WorldWideScience

Sample records for multiple echo sequences

  1. Fast spine echo and fast fluid attenuated inversion recovery sequences in multiple sclerosis

    International Nuclear Information System (INIS)

    Paolillo, Andrea; Giugni, Elisabetta; Bozzao, Alessandro; Bastianello, Stefano

    1997-01-01

    Fast spin echo (FSE) and fast fluid attenuated inversion recovery (fast-FLAIR) sequences, were compared with conventional spin echo (CSE) in quantitating multiple sclerosis (MS) lesion burden. For each sequence, the total number and volume of MS lesions were calculated in 38 remitting multiple sclerosis patients using a semiautomated lesion detection program. Conventional spin echo, fast spin echo, and fast fluid attenuated inversion recovery image were reported on randomly and at different times by two expert observers. Interobserver differences, the time needed to quantitative multiple sclerosis lesions and lesion signal intensity (contrast-to-noise ratio and overall contrast) were considered. The lesions were classified by site into infratentorial, white matter and cortical/subcortical. A total of 2970 lesions with a volume of 961.7 cm 3 was calculated on conventional spin echo images. Fast spin echo images depicted fewer (16.6%; p < .005) and smaller (24.9%; p < .0001) lesions and the differences were statistically significant. Despite an overall nonsignificant reduction for fast-FLAIR images (-5% and 4.8% for lesion number and volume, respectively), significantly lower values (lesion number: p < 0.1; volume: p < .04)were observed for infratentorial lesions, while significantly higher values were seen for cortical/subcortical lesions (lesion number: p < .01; volume: p < .02). A higher lesion/white matter contrast (p < .002), a significant time saving for lesion burden quantitation (p < .05) and very low interobserver variability were found in favor of fast-FLAIR. Our data suggest that, despite the limitations regarding infratentorial lesions, fast-FLAIR sequences are indicated in R studies because of their good identification of cortical/subcortical lesions, almost complete interobserver agreement, higher contrast-to-noise ratio and limited time needed for semiautomated quantitation

  2. Optimized, unequal pulse spacing in multiple echo sequences improves refocusing in magnetic resonance.

    Science.gov (United States)

    Jenista, Elizabeth R; Stokes, Ashley M; Branca, Rosa Tamara; Warren, Warren S

    2009-11-28

    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 "Uhrig dynamic decoupling (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 time scales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T(2)-weighted contrast than do CPMG sequences with the same number of pulses and total delay, with substantial enhancements in most regions. This permits improved characterization of low-frequency spectral density functions in a wide range of applications.

  3. Comparison of a conventional cardiac-triggered dual spin-echo and a fast STIR sequence in detection of spinal cord lesions in multiple sclerosis

    International Nuclear Information System (INIS)

    Bot, J.C.J.; Barkhof, F.; Lycklama a Nijeholt, G.J.; Bergers, E.; Castelijns, J.A.; Polman, C.H.; Ader, H.J.

    2000-01-01

    The current optimal imaging protocol in spinal cord MR imaging in patients with multiple sclerosis includes a long TR conventional spin-echo (CSE) sequence, requiring long acquisition times. Using short tau inversion recovery fast spin-echo (fast STIR) sequences both acquisition time can be shortened and sensitivity in the detection of multiple sclerosis (MS) abnormalities can be increased. This study compares both sequences for the potential to detect both focal and diffuse spinal abnormalities. Spinal cords of 5 volunteers and 20 MS patients were studied at 1.0 T. Magnetic resonance imaging included cardiac-gated sagittal dual-echo CSE and a cardiac-gated fast STIR sequence. Images were scored regarding number, size, and location of focal lesions, diffuse abnormalities and presence/hindrance of artifacts by two experienced radiologists. Examinations were scored as being definitely normal, indeterminate, or definitely abnormal. Interobserver agreement regarding focal lesions was higher for CSE (κ=0.67) than for fast STIR (κ=0.57) but did not differ significantly. Of all focal lesions scored in consensus, 47 % were scored on both sequences, 31 % were only detected by fast STIR, and 22 % only by dual-echo CSE (n. s.). Interobserver agreement for diffuse abnormalities was lower with fast STIR (κ=0.48) than dual-echo CSE (κ=0.65; n. s.). After consensus, fast STIR showed in 10 patients diffuse abnormalities and dual-echo CSE in 3. After consensus, in 19 of 20 patients dual-echo CSE scans were considered as definitely abnormal compared with 17 for fast STIR. The fast STIR sequence is a useful adjunct to dual-echo CSE in detecting focal abnormalities and is helpful in detecting diffuse MS abnormalities in the spinal cord. Due to the frequent occurrence of artifacts and the lower observer concordance, fast STIR cannot be used alone. (orig.)

  4. Performance of a fast and high-resolution multi-echo spin-echo sequence for prostate T2 mapping across multiple systems.

    Science.gov (United States)

    van Houdt, Petra J; Agarwal, Harsh K; van Buuren, Laurens D; Heijmink, Stijn W T P J; Haack, Søren; van der Poel, Henk G; Ghobadi, Ghazaleh; Pos, Floris J; Peeters, Johannes M; Choyke, Peter L; van der Heide, Uulke A

    2018-03-01

    To evaluate the performance of a multi-echo spin-echo sequence with k-t undersampling scheme (k-t T 2 ) in prostate cancer. Phantom experiments were performed at five systems to estimate the bias, short-term repeatability, and reproducibility across all systems expressed with the within-subject coefficient of variation (wCV). Monthly measurements were performed on two systems for long-term repeatability estimation. To evaluate clinical repeatability, two T 2 maps (voxel size 0.8 × 0.8 × 3 mm 3 ; 5 min) were acquired at separate visits on one system for 13 prostate cancer patients. Repeatability was assessed per patient in relation to spatial resolution. T 2 values were compared for tumor, peripheral zone, and transition zone. Phantom measurements showed a small bias (median = -0.9 ms) and good short-term repeatability (median wCV = 0.5%). Long-term repeatability was 0.9 and 1.1% and reproducibility between systems was 1.7%. The median bias observed in patients was -1.1 ms. At voxel level, the median wCV was 15%, dropping to 4% for structures of 0.5 cm 3 . The median tumor T 2 values (79 ms) were significantly lower (P < 0.001) than in the peripheral zone (149 ms), but overlapped with the transition zone (91 ms). Reproducible T 2 mapping of the prostate is feasible with good spatial resolution in a clinically reasonable scan time, allowing reliable measurement of T 2 in structures as small as 0.5 cm 3 . Magn Reson Med 79:1586-1594, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  5. Magnetic resonance imaging of multiple sclerosis brain lesions: A semeiologic study by multiple spin-echo sequences

    International Nuclear Information System (INIS)

    Caires, M.C.; Scheiber, C.; Rumbach, L.; Gounot, D.; Dumitresco, B.; Warter, J.M.; Collard, M.; Chambron, J.

    1986-01-01

    Nuclear magnetic resonance imaging (MRI) if the brain is now known as a very sensitive tool for clearly revealing lesions in white matter, and has thus become important in the study of multiple sclerosis (MS). Since 1981, others have shown the best of MRI: we can see 6 x more lesions than CT. MRI contrast bases mainly on the spatial heterogeneity of the relaxation time of different tissues. The sensitivity depends on the longer T1 and/or T2 of the pathological tissues compared to those of normal tissues. In our series, the authors use mainly T2 weighted MR images and they evaluate their interest for the diagnosis of MS. They study the frequency of the abnormalities and their semeiology in a small number of transversal sections imaged at the level of the lateral ventricles. The authors' aim is to describe the NMR-derived morphological signs of MS and to prospect its interest in the physiopathological studies of this disease

  6. 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.)

  7. MRI in multiple sclerosis of the spinal cord: evaluation of fast short-tan inversion-recovery and spin-echo sequences

    International Nuclear Information System (INIS)

    Dietemann, J.L.; Thibaut-Menard, A.; Neugroschl, C.; Gillis, C.; Abu Eid, M.; Bogorin, A.; Warter, J.M.; Tranchant, C.

    2000-01-01

    We compared the sensitivity of T2-weighted spin-echo (FSE) and fast short-tau inversion-recovery (fSTIR) sequences in detection of multiple sclerosis of the spinal cord in 100 consecutive patients with clinically confirmed multiple sclerosis (MS); 86 patients underwent also brain MRI. In all, 310 focal lesions were detected on fSTIR and 212 on T2-weighted FSE, spinal cord lesions were seen better on fSTIR images, with a higher contrast between the lesion and the normal spinal cord. In 24 patients in whom cord plaques were shown with both sequences, the cranial study was normal or inconclusive. Assessment of spinal plaques can be particularly important when MRI of the brain is inconclusive, and in there situations fSTIR can be helpful. (orig.)

  8. Self-normalizing multiple-echo technique for measuring the in vivo apparent diffusion coefficient

    International Nuclear Information System (INIS)

    Perman, W.H.; Gado, M.; Sandstrom, J.C.

    1989-01-01

    This paper presents work to develop a new technique for quantitating the in vivo apparent diffusion/perfusion coefficient (ADC) by obtaining multiple data points from only two images with the capability to normalize the data from consecutive images, thus minimizing the effect of interimage variation. Two multiple-echo (six-to eight-echo) cardiac-gated images are obtained, one without and one with additional diffusion/perfusion encoding gradients placed about the 180 RF pulses of all but the first echo. Since the first echoes of both images have identical pulse sequence parameters, variations in signal intensity-between the first echoes represent image-to-image variation. The signal intensities of the subsequent echoes with additional diffusion/perfusion encoding gradients are then normalized by using the ratio of the first-echo signal intensities

  9. A short TE gradient-echo sequence using asymmetric sampling

    International Nuclear Information System (INIS)

    Fujita, Norihiko; Harada, Kohshi; Sakurai, Kosuke; Nakanishi, Katsuyuki; Kim, Shyogen; Kozuka, Takahiro

    1990-01-01

    We have developed a gradient-echo pulse sequence with a short TE less than 4 msec using a data set of asymmetric off-center sampling with a broad bandwidth. The use of such a short TE significantly reduces T 2 * dephasing effect even in a two-dimensional mode, and by collecting an off-center echo, motion-induced phase dispersion is also considerably decreased. High immunity of this sequence to these dephasing effects permits clear visualization of anatomical details near the skull base where large local field inhomogeneities and rapid blood flow such as in the internal carotid artery are present. (author)

  10. In vivo quantitative NMR imaging of fruit tissues during growth using Spoiled Gradient Echo sequence

    DEFF Research Database (Denmark)

    Kenouche, S.; Perrier, M.; Bertin, N.

    2014-01-01

    of this study was to design a robust and accurate quantitative measurement method based on NMR imaging combined with contrast agent (CA) for mapping and quantifying water transport in growing cherry tomato fruits. A multiple flip-angle Spoiled Gradient Echo (SGE) imaging sequence was used to evaluate...

  11. Comparison of multi-echo and single-echo gradient-recalled echo sequences for SPIO-enhanced Liver MRI at 3 T

    International Nuclear Information System (INIS)

    Choi, J.S.; Kim, M.-J.; Kim, J.H.; Choi, J.-Y.; Chung, Y.E.; Park, M.-S.; Kim, K.W.

    2010-01-01

    Aim: To assess the utility of a T2*-weighted, multi-echo data imaging combination sequenced on superparamagnetic iron oxide (SPIO)-enhanced liver magnetic resonance imaging (MRI) using a 3 T system. Materials and methods: Fifty patients underwent SPIO-enhanced MRI at 3 T using T2*-weighted, single-echo, gradient-recalled echo (GRE) sequences [fast imaging with steady precession; repetition time (TR)/echo time (TE), 126 ms/9 ms; flip angle, 30 o ] and multi-echo GRE (multi-echo data image combination) sequences (TR/TE, 186 ms/9 ms; flip angle, 30 o ). Three radiologists independently reviewed the images in a random order. The sensitivity and accuracy for the detection of focal hepatic lesions (a total of 76 lesions in 33 patients; 48 solid lesions, 28 non-solid lesions) were compared by analysing the area under the receiver operating characteristic curves. Image artefacts (flow artefacts, susceptibility artefacts, dielectric artefacts, and motion artefacts), lesion conspicuity, and overall image quality were evaluated according to a four-point scale: 1, poor; 2, fair; 3, good; 4, excellent. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of the lesions were compared. Results: Image artefacts were more frequent with single-echo GRE (p < 0.05). The mean scale of image quality assessment for flow, susceptibility, dielectric, and motion artefacts were 2.76, 3.13, 3.42, and 2.89 with singe-echo, respectively, compared with 3.47, 3.43, 3.47, and 3.39, respectively, with multi-echo GRE. There was no significant difference in lesion conspicuity between single-echo (3.15) and multi-echo (3.30) GRE sequences. The overall image quality was significantly (p < 0.05) better with multi-echo (3.37) than with single-echo GRE (2.89). The mean SNR and CNR of the lesions were significantly (p < 0.05) higher on multi-echo (79 ± 23 and 128 ± 59, respectively) images than on single-echo (38 ± 11 and 102 ± 44, respectively) images. Lesion detection accuracy and

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

    International Nuclear Information System (INIS)

    Marcar, V.L.; Girard, F.; Rinkel, Y.; Schneider, J.F.; Martin, E.

    2002-01-01

    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.)

  13. 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.)

  14. Single-shot echo-planar imaging of multiple sclerosis: effects of varying echo time

    International Nuclear Information System (INIS)

    Wolansky, L.J.; Chong, S.; Liu, W.C.; Kang, E.; Simpson, S.W.; Karimi, S.; Akbari, H.

    1999-01-01

    Our aim was to determine the relative merits of short and long echo times (TE) with single-shot echo-planar imaging for imaging cerebral lesions such as multiple sclerosis. We examined seven patients with clinically definite multiple sclerosis were imaged at 1.5 T. Patients were scanned with spin-echo, single-shot echo-planar imaging, using TEs of 45, 75, 105, and 135 ms. Region of interest (ROI) measurements were performed on 36 lesions at or above the level of the corona radiata. The mean image contrast (IC) was highest (231.1) for a TE of 45 ms, followed by 75 ms (218.9), 105 ms (217.9), and 135 ms (191.6). When mean contrast-to-noise ratios (C/N) were compared, the value was again highest (29.7) for TE 45 ms, followed by 75 ms (28.9), 105 ms (28.5), and 135 ms (26.3). In a lesion-by-lesion comparison, TE 45 ms had the highest IC and C/N in the largest number of cases (50 % and 47.2 %, respectively). IC and C/N for TE 45 ms were superior to those of 75 ms in 64 % and 58 %, respectively. These results support the use of relatively short TEs for single-shot echo-planar imaging in the setting of cerebral lesions such as multiple sclerosis. (orig.) (orig.)

  15. A comparison between fast and conventional spin-echo in the detection of multiple sclerosis lesions

    International Nuclear Information System (INIS)

    Thorpe, J.W.; Halpin, S.F.; MacManus, D.G.; Barker, G.J.; Kendall, B.E.; Miller, D.H.

    1994-01-01

    Long repetition time (TR) spin-echo (SE) with T 2 - or proton density weighting is the sequence of choice to detect the brain lesions of multiple sclerosis (MS). Fast spin-echo (FSE) permits the generation of T 2 -weighted images with similar contrast to SE but in a fraction of the time. We compared the sensitivity of FSE and SE in the detection of the brain lesions of MS. Six patients with clinically definite MS underwent brain imaging with both dual echo (long TR, long and short echo time (TE) SE and dual echo FSE. The SE and FSE images were first reviewed independently and then compared. A total of 404 lesions was detected on SE and 398 on FSE. Slightly more periventricular lesions were detected using SE than FSE (145 vs 127), whereas more posterior cranial fossa lesions were detected by FSE (77 vs 57). With both SE and FSE the short TE images revealed more lesions than the long echo. These results suggest that FSE could replace SE as the long TR sequence of choice in the investigation of MS. (orig.)

  16. Benefits of the Multiple Echo Technique for Ultrasonic Thickness Testing

    Energy Technology Data Exchange (ETDEWEB)

    Elder, J.; Vandekamp, R.

    2011-02-10

    Much effort has been put into determining methods to make accurate thickness measurements, especially at elevated temperatures. An accuracy of +/- 0.001 inches is typically noted for commercial ultrasonic thickness gauges and ultrasonic thickness techniques. Codes and standards put limitations on many inspection factors including equipment, calibration tolerance and temperature variations. These factors are important and should be controlled, but unfortunately do not guarantee accurate and repeatable measurements in the field. Most technicians long for a single technique that is best for every situation, unfortunately, there are no 'silver bullets' when it comes to nondestructive testing. This paper will describe and discuss some of the major contributors to measurement error as well as some advantages and limitations of multiple echo techniques and why multiple echo techniques should be more widely utilized for ultrasonic thickness measurements.

  17. NMR multiple-echo phase-contrast blood flow imaging

    International Nuclear Information System (INIS)

    O'Donnell, M.

    1986-01-01

    A method is described for magnetic resonance imaging of fluid flow in a sample, comprising the steps of: (a) immersing the sample in a static magnetic field disposed in a first direction; (b) applying a first sequence of magnetic field gradients and radio-frequency signals to the sample to both define a slab, of the sample to be imaged, in a plane substantially orthogonal to a selected direction for which flow velocity is to be measured, and to obtain a plurality N of spin-echo response signals form that slab; (c) processing the plurality of first sequence spin-echo signals to obtain a complex value A/sub 1/(X,Y,Z) relating both the spin density rho'(X,Y,Z),... and the phase rotation phi(X,Y,Z), induced by the first sequence, for each of a selected number of sequential locations (X,Y,Z) in the sample slab; (d) applying a second sequence of magnetic field gradient and radio-frequency signals to both define the same sample slab as in step (b) and to obtain another plurality N of spin-echo response signals from that slab; (e) including a waveform in at least one of the magnetic field gradient and radio-frequency signals applied in step (d) for imparting to each of the spin-echo signal components from each slab location having a flowing material therein a phase rotation dependent upon the magnitude of the flow velocity therein in the selected direction; (f) processing the plurality of second sequence spin-echo signals to obtain a complex value A/sub 2/(X,Y,Z) relating the spin density rho'(X,Y,Z) and the imparted phase rotation of the sample material along the selected flow measurement direction for each of the sequential locations (X,Y,Z) in the sample slab; and (g) processing the complex values A/sub 1/(X,Y,Z) and A/sub 2/(X,Y,Z) for each sample location to obtain a differential phase-contrast value related to the velocity of the flowing material therein in the selected measurement direction

  18. Correction of echo shift in reconstruction processing for ultra-short TE pulse sequence

    International Nuclear Information System (INIS)

    Takizawa, Masahiro; Ootsuka, Takehiro; Abe, Takayuki; Takahashi, Tetsuhiko

    2010-01-01

    An ultra-short echo time (TE) pulse sequence is composed of a radial sampling that acquires echo signals radially in the K-space and a half-echo acquisition that acquires only half of the echo signal. The shift in the position of the echo signal (echo shift) caused by the timing errors in the gradient magnetic field pulses affects the image quality in the radial sampling with the half-echo acquisition. To improve image quality, we have developed a signal correction algorithm that detects and eliminates this echo shift during reconstruction by performing a pre-scan within 10 seconds. The results showed that image quality is improved under oblique and/or off-centering conditions that frequently cause image distortion due to hardware error. In conclusion, we have developed a robust ultra-short TE pulse sequence that allows wide latitude in the scan parameters, including oblique and off-centering conditions. (author)

  19. 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.

  20. Cardiac T2-mapping using a fast gradient echo spin echo sequence - first in vitro and in vivo experience

    OpenAIRE

    Baessler, Bettina; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Maintz, David; Bunck, Alexander C.

    2015-01-01

    Background: The aim of this study was the evaluation of a fast Gradient Spin Echo Technique (GraSE) for cardiac T2-mapping, combining a robust estimation of T2 relaxation times with short acquisition times. The sequence was compared against two previously introduced T2-mapping techniques in a phantom and in vivo. Methods: Phantom experiments were performed at 1.5 T using a commercially available cylindrical gel phantom. Three different T2-mapping techniques were compared: a Multi Echo Spin Ec...

  1. Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging

    Energy Technology Data Exchange (ETDEWEB)

    Nolte-Ernsting, C.C.A.; Tacke, J.; Adam, G.B.; Haage, P.; Guenther, R.W. [Univ. of Technology, Aachen (Germany). Dept. of Diagnostic Radiology; Jung, P.; Jakse, G. [Univ. of Technology, Aachen (Germany). Dept. of Urology

    2001-01-01

    The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. (orig.)

  2. Proton T2 relaxation effect of superparamagnetic iron oxide. Comparison between fast spin echo and conventional spin echo sequence

    International Nuclear Information System (INIS)

    Tanimoto, Akihiro; Satoh, Yoshinori; Higuchi, Nobuya; Izutsu, Mutsumu; Yuasa, Yuji; Hiramatsu, Kyoichi

    1995-01-01

    Superparamagnetic iron oxide (SPIO) particles have been known to show a great T 2 relaxation effect in the liver, which contributes to significant liver signal decrease and detection of hepatic neoplasms. Recently, fast spin echo (FSE) sequence with less scanning time than conventional spin echo (SE) sequence has been rapidly introduced in clinical MR imaging. To investigate whether SPIO would show decreased T 2 relaxation effect on FSE, we obtained T 2 relaxivity (R2) of SPIO in vitro and liver signal decrease caused by SPIO in vivo. SPIO showed 20% less R2 on Carr-Purcell-Meiboom-Gill (CPMG) sequence than on SE. Relative liver signal-to-noise ratio (SNR) decrease caused by SPIO was significantly smaller (p 2 relaxation effect on FSE than on SE. However, further studies will be required to assess the diagnostic capability of SPIO on FSE, in the detection of hepatic neoplasms. (author)

  3. 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).

  4. Visual Perceptual Echo Reflects Learning of Regularities in Rapid Luminance Sequences.

    Science.gov (United States)

    Chang, Acer Y-C; Schwartzman, David J; VanRullen, Rufin; Kanai, Ryota; Seth, Anil K

    2017-08-30

    A novel neural signature of active visual processing has recently been described in the form of the "perceptual echo", in which the cross-correlation between a sequence of randomly fluctuating luminance values and occipital electrophysiological signals exhibits a long-lasting periodic (∼100 ms cycle) reverberation of the input stimulus (VanRullen and Macdonald, 2012). As yet, however, the mechanisms underlying the perceptual echo and its function remain unknown. Reasoning that natural visual signals often contain temporally predictable, though nonperiodic features, we hypothesized that the perceptual echo may reflect a periodic process associated with regularity learning. To test this hypothesis, we presented subjects with successive repetitions of a rapid nonperiodic luminance sequence, and examined the effects on the perceptual echo, finding that echo amplitude linearly increased with the number of presentations of a given luminance sequence. These data suggest that the perceptual echo reflects a neural signature of regularity learning.Furthermore, when a set of repeated sequences was followed by a sequence with inverted luminance polarities, the echo amplitude decreased to the same level evoked by a novel stimulus sequence. Crucially, when the original stimulus sequence was re-presented, the echo amplitude returned to a level consistent with the number of presentations of this sequence, indicating that the visual system retained sequence-specific information, for many seconds, even in the presence of intervening visual input. Altogether, our results reveal a previously undiscovered regularity learning mechanism within the human visual system, reflected by the perceptual echo. SIGNIFICANCE STATEMENT How the brain encodes and learns fast-changing but nonperiodic visual input remains unknown, even though such visual input characterizes natural scenes. We investigated whether the phenomenon of "perceptual echo" might index such learning. The perceptual echo is a

  5. A new technique for MR elastography of the supraspinatus muscle: A gradient-echo type multi-echo sequence.

    Science.gov (United States)

    Ito, Daiki; Numano, Tomokazu; Mizuhara, Kazuyuki; Takamoto, Koichi; Onishi, Takaaki; Nishijo, Hisao

    2016-10-01

    Magnetic resonance elastography (MRE) can measure tissue stiffness quantitatively and noninvasively. Supraspinatus muscle injury is a significant problem among throwing athletes. The purpose of this study was to develop an MRE technique for application to the supraspinatus muscle by using a conventional magnetic resonance imaging (MRI). MRE acquisitions were performed with a gradient-echo type multi-echo MR sequence at 100Hz pneumatic vibration. A custom-designed vibration pad was used as a pneumatic transducer in order to adapt to individual shoulder shapes. In a gradient-echo type multi-echo MR sequence, without motion encoding gradient (MEG) that synchronizes with vibrations, bipolar readout gradient lobes achieved a similar function to MEG (MEG-like effect). In other words, a dedicated MRE sequence (built-in MEG) is not always necessary for MRE. In this study, 7 healthy volunteers underwent MRE. We investigated the effects of direction of the MEG-like effect and selected imaging planes on the patterns of wave propagation (wave image). The results indicated that wave images showed clear wave propagation on a condition that the direction of the MEG-like effect was nearly perpendicular to the long axis of the supraspinatus muscle, and that the imaging plane was superior to the proximal supraspinatus muscle. This limited condition might be ascribed to specific features of fibers in the supraspinatus muscle and wave reflection from the boundaries of the supraspinous fossa. The mean stiffness of the supraspinatus muscle was 10.6±3.17kPa. Our results demonstrated that using MRE, our method can be applied to the supraspinatus muscle by using conventional MRI. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. MRI of the breast with 2D spin-echo and gradient echo sequences in diagnostically difficult cases

    International Nuclear Information System (INIS)

    Allgayer, B.; Lukas, P.; Loos, W.; Kersting-Sommerhoff, B.

    1993-01-01

    One or both breasts of 296 patients with equivocal clinical or mammographical findings were examined with MRI. T 1 weighted spinecho (SE) and gradient echo (FFE) sequences were acquired before and after i.v. application of Gadolinium DTPA. 50 lesions with enhancement after Gd-DTPA were biopsied -26 carcinomas, 17 proliferating mastopathic tissues, 5 fibroadenomas and 1 abscess were found. Contrast enhanced MRI with 2D-SE and FFE sequences is an effective technqiue for evaluating suspicious breast lesions with high diagnostic acurracy. (orig.) [de

  7. Quantification of liver iron concentration with magnetic resonance imaging by combining T1-, T2-weighted spin echo sequences and a gradient echo sequence

    NARCIS (Netherlands)

    Kreeftenberg, HG; Mooyaart, EL; Sluiter, WJ; Kreeftenberg, HG; Huizenga, Reint

    Background: The aim of the study was to quantify hepatic iron by MRI for practical use. Methods: In twenty-three patients with various degrees of iron overload, measurements were carried out with a 1.5 Tesla MR unit. A combination of pulse sequences (T1, T2 and gradient echo) enabled us to quantify

  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. MRI detection of hypointense brain lesions in patients with multiple sclerosis: T1 spin-echo vs. gradient-echo

    International Nuclear Information System (INIS)

    Dupuy, Sheena L.; Tauhid, Shahamat; Kim, Gloria; Chu, Renxin; Tummala, Subhash; Hurwitz, Shelley; Bakshi, Rohit

    2015-01-01

    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

  10. MR contrast of ferritin and hemosiderin in the brain: comparison among gradient-echo, conventional spin-echo and fast spin-echo sequences

    Energy Technology Data Exchange (ETDEWEB)

    Haque, Tabassum Laz; Miki, Yukio; Kanagaki, Mitsunori; Takahashi, Takahiro; Yamamoto, Akira; Konishi, Junya; Nozaki, Kazuhiko; Hashimoto, Nobuo; Konishi, Junji

    2003-12-01

    Objective: To compare the magnetic resonance image contrasts due to ferritin and hemosiderin in the brain tissue among different pulse sequences. Materials and methods: Fourteen patients with cavernous hemangioma in the brain prospectively underwent MR imaging with T2*-weighted gradient-echo (GRE), T2-weighted conventional spin-echo (SE) and fast spin-echo (FSE) sequences. The relative contrast ratios (CRs) of the hypointense part of cavernous hemangioma, globus pallidus and putamen to the deep frontal white matter were measured on each pulse sequence and statistically analyzed using analysis of variance followed by paired t-test. Results: In the hypointense part of cavernous hemangioma, relative CRs were significantly lower on T2*-weighted GRE than on T2-weighted SE images (P=0.0001), and on T2-weighted SE than on T2-weighted FSE images (P=0.0001). In the globus pallidus, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.002), and on T2*-weighted GRE than on T2-weighted FSE images (P=0.0002). In the putamen, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.001), and there was no significant difference between CRs on T2-weighted FSE and T2*-weighted GRE images (P=0.90). Conclusion: Hemosiderin showed best image contrast on T2*-weighted GRE images but ferritin showed more prominent image contrast on T2-weighted SE than on T2*-weighted GRE images, which may help to determine an appropriate pulse sequence in neurological diseases associated with excessive ferritin accumulation.

  11. MR contrast of ferritin and hemosiderin in the brain: comparison among gradient-echo, conventional spin-echo and fast spin-echo sequences

    International Nuclear Information System (INIS)

    Haque, Tabassum Laz; Miki, Yukio; Kanagaki, Mitsunori; Takahashi, Takahiro; Yamamoto, Akira; Konishi, Junya; Nozaki, Kazuhiko; Hashimoto, Nobuo; Konishi, Junji

    2003-01-01

    Objective: To compare the magnetic resonance image contrasts due to ferritin and hemosiderin in the brain tissue among different pulse sequences. Materials and methods: Fourteen patients with cavernous hemangioma in the brain prospectively underwent MR imaging with T2*-weighted gradient-echo (GRE), T2-weighted conventional spin-echo (SE) and fast spin-echo (FSE) sequences. The relative contrast ratios (CRs) of the hypointense part of cavernous hemangioma, globus pallidus and putamen to the deep frontal white matter were measured on each pulse sequence and statistically analyzed using analysis of variance followed by paired t-test. Results: In the hypointense part of cavernous hemangioma, relative CRs were significantly lower on T2*-weighted GRE than on T2-weighted SE images (P=0.0001), and on T2-weighted SE than on T2-weighted FSE images (P=0.0001). In the globus pallidus, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.002), and on T2*-weighted GRE than on T2-weighted FSE images (P=0.0002). In the putamen, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.001), and there was no significant difference between CRs on T2-weighted FSE and T2*-weighted GRE images (P=0.90). Conclusion: Hemosiderin showed best image contrast on T2*-weighted GRE images but ferritin showed more prominent image contrast on T2-weighted SE than on T2*-weighted GRE images, which may help to determine an appropriate pulse sequence in neurological diseases associated with excessive ferritin accumulation

  12. Contrast-enhanced dynamic MR imaging of parasellar tumor using fast spin-echo sequence

    International Nuclear Information System (INIS)

    Kusunoki, Katsusuke; Ohue, Shiro; Ichikawa, Haruhisa; Saito, Masahiro; Sadamoto, Kazuhiko; Sakaki, Saburo; Miki, Hitoshi.

    1995-01-01

    We have applied a new dynamic MRI technique that uses a fast spin-echo sequence to parasellar tumors. This sequence has less susceptible effect and better spatial resolution than a gradient echo sequence, providing faster images than a short spin-echo sequence does. Image was obtained in the coronal or sagittal plane using a 1.5T clinical MRI system, and then, dynamic MR images were acquired every 10 to 20 sec after administration of Gd-DTPA (0.1 mmol/kg). The subjects were 12 patients (5 microadenomas, 5 macroadenomas and 2 Rathke's cleft cysts) and 5 normal volunteers. As for volunteers, the cavernous sinus, pituitary stalk and posterior pituitary gland were contrasted on the first image, followed by visualization of the proximal portion adjacent to the junction of the infundibulum and the anterior pituitary gland, and finally by contrasting the distal portion of the anterior pituitary gland. There was a difference with respect to tumor contrast between microadenomas and macroadenomas. In the case of the macroadenomas, the tumor was contrasted at the same time as, or faster than the anterior pituitary gland, while with the microadenomas the tumor was enhanced later than the anterior pituitary gland. No enhancement with contrast medium was seen in Rathke's cleft cysts. In addition, it was possible to differentiate a recurrent tumor from a piece of muscle placed at surgery since the images obtained by the fast spin-echo sequence were clearer than those obtained by gradient echo sequence. (author)

  13. Comparison between two.magnetic resonance sequences (spin-echo and gradient-echo) in the analysis of lesions of the knee joint meniscus

    International Nuclear Information System (INIS)

    Marti-Bonati, L.; Casillas, C.

    1999-01-01

    To compare the diagnostic reliability, the proportion of common diagnoses and the degree of agreement between the results of two magnetic resonance (MR) sequences in the diagnosis of lesions of the meniscus of the knee. One hundred consecutive patients were studied prospectively by MR (1,5 Teslas). All of them underwent T1-weighted spin-echo and T1 and T2-weighted gradient-echo sequences. The final diagnosis was based on the combined results of four imaging sequences. The sensitivity, specificity, positive predictive value (PPV) and negative predictive (NPV) in terms of the final diagnosis were calculated for each meniscus and MR technique. The chi.squared test and kappa test were employed for the statistical analysis. There were discrepancies between the final diagnosis and the spin-echo sequence in 4 cases and between the final diagnosis and the gradient-echo sequences in 5 Both spin-echo and gradient-echo sequences showed the same diagnostic reliabilities: sensitivity of 0.98, specificity of 0.99, PPV of 0.98 and NPV of 0.99. The correlation between the two sequences was highly significant (chi-squared, p < 0.001) with a very high rate of agreement (kappa=0.84). The two sequences can be considered equally reliable in the study of meniscal lesions. (Author) 7 refs

  14. Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

    Science.gov (United States)

    Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

    2012-06-01

    The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Optimal control design of turbo spin-echo sequences with applications to parallel-transmit systems

    NARCIS (Netherlands)

    Sbrizzi, Alessandro; Hoogduin, Hans; Hajnal, Joseph V; van den Berg, CAT; Luijten, Peter R; Malik, Shaihan J

    PURPOSE: The design of turbo spin-echo sequences is modeled as a dynamic optimization problem which includes the case of inhomogeneous transmit radiofrequency fields. This problem is efficiently solved by optimal control techniques making it possible to design patient-specific sequences online.

  16. Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

    International Nuclear Information System (INIS)

    Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L.

    2008-01-01

    The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

  17. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    International Nuclear Information System (INIS)

    Hopper, M.A.; Robinson, P.; Grainger, A.J.

    2011-01-01

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  18. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    Energy Technology Data Exchange (ETDEWEB)

    Hopper, M.A.; Robinson, P. [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom); Grainger, A.J., E-mail: andrew.grainger@leedsth.nhs.u [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom)

    2011-04-15

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  19. Magnetic resonance imaging of lumbar spine. Comparison of multiple spin echo and low flip angle gradient echo imaging

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, Takamichi; Fujita, Norihiko; Harada, Koushi; Kozuka, Takahiro (Osaka Univ. (Japan). Faculty of Medicine)

    1989-07-01

    Sixteen patients including 13 cases with disk herniation and 3 cases with spondylosis of lumbar spine were examined on a resistive MRI system operating at 0.1 T. All lesions were studied with both multiple spin echo (MSE) and low flip angle gradient echo (LF) techniques to evaluate which technique is more effective in detecting the disk degeneration and the indentation on subarachnoid space. MSE images were obtained with repetition time (TR) of 1100-1500 ms or cardiac gating, an echo time (TE) of 30, 60, 90, 120, 150, and 180 ms symmetrical 6 echoes, and total acquisition time of more than 281 sec. LF images were obtained with TR of 500, 250, and 100 ms, TE of 18 ms, a flip angle of 30 degree, and total acquisition time of 128 sec. Eleven lesions of spinal disk degeneration and 12 of indentation on subarachnoid space were detected with LF. On the other hand, 26 lesions of spinal disk degeneration and 38 of indentation on subarachnoid space were detected with MSE. Although the parameters of LF employed in this study were relatively effective to emphasize T2{sup *}-based contrast, the ability of LF in detection of spinal disk degeneration and indentation on subarachnoid space is less than that of MSE. Signal contrast to noise ratios for normal disk and degenerative disk, epidural-fat and disk herniated material, CSF and disk herniated material, and epidural-fat and CSF were less than 4 with LF, but more than 4 with MSE. This difference of contrast to noise ratio between MSE and LF was one of the main causes of the difference of the detection rate of spinal disk degeneration and indentation on subarachnoid space. (author).

  20. Comparison of spin echo T1-weighted sequences versus fast spin-echo proton density-weighted sequences for evaluation of meniscal tears at 1.5 T

    International Nuclear Information System (INIS)

    Wolff, Andrew B.; Pesce, Lorenzo L.; Wu, Jim S.; Smart, L.R.; Medvecky, Michael J.; Haims, Andrew H.

    2009-01-01

    At our institution, fast spin-echo (FSE) proton density (PD) imaging is used to evaluate articular cartilage, while conventional spin-echo (CSE) T1-weighted sequences have been traditionally used to characterize meniscal pathology. We sought to determine if FSE PD-weighted sequences are equivalent to CSE T1-weighted sequences in the detection of meniscal tears, obviating the need to perform both sequences. We retrospectively reviewed the records of knee arthroscopies performed by two arthroscopy-focused surgeons from an academic medical center over a 2-year period. The preoperative MRI images were interpreted independently by two fellowship-trained musculoskeletal radiologists who graded the sagittal CSE T1 and FSE PD sequences at different sittings with grades 1-5, where 1 = normal meniscus, 2 = probable normal meniscus, 3 indeterminate, 4 = probable torn meniscus, and 5 = torn meniscus. Each meniscus was divided into an anterior and posterior half, and these halves were graded separately. Operative findings provided the gold standard. Receiver operating characteristic (ROC) analysis was performed to compare the two sequences. There were 131 tears in 504 meniscal halves. Using ROC analysis, the reader 1 area under curve for FSE PD was significantly better than CSE T1 (0.939 vs. 0.902, >95% confidence). For reader 2, the difference met good criteria for statistical non-inferiority but not superiority (0.913 for FSE PD and 0.908 for CSE T1; >95% non-inferiority for difference at most of -0.027). FSE PD-weighted sequences, using our institutional protocol, are not inferior to CSE T1-weighted sequences for the detection of meniscal tears and may be superior. (orig.)

  1. Proton T2 Relaxation effect of superparamagnetic iron oxide on fast spin echo sequence. Influence of echo number (even or odd) of effective TE

    International Nuclear Information System (INIS)

    Tsuchihashi, Toshio; Maki, Toshio; Kitagawa, Matsuo; Suzuki, Takeshi; Fujita, Isao

    1999-01-01

    The T 2 relaxation effect of the fast spin echo sequence (FSE) was investigated using superparamagnetic iron oxide (SPIO) particles. When even echoes were used as the effective TE of FSE, the signal intensity ratio [signal intensity of FSE/signal intensity of conventional spin echo sequence (CSE)] of FSE and CSE increased, whereas the T 2 relaxation effect of SPIO with FSE was reduced. However, when odd echoes were used, neither signal intensity changed, and weakening of the T 2 relaxation effect, considered a problem with FSE, was reduced. This phenomenon was not observed when the refocusing flip angle was changed to 30 and 60 degrees. However, it was observed when the refocusing flip angle was 120 and 150 degrees. Thus, this phenomenon can be considered to be related to oscillation in longitudinal magnetization when using the Carr-Purcell-Meiboom-Gill (CPMG) technique. (author)

  2. MRI in neuro-Behcet's syndrome: comparison of conventional spin-echo and FLAIR pulse sequences

    International Nuclear Information System (INIS)

    Jaeger, H.R.; Albrecht, T.; Curati-Alasonatti, W.L.; Williams, E.J.; Haskard, D.O.

    1999-01-01

    We compared the sensitivity of a fluid-attenuated inversion-recovery (FLAIR) sequence with that of a conventional dual-echo spin-echo (SE) sequence to brain lesions in 20 patients with Behcet's syndrome. They underwent 25 MRI examinations. The images were independently analysed for the number, type and anatomical location of lesions shown. There were 18 abnormal studies (13 initial and 5 follow-up). The FLAIR sequence detected significantly more lesions than the SE TE 80 (P < 0.05) and SE TE 20 (P < 0.01) sequences. It was particularly useful for demonstrating lesions in the juxtacortical white matter, which accounted for over half the lesions detected on the FLAIR images. Of patients presenting with nonspecific symptoms such as headache, seven had normal and five had abnormal studies. All patients presenting with focal neurological signs had abnormal imaging. We found supratentorial and, in particular, juxtacortical lesions to be more frequent than previously described. (orig.)

  3. Calculation of T2 relaxation time from ultrafast single shot sequences for differentiation of liver tumors. Comparison of echo-planar, HASTE, and spin-echo sequences

    International Nuclear Information System (INIS)

    Abe, Yasuko; Yamashita, Yasuyuki; Tang, Yi; Namimoto, Tomohiro; Takahashi, Mutsumasa

    2000-01-01

    The purpose of this study was to evaluate the accuracy of T2 calculation from single shot imaging sequences such as echo-planar imaging (EPI) and half-Fourier single shot turbo spin-echo (HASTE) imaging. For the phantom study, we prepared vials containing different concentrations of agarose, copper sulfate, and nickel chloride. The temperature of the phantom was kept at 22 deg C. MR images were obtained with a 1.5-Tesla superconductive magnet. Spin-echo (SE)-type EPI and HASTE sequences with different TEs were obtained for T2 calculation, and the T2 values were compared with those obtained from the Carr-Purcell-Meiborm-Gill (CPMG) sequence. The clinical study group consisted of 30 consecutive patients referred for MR imaging to characterize focal liver lesions. A total of 40 focal liver lesions were evaluated, including 25 primary or metastatic solid masses and 15 non-solid lesions. Single shot SE-type EPI and HASTE were both performed with TEs of 64 and 90 msec. In the phantom study, the T2 values obtained from both single shot sequences showed significant correlations with those from the CPMG sequence (T2 on EPI vs. T2 on CPMG: r=0.98, p<0.01; T2 on HASTE vs. T2 on CPMG: r=0.99, p<0.01). In the clinical study, mean T2 values for liver calculated from EPI (42 msec) were significantly shorter than those calculated from the HASTE sequence (58 msec) (p<0.001). Mean T2 values for solid tumors were 95 msec with HASTE and 72 msec with EPI, and mean T2 values for non-solid lesions were 128 msec with HASTE and 159 msec with EPI. Although mean T2 values between solid and non-solid lesions were significantly different for both EPI and HASTE sequences (p=0.01 for HASTE, p<0.001 for EPI), the overlap of solid and non-solid lesions was less frequent in EPI than in HASTE. With single shot sequences, it is possible to obtain the T2 values that show excellent correlation with the CPMG sequence. Although both HASTE and EPI are useful to calculate T2 values, EPI appears to be more

  4. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  5. Time-resolved echo-shared parallel MRA of the lung: observer preference study of image quality in comparison with non-echo-shared sequences

    International Nuclear Information System (INIS)

    Fink, C.; Puderbach, M.; Zaporozhan, J.; Plathow, C.; Kauczor, H.-U.; Ley, S.

    2005-01-01

    The aim of this study was to evaluate the image quality of time-resolved echo-shared parallel MRA of the lung. The pulmonary vasculature of nine patients (seven females, two males; median age: 44 years) with pulmonary disease was examined using a time-resolved MRA sequence combining echo sharing with parallel imaging (time-resolved echo-shared angiography technique, or TREAT). The sharpness of the vessel borders, conspicuousness of peripheral lung vessels, artifact level, and overall image quality of TREAT was assessed independently by four readers in a side-by-side comparison with non-echo-shared time-resolved parallel MRA data (pMRA) previously acquired in the same patients. Furthermore, the SNR of pulmonary arteries (PA) and veins (PV) achieved with both pulse sequences was compared. The mean voxel size of TREAT MRA was decreased by 24% compared with the non-echo-shared MRA. Regarding the sharpness of the vessel borders, conspicuousness of peripheral lung vessels, and overall image quality the TREAT sequence was rated superior in 75-76% of all cases. If the TREAT images were preferred over the pMRA images, the advantage was rated as major in 61-71% of all cases. The level of artifacts was not increased with the TREAT sequence. The mean interobserver agreement for all categories ranged between fair (artifact level) and good (overall image quality). The maximum SNR of TREAT did not differ from non-echo-shared parallel MRA (PA: TREAT: 273±45; pMRA: 280±71; PV: TREAT: 273±33; pMRA: 258±62). TREAT achieves a higher spatial resolution than non-echo-shared parallel MRA which is also perceived as an improved image quality. (orig.)

  6. Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L. [David Geffen School of Medicine at UCLA, Department of Radiology, 200 UCLA Medical Plaza, Suite 165-59, Box 956952, Los Angeles, CA (United States)

    2008-01-15

    The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p < 0.05). Subdividing the labrum, GRE was significantly more sensitive for the posterior labrum (75% versus 25%; p < 0.05) with a trend toward greater sensitivity at the anterior labrum (78% versus 56%; p = 0.157) but not significantly different for the superior labrum (50% versus 57%; p > 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

  7. Comparison of Multiple-Microphone and Single-Loudspeaker Adaptive Feedback/Echo Cancellation Systems

    DEFF Research Database (Denmark)

    Guo, Meng; Elmedyb, Thomas Bo; Jensen, Søren Holdt

    2011-01-01

    Recently, we introduced a frequency domain measure - the power transfer function - to predict the convergence rate, system stability bound and the steady-state behavior across time and frequency of a least mean square based feedback/echo cancellation algorithm in a general multiple-microphone and......Recently, we introduced a frequency domain measure - the power transfer function - to predict the convergence rate, system stability bound and the steady-state behavior across time and frequency of a least mean square based feedback/echo cancellation algorithm in a general multiple...

  8. Myocardial viability: comparison of free-breathing navigator-echo-gated three-dimensional inversion-recovery gradient-echo MR and standard multiple breath-hold two-dimensional inversion-recovery gradient-echo MR

    International Nuclear Information System (INIS)

    Kim, Jin Hee; Seo, Joon Beom; Do, Kyung Hyun; Yang, Dong Hyun; Lee, Soo Hyun; Ko, Sung Min; Heo, Jeong Nam; Lim, Tae Hwan

    2004-01-01

    To compare a free-breathing, navigator-echo-gated, three-dimensional, inversion-recovery, gradient-echo, MR pulse sequence (3D-MRI) with standard, multiple breath-hold, two-dimensional, inversion-recovery, gradient-echo MR (2D-MRI) for the evaluation of delayed hyperenhancement of nonviable myocardium in patients with chronic ischemic heart disease. Ten patients with chronic ischemic heart disease were enrolled in this study. MRI was performed on a 1.5-T system. 3D-MRI was obtained in the short axis plane at 10 minutes after the administration of Gd-DTPA (0.2 mmol/kg, 4 cc/sec). Prospective gating of the acquisition based on the navigator echo was applied. 2D-MRI was performed immediately after finishing 3D-MRI. The area of total and hyperenhanced myocardium measured on both image sets was compared with paired Student t-test and Bland-Altman method. By using a 60-segment model, the transmural extent and segment width of the hyperenhanced area were recorded by 3-scale grading method. The agreement between the two sequences was evaluated with kappa statistics. We also evaluated the agreement of hyperenhancement among the three portions (apical, middle and basal portion) of the left ventricle with kappa statistics. The two sequences showed good agreement for the measured area of total and hyperenhanced myocardium on paired t-test (ρ = 0.11 and ρ = 0.34, respectively). No systematic bias was shown on Bland-Altman analysis. Good agreement was found for the segmental width (Κ = 0.674) and transmural extent (Κ = 0.615) of hyperenhancement on the segmented analysis. However, the agreement of the transmural extent of hyperenhancement in the apical segments was relatively poor compared with that in the middle or basal portions. This study showed good agreement between 3D-MRI and 2D-MRI in evaluation of non-viable myocardium. Therefore, 3D-MRI may be useful in the assessment of myocardial viability in patients with dyspnea and children because it allows free

  9. 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

  10. Fast triple-spin-echo Dixon (FTSED) sequence for water and fat imaging

    Czech Academy of Sciences Publication Activity Database

    Kořínek, Radim; Bartušek, Karel; Starčuk jr., Zenon

    2017-01-01

    Roč. 37, APR (2017), s. 164-170 ISSN 0730-725X R&D Projects: GA MŠk ED0017/01/01; GA MŠk(CZ) LO1212 Institutional support: RVO:68081731 Keywords : fast triple-spin-echo Dixon * sequence * MRI * fat fraction * water-fat * ultra-high field * 9.4 T * FTSED Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Radiology, nuclear medicine and medical imaging Impact factor: 2.225, year: 2016

  11. Can a single-shot black-blood T2-weighted spin-echo echo-planar imaging sequence with sensitivity encoding replace the respiratory-triggered turbo spin-echo sequence for the liver? An optimization and feasibility study.

    Science.gov (United States)

    Hussain, Shahid M; De Becker, Jan; Hop, Wim C J; Dwarkasing, Soendersing; Wielopolski, Piotr A

    2005-03-01

    To optimize and assess the feasibility of a single-shot black-blood T2-weighted spin-echo echo-planar imaging (SSBB-EPI) sequence for MRI of the liver using sensitivity encoding (SENSE), and compare the results with those obtained with a T2-weighted turbo spin-echo (TSE) sequence. Six volunteers and 16 patients were scanned at 1.5T (Philips Intera). In the volunteer study, we optimized the SSBB-EPI sequence by interactively changing the parameters (i.e., the resolution, echo time (TE), diffusion weighting with low b-values, and polarity of the phase-encoding gradient) with regard to distortion, suppression of the blood signal, and sensitivity to motion. The influence of each change was assessed. The optimized SSBB-EPI sequence was applied in patients (N = 16). A number of items, including the overall image quality (on a scale of 1-5), were used for graded evaluation. In addition, the signal-to-noise ratio (SNR) of the liver was calculated. Statistical analysis was carried out with the use of Wilcoxon's signed rank test for comparison of the SSBB-EPI and TSE sequences, with P = 0.05 considered the limit for significance. The SSBB-EPI sequence was improved by the following steps: 1) less frequency points than phase-encoding steps, 2) a b-factor of 20, and 3) a reversed polarity of the phase-encoding gradient. In patients, the mean overall image quality score for the optimized SSBB-EPI (3.5 (range: 1-4)) and TSE (3.6 (range: 3-4)), and the SNR of the liver on SSBB-EPI (mean +/- SD = 7.6 +/- 4.0) and TSE (8.9 +/- 4.6) were not significantly different (P > .05). Optimized SSBB-EPI with SENSE proved to be feasible in patients, and the overall image quality and SNR of the liver were comparable to those achieved with the standard respiratory-triggered T2-weighted TSE sequence. (c) 2005 Wiley-Liss, Inc.

  12. Anomalous diffusion measured by a twice-refocused spin echo pulse sequence: analysis using fractional order calculus.

    Science.gov (United States)

    Gao, Qing; Srinivasan, Girish; Magin, Richard L; Zhou, Xiaohong Joe

    2011-05-01

    To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2600 s/mm(2). For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β, and μ values and the goodness-of-fit in three specific regions of interest (ROIs) in white matter, gray matter, and cerebrospinal fluid, respectively, were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. The diffusion-induced signal attenuation in a TRSE pulse sequence

  13. Magnetic resonance urography in pediatrics: utilization of ultrafast single-shot spin echo sequences

    International Nuclear Information System (INIS)

    Martin, C.; Martin, J.; Duran, C.; Rigol, S.; Rojo, J. C.

    1999-01-01

    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 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 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

  14. MRI of the cervical spine with 3D gradient echo sequence at 3 T: initial experience

    International Nuclear Information System (INIS)

    Xiao, L.; Siu, C.W.J.; Yeung, K.; Leung, A.; Yuen, M.K.; Wong, Y.C.

    2015-01-01

    Aim: The aim of this study was to compare three-dimensional (3D) high resolution T2*-weighted gradient echo (3D FFE) magnetic resonance (MR) sequence with conventional 2D T2-weighted turbo spin echo (TSE) MR sequence for imaging of the cervical spine, especially to assess the detectability of the internal anatomy of the cervical spinal cord, i.e. to distinguish the grey and white matter. Methods: Fifteen volunteers were examined at 3.0T MR unit. Signal-to-noise (SNR), contrast-to-noise (CNR) and image homogeneity were evaluated. In the visual analysis, the visibility of anatomical structures of the cervical spine and artifacts were assessed. The nonparametric method of paired sample t-test was adopted to evaluate the differences between the sequences. Results: The 3D FFE sequence provided better results for CNR, cerebrospinal fluid (CSF) versus white matter, grey matter, disk and bone. Moreover, it yielded good results for the CNR grey matter versus white matter. The butterfly-shaped “H” is clearly displayed in the 3D FFE sequence. The statistical analysis revealed the statistically significant difference between the 2D TSE and 3D FFE sequences for the contrast of CSF versus spinal cord (both grey matter and white matter). Conclusion: The 3D FFE sequence in MR imaging of the cervical spinal cord is superior in delineation of spinal cord anatomical structures compared to 2D TSE sequence. -- Highlights: •We investigate the potential of 3D FFE sequence to distinguish the grey-white of the cervical spinal cord at 3T MRI system. •We optimized The 3D FFE sequence was optimized to increase the grey-white contrast. •Utilizing medium TE for T2W and the shortest TR for reduction of susceptibility related artifacts and motion artefacts. •This technique may increase the confidence in the diagnosis of disease with the improved delineation of cord anatomy

  15. 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.)

  16. Liver imaging at 3.0 T: Diffusion-induced black-blood echo-planar imaging with large anatomic volumetric coverage as an alternative for specific absorption rate-intensive echo-train spin-echo sequences: Feasibility study

    NARCIS (Netherlands)

    I.C. van den Bos (Indra); S.M. Hussain (Shahid); G.P. Krestin (Gabriel); P.A. Wielopolski (Piotr)

    2008-01-01

    textabstractInstitutional Review Board approval and signed informed consent were obtained by all participants for an ongoing sequence optimization project at 3.0 T. The purpose of this study was to evaluate breath-hold diffusion-induced blackblood echo-planar imaging (BBEPI) as a potential

  17. Detection-Discrimination Method for Multiple Repeater False Targets Based on Radar Polarization Echoes

    Directory of Open Access Journals (Sweden)

    Z. W. ZONG

    2014-04-01

    Full Text Available Multiple repeat false targets (RFTs, created by the digital radio frequency memory (DRFM system of jammer, are widely used in practical to effectively exhaust the limited tracking and discrimination resource of defence radar. In this paper, common characteristic of radar polarization echoes of multiple RFTs is used for target recognition. Based on the echoes from two receiving polarization channels, the instantaneous polarization radio (IPR is defined and its variance is derived by employing Taylor series expansion. A detection-discrimination method is designed based on probability grids. By using the data from microwave anechoic chamber, the detection threshold of the method is confirmed. Theoretical analysis and simulations indicate that the method is valid and feasible. Furthermore, the estimation performance of IPRs of RFTs due to the influence of signal noise ratio (SNR is also covered.

  18. Comparison of single-shot fast spin-echo sequence and T2-weighted fast spin-echo sequence in MR imaging of the brain

    International Nuclear Information System (INIS)

    Cha, Sung Ho; Seo, Jeong Jin; Jeong, Gwang Woo; Kim, Jae Kyu; Kim, Yun Hyeon; Jeong, Yong Yeon; Kang, Heoung Keun; Oh, Hee Yeon; Yoon, Jong Hoon

    1998-01-01

    The purpose of this study was to evaluate the usefulness of the single-shot fast spinecho (SS-FSE) sequence in comparison with the T2-weighted fast spin-echo (T2-FSE) sequence in brain MR imaging. In 41 patients aged 15-75 years with intracranial lesion, both SS-FSE and T2-FES images were obtained using a 1.5-T MR system. Lesions included cerebral ischemia or infarcts (n=3D23), tumors (n=3D10), hemorrhages (n=3D3), inflammatory diseases (n=3D2), arachnoid cysts(n=3D2), and vascular disease (n=3D1), and the MR images were retrospectively evaluated. To calculate contrast-to-noise ratio (CNR), percentage contrast, and signal-to-noise ratio (SNR)-and thus make a quantitative comparison-the mean signal intensities of lesions, normal brain tissue, and noise out-side the patient were measured. For qualitative comparison, the visibility, margin, and extent of the lesions were rated using a five-grade system, and the degree of MR artifacts was also evaluated. Wilcoxon's signed ranks test was used for statistical analysis. The mean CNR of lesions was significantly higher on SS-FSE (31.3) than on T2-FSE images (27.5) (p=3D0.0131). Mean percentage contrast was also higher on SS-FSE (159.0) than on T2-FSE images (108.5) (p=3D0.0222), but mean SNR was higher on T2-FSE (80.3) than on SS-FSE images (53.5) (p=3D0.0000). No significant differences in lesion visibility were observed between the two imaging sequences, though margin and extent of the lesion were worse on SS-FSE images. For MR artifacts, no significant differences were demonstrated. For the evaluation of most intracranial lesions, MR imaging using the SS-FSE sequence appears to be slightly inferior to the T2-FSE sequence, but may be useful where patients are ill or uncooperative, or where children require sedation.=20

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

    International Nuclear Information System (INIS)

    Bruine, Francisca T. de; Berg-Huysmans, Annette A. van den; Buchem, Mark A. van; Grond, Jeroen van der; Steggerda, Sylke J.; Leijser, Lara M.; Rijken, Monique; Wezel-Meijler, Gerda van

    2014-01-01

    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 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. Three-dimensional gradient echo versus spin echo sequence in contrast-enhanced imaging of the pituitary gland at 3 T

    Energy Technology Data Exchange (ETDEWEB)

    Kakite, Suguru, E-mail: sugkaki@med.tottori-u.ac.jp [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Fujii, Shinya [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Kurosaki, Masamichi [Department of Neurosurgery, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Kanasaki, Yoshiko; Matsusue, Eiji; Kaminou, Toshio; Ogawa, Toshihide [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan)

    2011-07-15

    Introduction: To clarify whether a three-dimensional-gradient echo (3D-GRE) or spin echo (SE) sequence is more useful for evaluating sellar lesions on contrast-enhanced T1-weighted MR imaging at 3.0 Tesla (T). Methods: We retrospectively assessed contrast-enhanced T1-weighted images using 3D-GRE and SE sequences at 3.0 T obtained from 33 consecutive patients with clinically suspected sellar lesions. Two experienced neuroradiologists evaluated the images qualitatively in terms of the following criteria: boundary edge of the cavernous sinus and pituitary gland, border of sellar lesions, delineation of the optic nerve and cranial nerves within the cavernous sinus, susceptibility and flow artifacts, and overall image quality. Results: At 3.0 T, 3D-GRE provided significantly better images than the SE sequence in terms of the border of sellar lesions, delineation of cranial nerves, and overall image quality; there was no significant difference regarding the boundary edge of the cavernous sinus and pituitary gland. In addition, the 3D-GRE sequence showed fewer pulsation artifacts but more susceptibility artifacts. Conclusion: Our results indicate that 3D-GRE is the more suitable sequence for evaluating sellar lesions on contrast-enhanced T1-weighted imaging at 3.0 T.

  1. 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.

  2. 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

    International Nuclear Information System (INIS)

    Park, Jung Hyun; Kim, Eun Hee; Park, Jong Bin; Kim, Jae Hyoung; Choi, Byung Se; Jung, Cheol Kyu; Bae, Yun Jung; Lee, Kyung Mi

    2015-01-01

    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

  3. Optimizing the magnetization-prepared rapid gradient-echo (MP-RAGE sequence.

    Directory of Open Access Journals (Sweden)

    Jinghua Wang

    Full Text Available The three-dimension (3D magnetization-prepared rapid gradient-echo (MP-RAGE sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.

  4. MRI of bone marrow: opposed-phase gradient-echo sequences with long repetition time

    International Nuclear Information System (INIS)

    Seiderer, M.; Staebler, A.; Wagner, H.

    1999-01-01

    Signal intensity for opposed-phase gradient-echo (GE) sequences of tissues composed of fat- and water-equivalent cells such as red bone marrow is extremely sensitive to variation of the ratio of both cell populations (fat-to-water ratio Q F/W ). Because most bone marrow pathology results in variation of Q F/W , GE sequences are characterized by high-contrast imaging of pathology. The aim of this study was to evaluate the influence of TR, TE, FA, Q F/W and histology on signal intensity. Signal intensity of opposed-phase GE sequences as a function of TR, TE, FA, and Q F/W was measured for a fat-water phantom and cadaver specimens of normal bone marrow (red and yellow) and pathological bone marrow (tumors). All specimens were correlated to histology. Opposed-phase GE imaging of red bone marrow pathology results in low-signal-intensity imaging of intact red bone marrow and high-signal-intensity positive contrast imaging of pathology associated with a change in Q F/W . In first-order approximation the signal intensity of pathology is linearly correlated to the change in Q F/W . Opposed-phase GE imaging is a sensitive imaging technique for red bone marrow pathology. Relative contrast of red bone marrow pathology is similar to fat-suppressed imaging techniques. Acquisition time is identical to T1-weighted SE sequences. (orig.)

  5. The optimization of balanced turbo field echo sequence for depicting pelvic venous plexuses

    International Nuclear Information System (INIS)

    Takatsu, Yasuo; Koyama, Takashi

    2010-01-01

    Evaluating the relation between the developing range and the extent of invasion of a malignant tumor around the pelvic venous plexus is an important index for making strategic therapeutic decisions. In this study, we tried to depict a venous plexus in the pelvis using Balanced Turbo Field Echo (B-TFE). At first, we used an original phantom (derived from one layer of lard and another of agar (0.1%gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA), 0.9%NaCl), each 500 ml, and we changed the Start Up Echo (SUE); 0-30, spectral attenuated inversion recovery (SPAIR) inversion delay time (delay time); 0-200 ms, shot interval (SI); 1150, 1500 ms and evaluated the degree of fat suppression in signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) (the air signal method). The fat suppression-effect was found to be high in delay time; 120 ms in SUE; 0, SI; 1150 ms and 160 ms in SUE; 0, SI; 1500 ms was different SUE>0 each delay time. As for the images of healthy volunteers (5 men and 5 women), after fixing optimum conditions, we evaluated the images visually, as assessed by two radiologists and two radiographers, comparing between SUE; 0-30 and SI; 1150 and 1500 ms. According to the visual evaluation, the fat suppression-effect was worse, more than with the delay time; 20. We judged the best image of the venous plexus in the pelvis as being at SUE; 10, SI; 1500 ms. We think that using the B-TFE can help distinguish pelvic venous plexuses, by setting an optimum sequence. (author)

  6. High-resolution T2-weighted MR imaging of the inner ear using a long echo-train-length 3D fast spin-echo sequence

    International Nuclear Information System (INIS)

    Naganawa, S.; Yamakawa, K.; Fukatsu, H.; Ishigaki, T.; Nakashima, T.; Sugimoto, H.; Aoki, I.; Miyazaki, M.; Takai, H.

    1996-01-01

    The purpose of this study was to assess the value of a long echo-train-length 3D fast spin-echo (3D-FSE) sequence in visualizing the inner ear structures. Ten normal ears and 50 patient ears were imaged on a 1.5T MR unit using a head coil. Axial high-resolution T2-weighted images of the inner ear and the internal auditory canal (IAC) were obtained in 15 min. In normal ears the reliability of the visualization for the inner ear structures was evaluated on original images and the targeted maximum intensity projection (MIP) images of the labyrinth. In ten normal ears, 3D surface display (3D) images were also created and compared with MIP images. On the original images the cochlear aqueduct, the vessels in the vicinity of the IAC, and more than three branches of the cranial nerves were visualized in the IAC in all the ears. The visibility of the endolympathic duct was 80%. On the MIP images the visibility of the three semicircular canals, anterior and posterior ampulla, and of more than two turns of the cochlea was 100%. The MIP images and 3D images were almost comparable. The visibility of the endolymphatic duct was 80% in normal ears and 0% in the affected ears of the patients with Meniere's disease (p<0.001). In one patient ear a small intracanalicular tumor was depicted clearly. In conclusion, the long echo train length T2-weighted 3D-FSE sequence enables the detailed visualization of the tiny structures of the inner ear and the IAC within a clinically acceptable scan time. Furthermore, obtaining a high contrast between the soft/bony tissue and the cerebrospinal/endolymph/perilymph fluid would be of significant value in the diagnosis of the pathologic conditions around the labyrinth and the IAC. (orig.)

  7. [The use of the T2-weighted turbo-spin-echo sequence in studying the neurocranium. A comparison with the conventional T2-weighted spin-echo sequence].

    Science.gov (United States)

    Siewert, C; Hosten, N; Felix, R

    1994-07-01

    T2-weighted spin-echo imaging is the standard screening procedure in MR imaging of the neurocranium. We evaluated fast spin-echo T2-weighted imaging (TT2) of the neurocranium in comparison to conventional spin-echo T2-weighted imaging (T2). Signal-to-noise and contrast-to-noise ratio of normal brain tissues (basal ganglia, grey and white matter, CSF fluid) and different pathologies were calculated. Signal-to-noise ratio and contrast-to-noise ratio were significantly higher in TT2 than in T2 (with the exception of gray-to-white matter contrast). Tissues with increased content of water protons (mobile protons) showed the highest contrast to surrounding tissues. The increased signal intensity of fat must be given due attention in fatty lesions. Because the contrast-to-noise ratio between white matter and basal ganglia is less in TT2, Parkinson patients have to be examined by conventional T2. If these limitations are taken into account, fast spin-echo T2-weighted imaging is well appropriate for MR imaging of the neurocranium, resulting in heavy T2-weighting achieved in a short acquisition time.

  8. Self-calibrated multiple-echo acquisition with radial trajectories using the conjugate gradient method (SMART-CG).

    Science.gov (United States)

    Jung, Youngkyoo; Samsonov, Alexey A; Bydder, Mark; Block, Walter F

    2011-04-01

    To remove phase inconsistencies between multiple echoes, an algorithm using a radial acquisition to provide inherent phase and magnitude information for self correction was developed. The information also allows simultaneous support for parallel imaging for multiple coil acquisitions. Without a separate field map acquisition, a phase estimate from each echo in multiple echo train was generated. When using a multiple channel coil, magnitude and phase estimates from each echo provide in vivo coil sensitivities. An algorithm based on the conjugate gradient method uses these estimates to simultaneously remove phase inconsistencies between echoes, and in the case of multiple coil acquisition, simultaneously provides parallel imaging benefits. The algorithm is demonstrated on single channel, multiple channel, and undersampled data. Substantial image quality improvements were demonstrated. Signal dropouts were completely removed and undersampling artifacts were well suppressed. The suggested algorithm is able to remove phase cancellation and undersampling artifacts simultaneously and to improve image quality of multiecho radial imaging, the important technique for fast three-dimensional MRI data acquisition. Copyright © 2011 Wiley-Liss, Inc.

  9. Abdominal MR imaging using a HASTE sequence : image comparison on the different echo times

    International Nuclear Information System (INIS)

    Park, Kwang Bo; Lee, Moon Gyu; Lim, Tae Hwan; Jeong, Yoong Ki; Ha, Hyun Kwon; Kim, Pyo Nyun; Auh, Yong Ho

    1999-01-01

    To determine the optimal parameters of abdominal HASTE imaging by means of a comparison of intermediate and long TE (echo time). We evaluated 30 consecutive patients who had undergone liver MR during a three-month period. Twelve patients were diagnosed as normal, four as having liver cirrhosis, and 14 were found to be suffering form hepatic hemangioma. On the basis of measured signal intensity of the liver, spleen, pancreas and gallbladder, and of fat, muscle, hemangioma, and background, we calculated the ratios of signal to noise (S/N), signal difference to noise (SD/N), and signal intensity (SI). Image quality was compared using these three ratios, and using two HASTE sequences with TEs of 90 msec and 134 msec, images were qualitatively evaluated. S/N ratio of the liver was higher when TE was 90 msec(p<.05), though S/N, SD/N and SI rations of the spleen, gallbladder, and pancreas-and of hemangiom-were higher when TE was 134 msec (p<.05). However, in muscle, all these three ratios were higher at a TE of 90 msec. SD/N ratio and SI of fat were higher at a TE of 134 msec. Overall image quality was better at a TE of 134 msec than at one of 90msec. A HASTE sequence with a TE of 134msec showed greater tissue contrast and stronger T2-weighted images than one with a TE of 90msec

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

    International Nuclear Information System (INIS)

    Tsuchiya, Kazuhiro; Katase, Shichiro; Yoshino, Ayako; Yamakami, Norio; Hachiya, Junichi

    1998-01-01

    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 2 -weighted (T 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 2 W imaging was performed, EPI-T 2 W imaging yielded superior results compared with SE-T 2 W imaging in 3 patients as a consequence of patient motion and equal results compared with SE-T 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 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)

  11. 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)

  12. Evaluation of turbo spin echo sequences for MRI of focal liver lesions at 0.5 T

    International Nuclear Information System (INIS)

    Kreft, B.; Layer, G.; Steudel, A.; Spiller, L.; Heuck, A.; Mueller, A.; Gieseke, J.; Reiser, M.F.

    1994-01-01

    To determine whether turbo spin echo (TSE) sequences can replace conventional T2-weighted spin echo (SE) sequences in MRI of the liver, 40 patients with focal liver lesions were imaged at 0.5 T. A T2-weighted SE sequence (TR/TE 1800/90 ms, number of signals averaged [NEX] = 2, scan time 7:16 min), a TSE sequence (TR/TE 1800/90 ms, NEX = 4, number of echos per excitation = 13, echo spacing = 12.9 ms, scan time = 4:16 min) and a T1-weighted SE sequence (TR/TE 350/15 ms, NEX = 2, scan time = 4:21 min) were obtained and image quality, lesion detectability and lesion differentiation were evaluated qualitatively by subjective assessment using scores and quantitatively by lesion-liver contrast-to-noise (CNR) and tumour/liver signal intensity (SI) ratios. The image quality of the TSE sequence was substantially better compared with the T2-weighted SE sequence due to a reduction in motion artefacts and better delineation of anatomical details. Of a total of 158 visible lesions the T1-weighted SE, TSE and T2-weighted SE sequences showed 91 %, 81 % and 65 % of the lesions, respectively. Thus the TSE sequence depicted 24 % (P < 0.001) more lesions than the T2-weighted SE sequence. In all types of pathology the lesion-liver CNR of the TSE sequence was significantly (P < 0.001) higher compared to the CNR of the T2-weighted SE sequence ( +55-65 %), indicating superior lesion conspicuity. Lesion characterization was equally good on the two T2-weighted sequences with no difference in the tumour/liver SI ratio. Using a criterion of tumour/liver SI ratio equal to or higher than 2, haemangiomas larger than 1 cm in diameter could be differentiated from other lesions with a sensitivity and specificity of 95 % and 96 %, respectively. Our results indicate that the TSE sequence is suitable for replacing the conventional T2-weighted SE sequence in MRI of focal liver lesions. (orig.)

  13. Evaluation of MR cisternography of the cerebellopontine angle using a balanced fast-field-echo sequence: preliminary findings

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Kazuhiro; Aoki, Chinatsu; Hachiya, Junichi [Department of Radiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, 181-8611, Tokyo (Japan)

    2004-02-01

    We evaluated the feasibility of MR cisternography by the balanced fast-field-echo (bFFE) sequence, comparing with that by a turbo-spin-echo (TSE) sequence, for cerebellopontine angle lesions on a 1.5-T imager (Gyroscan Intera, Philips, Best, The Netherlands). The bFFE MR cisternograms depicted target cranial nerves with less cerebrospinal fluid pulsation artifacts than TSE cisternograms and visualized an acoustic schwannoma in 6 of 44 patients with suspicion and a causative vessel of hemifacial spasm in all of 3 patients in a short scanning time (1 min 53 s). The bFFE sequence can be promising for MR cisternography in the diagnosis of cerebellopontine angle lesions. (orig.)

  14. 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

    International Nuclear Information System (INIS)

    Martin, J.; Villajos, M.; Oses, M. J.; Veintemillas, M.; Rue, M.; Puig, J.; Sentis, M.

    2000-01-01

    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

  15. 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.)

  16. Fat-saturated, contrast-enhanced spin echo sequences in magnetic resonance tomographic diagnosis of peritoneal carcinosis

    International Nuclear Information System (INIS)

    Ricke, J.; Hosten, N.; Stroszczynski, C.; Amthauer, H.; Felix, R.; Sehouli, J.; Buchmann, E.; Rieger, J.

    1999-01-01

    Purpose: To evaluate contrast-enhanced, fat-saturated spin echo sequences for the detection of peritoneal carcinosis with MRI. Material and Methods: 61 patients, 35 with and 26 without peritoneal carcinosis, were examined with abdominal MRI. Fat-saturated, T 1 -weighted spin echo sequences were performed before and after administration of Gd-DTPA. In addition, 22 patients with peritoneal carcinosis were examined with contrast-enhanced abdominal CT. Results: 32 of 35 patients with peritoneal carcinosis demonstrated contrast enhancement of the visceral and 30 to 35 enhancement of the parietal peritoneum (91 and 86%, respectively). Wall thickening of the intestine or parietal peritoneum were noted in 21 and 20 of 35 patients (60 and 57%, respectively), ascites in 18 of 35 patients (51%). False positive contrast enhancement of the peritoneum was noted in 4 of 26 patients (15%). In the direct comparison of MRI and CT, 22 of 22 patients versus 7 of 22 patients showed contrast enhancement of the visceral peritoneum (100 and 32%, respectively). For other signs of peritoneal carcinosis (e.g., ascites, peritoneal seedings), no differences in diagnostic reliability were demonstrated. Conclusions: The use of fat-saturated, spin echo sequences facilitates the diagnosis of peritoneal carcinosis by artifact reduction and improved detection of peritoneal contrast enhancement. MRI with fat-saturated sequences was superior to CT. (orig.) [de

  17. WE-DE-206-04: MRI Pulse Sequences - Spin Echo, Gradient Echo, EPI, Non-Cartesia

    Energy Technology Data Exchange (ETDEWEB)

    Pooley, R. [Mayo Clinic (United States)

    2016-06-15

    Magnetic resonance imaging (MRI) has become an essential part of clinical imaging due to its ability to render high soft tissue contrast. Instead of ionizing radiation, MRI use strong magnetic field, radio frequency waves and field gradients to create diagnostic useful images. It can be used to image the anatomy and also functional and physiological activities within the human body. Knowledge of the basic physical principles underlying MRI acquisition is vitally important to successful image production and proper image interpretation. This lecture will give an overview of the spin physics, imaging principle of MRI, the hardware of the MRI scanner, and various pulse sequences and their applications. It aims to provide a conceptual foundation to understand the image formation process of a clinical MRI scanner. Learning Objectives: Understand the origin of the MR signal and contrast from the spin physics level. Understand the main hardware components of a MRI scanner and their purposes Understand steps for MR image formation including spatial encoding and image reconstruction Understand the main kinds of MR pulse sequences and their characteristics.

  18. Comparison of a T1-weighted inversion-recovery-, gradient-echo- and spin-echo sequence for imaging of the brain at 3.0 Tesla

    International Nuclear Information System (INIS)

    Stehling, C.; Niederstadt, T.; Kraemer, S.; Kugel, H.; Schwindt, W.; Heindel, W.; Bachmann, R.

    2005-01-01

    Purpose: The increased T1 relaxation times at 3.0 Tesla lead to a reduced T1 contrast, requiring adaptation of imaging protocols for high magnetic fields. This prospective study assesses the performance of three techniques for T1-weighted imaging (T1w) at 3.0 T with regard to gray-white differentiation and contrast-to-noise-ratio (CNR). Materials and Methods: Thirty-one patients were examined at a 3.0 T system with axial T1 w inversion recovery (IR), spin-echo (SE) and gradient echo (GE) sequences and after contrast enhancement (CE) with CE-SE and CE-GE sequences. For qualitative analysis, the images were ranked with regard to artifacts, gray-white differentiation, image noise and overall diagnostic quality. For quantitative analysis, the CNR was calculated, and cortex and basal ganglia were compared with the white matter. Results: In the qualitative analysis, IR was judged superior to SE and GE for gray-white differentiation, image noise and overall diagnostic quality, but inferior to the GE sequence with regard to artifacts. CE-GE proved superior to CE-SE in all categories. In the quantitative analysis, CNR of the based ganglia was highest for IR, followed by GE and SE. For the CNR of the cortex, no significant difference was found between IR (16.9) and GE (15.4) but both were superior to the SE (9.4). The CNR of the cortex was significantly higher for CE-GE compared to CE-SE (12.7 vs. 7.6, p<0.001), but the CNR of the basal ganglia was not significantly different. Conclusion: For unenhanced T1w imaging at 3.0 T, the IR technique is, despite increased artifacts, the method of choice due to its superior gray-white differentiation and best overall image quality. For CE-studies, GE sequences are recommended. For cerebral imaging, SE sequences give unsatisfactory results at 3.0 T. (orig.)

  19. Detection and quantification of regional cortical gray matter damage in multiple sclerosis utilizing gradient echo MRI

    Directory of Open Access Journals (Sweden)

    Jie Wen

    2015-01-01

    Full Text Available Cortical gray matter (GM damage is now widely recognized in multiple sclerosis (MS. The standard MRI does not reliably detect cortical GM lesions, although cortical volume loss can be measured. In this study, we demonstrate that the gradient echo MRI can reliably and quantitatively assess cortical GM damage in MS patients using standard clinical scanners. High resolution multi-gradient echo MRI was used for regional mapping of tissue-specific MRI signal transverse relaxation rate values (R2* in 10 each relapsing–remitting, primary-progressive and secondary-progressive MS subjects. A voxel spread function method was used to correct artifacts induced by background field gradients. R2* values from healthy controls (HCs of varying ages were obtained to establish baseline data and calculate ΔR2* values – age-adjusted differences between MS patients and HC. Thickness of cortical regions was also measured in all subjects. In cortical regions, ΔR2* values of MS patients were also adjusted for changes in cortical thickness. Symbol digit modalities (SDMT and paced auditory serial addition (PASAT neurocognitive tests, as well as Expanded Disability Status Score, 25-foot timed walk and nine-hole peg test results were also obtained on all MS subjects. We found that ΔR2* values were lower in multiple cortical GM and normal appearing white matter (NAWM regions in MS compared with HC. ΔR2* values of global cortical GM and several specific cortical regions showed significant (p < 0.05 correlations with SDMT and PASAT scores, and showed better correlations than volumetric measures of the same regions. Neurological tests not focused on cognition (Expanded Disability Status Score, 25-foot timed walk and nine-hole peg tests showed no correlation with cortical GM ΔR2* values. The technique presented here is robust and reproducible. It requires less than 10 min and can be implemented on any MRI scanner. Our results show that quantitative tissue-specific R2

  20. Magnetic field mapping around metal implants using an asymmetric spin-echo sequence

    Czech Academy of Sciences Publication Activity Database

    Bartušek, Karel; Dokoupil, Zdeněk; Gescheidtová, E.

    2006-01-01

    Roč. 17, č. 12 (2006), s. 3293-3300 ISSN 0957-0233 R&D Projects: GA MZd NR8110 Institutional research plan: CEZ:AV0Z20650511 Keywords : nuclear magnetic resonance * spin echo * MRI * B0 mapping * dental material Subject RIV: FS - Medical Facilities ; Equipment Impact factor: 1.228, year: 2006

  1. Heuristics for multiobjective multiple sequence alignment.

    Science.gov (United States)

    Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

    2016-07-15

    Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

  2. The role of envelope shape in the localization of multiple sound sources and echoes in the barn owl.

    Science.gov (United States)

    Baxter, Caitlin S; Nelson, Brian S; Takahashi, Terry T

    2013-02-01

    Echoes and sounds of independent origin often obscure sounds of interest, but echoes can go undetected under natural listening conditions, a perception called the precedence effect. How does the auditory system distinguish between echoes and independent sources? To investigate, we presented two broadband noises to barn owls (Tyto alba) while varying the similarity of the sounds' envelopes. The carriers of the noises were identical except for a 2- or 3-ms delay. Their onsets and offsets were also synchronized. In owls, sound localization is guided by neural activity on a topographic map of auditory space. When there are two sources concomitantly emitting sounds with overlapping amplitude spectra, space map neurons discharge when the stimulus in their receptive field is louder than the one outside it and when the averaged amplitudes of both sounds are rising. A model incorporating these features calculated the strengths of the two sources' representations on the map (B. S. Nelson and T. T. Takahashi; Neuron 67: 643-655, 2010). The target localized by the owls could be predicted from the model's output. The model also explained why the echo is not localized at short delays: when envelopes are similar, peaks in the leading sound mask corresponding peaks in the echo, weakening the echo's space map representation. When the envelopes are dissimilar, there are few or no corresponding peaks, and the owl localizes whichever source is predicted by the model to be less masked. Thus the precedence effect in the owl is a by-product of a mechanism for representing multiple sound sources on its map.

  3. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

    Full Text Available Abstract Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mismatch scores.

  4. Analysis of Acoustic Feedback/Echo Cancellation in Multiple-Microphone and Single-Loudspeaker Systems Using a Power Transfer Function Method

    DEFF Research Database (Denmark)

    Guo, Meng; Bo Elmedyb, Thomas; Jensen, Søren Holdt

    2011-01-01

    In this work, we analyze a general multiple-microphone and single-loudspeaker audio processing system, where a multichannel adaptive system is used to cancel the effect of acoustic feedback/echo, and a beamformer processes the feedback/echo canceled signals. We introduce and derive an accurate...

  5. Turbo-Proton Echo Planar Spectroscopic Imaging (t-PEPSI) MR technique in the detection of diffuse axonal damage in brain injury. Comparison with Gradient-Recalled Echo (GRE) sequence.

    Science.gov (United States)

    Giugni, E; Sabatini, U; Hagberg, G E; Formisano, R; Castriota-Scanderbeg, A

    2005-01-01

    Diffuse axonal injury (DAI) is a common type of primary neuronal injury in patients with severe traumatic brain injury, and is frequently accompanied by tissue tear haemorrhage. The T2*-weighted gradient-recalled echo (GRE) sequences are more sensitive than T2-weighted spin-echo images for detection of haemorrhage. This study was undertaken to determine whether turbo-PEPSI, an extremely fast multi-echo-planar-imaging sequence, can be used as an alternative to the GRE sequence for detection of DAI. Nineteen patients (mean age 24,5 year) with severe traumatic brain injury (TBI), occurred at least 3 months earlier, underwent a brain MRI study on a 1.5-Tesla scanner. A qualitative evaluation of the turbo-PEPSI sequences was performed by identifying the optimal echo time and in-plane resolution. The number and size of DAI lesions, as well as the signal intensity contrast ratio (SI CR), were computed for each set of GRE and turbo-PEPSI images, and divided according to their anatomic location into lobar and/or deep brain. There was no significant difference between GRE and turbo-PEPSI sequences in the total number of DAI lesions detected (283 vs 225 lesions, respectively). The GRE sequence identified a greater number of hypointense lesions in the temporal lobe compared to the t-PEPSI sequence (72 vs 35, pPEPSI than for the GRE sequence (pPEPSI sequence can be used as an alternative to the GRE to assess brain DAI in severe TBI patients, especially if uncooperative and medically unstable.

  6. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  7. Assessment of the characteristics of MRI coils in terms of RF non-homogeneity using routine spin echo sequences

    International Nuclear Information System (INIS)

    Oghabian, M. A.; Mehdipour, Sh.; RiahicAlam, N.; Rafie, B.; Ghanaati, H.

    2005-01-01

    One of the major causes of image non-uniformity in MRI is due to the existence of non-homogeneity in RF receive and transmit. This can be the most effective source of error in quantitative studies in MRI imaging. Part of this non-homogeneity demonstrates the characteristics of RF coil and part of it is due to the interaction of RF field with the material being imaged. In this study, RF field non-homogeneity of surface and volume coils is measured using an oil phantom. The method employed in this work is based on a routine Spin Echo based sequence as proposed by this group previously. Materials and Methods: For the determination of RF non-uniformity, a method based on Spin Echo sequence (8θ-180) was used as reported previously by the same author. In this method, several images were obtained from one slice using different flip angles while keeping all other imaging parameters constant. Then, signal intensity at a ROI from all of these images were measured and fitted to the MRI defined mathematical model. Since this mathematical model describes the relation between signal intensity and flip angle in a (8θ-180) Spin Echo sequence, it is possible to obtain the variation in receive and transmit sensitivity in terms of the variation of signal intensity from the actual expected values. Since surface coils are functioning as only receiver (RF transmission is done by Body coil), first the results of receive coil homogeneity is measured, then characteristic of transmit coil (for the body coil) is evaluated Results: The coefficient of variation (C.V.) found for T(r) value obtained from images using head coils was in the order of 0.6%. Since the head coil is functioning as both transmitter and receiver, any non-uniformity in either transmit or receive stage can lead to non-homogeneity in RF field. A part from the surface coils, the amount of non-homogeneity due to receive coil was less than that of the transmit coil. In the case of the surface coils the variation in receive

  8. Evaluation of short repetition time, partial flip angle, gradient recalled echo pulse sequences in cervical spine imaging

    International Nuclear Information System (INIS)

    Enzmann, D.; Rubin, J.B.

    1987-01-01

    A short repetition time (TR), partial flip angle, gradient recalled echo pulse sequence (GRASS) was prospectively studied to optimize it for the diagnosis of cervical disk and cord disease in 98 patients. Changes in signal-to-noise ratio (SNR) and contrast were measured as the following parameters were varied: flip angle (3 0 to 18 0 ), TR (22-60 msec), and echo time (TE) (12.5-25 msec). Flip angle was the single most important parameter. For disk disease, cerebrospinal fluid (CSF) SNR peaked at an 8 0 flip angle in the axial view but at a 4 0 flip angle in the sagittal view. In the sagittal view, disk-CSF contrast decreased progressively from a flip angle of 3 0 , while in the axial view it peaked at 10 0 . For cord lesions the findings were similar except that lesion-cord contrast could be increased by lengthening both TR and TE. No one combination of parameters proved greatly superior for either disk disease or cord disease. The selection of parameters required balancing of several factors that often had opposing effects

  9. Measuring the distance between multiple sequence alignments.

    Science.gov (United States)

    Blackburne, Benjamin P; Whelan, Simon

    2012-02-15

    Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.

  10. 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.)

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

    International Nuclear Information System (INIS)

    Jung, Joon-Yong; Jee, Won-Hee; Park, Michael Y.; Lee, So-Yeon; Kim, Yang-Soo

    2012-01-01

    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 (κ) 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.)

  12. Application of fast spin-echo T2-weighted imaging for examination of the neurocranium. Comparison with the conventional T2-weighted spin-echo sequence

    International Nuclear Information System (INIS)

    Siewert, C.; Hosten, N.; Felix, R.

    1994-01-01

    T 2 -weighted spin-echo imaging is the standard screening procedure in MR imaging of the neutrocranium. We evaluated fast spin-echo T 2 -weighted imaging (TT 2 ) of the neurocranium in comparison to conventional spin-echo T 2 -weighted imaging (T 2 ). Signal-to-noise and contrast-to-noise ratio of normal brain tissues (basal ganglia, grey and white matter, CSF fluid) and different pathologies were calculated. Signal-to-noise ratio and contrast-to-noise ratio were significantly higher than TT 2 than in T 2 (with the exception of grey-to-white matter contrast). Tissues with increased content of water protons (mobile protons) showed the highest contrast to surrounding tissues. The increased signal intensity of fat must be given due attention in fatty lesions. Because the contrast-to-noise ratio between white matter and basal ganglia is less in TT 2 , Parkinson patients have to be examined by conventional T 2 . If these limitations are taken into account, fast spin-echo T 2 -weighted imaging is well appropriate for MR imaging of the neurocranium, resulting in heavy T 2 -weighting achieved in a short acquisition time. (orig.) [de

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

    International Nuclear Information System (INIS)

    Kim, Yong Pyo; Kim, Sung Jun; Chung, Tae Sub; Yoo, Yeon Hwa; Yoon, Choon Sik; Kanneengiesser, Stephan; Paek, Moon Young; Song, Ho Taek; Lee, Young Han; Suh, Jin Suck

    2014-01-01

    To assess the feasibility of T2 * -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 * -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.

  14. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

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

    International Nuclear Information System (INIS)

    Uhl, M.; Allmann, K.H.; Hauer, M.P.; Langer, M.; Ihling, C.; Conca, W.

    1998-01-01

    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.)

  16. 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.

  17. 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.)

  18. Ultrafast T2-weighted single shot spin-echo sequences: applications on abdominal and pelvic pathologies

    International Nuclear Information System (INIS)

    Martin, J.; Martin, C.; Falco, J.; Esteban, L.

    1999-01-01

    The magnetic resonance imaging (MRI) sequences that obtain all the data using a sole excitation pulse of 90 degree centigrade, filling the K space in a single repetition time (TR) is known as snap shot or single shot (SS). The SS sequence based on the rapid acquisition with relaxation enhancement (SS-RARE) method, designed by Hening (1) and a variation of it with a half-Fourier reconstruction (SS-HF-RARE (HASTEL)) (2, 3) are capable of obtaining high contrast images in T2, in very short times, that oscillate between one to several seconds. The clinical application of these sequences to abdominal and pelvic pathologies is increasing, providing and improvement in the contrast resolution, but also in the spatial resolution, with a high relation signal/noise ratio, high contrast and absence of movement artifacts. (Author)

  19. MRI of the breast with 2D spin-echo and gradient echo sequences in diagnostically difficult cases. MRT der Mamma mit 2D-Spinecho- und Gradientenecho-Sequenzen in diagnostischen Problemfaellen

    Energy Technology Data Exchange (ETDEWEB)

    Allgayer, B. (Technische Univ. Muenchen (Germany). Inst. fuer Roentgendiagnostik); Lukas, P. (Technische Univ. Muenchen (Germany). Inst. und Poliklinik fuer Strahlentherapie und Radiologische Onkologie); Loos, W. (Technische Univ. Muenchen (Germany). Frauenklinik und Poliklinik); Kersting-Sommerhoff, B. (Technische Univ. Muenchen (Germany). Inst. fuer Roentgendiagnostik)

    1993-05-01

    One or both breasts of 296 patients with equivocal clinical or mammographical findings were examined with MRI. T[sub 1] weighted spinecho (SE) and gradient echo (FFE) sequences were acquired before and after i.v. application of Gadolinium DTPA. 50 lesions with enhancement after Gd-DTPA were biopsied - 26 carcinomas, 17 proliferating mastopathic tissues, 5 fibroadenomas and 1 abscess were found. Contrast enhanced MRI with 2D-SE and FFE sequences is an effective technqiue for evaluating suspicious breast lesions with high diagnostic acurracy. (orig.)

  20. 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

  1. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  2. Propagation of error from parameter constraints in quantitative MRI: Example application of multiple spin echo T2 mapping.

    Science.gov (United States)

    Lankford, Christopher L; Does, Mark D

    2018-02-01

    Quantitative MRI may require correcting for nuisance parameters which can or must be constrained to independently measured or assumed values. The noise and/or bias in these constraints propagate to fitted parameters. For example, the case of refocusing pulse flip angle constraint in multiple spin echo T 2 mapping is explored. An analytical expression for the mean-squared error of a parameter of interest was derived as a function of the accuracy and precision of an independent estimate of a nuisance parameter. The expression was validated by simulations and then used to evaluate the effects of flip angle (θ) constraint on the accuracy and precision of T⁁2 for a variety of multi-echo T 2 mapping protocols. Constraining θ improved T⁁2 precision when the θ-map signal-to-noise ratio was greater than approximately one-half that of the first spin echo image. For many practical scenarios, constrained fitting was calculated to reduce not just the variance but the full mean-squared error of T⁁2, for bias in θ⁁≲6%. The analytical expression derived in this work can be applied to inform experimental design in quantitative MRI. The example application to T 2 mapping provided specific cases, depending on θ⁁ accuracy and precision, in which θ⁁ measurement and constraint would be beneficial to T⁁2 variance or mean-squared error. Magn Reson Med 79:673-682, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  3. Magnetic resonance imaging (MRI) of articular cartilage of the knee using ultrashort echo time (uTE) sequences with spiral acquisition

    International Nuclear Information System (INIS)

    Goto, Hajimu; Fujii, Masahiko; Iwama, Yuki; Aoyama, Nobukazu; Ohno, Yoshiharu; Sugimura, Kazuro

    2012-01-01

    The objective of this study was to evaluate the sensitivity of ultrashort echo time (uTE) sequence for visualisation of calcified deep layers of articular cartilage. MRI with a uTE sequence was performed on five healthy volunteers. Signals from the calcified deep layers of the articular knee cartilage were evaluated on uTE subtraction images and computed tomography images. The calcified deep layers of the articular cartilage changed from having a low to a high signal when imaged with a uTE sequence. The reported uTE sequence was effective in imaging the deep layers of the knee cartilage.

  4. 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

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

    International Nuclear Information System (INIS)

    Ohno, Yoshiharu; Hatabu, Hiroto; Higashino, Takanori; Kawamitsu, Hideaki; Watanabe, Hirokazu; Takenaka, Daisuke; Cauteren, Marc van; Sugimura, Kazuro

    2004-01-01

    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

  6. Lacunary ideal convergence of multiple sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2016-01-01

    Full Text Available An ideal I is a family of subsets of N×N which is closed under taking finite unions and subsets of its elements. In this article, the concept of lacunary ideal convergence of double sequences has been introduced. Also the relation between lacunary ideal convergent and lacunary Cauchy double sequences has been established. Furthermore, the notions of lacunary ideal limit point and lacunary ideal cluster points have been introduced and find the relation between these two notions. Finally, we have studied the properties such as solidity, monotonic.

  7. A 3D T1-weighted gradient-echo sequence for routine use in 3D radiosurgical treatment planning of brain metastases: first clinical results

    International Nuclear Information System (INIS)

    Hawighorst, H.; Schad, L.R.; Gademann, G.; Knopp, M.V.; Wenz, F.; Kaick, G. van

    1995-01-01

    The authors report on a 3D sequence for MRI of the brain and its application in radiosurgical treatment planning of 35 brain metastases. The measuring sequence, called magnetization - prepared rapid gradient echo (MPRAGE), was compared with 2D T1-weighted spin-echo (SE) sequences following intravenous contrast-medium application in 19 patients with brain metastases. The average diameter of all lesions was similar in both sequences, with 16.8 and 17.0 mm for SE and MPRAGE, respectively. Target point definition was equal in 29 metastases, and in 6 cases superior on MPRAGE, due to better gray-white matter contrast and increased contrast enhancement. In cases of bleeding metastases there was improved depiction of internal structures in 3D MRI. Postprocessing of 3D MPRAGE data created multiplanar reconstruction along any chosen plane with isotropic spatial resolution, which helped to improve radiosurgical isodose distribution in 4 cases when compared to 2D SE. However, sensitivity of 3D MPRAGE to detect small lesions (< 3 mm) was decreased in one patient with more than 50 metastases. We conclude that 3D gradient-echo (GE) imaging might be of great value for radiosurgical treatment planning, but does not replace 2D SE with its current parameters. (orig.)

  8. 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

    International Nuclear Information System (INIS)

    Dornia, C.; Hoffstetter, P.; Asklepios Klinikum, Bad Abbach; Fleck, M.; Asklepios Klinikum, Bad Abbach; Hartung, W.; Niessen, C.; Stroszczynski, C.

    2015-01-01

    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 * 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 * GRE showed a high interobserver reliability in the detection of structural alterations in patients with SpA. However, T2 * 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.

  9. Multiple Genome Sequences of Lactobacillus plantarum Strains

    OpenAIRE

    Kafka, Thomas A.; Geissler, Andreas J.; Vogel, Rudi F.

    2017-01-01

    ABSTRACT We report here the genome sequences of four Lactobacillus plantarum strains which vary in surface hydrophobicity. Bioinformatic analysis, using additional genomes of Lactobacillus plantarum strains, revealed a possible correlation between the cell wall teichoic acid-type and cell surface hydrophobicity and provide the basis for consecutive analyses.

  10. MRI of the lumbar spine: comparison of 3D isotropic turbo spin-echo SPACE sequence versus conventional 2D sequences at 3.0 T.

    Science.gov (United States)

    Lee, Sungwon; Jee, Won-Hee; Jung, Joon-Yong; Lee, So-Yeon; Ryu, Kyeung-Sik; Ha, Kee-Yong

    2015-02-01

    Three-dimensional (3D) fast spin-echo sequence with variable flip-angle refocusing pulse allows retrospective alignments of magnetic resonance imaging (MRI) in any desired plane. To compare isotropic 3D T2-weighted (T2W) turbo spin-echo sequence (TSE-SPACE) with standard two-dimensional (2D) T2W TSE imaging for evaluating lumbar spine pathology at 3.0 T MRI. Forty-two patients who had spine surgery for disk herniation and had 3.0 T spine MRI were included in this study. In addition to standard 2D T2W TSE imaging, sagittal 3D T2W TSE-SPACE was obtained to produce multiplanar (MPR) images. Each set of MR images from 3D T2W TSE and 2D TSE-SPACE were independently scored for the degree of lumbar neural foraminal stenosis, central spinal stenosis, and nerve compression by two reviewers. These scores were compared with operative findings and the sensitivities were evaluated by McNemar test. Inter-observer agreements and the correlation with symptoms laterality were assessed with kappa statistics. The 3D T2W TSE and 2D TSE-SPACE had similar sensitivity in detecting foraminal stenosis (78.9% versus 78.9% in 32 foramen levels), spinal stenosis (100% versus 100% in 42 spinal levels), and nerve compression (92.9% versus 81.8% in 59 spinal nerves). The inter-observer agreements (κ = 0.849 vs. 0.451 for foraminal stenosis, κ = 0.809 vs. 0.503 for spinal stenosis, and κ = 0.681 vs. 0.429 for nerve compression) and symptoms correlation (κ = 0.449 vs. κ = 0.242) were better in 3D TSE-SPACE compared to 2D TSE. 3D TSE-SPACE with oblique coronal MPR images demonstrated better inter-observer agreements compared to 3D TSE-SPACE without oblique coronal MPR images (κ = 0.930 vs. κ = 0.681). Isotropic 3D T2W TSE-SPACE at 3.0 T was comparable to 2D T2W TSE for detecting foraminal stenosis, central spinal stenosis, and nerve compression with better inter-observer agreements and symptom correlation. © The Foundation Acta Radiologica 2014 Reprints and

  11. MANGO: a new approach to multiple sequence alignment.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

    Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

  12. Fast spin echo MRI techniques. Contrast characteristics and clinical potential

    International Nuclear Information System (INIS)

    Melki, P.; Mulkern, R.V.; Dacher, J.N.; Helenon, O.; Higuchi, N.; Oshio, K.; Jolesz, F.; Pourcelot, L.; Einstein, S.

    1993-01-01

    Based on partial RF echo planar principles, Fast Spin Echo techniques (FSE) were implemented on high field systems. These methods produce image quality and contrast which resemble to conventional spin echo (SE) techniques. By reducing acquisition times by factors between 1.4 and 16 over SE methods, FSE allows for several imaging options usually prohibitive with conventional spin echo (SE) sequences. These include fast scans (especially breathold acquisitions); improved T2 contrast with longer TR intervals; increased spatial resolution with the use of larger image matrices and/or smaller fields of view; and 3D volume imaging with a 3D multislab FSE technique. Contrast features of FSE techniques are directly comparable to those of multiple echo SE sequences using the same echo spacing than FSE methods. However, essential contrast differences existing between the FSE sequences and their routine asymmetric dual SE counterpart can be identified. Decreased magnetic susceptibility effects and increased fat signal present within T2 weighted images compared to conventional dual SE images are due to the use of shorter echo spacings employed in FSE sequences. Off-resonance irradiation inherent to the use of a large number of radio frequency pulses in shown to results in dramatic magnetization contrast transfer effects in FSE images acquired in multislice mode

  13. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    DEFF Research Database (Denmark)

    Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah

    2016-01-01

    have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32...

  14. 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 can lead ...

  15. 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.

  16. Comparison between arthroscopy and 3 dimensional double echo steady state 3D-DESS sequences in magnetic resonance imaging of internal derangements of the knee

    International Nuclear Information System (INIS)

    Dongola, Nagwa A.; Gishen, Philip

    2004-01-01

    This study was performed with the aim of evaluating the usefulness of 3 dimensional double-echo steady state sequences in examining the internal derangements of the knee. Arthroscopy was used as a referral standard. The study was performed in the Radiology and Arthroscopy Departments of Kings College Hospital, London, United Kingdom, during a 6-month period from January 1997 to June 1997. All patients who had knee magnetic resonance imaging within 3 months of arthroscopy were retrospectively studied. Thirty-three patients fulfilled these criteria and were selected. Three dimensional double-echo steady state sequences produced sensitivity for detecting meniscal tears of 87.5% for medial menisci (MM) and 75% for lateral menisci (LM). Specificity was 76% for MM and 96% for LM; positive predictive value (PPV) was 46.1% for MM and 85.7% for LM and negative predictive value (NPV) of 95% for MM and 96% for LM. The sensitivity for the anterior cruciate ligament was 83.3%, specificity was 77.7%, PPV was 45.4% and NPV was 95.4%. Three dimensional double-echo steady state sequences are useful in evaluating internal derangement of the knee, especially in advanced cartilage lesions. (author)

  17. First results in rapid MR imaging of focal liver and spleen lesions using field echos and small angle excitation (gradient echo sequences)

    International Nuclear Information System (INIS)

    Griebel, J.; Hess, C.F.; Kurtz, B.; Klose, U.; Kueper, K.

    1987-01-01

    15 healthy subjects and 39 patients with focal liver and spleen lesions were examined via MR tomography at 1.5 tesla. Gradient field echos at small angle excitation ( 0 ) were employed. The imaging time per layer was 10 seconds so that rapid imaging could be carried out at respiratory standstill. This enabled visualisation of liver and spleen without interference by breathing artifacts and with accurate localisation. Focal lesions can be imaged best at low flip-angle pulses (liver) or low to medium-angle pulses (spleen). The primary liver cell carcinoma is visualised as an inhomogeneous structure with similar signal intensity as the surrounding tissue. All other examined liver lesions (metastases, haemangiomas, lymphatic infiltrates, echinococcus cysts, FNH, gummae) showed greater signal intensity than the remaining organ at small angle excitation. Furthermore, contrast reversals were seen at medium-angle pulses. Contrariwise, with the exception of the light-coloured spleen infarcts, spleen lesions (lymphatic infiltrate, Boeck's disease or sarcoidosis) appeared darker at all excitation angles than the surrounding tissue. (orig.) [de

  18. First results in rapid MR imaging of focal liver and spleen lesions using field echos and small angle excitation (gradient echo sequences)

    Energy Technology Data Exchange (ETDEWEB)

    Griebel, J.; Hess, C.F.; Kurtz, B.; Klose, U.; Kueper, K.

    1987-01-01

    15 healthy subjects and 39 patients with focal liver and spleen lesions were examined via MR tomography at 1.5 tesla. Gradient field echos at small angle excitation (< 90/sup 0/) were employed. The imaging time per layer was 10 seconds so that rapid imaging could be carried out at respiratory standstill. This enabled visualisation of liver and spleen without interference by breathing artifacts and with accurate localisation. Focal lesions can be imaged best at low flip-angle pulses (liver) or low to medium-angle pulses (spleen). The primary liver cell carcinoma is visualised as an inhomogeneous structure with similar signal intensity as the surrounding tissue. All other examined liver lesions (metastases, haemangiomas, lymphatic infiltrates, echinococcus cysts, FNH, gummae) showed greater signal intensity than the remaining organ at small angle excitation. Furthermore, contrast reversals were seen at medium-angle pulses. Contrariwise, with the exception of the light-coloured spleen infarcts, spleen lesions (lymphatic infiltrate, Boeck's disease or sarcoidosis) appeared darker at all excitation angles than the surrounding tissue.

  19. 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

    International Nuclear Information System (INIS)

    Hui Lihong; Zhang Xiaodong; He Chao; Xie Sheng; Xiao Jiangxi; Zhang jue; Wang Xiaoying; Jiang Xuexiang

    2010-01-01

    Objective: To evaluate the stability and repeatability of gradient-echo sampling of spin- echo (GESSE) sequence in measuring the R 2 ' value in volunteers, by comparison with traditional GRE sequence (T 2 * ]nap and T 2 map). Methods: Eight normal healthy volunteers were enrolled in this study and written informed consents were obtained from all subjects. MR scanning including sequences of GESSE, T 2 map and T 2 * map were performed in these subjects at resting status. The same protocol was repeated one day later. Raw data from GESSE sequence were transferred to PC to conduct postprocessing with the software built in house. R 2 ' map and OEF map were got consequently. To obtain quantitative R 2 ' and OEF values in the brain parenchyma, six ROIs were equally placed in the anterior, middle and posterior part of bilateral hemispheres. Both mean and standard deviation of R 2 ' and OEF were recorded. All images from T 2 * map and T 2 map were transferred to the Workstation for postprocessing. The ROIs were put at the same areas as those for GESSE sequence. R 2 ' is defined as R 2 ' = R 2 * - R 2 , R 2 * = 1/T 2 * . The R 2 ' value of GESSE sequence were compared with that of GRE sequence. Results: The mean R 2 ' values of GESSE at the first and second scan and those of the GRE were (4.21±0.92), (4.45±0.94) Hz and (7.37±1.47), (6.42±2.33) Hz respectively. The mean OEF values of GESSE at the first and second scan is 0.327±0.036 and 0.336± 0.035 respectively. The R 2 ' value and OEF value obtained from GESSE were not significantly different between the first and second scan (t=-0.83, -1.48, P>0.05). The R 2 ' value of first GRE imaging had significantly statistical difference from that of second GRE imaging (t=1.80, P 2 ' value of GESSE sequence was less than that of GRE sequence, and there was significantly statistical difference between them (t=1.71, P<0.05). Conclusion: The GESSE sequence has good stability and repeatability with promising clinical practicability

  20. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  1. Improved imaging of cochlear nerve hypoplasia using a 3-Tesla variable flip-angle turbo spin-echo sequence and a 7-cm surface coil.

    Science.gov (United States)

    Giesemann, Anja M; Raab, Peter; Lyutenski, Stefan; Dettmer, Sabine; Bültmann, Eva; Frömke, Cornelia; Lenarz, Thomas; Lanfermann, Heinrich; Goetz, Friedrich

    2014-03-01

    Magnetic resonance imaging of the temporal bone has an important role in decision making with regard to cochlea implantation, especially in children with cochlear nerve deficiency. The purpose of this study was to evaluate the usefulness of the combination of an advanced high-resolution T2-weighted sequence with a surface coil in a 3-Tesla magnetic resonance imaging scanner in cases of suspected cochlear nerve aplasia. Prospective study. Seven patients with cochlear nerve hypoplasia or aplasia were prospectively examined using a high-resolution three-dimensional variable flip-angle turbo spin-echo sequence using a surface coil, and the images were compared with the same sequence in standard resolution using a standard head coil. Three neuroradiologists evaluated the magnetic resonance images independently, rating the visibility of the nerves in diagnosing hypoplasia or aplasia. Eight ears in seven patients with hypoplasia or aplasia of the cochlear nerve were examined. The average age was 2.7 years (range, 9 months-5 years). Seven ears had accompanying malformations. The inter-rater reliability in diagnosing hypoplasia or aplasia was greater using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence (fixed-marginal kappa: 0.64) than with the same sequence in lower resolution (fixed-marginal kappa: 0.06). Examining cases of suspected cochlear nerve aplasia using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence in combination with a surface coil shows significant improvement over standard methods. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  2. Analysis of artefacts and detail resolution of lung MRI with breath-hold T1-weighted gradient-echo and T2-weighted fast spin-echo sequences with respiratory triggering

    International Nuclear Information System (INIS)

    Biederer, J.; Reuter, M.; Both, M.; Grimm, J.; Heller, M.; Muhle, C.; Graessner, J.

    2002-01-01

    The aim of this study was to evaluate feasibility and limitations of two MR sequences for imaging of the lung using a semi-quantitative rating scale. Ten healthy volunteers were assessed with a breath-hold T1-weighted gradient-recalled-echo (TR/TE=129/2.2 ms, matrix 173 x 256) and a T2-weighted turbo spin-echo (TSE) sequence with respiratory triggering (TR/TE=3000-5000/120 ms, matrix 270 x 512) in axial 6-mm slices. The T1-weighted GRE protocol included a pre-saturation pulse over the mediastinal structures. Artefacts and resolution of vessel/airway structures in each lung segment were evaluated by two observers (10 volunteers, 180 segments). Cardiac and vessel pulsation artefacts predominated on T1-weighted GRE, respiration artefacts on T2-weighted TSE (lingula and middle lobe). Pre-saturation of the mediastinum reduced pulsation artefacts on T1-weighted GRE. T1-weighted GRE images were improved by bright flow signal of vessels, whereas image quality of T2-weighted TSE was reduced by black-blood effects in central parts of the lung. Delineation of lung periphery and the mediastinum was superior with T2-weighted TSE. Segmental/sub-segmental vessels (up to fourth/fifth order) and bronchi (up to third order) were identified. All 180 lung segments were imaged in diagnostic quality with at least one of the two sequences (T1-weighted GRE not diagnostic in 9 of 180, T2-weighted TSE in 4 of 180). Both sequences were found to be complementary: superior identification of gross lung anatomy with T1-weighted GRE and higher detail resolution in the periphery and the mediastinum with T2-weighted TSE. (orig.)

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

    International Nuclear Information System (INIS)

    Drejer, J.; Thomsen, H.S.; Tanttu, J.

    1995-01-01

    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)

  4. 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).

  5. 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.

  6. Differential evolution-simulated annealing for multiple sequence alignment

    Science.gov (United States)

    Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

    2017-10-01

    Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

  7. Cartilage volume quantification with multi echo data image combination sequence in swine knee at 3.0 T MRI

    International Nuclear Information System (INIS)

    Zhang Lirong; Wang Dongqing; Wei Chuanshe; Ma Cong; Wang Dehang

    2010-01-01

    Objective: To investigate the accuracy and reproducibility of multi echo data imagine combination (MEDIC) sequence with water excitation at 3.0 T in swine knee cartilage. Methods: Sagittal MEDIC sequences (0.6 mm slice thickness, isotropic) were acquired twice at 3.0 T MRI in 30 swine knees. The knee cartilage was then removed and the volume was directly measured with water substitution method. The cartilage volume was also determined with a validated open source image software OsiriX by two observers (A and B). The cartilage volumes obtained by two methods were compared. The reproducibility of MEDIC for quantitative measurement was accessed by the root-mean-square (RMS) of variation coefficient. Interobserver and intraobserver precision errors were compared using a paired students t-test. The accuracy of MEDIC for quantitative measurement was determined by the random pairwise differences, systematic pairwise differences and the Pearson, correlation coefficients. Time of semiautomatic and manual segmentation were recorded. Results: Time was saved about 75% by using semiautomatic segmentation methods [(4.0± 1.5) min] versus manual segmentation [(16.0±0.9) min]. Interobserver precision errors (RMS CV% for paired analysis) between A and B for cartilage volume measurement were (2.66±0.82) ml and(2.61± 0.81) ml, t=0.24, P=0.81 (patella); (2.40±0.69) ml and (2.49±0.85) ml, t=-0.45, P=0.65 (medial femoral condyle); (2.28±0.74) ml and(2.41±0.78) ml, t=-0.66, P=0.51 (lateral femoral condyle); (3.43±1.28) ml and (3.51±1.08) ml, t=-0.26, P=0.79 (femora trochlea) with sagittal MEDIC. Intraobserver precision errors (RMS CV% for paired analysis) of observer A for the first and second cartilage volume measurement were (2.64±0.62) ml and (2.67±0.60) ml, t=-0.19, P=0.85 (patella); (2.43±0.60) ml and (2.39±0.59) ml, t=0.26, P=0.80 (medial femoral condyle); (2.26±0.56) ml and (2.30±0.57) ml, t=-0.27, P=0.78 (lateral femoral condyle); (3.40± 1.20) ml and (3.47±1

  8. 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.)

  9. Characterization of anomalous relaxation using the time-fractional Bloch equation and multiple echo T2 *-weighted magnetic resonance imaging at 7 T.

    Science.gov (United States)

    Qin, Shanlin; Liu, Fawang; Turner, Ian W; Yu, Qiang; Yang, Qianqian; Vegh, Viktor

    2017-04-01

    To study the utility of fractional calculus in modeling gradient-recalled echo MRI signal decay in the normal human brain. We solved analytically the extended time-fractional Bloch equations resulting in five model parameters, namely, the amplitude, relaxation rate, order of the time-fractional derivative, frequency shift, and constant offset. Voxel-level temporal fitting of the MRI signal was performed using the classical monoexponential model, a previously developed anomalous relaxation model, and using our extended time-fractional relaxation model. Nine brain regions segmented from multiple echo gradient-recalled echo 7 Tesla MRI data acquired from five participants were then used to investigate the characteristics of the extended time-fractional model parameters. We found that the extended time-fractional model is able to fit the experimental data with smaller mean squared error than the classical monoexponential relaxation model and the anomalous relaxation model, which do not account for frequency shift. We were able to fit multiple echo time MRI data with high accuracy using the developed model. Parameters of the model likely capture information on microstructural and susceptibility-induced changes in the human brain. Magn Reson Med 77:1485-1494, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  10. MRI of normal pancreas : comparison of T2-weighted pulse sequences using turbo spin echo, turbo spin echo with fat suppression, HASTE and HASTE with fat suppression

    International Nuclear Information System (INIS)

    Lee, Kyoung Ho; Kim, Tae Kyoung; Jang, Hyun Jung; Kim, Young Hoon; Han, Sang Wook; Han, Joon Koo; Choi, Byung Ihn

    1998-01-01

    To compare various breath-hold T2 weighted sequences in imaging normal pancreas with a phased-array coil. HASTE showed higher SD/N than TSE or FS-HASTE (p<0.01). TSE was superior to TSE in the delineation of pancreatic duct (p<0.001). TSE showed more artifacts than FS-TSE (p<0.001): HASTE and FS-HASTE showed no artifact. TSE is better than HASTE for the delineation of pancreatic margin but HASTE shows less artifacts and a more conspicuous pancreatic duct. Fat suppression decreases artifacts but makes the pancreatic margin indistinct. (author). 19 refs., 1 tab., 2 figs

  11. Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

    Science.gov (United States)

    Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

    2018-06-12

    This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

  12. Fast spin-echo imaging

    International Nuclear Information System (INIS)

    Mackey, K.; Zoarski, G.; Bentson, J.R.; Lufkin, R.B.; Melki, P.; Jolesz, F.

    1991-01-01

    This paper reports on a partial radio-frequency (RF) echo-planar pulse sequence called contiguous slice fast spin echo (CSFSE) which is undergoing clinical trials for spine MR imaging. In this variation of rapid acquisition relaxation enhanced (RARE) spin-echo imaging, rapid 180 degrees RF pulse generated refocused echoes, producing T2-weighted images in about one-third the time of conventional double-echo technique. Forty patients with suspected pathology of the spine were imaged with conventional double-echo and closely matched CSFSE techniques on a GE Signa 1.5-T Advantage system. Cases were reviewed by two board-certified neuroradiologists. In all cases the CSFSE images were of equal or superior quality compared with those obtained with the conventional double-echo technique. Pathologic processes that were imaged consisted of inflammatory, neoplastic, posttraumatic, and degenerative conditions

  13. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

    Science.gov (United States)

    Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

    2004-09-22

    Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

  14. Variability at Multiple Scales: Using an Array of Current and Pressure Sensor Equipped Inverted Echo Sounders to Measure the Ocean

    Science.gov (United States)

    2016-11-29

    of Current- and Pressure - Sensor Equipped Inverted Echo Sounders to Measure the Ocean 5b. GRANT NUMBER NOOO 14-15-1-2857 5c. PROGRAM ELEMENT NUMBER...inverted echo sounders (lESs) equipped with pressure and current sensors (CPIESs). CPIESs are moored instruments that measure the round-trip acoustic...at a range of spatial and temporal scales. The goals of this project were to enhance the pool of pressure - sensor equipped lESs available at the

  15. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  16. MR Imaging of the Internal Auditory Canal and Inner Ear at 3T: Comparison between 3D Driven Equilibrium and 3D Balanced Fast Field Echo Sequences

    Energy Technology Data Exchange (ETDEWEB)

    Byun, Jun Soo; Kim, Hyung Jin; Yim, Yoo Jeong; Kim, Sung Tae; Jeon, Pyoung; Kim, Keon Ha [Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Sam Soo; Jeon, Yong Hwan; Lee, Ji Won [Kangwon National University College of Medicine, Chuncheon (Korea, Republic of)

    2008-06-15

    To compare the use of 3D driven equilibrium (DRIVE) imaging with 3D balanced fast field echo (bFFE) imaging in the assessment of the anatomic structures of the internal auditory canal (IAC) and inner ear at 3 Tesla (T). Thirty ears of 15 subjects (7 men and 8 women; age range, 22 71 years; average age, 50 years) without evidence of ear problems were examined on a whole-body 3T MR scanner with both 3D DRIVE and 3D bFFE sequences by using an 8-channel sensitivity encoding (SENSE) head coil. Two neuroradiologists reviewed both MR images with particular attention to the visibility of the anatomic structures, including four branches of the cranial nerves within the IAC, anatomic structures of the cochlea, vestibule, and three semicircular canals. Although both techniques provided images of relatively good quality, the 3D DRIVE sequence was somewhat superior to the 3D bFFE sequence. The discrepancies were more prominent for the basal turn of the cochlea, vestibule, and all semicircular canals, and were thought to be attributed to the presence of greater magnetic susceptibility artifacts inherent to gradient-echo techniques such as bFFE. Because of higher image quality and less susceptibility artifacts, we highly recommend the employment of 3D DRIVE imaging as the MR imaging choice for the IAC and inner ear

  17. Sequence embedding for fast construction of guide trees for multiple sequence alignment

    LENUS (Irish Health Repository)

    Blackshields, Gordon

    2010-05-14

    Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

  18. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    International Nuclear Information System (INIS)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

    2017-01-01

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  19. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    Energy Technology Data Exchange (ETDEWEB)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

    2017-08-15

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  20. Readout-segmented echo-planar imaging improves the image quality of diffusion-weighted MR imaging in rectal cancer: Comparison with single-shot echo-planar diffusion-weighted sequences

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Chun-chao; Liu, Xi; Peng, Wan-lin; Li, Lei; Zhang, Jin-ge [Department of Radiology, West China Hospital, Sichuan University, 37# Guo Xue Xiang, Chengdu, Sichuan 610041 (China); Meng, Wen-jian; Deng, Xiang-bing [Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, 37# Guo Xue Xiang, Chengdu, Sichuan 610041 (China); Zuo, Pan-li [Siemens Healthcare, MR Collaborations NE Asia, 100010, Beijing (China); Li, Zhen-lin, E-mail: lzlcd01@126.com [Department of Radiology, West China Hospital, Sichuan University, 37# Guo Xue Xiang, Chengdu, Sichuan 610041 (China)

    2016-10-15

    Purpose: To determine whether readout-segmented echo-planar imaging (rs-EPI) diffusion-weighted imaging (DWI) can improve the image quality in patients with rectal cancer compared with single-shot echo-planar imaging (ss-EPI) DWI using 3.0 T magnetic resonance (MR) imaging. Materials and methods: This study was approved by the Institutional Review Board, and informed consent was obtained from all patients. Seventy-one patients with rectal cancer were enrolled in this study. For all patients, both rs-EPI and ss-EPI DWI were performed using a 3T MR scanner. Two radiologists independently assessed the overall image quality, lesion conspicuity, geometric distortion and distinction of anatomical structures. The signal-to-noise ratio (SNR), lesion contrast, contrast-to-noise ratio (CNR), and apparent diffusion coefficient (ADC) were also measured. Comparisons of the quantitative and qualitative parameters between the two sequences were performed using the paired t-test and the Wilcoxon signed rank test. Results: The scores of overall image quality, lesion conspicuity, geometric distortion and distinction of anatomical structures of rs-EPI were all significantly higher than those of ss-EPI (all p < 0.05). The SNR and CNR were higher in rs-EPI than those in ss-EPI (all p < 0.05). There was no significant difference between ss-EPI and rs-EPI with regard to ROI size and mean ADCs of the tumour (p = 0.574 and p = 0.479, respectively), but the mean ADC of the normal tissue was higher in rs-EPI than in ss-EPI (1.73 ± 0.30 × 10{sup −3} mm{sup 2}/s vs. 1.60 ± 0.31 × 10{sup −3} mm{sup 2}/s, p = 0.001). Conclusions: DW imaging based on readout-segmented echo-planar imaging is a clinically useful technique to improve the image quality for the purpose of evaluating lesions in patients with rectal tumours.

  1. Evaluation of a multiple spin- and gradient-echo (SAGE) EPI acquisition with SENSE acceleration: applications for perfusion imaging in and outside the brain.

    Science.gov (United States)

    Skinner, Jack T; Robison, Ryan K; Elder, Christopher P; Newton, Allen T; Damon, Bruce M; Quarles, C Chad

    2014-12-01

    Perfusion-based changes in MR signal intensity can occur in response to the introduction of exogenous contrast agents and endogenous tissue properties (e.g. blood oxygenation). MR measurements aimed at capturing these changes often implement single-shot echo planar imaging (ssEPI). In recent years ssEPI readouts have been combined with parallel imaging (PI) to allow fast dynamic multi-slice imaging as well as the incorporation of multiple echoes. A multiple spin- and gradient-echo (SAGE) EPI acquisition has recently been developed to allow measurement of transverse relaxation rate (R2 and R2(*)) changes in dynamic susceptibility contrast (DSC)-MRI experiments in the brain. With SAGE EPI, the use of PI can influence image quality, temporal resolution, and achievable echo times. The effect of PI on dynamic SAGE measurements, however, has not been evaluated. In this work, a SAGE EPI acquisition utilizing SENSE PI and partial Fourier (PF) acceleration was developed and evaluated. Voxel-wise measures of R2 and R2(*) in healthy brain were compared using SAGE EPI and conventional non-EPI multiple echo acquisitions with varying SENSE and PF acceleration. A conservative SENSE factor of 2 with PF factor of 0.73 was found to provide accurate measures of R2 and R2(*) in white (WM) (rR2=[0.55-0.79], rR2*=[0.47-0.71]) and gray (GM) matter (rR2=[0.26-0.59], rR2*=[0.39-0.74]) across subjects. The combined use of SENSE and PF allowed the first dynamic SAGE EPI measurements in muscle, with a SENSE factor of 3 and PF factor of 0.6 providing reliable relaxation rate estimates when compared to multi-echo methods. Application of the optimized SAGE protocol in DSC-MRI of high-grade glioma patients provided T1 leakage-corrected estimates of CBV and CBF as well as mean vessel diameter (mVD) and simultaneous measures of DCE-MRI parameters K(trans) and ve. Likewise, application of SAGE in a muscle reperfusion model allowed dynamic measures of R2', a parameter that has been shown to correlate

  2. Heuristic for Solving the Multiple Alignment Sequence Problem

    Directory of Open Access Journals (Sweden)

    Roman Anselmo Mora Gutiérrez

    2011-03-01

    Full Text Available In this paper we developed a new algorithm for solving the problem of multiple sequence alignment (AM S, which is a hybrid metaheuristic based on harmony search and simulated annealing. The hybrid was validated with the methodology of Julie Thompson. This is a basic algorithm and and results obtained during this stage are encouraging.

  3. Correction of inhomogeneous RF field using multiple SPGR signals for high-field spin-echo MRI

    International Nuclear Information System (INIS)

    Ishimori, Yoshiyuki; Monma, Masahiko; Yamada, Kazuhiro; Kimura, Hirohiko; Uematsu, Hidemasa; Fujiwara, Yasuhiro; Yamaguchi, Isao

    2007-01-01

    The purpose of this study was to propose a simple and useful method for correcting nonuniformity of high-field (3 Tesla) T 1 -weighted spin-echo (SE) images based on a B1 field map estimated from gradient recalled echo (GRE) signals. The method of this study was to estimate B1 inhomogeneity, spoiled gradient recalled echo (SPGR) images were collected using a fixed repetition time of 70 ms, flip angles of 45 and 90 degrees, and echo times of 4.8 and 10.4 ms. Selection of flip angles was based on the observation that the relative intensity changes in SPGR signals were very similar among different tissues at larger flip angles than the Ernst angle. Accordingly, spatial irregularity that was observed on a signal ratio map of the SPGR images acquired with these 2 flip angles was ascribed to inhomogeneity of the B1 field. Dual echo time was used to eliminate T 2 * effects. The ratio map that was acquired was scaled to provide an intensity correction map for SE images. Both phantom and volunteer studies were performed using a 3T magnetic resonance scanner to validate the method. In the phantom study, the uniformity of the T 1 -weighted SE image improved by 23%. Images of human heads also showed practically sufficient improvement in the image uniformity. The present method improves the image uniformity of high-field T 1 -weighted SE images. (author)

  4. Sensory neuronopathy involves the spinal cord and brachial plexus: a quantitative study employing multiple-echo data image combination (MEDIC) and turbo inversion recovery magnitude (TIRM)

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Yi-Fang; Tang, Wei-Jun; Li, Yu-Xin; Geng, Dao-Ying [Fudan University, Department of Radiology, Huashan Hospital, Shanghai (China); Zhu, Dong-Qing; Chen, Xiang-Jun [Fudan University, Department of Neurology, Huashan Hospital, Shanghai (China); Zee, Chi-Shing [University of Southern California Keck School of Medicine, Department of Radiology, Los Angeles, CA (United States)

    2013-01-15

    Sensory neuronopathy (SNN) is a distinctive subtype of peripheral neuropathies, specifically targeting dorsal root ganglion (DRG). We utilized MRI to demonstrate the imaging characteristics of DRG, spinal cord (SC), and brachial plexus at C7 level in SNN. We attempted multiple-echo data image combination (MEDIC) and turbo inversion recovery magnitude (TIRM) methods in nine patients with sensory neuronopathy and compared with those in 16 disease controls and 20 healthy volunteers. All participants underwent MRI for the measurement of DRG, posterior column (PC), lateral column, and spinal cord area (SCA) at C7 level. DRG diameters were obtained through its largest cross section, standardized by dividing sagittal diameter of mid-C7 vertebral canal. We also made comparisons of standardized anteroposterior diameter (APD) and left-right diameters of SC and PC in these groups. Signal intensity and diameter of C7 spinal nerve were assessed on TIRM. Compared to control groups, signal intensities of DRG and PC were higher in SNN patients when using MEDIC, but the standardized diameters were shorter in either DRG or PC. Abnormal PC signal intensities were identified in eight out of nine SNN patients (89 %) with MEDIC and five out of nine (56 %) with T2-weighted images. SCA, assessed with MEDIC, was smaller in SNN patients than in the other groups, with significant reduction of its standardized APD. C7 nerve root diameters, assessed with TIRM, were decreased in SNN patients. MEDIC and TIRM sequences demonstrate increased signal intensities and decreased area of DRG and PC, and decreased diameter of nerve roots in patients with SNN, which can play a significant role in early diagnosis. (orig.)

  5. Sensory neuronopathy involves the spinal cord and brachial plexus: a quantitative study employing multiple-echo data image combination (MEDIC) and turbo inversion recovery magnitude (TIRM)

    International Nuclear Information System (INIS)

    Bao, Yi-Fang; Tang, Wei-Jun; Li, Yu-Xin; Geng, Dao-Ying; Zhu, Dong-Qing; Chen, Xiang-Jun; Zee, Chi-Shing

    2013-01-01

    Sensory neuronopathy (SNN) is a distinctive subtype of peripheral neuropathies, specifically targeting dorsal root ganglion (DRG). We utilized MRI to demonstrate the imaging characteristics of DRG, spinal cord (SC), and brachial plexus at C7 level in SNN. We attempted multiple-echo data image combination (MEDIC) and turbo inversion recovery magnitude (TIRM) methods in nine patients with sensory neuronopathy and compared with those in 16 disease controls and 20 healthy volunteers. All participants underwent MRI for the measurement of DRG, posterior column (PC), lateral column, and spinal cord area (SCA) at C7 level. DRG diameters were obtained through its largest cross section, standardized by dividing sagittal diameter of mid-C7 vertebral canal. We also made comparisons of standardized anteroposterior diameter (APD) and left-right diameters of SC and PC in these groups. Signal intensity and diameter of C7 spinal nerve were assessed on TIRM. Compared to control groups, signal intensities of DRG and PC were higher in SNN patients when using MEDIC, but the standardized diameters were shorter in either DRG or PC. Abnormal PC signal intensities were identified in eight out of nine SNN patients (89 %) with MEDIC and five out of nine (56 %) with T2-weighted images. SCA, assessed with MEDIC, was smaller in SNN patients than in the other groups, with significant reduction of its standardized APD. C7 nerve root diameters, assessed with TIRM, were decreased in SNN patients. MEDIC and TIRM sequences demonstrate increased signal intensities and decreased area of DRG and PC, and decreased diameter of nerve roots in patients with SNN, which can play a significant role in early diagnosis. (orig.)

  6. Optimal MR pulse sequences for hepatic hemangiomas : comparison of T2-weighted turbo-spin-echo, T2-weighted breath-hold turbo-spin-echo, and T1-weighted FLASH dynamic imaging

    International Nuclear Information System (INIS)

    Wang, Wen Chao; Choi, Byung Ihn; Han, Joon Koo; Kim, Tae Kyoung; Cho, Soon Gu

    1997-01-01

    To optimize MR imaging pulse sequences in the imaging of hepatic hemangioma and to evaluate on dynamic MR imaging the enhancing characteristics of the lesions. Twenty patients with 35 hemangiomas were studied by using Turbo-spin-echo (TSE) sequence (T2-weighted, T2- and heavily T2-weighted breath-hold) and T1-weighted FLASH imaging acquired before, immediately on, and 1, 3 and 5 minutes after injection of a bolus of Gd-DTPA (0.1mmol/kg). Phased-array multicoil was employed. Images were quantitatively analyzed for lesion-to-liver signal difference to noise ratios (SD/Ns), and lesion-to-liver signal ratios (H/Ls), and qualitatively analyzed for lesion conspicuity. The enhancing characteristics of the hemangiomas were described by measuring the change of signal intensity as a curve in T1-weighted FLASH dynamic imaging. For T2-weighted images, breath-hold T2-weighted TSE had a slightly higher SD/N than other pulse sequences, but there was no statistical difference in three fast pulse sequences (p=0.211). For lesion conspicuity, heavily T2-weighted breath-hold TSE images was superior to T2-weighted breath-hold or non-breath-hold TSE (H/L, 5.75, 3.81, 2.87, respectively, p<0.05). T2-weighted breath-hold TSE imaging was more effective than T2-weighted TSE imaging in removing lesion blurring or lack of sharpness, and there was a 12-fold decrease in acquisition time (20sec versus 245 sec). T1-weighted FLASH dynamic images of normal liver showed peak enhancement at less than 1 minute, and of hemangioma at more than 3 minutes;the degree of enhancement for hemangioma decreased after a 3 minute delay. T2-weighed breath-hold TSE imaging and Gd-DTPA enhanced FLASH dynamic imaging with 5 minutes delay are sufficient for imaging hepatic hemangiomas

  7. 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

    International Nuclear Information System (INIS)

    Zhang, Jing; Chen, Lang; Wang, Qiu-Xia; Zhu, Wen-Zhen; Luo, Xin; Peng, Li; Liu, Rong; Xiong, Wei

    2015-01-01

    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 0.05). In comparison with the conventional protocol, Cube MRD demonstrates satisfactory image quality and similar diagnostic capability for cases of possible LDS disease. (orig.)

  8. MR imaging of the knee: Improvement of signal and contrast efficiency of T1-weighted turbo spin echo sequences by applying a driven equilibrium (DRIVE) pulse

    Energy Technology Data Exchange (ETDEWEB)

    Radlbauer, Rudolf, E-mail: rudolf.radlbauer@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Lomoschitz, Friedrich, E-mail: friedrich.lomoschitz@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Salomonowitz, Erich, E-mail: erich.salomonowitz@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Eberhardt, Knut E., E-mail: info@mrt-kompetenzzentrum.d [MRT Competence Center Schloss Werneck, Balthasar-Neumann-Platz 2, 97440 Werneck (Germany); Stadlbauer, Andreas, E-mail: andi@nmr.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany)

    2010-08-15

    The purpose of this study was to assess the effect of a driven equilibrium (DRIVE) pulse incorporated in a standard T1-weighted turbo spin echo (TSE) sequence as used in our routine MRI protocol for examination of pathologies of the knee. Sixteen consecutive patients with knee disorders were examined using the routine MRI protocol, including T1-weighted TSE-sequences with and without a DRIVE pulse. Signal-to-noise ratios (SNRs) and contrast-to-noise ratio (CNR) of anatomical structures and pathologies were calculated and compared for both sequences. The differences in diagnostic value of the T1-weighted images with and without DRIVE pulse were assessed. SNR was significantly higher on images acquired with DRIVE pulse for fluid, effusion, cartilage and bone. Differences in the SNR of meniscus and muscle between the two sequences were not statistically significant. CNR was significantly increased between muscle and effusion, fluid and cartilage, fluid and meniscus, cartilage and meniscus, bone and cartilage on images acquired using the DRIVE pulse. Diagnostic value of the T1-weighted images was found to be improved for delineation of anatomic structures and for diagnosing a variety of pathologies when a DRIVE pulse is incorporated in the sequence. Incorporation of a DRIVE pulse into a standard T1-weighted TSE-sequence leads to significant increase of SNR and CNR of both, anatomical structures and pathologies, and consequently to an increase in diagnostic value within the same acquisition time.

  9. MR imaging of the knee: Improvement of signal and contrast efficiency of T1-weighted turbo spin echo sequences by applying a driven equilibrium (DRIVE) pulse

    International Nuclear Information System (INIS)

    Radlbauer, Rudolf; Lomoschitz, Friedrich; Salomonowitz, Erich; Eberhardt, Knut E.; Stadlbauer, Andreas

    2010-01-01

    The purpose of this study was to assess the effect of a driven equilibrium (DRIVE) pulse incorporated in a standard T1-weighted turbo spin echo (TSE) sequence as used in our routine MRI protocol for examination of pathologies of the knee. Sixteen consecutive patients with knee disorders were examined using the routine MRI protocol, including T1-weighted TSE-sequences with and without a DRIVE pulse. Signal-to-noise ratios (SNRs) and contrast-to-noise ratio (CNR) of anatomical structures and pathologies were calculated and compared for both sequences. The differences in diagnostic value of the T1-weighted images with and without DRIVE pulse were assessed. SNR was significantly higher on images acquired with DRIVE pulse for fluid, effusion, cartilage and bone. Differences in the SNR of meniscus and muscle between the two sequences were not statistically significant. CNR was significantly increased between muscle and effusion, fluid and cartilage, fluid and meniscus, cartilage and meniscus, bone and cartilage on images acquired using the DRIVE pulse. Diagnostic value of the T1-weighted images was found to be improved for delineation of anatomic structures and for diagnosing a variety of pathologies when a DRIVE pulse is incorporated in the sequence. Incorporation of a DRIVE pulse into a standard T1-weighted TSE-sequence leads to significant increase of SNR and CNR of both, anatomical structures and pathologies, and consequently to an increase in diagnostic value within the same acquisition time.

  10. MR venography using the 3D-MEDIC (multi echo data imaging combination) sequence for lower extremities

    International Nuclear Information System (INIS)

    Kitagawa, Hisashi; Kishi, Takayuki; Saito, Ryo; Shohji, Tomokazu; Noguchi, Keiji; Sunohara, Nobuo

    2008-01-01

    It is possible to diagnose varicose vein from medical history and physical examinations including inspection and palpation. Non-contrast enhanced MRV (magnetic resonance venography) is becoming popular because it can be easily performed without being affected by the radiographer's skill. We thought that the use of MEDIC (multi echo data imaging combination) would enable us to delineate varicose veins within a short acquisition time and without need for synchronization or contrast enhancement. We used the SIEMENS MAGNETOM Avanto 1.5-Tesla unit to acquire images. Our subjects were five healthy volunteers and five patients with varicose vein. The signal strength of deep veins and muscles were measured. The SNR (signal-to-nose ratio) of deep veins and the CNR (contrast-to-noise ratio) between deep veins and muscles were also measured. Flip angle, fat suppression methods, MTC (magnetic transfer contrast) pulse, and combined echo. Using the optimum image acquisition protocol following our preliminary study with varicose vein patients, the ability of the 3D-MEDIC method to delineate varicose veins was compared with that of the electrocardiogram (ECG)-synchronized two-dimensional time of flight (2D-TOF) method. We found that the following settings would enable us to acquire images from a wide range=coronal, within short acquisition time and needless ECG-triggering. Flip angle=20 degrees, fat suppression method=water excitation, MTC pulse=ON, combined echo=2. 3D-MEDIC was better than the 2D-TOF method in delineating the varicose vein itself and the connection between the varicose vein and deep veins. It is expected that 3D-MEDIC may be useful in the clinical diagnosis of varicose veins. (author)

  11. Genomic multiple sequence alignments: refinement using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

    Full Text Available Abstract Background Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. Results We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned regions of the orthopoxvirus alignment. Overall sequence identity increased only

  12. A time warping approach to multiple sequence alignment.

    Science.gov (United States)

    Arribas-Gil, Ana; Matias, Catherine

    2017-04-25

    We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a median path that represents the MSA we are looking for. We establish a proof of concept that our method could be an interesting ingredient to include into refined MSA techniques. We present a simple synthetic experiment as well as the study of a benchmark dataset, together with comparisons with 2 widely used MSA softwares.

  13. Fast spin echo MRI techniques. Contrast characteristics and clinical potential. Techniques d'IRM en fast spin echo. Caracteristiques de contraste et potentiels cliniques

    Energy Technology Data Exchange (ETDEWEB)

    Melki, P.; Mulkern, R.V.; Dacher, J.N.; Helenon, O.; Higuchi, N. (Harvard Medical School, Boston, MA (United States)); Oshio, K.; Jolesz, F. (Keio Univ., Tokyo (Japan)); Pourcelot, L. (Hopital Bretonneau, 37 - Tours (France)); Einstein, S. (General Electric Medical System, Milwaukee, WI (United States))

    1993-03-01

    Based on partial RF echo planar principles, Fast Spin Echo techniques (FSE) were implemented on high field systems. These methods produce image quality and contrast which resemble to conventional spin echo (SE) techniques. By reducing acquisition times by factors between 1.4 and 16 over SE methods, FSE allows for several imaging options usually prohibitive with conventional spin echo (SE) sequences. These include fast scans (especially breathold acquisitions); improved T2 contrast with longer TR intervals; increased spatial resolution with the use of larger image matrices and/or smaller fields of view; and 3D volume imaging with a 3D multislab FSE technique. Contrast features of FSE techniques are directly comparable to those of multiple echo SE sequences using the same echo spacing than FSE methods. However, essential contrast differences existing between the FSE sequences and their routine asymmetric dual SE counterpart can be identified. Decreased magnetic susceptibility effects and increased fat signal present within T2 weighted images compared to conventional dual SE images are due to the use of shorter echo spacings employed in FSE sequences. Off-resonance irradiation inherent to the use of a large number of radio frequency pulses in shown to results in dramatic magnetization contrast transfer effects in FSE images acquired in multislice mode.

  14. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    DEFF Research Database (Denmark)

    Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah

    2016-01-01

    non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified......Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We...... have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32...

  15. 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.

  16. 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.

  17. The role of MR imaging with Half Fourier Acquired Single Shot Turbo Spin Echo sequence in the diagnosis of lung lesions in comparison with multislice CT

    International Nuclear Information System (INIS)

    Hekimoglu, B.; Gurgen, F.; Tatar, I.G.; Aydin, H.; Kizilgoz, V.; Keyik, B.

    2013-01-01

    Objective: To compare the diagnostic values of magnetic resonance imaging using Half Fourier Acquired Single Shot Turbo Spin Echo sequence and multidetector computed tomography in patients with pathologically examined pulmonary lesions. Methods: The retrospective, descriptive study was conducted at Radiology Department, Diskapi Research Hospital, Ankara, Turkey, and comprised records of patients with pathologically examined pulmonary lesions between May 2009 and March 2012. Patients were divided into three groups and examined by both multi dedector computed tomography and magnetic resonance imaging. During the imaging, patients were not administered any intravenous contrast medium. Electrocardiogram gating and breath holding were not performed in echo sequence. Pulmonary lesions were evaluated on the basis of their dimensions, numbers, differentiation from atelectasis and consolidation, invasion to the thoracic wall-mediastinal structures and presence of lymphadenopathies. Results: Sensitivity of all patients was 50% (p=0.214) and specificity of CT and MRI were 82.5% (p=0.134) for the detectability of submilimetric nodules . For differentiation of the mass from atelectasis and consolidation, the sensitivity of computed tomography was statistically more significant compared to magnetic resonance imaging (86.6%; p=0.035). For the invasion of the mass to the mediastinal structures and the thoracic wall, the sensitivity of magnetic resonance imaging was statistically more significant compared to tomography (86.6%; p=0.035). Conclusion: HASTE sequence can be used to determine the invasion of the pulmonary mass to the mediastinal structures and the thoracic wall since it is more sensitive than computed tomography. It can also be used to detect submilimetric nodules. It has equal sensitivity and specificity compared to computed tomography. But computed tomography is superior for the differentiation of the mass from atelectasis and consolidation. (author)

  18. MACSIMS : multiple alignment of complete sequences information management system

    Directory of Open Access Journals (Sweden)

    Plewniak Frédéric

    2006-06-01

    Full Text Available Abstract Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at http://bips.u-strasbg.fr/MACSIMS/.

  19. Comparison of MRI sequences for evaluation of multiple sclerosis of the cervical spinal cord at 3 T

    International Nuclear Information System (INIS)

    Philpott, Cristina; Brotchie, Peter

    2011-01-01

    Purpose: Debate remains regarding the utility of the traditional STIR (short inversion time recovery) sequence in aiding MRI diagnosis of spinal cord lesions in patients with multiple sclerosis (MS) and this sequence is not included in the current imaging guidelines. A recent study proposed a T1 weighted STIR as a superior alternative to the traditional STIR and T2 fast spin echo (FSE). Thus, the aim of this study was to compare the sensitivity of T2, standard STIR and T1 weighted STIR sequences in the evaluation of MS plaques on our 3 T system. Methods and materials: A retrospective analysis of patients with multiple sclerosis who presented to our institution over a period of 5 months and who had cervical cord lesions was undertaken. Patients had been examined with our institutional protocol which included T2 FSE, STIR and the recommended T1 STIR. Quantitative analysis of the lesions versus background cord using sample T-tests was performed for each sequence, and comparative analysis of the lesion contrast:background cord ratios of the 3 sequences (using two-way ANOVA tests) was performed. Results: The T2 sequence was not as sensitive in detecting lesions versus the traditional STIR and T1 weighted STIR, with 10% of lesions not detected using statistical analysis (p < 0.05). The traditional STIR also demonstrated greater contrast ratios than the T2 sequence (p < 0.05) suggesting increased sensitivity. However, the T1 STIR demonstrated even greater contrast ratios than both the traditional STIR and T2 sequences (p < 0.05). Conclusion: This study confirms earlier findings of the traditional STIRs increased sensitivity versus the T2 sequence. However, the new “T1 weighted STIR” appears to be even more sensitive than both these sequences showing potential promise as an alternative method to monitor demyelinating plaques of MS.

  20. Skeleton-based human action recognition using multiple sequence alignment

    Science.gov (United States)

    Ding, Wenwen; Liu, Kai; Cheng, Fei; Zhang, Jin; Li, YunSong

    2015-05-01

    Human action recognition and analysis is an active research topic in computer vision for many years. This paper presents a method to represent human actions based on trajectories consisting of 3D joint positions. This method first decompose action into a sequence of meaningful atomic actions (actionlets), and then label actionlets with English alphabets according to the Davies-Bouldin index value. Therefore, an action can be represented using a sequence of actionlet symbols, which will preserve the temporal order of occurrence of each of the actionlets. Finally, we employ sequence comparison to classify multiple actions through using string matching algorithms (Needleman-Wunsch). The effectiveness of the proposed method is evaluated on datasets captured by commodity depth cameras. Experiments of the proposed method on three challenging 3D action datasets show promising results.

  1. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

    Science.gov (United States)

    Edgar, Robert C

    2004-01-01

    We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

  2. Correlations of pseudo-random numbers of multiplicative sequence

    International Nuclear Information System (INIS)

    Bukin, A.D.

    1989-01-01

    An algorithm is suggested for searching with a computer in unit n-dimensional cube the sets of planes where all the points fall whose coordinates are composed of n successive pseudo-random numbers of multiplicative sequence. This effect should be taken into account in Monte-Carlo calculations with definite constructive dimension. The parameters of these planes are obtained for three random number generators. 2 refs.; 2 tabs

  3. Application of fast spin-echo T[sub 2]-weighted imaging for examination of the neurocranium. Comparison with the conventional T[sub 2]-weighted spin-echo sequence. Die Anwendung der T[sub 2]-gewichteten Turbo-Spin-Echo-Sequenz zur Untersuchung des Neurokraniums. Vergleich mit der konventionellen T[sub 2]-gewichteten Spin-Echo-Sequenz

    Energy Technology Data Exchange (ETDEWEB)

    Siewert, C. (Strahlenklinik und Poliklinik, Universitaets-Klinikum Rudolf Virchow, Standort Wedding, Freie Univ. Berlin (Germany)); Hosten, N. (Strahlenklinik und Poliklinik, Universitaets-Klinikum Rudolf Virchow, Standort Wedding, Freie Univ. Berlin (Germany)); Felix, R. (Strahlenklinik und Poliklinik, Universitaets-Klinikum Rudolf Virchow, Standort Wedding, Freie Univ. Berlin (Germany))

    1994-07-01

    T[sub 2]-weighted spin-echo imaging is the standard screening procedure in MR imaging of the neutrocranium. We evaluated fast spin-echo T[sub 2]-weighted imaging (TT[sub 2]) of the neurocranium in comparison to conventional spin-echo T[sub 2]-weighted imaging (T[sub 2]). Signal-to-noise and contrast-to-noise ratio of normal brain tissues (basal ganglia, grey and white matter, CSF fluid) and different pathologies were calculated. Signal-to-noise ratio and contrast-to-noise ratio were significantly higher than TT[sub 2] than in T[sub 2] (with the exception of grey-to-white matter contrast). Tissues with increased content of water protons (mobile protons) showed the highest contrast to surrounding tissues. The increased signal intensity of fat must be given due attention in fatty lesions. Because the contrast-to-noise ratio between white matter and basal ganglia is less in TT[sub 2], Parkinson patients have to be examined by conventional T[sub 2]. If these limitations are taken into account, fast spin-echo T[sub 2]-weighted imaging is well appropriate for MR imaging of the neurocranium, resulting in heavy T[sub 2]-weighting achieved in a short acquisition time. (orig.)

  4. Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE.

    Science.gov (United States)

    Van Eygen, Veerle; Thys, Kim; Van Hove, Carl; Rimsky, Laurence T; De Meyer, Sandra; Aerssens, Jeroen; Picchio, Gaston; Vingerhoets, Johan

    2016-05-01

    Minority variants (1.0-25.0%) were evaluated by deep sequencing (DS) at baseline and virological failure (VF) in a selection of antiretroviral treatment-naïve, HIV-1-infected patients from the rilpivirine ECHO/THRIVE phase III studies. Linkage between frequently emerging resistance-associated mutations (RAMs) was determined. DS (llIumina®) and population sequencing (PS) results were available at baseline for 47 VFs and time of failure for 48 VFs; and at baseline for 49 responders matched for baseline characteristics. Minority mutations were accurately detected at frequencies down to 1.2% of the HIV-1 quasispecies. No baseline minority rilpivirine RAMs were detected in VFs; one responder carried 1.9% F227C. Baseline minority mutations associated with resistance to other non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 8/47 VFs (17.0%) and 7/49 responders (14.3%). Baseline minority nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) RAMs M184V and L210W were each detected in one VF (none in responders). At failure, two patients without NNRTI RAMs by PS carried minority rilpivirine RAMs K101E and/or E138K; and five additional patients carried other minority NNRTI RAMs V90I, V106I, V179I, V189I, and Y188H. Overall at failure, minority NNRTI RAMs and NRTI RAMs were found in 29/48 (60.4%) and 16/48 VFs (33.3%), respectively. Linkage analysis showed that E138K and K101E were usually not observed on the same viral genome. In conclusion, baseline minority rilpivirine RAMs and other NNRTI/NRTI RAMs were uncommon in the rilpivirine arm of the ECHO and THRIVE studies. DS at failure showed emerging NNRTI resistant minority variants in seven rilpivirine VFs who had no detectable NNRTI RAMs by PS. © 2015 Wiley Periodicals, Inc.

  5. MRI of intracranial vertebral artery dissection: evaluation of intramural haematoma using a black blood, variable-flip-angle 3D turbo spin-echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Takano, Koichi; Yamashita, Shinnichi; Kuwabara, Yasuo; Yoshimitsu, Kengo [Fukuoka University, Department of Radiology, Faculty of Medicine, Fukuoka-shi, Fukuoka (Japan); Takemoto, Koichiro; Inoue, Tooru [Fukuoka University, Department of Neurosurgery, Faculty of Medicine, Fukuoka (Japan)

    2013-07-15

    We investigated the efficacy of three-dimensional black blood T1-weighted imaging (3D-BB-T1WI) using a variable refocusing flip angle turbo spin-echo sequence in the diagnosis of intracranial vertebral artery dissection (VAD). Sixteen consecutive patients diagnosed with intracranial VAD underwent magnetic resonance imaging that included 3D time-of-flight-MRA, axial spin-echo T1-weighted images (SE-T1WI) and oblique coronal 3D-BB-T1WI sequences. The visualization, morphology and extent of intramural haematomas were assessed and compared among the sequences. Results obtained by digital subtraction angiography (DSA), 3D-angiography and/or 3D-CT angiography (CTA) were used as standards of reference. 3D-BB-T1WI revealed intramural haematomas in all cases, whereas SE-T1WI and magnetic resonance angiography (MRA) failed to reveal a haematoma in one case and three cases, respectively. The mean visualization grading score for the intramural haematoma was the highest for 3D-BB-T1WI, and there was a statistically significant difference among the sequences (p < 0.001). At least a portion of the intramural haematoma was distinguishable from the lumen on 3D-BB-T1WI, whereas the haematomas were entirely indistinguishable from intraluminal signals on MRA in two cases (12.5 %) and on SE-T1WI in one case (6.3 %). 3D-BB-T1WI revealed the characteristic crescent shape of the intramural haematoma in 14 cases (87.5 %), whereas SE-T1WI and MRA revealed a crescent shape in only 7 cases (43.8 %) and 8 cases (50 %), respectively. In a consensus reading, 3D-BB-T1WI was considered the most consistent sequence in representing the extent and morphology of the lesion in 14 cases (87.5 %), compared to DSA and CTA. 3D-BB-T1WI is a promising method to evaluate intramural haematoma in patients with suspected intracranial VAD. (orig.)

  6. Rational examination of the greater abdominal veins with 2D-TOF- and turbo-spin-echo sequences

    International Nuclear Information System (INIS)

    Lutterbey, G.; Sommer, T.; Keller, E.; Kuhl, C.; Schild, H.H.

    1998-01-01

    Purpose: Development of a fast and reliable protocol for the detection and exclusion of abdominal venous thrombosis with an optimised T 2 -TSE- and 2D-TOF sequence. Results: The most effective combination of strong flow-void phenomena, signal/noise ratio and scan time was found with the following parameters: T E 120 ms, T R 2000 ms, 5 mm slice gap. In the patient group two complete and two partial thromboses were diagnosed with both sequences. One wrong positive thrombosis occurred in a stenotic anastomosis with the 2D-inflow sequence. Conclusion: With optimum parameters the T 2 -TSE sequence produces a strong 'flow-void' phenomenon suitable for 'black-blood'-MRA. The use of this sequence alone or in combination with 2D-inflow MRA, if 'bright-blood' MRA is recommended, allows a reliable evaluation of thrombosis in abdominal veins without high-tech MRA equipment and contrast media. (orig./AJ) [de

  7. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

    Science.gov (United States)

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

  8. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  9. Noisy: Identification of problematic columns in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2008-06-01

    Full Text Available Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i phylogenetically informative and (ii effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1 the average bootstrap support obtained from the original alignment is low, and (2 there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

  10. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  11. Magnetic resonance imaging in cadaver dogs with metallic vertebral implants at 3 Tesla: evaluation of the WARP-turbo spin echo sequence.

    Science.gov (United States)

    Griffin, John F; Archambault, Nicholas S; Mankin, Joseph M; Wall, Corey R; Thompson, James A; Padua, Abraham; Purdy, David; Kerwin, Sharon C

    2013-11-15

    Laboratory investigation, ex vivo. Postoperative complications are common after spinal implantation procedures, and magnetic resonance imaging (MRI) would be the ideal modality to image these patients. Unfortunately, the implants cause artifacts that can render MRI nondiagnostic. The WARP-turbo spin echo (TSE) sequence has been developed to mitigate artifacts caused by metal. The objective of this investigation was to evaluate the performance of the WARP-TSE sequence in canine cadaver specimens after implantation with metallic vertebral implants. Magnetic field strength, implant type, and MRI acquisition technique all play a role in the severity of susceptibility artifacts. The WARP-TSE sequence uses increased bandwidth, view angle tilting, and SEMAC (slice-encoding metal artifact correction) to correct for susceptibility artifact. The WARP-TSE technique has outperformed conventional techniques in patients, after total hip arthroplasty. However, published reports of its application in subjects with vertebral column implants are lacking. Ex vivo anterior stabilization of the atlantoaxial joint was performed on 6 adult small breed (implantation with stainless steel implants. N/A.

  12. Cerebral staging of lung cancer: is one single contrast-enhanced T1-weighted three-dimensional gradient-echo sequence sufficient?

    Energy Technology Data Exchange (ETDEWEB)

    Ohana, Mickael; Jeung, Mi-Young; Roy, Catherine [Nouvel Hopital Civil-Hopitaux Universitaires de Strasbourg, Service de Radiologie B/Radiology Department, Strasbourg (France); Bazille, Gauthier [Clinique Saint Anne-Groupe Radiologique MIM, Strasbourg (France)

    2014-08-15

    Gadolinium-enhanced magnetic resonance imaging (MRI) is the gold standard for cerebral staging in thoracic oncology. We hypothesize that a minimalist examination, consisting of a single contrast-enhanced T1-weighted three-dimensional gradient-echo sequence (CE 3D-GRE), would be sufficient for the cerebral staging of nonsymptomatic lung cancer patients. Seventy nonsymptomatic patients (50 % men; 62 years ± 10.2) referred for cerebral staging of a lung cancer were retrospectively included. All underwent a standard 3 T MRI examination with T1, FLAIR, T2* GRE, diffusion, and CE 3D-GRE sequences, for a total examination time of 20 min. The sole CE 3D-GRE (acquisition time: 6 min) was extracted and blindly interpreted by two radiologists in search of brain metastases. Hemorrhagic features of potential lesions and relevant incidental findings were also noted. Discrepant cases were reviewed by a third reader. The full MRI examination and follow-up studies were used as a reference to calculate sensitivity and specificity of the sole CE 3D-GRE. Thirty-eight point six percent (27 out of 70) of the patients had brain metastases. Performances and reader's agreement with the sole CE 3D-GRE sequence were excellent for the diagnosis of brain metastases (sensitivity = 96.3 %, specificity = 100 %, κ = 0.91) and incidental findings (sensitivity = 85.7 %, specificity = 100 %, κ = 0.62) but insufficient for the identification of hemorrhages within the metastases (sensitivity = 33.3 %, specificity = 85.7 %, κ = 0.47). In the specific case of lung cancer, cerebral staging in nonsymptomatic patients can be efficiently achieved with a minimalistic protocol consisting of a single CE 3D-GRE sequence, completed if positive with a T2* sequence for hemorrhagic assessment, thus halving appointment delays. (orig.)

  13. Investigation of timing effects in modified composite quadrupolar echo pulse sequences by mean of average Hamiltonian theory

    Science.gov (United States)

    Mananga, Eugene Stephane

    2018-01-01

    The utility of the average Hamiltonian theory and its antecedent the Magnus expansion is presented. We assessed the concept of convergence of the Magnus expansion in quadrupolar spectroscopy of spin-1 via the square of the magnitude of the average Hamiltonian. We investigated this approach for two specific modified composite pulse sequences: COM-Im and COM-IVm. It is demonstrated that the size of the square of the magnitude of zero order average Hamiltonian obtained on the appropriated basis is a viable approach to study the convergence of the Magnus expansion. The approach turns to be efficient in studying pulse sequences in general and can be very useful to investigate coherent averaging in the development of high resolution NMR technique in solids. This approach allows comparing theoretically the two modified composite pulse sequences COM-Im and COM-IVm. We also compare theoretically the current modified composite sequences (COM-Im and COM-IVm) to the recently published modified composite pulse sequences (MCOM-I, MCOM-IV, MCOM-I_d, MCOM-IV_d).

  14. Rapid Gradient-Echo Imaging

    Science.gov (United States)

    Hargreaves, Brian

    2012-01-01

    Gradient echo sequences are widely used in magnetic resonance imaging (MRI) for numerous applications ranging from angiography to perfusion to functional MRI. Compared with spin-echo techniques, the very short repetition times of gradient-echo methods enable very rapid 2D and 3D imaging, but also lead to complicated “steady states.” Signal and contrast behavior can be described graphically and mathematically, and depends strongly on the type of spoiling: fully balanced (no spoiling), gradient spoiling, or RF-spoiling. These spoiling options trade off between high signal and pure T1 contrast while the flip angle also affects image contrast in all cases, both of which can be demonstrated theoretically and in image examples. As with spin-echo sequences, magnetization preparation can be added to gradient-echo sequences to alter image contrast. Gradient echo sequences are widely used for numerous applications such as 3D perfusion imaging, functional MRI, cardiac imaging and MR angiography. PMID:23097185

  15. Optimal update with multiple out-of-sequence measurements

    Science.gov (United States)

    Zhang, Shuo; Bar-Shalom, Yaakov

    2011-06-01

    In multisensor target tracking systems receiving out-of-sequence measurements from local sensors is a common situation. In the last decade many algorithms have been proposed to update a target state with an OOSM optimally or suboptimally. However, what one faces in the real world is multiple OOSMs, which arrive at the fusion center in, generally, arbitrary orders, e.g., in succession or interleaved with in-sequence measurements. A straightforward approach to deal with this multi-OOSM problem is by sequentially applying a given OOSM algorithm; however, this simple solution does not guarantee optimal update under the multi-OOSM scenario. The present paper discusses the differences between the single-OOSM processing and the multi-OOSM processing, and presents the general solution to the multi-OOSM problem, called the complete in-sequence information (CISI) approach. Given an OOSM, in addition to updating the target state at the most recent time, the CISI approach also updates the states between the OOSM time and the most recent time, including the state at the OOSM time. Three novel CISI methods are developed in this paper: the information filter-equivalent measurement (IF-EqM) method, the CISI fixed-point smoothing (CISI-FPS) method and the CISI fixed-interval smoothing (CISI-FIS) method. Numerical examples are given to show the optimality of these CISI methods under various multi-OOSM scenarios.

  16. Programmable pulse sequence generator with multiple output lines

    Science.gov (United States)

    Drabczyk, Hubert

    2006-10-01

    This paper presents a novel concept of pulse sequence generator and its prototype as an electronic circuit testing laboratory tool. The generator has multiple output lines and is capable of using control data defining different pulse sequences to be given to the outputs. It is also possible to use different voltage levels in output signal and switch output lines for reading data from driven system. The pulse sequence generator can be used for runtime environment simulation, as hardware tester or auxiliary tool in new designs. Important design factors were to keep cost of the tool low and allow integration with other projects by using flexible architecture. The prototype was based on universal programmer with adjustable power supply, '51 microcontroller and Altera Cyclone chip. The generator communicates witch PC computer via RS232 port. Dedicated software was developed in the course of this project, to control the tool and data transmission. The prototype confirmed the possibility to create an inexpensive multipurpose laboratory tool for programming, testing and simulation of digital devices.

  17. Using hidden Markov models to align multiple sequences.

    Science.gov (United States)

    Mount, David W

    2009-07-01

    A hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a "state"), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.

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

    International Nuclear Information System (INIS)

    Subashi, Ergys; Choudhury, Kingshuk R.; Johnson, G. Allan

    2014-01-01

    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 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 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 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 were found to be

  19. 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.)

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

    International Nuclear Information System (INIS)

    Hodel, Jerome; Silvera, Jonathan; Bekaert, Olivier; Decq, Philippe; Rahmouni, Alain; Bastuji-Garin, Sylvie; Vignaud, Alexandre; Petit, Eric; Durning, Bruno

    2011-01-01

    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.)

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

    International Nuclear Information System (INIS)

    Oppenheim, C.; Dormont, D.; Lehericy, S.; Marsault, C.; Hasboun, D.; Bazin, B.; Samson, S.; Baulac, M.

    1999-01-01

    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.)

  3. MRT versus CT in the diagnosis of pneumonia. Evaluation of a T2-weighted utrafast turbo-spin-echo sequence (UTSE)

    International Nuclear Information System (INIS)

    Leutner, C.; Lutterbey, G.; Kuhl, C.K.; Flacke, S.; Schild, H.H.; Glasmacher, A.; Theisen, A.; Wardelmann, E.; Grohe, C.

    1999-01-01

    Purpose: To evaluate a T 2 -weighted URSE sequence for the assessment of pulmonary infiltrations in comparison to CT. Methods: 28 MRT scans of 22 patients with confirmed pneumonia were recorded on a 1.5 Tesla apparatus with an expiratory and diastolic triggered, T 2 -weighted ultrafast-spin-echo sequence in axial slice mode with the following parameters: TR eff /T E /Turbofactor 2000-4000/90 ms/21-23; slice thickness/separation 6/0.6 mm; FOV 360 mm; 24 slices. 24 spiral CTs (sice thickness/table advance: 1-2 mm/10 mm) were available for comparison. The separate evaluation of MRTs and CTs was performed by three radiologists in a consensus procedure with regard to pulmonary lesions (e.g., infiltration, round foci, net patterns) and image quality of the MRTs (4-step scale). Results: In 71% of the cases the CTs and MRTs agreed with the diagnosis and representation of the lesions, in 25% MRT was superior. MRT was better for the detection of pulmonary abscesses. In 93% the image quality of the MRT was very good to good. Conclusions: MRT in the technique presented here is in most cases equal to CT for the detection of pneumonia. Diagnosis of pulmonary abscesses seems to be better with MRT. (orig.) [de

  4. 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...... mothers and demonology (Kathy Acker’s property deals in the UK), and more; and future materials formalized as poster texts . . ....

  5. Effectiveness of the STIR turbo spin–echo sequence MR imaging in evaluation of lymphadenopathy in esophageal cancer

    International Nuclear Information System (INIS)

    Alper, Fatih; Turkyilmaz, Atila; Kurtcan, Serpil; Aydin, Yener; Onbas, Omer; Acemoglu, Hamit; Eroglu, Atilla

    2011-01-01

    Purpose: We have investigated the utility of the STIR TSE sequence in the differentiation of benign from malignant mediastinal lymph nodes in patients with esophageal cancer. Patients and methods: This study included 35 consecutive patients who were diagnosed as esophageal cancer and were undergone surgery. STIR TSE sequences were obtained as the ECG trigger. The signal intensity of the benign and malign lymph nodes, normal esophagus, and pathologic esophagus can be calculated on STIR sequence. Results: Pathologically, the number of total lymph nodes in 35 operated cases was 482. Approximately 152 lymph nodes were detected with MR imaging. Of these, 28 were thought to be malignant, and 124 were thought to be benign, although 32 were malignant and 120 were benign according pathological results. The ratio of benign lymph node intensity value to normal esophagus intensity value was 0.73 ± 0.3. The ratio of malignant lymph node intensity value to normal esophagus intensity value ratio was 2.03 ± 0.4. According to these results, the sensitivity of MR was 81.3%, the specificity was 98.3%. Conclusion: We think that if motionless images can be obtained with MRI, we may be able to differentiate benign lymph nodes from malignant ones.

  6. Frequency bandwidth extension by use of multiple Zeeman field offsets for electron spin-echo EPR oxygen imaging of large objects

    Science.gov (United States)

    Seifi, Payam; Epel, Boris; Sundramoorthy, Subramanian V.; Mailer, Colin; Halpern, Howard J.

    2011-01-01

    Purpose: Electron spin-echo (ESE) oxygen imaging is a new and evolving electron paramagnetic resonance (EPR) imaging (EPRI) modality that is useful for physiological in vivo applications, such as EPR oxygen imaging (EPROI), with potential application to imaging of multicentimeter objects as large as human tumors. A present limitation on the size of the object to be imaged at a given resolution is the frequency bandwidth of the system, since the location is encoded as a frequency offset in ESE imaging. The authors’ aim in this study was to demonstrate the object size advantage of the multioffset bandwidth extension technique.Methods: The multiple-stepped Zeeman field offset (or simply multi-B) technique was used for imaging of an 8.5-cm-long phantom containing a narrow single line triaryl methyl compound (trityl) solution at the 250 MHz imaging frequency. The image is compared to a standard single-field ESE image of the same phantom.Results: For the phantom used in this study, transverse relaxation (T2e) electron spin-echo (ESE) images from multi-B acquisition are more uniform, contain less prominent artifacts, and have a better signal to noise ratio (SNR) compared to single-field T2e images.Conclusions: The multi-B method is suitable for imaging of samples whose physical size restricts the applicability of the conventional single-field ESE imaging technique. PMID:21815379

  7. MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

    Science.gov (United States)

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

    2016-11-15

    The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

  8. Comparison of two-dimensional fast spin echo T2 weighted sequences and three-dimensional volume isotropic T2 weighted fast spin echo (VISTA) MRI in the evaluation of triangular fibrocartilage of the wrist.

    Science.gov (United States)

    Park, Hee Jin; Lee, So Yeon; Kang, Kyung A; Kim, Eun Young; Shin, Hun Kyu; Park, Se Jin; Park, Jai Hyung; Kim, Eugene

    2018-04-01

    To compare image quality of three-dimensional volume isotropic T 2 weighted fast spin echo (3D VISTA) and two-dimensional (2D) T 2 weighted images (T2WI) for evaluation of triangular fibrocartilage (TFC) and to investigate whether 3D VISTA can replace 2D T 2 WI in evaluating TFC injury. This retrospective study included 69 patients who received wrist MRIs using both 2D T 2 WI and 3D VISTA techniques for assessment of wrist pathology, including TFC injury. Two radiologists measured the signal-to-noise ratio (SNR) and the contrast-to-noise ratio (CNR) of the two sequences. The anatomical identification score and diagnostic performance were independently assessed by two interpreters. The diagnostic abilities of 3D VISTA and 2D T 2 WI were analysed by sensitivity, specificity and accuracy for diagnosing TFC injury using surgically or clinically confirmed diagnostic reference standards. 17 cases (25%) were classified as having TFC injury. 2 cases (12%) were diagnosed surgically, and 15 cases (88%) were diagnosed by physical examination. 52 cases (75%) were diagnosed as having intact TFC. 8 of these cases (15%) were surgically confirmed, while the others were diagnosed by physical examination and clinical findings. The 3D VISTA images had significantly higher SNR and CNR values for the TFC than 2D T 2 WI images. The scores of 3D VISTA's total length, full width and sharpness were similar to those of 2D T 2 WI. We were unable to find a significant difference between 3D VISTA and 2D T 2 WI in the ability to diagnose TFC injury. 3D VISTA image quality is similar to that of 2D T 2 WI for TFC evaluation and is also excellent for tissue contrast. 3D VISTA can replace 2D images in TFC injury assessment. Advances in knowledge: 3D VISTA image quality is similar to that of 2D T 2 WI for TFC evaluation and is also excellent for tissue contrast. 3D VISTA can replace 2D images in TFC injury assessment.

  9. Value of MR cisternography using three-dimensional half-fourier single-shot fast spin-echo sequences in the diagnosis of diseases related to cranial nerves VII and VIII

    Energy Technology Data Exchange (ETDEWEB)

    Yamakami, Norio [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1999-05-01

    The purpose of this study was to evaluate the value of MR cisternography using three-dimensional half-Fourier single-shot fast spin-echo sequences in the diagnosis of diseasea related to cranial nerves VII and VIII. With a 0.5-T imager, the most appropriate setting of echo time and section thickness was first assessed in five volunteers. This resulted in echo time of 250 msec and section thickness of 2 mm as the most effective parameters. Second, using echo time of 120 msec and section thickness of 1.5 mm that were available from the beginning of this study, the demonstration of four nerves within the audistory canal was assessed in seven volunteers. In all of the volunteers, the facial, cochlear, and vestibular nerves were determined with demonstration of each of superior and inferior vestibular nerves in four of them. Next, MR cisternography using the same echo time and section thickness was applied in 368 patients with suspicion of acoustic neurinoma and 14 with hemifacial spasm. In 28 of the 368 patients, MR cisternograms depicted an acoustic neurinoma that was confirmed on postcontrast T1-weighted images. Meanwhile, in five of the 14 patients with hemifacial spasm, MR cisternograms revealed a vessel compressing the root exit zone of the affected facial nerve. It is concluded that MR cisternography using three-dimensional half-Fourier single-shot fast spin-echo sequences can be a useful means for demonstrating nerves within the auditory nerve as well as for the screening of acoustic neurionoma. (author)

  10. Value of MR cisternography using three-dimensional half-fourier single-shot fast spin-echo sequences in the diagnosis of diseases related to cranial nerves VII and VIII

    International Nuclear Information System (INIS)

    Yamakami, Norio

    1999-01-01

    The purpose of this study was to evaluate the value of MR cisternography using three-dimensional half-Fourier single-shot fast spin-echo sequences in the diagnosis of diseasea related to cranial nerves VII and VIII. With a 0.5-T imager, the most appropriate setting of echo time and section thickness was first assessed in five volunteers. This resulted in echo time of 250 msec and section thickness of 2 mm as the most effective parameters. Second, using echo time of 120 msec and section thickness of 1.5 mm that were available from the beginning of this study, the demonstration of four nerves within the audistory canal was assessed in seven volunteers. In all of the volunteers, the facial, cochlear, and vestibular nerves were determined with demonstration of each of superior and inferior vestibular nerves in four of them. Next, MR cisternography using the same echo time and section thickness was applied in 368 patients with suspicion of acoustic neurinoma and 14 with hemifacial spasm. In 28 of the 368 patients, MR cisternograms depicted an acoustic neurinoma that was confirmed on postcontrast T1-weighted images. Meanwhile, in five of the 14 patients with hemifacial spasm, MR cisternograms revealed a vessel compressing the root exit zone of the affected facial nerve. It is concluded that MR cisternography using three-dimensional half-Fourier single-shot fast spin-echo sequences can be a useful means for demonstrating nerves within the auditory nerve as well as for the screening of acoustic neurionoma. (author)

  11. 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

  12. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

    2014-01-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

  13. Suppression of Protonated Organic Solvents in NMR Spectroscopy Using a Perfect Echo Low-Pass Filtration Pulse Sequence.

    Science.gov (United States)

    Howe, Peter W A

    2018-04-03

    Proton NMR spectra are usually acquired using deuterated solvents, but in many cases it is necessary to obtain spectra on samples in protonated solvents. In these cases, the intense resonances of the protonated solvents need to be suppressed to maximize sensitivity and spectral quality. A wide range of highly effective solvent suppression methods have been developed, but additional measures are needed to suppress the 13 C satellites of the solvent. Because the satellites represent 1.1% of the original solvent signal, they remain problematic if unsuppressed. The recently proposed DISPEL pulse sequences suppress 13 C satellites extremely effectively, and this Technical Note demonstrates that combining DISPEL and presaturation results in exceptionally effective solvent suppression. An important element in the effectiveness is volume selection, which is inherent within the DISPEL sequence. Spectra acquired in protonated dimethlysulfoxide and tetrahydrofuran show that optimum results are obtained by modifying the phase cycle, cycling the pulse-field gradients, and using broadband 13 C inversion pulses to reduce the effects of radiofrequency offset and inhomogeneity.

  14. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    2007-02-01

    Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

  15. 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

    International Nuclear Information System (INIS)

    Komada, Tomohiro; Naganawa, Shinji; Ogawa, Hiroshi

    2008-01-01

    We evaluated the newly developed whole-brain, isotropic, 3-dimensional turbo spin-echo imaging with variable flip angle echo train (SPACE) for contrast-enhanced T 1 -weighted imaging in detecting brain metastases at 3 tesla (T). Twenty-two patients with suspected brain metastases underwent postcontrast study with SPACE, magnetization-prepared rapid gradient-echo (MP-RAGE), and 2-dimensional T 1 -weighted spin echo (2D-SE) imaging at 3 T. 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) and contrast-to-noise ratios (CNRs) for GM-to-WM, lesion-to-GM, and lesion-to-WM. Two blinded radiologists evaluated the detection of brain metastases by segment-by-segment analysis and continuously-distributed test. The CNR between GM and WM was significantly higher on MP-RAGE images than on SPACE images (P 1 -weighted imaging. (author)

  16. 3D double-echo steady-state sequence assessment of hip joint cartilage and labrum at 3 Tesla: comparative analysis of magnetic resonance imaging and intraoperative data

    Energy Technology Data Exchange (ETDEWEB)

    Schleich, Christoph; Antoch, Gerald [University of Dusseldorf, Department of Diagnostic and Interventional Radiology, Medical Faculty, Duesseldorf (Germany); Hesper, Tobias; Rettegi, Fanni; Zilkens, Christoph; Krauspe, Ruediger; Bittersohl, Bernd [University of Dusseldorf, Department of Orthopedic Surgery, Medical Faculty, Duesseldorf (Germany); Hosalkar, Harish S. [Paradise Valley Hospital, Joint Preservation and Deformity Correction, San Diego, CA (United States); Tri-city Medical Center, Hip Preservation, San Diego, CA (United States)

    2017-10-15

    To assess the diagnostic accuracy of a high-resolution, three-dimensional (3D) double-echo steady-state (DESS) sequence with radial imaging at 3 Tesla (T) for evaluating cartilage and labral alterations in the hip. Magnetic resonance imaging (MRI) data obtained at 3 T, including radially reformatted DESS images and intraoperative data of 45 patients (mean age 42 ± 13.7 years) who underwent hip arthroscopy, were compared. The acetabular cartilage and labrum of the upper hemisphere of the acetabulum and the central femoral head cartilage were evaluated. Sensitivity, specificity, accuracy, and negative and positive predictive values were determined. Sensitivity, specificity and accuracy of the DESS technique were 96.7%, 75% and 93.7% for detecting cartilage lesions and 98%, 76.2% and 95.9% for detecting labral lesions. The positive and negative predictive values for detecting or ruling out cartilage lesions were 96% and 78.9%. For labral lesions, the positive and negative predictive values were 97.5% and 80%. A high-resolution, 3D DESS technique with radial imaging at 3 T demonstrated high accuracy for detecting hip cartilage and labral lesions with excellent interobserver agreement and moderate correlation between MRI and intraoperative assessment. (orig.)

  17. 3D Ultrashort TE MRI for Evaluation of Cartilaginous Endplate of Cervical Disk In Vivo: Feasibility and Correlation With Disk Degeneration in T2-Weighted Spin-Echo Sequence.

    Science.gov (United States)

    Kim, Yeo Ju; Cha, Jang Gyu; Shin, Yoon Sang; Chaudhari, Akshay S; Suh, Young Ju; Hwan Yoon, Seung; Gold, Garry E

    2018-05-01

    The purpose of this study was to evaluate the feasibility of 3D ultrashort TE (UTE) MRI in depicting the cartilaginous endplate (CEP) and its abnormalities and to investigate the association between CEP abnormalities and disk degeneration on T2-weighted spin-echo (SE) MR images in cervical disks in vivo. Eight healthy volunteers and 70 patients were examined using 3-T MRI with the 3D UTE cones trajectory technique (TR/TE, 16.1/0.032, 6.6). In the volunteer study, quantitative and qualitative assessments of CEP depiction were conducted for the 3D UTE and T2-weighted SE imaging. In the patient study, CEP abnormalities were analyzed. Intersequence agreement between the images obtained with the first-echo 3D UTE sequence and the images created by subtracting the second-echo from the first-echo 3D UTE sequence (subtracted 3D UTE) and the intraobserver and interobserver agreements for 3D UTE overall were also tested. The CEP abnormalities on the 3D UTE images correlated with the Miyazaki grading of the T2-weighted SE images. In the volunteer study, the CEP was well visualized on 3D UTE images but not on T2-weighted SE images (p evaluation of CEP abnormalities, intersequence agreements were substantial to almost perfect, intraobserver agreements were substantial to almost perfect, and interobserver agreements were moderate to substantial (p T2-weighted SE MRI.

  18. 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.

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

    International Nuclear Information System (INIS)

    Schaefer, F.K.W.; Schaefer, P.J.; Brossmann, J.; Frahm, C.; Hilgert, R.E.; Heller, M.; Jahnke, T.

    2006-01-01

    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

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

    International Nuclear Information System (INIS)

    Grosse, U.; Syha, R.; Kessler, D.E.; Bongers, M.; Seith, F.; Nikolaou, K.; Springer, F.; Partovi, S.; Robbin, M.; Schick, F.

    2015-01-01

    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.

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

    International Nuclear Information System (INIS)

    Hickman, S.J.; Brex, P.A.; Silver, N.C.; Barker, G.J.; Miller, D.H.; Brierley, C.M.H.; Compston, D.A.S.; Scolding, N.J.; Moseley, I.F.; Plant, G.T.

    2001-01-01

    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 2 in the affected eye of the patients, 12.9mm 2 in the contralateral eye (P = 0.006 compared to the affected eye) and 12.8mm 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.)

  2. Quantitative T1 and T2* carotid atherosclerotic plaque imaging using a three-dimensional multi-echo phase-sensitive inversion recovery sequence: a feasibility study.

    Science.gov (United States)

    Fujiwara, Yasuhiro; Maruyama, Hirotoshi; Toyomaru, Kanako; Nishizaka, Yuri; Fukamatsu, Masahiro

    2018-06-01

    Magnetic resonance imaging (MRI) is widely used to detect carotid atherosclerotic plaques. Although it is important to evaluate vulnerable carotid plaques containing lipids and intra-plaque hemorrhages (IPHs) using T 1 -weighted images, the image contrast changes depending on the imaging settings. Moreover, to distinguish between a thrombus and a hemorrhage, it is useful to evaluate the iron content of the plaque using both T 1 -weighted and T 2 *-weighted images. Therefore, a quantitative evaluation of carotid atherosclerotic plaques using T 1 and T 2 * values may be necessary for the accurate evaluation of plaque components. The purpose of this study was to determine whether the multi-echo phase-sensitive inversion recovery (mPSIR) sequence can improve T 1 contrast while simultaneously providing accurate T 1 and T 2 * values of an IPH. T 1 and T 2 * values measured using mPSIR were compared to values from conventional methods in phantom and in vivo studies. In the phantom study, the T 1 and T 2 * values estimated using mPSIR were linearly correlated with those of conventional methods. In the in vivo study, mPSIR demonstrated higher T 1 contrast between the IPH phantom and sternocleidomastoid muscle than the conventional method. Moreover, the T 1 and T 2 * values of the blood vessel wall and sternocleidomastoid muscle estimated using mPSIR were correlated with values measured by conventional methods and with values reported previously. The mPSIR sequence improved T 1 contrast while simultaneously providing accurate T 1 and T 2 * values of the neck region. Although further study is required to evaluate the clinical utility, mPSIR may improve carotid atherosclerotic plaque detection and provide detailed information about plaque components.

  3. 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.)

  4. 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.)

  5. 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.

  6. 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.)

  7. Iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) imaging of multiple myeloma: initial clinical efficiency results

    International Nuclear Information System (INIS)

    Takasu, Miyuki; Tani, Chihiro; Sakoda, Yasuko; Ishikawa, Miho; Tanitame, Keizo; Date, Shuji; Akiyama, Yuji; Awai, Kazuo; Sakai, Akira; Asaoku, Hideki; Kajima, Toshio

    2012-01-01

    To evaluate the effectiveness of the iterative decomposition of water and fat with echo asymmetric and least-squares estimation (IDEAL) MRI to quantify tumour infiltration into the lumbar vertebrae in myeloma patients without visible focal lesions. The lumbar spine was examined with 3 T MRI in 24 patients with multiple myeloma and in 26 controls. The fat-signal fraction was calculated as the mean value from three vertebral bodies. A post hoc test was used to compare the fat-signal fraction in controls and patients with monoclonal gammopathy of undetermined significance (MGUS), asymptomatic myeloma or symptomatic myeloma. Differences were considered significant at P 2 -microglobulin-to-albumin ratio were entered into the discriminant analysis. Fat-signal fractions were significantly lower in patients with symptomatic myelomas (43.9 ±19.7%, P 2 -microglobulin-to-albumin ratio facilitated discrimination of symptomatic myeloma from non-symptomatic myeloma in patients without focal bone lesions. circle A new magnetic resonance technique (IDEAL) offers new insights in multiple myeloma. (orig.)

  8. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  9. 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.

  10. 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.

  11. Multi-slice echo-planar spectroscopic MR imaging provides both global and local metabolite measures in multiple sclerosis

    DEFF Research Database (Denmark)

    Mathiesen, Henrik Kahr; Tscherning, Thomas; Sorensen, Per Soelberg

    2005-01-01

    MR spectroscopy (MRS) provides information about neuronal loss or dysfunction by measuring decreases in N-acetyl aspartate (NAA), a metabolite widely believed to be a marker of neuronal viability. In multiple sclerosis (MS), whole-brain NAA (WBNAA) has been suggested as a marker of disease...... progression and treatment efficacy in treatment trials, and the ability to measure NAA loss in specific brain regions early in the evolution of this disease may have prognostic value. Most spectroscopic studies to date have been limited to single voxels or nonlocalized measurements of WBNAA only...

  12. Multi-slice echo-planar spectroscopic MR imaging provides both global and local metabolite measures in multiple sclerosis

    DEFF Research Database (Denmark)

    Mathiesen, Henrik Kahr; Tscherning, Thomas; Sorensen, Per Soelberg

    2005-01-01

    MR spectroscopy (MRS) provides information about neuronal loss or dysfunction by measuring decreases in N-acetyl aspartate (NAA), a metabolite widely believed to be a marker of neuronal viability. In multiple sclerosis (MS), whole-brain NAA (WBNAA) has been suggested as a marker of disease...... progression and treatment efficacy in treatment trials, and the ability to measure NAA loss in specific brain regions early in the evolution of this disease may have prognostic value. Most spectroscopic studies to date have been limited to single voxels or nonlocalized measurements of WBNAA only......, measurements of metabolites in specific brain areas chosen after image acquisition (e.g., normal-appearing white matter (NAWM), gray matter (GM), and lesions) can be obtained. The identification and exclusion of regions that are inadequate for spectroscopic evaluation in global assessments can significantly...

  13. Optimal pulse-sequence parameters for MR imaging of the immature brain

    International Nuclear Information System (INIS)

    Nowell, M.A.; Hackney, D.B.; Zimmerman, R.A.; Bilaniuk, L.T.; Grossman, R.I.; Goldberg, H.I.

    1986-01-01

    Appropriate spin-echo pulse sequence parameters generate MR images with very high gray matter/white matter contrast in neonates and young infants. Low-contrast images appear to result from utilization of ''adult-type'' parameters to investigate tissues that have relaxation characteristics quite different than those of adult brain. In these young patients long spin-echo sequences with repetition times of 3,000-3,500 msec and multiple echoes with the longest echo time set at 120-160 msec are employed to yield high-contrast ''T2-weighted'' images

  14. Variability at Multiple Scales: Using an Array of Current- and Pressure-Sensor Equipped Inverted Echo Sounders to Measure the Ocean

    Science.gov (United States)

    2016-11-29

    of Current- and Pressure - Sensor Equipped Inverted Echo Sounders to Measure the Ocean 5b. GRANT NUMBER NOOO 14-15-1-2857 5c. PROGRAM ELEMENT NUMBER...inverted echo sounders (lESs) equipped with pressure and current sensors (CPIESs). CPIESs are moored instruments that measure the round-trip acoustic...at a range of spatial and temporal scales. The goals of this project were to enhance the pool of pressure - sensor equipped lESs available at the

  15. Improved nonparametric inference for multiple correlated periodic sequences

    KAUST Repository

    Sun, Ying; Hart, Jeffrey D.; Genton, Marc G.

    2013-01-01

    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

  16. Long multiplication by instruction sequences with backward jump instructions

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2013-01-01

    For each function on bit strings, its restriction to bit strings of any given length can be computed by a finite instruction sequence that contains only instructions to set and get the content of Boolean registers, forward jump instructions, and a termination instruction. Backward jump instructions

  17. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    Science.gov (United States)

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  18. The facial nerve in the temporal bone as visualised via thin-layer paratransversal and sagittal MR tomographic images by means of T1 spin-echo and FLASH sequences

    International Nuclear Information System (INIS)

    Mueller-Lisse, U.; Jaeger, L.J.E.; Bruegel, F.J.; Grevers, G.; Reiser, M.F.

    1995-01-01

    It is difficult to effect visualization and delineation of the facial nerve and its neighbouring structures in the temporal bone with conventional MRI examination protocols. We tested temporal bone MRI with 2 mm slices and compared T 1 -weighted FLASH (T R =400 ms, T E =10 ms, 90 flip angle) and spin-echo (T R =540 ms, T E =15 ms) sequences. 5 volunteers and 14 patients were examined with the head coil of a 1.0 T whole body MRI scanner (Impact, Siemens, Erlangen) with para-transversal images orientated parallel to the inferior outline of the clivus and sagittal images orientated along the brainstem. The facial nerve and its neighbouring structures could be reliably visualized and differentiated along its entire course. The FLASH sequence was superior to the spin-echo sequence. 8 of 11 patients with peripheral facial nerve palsy showed contrast enhancement. In two patients, local swelling of the affected facial nerve was evident. (orig./MG) [de

  19. Experimental investigation of the accuracy for absolute quantification of brain creatine concentration using long time echo point resolved spectroscopy sequence with an external standard and linear combination of model spectra

    International Nuclear Information System (INIS)

    Lin Yan; Shen Zhiwei; Xiao Yeyu; Zheng Wenbin; Wu Renhua; Li Hui; Xiao Zhuanwei

    2008-01-01

    Objective: To investigate the accuracy for absolute quantification of brain creatine (Cr) concentration using long time echo (TE) point resolved spectroscopy (PRESS) sequence performed with an extemal standard and postprocessed with the linear combination of model spectra ( LCModel). Methods: Ten swine (3.1 ± 0.6 kg) and an external standard phantom containing detectable compounds of known concentration were investigated in this study by using 1.5 T GE Signa scanner and a standard head coil. The single-voxel proton magnetic resonance spectroscopy ( 1 H-MRS) data were acquired from the two ROIs (2 cm x 2 cm x 2 cm) placed in swine brain and external standard solution using PRESS sequence with TE 135 ms, TR 1500 ms, and 128 scan averages. The in vivo quantification of Cr was accomplished by LCModel. After 1 H-MRS examination, each animal was sacrificed immediately. In vitro Cr concentration was analyzed by high performance liquid chromatography (HPLC). Results: In the 1 H-MRS group, the Cr concentration was (9.37±0.14)mmol/kg. In the HPLC group, the Cr concentration was (8.91± 0.13)mmol/kg. Good agreement was obtained between these two methods (t=9.038, P=0.491). Conclusion: The long echo time PRESS sequence performed with an external standard and processed with LCModel is proven to be an accurate technique to detect the in vivo brain Cr concentration. (authors)

  20. Short echo time, fast gradient-echo imaging

    International Nuclear Information System (INIS)

    Haacke, E.M.; Lenz, G.W.

    1987-01-01

    Present fast-gradient-echoes schemes can acquire volume data rapidly and are flexible in T1 or T1/T2 contrast behavior. However, sequences used to date employ echo time (TE) values of about 15 ms +- 5 and, because of in vivo field inhomogeneities (short T2), they suffer badly from signal loss near sinuses and tissue boundaries. The authors implemented sequences with TE = 4-6 ms and found significant improvement in image quality, especially at high fields. Examples with long TEs vs. short TEs are given in the knee, spine, head, and orbits. Further advantages include (1) faster repetition times (15 ms), (2) higher-quality spin-density or T1-weighted images, and (3) reduction of blood motion artifacts

  1. 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.

  2. RNAblueprint: flexible multiple target nucleic acid sequence design.

    Science.gov (United States)

    Hammer, Stefan; Tschiatschek, Birgit; Flamm, Christoph; Hofacker, Ivo L; Findeiß, Sven

    2017-09-15

    Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility. We developed a C ++  library implementing a graph coloring approach to stochastically sample sequences compatible with structural and sequence constraints from the typically very large solution space. The approach allows to specify and explore the solution space in a well defined way. Our library also guarantees uniform sampling, which makes optimization runs performant by not only avoiding re-evaluation of already found solutions, but also by raising the probability of finding better solutions for long optimization runs. We show that our software can be combined with any other software package to allow diverse RNA design applications. Scripting interfaces allow the easy adaption of existing code to accommodate new scenarios, making the whole design process very flexible. We implemented example design approaches written in Python to demonstrate these advantages. RNAblueprint , Python implementations and benchmark datasets are available at github: https://github.com/ViennaRNA . s.hammer@univie.ac.at, ivo@tbi.univie.ac.at or sven@tbi.univie.ac.at. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  3. ECHO Gov Login | 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.

  4. 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.)

  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

    International Nuclear Information System (INIS)

    Yi, Jisook; Cha, Jang Gyu; Lee, Young Koo; Lee, Bo Ra; Jeon, Chan Hong

    2016-01-01

    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. Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

    Science.gov (United States)

    Hormozdiari, Fereydoun; Hajirasouliha, Iman; McPherson, Andrew; Eichler, Evan E.; Sahinalp, S. Cenk

    Next generation sequencing technologies have been decreasing the costs and increasing the world-wide capacity for sequence production at an unprecedented rate, making the initiation of large scale projects aiming to sequence almost 2000 genomes [1]. Structural variation detection promises to be one of the key diagnostic tools for cancer and other diseases with genomic origin. In this paper, we study the problem of detecting structural variation events in two or more sequenced genomes through high throughput sequencing . We propose to move from the current model of (1) detecting genomic variations in single next generation sequenced (NGS) donor genomes independently, and (2) checking whether two or more donor genomes indeed agree or disagree on the variations (in this paper we name this framework Independent Structural Variation Discovery and Merging - ISV&M), to a new model in which we detect structural variation events among multiple genomes simultaneously.

  7. 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

  8. Grating stimulated echo

    International Nuclear Information System (INIS)

    Dubetsky, B.; Berman, P.R.; Sleator, T.

    1992-01-01

    A theory of a grating simulated echo (GTE) is developed. The GSE involves the sequential excitation of atoms by two counterpropagating traveling waves, a standing wave, and a third traveling wave. It is shown that the echo signal is very sensitive to small changes in atomic velocity, much more sensitive than the normal stimulated echo. Use of the GSE as a collisional probe or accelerometer is discussed

  9. Multiple Access Interference Reduction Using Received Response Code Sequence for DS-CDMA UWB System

    Science.gov (United States)

    Toh, Keat Beng; Tachikawa, Shin'ichi

    This paper proposes a combination of novel Received Response (RR) sequence at the transmitter and a Matched Filter-RAKE (MF-RAKE) combining scheme receiver system for the Direct Sequence-Code Division Multiple Access Ultra Wideband (DS-CDMA UWB) multipath channel model. This paper also demonstrates the effectiveness of the RR sequence in Multiple Access Interference (MAI) reduction for the DS-CDMA UWB system. It suggests that by using conventional binary code sequence such as the M sequence or the Gold sequence, there is a possibility of generating extra MAI in the UWB system. Therefore, it is quite difficult to collect the energy efficiently although the RAKE reception method is applied at the receiver. The main purpose of the proposed system is to overcome the performance degradation for UWB transmission due to the occurrence of MAI during multiple accessing in the DS-CDMA UWB system. The proposed system improves the system performance by improving the RAKE reception performance using the RR sequence which can reduce the MAI effect significantly. Simulation results verify that significant improvement can be obtained by the proposed system in the UWB multipath channel models.

  10. 3D hybrid profile order technique in a single breath-hold 3D T2-weighted fast spin-echo sequence: Usefulness in diagnosis of small liver lesions.

    Science.gov (United States)

    Hirata, Kenichiro; Nakaura, Takeshi; Okuaki, Tomoyuki; Tsuda, Noriko; Taguchi, Narumi; Oda, Seitaro; Utsunomiya, Daisuke; Yamashita, Yasuyuki

    2018-01-01

    We compared the efficacy of three-dimensional (3D) isotropic T2-weighted fast spin-echo imaging using a 3D hybrid profile order technique with a single-breath-hold (3D-Hybrid BH) with a two-dimensional (2D) T2-weighted fast spin-echo conventional respiratory-gated (2D-Conventional RG) technique for visualising small liver lesions. This study was approved by our institutional review board. The requirement to obtain written informed consent was waived. Fifty patients with small (≤15mm) hepatocellular carcinomas (HCC) (n=26), or benign cysts (n=24), had undergone hepatic MRI including both 2D-Conventional RG and 3D-Hybrid BH. We calculated the signal-to-noise ratio (SNR) and tumour-to-liver contrast (TLC). The diagnostic performance of the two protocols was analysed. The image acquisition time was 89% shorter with the 3D-Hybrid BH than with 2D-Conventional RG. There was no significant difference in the SNR between the two protocols. The area under the curve (AUC) of the TLC was significantly higher on 3D-Hybrid BH than on 2D-Conventional RG. The 3D-Hybrid BH sequence significantly improved diagnostic performance for small liver lesions with a shorter image acquisition time without sacrificing accuracy. Copyright © 2017. Published by Elsevier B.V.

  11. Differentiation between hepatic haemangiomas and cysts with an inversion recovery single-shot turbo spin-echo (SSTSE) sequence using the TI nulling value of hepatic haemangioma with sensitivity encoding

    International Nuclear Information System (INIS)

    Katada, Yoshiaki; Nozaki, Miwako; Yasumoto, Mayumi; Ishii, Chikako; Tanaka, Hiroshi; Nakamoto, Kazuya; Ohashi, Isamu

    2010-01-01

    To evaluate the additional value of inversion recovery (IR) single-shot turbo spin-echo (SSTSE) imaging with sensitivity encoding (SENSE) using the inversion time (TI) value of hepatic haemangioma as a supplement to conventional T2-weighted turbo spin-echo (TSE) imaging for the discrimination of hepatic haemangiomas and cysts. A total of 134 lesions (77 hepatic haemangiomas, 57 hepatic cysts) in 59 patients were evaluated. Three readers evaluated these images and used a five-point scale to evaluate the lesion status. A receiver operating characteristic (ROC) analysis and 2 x 2 table analysis were used. The ROC analysis for all the readers and all the cases revealed a significantly higher area under the curve (AUC) for the combination of moderately and heavily T2-weighted TSE with IR-SSTSE images (0.945) than for moderately and heavily T2-weighted TSE images alone (0.894) (P < 0.001). For the combination of T2-weighted TSE with IR-SSTSE versus T2-weighted TSE alone, the 2 x 2 table analysis revealed a higher true-positive rate; this difference was statistically significant (P < 0.0001). The introduction of IR-SSTSE with SENSE sequences significantly improves the diagnostic accuracy of the differentiation of hepatic haemangioma and cysts while increasing the time required for routine abdominal imaging by only 20 s. (orig.)

  12. Characteristics of spondylotic myelopathy on 3D driven-equilibrium fast spin echo and 2D fast spin echo magnetic resonance imaging: a retrospective cross-sectional study.

    Science.gov (United States)

    Abdulhadi, Mike A; Perno, Joseph R; Melhem, Elias R; Nucifora, Paolo G P

    2014-01-01

    In patients with spinal stenosis, magnetic resonance imaging of the cervical spine can be improved by using 3D driven-equilibrium fast spin echo sequences to provide a high-resolution assessment of osseous and ligamentous structures. However, it is not yet clear whether 3D driven-equilibrium fast spin echo sequences adequately evaluate the spinal cord itself. As a result, they are generally supplemented by additional 2D fast spin echo sequences, adding time to the examination and potential discomfort to the patient. Here we investigate the hypothesis that in patients with spinal stenosis and spondylotic myelopathy, 3D driven-equilibrium fast spin echo sequences can characterize cord lesions equally well as 2D fast spin echo sequences. We performed a retrospective analysis of 30 adult patients with spondylotic myelopathy who had been examined with both 3D driven-equilibrium fast spin echo sequences and 2D fast spin echo sequences at the same scanning session. The two sequences were inspected separately for each patient, and visible cord lesions were manually traced. We found no significant differences between 3D driven-equilibrium fast spin echo and 2D fast spin echo sequences in the mean number, mean area, or mean transverse dimensions of spondylotic cord lesions. Nevertheless, the mean contrast-to-noise ratio of cord lesions was decreased on 3D driven-equilibrium fast spin echo sequences compared to 2D fast spin echo sequences. These findings suggest that 3D driven-equilibrium fast spin echo sequences do not need supplemental 2D fast spin echo sequences for the diagnosis of spondylotic myelopathy, but they may be less well suited for quantitative signal measurements in the spinal cord.

  13. Distortion-free diffusion tensor imaging for evaluation of lumbar nerve roots: Utility of direct coronal single-shot turbo spin-echo diffusion sequence.

    Science.gov (United States)

    Sakai, Takayuki; Doi, Kunio; Yoneyama, Masami; Watanabe, Atsuya; Miyati, Tosiaki; Yanagawa, Noriyuki

    2018-06-01

    Diffusion tensor imaging (DTI) based on a single-shot echo planer imaging (EPI-DTI) is an established method that has been used for evaluation of lumbar nerve disorders in previous studies, but EPI-DTI has problems such as a long acquisition time, due to a lot of axial slices, and geometric distortion. To solve these problems, we attempted to apply DTI based on a single-shot turbo spin echo (TSE-DTI) with direct coronal acquisition. Our purpose in this study was to investigate whether TSE-DTI may be more useful for evaluation of lumbar nerve disorders than EPI-DTI. First, lumbar nerve roots of five healthy volunteers were evaluated for optimization of imaging parameters with TSE-DTI including b-values and the number of motion proving gradient (MPG) directions. Subsequently, optimized TSE-DTI was quantitatively compared with conventional EPI-DTI by using fractional anisotropy (FA) values and visual scores in subjective visual evaluation of tractography. Lumbar nerve roots of six patients, who had unilateral neurologic symptoms in one leg, were evaluated by the optimized TSE-DTI. TSE-DTI with b-value of 400 s/mm 2 and 32 diffusion-directions could reduce the image distortion compared with EPI-DTI, and showed that the average FA values on the symptomatic side for six patients were significantly lower than those on the non-symptomatic side (P DTI might show damaged areas of lumbar nerve roots without severe image distortion. TSE-DTI might improve the reproducibility in measurements of FA values for quantification of a nerve disorder, and would become a useful tool for diagnosis of low back pain. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. NMR polarization echoes in a nematic liquid crystal

    Science.gov (United States)

    Levstein, Patricia R.; Chattah, Ana K.; Pastawski, Horacio M.; Raya, Jésus; Hirschinger, Jérôme

    2004-10-01

    We have modified the polarization echo (PE) sequence through the incorporation of Lee-Goldburg cross polarization steps to quench the 1H-1H dipolar dynamics. In this way, the 13C becomes an ideal local probe to inject and detect polarization in the proton system. This improvement made possible the observation of the local polarization P00(t) and polarization echoes in the interphenyl proton of the liquid crystal N-(4-methoxybenzylidene)-4-butylaniline. The decay of P00(t) was well fitted to an exponential law with a characteristic time τC≈310 μs. The hierarchy of the intramolecular dipolar couplings determines a dynamical bottleneck that justifies the use of the Fermi Golden Rule to obtain a spectral density consistent with the structural parameters. The time evolution of P00(t) was reversed by the PE sequence generating echoes at the time expected by the scaling of the dipolar Hamiltonian. This indicates that the reversible 1H-1H dipolar interaction is the main contribution to the local polarization decrease and that the exponential decay for P00(t) does not imply irreversibility. The attenuation of the echoes follows a Gaussian law with a characteristic time τφ≈527 μs. The shape and magnitude of the characteristic time of the PE decay suggest that it is dominated by the unperturbed homonuclear dipolar Hamiltonian. This means that τφ is an intrinsic property of the dipolar coupled network and not of other degrees of freedom. In this case, one cannot unambiguously identify the mechanism that produces the decoherence of the dipolar order. This is because even weak interactions are able to break the fragile multiple coherences originated on the dipolar evolution, hindering its reversal. Other schemes to investigate these underlying mechanisms are proposed.

  15. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

    OpenAIRE

    Morgenstern, Burkhard

    2004-01-01

    DIALIGN is a widely used software tool for multiple DNA and protein sequence alignment. The program combines local and global alignment features and can therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online through Bielefeld Bioinformatics Server (BiBiServ). The downloadable version of the program offers several new program features. To compare the output of different alignment programs, we developed the program AltA...

  16. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2004-09-01

    Full Text Available Abstract Background Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. Conclusions By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

  17. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

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

    International Nuclear Information System (INIS)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M.; Koch, Kevin M.

    2015-01-01

    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.)

  19. 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.)

  20. Optical orthogonal code-division multiple-access system - Part 2: Multibits/sequence-period OOCDMA

    Science.gov (United States)

    Kwon, Hyuck M.

    1994-08-01

    In a recently proposed optical orthogonal code division multiple-access (OOCDMA) system, one bit of user's data is transmitted per sequence-period, and a threshold is employed for the final bit decision. In this paper, a system that can transmit multibits per sequence-period is introduced, and avalanche photodiode (APD) noise, thermal noise, and interference, are included. This system, derived by exploiting orthogonal properties of the OOCDMA code sequence and using a maximum search (instead of a threshold) in the final decision, is log(sub 2) F times higher in throughput, where F is sequence-period. For example, four orders of magnitude are better in bit error probability at - 56 dBW received laser power, with F = 1000 chips, 10 'marks' in a sequence, and 10 users of 30 Mb/s data rate for one-bit/sequence-period and 270 Mb/s data rate for multibits/sequence-period system. Furthermore, an exact analysis is performed for the log(sub 2)F bits/sequence-period system with a hard-limiter placed before the receiver, and its performance is compared to the performance without hard-limiter, for the chip-synchronous case. The improvement from using a hard-limiter is significant in the log(sub 2)F bits/sequence-period OCCDMA system.

  1. A prospective comparison study of fast T1 weighted fluid attenuation inversion recovery and T1 weighted turbo spin echo sequence at 3 T in degenerative disease of the cervical spine.

    Science.gov (United States)

    Ganesan, K; Bydder, G M

    2014-09-01

    This study compared T1 fluid attenuation inversion recovery (FLAIR) and T1 turbo spin echo (TSE) sequences for evaluation of cervical spine degenerative disease at 3 T. 72 patients (44 males and 28 females; mean age of 39 years; age range, 27-75 years) with suspected cervical spine degenerative disease were prospectively evaluated. Sagittal images of the spine were obtained using T1 FLAIR and T1 TSE sequences. Two experienced neuroradiologists compared the sequences qualitatively and quantitatively. On qualitative evaluation, cerebrospinal fluid (CSF) nulling and contrast at cord-CSF, disc-CSF and disc-cord interfaces were significantly higher on fast T1 FLAIR images than on T1 TSE images (p degenerative disease, owing to higher cord-CSF, disc-cord and disc-CSF contrast. However, intrinsic cord contrast is low on T1 FLAIR images. T1 FLAIR is more promising and sensitive than T1 TSE for evaluation of degenerative spondyloarthropathy and may provide a foundation for development of MR protocols for early detection of degenerative and neoplastic diseases.

  2. Fat suppression with short inversion time inversion-recovery and chemical-shift selective saturation: a dual STIR-CHESS combination prepulse for turbo spin echo pulse sequences.

    Science.gov (United States)

    Tanabe, Koji; Nishikawa, Keiichi; Sano, Tsukasa; Sakai, Osamu; Jara, Hernán

    2010-05-01

    To test a newly developed fat suppression magnetic resonance imaging (MRI) prepulse that synergistically uses the principles of fat suppression via inversion recovery (STIR) and spectral fat saturation (CHESS), relative to pure CHESS and STIR. This new technique is termed dual fat suppression (Dual-FS). To determine if Dual-FS could be chemically specific for fat, the phantom consisted of the fat-mimicking NiCl(2) aqueous solution, porcine fat, porcine muscle, and water was imaged with the three fat-suppression techniques. For Dual-FS and STIR, several inversion times were used. Signal intensities of each image obtained with each technique were compared. To determine if Dual-FS could be robust to magnetic field inhomogeneities, the phantom consisting of different NiCl(2) aqueous solutions, porcine fat, porcine muscle, and water was imaged with Dual-FS and CHESS at the several off-resonance frequencies. To compare fat suppression efficiency in vivo, 10 volunteer subjects were also imaged with the three fat-suppression techniques. Dual-FS could suppress fat sufficiently within the inversion time of 110-140 msec, thus enabling differentiation between fat and fat-mimicking aqueous structures. Dual-FS was as robust to magnetic field inhomogeneities as STIR and less vulnerable than CHESS. The same results for fat suppression were obtained in volunteers. The Dual-FS-STIR-CHESS is an alternative and promising fat suppression technique for turbo spin echo MRI. Copyright 2010 Wiley-Liss, Inc.

  3. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

    Science.gov (United States)

    Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

    2011-01-01

    The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

  4. Sedimentation and lithostratigraphy of the Vuosaari multiple till sequence in Helsinki, southern Finland

    Directory of Open Access Journals (Sweden)

    Hirvas, H.

    1995-12-01

    Full Text Available A multiple till sequence interbedded with sorted sediments has been investigated at Vuosaari, Helsinki, Finland. The investigation was carried out using standard sedimentological procedures combined with microfossil analysis in order to determine the genesis of the exposed sediments. This evidence is used to correlate lithostratigraphically the sequence with adjacent multiple till sequences in other parts of southern Finland (south of the Salpausselkä zone. It is concluded that all three till beds at Vuosaari are of basal origin that were laid down by separate ice flow phases. In contrast two rhythmite beds between the tills are thought to have been deposited in open water. The sediments at Vuosaari may have been laid down during the Weichselian glaciation although it is also possible that the lowermost till bed represents Saalian till.

  5. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Science.gov (United States)

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  6. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Directory of Open Access Journals (Sweden)

    Steven Kelly

    Full Text Available The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  7. Applying Agrep to r-NSA to solve multiple sequences approximate matching.

    Science.gov (United States)

    Ni, Bing; Wong, Man-Hon; Lam, Chi-Fai David; Leung, Kwong-Sak

    2014-01-01

    This paper addresses the approximate matching problem in a database consisting of multiple DNA sequences, where the proposed approach applies Agrep to a new truncated suffix array, r-NSA. The construction time of the structure is linear to the database size, and the computations of indexing a substring in the structure are constant. The number of characters processed in applying Agrep is analysed theoretically, and the theoretical upper-bound can approximate closely the empirical number of characters, which is obtained through enumerating the characters in the actual structure built. Experiments are carried out using (synthetic) random DNA sequences, as well as (real) genome sequences including Hepatitis-B Virus and X-chromosome. Experimental results show that, compared to the straight-forward approach that applies Agrep to multiple sequences individually, the proposed approach solves the matching problem in much shorter time. The speed-up of our approach depends on the sequence patterns, and for highly similar homologous genome sequences, which are the common cases in real-life genomes, it can be up to several orders of magnitude.

  8. MRI evaluation of myometrial invasion by endometrial carcinoma. Comparison between fast-spin-echo T2W and coronal FMPSPGR Gadolinium-Dota-Enhanced Sequences

    International Nuclear Information System (INIS)

    Nasi, Francesca; Fiocchi, Federica; Pecchi, Annarita; Torricelli, Pietro; Rivasi, Francesco

    2005-01-01

    Purpose. The depth of myometrial invasion by endometrial carcinoma strongly affects the incidence of metastasis to regional nodes and influences the surgical strategies. The aim of this paper is to compare the results of FSE T2-w and Gadolinium-enhanced FMPSGR MR sequences in assessing the depth of myometrial invasion by endometrial cancer. Materials and methods. Forty-five women with histopathologically-proven endometrial carcinoma underwent preoperative MRI. Axial SE TI w, axial, sagittal and para-coronal FSE T2w and para-coronal Gadolinium enhanced FMPSGR sequences were performed using a high field strength magnet (1.5T). Within one month of MR all patients underwent hysterectomy, and anatomical evaluation of the surgical specimen was done sectioning the uterus along the short axis. Based upon the results of the histological evaluation the results of the FSE T2w and Gadolinium-enhanced sequences were compared and the statistical difference between the results obtained was statistically evaluated. Results. The histological evaluation showed intra mucosal neoplasm in 11 patients, myometrial infiltration less than 50% in 31 patients, myometrial infiltration more than 50% in 12 patients and transmural cancer 1 patient. Statistical evaluation showed that the FSE T2w sequence had a global sensitivity and specificity of 80.6% and 87.6%, respectively, with a mean Negative Predictive Value of 92.6% and a mean Positive Predictive Value of 86%. Gadolinium-enhanced FMPSPGR sequence had a global sensitivity and specificity of 90.6% and 93.3%, respectively, with a mean Negative Predictive Value of 96,3% and a mean Positive Predictive Value of 88%. The staging accuracy (χ 2 test) on FMPSPGR images (95%) was higher than that on FSE T2w images (78%). Conclusions. In our experience Gadolinium-enhanced dynamic sequences increase the accuracy of MR imaging in diagnosing the depth of myometrial invasion. In particular they improve the visualisation of the inner myometrium, the so

  9. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    International Nuclear Information System (INIS)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar

    2017-01-01

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol

  10. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    Energy Technology Data Exchange (ETDEWEB)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar [SGRR Institute of Medical and Health Sciences, Patel Nagar, Dehradun (India)

    2017-11-15

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol.

  11. BLADE acquisition method improves T2-weighted MR images of the female pelvis compared with a standard fast spin-echo sequence

    International Nuclear Information System (INIS)

    Fujimoto, Koji; Koyama, Takashi; Tamai, Ken; Morisawa, Nobuko; Okada, Tomohisa; Togashi, Kaori

    2011-01-01

    Purpose: To investigate feasibility of the periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER or BLADE) T2-weighted imaging (T2WI) of the female pelvis by comparing it with standard fast spin-echo T2WI (STD-T2WI). Materials and methods: Sagittal STD-T2WI and BLADE-T2WI of the female pelvis were performed with (36 patients) or without (15 patients) administration of butylscopolamine on a 1.5 T MR unit. Two radiologists independently rated depiction of the uterus, ovary, intestines, bladder, gynecological lesions, overall quality, and artifacts using a four-point scale. Results were compared between STD-T2WI vs. BLADE-T2WI either with (B+) or without (B−) administration of butylscopolamine, BLADE-T2WI (B−) vs. BLADE-T2WI (B+), and STD-T2WI (B+) vs. BLADE-T2WI (B−). Results: When butylscopolamine was administrated, depiction of the uterus, ovary, intestines, gynecological lesions, and overall image quality was rated higher and artifacts were rated fewer for BLADE-T2WI with significance compared with STD-T2WI. When the drug was not administrated, significant difference was observed in depiction of the lesion, overall quality, and artifacts. Depiction of the uterus, gynecological lesion, and overall quality was rated significantly higher and artifacts were fewer in BLADE-T2WI (B+) than in BLADE-T2WI (B−). Conclusion: BLADE method was feasible for female pelvic MRI, with best image quality in BLADE-T2WI (B+).

  12. Echo Shaping Using Sums of Damped Complex Sinusoids

    DEFF Research Database (Denmark)

    Putnam, Lance Jonathan

    2015-01-01

    Feedback delay lines are the basis of myriad audio effects and reverberation schemes. The feedback delay line, by itself, is limited to producing an infinite sequence of exponentially decaying echoes. We introduce a new type of linear time-invariant echo effect whose impulse response is a general...

  13. 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.

  14. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

    Science.gov (United States)

    Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

    2012-07-15

    In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

  15. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  16. An intuitive graphical webserver for multiple-choice protein sequence search.

    Science.gov (United States)

    Banky, Daniel; Szalkai, Balazs; Grolmusz, Vince

    2014-04-10

    Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Happy birthday Echo!

    CERN Document Server

    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...

  18. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  19. AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

    Full Text Available Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used

  20. The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Menzel, Karl Peter; Backofen, Rolf

    2011-01-01

    gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer...... to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/...

  1. Practical multipeptide synthesis: dedicated software for the definition of multiple, overlapping peptides covering polypeptide sequences.

    Science.gov (United States)

    Heegaard, P M; Holm, A; Hagerup, M

    1993-01-01

    A personal computer program for the conversion of linear amino acid sequences to multiple, small, overlapping peptide sequences has been developed. Peptide lengths and "jumps" (the distance between two consecutive overlapping peptides) are defined by the user. To facilitate the use of the program for parallel solid-phase chemical peptide syntheses for the synchronous production of multiple peptides, amino acids at each acylation step are laid out by the program in a convenient standard multi-well setup. Also, the total number of equivalents, as well as the derived amount in milligrams (depend-ending on user-defined equivalent weights and molar surplus), of each amino acid are given. The program facilitates the implementation of multipeptide synthesis, e.g., for the elucidation of polypeptide structure-function relationships, and greatly reduces the risk of introducing mistakes at the planning step. It is written in Pascal and runs on any DOS-based personal computer. No special graphic display is needed.

  2. Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.

    Science.gov (United States)

    Kinjo, Akira R

    2017-01-01

    A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are used for both parameter optimization of the model and production runs to explore the sequence subspace around a given protein family. In this Note, I describe the details of the MC algorithm as well as some preliminary results of MC simulations with various temperatures and chemical potentials, and compare them with the mean-field approximation. The existence of a two-state transition in the sequence space is suggested for the SH3 domain family, and inappropriateness of the mean-field approximation for the LGM is demonstrated.

  3. Security Analysis of a Block Encryption Algorithm Based on Dynamic Sequences of Multiple Chaotic Systems

    Science.gov (United States)

    Du, Mao-Kang; He, Bo; Wang, Yong

    2011-01-01

    Recently, the cryptosystem based on chaos has attracted much attention. Wang and Yu (Commun. Nonlin. Sci. Numer. Simulat. 14 (2009) 574) proposed a block encryption algorithm based on dynamic sequences of multiple chaotic systems. We analyze the potential flaws in the algorithm. Then, a chosen-plaintext attack is presented. Some remedial measures are suggested to avoid the flaws effectively. Furthermore, an improved encryption algorithm is proposed to resist the attacks and to keep all the merits of the original cryptosystem.

  4. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification

    OpenAIRE

    Yi Wang; Yan Wang; Ai-Jing Ma; Dong-Xun Li; Li-Juan Luo; Dong-Xin Liu; Dong Jin; Kai Liu; Chang-Yun Ye

    2015-01-01

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61?65??C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primer...

  5. Evaluation of the Subscapularis Tendon Tears on 3T Magnetic Resonance Arthrography: Comparison of Diagnostic Performance of T1-Weighted Spectral Presaturation with Inversion-Recovery and T2-Weighted Turbo Spin-Echo Sequences.

    Science.gov (United States)

    Lee, Hoseok; Ahn, Joong Mo; Kang, Yusuhn; Oh, Joo Han; Lee, Eugene; Lee, Joon Woo; Kang, Heung Sik

    2018-01-01

    To compare the T1-weighted spectral presaturation with inversion-recovery sequences (T1 SPIR) with T2-weighted turbo spin-echo sequences (T2 TSE) on 3T magnetic resonance arthrography (MRA) in the evaluation of the subscapularis (SSC) tendon tear with arthroscopic findings as the reference standard. This retrospective study included 120 consecutive patients who had undergone MRA within 3 months between April and December 2015. Two musculoskeletal radiologists blinded to the arthroscopic results evaluated T1 SPIR and T2 TSE images in separate sessions for the integrity of the SSC tendon, examining normal/articular-surface partial-thickness tear (PTTa)/full-thickness tear (FTT). Diagnostic performance of T1 SPIR and T2 TSE was calculated with arthroscopic results as the reference standard, and sensitivity, specificity, and accuracy were compared using the McNemar test. Interobserver agreement was measured with kappa (κ) statistics. There were 74 SSC tendon tears (36 PTTa and 38 FTT) confirmed by arthroscopy. Significant differences were found in the sensitivity and accuracy between T1 SPIR and T2 TSE using the McNemar test, with respective rates of 95.9-94.6% vs. 71.6-75.7% and 90.8-91.7% vs. 79.2-83.3% for detecting tear; 55.3% vs. 31.6-34.2% and 85.8% vs. 78.3-79.2%, respectively, for FTT; and 91.7-97.2% vs. 58.3-61.1% and 89% vs. 78-79.3%, respectively, for PTTa. Interobserver agreement for T1 SPIR was almost perfect for T1 SPIR (κ = 0.839) and substantial for T2 TSE (κ = 0.769). T1-weighted spectral presaturation with inversion-recovery sequences is more sensitive and accurate compared to T2 TSE in detecting SSC tendon tear on 3T MRA.

  6. 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.

  7. Comparison of T1rho imaging between spoiled gradient echo (SPGR) and balanced steady state free precession (b-FFE) sequence of knee cartilage at 3 T MRI

    Energy Technology Data Exchange (ETDEWEB)

    Nozaki, Taiki; Kaneko, Yasuhito; Yu, Hon J. [Department of Radiological Sciences, University of California, Irvine, CA (United States); Kaneshiro, Kayleigh [School of Medicine, University of California, Irvine, CA (United States); Schwarzkopf, Ran [Department of Orthopaedic Surgery, University of California, Irvine, CA (United States); Yoshioka, Hiroshi, E-mail: hiroshi@uci.edu [Department of Radiological Sciences, University of California, Irvine, CA (United States)

    2015-07-15

    Highlights: • T1rho values on b-FFE tend to be higher than those on SPGR. • The reproducibility of T1rho cartilage segmentation is higher on SPGR than b-FFE. • There is angular variation of T1rho profiles. • Average T1rho values in the superficial layer are higher than in the deep layer. - Abstract: Purpose: To investigate the difference in T1rho profiles of the entire femoral cartilage between SPGR and b-FFE sequences at 3.0 T. Materials and methods: 20 healthy volunteers were enrolled in this study. T1rho images of each subject were acquired with two types of pulse sequences: SPGR and b-FFE. Femoral cartilage segmentation was performed by two independent raters slice-by-slice using Matlab. Inter- and intra-observer reproducibility between the two imaging protocols was calculated. The relative signal intensity (SI) of cartilage, subchondral bone marrow, joint effusion, and the relative signal contrast between structures of the knee were quantitatively measured. The difference in T1rho values between SPGR and b-FFE sequences was statistically analyzed using the Wilcoxon signed-rank test. Results: The average T1rho value of the entire femoral cartilage with b-FFE was significantly higher compared to SPGR (p < 0.05). The reproducibility of the segmented area and T1rho values was superior with SPGR compared to b-FFE. The inter-class correlation coefficient was 0.846 on SPGR and 0.824 on b-FFE. The intra-class correlation coefficient of T1rho values was 0.878 on SPGR and 0.836 on b-FFE. The two imaging techniques demonstrated different signal and contrast characteristics. The relative SI of fluid was significantly higher on SPGR, while the relative SI of subchondral bone was significantly higher on b-FFE (p < 0.001). There were also significant differences in the relative contrast between fluid–cartilage, fluid–subchondral bone, and cartilage–subchondral bone between the two sequences (all p < 0.001). Conclusion: We need to pay attention to differences in

  8. Free-breathing dynamic liver examination using a radial 3D T1-weighted gradient echo sequence with moderate undersampling for patients with limited breath-holding capacity

    Energy Technology Data Exchange (ETDEWEB)

    Kaltenbach, Benjamin, E-mail: benjamin.kaltenbach@kgu.de [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Roman, Andrei; Polkowski, Christoph; Gruber-Rouh, Tatjana [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Bauer, Ralf W. [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Divison of Radiology and Nuclear Medicine, Kantonsspital, St. Gallen (Switzerland); Hammerstingl, Renate; Vogl, Thomas J.; Zangos, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany)

    2017-01-15

    Highlights: • Respiratory artifacts are a frequent problem in abdominal MR imaging. • Non-diagnostic examinations could be reduced using free-breathing us-radial-VIBE for dynamic liver examination in challenging patients. • Streak artifacts are characteristic for an undersampled radial acquisition but do not affect diagnostic validity. - Abstract: Purpose: To compare free-breathing radial VIBE with moderate undersampling (us-radial-VIBE) with a standard breathhold T1-weighted volumetric interpolated sequence (3D GRE VIBE) in patients unable to suspend respiration during dynamic liver examination. Material and methods: 23 consecutive patients underwent dynamic liver MR examination using the free-breathing us-radial-VIBE sequence as part of their oncologic follow-up. All patients were eligible for the free-breathing protocol due to severe respiratory artifacts at the planning or precontrast sequences. The us-radial-VIBE acquisitions were compared to the patientś last staging liver MRI including a standard breathhold 3D GRE VIBE. For an objective image evaluation, signal intensity (SI), image noise (IN), signal-to-noise ratio (SNR) and contrast-enhancement ratio (CER) were compared. Representative image quality parameters, including typical artifacts were independently, retrospectively and blindly scored by four readers. Results: Us-radial-VIBE had significant lower SNR (p < 0.0001) and higher IN (p < 0.0001), whereas SI did not differ (p = 0.62). Temporal resolution assessed with CER in the arterial phase showed higher values for us-radial-VIBE (p = 0.028). Subjective image quality parameters received generally slightly higher scores for 3D GRE VIBE. In a smaller subgroup comprising patients with severe respiratory artifacts also at reference breathhold 3D GRE VIBE examination, us-radial-VIBE showed significantly higher image quality scores. Furthermore, there were generally more severe respiratory artifacts in 3D GRE VIBE, whereas streaking was characteristic

  9. Prognostic value of deep sequencing method for minimal residual disease detection in multiple myeloma

    Science.gov (United States)

    Lahuerta, Juan J.; Pepin, François; González, Marcos; Barrio, Santiago; Ayala, Rosa; Puig, Noemí; Montalban, María A.; Paiva, Bruno; Weng, Li; Jiménez, Cristina; Sopena, María; Moorhead, Martin; Cedena, Teresa; Rapado, Immaculada; Mateos, María Victoria; Rosiñol, Laura; Oriol, Albert; Blanchard, María J.; Martínez, Rafael; Bladé, Joan; San Miguel, Jesús; Faham, Malek; García-Sanz, Ramón

    2014-01-01

    We assessed the prognostic value of minimal residual disease (MRD) detection in multiple myeloma (MM) patients using a sequencing-based platform in bone marrow samples from 133 MM patients in at least very good partial response (VGPR) after front-line therapy. Deep sequencing was carried out in patients in whom a high-frequency myeloma clone was identified and MRD was assessed using the IGH-VDJH, IGH-DJH, and IGK assays. The results were contrasted with those of multiparametric flow cytometry (MFC) and allele-specific oligonucleotide polymerase chain reaction (ASO-PCR). The applicability of deep sequencing was 91%. Concordance between sequencing and MFC and ASO-PCR was 83% and 85%, respectively. Patients who were MRD– by sequencing had a significantly longer time to tumor progression (TTP) (median 80 vs 31 months; P < .0001) and overall survival (median not reached vs 81 months; P = .02), compared with patients who were MRD+. When stratifying patients by different levels of MRD, the respective TTP medians were: MRD ≥10−3 27 months, MRD 10−3 to 10−5 48 months, and MRD <10−5 80 months (P = .003 to .0001). Ninety-two percent of VGPR patients were MRD+. In complete response patients, the TTP remained significantly longer for MRD– compared with MRD+ patients (131 vs 35 months; P = .0009). PMID:24646471

  10. Rotary spin echoes

    Energy Technology Data Exchange (ETDEWEB)

    Solomon, I. [Commissariat a l' energie atomique et aux energies alternatives - CEA, Centre d' Etudes Nucleaires de Saclay, BP2, Gif-sur-Yvette (France)

    1959-07-01

    Torrey has observed the free precession of nuclear spins around an r-f field H{sub 1}, fixed in a frame rotating at the Larmor frequency ω{sub 0} = γH{sub 0} around a large d-c magnetic field H{sub 0}. He showed that for an H{sub 1}, much larger than inhomogeneity of H{sub 0}, the latter has a negligible effect on the decay of the spin magnetization which is mainly due to the inhomogeneity of H{sub 1}. We report here on a method of overcoming the inhomogeneity of H{sub 1}, by production of echoes in the rotating frame ('rotary echoes'). These echoes are obtained by a 180 deg. phase shift at t = τ on the r-f field so that H{sub 1}, is suddenly reversed, producing a re-focussing of the magnetization vectors at the time t = 2 τ. The rotary echoes so obtained are very similar to the usual spin-echoes with, however some specific features that make them particularly suitable for the measurement of long relaxation times. Reprint of a paper published in Physical Review Letters, vol. 2, no. 7, Apr 1959, p. 301-302.

  11. Rotary spin echoes

    International Nuclear Information System (INIS)

    Solomon, I.

    1959-01-01

    Torrey has observed the free precession of nuclear spins around an r-f field H 1 , fixed in a frame rotating at the Larmor frequency ω 0 = γH 0 around a large d-c magnetic field H 0 . He showed that for an H 1 , much larger than inhomogeneity of H 0 , the latter has a negligible effect on the decay of the spin magnetization which is mainly due to the inhomogeneity of H 1 . We report here on a method of overcoming the inhomogeneity of H 1 , by production of echoes in the rotating frame ('rotary echoes'). These echoes are obtained by a 180 deg. phase shift at t = τ on the r-f field so that H 1 , is suddenly reversed, producing a re-focussing of the magnetization vectors at the time t = 2 τ. The rotary echoes so obtained are very similar to the usual spin-echoes with, however some specific features that make them particularly suitable for the measurement of long relaxation times. Reprint of a paper published in Physical Review Letters, vol. 2, no. 7, Apr 1959, p. 301-302

  12. Gadolinium-enhanced MR imaging of normal renal transplants. An evaluation of a T1-weighted dynamic echo-planar sequence

    International Nuclear Information System (INIS)

    Dupas, B.; Blancho, G.; Havet, T.; Leaute, F.

    1999-01-01

    Purpose: To evaluate the potential usefulness of dynamic MR with echoplanar imaging (EPI) in assessing the renal function in patients with renal allografts. Material and methods: Using a T1-weighted sequence, EPI was performed after injection of a Gd-chelate in 17 patients with normally functioning renal allografts. Time-intensity curves were plotted from the signal intensity (SI) measurements of the cortex and the medulla. Results: The pattern of corticomedullar differentiation (CMD) observed after constrast enhancement was divided into four phases using the T1-EPI. After a rapid decrease in the SI of cortical structures, and a subsequent return to precontrast levels, a gradual fall in the SI of the medulla was observed. The average time between the two periods of signal loss was 60 s. Conclusion: This study illustrated the potential use of dynamic T1-EPI to demonstrate contrast-induced CMD in renal allografts. (orig.)

  13. Evaluation of cardiac function using multi-shot echo planar imaging

    Energy Technology Data Exchange (ETDEWEB)

    Nakanishi, Tadashi; Tanitame, Nobuko; Hata, Ryoichiro; Hirai, Nobuhiko; Ikeda, Midori; Ono, Chiaki; Fukuoka, Haruhito; Ito, Katsuhide [Hiroshima Univ. (Japan). School of Medicine

    1998-01-01

    In this study, we performed multi-shot echo planar imaging (8 shot, TR/TE/FL=55 ms/18 ms/60 degrees) and k-space segmented fast gradient echo sequence (8 views per segment, TR/TE/FL=9.9 ms/1.8 ms/30 degrees) to assess cardiac function in healthy volunteers. Transaxial sections of the entire heart were obtained with both sequences in ECG triggered, breath hold, and with a 256 x 128 matrix. Resulting temporal resolution was 55 ms for echo planar imaging, and 71 ms for k-space segmented fast gradient echo sequence, respectively. Ventricular volume and ejection fraction of both ventricles and left ventricular mass obtained with multi-shot echo planar imaging were assessed in comparison with k-space segmented fast gradient echo sequence. Measurements of left ventricular volume, ejection fraction and mass obtained with multi-shot echo planar imaging demonstrated close correlation with those obtained with k-space segmented fast gradient echo sequence. Right ventricular volumes obtained with echo planar imaging were significantly higher than those obtained with k-space segmented fast gradient echo sequence. This tendency is considered to be due to differing contrast between right ventricular myocardium and fat tissue observed with echo planar imaging relative to that observed with fast gradient echo sequence, because fat suppression is always performed in echo planar images. Multi-shot echo planar imaging can be a reliable tool for measurement of cardiac functional parameters, although wall motion analysis of the left ventricle requires higher temporal resolution and a short axial section. (K.H.)

  14. MRI before and after external beam intensity-modulated radiotherapy of patients with prostate cancer: The feasibility of monitoring of radiation-induced tissue changes using a dynamic contrast-enhanced inversion-prepared dual-contrast gradient echo sequence

    International Nuclear Information System (INIS)

    Franiel, Tobias; Luedemann, Lutz; Taupitz, Matthias; Boehmer, Dirk; Beyersdorff, Dirk

    2009-01-01

    Purpose: To identify and quantify suitable pharmacokinetic MRI parameters for monitoring tissue changes after external beam intensity-modulated radiotherapy of prostate cancer. Material and methods: Six patients with biopsy-proven prostate cancer (initial PSA, 6.0-81.4 ng/ml) underwent MRI at 1.5 T using a combined endorectal/body phased-array coil and a dynamic contrast-enhanced inversion-prepared dual-contrast gradient echo sequence (T1/T2*w; 1.65 s temporal resolution). MRI was performed before and immediately after radiotherapy, at 3 months and at 1 year. Perfusion, blood volume, mean transit time, delay, dispersion, interstitial volume, and extraction coefficient were calculated in prostate cancer and normal prostate for all four time points using a sequential 3-compartment model. Results: Prostate cancer and normal prostate tissue showed a statistically significant decrease in perfusion (p = 0.006, p = 0.001) and increase in extraction coefficient (p = 0.004, p 3 min, p = 0.028) and a smaller extraction coefficient (0.42 vs. 0.64, p = 0.028). Conclusions: Two pharmacokinetic parameters, perfusion and extraction coefficient, appear to be suitable candidates for monitoring the response to percutaneous intensity-modulated radiotherapy of prostate cancer.

  15. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

    2007-01-01

    BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

  16. The role of Acinetobacter in the pathogenesis of multiple sclerosis examined by using Popper sequences.

    Science.gov (United States)

    Ebringer, Alan; Rashid, Taha; Wilson, Clyde

    2012-06-01

    Multiple sclerosis (MS) is an autoimmune neurological disorder. The role of 'Acinetobacter' has been examined using the method of Karl Popper and involves nine "Popper sequences". (1) The frequency of MS increases with latitudes in the Northern Hemisphere, and the reverse is found in the Southern Hemisphere. (2) Sinusitis is found frequently at colder latitudes. (3) Sinusitis occurs frequently in patients with MS. (4) Specific sequences of bovine myelin when injected into experimental animals will produce a neurological disorder resembling MS which is called "experimental allergic encephalomyelitis". (5) Computer analysis of myelin shows molecular mimicry with sequences found in Acinetobacter. (6) Antibodies to Acinetobacter bacteria are found in MS patients. (7) Acinetobacter bacteria are located on human skin and in the nasal sinuses. (8) IgA antibodies are preferentially elevated in the sera of MS patients, thereby suggesting the trigger microbe is acting across a mucosal surface probably located in the nasal sinuses. (9) Only Acinetobacter bacteria and no other microbes evoke statistically significant titres of antibodies in MS patients. These nine Popper sequences suggest that MS is most probably caused by infections with Acinetobacter bacteria in the nasal sinuses, and this could have therapeutic implications. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. No counterpart of visual perceptual echoes in the auditory system.

    Directory of Open Access Journals (Sweden)

    Barkın İlhan

    Full Text Available It has been previously demonstrated by our group that a visual stimulus made of dynamically changing luminance evokes an echo or reverberation at ~10 Hz, lasting up to a second. In this study we aimed to reveal whether similar echoes also exist in the auditory modality. A dynamically changing auditory stimulus equivalent to the visual stimulus was designed and employed in two separate series of experiments, and the presence of reverberations was analyzed based on reverse correlations between stimulus sequences and EEG epochs. The first experiment directly compared visual and auditory stimuli: while previous findings of ~10 Hz visual echoes were verified, no similar echo was found in the auditory modality regardless of frequency. In the second experiment, we tested if auditory sequences would influence the visual echoes when they were congruent or incongruent with the visual sequences. However, the results in that case similarly did not reveal any auditory echoes, nor any change in the characteristics of visual echoes as a function of audio-visual congruence. The negative findings from these experiments suggest that brain oscillations do not equivalently affect early sensory processes in the visual and auditory modalities, and that alpha (8-13 Hz oscillations play a special role in vision.

  18. Initial experience in perfusion MR imaging of intracranial major artery occlusion with echo-planar technique

    International Nuclear Information System (INIS)

    Tsuchiya, Kazuhiro; Mizutani, Yoshiyuki; Inaoka, Sayuki; Hachiya, Junichi

    1997-01-01

    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. [Exome sequencing revealed Allan-Herndon-Dudley syndrome underlying multiple disabilities].

    Science.gov (United States)

    Arvio, Maria; Philips, Anju K; Ahvenainen, Minna; Somer, Mirja; Kalscheuer, Vera; Järvelä, Irma

    2014-01-01

    Normal function of the thyroid gland is the cornerstone of a child's mental development and physical growth. We describe a Finnish family, in which the diagnosis of three brothers became clear after investigations that lasted for more than 30 years. Two of the sons have already died. DNA analysis of the third one, a 16-year-old boy, revealed in exome sequencing of the complete X chromosome a mutation in the SLC16A2 gene, i.e. MCT8, coding for a thyroid hormone transport protein. Allan-Herndon-Dudley syndrome was thus shown to be the cause of multiple disabilities.

  20. Observation of Multiple Volume Reflection of Ultrarelativistic Protons by a Sequence of Several Bent Silicon Crystals

    CERN Document Server

    Scandale, Walter; Baricordi, S; Dalpiaz, P; Fiorini, M; Guidi, V; Mazzolari, A; Della Mea, G; Milan, R; Ambrosi, G; Zuccon, P; Bertucci, B; Bürger, W; Duranti, M; Cavoto, G; Santacesaria, R; Valente, P; Luci, C; Iacoangeli, F; Vallazza, E; Afonin, A G; Chesnokov, Yu A; Kotov, V I; Maisheev, V A; Yazynin, I A; Kovalenko, A D; Taratin, A M; Denisov, A S; Gavrikov, Y A; Ivanov, Yu M; Lapina, L P; Malyarenko, L G; Skorogobogatov, V V; Suvorov, V M; Vavilov, S A; Bolognini, D; Hasan, S; Mozzanica, A; Prest, M

    2009-01-01

    The interactions of 400 GeV protons with different sequences of bent silicon crystals have been investigated at the H8 beam line of the CERN Super Proton Synchrotron. The multiple volume reflection of the proton beam has been studied in detail on a five-crystal reflector measuring an angular beam deflection =52.96±0.14 µrad. The efficiency was found larger than 80% for an angular acceptance at the reflector entrance of 70 µrad, with a maximal efficiency value of =0.90±0.01±0.03.

  1. Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci

    Science.gov (United States)

    Chapman, Michael A.; Donaldson, Ian J.; Gilbert, James; Grafham, Darren; Rogers, Jane; Green, Anthony R.; Göttgens, Berthold

    2004-01-01

    Comparative analysis of genomic sequences is becoming a standard technique for studying gene regulation. However, only a limited number of tools are currently available for the analysis of multiple genomic sequences. An extensive data set for the testing and training of such tools is provided by the SCL gene locus. Here we have expanded the data set to eight vertebrate species by sequencing the dog SCL locus and by annotating the dog and rat SCL loci. To provide a resource for the bioinformatics community, all SCL sequences and functional annotations, comprising a collation of the extensive experimental evidence pertaining to SCL regulation, have been made available via a Web server. A Web interface to new tools specifically designed for the display and analysis of multiple sequence alignments was also implemented. The unique SCL data set and new sequence comparison tools allowed us to perform a rigorous examination of the true benefits of multiple sequence comparisons. We demonstrate that multiple sequence alignments are, overall, superior to pairwise alignments for identification of mammalian regulatory regions. In the search for individual transcription factor binding sites, multiple alignments markedly increase the signal-to-noise ratio compared to pairwise alignments. PMID:14718377

  2. Study on multiple-hops performance of MOOC sequences-based optical labels for OPS networks

    Science.gov (United States)

    Zhang, Chongfu; Qiu, Kun; Ma, Chunli

    2009-11-01

    In this paper, we utilize a new study method that is under independent case of multiple optical orthogonal codes to derive the probability function of MOOCS-OPS networks, discuss the performance characteristics for a variety of parameters, and compare some characteristics of the system employed by single optical orthogonal code or multiple optical orthogonal codes sequences-based optical labels. The performance of the system is also calculated, and our results verify that the method is effective. Additionally it is found that performance of MOOCS-OPS networks would, negatively, be worsened, compared with single optical orthogonal code-based optical label for optical packet switching (SOOC-OPS); however, MOOCS-OPS networks can greatly enlarge the scalability of optical packet switching networks.

  3. Assessment of diagnosing metastatic bone tumor on T2*-weighted images. Comparison between turbo spin echo (TSE) method and gradient echo (GE) method

    International Nuclear Information System (INIS)

    Hayashi, Takahiko; Sugiyama, Akira; Katayama, Motoyuki

    1996-01-01

    We examined the usefulness of T2 * weighted gradient field echo images for diagnosis for metastatic bone tumors in comparison with T2 weighted turbo spin echo (fast spin echo) images. In T2 * weighted gradient field echo sequence to obtain maximum contrast-to-noise ratio (CNR), we experimentally manipulated flip angle (FA) (5deg-90deg), repetition time (TR) (400, 700 msec), and echo time (TE) (10-50 msec). The best CNR was 16.4 in fast low angle shot (FLASH) (TE: 24 msec, TR: 700 msec, FA: 40deg). Magnetic resonance imaging was carried out in 28 patients with metastatic bone tumors. In addition to conventional T1 weighted spin echo images, T2 weighted turbo spin echo (fast spin echo images) and T2 * weighted gradient field echo images were obtained. T2 * weighted gradient field echo images were superior to T2 weighted turbo spin echo (fast spin echo) images in delineating the tumors, adjacent fat tissues, and bone marrow. (author)

  4. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  5. Whole exome sequencing reveals concomitant mutations of multiple FA genes in individual Fanconi anemia patients.

    Science.gov (United States)

    Chang, Lixian; Yuan, Weiping; Zeng, Huimin; Zhou, Quanquan; Wei, Wei; Zhou, Jianfeng; Li, Miaomiao; Wang, Xiaomin; Xu, Mingjiang; Yang, Fengchun; Yang, Yungui; Cheng, Tao; Zhu, Xiaofan

    2014-05-15

    Fanconi anemia (FA) is a rare inherited genetic syndrome with highly variable clinical manifestations. Fifteen genetic subtypes of FA have been identified. Traditional complementation tests for grouping studies have been used generally in FA patients and in stepwise methods to identify the FA type, which can result in incomplete genetic information from FA patients. We diagnosed five pediatric patients with FA based on clinical manifestations, and we performed exome sequencing of peripheral blood specimens from these patients and their family members. The related sequencing data were then analyzed by bioinformatics, and the FANC gene mutations identified by exome sequencing were confirmed by PCR re-sequencing. Homozygous and compound heterozygous mutations of FANC genes were identified in all of the patients. The FA subtypes of the patients included FANCA, FANCM and FANCD2. Interestingly, four FA patients harbored multiple mutations in at least two FA genes, and some of these mutations have not been previously reported. These patients' clinical manifestations were vastly different from each other, as were their treatment responses to androstanazol and prednisone. This finding suggests that heterozygous mutation(s) in FA genes could also have diverse biological and/or pathophysiological effects on FA patients or FA gene carriers. Interestingly, we were not able to identify de novo mutations in the genes implicated in DNA repair pathways when the sequencing data of patients were compared with those of their parents. Our results indicate that Chinese FA patients and carriers might have higher and more complex mutation rates in FANC genes than have been conventionally recognized. Testing of the fifteen FANC genes in FA patients and their family members should be a regular clinical practice to determine the optimal care for the individual patient, to counsel the family and to obtain a better understanding of FA pathophysiology.

  6. Quantitative evaluation of benign and malignant vertebral fractures with diffusion-weighted MRI: what is the optimum combination of b values for ADC-based lesion differentiation with the single-shot turbo spin-echo sequence?

    Science.gov (United States)

    Geith, Tobias; Schmidt, Gerwin; Biffar, Andreas; Dietrich, Olaf; Duerr, Hans Roland; Reiser, Maximilian; Baur-Melnyk, Andrea

    2014-09-01

    The purpose of our study was to determine the optimum combination of b values for calculating the apparent diffusion coefficient (ADC) using a diffusion-weighted (DW) single-shot turbo spin-echo (TSE) sequence in the differentiation between acute benign and malignant vertebral body fractures. Twenty-six patients with osteoporotic (mean age, 69 years; range, 31.5-86.2 years) and 20 patients with malignant vertebral fractures (mean age, 63.4 years; range, 24.7-86.4 years) were studied. T1-weighted, STIR, and T2-weighted sequences were acquired at 1.5 T. A DW single-shot TSE sequence at different b values (100, 250, 400, and 600 s/mm(2)) was applied. On the DW images for each evaluated fracture, an ROI was manually adapted to the area of hyperintense signal intensity on STIR-hypointense signal on T1-weighted images. For each ROI, nine different combinations of two, three, and four b values were used to calculate the ADC using a least-squares algorithm. The Student t test and Mann-Whitney U test were used to determine significant differences between benign and malignant fractures. An ROC analysis and the Youden index were used to determine cutoff values for assessment of the highest sensitivity and specificity for the different ADC values. The positive (PPV) and negative predictive values (NPV) were also determined. All calculated ADCs (except the combination of b = 400 s/mm(2) and b = 600 s/mm(2)) showed statistically significant differences between benign and malignant vertebral body fractures, with benign fractures having higher ADCs than malignant ones. The use of higher b values resulted in lower ADCs than those calculated with low b values. The highest AUC (0.85) showed the ADCs calculated with b = 100 and 400 s/mm(2), and the second highest AUC (0.829) showed the ADCs calculated with b = 100, 250, and 400 s/mm(2). The Youden index with equal weight given to sensitivity and specificity suggests use of an ADC calculated with b = 100, 250, and 400 s/mm(2) (cutoff

  7. SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

    Science.gov (United States)

    Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

    2010-07-01

    We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

  8. Maximum-Likelihood Sequence Detection of Multiple Antenna Systems over Dispersive Channels via Sphere Decoding

    Directory of Open Access Journals (Sweden)

    Hassibi Babak

    2002-01-01

    Full Text Available Multiple antenna systems are capable of providing high data rate transmissions over wireless channels. When the channels are dispersive, the signal at each receive antenna is a combination of both the current and past symbols sent from all transmit antennas corrupted by noise. The optimal receiver is a maximum-likelihood sequence detector and is often considered to be practically infeasible due to high computational complexity (exponential in number of antennas and channel memory. Therefore, in practice, one often settles for a less complex suboptimal receiver structure, typically with an equalizer meant to suppress both the intersymbol and interuser interference, followed by the decoder. We propose a sphere decoding for the sequence detection in multiple antenna communication systems over dispersive channels. The sphere decoding provides the maximum-likelihood estimate with computational complexity comparable to the standard space-time decision-feedback equalizing (DFE algorithms. The performance and complexity of the sphere decoding are compared with the DFE algorithm by means of simulations.

  9. An integrated multiple capillary array electrophoresis system for high-throughput DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X.

    1998-03-27

    A capillary array electrophoresis system was chosen to perform DNA sequencing because of several advantages such as rapid heat dissipation, multiplexing capabilities, gel matrix filling simplicity, and the mature nature of the associated manufacturing technologies. There are two major concerns for the multiple capillary systems. One concern is inter-capillary cross-talk, and the other concern is excitation and detection efficiency. Cross-talk is eliminated through proper optical coupling, good focusing and immersing capillary array into index matching fluid. A side-entry excitation scheme with orthogonal detection was established for large capillary array. Two 100 capillary array formats were used for DNA sequencing. One format is cylindrical capillary with 150 {micro}m o.d., 75 {micro}m i.d and the other format is square capillary with 300 {micro}m out edge and 75 {micro}m inner edge. This project is focused on the development of excitation and detection of DNA as well as performing DNA sequencing. The DNA injection schemes are discussed for the cases of single and bundled capillaries. An individual sampling device was designed. The base-calling was performed for a capillary from the capillary array with the accuracy of 98%.

  10. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    Science.gov (United States)

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  11. 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)

    International Nuclear Information System (INIS)

    Kretzschmar, M.; Hainc, N.; Studler, U.; Bieri, O.; Miska, M.; Wiewiorski, M.; Valderrabano, V.

    2015-01-01

    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 2 /ms) was significantly higher compared to normal cartilage (1.46 μm 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.)

  12. 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.)

  13. Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

    Directory of Open Access Journals (Sweden)

    Lee DT

    2007-02-01

    Full Text Available Abstract Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.

  14. Diffusion-weighted echo-planar MRI of lacunar infarcts

    International Nuclear Information System (INIS)

    Noguchi, K.; Nagayoshi, T.; Watanabe, N.; Kanazawa, T.; Toyoshima, S.; Morijiri, M.; Shojaku, H.; Shimizu, M.; Seto, H.

    1998-01-01

    We studied 35 patients with lacunar infarcts, using diffusion-weighted echo-planar imaging (DW-EPI) at 1.5 T. The relative apparent diffusion coefficient ratio (ADCR) of each lesion was calculated and lesion conspicuity on DW-EPI was compared to that on images aquired with fast fluid-attenuated inversion recovery and T2-weighted fast spin-echo sequences. Acute small infarcts (within 3 days) were identified with DW-EPI as an area of decreased ADCR (range 0.33-0.87; mean 0.67) and high signal, subacute small infarcts (4-30 days) as a high-signal or isointense areas of decreased or nearly normal ADCR (0.54-0.98; 0.73), and chronic small infarcts (> 30 days) as low- or high-signal areas of nearly normal or increased ADCR (0.97-1.92; 1.32). In three patients, small infarcts of the brain stem in the hyperacute phase (within 6 h) were seen only with DW-EPI. In five patients, fresh small infarcts adjacent to multiple old infarcts could be distinguished only with DW-EPI. (orig.)

  15. ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kim Taeho

    2010-09-01

    Full Text Available Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA. The new editing option and the graphical user interface (GUI provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1 the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2 Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3 Support for both single PC and distributed cluster systems.

  16. Whole brain, high resolution multiband spin-echo EPI fMRI at 7 T: A comparison with gradient-echo EPI using a color-word Stroop task

    NARCIS (Netherlands)

    Boyacioglu, R.; Schulz, J.; Müller, N.C.J.; Koopmans, P.J.; Barth, M.; Norris, David Gordon

    2014-01-01

    A whole brain, multiband spin-echo (SE) echo planar imaging (EPI) sequence employing a high spatial (1.5 mm isotropic) and temporal (TR of 2 s) resolution was implemented at 7 T. Its overall performance (tSNR, sensitivity and CNR) was assessed and compared to a geometrically matched gradient-echo

  17. Computer experiments of the time-sequence of individual steps in multiple Coulomb-excitation

    International Nuclear Information System (INIS)

    Boer, J. de; Dannhaueser, G.

    1982-01-01

    The way in which the multiple E2 steps in the Coulomb-excitation of a rotational band of a nucleus follow one another is elucidated for selected examples using semiclassical computer experiments. The role a given transition plays for the excitation of a given final state is measured by a quantity named ''importance function''. It is found that these functions, calculated for the highest rotational state, peak at times forming a sequence for the successive E2 transitions starting from the ground state. This sequential behaviour is used to approximately account for the effects on the projectile orbit of the sequential transfer of excitation energy and angular momentum from projectile to target. These orbits lead to similar deflection functions and cross sections as those obtained from a symmetrization procedure approximately accounting for the transfer of angular momentum and energy. (Auth.)

  18. ON THE MULTIPLICITY OF THE ZERO-AGE MAIN-SEQUENCE O STAR HERSCHEL 36

    International Nuclear Information System (INIS)

    Arias, Julia I.; Barba, Rodolfo H.; Gamen, Roberto C.; Morrell, Nidia I.; Apellaniz, Jesus MaIz; Alfaro, Emilio J.; Sota, Alfredo; Walborn, Nolan R.; Bidin, Christian Moni

    2010-01-01

    We present the analysis of high-resolution optical spectroscopic observations of the zero-age main-sequence O star Herschel 36 spanning six years. This star is definitely a multiple system, with at least three components detected in its spectrum. Based on our radial-velocity (RV) study, we propose a picture of a close massive binary and a more distant companion, most probably in wide orbit about each other. The orbital solution for the binary, whose components we identify as O9 V and B0.5 V, is characterized by a period of 1.5415 ± 0.0006 days. With a spectral type O7.5 V, the third body is the most luminous component of the system and also presents RV variations with a period close to 498 days. Some possible hypotheses to explain the variability are briefly addressed and further observations are suggested.

  19. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

    Science.gov (United States)

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-07-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Sequence-specific electrochemical recognition of multiple species using nanoparticle labels

    International Nuclear Information System (INIS)

    Cai Hong; Shang, Chii; Hsing, I.-Ming

    2004-01-01

    In this work, we report an electrochemical methodology that enables the rapid identification of different DNA sequences on the microfabricated electrodes. Our approach starts with an electropolymerization process on a patterned indium tin oxide (ITO)-coated glass electrode, followed by a selective immobilization of biotin-tagged probes on individually addressable spots via the biotin-streptavidin linkage. An exemplary target mixture containing E. coli and Stachybotrys Chartarum, an airborne pathogen, is then introduced. Recognition of the DNA hybridization event of the immobilized probes with the target pathogen PCR products or synthetic oligonucleotides is achieved by a novel electrochemistry-based technique utilizing the preferential catalytic silver electrodeposition process on the DNA-linked nanogold shells. The ability to selectively immobilize different oligonucleotide probes together with a sensitive electrochemistry-based detection for multiple species, as demonstrated in this study, is an important step forward for the realization of a portable bioanalytical microdevice for the rapid detection of pathogens

  1. A Next-Generation Sequencing Strategy for Evaluating the Most Common Genetic Abnormalities in Multiple Myeloma.

    Science.gov (United States)

    Jiménez, Cristina; Jara-Acevedo, María; Corchete, Luis A; Castillo, David; Ordóñez, Gonzalo R; Sarasquete, María E; Puig, Noemí; Martínez-López, Joaquín; Prieto-Conde, María I; García-Álvarez, María; Chillón, María C; Balanzategui, Ana; Alcoceba, Miguel; Oriol, Albert; Rosiñol, Laura; Palomera, Luis; Teruel, Ana I; Lahuerta, Juan J; Bladé, Joan; Mateos, María V; Orfão, Alberto; San Miguel, Jesús F; González, Marcos; Gutiérrez, Norma C; García-Sanz, Ramón

    2017-01-01

    Identification and characterization of genetic alterations are essential for diagnosis of multiple myeloma and may guide therapeutic decisions. Currently, genomic analysis of myeloma to cover the diverse range of alterations with prognostic impact requires fluorescence in situ hybridization (FISH), single nucleotide polymorphism arrays, and sequencing techniques, which are costly and labor intensive and require large numbers of plasma cells. To overcome these limitations, we designed a targeted-capture next-generation sequencing approach for one-step identification of IGH translocations, V(D)J clonal rearrangements, the IgH isotype, and somatic mutations to rapidly identify risk groups and specific targetable molecular lesions. Forty-eight newly diagnosed myeloma patients were tested with the panel, which included IGH and six genes that are recurrently mutated in myeloma: NRAS, KRAS, HRAS, TP53, MYC, and BRAF. We identified 14 of 17 IGH translocations previously detected by FISH and three confirmed translocations not detected by FISH, with the additional advantage of breakpoint identification, which can be used as a target for evaluating minimal residual disease. IgH subclass and V(D)J rearrangements were identified in 77% and 65% of patients, respectively. Mutation analysis revealed the presence of missense protein-coding alterations in at least one of the evaluating genes in 16 of 48 patients (33%). This method may represent a time- and cost-effective diagnostic method for the molecular characterization of multiple myeloma. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  2. Liver iron content determined by MRI. Spin-echo vs. gradient-echo

    Energy Technology Data Exchange (ETDEWEB)

    Juchems, M.S.; Wunderlich, A.P. [Universitaetskliniken Ulm (Germany). Klinik fuer Diagnostische und Interventionelle Radiologie; Cario, H. [Universitaetskliniken Ulm (Germany). Klinik fuer Kinder- und Jugendmedizin; Schmid, M. [Stadtspital Triemli, Zuerich (Switzerland). Medizinische Onkologie und Haematologie

    2012-05-15

    Purpose: Liver iron content (LIC) measurement plays a central role in the management of patients with transfusional iron overload. Calculating the LIC with data obtained from standardized MRI sequences represents an attractive alternative diagnostic possibility. The purpose of this study was to compare the LIC measurement obtained with gradient-echo (GRE) sequences to the mean liver proton transverse relaxation (R2) acquired with SE sequences. Materials and Methods: 68 patients with iron overload (median age: 24, range: 3 - 88) underwent 1.5 T MRI for liver iron content measurement. All patients received spin-echo (SE) and gradient-echo (GRE) sequences. Results: The two MRI methods revealed different liver iron content results although a significant correlation was found (r = 0.85, p < 0.001). Values evaluated using GRE sequences (median: 260 {mu}mol/g dry weight [d.w.], range: 6 - 732) were generally higher than those obtained by SE examinations (median: 161 {mu}mol /g d.w., range: 5 - 830). Conclusion: In conclusion, our study revealed different results for both MRI measurements, which could lead to different decisions concerning the management of chelation therapy in individual patients. (orig.)

  3. EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression.

    Science.gov (United States)

    Lian, Yao; Ge, Meng; Pan, Xian-Ming

    2014-12-19

    B-cell epitopes have been studied extensively due to their immunological applications, such as peptide-based vaccine development, antibody production, and disease diagnosis and therapy. Despite several decades of research, the accurate prediction of linear B-cell epitopes has remained a challenging task. In this work, based on the antigen's primary sequence information, a novel linear B-cell epitope prediction model was developed using the multiple linear regression (MLR). A 10-fold cross-validation test on a large non-redundant dataset was performed to evaluate the performance of our model. To alleviate the problem caused by the noise of negative dataset, 300 experiments utilizing 300 sub-datasets were performed. We achieved overall sensitivity of 81.8%, precision of 64.1% and area under the receiver operating characteristic curve (AUC) of 0.728. We have presented a reliable method for the identification of linear B cell epitope using antigen's primary sequence information. Moreover, a web server EPMLR has been developed for linear B-cell epitope prediction: http://www.bioinfo.tsinghua.edu.cn/epitope/EPMLR/ .

  4. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Sadreyev Ruslan I

    2004-08-01

    Full Text Available Abstract Background Profile-based analysis of multiple sequence alignments (MSA allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1 MSA position and a set of predicted residue frequencies, and (2 between two MSA positions. These problems are important for (i evaluation and optimization of methods predicting residue occurrence at protein positions; (ii detection of potentially misaligned regions in automatically produced alignments and their further refinement; and (iii detection of sites that determine functional or structural specificity in two related families. Results For problems (1 and (2, we propose analytical estimates of P-value and apply them to the detection of significant positional dissimilarities in various experimental situations. (a We compare structure-based predictions of residue propensities at a protein position to the actual residue frequencies in the MSA of homologs. (b We evaluate our method by the ability to detect erroneous position matches produced by an automatic sequence aligner. (c We compare MSA positions that correspond to residues aligned by automatic structure aligners. (d We compare MSA positions that are aligned by high-quality manual superposition of structures. Detected dissimilarities reveal shortcomings of the automatic methods for residue frequency prediction and alignment construction. For the high-quality structural alignments, the dissimilarities suggest sites of potential functional or structural importance. Conclusion The proposed computational method is of significant potential value for the analysis of protein families.

  5. Phylogenetic Relationships of Pseudorasbora, Pseudopungtungia, and Pungtungia (Teleostei; Cypriniformes; Gobioninae Inferred from Multiple Nuclear Gene Sequences

    Directory of Open Access Journals (Sweden)

    Keun-Yong Kim

    2013-01-01

    Full Text Available Gobionine species belonging to the genera Pseudorasbora, Pseudopungtungia, and Pungtungia (Teleostei; Cypriniformes; Cyprinidae have been heavily studied because of problems on taxonomy, threats of extinction, invasion, and human health. Nucleotide sequences of three nuclear genes, that is, recombination activating protein gene 1 (rag1, recombination activating gene 2 (rag2, and early growth response 1 gene (egr1, from Pseudorasbora, Pseudopungtungia, and Pungtungia species residing in China, Japan, and Korea, were analyzed to elucidate their intergeneric and interspecific phylogenetic relationships. In the phylogenetic tree inferred from their multiple gene sequences, Pseudorasbora, Pseudopungtungia and Pungtungia species ramified into three phylogenetically distinct clades; the “tenuicorpa” clade composed of Pseudopungtungia tenuicorpa, the “parva” clade composed of all Pseudorasbora species/subspecies, and the “herzi” clade composed of Pseudopungtungia nigra, and Pungtungia herzi. The genus Pseudorasbora was recovered as monophyletic, while the genus Pseudopungtungia was recovered as polyphyletic. Our phylogenetic result implies the unstable taxonomic status of the genus Pseudopungtungia.

  6. Multiple ECG Fiducial Points-Based Random Binary Sequence Generation for Securing Wireless Body Area Networks.

    Science.gov (United States)

    Zheng, Guanglou; Fang, Gengfa; Shankaran, Rajan; Orgun, Mehmet A; Zhou, Jie; Qiao, Li; Saleem, Kashif

    2017-05-01

    Generating random binary sequences (BSes) is a fundamental requirement in cryptography. A BS is a sequence of N bits, and each bit has a value of 0 or 1. For securing sensors within wireless body area networks (WBANs), electrocardiogram (ECG)-based BS generation methods have been widely investigated in which interpulse intervals (IPIs) from each heartbeat cycle are processed to produce BSes. Using these IPI-based methods to generate a 128-bit BS in real time normally takes around half a minute. In order to improve the time efficiency of such methods, this paper presents an ECG multiple fiducial-points based binary sequence generation (MFBSG) algorithm. The technique of discrete wavelet transforms is employed to detect arrival time of these fiducial points, such as P, Q, R, S, and T peaks. Time intervals between them, including RR, RQ, RS, RP, and RT intervals, are then calculated based on this arrival time, and are used as ECG features to generate random BSes with low latency. According to our analysis on real ECG data, these ECG feature values exhibit the property of randomness and, thus, can be utilized to generate random BSes. Compared with the schemes that solely rely on IPIs to generate BSes, this MFBSG algorithm uses five feature values from one heart beat cycle, and can be up to five times faster than the solely IPI-based methods. So, it achieves a design goal of low latency. According to our analysis, the complexity of the algorithm is comparable to that of fast Fourier transforms. These randomly generated ECG BSes can be used as security keys for encryption or authentication in a WBAN system.

  7. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

    KAUST Repository

    Wong, Ka-Chun; Peng, Chengbin; Li, Yue

    2015-01-01

    With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene's function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

  8. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

    KAUST Repository

    Wong, Ka-Chun

    2015-04-20

    With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene\\'s function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins\\' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

  9. THE MULTIPLE PRE-MAIN-SEQUENCE SYSTEM HBC 515 IN L1622

    International Nuclear Information System (INIS)

    Reipurth, Bo; Aspin, Colin; Herbig, George

    2010-01-01

    The bright pre-main-sequence star HBC 515 (HD 288313) located in the L1622 cometary cloud in Orion has been studied extensively with optical/infrared imaging and ultraviolet/optical/infrared spectroscopy. The spectra indicate that HBC 515 is a weakline T Tauri star (TTS) of spectral type K2V. Adaptive optics imaging in the K band reveals that HBC 515 is a binary with two equally bright components separated by 0.''5. A very faint third component is found 5'' to the northwest. Spitzer IRAC and MIPS observations show that at mid-infrared wavelengths this third source dominates the system, suggesting that it is a protostar still embedded in the nascent cloud of HBC 515. The close association of a weakline TTS with a newborn protostar in a multiple system is noteworthy. Two nearby TTSs are likely associated with the HBC 515 multiple system, and the dynamical evolution of the complex that would lead to such a configuration is considered.

  10. OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

    Directory of Open Access Journals (Sweden)

    Searle Stephen MJ

    2003-10-01

    Full Text Available Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. Results The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with http://www.compbio.dundee.ac.uk. Conclusions The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94

  11. Improved sensitivity and specificity for resting state and task fMRI with multiband multi-echo EPI compared to multi-echo EPI at 7T.

    NARCIS (Netherlands)

    Boyacioglu, R.; Schulz, J.; Koopmans, P.J.; Barth, M.; Norris, David Gordon

    2015-01-01

    A multiband multi-echo (MBME) sequence is implemented and compared to a matched standard multi-echo (ME) protocol to investigate the potential improvement in sensitivity and spatial specificity at 7 T for resting state and task fMRI. ME acquisition is attractive because BOLD sensitivity is less

  12. CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION

    Directory of Open Access Journals (Sweden)

    Nikolaos Alachiotis

    2013-03-01

    Full Text Available Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG, an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

  13. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

    Science.gov (United States)

    Wan, Shixiang; Zou, Quan

    2017-01-01

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

  14. 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.

  15. Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

    OpenAIRE

    Deakin, Gregory; Dobbs, Edward; Bennett, Julie M.; Jones, Ian M.; Grogan, Helen M.; Burton, Kerry S.

    2017-01-01

    Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3′ motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interact...

  16. Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

    Science.gov (United States)

    Bernsen, M R; Dijkman, H B; de Vries, E; Figdor, C G; Ruiter, D J; Adema, G J; van Muijen, G N

    1998-10-01

    Molecular analysis of small tissue samples has become increasingly important in biomedical studies. Using a laser dissection microscope and modified nucleic acid isolation protocols, we demonstrate that multiple mRNA as well as DNA sequences can be identified from a single-cell sample. In addition, we show that the specificity of procurement of tissue samples is not compromised by smear contamination resulting from scraping of the microtome knife during sectioning of lesions. The procedures described herein thus allow for efficient RT-PCR or PCR analysis of multiple nucleic acid sequences from small tissue samples obtained by laser-assisted microdissection.

  17. Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Jyh-Da Wei

    2017-08-01

    Full Text Available High-end graphics processing units (GPUs, such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1, which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs. Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform. Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

  18. Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments.

    Science.gov (United States)

    Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

    2017-01-01

    High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

  19. 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.)

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

    Science.gov (United States)

    Juras, Vladimir; Bohndorf, Klaus; Heule, Rahel; Kronnerwetter, Claudia; Szomolanyi, Pavol; Hager, Benedikt; Bieri, Oliver; Zbyn, Stefan; Trattnig, Siegfried

    2016-06-01

    To assess the clinical relevance of T2 relaxation times, measured by 3D triple-echo steady-state (3D-TESS), in knee articular cartilage compared to conventional multi-echo spin-echo T2-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 T2 mapping, and 3D TESS with the same geometry settings, but variable acquisition times: standard (TESSs 4:35min) and quick (TESSq 2:05min). T2 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 T2 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 B1 and B0 changes. • 3D-TESS T 2 mapping provides clinically comparable results to CPMG in shorter scan-time. • Clinical and investigational studies may benefit from high temporal resolution of 3D-TESS. • 3D-TESS T 2 values are able to differentiate between healthy and damaged cartilage.

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

    International Nuclear Information System (INIS)

    Juras, Vladimir; Szomolanyi, Pavol; Bohndorf, Klaus; Kronnerwetter, Claudia; Hager, Benedikt; Zbyn, Stefan; Heule, Rahel; Bieri, Oliver; Trattnig, Siegfried

    2016-01-01

    To assess the clinical relevance of T 2 relaxation times, measured by 3D triple-echo steady-state (3D-TESS), in knee articular cartilage compared to conventional multi-echo spin-echo T 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 2 mapping, and 3D TESS with the same geometry settings, but variable acquisition times: standard (TESSs 4:35min) and quick (TESSq 2:05min). T 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 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 1 and B 0 changes. (orig.)

  2. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  3. GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Kedzierska Anna M

    2012-08-01

    Full Text Available Abstract Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages. Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site, the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

  4. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

    2015-07-08

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

  5. MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

    Science.gov (United States)

    González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

    2016-12-15

    MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Light chain deposition disease in multiple myeloma: MR imaging features correlated with histopathological findings

    International Nuclear Information System (INIS)

    Baur, A.; Staebler, A.; Reiser, M.; Lamerz, R.; Bartl, R.

    1998-01-01

    The clinical, histopathological, and imaging findings on MRI of a 56-year-old woman with light chain deposition disease occurring in multiple myeloma are presented. Light chain deposition disease is a variant of multiple myeloma with distinct clinical and histological characteristics. MRI of this patient also revealed an infiltration pattern in the bone marrow distinct from that of typical multiple myeloma. Multiple small foci of low signal intensity were present on T1- and T2-weighted spin echo and STIR images, corresponding to conglomerates of light chains in bone marrow biopsy. Contrast-enhanced T1-weighted spin echo images show diffuse enhancement of 51% over all vertebral bodies, with a minor enhancement of the focal conglomerates of light chains. Light chain deposition disease in multiple myeloma should be added to the list of those few entities with normal radiographs and discrete low-signal marrow lesions on T1- and T2-weighted spin echo pulse sequences. (orig.)

  7. Formation of a Multiple Protein Complex on the Adenovirus Packaging Sequence by the IVa2 Protein▿

    OpenAIRE

    Tyler, Ryan E.; Ewing, Sean G.; Imperiale, Michael J.

    2007-01-01

    During adenovirus virion assembly, the packaging sequence mediates the encapsidation of the viral genome. This sequence is composed of seven functional units, termed A repeats. Recent evidence suggests that the adenovirus IVa2 protein binds the packaging sequence and is involved in packaging of the genome. Study of the IVa2-packaging sequence interaction has been hindered by difficulty in purifying the protein produced in virus-infected cells or by recombinant techniques. We report the first ...

  8. Pseudo-random Trees: Multiple Independent Sequence Generators for Parallel and Branching Computations

    Science.gov (United States)

    Halton, John H.

    1989-09-01

    A class of families of linear congruential pseudo-random sequences is defined, for which it is possible to branch at any event without changing the sequence of random numbers used in the original random walk and for which the sequences in different branches show properties analogous to mutual statistical independence. This is a hitherto unavailable, and computationally desirable, tool.

  9. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  10. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

    Science.gov (United States)

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

  11. Molecular diagnostics of a single drug-resistant multiple myeloma case using targeted next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Ikeda H

    2015-10-01

    Full Text Available Hiroshi Ikeda,1 Kazuya Ishiguro,1 Tetsuyuki Igarashi,1 Yuka Aoki,1 Toshiaki Hayashi,1 Tadao Ishida,1 Yasushi Sasaki,1,2 Takashi Tokino,2 Yasuhisa Shinomura1 1Department of Gastroenterology, Rheumatology and Clinical Immunology, 2Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan Abstract: A 69-year-old man was diagnosed with IgG λ-type multiple myeloma (MM, Stage II in October 2010. He was treated with one cycle of high-dose dexamethasone. After three cycles of bortezomib, the patient exhibited slow elevations in the free light-chain levels and developed a significant new increase of serum M protein. Bone marrow cytogenetic analysis revealed a complex karyotype characteristic of malignant plasma cells. To better understand the molecular pathogenesis of this patient, we sequenced for mutations in the entire coding regions of 409 cancer-related genes using a semiconductor-based sequencing platform. Sequencing analysis revealed eight nonsynonymous somatic mutations in addition to several copy number variants, including CCND1 and RB1. These alterations may play roles in the pathobiology of this disease. This targeted next-generation sequencing can allow for the prediction of drug resistance and facilitate improvements in the treatment of MM patients. Keywords: multiple myeloma, drug resistance, genome-wide sequencing, semiconductor sequencer, target therapy

  12. Detection of generalized synchronization using echo state networks

    Science.gov (United States)

    Ibáñez-Soria, D.; Garcia-Ojalvo, J.; Soria-Frisch, A.; Ruffini, G.

    2018-03-01

    Generalized synchronization between coupled dynamical systems is a phenomenon of relevance in applications that range from secure communications to physiological modelling. Here, we test the capabilities of reservoir computing and, in particular, echo state networks for the detection of generalized synchronization. A nonlinear dynamical system consisting of two coupled Rössler chaotic attractors is used to generate temporal series consisting of time-locked generalized synchronized sequences interleaved with unsynchronized ones. Correctly tuned, echo state networks are able to efficiently discriminate between unsynchronized and synchronized sequences even in the presence of relatively high levels of noise. Compared to other state-of-the-art techniques of synchronization detection, the online capabilities of the proposed Echo State Network based methodology make it a promising choice for real-time applications aiming to monitor dynamical synchronization changes in continuous signals.

  13. Help Content for ECHO Reports | 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.

  14. ECHO-UseFY17.png | 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.

  15. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

    DEFF Research Database (Denmark)

    Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam

    2013-01-01

    Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced metageno......Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced...

  16. A 135-kilodalton surface antigen of Mycoplasma hominis PG21 contains multiple directly repeated sequences

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Birkelund, Svend; Hauge, S

    1995-01-01

    gene was sequenced, and its gene product was characterized with the goal of elucidating the structure and function of Lmp1. A total of 7,196 bp in the lmp1 region was sequenced. An open reading frame of 4,032 bp, encoding a protein of 1,344 amino acids with a calculated molecular weight of 147...

  17. Multiple Teaching Approaches, Teaching Sequence and Concept Retention in High School Physics Education

    Science.gov (United States)

    Fogarty, Ian; Geelan, David

    2013-01-01

    Students in 4 Canadian high school physics classes completed instructional sequences in two key physics topics related to motion--Straight Line Motion and Newton's First Law. Different sequences of laboratory investigation, teacher explanation (lecture) and the use of computer-based scientific visualizations (animations and simulations) were…

  18. Custom 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.

  19. Watershed Statistics | 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.

  20. Three-dimensional T1 and T2* mapping of human lung parenchyma using interleaved saturation recovery with dual echo ultrashort echo time imaging (ITSR-DUTE).

    Science.gov (United States)

    Gai, Neville D; Malayeri, Ashkan A; Bluemke, David A

    2017-04-01

    To develop and assess a new technique for three-dimensional (3D) full lung T1 and T2* mapping using a single free breathing scan during a clinically feasible time. A 3D stack of dual-echo ultrashort echo time (UTE) radial acquisition interleaved with and without a WET (water suppression enhanced through T1 effects) saturation pulse was used to map T1 and T2* simultaneously in a single scan. Correction for modulation due to multiple views per segment was derived. Bloch simulations were performed to study saturation pulse excitation profile on lung tissue. Optimization of the saturation delay time (for T1 mapping) and echo time (for T2* mapping) was performed. Monte Carlo simulation was done to predict accuracy and precision of the sequence with signal-to-noise ratio of in vivo images used in the simulation. A phantom study was carried out using the 3D interleaved saturation recovery with dual echo ultrashort echo time imaging (ITSR-DUTE) sequence and reference standard inversion recovery spin echo sequence (IR-SE) to compare accuracy of the sequence. Nine healthy volunteers were imaged and mean (SD) of T1 and T2* in lung parenchyma at 3T were estimated through manually assisted segmentation. 3D lung coverage with a resolution of 2.5 × 2.5 × 6 mm 3 was performed and nominal scan time was recorded for the scans. Repeatability was assessed in three of the volunteers. Regional differences in T1/T2* values were also assessed. The phantom study showed accuracy of T1 values to be within 2.3% of values obtained from IR-SE. Mean T1 value in lung parenchyma was 1002 ± 82 ms while T2* was 0.85 ± 0.1 ms. Scan time was ∼10 min for volunteer scans. Mean coefficient of variation (CV) across slices was 0.057 and 0.09, respectively. Regional variation along the gravitational direction and between right and left lung were not significant (P = 0.25 and P = 0.06, respectively) for T1. T2* showed significant variation (P = 0.03) along the

  1. MR imaging studies of multiple myeloma in the vertebral column

    International Nuclear Information System (INIS)

    Albert, S.; Leeds, N.E.

    1990-01-01

    This paper studies the sensitivity and characteristics of MR imaging in the diagnosis of myeloma in the vertebral column. The cervical, thoracic, and lumbar spines of 12 patients with known multiple myeloma were imaged with small flip angle, fast gradient-echo, proton-density (FPD) as well as spin-echo T1-weighted, T2-weighted, and intermediate (SE 2,000/20-30) imaging. The FPD images were acquired with pulse sequence gradient recalled acquisition in a steady state at a magnetic field strength of 1.5T with use of a license-plate and a circular surface coil

  2. Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system.

    Science.gov (United States)

    Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

    2007-02-01

    We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

  3. Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system

    Science.gov (United States)

    Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

    2007-02-01

    We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

  4. Learning multiple variable-speed sequences in striatum via cortical tutoring.

    Science.gov (United States)

    Murray, James M; Escola, G Sean

    2017-05-08

    Sparse, sequential patterns of neural activity have been observed in numerous brain areas during timekeeping and motor sequence tasks. Inspired by such observations, we construct a model of the striatum, an all-inhibitory circuit where sequential activity patterns are prominent, addressing the following key challenges: (i) obtaining control over temporal rescaling of the sequence speed, with the ability to generalize to new speeds; (ii) facilitating flexible expression of distinct sequences via selective activation, concatenation, and recycling of specific subsequences; and (iii) enabling the biologically plausible learning of sequences, consistent with the decoupling of learning and execution suggested by lesion studies showing that cortical circuits are necessary for learning, but that subcortical circuits are sufficient to drive learned behaviors. The same mechanisms that we describe can also be applied to circuits with both excitatory and inhibitory populations, and hence may underlie general features of sequential neural activity pattern generation in the brain.

  5. Realtime identification of the propagation direction of received echoes in long range ultrasonic testing

    International Nuclear Information System (INIS)

    Choi, Myoung Seon; Heo, Won Nyoung

    2013-01-01

    In long range ultrasonic testing, a phased array probe composed of multiple identical transducers with an uniform interval of one quarter wavelength is usually used for the transmission or reception directivity control. This paper shows that the propagation directions of individual echoes can be identified in real time by displaying the inputs of a process for summing the constitution reception signals after compensating the phase difference due to the transducer interval, together with the output of the process. A constructive interference of the constitution echoes indicates a forward direction echo propagating along an intended direction while a destructive interference implies a reverse direction echo propagating along the direction opposite to the intended one

  6. Spin-echo Echo-planar Imaging MR Elastography versus Gradient-echo MR Elastography for Assessment of Liver Stiffness in Children and Young Adults Suspected of Having Liver Disease.

    Science.gov (United States)

    Serai, Suraj D; Dillman, Jonathan R; Trout, Andrew T

    2017-03-01

    Purpose To compare two-dimensional (2D) gradient-recalled echo (GRE) and 2D spin-echo (SE) echo-planar imaging (EPI) magnetic resonance (MR) elastography for measurement of hepatic stiffness in pediatric and young adult patients suspected of having liver disease. Materials and Methods In this institutional review board-approved, HIPAA-compliant study, 58 patients underwent both 2D GRE and 2D SE-EPI MR elastography at 1.5 T during separate breath holds. Liver stiffness (mean of means; in kilopascals) was measured by five blinded reviewers. Pooled mean liver stiffness and region-of-interest (ROI) size were compared by using paired t tests. Intraclass correlation coefficients (ICCs) were used to assess agreement between techniques. Respiratory motion artifacts were compared across sequences by using the Fisher exact test. Results Mean patient age was 14.7 years ± 5.2 (standard deviation; age range, 0.7-20.5 years), and 55.2% (32 of 58) of patients were male. Mean liver stiffness was 2.92 kPa ± 1.29 measured at GRE MR elastography and 2.76 kPa ± 1.39 at SE-EPI MR elastography (n = 290; P = .15). Mean ROI sizes were 8495 mm 2 ± 4482 for 2D GRE MR elastography and 15 176 mm 2 ± 7609 for 2D SE-EPI MR elastography (n = 290; P range, 0.91-0.95). Moderate or severe breathing artifacts were observed on 27.5% (16 of 58) of 2D GRE images versus 0% 2D SE-EPI images (P < .001). Conclusion There is excellent agreement on measured hepatic stiffness between 2D GRE and 2D SE-EPI MR elastography across multiple reviewers. SE-EPI MR elastography allowed for stiffness measurement across larger areas of the liver and can be performed in a single breath hold. © RSNA, 2016.

  7. Echoes of China.

    Science.gov (United States)

    Chang, Pei-lan Li; Chao, Johanna T.; Chao, Yenshew Lynn; Chin, Ai-li S.; Hsieh, Charlotte Sheau-mann; Sun, Paul P.; Swartz, Leslie M.; Wang, Theresa; Wu, Fa Y.

    This curriculum guide is developed to accompany 7 Chinese Cultural Heritage kits for use in intermediate and middle school classrooms. The units in this guide may be used with or without the accompanying kits. When appropriate, units include: objectives, introductory information, suggested presentation sequence, activity instruction, evaluation…

  8. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

    Science.gov (United States)

    Kangaspeska, Sara; Hultsch, Susanne; Edgren, Henrik; Nicorici, Daniel; Murumägi, Astrid; Kallioniemi, Olli

    2012-01-01

    RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

  9. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

    Directory of Open Access Journals (Sweden)

    Sara Kangaspeska

    Full Text Available RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60% of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

  10. Practical and Scalable Transmission of Segmented Video Sequences to Multiple Players Using H.264

    Science.gov (United States)

    Quax, Peter; di Fiore, Fabian; Issaris, Panagiotis; Lamotte, Wim; van Reeth, Frank

    We present a practical way to distribute viewports on the same video sequence to large amounts of players. Each of them has personal preferences to be met or is limited by the physical properties of his/her device (e.g., screen size of a PDA or processing power of a mobile phone). Instead of taking the naïve approach, in which sections of the video sequence are decoded and re-encoded for each of the clients, we have exploited advanced features offered by the H.264 codec to enable selection of parts of the video sequence by directly manipulating the encoder-generated bitstream. At the same time, we have overcome several practical issues presented by the fact that support for these features is sadly lacking from the state-of-the-art encoders available on the market. Two alternative solutions are discussed and have been implemented, enabling the generation of measurement results and comparison to alternative approaches.

  11. The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques.

    Science.gov (United States)

    Farshidfar, Z; Faeghi, F; Haghighatkhah, H R; Abdolmohammadi, J

    2017-09-01

    Magnetic resonance imaging (MRI) is the most sensitive technique to detect multiple sclerosis (MS) plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don't have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR) by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

  12. A spin echo study of A15 intermetallic compounds

    International Nuclear Information System (INIS)

    Schoep, G.K.

    1976-01-01

    This thesis mainly concerns the measurement of spin-lattice relaxation times in intermetallic compounds of the bcc lattice structure, having the formula V 3 X (C = Pt, Ir, Os, Pd, Rh, Ni, Co, Au). When, in a spin echo experiment, a two-pulse sequence was applied, several quadrupolar echoes were observed. Special attention is given to the 'forbidden' echoes (absol.(Δm')GT1) in V 3 Au and V 3 Co. In relation to the V 3 X compounds, several characteristics are discussed including temperature dependence and concentration dependence of spin relaxation times, superconductivity and the importance of d-state electrons in determination of the spin relaxation times. Finally, the above characteristics were determined for 6 different samples of the vanadium-gold alloy, V 3 Au, specifically

  13. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

    DEFF Research Database (Denmark)

    Hellmann, Ines; Mang, Yuan; Gu, Zhiping

    2008-01-01

    We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate...... for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show...

  14. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

    Directory of Open Access Journals (Sweden)

    Robin Charles

    2011-03-01

    Full Text Available Abstract Background Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. Results Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability. We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at Conclusions Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among

  15. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

    International Nuclear Information System (INIS)

    Mango, Victoria L.; Morris, Elizabeth A.; David Dershaw, D.; Abramson, Andrea; Fry, Charles; Moskowitz, Chaya S.; Hughes, Mary; Kaplan, Jennifer; Jochelson, Maxine S.

    2015-01-01

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  16. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

    Energy Technology Data Exchange (ETDEWEB)

    Mango, Victoria L., E-mail: vlm2125@columbia.edu [Columbia University Medical Center, Herbert Irving Pavilion, 161 Fort Washington Avenue, 10th Floor, New York, NY 10032 (United States); Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Morris, Elizabeth A., E-mail: morrise@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); David Dershaw, D., E-mail: dershawd@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Abramson, Andrea, E-mail: abramsoa@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Fry, Charles, E-mail: charles_fry@nymc.edu [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); New York Medical College, 40 Sunshine Cottage Rd, Valhalla, NY 10595 (United States); Moskowitz, Chaya S. [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Hughes, Mary, E-mail: hughesm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Kaplan, Jennifer, E-mail: kaplanj@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Jochelson, Maxine S., E-mail: jochelsm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States)

    2015-01-15

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  17. Echo phenomena in a plasma

    International Nuclear Information System (INIS)

    Pavlenko, V.N.

    1983-01-01

    The mechanism of echo phenomenon in different plasma media: laboratory and cosmic plasma, metals and semiconductors is analyzed to get a more comprehensive idea on collective processes in a plasma and for practical applications in radiophysics and plasma diagnostics. The echo phenomenon permitted to confirm a reversible nature of the Landau damping, to prove the fact that the information on perturbation is conserved in a plasma (as non-damping oscillations of the distribution function) even after disappearing of the macroscopic field. The dependence of the diffusion coefficient on the velocity is measured, microturbulences in a plasma are investigated. New ways of the plasma wave conversion are suggested, as well as ''lightning'' of super-critical plasma layers and regions of plasma non-transparency. Prospective advantages of using echo for studying the mechanisms of charged particle interaction with the surface bounding a plasma are revealed

  18. Ultrafast bold fMRI using single-shot spin-echo echo planar imaging

    Directory of Open Access Journals (Sweden)

    Boujraf Said

    2009-01-01

    Full Text Available The choice of imaging parameters for functional MRI can have an impact on the accuracy of functional localization by affecting the image quality and the degree of blood oxygenation-dependent (BOLD contrast achieved. By improving sampling efficiency, parallel acquisition techniques such as sensitivity encoding (SENSE have been used to shorten readout trains in single-shot (SS echo planar imaging (EPI. This has been applied to susceptibility artifact reduction and improving spatial resolution. SENSE together with single-shot spin-echo (SS-SE imaging may also reduce off-resonance artifacts. The goal of this work was to investigate the BOLD response of a SENSE-adapted SE-EPI on a three Tesla scanner. Whole-brain fMRI studies of seven healthy right hand-dominant volunteers were carried out in a three Tesla scanner. fMRI was performed using an SS-SE EPI sequence with SENSE. The data was processed using statistical parametric mapping. Both, group and individual subject data analyses were performed. Individual average percentage and maximal percentage signal changes attributed to the BOLD effect in M1 were calculated for all the subjects as a function of echo time. Corresponding activation maps and the sizes of the activated clusters were also calculated. Our results show that susceptibility artifacts were reduced with the use of SENSE; and the acquired BOLD images were free of the typical quadrature artifacts of SS-EPI. Such measures are crucial at high field strengths. SS SE-EPI with SENSE offers further benefits in this regard and is more specific for oxygenation changes in the microvasculature bed. Functional brain activity can be investigated with the help of single-shot spin echo EPI using SENSE at high magnetic fields.

  19. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

    Science.gov (United States)

    Belyi, Vladimir A; Levine, Arnold J; Skalka, Anna Marie

    2010-07-29

    Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological

  20. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Vladimir A Belyi

    2010-07-01

    Full Text Available Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected, later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important

  1. Imaging of the brain using the fast-spin-echo and gradient-spin-echo techniques

    International Nuclear Information System (INIS)

    Umek, W.; Ba-Ssalamah, A.; Prokesch, R.; Mallek, R.; Heimberger, K.; Hittmair, K.

    1998-01-01

    The aim of our study was to compare gradient-spin-echo (GRASE) to fast-spin-echo (FSE) sequences for fast T2-weighted MR imaging of the brain. Thirty-one patients with high-signal-intensity lesions on T2-weighted images were examined on a 1.5-T MR system. The FSE and GRASE sequences with identical sequence parameters were obtained and compared side by side. Image assessment criteria included lesion conspicuity, contrast between different types of normal tissue, and image artifacts. In addition, signal-to-noise, contrast-to-noise, and contrast ratios and were determined. The FSE technique demonstrated more lesions than GRASE and with generally better conspicuity. Smaller lesions in particular were better demonstrated on FSE because of lower image noise and slightly weaker image artifacts. Gray-white differentiation was better on FSE. Ferritin and hemosiderin depositions appeared darker on GRASE, which resulted in better contrast. Fatty tissue was less bright on GRASE. With current standard hardware equipment, the FSE technique seems preferable to GRASE for fast T2-weighted routine MR imaging of the brain. For the assessment of hemosiderin or ferritin depositions, GRASE might be considered. (orig.)

  2. New spoiled spin-echo technique for three-dimensional MR imaging

    International Nuclear Information System (INIS)

    Darrasse, L.; Mao, L.; Saint-Jalmes, H.

    1989-01-01

    For 3D MR imaging within a convenient scanning time, the authors propose an improved spin-echo technique that permits the use of TRs shorter than 100 msec. They use a two-pulse RF sequence (α-π echo). The echo is read with conventional 3DFT encoding. To avoid steady-state signal refocusing before either α or (imperfect) π pulses, we apply randomized gradient spoilers both before each α pulse and on each side of the π pulse. So the sequence works like standard spin- echo sequences, with the z-magnetization recovery being adjusted by means of α rather than TR. The authors have investigated the method on a new 0.1-T Magnetom system dedicated for 3D MR imaging

  3. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

    Science.gov (United States)

    Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2012-02-15

    We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

  4. A survey of endogenous retrovirus (ERV) sequences in the vicinity of multiple sclerosis (MS)-associated single nucleotide polymorphisms (SNPs).

    Science.gov (United States)

    Brütting, Christine; Emmer, Alexander; Kornhuber, Malte; Staege, Martin S

    2016-08-01

    Although multiple sclerosis (MS) is one of the most common central nervous system diseases in young adults, little is known about its etiology. Several human endogenous retroviruses (ERVs) are considered to play a role in MS. We are interested in which ERVs can be identified in the vicinity of MS associated genetic marker to find potential initiators of MS. We analysed the chromosomal regions surrounding 58 single nucleotide polymorphisms (SNPs) that are associated with MS identified in one of the last major genome wide association studies. We scanned these regions for putative endogenous retrovirus sequences with large open reading frames (ORFs). We observed that more retrovirus-related putative ORFs exist in the relatively close vicinity of SNP marker indices in multiple sclerosis compared to control SNPs. We found very high homologies to HERV-K, HCML-ARV, XMRV, Galidia ERV, HERV-H/env62 and XMRV-like mouse endogenous retrovirus mERV-XL. The associated genes (CYP27B1, CD6, CD58, MPV17L2, IL12RB1, CXCR5, PTGER4, TAGAP, TYK2, ICAM3, CD86, GALC, GPR65 as well as the HLA DRB1*1501) are mainly involved in the immune system, but also in vitamin D regulation. The most frequently detected ERV sequences are related to the multiple sclerosis-associated retrovirus, the human immunodeficiency virus 1, HERV-K, and the Simian foamy virus. Our data shows that there is a relation between MS associated SNPs and the number of retroviral elements compared to control. Our data identifies new ERV sequences that have not been associated with MS, so far.

  5. Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

    2010-01-01

    of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

  6. Geographic isolates of Lymantria dispar multiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains.

    Science.gov (United States)

    Harrison, Robert L; Rowley, Daniel L; Keena, Melody A

    2016-06-01

    Isolates of the baculovirus species Lymantria dispar multiple nucleopolyhedrovirus have been formulated and applied to suppress outbreaks of the gypsy moth, L. dispar. To evaluate the genetic diversity in this species at the genomic level, the genomes of three isolates from Massachusetts, USA (LdMNPV-Ab-a624), Spain (LdMNPV-3054), and Japan (LdMNPV-3041) were sequenced and compared with four previously determined LdMNPV genome sequences. The LdMNPV genome sequences were collinear and contained the same homologous repeats (hrs) and clusters of baculovirus repeat orf (bro) gene family members in the same relative positions in their genomes, although sequence identities in these regions were low. Of 146 non-bro ORFs annotated in the genome of the representative isolate LdMNPV 5-6, 135 ORFs were found in every other LdMNPV genome, including the 37 core genes of Baculoviridae and other genes conserved in genus Alphabaculovirus. Phylogenetic inference with an alignment of the core gene nucleotide sequences grouped isolates 3041 (Japan) and 2161 (Korea) separately from a cluster containing isolates from Europe, North America, and Russia. To examine phenotypic diversity, bioassays were carried out with a selection of isolates against neonate larvae from three European gypsy moth (Lymantria dispar dispar) and three Asian gypsy moth (Lymantria dispar asiatica and Lymantria dispar japonica) colonies. LdMNPV isolates 2161 (Korea), 3029 (Russia), and 3041 (Japan) exhibited a greater degree of pathogenicity against all L. dispar strains than LdMNPV from a sample of Gypchek. This study provides additional information on the genetic diversity of LdMNPV isolates and their activity against the Asian gypsy moth, a potential invasive pest of North American trees and forests. Published by Elsevier Inc.

  7. The complete sequence of the first Spodoptera frugiperda Betabaculovirus genome: a natural multiple recombinant virus.

    Science.gov (United States)

    Cuartas, Paola E; Barrera, Gloria P; Belaich, Mariano N; Barreto, Emiliano; Ghiringhelli, Pablo D; Villamizar, Laura F

    2015-01-20

    Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs) and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs), 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.

  8. The Complete Sequence of the First Spodoptera frugiperda Betabaculovirus Genome: A Natural Multiple Recombinant Virus

    Directory of Open Access Journals (Sweden)

    Paola E. Cuartas

    2015-01-01

    Full Text Available Spodoptera frugiperda (Lepidoptera: Noctuidae is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008 has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV. The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs, 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.

  9. Sequence-based analysis of the microbial composition of water kefir from multiple sources.

    Science.gov (United States)

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2013-11-01

    Water kefir is a water-sucrose-based beverage, fermented by a symbiosis of bacteria and yeast to produce a final product that is lightly carbonated, acidic and that has a low alcohol percentage. The microorganisms present in water kefir are introduced via water kefir grains, which consist of a polysaccharide matrix in which the microorganisms are embedded. We aimed to provide a comprehensive sequencing-based analysis of the bacterial population of water kefir beverages and grains, while providing an initial insight into the corresponding fungal population. To facilitate this objective, four water kefirs were sourced from the UK, Canada and the United States. Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea. This information will assist in the ultimate identification of the microorganisms responsible for the potentially health-promoting attributes of these beverages. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  10. Seismic echo character northern Hatteras Abyssal Plain

    International Nuclear Information System (INIS)

    McCreery, C.J.; Laine, E.P.

    1985-01-01

    Latest efforts in echo-character mapping of the northern Hatteras Abyssal Plain have discerned variations in thickness in a near-surface sedimentary sequence which has been designated seismic unit A. This unit probably represents the last episode of progradation of the Hatteras Deep Sea Fan in the southern part of the study area, and has infilled probable paleochannels from the Wilmington Canyon and Sohm Gap in the north. Unit A thins to a minimum in the central part of the plain, where older sediments come within 1 meter of the surface. Variations in the character of the surface reflector probably represent differing degrees of microtopography developed on a Late Pleistocene surface overlain by Holocene sediments. With the exception of one area identified as a relict surface outcropping in the western plain, this microtopography seems related to present-day thalweg locations on the abyssal plain. 11 references, 13 figures

  11. Neutron spin echo scattering angle measurement (SESAME)

    International Nuclear Information System (INIS)

    Pynn, R.; Fitzsimmons, M.R.; Fritzsche, H.; Gierlings, M.; Major, J.; Jason, A.

    2005-01-01

    We describe experiments in which the neutron spin echo technique is used to measure neutron scattering angles. We have implemented the technique, dubbed spin echo scattering angle measurement (SESAME), using thin films of Permalloy electrodeposited on silicon wafers as sources of the magnetic fields within which neutron spins precess. With 30-μm-thick films we resolve neutron scattering angles to about 0.02 deg. with neutrons of 4.66 A wavelength. This allows us to probe correlation lengths up to 200 nm in an application to small angle neutron scattering. We also demonstrate that SESAME can be used to separate specular and diffuse neutron reflection from surfaces at grazing incidence. In both of these cases, SESAME can make measurements at higher neutron intensity than is available with conventional methods because the angular resolution achieved is independent of the divergence of the neutron beam. Finally, we discuss the conditions under which SESAME might be used to probe in-plane structure in thin films and show that the method has advantages for incident neutron angles close to the critical angle because multiple scattering is automatically accounted for

  12. Comparison of third-order plasma wave echoes with ballistic second-order plasma wave echoes

    International Nuclear Information System (INIS)

    Leppert, H.D.; Schuelter, H.; Wiesemann, K.

    1982-01-01

    The apparent dispersion of third-order plasma wave echoes observed in a high frequency plasma is compared with that of simultaneously observed ballistic second-order echoes. Amplitude and wavelength of third-order echoes are found to be always smaller than those of second-order echoes, however, the dispersion curves of both types of echoes are very similar. These observations are in qualitative agreement with calculations of special ballistic third-order echoes. The ballistic nature of the observed third-order echoes may, therefore, be concluded from these measurements. (author)

  13. The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

    Science.gov (United States)

    Nordborg, Magnus; Innan, Hideki

    2003-03-01

    A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

  14. Sequencing of disease-modifying therapies for relapsing-remitting multiple sclerosis: a theoretical approach to optimizing treatment.

    Science.gov (United States)

    Grand'Maison, Francois; Yeung, Michael; Morrow, Sarah A; Lee, Liesly; Emond, Francois; Ward, Brian J; Laneuville, Pierre; Schecter, Robyn

    2018-04-18

    Multiple sclerosis (MS) is a chronic disease which usually begins in young adulthood and is a lifelong condition. Individuals with MS experience physical and cognitive disability resulting from inflammation and demyelination in the central nervous system. Over the past decade, several disease-modifying therapies (DMTs) have been approved for the management of relapsing-remitting MS (RRMS), which is the most prevalent phenotype. The chronic nature of the disease and the multiple treatment options make benefit-risk-based sequencing of therapy essential to ensure optimal care. The efficacy and short- and long-term risks of treatment differ for each DMT due to their different mechanism of action on the immune system. While transitioning between DMTs, in addition to immune system effects, factors such as age, disease duration and severity, disability status, monitoring requirements, preference for the route of administration, and family planning play an important role. Determining a treatment strategy is therefore challenging as it requires careful consideration of the differences in efficacy, safety and tolerability, while at the same time minimizing risks of immune modulation. In this review, we discuss a sequencing approach for treating RRMS, with importance given to the long-term risks and individual preference when devising a treatment plan. Evidence-based strategies to counter breakthrough disease are also addressed.

  15. MRI of the brain stem using fluid attenuated inversion recivery pulse sequences

    International Nuclear Information System (INIS)

    De Coene, B.; Hajnal, J.V.; Pennock, J.M.; Bydder, G.M.

    1993-01-01

    Heavily T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences with inversion times of 2000-2500 ms and echo times of 130-200 ms were used to image the brain stem of a normal adult and five patients. These sequences produce high signal from many white matter tracts and display high lesion contrast. The corticospinal and parietopontine tracts, lateral and medial lemnisci, superior and inferior cerebellar peduncles, medial longitudinal fasciculi, thalamo-olivary tracts the cuneate and gracile fasiculi gave high signal and were directly visualised. The oculomotor and trigeminal nerves were demonstrated within the brain stem. Lesions not seen with conventional T2-weighted spin echo sequences were seen with high contrast in patients with infarction, multiple sclerosis, sarcoidosis, chunt obstruction and metastatic tumour. The anatomical detail and high lesion contrast given by the FLAIR pulse sequence appear likely to be of value in diagnosis of disease in the brain stem. (orig.)

  16. Multiband multi-echo imaging of simultaneous oxygenation and flow timeseries for resting state connectivity.

    Science.gov (United States)

    Cohen, Alexander D; Nencka, Andrew S; Lebel, R Marc; Wang, Yang

    2017-01-01

    A novel sequence has been introduced that combines multiband imaging with a multi-echo acquisition for simultaneous high spatial resolution pseudo-continuous arterial spin labeling (ASL) and blood-oxygenation-level dependent (BOLD) echo-planar imaging (MBME ASL/BOLD). Resting-state connectivity in healthy adult subjects was assessed using this sequence. Four echoes were acquired with a multiband acceleration of four, in order to increase spatial resolution, shorten repetition time, and reduce slice-timing effects on the ASL signal. In addition, by acquiring four echoes, advanced multi-echo independent component analysis (ME-ICA) denoising could be employed to increase the signal-to-noise ratio (SNR) and BOLD sensitivity. Seed-based and dual-regression approaches were utilized to analyze functional connectivity. Cerebral blood flow (CBF) and BOLD coupling was also evaluated by correlating the perfusion-weighted timeseries with the BOLD timeseries. These metrics were compared between single echo (E2), multi-echo combined (MEC), multi-echo combined and denoised (MECDN), and perfusion-weighted (PW) timeseries. Temporal SNR increased for the MECDN data compared to the MEC and E2 data. Connectivity also increased, in terms of correlation strength and network size, for the MECDN compared to the MEC and E2 datasets. CBF and BOLD coupling was increased in major resting-state networks, and that correlation was strongest for the MECDN datasets. These results indicate our novel MBME ASL/BOLD sequence, which collects simultaneous high-resolution ASL/BOLD data, could be a powerful tool for detecting functional connectivity and dynamic neurovascular coupling during the resting state. The collection of more than two echoes facilitates the use of ME-ICA denoising to greatly improve the quality of resting state functional connectivity MRI.

  17. Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria

    Science.gov (United States)

    2012-01-01

    Background Drug resistance in the malaria parasite Plasmodium falciparum severely compromises the treatment and control of malaria. A knowledge of the critical mutations conferring resistance to particular drugs is important in understanding modes of drug action and mechanisms of resistances. They are required to design better therapies and limit drug resistance. A mutation in the gene (pfcrt) encoding a membrane transporter has been identified as a principal determinant of chloroquine resistance in P. falciparum, but we lack a full account of higher level chloroquine resistance. Furthermore, the determinants of resistance in the other major human malaria parasite, P. vivax, are not known. To address these questions, we investigated the genetic basis of chloroquine resistance in an isogenic lineage of rodent malaria parasite P. chabaudi in which high level resistance to chloroquine has been progressively selected under laboratory conditions. Results Loci containing the critical genes were mapped by Linkage Group Selection, using a genetic cross between the high-level chloroquine-resistant mutant and a genetically distinct sensitive strain. A novel high-resolution quantitative whole-genome re-sequencing approach was used to reveal three regions of selection on chr11, chr03 and chr02 that appear progressively at increasing drug doses on three chromosomes. Whole-genome sequencing of the chloroquine-resistant parent identified just four point mutations in different genes on these chromosomes. Three mutations are located at the foci of the selection valleys and are therefore predicted to confer different levels of chloroquine resistance. The critical mutation conferring the first level of chloroquine resistance is found in aat1, a putative aminoacid transporter. Conclusions Quantitative trait loci conferring selectable phenotypes, such as drug resistance, can be mapped directly using progressive genome-wide linkage group selection. Quantitative genome-wide short

  18. Temporal Sequence of Visuo-Auditory Interaction in Multiple Areas of the Guinea Pig Visual Cortex

    Science.gov (United States)

    Nishimura, Masataka; Song, Wen-Jie

    2012-01-01

    Recent studies in humans and monkeys have reported that acoustic stimulation influences visual responses in the primary visual cortex (V1). Such influences can be generated in V1, either by direct auditory projections or by feedback projections from extrastriate cortices. To test these hypotheses, cortical activities were recorded using optical imaging at a high spatiotemporal resolution from multiple areas of the guinea pig visual cortex, to visual and/or acoustic stimulations. Visuo-auditory interactions were evaluated according to differences between responses evoked by combined auditory and visual stimulation, and the sum of responses evoked by separate visual and auditory stimulations. Simultaneous presentation of visual and acoustic stimulations resulted in significant interactions in V1, which occurred earlier than in other visual areas. When acoustic stimulation preceded visual stimulation, significant visuo-auditory interactions were detected only in V1. These results suggest that V1 is a cortical origin of visuo-auditory interaction. PMID:23029483

  19. Robust segmentation of focal lesions on multi-sequence MRI in multiple sclerosis

    International Nuclear Information System (INIS)

    Garcia-Lorenzo, Daniel

    2010-01-01

    Multiple sclerosis (MS) affects around 80.000 people in France. Magnetic resonance imaging (MRI) is an essential tool for diagnosis of MS and MRI-derived surrogate markers such as MS lesion volumes are often used as measures in MS clinical trials for the development of new treatments. The manual segmentation of these MS lesions is a time-consuming task that shows high inter- and intra-rater variability. We developed an automatic work flow for the segmentation of focal MS lesions on MRI. The segmentation method is based on the robust estimation of a parametric model of the intensities of the brain; lesions are detected as outliers to the model. We proposed two methods to include spatial information in the segmentation using mean shift and graph cut. We performed a quantitative evaluation of our work flow using synthetic and clinical images of two different centers to verify its accuracy and robustness. (author)

  20. The clinical potential of ultra-high-speed echo-planar imaging

    International Nuclear Information System (INIS)

    Worthington, B.S.; Firth, J.L.; Morris, G.K.; Johnson, I.R.; Coxon, R.; Blamire, A.M.; Gibbs, P.; Mansfield, P.

    1990-01-01

    Ultra-high-speed echo-planar imaging (EPI) allows acquisition of a complete two-dimensional image in 64 to 128 ms devoid of movement artefact and without sacrifice of contrast due to relaxation time effects. In conventional whole-body MRI, however, obtrusive movement artefact and extended imaging time, resulting from the need to apply multiple sequences to facilitate lesion detection and pathological characterization, remain limitations. Reduced total examination time increases patient tolerance and throughput; furthermore optimization of contrast to achieve maximal conspicuity of particular features in liver or brain pathology is achieved simply and interactively by real time adjustment of the imaging parameters. The method provides the opportunity to study in real time dynamic events such as flow phenomena in the vascular and cerebrospinal fluid compartments of the brain as well as the kinetics of administered contrast agents. EPI is the only means of capturing the irregular motion of aperiodic cardiac events and bowel peristalsis. (author)

  1. Storage and manipulation of light using a Raman gradient-echo process

    International Nuclear Information System (INIS)

    Hosseini, M; Sparkes, B M; Campbell, G T; Lam, P K; Buchler, B C

    2012-01-01

    The gradient-echo memory (GEM) scheme has potential to be a suitable protocol for storage and retrieval of optical quantum information. In this paper, we review the properties of the Λ-GEM method that stores information in the ground states of three-level atomic ensembles via Raman coupling. The scheme is versatile in that it can store and re-sequence multiple pulses of light. To date, this scheme has been implemented using warm rubidium gas cells. There are different phenomena that can influence the performance of these atomic systems. We investigate the impact of atomic motion and four-wave mixing and present experiments that show how parasitic four-wave mixing can be mitigated. We also use the memory to demonstrate preservation of pulse shape and the backward retrieval of pulses. (paper)

  2. Detection of lesions in multiple sclerosis by 2D FLAIR and single-slab 3D FLAIR sequences at 3.0 T: initial results

    International Nuclear Information System (INIS)

    Bink, Andrea; Gaa, Jochen; Lanfermann, Heinrich; Zanella, Friedhelm E.; Schmitt, Melanie; Mugler, John P.

    2006-01-01

    The aim of this study was to compare conventional 2D FLAIR and single-slab 3D FLAIR sequences in the detection of lesions in patients with multiple sclerosis. Eight patients with MS were examined at 3.0 T by using a 2D FLAIR sequence and a single-slab 3D FLAIR sequence. A comparison of lesion detectability was performed for the following regions: periventricular, nonperiventricular/juxtacortical and infratentorial. The contrast-to-noise ratios (CNRs) between lesions and brain tissue and CSF were calculated for each sequence. A total of 424 lesions were found using the 2D FLAIR sequence, while with the 3D FLAIR sequence 719 lesions were found. With the 2D FLAIR sequence, 41% fewer lesions were detected than with the 3D FLAIR sequence. Further, 40% fewer supratentorial and 62.5% fewer infratentorial lesions were found with the 2D FLAIR sequence. In images acquired with the 3D FLAIR sequence, the lesions had significantly higher CNRs than in images acquired with the 2D FLAIR sequence. These are the first results using a single-slab 3D FLAIR sequence at 3.0 T for detection of lesions in patients with MS. With the 3D FLAIR sequence significantly higher CNRs were achieved and significantly more lesions in patients with MS were detected. (orig.)

  3. Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events.

    Science.gov (United States)

    Armour, Christine M; Smith, Amanda; Hartley, Taila; Chardon, Jodi Warman; Sawyer, Sarah; Schwartzentruber, Jeremy; Hennekam, Raoul; Majewski, Jacek; Bulman, Dennis E; Suri, Mohnish; Boycott, Kym M

    2016-07-01

    In 1987 Fitzsimmons and Guilbert described identical male twins with progressive spastic paraplegia, brachydactyly with cone shaped epiphyses, short stature, dysarthria, and "low-normal" intelligence. In subsequent years, four other patients, including one set of female identical twins, a single female child, and a single male individual were described with the same features, and the eponym Fitzsimmons syndrome was adopted (OMIM #270710). We performed exome analysis of the patient described in 2009, and one of the original twins from 1987, the only patients available from the literature. No single genetic etiology exists that explains Fitzsimmons syndrome; however, multiple different genetic causes were identified. Specifically, the twins described by Fitzsimmons had heterozygous mutations in the SACS gene, the gene responsible for autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS), as well as a heterozygous mutation in the TRPS1, the gene responsible in Trichorhinophalangeal syndrome type 1 (TRPS1 type 1) which includes brachydactyly as a feature. A TBL1XR1 mutation was identified in the patient described in 2009 as contributing to his cognitive impairment and autistic features with no genetic cause identified for his spasticity or brachydactyly. The findings show that these individuals have multiple different etiologies giving rise to a similar phenotype, and that "Fitzsimmons syndrome" is in fact not one single syndrome. Over time, we anticipate that continued careful phenotyping with concomitant genome-wide analysis will continue to identify the causes of many rare syndromes, but it will also highlight that previously delineated clinical entities are, in fact, not syndromes at all. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Detection of generalized synchronization using echo state networks

    OpenAIRE

    Ibáñez-Soria, D.; García Ojalvo, Jordi; Soria Frisch, Aureli; Ruffini, G.

    2018-01-01

    Generalized synchronization between coupled dynamical systems is a phenomenon of relevance in applications that range from secure communications to physiological modelling. Here, we test the capabilities of reservoir computing and, in particular, echo state networks for the detection of generalized synchronization. A nonlinear dynamical system consisting of two coupled Rössler chaotic attractors is used to generate temporal series consisting of time-locked generalized synchronized sequences i...

  5. Modified echo peak correction for radial acquisition regime (RADAR).

    Science.gov (United States)

    Takizawa, Masahiro; Ito, Taeko; Itagaki, Hiroyuki; Takahashi, Tetsuhiko; Shimizu, Kanichirou; Harada, Junta

    2009-01-01

    Because radial sampling imposes many limitations on magnetic resonance (MR) imaging hardware, such as on the accuracy of the gradient magnetic field or the homogeneity of B(0), some correction of the echo signal is usually needed before image reconstruction. In our previous study, we developed an echo-peak-shift correction (EPSC) algorithm not easily affected by hardware performance. However, some artifacts remained in lung imaging, where tissue is almost absent, or in cardiac imaging, which is affected by blood flow. In this study, we modified the EPSC algorithm to improve the image quality of the radial aquisition regime (RADAR) and expand its application sequences. We assumed the artifacts were mainly caused by errors in the phase map for EPSC and used a phantom on a 1.5-tesla (T) MR scanner to investigate whether to modify the EPSC algorithm. To evaluate the effectiveness of EPSC, we compared results from T(1)- and T(2)-weighted images of a volunteer's lung region using the current and modified EPSC. We then applied the modified EPSC to RADAR spin echo (SE) and RADAR balanced steady-state acquisition with rewound gradient echo (BASG) sequence. The modified EPSC reduced phase discontinuity in the reference data used for EPSC and improved visualization of blood vessels in the lungs. Motion and blood flow caused no visible artifacts in the resulting images in either RADAR SE or RADAR BASG sequence. Use of the modified EPSC eliminated artifacts caused by signal loss in the reference data for EPSC. In addition, the modified EPSC was applied to RADAR SE and RADAR BASG sequences.

  6. Modified echo peak correction for radial acquisition regime (RADAR)

    International Nuclear Information System (INIS)

    Takizawa, Masahiro; Ito, Taeko; Itagaki, Hiroyuki; Takahashi, Tetsuhiko; Shimizu, Kanichirou; Harada, Junta

    2009-01-01

    Because radial sampling imposes many limitations on magnetic resonance (MR) imaging hardware, such as on the accuracy of the gradient magnetic field or the homogeneity of B 0 , some correction of the echo signal is usually needed before image reconstruction. In our previous study, we developed an echo-peak-shift correction (EPSC) algorithm not easily affected by hardware performance. However, some artifacts remained in lung imaging, where tissue is almost absent, or in cardiac imaging, which is affected by blood flow. In this study, we modified the EPSC algorithm to improve the image quality of the radial acquisition regime (RADAR) and expand its application sequences. We assumed the artifacts were mainly caused by errors in the phase map for EPSC and used a phantom on a 1.5-tesla (T) MR scanner to investigate whether to modify the EPSC algorithm. To evaluate the effectiveness of EPSC, we compared results from T 1 -and T 2 -weighted images of a volunteer's lung region using the current and modified EPSC. We then applied the modified EPSC to RADAR spin echo (SE) and RADAR balanced steady-state acquisition with rewound gradient echo (BASG) sequence. The modified EPSC reduced phase discontinuity in the reference data used for EPSC and improved visualization of blood vessels in the lungs. Motion and blood flow caused no visible artifacts in the resulting images in either RADAR SE or RADAR BASG sequence. Use of the modified EPSC eliminated artifacts caused by signal loss in the reference data for EPSC. In addition, the modified EPSC was applied to RADAR SE and RADAR BASG sequences. (author)

  7. A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

    Science.gov (United States)

    Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

    2017-01-01

    Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

  8. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.

    Science.gov (United States)

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2014-04-01

    Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Tori sequences as remnants of multiple accreting periods of Kerr SMBHs

    Science.gov (United States)

    Pugliese, D.; Stuchlík, Z.

    2018-03-01

    Super-massive black holes (SMBHs) hosted in active galactic nuclei (AGNs) can be characterized by multi-accreting periods as the attractors interact with the environment during their life-time. These multi-accretion episodes should leave traces in the matter orbiting the attractor. Counterrotating and even misaligned structures orbiting around the SMBHs would be consequences of these episodes. Our task in this work is to consider situations where such accretions occur and to trace their remnants represented by several toroidal accreting fluids, corotating or counterrotating relative to the central Kerr attractor, and created in various regimes during the evolution of matter configurations around SMBHs. We focus particularly on the emergence of matter instabilities, i.e., tori collisions, accretion onto the central Kerr black hole, or creation of jet-like structures (proto-jets). Each orbiting configuration is governed by the general relativistic hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluid. We prove that sequences of configurations and hot points, where an instability occurs, characterize the Kerr SMBHs, depending mainly on their spin-mass ratios. The occurrence of tori accretion or collision are strongly constrained by the fluid rotation with respect to the central black hole and the relative rotation with respect to each other. Our investigation provides characteristic of attractors where traces of multi-accreting episodes can be found and observed.

  10. 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.

  11. Significance of spin-echo intracardiac signal during cine cardiac MR imaging

    International Nuclear Information System (INIS)

    Feiglin, D.H.I.; O'Donnell, J.K.

    1987-01-01

    Thirty patient studies were performed using several multisection spin multi-echo pulse sequences (SEPS) formattable into the cine mode, with repetition time (TR)≤RR interval and 18 msec ≤ echo time (TE) ≤ 64 msec. Thirteen studies were performed in patients with various cardiomyopathies, ten in patients with cardiac tumors, and seven in healthy volunteers. The SEPS in the multi-echo acquisition format differentiated between tumor and stasis in terms of signal behavior. Healthy subjects may exhibit stasis of flow adjacent to the endocardium during the cardiac cycle

  12. 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...

  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. Comparison of 3D two-point Dixon and standard 2D dual-echo breath-hold sequences for detection and quantification of fat content in renal angiomyolipoma

    International Nuclear Information System (INIS)

    Rosenkrantz, Andrew B.; Raj, Sean; Babb, James S.; Chandarana, Hersh

    2012-01-01

    Purpose: To assess the utility of a 3D two-point Dixon sequence with water–fat decomposition for quantification of fat content of renal angiomyolipoma (AML). Methods: 84 patients underwent renal MRI including 2D in-and-opposed-phase (IP and OP) sequence and 3D two-point Dixon sequence that generates four image sets [IP, OP, water-only (WO), and fat-only (FO)] within one breath-hold. Two radiologists reviewed 2D and 3D images during separate sessions to identify fat-containing renal masses measuring at least 1 cm. For identified lesions subsequently confirmed to represent AML, ROIs were placed at matching locations on 2D and 3D images and used to calculate 2D and 3D SI index [(SI IP − SI OP )/SI IP ] and 3D fat fraction (FF) [SI FO /(SI FO + SI WO )]. 2D and 3D SI index were compared with 3D FF using Pearson correlation coefficients. Results: 41 AMLs were identified in 6 patients. While all were identified using the 3D sequence, 39 were identified using the 2D sequence, with the remaining 2 AMLs retrospectively visible on 2D images but measuring under 1 cm. Among 32 AMLs with a 3D FF of over 50%, both 2D and 3D SI index showed a statistically significant inverse correlation with 3D FF (2D SI index : r = −0.63, p = 0.0010; 3D SI index : r = −0.97, p index , is not limited by ambiguity of water or fat dominance. This may assist clinical management of AML given evidence that fat content predicts embolization response.

  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. Fast-gradient-echo variable-flip-angle imaging of the cervical spine

    International Nuclear Information System (INIS)

    Van Dyke, C.W.; Ross, J.S.; Masaryk, T.J.; Tkach, J.; Beale, S.; Hueftle, M.G.; Kaufman, B.; Modic, M.T.

    1987-01-01

    Two hundred consecutive patients were studied with 4-mm sagittal and axial T1-weighted images and gradient echo sequences with 6-msec or 13-msec echo time (TE) and 10 0 or 60 0 flip angles to evaluate cervical extradural disease. Images were independently evaluated for contrast behavior and anatomy, then directly compared for conspicuity of lesions. FLASH sequences produced better conspicuity of disease in half the imaging time. T1-weighted spin-echo (SE) sequences were more sensitive to marrow changes and intradural disease. Shorter TEs produced overall image improvement and reduced susceptibility effects. A fast and sensitive cervical examination combines sagittal T1-weighted SE with sagittal and axial FLASH 10 0 sequences with 6-msec TE

  17. Application of velocity imaging and gradient-recalled echo in neuroimaging

    International Nuclear Information System (INIS)

    Boyko, O.B.; Pelc, N.J.; Shimakawa, A.

    1990-01-01

    This paper describes the initial clinical experience with imaging blood flow at 1.5 T by means of a phase-sensitive gradient refocused pulse sequence. A spin-echo flow-encoding technique was modified to a gradient recalled acquisition in a steady state sequence, producing a velocity imaging and gradient recalled echo (VIGRE) sequence (TR = 24 msec, TE = 13 msec, flip angle = 45 degrees, 24-cm field of view, 7 mm contiguous sections). Two views per phase-encoding step are acquired; one using the first-moment flow-compensation gradient waveform and the second having a (selectable) nonzero first moment. A phase subtraction image is obtained where the signal is dependent on the direction and velocity of flow. The sequence was done following routine spin-echo imaging in 35 patients

  18. Short-scan-time multi-slice diffusion MRI of the mouse cervical spinal cord using echo planar imaging.

    Science.gov (United States)

    Callot, Virginie; Duhamel, Guillaume; Cozzone, Patrick J; Kober, Frank

    2008-10-01

    Mouse spinal cord (SC) diffusion-weighted imaging (DWI) provides important information on tissue morphology and structural changes that may occur during pathologies such as multiple sclerosis or SC injury. The acquisition scheme of the commonly used DWI techniques is based on conventional spin-echo encoding, which is time-consuming. The purpose of this work was to investigate whether the use of echo planar imaging (EPI) would provide good-quality diffusion MR images of mouse SC, as well as accurate measurements of diffusion-derived metrics, and thus enable diffusion tensor imaging (DTI) and highly resolved DWI within reasonable scan times. A four-shot diffusion-weighted spin-echo EPI (SE-EPI) sequence was evaluated at 11.75 T on a group of healthy mice (n = 10). SE-EPI-derived apparent diffusion coefficients of gray and white matter were compared with those obtained using a conventional spin-echo sequence (c-SE) to validate the accuracy of the method. To take advantage of the reduction in acquisition time offered by the EPI sequence, multi-slice DTI acquisitions were performed covering the cervical segments (six slices, six diffusion-encoding directions, three b values) within 30 min (vs 2 h for c-SE). From these measurements, fractional anisotropy and mean diffusivities were calculated, and fiber tracking along the C1 to C6 cervical segments was performed. In addition, high-resolution images (74 x 94 microm(2)) were acquired within 5 min per direction. Clear delineation of gray and white matter and identical apparent diffusion coefficient values were obtained, with a threefold reduction in acquisition time compared with c-SE. While overcoming the difficulties associated with high spatially and temporally resolved DTI measurements, the present SE-EPI approach permitted identification of reliable quantitative parameters with a reproducibility compatible with the detection of pathologies. The SE-EPI method may be particularly valuable when multiple sets of images

  19. Classification of radar echoes using fractal geometry

    International Nuclear Information System (INIS)

    Azzaz, Nafissa; Haddad, Boualem

    2017-01-01

    Highlights: • Implementation of two concepts of fractal geometry to classify two types of meteorological radar echoes. • A new approach, called a multi-scale fractal dimension is used for classification between fixed echoes and rain echoes. • An Automatic identification system of meteorological radar echoes was proposed using fractal geometry. - Abstract: This paper deals with the discrimination between the precipitation echoes and the ground echoes in meteorological radar images using fractal geometry. This study aims to improve the measurement of precipitations by weather radars. For this, we considered three radar sites: Bordeaux (France), Dakar (Senegal) and Me lbourne (USA). We showed that the fractal dimension based on contourlet and the fractal lacunarity are pertinent to discriminate between ground and precipitation echoes. We also demonstrated that the ground echoes have a multifractal structure but the precipitations are more homogeneous than ground echoes whatever the prevailing climate. Thereby, we developed an automatic classification system of radar using a graphic interface. This interface, based on the fractal geometry makes possible the identification of radar echoes type in real time. This system can be inserted in weather radar for the improvement of precipitation estimations.

  20. T1 Shortening in the Globus Pallidus after Multiple Administrations of Gadobutrol: Assessment with a Multidynamic Multiecho Sequence.

    Science.gov (United States)

    Kang, Koung Mi; Choi, Seung Hong; Hwang, Moonjung; Yun, Tae Jin; Kim, Ji-Hoon; Sohn, Chul-Ho

    2018-04-01

    Purpose To determine the association between the administration of the macrocyclic contrast medium gadobutrol and T1 relaxation time in the brains of patients with normal renal function by using multidynamic multiecho (MDME) magnetic resonance (MR) imaging sequences. Materials and Methods The institutional review board approved this retrospective study, and the need to obtain written informed consent was waived. This study included 46 patients (revealed by an electronic medical record search) who had received one or more gadobutrol injections and a maximum of one MR imaging contrast medium injection other than gadobutrol before MDME sequence acquisition. One radiologist performed quantitative analyses of regions of interest on quantitative T1 maps twice to cover the normal-appearing globus pallidus (GP), frontal white matter, frontal cortex, and thalamus. The number of administrations and the cumulative dose of gadobutrol, age, intervals between administrations, sex, and treatment were investigated. Univariable and multivariable linear regression analyses of the T1 values in four brain regions and the GP-to-thalamus signal intensity (SI) ratio were performed. P values of less than the Bonferroni-corrected value of .01 were considered to indicate significant differences. Results Intraobserver reproducibility was good to excellent (intraclass correlation coefficients, 0.62-0.81). Because of high multicollinearity between the number of gadobutrol administrations and accumulated dose (r = 0.96, P .01). Conclusion Multiple exposures to gadobutrol are associated with T1 shortening in the GP. © RSNA, 2017 Online supplemental material is available for this article.

  1. TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

    Science.gov (United States)

    Chang, Jia-Ming; Di Tommaso, Paolo; Notredame, Cedric

    2014-06-01

    Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications of MSAs. Both are known to be sensitive to the underlying MSA accuracy. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. For this purpose, we describe a novel lossless alternative to site filtering that involves overweighting the trustworthy columns. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees. The software is available from www.tcoffee.org/Projects/tcs. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Capture-based next-generation sequencing reveals multiple actionable mutations in cancer patients failed in traditional testing.

    Science.gov (United States)

    Xie, Jing; Lu, Xiongxiong; Wu, Xue; Lin, Xiaoyi; Zhang, Chao; Huang, Xiaofang; Chang, Zhili; Wang, Xinjing; Wen, Chenlei; Tang, Xiaomei; Shi, Minmin; Zhan, Qian; Chen, Hao; Deng, Xiaxing; Peng, Chenghong; Li, Hongwei; Fang, Yuan; Shao, Yang; Shen, Baiyong

    2016-05-01

    Targeted therapies including monoclonal antibodies and small molecule inhibitors have dramatically changed the treatment of cancer over past 10 years. Their therapeutic advantages are more tumor specific and with less side effects. For precisely tailoring available targeted therapies to each individual or a subset of cancer patients, next-generation sequencing (NGS) has been utilized as a promising diagnosis tool with its advantages of accuracy, sensitivity, and high throughput. We developed and validated a NGS-based cancer genomic diagnosis targeting 115 prognosis and therapeutics relevant genes on multiple specimen including blood, tumor tissue, and body fluid from 10 patients with different cancer types. The sequencing data was then analyzed by the clinical-applicable analytical pipelines developed in house. We have assessed analytical sensitivity, specificity, and accuracy of the NGS-based molecular diagnosis. Also, our developed analytical pipelines were capable of detecting base substitutions, indels, and gene copy number variations (CNVs). For instance, several actionable mutations of EGFR,PIK3CA,TP53, and KRAS have been detected for indicating drug susceptibility and resistance in the cases of lung cancer. Our study has shown that NGS-based molecular diagnosis is more sensitive and comprehensive to detect genomic alterations in cancer, and supports a direct clinical use for guiding targeted therapy.

  3. Single-nucleotide variant in multiple copies of a deleted in azoospermia (DAZ) sequence - a human Y chromosome quantitative polymorphism.

    Science.gov (United States)

    Szmulewicz, Martin N; Ruiz, Luis M; Reategui, Erika P; Hussini, Saeed; Herrera, Rene J

    2002-01-01

    The evolution of the deleted in azoospermia (DAZ) gene family supports prevalent theories on the origin and development of sex chromosomes and sexual dimorphism. The ancestral DAZL gene in human chromosome 3 is known to be involved in germline development of both males and females. The available phylogenetic data suggest that some time after the divergence of the New World and Old World monkey lineages, the DAZL gene, which is found in all mammals, was copied to the Y chromosome of an ancestor to the Old World monkeys, but not New World monkeys. In modern man, the Y-linked DAZ gene complex is located on the distal part of the q arm. It is thought that after being copied to the Y chromosome, and after the divergence of the human and great ape lineages, the DAZ gene in the former underwent internal rearrangements. This included tandem duplications as well as a T > C transition altering an MboI restriction enzyme site in a duplicated sequence. In this study, we report on the ratios of MboI-/MboI+ variant sequences in individuals from seven worldwide human populations (Basque, Benin, Egypt, Formosa, Kungurtug, Oman and Rwanda) in the DAZ complex. The ratio of PCR MboI- and MboI+ amplicons can be used to characterize individuals and populations. Our results show a nonrandom distribution of MboI-/MboI+ sequence ratios in all populations examined, as well as significant differences in ratios between populations when compared pairwise. The multiple ratios imply that there have been more than one recent reorganization events at this locus. Considering the dynamic nature of this locus and its involvement in male fertility, we investigated the extent and distribution of this polymorphism. Copyright 2002 S. Karger AG, Basel

  4. Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments.

    Science.gov (United States)

    Li, Man; Ling, Cheng; Xu, Qi; Gao, Jingyang

    2018-02-01

    Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To improve prediction accuracy, these algorithms must confront the key challenge of extracting valuable features. In this work, we propose a feature-enhanced protein classification approach, considering the rich generation of multiple sequence alignment algorithms, N-gram probabilistic language model and the deep learning technique. The essence behind the proposed method is that if each group of sequences can be represented by one feature sequence, composed of homologous sites, there should be less loss when the sequence is rebuilt, when a more relevant sequence is added to the group. On the basis of this consideration, the prediction becomes whether a query sequence belonging to a group of sequences can be transferred to calculate the probability that the new feature sequence evolves from the original one. The proposed work focuses on the hierarchical classification of G-protein Coupled Receptors (GPCRs), which begins by extracting the feature sequences from the multiple sequence alignment results of the GPCRs sub-subfamilies. The N-gram model is then applied to construct the input vectors. Finally, these vectors are imported into a convolutional neural network to make a prediction. The experimental results elucidate that the proposed method provides significant performance improvements. The classification error rate of the proposed method is reduced by at least 4.67% (family level I) and 5.75% (family Level II), in comparison with the current state-of-the-art methods. The implementation program of the proposed work is freely available at: https://github.com/alanFchina/CNN .

  5. Efficient Multichannel NLMS Implementation for Acoustic Echo Cancellation

    Directory of Open Access Journals (Sweden)

    Schüldt Christian

    2007-01-01

    Full Text Available An acoustic echo cancellation structure with a single loudspeaker and multiple microphones is, from a system identification perspective, generally modelled as a single-input multiple-output system. Such a system thus implies specific echo-path models (adaptive filter for every loudspeaker to microphone path. Due to the often large dimensionality of the filters, which is required to model rooms with standard reverberation time, the adaptation process can be computationally demanding. This paper presents a selective updating normalized least mean square (NLMS-based method which reduces complexity to nearly half in practical situations, while showing superior convergence speed performance as compared to conventional complexity reduction schemes. Moreover, the method concentrates the filter adaptation to the filter which is most misadjusted, which is a typically desired feature.

  6. Efficient Multichannel NLMS Implementation for Acoustic Echo Cancellation

    Directory of Open Access Journals (Sweden)

    Fredric Lindstrom

    2007-02-01

    Full Text Available An acoustic echo cancellation structure with a single loudspeaker and multiple microphones is, from a system identification perspective, generally modelled as a single-input multiple-output system. Such a system thus implies specific echo-path models (adaptive filter for every loudspeaker to microphone path. Due to the often large dimensionality of the filters, which is required to model rooms with standard reverberation time, the adaptation process can be computationally demanding. This paper presents a selective updating normalized least mean square (NLMS-based method which reduces complexity to nearly half in practical situations, while showing superior convergence speed performance as compared to conventional complexity reduction schemes. Moreover, the method concentrates the filter adaptation to the filter which is most misadjusted, which is a typically desired feature.

  7. MR imaging of articular cartilage : comparison of magnetization transfer contrast and fat-suppression in multiplanar and 3D gradient-echo, spin-echo, turbo spin-echo techniques

    International Nuclear Information System (INIS)

    Lee, Young Joon; Joo, Eun Young; Eun, Choong Ki

    1999-01-01

    The purpose of this study was to evaluate the effects of magnetization transfer contrast(MTC) and fat-suppression(FS) in variable spin-echo and gradient-echo sequences for articular cartilage imaging and to determine the optimal pulse sequences. Using variable 7-pulse sequences, the knees of 15 pigs were imaged Axial images were obtained using proton density and T2-weighted spin-echo (PDWSE and T2WSE), turbo spin-echo (TSE), multiplanar gradient-echo (MPGR), and 3D steady-state gradient-echo (3DGRE) sequences, and the same pulse sequences were then repeated using MTC. Also T1-weighted spin-echo(T1WSE) and 3D spoiled gradient-echo(3DSPGR) images of knees were also acquired, and the procedure was repeated using FS. For each knee, a total of 14 axial images were acquired, and using a 6-band scoring system, the visibility of and the visibilities of the the articular cartilage was analyzed. The visual effect of MTC and FS was scored using a 4-band scale. For each image, the signal intensities of articular cartilage, subchondral bone, muscles, and saline were measured, and signal-to-noise ratios(SNR) and contrast-to-noise ratios(CNR) were also calculated. Visibility of the cartilage was best when 3DSPGR and T1WSE sequences were used. MTC imaging increased the negative contrast between cartilage and saline, but FS imaging provided more positive contrast. CNR between cartilage and saline was highest when using TSE with FS(-351.1±15.3), though CNR between cartilage and bone then fell to -14.7±10.8. In MTC imaging using MPGR showed the greatest increase of negative contrast between cartilage and saline(CNR change=-74.7); the next highest was when 3DGRE was used(CNR change=-34.3). CNR between cartilage and bone was highest with MPGR(161.9±17.7), but with MTC, the greatest CNR decrease(-81.8) was observed. The greatest CNR increase between cartilage and bone was noted in T1WSE with FS. In all scans, FS provided a cartilage-only positive contrast image, though the absolute

  8. Determination of the amounts of C, CH, CH/sub 2/, and CH fragments by the spin echo method

    Energy Technology Data Exchange (ETDEWEB)

    Polonov, V.M.; Kalabin, G.A.; Kushnarev, D.F.; Latyshev, V.P.

    1984-01-01

    A new method has been developed for the quantitative determination of the amounts of primary, secondary, tertiary, and quaternary carbon atoms in soluble products of coal origin which is based on pulsed sequence of /sup 13/C NMR spin echo.

  9. Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

    Science.gov (United States)

    Vogel, Ulrich; Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

    2012-06-01

    Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.

  10. Automated statistical matching of multiple tephra records exemplified using five long maar sequences younger than 75 ka, Auckland, New Zealand

    Science.gov (United States)

    Green, Rebecca M.; Bebbington, Mark S.; Cronin, Shane J.; Jones, Geoff

    2014-09-01

    Detailed tephrochronologies are built to underpin probabilistic volcanic hazard forecasting, and to understand the dynamics and history of diverse geomorphic, climatic, soil-forming and environmental processes. Complicating factors include highly variable tephra distribution over time; difficulty in correlating tephras from site to site based on physical and chemical properties; and uncertain age determinations. Multiple sites permit construction of more accurate composite tephra records, but correctly merging individual site records by recognizing common events and site-specific gaps is complex. We present an automated procedure for matching tephra sequences between multiple deposition sites using stochastic local optimization techniques. If individual tephra age determinations are not significantly different between sites, they are matched and a more precise age is assigned. Known stratigraphy and mineralogical or geochemical compositions are used to constrain tephra matches. We apply this method to match tephra records from five long sediment cores (≤ 75 cal ka BP) in Auckland, New Zealand. Sediments at these sites preserve basaltic tephras from local eruptions of the Auckland Volcanic Field as well as distal rhyolitic and andesitic tephras from Okataina, Taupo, Egmont, Tongariro, and Tuhua (Mayor Island) volcanic centers. The new correlated record compiled is statistically more likely than previously published arrangements from this area.

  11. Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

    OpenAIRE

    Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

    2017-01-01

    Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

  12. A radar-echo model for Mars

    International Nuclear Information System (INIS)

    Thompson, T.W.; Moore, H.J.

    1990-01-01

    Researchers developed a radar-echo model for Mars based on 12.6 cm continuous wave radio transmissions backscattered from the planet. The model broadly matches the variations in depolarized and polarized total radar cross sections with longitude observed by Goldstone in 1986 along 7 degrees S. and yields echo spectra that are generally similiar to the observed spectra. Radar map units in the model include an extensive cratered uplands unit with weak depolarized echo cross sections, average thermal inertias, moderate normal refelectivities, and moderate rms slopes; the volcanic units of Tharsis, Elysium, and Amazonis regions with strong depolarized echo cross sections, low thermal inertia, low normal reflectivities, and large rms slopes; and the northern planes units with moderate to strong depolarized echo cross sections, moderate to very high thermal inertias, moderate to large normal reflectivities, and moderate rms slopes. The relevance of the model to the interpretation of radar echoes from Mars is discussed

  13. The acoustics of the echo cornet

    Science.gov (United States)

    Pyle, Robert W., Jr.; Klaus, Sabine K.

    2002-11-01

    The echo cornet was an instrument produced by a number of makers in several countries from about the middle of the nineteenth to the early twentieth centuries. It consists of an ordinary three-valve cornet to which a fourth valve has been added, downstream of the three normal valves. The extra valve diverts the airstream from the normal bell to an ''echo'' bell that gives a muted tone quality. Although the air column through the echo bell is typically 15 cm longer than the path through the normal bell, there is no appreciable change of playing pitch when the echo bell is in use. Acoustic input impedance and impulse response measurements and consideration of the standing-wave pattern within the echo bell show how this can be so. Acoustically, the echo bell is more closely related to hand-stopping on the French horn than to the mutes commonly used on the trumpet and cornet.

  14. Beam echoes in the presence of coupling

    Energy Technology Data Exchange (ETDEWEB)

    Gross, Axel [Case Western Reserve U.

    2017-10-03

    Transverse beam echoes could provide a new technique of measuring diusion characteristics orders of magnitude faster than the current methods; however, their interaction with many accelerator parameters is poorly understood. Using a program written in C, we explored the relationship between coupling and echo strength. We found that echoes could be generated in both dimensions, even with a dipole kick in only one dimension. We found that the echo eects are not destroyed even when there is strong coupling, falling o only at extremely high coupling values. We found that at intermediate values of skew quadrupole strength, the decoherence time of the beam is greatly increased, causing a destruction of the echo eects. We found that this is caused by a narrowing of the tune width of the particles. Results from this study will help to provide recommendations to IOTA (Integrable Optics Test Accelerator) for their upcoming echo experiment.

  15. MR fingerprinting using the quick echo splitting NMR imaging technique.

    Science.gov (United States)

    Jiang, Yun; Ma, Dan; Jerecic, Renate; Duerk, Jeffrey; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A

    2017-03-01

    The purpose of the study is to develop a quantitative method for the relaxation properties with a reduced radio frequency (RF) power deposition by combining magnetic resonance fingerprinting (MRF) technique with quick echo splitting NMR imaging technique (QUEST). A QUEST-based MRF sequence was implemented to acquire high-order echoes by increasing the gaps between RF pulses. Bloch simulations were used to calculate a dictionary containing the range of physically plausible signal evolutions using a range of T 1 and T 2 values based on the pulse sequence. MRF-QUEST was evaluated by comparing to the results of spin-echo methods. The specific absorption rate (SAR) of MRF-QUEST was compared with the clinically available methods. MRF-QUEST quantifies the relaxation properties with good accuracy at the estimated head SAR of 0.03 W/kg. T 1 and T 2 values estimated by MRF-QUEST are in good agreement with the traditional methods. The combination of the MRF and the QUEST provides an accurate quantification of T 1 and T 2 simultaneously with reduced RF power deposition. The resulting lower SAR may provide a new acquisition strategy for MRF when RF energy deposition is problematic. Magn Reson Med 77:979-988, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  16. Intraluminal filling defects of the bile ducts: differentiation of stones from tumors-the value of magnetic resonance cholangiography in conjunction with a 3D spoiled gradient echo gadolinium enhanced dynamic sequence

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Soo Jin; Kim, Suk; Kim, Chang Won [Busan National University Hospital, Busan (Korea, Republic of)] (and others)

    2006-05-15

    We wanted to determinate the value of a dynamic volumetric interpolated breath-hold examination (VIBE) as a supplement to MR cholangiography for differentiating biliary stones from tumors when patient are suspected of having intraluminal filling defects on direct cholangiography. A retrospective analysis was performed for 49 patients who underwent MRI among all the patients who showed intraluminal filling defects on direct cholangiography for evaluating the cause of their jaundice from June 2002 to June 2003. After dividing these patients into two groups; i.e., the group with stones and the group wth tumors, we analyzed and compared each MR patterns of 1) signal intensity, 2) shape, and 3) enhancement. High signal intensity on T1-weighted images ({rho} < 0.001, X{sup 2} test), dark signal intensity on T2-weighted images ({rho} < 0.01, Fisher' s exact test) or smooth contour of intraluminal filling defects ({rho} < 0.001, X{sup 2} test) could be significantly suggestive findings of stone rather than a tumor mass. Dynamic VIBE is the most specific sequence for differentiating non-enhancing stone from an enhancing mass ({rho} < 0.001, Fisher' s exact test). We showed that MR cholangiography, when added to the dynamic VIBE sequences, could be an important imaging technique for patients who are suspected of having intraluminal filling defects on direct cholangiography to differentiate stones from tumors. Especially, the addition of dynamic VIBE images can provide the increased level of confidence in the diagnosis.

  17. Comparison of gradient-recalled echo and spin-echo echo-planar imaging MR elastography in staging liver fibrosis. A meta-analysis

    International Nuclear Information System (INIS)

    Kim, Yong Seek; Jang, Yu Na; Song, Ji Soo

    2018-01-01

    To compare the diagnostic performance of gradient-recalled echo-based magnetic resonance elastography (GRE-MRE) and spin-echo echo-planar imaging-based MRE (SE-EPI-MRE) in liver fibrosis staging. A systematic literature search was performed to identify studies involving the performance of MRE for the diagnosis of liver fibrosis. Pooled sensitivity, specificity, positive and negative likelihood ratios, the diagnostic odds ratio, and a summary receiver operating characteristic (ROC) curve were estimated by using a bivariate random effects model. Subgroup analyses were performed between different study characteristics. Twenty-six studies with a total of 3,200 patients were included in the meta-analysis. Pooled sensitivity and specificity of GRE-MRE and SE-EPI-MRE did not differ significantly. The area under the summary ROC curve for stage diagnosis of any (F ≥ 1), significant (F ≥ 2), advanced (F ≥ 3), and cirrhosis (F = 4) on GRE-MRE and SE-EPI-MRE were 0.93 versus 0.94, 0.95 versus 0.94, 0.94 versus 0.95, and 0.92 versus 0.93, respectively. Substantial heterogeneity was detected for both sequences. Both GRE and SE-EPI-MRE show high sensitivity and specificity for detection of each stage of liver fibrosis, without significant differences. Magnetic resonance elastography (MRE) may be useful for noninvasive evaluation of liver fibrosis in chronic liver disease. (orig.)

  18. 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.

  19. In vitro and in vivo comparison of wrist MR imaging at 3.0 and 7.0 tesla using a gradient echo sequence and identical eight-channel coil array designs.

    Science.gov (United States)

    Nordmeyer-Massner, Jurek A; Wyss, Michael; Andreisek, Gustav; Pruessmann, Klaas P; Hodler, Juerg

    2011-03-01

    To evaluate in vivo MR imaging of the wrist at 3.0 Tesla (T) and 7.0T quantitatively and qualitatively. To enable unbiased signal-to-noise ratio (SNR) comparisons, geometrically identical eight-channel receiver arrays were used at both field strengths. First, in vitro images of a phantom bottle were acquired at 3.0T and 7.0T to obtain an estimate of the maximum SNR gain that can be expected. MR images of the dominant wrist of 10 healthy volunteers were acquired at both field strengths. All measurements were done using the same sequence parameters. Quantitative SNR maps were calculated on a pixel-by-pixel basis and analyzed in several regions-of-interest. Furthermore, the images were qualitatively evaluated by two independent radiologists. The quantitative analysis showed SNR increases of up to 100% at 7.0T compared with 3.0T, with considerable variation between different anatomical structures. The qualitative analysis revealed no significant difference in the visualization of anatomical structures comparing 3.0T and 7.0T MR images (P>0.05). The presented results establish the SNR benefits of the transition from 3.0T to 7.0T for wrist imaging without bias by different array designs and based on exact, algebraic SNR quantification. The observed SNR increase nearly reaches expected values but varies greatly between different tissues. It does not necessarily improve the visibility of anatomic structures but adds valuable latitude for sequence optimization. Copyright © 2011 Wiley-Liss, Inc.

  20. 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.

  1. Light echoes - Type II supernovae

    International Nuclear Information System (INIS)

    Schaefer, B.E.

    1987-01-01

    Type II supernovae (SNs) light curves show a remarkable range of shapes. Data have been collected for the 12 Type II SNs that have light curve information for more than four months past maximum. Contrary to previous reports, it is found that (1) the decay rate after 100 days past maximum varies by almost an order of magnitude and (2) the light curve shapes are not bimodally distributed, but actually form a continuum. In addition, it is found that the extinctions to the SNs are related to the light curve shapes. This implies that the absorbing dust is local to the SNs. The dust is likely to be part of a circumstellar shell emitted by the SN progenitor that Dwek (1983) has used to explain infrared echoes. The optical depth of the shell can get quite large. In such cases, it is found that the photons scattered and delayed by reflection off dust grains will dominate the light curve several months after peak brightness. This light echo offers a straightforward explanation of the diversity of Type II SN light curves. 22 references

  2. Clinical characteristics in normal healthy adults with microbleeds on echo-planar gradient-echo T2*-weighted MRI

    International Nuclear Information System (INIS)

    Takahashi, Wakoh; Ide, Michiru; Ohnuki, Tomohide; Takagi, Shigeharu; Shinohara, Yukito

    2004-01-01

    The gradient-echo T 2 * -weighted sequence in magnetic resonance imaging is known to be useful for detecting microbleeds (MBs) in patients with intracranial hemorrhage or lacunar stroke. We investigated the characteristics of apparently healthy adults with MBs but without stroke, employing echo-planar gradient-echo T 2 * -weighted MRI. The subjects were recruited from among 3,537 participants who underwent brain check-ups at the HIMEDIC Imaging Center. Of the 3,537 participants, 3,296 (mean age, 55±11 years) without any history of cerebrovascular disease or apparent focal neurological manifestations were selected for the present study. MBs on echo-planar gradient-echo T 2 * -weighted MRI were observed in 74 (2.2%) of the 3,296 subjects. Of a total of 133 lesions found in these 74 persons, 31 were located in the basal ganglia or cortico-subcortical regions. Thirty were in the deep white matter, 19 in the thalamus, 16 in the cerebellum, and 6 in the brain stem. The subjects with MBs were significantly older than the subjects without MBs, and the mean values for their systolic and diastolic blood pressures were higher than those in the subjects without MBs. Asymptomatic cerebral infarction, periventricular hyperintensity, and deep and subcortical white matter hyperintensity on T 1 - and T 2 -weighted MRI were more frequent in the subjects with MBs, as compared with those without MBs. Asymptomatic cerebral infarction, periventricular hyperintensity, and deep and subcortical white matter hyperintensity on T 1 - and T 2 -weighted MRI were more frequent in the subjects with MBs of the basal ganglia or thalamus than in those with MBs in other regions. MBs on echo-planar gradient-echo T 2 * -weighted MRI were thus relatively rare in apparently healthy adults. However, MBs in the basal ganglia or thalamus are suggested to be closely related to intracerebral microangiopathy. Persons with MBs in such regions should therefore be carefully checked for cerebrovascular risk

  3. Analysis and functional annotation of expressed sequence tags (ESTs from multiple tissues of oil palm (Elaeis guineensis Jacq.

    Directory of Open Access Journals (Sweden)

    Lee Weng-Wah

    2007-10-01

    Full Text Available Abstract Background Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST analysis on oil palm. Results In this study, six cDNA libraries from oil palm zygotic embryos, suspension cells, shoot apical meristems, young flowers, mature flowers and roots, were constructed. We have generated a total of 14537 expressed sequence tags (ESTs from these libraries, from which 6464 tentative unique contigs (TUCs and 2129 singletons were obtained. Approximately 6008 of these tentative unique genes (TUGs have significant matches to the non-redundant protein database, from which 2361 were assigned to one or more Gene Ontology categories. Predominant transcripts and differentially expressed genes were identified in multiple oil palm tissues. Homologues of genes involved in many aspects of flower development were also identified among the EST collection, such as CONSTANS-like, AGAMOUS-like (AGL2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP etc. Majority of them are the first representatives in oil palm, providing opportunities to explore the cause of epigenetic homeotic flowering abnormality in oil palm, given the importance of flowering in fruit production. The transcript levels of two flowering-related genes, EgSBP and EgSEP were analysed in the flower tissues of various developmental stages. Gene homologues for enzymes involved in oil biosynthesis, utilization of nitrogen sources, and scavenging of oxygen radicals, were also uncovered among the oil palm ESTs. Conclusion The EST sequences generated will allow comparative genomic studies between oil palm and other monocotyledonous and dicotyledonous plants, development of gene-targeted markers for the reference genetic map

  4. Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

    2016-01-01

    We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

  5. Importance of T2*-weighted gradient-echo MRI for diagnosis of cortical vein thrombosis

    Energy Technology Data Exchange (ETDEWEB)

    Fellner, Franz A. [Institut fuer Radiologie, Landes-Nervenklinik Wagner Jauregg, Linz (Austria) and Zentrales Radiologie Institut, Allgemeines Krankenhaus der Stadt Linz, Krankenhausstr. 9, 4020 Linz (Austria)]. E-mail: franz.fellner@akh.linz.at; Fellner, Claudia [Institut fuer Radiologie, Landes-Nervenklinik Wagner Jauregg, Linz (Austria); Aichner, Franz T. [Abteilung fuer Neurologie, Landes-Nervenklinik Wagner-Jauregg, Linz (Austria); Moelzer, Guenther [Institut fuer Radiologie, Landes-Nervenklinik Wagner Jauregg, Linz (Austria)

    2005-11-01

    We examined six patients with isolated venous thrombosis (n = 2), or venous thrombosis combined with sinus thrombosis (n = 4) (CVT). The clinical symptoms were non-specific (acute cephalea, paresis, epileptic seizure, progressive speech disorder). All examinations were performed on a 1.5 T system (Magnetom Symphony, Siemens, Erlangen, Germany), maximum gradient field strength 30 mT/m, minimal gradient rise time 450 {mu}s, according to the following protocol: Transverse T2-weighted turbo spin-echo (TSE), fluid attenuated inversion recovery (FLAIR), T1-weighted spin-echo (SE), before and after administration of contrast medium, T2*-weighted conventional gradient-echo (GRE), T2*-weighted spin-echo echo planar imaging (SE EPI), both without and with diffusion weighting as well as two-dimensional (2D) venous time-of-flight (TOF) MRA. The venous thromboses were best detectable in the T2*-weighted conventional GRE sequence in all patients. In two patients, the CVT was discernible only in this sequence. The sinus thrombosis was well discernible only in the T2*-weighted GRE sequence in only one case; in the remaining cases it was detectable only with difficulty. For these cases, other sequences such as SE, diffusion-weighted, or 2D-TOF-MRA sequence were superior. The T2*-weighted conventional GRE sequence was superior to the T2*-weighted SE EPI sequence in all patients. To sum up, it can be concluded, that T2*-weighted conventional GRE sequences are possibly the best method of detection of acute cortical vein thromboses. Therefore, it seems to be of benefit to integrate a T2*-weighted conventional GRE sequence into the MR-protocol for the diagnosis of isolated cortical vein thrombosis.

  6. Importance of T2*-weighted gradient-echo MRI for diagnosis of cortical vein thrombosis

    International Nuclear Information System (INIS)

    Fellner, Franz A.; Fellner, Claudia; Aichner, Franz T.; Moelzer, Guenther

    2005-01-01

    We examined six patients with isolated venous thrombosis (n = 2), or venous thrombosis combined with sinus thrombosis (n = 4) (CVT). The clinical symptoms were non-specific (acute cephalea, paresis, epileptic seizure, progressive speech disorder). All examinations were performed on a 1.5 T system (Magnetom Symphony, Siemens, Erlangen, Germany), maximum gradient field strength 30 mT/m, minimal gradient rise time 450 μs, according to the following protocol: Transverse T2-weighted turbo spin-echo (TSE), fluid attenuated inversion recovery (FLAIR), T1-weighted spin-echo (SE), before and after administration of contrast medium, T2*-weighted conventional gradient-echo (GRE), T2*-weighted spin-echo echo planar imaging (SE EPI), both without and with diffusion weighting as well as two-dimensional (2D) venous time-of-flight (TOF) MRA. The venous thromboses were best detectable in the T2*-weighted conventional GRE sequence in all patients. In two patients, the CVT was discernible only in this sequence. The sinus thrombosis was well discernible only in the T2*-weighted GRE sequence in only one case; in the remaining cases it was detectable only with difficulty. For these cases, other sequences such as SE, diffusion-weighted, or 2D-TOF-MRA sequence were superior. The T2*-weighted conventional GRE sequence was superior to the T2*-weighted SE EPI sequence in all patients. To sum up, it can be concluded, that T2*-weighted conventional GRE sequences are possibly the best method of detection of acute cortical vein thromboses. Therefore, it seems to be of benefit to integrate a T2*-weighted conventional GRE sequence into the MR-protocol for the diagnosis of isolated cortical vein thrombosis

  7. Incidence of a didactic sequence, based on multiple representations, for the strengthening of argumentative competence in high school students

    Directory of Open Access Journals (Sweden)

    Gustavo Bonilla

    2018-01-01

    Full Text Available The present article; seeks to identify the way in which a didactic sequence, based on the implementation of multiple representations, can have an impact on the strengthening of the argumentative competence in basic secondary school students. The methodological foundation on which is based the research, taking into account the mixed approach as a perspective that properly oriented, the exercise of research in the field of education. In view of the above, it performs a process of pedagogical intervention related to the general law of ideal gases, through the implementation of the elements presented in the didactic cycle with a research approach and with the application of a pretest and posttest. The techniques to be used for the process of intervention are the participant observation, the discussion group and the survey. Specifically, as instruments for the collection of information; the interview focused, semi-structured interview and the questions guide. The unit of work corresponds to 36 students --240, six students per each group of 9°-- the basic secondary educational institutions belonging to the Citadel New West, located in the Commune 60 and The Heart, located in the commune 13; both in the city of Medellín.

  8. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

    Science.gov (United States)

    Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

    2014-11-01

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia

    Institute of Scientific and Technical Information of China (English)

    Jinsong Tang; Fan He; Fengyu Zhang; Yin Yao Shugart; Chunyu Liu; Yanqing Tang; Raymond C.K.Chan; Chuan-Yue Wang; Yong-Gang Yao; Xiaogang Chen; Yu Fan; Hong Li; Qun Xiang; Deng-Feng Zhang; Zongchang Li; Ying He; Yanhui Liao; Ya Wang

    2017-01-01

    Schizophrenia is a common disorder with a high heritability,but its genetic architecture is still elusive.We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia.Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins,which were either located in previously reported schizophrenia risk genes (p.V24689I mutation in TTN,p.S2506T mutation in GCN1L1,IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis.By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes,we were able to distill genetic alterations in several schizophrenia risk genes,including GAD1,PLXNA2,RELN and FEZ1.Four inherited copy number variations (CNVs;including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families,respectively.Most of families carried both missense DNMs and inherited risk variants,which might suggest that DNMs,inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility.Our results support that schizophrenia is caused by a combination of multiple genetic factors,with each DNM/variant showing a relatively small effect size.

  10. Diagnostic equivalence of conventional and fast spin echo magnetic resonance imaging of the anterior cruciate ligament of the knee

    International Nuclear Information System (INIS)

    Munk, P.L.; Hilborn, M.D.; Vellet, A.D.; University of Calgary, Calgary, Alberta,; Romano, C.C.; University of Calgary, Calgary, Alberta,

    1997-01-01

    Many techniques and pulse sequences have been devised for the assessment of the anterior cruciate ligament. The present study compares fast spin echo (FSE) imaging to conventional spin echo imaging at a field strength of 1.5 T in an effort to determine if these sequences are diagnostically equivalent. Where available, arthroscopy was also done. A total of 52 patients were imaged using both FSE and conventional spin echo sequences. Eight volunteers were used as controls. Arthroscopy was performed on 10 patients. The anterior cruciate ligament was assessed in a blinded fashion by three radiologists. The Kappa statistic was then used to determine the percentage agreement between FSE and conventional spin echo imaging. Fast spin echo sequencing demonstrated a sensitivity of 100%, a specificity of 94.8% and an accuracy of 96.3% when compared to arthroscopy. Conventional spin echo imaging and arthroscopy had a sensitivity of 100%, specificity of 84.6% and an accuracy of 88.9%. The remaining 34 patients who did not undergo arthroscopy were followed clinically because clinical and imaging findings were not suggestive of ACL tears. These demonstrated 72% agreement between FSE and conventional spin echo imaging using the Kappa statistic, with regards to calling ACL normal or having only a low-grade partial tear. Fast spin echo imaging produces images of the anterior cruciate ligament that have similar diagnostic accuracy to conventional spin echo images (P<0.05) within a much shorter scan time. These results however, require further validation in a larger group, preferably with arthroscopic correlation. (author)

  11. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia.

    Science.gov (United States)

    Tang, Jinsong; Fan, Yu; Li, Hong; Xiang, Qun; Zhang, Deng-Feng; Li, Zongchang; He, Ying; Liao, Yanhui; Wang, Ya; He, Fan; Zhang, Fengyu; Shugart, Yin Yao; Liu, Chunyu; Tang, Yanqing; Chan, Raymond C K; Wang, Chuan-Yue; Yao, Yong-Gang; Chen, Xiaogang

    2017-06-20

    Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p.V24689I mutation in TTN, p.S2506T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations (CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. All rights reserved.

  12. Performance Analysis of Direct-Sequence Code-Division Multiple-Access Communications with Asymmetric Quadrature Phase-Shift-Keying Modulation

    Science.gov (United States)

    Wang, C.-W.; Stark, W.

    2005-01-01

    This article considers a quaternary direct-sequence code-division multiple-access (DS-CDMA) communication system with asymmetric quadrature phase-shift-keying (AQPSK) modulation for unequal error protection (UEP) capability. Both time synchronous and asynchronous cases are investigated. An expression for the probability distribution of the multiple-access interference is derived. The exact bit-error performance and the approximate performance using a Gaussian approximation and random signature sequences are evaluated by extending the techniques used for uniform quadrature phase-shift-keying (QPSK) and binary phase-shift-keying (BPSK) DS-CDMA systems. Finally, a general system model with unequal user power and the near-far problem is considered and analyzed. The results show that, for a system with UEP capability, the less protected data bits are more sensitive to the near-far effect that occurs in a multiple-access environment than are the more protected bits.

  13. Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

    Science.gov (United States)

    Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

    2013-09-01

    Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

  14. Gravitational wave sources: reflections and echoes

    Science.gov (United States)

    Price, Richard H.; Khanna, Gaurav

    2017-11-01

    The recent detection of gravitational waves has generated interest in alternatives to the black hole interpretation of sources. A subset of such alternatives involves a prediction of gravitational wave ‘echoes’. We consider two aspects of possible echoes: first, general features of echoes coming from spacetime reflecting conditions. We find that the detailed nature of such echoes does not bear any clear relationship to quasi-normal frequencies. Second, we point out the pitfalls in the analysis of local reflecting ‘walls’ near the horizon of rapidly rotating black holes.

  15. Gravitational wave sources: reflections and echoes

    International Nuclear Information System (INIS)

    Price, Richard H; Khanna, Gaurav

    2017-01-01

    The recent detection of gravitational waves has generated interest in alternatives to the black hole interpretation of sources. A subset of such alternatives involves a prediction of gravitational wave ‘echoes’. We consider two aspects of possible echoes: first, general features of echoes coming from spacetime reflecting conditions. We find that the detailed nature of such echoes does not bear any clear relationship to quasi-normal frequencies. Second, we point out the pitfalls in the analysis of local reflecting ‘walls’ near the horizon of rapidly rotating black holes. (paper)

  16. 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

  17. 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.

  18. Two-pulse and stimulated nuclear-quadrupole-resonance echoes in YAlO3:Pr3+

    International Nuclear Information System (INIS)

    Erickson, L.E.

    1991-01-01

    The dephasing of trivalent praseodymium dilute in yttrium aluminum oxide (YAlO 3 ) in the ground electronic state 3 H 4 state is evaluated using an optically detected method, to measure two-rf-pulse- and three-rf-pulse-stimulated nuclear quadrupole echoes. The magnitude of the echo is obtained by detecting the weak Raman optical field generated by the interaction of the magnetic moment of the echo and a light beam resonant with the 3 H 4 (0 cm 1 ) to 1 D 2 (16 374 cm -1 ) optical transition. This same light beam is used as an optical pump (37-ms duration) prior the rf-pulse sequence to increase the population difference of the hyperfine energy levels, thereby improving the echo signal. The light is turned off 9 ms before the rf-pulse sequence and remains off until the echo to avoid optical-pumping effects on the measured nuclear-quadrupole-resonance (NQR) echo lifetime. The dephasing time T 2 from two-pulse nuclear-quadrupole-echo measurement is found to be 366±29 μs

  19. Continuous Online Sequence Learning with an Unsupervised Neural Network Model.

    Science.gov (United States)

    Cui, Yuwei; Ahmad, Subutar; Hawkins, Jeff

    2016-09-14

    The ability to recognize and predict temporal sequences of sensory inputs is vital for survival in natural environments. Based on many known properties of cortical neurons, hierarchical temporal memory (HTM) sequence memory recently has been proposed as a theoretical framework for sequence learning in the cortex. In this letter, we analyze properties of HTM sequence memory and apply it to sequence learning and prediction problems with streaming data. We show the model is able to continuously learn a large number of variableorder temporal sequences using an unsupervised Hebbian-like learning rule. The sparse temporal codes formed by the model can robustly handle branching temporal sequences by maintaining multiple predictions until there is sufficient disambiguating evidence. We compare the HTM sequence memory with other sequence learning algorithms, including statistical methods: autoregressive integrated moving average; feedforward neural networks-time delay neural network and online sequential extreme learning machine; and recurrent neural networks-long short-term memory and echo-state networks on sequence prediction problems with both artificial and real-world data. The HTM model achieves comparable accuracy to other state-of-the-art algorithms. The model also exhibits properties that are critical for sequence learning, including continuous online learning, the ability to handle multiple predictions and branching sequences with high-order statistics, robustness to sensor noise and fault tolerance, and good performance without task-specific hyperparameter tuning. Therefore, the HTM sequence memory not only advances our understanding of how the brain may solve the sequence learning problem but is also applicable to real-world sequence learning problems from continuous data streams.

  20. Echoes in correlated neural systems

    International Nuclear Information System (INIS)

    Helias, M; Tetzlaff, T; Diesmann, M

    2013-01-01

    Correlations are employed in modern physics to explain microscopic and macroscopic phenomena, like the fractional quantum Hall effect and the Mott insulator state in high temperature superconductors and ultracold atoms. Simultaneously probed neurons in the intact brain reveal correlations between their activity, an important measure to study information processing in the brain that also influences the macroscopic signals of neural activity, like the electroencephalogram (EEG). Networks of spiking neurons differ from most physical systems: the interaction between elements is directed, time delayed, mediated by short pulses and each neuron receives events from thousands of neurons. Even the stationary state of the network cannot be described by equilibrium statistical mechanics. Here we develop a quantitative theory of pairwise correlations in finite-sized random networks of spiking neurons. We derive explicit analytic expressions for the population-averaged cross correlation functions. Our theory explains why the intuitive mean field description fails, how the echo of single action potentials causes an apparent lag of inhibition with respect to excitation and how the size of the network can be scaled while maintaining its dynamical state. Finally, we derive a new criterion for the emergence of collective oscillations from the spectrum of the time-evolution propagator. (paper)

  1. Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

    Directory of Open Access Journals (Sweden)

    Yi eWang

    2016-05-01

    Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

  2. PriFi - Using a Multiple Alignment of Related Sequences to Find Primers for  Amplification of Homologs

    DEFF Research Database (Denmark)

    Fredslund, Jakob; Schauser, Leif; Madsen, Lene Heegaard

    2005-01-01

    Using a comparative approach, the web program PriFi (http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main) designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available. The program works with an alignment of DNA sequences from phylog...

  3. Wind yield forecast with Echo State Networks; Windertragsprognose mit Echo State Networks

    Energy Technology Data Exchange (ETDEWEB)

    Kobialka, Hans-Ulrich [Fraunhofer IAIS, Sankt Augustin (Germany)

    2012-07-01

    Statistical methods are able to create models of complex system dynamics which are difficult to capture analytically. This paper describes a wind energy prediction system based on a machine learning method, called Echo State Networks. Echo State Networks enable the training of large recurrent neural networks which are able to model and predict highly non-linear system dynamics. This paper gives a short description of Echo State Networks and the realization of the wind energy prediction system. (orig.)

  4. 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).

  5. 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).

  6. MEASUREMENT OF TRANSVERSE ECHOES IN RHIC

    International Nuclear Information System (INIS)

    FISCHER, W.; SATOGATA, T.; TOMAS, R.

    2005-01-01

    Beam echoes are a very sensitive method to measure diffusion, and longitudinal echo measurements were performed in a number of machines. In RHIC, for the first time, a transverse beam echo was observed after applying a dipole kick followed by a quadrupole .kick. After application of the dipole kick, the dipole moment decohered completely due to lattice nonlinearities. When a quadrupole kick is applied at time τ after the dipole kick, the beam re-cohered at time 2τ thus showing an echo response. We describe the experimental setup and measurement results. In the measurements the dipole and quadrupole kick amplitudes, amplitude dependent tune shift, and the time between dipole and quadrupole kick were varied. In addition, measurements were taken with gold bunches of different intensities. These should exhibit different transverse diffusion rates due to intra-beam scattering

  7. Water Dashboard Help | ECHO | US EPA

    Science.gov (United States)

    The dashboards on the 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).

  8. Stellar Echo Imaging of Exoplanets, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — All stars exhibit intensity fluctuations over several time scales, from nanoseconds to days; these intensity fluctuations echo off planetary bodies in the star...

  9. Stellar Echo Imaging of Exoplanets, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — All stars exhibit intensity fluctuations over several time scales, from nanoseconds to days; these intensity fluctuations echo off planetary bodies in the star...

  10. 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.

  11. 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,...

  12. Imaging 2015 Mw 7.8 Gorkha Earthquake and Its Aftershock Sequence Combining Multiple Calibrated Global Seismic Arrays

    Science.gov (United States)

    LI, B.; Ghosh, A.

    2016-12-01

    The 2015 Mw 7.8 Gorkha earthquake provides a good opportunity to study the tectonics and earthquake hazards in the Himalayas, one of the most seismically active plate boundaries. Details of the seismicity patterns and associated structures in the Himalayas are poorly understood mainly due to limited instrumentation. Here, we apply a back-projection method to study the mainshock rupture and the following aftershock sequence using four large aperture global seismic arrays. All the arrays show eastward rupture propagation of about 130 km and reveal similar evolution of seismic energy radiation, with strong high-frequency energy burst about 50 km north of Kathmandu. Each single array, however, is typically limited by large azimuthal gap, low resolution, and artifacts due to unmodeled velocity structures. Therefore, we use a self-consistent empirical calibration method to combine four different arrays to image the Gorkha event. It greatly improves the resolution, can better track rupture and reveal details that cannot be resolved by any individual array. In addition, we also use the same arrays at teleseismic distances and apply a back-projection technique to detect and locate the aftershocks immediately following the Gorkha earthquake. We detect about 2.5 times the aftershocks recorded by the Advance National Seismic System comprehensive earthquake catalog during the 19 days following the mainshock. The aftershocks detected by the arrays show an east-west trend in general, with majority of the aftershocks located at the eastern part of the rupture patch and surrounding the rupture zone of the largest Mw 7.3 aftershock. Overall spatiotemporal aftershock pattern agrees well with global catalog, with our catalog showing more details relative to the standard global catalog. The improved aftershock catalog enables us to better study the aftershock dynamics, stress evolution in this region. Moreover, rapid and better imaging of aftershock distribution may aid rapid response

  13. Report Environmental Violations | 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.

  14. Denuncie violaciones ambientales | 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.

  15. 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.

  16. DWDashboard_Year.png | 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.

  17. summarytable.PNG | 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.

  18. dashboard_3.PNG | 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.

  19. ExampleDFR.PNG | 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.

  20. monperload_1.PNG | ECHO | US EPA