thanatephorus and Tulasnella that were originally described in the landmark mycorrhizal studies of Currah and Warcup. Detailed phylogenetic analyses reveal some inconsistencies in species concepts in these taxonomically challenging resupinate basidiomycetes, but also help to place several sequences from environmental samples.

  10. GESTATIONAL ECHO BIOMETRY IN BRACHYCEPHALIC PREGNANT BITCHES

    Directory of Open Access Journals (Sweden)

    Marcus Antônio Rossi Feliciano

    2015-07-01

    Full Text Available Ultrasonography is an accurate pregnancy diagnostic method, besides being completely innocuous for female and fetuses evaluation. The objective of this paper was to determine the reference values for gestational echo biometry of different breeds of bitches. A total of 25 multiparous females were included in the experiment, five English Bulldog bitches, five Pugs and 15 Shih Tzu, weighing 4-25 kg and aged 4-6 years. The echo biometric assessments were performed during the 2nd, 5th, 6th, 7th and 8th weeks of pregnancy, including gestational vesicle diameter, femur length, placenta thickness, parietal diameter, liver, heart and abdominal diameter and area. Early echo biometric study started at the second week of gestation. Measurements like fetal heart and liver diameter and area are still poorly studied, but can provide useful information for early detection of congenital anomalies that may reduce the viability of pregnancy. The significant results (P < 0.001 obtained for biometrics (P < 0.001 of the parietal (r2 = 81% and abdominal diameter (r2 = 86%, abdominal area (r2 = 80%, femur length (r2 = 84%, cardiac length (r2 = 79%, width (r2 = 79%, area (r2 = 82% and volume (r2 = 72% and liver area (r2 = 71% in brachycephalic conceptus may help to assess the development of fetuses, complementing the conventional gestational ultrasound of bitches and become a model for the study in other breeds of dogs and alternative animal species.

  11. An improved classification of G-protein-coupled receptors using sequence-derived features

    Directory of Open Access Journals (Sweden)

    Peng Zhen-Ling

    2010-08-01

    Full Text Available Abstract Background G-protein-coupled receptors (GPCRs play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and characterization of novel receptors, it is therefore very valuable to develop a computational method to accurately predict GPCRs from the protein primary sequences. Results We propose a new method called PCA-GPCR, to predict GPCRs using a comprehensive set of 1497 sequence-derived features. The principal component analysis is first employed to reduce the dimension of the feature space to 32. Then, the resulting 32-dimensional feature vectors are fed into a simple yet powerful classification algorithm, called intimate sorting, to predict GPCRs at five levels. The prediction at the first level determines whether a protein is a GPCR or a non-GPCR. If it is predicted to be a GPCR, then it will be further predicted into certain family, subfamily, sub-subfamily and subtype by the classifiers at the second, third, fourth, and fifth levels, respectively. To train the classifiers applied at five levels, a non-redundant dataset is carefully constructed, which contains 3178, 1589, 4772, 4924, and 2741 protein sequences at the respective levels. Jackknife tests on this training dataset show that the overall accuracies of PCA-GPCR at five levels (from the first to the fifth can achieve up to 99.5%, 88.8%, 80.47%, 80.3%, and 92.34%, respectively. We further perform predictions on a dataset of 1238 GPCRs at the second level, and on another two datasets of 167 and 566 GPCRs respectively at the fourth level. The overall prediction accuracies of our method are consistently higher than those of the existing methods to be compared. Conclusions The comprehensive set of 1497 features is believed to be capable of capturing information about amino acid

  12. Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

    Science.gov (United States)

    Utturkar, Sagar M; Bayer, Edward A; Borovok, Ilya; Lamed, Raphael; Hurt, Richard A; Land, Miriam L; Klingeman, Dawn M; Elias, Dwayne; Zhou, Jizhong; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Brown, Steven D

    2016-09-29

    We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

  13. Cardiac echo-lab productivity in times of economic austerity.

    Science.gov (United States)

    Katsi, Vasiliki K; Vrachatis, Dimitrios A; Politi, Anastasia; Papageorgiou, Manto; Koumoulidis, Anastasios; Vlasseros, Ioannis; Vavuranakis, Manolis; Tousoulis, Dimitrios; Stefanadis, Christodoulos; Kallikazaros, Ioannis; Souliotis, Kyriakos

    2014-01-01

    The present study attempts to offer insight into the volume, cost, and productivity of the operation of a cardiac echocardiographic laboratory (echo-lab) in a major public hospital of Greece and thus to contribute, on a practical level, to the widening of knowledge in the strategic field of secondary and tertiary healthcare management. The conducted research includes the basic step of the deployment of a primary data registry in the echo-lab and unfolds in three levels, i.e. the variability measurement of the quantity and cost of medical services provided to different patient populations, the assessment of operating costs and the development of productivity indexes. The results show that the mean costs of provision do change among distinct patient populations. The most important, from a financial standpoint, population cluster appears to be the one corresponding to outpatients. Productivity indices presented in this analysis constitute an essential piece of information which the public healthcare system is currently largely lacking, and which, combined with the pricing and the diagnosis-related group coding system of hospitals, can be used to improve efficiency in the management of secondary and tertiary care.

  14. Echo Meadows Project Winter Artificial Recharge.

    Energy Technology Data Exchange (ETDEWEB)

    Ziari, Fred

    2002-12-19

    This report discusses the findings of the Echo Meadows Project (BPA Project 2001-015-00). The main purpose of this project is to artificially recharge an alluvial aquifer, WITH water from Umatilla River during the winter high flow period. In turn, this recharged aquifer will discharge an increased flow of cool groundwater back to the river, thereby improving Umatilla River water quality and temperature. A considerable side benefit is that the Umatilla River should improve as a habitat for migration, spanning, and rearing of anadromous and resident fish. The scope of this project is to provide critical baseline information about the Echo Meadows and the associated reach of the Umatilla River. Key elements of information that has been gathered include: (1) Annual and seasonal groundwater levels in the aquifer with an emphasis on the irrigation season, (2) Groundwater hydraulic properties, particularly hydraulic conductivity and specific yield, and (3) Groundwater and Umatilla River water quality including temperature, nutrients and other indicator parameters. One of the major purposes of this data gathering was to develop input to a groundwater model of the area. The purpose of the model is to estimate our ability to recharge this aquifer using water that is only available outside of the irrigation season (December through the end of February) and to estimate the timing of groundwater return flow back to the river. We have found through the data collection and modeling efforts that this reach of the river had historically returned as much as 45 cubic feet per second (cfs) of water to the Umatilla River during the summer and early fall. However, this return flow was reduced to as low as 10 cfs primarily due to reduced quantities of irrigation application, gain in irrigation efficiencies and increased groundwater pumping. Our modeling indicated that it is possible to restore these critical return flows using applied water outside of the irrigation season. We further

  15. Echo Meadows Project Winter Artificial Recharge.

    Energy Technology Data Exchange (ETDEWEB)

    Ziari, Fred

    2002-12-19

    This report discusses the findings of the Echo Meadows Project (BPA Project 2001-015-00). The main purpose of this project is to artificially recharge an alluvial aquifer, WITH water from Umatilla River during the winter high flow period. In turn, this recharged aquifer will discharge an increased flow of cool groundwater back to the river, thereby improving Umatilla River water quality and temperature. A considerable side benefit is that the Umatilla River should improve as a habitat for migration, spanning, and rearing of anadromous and resident fish. The scope of this project is to provide critical baseline information about the Echo Meadows and the associated reach of the Umatilla River. Key elements of information that has been gathered include: (1) Annual and seasonal groundwater levels in the aquifer with an emphasis on the irrigation season, (2) Groundwater hydraulic properties, particularly hydraulic conductivity and specific yield, and (3) Groundwater and Umatilla River water quality including temperature, nutrients and other indicator parameters. One of the major purposes of this data gathering was to develop input to a groundwater model of the area. The purpose of the model is to estimate our ability to recharge this aquifer using water that is only available outside of the irrigation season (December through the end of February) and to estimate the timing of groundwater return flow back to the river. We have found through the data collection and modeling efforts that this reach of the river had historically returned as much as 45 cubic feet per second (cfs) of water to the Umatilla River during the summer and early fall. However, this return flow was reduced to as low as 10 cfs primarily due to reduced quantities of irrigation application, gain in irrigation efficiencies and increased groundwater pumping. Our modeling indicated that it is possible to restore these critical return flows using applied water outside of the irrigation season. We further

  16. Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.

    Science.gov (United States)

    Gupta, Sonal; Nawaz, Kashif; Parween, Sabiha; Roy, Riti; Sahu, Kamlesh; Kumar Pole, Anil; Khandal, Hitaishi; Srivastava, Rishi; Kumar Parida, Swarup; Chattopadhyay, Debasis

    2017-02-01

    Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. Taking Telemedicine to the Next Level in Diabetes Population Management: a Review of the Endo ECHO Model.

    Science.gov (United States)

    Bouchonville, Matthew F; Paul, Margaret M; Billings, John; Kirk, Jessica B; Arora, Sanjeev

    2016-10-01

    Worldwide increases in diabetes prevalence in the face of limited medical resources have prompted international interest in innovative healthcare delivery models. Project ECHO (Extension for Community Healthcare Outcomes) is a "telementoring" program which has been shown to increase capacity for complex disease management in medically underserved regions. In contrast to a traditional telemedicine model which might connect a specialist with one patient, the ECHO model allows for multiple patients to benefit simultaneously by building new expertise. We recently applied the ECHO model to improve health outcomes of patients with complex diabetes (Endo ECHO) living in rural New Mexico. We describe the design of the Endo ECHO intervention and a 4-year, prospective program evaluation assessing health outcomes, utilization patterns, and cost-effectiveness. The Endo ECHO evaluation will demonstrate whether and to what extent this intervention improves outcomes for patients with complex diabetes living in rural New Mexico, and will serve as proof-of-concept for academic medical centers wishing to replicate the model in underserved regions around the world.

  18. Initial experience in perfusion MR imaging of intracranial major artery occlusion with echo-planar technique

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Kazuhiro; Mizutani, Yoshiyuki; Inaoka, Sayuki; Hachiya, Junichi [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1997-09-01

    The purpose of this study was to evaluate the usefulness of perfusion MR imaging using a single-shot echo-planar technique in occlusion of intracranial main arteries. Our patient group consisted of 16 patients with internal carotid artery occlusion (n=9), Moyamoya disease (n=4), and middle cerebral artery occlusion (n=3). We performed the echo-planar perfusion studies with a 1.5-T unit using a free-induction-decay-type echo-planar sequence. With a bolus injection of Gd-DTPA, 30 consecutive scans were obtained at 10 sections every 2 seconds. The data were analyzed in three ways: a time-intensity curves in the territory of the involved artery (n=16); semiquantitative flow map of each section representing signal changes due to passage of Gd-DTPA (n=15); and serial images at a selected section (n=7). The time intensity curves were abnormal in 13 patients. The peak of signal drop was delayed in all of them. Flow maps showed focal flow abnormalities in 11 patients, but they were apparently normal in 4 patients probably due to collateral flow. In serial images, delay in appearance and/or disappearance of Gd-DTPA was noted in 6 patients. In patients with occlusion of intracranial main arteries, MR single-shot echo-planar technique is of clinical use because it can provide information about hemodynamic changes in a short examination time, in multiple sections, and with good temporal resolution. (author)

  19. The EChO science case

    Science.gov (United States)

    Tinetti, Giovanna; Drossart, Pierre; Eccleston, Paul; Hartogh, Paul; Isaak, Kate; Linder, Martin; Lovis, Christophe; Micela, Giusi; Ollivier, Marc; Puig, Ludovic; Ribas, Ignasi; Snellen, Ignas; Swinyard, Bruce; Allard, France; Barstow, Joanna; Cho, James; Coustenis, Athena; Cockell, Charles; Correia, Alexandre; Decin, Leen; de Kok, Remco; Deroo, Pieter; Encrenaz, Therese; Forget, Francois; Glasse, Alistair; Griffith, Caitlin; Guillot, Tristan; Koskinen, Tommi; Lammer, Helmut; Leconte, Jeremy; Maxted, Pierre; Mueller-Wodarg, Ingo; Nelson, Richard; North, Chris; Pallé, Enric; Pagano, Isabella; Piccioni, Guseppe; Pinfield, David; Selsis, Franck; Sozzetti, Alessandro; Stixrude, Lars; Tennyson, Jonathan; Turrini, Diego; Zapatero-Osorio, Mariarosa; Beaulieu, Jean-Philippe; Grodent, Denis; Guedel, Manuel; Luz, David; Nørgaard-Nielsen, Hans Ulrik; Ray, Tom; Rickman, Hans; Selig, Avri; Swain, Mark; Banaszkiewicz, Marek; Barlow, Mike; Bowles, Neil; Branduardi-Raymont, Graziella; du Foresto, Vincent Coudé; Gerard, Jean-Claude; Gizon, Laurent; Hornstrup, Allan; Jarchow, Christopher; Kerschbaum, Franz; Kovacs, Géza; Lagage, Pierre-Olivier; Lim, Tanya; Lopez-Morales, Mercedes; Malaguti, Giuseppe; Pace, Emanuele; Pascale, Enzo; Vandenbussche, Bart; Wright, Gillian; Ramos Zapata, Gonzalo; Adriani, Alberto; Azzollini, Ruymán; Balado, Ana; Bryson, Ian; Burston, Raymond; Colomé, Josep; Crook, Martin; Di Giorgio, Anna; Griffin, Matt; Hoogeveen, Ruud; Ottensamer, Roland; Irshad, Ranah; Middleton, Kevin; Morgante, Gianluca; Pinsard, Frederic; Rataj, Mirek; Reess, Jean-Michel; Savini, Giorgio; Schrader, Jan-Rutger; Stamper, Richard; Winter, Berend; Abe, L.; Abreu, M.; Achilleos, N.; Ade, P.; Adybekian, V.; Affer, L.; Agnor, C.; Agundez, M.; Alard, C.; Alcala, J.; Allende Prieto, C.; Alonso Floriano, F. J.; Altieri, F.; Alvarez Iglesias, C. A.; Amado, P.; Andersen, A.; Aylward, A.; Baffa, C.; Bakos, G.; Ballerini, P.; Banaszkiewicz, M.; Barber, R. J.; Barrado, D.; Barton, E. J.; Batista, V.; Bellucci, G.; Belmonte Avilés, J. A.; Berry, D.; Bézard, B.; Biondi, D.; Błęcka, M.; Boisse, I.; Bonfond, B.; Bordé, P.; Börner, P.; Bouy, H.; Brown, L.; Buchhave, L.; Budaj, J.; Bulgarelli, A.; Burleigh, M.; Cabral, A.; Capria, M. T.; Cassan, A.; Cavarroc, C.; Cecchi-Pestellini, C.; Cerulli, R.; Chadney, J.; Chamberlain, S.; Charnoz, S.; Christian Jessen, N.; Ciaravella, A.; Claret, A.; Claudi, R.; Coates, A.; Cole, R.; Collura, A.; Cordier, D.; Covino, E.; Danielski, C.; Damasso, M.; Deeg, H. J.; Delgado-Mena, E.; Del Vecchio, C.; Demangeon, O.; De Sio, A.; De Wit, J.; Dobrijévic, M.; Doel, P.; Dominic, C.; Dorfi, E.; Eales, S.; Eiroa, C.; Espinoza Contreras, M.; Esposito, M.; Eymet, V.; Fabrizio, N.; Fernández, M.; Femenía Castella, B.; Figueira, P.; Filacchione, G.; Fletcher, L.; Focardi, M.; Fossey, S.; Fouqué, P.; Frith, J.; Galand, M.; Gambicorti, L.; Gaulme, P.; García López, R. J.; Garcia-Piquer, A.; Gear, W.; Gerard, J.-C.; Gesa, L.; Giani, E.; Gianotti, F.; Gillon, M.; Giro, E.; Giuranna, M.; Gomez, H.; Gomez-Leal, I.; Gonzalez Hernandez, J.; González Merino, B.; Graczyk, R.; Grassi, D.; Guardia, J.; Guio, P.; Gustin, J.; Hargrave, P.; Haigh, J.; Hébrard, E.; Heiter, U.; Heredero, R. L.; Herrero, E.; Hersant, F.; Heyrovsky, D.; Hollis, M.; Hubert, B.; Hueso, R.; Israelian, G.; Iro, N.; Irwin, P.; Jacquemoud, S.; Jones, G.; Jones, H.; Justtanont, K.; Kehoe, T.; Kerschbaum, F.; Kerins, E.; Kervella, P.; Kipping, D.; Koskinen, T.; Krupp, N.; Lahav, O.; Laken, B.; Lanza, N.; Lellouch, E.; Leto, G.; Licandro Goldaracena, J.; Lithgow-Bertelloni, C.; Liu, S. J.; Lo Cicero, U.; Lodieu, N.; Lognonné, P.; Lopez-Puertas, M.; Lopez-Valverde, M. A.; Lundgaard Rasmussen, I.; Luntzer, A.; Machado, P.; MacTavish, C.; Maggio, A.; Maillard, J.-P.; Magnes, W.; Maldonado, J.; Mall, U.; Marquette, J.-B.; Mauskopf, P.; Massi, F.; Maurin, A.-S.; Medvedev, A.; Michaut, C.; Miles-Paez, P.; Montalto, M.; Montañés Rodríguez, P.; Monteiro, M.; Montes, D.; Morais, H.; Morales, J. C.; Morales-Calderón, M.; Morello, G.; Moro Martín, A.; Moses, J.; Moya Bedon, A.; Murgas Alcaino, F.; Oliva, E.; Orton, G.; Palla, F.; Pancrazzi, M.; Pantin, E.; Parmentier, V.; Parviainen, H.; Peña Ramírez, K. Y.; Peralta, J.; Perez-Hoyos, S.; Petrov, R.; Pezzuto, S.; Pietrzak, R.; Pilat-Lohinger, E.; Piskunov, N.; Prinja, R.; Prisinzano, L.; Polichtchouk, I.; Poretti, E.; Radioti, A.; Ramos, A. A.; Rank-Lüftinger, T.; Read, P.; Readorn, K.; Rebolo López, R.; Rebordão, J.; Rengel, M.; Rezac, L.; Rocchetto, M.; Rodler, F.; Sánchez Béjar, V. J.; Sanchez Lavega, A.; Sanromá, E.; Santos, N.; Sanz Forcada, J.; Scandariato, G.; Schmider, F.-X.; Scholz, A.; Scuderi, S.; Sethenadh, J.; Shore, S.; Showman, A.; Sicardy, B.; Sitek, P.; Smith, A.; Soret, L.; Sousa, S.; Stiepen, A.; Stolarski, M.; Strazzulla, G.; Tabernero, H. M.; Tanga, P.; Tecsa, M.; Temple, J.; Terenzi, L.; Tessenyi, M.; Testi, L.; Thompson, S.; Thrastarson, H.; Tingley, B. W.; Trifoglio, M.; Martín Torres, J.; Tozzi, A.; Turrini, D.; Varley, R.; Vakili, F.; de Val-Borro, M.; Valdivieso, M. L.; Venot, O.; Villaver, E.; Vinatier, S.; Viti, S.; Waldmann, I.; Waltham, D.; Ward-Thompson, D.; Waters, R.; Watkins, C.; Watson, D.; Wawer, P.; Wawrzaszk, A.; White, G.; Widemann, T.; Winek, W.; Wiśniowski, T.; Yelle, R.; Yung, Y.; Yurchenko, S. N.

    2015-12-01

    The discovery of almost two thousand exoplanets has revealed an unexpectedly diverse planet population. We see gas giants in few-day orbits, whole multi-planet systems within the orbit of Mercury, and new populations of planets with masses between that of the Earth and Neptune—all unknown in the Solar System. Observations to date have shown that our Solar System is certainly not representative of the general population of planets in our Milky Way. The key science questions that urgently need addressing are therefore: What are exoplanets made of? Why are planets as they are? How do planetary systems work and what causes the exceptional diversity observed as compared to the Solar System? The EChO (Exoplanet Characterisation Observatory) space mission was conceived to take up the challenge to explain this diversity in terms of formation, evolution, internal structure and planet and atmospheric composition. This requires in-depth spectroscopic knowledge of the atmospheres of a large and well-defined planet sample for which precise physical, chemical and dynamical information can be obtained. In order to fulfil this ambitious scientific program, EChO was designed as a dedicated survey mission for transit and eclipse spectroscopy capable of observing a large, diverse and well-defined planet sample within its 4-year mission lifetime. The transit and eclipse spectroscopy method, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allows us to measure atmospheric signals from the planet at levels of at least 10-4 relative to the star. This can only be achieved in conjunction with a carefully designed stable payload and satellite platform. It is also necessary to provide broad instantaneous wavelength coverage to detect as many molecular species as possible, to probe the thermal structure of the planetary atmospheres and to correct for the contaminating effects of the stellar photosphere. This requires wavelength

  20. Design of a fast echo matching algorithm to reduce crosstalk with Doppler shifts in ultrasonic ranging

    Science.gov (United States)

    Liu, Lei; Guo, Rui; Wu, Jun-an

    2017-02-01

    Crosstalk is a main factor for wrong distance measurement by ultrasonic sensors, and this problem becomes more difficult to deal with under Doppler effects. In this paper, crosstalk reduction with Doppler shifts on small platforms is focused on, and a fast echo matching algorithm (FEMA) is proposed on the basis of chaotic sequences and pulse coding technology, then verified through applying it to match practical echoes. Finally, we introduce how to select both better mapping methods for chaotic sequences, and algorithm parameters for higher achievable maximum of cross-correlation peaks. The results indicate the following: logistic mapping is preferred to generate good chaotic sequences, with high autocorrelation even when the length is very limited; FEMA can not only match echoes and calculate distance accurately with an error degree mostly below 5%, but also generates nearly the same calculation cost level for static or kinematic ranging, much lower than that by direct Doppler compensation (DDC) with the same frequency compensation step; The sensitivity to threshold value selection and performance of FEMA depend significantly on the achievable maximum of cross-correlation peaks, and a higher peak is preferred, which can be considered as a criterion for algorithm parameter optimization under practical conditions.

  1. Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes.

    Science.gov (United States)

    DeJesus, Michael A; Ioerger, Thomas R

    2016-06-01

    Sequencing of transposon-mutant libraries using next-generation sequencing (TnSeq) has become a popular method for determining which genes and non-coding regions are essential for growth under various conditions in bacteria. For methods that rely on quantitative comparison of counts of reads at transposon insertion sites, proper normalization of TnSeq datasets is vitally important. Real TnSeq datasets are often noisy and exhibit a significant skew that can be dominated by high counts at a small number of sites (often for non-biological reasons). If two datasets that are not appropriately normalized are compared, it might cause the artifactual appearance of Differentially Essential (DE) genes in a statistical test, constituting type I errors (false positives). In this paper, we propose a novel method for normalization of TnSeq datasets that corrects for the skew of read-count distributions by fitting them to a Beta-Geometric distribution. We show that this read-count correction procedure reduces the number of false positives when comparing replicate datasets grown under the same conditions (for which no genuine differences in essentiality are expected). We compare these results to results obtained with other normalization procedures, and show that it results in greater reduction in the number of false positives. In addition we investigate the effects of normalization on the detection of DE genes.

  2. Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.

    Science.gov (United States)

    Sameith, Katrin; Roscito, Juliana G; Hiller, Michael

    2017-01-01

    Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous k-mers occur in other copies of the repeat. We developed an iterative error correction pipeline that runs the previously published String Graph Assembler (SGA) in multiple rounds of k-mer-based correction with an increasing k-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads. We show that higher read accuracy increases contig lengths two to three times. We provide SGA-Iteratively Correcting Errors (https://github.com/hillerlab/IterativeErrorCorrection/) that implements iterative error correction by using modules from SGA.

  3. Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly

    Science.gov (United States)

    Sameith, Katrin; Roscito, Juliana G.

    2017-01-01

    Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous k-mers occur in other copies of the repeat. We developed an iterative error correction pipeline that runs the previously published String Graph Assembler (SGA) in multiple rounds of k-mer-based correction with an increasing k-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads. We show that higher read accuracy increases contig lengths two to three times. We provide SGA-Iteratively Correcting Errors (https://github.com/hillerlab/IterativeErrorCorrection/) that implements iterative error correction by using modules from SGA. PMID:26868358

  4. Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing

    Directory of Open Access Journals (Sweden)

    ElSharawy Abdou

    2012-08-01

    Full Text Available Abstract Background Compared to classical genotyping, targeted next-generation sequencing (tNGS can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages of increasing complexity (E. coli genes, multiplexed E. coli, and multiplexed HapMap BRCA1/2 regions. Results We successfully enriched barcoded NGS libraries instead of genomic DNA, achieving reproducible coverage profiles (Pearson correlation coefficients of up to 0.99 across multiplexed samples, with Conclusions We recommend applying our general ‘two-step’ mapping approach for more efficient SNP discovery in tNGS. Our study has also shown the benefit of computing inter-sample SNP-concordances and inspecting read alignments in order to attain more confident results.

  5. Some reasoning on the improvement of the ETAS modeling at the occurrence of the 2016 central Italy seismic sequence

    Directory of Open Access Journals (Sweden)

    Anna Maria Lombardi

    2016-12-01

    Full Text Available This study presents an application of the ETAS model to the first 20 days of the 2016 central Italy sequence. Despite of the provisional nature of data, the model is able to describe the occurrence rate, but for the first hours after the mainshock occurrence. A sensitivity analysis of the model to two uncertainty sources, the model parameters and the occurrence history, shows that the second has a main role in controlling the performance of the ETAS model, more than the uncertainty on parameters. Previous results, together with the clear inability of ETAS to forecast the occurrence of a sequence before its starting time, give important suggestions about possible improvements. Here, a very preliminary attempt in this sense is presented.

  6. Application of Multi-Scale Tracking Radar Echoes Scheme in Quantitative Precipitation Nowcasting

    Institute of Scientific and Technical Information of China (English)

    WANG Gaili; WONG Waikin; LIU Liping; WANG Hongyan

    2013-01-01

    A new radar echo tracking algorithm known as multi-scale tracking radar echoes by cross-correlation (MTREC) was developed in this study to analyze movements of radar echoes at different spatial scales.Movement of radar echoes,particularly associated with convective storms,exhibits different characteristics at various spatial scales as a result of complex interactions among meteorological systems leading to the formation of convective storms.For the null echo region,the usual correlation technique produces zero or a very small magnitude of motion vectors.To mitigate these constraints,MTREC uses the tracking radar echoes by correlation (TREC) technique with a large "box" to determine the systematic movement driven by steering wind,and MTREC applies the TREC technique with a small "box" to estimate small-scale internal motion vectors.Eventually,the MTREC vectors are obtained by synthesizing the systematic motion and the small scale internal motion.Performance of the MTREC technique was compared with TREC technique using case studies:the Khanun typhoon on 11 September 2005 observed by Wenzhou radar and a squall-line system on 23 June 2011 detected by Beijing radar.The results demonstrate that more spatially smoothed and continuous vector fields can be generated by the MTREC technique,which leads to improvements in tracking the entire radar reflectivity pattern.The new multi-scale tracking scheme was applied to study its impact on the performance of quantitative precipitation nowcasting.The location and intensity of heavy precipitation at a 1-h lead time was more consistent with quantitative precipitation estimates using radar and rain gauges.

  7. MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

    Science.gov (United States)

    Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

    2016-12-01

    In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner.

  8. MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

    Science.gov (United States)

    Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

    2017-06-01

    In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

  9. Real-Time Culture Change Improves Lean Success: Sequenced Culture Change Gets Failing Grades.

    Science.gov (United States)

    Kusy, Mitchell; Diamond, Marty; Vrchota, Scott

    2015-01-01

    Success with the Lean management system is rooted in a culture of stakeholder engagement and commitment. Unfortunately, many leaders view Lean as an "add-on" tool instead of one that requires a new way of thinking and approaching culture. This article addresses the "why, how, and what" to promote a Lean culture that works. We present a five-phased approach grounded in evidence-based practices of real-time culture change. We further help healthcare leaders understand the differences between traditional "sequenced" approaches to culture change and "real-time" methods--and why these real-time practices are more sustainable and ultimately more successful than traditional culture change methods.

  10. Targeted deep sequencing improves outcome stratification in chronic myelomonocytic leukemia with low risk cytogenetic features

    Science.gov (United States)

    Palomo, Laura; Garcia, Olga; Arnan, Montse; Xicoy, Blanca; Fuster, Francisco; Cabezón, Marta; Coll, Rosa; Ademà, Vera; Grau, Javier; Jiménez, Maria-José; Pomares, Helena; Marcé, Sílvia; Mallo, Mar; Millá, Fuensanta; Alonso, Esther; Sureda, Anna; Gallardo, David; Feliu, Evarist; Ribera, Josep-Maria; Solé, Francesc; Zamora, Lurdes

    2016-01-01

    Clonal cytogenetic abnormalities are found in 20-30% of patients with chronic myelomonocytic leukemia (CMML), while gene mutations are present in >90% of cases. Patients with low risk cytogenetic features account for 80% of CMML cases and often fall into the low risk categories of CMML prognostic scoring systems, but the outcome differs considerably among them. We performed targeted deep sequencing of 83 myeloid-related genes in 56 CMML patients with low risk cytogenetic features or uninformative conventional cytogenetics (CC) at diagnosis, with the aim to identify the genetic characteristics of patients with a more aggressive disease. Targeted sequencing was also performed in a subset of these patients at time of acute myeloid leukemia (AML) transformation. Overall, 98% of patients harbored at least one mutation. Mutations in cell signaling genes were acquired at time of AML progression. Mutations in ASXL1, EZH2 and NRAS correlated with higher risk features and shorter overall survival (OS) and progression free survival (PFS). Patients with SRSF2 mutations associated with poorer OS, while absence of TET2 mutations (TET2wt) was predictive of shorter PFS. A decrease in OS and PFS was observed as the number of adverse risk gene mutations (ASXL1, EZH2, NRAS and SRSF2) increased. On multivariate analyses, CMML-specific scoring system (CPSS) and presence of adverse risk gene mutations remained significant for OS, while CPSS and TET2wt were predictive of PFS. These results confirm that mutation analysis can add prognostic value to patients with CMML and low risk cytogenetic features or uninformative CC. PMID:27486981

  11. An improved hypothesis-feedback equalization algorithm for multicode direct-sequence spread-spectrum underwater communications

    Institute of Scientific and Technical Information of China (English)

    HAN Jing; HUANG Jianguo; SHEN Xiaohong; WANG Yu

    2007-01-01

    In underwater acoustic communication,because the available bandwidth of the channel is severely limited,the direct-sequence spread-spectrum scheme can only be realized at low bit rates.To improve the transmission speed,a multicode spread-spectrum scheme is considered.However,in this case,due to the rapid time-variability of the underwater channel,and the influence of inter-symbol interference(ISI)and inter-channel interference(ICI),the conventional rake receiver may fail to function.The hypothesis-feedback equalization algorithm has been proposed for the direct-sequence spread-spectrum system[1].By updating coefficients at chip rate and feeding back hypothesized chips,it can track time-variability and combat ISI effectively.However,for a multicode system,its performance will be degraded bv ICI.An improved algorithm is proposed in this paper,which combines parallel interference cancellation(PIC)with hypothesis-feedback equalization(HFE),with the capabilities of tracking the time-varying channel and suppressing the ISI and ICI at the same time.Simulation results prove that the proposed algorithm can significantly improve the performance of a multicode system.

  12. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

    DEFF Research Database (Denmark)

    Li, Ying-hui; Zhao, Shan-cen; Ma, Jian-xin;

    2013-01-01

    BACKGROUND:Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re...

  13. ECHO Ontario Chronic Pain & Opioid Stewardship: Providing Access and Building Capacity for Primary Care Providers in Underserviced, Rural, and Remote Communities.

    Science.gov (United States)

    Dubin, Ruth E; Flannery, John; Taenzer, Paul; Smith, Andrew; Smith, Karen; Fabico, Ralph; Zhao, Jane; Cameron, Lindsay; Chmelnitsky, Dana; Williams, Rob; Carlin, Leslie; Sidrak, Hannah; Arora, Sanjeev; Furlan, Andrea D

    2015-01-01

    Chronic pain is a prevalent and serious problem in the province of Ontario. Frontline primary care providers (PCPs) manage the majority of chronic pain patients, yet receive minimal training in chronic pain. ECHO (Extension for Community Healthcare Outcomes) Ontario Chronic Pain & Opioid Stewardship aims to address the problem of chronic pain management in Ontario. This paper describes the development, operation, and evaluation of the ECHO Ontario Chronic Pain project. We discuss how ECHO increases PCP access and capacity to manage chronic pain, the development of a community of practice, as well as the limitations of our approach. The ECHO model is a promising approach for healthcare system improvement. ECHO's strength lies in its simplicity, adaptability, and use of existing telemedicine infrastructure to increase both access and capacity of PCPs in underserviced, rural, and remote communities.

  14. Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system.

    Science.gov (United States)

    Wibberg, Daniel; Rupp, Oliver; Jelonek, Lukas; Kröber, Magdalena; Verwaaijen, Bart; Blom, Jochen; Winkler, Anika; Goesmann, Alexander; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

    2015-06-10

    The phytopathogenic fungus Rhizoctonia solani AG1-IB of the phylum Basidiomycota affects various economically important crops comprising bean, rice, soybean, figs, cabbage and lettuce. The R. solani isolate 7/3/14 of the anastomosis group AG1-IB was deeply resequenced on the Illumina MiSeq system applying the mate-pair mode to improve its genome sequence. Assembly of obtained sequence reads significantly reduced the amount of scaffolds and improved the genome sequence of the isolate compared to the previous sequencing approach. The genome sequence of the AG1-IB isolate 7/3/14 now provides an up-graded basis to analyze genome features predicted to play a role in pathogenesis and for the development of strategies to antagonize the pathogenic impact of this fungus.

  15. A New Definition and Classification of Echo Questions

    Institute of Scientific and Technical Information of China (English)

    王瑾琼; 张岭

    2014-01-01

    The frequent occurrence of echo questions in people’s daily conversation has not arouse enough interest in linguists yet; meanwhile, different scholars hold different views when it comes to such questions as how far the boundary of echo ques-tions should extend, how they should be classified, etc. The following paper gives the echo question a new definition and classifi-cation. It hopes to provide a more persuasive reference of future researchers.

  16. An Acoustic Echo Cancellation System based on Adaptive Algorithm

    OpenAIRE

    2012-01-01

    Adaptive filtering technique is one of the core technologies in digital signal processing and finds numerous application areas in science as well as in industry. Adaptive filtering technique is widely used in many applications, including echo cancellation, adaptive noise cancellation, adaptive beam forming and adaptive equalization. Acoustic echo is a common occurrence in today’s telecommunication systems. The distraction caused by the acoustic echo, reduces the speech quality in the communic...

  17. Decoherence and Spin Echo in Biological Systems

    CERN Document Server

    Nesterov, Alexander I

    2015-01-01

    The spin echo approach is extended to include bio-complexes for which the interaction with dynamical noise is strong. Significant restoration of the free induction decay signal due to homogeneous (decoherence) and inhomogeneous (dephasing) broadening is demonstrated analytically and numerically, for both an individual dimer of interacting chlorophylls and for an ensemble of dimers. This approach is based on an exact and closed system of ordinary differential equations that can be easily solved for a wide range of parameters that are relevant for bio-applications.

  18. Decoherence alias Loschmidt echo of the environment

    CERN Document Server

    Gorin, T; Seligman, T H; Strunz, W T

    2004-01-01

    Entanglement between a quantum system and its environment leads to loss of coherence in the former. In general, the temporal fate of coherences is complicated. Here, we establish the connection between decoherence of a central system and fidelity decay in the environment for a variety of situations, including both, energy conserving and dissipative couplings. We show how properties of unitary time evolution of the environment can be inferred from the non-unitary evolution of coherences in the central system. This opens up promising ways for measuring Loschmidt echoes in a variety of situations.

  19. Instances or Sequences? Improving the State of the Art of Qualitative Research

    Directory of Open Access Journals (Sweden)

    David Silverman

    2005-09-01

    Full Text Available Numbers apparently talk. With few numbers, qualitative researchers appear to rely on examples or instances to support their analysis. Hence research reports routinely display data extracts which serve as telling instances of some claimed phenomenon. However, the use of such an evidential base rightly provokes the charge of (possible anecdotalism, i.e. choosing just those extracts which support your argument. I suggest that this methodological problem is best addressed by returning to those features of our theoretical roots which tend to distinguish what we do from the work of quantitative social scientists. Although SAUSSURE is most cited in linguistics and structural anthropology, he provides a simple rule that applies to us all. In a rebuke to our reli­ance on instances, SAUSSURE tells us "no mean­ing exists in a single item". Everything depends upon how single items (elements are articulated. One everyday activity in which the social world is articulated is through the construction of se­quences. Just as participants attend to the se­quential placing of interactional "events", so should social scientists. Using examples drawn from focus groups, fieldnotes and audiotapes, I argue that the identification of such sequences rather than the citing of instances should constitute a prime test for the adequacy of any claim about qualitative data. URN: urn:nbn:de:0114-fqs0503301

  20. High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase.

    Science.gov (United States)

    Ditzler, Mark A; Lange, Margaret J; Bose, Debojit; Bottoms, Christopher A; Virkler, Katherine F; Sawyer, Andrew W; Whatley, Angela S; Spollen, William; Givan, Scott A; Burke, Donald H

    2013-02-01

    Systematic evolution of ligands through exponential enrichment (SELEX) is a well-established method for generating nucleic acid populations that are enriched for specified functions. High-throughput sequencing (HTS) enhances the power of comparative sequence analysis to reveal details of how RNAs within these populations recognize their targets. We used HTS analysis to evaluate RNA populations selected to bind type I human immunodeficiency virus reverse transcriptase (RT). The populations are enriched in RNAs of independent lineages that converge on shared motifs and in clusters of RNAs with nearly identical sequences that share common ancestry. Both of these features informed inferences of the secondary structures of enriched RNAs, their minimal structural requirements and their stabilities in RT-aptamer complexes. Monitoring population dynamics in response to increasing selection pressure revealed RNA inhibitors of RT that are more potent than the previously identified pseudoknots. Improved potency was observed for inhibition of both purified RT in enzymatic assays and viral replication in cell-based assays. Structural and functional details of converged motifs that are obscured by simple consensus descriptions are also revealed by the HTS analysis. The approach presented here can readily be generalized for the efficient and systematic post-SELEX development of aptamers for down-stream applications.

  1. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6

    Directory of Open Access Journals (Sweden)

    Creason Allison L

    2010-09-01

    Full Text Available Abstract Background Pseudomonas fluorescens is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metabolites with potential as natural products. P. fluorescens isolate WH6 produces Germination-Arrest Factor (GAF, a predicted small peptide or amino acid analog with herbicidal activity that specifically inhibits germination of seeds of graminaceous species. Results We used a hybrid next-generation sequencing approach to develop a high-quality draft genome sequence for P. fluorescens WH6. We employed automated, manual, and experimental methods to further improve the draft genome sequence. From this assembly of 6.27 megabases, we predicted 5876 genes, of which 3115 were core to P. fluorescens and 1567 were unique to WH6. Comparative genomic studies of WH6 revealed high similarity in synteny and orthology of genes with P. fluorescens SBW25. A phylogenomic study also placed WH6 in the same lineage as SBW25. In a previous non-saturating mutagenesis screen we identified two genes necessary for GAF activity in WH6. Mapping of their flanking sequences revealed genes that encode a candidate anti-sigma factor and an aminotransferase. Finally, we discovered several candidate virulence and host-association mechanisms, one of which appears to be a complete type III secretion system. Conclusions The improved high-quality draft genome sequence of WH6 contributes towards resolving the P. fluorescens species, providing additional impetus for establishing two separate lineages in P. fluorescens. Despite the high levels of orthology and synteny to SBW25, WH6 still had a substantial number of unique genes and represents another source for the discovery of genes with implications in affecting plant growth and health. Two genes are demonstrably necessary for GAF and further characterization of their proteins is important for developing

  2. ECHO - Search and Order Metadata Registry Post EDG to WIST Transition

    Science.gov (United States)

    Bories, C.; Pilone, D.

    2009-12-01

    (unclear what is meant by this), both in searches and orders. Currently, ECHO serves an average of over 25,000 queries and 2,500 orders on a weekly basis. Through targeted architectural changes and continued software tuning, ECHO has improved its performance metrics in a significant way. Average query performance has been more than halved since the beginning of 2009 and the standard deviation for queries has been reduced to an eighth in the same period. The increased system performance capability was highlighted during the first week of the ASTER GDEM June 2009 release by sustaining increased performance demands and higher rates of user service levels. This was seen through an increase of four times the demand for orders, 10 times the number of searches and more than double the number of registered users. The excellent response of the ECHO system and team is the result of months of focused and continuous improvements in ECHO’s performance, availability and stability. With availability metrics above 98% the ECHO system demonstrates full operational maturity; ready and available to fulfill NASA Science Missions Directorate mission of making EOSDIS data broadly available and usable by a variety of science applications.

  3. Comparison of multi-echo dixon methods with volume interpolated breath-hold gradient magnetic resonance imaging in fat-signal fraction quantification of paravaertebral muscle

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Yeon Hwa; Kim, Hak Sun; Lee, Young Han [Dept. of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); and others

    2015-10-15

    To assess whether multi-echo Dixon magnetic resonance (MR) imaging with simultaneous T2{sup *} estimation and correction yields more accurate fat-signal fraction (FF) measurement of the lumbar paravertebral muscles, in comparison with non-T2{sup *}-corrected two-echo Dixon or T2{sup *}-corrected three-echo Dixon, using the FF measurements from single-voxel MR spectroscopy as the reference standard. Sixty patients with low back pain underwent MR imaging with a 1.5T scanner. FF mapping images automatically obtained using T2{sup *}-corrected Dixon technique with two (non-T2{sup *}-corrected), three, and six echoes, were compared with images from single-voxel MR spectroscopy at the paravertebral muscles on levels L4 through L5. FFs were measured directly by two radiologists, who independently drew the region of interest on the mapping images from the three sequences. A total of 117 spectroscopic measurements were performed either bilaterally (57 of 60 subjects) or unilaterally (3 of 60 subjects). The mean spectroscopic FF was 14.3 ± 11.7% (range, 1.9-63.7%). Interobserver agreement was excellent between the two radiologists. Lin's concordance correlation between the spectroscopic findings and all the imaging-based FFs were statistically significant (p < 0.001). FFs obtained from the T2*-corrected six-echo Dixon sequences showed a significantly better concordance with the spectroscopic data, with its concordance correlation coefficient being 0.99 and 0.98 (p < 0.001), as compared with two- or three-echo methods. T2{sup *}-corrected six-echo Dixon sequence would be a better option than two- or three-echo methods for noninvasive quantification of lumbar muscle fat quantification.

  4. An Improved Particle Swarm Optimization for Selective Single Machine Scheduling with Sequence Dependent Setup Costs and Downstream Demands

    Directory of Open Access Journals (Sweden)

    Kun Li

    2015-01-01

    Full Text Available This paper investigates a special single machine scheduling problem derived from practical industries, namely, the selective single machine scheduling with sequence dependent setup costs and downstream demands. Different from traditional single machine scheduling, this problem further takes into account the selection of jobs and the demands of downstream lines. This problem is formulated as a mixed integer linear programming model and an improved particle swarm optimization (PSO is proposed to solve it. To enhance the exploitation ability of the PSO, an adaptive neighborhood search with different search depth is developed based on the decision characteristics of the problem. To improve the search diversity and make the proposed PSO algorithm capable of getting out of local optimum, an elite solution pool is introduced into the PSO. Computational results based on extensive test instances show that the proposed PSO can obtain optimal solutions for small size problems and outperform the CPLEX and some other powerful algorithms for large size problems.

  5. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes.

    Science.gov (United States)

    Fu, Yong-Bi; Peterson, Gregory W; Dong, Yibo

    2016-04-07

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.

  6. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

    Directory of Open Access Journals (Sweden)

    Yong-Bi Fu

    2016-04-01

    Full Text Available Genotyping-by-sequencing (GBS has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV in 12 plant species showed 1.7–6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0–16.7% missing observations than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.

  7. Evaluation of the Chondromalacia Patella Using a Microscopy Coil: Comparison of the Two-Dimensional Fast Spin Echo Techniques and the Three-Dimensional Fast Field Echo Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyun Joo; Lee, Sang Hoon; Kang, Chang Ho; Ryu, Jeong Ah; Shin, Myung Jin; Cho, Kyung Ja; Cho, Woo Shin [University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

    2011-02-15

    We wanted to compare the two-dimensional (2D) fast spin echo (FSE) techniques and the three-dimensional (3D) fast field echo techniques for the evaluation of the chondromalacia patella using a microscopy coil. Twenty five patients who underwent total knee arthroplasty were included in this study. Preoperative MRI evaluation of the patella was performed using a microscopy coil (47 mm). The proton density-weighted fast spin echo images (PD), the fat-suppressed PD images (FS-PD), the intermediate weighted-fat suppressed fast spin echo images (iw-FS-FSE), the 3D balanced-fast fi eld echo images (B-FFE), the 3D water selective cartilage scan (WATS-c) and the 3D water selective fluid scan (WATS-f) were obtained on a 1.5T MRI scanner. The patellar cartilage was evaluated in nine areas: the superior, middle and the inferior portions that were subdivided into the medial, central and lateral facets in a total of 215 areas. Employing the Noyes grading system, the MRI grade 0-I, II and III lesions were compared using the gross and microscopic findings. The sensitivity, specificity and accuracy were evaluated for each sequence. The significance of the differences for the individual sequences was calculated using the McNemar test. The gross and microscopic findings demonstrated 167 grade 0-I lesions, 40 grade II lesions and eight grade III lesions. Iw-FS-FSE had the highest accuracy (sensitivity/specificity/accuracy = 88%/98%/96%), followed by FSPD (78%/98%/93%, respectively), PD (76%/98%/93%, respectively), B-FFE (71%/100%/93%, respectively), WATS-c (67%/100%/92%, respectively) and WATS-f (58%/99%/89%, respectively). There were statistically significant differences for the iw-FS-FSE and WATS-f and for the PD-FS and WATS-f (p < 0.01). The iw-FS-FSE images obtained with a microscopy coil show best diagnostic performance among the 2D and 3D GRE images for evaluating the chondromalacia patella

  8. Light Echoes of Transients and Variables

    Science.gov (United States)

    Rest, Armin

    2012-04-01

    abstract-type="normal">SummaryTycho Brahe's observations of a supernova in 1572 challenged the contemporaneous European view of the cosmos that the celestial realm was unchanging. 439 years later we have once again seen the light that Tycho saw, as some of the light from the 1572 supernova is reflected off dust and is only now reaching Earth. These light echoes, as well as ones detected from other transients and variables, give us a very rare opportunity in astronomy: direct observation of the cause (the supernova explosion) and the effect (the supernova remnant) of the same astronomical event. Furthermore, in some cases we can compare light echoes at different angles around a supernova remnant, and thus investigate possible asymmetry in the supernova explosion. In addition, in cases where the scattering dust is favorably positioned, the geometric distance to the SN remnant can be determined using polarization measurements. These techniques have been successfully applied to various transients in the last decade, and the talk gave an overview of the scientific results and techniques, with a particular focus on the challenges we will face in the current and upcoming wide-field time-domain surveys.

  9. Caustic echoes from a Schwarzschild black hole

    CERN Document Server

    Zenginoğlu, Anıl

    2012-01-01

    We present the first numerical construction of the scalar Schwarzschild Green function in the time-domain, which reveals several universal features of wave propagation in black hole spacetimes. We demonstrate the trapping of energy near the photon sphere and confirm its exponential decay. The trapped wavefront propagates through caustics resulting in echoes that propagate to infinity. The arrival times and the decay rate of these caustic echoes are consistent with propagation along null geodesics and the large l-limit of quasinormal modes. We show that the four-fold singularity structure of the retarded Green function is due to the well-known action of a Hilbert transform on the trapped wavefront at caustics. A two-fold cycle is obtained for degenerate source-observer configurations along the caustic line, where the energy amplification increases with an inverse power of the scale of the source. Finally, we discuss the tail piece of the solution due to propagation within the light cone, up to and including nu...

  10. Impact echo scanning of concrete and wood

    Science.gov (United States)

    Sack, Dennis A.; Olson, Larry D.; Aouad, Marwan F.

    1995-05-01

    This paper presents an overview of a new nondestructive testing (NDT) system that allows rapid nondestructive assessment of many types of structural materials. The new system is based on scanning impact echo (IE), using a rolling receiver, digitally controlled impact source, and a distance measurement wheel integrated into a system that is capable of performing over 3000 IE tests per hour. The system has been successfully used on both concrete and wood for condition assessment. Previously, impact echo testing has been limited to point-by-point testing at rates of typically 30 - 60 points per hour. The new system is usable on any flat, relatively smooth surface such as floor slabs, pavements, walls, columns, beams, etc. In addition to IE scanning, the new system has recently been expanded to allow the performance of spectral analysis of surface waves (SASW) scanning on concrete and wood. The SASW method allows the measurement of material stiffness (modulus) versus depth, and therefore can give a profile of the material condition versus depth. Included in this paper are brief discussions of the IE and SASW methods, the scanner system hardware, and the software which was developed to enable efficient processing, analysis, and display of the test data and results. Also included are sample data plots and a case history presentation of the use of the system in the field, including one in which 23,000 IE tests were performed on an elevated floor slab in approximately 16 hours of testing time.

  11. The EChO science case

    CERN Document Server

    Tinetti, Giovanna; Eccleston, Paul; Hartogh, Paul; Isaak, Kate; Linder, Martin; Lovis, Christophe; Micela, Giusi; Ollivier, Marc; Puig, Ludovic; Ribas, Ignasi; Snellen, Ignas; Allard, Bruce Swinyard France; Barstow, Joanna; Cho, James; Coustenis, Athena; Cockell, Charles; Correia, Alexandre; Decin, Leen; de Kok, Remco; Deroo, Pieter; Encrenaz, Therese; Forget, Francois; Glasse, Alistair; Griffith, Caitlin; Guillot, Tristan; Koskinen, Tommi; Lammer, Helmut; Leconte, Jeremy; Maxted, Pierre; Mueller-Wodarg, Ingo; Nelson, Richard; North, Chris; Pallé, Enric; Pagano, Isabella; Piccioni, Guseppe; Pinfield, David; Selsis, Franck; Sozzetti, Alessandro; Stixrude, Lars; Tennyson, Jonathan; Turrini, Diego; Beaulieu, Mariarosa Zapatero-Osorio Jean-Philippe; Grodent, Denis; Guedel, Manuel; Luz, David; Nørgaard-Nielsen, Hans Ulrik; Ray, Tom; Rickman, Hans; Selig, Avri; Banaszkiewicz, Mark Swain Marek; Barlow, Mike; Bowles, Neil; Branduardi-Raymont, Graziella; Foresto, Vincent Coudé du; Gerard, Jean-Claude; Gizon, Laurent; Hornstrup, Allan; Jarchow, Christopher; Kerschbaum, Franz; Kovacs, Géza; Lagage, Pierre-Olivier; Lim, Tanya; Lopez-Morales, Mercedes; Malaguti, Giuseppe; Pace, Emanuele; Pascale, Enzo; Vandenbussche, Bart; Wright, Gillian; Adriani, Gonzalo Ramos Zapata Alberto; Azzollini, Ruymán; Balado, Ana; Bryson, Ian; Burston, Raymond; Colomé, Josep; Crook, Martin; Di Giorgio, Anna; Griffin, Matt; Hoogeveen, Ruud; Ottensamer, Roland; Irshad, Ranah; Middleton, Kevin; Morgante, Gianluca; Pinsard, Frederic; Rataj, Mirek; Reess, Jean-Michel; Savini, Giorgio; Schrader, Jan-Rutger; Stamper, Richard; Abe, Berend Winter L; Abreu, M; Achilleos, N; Ade, P; Adybekian, V; Affer, L; Agnor, C; Agundez, M; Alard, C; Alcala, J; Prieto, C Allende; Floriano, F J Alonso; Altieri, F; Iglesias, C A Alvarez; Amado, P; Andersen, A; Aylward, A; Baffa, C; Bakos, G; Ballerini, P; Banaszkiewicz, M; Barber, R J; Barrado, D; Barton, E J; Batista, V; Bellucci, G; Avilés, J A Belmonte; Berry, D; Bézard, B; Biondi, D; Błęcka, M; Boisse, I; Bonfond, B; Bordé, P; Börner, P; Bouy, H; Brown, L; Buchhave, L; Budaj, J; Bulgarelli, A; Burleigh, M; Cabral, A; Capria, M T; Cassan, A; Cavarroc, C; Cecchi-Pestellini, C; Cerulli, R; Chadney, J; Chamberlain, S; Charnoz, S; Jessen, N Christian; Ciaravella, A; Claret, A; Claudi, R; Coates, A; Cole, R; Collura, A; Cordier, D; Covino, E; Danielski, C; Damasso, M; Deeg, H J; Delgado-Mena, E; Del Vecchio, C; Demangeon, O; De Sio, A; De Wit, J; Dobrijévic, M; Doel, P; Dominic, C; Dorfi, E; Eales, S; Eiroa, C; Contreras, M Espinoza; Esposito, M; Eymet, V; Fabrizio, N; Fernández, M; Castella, B Femenía; Figueira, P; Filacchione, G; Fletcher, L; Focardi, M; Fossey, S; Fouqué, P; Frith, J; Galand, M; Gambicorti, L; Gaulme, P; López, R J García; Garcia-Piquer, A; Gear, W; Gerard, J -C; Gesa, L; Giani, E; Gianotti, F; Gillon, M; Giro, E; Giuranna, M; Gomez, H; Gomez-Leal, I; Hernandez, J Gonzalez; Merino, B González; Graczyk, R; Grassi, D; Guardia, J; Guio, P; Gustin, J; Hargrave, P; Haigh, J; Hébrard, E; Heiter, U; Heredero, R L; Herrero, E; Hersant, F; Heyrovsky, D; Hollis, M; Hubert, B; Hueso, R; Israelian, G; Iro, N; Irwin, P; Jacquemoud, S; Jones, G; Jones, H; Justtanont, K; Kehoe, T; Kerschbaum, F; Kerins, E; Kervella, P; Kipping, D; Koskinen, T; Krupp, N; Lahav, O; Laken, B; Lanza, N; Lellouch, E; Leto, G; Goldaracena, J Licandro; Lithgow-Bertelloni, C; Liu, S J; Cicero, U Lo; Lodieu, N; Lognonné, P; Lopez-Puertas, M; Lopez-Valverde, M A; Rasmussen, I Lundgaard; Luntzer, A; Machado, P; MacTavish, C; Maggio, A; Maillard, J -P; Magnes, W; Maldonado, J; Mall, U; Marquette, J -B; Mauskopf, P; Massi, F; Maurin, A -S; Medvedev, A; Michaut, C; Miles-Paez, P; Montalto, M; Rodríguez, P Montañés; Monteiro, M; Montes, D; Morais, H; Morales, J C; Morales-Calderón, M; Morello, G; Martín, A Moro; Moses, J; Bedon, A Moya; Alcaino, F Murgas; Oliva, E; Orton, G; Palla, F; Pancrazzi, M; Pantin, E; Parmentier, V; Parviainen, H; Ramírez, K Y Peña; Peralta, J; Perez-Hoyos, S; Petrov, R; Pezzuto, S; Pietrzak, R; Pilat-Lohinger, E; Piskunov, N; Prinja, R; Prisinzano, L; Polichtchouk, I; Poretti, E; Radioti, A; Ramos, A A; Rank-Lüftinger, T; Read, P; Readorn, K; López, R Rebolo; Rebordão, J; Rengel, M; Rezac, L; Rocchetto, M; Rodler, F; Béjar, V J Sánchez; Lavega, A Sanchez; Sanromá, E; Santos, N; Forcada, J Sanz; Scandariato, G; Schmider, F -X; Scholz, A; Scuderi, S; Sethenadh, J; Shore, S; Showman, A; Sicardy, B; Sitek, P; Smith, A; Soret, L; Sousa, S; Stiepen, A; Stolarski, M; Strazzulla, G; Tabernero, H M; Tanga, P; Tecsa, M; Temple, J; Terenzi, L; Tessenyi, M; Testi, L; Thompson, S; Thrastarson, H; Tingley, B W; Trifoglio, M; Torres, J Martín; Tozzi, A; Turrini, D; Varley, R; Vakili, F; de Val-Borro, M; Valdivieso, M L; Venot, O; Villaver, E; Vinatier, S; Viti, S; Waldmann, I; Waltham, D; Ward-Thompson, D; Waters, R; Watkins, C; Watson, D; Wawer, P; Wawrzaszk, A; White, G; Widemann, T; Winek, W; Wiśniowski, T; Yelle, R; Yung, Y; Yurchenko, S N

    2015-01-01

    The discovery of almost 2000 exoplanets has revealed an unexpectedly diverse planet population. Observations to date have shown that our Solar System is certainly not representative of the general population of planets in our Milky Way. The key science questions that urgently need addressing are therefore: What are exoplanets made of? Why are planets as they are? What causes the exceptional diversity observed as compared to the Solar System? EChO (Exoplanet Characterisation Observatory) has been designed as a dedicated survey mission for transit and eclipse spectroscopy capable of observing a large and diverse planet sample within its four-year mission lifetime. EChO can target the atmospheres of super-Earths, Neptune-like, and Jupiter-like planets, in the very hot to temperate zones (planet temperatures of 300K-3000K) of F to M-type host stars. Over the next ten years, several new ground- and space-based transit surveys will come on-line (e.g. NGTS, CHEOPS, TESS, PLATO), which will specifically focus on find...

  12. rTPPM: Towards Improving Solid-State NMR Two-Pulse Phase-Modulation Heteronuclear Dipolar Decoupling Sequence by Refocusing

    DEFF Research Database (Denmark)

    Equbal, Asif; Paul, Subhradip; Mithu, Venus Singh

    2014-01-01

    We present here a simple refocused modification, r TPPM, of the Two-Pulse Phase-Modulation (TPPM) heteronuclear decoupling method, which improves decoupling and makes the sequence much more robust with respect to essential experimental parameters. The modified sequence is compared with the establ...

  13. Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca.

    Science.gov (United States)

    Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Louati, Moussa; Nouioui, Imen; Ktari, Amir; Hezbri, Karima; Gueddou, Abdellatif; Chen, Amy; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Pagani, Ioanna; Sen, Arnab; Wall, Luis; Woyke, Tanja; Gtari, Maher; Tisa, Louis S

    2016-08-04

    Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content and 7,307 predicted protein-coding genes.

  14. Optimal Configuration for Relaxation Times Estimation in Complex Spin Echo Imaging

    Directory of Open Access Journals (Sweden)

    Fabio Baselice

    2014-01-01

    Full Text Available Many pathologies can be identified by evaluating differences raised in the physical parameters of involved tissues. In a Magnetic Resonance Imaging (MRI framework, spin-lattice T1 and spin-spin T2 relaxation time parameters play a major role in such an identification. In this manuscript, a theoretical study related to the evaluation of the achievable performances in the estimation of relaxation times in MRI is proposed. After a discussion about the considered acquisition model, an analysis on the ideal imaging acquisition parameters in the case of spin echo sequences, i.e., echo and repetition times, is conducted. In particular, the aim of the manuscript consists in providing an empirical rule for optimal imaging parameter identification with respect to the tissues under investigation. Theoretical results are validated on different datasets in order to show the effectiveness of the presented study and of the proposed methodology.

  15. Spectral editing of weakly coupled spins using variable flip angles in PRESS constant echo time difference spectroscopy: Application to GABA

    Science.gov (United States)

    Snyder, Jeff; Hanstock, Chris C.; Wilman, Alan H.

    2009-10-01

    A general in vivo magnetic resonance spectroscopy editing technique is presented to detect weakly coupled spin systems through subtraction, while preserving singlets through addition, and is applied to the specific brain metabolite γ-aminobutyric acid (GABA) at 4.7 T. The new method uses double spin echo localization (PRESS) and is based on a constant echo time difference spectroscopy approach employing subtraction of two asymmetric echo timings, which is normally only applicable to strongly coupled spin systems. By utilizing flip angle reduction of one of the two refocusing pulses in the PRESS sequence, we demonstrate that this difference method may be extended to weakly coupled systems, thereby providing a very simple yet effective editing process. The difference method is first illustrated analytically using a simple two spin weakly coupled spin system. The technique was then demonstrated for the 3.01 ppm resonance of GABA, which is obscured by the strong singlet peak of creatine in vivo. Full numerical simulations, as well as phantom and in vivo experiments were performed. The difference method used two asymmetric PRESS timings with a constant total echo time of 131 ms and a reduced 120° final pulse, providing 25% GABA yield upon subtraction compared to two short echo standard PRESS experiments. Phantom and in vivo results from human brain demonstrate efficacy of this method in agreement with numerical simulations.

  16. Pulse-echo ultrasound transit time spectroscopy: A comparison of experimental measurement and simulation prediction.

    Science.gov (United States)

    Wille, Marie-Luise; Almualimi, Majdi A; Langton, Christian M

    2016-01-01

    Considering ultrasound propagation through complex composite media as an array of parallel sonic rays, a comparison of computer-simulated prediction with experimental data has previously been reported for transmission mode (where one transducer serves as transmitter, the other as receiver) in a series of 10 acrylic step-wedge samples, immersed in water, exhibiting varying degrees of transit time inhomogeneity. In this study, the same samples were used but in pulse-echo mode, where the same ultrasound transducer served as both transmitter and receiver, detecting both 'primary' (internal sample interface) and 'secondary' (external sample interface) echoes. A transit time spectrum was derived, describing the proportion of sonic rays with a particular transit time. A computer simulation was performed to predict the transit time and amplitude of various echoes created, and compared with experimental data. Applying an amplitude-tolerance analysis, 91.7% ± 3.7% of the simulated data were within ±1 standard deviation of the experimentally measured amplitude-time data. Correlation of predicted and experimental transit time spectra provided coefficients of determination (R(2)%) ranging from 100.0% to 96.8% for the various samples tested. The results acquired from this study provide good evidence for the concept of parallel sonic rays. Furthermore, deconvolution of experimental input and output signals has been shown to provide an effective method to identify echoes otherwise lost due to phase cancellation. Potential applications of pulse-echo ultrasound transit time spectroscopy include improvement of ultrasound image fidelity by improving spatial resolution and reducing phase interference artefacts.

  17. Fast all-optical nuclear spin echo technique based on EIT

    Science.gov (United States)

    Walther, Andreas; Nilsson, Adam N.; Li, Qian; Rippe, Lars; Kröll, Stefan

    2016-08-01

    We demonstrate an all-optical Raman spin echo technique, using electromagnetically induced transparency (EIT) to create the pulses required for a spin echo sequence: initialization, pi-rotation, and readout. The first pulse of the sequence induces coherence directly from a mixed state, and the technique is used to measure the nuclear spin coherence of an inhomogeneously broadened ensemble of rare-earth ions (Pr3 +) in a crystal. The rephasing pi-rotation is shown to offer an advantage of combining the rephasing action with the operation of a phase gate, particularly useful in e.g. dynamic decoupling sequences. In contrast to many previous experiments the sequence does not require any preparatory hole burning, which greatly shortens the total duration of the sequence. The effect of the different pulses is characterized by quantum state tomography and compared with simulations. We demonstrate two applications of the technique: compensating the magnetic field across our sample by monitoring T 2 reductions from stray magnetic fields, and measuring coherence times at temperatures up to 11 K, where standard preparation techniques are difficult to implement. We explore the potential of the technique, in particular for systems with much shorter T 2, and other possible applications.

  18. [Application of brain diffusion-weighted imaging performed using readout segmentation of long variable echo trains].

    Science.gov (United States)

    Ishida, Go; Oishi, Makoto; Morii, Ken; Hasegawa, Kenji; Saito, Akihiko; Sato, Mitsuya; Takizawa, Osamu; Murata, Katsutoshi; Porter, D A; Matsuzawa, Hitoshi; Fujii, Yukihiko

    2015-01-01

    We report the preliminary use of the readout segmentation of long variable echo trains(RESOLVE)sequence, a novel magnetic resonance(MR)scanning technique based on a readout segmented echo planar imaging(EPI)strategy. RESOLVE enables high-resolution diffusion-weighted imaging(DWI)by minimizing susceptibility distortions and T2* blurring. The software for this sequence was provided by Siemens AG, Germany. Previously, we determined appropriate sequence parameters to obtain sufficiently high-resolution images through phantom studies. Then, we applied the sequence to some clinical cases with neurological disorders and analyzed the RESOLVE-DWI data with diffusion tensor imaging(DTI)techniques. In this article, we report clinical application of the RESOLVE sequence in two cases, one with cerebellar infarction and one with an intracranial epidermoid cyst. In both cases, RESOLVE-DWI clearly exposed structures that were obscured or severely distorted by artifacts on usual single-shot EPI-DWI. DTI analyses for RESOLVE-DWI data provided detailed information about fiber tracts and cranial nerves.

  19. Power Doppler sonography with and without echo-enhancing contrast agent and contrast-enhanced MRI for the evaluation of rheumatoid arthritis of the shoulder joint: differentiation between synovitis and joint effusion

    Energy Technology Data Exchange (ETDEWEB)

    Wamser, G. [Department of Diagnostic Radiology, Klinikum Augsburg, Augsburg (Germany); Diagnostic Radiology, Klinik Dr. Schindlbeck, Seestrasse 43, 82211, Herrsching (Germany); Bohndorf, K.; Vollert, K.; Buecklein, W. [Department of Diagnostic Radiology, Klinikum Augsburg, Augsburg (Germany); Schalm, J. [Department of Internal Medicine I, Klinikum Augsburg, Augsburg (Germany)

    2003-06-01

    To evaluate patients with clinically active rheumatoid arthritis (RA) of the shoulder for joint effusion and synovitis using conventional sonography, power Doppler (PD) sonography with and without echo-enhancing contrast agent, and contrast-enhanced MRI.Design and patients Twenty-four patients (mean age 64 years) with known RA had one symptomatic shoulder evaluated by conventional gray-scale sonography and PD sonography before and after intravenous administration of the echo-enhancing contrast agent Levovist (300 mg/ml, 2.5 g). The degree and extent of the altered echo pattern in the subacromial bursa, axillary recess and glenohumeral joint seen by conventional gray-scale sonography and the intensity of vascular signals of PD sonography were compared with the findings of MRI obtained with T2-weighted turbo spin-echo sequences and contrast-enhanced T1-weighted fat-saturated spin-echo sequences. MRI was evaluated by two readers in consensus without knowledge of the sonographic findings. MRI, which was used as the reference examination, detected joint effusion in 71% (17/24) and synovitis in 92% (22/24) of the patients. Conventional sonography revealed an abnormal articular echo pattern in 96% (23/24) of the patients, especially in the axillary recess and subacromial bursa, but failed to attribute the altered echo pattern to either fluid or specific synovitis. PD sonography allowed a specific diagnosis of synovitis in 33% (8 patients), which increased to 50% (12 patients) after administration of an echo-enhancing contrast agent. In 42% (10/24) of the patients, the findings of synovitis demonstrated by MRI corresponded to an altered echo pattern by conventional sonography, but vascular signals were absent by PD sonography with or without echo-enhancing contrast agent. Using MRI as the ''gold standard,'' PD sonography with and without echo-enhancing contrast agent cannot reliably identify synovitis or distinguish synovial inflammation from effusion

  20. The INGVterremoti blog: a new communication tool to improve earthquake information during the Po Plain seismic sequence

    Directory of Open Access Journals (Sweden)

    Maurizio Pignone

    2012-10-01

    Full Text Available During a seismic sequence, it is extremely important that the population shaken by the earthquakes has continuous and timely information about the ongoing seismic activity. For this reason, a few days after the beginning of the Po Plain sequence, we opened a new informative channel, namely a blog (http://ingvterremoti.wordpress.com, through which we released tens of updates and in-depth scientific explanations on the earthquake sequence, as well as the classical information provided on the INGV web sites. Through the collaboration of Istituto Nazionale di Geofisica e Vulcanologia (INGV researchers and technicians, we published more than 80 posts about the sequence, to describe ongoing activities during the emergency, and the first scientific results obtained from preliminary data processing. The response of the public was immediately encouraging, and reached its maximum on June 3, 2012, when a Ml 5.1 earthquake was strongly felt in the region previously shaken by the May 20, 2012, Ml 5.9 and the May 29, 2012, Ml 5.8 events. We recorded more than 850,000 views on that particular day, and had more than six million contacts (6,403,843 in the first two months (May 29 to July 29, mostly concentrated in the first 15 days. Even if the number of contacts is surely the main indicator of the effectiveness of a blog, it is important to carry out an in-depth analysis of the audience, to have useful material to further improve this blog. A broader research project could also include cross-media comparisons, taking into account the whole set of social media used by the INGV (YouTube, Twitter, Facebook, Flickr, Apple. Future developments include the creation of new categories and new articles for other regions of Italy, and in-depth scientific articles to explain the results of the research activities. We also plan to find a way to implement the interactions with the public, for answering questions and making comments. The INGVterremoti blog is an original

  1. Improved measurement of brain deformation during mild head acceleration using a novel tagged MRI sequence.

    Science.gov (United States)

    Knutsen, Andrew K; Magrath, Elizabeth; McEntee, Julie E; Xing, Fangxu; Prince, Jerry L; Bayly, Philip V; Butman, John A; Pham, Dzung L

    2014-11-07

    In vivo measurements of human brain deformation during mild acceleration are needed to help validate computational models of traumatic brain injury and to understand the factors that govern the mechanical response of the brain. Tagged magnetic resonance imaging is a powerful, noninvasive technique to track tissue motion in vivo which has been used to quantify brain deformation in live human subjects. However, these prior studies required from 72 to 144 head rotations to generate deformation data for a single image slice, precluding its use to investigate the entire brain in a single subject. Here, a novel method is introduced that significantly reduces temporal variability in the acquisition and improves the accuracy of displacement estimates. Optimization of the acquisition parameters in a gelatin phantom and three human subjects leads to a reduction in the number of rotations from 72 to 144 to as few as 8 for a single image slice. The ability to estimate accurate, well-resolved, fields of displacement and strain in far fewer repetitions will enable comprehensive studies of acceleration-induced deformation throughout the human brain in vivo. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait.

    Directory of Open Access Journals (Sweden)

    Ulrike Ober

    Full Text Available The ability to predict quantitative trait phenotypes from molecular polymorphism data will revolutionize evolutionary biology, medicine and human biology, and animal and plant breeding. Efforts to map quantitative trait loci have yielded novel insights into the biology of quantitative traits, but the combination of individually significant quantitative trait loci typically has low predictive ability. Utilizing all segregating variants can give good predictive ability in plant and animal breeding populations, but gives little insight into trait biology. Here, we used the Drosophila Genetic Reference Panel to perform both a genome wide association analysis and genomic prediction for the fitness-related trait chill coma recovery time. We found substantial total genetic variation for chill coma recovery time, with a genetic architecture that differs between males and females, a small number of molecular variants with large main effects, and evidence for epistasis. Although the top additive variants explained 36% (17% of the genetic variance among lines in females (males, the predictive ability using genomic best linear unbiased prediction and a relationship matrix using all common segregating variants was very low for females and zero for males. We hypothesized that the low predictive ability was due to the mismatch between the infinitesimal genetic architecture assumed by the genomic best linear unbiased prediction model and the true genetic architecture of chill coma recovery time. Indeed, we found that the predictive ability of the genomic best linear unbiased prediction model is markedly improved when we combine quantitative trait locus mapping with genomic prediction by only including the top variants associated with main and epistatic effects in the relationship matrix. This trait-associated prediction approach has the advantage that it yields biologically interpretable prediction models.

  3. Long-lasting inverted photon echo and optical memory

    Energy Technology Data Exchange (ETDEWEB)

    Akhmediev, N.N.; Borisov, B.S.; Zuikov, V.A.; Samartsev, V.V.; Stel' makh, M.F.

    1988-06-01

    Experimental results are presented on the formation of the long-lasting inverted stimulated photon echo in the LaF3:Pr(3+) crystal. The physics of this phenomenon is explained on the basis of a three-level model. The feasibility of using this echo effect in the development of optical-memory systems is considered. 18 references.

  4. Picosecond Photon Echoes Stimulated from an Accumulated Grating

    NARCIS (Netherlands)

    Hesselink, Wim H.; Wiersma, Douwe A.

    1979-01-01

    It is shown that in optical transitions with a bottleneck, a mode-locked cw dye laser may be used to generate and heterodyne detect picosecond photon echoes. These echoes are stimulated from an accumulated grating in the electronic ground state formed by a train of twin excitation pulses of constant

  5. Mean grain size mapping with single-beam echo sounders

    NARCIS (Netherlands)

    Van Walree, P.A.; Ainslie, M.A.; Simons, D.G.

    2006-01-01

    Echo energies of single-beam echo sounders are inverted for the sediment mean grain size via a combination of theoretical and empirical relationships. In situ measurements of the seafloor mass density have revealed the presence of a thin transition layer between the water and the sediment. Within th

  6. Improved method for linear B-cell epitope prediction using antigen's primary sequence.

    Directory of Open Access Journals (Sweden)

    Harinder Singh

    Full Text Available One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell's response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/.

  7. Antisense sequencing improves the accuracy and precision of A-to-I editing measurements using the peak height ratio method

    Directory of Open Access Journals (Sweden)

    Rinkevich Frank D

    2012-01-01

    Full Text Available Abstract Background A-to-I RNA editing is found in all phyla of animals and contributes to transcript diversity that may have profound impacts on behavior and physiology. Many transcripts of genes involved in axonal conductance, synaptic transmission and modulation are the targets of A-to-I RNA editing. There are a number of methods to measure the extent of A-to-I RNA editing, but they are generally costly and time consuming. One way to determine the frequency of A-to-I RNA editing is the peak height ratio method, which compares the size of peaks on electropherograms that represent unedited and edited sites. Findings Sequencing of 4 editing sites of the Dα6 nicotinic acetylcholine receptor subunit with an antisense primer (which uses T/C peaks to measure unedited and edited sites, respectively showed very accurate and precise measurements of A-to-I RNA editing. The accuracy and precision were excellent for all editing sites, including those edited with high or low frequencies. The frequency of A-to-I RNA editing was comparable to the editing frequency as measured by clone counting from the same sample. Sequencing these same sites with the sense primer (which uses A/G peaks yielded inaccurate and imprecise measurements. Conclusions We have validated and improved the accuracy and precision of the peak height ratio method to measure the frequency of A-to-I RNA editing, and shown that results are primer specific. Thus, the correct sequencing primer must be utilized for the most dependable data. When compared to other methods used to measure the frequency of A-to-I RNA editing, the major benefits of the peak height ratio are that this method is inexpensive, fast, non-labor intensive and easily adaptable to many laboratory and field settings.

  8. MRI detection of hypointense brain lesions in patients with multiple sclerosis: T1 spin-echo vs. gradient-echo

    Energy Technology Data Exchange (ETDEWEB)

    Dupuy, Sheena L.; Tauhid, Shahamat; Kim, Gloria; Chu, Renxin; Tummala, Subhash [Departments of Neurology, Brigham and Women' s Hospital, Laboratory for Neuroimaging Research, Partners MS Center, Harvard Medical School, Boston, MA (United States); Hurwitz, Shelley [Departments of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Bakshi, Rohit, E-mail: rbakshi@bwh.harvard.edu [Departments of Neurology, Brigham and Women' s Hospital, Laboratory for Neuroimaging Research, Partners MS Center, Harvard Medical School, Boston, MA (United States); Departments of Radiology, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States)

    2015-08-15

    Highlights: • Compared T1SE and T1GE in detecting hypointense brain lesions in MS patients. • T1GE detected a higher cerebral lesion volume and number than T1SE. • T1SE correlated significantly with disability, while T1GE did not. • Hypointense lesions on T1SE and T1GE are not interchangeable in patients with MS. - Abstract: Objective: Compare T1 spin-echo (T1SE) and T1 gradient-echo (T1GE) sequences in detecting hypointense brain lesions in multiple sclerosis (MS). Background: Chronic hypointense lesions on T1SE MRI scans are a surrogate of severe demyelination and axonal loss in MS. The role of T1GE images in the detection of such lesions has not been clarified. Design/methods: In 45 patients with MS [Expanded Disability Status Scale (EDSS) score (mean ± SD) 3.5 ± 2.0; 37 relapsing-remitting (RR); 8 secondary progressive (SP)], cerebral T1SE, T1GE, and T2-weighted fluid-attenuated inversion-recovery (FLAIR) images were acquired on a 1.5 T MRI scanner. Images were re-sampled to axial 5 mm slices before directly comparing lesion detectability using Jim (v.7, Xinapse Systems). Statistical methods included Wilcoxon signed rank tests to compare sequences and Spearman correlations to test associations. Results: Considering the entire cohort, T1GE detected a higher lesion volume (5.90 ± 6.21 vs. 4.17 ± 4.84 ml, p < 0.0001) and higher lesion number (27.82 ± 20.66 vs. 25.20 ± 20.43, p < 0.05) than T1SE. Lesion volume differences persisted when considering RR and SP patients separately (both p < 0.01). A higher lesion number by T1GE was seen only in the RR group (p < 0.05). When comparing correlations between lesion volume and overall neurologic disability (EDSS score), T1SE correlated with EDSS (Spearman r = 0.29, p < 0.05) while T1GE (r = 0.23, p = 0.13) and FLAIR (r = 0.24, p = 0.12) did not. Conclusion: Our data suggest that hypointense lesions on T1SE and T1GE are not interchangeable in patients with MS. Based on these results, we hypothesize that T1GE

  9. Excitation of spin echo by pulses with linear frequency modulation

    Science.gov (United States)

    Baruzdin, S. A.

    2015-03-01

    The excitation of a spin echo by two pulses with linear frequency modulation, upon which the pulse parameters ensure maximal compression of the response in time, is considered. The frequency of the excitation pulses was changed by a step law, approximating its linear rise. The transfer matrix of the state of the spin system for pulses with linear frequency modulation is found by solving the Bloch equations. The shape of the envelope of the spin echo in thin magnetic cobalt films, as well as the dependence of the echo amplitude on the parameters of the excitation pulses, is determined. The amplitudes of the excitation pulses, which ensure the excitation of the echo maximal amplitude for various values of the frequency deviation, are found. It is shown that the use of pulses with linear frequency modulation makes it possible to obtain the same echo amplitude as with the use of simple excitation pulses for a substantially smaller amplitude and power of excitation pulses.

  10. Echoes from Ancient supernovae in the Large Magellanic Cloud

    Energy Technology Data Exchange (ETDEWEB)

    Rest, A; Suntzeff, N B; Olsen, K; Prieto, J L; Smith, R C; Welch, D L; Becker, A; Bergmann, M; Clocchiatti, A; Cook, K; Garg, A; Huber, M; Miknaitis, G; Minniti, D; Nikolaev, S; Stubbs, C

    2005-06-15

    In principle, historical supernovae could still be visible as scattered-light echoes even centuries later [1, 2]. Searches for surface brightness variations using photographic plates have not recovered any echoes in the regions of historical Galactic supernovae [3]. Using differenced images, our SuperMACHO collaboration has discovered three faint new variable surface brightness complexes with high apparent proper motion pointing back to well-defined positions in the Large Magellanic Cloud (LMC). These correspond to three of the six smallest (and likely youngest) supernova remnants believed to be due to thermonuclear (Type Ia) supernovae [4]. A lower limit to the age of these remnants and echoes is 200 years given the lack of any reported LMC supernovae until 1987. The discovery of historical supernova echoes in the LMC suggests that similar echoes for Galactic supernovae such as Tycho, Kepler, Cas A, or SN1006 could be visible using standard image differencing techniques.

  11. Ultrasonic position and velocity measurement for a moving object by M-sequence pulse compression using Doppler velocity estimation by spectrum-pattern analysis

    Science.gov (United States)

    Ikari, Yohei; Hirata, Shinnosuke; Hachiya, Hiroyuki

    2015-07-01

    Pulse compression using a maximum-length sequence (M-sequence) can improve the signal-to-noise ratio (SNR) of the reflected echo in the pulse-echo method. In the case of a moving object, however, the echo is modulated owing to the Doppler effect. The Doppler-shifted M-sequence-modulated signal cannot be correlated with the reference signal that corresponds to the transmitted M-sequence-modulated signal. Therefore, Doppler velocity estimation by spectrum-pattern analysis of a cyclic M-sequence-modulated signal and cross correlations with Doppler-shifted reference signals that correspond to the estimated Doppler velocities has been proposed. In this paper, measurements of the position and velocity of a moving object by the proposed method are described. First, Doppler velocities of the object are estimated using a microphone array. Secondly, the received signal from each microphone is correlated with each Doppler-shifted reference signal. Then, the position of the object is determined from the B-mode image formed from all cross-correlation functions. After that, the velocity of the object is calculated from velocity components estimated from the Doppler velocities and the position. Finally, the estimated Doppler velocities, determined positions, and calculated velocities are evaluated.

  12. Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages

    Directory of Open Access Journals (Sweden)

    Jordyn Bergsveinson

    2017-01-01

    Full Text Available Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.

  13. Improving municipal wastewater nitrogen and phosphorous removal by feeding sludge fermentation products to sequencing batch reactor (SBR).

    Science.gov (United States)

    Yuan, Yue; Liu, Jinjin; Ma, Bin; Liu, Ye; Wang, Bo; Peng, Yongzhen

    2016-12-01

    This study presents a novel strategy to improve the removal efficiency of nitrogen and phosphorus from municipal wastewater by feeding sequencing batch reactor (SBR) with sludge alkaline fermentation products as carbon sources. The performances of two SBRs treating municipal wastewater (one was fed with sludge fermentation products; F-SBR, and the other without sludge fermentation products; B-SBR) were compared. The removal efficiencies of total nitrogen (TN) and phosphorus (PO4(3-)-P) were found to be 82.9% and 96.0% in F-SBR, while the corresponding values in B-SBR were 55.9% (TN) and -6.1% (PO4(3-)-P). Illumina MiSeq sequencing indicated that ammonium-oxidizing bacteria (Nitrosomonadaceae and Nitrosomonas) and denitrifying polyphosphate accumulating organisms (Dechloromonas) were enriched in F-SBR, which resulted in NO2(-)-N accumulation and denitrifying phosphorus removal via nitrite (DPRN). Moreover, feeding of sludge fermentation products reduced 862.1mg VSS/d of sludge in the F-SBR system (volume: 10L).

  14. Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel

    Science.gov (United States)

    Bravo-Gil, Nereida; Méndez-Vidal, Cristina; Romero-Pérez, Laura; González-del Pozo, María; Rodríguez-de la Rúa, Enrique; Dopazo, Joaquín; Borrego, Salud; Antiñolo, Guillermo

    2016-01-01

    Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management. PMID:27032803

  15. Spin Echo Studies on Cellular Water

    CERN Document Server

    Chang, D C; Nichols, B L; Rorschach, H E

    2014-01-01

    Previous studies indicated that the physical state of cellular water could be significantly different from pure liquid water. To experimentally investigate this possibility, we conducted a series of spin-echo NMR measurements on water protons in rat skeletal muscle. Our result indicated that the spin-lattice relaxation time and the spin-spin relaxation time of cellular water protons are both significantly shorter than that of pure water (by 4.3-fold and 34-fold, respectively). Furthermore, the spin diffusion coefficient of water proton is almost 1/2 of that of pure water. These data suggest that cellular water is in a more ordered state in comparison to pure water.

  16. Theory of electron spin echoes in solids

    CERN Document Server

    Asadullina, N Y; Asadullin, Y Y

    2002-01-01

    We propose modified Bloch equations (MBEs) with specific power-dependent relaxation and dispersion parameters characteristic for two-pulse excitation and when the magnetic dipole-dipole interactions in the electron spin system control the dephasing. We discriminate between the 'active' (excited by both pulses) and 'passive' (excited by the second pulse only) spins: it is shown that the 'active' spins participate in a new effect, an active spin frequency modulation effect giving rise to the power-dependent dispersion and multiple electron spin echoes (ESEs); the 'passive' spins contribute to the power-dependent relaxation. The MBEs are solved and a general expression for the two-pulse ESEs is obtained. Detailed numerical analysis of this expression gives results in good quantitative agreement with the recent experiments on the two-pulse ESEs at conventional low applied fields. The developed theory is applied also to high field ESEs, which are promising for future investigations. On the basis of published resul...

  17. Challenges in neutron spin echo spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Pappas, C., E-mail: c.pappas@tudelft.n [Helmholtz-Zentrum Berlin for Materials and Energy, Glienicker Str. 100, 14109 Berlin (Germany); Faculty of Applied Sciences, Delft University of Technology, Mekelweg 15, 2629 JB Delft (Netherlands); Lelievre-Berna, E.; Falus, P.; Farago, B. [Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble (France); Bentley, P. [Helmholtz-Zentrum Berlin for Materials and Energy, Glienicker Str. 100, 14109 Berlin (Germany); Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble (France); Moskvin, E. [Helmholtz-Zentrum Berlin for Materials and Energy, Glienicker Str. 100, 14109 Berlin (Germany); PNPI, 188300 Gatchina, Leningrad District (Russian Federation); Krist, Th. [Helmholtz-Zentrum Berlin for Materials and Energy, Glienicker Str. 100, 14109 Berlin (Germany); Grigoriev, S. [PNPI, 188300 Gatchina, Leningrad District (Russian Federation)

    2009-09-01

    With the new brilliant neutron sources and the developments of novel optical elements, neutron spin echo (NSE) spectroscopy evolves to tackle new problems and scientific fields. The new developments pave the way to complex experimental set-ups such as the intensity modulated variant of NSE (IMNSE), a powerful technique which was introduced some 20 years ago but found limited use up to now. With the new compact supermirror or He{sup 3} polarizers IMNSE becomes attractive for a broad range of applications in magnetism, soft matter and biology. A novel development along this line is the polarimetric NSE technique, which combines IMNSE and the zero-field polarimeter Cryopad to access components of the scattered polarization that are transverse to the incoming polarization. Polarimetric NSE is the method of choice for studying chiral fluctuations, as illustrated by new results on the reference helimagnet MnSi.

  18. Echo chambers in the age of misinformation

    CERN Document Server

    Del Vicario, Michela; Zollo, Fabiana; Petroni, Fabio; Scala, Antonio; Caldarelli, Guido; Stanley, H Eugene; Quattrociocchi, Walter

    2015-01-01

    The wide availability of user-provided content in online social media facilitates the aggregation of people around common interests, worldviews, and narratives. Despite the enthusiastic rhetoric on the part of some that this process generates "collective intelligence", the WWW also allows the rapid dissemination of unsubstantiated conspiracy theories that often elicite rapid, large, but naive social responses such as the recent case of Jade Helm 15 -- where a simple military exercise turned out to be perceived as the beginning of the civil war in the US. We study how Facebook users consume information related to two different kinds of narrative: scientific and conspiracy news. We find that although consumers of scientific and conspiracy stories present similar consumption patterns with respect to content, the sizes of the spreading cascades differ. Homogeneity appears to be the primary driver for the diffusion of contents, but each echo chamber has its own cascade dynamics. To mimic these dynamics, we introdu...

  19. Dual-rail optical gradient echo memory

    CERN Document Server

    Higginbottom, Daniel B; Campbell, Geoff T; Hosseini, Mahdi; Cao, Ming Tao; Sparkes, Ben M; Bernu, Julian; Robins, Nick P; Lam, Ping Koy; Buchler, Ben C

    2016-01-01

    We introduce a scheme for the parallel storage of frequency separated signals in an optical memory and demonstrate that this dual-rail storage is a suitable memory for high fidelity frequency qubits. The two signals are stored simultaneously in the Zeeman-split Raman absorption lines of a cold atom ensemble using gradient echo memory techniques. Analysis of the split-Zeeman storage shows that the memory can be configured to preserve the relative amplitude and phase of the frequency separated signals. In an experimental demonstration dual-frequency pulses are recalled with 35% efficiency, 82% interference fringe visibility, and 6 degrees phase stability. The fidelity of the frequency-qubit memory is limited by frequency-dependent polarisation rotation and ambient magnetic field fluctuations, our analysis describes how these can be addressed in an alternative configuration.

  20. Theoretical aspects of nonlinear echo image system

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ruiquan; FENG Shaosong

    2003-01-01

    In order to develop the nonlinear echo image system to diagnose pathological changes in biological tissue , a simple physical model to analyse the character of nonlinear reflected wave in biological medium is postulated. The propagation of large amplitude plane sound wave in layered biological media is analysed for the one dimensional case by the method of successive approximation and the expression for the second order wave reflected from any interface of layered biological media is obtained. The relations between the second order reflection coefficients and the nonlinear parameters of medium below the interface are studied in three layers interfaces. Finally, the second order reflection coefficients of four layered media are calculated numerically. The results indicate that the nonlinear parameter B/A of each layer of biological media can be determined by the reflection method.

  1. Dynamic hysteresis between gradient echo and spin echo attenuations in dynamic susceptibility contrast imaging.

    Science.gov (United States)

    Xu, Chao; Kiselev, Valerij G; Möller, Harald E; Fiebach, Jochen B

    2013-04-01

    Perfusion measurements using dynamic susceptibility contrast imaging provide additional information about the mean vessel size of microvasculature when supplemented with a dual gradient echo (GE) - spin echo (SE) contrast. Dynamic increase in the corresponding transverse relaxation rate constant changes, ΔR2GE and ΔR2SE , forms a loop on the (Δ R2SE3/2, ΔR2GE ) plane, rather than a reversible line. The shape of the loop and the direction of its passage differentiate between healthy brain and pathological tissue, such as tumour and ischemic tissue. By considering a tree model of microvasculature, the direction of the loop is found to be influenced mainly by the relative arterial and venous blood volume, as well as the tracer bolus dispersion. A parameter Λ is proposed to characterize the direction and shape of the loop, which might be considered as a novel imaging marker for describing the pathology of cerebrovascular network.

  2. Metastatic Kaposi’s Sarcoma with Perirectal Involvement Diagnosed with Endoscopic Ultrasound-Guided EchoBrush Cytology Sampling

    Directory of Open Access Journals (Sweden)

    Daniel Cornett

    2011-07-01

    Full Text Available AIDS-related Kaposi’s sarcoma (KS is a low-grade vascular tumor that occurs in association with human herpesvirus 8 infection. Here we report the case of a 21-year-old male with recently diagnosed cutaneous KS who presented with rectal bleeding and anal pruritus. Initial endoscopic evaluation was nondiagnostic. CT imaging showed diffuse lymphadenopathy including perirectal involvement which was suspicious for metastatic KS. Echoendoscopy with needle biopsies and EchoBrush sampling of the lymph nodes revealed spindle cells confirming metastatic KS. Treatment was initiated with liposomal doxorubicin resulting in rapid improvement of the skin lesions. After treatment completion, repeat CT imaging showed improved lymphadenopathy. No further rectal bleeding or perianal pruritus was reported. Although the EchoBrush has previously been used to aid in the diagnosis of pancreatic lesions, this report describes a novel use of EchoBrush to diagnose KS from perirectal lymph nodes.

  3. Echo-based screening of rheumatic heart disease in children: a cost-effectiveness Markov model.

    Science.gov (United States)

    Zachariah, Justin P; Samnaliev, Mihail

    2015-06-01

    To project the cost-effectiveness of population-based echo screening to prevent rheumatic heart disease (RHD) consequences. RHD is a leading cause of cardiovascular mortality and morbidity during adolescence and young adulthood in low- and middle-per capita income settings. Echocardiography-based screening approaches can dramatically expand the number of children identified at risk of progressive RHD. Cost-effectiveness analysis can inform public health agencies and payers about the net economic benefit of such large-scale population-based screening. A Markov model was constructed comparing a no-screen to echo screen approach. The echo screen program was modeled as a 2-staged screen of a cohort of 11-year-old children with initial short screening performed by dedicated technicians and follow-up complete echo by cardiologists. Penicillin RHD prophylaxis was modeled to only reduce rheumatic fever recurrence-related exacerbation. Quality-adjusted life years (QALYs) and societal costs (in 2010 Australian dollars) associated with each approach were estimated. One-way, two-way and probabilistic sensitivity analyses were performed on RHD prevalence and transition probabilities; echocardiography test characteristics; and societal level costs including supplies, transportation, and labor. The incremental costs and QALYs of the screen compared to no screen strategy were -$432 (95% CI = -$1357 to $575) and 0.007 (95% CI = -0.0101 to 0.0237), respectively. The joint probability that the screen was both less costly and more effective exceeded 80%. Sensitivity analyses suggested screen strategy dominance depends mostly on the probability of transitioning out of sub-clinical RHD. Two-stage echo RHD screening and secondary prophylaxis may achieve modestly improved outcomes at lower cost compared to clinical detection and deserves closer attention from health policy stakeholders.

  4. Improved abdominal MRI in non-breath-holding children using a radial k-space sampling technique

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jong Hyuk; Choi, Young Hun; Cheon, Jung Eun; Lee, So Mi; Cho, Hyun Hae; Kim, Woo Sun; Kim, In One [Seoul National University Children' s Hospital, Department of Radiology, Seoul (Korea, Republic of); Shin, Su Mi [SMG-SNU Boramae Medical Center, Department of Radiology, Seoul (Korea, Republic of)

    2015-06-15

    Radial k-space sampling techniques have been shown to reduce motion artifacts in adult abdominal MRI. To compare a T2-weighted radial k-space sampling MRI pulse sequence (BLADE) with standard respiratory-triggered T2-weighted turbo spin echo (TSE) in pediatric abdominal imaging. Axial BLADE and respiratory-triggered turbo spin echo sequences were performed without fat suppression in 32 abdominal MR examinations in children. We retrospectively assessed overall image quality, the presence of respiratory, peristaltic and radial artifact, and lesion conspicuity. We evaluated signal uniformity of each sequence. BLADE showed improved overall image quality (3.35 ± 0.85 vs. 2.59 ± 0.59, P < 0.001), reduced respiratory motion artifact (0.51 ± 0.56 vs. 1.89 ± 0.68, P < 0.001), and improved lesion conspicuity (3.54 ± 0.88 vs. 2.92 ± 0.77, P = 0.006) compared to respiratory triggering turbo spin-echo (TSE) sequences. The bowel motion artifact scores were similar for both sequences (1.65 ± 0.77 vs. 1.79 ± 0.74, P = 0.691). BLADE introduced a radial artifact that was not observed on the respiratory triggering-TSE images (1.10 ± 0.85 vs. 0, P < 0.001). BLADE was associated with diminished signal variation compared with respiratory triggering-TSE in the liver, spleen and air (P < 0.001). The radial k-space sampling technique improved the quality and reduced respiratory motion artifacts in young children compared with conventional respiratory-triggered turbo spin-echo sequences. (orig.)

  5. T2-weighted MRI of the uterus: fast spin echo vs. breath-hold fast spin echo.

    Science.gov (United States)

    Ascher, S M; O'Malley, J; Semelka, R C; Patt, R H; Rajan, S; Thomasson, D

    1999-03-01

    This study compared one routine T2-weighted fast spin echo (T2FSE) sequence with a breath-hold T2FSE (BH T2FSE) sequence of the female pelvis for image quality, uterine anatomy, lesion detection, and signal intensity measurements. Thirty-two consecutive women (mean age 41.7 years) were imaged at 1.5 T with one high-resolution routine T2FSE sequence and one BH T2FSE sequence in the sagittal plane as part of comprehensive pelvic magnetic resonance imaging. The different image sets were rated separately for imaging characteristics (overall image quality, uterine anatomy definition, lesion detection, and free fluid conspicuity) and then compared side by side. The image sets were also compared for artifacts (ghosting, blurring, pulsatility, and chemical shift misregistration). Signal-to-noise (S/N) and signal difference-to-noise (SD/N) ratios were calculated for the different uterine zones, uterine abnormalities, free fluid, rectus abdominis muscle, and bladder. Contrast-to-noise ratios (CNRs) were calculated for uterine abnormalities. Twenty-eight uterine abnormalities were detected in 20 patients and included leiomyomata (13 patients), adenomyosis (7 patients), benign endometrial polyps (6 patients), endometrial carcinoma (1 patient), and pregnancy (1 patient). BH T2FSE was superior or equivalent to T2FSE for overall image quality in 23/32 patients (71.8%), uterine anatomy definition in 19/32 patients (59.3%), and lesion detection in 13/20 patients (65%). BH T2FSE performed less well than T2FSE for free fluid conspicuity in 5/5 (100%) patients. BH T2FSE was equivalent to or less affected than T2FSE for ghosting artifact in 24/32 patients (75%) and blurring artifact in 29/32 patients (90.6%). Pulsatility and chemical shift artifacts were not problematic for either image set. S/N and SD/N were higher for all BH T2FSE determinations compared with T2FSE. For the endometrium, junctional zone, myometrium, and bladder, these differences were statistically significant. There

  6. Comparison of respiratory-triggered 3-D fast spin-echo and single-shot fast spin-echo radial slab MR cholangiopancreatography images in children

    Energy Technology Data Exchange (ETDEWEB)

    Chavhan, Govind B.; Almehdar, Abeer; Gupta, Sumeet [The Hospital for Sick Children and University of Toronto, Department of Diagnostic Imaging, Toronto (Canada); Moineddin, Rahim [University of Toronto, Department of Family and Community Medicine, Toronto (Canada); Babyn, Paul S. [Royal University Hospital, Department of Medical Imaging, Saskatoon (Canada)

    2013-09-15

    The two most commonly performed magnetic resonance cholangiopancreatography (MRCP) sequences, 3-D fast spin-echo (3-D FSE) and single-shot fast spin-echo radial slabs (radial slabs), have not been compared in children. The purpose of this study was to compare 3-D FSE and radial slabs MRCP sequences on a 3-T scanner to determine their ability to show various segments of pancreaticobiliary tree and presence of artifacts in children. We reviewed 79 consecutive MRCPs performed in 74 children on a 3-T scanner. We noted visibility of major ducts on 3-D FSE and radial slabs. We noted the order of branching of ducts in the right and left hepatic ducts and the degree of visibility of the pancreatic duct. Statistical analysis was performed using McNemar and signed rank tests. There was no significant difference in the visibility of major bile ducts and the order of branching in the right hepatic lobe between sequences. A higher order of branching in the left lobe was seen on radial slabs than 3-D FSE (mean order of branching 2.82 versus 2.27; P-value = 0.0002). The visibility of pancreatic duct was better on radial slabs as compared to 3-D FSE (mean value of 1.53 vs. 0.90; P-value < 0.0001). 3-D FSE sequence was artifact-free in 25/79 (31.6%) MRCP exams as compared to radial slabs, which were artifact-free in 18/79 (22.8%) MRCP exams (P-value = 0.0001). There is no significant difference in the visibility of major bile ducts between 3-D FSE and radial slab MRCP sequences at 3-T in children. However, radial slab MRCP shows a higher order of branching in the left hepatic lobe and superior visibility of the pancreatic duct than 3-D FSE. (orig.)

  7. Networks of echoes imitation, innovation and invisible leaders

    CERN Document Server

    West, Bruce J; Grigolini, Paolo

    2014-01-01

    Networks of Echoes: Imitation, Innovation and Invisible Leaders is a mathematically rigorous and data rich book on a fascinating area of the science and engineering of social webs.  There are hundreds of complex network phenomena whose statistical properties are described by inverse power laws.  The phenomena of interest are not arcane events that we encounter only fleetingly, but are events that dominate our lives. We examine how this intermittent statistical behavior intertwines itself with what appears to be the organized activity of social groups.  The book is structured as answers to a sequence of questions such as: How are decisions reached in elections and boardrooms?  How is the stability of a society undermined by zealots and committed minorities, and how is that stability re-established?  Can we learn to answer such questions about human behavior by studying the way flocks of birds retain their formation when eluding a predator?  These questions and others are answered using a generic model of...

  8. HMM-ModE – Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences

    Directory of Open Access Journals (Sweden)

    Nandi Soumyadeep

    2007-03-01

    Full Text Available Abstract Background Profile Hidden Markov Models (HMM are statistical representations of protein families derived from patterns of sequence conservation in multiple alignments and have been used in identifying remote homologues with considerable success. These conservation patterns arise from fold specific signals, shared across multiple families, and function specific signals unique to the families. The availability of sequences pre-classified according to their function permits the use of negative training sequences to improve the specificity of the HMM, both by optimizing the threshold cutoff and by modifying emission probabilities to minimize the influence of fold-specific signals. A protocol to generate family specific HMMs is described that first constructs a profile HMM from an alignment of the family's sequences and then uses this model to identify sequences belonging to other classes that score above the default threshold (false positives. Ten-fold cross validation is used to optimise the discrimination threshold score for the model. The advent of fast multiple alignment methods enables the use of the profile alignments to align the true and false positive sequences, and the resulting alignments are used to modify the emission probabilities in the original model. Results The protocol, called HMM-ModE, was validated on a set of sequences belonging to six sub-families of the AGC family of kinases. These sequences have an average sequence similarity of 63% among the group though each sub-group has a different substrate specificity. The optimisation of discrimination threshold, by using negative sequences scored against the model improves specificity in test cases from an average of 21% to 98%. Further discrimination by the HMM after modifying model probabilities using negative training sequences is provided in a few cases, the average specificity rising to 99%. Similar improvements were obtained with a sample of G-Protein coupled receptors

  9. Fast and tissue-optimized mapping of magnetic susceptibility and T2* with multi-echo and multi-shot spirals.

    Science.gov (United States)

    Wu, Bing; Li, Wei; Avram, Alexandru Vlad; Gho, Sung-Min; Liu, Chunlei

    2012-01-02

    Gradient-echo MRI of resonance-frequency shift and T2* values exhibit unique tissue contrast and offer relevant physiological information. However, acquiring 3D-phase images and T2* maps with the standard spoiled gradient echo (SPGR) sequence is lengthy for routine imaging at high-spatial resolution and whole-brain coverage. In addition, with the standard SPGR sequence, optimal signal-to-noise ratio (SNR) cannot be achieved for every tissue type given their distributed resonance frequency and T2* value. To address these two issues, a SNR optimized multi-echo sequence with a stack-of-spiral acquisition is proposed and implemented for achieving fast and simultaneous acquisition of image phase and T2* maps. The analytical behavior of the phase SNR is derived as a function of resonance frequency, T2* and echo time. This relationship is utilized to achieve tissue optimized SNR by combining phase images with different echo times. Simulations and in vivo experiments were designed to verify the theoretical predictions. Using the multi-echo spiral acquisition, whole-brain coverage with 1 mm isotropic resolution can be achieved within 2.5 min, shortening the scan time by a factor of 8. The resulting multi-echo phase map shows similar SNR to that of the standard SPGR. The acquisition can be further accelerated with non-Cartesian parallel imaging. The technique can be readily extended to other multi-shot readout trajectories besides spiral. It may provide a practical acquisition strategy for high resolution and simultaneous 3D mapping of magnetic susceptibility and T2*.

  10. A base-sequence-modulated Golay code improves the excitation and measurement of ultrasonic guided waves in long bones.

    Science.gov (United States)

    Song, Xiaojun; Ta, Dean; Wang, Weiqi

    2012-11-01

    Researchers are interested in using ultrasonic guided waves (GWs) to assess long bones. However, GWs suffer high attenuation when they propagate in long bones, resulting in a low SNR. To overcome this limitation, this paper introduces a base-sequence-modulated Golay code (BSGC) to produce larger amplitude and improve the SNR in the ultrasound evaluation of long bones. A 16-bit Golay code was used for excitation in computer simulation. The decoded GWs and the traditional GWs, which were generated by a single pulse, agreed well after decoding the received signals, and the SNR was improved by 26.12 dB. In the experiments using bovine bones, the BSGC excitation produced the amplitudes which were at least 237 times greater than those produced by a single pulse excitation. The BSGC excitation also allowed the GWs to be received over a longer distance between two transducers. The results suggest the BSGC excitation has the potential to measure GWs and assess long bones.

  11. Modification of cyclic NGR tumor neovasculature-homing motif sequence to human plasminogen kringle 5 improves inhibition of tumor growth.

    Directory of Open Access Journals (Sweden)

    Weiwei Jiang

    Full Text Available BACKGROUND: Blood vessels in tumors express higher level of aminopeptidase N (APN than normal tissues. Evidence suggests that the CNGRC motif is an APN ligand which targets tumor vasculature. Increased expression of APN in tumor vascular endothelium, therefore, offers an opportunity for targeted delivery of NGR peptide-linked drugs to tumors. METHODS/PRINCIPAL FINDINGS: To determine whether an additional cyclic CNGRC sequence could improve endothelial cell homing and antitumor effect, human plasminogen kringle 5 (hPK5 was modified genetically to introduce a CNGRC motif (NGR-hPK5 and was subsequently expressed in yeast. The biological activity of NGR-hPK5 was assessed and compared with that of wild-type hPK5, in vitro and in vivo. NGR-hPK5 showed more potent antiangiogenic activity than wild-type hPK5: the former had a stronger inhibitory effect on proliferation, migration and cord formation of vascular endothelial cells, and produced a stronger antiangiogenic response in the CAM assay. To evaluate the tumor-targeting ability, both wild-type hPK5 and NGR-hPK5 were (99 mTc-labeled, for tracking biodistribution in the in vivo tumor model. By planar imaging and biodistribution analyses of major organs, NGR-hPK5 was found localized to tumor tissues at a higher level than wild-type hPK5 (approximately 3-fold. Finally, the effects of wild-type hPK5 and NGR-modified hPK5 on tumor growth were investigated in two tumor model systems. NGR modification improved tumor localization and, as a consequence, effectively inhibited the growth of mouse Lewis lung carcinoma (LLC and human colorectal adenocarcinoma (Colo 205 cells in tumor-bearing mice. CONCLUSIONS/SIGNIFICANCE: These studies indicated that the addition of an APN targeting peptide NGR sequence could improve the ability of hPK5 to inhibit angiogenesis and tumor growth.

  12. Multiple-Echo Suppression Modeling and Experimental Verification for Acoustic Transmission along Periodic Drillstring Using Dual Receivers

    Directory of Open Access Journals (Sweden)

    Li Cheng

    2014-01-01

    Full Text Available In the oil industry, the accompanied reverberation is a major constraint in the transmission rate and distance because the drillstring is a heterogeneous assembly. Based on the transient impulse responses in uplink and downlink channels, an improved simplified echo suppression model with two acoustic receivers is presented in consideration of position optimization of single acoustic receiver. Then the acoustic receiving characteristics of transmitted signals in a length-limited periodic drillstring channel are obtained in single- and dual-receiver modes. An additive downward white Gaussian noise is also introduced in the channel. Moreover, an experimental rig is established by using a rotatable electromagnetic vibration exciter and two piezoelectric accelerometers, which are spaced one-quarter wavelength apart along a 6.3-meter simulated periodic drillstring. The ASK-, FSK-, and PSK-modulated square-wave pulse sequences at a transmission rate of 200 bit/s are applied to the simulated drillstring at a rotation speed of 0, 80, and 140 r/min, respectively. The experimental results show that the dual-receiver mode can exhibit a significantly improved average error bit ratio, which is approximately 2.5 to 3 times lower than that of the single-receiver mode, especially under the conditions of higher rotation speeds.

  13. First HF radar measurements of summer mesopause echoes at SURA

    Directory of Open Access Journals (Sweden)

    A. N. Karashtin

    Full Text Available HF sounding of the mesosphere was first carried out at SURA in summer 1994 at frequencies in the range 8–9 MHz using one of the sub-arrays of the SURA heating facility. The observations had a range resolution of 3 km. Almost all measurements indicated the presence of strong radar returns from altitudes between 83 and 90 km with features very similar to VHF measurements of mesopause summer echoes at mid-latitudes and polar mesopause summer echoes. In contrast to VHF observations, HF mesopause echoes are almost always present.

  14. First HF radar measurements of summer mesopause echoes at SURA

    Science.gov (United States)

    Karashtin, A. N.; Shlyugaev, Y. V.; Abramov, V. I.; Belov, I. F.; Berezin, I. V.; Bychkov, V. V.; Eryshev, E. B.; Komrakov, G. P.

    1997-07-01

    HF sounding of the mesosphere was first carried out at SURA in summer 1994 at frequencies in the range 8-9 MHz using one of the sub-arrays of the SURA heating facility. The observations had a range resolution of 3 km. Almost all measurements indicated the presence of strong radar returns from altitudes between 83 and 90 km with features very similar to VHF measurements of mesopause summer echoes at mid-latitudes and polar mesopause summer echoes. In contrast to VHF observations, HF mesopause echoes are almost always present.

  15. A Frequency-Domain Adaptive Filter (FDAF) Prediction Error Method (PEM) Framework for Double-Talk-Robust Acoustic Echo Cancellation

    DEFF Research Database (Denmark)

    Gil-Cacho, Jose M.; van Waterschoot, Toon; Moonen, Marc

    2014-01-01

    In this paper, we propose a new framework to tackle the double-talk (DT) problem in acoustic echo cancellation (AEC). It is based on a frequency-domain adaptive filter (FDAF) implementation of the so-called prediction error method adaptive filtering using row operations (PEM-AFROW) leading...... to the FDAF-PEM-AFROW algorithm. We show that FDAF-PEM-AFROW is by construction related to the best linear unbiased estimate (BLUE) of the echo path. We depart from this framework to show an improvement in performance with respect to other adaptive filters minimizing the BLUE criterion, namely the PEM...

  16. Embedded Object Detection with Radar Echo Data by Means of Wavelet Analysis of MRA: Multi-Resolution Analysis

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2011-09-01

    Full Text Available A method for embedded object detection with radar echo data by means of wavelet analysis of MRA: Multi-Resolution Analysis, in particular, three dimensional wavelet transformations is proposed. In order to improve embedded object detecting capability, not only one dimensional radar echo data but also three dimensional data are used. Through a comparison between one dimensional edge detection with Sobel operator and three dimensional wavelet transformation based edge detection, it is found that the proposed method is superior to the Sobel operator based method.

  17. Does Dopplersignal enhancement with Levovist improve the diagnostic confidence of duplex scanning of the iliac arteries?--(A pilot study with correlation to intravascular ultrasound)

    DEFF Research Database (Denmark)

    Vogt, K C; Jensen, F; Schroeder, T V

    1998-01-01

    To evaluate whether echo-enhancement with Levovist improves the diagnostic confidence of duplex scanning of the iliac arteries.......To evaluate whether echo-enhancement with Levovist improves the diagnostic confidence of duplex scanning of the iliac arteries....

  18. Predicting electrocardiogram and arterial blood pressure waveforms with different Echo State Network architectures.

    Science.gov (United States)

    Fong, Allan; Mittu, Ranjeev; Ratwani, Raj; Reggia, James

    2014-01-01

    Alarm fatigue caused by false alarms and alerts is an extremely important issue for the medical staff in Intensive Care Units. The ability to predict electrocardiogram and arterial blood pressure waveforms can potentially help the staff and hospital systems better classify a patient's waveforms and subsequent alarms. This paper explores the use of Echo State Networks, a specific type of neural network for mining, understanding, and predicting electrocardiogram and arterial blood pressure waveforms. Several network architectures are designed and evaluated. The results show the utility of these echo state networks, particularly ones with larger integrated reservoirs, for predicting electrocardiogram waveforms and the adaptability of such models across individuals. The work presented here offers a unique approach for understanding and predicting a patient's waveforms in order to potentially improve alarm generation. We conclude with a brief discussion of future extensions of this research.

  19. Acoustic Feedback and Echo Cancellation Strategies for Multiple-Microphone and Single-Loudspeaker Systems

    DEFF Research Database (Denmark)

    Guo, Meng; Elmedyb, Thomas Bo; Jensen, Søren Holdt;

    2011-01-01

    Acoustic feedback/echo cancellation in a multiple-microphone and single-loudspeaker system is often carried out using a cancellation filter for each microphone channel, and the filters are adaptively estimated, independently of each other. In this work, we consider another strategy by estimating...... cancellation performance is achievable compared to the independent estimation strategy. Furthermore, we relate the joint estimation strategy to a stereophonic echo cancellation system and provide analytic expressions for its system behavior....... all the cancellation filters jointly and in this way exploit information from all microphone channels. We determine the statistical system behavior for the joint estimation strategy in terms of the convergence rate and steady-state behavior across time and frequency. We assess if an improved...

  20. Theory of electron spin echoes in solids

    Energy Technology Data Exchange (ETDEWEB)

    Asadullina, N.Ya.; Asadullin, T.Ya.; Asadullin, Ya.Ya. [Kazan State Technical University, Department of General Physics, Karl Marx Street 10, Kazan (Russian Federation)

    2002-11-04

    We propose modified Bloch equations (MBEs) with specific power-dependent relaxation and dispersion parameters characteristic for two-pulse excitation and when the magnetic dipole-dipole interactions in the electron spin system control the dephasing. We discriminate between the 'active' (excited by both pulses) and 'passive' (excited by the second pulse only) spins: it is shown that the 'active' spins participate in a new effect, an active spin frequency modulation effect giving rise to the power-dependent dispersion and multiple electron spin echoes (ESEs); the 'passive' spins contribute to the power-dependent relaxation. The MBEs are solved and a general expression for the two-pulse ESEs is obtained. Detailed numerical analysis of this expression gives results in good quantitative agreement with the recent experiments on the two-pulse ESEs at conventional low applied fields. The developed theory is applied also to high field ESEs, which are promising for future investigations. On the basis of published results it is deduced that the instantaneous diffusion mechanism is ineffective.

  1. Echoes in X-ray Binaries

    CERN Document Server

    O'Brien, K; Hynes, R; Chen, W; Haswell, C; Still, M

    2002-01-01

    We present a method of analysing the correlated X-ray and optical/UV variability in X-ray binaries, using the observed time delays between the X-ray driving lightcurves and their reprocessed optical echoes. This allows us to determine the distribution of reprocessing sites within the binary. We model the time-delay transfer functions by simulating the distribution of reprocessing regions, using geometrical and binary parameters. We construct best-fit time-delay transfer functions, showing the regions in the binary responsible for the reprocessing of X-rays. We have applied this model to observations of the Soft X-ray Transient, GRO j1655-40. We find the optical variability lags the X-ray variability with a mean time delay of 19.3$pm{2.2}$ seconds. This means that the outer regions of the accretion disc are the dominant reprocessing site in this system. On fitting the data to a simple geometric model, we derive a best-fit disk half-opening angle of 13.5$^{+2.1}_{-2.8}$ degrees, which is similar to that observe...

  2. Decoupled echo state networks with lateral inhibition.

    Science.gov (United States)

    Xue, Yanbo; Yang, Le; Haykin, Simon

    2007-04-01

    Building on some prior work, in this paper we describe a novel structure termed the decoupled echo state network (DESN) involving the use of lateral inhibition. Two low-complexity implementation schemes, namely, the DESN with reservoir prediction (DESN + RP) and DESN with maximum available information (DESN + MaxInfo), are developed: (1) In the multiple superimposed oscillator (MSO) problem, DESN + MaxInfo exhibits three important attributes: lower generalization mean-square error (MSE), better robustness with respect to the random generation of reservoir weight matrix and feedback connections, and robustness to variations in the sparseness of reservoir weight matrix, compared to DESN + RP. (2) For a noiseless nonlinear prediction task, DESN + RP outperforms the DESN + MaxInfo and single reservoir-based ESN approach in terms of lower prediction MSE and better robustness to a change in the number of inputs and sparsity of the reservoir weight matrix. Finally, in a real-life prediction task using noisy sea clutter data, both schemes exhibit higher prediction accuracy and successful design ratio than a conventional ESN with a single reservoir.

  3. Geomagnetic control of polar mesosphere summer echoes

    Directory of Open Access Journals (Sweden)

    J. Bremer

    Full Text Available Using observations with the ALOMAR SOUSY radar near Andenes (69.3°N, 16.0°E from 1994 until 1997 polar mesosphere summer echoes (PMSE have been investigated in dependence on geomagnetic K indices derived at the Auroral Observatory Tromsø (69.66°N, 18.94°E. During night-time and morning hours a significant correlation between the signal-to-noise ratio (SNR of the radar results and the geomagnetic K indices could be detected with a maximum correlation near midnight. The correlation becomes markedly smaller in the afternoon and early evening hours with a minimum near 17 UT. This diurnal variation is in reasonable agreement with riometer absorption at Ivalo (68.55°N, 27.28°E and can be explained by the diurnal variation of ionization due to precipitating high energetic particles. Therefore, a part of the diurnal PMSE variation is caused by this particle precipitation. The variability of the solar EUV variation, however, has no significant influence on the PMSE during the observation period.

    Keywords: Ionosphere (auroral ionosphere - Magnetospheric physics (energetic particles, precipitating - Radio science (remote sensing

  4. Phase incremented echo train acquisition applied to magnetic resonance pore imaging

    Science.gov (United States)

    Hertel, S. A.; Galvosas, P.

    2017-02-01

    Efficient phase cycling schemes remain a challenge for NMR techniques if the pulse sequences involve a large number of rf-pulses. Especially complex is the Carr Purcell Meiboom Gill (CPMG) pulse sequence where the number of rf-pulses can range from hundreds to several thousands. Our recent implementation of Magnetic Resonance Pore Imaging (MRPI) is based on a CPMG rf-pulse sequence in order to refocus the effect of internal gradients inherent in porous media. While the spin dynamics for spin- 1 / 2 systems in CPMG like experiments are well understood it is still not straight forward to separate the desired pathway from the spectrum of unwanted coherence pathways. In this contribution we apply Phase Incremented Echo Train Acquisition (PIETA) to MRPI. We show how PIETA offers a convenient way to implement a working phase cycling scheme and how it allows one to gain deeper insights into the amplitudes of undesired pathways.

  5. Qualitative and quantitative assessment of wrist MRI at 3.0T: comparison between isotropic 3D turbo spin echo and isotropic 3D fast field echo and 2D turbo spin echo.

    Science.gov (United States)

    Jung, Jee Young; Yoon, Young Cheol; Jung, Jin Young; Choe, Bong-Keun

    2013-04-01

    Isotropic three-dimensional (3D) magnetic resonance imaging (MRI) has been applied to various joints. However, comparison for image quality between isotropic 3D MRI and two-dimensional (2D) turbo spin echo (TSE) sequence of the wrist at a 3T MR system has not been investigated. To compare the image quality of isotropic 3D MRI including TSE intermediate-weighted (VISTA) sequence and fast field echo (FFE) sequence with 2D TSE intermediate-weighted sequence of the wrist joint at 3.0 T. MRI was performed in 10 wrists of 10 healthy volunteers with isotropic 3D sequences (VISTA and FFE) and 2D TSE intermediate-weighted sequences at 3.0 T. The signal-to-noise ratio (SNR) was obtained by imaging phantom and noise-only image. Contrast ratios (CRs) were calculated between fluid and cartilage, triangular fibrocartilage complex (TFCC), and the scapholunate ligament. Two radiologists independently assessed the visibility of TFCC, carpal ligaments, cartilage, tendons and nerves with a four-point grading scale. Statistical analysis to compare CRs (one way ANOVA with a Tukey test) and grades of visibility (Kruskal-Wallis test) between three sequences and those for inter-observer agreement (kappa analysis) were performed. The SNR of 2D TSE (46.26) was higher than those of VISTA (23.34) and 3D FFE (19.41). CRs were superior in 2D TSE than VISTA (P = 0.02) for fluid-cartilage and in 2D TSE than 3D FFE (P < 0.01) for fluid-TFCC. The visibility was best in 2D TSE (P < 0.01) for TFCC and in VISTA (P = 0.01) for scapholunate ligament. The visibility was better in 2D TSE and 3D FFE (P = 0.04) for cartilage and in VISTA than 3D FFE (P < 0.01) for TFCC. The inter-observer agreement for the visibility of anatomic structures was moderate or substantial. Image quality of 2D TSE was superior to isotropic 3D MR imaging for cartilage, and TFCC. 3D FFE has better visibility for cartilage than VISTA and VISTA has superior visibility for TFCC to 3D FFE and the visibility for scapholunate ligament

  6. Qualitative and quantitative assessment of wrist MRI at 3.0T - Comparison between isotropic 3D turbo spin echo and isotropic 3D fast field echo and 2D turbo spin echo

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Jee Young [Dept. of Radiology, Chungang Univ. Hospital, School of Medicine, Chungang Univ. (Korea, Republic of); Yoon, Young Cheol [Dept. of Radiology, Samsung Medical Center, School of Medicine, Sungkyunkwan Univ. (Korea, Republic of)], e-mail: ycyoon@skku.edu; Jung, Jin Young [Dept. of Radiology, Saint Paul' s Hospital, The Catholic Univ. (Korea, Republic of); Choe, Bong-Keun [Dept. of Preventive Medicine, School of Medicine, Kyung Hee Univ., Seoul (Korea, Republic of)

    2013-04-15

    Background: Isotropic three-dimensional (3D) magnetic resonance imaging (MRI) has been applied to various joints. However, comparison for image quality between isotropic 3D MRI and two-dimensional (2D) turbo spin echo (TSE) sequence of the wrist at a 3T MR system has not been investigated. Purpose: To compare the image quality of isotropic 3D MRI including TSE intermediate-weighted (VISTA) sequence and fast field echo (FFE) sequence with 2D TSE intermediate-weighted sequence of the wrist joint at 3.0 T. Material and Methods: MRI was performed in 10 wrists of 10 healthy volunteers with isotropic 3D sequences (VISTA and FFE) and 2D TSE intermediate-weighted sequences at 3.0 T. The signal-to-noise ratio (SNR) was obtained by imaging phantom and noise-only image. Contrast ratios (CRs) were calculated between fluid and cartilage, triangular fibrocartilage complex (TFCC), and the scapholunate ligament. Two radiologists independently assessed the visibility of TFCC, carpal ligaments, cartilage, tendons a