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Sample records for inversion recovery sequences

  1. Pre- and Postcontrast 3D Double Inversion Recovery Sequence in Multiple Sclerosis: A Simple and Effective MR Imaging Protocol.

    PubMed

    Eichinger, P; Kirschke, J S; Hoshi, M-M; Zimmer, C; Mühlau, M; Riederer, I

    2017-07-27

    The double inversion recovery sequence is known to be very sensitive and specific for MS-related lesions. Our aim was to compare the sensitivity of pre- and postcontrast images of 3D double inversion recovery and conventional 3D T1-weighted images for the detection of contrast-enhancing MS-related lesions in the brain to analyze whether double inversion recovery could be as effective as T1WI. A postcontrast 3D double inversion recovery sequence was acquired in addition to the standard MR imaging protocol at 3T, including pre- and postcontrast 3D T1WI sequences as well as precontrast double inversion recovery of 45 consecutive patients with MS or clinically isolated syndrome between June and December 2013. Two neuroradiologists independently assessed precontrast, postcontrast, and subtraction images of double inversion recovery as well as T1WI to count the number of contrast-enhancing lesions. Afterward, a consensus reading was performed. Lin concordance was calculated between both radiologists, and differences in lesion detectability were assessed with the Student t test. Additionally, the contrast-to-noise ratio was calculated. Significantly more contrast-enhancing lesions could be detected with double inversion recovery compared with T1WI (16%, 214 versus 185, P = .007). The concordance between both radiologists was almost perfect (ρc = 0.94 for T1WI and ρc = 0.98 for double inversion recovery, respectively). The contrast-to-noise ratio was significantly higher in double inversion recovery subtraction images compared with T1-weighted subtraction images (double inversion recovery, 14.3 ± 5.5; T1WI, 6.3 ± 7.1; P < .001). Pre- and postcontrast double inversion recovery enables better detection of contrast-enhancing lesions in MS in the brain compared with T1WI and may be considered an alternative to the standard MR imaging protocol. © 2017 American Society of Neuroradiology.

  2. Comparison of Diffuse Weighted Imaging and Fluid Attenuation Inversion Recovery Sequences of MRI in Brain Multiple Sclerosis Plaques Detection.

    PubMed

    Nafisi-Moghadam, Reza; Rahimdel, Abolghasem; Shanbehzadeh, Tahereh; Fallah, Razieh

    2017-01-01

    Suitable magnetic resonance imaging (MRI) techniques from conventional to new devices can help physicians in diagnosis and follow up of Multiple Sclerosis (MS) patients. The aim of present research was to compare effectiveness of Fluid Attenuation Inversion Recovery (FLAIR) sequence of conventional MRI and Diffuse Weighted Imaging (DWI) sequence as a new technique in detection of brain MS plaques. In this analytic cross sectional study, sample size was assessed as 40 people to detect any significant difference between two sequences with a level of 0.05. DWI and FLAIR sequences of without contrast brain MRI of consecutive MS patients referred to MRI center of Shahid Sadoughi Hospital, Yazd, Iran from January to May 2012, were evaluated. Thirty-two females and 8 males with mean age of 35.20±9.80 yr (range = 11-66 yr) were evaluated and finally 340 plaques including 127(37.2%) in T2WI, 127(37.2%) in FLAIR, 63(18.5%) in DWI and 24(7.1%) in T1WI were detected. FLAIR sequence was more efficient than DWI in detection of brain MS plaques, oval, round, amorphous plaque shapes, frontal and occipital lobes, periventricular, intracapsular, corpus callosum, centrum semiovale, subcortical, basal ganglia plaques and diameter of detected MS plaques in DWI sequence was smaller than in FLAIR. Old lesion can be detected by conventional MRI and new techniques might be more useful in early inflammatory phase of MS and assessment of experimental treatments.

  3. Spinal cord infarction due to fibrocartilaginous embolization: the role of diffusion weighted imaging and short-tau inversion recovery sequences.

    PubMed

    Manara, Renzo; Calderone, Milena; Severino, Maria Savina; Citton, Valentina; Toldo, Irene; Laverda, Anna Maria; Sartori, Stefano

    2010-08-01

    Fibrocartilaginous embolization is a rare cause of ischemic myelopathy caused by embolization of intersomatic disk nucleus pulposus into spinal vasculature during Valsalva-like maneuvers. Diagnostic criteria are based on patient's clinical history, magnetic resonance evidence of T2-hyperintense spinal cord lesion, and exclusion of other causes of ischemic myelopathy. These criteria do not take into account the development of magnetic resonance techniques able to enhance signal abnormalities within the neighboring intersomatic disc or vertebral body and to early characterize central nervous system lesions according to the presence of cytotoxic edema. We present 2 pediatric cases of progressive paraplegia attributed to fibrocartilaginous embolization in which short-tau inversion recovery and diffusion-weighted imaging sequences played a pivotal role showing the ischemic nature of spinal cord lesions. Due to its specificity, diffusion-weighted imaging should be included in the magnetic resonance criteria of fibrocartilaginous embolization and in standard magnetic resonance analysis when dealing with acute transverse myelopathy.

  4. Combined saturation/inversion recovery sequences for improved evaluation of scar and diffuse fibrosis in patients with arrhythmia or heart rate variability.

    PubMed

    Weingärtner, Sebastian; Akçakaya, Mehmet; Basha, Tamer; Kissinger, Kraig V; Goddu, Beth; Berg, Sophie; Manning, Warren J; Nezafat, Reza

    2014-03-01

    To develop arrhythmia-insensitive inversion recovery sequences for improved visualization of myocardial scar and quantification of diffuse fibrosis. A novel preparation pre-pulse, called saturation pulse prepared heart-rate-independent inversion recovery, is introduced, which consists of a combination of saturation and inversion pulses to remove the magnetization history in each heartbeat in late gadolinium enhancement (LGE) imaging and eliminate the need for rest periods in T1 mapping. The proposed LGE and T1 mapping sequences were evaluated against conventional LGE and modified Look-Locker inversion sequences using numerical simulations, phantom and imaging in healthy subjects and patients with suspected or known cardiovascular disease. Simulations and phantom experiments show that the saturation pulse prepared heart-rate-independent inversion recovery pre-pulse in LGE reduces ghosting artifacts and results in perfect nulling of the healthy myocardium in the presence of arrhythmia. In T1 mapping, saturation pulse prepared heart-rate-independent inversion recovery results in (a) reduced scan time (17 vs. 9 heartbeats), (b) insensitivity to heart rate for long T1, and (c) increased signal homogeneity for short T1. LGE images in a patient in atrial fibrillation during the scan show improved myocardial nulling. In vivo T1 maps demonstrate increased signal homogeneity in blood pools and myocardium. The proposed sequences are insensitive to heart rate variability, yield improved LGE images in the presence of arrhythmias, as well as T1 mapping with shorter scan times. Copyright © 2013 Wiley Periodicals, Inc.

  5. Comparison of Diffuse Weighted Imaging and Fluid Attenuation Inversion Recovery Sequences of MRI in Brain Multiple Sclerosis Plaques Detection

    PubMed Central

    NAFISI-MOGHADAM, Reza; RAHIMDEL, Abolghasem; SHANBEHZADEH, Tahereh; FALLAH, Razieh

    2017-01-01

    Objective Suitable magnetic resonance imaging (MRI) techniques from conventional to new devices can help physicians in diagnosis and follow up of Multiple Sclerosis (MS) patients. The aim of present research was to compare effectiveness of Fluid Attenuation Inversion Recovery (FLAIR) sequence of conventional MRI and Diffuse Weighted Imaging (DWI) sequence as a new technique in detection of brain MS plaques. Materials & Methods In this analytic cross sectional study, sample size was assessed as 40 people to detect any significant difference between two sequences with a level of 0.05. DWI and FLAIR sequences of without contrast brain MRI of consecutive MS patients referred to MRI center of Shahid Sadoughi Hospital, Yazd, Iran from January to May 2012, were evaluated. Results Thirty-two females and 8 males with mean age of 35.20±9.80 yr (range = 11-66 yr) were evaluated and finally 340 plaques including 127(37.2%) in T2WI, 127(37.2%) in FLAIR, 63(18.5%) in DWI and 24(7.1%) in T1WI were detected. FLAIR sequence was more efficient than DWI in detection of brain MS plaques, oval, round, amorphous plaque shapes, frontal and occipital lobes, periventricular, intracapsular, corpus callosum, centrum semiovale, subcortical, basal ganglia plaques and diameter of detected MS plaques in DWI sequence was smaller than in FLAIR. Conclusion Old lesion can be detected by conventional MRI and new techniques might be more useful in early inflammatory phase of MS and assessment of experimental treatments. PMID:28277551

  6. Diagnostic accuracy of short-time inversion recovery sequence in Graves' Ophthalmopathy before and after prednisone treatment.

    PubMed

    Tortora, Fabio; Prudente, Mariaevelina; Cirillo, Mario; Elefante, Andrea; Belfiore, Maria Paola; Romano, Francesco; Cappabianca, Salvatore; Carella, Carlo; Cirillo, Sossio

    2014-05-01

    In Graves' Ophthalmopathy, it is important to distinguish active inflammatory phase, responsive to immunosuppressive treatment, from fibrotic unresponsive inactive one. The purpose of this study is, first, to identify the relevant orbital magnetic resonance imaging signal intensities before treatment, so to classify patients according to their clinical activity score (CAS), discriminating inactive (CAS < 3) from active Graves' Ophthalmopathy (GO) (CAS > 3) subjects and, second, to follow post-steroid treatment disease. An observational study was executed on 32 GO consecutive patients in different phases of disease, based on clinical and orbital Magnetic Resonance Imaging parameters, compared to 32 healthy volunteers. Orbital Magnetic Resonance Imaging was performed on a 1.5 tesla Magnetic Resonance Unit by an experienced neuroradiologist blinded to the clinical examinations. In pre-therapy patients, compared to controls, a medial rectus muscle statistically significant signal intensity ratio (SIR) in short-time inversion recovery (STIR) (long TR/TE) sequence was found, as well as when comparing patients before and after treatment, both medial and inferior rectus muscle SIR resulted significantly statistically different in STIR. These increased outcomes explain the inflammation oedematous phase of disease, moreover after steroid administration, compared to controls; patients presented lack of that statistically significant difference, thus suggesting treatment effectiveness. In our study, we proved STIR signal intensities increase in inflammation oedematous phase, confirming STIR sequence to define active phase of disease with more sensibility and reproducibility than CAS alone and to evaluate post-therapy involvement.

  7. Assessment of the evaluation of liver T1 mapping imaging applying virtual ECG gating on a modified look-locker inversion recovery (MOLLI) pulse sequence

    NASA Astrophysics Data System (ADS)

    Yu, Seung-Man; Goo, Eun-Hoe; Lee, Suk-Jun; Choe, Bo-Young

    2014-10-01

    A T1 mapping calculation error may occur in a physicochemical environment with large relaxivity. We evaluated through a simulated electrocardiogram (ECG) the administration of a contrast with high relaxivity and its effect on the heart rate by using a modified Look-Locker inversion recovery (MOLLI) pulse sequence. The agarose 2% phantom of high relaxivity environment was developed by diluting gadoxetic acid magnetic resonance imaging (MRI) T1 contrast media. The gold standard T1 determination was based on coronal single section imaging with a 2D inversion-recovery turbo spin echo sequence (2D-IRTSE) in a 3T MR unit. Using the identical 3T MR scanner, we acquired T1 mapping for the MOLLI pulse sequence with various virtual heart rates. T1 mapping data of the two different pulse sequences ( i.e., 2D-IRTSE and MOLLI) were measured to investigate the accuracy and the specificity. An in vivo study was conducted in the same manner as the phantom experiments for liver T1 mapping imaging in three healthy volunteers. The MOLLI pulse sequence showed an error rate of less than 10% at a contrast agent concentration of 0.4 mmol/L, and significant error, compared with the reference value, was observed at 0.6 mmol/L or higher. The percentage error of the T1 value did not correlated with the RR ( i.e., the time between heart beats) change that was observed (P =.270). Based on the in-vivo liver test, T1 mapping imaging of an abdominal organ as the liver can be successfully achieved using the applied virtual ECG gating on the MOLLI sequence.

  8. Saturation-inversion-recovery: A method for T1 measurement

    NASA Astrophysics Data System (ADS)

    Wang, Hongzhi; Zhao, Ming; Ackerman, Jerome L.; Song, Yiqiao

    2017-01-01

    Spin-lattice relaxation (T1) has always been measured by inversion-recovery (IR), saturation-recovery (SR), or related methods. These existing methods share a common behavior in that the function describing T1 sensitivity is the exponential, e.g., exp(- τ /T1), where τ is the recovery time. In this paper, we describe a saturation-inversion-recovery (SIR) sequence for T1 measurement with considerably sharper T1-dependence than those of the IR and SR sequences, and demonstrate it experimentally. The SIR method could be useful in improving the contrast between regions of differing T1 in T1-weighted MRI.

  9. Comparison of Maximum Signal Intensity of Contrast Agent on T1-Weighted Images Using Spin Echo, Fast Spin Echo and Inversion Recovery Sequences

    PubMed Central

    Nazarpoor, Mahmood; Poureisa, Masoud; Daghighi, Mohammad Hossein

    2012-01-01

    Background MRI is not able to directly measure the concentration of contrast agent. It is measured indirectly from the signal intensity (SI). It is very important to know how much contrast agent should be injected to receive a maximum SI in the region of interest (ROI). Objectives The aim of this study was to investigate the maximum relationship between contrast concentration and signal intensity (SI) on T1-weighted images using spin echo (SE), fast spin echo (FSE) and inversion recovery (IR) sequences. Materials and Methods To assess the relationship between SI and concentration, a water-filled phantom containing vials of different concentrations of gadolinium DTPA (Gd-DTPA) (0 to 19.77 mmol/L) or a constant concentration (1.2 mmol/L) of contrast agent was used. The vials of constant concentration were used to measure coil nonuniformity. The mean SI was obtained in the ROI using T1-weighted images. All studies were carried out using a 0.3 T clinical MR scanner with a standard head coil. Results This study shows that maximum SI will appear at different ranges in different sequences. The maximum SI can be seen at concentrations of 5.95, 4.96 and 3.98mmol/L for SE, FSE and IR, respectively. Conclusion Using standard imaging parameters, each MRI sequence reaches its maximum SI in a specific contrast concentration, which is highest in SE and least in IR in a comparison between SE, FSE and IR sequences. PMID:23599710

  10. An Inversion Recovery NMR Kinetics Experiment.

    PubMed

    Williams, Travis J; Kershaw, Allan D; Li, Vincent; Wu, Xinping

    2011-05-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a convenient template with which to acquire inversion recovery data on research samples.

  11. An Inversion Recovery NMR Kinetics Experiment

    PubMed Central

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a convenient template with which to acquire inversion recovery data on research samples. PMID:21552343

  12. Fast volumetric imaging of bound and pore water in cortical bone using three-dimensional ultrashort-TE (UTE) and inversion recovery UTE sequences.

    PubMed

    Chen, Jun; Carl, Michael; Ma, Yajun; Shao, Hongda; Lu, Xing; Chen, Bimin; Chang, Eric Y; Wu, Zhihong; Du, Jiang

    2016-10-01

    We report the three-dimensional ultrashort-TE (3D UTE) and adiabatic inversion recovery UTE (IR-UTE) sequences employing a radial trajectory with conical view ordering for bi-component T2 * analysis of bound water (T2 *(BW) ) and pore water (T2 *(PW) ) in cortical bone. An interleaved dual-echo 3D UTE acquisition scheme was developed for fast bi-component analysis of bound and pore water in cortical bone. A 3D IR-UTE acquisition scheme employing multiple spokes per IR was developed for bound water imaging. Two-dimensional UTE (2D UTE) and IR-UTE sequences were employed for comparison. The sequences were applied to bovine bone samples (n = 6) and volunteers (n = 6) using a 3-T scanner. Bi-component fitting of 3D UTE images of bovine samples showed a mean T2 *(BW) of 0.26 ± 0.04 ms and T2 *(PW) of 4.16 ± 0.35 ms, with fractions of 21.5 ± 3.6% and 78.5 ± 3.6%, respectively. The 3D IR-UTE signal showed a single-component decay with a mean T2 *(BW) of 0.29 ± 0.05 ms, suggesting selective imaging of bound water. Similar results were achieved with the 2D UTE and IR-UTE sequences. Bi-component fitting of 3D UTE images of the tibial midshafts of healthy volunteers showed a mean T2 *(BW) of 0.32 ± 0.08 ms and T2 *(PW) of 5.78 ± 1.24 ms, with fractions of 34.2 ± 7.4% and 65.8 ± 7.4%, respectively. Single-component fitting of 3D IR-UTE images showed a mean T2 *(BW) of 0.35 ± 0.09 ms. The 3D UTE and 3D IR-UTE techniques allow fast volumetric mapping of bound and pore water in cortical bone. Copyright © 2016 John Wiley & Sons, Ltd.

  13. An Inversion Recovery NMR Kinetics Experiment

    ERIC Educational Resources Information Center

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  14. An Inversion Recovery NMR Kinetics Experiment

    ERIC Educational Resources Information Center

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  15. Magnetic resonance imaging fluid-attenuated inversion recovery sequence signal reduction after endoscopic endonasal transcribiform total resection of olfactory groove meningiomas

    PubMed Central

    Prevedello, Daniel M.; Ditzel Filho, Leo F. S.; Fernandez-Miranda, Juan C.; Solari, Domenico; do Espírito Santo, Marcelo Prudente; Wehr, Allison M.; Carrau, Ricardo L.; Kassam, Amin B.

    2015-01-01

    Background: Olfactory groove meningiomas grow insidiously and compress adjacent cerebral structures. Achieving complete removal without further damage to frontal lobes can be difficult. Microsurgical removal of large lesions is a challenging procedure and usually involves some brain retraction. The endoscopic endonasal approaches (EEAs) for tumors arising from the anterior fossa have been well described; however, their effect on the adjacent brain tissue has not. Herein, the authors utilized the magnetic resonance imaging fluid attenuated inversion recovery (FLAIR) sequence signal as a marker for edema and gliosis on pre- and post-operative images of olfactory groove meningiomas, thus presenting an objective parameter for brain injury after surgical manipulation. Methods: Imaging of 18 olfactory groove meningiomas removed through EEAs was reviewed. Tumor and pre/postoperative FLAIR signal volumes were assessed utilizing the DICOM image viewer OsiriX®. Inclusion criteria were: (1) No previous treatment; (2) EEA gross total removal; (3) no further treatment. Results: There were 14 females and 4 males; the average age was 53.8 years (±8.85 years). Average tumor volume was 24.75 cm3 (±23.26 cm3, range 2.8–75.7 cm3), average preoperative FLAIR volume 31.17 cm3 (±39.38 cm3, range 0–127.5 cm3) and average postoperative change volume, 4.16 cm3 (±6.18 cm3, range 0–22.2 cm3). Average time of postoperative scanning was 6 months (range 0.14–20 months). In all cases (100%) gross total tumor removal was achieved. Nine patients (50%) had no postoperative FLAIR changes. In 2 patients (9%) there was minimal increase of changes postoperatively (2.2 cm3 and 6 cm3 respectively); all others demonstrated image improvement. The most common complication was postoperative cerebrospinal fluid leakage (27.8%); 1 patient (5.5%) died due to systemic complications and pulmonary sepsis. Conclusions: FLAIR signal changes tend to resolve after endonasal tumor resection and do not seem

  16. Chondral lesions in the patellofemoral joint in MRI: Intra-individual comparison of short-tau inversion recovery sequence (STIR) with 2D multiple-echo data image combination sequence (MEDIC).

    PubMed

    Bodelle, Boris; Luboldt, Wolfgang; Wichmann, Julian L; Fischer, Sebastian; Vogl, Thomas J; Beeres, Martin

    2016-01-01

    To determine the value of the 2D multiple-echo data image combination (MEDIC) sequence relative to the short-tau inversion recovery (STIR) sequence regarding the depiction of chondral lesions in the patellofemoral joint. During a period of 6 month patients with acute pain at the anterior aspect of the knee, joint effusion and suspected chondral lesion defect in the patellofemoral joint underwent MRI including axial MEDIC and STIR imaging. Patients with chondral lesions in the patellofemoral joint on at least one sequence were included. The MEDIC and STIR sequence were quantitatively compared regarding the patella cartilage-to-effusion contrast-to-noise ratio (CNR) and qualitatively regarding the depiction of chondral lesions independently scored by two radiologists on a 3-point scale (1 = not depicted; 2 = blurred depicted; 3 = clearly depicted) using the Wilcoxon-Mann-Whitney-Test. For the analysis of inter-observer agreement the Cohen's Weighted Kappa test was used. 30 of 58 patients (male: female, 21:9; age: 44 ± 12 yrs) revealed cartilage lesions (fissures, n = 5 including fibrillation; gaps, n = 15; delamination, n = 7; osteoarthritis, n = 3) and were included in this study. The STIR-sequence was significantly (p < 0.001) superior to the MEDIC-sequence regarding both, the patella cartilage-to-effusion CNR (mean CNR: 232 ± 61 vs. 40 ± 16) as well as the depiction of chondral lesion (mean score: 2.83 ± 0.4 vs. 1.75 ± 0.7) with substantial inter-observer agreement in the rating of both sequences (κ = 0.76-0.89). For the depiction of chondral lesions in the patellofemoral joint, the axial STIR-sequence should be chosen in preference to the axial MEDIC-sequence.

  17. Non-enhanced MR angiography of renal artery using inflow-sensitive inversion recovery pulse sequence: a prospective comparison with enhanced CT angiography.

    PubMed

    Xu, Jun-ling; Shi, Da-Peng; Li, Yong-Li; Zhang, Ji-liang; Zhu, Shao-cheng; Shen, Hao

    2011-11-01

    To prospectively evaluate the diagnostic value of non-enhanced inflow-sensitive inversion recovery (IFIR) MR angiography for the detection of renal artery stenosis (RAS), with enhanced CT angiography performed as the reference standard. Sixty consecutive patients suspected of RAS underwent both of IFIR MR and enhanced CT angiography. Subjective image quality, renal artery depiction and renal artery grading were all evaluated on artery-by-artery basis. Spearman rank correlation analysis was used to assess agreement between the two techniques. The diagnostic sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for RAS detection at IFIR MR angiography were calculated. One hundred twenty-six main renal arteries were visualized on enhanced CT and non-enhanced MR angiographic images, respectively. The Spearman rank correlation was 0.773 (P<.001) for renal artery depiction, 0.998 (P<.001) for renal arteries grading and 0.833 (P<.001) for RAS detection between the two modalities. The sensitivity, specificity, PPV and NPV of IFIR MR angiography for RAS detection demonstrated 100%, 99.0%, 92.0% and 100%, respectively. Non-enhanced IFIR MR angiography had high sensitivity, specificity, PPV and NPV for RAS detection. It could be the first choice of renal artery imaging methods to avoid ionizing irradiation and renal toxicity from contrast media. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  18. Inversion Recovery with Embedded Self-Calibration (IRES)

    PubMed Central

    Tan, Ek T.; Riederer, Stephen J.

    2009-01-01

    With self-calibrated parallel acquisition, the calibration data used to characterize coil response are acquired within the actual, parallel scan. Although this eliminates the need for a separate calibration scan, it reduces the net acceleration factor of the parallel scan. Furthermore, this reduction gets worse at higher accelerations. A method is described for 3D inversion recovery gradient-echo imaging in which calibration is incorporated into the sequence but with no loss of net acceleration. This is done by acquiring the calibration data using very small (≤4°) tip angle acquisitions during the delay interval after acquisition of the accelerated imaging data. The technique is studied at 3T with simulation, phantom and in vivo experiments using both image space-based and k-space-based parallel reconstruction methods. At nominal acceleration factors of three and four, the newly described Inversion Recovery with Embedded Self-calibration (IRES) method can retain effective acceleration with comparable SNR and contrast to standard self-calibration. At a net 2D acceleration factor of four, IRES can achieve higher SNR than standard self-calibration having a nominal acceleration factor of six but the same acquisition time. PMID:19365864

  19. Magnetic resonance separation imaging using a divided inversion recovery technique (DIRT).

    PubMed

    Goldfarb, James W

    2010-04-01

    The divided inversion recovery technique is an MRI separation method based on tissue T(1) relaxation differences. When tissue T(1) relaxation times are longer than the time between inversion pulses in a segmented inversion recovery pulse sequence, longitudinal magnetization does not pass through the null point. Prior to additional inversion pulses, longitudinal magnetization may have an opposite polarity. Spatial displacement of tissues in inversion recovery balanced steady-state free-precession imaging has been shown to be due to this magnetization phase change resulting from incomplete magnetization recovery. In this paper, it is shown how this phase change can be used to provide image separation. A pulse sequence parameter, the time between inversion pulses (T180), can be adjusted to provide water-fat or fluid separation. Example water-fat and fluid separation images of the head, heart, and abdomen are presented. The water-fat separation performance was investigated by comparing image intensities in short-axis divided inversion recovery technique images of the heart. Fat, blood, and fluid signal was suppressed to the background noise level. Additionally, the separation performance was not affected by main magnetic field inhomogeneities.

  20. 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

    PubMed Central

    Bydder, G M

    2014-01-01

    Objective: 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. Methods: 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. Results: 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 < 0.001). No significant difference was seen between the sequences in evaluation of neural foramina and bone–disc interface. On quantitative evaluation, the signal-to-noise ratios of cord and CSF on fast T1 FLAIR images were significantly higher than those on T1 TSE images (p < 0.05). Contrast-to-noise ratios (CNRs) of cord to CSF on T1 FLAIR images were significantly higher than those of T1 TSE images (p < 0.05). CNRs of bone to disc for T1 weighted TSE images were significantly higher than those of T1 FLAIR images (p < 0.05). Conclusion: At 3 T, T1 FLAIR imaging is superior to T1 TSE for evaluating cervical spine degenerative disease, owing to higher cord–CSF, disc–cord and disc–CSF contrast. However, intrinsic cord contrast is low on T1 FLAIR images. Advances in knowledge: 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. PMID:25010068

  1. Spectral presaturation inversion recovery MR imaging sequence after gadolinium injection to differentiate fibrotic scar tissue and neoplastic strands in the mesorectal fat in patients undergoing restaging of rectal carcinoma after neoadjuvant chemo- and radiation therapy.

    PubMed

    Quaia, Emilio; Ulcigrai, Veronica; Coss, Matteo; De Paoli, Luca; Ukmar, Maja; Zanconati, Fabrizio; De Pellegrin, Alessandro; De Manzini, Nicolò; Cova, Maria Assunta

    2011-11-01

    To retrospectively assess the value of spectral presaturation by inversion-recovery (SPIR) magnetic resonance (MR) imaging sequence after gadolinium injection to differentiate fibrotic scar tissue and tumoral infiltration within the mesorectal fat in patients with rectal carcinoma undergoing MR restaging after neoadjuvant chemo- and radiation therapy (CRT). Forty-three consecutive patients (mean age, 65.8 years; range, 46-85 years; male:female, 29:14) with locally advanced rectal carcinoma underwent CRT followed by surgery. MR imaging was performed before and after completion of CRT by using T2-weighted turbo spin-echo and T1-weighted SPIR sequences before and after gadolinium injection, and MR images were assessed by two radiologists in consensus. Logistic regression was conducted to test the significance of the MR image findings with histology. After CRT the disease was either limited to the rectal wall (n = 18 patients) or presented perirectal infiltration (n = 25) on histology. In 21 patients, mesorectal enhancing strands were observed. Reticular-shaped enhancing strands reaching the mesorectal fascia presented the highest correlation with tumor infiltration of the mesorectal fat (OR 130.33, 95% CI: 4.1-4220.29; logistic regression), whereas linear-shaped enhancing strands either reaching or not reaching the mesorectal fascia (OR 0.25 or 0.1, 95% CI: 0.024-2.6 or 0.01-1.07) revealed the lowest correlation. Reticular-shaped enhancing strands on SPIR MR imaging after gadolinium injection are associated with tumor infiltration of the mesorectal fat. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

  2. Double Resonance Inversion Recovery in a Heteronuclear Two Spin System

    NASA Astrophysics Data System (ADS)

    Ishiwata, Mitsumasa; Koizumi, Jun-ichi

    1988-09-01

    For a heteronuclear coupled AX spin system, recovery after inversion of the A spin lines in A-\\{X\\} double resonance spectra is observed under a spin tickling condition. Oscillations in the A lines after inversion are found to decay more rapidly than expected and depend on inhomogeneity of an applied static field. After the initial oscillating stage, the recovery of the tickling spectra can considerably be accelerated by an irradiation field which is applied near a resonance of an X line. A simple mathematical method is presented for calculating the double resonance recovery process under the inhomogeneity of the static field. Such an inhomogeneity modifies a recovery time near the resonance. Experimental results for 13C-enriched formic acid are reproduced by numerical computation. Acceleration of the recovery is explained in terms of a saturation effect of the irradiated line.

  3. Utility of double inversion recovery MRI in paediatric epilepsy

    PubMed Central

    Porter, Samuel G; Saindane, Amit M; Dehkharghani, Seena; Desai, Nilesh K

    2016-01-01

    Detecting focal abnormalities in MRI examinations of children with epilepsy can be a challenging task given the frequently subtle appearance of cortical dysplasia, mesial temporal sclerosis and similar lesions. In this report, we demonstrate the utility of double inversion recovery MRI in the detection of paediatric epileptogenic abnormalities, promoted primarily by increased lesion conspicuity due to complementary suppression of both cerebrospinal fluid and normal white matter signal. PMID:26529229

  4. Flow-independent T(2)-prepared inversion recovery black-blood MR imaging.

    PubMed

    Liu, Chia-Ying; Bley, Thorsten A; Wieben, Oliver; Brittain, Jean H; Reeder, Scott B

    2010-01-01

    To develop a magnetization preparation method to achieve robust, flow-independent blood suppression for cardiac and vascular magnetic resonance imaging (MRI). T(2)Prep-IR sequence consists of a T(2) preparation followed by a nonselective adiabatic inversion pulse. T(2)Prep separates the initial longitudinal magnetization of arterial wall from lumen blood. After the inversion recovery pulse the imaging acquisition is then delayed for a period that allows the blood signal to approach the zero-crossing point. Compared to the conventional double inversion recovery (DIR) preparation, T(2)Prep-IR prepares all the spins regardless of their velocity and direction. T(2)Prep-IR was incorporated into the fast spin echo and fast gradient echo acquisition sequences and images in various planes were acquired in the carotid arteries, thoracic aorta, and heart of normal volunteers. Blood suppression and image quality were compared qualitatively between two different preparations. For in-plane flow carotid images, persistent flow-related artifacts on the DIR images were removed with T(2)Prep-IR. For cardiac applications, T(2)Prep-IR provided robust blood suppression regardless of the flow direction and velocity, including the cardiac long-axis views and the aorta that are often problematic with DIR. T(2)Prep-IR may overcome the flow dependence of DIR by providing robust flow-independent black-blood images. (c) 2009 Wiley-Liss, Inc.

  5. Double inversion recovery magnetic resonance imaging of subcortical band heterotopia: a report of 2 cases.

    PubMed

    Zhang, Quan; Zhang, Yunting; Zhang, Jing; Li, Qiong

    2011-01-01

    We report 2 cases of subcortical band heterotopia (SBH) with emphasis on double inversion recovery (DIR) magnetic resonance imaging (MRI). The heterotopic gray matter demonstrated homogeneous high signal intensity and the delineation between the SBH and white matter was distinctly depicted on DIR MRI. Double inversion recovery is a useful adjunct to conventional MRI for the diagnosis of SBH.

  6. Limitations in biexponential fitting of NMR inversion-recovery curves

    NASA Astrophysics Data System (ADS)

    Shazeeb, Mohammed Salman; Sotak, Christopher H.

    2017-03-01

    NMR relaxation agents have long been employed as contrast agents in MRI. In many cases, the contrast agent is confined to either (i) the vascular and/or extracellular compartment (EC), as is the case with gadolinium(III)-based agents, or (ii) the intracellular compartment (IC), as is the case with manganese(II) ions. The compartmentalization of contrast agents often results in tissue-water 1H relaxation profiles that are well modeled as biexponential. It has long been recognized that water exchange between compartments modifies the biexponential relaxation parameters (amplitudes and rate constants) from those that would be found in the absence of exchange. Nevertheless, interpretation in terms of an ;apparent; two-compartment biophysical model, apparent EC vs. apparent IC, can provide insight into tissue structure and function, and changes therein, in the face of physiologic challenge. The accuracy of modeling biexponential data is highly dependent upon the amplitudes, rate constants, and signal-to-noise characterizing the data. Herein, simulated (in silico) inversion-recovery relaxation data are modeled by standard, nonlinear-least-squares analysis and the error in parameter values assessed for a range of amplitudes and rate constants characteristic of in vivo systems following administration of contrast agent. The findings provide guidance for laboratories seeking to exploit contrast-agent-driven, biexponential relaxation to differentiate MRI-based compartmental properties, including the apparent diffusion coefficient.

  7. Sodium inversion recovery MRI on the knee joint at 7 T with an optimal control pulse

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Xia, Ding; Madelin, Guillaume; Regatte, Ravinder R.

    2016-01-01

    In the field of sodium magnetic resonance imaging (MRI), inversion recovery (IR) is a convenient and popular method to select sodium in different environments. For the knee joint, IR has been used to suppress the signal from synovial fluids, which improves the correlation between the sodium signal and the concentration of glycosaminoglycans (GAGs) in cartilage tissues. For the better inversion of the magnetization vector under the spatial variations of the B0 and B1 fields, the IR sequence usually employ adiabatic pulses as the inversion pulse. On the other hand, it has been shown that RF shapes robust against the variations of the B0 and B1 fields can be generated by numerical optimization based on optimal control theory. In this work, we compare the performance of fluid-suppressed sodium MRI on the knee joint in vivo, between one implemented with an adiabatic pulse in the IR sequence and the other with the adiabatic pulse replaced by an optimal-control shaped pulse. While the optimal-control pulse reduces the RF power deposited to the body by 58%, the quality of fluid suppression and the signal level of sodium within cartilage are similar between two implementations.

  8. Sodium inversion recovery MRI of the knee joint in vivo at 7T

    NASA Astrophysics Data System (ADS)

    Madelin, Guillaume; Lee, Jae-Seung; Inati, Souheil; Jerschow, Alexej; Regatte, Ravinder R.

    2010-11-01

    The loss of proteoglycans (PG) in the articular cartilage is an early signature of osteoarthritis (OA). The ensuing changes in the fixed charge density in the cartilage can be directly linked to sodium concentration via charge balance. Sodium ions in the knee joint appear in two pools: in the synovial fluids or joint effusion where the ions are in free motion and bound within the cartilage tissue where the Na+ ions have a restricted motion. The ions in these two compartments have therefore different T1 and T2 relaxation times. The purpose of this study is to demonstrate the feasibility of a fluid-suppressed 3D ultrashort TE radial sodium sequence by implementing an inversion recovery (IR) preparation of the magnetization at 7T. This method could allow a more accurate and more sensitive quantification of loss of PG in patients with OA. It is shown that adiabatic pulses offer significantly improved performance in terms of robustness to B1 and B0 inhomogeneities when compared to the hard pulse sequence. Power deposition considerations further pose a limit to the RF inversion power, and we demonstrate in simulations and experiments how a practical compromise can be struck between clean suppression of fluid signals and power deposition levels. Two IR sequences with different types of inversion pulses (a rectangular pulse and an adiabatic pulse) were tested on a liquid phantom, ex vivo on a human knee cadaver and then in vivo on five healthy volunteers, with a (Nyquist) resolution of ∼3.6 mm and a signal-to-noise ratio of ∼30 in cartilage without IR and ∼20 with IR. Due to specific absorption rate limitations, the total acquisition time was ∼17 min for the 3D radial sequence without inversion or with the rectangular IR, and 24:30 min for the adiabatic IR sequence. It is shown that the adiabatic IR sequence generates a more uniform fluid suppression over the whole sample than the rectangular IR sequence.

  9. Identifying micro-inversions using high-throughput sequencing reads.

    PubMed

    He, Feifei; Li, Yang; Tang, Yu-Hang; Ma, Jian; Zhu, Huaiqiu

    2016-01-11

    The identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MIs are important genomic variation and may play roles in causing genetic disease. However, current alignment methods are generally insensitive to detect MIs. Here we develop a novel tool, MID (Micro-Inversion Detector), to identify MIs in human genomes using next-generation sequencing reads. The algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID different from other variant detection tools is that MID can handle small MIs and multiple breakpoints within an unmapped read. Moreover, MID improves reliability in low coverage data by integrating multiple samples. Our evaluation demonstrated that MID outperforms Gustaf, which can currently detect inversions from 30 bp to 500 bp. To our knowledge, MID is the first method that can efficiently and reliably identify MIs from unmapped short next-generation sequencing reads. MID is reliable on low coverage data, which is suitable for large-scale projects such as the 1000 Genomes Project (1KGP). MID identified previously unknown MIs from the 1KGP that overlap with genes and regulatory elements in the human genome. We also identified MIs in cancer cell lines from Cancer Cell Line Encyclopedia (CCLE). Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID .

  10. Phase-Sensitive Inversion Recovery for Detecting Myocardial Infarction Using Gadolinium-Delayed Hyperenhancement

    PubMed Central

    Kellman, Peter; Arai, Andrew E.; McVeigh, Elliot R.; Aletras, Anthony H.

    2007-01-01

    After administration of gadolinium, infarcted myocardium exhibits delayed hyperenhancement and can be imaged using an inversion recovery (IR) sequence. The performance of such a method when using magnitude-reconstructed images is highly sensitive to the inversion recovery time (TI) selected. Using phase-sensitive reconstruction, it is possible to use a nominal value of TI, eliminate several breath-holds otherwise needed to find the precise null time for normal myocardium, and achieve a consistent contrast. Phase-sensitive detection is used to remove the background phase while preserving the sign of the desired magnetization during IR. Experimental results are presented which demonstrate the benefits of both phase-sensitive IR image reconstruction and surface coil intensity normalization for detecting myocardial infarction (MI). The phase-sensitive reconstruction method reduces the variation in apparent infarct size that is observed in the magnitude images as TI is changed. Phase-sensitive detection also has the advantage of decreasing the sensitivity to changes in tissue T1 with increasing delay from contrast agent injection. PMID:11810682

  11. 3D inversion of full gravity gradient tensor data using SL0 sparse recovery

    NASA Astrophysics Data System (ADS)

    Meng, Zhaohai

    2016-04-01

    We present a new method dedicated to the interpretation of full gravity gradient tensor data, based on SL0 sparse recovery inversion. The SL0 sparse recovery method aims to find out the minimum value of the objective function to fit the data function and to solve the non-zero solution to the objective function. Based on continuous iteration, we can easily obtain the final global minimum (namely the property and space attribute of the inversion target). We consider which type of tensor data combination produces the best inversion results based on the inversion results of different full gravity gradient tensor data combinations (separate tensor data and combined tensor data). We compare the recovered models obtained by inverting the different combinations of different gravity gradient tensor components to understand how different component combinations contribute to the resolution of the recovered model. Based on the comparison between the SL0 sparse recovery inversion results and the smoothest and focusing inversion results of the full gravity gradient tensor data, we show that SL0 sparse recovery inversion can obtain more stable and efficient inversion results with relatively sharp edge information, and that this method can also produce a stable solution of the inverse problem for complex geological structures. This new method to resolve very large full gravity gradient tensor datasets has the considerable advantage of being highly efficient; the full gravity gradient tensor inversion requires very little time. This new method is very effective in explaining the full gravity tensor which is very sensitive to small changes in local anomaly. The numerical simulation and inversion results of the compositional model indicates that including multiple components for inversion increases the resolution of the recovered density model and improves the structure delineation. We apply our inversion method to invert the gravity gradient tensor survey data from the Vinton salt

  12. Pre- and post-contrast three-dimensional double inversion-recovery MRI in human glioblastoma

    PubMed Central

    Harris, Robert J.; Cloughesy, Timothy F.; Pope, Whitney B.; Godinez, Sergio; Natsuaki, Yutaka; Nghiemphu, Phioanh L.; Meyer, Heiko; Paul, Dominik; Behbahanian, Yalda; Lai, Albert

    2013-01-01

    Fluid attenuated inversion recovery (FLAIR) MRI sequences have become an indispensible tool for defining the malignant boundary in patients with brain tumors by nulling the signal contribution from cerebro-spinal fluid allowing both regions of edema and regions of non-enhancing, infiltrating tumor to become hyperintense on resulting images. In the current study we examined the utility of a three-dimensional double inversion recovery (DIR) sequence that additionally nulls the MR signal associated with white matter, implemented either pre-contrast or post-contrast, in order to determine whether this sequence allows for better differentiation between tumor and normal brain tissue. T1- and T2-weighted, FLAIR, dynamic susceptibility contrast (DSC)-MRI estimates of cerebral blood volume (rCBV), contrast-enhanced T1-weighted images (T1+C), and DIR data (pre- or post-contrast) were acquired in 22 patients with glioblastoma. Contrast-to-noise (CNR) and tumor volumes were compared between DIR and FLAIR sequences. Line profiles across regions of tumor were generated to evaluate similarities between image contrasts. Additionally, voxel-wise associations between DIR and other sequences were examined. Results suggested post-contrast DIR images were hyperintense (bright) in regions spatially similar those having FLAIR hyperintensity and hypointense (dark) in regions with contrast-enhancement or elevated rCBV due to the high sensitivity of 3D turbo spin echo sequences to susceptibility differences between different tissues. DIR tumor volumes were statistically smaller than tumor volumes as defined by FLAIR (Paired t test, P = 0.0084), averaging a difference of approximately 14 mL or 24 %. DIR images had approximately 1.5× higher lesion CNR compared with FLAIR images (Paired t test, P = 0.0048). Line profiles across tumor regions and scatter plots of voxel-wise coherence between different contrasts confirmed a positive correlation between DIR and FLAIR signal intensity and a

  13. Pre- and post-contrast three-dimensional double inversion-recovery MRI in human glioblastoma.

    PubMed

    Harris, Robert J; Cloughesy, Timothy F; Pope, Whitney B; Godinez, Sergio; Natsuaki, Yutaka; Nghiemphu, Phioanh L; Meyer, Heiko; Paul, Dominik; Behbahanian, Yalda; Lai, Albert; Ellingson, Benjamin M

    2013-04-01

    Fluid attenuated inversion recovery (FLAIR) MRI sequences have become an indispensible tool for defining the malignant boundary in patients with brain tumors by nulling the signal contribution from cerebrospinal fluid allowing both regions of edema and regions of non-enhancing, infiltrating tumor to become hyperintense on resulting images. In the current study we examined the utility of a three-dimensional double inversion recovery (DIR) sequence that additionally nulls the MR signal associated with white matter, implemented either pre-contrast or post-contrast, in order to determine whether this sequence allows for better differentiation between tumor and normal brain tissue. T1- and T2-weighted, FLAIR, dynamic susceptibility contrast (DSC)-MRI estimates of cerebral blood volume (rCBV), contrast-enhanced T1-weighted images (T1+C), and DIR data (pre- or post-contrast) were acquired in 22 patients with glioblastoma. Contrast-to-noise (CNR) and tumor volumes were compared between DIR and FLAIR sequences. Line profiles across regions of tumor were generated to evaluate similarities between image contrasts. Additionally, voxel-wise associations between DIR and other sequences were examined. Results suggested post-contrast DIR images were hyperintense (bright) in regions spatially similar those having FLAIR hyperintensity and hypointense (dark) in regions with contrast-enhancement or elevated rCBV due to the high sensitivity of 3D turbo spin echo sequences to susceptibility differences between different tissues. DIR tumor volumes were statistically smaller than tumor volumes as defined by FLAIR (Paired t test, P = 0.0084), averaging a difference of approximately 14 mL or 24 %. DIR images had approximately 1.5× higher lesion CNR compared with FLAIR images (Paired t test, P = 0.0048). Line profiles across tumor regions and scatter plots of voxel-wise coherence between different contrasts confirmed a positive correlation between DIR and FLAIR signal intensity and a

  14. Effects of Inversion Time on Inversion Recovery Prepared Ultrashort Echo Time (IR-UTE) Imaging of Free and Bound Water in Cortical Bone

    PubMed Central

    Li, Shihong; Ma, Lanqing; Chang, Eric Y; Shao, Hongda; Chen, Jun; Chung, Christine B; Bydder, Graeme M; Du, Jiang

    2014-01-01

    Water is present in cortical bone in different binding states. In this study we aimed to investigate the effects of inversion time (TI) on the signal from bound and pore water in cortical bone using an adiabatic inversion recovery prepared ultrashort echo time (IR-UTE) sequence on a clinical 3T scanner. In total ten bovine midshaft samples and four human tibial midshaft samples were harvested for this study. Each cortical sample was imaged with the UTE and IR-UTE sequences with a TR of 300 ms and a series of TIs ranging from 10 to 240 ms. Five healthy volunteers were also imaged with the same sequence. Single- and bi-component models were utilized to calculate the T2* and relative fractions of short and long T2* components. Bi-component behavior of the signal from cortical bone was seen with the IR-UTE sequence except with a TI of around 80 ms where the short T2* component alone were seen and a mono-exponential decay pattern was observed. In vivo imaging with the IR-UTE sequence provided high contrast-to-noise images with direct visualization of bound water and reduced signal from long T2 muscle and fat. Our preliminary results demonstrate that selective nulling of the pore water component can be achieved with the IR-UTE sequence with an appropriate TI, allowing selective imaging of the bound water component in cortical bone in vivo using clinical MR scanners. PMID:25348196

  15. Three-dimensional (3D) visualization of endolymphatic hydrops after intratympanic injection of Gd-DTPA: optimization of a 3D-real inversion-recovery turbo spin-echo (TSE) sequence and application of a 32-channel head coil at 3T.

    PubMed

    Naganawa, Shinji; Ishihara, Shunichi; Iwano, Shingo; Sone, Michihiko; Nakashima, Tsutomu

    2010-01-01

    To enable volume visualization of endolymphatic hydrops of Ménière's disease via a volume rendering (VR) technique, a three-dimensional (3D) inversion-recovery (IR) sequence with real reconstruction (3D-real IR) sequence after intratympanic injection of Gd-DTPA was optimized for higher spatial resolution using a 32-channel head coil at 3T. Pulse sequence parameters were optimized using a diluted Gd-DTPA phantom. Then, 11 patients who had been clinically diagnosed with Ménière's disease and a patient with sudden hearing loss were scanned. Images were processed using commercially available 3D-VR software. 3D-real IR data was processed to produce endolymph and perilymph fluid volume images in different colors. 3D-CISS data was processed to generate total fluid volume images. While maintaining a comparable signal-to-noise ratio (SNR) and scan time, the voxel volume could be reduced from 0.4 x 0.4 x 2 mm(3) with a 12-channel coil to 0.4 x 0.4 x 0.8 mm(3) with a 32-channel coil. A newly-optimized protocol allowed the smooth, three-dimensional visualization of endolymphatic hydrops in all patients with Ménière's disease. Volumetrically separate visualization of endo-/perilymphatic space is now feasible in patients with Ménière's disease using an optimized 3D-real IR sequence, a 32-channel head coil, at 3T, after intratympanic administration of Gd-DTPA. This will aid the understanding of the pathophysiology of Ménière's disease. (c) 2009 Wiley-Liss, Inc.

  16. Assessment of cardiac function and myocardial morphology using small animal Look-Locker inversion recovery (SALLI) MRI in rats.

    PubMed

    Jeuthe, Sarah; O H-Ici, Darach; Kemnitz, Ulrich; Dietrich, Thore; Schnackenburg, Bernhard; Berger, Felix; Kuehne, Titus; Messroghli, Daniel

    2013-07-19

    Small animal magnetic resonance imaging is an important tool to study cardiac function and changes in myocardial tissue. The high heart rates of small animals (200 to 600 beats/min) have previously limited the role of CMR imaging. Small animal Look-Locker inversion recovery (SALLI) is a T1 mapping sequence for small animals to overcome this problem. T1 maps provide quantitative information about tissue alterations and contrast agent kinetics. It is also possible to detect diffuse myocardial processes such as interstitial fibrosis or edema. Furthermore, from a single set of image data, it is possible to examine heart function and myocardial scarring by generating cine and inversion recovery-prepared late gadolinium enhancement-type MR images. The presented video shows step-by-step the procedures to perform small animal CMR imaging. Here it is presented with a healthy Sprague-Dawley rat, however naturally it can be extended to different cardiac small animal models.

  17. Three-dimensional T(1), T(2) and proton density mapping with inversion recovery balanced SSFP.

    PubMed

    Newbould, Rexford D; Skare, Stefan T; Alley, Marcus T; Gold, Garry E; Bammer, Roland

    2010-11-01

    By combining a balanced steady-state free precession (bSSFP) readout with an initial inversion pulse, all three contrast parameters, T(1), T(2) and proton density (M(0)), may be rapidly calculated from the signal progression in time. However, here it is shown that this technique is quite sensitive to variation in the applied transmit RF (B(1)) field, leading to pronounced errors in calculated values. Two-dimensional (2D) acquisitions are taxed to accurately quantify the relaxation, as the short RF pulses required by SSFP's rapid TR contain a broad spectrum of excitation angles. A 3D excitation using a large diameter excitation coil was able to correctly quantify the parameters. While the extreme B(1) sensitivity was previously problematic and has precluded use of IR-bSSFP for relaxometry, in this work these obstacles were significantly reduced, allowing the rapid quantification of T(1), T(2) and M(0). The results may further be used to simulate image contrast from common sequences, such as a T(1)-weighted or fluid-attenuated inversion recovery (FLAIR) examination.

  18. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  19. Multiplexed microsatellite recovery using massively parallel sequencing.

    PubMed

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  20. Multiplexed microsatellite recovery using massively parallel sequencing

    Treesearch

    T.N. Jennings; B.J. Knaus; T.D. Mullins; S.M. Haig; R.C. Cronn

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of...

  1. Importance of Contrast-Enhanced Fluid-Attenuated Inversion Recovery Magnetic Resonance Imaging in Various Intracranial Pathologic Conditions

    PubMed Central

    Lee, Eun Kyoung; Kim, Sungwon; Lee, Yong Seok

    2016-01-01

    Intracranial lesions may show contrast enhancement through various mechanisms that are closely associated with the disease process. The preferred magnetic resonance sequence in contrast imaging is T1-weighted imaging (T1WI) at most institutions. However, lesion enhancement is occasionally inconspicuous on T1WI. Although fluid-attenuated inversion recovery (FLAIR) sequences are commonly considered as T2-weighted imaging with dark cerebrospinal fluid, they also show mild T1-weighted contrast, which is responsible for the contrast enhancement. For several years, FLAIR imaging has been successfully incorporated as a routine sequence at our institution for contrast-enhanced (CE) brain imaging in detecting various intracranial diseases. In this pictorial essay, we describe and illustrate the diagnostic importance of CE-FLAIR imaging in various intracranial pathologic conditions. PMID:26798225

  2. Adaptive Lp inversion for simultaneous recovery of both blocky and smooth features in a geophysical model

    NASA Astrophysics Data System (ADS)

    Sun, Jiajia; Li, Yaoguo

    2014-05-01

    Minimum-structure inversions using L2-norm measures have been widely applied to geophysical exploration problems. However, the smeared-out models resulting from L2-norm inversions are not always consistent with the real or expected geological structures, especially in regions where distinct interfaces between different rock units exist. To obtain sharp boundaries and blocky features, non-L2 inversions have been used successfully in geophysical imaging problems. In reality, however, both smooth and blocky features can be present in the subsurface physical properties or interfaces to be recovered. To deal with this situation, we develop a new method for adaptively recovering both smooth and blocky features in the constructed model from geophysical inversions. This method first detects different regions of the smoothness or blockiness in a model based on a sequence of inversions and then adaptively applies appropriate Lp model norm with different p values at different locations to complete the final inversion. We present two synthetic examples from basement inversion using gravity data and crosswell seismic traveltime tomography before demonstrating our method on a field data example at the U.S. Geological Survey Fractured Rock Research Site in central New Hampshire.

  3. Using the dGEMRIC technique to evaluate cartilage health in the presence of surgical hardware at 3T: comparison of inversion recovery and saturation recovery approaches.

    PubMed

    d'Entremont, Agnes G; Kolind, Shannon H; Mädler, Burkhard; Wilson, David R; MacKay, Alexander L

    2014-03-01

    To evaluate the effect of metal artifact reduction techniques on dGEMRIC T(1) calculation with surgical hardware present. We examined the effect of stainless-steel and titanium hardware on dGEMRIC T(1) maps. We tested two strategies to reduce metal artifact in dGEMRIC: (1) saturation recovery (SR) instead of inversion recovery (IR) and (2) applying the metal artifact reduction sequence (MARS), in a gadolinium-doped agarose gel phantom and in vivo with titanium hardware. T(1) maps were obtained using custom curve-fitting software and phantom ROIs were defined to compare conditions (metal, MARS, IR, SR). A large area of artifact appeared in phantom IR images with metal when T(I) ≤ 700 ms. IR maps with metal had additional artifact both in vivo and in the phantom (shifted null points, increased mean T(1) (+151 % IR ROI(artifact)) and decreased mean inversion efficiency (f; 0.45 ROI(artifact), versus 2 for perfect inversion)) compared to the SR maps (ROI(artifact): +13 % T(1) SR, 0.95 versus 1 for perfect excitation), however, SR produced noisier T(1) maps than IR (phantom SNR: 118 SR, 212 IR). MARS subtly reduced the extent of artifact in the phantom (IR and SR). dGEMRIC measurement in the presence of surgical hardware at 3T is possible with appropriately applied strategies. Measurements may work best in the presence of titanium and are severely limited with stainless steel. For regions near hardware where IR produces large artifacts making dGEMRIC analysis impossible, SR-MARS may allow dGEMRIC measurements. The position and size of the IR artifact is variable, and must be assessed for each implant/imaging set-up.

  4. Characterization and optimization of the visualization performance of continuous flow overhauser DNP hyperpolarized water MRI: Inversion recovery approach.

    PubMed

    Terekhov, Maxim; Krummenacker, Jan; Denysenkov, Vasyl; Gerz, Kathrin; Prisner, Thomas; Schreiber, Laura Maria

    2016-03-01

    Overhauser dynamic nuclear polarization (DNP) allows the production of liquid hyperpolarized substrate inside the MRI magnet bore as well as its administration in continuous flow mode to acquire MR images with enhanced signal-to-noise ratio. We implemented inversion recovery preparation in order to improve contrast-to-noise ratio and to quantify the overall imaging performance of Overhauser DNP-enhanced MRI. The negative enhancement created by DNP in combination with inversion recovery (IR) preparation allows canceling selectively the signal originated from Boltzmann magnetization and visualizing only hyperpolarized fluid. The theoretical model describing gain of MR image intensity produced by steady-state continuous flow DNP hyperpolarized magnetization was established and proved experimentally. A precise quantification of signal originated purely from DNP hyperpolarization was achieved. A temperature effect on longitudinal relaxation had to be taken into account to fit experimental results with numerical prediction. Using properly adjusted IR preparation, the complete zeroing of thermal background magnetization was achieved, providing an essential increase of contrast-to-noise ratio of DNP-hyperpolarized water images. To quantify and optimize the steady-state conditions for MRI with continuous flow DNP, an approach similar to that incorporating transient-state thermal magnetization equilibrium in spoiled fast field echo imaging sequences can be used. © 2015 Wiley Periodicals, Inc.

  5. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).

    PubMed

    Walker, Joseph F; Zanis, Michael J; Emery, Nancy C

    2014-04-01

    Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

  6. Diagnosis of retrodiscal tissue in painful temporomandibular joint (TMJ) by fluid-attenuated inversion recovery (FLAIR) signal intensity.

    PubMed

    Kuroda, Migiwa; Otonari-Yamamoto, Mika; Sano, Tsukasa; Fujikura, Mamiko; Wakoh, Mamoru

    2015-10-01

    The purpose of the present study is to analyze the fluid-attenuated inversion recovery (FLAIR) signal intensity of the retrodiscal tissue in a painful temporomandibular joint (TMJ), and to develop a diagnostic system based on FLAIR data. The study was based on 33 joints of 17 patients referred for MR imaging of the TMJ. Regions of interest were placed over retrodiscal tissue and gray matter (GM) on FLAIR images. Using signal intensities of GM as reference points, signal intensity ratios (SIR) of retrodiscal tissue were calculated. SIRs in painful TMJ were compared with those in painless TMJ. Wilcoxon's Rank Sum Test was used to analyze the difference in SIRs between the painful and painless groups (P<0·05). The SIRs of retrodiscal tissue were significantly higher in painful joints than in painless joints. FLAIR sequences provide a high signal in patients having painful TMJ, and it suggests that retrodiscal tissue in painful TMJ contains elements such as protein.

  7. Cross-borehole resistivity inversion: Theory and application to monitoring enhanced oil recovery

    SciTech Connect

    Beasley, C.W.

    1989-01-01

    An algorithm capable of both forward and inverse modeling of cross-borehole resistivity data has been developed. The method of finite elements (FEM) forms the basis of the forward algorithm which computes the secondary electric potential response of a two-dimensional (2-D) earth excited by a three-dimensional (3-D) point source of direct current. The inverse algorithm which is applied to the forward algorithm is an iterative, smoothed least-squares minimization applied to an objective function. As is typical with any 2-D/3-D problem, the governing differential equation for the forward problem is formulated in wavenumber domain via a Fourier transform which removes the effects of the source in the strike direction. The FEM is applied to the transformed equation and potentials in wavenumber domain are computer for a discrete number of transform variables. These potentials are then numerically inverse transformed to obtain potentials in 3-D Cartesian domain. The inverse transform method presented here allows for a cosine transform so that transmitters and receivers are not required to be contained within the plane perpendicular to strike. The inverse program is then used to evaluate the applicability of cross-borehole resistivity inversion to monitoring enhanced oil recovery (EOR) processes. The synthetic model study, which is generic rather than site specific, is directed towards tracking hot water and steam floods. Also included is a discussion of EOR induced rock resistivity variations. The analysis shows that for typical resistivity contrasts associated with EOR processes, repeatedly performing cross-borehole resistivity surveys can be a successful method of tracking EOR fronts.

  8. Matched-field processing, geoacoustic inversion, and source signature recovery of blue whale vocalizations.

    PubMed

    Thode, A M; D'Spain, G L; Kuperman, W A

    2000-03-01

    Matched-field processing (MFP) and global inversion techniques have been applied to vocalizations from four whales recorded on a 48-element tilted vertical array off the Channel Islands in 1996. Global inversions from selected whale calls using as few as eight elements extracted information about the surrounding ocean bottom composition, array shape, and the animal's position. These inversion results were then used to conduct straightforward MFP on other calls. The sediment sound-speed inversion estimates are consistent with those derived from sediment samples collected in the area. In general, most animals swam from the east to west, but one animal remained within approximately 500 m of its original position over 45 min. All whales vocalized between 10 and 40 m depth. Three acoustic sequences are discussed in detail: the first illustrating a match between an acoustic track and visual sighting, the second tracking two whales to ranges out to 8 km, and the final sequence demonstrating high-resolution dive profiles from an animal that changed its course to avoid the research platform FLIP (floating instrument platform). This last whale displayed an unusual diversity of signals that include three strong frequency-modulated (FM) downsweeps which contain possible signs of an internal resonance. The arrival of this same whale coincided with a sudden change in oceanographic conditions.

  9. Optimal recovery sequencing for critical infrastructure resilience assessment.

    SciTech Connect

    Vugrin, Eric D.; Brown, Nathanael J. K.; Turnquist, Mark Alan

    2010-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the identification of optimal recovery strategies that maximize resilience. To this goal, we formulate a bi-level optimization problem for infrastructure network models. In the 'inner' problem, we solve for network flows, and we use the 'outer' problem to identify the optimal recovery modes and sequences. We draw from the literature of multi-mode project scheduling problems to create an effective solution strategy for the resilience optimization model. We demonstrate the application of this approach to a set of network models, including a national railroad model and a supply chain for Army munitions production.

  10. TIME-LAPSE SEISMIC MODELING & INVERSION OF CO2 SATURATION FOR SEQUESTRATION AND ENHANCED OIL RECOVERY

    SciTech Connect

    Mark A. Meadows

    2006-03-31

    Injection of carbon dioxide (CO2) into subsurface aquifers for geologic storage/sequestration, and into subsurface hydrocarbon reservoirs for enhanced oil recovery, has become an important topic to the nation because of growing concerns related to global warming and energy security. In this project we developed new ways to predict and quantify the effects of CO2 on seismic data recorded over porous reservoir/aquifer rock systems. This effort involved the research and development of new technology to: (1) Quantitatively model the rock physics effects of CO2 injection in porous saline and oil/brine reservoirs (both miscible and immiscible). (2) Quantitatively model the seismic response to CO2 injection (both miscible and immiscible) from well logs (1D). (3) Perform quantitative inversions of time-lapse 4D seismic data to estimate injected CO2 distributions within subsurface reservoirs and aquifers. This work has resulted in an improved ability to remotely monitor the injected CO2 for safe storage and enhanced hydrocarbon recovery, predict the effects of CO2 on time-lapse seismic data, and estimate injected CO2 saturation distributions in subsurface aquifers/reservoirs. We applied our inversion methodology to a 3D time-lapse seismic dataset from the Sleipner CO2 sequestration project, Norwegian North Sea. We measured changes in the seismic amplitude and traveltime at the top of the Sleipner sandstone reservoir and used these time-lapse seismic attributes in the inversion. Maps of CO2 thickness and its standard deviation were generated for the topmost layer. From this information, we estimated that 7.4% of the total CO2 injected over a five-year period had reached the top of the reservoir. This inversion approach could also be applied to the remaining levels within the anomalous zone to obtain an estimate of the total CO2 injected.

  11. Inversions

    ERIC Educational Resources Information Center

    Brown, Malcolm

    2009-01-01

    Inversions are fascinating phenomena. They are reversals of the normal or expected order. They occur across a wide variety of contexts. What do inversions have to do with learning spaces? The author suggests that they are a useful metaphor for the process that is unfolding in higher education with respect to education. On the basis of…

  12. Inversions

    ERIC Educational Resources Information Center

    Brown, Malcolm

    2009-01-01

    Inversions are fascinating phenomena. They are reversals of the normal or expected order. They occur across a wide variety of contexts. What do inversions have to do with learning spaces? The author suggests that they are a useful metaphor for the process that is unfolding in higher education with respect to education. On the basis of…

  13. Viral Discovery and Sequence Recovery Using DNA Microarrays

    PubMed Central

    Wang, David; Urisman, Anatoly; Liu, Yu-Tsueng; Springer, Michael; Ksiazek, Thomas G; Erdman, Dean D; Mardis, Elaine R; Hickenbotham, Matthew; Magrini, Vincent; Eldred, James; Latreille, J. Phillipe; Wilson, Richard K; Ganem, Don

    2003-01-01

    Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease. PMID:14624234

  14. SAR and scan-time optimized 3D whole-brain double inversion recovery imaging at 7T.

    PubMed

    Pracht, Eberhard D; Feiweier, Thorsten; Ehses, Philipp; Brenner, Daniel; Roebroeck, Alard; Weber, Bernd; Stöcker, Tony

    2017-09-14

    The aim of this project was to implement an ultra-high field (UHF) optimized double inversion recovery (DIR) sequence for gray matter (GM) imaging, enabling whole brain coverage in short acquisition times ( ≈5 min, image resolution 1 mm(3) ). A 3D variable flip angle DIR turbo spin echo (TSE) sequence was optimized for UHF application. We implemented an improved, fast, and specific absorption rate (SAR) efficient TSE imaging module, utilizing improved reordering. The DIR preparation was tailored to UHF application. Additionally, fat artifacts were minimized by employing water excitation instead of fat saturation. GM images, covering the whole brain, were acquired in 7 min scan time at 1 mm isotropic resolution. SAR issues were overcome by using a dedicated flip angle calculation considering SAR and SNR efficiency. Furthermore, UHF related artifacts were minimized. The suggested sequence is suitable to generate GM images with whole-brain coverage at UHF. Due to the short total acquisition times and overall robustness, this approach can potentially enable DIR application in a routine setting and enhance lesion detection in neurological diseases. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  15. Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

    PubMed

    Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

    2017-01-01

    Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

  16. Optimization of flow-sensitive alternating inversion recovery (FAIR) for perfusion functional MRI of rodent brain.

    PubMed

    Nasrallah, Fatima A; Lee, Eugene L Q; Chuang, Kai-Hsiang

    2012-11-01

    Arterial spin labeling (ASL) MRI provides a noninvasive method to image perfusion, and has been applied to map neural activation in the brain. Although pulsed labeling methods have been widely used in humans, continuous ASL with a dedicated neck labeling coil is still the preferred method in rodent brain functional MRI (fMRI) to maximize the sensitivity and allow multislice acquisition. However, the additional hardware is not readily available and hence its application is limited. In this study, flow-sensitive alternating inversion recovery (FAIR) pulsed ASL was optimized for fMRI of rat brain. A practical challenge of FAIR is the suboptimal global inversion by the transmit coil of limited dimensions, which results in low effective labeling. By using a large volume transmit coil and proper positioning to optimize the body coverage, the perfusion signal was increased by 38.3% compared with positioning the brain at the isocenter. An additional 53.3% gain in signal was achieved using optimized repetition and inversion times compared with a long TR. Under electrical stimulation to the forepaws, a perfusion activation signal change of 63.7 ± 6.3% can be reliably detected in the primary somatosensory cortices using single slice or multislice echo planar imaging at 9.4 T. This demonstrates the potential of using pulsed ASL for multislice perfusion fMRI in functional and pharmacological applications in rat brain.

  17. Non-contrast-enhanced pulmonary vein MRI with a spatially selective slab inversion preparation sequence.

    PubMed

    Hu, Peng; Chuang, Michael L; Kissinger, Kraig V; Goddu, Beth; Goepfert, Lois A; Rofsky, Neil M; Manning, Warren J; Nezafat, Reza

    2010-02-01

    We propose a non-contrast-enhanced, three-dimensional, free-breathing, electrocardiogram-gated, gradient recalled echo sequence with a slab-selective inversion for pulmonary vein (PV) MRI. A sagittal inversion slab was applied prior to data acquisition to suppress structures adjacent to the left atrium (LA) and PVs, thereby improving the conspicuity of the PV and LA. Compared with other MR angiography methods using an inversion pulse, the proposed method does not require signal subtraction and the inversion slab is not parallel to the imaging slab. The feasibility of the proposed method was demonstrated in healthy subjects. The inversion slab thickness and inversion time were optimized to be 60 mm and 500 ms, respectively. Compared to conventional gradient recalled echo imaging without inversion, the proposed technique significantly increased the contrast-to-noise ratios between the LA and the right atrium by 20-fold (P < 0.01), increased the contrast-to-noise ratios between the PVs and right atrium by 10-fold (P < 0.03), and increased the contrast-to-noise ratios between the PVs, LA and pulmonary artery by 4-fold (P < 0.01 for both). The signal-to-noise ratios of the PVs and the LA were similar with and without the inversion slab (P > 0.3). The proposed technique greatly enhances the conspicuity of the PVs and LA without significant loss of signal-to-noise ratio.

  18. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

    PubMed

    Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

    2013-05-01

    Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

  19. An adaptive joint focal-mechanism inversion method for microseismic data: Application to Aneth CO2 Enhanced Oil Recovery Field

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Chen, T.; Huang, L.

    2016-12-01

    A good azimuthal coverage of geophones is essentially important for focal-mechanism inversion of passive seismic data. However, microseismic monitoring for CO2 injection-induced seisimicity using borehole geophones often suffers from a poor azimuthal coverage of geophones, leading to large uncertainties in inversion. The focal mechanisms of microseismic events occurred within a small region are often similar to one another. We develop an adaptive focal-mechanism inversion method to invert microseismic events with similar focal mechanisms. We first classify microseismic events with similar focal mechanisms into clusters, and then invert the events in a cluster with the same focal mechanism simultaneously. Such inversion strategy is capable of improving convergent rate and reducing inversion uncertainty with abundant data from different azimuths. We develop a new double-difference focal-mechanism inversion method to further improve focal-mechanism inversion by minimizing the residual between observed and synthetic waveforms for pairs of microseismic events at adjacent locations. Our new algorithm allows us to constrain the focal mechanisms among events adjacent to one another. We apply our new adaptive joint focal-mechanism inversion method to microseismic data acquired using a borehole geophone string at a CO2 enhanced oil recovery field in Aneth, Utah. We compare our inversion results with those obtained from inverting focal mechanism for each microseismic event independently, demonstrating that our new inversion method greatly reduce the inversion uncertainty caused by the limited azimuthal coverage of borehole geophones.

  20. Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats.

    PubMed

    Ling, Alison; Cordaux, Richard

    2010-12-20

    Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.

  1. Inversion group (IG) fitting: A new T1 mapping method for modified look-locker inversion recovery (MOLLI) that allows arbitrary inversion groupings and rest periods (including no rest period).

    PubMed

    Sussman, Marshall S; Yang, Issac Y; Fok, Kai-Ho; Wintersperger, Bernd J

    2016-06-01

    The Modified Look-Locker Inversion Recovery (MOLLI) technique is used for T1 mapping in the heart. However, a drawback of this technique is that it requires lengthy rest periods in between inversion groupings to allow for complete magnetization recovery. In this work, a new MOLLI fitting algorithm (inversion group [IG] fitting) is presented that allows for arbitrary combinations of inversion groupings and rest periods (including no rest period). Conventional MOLLI algorithms use a three parameter fitting model. In IG fitting, the number of parameters is two plus the number of inversion groupings. This increased number of parameters permits any inversion grouping/rest period combination. Validation was performed through simulation, phantom, and in vivo experiments. IG fitting provided T1 values with less than 1% discrepancy across a range of inversion grouping/rest period combinations. By comparison, conventional three parameter fits exhibited up to 30% discrepancy for some combinations. The one drawback with IG fitting was a loss of precision-approximately 30% worse than the three parameter fits. IG fitting permits arbitrary inversion grouping/rest period combinations (including no rest period). The cost of the algorithm is a loss of precision relative to conventional three parameter fits. Magn Reson Med 75:2332-2340, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  2. Dual Inversion Recovery Ultrashort Echo Time (DIR-UTE) Imaging and Quantification of the Zone of Calcified Cartilage (ZCC)

    PubMed Central

    Du, Jiang; Carl, Michael; Bae, Won C.; Statum, Sheronda; Chang, Eric; Bydder, Graeme M; Chung, Christine B.

    2012-01-01

    OBJECTIVE To develop ultrashort echo time (UTE) magnetic resonance imaging (MRI) techniques to image the zone of calcified cartilage (ZCC), and quantify its T2*, T1 and T1ρ. DESIGN In this feasibility study a dual inversion recovery ultrashort echo time (DIR-UTE) sequence was developed for high contrast imaging of the ZCC. T2* of the ZCC was measured with DIR-UTE acquisitions at progressively increasing TEs. T1 of the ZCC was measured with saturation recovery UTE acquisitions at progressively increasing saturation recovery times. T1ρ of the ZCC was measured with spin-locking prepared DIR-UTE acquisitions at progressively increasing spin-locking times. RESULTS The feasibility of the qualitative and quantitative DIR-UTE techniques was demonstrated on phantoms and in six cadaveric patellae using a clinical 3T scanner. On average the ZCC has a short T2* ranging from 1.0 to 3.3 ms (mean ± standard deviation = 2.0 ± 1.2 ms), a short T1 ranging from 256 to 389 ms (mean ± standard deviation = 305 ± 45 ms), and a short T1ρ ranging from 2.2 to 4.6 ms (mean ± standard deviation = 3.6 ± 1.2 ms). CONCLUSION UTE MR based techniques have been developed for high resolution imaging of the ZCC and quantitative evaluation of its T2*, T1 and T1ρ relaxation times, providing noninvasive assessment of collagen orientation and proteoglycan content at the zone of calcified cartilage and the bone cartilage interface. These measurements may be useful for non-invasive assessment of the ZCC, including understanding the involvement of this tissue component in osteoarthritis. PMID:23025927

  3. Sequence analysis of the inversion region containing the pilin genes of Moraxella bovis.

    PubMed Central

    Fulks, K A; Marrs, C F; Stevens, S P; Green, M R

    1990-01-01

    Moraxella bovis EPP63 is able to produce two antigenically distinct pili called Q and I pili (previously called beta and alpha pili). Hybridization studies have shown that the transition between the types is due to inversion of a 2.1-kilobase segment of chromosomal DNA. We present the sequence of a 4.1-kilobase region of cloned DNA spanning the entire inversion region in orientation 1 (Q pilin expressed). Comparison of this sequence with the sequence of the polymerase chain reaction-amplified genomic DNA from orientation 2 (I pilin expressed) allows the site-specific region of recombination to be localized to a 26-base-pair region in which sequence similarity to the left inverted repeat of the Salmonella typhimurium hin system was previously noted. In addition, 50% sequence similarity was seen in a 60-base-pair segment of our sequence to the recombinational enhancer of bacteriophage P1, an inversion system related to the hin system of S. typhimurium. Finally, two open reading frames representing potential genes were identified. PMID:2403542

  4. Sequence analysis of the inversion region containing the pilin genes of Moraxella bovis.

    PubMed

    Fulks, K A; Marrs, C F; Stevens, S P; Green, M R

    1990-01-01

    Moraxella bovis EPP63 is able to produce two antigenically distinct pili called Q and I pili (previously called beta and alpha pili). Hybridization studies have shown that the transition between the types is due to inversion of a 2.1-kilobase segment of chromosomal DNA. We present the sequence of a 4.1-kilobase region of cloned DNA spanning the entire inversion region in orientation 1 (Q pilin expressed). Comparison of this sequence with the sequence of the polymerase chain reaction-amplified genomic DNA from orientation 2 (I pilin expressed) allows the site-specific region of recombination to be localized to a 26-base-pair region in which sequence similarity to the left inverted repeat of the Salmonella typhimurium hin system was previously noted. In addition, 50% sequence similarity was seen in a 60-base-pair segment of our sequence to the recombinational enhancer of bacteriophage P1, an inversion system related to the hin system of S. typhimurium. Finally, two open reading frames representing potential genes were identified.

  5. Consideration of slice profiles in inversion recovery Look-Locker relaxation parameter mapping.

    PubMed

    Tran-Gia, Johannes; Wech, Tobias; Hahn, Dietbert; Bley, Thorsten A; Köstler, Herbert

    2014-10-01

    To include the flip angle distribution caused by the slice profile into the model used for describing the relaxation curves observed in inversion recovery Look-Locker FLASH T1 mapping for a more accurate determination of the relaxation parameters. For each inversion time, the flip angle dependent signal of the mono-exponential relaxation model is integrated across the slice profile. The resulting Consideration of Slice Profiles (CSP) relaxation curves are compared to the mono-exponential signal model in numerical simulations as well as in phantom and in-vivo experiments. All measured relaxation curves showed systematic deviations from a mono-exponential curve increasing with flip angle and T1 but decreasing with repetition time. Additionally, the accuracy of T1 was found to be largely dependent on the temporal coverage of the relaxation curve. All these systematic errors were largely reduced by the CSP model. The proposed CSP model represents a useful extension of the conventionally used mono-exponential relaxation model. Despite inherent model inaccuracies, the mono-exponential model was found to be sufficient for many T1 mapping situations. However, if only a poor temporal coverage of the relaxation process is achievable or a very precise modeling of the relaxation course is needed as in model-based techniques, the mono-exponential model leads to systematic errors and the CSP model should be used instead. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Geoid Recovery Using Geophysical Inverse Theory Applied to Satellite to Satellite Tracking Data

    NASA Technical Reports Server (NTRS)

    Gaposchkin, E. M.

    2000-01-01

    This report describes a new method for determination of the geopotential, or the equivalent geoid. It is based on Satellite-to-Satellite Tracking (SST) of two co-orbiting low earth satellites separated by a few hundred kilometers. The analysis is aimed at the GRACE Mission, though it is generally applicable to any SST data. It is proposed that the SST be viewed as a mapping mission. That is, the result will be maps of the geoid or gravity, as contrasted with determination of spherical harmonics or Fourier coefficients. A method has been developed, based on Geophysical Inverse Theory (GIT), that can provide maps at a prescribed (desired) resolution and the corresponding error map from the SST data. This computation can be done area by area avoiding simultaneous recovery of all the geopotential information. The necessary elements of potential theory, celestial mechanics, and Geophysical Inverse Theory are described, a computation architecture is described, and the results of several simulations presented. Centimeter accuracy geoids with 50 to 100 km resolution can be recovered with a 30 to 60 day mission.

  7. Characterization of myocardial T1-mapping bias caused by intramyocardial fat in inversion recovery and saturation recovery techniques.

    PubMed

    Kellman, Peter; Bandettini, W Patricia; Mancini, Christine; Hammer-Hansen, Sophia; Hansen, Michael S; Arai, Andrew E

    2015-05-10

    Quantitative measurement of T1 in the myocardium may be used to detect both focal and diffuse disease processes such as interstitial fibrosis or edema. A partial volume problem exists when a voxel in the myocardium also contains fat. Partial volume with fat occurs at tissue boundaries or within the myocardium in the case of lipomatous metaplasia of replacement fibrosis, which is commonly seen in chronic myocardial infarction. The presence of fat leads to a bias in T1 measurement. The mechanism for this artifact for widely used T1 mapping protocols using balanced steady state free precession readout and the dependence on off-resonance frequency are described in this paper. Simulations were performed to illustrate the behavior of mono-exponential fitting to bi-exponential mixtures of myocardium and fat with varying fat fractions. Both inversion recovery and saturation recovery imaging protocols using balanced steady state free precession are considered. In-vivo imaging with T1-mapping, water/fat separated imaging, and late enhancement imaging was performed on subjects with chronic myocardial infarction. In n = 17 subjects with chronic myocardial infarction, lipomatous metaplasia is evident in 8 patients (47%). Fat fractions as low as 5% caused approximately 6% T1 elevation for the out-of-phase condition, and approximately 5% reduction of T1 for the in-phase condition. T1 bias in excess of 1000 ms was observed in lipomatous metaplasia with fat fraction of 38% in close agreement with simulation of the specific imaging protocols. Measurement of the myocardial T1 by widely used balanced steady state free precession mapping methods is subject to bias when there is a mixture of water and fat in the myocardium. Intramyocardial fat is frequently present in myocardial scar tissue due lipomatous metaplasia, a process affecting myocardial infarction and some non-ischemic cardiomyopathies. In cases of lipomatous metaplasia, the T1 biases will be additive or subtractive

  8. Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes

    NASA Astrophysics Data System (ADS)

    José, Marco V.; Govezensky, Tzipe; Bobadilla, Juan R.

    2005-06-01

    Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in the other half. This is due to the inverse bilateral symmetry of bacterial chromosomes. Contrary to the classical result that DNA coding regions of bacterial genomes are purely uncorrelated random sequences, here it is shown, via a renormalization group approach, that DNA random fluctuations of single bases are modulated by log-periodic variations. Distance series of triplets display long-range correlations in each half of the intact chromosome and in protein-coding sequences, or both long-range correlations and log-periodic modulations along the whole chromosome. Hence scaling analyses of distance series of DNA sequences have to consider the functional units of bacterial chromosomes.

  9. Information recovery from low coverage whole-genome bisulfite sequencing

    PubMed Central

    Libertini, Emanuele; Heath, Simon C.; Hamoudi, Rifat A.; Gut, Marta; Ziller, Michael J.; Czyz, Agata; Ruotti, Victor; Stunnenberg, Hendrik G.; Frontini, Mattia; Ouwehand, Willem H.; Meissner, Alexander; Gut, Ivo G.; Beck, Stephan

    2016-01-01

    The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future. PMID:27346250

  10. Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.

    PubMed

    Suzuki, Toshifumi; Tsurusaki, Yoshinori; Nakashima, Mitsuko; Miyake, Noriko; Saitsu, Hirotomo; Takeda, Satoru; Matsumoto, Naomichi

    2014-12-01

    Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  12. Sequence differentiation associated with an inversion on the neo-X chromosome of Drosophila americana.

    PubMed

    McAllister, Bryant F

    2003-11-01

    Sex chromosomes originate from pairs of autosomes that acquire controlling genes in the sex-determining cascade. Universal mechanisms apparently influence the evolution of sex chromosomes, because this chromosomal pair is characteristically heteromorphic in a broad range of organisms. To examine the pattern of initial differentiation between sex chromosomes, sequence analyses were performed on a pair of newly formed sex chromosomes in Drosophila americana. This species has neo-sex chromosomes as a result of a centromeric fusion between the X chromosome and an autosome. Sequences were analyzed from the Alcohol dehydrogenase (Adh), big brain (bib), and timeless (tim) gene regions, which represent separate positions along this pair of neo-sex chromosomes. In the northwestern range of the species, the bib and Adh regions exhibit significant sequence differentiation for neo-X chromosomes relative to neo-Y chromosomes from the same geographic region and other chromosomal populations of D. americana. Furthermore, a nucleotide site defining a common haplotype in bib is shown to be associated with a paracentric inversion [In(4)ab] on the neo-X chromosome, and this inversion suppresses recombination between neo-X and neo-Y chromosomes. These observations are consistent with the inversion acting as a recombination modifier that suppresses exchange between these neo-sex chromosomes, as predicted by models of sex chromosome evolution.

  13. The inverse hexagonal - inverse ribbon - lamellar gel phase transition sequence in low hydration DOPC:DOPE phospholipid mixtures

    SciTech Connect

    Kent, B; Garvey, C J; Cookson, D; Bryant, G

    2009-01-05

    The inverse hexagonal to inverse ribbon phase transition in a mixed phosphatidylcholine-phosphatidylethanolamine system at low hydration is studied using small and wide angle X-ray scattering. It is found that the structural parameters of the inverse hexagonal phase are independent of temperature. By contrast the length of each ribbon of the inverse ribbon phase increases continuously with decreasing temperature over a range of 50 ºC. At low temperatures the inverse ribbon phase is observed to have a transition to a gel lamellar phase, with no intermediate fluid lamellar phase. This phase transition is confirmed by differential scanning calorimetry.

  14. Dual Inversion Recovery Ultrashort Echo Time (DIR UTE) Imaging: Creating High Contrast for Short-T2 Species

    PubMed Central

    Du, Jiang; Takahashi, Atsushi M.; Bae, Won C.; Chung, Christine B.; Bydder, Graeme M.

    2015-01-01

    Imaging of short-T2 species requires not only a short echo time (TE) but also efficient suppression of long-T2 species in order to maximize the short-T2 contrast and dynamic range. This paper introduces a method of long-T2 suppression using two long adiabatic inversion pulses. The first adiabatic inversion pulse inverts the magnetization of long-T2 water and the second one inverts that of fat. Short-T2 species experience a significant transverse relaxation during the long adiabatic inversion process, and are minimally affected by the inversion pulses. Data acquisition with a short TE of 8 μs starts following a time delay of TI1 for the inverted water magnetization to reach a null point, and a time delay of TI2 for the inverted fat magnetization to reach a null point. The suppression of long-T2 species depends on proper combination of TI1, TI2 and TR. It is insensitive to RF inhomogeneities because of the adiabatic inversion pulses. The feasibility of this dual inversion recovery ultrashort TE (DIR UTE) technique was demonstrated on phantoms, cadaveric specimens and healthy volunteers using a clinical 3T scanner. High image contrast was achieved for the deep radial and calcified layers of articular cartilage, cortical bone and the Achilles tendon. PMID:20099332

  15. Evaluation of chondromalacia of the patella with axial inversion recovery-fast spin-echo imaging.

    PubMed

    Lee, S H; Suh, J S; Cho, J; Kim, S J; Kim, S J

    2001-03-01

    The purpose of our study was to assess the accuracy of inversion recovery-fast spin-echo (IR-FSE) imaging for the evaluation of chondromalacia of the patella. Eighty-six patients were included, they underwent magnetic resonance (MR) examination and subsequent knee arthroscopy. Medial and lateral facets of the patella were evaluated separately. Axial images were obtained by using IR-FSE (TR/TE/TI = 3000/25/150 msec; echo train length, 8; 4-mm thickness; 12-cm field of view; 512 x 256 matrix; two, number of excitations) with a 1.5-T MR machine. MR interpretation of chondromalacia was made on the basis of the arthroscopic grading system. Of a total of 172 facets graded, arthroscopy revealed chondromalacia in 14 facets with various grades (G0, 158; G1, 1; G2, 3; G3, 6; G4, 4). Sensitivity, specificity, and accuracy in the chondromalacia grades were 57.1%, 93.0%, and 90.1%, respectively. There was one false-negative case (G4) and 11 false-positive cases (G1, eight; G2, two; G3, one). Sensitivity and specificity corrected by one grade difference were improved to 85.7% and 98.1%, respectively. When cartilage changes were grouped into early (corresponding to grade 1 and 2) and advanced (grade 3 and 4) diseases, sensitivity and specificity of the early and advanced diseases were 75% and 94% and 80% and 99%, respectively. IR-FSE imaging of the knee revealed high specificity but low sensitivity for the evaluation of chondromalacia of the patella.

  16. Pulmonary perfusion quantification with flow-sensitive inversion recovery (FAIR) UTE MRI in small animal imaging.

    PubMed

    Tibiletti, Marta; Bianchi, Andrea; Stiller, Detlef; Rasche, Volker

    2016-12-01

    Blood perfusion in lung parenchyma is an important property for assessing lung function. In small animals, its quantitation is limited even with radioactive isotopes or dynamic contrast-enhanced MRI techniques. In this study, the feasibility flow-sensitive alternating inversion recovery (FAIR) for the quantification of blood flow in lung parenchyma in free breathing rats at 7 T has been investigated. In order to obtain sufficient signal from the short T2 * lung parenchyma, a 2D ultra-short echo time (UTE) Look-Locker read-out has been implemented. Acquisitions were segmented to maintain acquisition time within an acceptable range. A method to perform retrospective respiratory gating (DC-SG) has been applied to investigate the impact of respiratory movement. Reproducibilities within and between sessions were estimated, and the ability of FAIR-UTE to identify the decrease of lung perfusion under hyperoxic conditions was tested. The implemented technique allowed for the visualization of lung parenchyma with excellent SNR and no respiratory artifact even in ungated acquisitions. Lung parenchyma perfusion was obtained as 32.54 ± 2.26 mL/g/min in the left lung, and 34.09 ± 2.75 mL/g/min in the right lung. Application of retrospective gating significantly but minimally changes the perfusion values, implying that respiratory gating may not be necessary with this center-our acquisition method. A decrease of 10% in lung perfusion was found between normoxic and hyperoxic conditions, proving the feasibility of the FAIR-UTE approach to quantify lung perfusion changes. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Fluid-attenuated inversion recovery evolution within 12 hours from stroke onset: a reliable tissue clock?

    PubMed

    Ebinger, Martin; Galinovic, Ivana; Rozanski, Michal; Brunecker, Peter; Endres, Matthias; Fiebach, Jochen B

    2010-02-01

    It has recently been proposed that fluid-attenuated inversion recovery (FLAIR) imaging may serve as a surrogate marker for time of symptom onset after stroke. We assessed the hypothesis that FLAIR imaging could be used to decide if an MRI was performed within 4.5 hours from symptom onset or later. All consecutive patients with presumed stroke who underwent an MRI within 12 hours after known symptom onset were included regardless of stroke subtype and severity between May 2008 and May 2009. Blinded to time of symptom onset, 2 raters judged the visibility of lesions on FLAIR. Apparent diffusion coefficient values, lesion volume on diffusion-weighted imaging, and relative signal intensity of FLAIR lesions were determined. In 94 consecutive patients with stroke, we found that median time from symptom onset for FLAIR-positive patients (189 minutes; interquartile range, 110 to 369 minutes) was significantly longer compared with FLAIR-negative patients (103 minutes; interquartile range, 75 to 183 minutes; P=0.011). Negative FLAIR had a sensitivity of 46% and a specificity of 79% for allocating patients to a time window of less than 4.5 hours. FLAIR positivity increased with diffusion-weighted imaging lesion volume (P<0.001) but showed no correlation with apparent diffusion coefficient values (P=0.795). There was no significant correlation between relative signal intensity and time from symptom onset (Spearman correlation coefficient -0.152, P=0.128). Based on our findings, we cannot recommend the use of FLAIR visibility as an estimate of time from symptom onset within the first 4.5 hours.

  18. Seismic inversion for incoming sedimentary sequence in the Nankai Trough margin off Kumano Basin, southwest Japan

    NASA Astrophysics Data System (ADS)

    Naito, K.; Park, J.

    2012-12-01

    The Nankai Trough off southwest Japan is one of the best subduction-zone to study megathrust earthquake mechanism. Huge earthquakes have been repeated in the cycle of 100-150 years in the area, and in these days the next emergence of the earthquake becomes one of the most serious issue in Japan. Therefore, detailed descriptions of geological structure are urgently needed there. IODP (Integrated Ocean Drilling Program) have investigated this area in the NanTroSEIZE science plan. Seismic reflection, core sampling and borehole logging surveys have been executed during the NanTroSEIZE expeditions. Core-log-seismic data integration (CLSI) is useful for understanding the Nankai seismogenic zone. We use the seismic inversion method to do the CLSI. The seismic inversion (acoustic impedance inversion, A.I. inversion) is a method to estimate rock physical properties using seismic reflection and logging data. Acoustic impedance volume is inverted for seismic data with density and P-wave velocity of several boreholes with the technique. We use high-resolution 3D multi-channel seismic (MCS) reflection data obtained during KR06-02 cruise in 2006, and measured core sample properties by IODP Expeditions 322 and 333. P-wave velocities missing for some core sample are interpolated by the relationship between acoustic impedance and P-wave velocity. We used Hampson-Russell software for the seismic inversion. 3D porosity model is derived from the 3D acoustic impedance model to figure out rock physical properties of the incoming sedimentary sequence in the Nankai Trough off Kumano Basin. The result of our inversion analysis clearly shows heterogeneity of sediments; relatively high porosity sediments on the shallow layer of Kashinosaki Knoll, and distribution of many physical anomaly bands on volcanic and turbidite sediment layers around the 3D MCS survey area. In this talk, we will show 3D MCS, acoustic impedance, and porosity data for the incoming sedimentary sequence and discuss its

  19. Three Dimensional T1, T2, and Proton Density Mapping with Inversion Recovery Balanced SSFP

    PubMed Central

    Newbould, Rexford D.; Skare, Stefan T.; Alley, Marcus T.; Gold, Garry E.; Bammer, Roland

    2010-01-01

    By combining a bSSFP readout with an initial inversion pulse, all three contrast parameters, T1, T2, and proton density (M0), may be rapidly calculated from the signal progression in time. However, here it is shown that this technique is quite sensitive to variation in the applied transmit RF (B1) field, leading to pronounced errors in calculated values. 2D acquisitions are taxed to accurately quantify the relaxation, as the short RF pulses required by SSFP's rapid TR contain a broad spectrum of excitation angles. A 3D excitation using a large diameter excitation coil was able to correctly quantify the parameters. While the extreme B1 sensitivity was previously problematic, and has precluded use of IR-bSSFP for relaxometry, in this work these obstacles were significantly reduced, allowing the rapid quantification of T1, T2, and M0. The results may further be used to simulate image contrast from common sequences, such as a T1-weighted or FLAIR examination. PMID:20692784

  20. Inversions and adaptation to the plant toxin ouabain shape DNA sequence variation within and between chromosomal inversions of Drosophila subobscura.

    PubMed Central

    Pegueroles, Cinta; Ferrés-Coy, Albert; Martí-Solano, Maria; Aquadro, Charles F; Pascual, Marta; Mestres, Francesc

    2016-01-01

    Adaptation is defined as an evolutionary process allowing organisms to succeed in certain habitats or conditions. Chromosomal inversions have the potential to be key in the adaptation processes, since they can contribute to the maintenance of favoured combinations of adaptive alleles through reduced recombination between individuals carrying different inversions. We have analysed six genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1), located inside and outside three inversions of the O chromosome in European populations of Drosophila subobscura. Genetic differentiation was significant between inversions despite extensive recombination inside inverted regions, irrespective of gene distance to the inversion breakpoints. Surprisingly, the highest level of genetic differentiation between arrangements was found for the Atpα gene, which is located outside the O1 and O7 inversions. Two derived unrelated arrangements (O3+4+1 and O3+4+7) are nearly fixed for several amino acid substitutions at the Atpα gene that have been described to confer resistance in other species to the cardenolide ouabain, a plant toxin capable of blocking ATPases. Similarities in the Atpα variants, conferring ouabain resistance in both arrangements, may be the result of convergent substitution and be favoured in response to selective pressures presumably related to the presence of plants containing ouabain in the geographic locations where both inversions are present. PMID:27029337

  1. Inversions and adaptation to the plant toxin ouabain shape DNA sequence variation within and between chromosomal inversions of Drosophila subobscura.

    PubMed

    Pegueroles, Cinta; Ferrés-Coy, Albert; Martí-Solano, Maria; Aquadro, Charles F; Pascual, Marta; Mestres, Francesc

    2016-03-31

    Adaptation is defined as an evolutionary process allowing organisms to succeed in certain habitats or conditions. Chromosomal inversions have the potential to be key in the adaptation processes, since they can contribute to the maintenance of favoured combinations of adaptive alleles through reduced recombination between individuals carrying different inversions. We have analysed six genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1), located inside and outside three inversions of the O chromosome in European populations of Drosophila subobscura. Genetic differentiation was significant between inversions despite extensive recombination inside inverted regions, irrespective of gene distance to the inversion breakpoints. Surprisingly, the highest level of genetic differentiation between arrangements was found for the Atpα gene, which is located outside the O1 and O7 inversions. Two derived unrelated arrangements (O3+4+1 and O3+4+7) are nearly fixed for several amino acid substitutions at the Atpα gene that have been described to confer resistance in other species to the cardenolide ouabain, a plant toxin capable of blocking ATPases. Similarities in the Atpα variants, conferring ouabain resistance in both arrangements, may be the result of convergent substitution and be favoured in response to selective pressures presumably related to the presence of plants containing ouabain in the geographic locations where both inversions are present.

  2. Characterizing polymorphic inversions in human genomes by single-cell sequencing

    PubMed Central

    Sanders, Ashley D.; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M.

    2016-01-01

    Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery. PMID:27472961

  3. Characterizing polymorphic inversions in human genomes by single-cell sequencing.

    PubMed

    Sanders, Ashley D; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M

    2016-11-01

    Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery.

  4. Myocardial Late Gadolinium Enhancement: Accuracy of T1 Mapping-based Synthetic Inversion-Recovery Imaging.

    PubMed

    Varga-Szemes, Akos; van der Geest, Rob J; Spottiswoode, Bruce S; Suranyi, Pal; Ruzsics, Balazs; De Cecco, Carlo N; Muscogiuri, Giuseppe; Cannaò, Paola M; Fox, Mary A; Wichmann, Julian L; Vliegenthart, Rozemarijn; Schoepf, U Joseph

    2016-02-01

    To compare the accuracy of detection and quantification of myocardial late gadolinium enhancement (LGE) with a synthetic inversion-recovery (IR) approach with that of conventional IR techniques. This prospective study was approved by the institutional review board and compliant with HIPAA. All patients gave written informed consent. Between June and November 2014, 43 patients (25 men; mean age, 54 years ± 16) suspected of having previous myocardial infarction underwent magnetic resonance (MR) imaging, including contrast material-enhanced LGE imaging and T1 mapping. Synthetic magnitude and phase-sensitive IR images were generated on the basis of T1 maps. Images were assessed by two readers. Differences in the per-patient and per-segment LGE detection rates between the synthetic and conventional techniques were analyzed with the McNemar test, and the accuracy of LGE quantification was calculated with the paired t test and Bland-Altman statistics. Interreader agreement for the detection and quantification of LGE was analyzed with κ and Bland-Altman statistics, respectively. Seventeen of the 43 patients (39%) had LGE patterns consistent with myocardial infarction. The sensitivity and specificity of synthetic magnitude and phase-sensitive IR techniques in the detection of LGE were 90% and 95%, respectively, with patient-based analysis and 94% and 99%, respectively, with segment-based analysis. The area of LGE measured with synthetic IR techniques showed excellent agreement with that of conventional techniques (4.35 cm(2) ± 1.88 and 4.14 cm(2)± 1.62 for synthetic magnitude and phase-sensitive IR, respectively, compared with 4.25 cm(2) ± 1.92 and 4.22 cm(2) ± 1.86 for conventional magnitude and phase-sensitive IR, respectively; P > .05). Interreader agreement was excellent for the detection (κ > 0.81) and quantification (bias range, -0.34 to 0.40; P > .05) of LGE. The accuracy of the T1 map-based synthetic IR approach in the detection and quantification of

  5. Validation of net joint loads calculated by inverse dynamics in case of complex movements: application to balance recovery movements.

    PubMed

    Robert, T; Chèze, L; Dumas, R; Verriest, J-P

    2007-01-01

    The joint forces and moments driving the motion of a human subject are classically computed by an inverse dynamic calculation. However, even if this process is theoretically simple, many sources of errors may lead to huge inaccuracies in the results. Moreover, a direct comparison with in vivo measured loads or with "gold standard" values from literature is only possible for very specific studies. Therefore, assessing the inaccuracy of inverse dynamic results is not a trivial problem and a simple method is still required. This paper presents a simple method to evaluate both: (1) the consistency of the results obtained by inverse dynamics; (2) the influence of possible modifications in the inverse dynamic hypotheses. This technique concerns recursive calculation performed on full kinematic chains, and consists in evaluating the loads obtained by two different recursive strategies. It has been applied to complex 3D whole body movements of balance recovery. A recursive Newton-Euler procedure was used to compute the net joint loads. Two models were used to represent the subject bodies, considering or not the upper body as a unique rigid segment. The inertial parameters of the body segments were estimated from two different sets of scaling equations [De Leva, P., 1996. Adjustments to Zatsiorsky-Suleyanov's segment inertia parameters. Journal of Biomechanics 29, 1223-1230; Dumas, R., Chèze, L., Verriest, J.-P., 2006b. Adjustments to McConville et al. and Young et al. Body Segment Inertial Parameters. Journal of Biomechanics, in press]. Using this comparison technique, it has been shown that, for the balance recovery motions investigated: (1) the use of the scaling equations proposed by Dumas et al., instead of those proposed by De Leva, improves the consistency of the results (average relative influence up to 30% for the transversal moment); (2) the arm motions dynamically influence the recovery motion in a non negligible way (average relative influence up to 15% and 30

  6. Accuracy for detection of simulated lesions: comparison of fluid-attenuated inversion-recovery, proton density--weighted, and T2-weighted synthetic brain MR imaging

    NASA Technical Reports Server (NTRS)

    Herskovits, E. H.; Itoh, R.; Melhem, E. R.

    2001-01-01

    OBJECTIVE: The objective of our study was to determine the effects of MR sequence (fluid-attenuated inversion-recovery [FLAIR], proton density--weighted, and T2-weighted) and of lesion location on sensitivity and specificity of lesion detection. MATERIALS AND METHODS: We generated FLAIR, proton density-weighted, and T2-weighted brain images with 3-mm lesions using published parameters for acute multiple sclerosis plaques. Each image contained from zero to five lesions that were distributed among cortical-subcortical, periventricular, and deep white matter regions; on either side; and anterior or posterior in position. We presented images of 540 lesions, distributed among 2592 image regions, to six neuroradiologists. We constructed a contingency table for image regions with lesions and another for image regions without lesions (normal). Each table included the following: the reviewer's number (1--6); the MR sequence; the side, position, and region of the lesion; and the reviewer's response (lesion present or absent [normal]). We performed chi-square and log-linear analyses. RESULTS: The FLAIR sequence yielded the highest true-positive rates (p < 0.001) and the highest true-negative rates (p < 0.001). Regions also differed in reviewers' true-positive rates (p < 0.001) and true-negative rates (p = 0.002). The true-positive rate model generated by log-linear analysis contained an additional sequence-location interaction. The true-negative rate model generated by log-linear analysis confirmed these associations, but no higher order interactions were added. CONCLUSION: We developed software with which we can generate brain images of a wide range of pulse sequences and that allows us to specify the location, size, shape, and intrinsic characteristics of simulated lesions. We found that the use of FLAIR sequences increases detection accuracy for cortical-subcortical and periventricular lesions over that associated with proton density- and T2-weighted sequences.

  7. Accuracy for detection of simulated lesions: comparison of fluid-attenuated inversion-recovery, proton density--weighted, and T2-weighted synthetic brain MR imaging

    NASA Technical Reports Server (NTRS)

    Herskovits, E. H.; Itoh, R.; Melhem, E. R.

    2001-01-01

    OBJECTIVE: The objective of our study was to determine the effects of MR sequence (fluid-attenuated inversion-recovery [FLAIR], proton density--weighted, and T2-weighted) and of lesion location on sensitivity and specificity of lesion detection. MATERIALS AND METHODS: We generated FLAIR, proton density-weighted, and T2-weighted brain images with 3-mm lesions using published parameters for acute multiple sclerosis plaques. Each image contained from zero to five lesions that were distributed among cortical-subcortical, periventricular, and deep white matter regions; on either side; and anterior or posterior in position. We presented images of 540 lesions, distributed among 2592 image regions, to six neuroradiologists. We constructed a contingency table for image regions with lesions and another for image regions without lesions (normal). Each table included the following: the reviewer's number (1--6); the MR sequence; the side, position, and region of the lesion; and the reviewer's response (lesion present or absent [normal]). We performed chi-square and log-linear analyses. RESULTS: The FLAIR sequence yielded the highest true-positive rates (p < 0.001) and the highest true-negative rates (p < 0.001). Regions also differed in reviewers' true-positive rates (p < 0.001) and true-negative rates (p = 0.002). The true-positive rate model generated by log-linear analysis contained an additional sequence-location interaction. The true-negative rate model generated by log-linear analysis confirmed these associations, but no higher order interactions were added. CONCLUSION: We developed software with which we can generate brain images of a wide range of pulse sequences and that allows us to specify the location, size, shape, and intrinsic characteristics of simulated lesions. We found that the use of FLAIR sequences increases detection accuracy for cortical-subcortical and periventricular lesions over that associated with proton density- and T2-weighted sequences.

  8. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

    PubMed Central

    Stefan, Christopher P.; Koehler, Jeffrey W.; Minogue, Timothy D.

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

  9. Anterior temporal lobe white matter abnormal signal (ATLAS) as an indicator of seizure focus laterality in temporal lobe epilepsy: comparison of double inversion recovery, FLAIR and T2W MR imaging.

    PubMed

    Morimoto, Emiko; Kanagaki, Mitsunori; Okada, Tomohisa; Yamamoto, Akira; Mori, Nobuyuki; Matsumoto, Riki; Ikeda, Akio; Mikuni, Nobuhiro; Kunieda, Takeharu; Paul, Dominik; Miyamoto, Susumu; Takahashi, Ryosuke; Togashi, Kaori

    2013-01-01

    To investigate the diagnostic capability of anterior temporal lobe white matter abnormal signal (ATLAS) for determining seizure focus laterality in temporal lobe epilepsy (TLE) by comparing different MR sequences. This prospective study was approved by the institutional review board and written informed consent was obtained. Three 3D sequences (double inversion recovery (DIR), fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging (T2WI)) and two 2D sequences (FLAIR and T2WI) were acquired at 3 T. Signal changes in the anterior temporal white matter of 21 normal volunteers were evaluated. ATLAS laterality was evaluated in 21 TLE patients. Agreement of independent evaluations by two neuroradiologists was assessed using κ statistics. Differences in concordance between ATLAS laterality and clinically defined seizure focus laterality were analysed using McNemar's test with multiple comparisons. Pre-amygdala high signals (PAHS) were detected in all volunteers only on 3D-DIR. Inter-evaluator agreement was moderate to almost perfect for each sequence. Correct diagnosis of seizure laterality was significantly more frequent on 3D-DIR than on any other sequences (P ≤ 0.031 for each evaluator). The most sensitive sequence for detecting ATLAS laterality was 3D-DIR. ATLAS laterality on 3D-DIR can be a good indicator for determining seizure focus localization in TLE.

  10. Does b1000-b0 Mismatch Challenge Diffusion-Weighted Imaging-Fluid Attenuated Inversion Recovery Mismatch in Stroke?

    PubMed

    Geraldo, Ana Filipa; Berner, Lise-Prune; Haesebaert, Julie; Chabrol, Aurélie; Cho, Tae-Hee; Derex, Laurent; Hermier, Marc; Louis-Tisserand, Guy; Chamard, Leila; Klaerke Mikkelsen, Irene; Ribe, Lars; Østergaard, Leif; Hjort, Niels; Pedraza, Salvador; Thomalla, Götz; Baron, Jean-Claude; Nighoghossian, Norbert; Berthèzene, Yves

    2016-03-01

    Our aim was to explore whether the mismatch in lesion visibility between b1000 and b0 images is an alternative to mismatch between diffusion-weighted imaging and fluid-attenuated inversion recovery imaging as a surrogate marker of stroke age. We analyzed patients from the European multicenter I-KNOW database. Independent readers assessed the visibility of ischemic lesions of the anterior circulation on b0 and fluid-attenuated inversion recovery imaging images. The signal-intensity ratio for b0 and fluid-attenuated inversion recovery imaging images was also measured from the segmented stroke lesion volume on b1000 images. This study included 112 patients (68 men; mean age, 67.4 years) with stroke onset within (n=85) or longer than (n=27) 4.5 hours. b1000-b0 mismatch identified patients within 4.5 hours of stroke onset with moderate sensitivity (72.9%; 95% confidence interval [CI], 63.5-82.4) and specificity (70.4%; 95% CI, 53.2-87.6), high positive predictive value (88.6%; 95% CI, 81.1-96.0), and low negative predictive value (45.2%; 95% CI, 30.2-60.3). Global comparison of b1000-b0 mismatch with diffusion-weighted imaging-fluid-attenuated inversion recovery imaging mismatch (considered the imaging gold standard) indicated high sensitivity (85.9%; 95% CI, 78.2-93.6), specificity (91.2%; 95% CI, 76.3-98.1), and positive predictive value (96.7%; 95% CI, 88.0-99.1) and moderate negative predictive value (73.8%; 95% CI, 60.5-87.1) of this new approach. b0 signal-intensity ratio (r=0.251; 95% CI, 0.069-0.417; P=0.008) was significantly although weakly correlated with delay between stroke onset and magnetic resonance imaging. b1000-b0 mismatch may identify patients with ischemic stroke of the within 4.5 hours of onset with high positive predictive value, perhaps constituting an alternative imaging tissue clock. © 2016 American Heart Association, Inc.

  11. Spectral recovery of outdoor illumination by an extension of the Bayesian inverse approach to the Gaussian mixture model.

    PubMed

    Peyvandi, Shahram; Amirshahi, Seyed Hossein; Hernández-Andrés, Javier; Nieves, Juan Luis; Romero, Javier

    2012-10-01

    The Bayesian inference approach to the inverse problem of spectral signal recovery has been extended to mixtures of Gaussian probability distributions of a training dataset in order to increase the efficiency of estimating the spectral signal from the response of a transformation system. Bayesian (BIC) and Akaike (AIC) information criteria were assessed in order to provide the Gaussian mixture model (GMM) with the optimum number of clusters within the spectral space. The spectra of 2600 solar illuminations measured in Granada (Spain) were recovered over the range of 360-830 nm from their corresponding tristimulus values using a linear model of basis functions, the Wiener inverse (WI) method, and the Bayesian inverse approach extended to the GMM (BGMM). A model of Gaussian mixtures for solar irradiance was deemed to be more appropriate than a single Gaussian distribution for representing the probability distribution of the solar spectral data. The results showed that the estimation performance of the BGMM method was better than either the linear model or the WI method for the spectral approximation of daylight from the three-dimensional tristimulus values.

  12. Using waveform cross correlation for automatic recovery of aftershock sequences

    NASA Astrophysics Data System (ADS)

    Bobrov, Dmitry; Kitov, Ivan; Rozhkov, Mikhail

    2017-04-01

    Aftershock sequences of the largest earthquakes are difficult to recover. There can be several hundred mid-sized aftershocks per hour within a few hundred km from each other recorded by the same stations. Moreover, these events generate thousands of reflected/refracted phases having azimuth and slowness close to those from the P-waves. Therefore, aftershock sequences with thousands of events represent a major challenge for automatic and interactive processing at the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Organization (CTBTO). Standard methods of detection and phase association do not use all information contained in signals. As a result, wrong association of the first and later phases, both regular and site specific, produces enormous number of wrong event hypotheses and destroys valid event hypotheses in automatic IDC processing. In turn, the IDC analysts have to reject false and recreate valid hypotheses wasting precious human resources. At the current level of the IDC catalogue completeness, the method of waveform cross correlation (WCC) can resolve most of detection and association problems fully utilizing the similarity of waveforms generated by aftershocks. Array seismic stations of the International monitoring system (IMS) can enhance the performance of the WCC method: reduce station-specific detection thresholds, allow accurate estimate of signal attributes, including relative magnitude, and effectively suppress irrelevant arrivals. We have developed and tested a prototype of an aftershock tool matching all IDC processing requirements and merged it with the current IDC pipeline. This tool includes creation of master events consisting of real or synthetic waveform templates at ten and more IMS stations; cross correlation (CC) of real-time waveforms with these templates, association of arrivals detected at CC-traces in event hypotheses; building events matching the IDC quality criteria; and resolution of conflicts between events

  13. Distillation sequence for the purification and recovery of hydrocarbons

    DOEpatents

    Reyneke, Rian; Foral, Michael; Papadopoulos, Christos G.; Logsdon, Jeffrey S.; Eng, Wayne W. Y.; Lee, Guang-Chung; Sinclair, Ian

    2007-12-25

    This invention is an improved distillation sequence for the separation and purification of ethylene from a cracked gas. A hydrocarbon feed enters a C2 distributor column. The top of the C2 distributor column is thermally coupled to an ethylene distributor column, and the bottoms liquid of a C2 distributor column feeds a deethanizer column. The C2 distributor column utilizes a conventional reboiler. The top of the ethylene distributor is thermally coupled with a demethanizer column, and the bottoms liquid of the ethylene distributor feeds a C2 splitter column. The ethylene distributor column utilizes a conventional reboiler. The deethanizer and C2 splitter columns are also thermally coupled and operated at a substantially lower pressure than the C2 distributor column, the ethylene distributor column, and the demethanizer column. Alternatively, a hydrocarbon feed enters a deethanizer column. The top of the deethanizer is thermally coupled to an ethylene distributor column, and the ethylene distributor column utilizes a conventional reboiler. The top of the ethylene distributor column is thermally coupled with a demethanizer column, and the bottoms liquid of the ethylene distributor column feeds a C2 splitter column. The C2 splitter column operates at a pressure substantially lower than the ethylene distributor column, the demethanizer column, and the deethanizer column.

  14. Damped regional-scale stress inversions: Methodology and examples for southern California and the Coalinga aftershock sequence

    USGS Publications Warehouse

    Hardebeck, J.L.; Michael, A.J.

    2006-01-01

    We present a new focal mechanism stress inversion technique to produce regional-scale models of stress orientation containing the minimum complexity necessary to fit the data. Current practice is to divide a region into small subareas and to independently fit a stress tensor to the focal mechanisms of each subarea. This procedure may lead to apparent spatial variability that is actually an artifact of overfitting noisy data or nonuniquely fitting data that does not completely constrain the stress tensor. To remove these artifacts while retaining any stress variations that are strongly required by the data, we devise a damped inversion method to simultaneously invert for stress in all subareas while minimizing the difference in stress between adjacent subareas. This method is conceptually similar to other geophysical inverse techniques that incorporate damping, such as seismic tomography. In checkerboard tests, the damped inversion removes the stress rotation artifacts exhibited by an undamped inversion, while resolving sharper true stress rotations than a simple smoothed model or a moving-window inversion. We show an example of a spatially damped stress field for southern California. The methodology can also be used to study temporal stress changes, and an example for the Coalinga, California, aftershock sequence is shown. We recommend use of the damped inversion technique for any study examining spatial or temporal variations in the stress field.

  15. A high resolution and high contrast MRI for differentiation of subcortical structures for DBS targeting: the Fast Gray Matter Acquisition T1 Inversion Recovery (FGATIR).

    PubMed

    Sudhyadhom, Atchar; Haq, Ihtsham U; Foote, Kelly D; Okun, Michael S; Bova, Frank J

    2009-08-01

    DBS depends on precise placement of the stimulating electrode into an appropriate target region. Image-based (direct) targeting has been limited by the ability of current technology to visualize DBS targets. We have recently developed and employed a Fast Gray Matter Acquisition T1 Inversion Recovery (FGATIR) 3T MRI sequence to more reliably visualize these structures. The FGATIR provides significantly better high resolution thin (1 mm) slice visualization of DBS targets than does either standard 3T T1 or T2-weighted imaging. The T1 subcortical image revealed relatively poor contrast among the targets for DBS, though the sequence did allow localization of striatum and thalamus. T2 FLAIR scans demonstrated better contrast between the STN, SNr, red nucleus (RN), and pallidum (GPe/GPi). The FGATIR scans allowed for localization of the thalamus, striatum, GPe/GPi, RN, and SNr and displayed sharper delineation of these structures. The FGATIR also revealed features not visible on other scan types: the internal lamina of the GPi, fiber bundles from the internal capsule piercing the striatum, and the boundaries of the STN. We hope that use of the FGATIR to aid initial targeting will translate in future studies to faster and more accurate procedures with consequent improvements in clinical outcomes.

  16. Geoid Recovery using Geophysical Inverse Theory Applied to Satellite to Satellite Tracking Data

    NASA Technical Reports Server (NTRS)

    Gaposchkin, E. M.; Frey, H. (Technical Monitor)

    2000-01-01

    This report describes a new method for determination of the geopotential. The analysis is aimed at the GRACE mission. This Satellite-to-Satellite Tracking (SST) mission is viewed as a mapping mission The result will be maps of the geoid. The elements of potential theory, celestial mechanics, and Geophysical Inverse Theory are integrated into a computation architecture, and the results of several simulations presented Centimeter accuracy geoids with 50 to 100 km resolution can be recovered with a 30 to 60 day mission.

  17. TIME-LAPSE MODELING AND INVERSION OF CO2 SATURATION FOR SEQUESTRATION AND ENHANCED OIL RECOVERY

    SciTech Connect

    Mark A. Meadows

    2005-05-25

    In this quarter we have continued our development of the inversion procedure for Phase III, in which time-lapse changes in seismic attributes are inverted to yield changes in CO{sub 2} fluid properties over time. In order to extract seismic attributes from the Sleipner North Sea CO{sub 2} time-lapse data set, a new, detailed interpretation was performed and multiple horizons were picked for the 1994 and 2002 vintages. Traveltime difference maps were constructed at several levels within the Sleipner CO{sub 2} injection zone, and were quantitatively analyzed. No traveltime change was seen in the overburden, as expected, while significant changes were seen in the upper half of the CO{sub 2} injection zone. Evidence of thin-bed tuning and undershooting was also found. A new semi-automated, quantitative method for estimating time sag anomalies was developed, and was used to calculate the amount of time sag along a selected horizon. The resulting time sag estimates matched those seen in the traveltime difference maps. Such a method will be useful for obtaining rapid, accurate quantitative measurements of traveltime changes in the Sleipner data cubes. The traveltime changes will be combined with other attributes, such as amplitude and frequency changes, for input into the real-data inversion.

  18. A selective inversion recovery method for the improvement of 23Na NMR spectral resolution in isolated perfused rat hearts.

    PubMed

    Simor, T; Kim, S K; Chu, W J; Pohost, G M; Elgavish, G A

    1993-01-01

    Shift-reagent-aided 23Na NMR spectroscopy allows differentiation of the intracellular (Na(i)) and extracellular sodium (Na(o)) signals. The goal of the present study has been to develop a 23Na NMR spectroscopic method to minimize the intensity of the shift-reagent-shifted Na(o) signal and thus increase Na(i) resolution. This is achieved by a selective inversion recovery (SIR) method which enhances the resolution between the Na(i) and Na(o) peaks in shift-reagent-aided 23Na NMR spectroscopy. The application of SIR with Dy(TTHA), Tm(DOTP), or with low concentrations of Dy(PPP)2 results in both good spectral resolution and physiologically acceptable contractile function in the isolated, perfused rat heart model.

  19. Flow-sensitive alternating inversion recovery (fair) imaging for retrograde cortical venous drainage related to intracranial dural arteriovenous fistula.

    PubMed

    Noguchi, Kyo; Kuwayama, Naoya; Kubo, Michiya; Kamisaki, Yuichi; Kameda, Keisuke; Tomizawa, Gakuto; Kawabe, Hideto; Seto, Hikaru

    2011-03-01

    To evaluate the hypothesis that flow-sensitive alternating inversion recovery (FAIR) magnetic resonance (MR) imaging can detect retrograde cortical venous drainage (RCVD) in patients with intracranial dural arteriovenous fistula (DAVF). Seven patients with angiographically confirmed DAVF with RCVD and two DAVF patients without RCVD underwent examinations with conventional MR imaging and FAIR, five of these seven patients with RCVD also underwent examination with dynamic susceptibility contrast (DSC) MR imaging. The ability of FAIR to depict prominent cerebral veins was evaluated, and FAIR was compared with the relative cerebral blood volume (rCBV) maps created with DSC. In all DAVF patients with RCVD, FAIR clearly showed prominent veins on the surface of the brain in affected hemisphere, and FAIR corresponded well with the areas of increased rCBV. In all DAVF patients without RCVD, FAIR showed no prominent veins. FAIR can detect RCVD in patients with DAVF.

  20. Application of (13)C NMR cross-polarization inversion recovery experiments for the analysis of solid dosage forms.

    PubMed

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Szeleszczuk, Łukasz

    2016-11-20

    Solid-state nuclear magnetic resonance (ssNMR) is a powerful and unique method for analyzing solid forms of the active pharmaceutical ingredients (APIs) directly in their original formulations. Unfortunately, despite their wide range of application, the ssNMR experiments often suffer from low sensitivity and peaks overlapping between API and excipients. To overcome these limitations, the crosspolarization inversion recovery method was successfully used. The differences in the spin-lattice relaxation time constants for hydrogen atoms T1(H) between API and excipients were employed in order to separate and discriminate their peaks in ssNMR spectra as well as to increase the intensity of API signals in low-dose formulations. The versatility of this method was demonstrated by different examples, including the excipients mixture and commercial solid dosage forms (e.g. granules and tablets). Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering.

    PubMed

    Hong, Kuk-Ki; Nielsen, Jens

    2012-11-01

    In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the mutations RAS2(Lys77), RAS2(Tyr112), and ERG5(Pro370) were constructed and evaluated. The mutants were also combined with overexpression of PGM2, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites, and the results were compared to those obtained from reference strains and the evolved strains. The RAS2(Lys77) mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The RAS2(Tyr112) mutation also improved the specific galactose uptake rate and also resulted in many transcriptional changes, including ergosterol metabolism. The ERG5(Pro370) mutation only showed a small improvement, but when it was combined with PGM2 overexpression, the phenotype was almost the same as that of the evolved mutants. Combination of the RAS2 mutations with PGM2 overexpression also led to a complete recovery of the adaptive phenotype in galactose utilization. Recovery of the gross phenotype by the reconstructed mutants was achieved with much fewer changes in the genome and transcriptome than for the evolved mutants. Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast.

  2. [Introns 1 and 22 inversions and F8 gene sequencing for molecular diagnosis of hemophilia A in Chile].

    PubMed

    Poggi, Helena; Honorato, Josefina; Romeo, Eliana; Zúñiga, Pamela; Quiroga, Teresa; Lagos, Marcela

    2011-02-01

    Hemophilia A is an inherited disorder caused by alterations in factor VIII gene (F8) located on the X-chromosome, the intron 22 inversion being the most common mutation. The rest are predominantly point mutations distributed along this large gene of 26 exons. To implement a molecular diagnostic test to detect mutations in the F8 gene in Chilean patients with Hemophilia A. To validate the testing methods, we analyzed samples with intron 22 and intron 1 inversion, and with point mutations previously studied, as well as one subject without Hemophilia. We also studied unrelated Chilean patients with Hemophilia A and their female relatives for carrier testing. Intron 22 and intron 1 inversions were studied by long distance polymerase chain reaction (PCR) and point mutations by sequencing the coding and promoter regions of the F8 gene. The results obtained in all samples used for validation were concordant with those obtained previously. In the Chilean patients, the intron 22 inversion and point mutations previously described were observed. In 6 out of 9 patients with mild Hemophilia A we found the same mutation (Arg2159Cys) in exon 23, which has been described as prevalent in mild Hemophilia A. The analysis of intron 22 and intron 1 inversions, as well as of point mutations in the F8 gene will help us to confirm the diagnosis in patients with severe, moderate and mild Hemophilia A, and also it will allow us to perform carrier testing and to provide better genetic counseling.

  3. Usefulness of three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging to detect inner-ear abnormalities in patients with sudden sensorineural hearing loss.

    PubMed

    Tanigawa, T; Shibata, R; Tanaka, H; Gosho, M; Katahira, N; Horibe, Y; Nakao, Y; Ueda, H

    2015-01-01

    Three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging has been used to detect alterations in the composition of inner-ear fluid. This study investigated the association between hearing level and the signal intensity of pre- and post-contrast three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging in patients with sudden-onset sensorineural hearing loss. Three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging was performed in 18 patients with sudden-onset sensorineural hearing loss: 12 patients with mild-to-moderate sensorineural hearing loss (baseline hearing levels of 60 dB or less) and 6 patients with severe-to-profound sensorineural hearing loss (baseline hearing levels of more than 60 dB). High-intensity signals in the inner ear were observed in two of the six patients (33 per cent) with severe-to-profound sensorineural hearing loss, but not in those with mild-to-moderate sensorineural hearing loss (mid-p test, p = 0.049). These signals were observed on magnetic resonance imaging scans 6 or 18 days after sensorineural hearing loss onset. The results indicate that three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging is not a useful tool for detecting inner-ear abnormalities in patients with mild sensorineural hearing loss.

  4. Fast perfusion measurements in rat skeletal muscle at rest and during exercise with single-voxel FAIR (flow-sensitive alternating inversion recovery).

    PubMed

    Pohmann, Rolf; Künnecke, Basil; Fingerle, Jürgen; von Kienlin, Markus

    2006-01-01

    Non-invasive measurement of perfusion in skeletal muscle by in vivo magnetic resonance remains a challenge due to its low level and the correspondingly low signal-to-noise ratio. To enable accurate, quantitative, and time-resolved perfusion measurements in the leg muscle, a technique with a high sensitivity is required. By combining a flow-sensitive alternating inversion recovery (FAIR)-sequence with a single-voxel readout, we have developed a new technique to measure the perfusion in the rat gastrocnemius muscle at rest, yielding an average value of 19.4 +/- 4.8 mL/100 g/min (n = 22). In additional experiments, perfusion changes were elicited by acute ischemia and reperfusion or by exercise induced by electrical, noninvasive muscle stimulation with varying duration and intensity. The perfusion time courses during these manipulations were measured with a temporal resolution of 2.2 min, showing increases in perfusion of a factor of up to 2.5. In a direct comparison, the results agreed closely with values found with microsphere measurements in the same animals. The quantitative and noninvasive method can significantly facilitate the investigation of atherosclerotic diseases and the examination of drug efficacy.

  5. Masking of earthquake triggering behavior by a high background rate and implications for epidemic-type aftershock sequence inversions

    NASA Astrophysics Data System (ADS)

    Touati, S.; Naylor, M.; Main, I. G.; Christie, M.

    2011-03-01

    We examine the effects of the spontaneous background event rate and aftershock triggering characteristics on the temporal statistics of seismicity in the epidemic-type aftershock sequence model. Recent work has shown that the earthquake interevent time distribution is generally bimodal: a superposition of a gamma component from triggered aftershocks at short time intervals and an exponential component at longer intervals from spontaneous events and the overlapping of independent aftershock sequences. The relative size of these two components varies between catalogs, so there is no simple, universal scaling; at the extreme of high spontaneous rate, e.g., in large regions, the high probability of temporally overlapping aftershock sequences causes the exponential component to dominate. Here we further explore the effects of both the spontaneous rate and the aftershock triggering parameters. We show that the analytical theory of Saichev and Sornette (2007), although valid under their assumptions, gives the impression of a more "universal" behavior if used outside its stated range of applicability. We also show that within the high-overlap (high-spontaneous rate) regime, a maximum likelihood inversion of the model's temporal parameters is both less accurate and biased; specifically, the background rate is systematically overestimated. This has implications on the suitable range of region sizes for which parameter inversion may be reliable and must therefore be taken into account in any inversion for temporal variations in background rate in time-dependent hazard calculation.

  6. Fluid-Attenuated Inversion Recovery Vascular Hyperintensity Topography, Novel Imaging Marker for Revascularization in Middle Cerebral Artery Occlusion.

    PubMed

    Liu, Dezhi; Scalzo, Fabien; Rao, Neal M; Hinman, Jason D; Kim, Doojin; Ali, Latisha K; Saver, Jeffrey L; Sun, Wen; Dai, Qiliang; Liu, Xinfeng; Liebeskind, David S

    2016-11-01

    In acute arterial occlusion, fluid-attenuated inversion recovery vascular hyperintensity (FVH) has been linked to slow flow in leptomeningeal collaterals and cerebral hypoperfusion, but the impact on clinical outcome is still controversial. In this study, we aimed to investigate the association between FVH topography or FVH-Alberta Stroke Program Early CT Score (ASPECTS) pattern and outcome in acute M1-middle cerebral artery occlusion patients with endovascular treatment. We included acute M1-middle cerebral artery occlusion patients treated with endovascular therapy (ET). All patients had diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery before ET. Distal FVH-ASPECTS was evaluated according to distal middle cerebral artery-ASPECT area (M1-M6) and acute DWI lesion was also reviewed. The presence of FVH inside and outside DWI-positive lesions was separately analyzed. Clinical outcome after ET was analyzed with respect to different distal FVH-ASPECTS topography. Among 101 patients who met inclusion criteria for the study, mean age was 66.2±17.8 years and median National Institutes of Health Stroke Scale was 17.0 (interquartile range, 12.0-21.0). FVH-ASPECTS measured outside of the DWI lesion was significantly higher in patients with good outcome (modified Rankin Scale [mRS] score of 0-2; 8.0 versus 4.0, P<0.001). Logistic regression demonstrated that FVH-ASPECTS outside of the DWI lesion was independently associated with clinical outcome of these patients (odds ratio, 1.3; 95% confidence interval, 1.06-1.68; P=0.013). FVH-ASPECTS inside the DWI lesion was associated with hemorrhagic transformation (odds ratio, 1.3; 95% confidence interval, 1.04-1.51; P=0.019). Higher FVH-ASPECTS measured outside the DWI lesion is associated with good clinical outcomes in patients undergoing ET. FVH-ASPECTS measured inside the DWI lesion was predictive of hemorrhagic transformation. The FVH pattern, not number, can serve as an imaging selection marker for ET in

  7. Characteristic MRI findings in hyperglycaemia-induced seizures: diagnostic value of contrast-enhanced fluid-attenuated inversion recovery imaging.

    PubMed

    Lee, E J; Kim, K K; Lee, E K; Lee, J E

    2016-12-01

    To describe characteristic magnetic resonance imaging (MRI) abnormalities in hyperglycaemia-induced seizures, and evaluate the diagnostic value of contrast-enhanced fluid-attenuated inversion recovery (FLAIR) imaging. Possible underlying mechanisms of this condition are also discussed. Eleven patients with hyperglycaemia-induced seizures and MRI abnormalities were retrospectively studied. Clinical manifestations, laboratory findings, MRI findings, and clinical outcomes were analysed. All patients, except one, presented with focal seizures, simple or complex partial seizures, or negative motor seizures. All patients had long-standing uncontrolled diabetes mellitus. The MRI abnormalities observed acutely were focal subcortical hypointensities on T2-weighted imaging and FLAIR imaging in all patients with overlying cortical gyral T2 hyperintensities in five. Focal overlying cortical or leptomeningeal enhancement on contrast-enhanced T1-weighted imaging or contrast-enhanced FLAIR imaging was observed in all patients. Contrast-enhanced FLAIR imaging was superior to contrast-enhanced T1-weighted imaging for detecting characteristic cortical or leptomeningeal enhancement. Diffusion-weighted imaging showed mildly restricted diffusion in four of five patients with cortical gyral T2 hyperintensity. In nine patients, the lesions were localised in the parietal or parieto-occipital lobes. The other two patients showed localised precentral gyral lesions. After treatment, the neurological symptoms, including the seizures, improved in all patients. On clinical recovery, the subcortical T2 hypointensity, gyral or leptomeningeal enhancement, and overlying cortical T2 hyperintensities resolved. Recognition of these radiological abnormalities in patients with hyperglycaemia-induced seizures is important in restricting unwarranted investigations and initiating early therapy. These patients generally have a good prognosis. Copyright © 2016 The Royal College of Radiologists. Published by

  8. Assessment of left ventricular myocardial scar in infiltrative and non-ischemic cardiac diseases by free breathing three dimensional phase sensitive inversion recovery (PSIR) TurboFLASH.

    PubMed

    Kino, Aya; Keeling, Aoife N; Farrelly, Cormac T; Sheehan, John J; Davarpanah, Amir H; Weele, Peter J; Zuehldorff, Sven; Carr, James C

    2011-04-01

    The purpose of this study was to compare a navigator gated free breathing 3D Phase Sensitive Inversion Recovery (PSIR) TurboFLASH to an established 2D PSIR TurboFLASH method for detecting myocardial late gadolinium hyperenhanced lesions caused by infiltrative and non-ischemic cardiomyopathy. Under an IRB approved protocol; patients with suspected non-ischemic infiltrative myocardial heart disease were examined on a 1.5T MR scanner for late enhancement after the administration of gadolinium using a segmented 2D PSIR TurboFLASH sequence followed by a navigator-gated 3D PSIR TurboFLASH sequence. Two independent readers analyzed image quality using a four point Likert scale for qualitative analysis (0 = poor, non diagnostic; 1 = fair, diagnostic may be impaired; 2 = good, some artifacts but not interfering in diagnostics, 3 = excellent, no artifacts) and also reported presence or absence of scar. Detected scars were classified based on area and location and also compared quantitatively in volume. Twenty-seven patients were scanned using both protocols. Image quality score did not differ significantly (p = 0.358, Wilcoxon signed rank test) for both technique. Scars were detected in 24 patients. Larger numbers of hyperenhanced scars were detected with 3D PSIR (200) compared to 2D PSIR (167) and scar volume were significant larger in 3D PSIR (p = 0.004). The mean scar volume over all cases was 49.95 cm(3) for 2D PSIR and 70.02 cm(3) for 3D PSIR. The navigator gated free breathing 3D PSIR approach is a suitable method for detecting myocardial late gadolinium hyperenhanced lesions caused by non-ischemic cardiomyopathy due to its complete isotropic coverage of the left ventricle, improving detection of scar lesions compared to 2D PSIR imaging.

  9. Simultaneous acquisition of high-contrast and quantitative liver T1 images using 3D phase-sensitive inversion recovery: a feasibility study.

    PubMed

    Fujiwara, Yasuhiro; Maruyama, Hirotoshi; Kosaka, Nobuyuki; Ishimori, Yoshiyuki

    2017-08-01

    Background Tumor-to-liver contrast is low in images of chronically diseased livers because gadolinium-based hepatocyte-specific contrast agents (Gd-EOB-DTPA) accumulate less to hepatocytes. Purpose To determine whether phase-sensitive inversion recovery (PSIR) could improve the T1 contrasts of Gd-based contrast agents and liver parenchyma and simultaneously provide accurate T1 values for abdominal organs. Material and Methods The image contrasts of phantoms with different Gd concentrations that were obtained using PSIR were compared to conventional turbo field echo (TFE) results. T1 value was estimated using PSIR by performing iterations to investigate the two IR magnetization evolutions. The estimated T1 values were validated using IR-spin echo (IR-SE) and Look-Locker (L-L) sequences. In an in vivo study, the liver-to-spleen and liver-to-muscle contrasts of the PSIR and TFE images of seven volunteers were compared, as were the T1 values of liver parenchyma, spleen, and muscle obtained using PSIR and L-L sequences. Results The PSIR images showed T1 contrasts higher than those in the TFE results. The PSIR and IR-SE T1 values were linearly correlated. Additionally, the R1 estimated using PSIR were correlated with those measured using IR-SE and L-L. In the in vivo study, the liver-to-spleen and liver-to-muscle contrasts of PSIR were significantly higher than those obtained using TFE. T1 values of abdominal organs obtained using PSIR and L-L were clearly correlated. Conclusion PSIR may be capable of improving liver image T1 contrasts when Gd-based contrast agents are employed and simultaneously yielding accurate T1 values of abdominal organs.

  10. Regional Fluid-Attenuated Inversion Recovery (FLAIR) at 7 Tesla correlates with amyloid beta in hippocampus and brainstem of cognitively normal elderly subjects

    PubMed Central

    Schreiner, Simon J.; Liu, Xinyang; Gietl, Anton F.; Wyss, Michael; Steininger, Stefanie C.; Gruber, Esmeralda; Treyer, Valerie; Meier, Irene B.; Kälin, Andrea M.; Leh, Sandra E.; Buck, Alfred; Nitsch, Roger M.; Pruessmann, Klaas P.; Hock, Christoph; Unschuld, Paul G.

    2014-01-01

    Background: Accumulation of amyloid beta (Aβ) may occur during healthy aging and is a risk factor for Alzheimer Disease (AD). While individual Aβ-accumulation can be measured non-invasively using Pittsburgh Compund-B positron emission tomography (PiB-PET), Fluid-attenuated inversion recovery (FLAIR) is a Magnetic Resonance Imaging (MRI) sequence, capable of indicating heterogeneous age-related brain pathologies associated with tissue-edema. In the current study cognitively normal elderly subjects were investigated for regional correlation of PiB- and FLAIR intensity. Methods: Fourteen healthy elderly subjects without known history of cognitive impairment received 11C-PiB-PET for estimation of regional Aβ-load. In addition, whole brain T1-MPRAGE and FLAIR-MRI sequences were acquired at high field strength of 7 Tesla (7T). Volume-normalized intensities of brain regions were assessed by applying an automated subcortical segmentation algorithm for spatial definition of brain structures. Statistical dependence between FLAIR- and PiB-PET intensities was tested using Spearman's rank correlation coefficient (rho), followed by Holm–Bonferroni correction for multiple testing. Results: Neuropsychological testing revealed normal cognitive performance levels in all participants. Mean regional PiB-PET and FLAIR intensities were normally distributed and independent. Significant correlation between volume-normalized PiB-PET signals and FLAIR intensities resulted for Hippocampus (right: rho = 0.86; left: rho = 0.84), Brainstem (rho = 0.85) and left Basal Ganglia vessel region (rho = 0.82). Conclusions: Our finding of a significant relationship between PiB- and FLAIR intensity mainly observable in the Hippocampus and Brainstem, indicates regional Aβ associated tissue-edema in cognitively normal elderly subjects. Further studies including clinical populations are necessary to clarify the relevance of our findings for estimating individual risk for age-related neurodegenerative

  11. Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

    PubMed

    Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

    2015-01-01

    In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles

  12. Application of variable threshold intensity to segmentation for white matter hyperintensities in fluid attenuated inversion recovery magnetic resonance images.

    PubMed

    Yoo, Byung Il; Lee, Jung Jae; Han, Ji Won; Oh, San Yeo Wool; Lee, Eun Young; MacFall, James R; Payne, Martha E; Kim, Tae Hui; Kim, Jae Hyoung; Kim, Ki Woong

    2014-04-01

    White matter hyperintensities (WMHs) are regions of abnormally high intensity on T2-weighted or fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI). Accurate and reproducible automatic segmentation of WMHs is important since WMHs are often seen in the elderly and are associated with various geriatric and psychiatric disorders. We developed a fully automated monospectral segmentation method for WMHs using FLAIR MRIs. Through this method, we introduce an optimal threshold intensity (I O ) for segmenting WMHs, which varies with WMHs volume (V WMH), and we establish the I O -V WMH relationship. Our method showed accurate validations in volumetric and spatial agreements of automatically segmented WMHs compared with manually segmented WMHs for 32 confirmatory images. Bland-Altman values of volumetric agreement were 0.96 ± 8.311 ml (bias and 95 % confidence interval), and the similarity index of spatial agreement was 0.762 ± 0.127 (mean ± standard deviation). Furthermore, similar validation accuracies were obtained in the images acquired from different scanners. The proposed segmentation method uses only FLAIR MRIs, has the potential to be accurate with images obtained from different scanners, and can be implemented with a fully automated procedure. In our study, validation results were obtained with FLAIR MRIs from only two scanner types. The design of the method may allow its use in large multicenter studies with correct efficiency.

  13. Problems with diagnosis by fluid-attenuated inversion recovery magnetic resonance imaging in patients with acute aneurysmal subarachnoid hemorrhage.

    PubMed

    Shimoda, Masami; Hoshikawa, Kaori; Shiramizu, Hideki; Oda, Shinri; Matsumae, Mitsunori

    2010-01-01

    The diagnostic efficacy of fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging and computed tomography (CT) for acute subarachnoid hemorrhage (SAH) were compared and the problems with diagnosis were investigated in 81 patients with aneurysmal SAH within 24 hours after onset who underwent FLAIR imaging and CT on admission. The number of hematomas in the cisterns and ventricles were evaluated by clot scores. In addition, the frequency of undetected hematomas was calculated for the cisterns and ventricles. Clot scores were significantly higher for FLAIR imaging than for CT in the lateral sylvian, quadrigeminal, and convexity cisterns. On the other hand, clot scores were significantly higher for CT than for FLAIR imaging in the interhemispheric and medial sylvian cisterns. The overall frequency of undetected SAH was 2% for FLAIR imaging and 14% for CT. With the exception of the interhemispheric and medial sylvian cisterns, the frequency of undetected SAH was higher for CT than for FLAIR imaging. In this study, FLAIR imaging was more sensitive than CT for the detection of acute SAH within 24 hours after onset. However, the diagnostic efficacy of FLAIR imaging was reduced in comparatively tight cisterns.

  14. Partitioning of main and side-chain units between different phases: a solid-state 13C NMR inversion-recovery cross-polarization study on a homogeneous, metallocene-based, ethylene-1-octene copolymer.

    PubMed

    Litvinov, Victor M; Mathot, Vincent B F

    2002-01-01

    13C NMR inversion-recovery cross-polarization experiments are used to study the phase structure and partitioning of main and side-chain groups in a homogeneous, metallocene-based, ethylene-1-octene copolymer. The results provide strong evidence for a three-phase model, i.e. a rigid, (imperfect) crystalline phase, which is mainly composed of long sequences of methylene carbon atoms of the main chain, a semi-rigid, amorphous interphase (also denoted as 'rigid amorphous'), which is enriched by chain segments bearing methylene and methine carbon atoms of the main chain, and a soft fraction of the amorphous phase (also denoted as 'mobile amorphous'), which is largely composed of side chains and short methylene sequences of the main chain.

  15. Prediction of Stroke Onset Is Improved by Relative Fluid-Attenuated Inversion Recovery and Perfusion Imaging Compared to the Visual Diffusion-Weighted Imaging/Fluid-Attenuated Inversion Recovery Mismatch.

    PubMed

    Wouters, Anke; Dupont, Patrick; Norrving, Bo; Laage, Rico; Thomalla, Götz; Albers, Gregory W; Thijs, Vincent; Lemmens, Robin

    2016-10-01

    Acute stroke patients with unknown time of symptom onset are ineligible for thrombolysis. The diffusion-weighted imaging and fluid-attenuated inversion recovery (FLAIR) mismatch is a reasonable predictor of stroke within 4.5 hours of symptom onset, and its clinical usefulness in selecting patients for thrombolysis is currently being investigated. The accuracy of the visual mismatch rating is moderate, and we hypothesized that the predictive value of stroke onset within 4.5 hours could be improved by including various clinical and imaging parameters. In this study, 141 patients in whom magnetic resonance imaging was obtained within 9 hours after symptom onset were included. Relative FLAIR signal intensity was calculated in the region of nonreperfused core. Mean Tmax was calculated in the total region with Tmax >6 s. Mean relative FLAIR, mean Tmax, lesion volume with Tmax >6 s, age, site of arterial stenosis, core volume, and location of infarct were analyzed by logistic regression to predict stroke onset time before or after 4.5 hours. Receiver-operating characteristic curve analysis revealed an area under the curve of 0.68 (95% confidence interval 0.59-0.78) for the visual diffusion-weighted imaging/FLAIR mismatch, thereby correctly classifying 69% of patients with an onset time before or after 4.5 hours. Age, relative FLAIR, and Tmax increased the accuracy significantly (P<0.01) to an area under the curve of 0.82 (95% confidence interval 0.74-0.89). This new predictive model correctly categorized 77% of patients according to stroke onset before versus after 4.5 hours. In patients with unknown stroke onset, the accuracy of predicting time from symptom onset within 4.5 hours is improved by obtaining relative FLAIR and perfusion imaging. © 2016 American Heart Association, Inc.

  16. Hyperintense vessels on acute stroke Fluid-attenuated Inversion Recovery imaging: Associations with clinical and other MRI findings

    PubMed Central

    Cheng, Bastian; Ebinger, Martin; Kufner, Anna; Köhrmann, Martin; Wu, Ona; Kang, Dong-Wha; Liebeskind, David; Tourdias, Thomas; Singer, Oliver C.; Christensen, Soren; Warach, Steve; Luby, Marie; Fiebach, Jochen B.; Fiehler, Jens; Gerloff, Christian; Thomalla, Götz

    2012-01-01

    Background and Purpose Hyperintense vessels (HV) have been observed in Fluid-Attenuated Inversion Recovery (FLAIR) imaging of patients with acute ischemic stroke and been linked to slow flow in collateral arterial circulation. Given the potential importance of HV, we used a large, multicentre dataset of stroke patients to clarify which clinical and imaging factors play a role in HV. Methods We analyzed data of 516 patients from the previously published PRE-FLAIR study. Patients were studied by MRI within 12 hours of symptom onset. HV were defined as hyperintensities in FLAIR corresponding to the typical course of a blood vessel that was not considered the proximal, occluded main artery ipsilateral to the diffusion restriction. Presence of HV was rated by two observers and related to clinical and imaging findings. Results Presence of HV was identified in 240 of all 516 patients (47%). Patients with HV showed larger initial ischemic lesion volumes (median 12.3 vs. 4.9 ml; p<0.001) and a more severe clinical impairment (median NIHSS 10.5 vs. 6; p<0.001). In 198 patients with MR-angiography, HV were found in 80% of patients with vessel occlusion and in 17% without vessel occlusion. In a multivariable logistic regression model, vessel occlusion was associated with HV (OR 21.7%; 95% CI 9.6–49.9, p < 0.001). HV detected vessel occlusion with a specificity of 0.86 (95% CI 0.80–0.90) and sensitivity of 0.76 (95% CI 0.69–0.83). Conclusions HV are a common finding associated with proximal arterial occlusions and more severe strokes. HV predict arterial occlusion with high diagnostic accuracy. PMID:22933582

  17. Fluid-attenuated inversion recovery hyperintensity correlates with matrix metalloproteinase-9 level and hemorrhagic transformation in acute ischemic stroke.

    PubMed

    Jha, Ruchira; Battey, Thomas W K; Pham, Ly; Lorenzano, Svetlana; Furie, Karen L; Sheth, Kevin N; Kimberly, W Taylor

    2014-04-01

    Matrix metalloproteinase-9 (MMP-9) is elevated in patients with acute stroke who later develop hemorrhagic transformation (HT). It is controversial whether early fluid-attenuated inversion recovery (FLAIR) hyperintensity on brain MRI predicts hemorrhagic transformation (HT). We assessed whether FLAIR hyperintensity was associated with MMP-9 and HT. We analyzed a prospectively collected cohort of acute stroke subjects with acute brain MRI images and MMP-9 values within the first 12 hours after stroke onset. FLAIR hyperintensity was measured using a signal intensity ratio between the stroke lesion and corresponding normal contralateral hemisphere. MMP-9 was measured using enzyme-linked immunosorbent assay. The relationships between FLAIR ratio (FR), MMP-9, and HT were evaluated. A total of 180 subjects were available for analysis. Patients were imaged with brain MRI at 5.6±4.3 hours from last seen well time. MMP-9 blood samples were drawn within 7.7±4.0 hours from last seen well time. The time to MRI (r=0.17, P=0.027) and MMP-9 level (r=0.29, P<0.001) were each associated with FR. The association between MMP-9 and FR remained significant after multivariable adjustment (P<0.001). FR was also associated with HT and symptomatic hemorrhage (P=0.012). FR correlates with both MMP-9 level and risk of hemorrhage. FLAIR changes in the acute phase of stroke may predict hemorrhagic transformation, possibly as a reflection of altered blood-brain barrier integrity.

  18. Ivy Sign on Fluid-Attenuated Inversion Recovery Images in Moyamoya Disease: Correlation with Clinical Severity and Old Brain Lesions

    PubMed Central

    Seo, Kwon-Duk; Suh, Sang Hyun; Kim, Yong Bae; Kim, Ji Hwa; Ahn, Sung Jun; Kim, Dong-Seok

    2015-01-01

    Purpose Leptomeningeal collateral, in moyamoya disease (MMD), appears as an ivy sign on fluid-attenuated inversion-recovery (FLAIR) images. There has been little investigation into the relationship between presentation of ivy signs and old brain lesions. We aimed to evaluate clinical significance of ivy signs and whether they correlate with old brain lesions and the severity of clinical symptoms in patients with MMD. Materials and Methods FLAIR images of 83 patients were reviewed. Each cerebral hemisphere was divided into 4 regions and each region was scored based on the prominence of the ivy sign. Total ivy score (TIS) was defined as the sum of the scores from the eight regions and dominant hemispheric ivy sign (DHI) was determined by comparing the ivy scores from each hemisphere. According to the degree of ischemic symptoms, patients were classified into four subgroups: 1) nonspecific symptoms without motor weakness, 2) single transient ischemic attack (TIA), 3) recurrent TIA, or 4) complete stroke. Results TIS was significantly different as follows: 4.86±2.55 in patients with nonspecific symptoms, 5.89±3.10 in patients with single TIA, 9.60±3.98 in patients with recurrent TIA and 8.37±3.39 in patients with complete stroke (p=0.003). TIS associated with old lesions was significantly higher than those not associated with old lesions (9.35±4.22 vs. 7.49±3.37, p=0.032). We found a significant correlation between DHI and motor symptoms (p=0.001). Conclusion Because TIS has a strong tendency with severity of ischemic motor symptom and the presence of old lesions, the ivy sign may be useful in predicting severity of disease progression. PMID:26256975

  19. Ivy Sign on Fluid-Attenuated Inversion Recovery Images in Moyamoya Disease: Correlation with Clinical Severity and Old Brain Lesions.

    PubMed

    Seo, Kwon-Duk; Suh, Sang Hyun; Kim, Yong Bae; Kim, Ji Hwa; Ahn, Sung Jun; Kim, Dong-Seok; Lee, Kyung-Yul

    2015-09-01

    Leptomeningeal collateral, in moyamoya disease (MMD), appears as an ivy sign on fluid-attenuated inversion-recovery (FLAIR) images. There has been little investigation into the relationship between presentation of ivy signs and old brain lesions. We aimed to evaluate clinical significance of ivy signs and whether they correlate with old brain lesions and the severity of clinical symptoms in patients with MMD. FLAIR images of 83 patients were reviewed. Each cerebral hemisphere was divided into 4 regions and each region was scored based on the prominence of the ivy sign. Total ivy score (TIS) was defined as the sum of the scores from the eight regions and dominant hemispheric ivy sign (DHI) was determined by comparing the ivy scores from each hemisphere. According to the degree of ischemic symptoms, patients were classified into four subgroups: 1) nonspecific symptoms without motor weakness, 2) single transient ischemic attack (TIA), 3) recurrent TIA, or 4) complete stroke. TIS was significantly different as follows: 4.86±2.55 in patients with nonspecific symptoms, 5.89±3.10 in patients with single TIA, 9.60±3.98 in patients with recurrent TIA and 8.37±3.39 in patients with complete stroke (p=0.003). TIS associated with old lesions was significantly higher than those not associated with old lesions (9.35±4.22 vs. 7.49±3.37, p=0.032). We found a significant correlation between DHI and motor symptoms (p=0.001). Because TIS has a strong tendency with severity of ischemic motor symptom and the presence of old lesions, the ivy sign may be useful in predicting severity of disease progression.

  20. Noninvasive investigation of exocrine pancreatic function: Feasibility of cine dynamic MRCP with a spatially selective inversion-recovery pulse.

    PubMed

    Yasokawa, Kazuya; Ito, Katsuyoshi; Tamada, Tsutomu; Yamamoto, Akira; Hayashida, Minoru; Tanimoto, Daigo; Higaki, Atsushi; Noda, Yasufumi; Kido, Ayumu

    2015-11-01

    To investigate the feasibility of noncontrast-enhanced cine dynamic magnetic resonance cholangiopancreatography (MRCP) with a spatially selective inversion-recovery (IR) pulse for evaluating exocrine pancreatic function in comparison with the N-benzoyl-L-tyrosyl-p-aminobenzoic acid (BT-PABA) test as a pancreatic exocrine function test. Twenty subjects with or without chronic pancreatitis were included. MRCP with a spatially selective IR pulse was repeated every 15 seconds for 5 minutes to acquire a total of 20 images (cine-dynamic MRCP). The median and mean frequency of the observation (the number of times) and the moving distance (mean secretion grading scores) of pancreatic juice inflow on cine-dynamic MRCP were compared with a BT-PABA test. The urinary PABA excretion rate (%) had significant positive correlations with both the mean secretion grade (r = 0.66, P = 0.002) and frequency of secretory inflow (r = 0.62, P = 0.004) in cine dynamic MRCP. Both the mean frequency of observations of pancreatic secretory inflow (1.4 ± 1.6 times vs. 14.3 ± 4.2 times, P < 0.001) and the mean secretion grade (grade = 0.16 ± 0.24 vs. grade = 1.81 ± 0.81, P < 0.001) was significantly lower in the chronic pancreatitis group than in the normal subject group. Cine dynamic MRCP with a spatially selective IR pulse may have potential for estimating the pancreatic exocrine function noninvasively as a substitute for the BT-PABA test. © 2015 Wiley Periodicals, Inc.

  1. Identifying odd/even-order binary kernel slices for a nonlinear system using inverse repeat m-sequences.

    PubMed

    Hu, Jin-Yan; Yan, Gang; Wang, Tao

    2015-01-01

    The study of various living complex systems by system identification method is important, and the identification of the problem is even more challenging when dealing with a dynamic nonlinear system of discrete time. A well-established model based on kernel functions for input of the maximum length sequence (m-sequence) can be used to estimate nonlinear binary kernel slices using cross-correlation method. In this study, we examine the relevant mathematical properties of kernel slices, particularly their shift-and-product property and overlap distortion problem caused by the irregular shifting of the estimated kernel slices in the cross-correlation function between the input m-sequence and the system output. We then derive the properties of the inverse repeat (IR) m-sequence and propose a method of using IR m-sequence as an input to separately estimate odd- and even-order kernel slices to reduce the chance of kernel-slice overlapping. An instance of third-order Wiener nonlinear model is simulated to justify the proposed method.

  2. Identifying Odd/Even-Order Binary Kernel Slices for a Nonlinear System Using Inverse Repeat m-Sequences

    PubMed Central

    Hu, Jin-yan; Yan, Gang

    2015-01-01

    The study of various living complex systems by system identification method is important, and the identification of the problem is even more challenging when dealing with a dynamic nonlinear system of discrete time. A well-established model based on kernel functions for input of the maximum length sequence (m-sequence) can be used to estimate nonlinear binary kernel slices using cross-correlation method. In this study, we examine the relevant mathematical properties of kernel slices, particularly their shift-and-product property and overlap distortion problem caused by the irregular shifting of the estimated kernel slices in the cross-correlation function between the input m-sequence and the system output. We then derive the properties of the inverse repeat (IR) m-sequence and propose a method of using IR m-sequence as an input to separately estimate odd- and even-order kernel slices to reduce the chance of kernel-slice overlapping. An instance of third-order Wiener nonlinear model is simulated to justify the proposed method. PMID:25873988

  3. 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).

    PubMed

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

    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.

  4. Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

    PubMed Central

    Dasenko, Mark A.

    2015-01-01

    In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles

  5. Myocardial T1 Mapping at 3.0T Using an Inversion Recovery Spoiled Gradient Echo Readout and Bloch Equation Simulation with Slice Profile Correction (BLESSPC) T1 Estimation Algorithm

    PubMed Central

    Shao, Jiaxin; Rapacchi, Stanislas; Nguyen, Kim-Lien; Hu, Peng

    2015-01-01

    Purpose To develop an accurate and precise myocardial T1 mapping technique using an inversion recovery spoiled gradient echo readout at 3.0T. Materials and Methods The modified Look-Locker inversion-recovery (MOLLI) sequence was modified to use fast low angle shot (FLASH) readout, incorporating a BLESSPC (Bloch Equation Simulation with Slice Profile Correction) T1 estimation algorithm, for accurate myocardial T1 mapping. The FLASH-MOLLI with BLESSPC fitting was compared to different approaches and sequences with regards to T1 estimation accuracy, precision and image artifact based on simulation, phantom studies, and in vivo studies of 10 healthy volunteers and 3 patients at 3.0T. Results The FLASH-MOLLI with BLESSPC fitting yields accurate T1 estimation (average error = −5.4±15.1 ms, percentage error = −0.5%±1.2%) for T1 from 236–1852 ms and heart rate from 40–100 bpm in phantom studies. The FLASH-MOLLI sequence prevented off-resonance artifacts in all 10 healthy volunteers at 3.0T. In vivo, there was no significant difference between FLASH-MOLLI-derived myocardial T1 values and “ShMOLLI+IE” derived values (1458.9±20.9 ms vs. 1464.1±6.8 ms, p=0.50); However, the average precision by FLASH-MOLLI was significantly better than that generated by “ShMOLLI+IE” (1.84±0.36% variance vs. 3.57±0.94%, p<0.001). Conclusion The FLASH-MOLLI with BLESSPC fitting yields accurate and precise T1 estimation, and eliminates banding artifacts associated with bSSFP at 3.0T. PMID:26214152

  6. Influence of the Amino-Acid Sequence on the Inverse Temperature Transition of Elastin-Like Polymers

    PubMed Central

    Ribeiro, Artur; Arias, F. Javier; Reguera, Javier; Alonso, Matilde; Rodríguez-Cabello, J. Carlos

    2009-01-01

    Abstract This work explores the dependence of the inverse temperature transition of elastin-like polymers (ELPs) on the amino-acid sequence, i.e., the amino-acid arrangement along the macromolecule and the resulting linear distribution of the physical properties (mainly polarity) derived from it. The hypothesis of this work is that, in addition to mean polarity and molecular mass, the given amino-acid sequence, or its equivalent—the way in which polarity is arranged along the molecule—is also relevant for determining the transition temperature and the latent heat of that transition. To test this hypothesis, a set of linear and di- and triblock ELP copolymers were designed and produced as recombinant proteins. The absolute sequence control provided by recombinant technologies allows the effect of the amino-acid arrangement to be isolated while keeping the molecular mass or mean polarity under strict control. The selected block copolymers were made of two different ELPs: one exhibiting temperature and pH responsiveness, and one exhibiting temperature responsiveness only. By changing the arrangement and length of the blocks while keeping other parameters, such as the molecular mass or mean polarity, constant, we were able to show that the sequence plays a key role in the smart behavior of ELPs. PMID:19580769

  7. The Effects of Concrete-Representational-Abstract Sequence of Instruction on Solving Equations Using Inverse Operations with High School Students with Mild Intellectual Disability

    ERIC Educational Resources Information Center

    Cease-Cook, Jennifer Jo

    2013-01-01

    This study used a multiple probe across participants design to examine the effects of concrete-representational-abstract sequence of instruction on solving equations using inverse operations with high school students with mild intellectual disability. Results demonstrated a functional relation between the Abstract sequence of instruction and…

  8. Evolution of Volume and Signal Intensity on Fluid-attenuated Inversion Recovery MR Images after Endovascular Stroke Therapy.

    PubMed

    Federau, Christian; Mlynash, Michael; Christensen, Soren; Zaharchuk, Greg; Cha, Brannon; Lansberg, Maarten G; Wintermark, Max; Albers, Gregory W

    2016-07-01

    Purpose To analyze both volume and signal evolution on magnetic resonance (MR) fluid-attenuated inversion recovery (FLAIR) images between the images after endovascular therapy and day 5 (which was the prespecified end point for infarct volume in the Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution [DEFUSE 2] trial) in a subset of patients enrolled in the DEFUSE 2 study. Materials and Methods This study was approved by the local ethics committee at all participating sites. Informed written consent was obtained from all patients. In this post hoc analysis of the DEFUSE 2 study, 35 patients with FLAIR images acquired both after endovascular therapy (median time after symptom onset, 12 hours) and at day 5 were identified. Patients were separated into two groups based on the degree of reperfusion achieved on time to maximum greater than 6-second perfusion imaging (≥90% vs <90%). After coregistration and signal normalization, lesion volumes and signal intensity were assessed by using FLAIR imaging for the initial lesion (ie, visible after endovascular therapy) and the recruited lesion (the additional lesion visible on day 5, but not visible after endovascular therapy). Statistical significance was assessed by using Wilcoxon signed-rank, Mann-Whitney U, and Fisher exact tests. Results All 35 patients had FLAIR lesion growth between the after-revascularization examination and day 5. Median lesion growth was significantly larger in patients with <90% reperfusion (27.85 mL) compared with ≥90% (8.12 mL; P = .003). In the initial lesion, normalized signal did not change between after endovascular therapy (median, 1.60) and day 5 (median, 1.58) in the ≥90% reperfusion group (P = .97), but increased in the <90% reperfusion group (from 1.60 to 1.73; P = .01). In the recruited lesion, median normalized signal increased significantly in both groups between after endovascular therapy and day 5 (after endovascular therapy, from 1.19 to 1.56, P

  9. Triple-layer appearance of Brodmann area 4 at thin-section double inversion-recovery MR imaging.

    PubMed

    Kim, Eung Yeop; Kim, Dong-Hyun; Chang, Jong-Hee; Yoo, Eunhye; Lee, Jae-Wook; Park, Hae-Jeong

    2009-02-01

    To investigate whether thin-section axial double inversion-recovery (DIR) brain magnetic resonance (MR) imaging at 3.0 T can help distinguish the primary motor cortex (PMC), or Brodmann area 4, from other selected cortical regions, including the primary sensory cortex (PSC), or Brodmann areas 1-3, on the basis of the presence of a "triple-layer" appearance. This prospective study was approved by the institutional review board; informed consent was obtained from patients. This study included 191 patients (94 female, age range, 5-80 years; 97 male, age range, 5-76 years) with normal findings at 3.0-T MR imaging. The presence or absence of a triple-layer appearance within selected cortical regions on DIR images was graded independently by two neuroradiologists as definitely present (grade 2), probably present (grade 1), or definitely absent (grade 0). Ten additional patients with tumors underwent DIR imaging and intraoperative cortical mapping for further validation of the PMC. A myelin-stained brain specimen image in a patient not imaged with DIR was correlated with a representative set of DIR images. A triple-layer appearance was found in the PMC bilaterally in 184 of 191 patients; grade 0 was assigned in only seven patients, who were all younger than 10 years. Grades were significantly lower in patients younger than 10 years than in others (P < .0001) but were not significantly different between older age groups (P > .0018). Interobserver agreement was excellent (weighted kappa = 0.843). The PMC determined on DIR images was confirmed with cortical mapping in all 10 patients with tumors. Triple-layer appearance was not present in the other cortical regions examined, including the PSC (P < .01). The triple-layer appearance on DIR images corresponded to the myelin band within the PMC present on the myelin-stained specimen image. A triple-layer appearance was found in the PMC at thin-section 3.0-T DIR imaging but not in other examined brain regions and therefore might

  10. Modified look-locker inversion recovery T1 mapping indices: assessment of accuracy and reproducibility between magnetic resonance scanners

    PubMed Central

    2013-01-01

    Background Cardiovascular magnetic resonance (CMR) T1 mapping indices, such as T1 time and partition coefficient (λ), have shown potential to assess diffuse myocardial fibrosis. The purpose of this study was to investigate how scanner and field strength variation affect the accuracy and precision/reproducibility of T1 mapping indices. Methods CMR studies were performed on two 1.5T and three 3T scanners. Eight phantoms were made to mimic the T1/T2 of pre- and post-contrast myocardium and blood at 1.5T and 3T. T1 mapping using MOLLI was performed with simulated heart rate of 40-100 bpm. Inversion recovery spin echo (IR-SE) was the reference standard for T1 determination. Accuracy was defined as the percent error between MOLLI and IR-SE, and scan/re-scan reproducibility was defined as the relative percent mean difference between repeat MOLLI scans. Partition coefficient was estimated by ΔR1myocardium phantom/ΔR1blood phantom. Generalized linear mixed model was used to compare the accuracy and precision/reproducibility of T1 and λ across field strength, scanners, and protocols. Results Field strength significantly affected MOLLI T1 accuracy (6.3% error for 1.5T vs. 10.8% error for 3T, p<0.001) but not λ accuracy (8.8% error for 1.5T vs. 8.0% error for 3T, p=0.11). Partition coefficients of MOLLI were not different between two 1.5T scanners (47.2% vs. 47.9%, p=0.13), and showed only slight variation across three 3T scanners (49.2% vs. 49.8% vs. 49.9%, p=0.016). Partition coefficient also had significantly lower percent error for precision (better scan/re-scan reproducibility) than measurement of individual T1 values (3.6% for λ vs. 4.3%-4.8% for T1 values, approximately, for pre/post blood and myocardium values). Conclusion Based on phantom studies, T1 errors using MOLLI ranged from 6-14% across various MR scanners while errors for partition coefficient were less (6-10%). Compared with absolute T1 times, partition coefficient showed less variability across

  11. The leptomeningeal ivy sign on fluid-attenuated inversion recovery images in moyamoya disease: positron emission tomography study.

    PubMed

    Kaku, Yasuyuki; Iihara, Koji; Nakajima, Norio; Kataoka, Hiroharu; Fukushima, Kazuhito; Iida, Hidehiro; Hashimoto, Nobuo

    2013-01-01

    The ivy sign is sometimes seen on fluid-attenuated inversion recovery (FLAIR) images in moyamoya disease (MMD). In recent studies using single-photon emission computed tomography, ivy sign proliferation correlated with decreases in cerebrovascular reserve. However, a decreased vascular reserve is not concrete. The purpose of this study was to evaluate the correlation between ivy sign proliferation and the findings of 15O gas positron emission tomography (PET). In 19 MMD patients (12 women, age 31-69 years) with ischemic symptoms, FLAIR magnetic resonance imaging and 15O gas PET were performed. We classified the middle cerebral artery (MCA) territory into 2 regions in each hemisphere, and the degree of the ivy sign (ivy sign score) in each region was classified into 3 grades (0-2), where grade 0 indicated an absence of the ivy sign, grade 1 indicated that the ivy sign was seen on less than half of the cortical surface in each region, and grade 2 indicated that the ivy sign was seen on more than half of the cortical surface. We examined the relationship among the ivy sign score, the severity of ischemic symptoms and PET parameters in 76 MCA regions of 19 patients. Ivy sign scores of the regions were 0 (n = 19), 1 (n = 40), and 2 (n = 17). Total ivy sign score of a hemisphere increased as clinical symptoms became more severe. Cerebral blood flow (CBF) values were lower, cerebral blood volume (CBV) values were higher, and CBF/CBV values were lower than those of controls as symptoms became severe (p < 0.05). CBF and CBF/CBV values decreased and CBV values increased as the ivy sign score increased, and were significantly higher and lower, respectively, than control values (p < 0.05). No significant differences in cerebral metabolic rate of oxygen and oxygen extraction fraction were found between the 3 ivy sign scores. A positive correlation was found between ivy sign score and increases in CBV (p < 0.01), and a more obvious negative correlation was found between ivy sign

  12. High-resolution myocardial T1 mapping using single-shot inversion recovery fast low-angle shot MRI with radial undersampling and iterative reconstruction

    PubMed Central

    Joseph, Arun A; Kalentev, Oleksandr; Merboldt, Klaus-Dietmar; Voit, Dirk; Roeloffs, Volkert B; van Zalk, Maaike; Frahm, Jens

    2016-01-01

    Objective: To develop a novel method for rapid myocardial T1 mapping at high spatial resolution. Methods: The proposed strategy represents a single-shot inversion recovery experiment triggered to early diastole during a brief breath-hold. The measurement combines an adiabatic inversion pulse with a real-time readout by highly undersampled radial FLASH, iterative image reconstruction and T1 fitting with automatic deletion of systolic frames. The method was implemented on a 3-T MRI system using a graphics processing unit-equipped bypass computer for online application. Validations employed a T1 reference phantom including analyses at simulated heart rates from 40 to 100 beats per minute. In vivo applications involved myocardial T1 mapping in short-axis views of healthy young volunteers. Results: At 1-mm in-plane resolution and 6-mm section thickness, the inversion recovery measurement could be shortened to 3 s without compromising T1 quantitation. Phantom studies demonstrated T1 accuracy and high precision for values ranging from 300 to 1500 ms and up to a heart rate of 100 beats per minute. Similar results were obtained in vivo yielding septal T1 values of 1246 ± 24 ms (base), 1256 ± 33 ms (mid-ventricular) and 1288 ± 30 ms (apex), respectively (mean ± standard deviation, n = 6). Conclusion: Diastolic myocardial T1 mapping with use of single-shot inversion recovery FLASH offers high spatial resolution, T1 accuracy and precision, and practical robustness and speed. Advances in knowledge: The proposed method will be beneficial for clinical applications relying on native and post-contrast T1 quantitation. PMID:27759423

  13. Recovery

    NASA Image and Video Library

    This video discusses the recovery events that occur in high-power rocketry and the various devices used in safely recovering the rocket. The video includes a discussion of black powder and ejection...

  14. An analytical model which determines the apparent T1 for Modified Look-Locker Inversion Recovery - Analysis of the longitudinal relaxation under the influence of discontinuous balanced (classical MOLLI) and spoiled gradient echo readouts.

    PubMed

    Kampf, Thomas; Reiter, Theresa; Bauer, Wolfgang Rudolf

    2017-08-09

    Quantitative nuclear magnetic resonance imaging (MRI) shifts more and more into the focus of clinical research. Especially determination of relaxation times without/and with contrast agents becomes the foundation of tissue characterization, e.g. in cardiac MRI for myocardial fibrosis. Techniques which assess longitudinal relaxation times rely on repetitive application of readout modules, which are interrupted by free relaxation periods, e.g. the Modified Look-Locker Inversion Recovery = MOLLI sequence. These discontinuous sequences reveal an apparent relaxation time, and, by techniques extrapolated from continuous readout sequences, a putative real T1 is determined. What is missing is a rigorous analysis of the dependence of the apparent relaxation time on its real partner, readout sequence parameters and biological parameters as heart rate. This is provided in this paper for the discontinuous balanced steady state free precession (bSSFP) and spoiled gradient echo readouts. It turns out that the apparent longitudinal relaxation rate is the time average of the relaxation rates during the readout module, and free relaxation period. Knowing the heart rate our results vice versa allow to determine the real T1 from its measured apparent partner. Copyright © 2017. Published by Elsevier GmbH.

  15. An inverse problem approach to recovery of in vivo nanoparticle concentrations from thermal image monitoring of MR-guided laser induced thermal therapy.

    PubMed

    Fuentes, D; Elliott, A; Weinberg, J S; Shetty, A; Hazle, J D; Stafford, R J

    2013-01-01

    Quantification of local variations in the optical properties of tumor tissue introduced by the presence of gold-silica nanoparticles (NP) presents significant opportunities in monitoring and control of NP-mediated laser induced thermal therapy (LITT) procedures. Finite element methods of inverse parameter recovery constrained by a Pennes bioheat transfer model were applied to estimate the optical parameters. Magnetic resonance temperature imaging (MRTI) acquired during a NP-mediated LITT of a canine transmissible venereal tumor in brain was used in the presented statistical inverse problem formulation. The maximum likelihood (ML) value of the optical parameters illustrated a marked change in the periphery of the tumor corresponding with the expected location of NP and area of selective heating observed on MRTI. Parameter recovery information became increasingly difficult to infer in distal regions of tissue where photon fluence had been significantly attenuated. Finite element temperature predictions using the ML parameter values obtained from the solution of the inverse problem are able to reproduce the NP selective heating within 5 °C of measured MRTI estimations along selected temperature profiles. Results indicate the ML solution found is able to sufficiently reproduce the selectivity of the NP mediated laser induced heating and therefore the ML solution is likely to return useful optical parameters within the region of significant laser fluence.

  16. Noninvasive reconstruction of three-dimensional ventricular activation sequence from the inverse solution of distributed equivalent current density.

    PubMed

    Liu, Zhongming; Liu, Chenguang; He, Bin

    2006-10-01

    We propose a new electrocardiographic (ECG) inverse approach for imaging the three-dimensional (3-D) ventricular activation sequence based on the modeling and estimation of the equivalent current density throughout the entire volume of the ventricular myocardium. The spatio-temporal coherence of the ventricular excitation process has been utilized to derive the activation time from the estimated time course of the equivalent current density. In the present study, we explored four different linear inverse algorithms (the minimum norm and weighted minimum norm estimates in combination with two regularization schemes: the instant-by-instant regularization and the isotropy method) to estimate the current density at each time instant during the ventricular depolarization. The activation time at any given location within the ventricular myocardium was determined as the time point with the occurrence of the maximum local current density estimate. Computer simulations were performed to evaluate this approach using single- and dual-site pacing protocols in a physiologically realistic cellular automaton heart model. The performance and stability of the proposed approach was evaluated with respect to the various levels of measurement noise (0, 5, 10, 20, 40, and 60 microV), the various numbers of ECG electrodes and the modeling errors on the torso geometry and heart position. The simulation results demonstrate that: 1) the single-site paced 3-D activation sequence can be well reconstructed from 200-channel body surface potential maps with additive Gaussian white noise of 20 microV (correlation coefficient = 0.90, relative error = 0.19, and localization error = 5.49 mm); 2) a higher imaging accuracy can be obtained when the activation is initiated from the left/right ventricle (LV/RV) compared to from the septum; 3) the isotropy method gives rise to a better performance than the conventional instant-by-instant regularization; 4) a decreased imaging accuracy results from a

  17. CO-induced inversion of the layer sequence of a model CoCu catalyst

    NASA Astrophysics Data System (ADS)

    Collinge, Greg; Xiang, Yizhi; Barbosa, Roland; McEwen, Jean-Sabin; Kruse, Norbert

    2016-06-01

    Experimental X-ray photoelectron spectroscopy (XPS) and theoretical density functional theory (DFT) calculations reveal the electronic and structural properties of CoCu catalysts before and after CO adsorption. DFT calculations show that, prior to CO adsorption, CoCu has a high tendency to self-assemble into a Co@Cu core-shell structure, which is in accordance with previous atom probe tomography (APT) results for CoCu-based systems and the known mutually low miscibility of Co and Cu. We demonstrate that Co and Cu are electronically immiscible using a density of states (DOS) analysis wherein neither metal's electronic structure is greatly perturbed by the other in ;mixed; CoCu. However, CO adsorption on Co is in fact weakened in CoCu compared to CO adsorption on pure Co despite being electronically unchanged in the alloy. Differential charge density analysis suggests that this is likely due to a lower electron density made available to Co by Cu. CO adsorption at coverages up to 1.00 ML are then investigated on a Cu/Co(0001) model slab to demonstrate CO-induced segregation effects in CoCu. Accordingly, a large driving force for a Co surface enrichment is found. At high coverages, CO can completely invert the layer sequence of Co and Cu. This result is echoed by XPS evidence, which shows that the surface Co/Cu ratio of CoCu is much larger in the presence of CO than in H2.

  18. Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing.

    PubMed

    Zhan, Aibin; Xiong, Wei; He, Song; Macisaac, Hugh J

    2014-01-01

    Large-scale high-throughput sequencing techniques are rapidly becoming popular methods to profile complex communities and have generated deep insights into community biodiversity. However, several technical problems, especially sequencing artifacts such as nucleotide calling errors, could artificially inflate biodiversity estimates. Sequence filtering for artifact removal is a conventional method for deleting error-prone sequences from high-throughput sequencing data. As rare species represented by low-abundance sequences in datasets may be sensitive to artifact removal process, the influence of artifact removal on rare species recovery has not been well evaluated in natural complex communities. Here we employed both internal (reliable operational taxonomic units selected from communities themselves) and external (indicator species spiked into communities) references to evaluate the influence of artifact removal on rare species recovery using 454 pyrosequencing of complex plankton communities collected from both freshwater and marine habitats. Multiple analyses revealed three clear patterns: 1) rare species were eliminated during sequence filtering process at all tested filtering stringencies, 2) more rare taxa were eliminated as filtering stringencies increased, and 3) elimination of rare species intensified as biomass of a species in a community was reduced. Our results suggest that cautions be applied when processing high-throughput sequencing data, especially for rare taxa detection for conservation of species at risk and for rapid response programs targeting non-indigenous species. Establishment of both internal and external references proposed here provides a practical strategy to evaluate artifact removal process.

  19. Computational issues of importance to the inverse recovery of epicardial potentials in a realistic heart-torso geometry.

    PubMed

    Messinger-Rapport, B J; Rudy, Y

    1989-11-01

    In vitro data from a realistic-geometry electrolytic tank were used to demonstrate the consequences of computational issues critical to the ill-posed inverse problem in electrocardiography. The boundary element method was used to discretize the relationship between the body surface potentials and epicardial cage potentials. Variants of Tikhonov regularization were used to stabilize the inversion of the body surface potentials in order to reconstruct the epicardial surface potentials. The computational issues investigated were (1) computation of the regularization parameter; (2) effects of inaccuracy in locating the position of the heart; and (3) incorporation of a priori information on the properties of epicardial potentials into the regularization methodology. Two methods were suggested by which a priori information could be incorporated into the regularization formulation: (1) use of an estimate of the epicardial potential distribution everywhere on the surface and (2) use of regional bounds on the excursion of the potential. Results indicate that the a posteriori technique called CRESO, developed by Colli Franzone and coworkers, most consistently derives the regularization parameter closest to the optimal parameter for this experimental situation. The sensitivity of the inverse computation in a realistic-geometry torso to inaccuracies in estimating heart position are consistent with results from the eccentric spheres model; errors of 1 cm are well tolerated, but errors of 2 cm or greater result in a loss of position and amplitude information. Finally, estimates and bounds based on accurate, known information successfully lower the relative error associated with the inverse and have the potential to significantly enhance the amplitude and feature position information obtainable from the inverse-reconstructed epicardial potential map.

  20. Geometry of the 1954 Fairview Peak-Dixie Valley earthquake sequence from a joint inversion of leveling and triangulation data

    USGS Publications Warehouse

    Hodgkinson, K.M.; Stein, R.S.; Marshall, G.

    1996-01-01

    In 1954, four earthquakes greater than Ms=6.0 occurred within a 30-km radius and in a period of 6 months. Elevation and angle changes calculated from repeated leveling and triangulation surveys which span the coseismic period provide constraints on the fault geometries and coseismic slip of the faults which were activated. The quality of the coseismic geodetic data is assessed. Corrections are applied to the leveling data for subsidence due to groundwater withdrawal in the Fallon area, and a rod miscalibration error of 150??30 ppm is isolated in leveling surveys made in 1967. The leveling and triangulation observations are then simultaneously inverted using the single value decomposition (SVD) inversion method to determine fault geometries and coseismic slip. Using SVD, it is possible to determine on which faults slip is resolvable given the data distribution. The faults are found to dip between 50?? and 80?? and extend to depths of 5 to 14 km. The geodetically derived slip values are generally equal to, or greater than, the maximum observed displacement along the surface scarps. Where slip is resolvable the geodetic data indicates the 1954 sequence contained a significant component of right-lateral slip. This is consistent with the N15??W trending shear zone which geodetic surveys have detected in western Nevada. Copyright 1996 by the American Geophysical Union.

  1. Studying the Sequence of the April 17, 2003 Delingha Earthquake (ML=6.7) by Regional Moment Tensor Inversion

    NASA Astrophysics Data System (ADS)

    Jiao, W.; Qian, R.; Chan, W.; Zeng, X.; Zhang, M.

    2004-12-01

    On April 17, 2003, a strong earthquake of ML = 6.7 occurred to the northwest of the Delingha City, Qinghai Province, northwest China. The epicenter (37o33¡_N, 96o27¡_E) lies in the Zongwulong Mountain, where the Dachaidan-Zongwulong Mountain fault (DZMF) zone runs through. In this study, we analyzed the focal mechanism of the main shock and several strong immediate aftershocks by regional waveform moment tensor inversion. We collected a comprehensive regional waveform data set that includes the broadband waveforms from the China Digital Seismic Network, the GSN, and a portable broadband seismic network deployed in the near regional distance to the earthquake at the time. One very broadband station equipped with the STS-2 seismometer and 24-bit digital data logger was only 80km from the epicenter, which gave tremendous constraint on the mechanism of the aftershock sequence (Fan and Wallace, 1991; Dreger and Helmberger, 1993). Our results show the dominance of the high angle thrust faulting striking NWW-NW. The distribution of the fault plane solutions reflects the turning and/or branching of the DZMF zone in the area, which has been confirmed by the field geological survey.

  2. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome.

    PubMed

    Li, Runsheng; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Ren, Xiaoliang; Zhao, Zhongying

    2015-06-03

    Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24 × reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads.

  3. A paracentric inversion suppresses genetic recombination at the FON3 locus with breakpoints corresponding to sequence gaps on rice chromosome 11L.

    PubMed

    Jiang, Li; Zhang, Wenli; Xia, Zhihui; Jiang, Guanghuai; Qian, Qian; Li, Aili; Cheng, Zhukuan; Zhu, Lihuang; Mao, Long; Zhai, Wenxue

    2007-03-01

    Paracentric inversion is known to inhibit genetic recombination between normal and inverted chromosomal segments in heterozygous arrangements. Insect inversion polymorphisms have been studied to reveal adaptive processes for maintaining genetic variation. We report the first paracentric inversion in rice (Oryza sativa), which was discovered in our effort to clone the floral organ number gene FON3. Recombination at the FON3 locus on the long arm of chromosome 11 was severely suppressed over a distance of more than 36 cM. An extensive screening among 8,242 F(2) progeny failed to detect any recombinants. Cytological analysis revealed a loop-like structure on pachytene chromosomes, whereas FISH analysis showed the migration of a BAC clone from a distal location to a position closer to the centromere. Interestingly, the locations where the genetic recombination suppression began were coincided with the positions of two physical gaps on the chromosome 11, suggesting a correlation between the physical gaps, the inversion breakpoints. Transposons and retrotransposons, and tandemly arranged members of gene families were among the sequences immediately flanking the gaps. Taken together, we propose that the genetic suppression at the FON3 locus was caused by a paracentric inversion. The possible genetic mechanism causing such a spontaneous inversion was proposed.

  4. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

    USGS Publications Warehouse

    Barker, F. Keith; Oyler-McCance, Sara; Tomback, Diana F.

    2015-01-01

    Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

  5. The hyperintense acute reperfusion marker on fluid-attenuated inversion recovery magnetic resonance imaging is caused by gadolinium in the cerebrospinal fluid.

    PubMed

    Köhrmann, Martin; Struffert, Tobias; Frenzel, Thomas; Schwab, Stefan; Doerfler, Arnd

    2012-01-01

    The hyperintense acute reperfusion marker (HARM) on fluid-attenuated inversion recovery MRI is believed to be caused by gadolinium-based contrast agents crossing a disrupted blood-brain barrier. However, this hypothesis has never been directly verified in humans. In this study, we analyzed cerebrospinal fluid samples of patients with HARM on imaging regarding the presence and concentration of gadolinium-based contrast agents. Gadobutrol was found in concentrations of approximately 50 μmol/L. Using phantom MRI experiments, we demonstrate that the detected concentrations are consistent with the observed HARM imaging pattern. Our study yields first direct evidence in humans that the imaging phenomenon HARM is indeed caused by leakage of gadolinium-based contrast agents into the cerebrospinal fluid.

  6. A-T linker adapter polymerase chain reaction for determining flanking sequences by rescuing inverse PCR or thermal asymmetric interlaced PCR products.

    PubMed

    Trinh, Quoclinh; Zhu, Pengyu; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2014-12-01

    The polymerase chain reaction (PCR)-based genome walking method has been extensively used to isolate unknown flanking sequences, whereas nonspecific products are always inevitable. To resolve these problems, we developed a new strategy to isolate the unknown flanking sequences by combining A-T linker adapter PCR with inverse PCR (I-PCR) or thermal asymmetric interlaced PCR (TAIL-PCR). The result showed that this method can be efficiently achieved with the flanking sequence from the Arabidopsis mutant and papain gene. Our study provides researchers with an additional method for determining genomic DNA flanking sequences to identify the target band from bulk of bands and to eliminate the cloning step for sequencing. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Improving parenchyma segmentation by simultaneous estimation of tissue property T1 map and group-wise registration of inversion recovery MR breast images.

    PubMed

    Xing, Ye; Xue, Zhong; Englander, Sarah; Schnall, Mitchell; Shen, Dinggang

    2008-01-01

    The parenchyma tissue in the breast has a strong relation with predictive biomarkers of breast cancer. To better segment parenchyma, we perform segmentation on estimated tissue property T1 map. To improve the estimation of tissue property (T1) which is the basis for parenchyma segmentation, we present an integrated algorithm for simultaneous T1 map estimation, T1 map based parenchyma segmentation and group-wise registration on series of inversion recovery magnetic resonance (MR) breast images. The advantage of using this integrated algorithm is that the simultaneous T1 map estimation (E-step) and group-wise registration (R-step) could benefit each other and jointly improve parenchyma segmentation. In particular, in E-step, T1 map based segmentation could help perform an edge-preserving smoothing on the tentatively estimated noisy T1 map, and could also help provide tissue probability maps to be robustly registered in R-step. Meanwhile, the improved estimation of T1 map could help segment parenchyma in a more accurate way. In R-step, for robust registration, the group-wise registration is performed on the tissue probability maps produced in E-step, rather than the original inversion recovery MR images, since tissue probability maps are the intrinsic tissue property which is invariant to the use of different imaging parameters. The better alignment of images achieved in R-step can help improve T1 map estimation and indirectly the T1 map based parenchyma segmentation. By iteratively performing E-step and R-step, we can simultaneously obtain better results for T1 map estimation, T1 map based segmentation, group-wise registration, and finally parenchyma segmentation.

  8. Inversion recovery ultrashort echo time magnetic resonance imaging: A method for simultaneous direct detection of myelin and high signal demonstration of iron deposition in the brain - A feasibility study.

    PubMed

    Sheth, Vipul R; Fan, Shujuan; He, Qun; Ma, Yajun; Annese, Jacopo; Switzer, Robert; Corey-Bloom, Jody; Bydder, Graeme M; Du, Jiang

    2017-05-01

    Multiple sclerosis (MS) causes demyelinating lesions in the white matter and increased iron deposition in the subcortical gray matter. Myelin protons have an extremely short T2* (<1ms) and are not directly detected with conventional clinical magnetic resonance (MR) imaging sequences. Iron deposition also reduces T2*, leading to reduced signal on clinical sequences. In this study we tested the hypothesis that the inversion recovery ultrashort echo time (IR-UTE) pulse sequence can directly and simultaneously image myelin and iron deposition using a clinical 3T scanner. The technique was first validated on a synthetic myelin phantom (myelin powder in D2O) and a Feridex iron phantom. This was followed by studies of cadaveric MS specimens, healthy volunteers and MS patients. UTE imaging of the synthetic myelin phantom showed an excellent bi-component signal decay with two populations of protons, one with a T2* of 1.2ms (residual water protons) and the other with a T2* of 290μs (myelin protons). IR-UTE imaging shows sensitivity to a wide range of iron concentrations from 0.5 to ~30mM. The IR-UTE signal from white matter of the brain of healthy volunteers shows a rapid signal decay with a short T2* of ~300μs, consistent with the T2* values of myelin protons in the synthetic myelin phantom. IR-UTE imaging in MS brain specimens and patients showed multiple white matter lesions as well as areas of high signal in subcortical gray matter. This in specimens corresponded in position to Perl's diaminobenzide staining results, consistent with increased iron deposition. IR-UTE imaging simultaneously detects lesions with myelin loss in the white matter and iron deposition in the gray matter. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Recovery and Analysis of Formyltetrahydrofolate Synthetase Gene Sequences from Natural Populations of Acetogenic Bacteria

    PubMed Central

    Leaphart, Adam B.; Lovell, Charles R.

    2001-01-01

    Primers for PCR amplification of partial (1,102 of 1,680 bp) formyltetrahydrofolate synthetase (FTHFS) gene sequences were developed and tested. Partial FTHFS sequences were successfully amplified from DNA from pure cultures of known acetogens, from other FTHFS-producing organisms, from the roots of the smooth cordgrass, Spartina alterniflora, and from fresh horse manure. The amplimers recovered were cloned, their nucleotide sequences were determined, and their translated amino acid sequences were used to construct phylogenetic trees. We found that FTHFS sequences from homoacetogens formed a monophyletic cluster that did not contain sequences from nonhomoacetogens and that FTHFS sequences appear to be informative regarding major physiological features of FTHFS-producing organisms. PMID:11229939

  10. Electrical Monitoring of Fresh Water Displacement in a Brackish Aquifer During Aquifer Storage and Recovery: Forward and Inverse Modeling Results

    NASA Astrophysics Data System (ADS)

    Levannier, A.; Delhomme, J.

    2003-12-01

    Aquifer storage and recovery (ASR) projects are now used to temporarily store water in the subsurface and to recover it when needed. When freshwater is injected into a brackish aquifer, a transition zone forms, due to mixing, diffusion and gravity. The front displacement and the width of the transition zone depend on the characteristics of the aquifer but, from repeated surveys conducted with an array of downhole electrodes placed against the borehole wall, the changes in the front position/shape can be continuously monitored. Synthetic data were created for a targeted ASR situation through hydrodynamic and hydrodispersive modeling (performed with a finite difference scheme) that gave the salt concentration distribution in the aquifer, as a function of space and time, during ASR inject/store/pump cycles. Concentrations were converted first into water resistivity values Rw, and then into formation resistivity values Rt through Archie's law (1) calibrated on logging data: \\begin{equation} R_{t}=\\frac{a}{\\phi^{m}}R_w where φ is the porosity, and a and m depend on the lithology. Based on this information, the response of downhole electrodes was computed by solving equation (2) (using a finite element modeling code) for electrical surveys conducted at repeated times during the planned ASR cycles, and in particular during the initial ASR testing phase: \\begin{equation} \

  11. Mask pattern recovery by level set method based inverse inspection technology (IIT) and its application on defect auto disposition

    NASA Astrophysics Data System (ADS)

    Park, Jin-Hyung; Chung, Paul D. H.; Jeon, Chan-Uk; Cho, Han Ku; Pang, Linyong; Peng, Danping; Tolani, Vikram; Cecil, Tom; Kim, David; Baik, KiHo

    2009-10-01

    At the most advanced technology nodes, such as 32nm and 22nm, aggressive OPC and Sub-Resolution Assist Features (SRAFs) are required. However, their use results in significantly increased mask complexity, making mask defect disposition more challenging than ever. This paper describes how mask patterns can first be recovered from the inspection images by applying patented algorithms using Level Set Methods. The mask pattern recovery step is then followed by aerial/wafer image simulation, the results of which can be plugged into an automated mask defect disposition system based on aerial/wafer image. The disposition criteria are primarily based on wafer-plane CD variance. The system also connects to a post-OPC lithography verification tool that can provide gauges and CD specs, thereby enabling them to be used in mask defect disposition as well. Results on both programmed defects and production defects collected at Samsung mask shop are presented to show the accuracy and consistency of using the Level Set Methods and aerial/wafer image based automated mask disposition.

  12. Inversely repeating integrated hepatitis B virus DNA and cellular flanking sequences in the human hepatoma-derived cell line huSP.

    PubMed Central

    Mizusawa, H; Taira, M; Yaginuma, K; Kobayashi, M; Yoshida, E; Koike, K

    1985-01-01

    Among recombinant phages carrying integrated hepatitis B virus (HBV) DNA sequences cloned from the human hepatoma-derived cell line huSP, one clone, lambda hu-489, revealed some unusual features. The 2.25-kilobase Eco D fragment from the insert of this clone hybridized to the HBV DNA probe only and its nucleotide sequence was determined. The viral sequence, as well as a cellular flanking sequence, showed extensive rearrangement accompanied by inverted repetition. The Eco D fragment contained HBV DNA from the 5'-end region of gene S to the middle of gene X, followed by a long cellular flanking sequence. Moreover, a part of gene X was found inversely repeated at the head of the same gene S in a head-to-head configuration truncated by the same cellular sequence. Therefore, the same junction sequence of viral DNA and the cellular sequence was found at two different sites in the Eco D fragment in opposite polarities. Images PMID:2982143

  13. Three-dimensional inversion recovery manganese-enhanced MRI of mouse brain using super-resolution reconstruction to visualize nuclei involved in higher brain function.

    PubMed

    Poole, Dana S; Plenge, Esben; Poot, Dirk H J; Lakke, Egbert A J F; Niessen, Wiro J; Meijering, Erik; van der Weerd, Louise

    2014-07-01

    The visualization of activity in mouse brain using inversion recovery spin echo (IR-SE) manganese-enhanced MRI (MEMRI) provides unique contrast, but suffers from poor resolution in the slice-encoding direction. Super-resolution reconstruction (SRR) is a resolution-enhancing post-processing technique in which multiple low-resolution slice stacks are combined into a single volume of high isotropic resolution using computational methods. In this study, we investigated, first, whether SRR can improve the three-dimensional resolution of IR-SE MEMRI in the slice selection direction, whilst maintaining or improving the contrast-to-noise ratio of the two-dimensional slice stacks. Second, the contrast-to-noise ratio of SRR IR-SE MEMRI was compared with a conventional three-dimensional gradient echo (GE) acquisition. Quantitative experiments were performed on a phantom containing compartments of various manganese concentrations. The results showed that, with comparable scan times, the signal-to-noise ratio of three-dimensional GE acquisition is higher than that of SRR IR-SE MEMRI. However, the contrast-to-noise ratio between different compartments can be superior with SRR IR-SE MEMRI, depending on the chosen inversion time. In vivo experiments were performed in mice receiving manganese using an implanted osmotic pump. The results showed that SRR works well as a resolution-enhancing technique in IR-SE MEMRI experiments. In addition, the SRR image also shows a number of brain structures that are more clearly discernible from the surrounding tissues than in three-dimensional GE acquisition, including a number of nuclei with specific higher brain functions, such as memory, stress, anxiety and reward behavior.

  14. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

    PubMed

    Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

    2014-01-01

    High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

  15. Evaluation of a Secondary School Science Program Inversion: Moving from a Traditional to a Modifified-PCB Sequence

    ERIC Educational Resources Information Center

    Gaubatz, Julie

    2013-01-01

    Studies of high-school science course sequences have been limited primarily to a small number of site-specific investigations comparing traditional science sequences (e.g., Biology-Chemistry-Physics: BCP) to various Physics First-influenced sequences (Physics-Chemistry-Biology: PCB). The present study summarizes a five-year program evaluation…

  16. Evaluation of a Secondary School Science Program Inversion: Moving from a Traditional to a Modifified-PCB Sequence

    ERIC Educational Resources Information Center

    Gaubatz, Julie

    2013-01-01

    Studies of high-school science course sequences have been limited primarily to a small number of site-specific investigations comparing traditional science sequences (e.g., Biology-Chemistry-Physics: BCP) to various Physics First-influenced sequences (Physics-Chemistry-Biology: PCB). The present study summarizes a five-year program evaluation…

  17. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

    PubMed Central

    2013-01-01

    Background Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities. Results Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance. Conclusions The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity. PMID:23587339

  18. Cerebrospinal Fluid Enhancement on Fluid Attenuated Inversion Recovery Images After Carotid Artery Stenting with Neuroprotective Balloon Occlusions: Hemodynamic Instability and Blood-Brain Barrier Disruption

    SciTech Connect

    Ogami, Ryo Nakahara, Toshinori; Hamasaki, Osamu; Araki, Hayato; Kurisu, Kaoru

    2011-10-15

    Purpose: A rare complication of carotid artery stenting (CAS), prolonged reversible neurological symptoms with delayed cerebrospinal fluid (CSF) space enhancement on fluid attenuated inversion recovery (FLAIR) images, is associated with blood-brain barrier (BBB) disruption. We prospectively identified patients who showed CSF space enhancement on FLAIR images. Methods: Nineteen patients-5 acute-phase and 14 scheduled-underwent 21 CAS procedures. Balloon catheters were navigated across stenoses, angioplasty was performed using a neuroprotective balloon, and stents were placed with after dilation under distal balloon protection. CSF space hyperintensity or obscuration on FLAIR after versus before CAS indicated CSF space enhancement. Correlations with clinical factors were examined. Results: CSF space was enhanced on FLAIR in 12 (57.1%) cases. Postprocedural CSF space enhancement was significantly related to age, stenosis rate, acute-stage procedure, and total occlusion time. All acute-stage CAS patients showed delayed enhancement. Only age was associated with delayed CSF space enhancement in scheduled CAS patients. Conclusions: Ischemic intolerance for severe carotid artery stenosis and temporary neuroprotective balloon occlusion, causing reperfusion injury, seem to be the main factors that underlie BBB disruption with delayed CSF space enhancement shortly after CAS, rather than sudden poststenting hemodynamic change. Our results suggest that factors related to hemodynamic instability or ischemic intolerance seem to be associated with post-CAS BBB vulnerability. Patients at risk for hemodynamic instability or with ischemic intolerance, which decrease BBB integrity, require careful management to prevent intracranial hemorrhagic and other post-CAS complications.

  19. T1-weighted gradient-echo imaging, with and without inversion recovery, in the identification of anatomical structures on the lateral surface of the brain*

    PubMed Central

    Georgeto, Sergio Murilo; Zicarelli, Carlos Alexandre Martins; Gariba, Munir Antônio; Aguiar, Luiz Roberto

    2016-01-01

    Objective To compare brain structures using volumetric magnetic resonance imaging with isotropic resolution, in T1-weighted gradient-echo (GRE) acquisition, with and without inversion recovery (IR). Materials and methods From 30 individuals, we evaluated 120 blocks of images of the left and right cerebral hemispheres being acquired by T1 GRE and by T1 IR GRE. On the basis of the Naidich et al. method for localization of anatomical landmarks, 27 anatomical structures were divided into two categories: identifiable and inconclusive. Those two categories were used in the analyses of repeatability (intraobserver agreement) and reproducibility (interobserver agreement). McNemar's test was used in order to compare the T1 GRE and T1 IR GRE techniques. Results There was good agreement in the intraobserver and interobserver analyses (mean kappa > 0.60). McNemar's test showed that the frequency of identifiable anatomical landmarks was slightly higher when the T1 IR GRE technique was employed than when the T1 GRE technique was employed. The difference between the two techniques was statistically significant. Conclusion In the identification of anatomical landmarks, the T1 IR GRE technique appears to perform slightly better than does the T1 GRE technique. PMID:28057964

  20. Potential of fluid-attenuated inversion recovery MRI as an alternative to contrast-enhanced MRI for oral and maxillofacial vascular malformations: experimental and clinical studies.

    PubMed

    Sasaki, Yoshinori; Sakamoto, Junichiro; Otonari-Yamamoto, Mika; Nishikawa, Keiichi; Sano, Tsukasa

    2013-10-01

    To determine the potential of fluid-attenuated inversion recovery (FLAIR) imaging of oral and maxillofacial vascular malformations as an alternative to contrast-enhanced magnetic resonance imaging (MRI), we investigated the influence of differences in T1 and T2 values on image contrast in FLAIR images and evaluated the diagnostic utility of such images. FLAIR imaging and heavily T2-weighted (hT2-weighted) imaging were performed using a phantom. FLAIR and hT2-weighted images of 32 lesions (11 mucous cysts, 12 vascular malformations, and 9 tumors) were also studied retrospectively. The contrast-to-noise ratios (CNRs) and CNR change ratios were compared. All aqueous solutions except those with a short T2 value were discriminated by CNR change ratio (P < .05). All 3 types of lesions were discriminated by CNR change ratio (P < .05). FLAIR imaging has potential as an alternative to contrast-enhanced MRI in differentiating vascular malformations from other types of lesions in the oral and maxillofacial region. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Time course of arterial hyperintensity with fast fluid-attenuated inversion-recovery imaging in acute and subacute middle cerebral arterial infarction.

    PubMed

    Maeda, M; Koshimoto, Y; Uematsu, H; Yamada, H; Kimura, H; Kawamura, Y; Itoh, H; Sakuma, H; Takeda, K

    2001-06-01

    The purpose of this study was to evaluate the time course of arterial hyperintensity (AH) in acute and subacute cerebral infarctions of the middle cerebral artery (MCA) distribution by using fast fluid-attenuated inversion-recovery (FLAIR) imaging. A total of 40 FLAIR MR examinations were performed in 27 patients with MCA infarction within 13 days after ictus. Thirteen patients underwent two MR examinations during this period. Thrombotic or embolic infarctions were included in this study, but lacunar infarctions were excluded. The presence or absence of AH and the location of AH were analyzed. Overall, AH was found in 24 (60%) of 40 FLAIR examinations within 13 days after onset. AH was seen in 17 (100%) examinations less than 24 hours old, four (40%) of 10 examinations 1-4 days old, two (18%) of 11 examinations 5-9 days old, and one (50%) of two examinations 10-13 days old. AH was most frequently found at the sylvian fissure (87%), followed by the sulci (54%), and the horizontal segment of MCA (29%) in the affected MCA distribution. Although AH could be seen even at 13 days after ictus, the presence of AH declined over time. AH represented an early sign of acute embolic or thrombotic infarction. J. Magn. Reson. Imaging 2001;13:987-990. Copyright 2001 Wiley-Liss, Inc.

  2. Quantitative measurements of relative fluid-attenuated inversion recovery (FLAIR) signal intensities in acute stroke for the prediction of time from symptom onset

    PubMed Central

    Cheng, Bastian; Brinkmann, Mathias; Forkert, Nils D; Treszl, Andras; Ebinger, Martin; Köhrmann, Martin; Wu, Ona; Kang, Dong-Wha; Liebeskind, David S; Tourdias, Thomas; Singer, Oliver C; Christensen, Soren; Luby, Marie; Warach, Steven; Fiehler, Jens; Fiebach, Jochen B; Gerloff, Christian; Thomalla, Götz

    2013-01-01

    In acute stroke magnetic resonance imaging, a ‘mismatch' between visibility of an ischemic lesion on diffusion-weighted imaging (DWI) and missing corresponding parenchymal hyperintensities on fluid-attenuated inversion recovery (FLAIR) data sets was shown to identify patients with time from symptom onset ≤4.5 hours with high specificity. However, moderate sensitivity and suboptimal interpreter agreement are limitations of a visual rating of FLAIR lesion visibility. We tested refined image analysis methods in patients included in the previously published PREFLAIR study using refined visual analysis and quantitative measurements of relative FLAIR signal intensity (rSI) from a three-dimensional, segmented stroke lesion volume. A total of 399 patients were included. The rSI of FLAIR lesions showed a moderate correlation with time from symptom onset (r=0.382, P<0.001). A FLAIR rSI threshold of <1.0721 predicted symptom onset ≤4.5 hours with slightly increased specificity (0.85 versus 0.78) but also slightly decreased sensitivity (0.47 versus 0.58) as compared with visual analysis. Refined visual analysis differentiating between ‘subtle' and ‘obvious' FLAIR hyperintensities and classification and regression tree algorithms combining information from visual and quantitative analysis also did not improve diagnostic accuracy. Our results raise doubts whether the prediction of stroke onset time by visual image judgment can be improved by quantitative rSI measurements. PMID:23047272

  3. The leptomeningeal "ivy sign" on fluid-attenuated inversion recovery MR imaging in Moyamoya disease: a sign of decreased cerebral vascular reserve?

    PubMed

    Mori, N; Mugikura, S; Higano, S; Kaneta, T; Fujimura, M; Umetsu, A; Murata, T; Takahashi, S

    2009-05-01

    Moyamoya disease is an idiopathic occlusive cerebrovascular disorder with abnormal microvascular proliferation. We investigated the clinical utility of leptomeningeal high signal intensity (ivy sign) sometimes seen on fluid-attenuated inversion recovery images in Moyamoya disease. We examined the relationship between the degree of the ivy sign and the severity of the ischemic symptoms in 96 hemispheres of 48 patients with Moyamoya disease. We classified each cerebral hemisphere into 4 regions from anterior to posterior. In 192 regions of 24 patients, we examined the relationship between the degree of the ivy sign and findings of single-photon emission CT, including the resting cerebral blood flow (CBF) and cerebral vascular reserve (CVR). The degree of the ivy sign showed a significant positive relationship with the severity of the ischemic symptoms (P < .001). Of the 4 regions, the ivy sign was most frequently and prominently seen in the anterior part of the middle cerebral artery region. The degree of the ivy sign showed a negative relationship with the resting CBF (P < .0034) and a more prominent negative relationship with the CVR (P < .001). The leptomeningeal ivy sign indicates decreased CVR in Moyamoya disease.

  4. The Ivy Sign on Fluid Attenuated Inversion Recovery Images Related to Single-Photon Emission Computed Tomography Cerebral Blood Flow in Moyamoya Disease: A Case Report.

    PubMed

    Matano, Fumihiro; Murai, Yasuo; Kubota, Asami; Mizunari, Takayuki; Kobayashi, Shiro; Morita, Akio

    2017-01-17

    Moyamoya disease is an idiopathic progressive cerebrovascular steno-occlusive disorder characterized by the formation of numerous collaterals called moyamoya vessels. Accurate evaluation of vascular status and CBF is needed for prompt treatment to prevent ischemic and/or hemorrhagic events. The pathogenesis of the ivy sign on fluid attenuated inversion recovery (FLAIR) images of moyamoya disease patients is unclear. We report a moyamoya disease case wherein the ivy sign changed in relation to SPECT-measured CBF during progression and following treatment. A 49-year-old female presented with slight aphasia and right hemiparesis. MRI diffusion-weighted image revealed cerebral infarction in the left frontal lobe. Cerebral angiography images showed bilateral distal internal carotid artery stenosis and moyamoya vessels. FLAIR images exhibited the ivy sign. We performed superficial temporal artery-middle cerebral artery(STA-MCA) bypass surgery with encephalogaleosynangiosis(EGS) and encephalomyosynangiosis(EMS) on the left side 6 months after first presentation. After operation, left-side resting CBF gradually improved on SPECT and the ivy sign decreased. On the other hand, right-side CBF gradually deteriorated at rest, and the ivy sign increased. Therefore, we performed STA-MCA bypass with EGS and EMS on the right side 4 years after first presentation. After operation, resting CBF increased and ivy sign decreased. The FLAIR ivy sign may be a useful indicator of both deterioration and improvement of CBF status without the need for CBF imaging using contrast material.

  5. A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome.

    PubMed

    Watson, Christopher M; Crinnion, Laura A; Harrison, Sally M; Lascelles, Carolina; Antanaviciute, Agne; Carr, Ian M; Bonthron, David T; Sheridan, Eamonn

    2016-01-01

    Next generation sequencing methodologies are facilitating the rapid characterisation of novel structural variants at nucleotide resolution. These approaches are particularly applicable to variants initially identified using alternative molecular methods. We report a child born with bilateral postaxial syndactyly of the feet and bilateral fifth finger clinodactyly. This was presumed to be an autosomal recessive syndrome, due to the family history of consanguinity. Karyotype analysis revealed a homozygous pericentric inversion of chromosome 7 (46,XX,inv(7)(p15q21)x2) which was confirmed to be heterozygous in both unaffected parents. Since the resolution of the karyotype was insufficient to identify any putatively causative gene, we undertook medium-coverage whole genome sequencing using paired-end reads, in order to elucidate the molecular breakpoints. In a two-step analysis, we first narrowed down the region by identifying discordant read-pairs, and then determined the precise molecular breakpoint by analysing the mapping locations of "soft-clipped" breakpoint-spanning reads. PCR and Sanger sequencing confirmed the identified breakpoints, both of which were located in intergenic regions. Significantly, the 7p15 breakpoint was located 523 kb upstream of HOXA13, the locus for hand-foot-genital syndrome. By inference from studies of HOXA locus control in the mouse, we suggest that the inversion has delocalised a HOXA13 enhancer to produce the phenotype observed in our patient. This study demonstrates how modern genetic diagnostic approach can characterise structural variants at nucleotide resolution and provide potential insights into functional regulation.

  6. New insights into the tectonic inversion of North Canterbury and the regional structural context of the 2010-2011 Canterbury earthquake sequence, New Zealand

    NASA Astrophysics Data System (ADS)

    Barnes, Philip M.; Ghisetti, Francesca C.; Gorman, Andrew R.

    2016-02-01

    The 2010-2011 Canterbury earthquake sequence highlighted the existence of previously unknown active faults beneath the North Canterbury plains and Pegasus Bay, South Island, New Zealand. We provide new insights into the geometry and kinematics of ongoing deformation by analyzing marine seismic data to produce new maps of regional faults and cross-sectional reconstructions of deformation history. Active faulting and folding extends up to 30 km offshore, and involves reactivation of sets of Late Cretaceous-Paleogene normal faults under NW-SE tectonic compression. The active faults consist predominantly of NE-SW striking, SE-dipping reverse faults, and less commonly E-W to NW-SE faults suitably oriented for strike-slip reactivation. Additionally, newly developing reverse faults obliquely segment and overprint the inherited basement fabric and impose geometric and kinematic complexities revealed by mapping and reverse displacement profiles of markers. The Quaternary reverse slip rates decrease from 0.1-0.3 mm/yr beneath northern Pegasus Bay to <0.05 mm/yr approaching Banks Peninsula. Fault growth modeling involving trishear fault-propagation folding mechanisms successfully restores an evolutionary sequence of progressive fault inversion, revealing a history of reactivated individual faults. Tectonic inversion and overprinting processes beneath Pegasus Bay are immature and <1.2 ± 0.4 Ma old, with no evidence of systematic spatial migration of deformation. Our marine data analyses give insights into the structural context of the 2010-2011 Canterbury earthquake sequence, while the combined onshore to offshore data provide an excellent illustration of fault growth associated with immature inversion tectonics, in which selective fault reactivation results from compressive stress imposed across a complex network of inherited faults.

  7. Response and recovery lessons from the 2010-2011 earthquake sequence in Canterbury, New Zealand

    USGS Publications Warehouse

    Pierepiekarz, Mark; Johnston, David; Berryman, Kelvin; Hare, John; Gomberg, Joan S.; Williams, Robert A.; Weaver, Craig S.

    2014-01-01

    The impacts and opportunities that result when low-probability moderate earthquakes strike an urban area similar to many throughout the US were vividly conveyed in a one-day workshop in which social and Earth scientists, public officials, engineers, and an emergency manager shared their experiences of the earthquake sequence that struck the city of Christchurch and surrounding Canterbury region of New Zealand in 2010-2011. Without question, the earthquake sequence has had unprecedented impacts in all spheres on New Zealand society, locally to nationally--10% of the country's population was directly impacted and losses total 8-10% of their GDP. The following paragraphs present a few lessons from Christchurch.

  8. Temporal sequence of recovery-related events following maximal exercise assessed by heart rate variability and blood lactate concentration.

    PubMed

    Hoshi, Rosangela Akemi; Vanderlei, Luiz Carlos Marques; de Godoy, Moacir Fernandes; Bastos, Fábio do Nascimento; Netto, Jayme; Pastre, Carlos Marcelo

    2017-09-01

    To analyse the temporal sequence of recovery events related to autonomic nervous system and metabolic processes following maximal exercise, applying linear and nonlinear indices of heart rate variability (HRV) and blood lactate concentration. On the following day of the maximum oxygen consumption test, 20 participants firstly lay down for 20 min for resting data collection and then underwent the constant velocity exhaustive test, which consisted in running at 100% of maximal velocity reached on the previous day until exhaustion. Immediately after the end of exercise, the participants kept a supine position for 120 min recovering passively. Prior to exercise and at every 10 min during the recovery time, blood samples were collected to determine lactate concentration, and heart rate variability analysis (time and frequency domain indices and recurrence plot variables) was performed. Friedman's test, complemented with Dunn's multiple comparison test, was used to compare recovery moments and baseline values. From 70 min, no significant differences were detected between lactate concentration and baseline. HRV indices were considered recovered at different timings: at 60 min for SD2; at 70 min for SDNN and LF; at 80 min for RMSSD, HF and SD1 and at 90 min for recurrence plot variables. During passive recovery after maximal exercise, restoration processes seem to comply an order, considering analysed HRV indices and lactate removal: at first, lactate concentration reaches normal values, allowing sympathovagal reorganization, and then, parasympathetic function is able to complete its reestablishment followed by system complexity recovering. © 2016 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

  9. Lipid suppression via double inversion recovery with symmetric frequency sweep for robust 2D‐GRAPPA‐accelerated MRSI of the brain at 7 T

    PubMed Central

    Hangel, Gilbert; Strasser, Bernhard; Považan, Michal; Gruber, Stephan; Chmelík, Marek; Gajdošík, Martin; Trattnig, Siegfried

    2015-01-01

    This work presents a new approach for high‐resolution MRSI of the brain at 7 T in clinically feasible measurement times. Two major problems of MRSI are the long scan times for large matrix sizes and the possible spectral contamination by the transcranial lipid signal. We propose a combination of free induction decay (FID)‐MRSI with a short acquisition delay and acceleration via in‐plane two‐dimensional generalised autocalibrating partially parallel acquisition (2D‐GRAPPA) with adiabatic double inversion recovery (IR)‐based lipid suppression to allow robust high‐resolution MRSI. We performed Bloch simulations to evaluate the magnetisation pathways of lipids and metabolites, and compared the results with phantom measurements. Acceleration factors in the range 2–25 were tested in a phantom. Five volunteers were scanned to verify the value of our MRSI method in vivo. GRAPPA artefacts that cause fold‐in of transcranial lipids were suppressed via double IR, with a non‐selective symmetric frequency sweep. The use of long, low‐power inversion pulses (100 ms) reduced specific absorption rate requirements. The symmetric frequency sweep over both pulses provided good lipid suppression (>90%), in addition to a reduced loss in metabolite signal‐to‐noise ratio (SNR), compared with conventional IR suppression (52–70%). The metabolic mapping over the whole brain slice was not limited to a rectangular region of interest. 2D‐GRAPPA provided acceleration up to a factor of nine for in vivo FID‐MRSI without a substantial increase in g‐factors (<1.1). A 64 × 64 matrix can be acquired with a common repetition time of ~1.3 s in only 8 min without lipid artefacts caused by acceleration. Overall, we present a fast and robust MRSI method, using combined double IR fat suppression and 2D‐GRAPPA acceleration, which may be used in (pre)clinical studies of the brain at 7 T. © 2015 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd

  10. Targeted recovery of novel phylogenetic diversity from next-generation sequence data.

    PubMed

    Lynch, Michael D J; Bartram, Andrea K; Neufeld, Josh D

    2012-11-01

    Next-generation sequencing technologies have led to recognition of a so-called 'rare biosphere'. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts. Here, we test this hypothesis by combining molecular and bioinformatic approaches for targeted retrieval of phylogenetic novelty within rare biosphere OTUs. We combined BLASTN network analysis, phylogenetics and targeted primer design to amplify 16S rRNA gene sequences from unique potential bacterial lineages, comprising part of the rare biosphere from a multi-million sequence data set from an Arctic tundra soil sample. Demonstrating the feasibility of the protocol developed here, three of seven recovered phylogenetic lineages represented extremely divergent taxonomic entities. These divergent target sequences correspond to (a) a previously unknown lineage within the BRC1 candidate phylum, (b) a sister group to the early diverging and currently recognized monospecific Cyanobacteria Gloeobacter, a genus containing multiple plesiomorphic traits and (c) a highly divergent lineage phylogenetically resolved within mitochondria. A comparison to twelve next-generation data sets from additional soils suggested persistent low-abundance distributions of these novel 16S rRNA genes. The results demonstrate this sequence analysis and retrieval pipeline as applicable for exploring underrepresented phylogenetic novelty and recovering taxa that may represent significant steps in bacterial evolution.

  11. Seismic moment tensor inversion using 3D velocity model and its application to the 2013 Lushan earthquake sequence

    NASA Astrophysics Data System (ADS)

    Zhu, Lupei; Zhou, Xiaofeng

    2016-10-01

    Source inversion of small-magnitude events such as aftershocks or mine collapses requires use of relatively high frequency seismic waveforms which are strongly affected by small-scale heterogeneities in the crust. In this study, we developed a new inversion method called gCAP3D for determining general moment tensor of a seismic source using Green's functions of 3D models. It inherits the advantageous features of the "Cut-and-Paste" (CAP) method to break a full seismogram into the Pnl and surface-wave segments and to allow time shift between observed and predicted waveforms. It uses grid search for 5 source parameters (relative strengths of the isotropic and compensated-linear-vector-dipole components and the strike, dip, and rake of the double-couple component) that minimize the waveform misfit. The scalar moment is estimated using the ratio of L2 norms of the data and synthetics. Focal depth can also be determined by repeating the inversion at different depths. We applied gCAP3D to the 2013 Ms 7.0 Lushan earthquake and its aftershocks using a 3D crustal-upper mantle velocity model derived from ambient noise tomography in the region. We first relocated the events using the double-difference method. We then used the finite-differences method and reciprocity principle to calculate Green's functions of the 3D model for 20 permanent broadband seismic stations within 200 km from the source region. We obtained moment tensors of the mainshock and 74 aftershocks ranging from Mw 5.2 to 3.4. The results show that the Lushan earthquake is a reverse faulting at a depth of 13-15 km on a plane dipping 40-47° to N46° W. Most of the aftershocks occurred off the main rupture plane and have similar focal mechanisms to the mainshock's, except in the proximity of the mainshock where the aftershocks' focal mechanisms display some variations.

  12. In-season changes in heart rate recovery are inversely related to time to exhaustion but not aerobic capacity in rowers.

    PubMed

    Haraldsdottir, K; Brickson, S; Sanfilippo, J; Dunn, W; Watson, A

    2017-06-26

    To determine if in-season changes in heart rate recovery (HRR) are related to aerobic fitness and performance in collegiate rowers. Twenty-two female collegiate rowers completed testing before and after their competitive season. Body fat percentage (BF%) was determined by dual-energy X-ray absorptiometry. Maximal aerobic capacity (VO2max ) and time to exhaustion (Tmax ) were determined during maximal rowing ergometer testing followed by 1 minute of recovery. HRR was expressed absolutely and as a percentage of maximal HR (HRR%1 min ). Variables were compared using paired Wilcoxon tests. Multivariable regression models were used to predict in-season changes in HRR using changes in VO2max and Tmax , while accounting for changes in BF%. From preseason to post-season, VO2max and BF% decreased (3.98±0.42 vs 3.78±0.35 L/min, P=.002 and 23.8±3.4 vs 21.3±3.9%, P<.001, respectively), while Tmax increased (11.7±1.3 vs 12.6±1.3 min, P=.002), and HRR%1 min increased (11.1±2.7 vs 13.8±3.8, P=.001). In-season changes in VO2max were not associated with HRR%1 min (P>.05). In-season changes in Tmax were related to changes in HRR%1 min (β=-1.67, P=.006). In-season changes in BF% were not related to changes in HRR (P>.05 for all). HRR1 min and HRR%1 min were faster preseason to post-season, although the changes were unrelated to VO2max . Faster HRR%1 min post-season was inversely related to changes in Tmax . This suggests that HRR should not be used as a measure of aerobic capacity in collegiate rowers, but is a promising measure of training status in this population. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. The Orion GN and C Data-Driven Flight Software Architecture for Automated Sequencing and Fault Recovery

    NASA Technical Reports Server (NTRS)

    King, Ellis; Hart, Jeremy; Odegard, Ryan

    2010-01-01

    The Orion Crew Exploration Vehicle (CET) is being designed to include significantly more automation capability than either the Space Shuttle or the International Space Station (ISS). In particular, the vehicle flight software has requirements to accommodate increasingly automated missions throughout all phases of flight. A data-driven flight software architecture will provide an evolvable automation capability to sequence through Guidance, Navigation & Control (GN&C) flight software modes and configurations while maintaining the required flexibility and human control over the automation. This flexibility is a key aspect needed to address the maturation of operational concepts, to permit ground and crew operators to gain trust in the system and mitigate unpredictability in human spaceflight. To allow for mission flexibility and reconfrgurability, a data driven approach is being taken to load the mission event plan as well cis the flight software artifacts associated with the GN&C subsystem. A database of GN&C level sequencing data is presented which manages and tracks the mission specific and algorithm parameters to provide a capability to schedule GN&C events within mission segments. The flight software data schema for performing automated mission sequencing is presented with a concept of operations for interactions with ground and onboard crew members. A prototype architecture for fault identification, isolation and recovery interactions with the automation software is presented and discussed as a forward work item.

  14. [Study of optimal flip angle for inversion-recovery gradient echo method in delayed contrast-enhanced cardiac magnetic resonance imaging].

    PubMed

    Ogawa, Masashi; Matsumura, Yoshio; Tsuchihashi, Toshio

    2013-04-01

    Delayed contrast-enhanced cardiac magnetic resonance imaging (MRI) is a valuable tool for detecting myocardial infarction and assessing myocardial viability. The standard viability MRI technique is the inversion-recovery gradient echo (IR-GRE) method. Several previous studies have demonstrated that this imaging technique provides superior image quality at high magnetic field strengths, e.g., 3.0 T. However, there are numerous possible flip angles. We investigated the optimal flip angle of IR-GRE in delayed contrast-enhanced cardiac MRI. Phantoms were made that modeled infarcted myocardium and normal myocardium after administration of contrast agent. To determine optimal flip angle, we compared the contrast-to-noise ratio (CNR) among these phantoms and evaluated the degree of artifacts induced by increased flip angle. The flip angle that showed the highest CNR for 2D IR-GRE and 3D IR-GRE was 30°/15° at 1.5 T and 25°/15° at 3.0 T. The flip angle that showed the highest CNR was independent of R-R interval. Streak artifacts induced by increased flip angle tended to occur more readily at 3.0 T than 1.5 T. The optimal flip angle for 2D IR-GRE and 3D IR-GRE at 1.5 T was 30° and 15°, respectively. At 3.0 T, taking into account the results for both CNR and streak artifacts, we concluded the optimal flip angle of 2D IR-GRE to be 15-20°.

  15. 2D phase-sensitive inversion recovery imaging to measure in vivo spinal cord gray and white matter areas in clinically feasible acquisition times.

    PubMed

    Papinutto, Nico; Schlaeger, Regina; Panara, Valentina; Caverzasi, Eduardo; Ahn, Sinyeob; Johnson, Kevin J; Zhu, Alyssa H; Stern, William A; Laub, Gerhard; Hauser, Stephen L; Henry, Roland G

    2015-09-01

    To present and assess a procedure for measurement of spinal cord total cross-sectional areas (TCA) and gray matter (GM) areas based on phase-sensitive inversion recovery imaging (PSIR). In vivo assessment of spinal cord GM and white matter (WM) could become pivotal to study various neurological diseases, but it is challenging because of insufficient GM/WM contrast provided by conventional magnetic resonance imaging (MRI). We acquired 2D PSIR images at 3T at each disc level of the spinal axis in 10 healthy subjects and measured TCA, cord diameters, WM and GM areas, and GM area/TCA ratios. Second, we investigated 32 healthy subjects at four selected levels (C2-C3, C3-C4, T8-T9, T9-T10, total acquisition time <8 min) and generated normative reference values of TCA and GM areas. We assessed test-retest, intra- and interoperator reliability of the acquisition strategy, and measurement steps. The measurement procedure based on 2D PSIR imaging allowed TCA and GM area assessments along the entire spinal cord axis. The tests we performed revealed high test-retest/intraoperator reliability (mean coefficient of variation [COV] at C2-C3: TCA = 0.41%, GM area = 2.75%) and interoperator reliability of the measurements (mean COV on the 4 levels: TCA = 0.44%, GM area = 4.20%; mean intraclass correlation coefficient: TCA = 0.998, GM area = 0.906). 2D PSIR allows reliable in vivo assessment of spinal cord TCA, GM, and WM areas in clinically feasible acquisition times. The area measurements presented here are in agreement with previous MRI and postmortem studies. © 2014 Wiley Periodicals, Inc.

  16. Diffusion-weighted imaging-fluid-attenuated inversion recovery mismatch is associated with better neurologic response to intravenous thrombolytic therapy in acute ischemic stroke patients.

    PubMed

    Jeong, Jong Yeong; Han, Sang Kuk; Shin, Dong Hyuk; Na, Ji Ung; Lee, Hyun Jung; Choi, Pil Cho; Lee, Jeong Hun

    2015-03-01

    To investigate differences in the effect of intravenous (IV) thrombolysis regarding the mismatch of diffusion-weighted imaging-fluid-attenuated inversion recovery (DWI-FLAIR) among acute ischemic stroke patients who visited the emergency department (ED) within 3 hours from the onset of symptoms. Among ED patients presenting with an acute ischemic stroke between January 2011 and May 2013 at a tertiary hospital, those who underwent magnetic resonance imaging before IV thrombolytic therapy were included in this retrospective study. Patients were divided into DWI-FLAIR mismatch and match groups. National Institutes of Health Stroke Scale (NIHSS) scores obtained initially, 24 hours after thrombolytic therapy, and on discharge, and early neurologic improvement (ENI) and major neurologic improvement (MNI) were compared. During the study period, 50 of the 213 acute ischemic stroke patients who presented to the ED were included. The DWI-FLAIR mismatch group showed a statistically significantly greater reduction in NIHSS both at 24 hours after thrombolytic therapy and upon discharge than did the match group (5.5 vs. 1.2, P<0.001; 6.0 vs. 2.3, P<0.01, respectively). Moreover, ENI and MNI were significantly greater for the DWI-FLAIR mismatch group than for the match group (27/36 vs. 2/14, P<0.001; 12/36 vs. 0/14, P=0.012, respectively). Among acute ischemic stroke patients who visited the ED within 3 hours from the onset of symptoms, patients who showed DWI-FLAIR mismatch showed a significantly better response to IV thrombolytic therapy than did the DWI-FLAIR match group in terms of neurologic outcome.

  17. Localisation of the central sulcus region in glioma patients with three-dimensional fluid-attenuated inversion recovery and volume rendering: comparison with functional and conventional magnetic resonance.

    PubMed

    Willemse, Ronald B; Pouwels, Petra J W; Barkhof, Frederik; Vandertop, W Peter

    2011-04-01

    Volume rendering (VR) of three-dimensional (3D) fluid-attenuated inversion recovery (FLAIR) magnetic resonance (MR) images shows regional intensity differences, reflecting the central sulcus (CS) region and occipital cortex. The purpose of this study was to determine whether 3D FLAIR with VR could be used as an alternative method to localise the CS region in comparison with functional and conventional MR-imaging in patients with perirolandic glioma. Eleven patients with intracranial gliomas were studied with single-slab 3D FLAIR including VR and conventional T1-weighted imaging. In all patients, preoperative functional magnetic resonance imaging (fMRI) was performed with a motor paradigm of the hand. The hypo-intense central gyri on 3D FLAIR with VR were interpreted as the CS area. Localisation of the motor hand knob on anatomical images and fMRI results were used for identification of the primary motor cortex. Anatomical localisation of the motor hand knob on T1-weighted images was possible in 91% of both hemispheres. In 73% of the affected hemispheres (AH) and 91% of the unaffected hemispheres (UH) the hand knob and CS region could be identified on 3D FLAIR axial and VR images, respectively. With one exception, fMRI activation confirmed the CS region as observed with 3D FLAIR with VR. Volume rendering of 3D FLAIR MR images shows central hypo-intensities frequently corresponding with the CS region. Two-dimensional localisation of the CS region on conventional T1-weighted images and fMRI seems favourable compared to 3D FLAIR. However, in selected cases, especially where fMRI is not possible or feasible, volume rendering with 3D FLAIR may enhance the 3D visualisation of gliomas in relation to the CS region which can be used as an alternative method in the presurgical structural and functional evaluation of neurosurgical patients.

  18. [Three-dimensional fluid attenuated inversion recovery imaging at 3T MRI in sudden deafness: its findings and relationship with the prognosis].

    PubMed

    Qian, Yin-feng; Wu, Ji-chun; Zhang, Cheng; Yu, Yong-qiang

    2011-10-01

    To investigate inner ear of patients with sudden deafness with three-dimensional fluid attenuated inversion recovery (3D FLAIR) MRI, and the relationship between the results of 3D FLAIR and the prognosis. Twenty-three patients with sudden deafness received 3D FLAIR at 3T MRI, and the signals of inner ear were recorded. Hearing levels were evaluated at initial visit and after treatment. The relationship between 3D FLAIR findings and hearing prognosis was evaluated. Eight patients with sudden deafness showed high signals in the affected cochlea on 3D FLAIR, the others of affected cochlea and all of contralateral cochlea showed no signal on 3D FLAIR. The age, sex, affected side, period to initial visit and initial audiogram had no difference between cochlea no signal group and high signal group. The average auditory threshold (x±s) in cochlea high signal group (90±21) dB HL was significant higher than that in cochlea no signal group (60±28) dB HL, P<0.05 at patients' discharge. After treatment, in cochlea no signal group, two cases' hearing was complete recovered, remarkable improvement in five cases, slight improvement in two cases and no change in six cases. In cochlea high signal group, hearing was slight improvement in one case and no change in seven cases. The prognosis was significant difference between two groups. Five of seven patients with vertigo and sudden deafness showed high signal in affected side vestibule on 3D FLAIR, and the hearing of whom had no change after treatment. 3D FLAIR can show high signal in affected inner ear in sudden deafness patients, and which is related to a poor hearing prognosis.

  19. Unilateral hemispheric proliferation of ivy sign on fluid-attenuated inversion recovery images in moyamoya disease correlates highly with ipsilateral hemispheric decrease of cerebrovascular reserve.

    PubMed

    Kawashima, M; Noguchi, T; Takase, Y; Ootsuka, T; Kido, N; Matsushima, T

    2009-10-01

    An ivy sign is considered to represent diffuse leptomeningeal collaterals found on fluid-attenuated inversion recovery (FLAIR) images of patients with Moyamoya disease. We evaluated the correlation between unilateral ivy proliferation in a hemisphere and cerebrovascular hemodynamic status to learn the clinical significance of the ivy sign. A total of 35 patients with Moyamoya disease were included. Correlation between ivy dominance on FLAIR images and hemodynamic status with use of iodine 123 N-isopropyl-p-iodoamphetamine ((123)I-IMP) single-photon emission CT (SPECT) was evaluated. Distributional differences of ivy signs between both hemispheres were observed in 22 (64.7%) of 34 patients with a positive ivy sign, all of whom showed decreased vascular reserve/reactivity in the ivy-dominant hemisphere (IDH). The proportion of the stage II (misery perfusion) area to IDH was higher than that in the ivy less-dominant hemisphere (ILDH) in the quantitative analysis. The mean vascular reserve was lower in IDH than ILDH. There were 15 of 22 patients who had bypass surgery on IDH because of transient ischemic attack from ischemia of IDH. Patients with symmetric ivy distributions showed a variety of hemodynamic status. MR angiography (MRA) stage of IDH (2.95 +/- 0.39) was higher compared with ILDH (2.60 +/- 0.50; P < .05). Regional arteriocapillary circulation time ratio in IDH was longer compared with ILDH (P < .05). Ivy proliferation decreased in 10 (55.6%) of 18 patients who underwent bypass surgery during the follow-up period. Unilateral hemispheric ivy proliferation correlated highly with the existence of an ipsilateral decreased vascular reserve associated with the development of leptomeningeal collaterals in patients with Moyamoya disease.

  20. Evaluation of focus laterality in temporal lobe epilepsy: a quantitative study comparing double inversion-recovery MR imaging at 3T with FDG-PET.

    PubMed

    Morimoto, Emiko; Okada, Tomohisa; Kanagaki, Mitsunori; Yamamoto, Akira; Fushimi, Yasutaka; Matsumoto, Riki; Takaya, Shigetoshi; Ikeda, Akio; Kunieda, Takeharu; Kikuchi, Takayuki; Paul, Dominik; Miyamoto, Susumu; Takahashi, Ryosuke; Togashi, Kaori

    2013-12-01

    To quantitatively compare the diagnostic capability of double inversion-recovery (DIR) with F-18 fluorodeoxyglucose positron emission tomography (FDG-PET) for detection of seizure focus laterality in temporal lobe epilepsy (TLE). This study was approved by the institutional review board, and written informed consent was obtained. Fifteen patients with TLE and 38 healthy volunteers were enrolled. All magnetic resonance (MR) images were acquired using a 3T-MRI system. Voxel-based analysis (VBA) was conducted for FDG-PET images and white matter segments of DIR images (DIR-WM) focused on the whole temporal lobe (TL) and the anterior part of the temporal lobe (ATL). Distribution of hypometabolic areas on FDG-PET and increased signal intensity areas on DIR-WM were evaluated, and their laterality was compared with clinically determined seizure focus laterality. Correct diagnostic rates of laterality were evaluated, and agreement between DIR-WM and FDG-PET was assessed using κ statistics. Increased signal intensity areas on DIR-WM were located at the vicinity of the hypometabolic areas on FDG-PET, especially in the ATL. Correct diagnostic rates of seizure focus laterality for DIR-WM (0.80 and 0.67 for the TL and the ATL, respectively) were slightly higher than those for FDG-PET (0.67 and 0.60 for the TL and the ATL, respectively). Agreement of laterality between DIR-WM and FDG-PET was substantial for the TL and almost perfect for the ATL (κ = 0.67 and 0.86, respectively). High agreement in localization between DIR-WM and FDG-PET and nearly equivalent detectability of them show us an additional role of MRI in TLE. Wiley Periodicals, Inc. © 2013 International League Against Epilepsy.

  1. Postprandial changes in secretory flow of pancreatic juice in the main pancreatic duct: evaluation with cine-dynamic MRCP with a spatially selective inversion-recovery (IR) pulse.

    PubMed

    Yasokawa, Kazuya; Ito, Katsuyoshi; Tamada, Tsutomu; Yamamoto, Akira; Hayashida, Minoru; Torigoe, Teruyuki; Tanimoto, Daigo; Higaki, Atsushi; Noda, Yasufumi; Kido, Ayumu

    2016-12-01

    To evaluate the influence of oral ingestion on the secretory flow dynamics of physiological pancreatic juice within the main pancreatic duct in healthy subjects by using cine-dynamic MRCP with spatially-selective inversion-recovery (IR) pulse non-invasively. Thirty-eight healthy subjects were investigated. MRCP with spatially-selective IR pulse was repeated every 15 s for 5 min to acquire a total of 20 images (cine-dynamic MRCP). A set of 20 MRCP images was repeatedly obtained before and after liquid oral ingestion every 7 min (including 2-min interval) for 40 min (a total of seven sets). Secretion grade of pancreatic juice on cine-dynamic MRCP was compared before and after oral ingestion using the nonparametric Wilcoxon signed-rank test. Median secretion grades of pancreatic juice at 5 min (score = 2.15), 12 min (score = 1.95) and 19 min (score = 2.05) after ingestion were significantly higher than that before ingestion (score = 1.40) (P = 0.004, P = 0.032, P = 0.045, respectively). Secretion grade of pancreatic juice showed a maximum peak of 2.15 at 5 min after ingestion. Thereafter, the secretion grade of pancreatic juice tended to gradually decline. Non-invasive cine-dynamic MRCP using spatially-selective IR pulse showed potential for evaluating postprandial changes in the secretory flow dynamics of pancreatic juice as a physiological reaction. • Secretion grade of pancreatic juice at cine-dynamic MRCP after ingestion was evaluated. • Secretion grade was significantly increased within 19 min after liquid meal ingestion. • Secretion grade showed maximum peak of 2.15 at 5 min after ingestion. • Postprandial changes in pancreatic juice flow can be assessed by cine-dynamic MRCP.

  2. Multicentre multiobserver study of diffusion-weighted and fluid-attenuated inversion recovery MRI for the diagnosis of sporadic Creutzfeldt-Jakob disease: a reliability and agreement study.

    PubMed

    Fujita, Koji; Harada, Masafumi; Sasaki, Makoto; Yuasa, Tatsuhiko; Sakai, Kenji; Hamaguchi, Tsuyoshi; Sanjo, Nobuo; Shiga, Yusei; Satoh, Katsuya; Atarashi, Ryuichiro; Shirabe, Susumu; Nagata, Ken; Maeda, Tetsuya; Murayama, Shigeo; Izumi, Yuishin; Kaji, Ryuji; Yamada, Masahito; Mizusawa, Hidehiro

    2012-01-01

    Objectives To assess the utility of the display standardisation of diffusion-weighted MRI (DWI) and to compare the effectiveness of DWI and fluid-attenuated inversion recovery (FLAIR) MRI for the diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD). Design A reliability and agreement study. Setting Thirteen MRI observers comprising eight neurologists and five radiologists at two universities in Japan. Participants Data of 1.5-Tesla DWI and FLAIR were obtained from 29 patients with sCJD and 13 controls. Outcome measures Standardisation of DWI display was performed utilising b0 imaging. The observers participated in standardised DWI, variable DWI (the display adjustment was observer dependent) and FLAIR sessions. The observers independently assessed each MRI for CJD-related lesions, that is, hyperintensity in the cerebral cortex or striatum, using a continuous rating scale. Performance was evaluated by the area under the receiver operating characteristics curve (AUC). Results The mean AUC values were 0.84 (95% CI 0.81 to 0.87) for standardised DWI, 0.85 (95% CI 0.82 to 0.88) for variable DWI and 0.68 (95% CI 0.63 to 0.72) for FLAIR, demonstrating the superiority of DWI (p<0.05). There was a trend for higher intraclass correlations of standardised DWI (0.74, 95% CI 0.66 to 0.83) and variable DWI (0.72, 95% CI 0.62 to 0.81) than that of FLAIR (0.63, 95% CI 0.53 to 0.74), although the differences were not statistically significant. Conclusions Standardised DWI is as reliable as variable DWI, and the two DWI displays are superior to FLAIR for the diagnosis of sCJD. The authors propose that hyperintensity in the cerebral cortex or striatum on 1.5-Tesla DWI but not FLAIR can be a reliable diagnostic marker for sCJD.

  3. [A method using long primers for cloning the upstream sequence of delta-6 fatty acid desaturases gene of Thamnidium elegans by nested inverse PCR].

    PubMed

    Wang, De-Pei; Sun, Wei; Li, Ming-Chun; Wei, Dong-Sheng; Zhang, Ying-Hui; Xing, Lai-Jun

    2006-07-01

    Thamnidium elegans is a kind of phycomycete that produces essential unsaturated fatty acids, particularly y-linolenic acid. In this process, delta6-Fatty acid desaturase (D6D) plays a key role due to its enzymatic properties that catalyze the delta6 site dehydrogenation of precursor linoleic acid (18:2delta(9, 12) n-6) and a-linolenic acid (18:3delta(9, 12, 15) n-3). This reaction is the first and rate-limiting step of highly unsaturated fatty acids (HUFA) synthesis pathways. After we have isolated and cloned the gene coding delta6-fatty acid desaturase from Thamnidium elegans As3.2806 (GenBank accession number DQ099380), our interest focuses on the promotion and regulation of the gene transcription. To achieve this aim, we designed long primers and used nested inverse PCR to amplify DNA flanking sequences. First, genome of Thamnidium elegans was extracted and digested with restriction enzymes EcoR I and Kpn I , respectively. Then we ligated the digested DNA with T4 ligase at low concentration which is propitious for linear DNA to joint intromolecule. According to the sequence of delta6-fatty acid desaturase gene of Thamnidium elegans, we designed a couple of 35nt long inverse primers and two couples of shorter inverse primers for inverse PCR. Three rounds of PCR reactions were performed. In the primary reaction, the ligated DNA was used as a template, and the product was used as the template of the secondary reaction, the tertiary reaction was achieved in the same way. After all the three rounds of reactions, we got a nice product about 4 kb from the EcoR I digested sample, in which a 1.3kb 5' upstream sequence (GenBank accession number DQ309425) of delta6-fatty acid desaturase gene containing several putative regulatory elements including TATA. box, FSE-2, AP-1 sites, CCAAT cis-element site and STRE-binding site was derived after sequencing. All of these implied intensely that this 1.3kb fragment is a condition-regulated promoter. It is the first report about

  4. Recursive Recovery of Sparse Signal Sequences From Compressive Measurements: A Review

    NASA Astrophysics Data System (ADS)

    Vaswani, Namrata; Zhan, Jinchun

    2016-07-01

    In this article, we review the literature on design and analysis of recursive algorithms for reconstructing a time sequence of sparse signals from compressive measurements. The signals are assumed to be sparse in some transform domain or in some dictionary. Their sparsity patterns can change with time, although, in many practical applications, the changes are gradual. An important class of applications where this problem occurs is dynamic projection imaging, e.g., dynamic magnetic resonance imaging (MRI) for real-time medical applications such as interventional radiology, or dynamic computed tomography.

  5. Deep Sequencing of Suppression Subtractive Hybridisation Drought and Recovery Libraries of the Non-model Crop Trifolium repens L.

    PubMed

    Bisaga, Maciej; Lowe, Matthew; Hegarty, Matthew; Abberton, Michael; Ravagnani, Adriana

    2017-01-01

    White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data. The pipeline generated four robust sets of transcripts induced and repressed in the leaves of plants subjected to water deficit stress (6,937 and 3,142, respectively) and following re-hydration (6,695 and 4,897, respectively). Semi-quantitative polymerase chain reaction was used to verify the expression pattern of 16 genes. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways. In agreement with similar studies in other crops, the majority of transcripts up-regulated in response to drought belonged to metabolic processes, such as amino acid, carbohydrate, and lipid metabolism, while transcripts involved in photosynthesis, such as components of the photosystem and the biosynthesis of photosynthetic pigments, were up-regulated during recovery. The data also highlighted the role of raffinose family oligosaccharides (RFOs) and the possible delayed response of the flavonoid pathways in the initial response of white clover to water withdrawal. The work presented in this paper is to our knowledge the first large scale molecular analysis of the white clover response to drought stress and re-hydration. The data generated provide a valuable genomic resource for marker

  6. Deep Sequencing of Suppression Subtractive Hybridisation Drought and Recovery Libraries of the Non-model Crop Trifolium repens L.

    PubMed Central

    Bisaga, Maciej; Lowe, Matthew; Hegarty, Matthew; Abberton, Michael; Ravagnani, Adriana

    2017-01-01

    White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data. The pipeline generated four robust sets of transcripts induced and repressed in the leaves of plants subjected to water deficit stress (6,937 and 3,142, respectively) and following re-hydration (6,695 and 4,897, respectively). Semi-quantitative polymerase chain reaction was used to verify the expression pattern of 16 genes. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways. In agreement with similar studies in other crops, the majority of transcripts up-regulated in response to drought belonged to metabolic processes, such as amino acid, carbohydrate, and lipid metabolism, while transcripts involved in photosynthesis, such as components of the photosystem and the biosynthesis of photosynthetic pigments, were up-regulated during recovery. The data also highlighted the role of raffinose family oligosaccharides (RFOs) and the possible delayed response of the flavonoid pathways in the initial response of white clover to water withdrawal. The work presented in this paper is to our knowledge the first large scale molecular analysis of the white clover response to drought stress and re-hydration. The data generated provide a valuable genomic resource for marker

  7. Improved border sharpness of post-infarct scar by a novel self-navigated free-breathing high-resolution 3D whole-heart inversion recovery magnetic resonance approach.

    PubMed

    Rutz, Tobias; Piccini, Davide; Coppo, Simone; Chaptinel, Jerome; Ginami, Giulia; Vincenti, Gabriella; Stuber, Matthias; Schwitter, Juerg

    2016-12-01

    The border zone of post-infarction myocardial scar as identified by late gadolinium enhancement (LGE) has been identified as a substrate for arrhythmias and consequently, high-resolution 3D scar information is potentially useful for planning of electrophysiological interventions. This study evaluates the performance of a novel high-resolution 3D self-navigated free-breathing inversion recovery magnetic resonance pulse sequence (3D-SN-LGE) vs. conventional 2D breath-hold LGE (2D-LGE) with regard to sharpness of borders (SBorder) of post-infarction scar. Patients with post-infarction scar underwent two magnetic resonance examinations for conventional 2D-LGE and high-resolution 3D-SN-LGE acquisitions (both 15 min after 0.2 mmol/kg Gadobutrol IV) at 1.5T. In the prototype 3D-SN-LGE sequence, each ECG-triggered radial steady-state-free-precession read-out segment is preceded by a non-slice-selective inversion pulse. Scar volume and SBorder were assessed on 2D-LGE and matching reconstructed high-resolution 3D-SN-LGE short-axis slices. In 16 patients (four females, 58 ± 10y) all scars visualized by 2D-LGE could be identified on 3D-SN-LGE (time between 2D-LGE and 3D-SN-LGE 48 ± 53 days). A good agreement of scar volume by 3D-SN-LGE vs. 2D-LGE was found (Bland-Altman: -3.7 ± 3.4 ml, correlation: r = 0.987, p < 0.001) with a small difference in scar volume (20.5 (15.8, 35.2) ml vs. 24.5 (20.0, 41.9)) ml, respectively, p = 0.002] and a good intra- and interobserver variability (1.1 ± 4.1 and -1.1 ± 11.9 ml, respectively). SBorder of border "scar to non-infarcted myocardium" was superior on 3D-SN-LGE vs. 2D-LGE: 0.180 ± 0.044 vs. 0.083 ± 0.038, p < 0.001. Detection and quantification of myocardial scar by 3D-SN-LGE is feasible and accurate in comparison to 2D-LGE. The high spatial resolution of the 3D sequence improves delineation of scar borders.

  8. Automatic recovery of aftershock sequences at the International Data Centre: from concept to pipeline

    NASA Astrophysics Data System (ADS)

    Kitov, I.; Bobrov, D.; Rozhkov, M.

    2016-12-01

    Aftershocks of larger earthquakes represent an important source of information on the distribution and evolution of stresses and deformations in pre-seismic, co-seismic and post-seismic phases. For the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Organization (CTBTO) largest aftershocks sequences are also a challenge for automatic and interactive processing. The highest rate of events recorded by two and more seismic stations of the International Monitoring System from a relatively small aftershock area may reach hundreds per hour (e.g. Sumatra 2004 and Tohoku 2011). Moreover, there are thousands of reflected/refracted phases per hour with azimuth and slowness within the uncertainty limits of the first P-waves. Misassociation of these later phases, both regular and site specific, as the first P-wave results in creation of numerous wrong event hypotheses in automatic IDC pipeline. In turn, interactive review of such wrong hypotheses is direct waste of analysts' resources. Waveform cross correlation (WCC) is a powerful tool to separate coda phases from actual P-wave arrivals and to fully utilize the repeat character of waveforms generated by events close in space. Array seismic stations of the IMS enhance the performance of the WCC in two important aspects - they reduce detection threshold and effectively suppress arrivals from all sources except master events. An IDC specific aftershock tool has been developed and merged with standard IDC pipeline. The tool includes several procedures: creation of master events consisting of waveform templates at ten and more IMS stations; cross correlation (CC) of real-time waveforms with these templates, association of arrivals detected at CC-traces in event hypotheses; building events matching IDC quality criteria; and resolution of conflicts between events hypotheses created by neighboring master-events. The final cross correlation standard event lists (XSEL) is a start point of interactive analysis

  9. Reliability of cortical lesion detection on double inversion recovery MRI applying the MAGNIMS-Criteria in multiple sclerosis patients within a 16-months period

    PubMed Central

    Thaler, Christian; Ceyrowski, Tim; Broocks, Gabriel; Treffler, Natascha; Sedlacik, Jan; Stürner, Klarissa; Stellmann, Jan-Patrick; Heesen, Christoph; Fiehler, Jens; Siemonsen, Susanne

    2017-01-01

    Purpose In patients with multiple sclerosis (MS), Double Inversion Recovery (DIR) magnetic resonance imaging (MRI) can be used to identify cortical lesions (CL). We sought to evaluate the reliability of CL detection on DIR longitudinally at multiple subsequent time-points applying the MAGNIMs scoring criteria for CLs. Methods 26 MS patients received a 3T-MRI (Siemens, Skyra) with DIR at 12 time-points (TP) within a 16 months period. Scans were assessed in random order by two different raters. Both raters separately marked all CLs on each scan and total lesion numbers were obtained for each scan-TP and patient. After a retrospective re-evaluation, the number of consensus CLs (conL) was defined as the total number of CLs, which both raters finally agreed on. CLs volumes, relative signal intensities and CLs localizations were determined. Both ratings (conL vs. non-consensus scoring) were compared for further analysis. Results A total number of n = 334 CLs were identified by both raters in 26 MS patients with a first agreement of both raters on 160 out of 334 of the CLs found (κ = 0.48). After the retrospective re-evaluation, consensus agreement increased to 233 out of 334 CL (κ = 0.69). 93.8% of conL were visible in at least 2 consecutive TP. 74.7% of the conL were visible in all 12 consecutive TP. ConL had greater mean lesion volumes and higher mean signal intensities compared to lesions that were only detected by one of the raters (p<0.05). A higher number of CLs in the frontal, parietal, temporal and occipital lobe were identified by both raters than the number of those only identified by one of the raters (p<0.05). Conclusions After a first assessment, slightly less than a half of the CL were considered as reliably detectable on longitudinal DIR images. A retrospective re-evaluation notably increased the consensus agreement. However, this finding is narrowed, considering the fact that retrospective evaluation steps might not be practicable in clinical routine

  10. Reliability of cortical lesion detection on double inversion recovery MRI applying the MAGNIMS-Criteria in multiple sclerosis patients within a 16-months period.

    PubMed

    Faizy, Tobias Djamsched; Thaler, Christian; Ceyrowski, Tim; Broocks, Gabriel; Treffler, Natascha; Sedlacik, Jan; Stürner, Klarissa; Stellmann, Jan-Patrick; Heesen, Christoph; Fiehler, Jens; Siemonsen, Susanne

    2017-01-01

    In patients with multiple sclerosis (MS), Double Inversion Recovery (DIR) magnetic resonance imaging (MRI) can be used to identify cortical lesions (CL). We sought to evaluate the reliability of CL detection on DIR longitudinally at multiple subsequent time-points applying the MAGNIMs scoring criteria for CLs. 26 MS patients received a 3T-MRI (Siemens, Skyra) with DIR at 12 time-points (TP) within a 16 months period. Scans were assessed in random order by two different raters. Both raters separately marked all CLs on each scan and total lesion numbers were obtained for each scan-TP and patient. After a retrospective re-evaluation, the number of consensus CLs (conL) was defined as the total number of CLs, which both raters finally agreed on. CLs volumes, relative signal intensities and CLs localizations were determined. Both ratings (conL vs. non-consensus scoring) were compared for further analysis. A total number of n = 334 CLs were identified by both raters in 26 MS patients with a first agreement of both raters on 160 out of 334 of the CLs found (κ = 0.48). After the retrospective re-evaluation, consensus agreement increased to 233 out of 334 CL (κ = 0.69). 93.8% of conL were visible in at least 2 consecutive TP. 74.7% of the conL were visible in all 12 consecutive TP. ConL had greater mean lesion volumes and higher mean signal intensities compared to lesions that were only detected by one of the raters (p<0.05). A higher number of CLs in the frontal, parietal, temporal and occipital lobe were identified by both raters than the number of those only identified by one of the raters (p<0.05). After a first assessment, slightly less than a half of the CL were considered as reliably detectable on longitudinal DIR images. A retrospective re-evaluation notably increased the consensus agreement. However, this finding is narrowed, considering the fact that retrospective evaluation steps might not be practicable in clinical routine. Lesions that were not reliably

  11. A comparison of inner ear imaging features at different time points of sudden sensorineural hearing loss with three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging.

    PubMed

    Zhu, Honglei; Ou, Yongkang; Fu, Jia; Zhang, Ya; Xiong, Hao; Xu, Yaodong

    2015-10-01

    It has been reported that about half of patients with sudden sensorineural hearing loss (SSNHL) show high signals in the affected inner ear on three-dimensional, fluid-attenuated inversion recovery magnetic resonance imaging (3D-FLAIR MRI). These signals may reflect minor hemorrhage or an increased concentration of protein in the inner ear, which has passed through blood vessels with increased permeability. Our objective was to compare the positive ratio of the high signal in affected inner ears at different time points to determine the suitable imaging time point for 3D-FLAIR MRI in SSNHL. 3D-FLAIR MRI images were taken at three times, precontrast and approximately 10 min and 4 h after intravenous injection of a single dose of gadodiamide (Gd) (0.1 mmol/kg), in 46 patients with SNHL. We compared the positive findings of the high signals in the inner ear of patients with SNHL as well as the signal intensity ratio (SIR) between the affected cochleae and unaffected cochleae at three time points. The positive ratios of the high signals in the affected inner ear at the time points of precontrast and 10 min and 4 h after the intravenous Gd injection were 26.1, 32.6, and 41.3%, respectively. The high signal intensity ratios of affected inner ears at the three time points were 1.28, 1.31, and 1.48, respectively. The difference between the positive ratios precontrast and at 10 min after the intravenous Gd injection was statistically significant (P = 0.006); the differences between the positive ratios at 4 h after the intravenous Gd injection and precontrast and between the ratios at 4 h and 10 min after the intravenous Gd injection were not statistically significant. The time effects of the median value of SIR were not significant (P = 0.064). We do not recommend 4 h after intravenous Gd injection as a time point to image the inner ear in SNHL. We believe that imaging precontrast and at 10 min after the intravenous Gd injection are suitable time points.

  12. The cannabinoid CB1 receptor inverse agonist AM 251 and antagonist AM 4113 produce similar effects on the behavioral satiety sequence in rats.

    PubMed

    Hodge, Janel; Bow, Joshua P; Plyler, Kimberly S; Vemuri, V Kiran; Wisniecki, Ania; Salamone, John D; Makriyannis, Alexandros; McLaughlin, Peter J

    2008-11-21

    Cannabinoid CB1 inverse agonists such as rimonabant and AM 251 hold therapeutic promise as appetite suppressants, but the extent to which non-motivational factors contribute to their anorectic effects is not fully known. Examination of the behavioral satiety sequence (BSS) in rats, the orderly progression from eating to post-prandial grooming and then resting, has revealed that these compounds preserve the order of events but differ markedly from natural satiation. The most notable difference is that grooming (particularly scratching) is profoundly enhanced at anorectic doses, while eating and resting are diminished, raising the possibility that the anorectic effect is simply secondary to the grooming effect. In the current design, the neutral CB1 antagonist AM 4113, which has been found to lack some of the undesirable effects of AM 251, produced nearly identical effects on the BSS as AM 251. The possibility that competition from enhanced grooming could account for the anorectic effect of AM 4113 was examined by yoking the pattern of disruptions caused by grooming in the AM 4113-treated group to forced locomotion in a different group fed in a modified running wheel. This response competition did not significantly reduce food intake. It was concluded that AM 4113, a CB1 neutral antagonist, produces the same effects on the BSS as AM 251, but that response competition from enhanced grooming may not be a sufficient explanation for the anorectic effects of CB1 antagonists/inverse agonists.

  13. Ion/Ion Reactions of MALDI-Derived Peptide Ions: Increased Sequence Coverage via Covalent and Electrostatic Modification upon Charge Inversion

    PubMed Central

    Stutzman, John R.; McLuckey, Scott A.

    2012-01-01

    Atmospheric pressure matrix assisted laser desorption/ionization (AP-MALDI)-derived tryptic peptide ions have been subjected to ion/ion reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The ion/ion reaction produces a negatively charged electrostatic complex composed of the peptide cation and reagent dianion, whereupon dehydration of the complex via collision-induced dissociation (CID) produces a Schiff base product anion. Collisional activation of modified lysine-terminated tryptic peptide anions is consistent with a covalent modification of unprotonated primary amines (i.e. N-terminus and ε-NH2 of lysine). Modified arginine-terminated tryptic peptides have shown evidence of a covalent modification at the N-terminus and a non-covalent interaction with the arginine residue. The modified anions yield at least as much sequence information upon CID as the unmodified cations for the small tryptic peptides examined here and more sequence information for the large tryptic peptides. This study represents the first demonstration of gas phase ion/ion reactions involving MALDI-derived ions. In this case, covalent modification upon charge inversion is shown to enhance MALDI tandem mass spectrometry of tryptic peptides. PMID:23078018

  14. Ion/ion reactions of MALDI-derived peptide ions: increased sequence coverage via covalent and electrostatic modification upon charge inversion.

    PubMed

    Stutzman, John R; McLuckey, Scott A

    2012-12-18

    Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI)-derived tryptic peptide ions have been subjected to ion/ion reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas-phase. The ion/ion reaction produces a negatively charged electrostatic complex composed of the peptide cation and reagent dianion, whereupon dehydration of the complex via collision-induced dissociation (CID) produces a Schiff base product anion. Collisional activation of modified lysine-terminated tryptic peptide anions is consistent with a covalent modification of unprotonated primary amines (i.e., N-terminus and ε-NH(2) of lysine). Modified arginine-terminated tryptic peptides have shown evidence of a covalent modification at the N-terminus and a noncovalent interaction with the arginine residue. The modified anions yield at least as much sequence information upon CID as the unmodified cations for the small tryptic peptides examined here and more sequence information for the large tryptic peptides. This study represents the first demonstration of gas-phase ion/ion reactions involving MALDI-derived ions. In this case, covalent and electrostatic modification charge inversion is shown to enhance MALDI tandem mass spectrometry of tryptic peptides.

  15. The time window of MRI of murine atherosclerotic plaques after administration of CB2 receptor targeted micelles: inter-scan variability and relation between plaque signal intensity increase and gadolinium content of inversion recovery prepared versus non-prepared fast spin echo.

    PubMed

    te Boekhorst, B C M; Bovens, S M; van de Kolk, C W A; Cramer, M J M; Doevendans, P A F M; ten Hove, M; van der Weerd, L; Poelmann, R; Strijkers, G J; Pasterkamp, G; van Echteld, C J A

    2010-10-01

    Single fast spin echo scans covering limited time frames are mostly used for contrast-enhanced MRI of atherosclerotic plaque biomarkers. Knowledge on inter-scan variability of the normalized enhancement ratio of plaque (NER(plaque)) and relation between NER(plaque) and gadolinium content for inversion-recovery fast spin echo is limited. Study aims were: evaluation of (1) timing of MRI after intravenous injection of cannabinoid-2 receptor (CB2-R) (expressed by human and mouse plaque macrophages) targeted micelles; (2) inter-scan variability of inversion-recovery fast spin echo and fast spin echo; (3) relation between NER(plaque) and gadolinium content for inversion-recovery fast spin echo and fast spin echo. Inversion-recovery fast spin echo/fast spin echo imaging was performed before and every 15 min up to 48 h after injection of CB2-R targeted or control micelles using several groups of mice measured in an interleaved fashion. NER(plaque) (determined on inversion-recovery fast spin echo images) remained high (∼2) until 48 h after injection of CB2-R targeted micelles, whereas NER(plaque) decreased after 36 h in the control group. The inter-scan variability and relation between NER(plaque) and gadolinium (assessed with inductively coupled plasma- mass spectrometry) were compared between inversion-recovery fast spin echo and fast spin echo. Inter-scan variability was higher for inversion-recovery fast spin echo than for fast spin echo. Although gadolinium and NER(plaque) correlated well for both techniques, the NER of plaque was higher for inversion-recovery fast spin echo than for fast spin echo. In mice injected with CB2-R targeted micelles, NER(plaque) can be best evaluated at 36-48 h post-injection. Because NER(plaque) was higher for inversion-recovery fast spin echo than for fast spin echo, but with high inter-scan variability, repeated inversion-recovery fast spin echo imaging and averaging of the obtained NER(plaque) values is recommended.

  16. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Peng, Ze [DOE JGI

    2016-07-12

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    Peng, Ze

    2012-06-01

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  18. Rearrangement of the bacterial chromosome: forbidden inversions.

    PubMed

    Segall, A; Mahan, M J; Roth, J R

    1988-09-09

    The order of genes in the chromosome of enteric bacteria has been evolutionarily conserved despite the existence of mechanisms for rearrangement. Homologous chromosomal sequences in the same orientation recombine to form deletions or duplications. When homologous sequences in inverse orientation recombine, one expects to form an inversion of the intervening chromosomal segment. This expectation was tested by placing pairs of homologous sequences in inverse order at various points in the chromosome. Sequences at many pairs of sites (permissive) do recombine to generate the expected inversion, while the same sequences placed at other pairs of sites (nonpermissive) do not form an inversion. For the one nonpermissive interval tested, the missing inversion type can be constructed by an alternative transductional method; strains with this inversion are viable. Thus mechanistic limitations must prevent sequences at particular sites from undergoing the recombination event required to form an inversion.

  19. [Uterine inversion].

    PubMed

    Neves, J; Cardoso, E; Araújo, C; Santo, S; Gonçalves, P; Melo, A; Rodrigues, R; Coelho, A Pereira

    2006-01-01

    The uterine inversion is a rare but serious pathology of the delivery. We describe two cases of uterine inversion of secondary and quaternary degree; the first had a delay diagnosis and the second having a return after the manual replacement, finishing both on surgical resolution. The authors describe the causal factors, the diagnosis and the therapeutic of uterine inversion.

  20. Source rupture processes of the foreshock and mainshock in the 2016 Kumamoto earthquake sequence estimated from the kinematic waveform inversion of strong motion data

    NASA Astrophysics Data System (ADS)

    Asano, Kimiyuki; Iwata, Tomotaka

    2016-08-01

    The 2016 Kumamoto earthquake sequence started with an MJMA 6.5 foreshock occurring along the northern part of the Hinagu fault, central Kyushu, Japan, and the MJMA 7.3 mainshock occurred just 28 h after the foreshock. We analyzed the source rupture processes of the foreshock and mainshock by using the kinematic waveform inversion technique on strong motion data. The foreshock was characterized by right-lateral strike-slip occurring on a nearly vertical fault plane along the northern part of the Hinagu fault, and it had two large-slip areas: one near the hypocenter and another at a shallow depth. The rupture of the mainshock started from the deep portion of a northwest-dipping fault plane along the northern part of the Hinagu fault, then continued to transfer to the Futagawa fault. Most of the significant slip occurred on the Futagawa fault, and the shallow portion of the Hinagu fault also had a relatively large slip. The slip amount on the shallowest subfaults along the Futagawa fault was approximately 1-4 m, which is consistent with the emergence of surface breaks associated with this earthquake. Right-lateral strike-slip dominated on the fault segment along the Hinagu fault, but normal-slip components were estimated to make a significant contribution on the fault segment along the Futagawa fault. The large fault-parallel displacements recorded at two near-fault strong motion stations coincided with the spatiotemporal pattern of the fault slip history during the mainshock. The spatial relationship between the rupture areas of the foreshock and mainshock implies a complex fault structure in this region.

  1. [Uterine inversion].

    PubMed

    Dirken, J J; Vlaanderen, W

    1994-01-01

    Inversion of the uterus is a rare complication of childbirth. A primigravida aged 21 and a multigravida aged 32, hospitalized as emergency cases because of inversion of the uterus with major blood loss, were treated with infusion of liquids (to combat shock), repositioning of the uterus under anaesthesia and prevention of reinversion by uterine tonics. Inversion of the uterus should be part of the differential diagnosis in every case of fluxus post partum.

  2. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes.

    PubMed

    Gan, Han Ming; Schultz, Mark B; Austin, Christopher M

    2014-02-03

    Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.

  3. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

    PubMed Central

    2014-01-01

    Background Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. Results The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. Conclusions We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer. PMID:24484414

  4. Recovery of partial 16S rDNA sequences suggests the presence of Crenarchaeota in the human digestive ecosystem.

    PubMed

    Rieu-Lesme, Françoise; Delbès, Céline; Sollelis, Lauriane

    2005-11-01

    Human feces collected from 10 healthy teenagers was analyzed for the presence of Crenarchaeota. After a first polymerase chain reaction (PCR) with Archaea-specific primers, a nested real-time PCR was performed using Crenarchaeota-specific primers. Real-time Crenarchaeotal PCR products detected from four subjects were cloned and the sequencing revealed that most of the partial 16S rRNA gene sequences were highly similar (> or = 97% homology) to sequences affiliated to the Sulfolobus group of the Crenarchaeota phylum. Our findings suggest for the first time that Crenarchaeota might be present in the microbiota of the human digestive ecosystem in which this phylum has never been found yet.

  5. Rapid quantification of oxygen tension in blood flow with a fluorine nanoparticle reporter and a novel blood flow-enhanced-saturation-recovery sequence.

    PubMed

    Hu, Lingzhi; Chen, Junjie; Yang, Xiaoxia; Caruthers, Shelton D; Lanza, Gregory M; Wickline, Samuel A

    2013-07-01

    We present a novel blood flow-enhanced-saturation-recovery (BESR) sequence, which allows rapid in vivo T1 measurement of blood for both (1)H and (19)F nuclei. BESR sequence is achieved by combining homogeneous spin preparation and time-of-flight image acquisition and therefore preserves high time efficiency and signal-to-noise ratio for (19)F imaging of circulating perfluorocarbon nanoparticles comprising a perfluoro-15-crown-5-ether core and a lipid monolayer (nominal size = 250 nm). The consistency and accuracy of the BESR sequence for measuring T1 of blood was validated experimentally. With a confirmed linear response feature of (19)F R1 with oxygen tension in both salt solution and blood sample, we demonstrated the feasibility of the BESR sequence to quantitatively determine the oxygen tension within mouse left and right ventricles under both normoxia and hyperoxia conditions. Thus, (19)F BESR MRI of circulating perfluorocarbon nanoparticles represents a new approach to noninvasively evaluate intravascular oxygen tension. Copyright © 2012 Wiley Periodicals, Inc.

  6. Rapid quantification of oxygen tension in blood flow with a fluorine nanoparticle reporter and a novel Blood flow-Enhanced-Saturation-Recovery (BESR) sequence

    PubMed Central

    Hu, Lingzhi; Chen, Junjie; Yang, Xiaoxia; Caruthers, Shelton D.; Lanza, Gregory M.; Wickline, Samuel A.

    2013-01-01

    We present a novel Blood flow-Enhanced-Saturation-Recovery (BESR) sequence, which allows rapid in vivo T1 measurement of blood for both 1H and 19F nuclei. BESR sequence is achieved by combining homogeneous spin preparation and time-of-flight image acquisition and therefore preserves high time efficiency and SNR for 19F imaging of circulating Perfluorocarbon (PFC) Nanoparticles (NPs) comprising a perfluoro-15-crown-5-ether core and a lipid monolayer (nominal size = 250 nm). The consistency and accuracy of the BESR sequence for measuring T1 of blood was validated experimentally. With a confirmed linear response feature of 19F R1 with oxygen tension in both salt solution and blood sample, we demonstrated the feasibility of the BESR sequence to quantitatively determine the oxygen tension within mouse left and right ventricles under both normoxia and hyperoxia conditions. Thus, 19F BESR MRI of circulating PFC NPs represents a new approach to non-invasively evaluate intravascular oxygen tension. PMID:22915328

  7. SirX: a selective inversion recovery experiment on X-nuclei for the determination of the exchange rate of slow chemical exchanges between two sites.

    PubMed

    Xie, Xiulan; Bönisch, Friedrich

    2015-10-01

    Nuclear magnetic resonance spectroscopy has proven to be powerful for the study of dynamic processes. A new pulse sequence, SirX, is designed to provide boundary conditions that simplify the McConnell equations. Both an initial rate approximation and a whole curve fitting to the time course of magnetization can be used to calculate the exchange rate. These methods were used to study the exchange kinetics of N,N-dimethylacetamide. As compared with the well-established exchange spectroscopy suitable to studies of slow exchange, SirX has the advantage of being less time consuming and capable of providing more reliable kinetic data. Furthermore, by setting the observation on X-nuclei with larger chemical shift dispersion as compared with an observation on (1)H resonance, SirX extends the upper limit of a reliable determination of exchange rates.

  8. Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing

    SciTech Connect

    Williams, L.E.; Detter, C,; Barrie, K.; Lapidus, A.; Summers, A.O.

    2006-06-01

    Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for effective preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli, Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for construction of highcoverage libraries, as shown by sequencing five native plasmids ranging in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on mobile genetic element biology derived from these sequences. Adaptation of this BAC method for large plasmid isolation removes one major technical hurdle to expanding our knowledge of the natural plasmid gene pool.

  9. Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths.

    PubMed

    Hernández-Triana, L M; Prosser, S W; Rodríguez-Perez, M A; Chaverri, L G; Hebert, P D N; Gregory, T Ryan

    2014-05-01

    In this study, we evaluated the efficacy of various primers for the purpose of DNA barcoding old, pinned museum specimens of blackflies (Diptera: Simuliidae). We analysed 271 pinned specimens representing two genera and at least 36 species. Due to the age of our material, we targeted overlapping DNA fragments ranging in size from 94 to 407 bp. We were able to recover valid sequences from 215 specimens, of which 18% had 500- to 658-bp barcodes, 36% had 201- to 499-bp barcodes and 46% had 65- to 200-bp barcodes. Our study demonstrates the importance of choosing suitable primers when dealing with older specimens and shows that even very short sequences can be diagnostically informative provided that an appropriate gene region is used. Our study also highlights the lack of knowledge surrounding blackfly taxonomy, and we briefly discuss the need for further phylogenetic studies in this socioeconomically important family of insects.

  10. Indirect inversions

    NASA Astrophysics Data System (ADS)

    Sergienko, Olga

    2013-04-01

    Since Doug MacAyeal's pioneering studies of the ice-stream basal traction optimizations by control methods, inversions for unknown parameters (e.g., basal traction, accumulation patterns, etc) have become a hallmark of the present-day ice-sheet modeling. The common feature of such inversion exercises is a direct relationship between optimized parameters and observations used in the optimization procedure. For instance, in the standard optimization for basal traction by the control method, ice-stream surface velocities constitute the control data. The optimized basal traction parameters explicitly appear in the momentum equations for the ice-stream velocities (compared to the control data). The inversion for basal traction is carried out by minimization of the cost (or objective, misfit) function that includes the momentum equations facilitated by the Lagrange multipliers. Here, we build upon this idea, and demonstrate how to optimize for parameters indirectly related to observed data using a suite of nested constraints (like Russian dolls) with additional sets of Lagrange multipliers in the cost function. This method opens the opportunity to use data from a variety of sources and types (e.g., velocities, radar layers, surface elevation changes, etc.) in the same optimization process.

  11. Recovery of community genomes to assess subsurface metabolic potential: exploiting the capacity of next generation sequencing-based metagenomics

    NASA Astrophysics Data System (ADS)

    Wrighton, K. C.; Thomas, B.; Miller, C. S.; Sharon, I.; Wilkins, M. J.; VerBerkmoes, N. C.; Handley, K. M.; Lipton, M. S.; Hettich, R. L.; Williams, K. H.; Long, P. E.; Banfield, J. F.

    2011-12-01

    , the capacity to oxidize complex organic carbon, as well as lack of membrane bound electron transport chains and an incomplete citric acid cycle. We propose that these organisms grow cryptically on residual biomass from previous biostimulation experiments and thus demonstrate that resource utilization and turnover in the aquifer can be decoupled from existing acetate amendment and external terminal electron accepting processes. In addition to the first recovery of multiple genomes from these novel candidate divisions, our community genomic approach uncovered viral diversity not yet observed at the site, with the reconstruction of six phage genomes and the presence of CRISPR loci detected in bacterial genomes from diverse lineages. These findings have implications for predictive ecosystem modeling, highlighting the importance of integrating the response, adaptation, as well as biological and geochemical feedback mechanisms existing within complex subsurface communities to long term organic carbon amendment.

  12. Left-lateral shear inside the North Gulf of Evia Rift, Central Greece, evidenced by relocated earthquake sequences and moment tensor inversion

    NASA Astrophysics Data System (ADS)

    Ganas, Athanassios; Mouzakiotis, Evangelos; Moshou, Alexandra; Karastathis, Vassilios

    2016-07-01

    The use of local velocity model in the analysis of seismicity recorded by the Hellenic Unified Seismological Network (HUSN), provides the opportunity to determine accurate hypocentral solutions using the weighted P- and S-wave arrival times for the November 2013, November 2014 and June 2015 North Gulf of Evia (Euboea) sequences. The hypocentral locations, including the determination of the location uncertainties, are obtained applying the non-linear probabilistic analysis. We also calculated the moment tensor solutions for the main events as well as for the strongest aftershocks. The accurate determination of seismicity showed the activation of two left-lateral, NW-SE striking, near-vertical faults, one onshore near village Taxiarchis (2013 sequence) and one offshore (offshore Malessina Peninsula, 2015 sequence). The 2014 sequence, also offshore Malessina Peninsula ruptured an oblique-slip, north-dipping normal fault with a strike of N280-290°E. All three faults occur at depths 10-16 km, with rupture zone dimensions 5-6 km along strike and 3-4 km along dip. These aftershock depths indicate a seismogenic (brittle) zone of about 15 km in depth for this rift. The left-lateral kinematics indicates strain partitioning inside the rift because of E-W horizontal compression, also evidenced by GPS data. The moderate magnitude of earthquakes (M5.2 ± 0.1) indicates that strike-slip events have a minor contribution to the crustal deformation and to active tectonics of the Gulf.

  13. Added value of high-b-value (b = 3000 s/mm2) diffusion-weighted imaging at 3 T in relation to fluid-attenuated inversion recovery images for the evaluation of cortical lesions in inflammatory brain diseases.

    PubMed

    Iwashita, Koya; Hirai, Toshinori; Kitajima, Mika; Shigematsu, Yoshinori; Uetani, Hiroyuki; Iryo, Yasuhiko; Azuma, Minako; Hayashida, Eri; Ando, Yukio; Murakami, Ryuji; Yamashita, Yasuyuki

    2013-01-01

    The purpose of this study was to determine how the gray-to-white matter contrast in healthy subjects changes on high-b-value diffusion-weighted imaging (DWI) acquired at 3 T and evaluate whether high-b-value DWI at 3 T is useful for the detection of cortical lesions in inflammatory brain diseases. Ten healthy volunteers underwent DWI at b = 1000, 2000, 3000, 4000, and 5000 s/mm(2) on a 3-T MRI unit. On DW images, 1 radiologist performed region-of-interest measurements of the signal intensity of 8 gray matter structures. The gray-to-white matter contrast ratio (GWCR) was calculated. Ten patients with inflammatory cortical lesions were also included. All patients underwent conventional MRI and DWI at b = 1000 and 3000 s/mm(2). Using a 4-point grading system, 2 radiologists independently assessed the presence of additional information on DW images compared with fluid-attenuated inversion recovery images. Interobserver agreement was assessed by κ statistics. In the healthy subjects, the b value increased as the GWCR decreased in all evaluated gray matter structures. On DW images acquired at b = 3000 s/mm(2), mean GWCR was less than 1.0 in 7 of 8 structures. For both reviewers, DWI at b = 3000 s/mm(2) yielded significantly more additional information than did DWI at b = 1000 s/mm(2) (P < 0.05). Interobserver agreement for DWI at b = 1000 s/mm(2) and b = 3000 s/mm(2) was fair (κ = 0.35) and excellent (κ = 1.0), respectively. At 3-T DWI, the gray-to-white matter contrast in most gray matter structures reverses at b = 3000 s/mm. In the evaluation of cortical lesions in patients with inflammatory brain diseases, 3-T DWI at b = 3000 s/mm was more useful than b = 1000 s/mm(2).

  14. Inverse Floatation

    NASA Astrophysics Data System (ADS)

    Nath, Saurabh; Mukherjee, Anish; Chatterjee, Souvick; Ganguly, Ranjan; Sen, Swarnendu; Mukhopadhyay, Achintya; Boreyko, Jonathan

    2014-11-01

    We have observed that capillarity forces may cause floatation in a few non-intuitive configurations. These may be divided into 2 categories: i) floatation of heavier liquid droplets on lighter immiscible ones and ii) fully submerged floatation of lighter liquid droplets in a heavier immiscible medium. We call these counter-intuitive because of the inverse floatation configuration. For case (i) we have identified and studied in detail the several factors affecting the shape and maximum volume of the floating drop. We used water and vegetable oil combinations as test fluids and established the relation between Bond Number and maximum volume contained in a floating drop (in the order of μL). For case (ii), we injected vegetable oil drop-wise into a pool of water. The fully submerged configuration of the drop is not stable and a slight perturbation to the system causes the droplet to burst and float in partially submerged condition. Temporal variation of a characteristic length of the droplet is analyzed using MATLAB image processing. The constraint of small Bond Number establishes the assumption of lubrication regime in the thin gap. A brief theoretical formulation also shows the temporal variation of the gap thickness. Jadavpur University, Jagadis Bose Centre of Excellence, Virginia Tech.

  15. The origin of the 5S ribosomal RNA molecule could have been caused by a single inverse duplication: strong evidence from its sequences.

    PubMed

    Branciamore, Sergio; Di Giulio, Massimo

    2012-04-01

    The secondary structure of the 5S ribosomal RNA (5S rRNA) molecule shows a high degree of symmetry. In order to explain the origin of this symmetry, it has been conjectured that one half of the 5S rRNA molecule was its precursor and that an indirect duplication of this precursor created the other half and thus the current symmetry of the molecule. Here, we have subjected to an empirical test both the indirect duplication model, analysing a total of 684 5S rRNA sequences for complementarity between the two halves of the 5S rRNA, and the direct duplication model analysing in this case the similarity between the two halves of this molecule. In intra- and inter-molecule and intra- and inter-domain comparisons, we find a high statistical support to the hypothesis of a complementarity relationship between the two halves of the 5S rRNA molecule, denying vice versa the hypothesis of similarity between these halves. Therefore, these observations corroborate the indirect duplication model at the expense of the direct duplication model, as reason of the origin of the 5S rRNA molecule. More generally, we discuss and favour the hypothesis that all RNAs and proteins, which present symmetry, did so through gene duplication and not by gradualistic accumulation of few monomers or segments of molecule into a gradualistic growth process. This would be the consequence of the very high propensity that nucleic acids have to be subjected to duplications.

  16. Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256's Spread, and Evolution of Russia ST8-IV.

    PubMed

    Wan, Tsai-Wen; Khokhlova, Olga E; Iwao, Yasuhisa; Higuchi, Wataru; Hung, Wei-Chun; Reva, Ivan V; Singur, Olga A; Gostev, Vladimir V; Sidorenko, Sergey V; Peryanova, Olga V; Salmina, Alla B; Reva, Galina V; Teng, Lee-Jene; Yamamoto, Tatsuo

    2016-01-01

    ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256's strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages.

  17. Recursive inversion of externally defined linear systems

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1988-01-01

    The approximate inversion of an internally unknown linear system, given by its impulse response sequence, by an inverse system having a finite impulse response, is considered. The recursive least squares procedure is shown to have an exact initialization, based on the triangular Toeplitz structure of the matrix involved. The proposed approach also suggests solutions to the problems of system identification and compensation.

  18. Multidimensional NMR inversion without Kronecker products: Multilinear inversion

    NASA Astrophysics Data System (ADS)

    Medellín, David; Ravi, Vivek R.; Torres-Verdín, Carlos

    2016-08-01

    Multidimensional NMR inversion using Kronecker products poses several challenges. First, kernel compression is only possible when the kernel matrices are separable, and in recent years, there has been an increasing interest in NMR sequences with non-separable kernels. Second, in three or more dimensions, the singular value decomposition is not unique; therefore kernel compression is not well-defined for higher dimensions. Without kernel compression, the Kronecker product yields matrices that require large amounts of memory, making the inversion intractable for personal computers. Finally, incorporating arbitrary regularization terms is not possible using the Lawson-Hanson (LH) or the Butler-Reeds-Dawson (BRD) algorithms. We develop a minimization-based inversion method that circumvents the above problems by using multilinear forms to perform multidimensional NMR inversion without using kernel compression or Kronecker products. The new method is memory efficient, requiring less than 0.1% of the memory required by the LH or BRD methods. It can also be extended to arbitrary dimensions and adapted to include non-separable kernels, linear constraints, and arbitrary regularization terms. Additionally, it is easy to implement because only a cost function and its first derivative are required to perform the inversion.

  19. Atypical appearance of lipomatous tumors on MR images: high signal intensity with fat-suppression STIR sequences.

    PubMed

    Murphy, W D; Hurst, G C; Duerk, J L; Feiglin, D H; Christopher, M; Bellon, E M

    1991-01-01

    Lipomatous tumors generally have signal characteristics that allow them to be diagnosed with great accuracy by means of magnetic resonance imaging. These tumors usually have signal intensities similar to those of subcutaneous fat on both T1- and T2-weighted spin-echo images. Previous reports have not, to the authors' knowledge, described the appearance of lipomatous tumors on images obtained with a short-inversion-time inversion-recovery (STIR) sequence, which can be used to suppress signal from fat. Three lipomatous tumors (two liposarcomas and one lipoma) with signal characteristics unlike those of normal subcutaneous fat at all pulse sequences are presented.

  20. Adiabatic inversion pulses for myocardial T1-mapping

    PubMed Central

    Kellman, Peter; Herzka, Daniel A.; Hansen, Michael Schacht

    2013-01-01

    Purpose To evaluate the error in T1-estimates using inversion recovery based T1-mapping due to imperfect inversion, and perform a systematic study of adiabatic inversion pulse designs in order to maximize inversion efficiency for values of transverse relaxation (T2) in the myocardium subject to a peak power constraint. Methods The inversion factor for hyperbolic secant (HS) and tangent/hyperbolic tangent (tan/tanh) adiabatic full passage waveforms was calculated using Bloch equations. A brute force search was conducted of design parameters: pulse duration, frequency range, shape parameters, and peak amplitude. A design was selected that maximized the inversion factor over a specified range of amplitude and off-resonance and validated using phantom measurements. Empirical correction for imperfect inversion was performed. Results The tan/tanh adiabatic pulse was found to outperform HS designs, and achieve an inversion factor of 0.96 within ±150 Hz over 25% amplitude range with 14.7 μTesla peak amplitude. T1-mapping errors of the selected design due to imperfect inversion was approx. 4% and could be corrected to <1%. Conclusion Non-ideal inversion leads to significant errors in inversion recovery based T1-mapping. The inversion efficiency of adiabatic pulses is sensitive to transverse relaxation. The tan/tanh design achieved the best performance subject to the peak amplitude constraint. PMID:23722695

  1. A simplified sequence for observing deoxymyoglobin signals in vivo: myoglobin excitation with dynamic unexcitation and saturation of water and fat (MEDUSA).

    PubMed

    Noyszewski, E A; Chen, E L; Reddy, R; Wang, Z; Leigh, J S

    1997-11-01

    This paper describes a new, simplified pulse sequence for observing NMR signals from deoxymyoglobin in vivo. Paramagnetically shifted resonances from deoxymyoglobin can be exploited to noninvasively calculate intracellular oxygen tension in striated muscle. However, special sequences are required to observe these weak signals against the larger water and fat signals encountered in vivo. The pulse sequence described here, which is based on inversion recovery sequences, efficiently suppresses both water and fat resonances and can be implemented with short repetition rates. Moreover, it is perfectly suited for studies with surface coils, where RF inhomogeneities render other popular suppression sequences ineffective.

  2. Locative Inversion in Cantonese.

    ERIC Educational Resources Information Center

    Mok, Sui-Sang

    This study investigates the phenomenon of "Locative Inversion" in Cantonese. The term "Locative Inversion" indicates that the locative phrase (LP) syntactic process in Cantonese and the appears at the sentence-initial position and its logical subject occurs postverbally. It is demonstrated that this Locative Inversion is a…

  3. Recovery and characterization of a Citrus clementina Hort. ex Tan. 'Clemenules' haploid plant selected to establish the reference whole Citrus genome sequence.

    PubMed

    Aleza, Pablo; Juárez, José; Hernández, María; Pina, José A; Ollitrault, Patrick; Navarro, Luis

    2009-08-22

    In recent years, the development of structural genomics has generated a growing interest in obtaining haploid plants. The use of homozygous lines presents a significant advantage for the accomplishment of sequencing projects. Commercial citrus species are characterized by high heterozygosity, making it difficult to assemble large genome sequences. Thus, the International Citrus Genomic Consortium (ICGC) decided to establish a reference whole citrus genome sequence from a homozygous plant. Due to the existence of important molecular resources and previous success in obtaining haploid clementine plants, haploid clementine was selected as the target for the implementation of the reference whole genome citrus sequence. To obtain haploid clementine lines we used the technique of in situ gynogenesis induced by irradiated pollen. Flow cytometry, chromosome counts and SSR marker (Simple Sequence Repeats) analysis facilitated the identification of six different haploid lines (2n = x = 9), one aneuploid line (2n = 2x+4 = 22) and one doubled haploid plant (2n = 2x = 18) of 'Clemenules' clementine. One of the haploids, obtained directly from an original haploid embryo, grew vigorously and produced flowers after four years. This is the first haploid plant of clementine that has bloomed and we have, for the first time, characterized the histology of haploid and diploid flowers of clementine. Additionally a double haploid plant was obtained spontaneously from this haploid line. The first haploid plant of 'Clemenules' clementine produced directly by germination of a haploid embryo, which grew vigorously and produced flowers, has been obtained in this work. This haploid line has been selected and it is being used by the ICGC to establish the reference sequence of the nuclear genome of citrus.

  4. Reading Recovery.

    ERIC Educational Resources Information Center

    Jones, Joanna R., Ed.

    1992-01-01

    This issue of the Arizona Reading Journal focuses on the theme "reading recovery" and includes the following articles: "Why Is an Inservice Programme for Reading Recovery Teachers Necessary?" (Marie M. Clay); "What Is Reading Recovery?" (Gay Su Pinnell); "Teaching a Hard To Teach Child" (Constance A.…

  5. Reading Recovery.

    ERIC Educational Resources Information Center

    Jones, Joanna R., Ed.

    1992-01-01

    This issue of the Arizona Reading Journal focuses on the theme "reading recovery" and includes the following articles: "Why Is an Inservice Programme for Reading Recovery Teachers Necessary?" (Marie M. Clay); "What Is Reading Recovery?" (Gay Su Pinnell); "Teaching a Hard To Teach Child" (Constance A.…

  6. Three-dimensional SPACE fluid-attenuated inversion recovery at 3 T to improve subthalamic nucleus lead placement for deep brain stimulation in Parkinson's disease: from preclinical to clinical studies.

    PubMed

    Senova, Suhan; Hosomi, Koichi; Gurruchaga, Jean-Marc; Gouello, Gaëtane; Ouerchefani, Naoufel; Beaugendre, Yara; Lepetit, Hélène; Lefaucheur, Jean-Pascal; Badin, Romina Aron; Dauguet, Julien; Jan, Caroline; Hantraye, Philippe; Brugières, Pierre; Palfi, Stéphane

    2016-08-01

    OBJECTIVE Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a well-established therapy for motor symptoms in patients with pharmacoresistant Parkinson's disease (PD). However, the procedure, which requires multimodal perioperative exploration such as imaging, electrophysiology, or clinical examination during macrostimulation to secure lead positioning, remains challenging because the STN cannot be reliably visualized using the gold standard, T2-weighted imaging (T2WI) at 1.5 T. Thus, there is a need to improve imaging tools to better visualize the STN, optimize DBS lead implantation, and enlarge DBS diffusion. METHODS Gradient-echo sequences such as those used in T2WI suffer from higher distortions at higher magnetic fields than spin-echo sequences. First, a spin-echo 3D SPACE (sampling perfection with application-optimized contrasts using different flip angle evolutions) FLAIR sequence at 3 T was designed, validated histologically in 2 nonhuman primates, and applied to 10 patients with PD; their data were clinically compared in a double-blind manner with those of a control group of 10 other patients with PD in whom STN targeting was performed using T2WI. RESULTS Overlap between the nonhuman primate STNs segmented on 3D-histological and on 3D-SPACE-FLAIR volumes was high for the 3 most anterior quarters (mean [± SD] Dice scores 0.73 ± 0.11, 0.74 ± 0.06, and 0.60 ± 0.09). STN limits determined by the 3D-SPACE-FLAIR sequence were more consistent with electrophysiological edges than those determined by T2WI (0.9 vs 1.4 mm, respectively). The imaging contrast of the STN on the 3D-SPACE-FLAIR sequence was 4 times higher (p < 0.05). Improvement in the Unified Parkinson's Disease Rating Scale Part III score (off medication, on stimulation) 12 months after the operation was higher for patients who underwent 3D-SPACE-FLAIR-guided implantation than for those in whom T2WI was used (62.2% vs 43.6%, respectively; p < 0.05). The total electrical energy

  7. A "voice inversion effect?".

    PubMed

    Bédard, Catherine; Belin, Pascal

    2004-07-01

    Voice is the carrier of speech but is also an "auditory face" rich in information on the speaker's identity and affective state. Three experiments explored the possibility of a "voice inversion effect," by analogy to the classical "face inversion effect," which could support the hypothesis of a voice-specific module. Experiment 1 consisted of a gender identification task on two syllables pronounced by 90 speakers (boys, girls, men, and women). Experiment 2 consisted of a speaker discrimination task on pairs of syllables (8 men and 8 women). Experiment 3 consisted of an instrument discrimination task on pairs of melodies (8 string and 8 wind instruments). In all three experiments, stimuli were presented in 4 conditions: (1) no inversion; (2) temporal inversion (e.g., backwards speech); (3) frequency inversion centered around 4000 Hz; and (4) around 2500 Hz. Results indicated a significant decrease in performance caused by sound inversion, with a much stronger effect for frequency than for temporal inversion. Interestingly, although frequency inversion markedly affected timbre for both voices and instruments, subjects' performance was still above chance. However, performance at instrument discrimination was much higher than for voices, preventing comparison of inversion effects for voices vs. non-vocal stimuli. Additional experiments will be necessary to conclude on the existence of a possible "voice inversion effect."

  8. Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.

    PubMed

    Pan, Luyuan; Shah, Arish N; Phelps, Ian G; Doherty, Dan; Johnson, Eric A; Moens, Cecilia B

    2015-02-14

    Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive. Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified. Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.

  9. INVERSE STABLE SUBORDINATORS

    PubMed Central

    MEERSCHAERT, MARK M.; STRAKA, PETER

    2013-01-01

    The inverse stable subordinator provides a probability model for time-fractional differential equations, and leads to explicit solution formulae. This paper reviews properties of the inverse stable subordinator, and applications to a variety of problems in mathematics and physics. Several different governing equations for the inverse stable subordinator have been proposed in the literature. This paper also shows how these equations can be reconciled. PMID:25045216

  10. The Inverse of Banded Matrices

    DTIC Science & Technology

    2013-01-01

    of Br,n. For these sequences to be well-defined, we assume that none of the denominators kis are zero (which is equivalent to the below-defined U...numbers of summed or subtracted terms in computing the inverse of a term of an upper (lower) triangular matrix are the generalized order-k Fibonacci ... Fibonacci numbers are the usual Fibonacci numbers, that is, f 2m = Fm (mth Fibonacci number). When also k = 3, c1 = c2 = c3 = 1, then the generalized order-3

  11. Tiling spaces are inverse limits

    NASA Astrophysics Data System (ADS)

    Sadun, Lorenzo

    2003-11-01

    Let M be an arbitrary Riemannian homogeneous space, and let Ω be a space of tilings of M, with finite local complexity (relative to some symmetry group Γ) and closed in the natural topology. Then Ω is the inverse limit of a sequence of compact finite-dimensional branched manifolds. The branched manifolds are (finite) unions of cells, constructed from the tiles themselves and the group Γ. This result extends previous results of Anderson and Putnam, of Ormes, Radin, and Sadun, of Bellissard, Benedetti, and Gambaudo, and of Gähler. In particular, the construction in this paper is a natural generalization of Gähler's.

  12. Teaching about Inverse Functions

    ERIC Educational Resources Information Center

    Esty, Warren

    2005-01-01

    In their sections on inverses most precalculus texts emphasize an algorithm for finding f [superscript -1] given f. However, inspection of precalculus and calculus texts shows that students will never again use the algorithm, which suggests the textbook emphasis may be misplaced. Inverses appear primarily when equations need to be solved, which…

  13. A ''Voice Inversion Effect?''

    ERIC Educational Resources Information Center

    Bedard, Catherine; Belin, Pascal

    2004-01-01

    Voice is the carrier of speech but is also an ''auditory face'' rich in information on the speaker's identity and affective state. Three experiments explored the possibility of a ''voice inversion effect,'' by analogy to the classical ''face inversion effect,'' which could support the hypothesis of a voice-specific module. Experiment 1 consisted…

  14. A ''Voice Inversion Effect?''

    ERIC Educational Resources Information Center

    Bedard, Catherine; Belin, Pascal

    2004-01-01

    Voice is the carrier of speech but is also an ''auditory face'' rich in information on the speaker's identity and affective state. Three experiments explored the possibility of a ''voice inversion effect,'' by analogy to the classical ''face inversion effect,'' which could support the hypothesis of a voice-specific module. Experiment 1 consisted…

  15. Seismic Inversion Methods

    NASA Astrophysics Data System (ADS)

    Jackiewicz, Jason

    2009-09-01

    With the rapid advances in sophisticated solar modeling and the abundance of high-quality solar pulsation data, efficient and robust inversion techniques are crucial for seismic studies. We present some aspects of an efficient Fourier Optimally Localized Averaging (OLA) inversion method with an example applied to time-distance helioseismology.

  16. Seismic Inversion Methods

    SciTech Connect

    Jackiewicz, Jason

    2009-09-16

    With the rapid advances in sophisticated solar modeling and the abundance of high-quality solar pulsation data, efficient and robust inversion techniques are crucial for seismic studies. We present some aspects of an efficient Fourier Optimally Localized Averaging (OLA) inversion method with an example applied to time-distance helioseismology.

  17. Dewpoint temperature inversions analyzed

    NASA Technical Reports Server (NTRS)

    Ashby, W. C.; Bogner, M. A.; Moses, H.

    1969-01-01

    Dewpoint temperature inversion, with regard to other simultaneous meteorological conditions, was examined to establish the influence of meteorological variables on the variation of dewpoint temperature with height. This report covers instrumentation and available data, all the climatological features of dewpoint inversions, and specific special cases.

  18. Rehabilitation in a convalescent rehabilitation ward following an acute ward improves functional recovery and mortality for hip fracture patients: a sequence in a single hospital.

    PubMed

    Yoshizawa, Tomohiro; Nishino, Tomofumi; Mishima, Hajime; Ainoya, Takeshi; Yamazaki, Masashi

    2017-06-01

    [Purpose] The convalescent rehabilitation ward (CRW) plays an important role for hip fracture patients in Japanese super-aged society. The purpose of this study is to clarify the usefulness of the CRW concomitant with acute wards in a single hospital. [Subjects and Methods] 110 hip fracture patients were evaluated; 63 patients were moved from acute wards to the CRW in the same hospital (Group C) and 47 patients were treated in acute wards only (Group A). Patient selection was determined by each attending doctor. The outcomes were examined from medical records. [Results] 90.5% of patients in the group C were discharged to home and 57.4% in the group A. 92.9% of patients in the group C had regained their ambulatory ability at discharge and 88.9% in the group A. The average total functional independence measure scores at discharge were 96.4 in the group C and 85.0 in the group A. The one-year mortality was 2.4% in the group C and 8.3% in the group A. [Conclusion] Using a CRW concomitant with acute wards in a single hospital could achieve a high home-discharge rate, good functional recovery, and low mortality in hip fracture patients.

  19. Recovery Online

    ERIC Educational Resources Information Center

    Clark, John R.

    2007-01-01

    Since the founding of Alcoholics Anonymous (AA) in 1935, programs offering opportunity for recovery from alcoholism and other addictions have undergone vast changes. The Internet has created nearly limitless opportunities for recovering people and those seeking recovery to find both meetings and places where they can gather virtually and discuss…

  20. Recovery Online

    ERIC Educational Resources Information Center

    Clark, John R.

    2007-01-01

    Since the founding of Alcoholics Anonymous (AA) in 1935, programs offering opportunity for recovery from alcoholism and other addictions have undergone vast changes. The Internet has created nearly limitless opportunities for recovering people and those seeking recovery to find both meetings and places where they can gather virtually and discuss…

  1. A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses.

    PubMed

    Brooks, S A; Lear, T L; Adelson, D L; Bailey, E

    2007-01-01

    Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern.

  2. Recursive inversion of externally defined linear systems by FIR filters

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1989-01-01

    The approximate inversion of an internally unknown linear system, given by its impulse response sequence, by an inverse system having a finite impulse response, is considered. The recursive least-squares procedure is shown to have an exact initialization, based on the triangular Toeplitz structure of the matrix involved. The proposed approach also suggests solutions to the problem of system identification and compensation.

  3. Recursive inversion of externally defined linear systems by FIR filters

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1989-01-01

    The approximate inversion of an internally unknown linear system, given by its impulse response sequence, by an inverse system having a finite impulse response, is considered. The recursive least-squares procedure is shown to have an exact initialization, based on the triangular Toeplitz structure of the matrix involved. The proposed approach also suggests solutions to the problem of system identification and compensation.

  4. The inverse electroencephalography pipeline

    NASA Astrophysics Data System (ADS)

    Weinstein, David Michael

    The inverse electroencephalography (EEG) problem is defined as determining which regions of the brain are active based on remote measurements recorded with scalp EEG electrodes. An accurate solution to this problem would benefit both fundamental neuroscience research and clinical neuroscience applications. However, constructing accurate patient-specific inverse EEG solutions requires complex modeling, simulation, and visualization algorithms, and to date only a few systems have been developed that provide such capabilities. In this dissertation, a computational system for generating and investigating patient-specific inverse EEG solutions is introduced, and the requirements for each stage of this Inverse EEG Pipeline are defined and discussed. While the requirements of many of the stages are satisfied with existing algorithms, others have motivated research into novel modeling and simulation methods. The principal technical results of this work include novel surface-based volume modeling techniques, an efficient construction for the EEG lead field, and the Open Source release of the Inverse EEG Pipeline software for use by the bioelectric field research community. In this work, the Inverse EEG Pipeline is applied to three research problems in neurology: comparing focal and distributed source imaging algorithms; separating measurements into independent activation components for multifocal epilepsy; and localizing the cortical activity that produces the P300 effect in schizophrenia.

  5. Localization and characterization of X chromosome inversion breakpoints separating Drosophila mojavensis and Drosophila arizonae.

    PubMed

    Cirulli, Elizabeth T; Noor, Mohamed A F

    2007-01-01

    Ectopic exchange between transposable elements or other repetitive sequences along a chromosome can produce chromosomal inversions. As a result, genome sequence studies typically find sequence similarity between corresponding inversion breakpoint regions. Here, we identify and investigate the breakpoint regions of the X chromosome inversion distinguishing Drosophila mojavensis and Drosophila arizonae. We localize one inversion breakpoint to 13.7 kb and localize the other to a 1-Mb interval. Using this localization and assuming microsynteny between Drosophila melanogaster and D. arizonae, we pinpoint likely positions of the inversion breakpoints to windows of less than 3000 bp. These breakpoints define the size of the inversion to approximately 11 Mb. However, in contrast to many other studies, we fail to find significant sequence similarity between the 2 breakpoint regions. The localization of these inversion breakpoints will facilitate future genetic and molecular evolutionary studies in this species group, an emerging model system for ecological genetics.

  6. Dynamic inversion time for improved 3D late gadolinium enhancement imaging in patients with atrial fibrillation.

    PubMed

    Keegan, Jennifer; Gatehouse, Peter D; Haldar, Shouvik; Wage, Ricardo; Babu-Narayan, Sonya V; Firmin, David N

    2015-02-01

    High resolution three-dimensional (3D) late gadolinium enhancement (LGE) imaging is performed with single R-wave gating to minimize lengthy acquisition durations. In patients with atrial fibrillation (AF), heart rate variability results in variable magnetization recovery between sequence repeats, and image quality is often poor. In this study, we implemented and tested a dynamic inversion time (dynamic-TI) scheme designed to reduce sequence sensitivity to heart rate variations. An inversion-prepared 3D segmented gradient echo sequence was modified so that the TI varied automatically from beat-to-beat (dynamic-TI) based on the time since the last sequence repeat. 3D LGE acquisitions were performed in 17 patients prior to radio frequency ablation of persistent AF both with and without dynamic-TI. Qualitative image quality scores, blood signal-to-ghosting ratios (SGRs). and blood-myocardium contrast-to-ghosting ratios (CGRs) were compared. Image quality scores were higher with dynamic-TI than without dynamic-TI (2.2 ± 0.9 vs. 1.8 ± 1.1, P = 0.008), as were blood-myocardium CGRs (13.8 ± 7.6 vs. 8.3 ± 6.1, P = 0.003) and blood SGRs (19.6 ± 8.5 vs. 13.1 ± 8.0, P = 0.003). The dynamic-TI algorithm improves image quality of 3D LGE imaging in this difficult patient population by reducing the sequence sensitivity to RR interval variations © 2014 Wiley Periodicals, Inc.

  7. 'Inverse' temporomandibular joint dislocation.

    PubMed

    Alemán Navas, R M; Martínez Mendoza, M G

    2011-08-01

    Temporomandibular joint (TMJ) dislocation can be classified into four groups (anterior, posterior, lateral, and superior) depending on the direction of displacement and the location of the condylar head. All the groups are rare except for anterior dislocation. 'Inverse' TMJ dislocation is a bilateral anterior and superior dislocation with impaction of the mandible over the maxilla; to the authors' knowledge only two cases have previously been reported in the literature. Inverse TMJ dislocation has unique clinical and radiographic findings, which are described for this case. Copyright © 2011 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  8. Estimating nuisance parameters in inverse problems

    NASA Astrophysics Data System (ADS)

    Aravkin, Aleksandr Y.; van Leeuwen, Tristan

    2012-11-01

    Many inverse problems include nuisance parameters which, while not of direct interest, are required to recover primary parameters. The structure of these problems allows efficient optimization strategies—a well-known example is variable projection, where nonlinear least-squares problems which are linear in some parameters can be very efficiently optimized. In this paper, we extend the idea of projecting out a subset over the variables to a broad class of maximum likelihood and maximum a posteriori likelihood problems with nuisance parameters, such as variance or degrees of freedom (d.o.f.). As a result, we are able to incorporate nuisance parameter estimation into large-scale constrained and unconstrained inverse problem formulations. We apply the approach to a variety of problems, including estimation of unknown variance parameters in the Gaussian model, d.o.f. parameter estimation in the context of robust inverse problems, and automatic calibration. Using numerical examples, we demonstrate improvement in recovery of primary parameters for several large-scale inverse problems. The proposed approach is compatible with a wide variety of algorithms and formulations, and its implementation requires only minor modifications to existing algorithms.

  9. Inverse Gas Chromatography

    DTIC Science & Technology

    1990-09-01

    4 PHASE III: CHARACTERIZATION .......... .,. ........... * . 4 Task 1 . Inverse GLC of Selected Lots of R-45M ...................... 4 Task 2 ...129 Phase 1 %, Task 2 . Chain Branching ................. 136 SUMMARY AND CONCLUSIONS ... ,.........oa. * s *..... .* 136 REFERENCES...o*, *..... .*.......* . . *. . .,,. *... .. 45 33 Enthalpies of Solution -AI9s/kJ mol 1 for Listed Probe Solutes with lndicated Lots of Poly bd R

  10. Recursive Inversion Of Externally Defined Linear Systems

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1992-01-01

    Technical memorandum discusses mathematical technique described in "Recursive Inversion by Finite-Impulse-Response Filters" (ARC-12247). Technique is recursive algorithm yielding finite-impulse-response approximation of unknown single-input/single-output, causal, time-invariant, linear, real system, response of which is sequence of impulses. Useful in such diverse applications as medical diagnoses, identification of military targets, geophysical exploration, and nondestructive testing.

  11. Recursive Inversion Of Externally Defined Linear Systems

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1992-01-01

    Technical memorandum discusses mathematical technique described in "Recursive Inversion by Finite-Impulse-Response Filters" (ARC-12247). Technique is recursive algorithm yielding finite-impulse-response approximation of unknown single-input/single-output, causal, time-invariant, linear, real system, response of which is sequence of impulses. Useful in such diverse applications as medical diagnoses, identification of military targets, geophysical exploration, and nondestructive testing.

  12. Inverse heat conduction problems

    NASA Astrophysics Data System (ADS)

    Orlande, Helcio Rangel Barreto

    We present the solution of the following inverse problems: (1) Inverse Problem of Estimating Interface Conductance Between Periodically Contacting Surfaces; (2) Inverse Problem of Estimating Interface Conductance During Solidification via Conjugate Gradient Method; (3) Determination of the Reaction Function in a Reaction-Diffusion Parabolic Problem; and (4) Simultaneous Estimation of Thermal Diffusivity and Relaxation Time with Hyperbolic Heat Conduction Model. Also, we present the solution of a direct problem entitled: Transient Thermal Constriction Resistance in a Finite Heat Flux Tube. The Conjugate Gradient Method with Adjoint Equation was used in chapters 1-3. The more general function estimation approach was treated in these chapters. In chapter 1, we solve the inverse problem of estimating the timewise variation of the interface conductance between periodically contacting solids, under quasi-steady-state conditions. The present method is found to be more accurate than the B-Spline approach for situations involving small periods, which are the most difficult on which to perform the inverse analysis. In chapter 2, we estimate the timewise variation of the interface conductance between casting and mold during the solidification of aluminum. The experimental apparatus used in this study is described. In chapter 3, we present the estimation of the reaction function in a one dimensional parabolic problem. A comparison of the present function estimation approach with the parameter estimation technique, wing B-Splines to approximate the reaction function, revealed that the use of function estimation reduces the computer time requirements. In chapter 4 we present a finite difference solution for the transient constriction resistance in a cylinder of finite length with a circular contact surface. A numerical grid generation scheme was used to concentrate grid points in the regions of high temperature gradients in order to reduce discretization errors. In chapter 6, we

  13. Value of Cine-MRI sequences before and after injection in the diagnosis of acute myocarditis.

    PubMed

    Zidi, Asma; Zairi, Ihsen; Mzoughi, Khadija; Zakhama, Lilia; Kamoun, Ikram; Ben Halima, Afef; Ridene, Imen

    2016-11-01

    Cardiovascular magnetic resonance (CMR) has become the examination of choice in case of suspicion of acute myocarditis. Late gadolinium enhancement (LGE) imaging is very important to establish this diagnosis. Cine MRI sequences are useful for the study of the myocardial contractility.   The purpose is to estimate the value of cine MRI sequences before and after injection for the diagnosis of acute myocarditis compared with late gadolinium enhanced sequences. We prospectively included 40 patients having a high suspicion of acute myocarditis and examined using a 1.5 Tesla CMR. Cine MRI sequences before and after injection were performed. The protocol also include  T2-weighted  short- tau-inversion-recovery (STIR T2) fast spin echo MRI and LGE imaging eight minutes after injection with visual adjustment of inversion time. Delayed enhancement was found among 23 patients. Fifteen patients (65 %) presented a spontaneous hyper signal detected visually on Cine MRI sequences before injection and 11 patients (48 %) on STIR T2. The hyper signal on Cine MRI sequences after injection of gadolinium was the same topography that the late raising at 23 patients. In addition, we highlighted a significant difference between this hyper signal before injection and the left ventricle ejection fraction (p=0.022) as well as with the telesystolic volume of the left ventricle (LV) indexed by the body mass (p=0.039). Our study suggests that Cine MRI sequences after injection are of equal performance in the diagnosis of acute myocarditis as the LGE sequences and its contibution is important when we want to shorten the examination or when inversion time isn't optimal.

  14. Multichannel sparse spike inversion

    NASA Astrophysics Data System (ADS)

    Pereg, Deborah; Cohen, Israel; Vassiliou, Anthony A.

    2017-10-01

    In this paper, we address the problem of sparse multichannel seismic deconvolution. We introduce multichannel sparse spike inversion as an iterative procedure, which deconvolves the seismic data and recovers the Earth two-dimensional reflectivity image, while taking into consideration the relations between spatially neighboring traces. We demonstrate the improved performance of the proposed algorithm and its robustness to noise, compared to competitive single-channel algorithm through simulations and real seismic data examples.

  15. Intersections, ideals, and inversion

    SciTech Connect

    Vasco, D.W.

    1998-10-01

    Techniques from computational algebra provide a framework for treating large classes of inverse problems. In particular, the discretization of many types of integral equations and of partial differential equations with undetermined coefficients lead to systems of polynomial equations. The structure of the solution set of such equations may be examined using algebraic techniques.. For example, the existence and dimensionality of the solution set may be determined. Furthermore, it is possible to bound the total number of solutions. The approach is illustrated by a numerical application to the inverse problem associated with the Helmholtz equation. The algebraic methods are used in the inversion of a set of transverse electric (TE) mode magnetotelluric data from Antarctica. The existence of solutions is demonstrated and the number of solutions is found to be finite, bounded from above at 50. The best fitting structure is dominantly onedimensional with a low crustal resistivity of about 2 ohm-m. Such a low value is compatible with studies suggesting lower surface wave velocities than found in typical stable cratons.

  16. [Total inversion of the uterus].

    PubMed

    Novachkov, V; Baltadzhieva, B; Ilieva, A; Rachev, E

    2008-01-01

    Non puerperal inversion of the uterus is very uncommon. Patients may present with pelvic pain, vaginal bleeding or hemodynamic shock. We report a fifty five old woman with uterus inversion second stage.

  17. Inverse Functions and their Derivatives.

    ERIC Educational Resources Information Center

    Snapper, Ernst

    1990-01-01

    Presented is a method of interchanging the x-axis and y-axis for viewing the graph of the inverse function. Discussed are the inverse function and the usual proofs that are used for the function. (KR)

  18. [Serial T2 short inversion time inversion recovery images in a patient with medullary hemorrhage].

    PubMed

    Okada, Yoko; Shibazaki, Kensaku; Iguchi, Yasuyuki; Inoue, Takeshi; Kimura, Kazumi

    2007-08-01

    A 52-year-old man was admitted to our hospital because of hypesthesia on the right side of his body. He had no medical history. On admission, he exhibited hypesthesia and disturbance of the touch and the vibratory sense on the right side of his body excluding the face. A brain T2* -weighted image revealed the a dot like lesion surrounded by an iso-signal lesion in the medial medulla oblongata. Therefore a diagnosis of medullary hemorrhage was made. Although a vascular malformation was considered as the cause of the hemorrhage, cerebral angiography did not reveal any vascular malformations. After admission, he developed left hypoglossal nerve palsy on day 6, and intractable hiccups on day 11. A T2* -weighted image and a FLAIR image disclosed edema surrounding the hematoma in the medial medullary lesion. T2* weighted images are useful for diagnosing and evaluating serial changes of medullary hemorrhage.

  19. Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

    PubMed Central

    Corbett-Detig, Russell B.; Hartl, Daniel L.

    2012-01-01

    Chromosomal inversions have been an enduring interest of population geneticists since their discovery in Drosophila melanogaster. Numerous lines of evidence suggest powerful selective pressures govern the distributions of polymorphic inversions, and these observations have spurred the development of many explanatory models. However, due to a paucity of nucleotide data, little progress has been made towards investigating selective hypotheses or towards inferring the genealogical histories of inversions, which can inform models of inversion evolution and suggest selective mechanisms. Here, we utilize population genomic data to address persisting gaps in our knowledge of D. melanogaster's inversions. We develop a method, termed Reference-Assisted Reassembly, to assemble unbiased, highly accurate sequences near inversion breakpoints, which we use to estimate the age and the geographic origins of polymorphic inversions. We find that inversions are young, and most are African in origin, which is consistent with the demography of the species. The data suggest that inversions interact with polymorphism not only in breakpoint regions but also chromosome-wide. Inversions remain differentiated at low levels from standard haplotypes even in regions that are distant from breakpoints. Although genetic exchange appears fairly extensive, we identify numerous regions that are qualitatively consistent with selective hypotheses. Finally, we show that In(1)Be, which we estimate to be ∼60 years old (95% CI 5.9 to 372.8 years), has likely achieved high frequency via sex-ratio segregation distortion in males. With deeper sampling, it will be possible to build on our inferences of inversion histories to rigorously test selective models—particularly those that postulate that inversions achieve a selective advantage through the maintenance of co-adapted allele complexes. PMID:23284285

  20. Inverse nodal problems

    NASA Astrophysics Data System (ADS)

    Klawonn, David

    2009-05-01

    It is shown that nodal sequences determine the underlying manifold up to scaling within classes of rectangles with Dirichlet boundary conditions, separable two-dimensional tori, two-dimensional flat Klein bottles and flat tori in two and three dimensions.

  1. Course of Recovery from Alcoholism

    PubMed Central

    Venner, Kamilla L.; Matzger, Helen; Forcehimes, Alyssa A.; Moos, Rudolf H.; Feldstein, Sarah W.; Willenbring, Mark L.; Weisner, Constance

    2010-01-01

    This article represents the proceedings of a symposium at the 2005 Research Society on Alcoholism meeting in Santa Barbara, California, organized and chaired by Kamilla L. Venner. This symposium integrated current empirical research on the course of recovery from alcoholism from multiple perspectives, an aim that is consistent with NIAAA's new focus on the process of recovery. The presentations and presenters were as follows: (1) The Role of Community Services and Informal Support on 7-Year Drinking Outcomes in Treated and Untreated Drinkers, by Helen Matzger; (2) The Sequence of Recovery Events in a Native American Sample, by Kamilla L. Venner; (3) Transformational Change in Recovery, by Alyssa A. Forcehimes; (4) Social Settings and Substance Use: Contextual Factors in Recovery, by Rudolf H. Moos; and (5) A Broader View of Change in Drinking Behavior, by discussant Mark L. Willenbring. A theme connecting the presentations was that treatment is but one discrete aspect to recovery and that sustained recovery is often influenced by an individual interaction with others within a social context. Collectively, presentations underscored the need to think more broadly about factors contributing to the remission of alcohol dependence. PMID:16737468

  2. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  3. Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256’s Spread, and Evolution of Russia ST8-IV

    PubMed Central

    Wan, Tsai-Wen; Higuchi, Wataru; Hung, Wei-Chun; Reva, Ivan V.; Singur, Olga A.; Gostev, Vladimir V.; Sidorenko, Sergey V.; Peryanova, Olga V.; Salmina, Alla B.; Reva, Galina V.; Teng, Lee-Jene; Yamamoto, Tatsuo

    2016-01-01

    ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256’s strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages. PMID:27741255

  4. Comparison of pulse sequences for R1-based electron paramagnetic resonance oxygen imaging

    NASA Astrophysics Data System (ADS)

    Epel, Boris; Halpern, Howard J.

    2015-05-01

    Electron paramagnetic resonance (EPR) spin-lattice relaxation (SLR) oxygen imaging has proven to be an indispensable tool for assessing oxygen partial pressure in live animals. EPR oxygen images show remarkable oxygen accuracy when combined with high precision and spatial resolution. Developing more effective means for obtaining SLR rates is of great practical, biological and medical importance. In this work we compared different pulse EPR imaging protocols and pulse sequences to establish advantages and areas of applicability for each method. Tests were performed using phantoms containing spin probes with oxygen concentrations relevant to in vivo oxymetry. We have found that for small animal size objects the inversion recovery sequence combined with the filtered backprojection reconstruction method delivers the best accuracy and precision. For large animals, in which large radio frequency energy deposition might be critical, free induction decay and three pulse stimulated echo sequences might find better practical usage.

  5. Optimization based inversion method for the inverse heat conduction problems

    NASA Astrophysics Data System (ADS)

    Mu, Huaiping; Li, Jingtao; Wang, Xueyao; Liu, Shi

    2017-05-01

    Precise estimation of the thermal physical properties of materials, boundary conditions, heat flux distributions, heat sources and initial conditions is highly desired for real-world applications. The inverse heat conduction problem (IHCP) analysis method provides an alternative approach for acquiring such parameters. The effectiveness of the inversion algorithm plays an important role in practical applications of the IHCP method. Different from traditional inversion models, in this paper a new inversion model that simultaneously highlights the measurement errors and the inaccurate properties of the forward problem is proposed to improve the inversion accuracy and robustness. A generalized cost function is constructed to convert the original IHCP into an optimization problem. An iterative scheme that splits a complicated optimization problem into several simpler sub-problems and integrates the superiorities of the alternative optimization method and the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm is developed for solving the proposed cost function. Numerical experiment results validate the effectiveness of the proposed inversion method.

  6. Widespread occurrence of small inversions in the chloroplast genomes of land plants.

    PubMed

    Kim, Ki-Joong; Lee, Hae-Lim

    2005-02-28

    Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

  7. Multiresolution MR elastography using nonlinear inversion

    PubMed Central

    McGarry, M. D. J.; Van Houten, E. E. W.; Johnson, C. L.; Georgiadis, J. G.; Sutton, B. P.; Weaver, J. B.; Paulsen, K. D.

    2012-01-01

    Purpose: Nonlinear inversion (NLI) in MR elastography requires discretization of the displacement field for a finite element (FE) solution of the “forward problem”, and discretization of the unknown mechanical property field for the iterative solution of the “inverse problem”. The resolution requirements for these two discretizations are different: the forward problem requires sufficient resolution of the displacement FE mesh to ensure convergence, whereas lowering the mechanical property resolution in the inverse problem stabilizes the mechanical property estimates in the presence of measurement noise. Previous NLI implementations use the same FE mesh to support the displacement and property fields, requiring a trade-off between the competing resolution requirements. Methods: This work implements and evaluates multiresolution FE meshes for NLI elastography, allowing independent discretizations of the displacements and each mechanical property parameter to be estimated. The displacement resolution can then be selected to ensure mesh convergence, and the resolution of the property meshes can be independently manipulated to control the stability of the inversion. Results: Phantom experiments indicate that eight nodes per wavelength (NPW) are sufficient for accurate mechanical property recovery, whereas mechanical property estimation from 50 Hz in vivo brain data stabilizes once the displacement resolution reaches 1.7 mm (approximately 19 NPW). Viscoelastic mechanical property estimates of in vivo brain tissue show that subsampling the loss modulus while holding the storage modulus resolution constant does not substantially alter the storage modulus images. Controlling the ratio of the number of measurements to unknown mechanical properties by subsampling the mechanical property distributions (relative to the data resolution) improves the repeatability of the property estimates, at a cost of modestly decreased spatial resolution. Conclusions: Multiresolution

  8. A passive inverse filter for Green's function retrieval.

    PubMed

    Gallot, Thomas; Catheline, Stefan; Roux, Philippe; Campillo, Michel

    2012-01-01

    Passive methods for the recovery of Green's functions from ambient noise require strong hypotheses, including isotropic distribution of the noise sources. Very often, this distribution is nonisotropic, which introduces bias in the Green's function reconstruction. To minimize this bias, a spatiotemporal inverse filter is proposed. The method is tested on a directive noise field computed from an experimental active seismic data set. The results indicate that the passive inverse filter allows the manipulation of the spatiotemporal degrees of freedom of a complex wave field, and it can efficiently compensate for the noise wavefield directivity.

  9. Inverse PCR for Point Mutation Introduction.

    PubMed

    Silva, Diogo; Santos, Gustavo; Barroca, Mário; Collins, Tony

    2017-01-01

    Inverse PCR is a powerful tool for the rapid introduction of desired mutations at desired positions in a circular double-stranded DNA sequence. Here, custom-designed mutant primers oriented in the inverse direction are used to amplify the entire circular template with incorporation of the required mutation(s). By careful primer design it can be used to perform such diverse modifications as the introduction of point mutations and multiple mutations, the insertion of new sequences, and even sequence deletions. Three primer formats are commonly used; nonoverlapping, partially overlapping and fully overlapping primers, and here we describe the use of nonoverlapping primers for introduction of a point mutation. Use of such a primer setup in the PCR reaction, with one of the primers containing the desired mismatch mutation, results in the amplification of a linear, double-stranded, mutated product. Methylated template DNA is removed from the nonmethylated PCR product by DpnI digestion and the PCR product is then phosphorylated by polynucleotide kinase treatment before being recircularized by ligation, and transformed to E. coli. This relatively simple site-directed mutagenesis procedure is of major importance in biology and biotechnology today where it is commonly employed for the study and engineering of DNA, RNA, and proteins.

  10. Inverse plasma equilibria

    SciTech Connect

    Hicks, H.R.; Dory, R.A.; Holmes, J.A.

    1983-01-01

    We illustrate in some detail a 2D inverse-equilibrium solver that was constructed to analyze tokamak configurations and stellarators (the latter in the context of the average method). To ensure that the method is suitable not only to determine equilibria, but also to provide appropriately represented data for existing stability codes, it is important to be able to control the Jacobian, tilde J is identical to delta(R,Z)/delta(rho, theta). The form chosen is tilde J = J/sub 0/(rho)R/sup l/rho where rho is a flux surface label, and l is an integer. The initial implementation is for a fixed conducting-wall boundary, but the technique can be extended to a free-boundary model.

  11. Asteroid lightcurve inversion

    NASA Technical Reports Server (NTRS)

    Ostro, Steven J.; Connelly, Robert

    1987-01-01

    One of the most fundamental physical properties of any asteroid is its shape. Lightcurves provide the only source of shape information for most asteroids. Unfortunately, the functional form of a lightcurve is determined by the viewing/illumination geometry and the asteroid's light scattering characteristics as well as its shape, and in general it is impossible to determine an asteroid's shape from lightcurves. A technique called convex-profile inversion (CPI) that obtains a convex profile, P, from any lightcurve is introduced. If certain ideal conditions are satisfied, then P is an estimator for the asteroid's mean cross section, C, a convex set defined as the average of all cross sections C(z) cut by planes a distance z above the asteroids's equatorial plane. C is therefore a 2-D average of the asteroid's 3-D shape.

  12. Inverse Compton for Compton

    NASA Astrophysics Data System (ADS)

    Suortti, Pekka

    2016-04-01

    A novel concept for a high resolution Compton spectrometer is introduced. 88 keV radiation from an Inverse Compton Compact Source is focused using crossed cylindrically bent Laue-type Si perfect crystals, and dispersed on the sample with a constant energy gradient. Dispersion is compensated exactly at a Ge crystal analyzer, so that the same wavelength shift is observed for all wavelengths of the incident beam. The ThomX source is used as a concrete example. Detailed dimensions and flux estimates at successive locations of the spectrometer are given, and the performance is compared with the dispersion compensating spectrometer at ID15 of the ESRF. The momentum resolution is better than 0.1 atomic units in both cases. The intensity of scattering with the compact source is an order of magnitude smaller, but still adequate for high resolution Compton profile measurements.

  13. Inverse magnetorheological fluids.

    PubMed

    Rodríguez-Arco, L; López-López, M T; Zubarev, A Y; Gdula, K; Durán, J D G

    2014-09-07

    We report a new kind of field-responsive fluid consisting of suspensions of diamagnetic (DM) and ferromagnetic (FM) microparticles in ferrofluids. We designate them as inverse magnetorheological (IMR) fluids for analogy with inverse ferrofluids (IFFs). Observations on the particle self-assembly in IMR fluids upon magnetic field application showed that DM and FM microparticles were assembled into alternating chains oriented along the field direction. We explain such assembly on the basis of the dipolar interaction energy between particles. We also present results on the rheological properties of IMR fluids and, for comparison, those of IFFs and bidispersed magnetorheological (MR) fluids. Interestingly, we found that upon magnetic field application, the rheological properties of IMR fluids were enhanced with respect to bidispersed MR fluids with the same FM particle concentration, by an amount greater than the sum of the isolated contribution of DM particles. Furthermore, the field-induced yield stress was moderately increased when up to 30% of the total FM particle content was replaced with DM particles. Beyond this point, the dependence of the yield stress on the DM content was non-monotonic, as expected for FM concentrations decreasing to zero. We explain these synergistic results by two separate phenomena: the formation of exclusion areas for FM particles due to the perturbation of the magnetic field by DM particles and the dipole-dipole interaction between DM and FM particles, which enhances the field-induced structures. Based on the second phenomenon, we present a theoretical model for the yield stress that semi-quantitatively predicts the experimental results.

  14. Birth and death of genes linked to chromosomal inversion

    PubMed Central

    Furuta, Yoshikazu; Kawai, Mikihiko; Yahara, Koji; Takahashi, Noriko; Handa, Naofumi; Tsuru, Takeshi; Oshima, Kenshiro; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo

    2011-01-01

    The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization. Helicobacter pylori, bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells. PMID:21212362

  15. Wavelet Sparse Approximate Inverse Preconditioners

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.; Tang, W.-P.; Wan, W. L.

    1996-01-01

    There is an increasing interest in using sparse approximate inverses as preconditioners for Krylov subspace iterative methods. Recent studies of Grote and Huckle and Chow and Saad also show that sparse approximate inverse preconditioner can be effective for a variety of matrices, e.g. Harwell-Boeing collections. Nonetheless a drawback is that it requires rapid decay of the inverse entries so that sparse approximate inverse is possible. However, for the class of matrices that, come from elliptic PDE problems, this assumption may not necessarily hold. Our main idea is to look for a basis, other than the standard one, such that a sparse representation of the inverse is feasible. A crucial observation is that the kind of matrices we are interested in typically have a piecewise smooth inverse. We exploit this fact, by applying wavelet techniques to construct a better sparse approximate inverse in the wavelet basis. We shall justify theoretically and numerically that our approach is effective for matrices with smooth inverse. We emphasize that in this paper we have only presented the idea of wavelet approximate inverses and demonstrated its potential but have not yet developed a highly refined and efficient algorithm.

  16. Disaster Debris Recovery Database - Recovery

    EPA Pesticide Factsheets

    The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 6,000 composting facilities, demolition contractors, transfer stations, landfills and recycling facilities for construction and demolition materials, electronics, household hazardous waste, metals, tires, and vehicles in the states of Illinois, Indiana, Iowa, Kentucky, Michigan, Minnesota, Missouri, North Dakota, Ohio, Pennsylvania, South Dakota, West Virginia and Wisconsin.In this update, facilities in the 7 states that border the EPA Region 5 states were added to assist interstate disaster debris management. Also, the datasets for composters, construction and demolition recyclers, demolition contractors, and metals recyclers were verified and source information added for each record using these sources: AGC, Biocycle, BMRA, CDRA, ISRI, NDA, USCC, FEMA Debris Removal Contractor Registry, EPA Facility Registry System, and State and local listings.

  17. Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis

    PubMed Central

    Ma, Jianzhong; Amos, Christopher I.

    2012-01-01

    Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1∶1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases. PMID:22808122

  18. Investigation of inversion polymorphisms in the human genome using principal components analysis.

    PubMed

    Ma, Jianzhong; Amos, Christopher I

    2012-01-01

    Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct "populations" of inversion homozygotes of different orientations and their 1:1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.

  19. Genomic Sequencing in Cancer

    PubMed Central

    Tuna, Musaffe; Amos, Christopher I.

    2013-01-01

    Genomic sequencing has provided critical insights into the etiology of both simple and complex diseases. The enormous reductions in cost for whole genome sequencing have allowed this technology to gain increasing use. Whole genome analysis has impacted research of complex diseases including cancer by allowing the systematic analysis of entire genomes in a single experiment, thereby facilitating the discovery of somatic and germline mutations, and identification of the function and impact of the insertions, deletions, and structural rearrangements, including translocations and inversions, in novel disease genes. Whole-genome sequencing can be used to provide the most comprehensive characterization of the cancer genome, the complexity of which we are only beginning to understand. Hence in this review, we focus on whole-genome sequencing in cancer. PMID:23178448

  20. Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

    PubMed Central

    Lee, Jungnam; Han, Kyudong; Meyer, Thomas J.; Kim, Heui-Soo; Batzer, Mark A.

    2008-01-01

    The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution. PMID:19112500

  1. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons.

    PubMed

    Lee, Jungnam; Han, Kyudong; Meyer, Thomas J; Kim, Heui-Soo; Batzer, Mark A

    2008-01-01

    The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution.

  2. Accuracy, Precision, and Reproducibility of Four T1 Mapping Sequences: A Head-to-Head Comparison of MOLLI, ShMOLLI, SASHA, and SAPPHIRE

    PubMed Central

    Roujol, Sébastien; Weingärtner, Sebastian; Foppa, Murilo; Chow, Kelvin; Kawaji, Keigo; Ngo, Long H.; Kellman, Peter; Manning, Warren J.; Thompson, Richard B.

    2014-01-01

    Purpose To compare accuracy, precision, and reproducibility of four commonly used myocardial T1 mapping sequences: modified Look-Locker inversion recovery (MOLLI), shortened MOLLI (ShMOLLI), saturation recovery single-shot acquisition (SASHA), and saturation pulse prepared heart rate independent inversion recovery (SAPPHIRE). Materials and Methods This HIPAA-compliant study was approved by the institutional review board. All subjects provided written informed consent. Accuracy, precision, and reproducibility of the four T1 mapping sequences were first compared in phantom experiments. In vivo analysis was performed in seven healthy subjects (mean age ± standard deviation, 38 years ± 19; four men, three women) who were imaged twice on two separate days. In vivo reproducibility of native T1 mapping and extracellular volume (ECV) were measured. Differences between the sequences were assessed by using Kruskal-Wallis and Wilcoxon rank sum tests (phantom data) and mixed-effect models (in vivo data). Results T1 mapping accuracy in phantoms was lower with ShMOLLI (62 msec) and MOLLI (44 msec) than with SASHA (13 msec; P < .05) and SAPPHIRE (12 msec; P < .05). MOLLI had similar precision to ShMOLLI (4.0 msec vs 5.6 msec; P = .07) but higher precision than SAPPHIRE (6.8 msec; P = .002) and SASHA (8.7 msec; P < .001). All sequences had similar reproducibility in phantoms (P = .1). The four sequences had similar in vivo reproducibility for native T1 mapping (∼25–50 msec; P > .05) and ECV quantification (∼0.01–0.02; P > .05). Conclusion SASHA and SAPPHIRE yield higher accuracy, lower precision, and similar reproducibility compared with MOLLI and ShMOLLI for T1 measurement. Different sequences yield different ECV values; however, all sequences have similar reproducibility for ECV quantification. © RSNA, 2014 Online supplemental material is available for this article. PMID:24702727

  3. Inverse problem in hydrogeology

    NASA Astrophysics Data System (ADS)

    Carrera, Jesús; Alcolea, Andrés; Medina, Agustín; Hidalgo, Juan; Slooten, Luit J.

    2005-03-01

    The state of the groundwater inverse problem is synthesized. Emphasis is placed on aquifer characterization, where modelers have to deal with conceptual model uncertainty (notably spatial and temporal variability), scale dependence, many types of unknown parameters (transmissivity, recharge, boundary conditions, etc.), nonlinearity, and often low sensitivity of state variables (typically heads and concentrations) to aquifer properties. Because of these difficulties, calibration cannot be separated from the modeling process, as it is sometimes done in other fields. Instead, it should be viewed as one step in the process of understanding aquifer behavior. In fact, it is shown that actual parameter estimation methods do not differ from each other in the essence, though they may differ in the computational details. It is argued that there is ample room for improvement in groundwater inversion: development of user-friendly codes, accommodation of variability through geostatistics, incorporation of geological information and different types of data (temperature, occurrence and concentration of isotopes, age, etc.), proper accounting of uncertainty, etc. Despite this, even with existing codes, automatic calibration facilitates enormously the task of modeling. Therefore, it is contended that its use should become standard practice. L'état du problème inverse des eaux souterraines est synthétisé. L'accent est placé sur la caractérisation de l'aquifère, où les modélisateurs doivent jouer avec l'incertitude des modèles conceptuels (notamment la variabilité spatiale et temporelle), les facteurs d'échelle, plusieurs inconnues sur différents paramètres (transmissivité, recharge, conditions aux limites, etc.), la non linéarité, et souvent la sensibilité de plusieurs variables d'état (charges hydrauliques, concentrations) des propriétés de l'aquifère. A cause de ces difficultés, le calibrage ne peut êtreséparé du processus de modélisation, comme c'est le

  4. Modular theory of inverse systems

    NASA Technical Reports Server (NTRS)

    1979-01-01

    The relationship between multivariable zeros and inverse systems was explored. A definition of zero module is given in such a way that it is basis independent. The existence of essential right and left inverses were established. The way in which the abstract zero module captured previous definitions of multivariable zeros is explained and examples are presented.

  5. Inversion exercises inspired by mechanics

    NASA Astrophysics Data System (ADS)

    Groetsch, C. W.

    2016-02-01

    An elementary calculus transform, inspired by the centroid and gyration radius, is introduced as a prelude to the study of more advanced transforms. Analysis of the transform, including its inversion, makes use of several key concepts from basic calculus and exercises in the application and inversion of the transform provide practice in the use of technology in calculus.

  6. DNA Inversions between Short Inverted Repeats in Escherichia Coli

    PubMed Central

    Schofield, M. A.; Agbunag, R.; Miller, J. H.

    1992-01-01

    Using site-specific mutagenesis in vitro, we have constructed Escherichia coli strains that allow the detection of the inversion of an 800-bp segment in the lac region. The invertible segment is bounded by inverted repeats of either 12 or 23 bp. Inversions occurring at these inverted repeats will restore the Lac(+) phenotype. Inversions can be detected at both short homologies at frequencies ranging from 0.5 X 10(-8) to 1 X 10(-7). These events, which have been verified by DNA sequence analysis, are reduced up to 1000-fold in strains deficient for either RecA, RecB or RecC. They are not reduced in strains deficient in the RecF,J pathway. These results show that the RecB,C,D system can mediate rearrangements at short sequence repeats, and probably plays a major role in cellular rearrangements. PMID:1427029

  7. Recovery position - series (image)

    MedlinePlus

    ... CPR, the victim should be placed in the recovery position. The recovery position helps keep the victim's airway open. To put the victim in the recovery position grab the victim's leg and shoulder and ...

  8. Recursive Inversion By Finite-Impulse-Response Filters

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1991-01-01

    Recursive approximation gives least-squares best fit to exact response. Algorithm yields finite-impulse-response approximation of unknown single-input/single-output, causal, time-invariant, linear, real system, response of which is sequence of impulses. Applicable to such system-inversion problems as suppression of echoes and identification of target from its scatter response to incident impulse.

  9. Recursive Inversion By Finite-Impulse-Response Filters

    NASA Technical Reports Server (NTRS)

    Bach, Ralph E., Jr.; Baram, Yoram

    1991-01-01

    Recursive approximation gives least-squares best fit to exact response. Algorithm yields finite-impulse-response approximation of unknown single-input/single-output, causal, time-invariant, linear, real system, response of which is sequence of impulses. Applicable to such system-inversion problems as suppression of echoes and identification of target from its scatter response to incident impulse.

  10. Effects of inversion and saturation times on relationships between contrast agent concentrations and signal intensities of T1-weighted magnetic resonance images.

    PubMed

    Nazarpoor, Mahmood

    2010-07-01

    The present study was an attempt to investigate the effect of variation of inversion time (T (I)) and saturation time (T (S)) on the linear relationship between contrast agent concentration and signal intensity (SI) on Turbo Fast Low Angle Shot (TurboFLASH) T (1)-weighted images in MRI. For this purpose, inversion recovery (IR) and saturation recovery (SR) sequences (Center out Phase-Encoding acquisition) were used. A phantom was designed to hold 25 vials which contained either different (between 0 and 19.77 mmol/L) or constant (1.20 mmol/L) concentrations of contrast agent. The vials of constant concentration were used for the measurement of coil non-uniformity, which was normalized to give a correction factor. The vials of different concentrations were used to measure the SI by using different sequences and different T (I) and T (S) values. To calculate the corrected SI for different concentrations, we multiplied the SI of each vial by its correction factor. The relationships between the corrected SI and the concentration [were evaluated], where the threshold of (R (2) = 0.95 and 0.99) was maintained. This study shows that different sequences and different T (I) and T (S) values can have an effect on the correlation between the SI and concentration. Regardless of the values of T (I), T (S), and the different IR and SR sequences chosen, the linear relationship between the SI and concentration was about twice that previously reported (i.e., 0.8 mmol/L, R (2) = 0.95).

  11. Creep and inverse stress relaxation behaviors of carbon nanotube yarns.

    PubMed

    Misak, H E; Sabelkin, V; Miller, L; Asmatulu, R; Mall, S

    2013-12-01

    Creep, creep recovery and inverse stress relaxation behaviors of carbon nanotube yarns that consisted of 1-, 30-, and 100-yarn(s) were characterized. Primary and secondary creep stages were observed over the duration of 336 h. The primary creep stage lasted for about 4 h at an applied load equal to 75% of the ultimate tensile strength. The total strain in the primary stage was significantly larger in the carbon nanotube multi-yarn than in the carbon nanotube 1-yarn. In the secondary stage, 1-yarn also had a smaller steady state strain rate than the multi-yarn, and it was independent of number of yarns in multi-yarn. Strain response under cyclic creep loading condition was comparable to its counterpart in non-cyclic (i.e., standard) creep test except that strain response during the first cycle was slightly different from the subsequent cycles. Inverse creep (i.e., strain recovery) was observed in the 100-yarn during the cyclic creep tests after the first unloading cycle. Furthermore, inverse stress relaxation of the multi-yarns was characterized. Inverse stress relaxation was larger and for longer duration with the larger number of yarns.

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

    PubMed Central

    Bidar, Fatemeh; Faeghi, Fariborz; Ghorbani, Askar

    2016-01-01

    Background: The purpose of this study is to demonstrate the advantages of gradient echo (GRE) sequences in the detection and characterization of cerebral venous sinus thrombosis compared to conventional magnetic resonance sequences. Methods: A total of 17 patients with cerebral venous thrombosis (CVT) were evaluated using different magnetic resonance imaging (MRI) sequences. The MRI sequences included T1-weighted spin echo (SE) imaging, T*2-weighted turbo SE (TSE), fluid attenuated inversion recovery (FLAIR), T*2-weighted conventional GRE, and diffusion weighted imaging (DWI). MR venography (MRV) images were obtained as the golden standard. Results: Venous sinus thrombosis was best detectable in T*2-weighted conventional GRE sequences in all patients except in one case. Venous thrombosis was undetectable in DWI. T*2-weighted GRE sequences were superior to T*2-weighted TSE, T1-weighted SE, and FLAIR. Enhanced MRV was successful in displaying the location of thrombosis. Conclusion: T*2-weighted conventional GRE sequences are probably the best method for the assessment of cerebral venous sinus thrombosis. The mentioned method is non-invasive; therefore, it can be employed in the clinical evaluation of cerebral venous sinus thrombosis. PMID:27326365

  13. Time-Lapse Joint Inversion of Cross-Well DC Resistivity and Seismic Data: A Numerical Investigation

    EPA Science Inventory

    Time-lapse joint inversion of geophysical data is required to image the evolution of oil reservoirs during production and enhanced oil recovery, CO2 sequestration, geothermal fields during production, and to monitor the evolution of contaminant plumes. Joint inversion schemes red...

  14. Time-Lapse Joint Inversion of Cross-Well DC Resistivity and Seismic Data: A Numerical Investigation

    EPA Science Inventory

    Time-lapse joint inversion of geophysical data is required to image the evolution of oil reservoirs during production and enhanced oil recovery, CO2 sequestration, geothermal fields during production, and to monitor the evolution of contaminant plumes. Joint inversion schemes red...

  15. The body-inversion effect.

    PubMed

    Reed, Catherine L; Stone, Valerie E; Bozova, Senia; Tanaka, James

    2003-07-01

    Researchers argue that faces are recognized via the configuration of their parts. An important behavioral finding supporting this claim is the face-inversion effect, in which inversion impairs recognition of faces more than nonface objects. Until recently, faces were the only class of objects producing the inversion effect for untrained individuals. This study investigated whether the inversion effect extends to human body positions, a class of objects whose exemplars are structurally similar to each other. Three experiments compared the recognition of upright and inverted faces, houses, and body positions using a forced-choice, same/different paradigm. For both reaction time and error data, the recognition of possible human body postures was more affected by inversion than the recognition of houses. Further, the recognition of possible human body postures and recognition of faces showed similar effects of inversion. The inversion effect was diminished for impossible body positions that violated the biomechanical constraints of human bodies. These data suggest that human body positions, like faces, may be processed configurally by untrained viewers.

  16. Localized recovery of complex networks against failure

    NASA Astrophysics Data System (ADS)

    Shang, Yilun

    2016-07-01

    Resilience of complex networks to failure has been an important issue in network research for decades, and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood, and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks, and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the “complement network” of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems.

  17. Localized recovery of complex networks against failure

    PubMed Central

    Shang, Yilun

    2016-01-01

    Resilience of complex networks to failure has been an important issue in network research for decades, and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood, and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks, and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the “complement network” of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems. PMID:27456202

  18. A Generalization of the Spherical Inversion

    ERIC Educational Resources Information Center

    Ramírez, José L.; Rubiano, Gustavo N.

    2017-01-01

    In the present article, we introduce a generalization of the spherical inversion. In particular, we define an inversion with respect to an ellipsoid, and prove several properties of this new transformation. The inversion in an ellipsoid is the generalization of the elliptic inversion to the three-dimensional space. We also study the inverse images…

  19. A Generalization of the Spherical Inversion

    ERIC Educational Resources Information Center

    Ramírez, José L.; Rubiano, Gustavo N.

    2017-01-01

    In the present article, we introduce a generalization of the spherical inversion. In particular, we define an inversion with respect to an ellipsoid, and prove several properties of this new transformation. The inversion in an ellipsoid is the generalization of the elliptic inversion to the three-dimensional space. We also study the inverse images…

  20. Improvements in Earthquake Location from Joint Inversion of Seismic and Gravity Observations – Application to the Iran Region

    SciTech Connect

    Syracuse, Ellen Marie; Maceira, Monica; Phillips, William Scott; Begnaud, Michael Lee; Nippress, Stuart; Bergman, Eric; Zhang, Haijiang

    2016-07-19

    These are slides which show many graphs and datasets for the above-mentioned topic and then concludes with the following: Joint inversion of multiple geophysical datasets improves recovery of velocity structures, particularly in Vs and in shallow parts of the model, in comparison to travel-time only models. Resulting fits to travel time data are minimally degraded by joint inversions. Correspondingly, fits to independent estimates of ground-truth locations are minimally affected by joint inversions.

  1. Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

    PubMed

    Freyhult, Eva; Moulton, Vincent; Ardell, David H

    2006-01-01

    Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure-function relationships in sequence families and superfamilies.

  2. Fair and Square Computation of Inverse "Z"-Transforms of Rational Functions

    ERIC Educational Resources Information Center

    Moreira, M. V.; Basilio, J. C.

    2012-01-01

    All methods presented in textbooks for computing inverse "Z"-transforms of rational functions have some limitation: 1) the direct division method does not, in general, provide enough information to derive an analytical expression for the time-domain sequence "x"("k") whose "Z"-transform is "X"("z"); 2) computation using the inversion integral…

  3. Fair and Square Computation of Inverse "Z"-Transforms of Rational Functions

    ERIC Educational Resources Information Center

    Moreira, M. V.; Basilio, J. C.

    2012-01-01

    All methods presented in textbooks for computing inverse "Z"-transforms of rational functions have some limitation: 1) the direct division method does not, in general, provide enough information to derive an analytical expression for the time-domain sequence "x"("k") whose "Z"-transform is "X"("z"); 2) computation using the inversion integral…

  4. Inverse problems in mathematical physics

    NASA Astrophysics Data System (ADS)

    Glasko, V. B.

    Procedures for the correct formulation and solution of inverse problems, which usually belong to the class of ill-posed problems, are discussed. Attention is given to the concept of the conditionally correct statement of a problem, the concept of quasi-solution, and the fundamentals of regularization theory. The discussion also covers the uniqueness of solutions to inverse problems in mathematical physics, with consideration given to problems involving layered media, impedance problems, gravimetric problems, and inverse problems of heat conduction. The problem of stability and regularizing operators are also discussed.

  5. Measurement of solute proton spin-lattice relaxation times in water using the 1,3,3,1 sequence

    SciTech Connect

    Sankar, S.S.; Mole, P.A.; Coulson, R.L.

    1986-12-01

    /sup 1/H NMR spin-lattice relaxation times (T1) of the N-CH3 proton resonances of phosphocreatine (PCr) and creatine (Cr) in water solutions were obtained using the 1,3,3,1 pulse sequence. These T1 values were equivalent to those obtained in D/sub 2/O and water using either the conventional inversion-recovery experiment or the 1,3,3,1 pulse sequence. Thus, the 1,3,3,1 sequence of proton NMR can provide an independent means along with phosphorous NMR for assess PCr and for the study of the creatine kinase reaction (PCr + ADP in equilibrium ATP + Cr) in aqueous solutions and perhaps in biological preparations.

  6. Inversion layer MOS solar cells

    NASA Technical Reports Server (NTRS)

    Ho, Fat Duen

    1986-01-01

    Inversion layer (IL) Metal Oxide Semiconductor (MOS) solar cells were fabricated. The fabrication technique and problems are discussed. A plan for modeling IL cells is presented. Future work in this area is addressed.

  7. Testing Earthquake Source Inversion Methodologies

    NASA Astrophysics Data System (ADS)

    Page, Morgan; Mai, P. Martin; Schorlemmer, Danijel

    2011-03-01

    Source Inversion Validation Workshop; Palm Springs, California, 11-12 September 2010; Nowadays earthquake source inversions are routinely performed after large earthquakes and represent a key connection between recorded seismic and geodetic data and the complex rupture process at depth. The resulting earthquake source models quantify the spatiotemporal evolution of ruptures. They are also used to provide a rapid assessment of the severity of an earthquake and to estimate losses. However, because of uncertainties in the data, assumed fault geometry and velocity structure, and chosen rupture parameterization, it is not clear which features of these source models are robust. Improved understanding of the uncertainty and reliability of earthquake source inversions will allow the scientific community to use the robust features of kinematic inversions to more thoroughly investigate the complexity of the rupture process and to better constrain other earthquake-related computations, such as ground motion simulations and static stress change calculations.

  8. Temperature Inversions Have Cold Bottoms.

    ERIC Educational Resources Information Center

    Bohren, Craig F.; Brown, Gail M.

    1982-01-01

    Uses discussion and illustrations of several demonstrations on air temperature differences and atmospheric stability to explain the phenomena of temperature inversions. Relates this to the smog in Los Angeles and discusses the implications. (DC)

  9. Donor states in inverse opals

    SciTech Connect

    Mahan, G. D.

    2014-09-21

    We calculate the binding energy of an electron bound to a donor in a semiconductor inverse opal. Inverse opals have two kinds of cavities, which we call octahedral and tetrahedral, according to their group symmetry. We put the donor in the center of each of these two cavities and obtain the binding energy. The binding energies become very large when the inverse opal is made from templates with small spheres. For spheres less than 50 nm in diameter, the donor binding can increase to several times its unconfined value. Then electrons become tightly bound to the donor and are unlikely to be thermally activated to the semiconductor conduction band. This conclusion suggests that inverse opals will be poor conductors.

  10. Donor states in inverse opals

    NASA Astrophysics Data System (ADS)

    Mahan, G. D.

    2014-09-01

    We calculate the binding energy of an electron bound to a donor in a semiconductor inverse opal. Inverse opals have two kinds of cavities, which we call octahedral and tetrahedral, according to their group symmetry. We put the donor in the center of each of these two cavities and obtain the binding energy. The binding energies become very large when the inverse opal is made from templates with small spheres. For spheres less than 50 nm in diameter, the donor binding can increase to several times its unconfined value. Then electrons become tightly bound to the donor and are unlikely to be thermally activated to the semiconductor conduction band. This conclusion suggests that inverse opals will be poor conductors.

  11. Temperature Inversions Have Cold Bottoms.

    ERIC Educational Resources Information Center

    Bohren, Craig F.; Brown, Gail M.

    1982-01-01

    Uses discussion and illustrations of several demonstrations on air temperature differences and atmospheric stability to explain the phenomena of temperature inversions. Relates this to the smog in Los Angeles and discusses the implications. (DC)

  12. Testing earthquake source inversion methodologies

    USGS Publications Warehouse

    Page, M.; Mai, P.M.; Schorlemmer, D.

    2011-01-01

    Source Inversion Validation Workshop; Palm Springs, California, 11-12 September 2010; Nowadays earthquake source inversions are routinely performed after large earthquakes and represent a key connection between recorded seismic and geodetic data and the complex rupture process at depth. The resulting earthquake source models quantify the spatiotemporal evolution of ruptures. They are also used to provide a rapid assessment of the severity of an earthquake and to estimate losses. However, because of uncertainties in the data, assumed fault geometry and velocity structure, and chosen rupture parameterization, it is not clear which features of these source models are robust. Improved understanding of the uncertainty and reliability of earthquake source inversions will allow the scientific community to use the robust features of kinematic inversions to more thoroughly investigate the complexity of the rupture process and to better constrain other earthquakerelated computations, such as ground motion simulations and static stress change calculations.

  13. Inversion-symmetric topological insulators

    NASA Astrophysics Data System (ADS)

    Hughes, Taylor L.; Prodan, Emil; Bernevig, B. Andrei

    2011-06-01

    We analyze translationally invariant insulators with inversion symmetry that fall outside the current established classification of topological insulators. These insulators exhibit no edge or surface modes in the energy spectrum and hence they are not edge metals when the Fermi level is in the bulk gap. However, they do exhibit protected modes in the entanglement spectrum localized on the cut between two entangled regions. Their entanglement entropy cannot be made to vanish adiabatically, and hence the insulators can be called topological. There is a direct connection between the inversion eigenvalues of the Hamiltonian band structure and the midgap states in the entanglement spectrum. The classification of protected entanglement levels is given by an integer N, which is the difference between the negative inversion eigenvalues at inversion symmetric points in the Brillouin zone, taken in sets of 2. When the Hamiltonian describes a Chern insulator or a nontrivial time-reversal invariant topological insulator, the entirety of the entanglement spectrum exhibits spectral flow. If the Chern number is zero for the former, or time reversal is broken in the latter, the entanglement spectrum does not have spectral flow, but, depending on the inversion eigenvalues, can still exhibit protected midgap bands similar to impurity bands in normal semiconductors. Although spectral flow is broken (implying the absence of real edge or surface modes in the original Hamiltonian), the midgap entanglement bands cannot be adiabatically removed, and the insulator is “topological.” We analyze the linear response of these insulators and provide proofs and examples of when the inversion eigenvalues determine a nontrivial charge polarization, a quantum Hall effect, an anisotropic three-dimensional (3D) quantum Hall effect, or a magnetoelectric polarization. In one dimension, we establish a link between the product of the inversion eigenvalues of all occupied bands at all inversion

  14. Inversion Algorithms for Geophysical Problems

    DTIC Science & Technology

    1987-12-16

    ktdud* Sccumy Oass/Kjoon) Inversion Algorithms for Geophysical Problems (U) 12. PERSONAL AUTHOR(S) Lanzano, Paolo 13 «. TYPE OF REPORT Final 13b...spectral density. 20. DISTRIBUTION/AVAILABILITY OF ABSTRACT 13 UNCLASSIFIED/UNLIMITED D SAME AS RPT n OTIC USERS 22a. NAME OF RESPONSIBLE...Research Laboratory ’^^ SSZ ’.Washington. DC 20375-5000 NRLrMemorandum Report-6138 Inversion Algorithms for Geophysical Problems p. LANZANO Space

  15. Computation of inverse magnetic cascades

    NASA Technical Reports Server (NTRS)

    Montgomery, D.

    1981-01-01

    Inverse cascades of magnetic quantities for turbulent incompressible magnetohydrodynamics are reviewed, for two and three dimensions. The theory is extended to the Strauss equations, a description intermediate between two and three dimensions appropriate to Tokamak magnetofluids. Consideration of the absolute equilibrium Gibbs ensemble for the system leads to a prediction of an inverse cascade of magnetic helicity, which may manifest itself as a major disruption. An agenda for computational investigation of this conjecture is proposed.

  16. Relevance of 3D magnetic resonance imaging sequences in diagnosing basal subarachnoid neurocysticercosis.

    PubMed

    Carrillo Mezo, Roger; Lara García, Javier; Arroyo, Mariana; Fleury, Agnès

    2015-12-01

    Imagenological diagnosis of subarachnoid neurocysticercosis is usually difficult when classical magnetic resonance imaging (MRI) sequences are used. The purpose of this study was to evaluate the advantages of 3D MRI sequences (Fast Imaging Employing Steady-state Acquisition (FIESTA) and Spoiled Gradient Recalled Echo (SPGR)) with respect to classical sequences (Fluid Attenuation Inversion Recovery (FLAIR) and T1) in visualizing Taenia solium cyst in these locations. Forty-seven T. solium cysts located in the basal cisterns of the subarachnoid space were diagnosed in eighteen Mexican patients. A pre-treatment MRI was performed on all patients, and all four sequences (FIESTA, FLAIR, T1 SPGR, and T2) were evaluated independently by two neuroradiologists. The sensitivity of each sequence to detect the parasite membrane and scolex was evaluated, along with its capacity to detect differences in signal intensity between cerebrospinal fluid (CSF) and cysts. FIESTA sequences allowed the visualization of cyst membrane in 87.2% of the parasites evaluated, FLAIR in 38.3%, SPGR in 23.4%, and T2 in 17.0%. The superiority of FIESTA sequences over the other three imaging methods was statistically significant (P<0.001). Scolices were detected by FIESTA twice as much as the other sequences did, although this difference was not significant (P>0.05). Differences in signal intensity between CSF and parasite cysts were significant in FIESTA (P<0.0001), SPGR (P<0.0001), and FLAIR (P=0.005) sequences. For the first time, the usefulness of 3D MRI sequences to diagnose T. solium cysts located in the basal cisterns of the subarachnoid space was demonstrated. The routine use of these sequences could favor an earlier diagnosis and greatly improve the prognosis of patients affected by this severe form of the disease.

  17. EDITORIAL: Inverse Problems in Engineering

    NASA Astrophysics Data System (ADS)

    West, Robert M.; Lesnic, Daniel

    2007-01-01

    Presented here are 11 noteworthy papers selected from the Fifth International Conference on Inverse Problems in Engineering: Theory and Practice held in Cambridge, UK during 11-15 July 2005. The papers have been peer-reviewed to the usual high standards of this journal and the contributions of reviewers are much appreciated. The conference featured a good balance of the fundamental mathematical concepts of inverse problems with a diverse range of important and interesting applications, which are represented here by the selected papers. Aspects of finite-element modelling and the performance of inverse algorithms are investigated by Autrique et al and Leduc et al. Statistical aspects are considered by Emery et al and Watzenig et al with regard to Bayesian parameter estimation and inversion using particle filters. Electrostatic applications are demonstrated by van Berkel and Lionheart and also Nakatani et al. Contributions to the applications of electrical techniques and specifically electrical tomographies are provided by Wakatsuki and Kagawa, Kim et al and Kortschak et al. Aspects of inversion in optical tomography are investigated by Wright et al and Douiri et al. The authors are representative of the worldwide interest in inverse problems relating to engineering applications and their efforts in producing these excellent papers will be appreciated by many readers of this journal.

  18. A boundary integral method for an inverse problem in thermal imaging

    NASA Technical Reports Server (NTRS)

    Bryan, Kurt

    1992-01-01

    An inverse problem in thermal imaging involving the recovery of a void in a material from its surface temperature response to external heating is examined. Uniqueness and continuous dependence results for the inverse problem are demonstrated, and a numerical method for its solution is developed. This method is based on an optimization approach, coupled with a boundary integral equation formulation of the forward heat conduction problem. Some convergence results for the method are proved, and several examples are presented using computationally generated data.

  19. Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction.

    PubMed

    Mathiopoulos, K D; della Torre, A; Predazzi, V; Petrarca, V; Coluzzi, M

    1998-10-13

    Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd' of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd' suggests that the inversion may be the result of the transposable element's activity. Characteristics of Odysseus' terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.

  20. Identification of elastic basin properties by large-scale inverse earthquake wave propagation

    NASA Astrophysics Data System (ADS)

    Epanomeritakis, Ioannis K.

    The importance of the study of earthquake response, from a social and economical standpoint, is a major motivation for the current study. The severe uncertainties involved in the analysis of elastic wave propagation in the interior of the earth increase the difficulty in estimating earthquake impact in seismically active areas. The need for recovery of information about the geological and mechanical properties of underlying soils motivates the attempt to apply inverse analysis on earthquake wave propagation problems. Inversion for elastic properties of soils is formulated as an constrained optimization problem. A series of trial mechanical soil models is tested against a limited-size set of dynamic response measurements, given partial knowledge of the target model and complete information on source characteristics, both temporal and geometric. This inverse analysis gives rise to a powerful method for recovery of a material model that produces the given response. The goal of the current study is the development of a robust and efficient computational inversion methodology for material model identification. Solution methods for gradient-based local optimization combine with robustification and globalization techniques to build an effective inversion framework. A Newton-based approach deals with the complications of the highly nonlinear systems generated in the inversion solution process. Moreover, a key addition to the inversion methodology is the application of regularization techniques for obtaining admissible soil models. Most importantly, the development and use of a multiscale strategy offers globalizing and robustifying advantages to the inversion process. In this study, a collection of results of inversion for different three-dimensional Lame moduli models is presented. The results demonstrate the effectiveness of the inversion methodology proposed and provide evidence for its capabilities. They also show the path for further study of elastic property

  1. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    PubMed

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  2. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints

    PubMed Central

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-01-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits. PMID:25712227

  3. Water Recovery Systems for Exploration Missions

    NASA Technical Reports Server (NTRS)

    Pickering, Karen D.

    2007-01-01

    As NASA prepares for the Vision for Space Exploration, advances in technology for water recovery systems are necessary to enable future missions. This paper examines the proposed water recovery systems for the initial Constellation exploration missions as well as the capability gaps that exist in the current technology portfolio. We discuss how these gaps will be addressed with future technology development. In addition, the paper reviews how the water recovery system matures throughout the sequence of planned exploration missions, to ultimately support a 180-day lunar mission.

  4. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  5. MR imaging of focal lung lesions: elimination of flow and motion artifact by breath-hold ECG-gated and black-blood techniques on T2-weighted turbo SE and STIR sequences.

    PubMed

    Yamashita, Y; Yokoyama, T; Tomiguchi, S; Takahashi, M; Ando, M

    1999-05-01

    Respiratory and cardiac motion correction may result in better turbo spin-echo (SE) imaging of the lung. To compare breath-hold cardiac-gated black-blood T2-weighted turbo SE and turbo short-inversion-time inversion-recovery (STIR) magnetic resonance (MR) imaging pulse sequences with conventional breath-hold turbo SE and half-Fourier acquisition single-shot turbo spin-echo (HASTE) sequences for lesion conspicuity of focal lung lesions, 42 patients with focal lung lesions were prospectively studied with MR imaging at 1.5 T. Helical computed tomography was used as a reference. In comparison with the conventional breath-hold turbo SE sequence, all black-blood sequences had fewer image artifacts arising from the heart and blood flow. The overall image quality for the black-blood turbo SE and turbo STIR sequences was superior to that for the breath-hold turbo SE and HASTE sequence (P < 0.01). Not only focal lung lesions but also surrounding inflammatory changes were clearly visualized with these two sequences. With the HASTE sequence, although several slices could be obtained in one breath-hold, both the tumor and vessels appeared blurred. We conclude that T2-weighted turbo SE and turbo STIR imaging of the lung with effective suppression of flow and motion artifacts provide high-quality images in patients with focal lung lesions.

  6. Aligning genomes with inversions and swaps

    SciTech Connect

    Holloway, J.L.; Cull, P.

    1994-12-31

    The decision about what operators to allow and how to charge for these operations when aligning strings that arise in a biological context is the decision about what model of evolution to assume. Frequently the operators used to construct an alignment between biological sequences axe limited to deletion, insertion, or replacement of a character or block of characters, but there is biological evidence for the evolutionary operations of exchanging the positions of two segments in a sequence and the replacement of a segment by its reversed complement. In this paper we describe a family of heuristics designed to compute alignments of biological sequences assuming a model of evolution with swaps and inversions. The heuristics will necessarily be approximate since the appropriate way to charge for the evolutionary events (delete, insert, substitute, swap, and invert) is not known. The paper concludes with a pair-wise comparison of 20 Picornavirus genomes, and a detailed comparison of the hepatitis delta virus with the citrus exocortis viroid.

  7. Recovery from schizophrenia and the recovery model.

    PubMed

    Warner, Richard

    2009-07-01

    The recovery model refers to subjective experiences of optimism, empowerment and interpersonal support, and to a focus on collaborative treatment approaches, finding productive roles for user/consumers, peer support and reducing stigma. The model is influencing service development around the world. This review will assess whether optimism about outcome from serious mental illness and other tenets of the recovery model are borne out by recent research. Remission of symptoms has been precisely defined, but the definition of 'recovery' is a more diffuse concept that includes such factors as being productive and functioning independently. Recent research and a large, earlier body of data suggest that optimism about outcome from schizophrenia is justified. A substantial proportion of people with the illness will recover completely and many more will regain good social functioning. Outcome is better for people in the developing world. Mortality for people with schizophrenia is increasing but is lower in the developing world. Working appears to help people recover from schizophrenia, and recent advances in vocational rehabilitation have been shown to be effective in countries with differing economies and labor markets. A growing body of research supports the concept that empowerment is an important component of the recovery process. Key tenets of the recovery model - optimism about recovery from schizophrenia, the importance of access to employment and the value of empowerment of user/consumers in the recovery process - are supported by the scientific research. Attempts to reduce the internalized stigma of mental illness should enhance the recovery process.

  8. Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in Drosophila melanogaster

    PubMed Central

    Miller, Danny E.; Cook, Kevin R.; Arvanitakis, Alexandra V.; Hawley, R. Scott

    2016-01-01

    Balancer chromosomes are multiply inverted chromosomes that suppress meiotic crossing over and prevent the recovery of crossover products. Balancers are commonly used in Drosophila melanogaster to maintain deleterious alleles and in stock construction. They exist for all three major chromosomes, yet the molecular location of the breakpoints and the exact nature of many of the mutations carried by the second and third chromosome balancers has not been available. Here, we precisely locate eight of 10 of the breakpoints on the third chromosome balancer TM3, six of eight on TM6, and nine of 11 breakpoints on TM6B. We find that one of the inversion breakpoints on TM3 bisects the highly conserved tumor suppressor gene p53—a finding that may have important consequences for a wide range of studies in Drosophila. We also identify evidence of single and double crossovers between several TM3 and TM6B balancers and their normal-sequence homologs that have created genetic diversity among these chromosomes. Overall, this work demonstrates the practical importance of precisely identifying the position of inversion breakpoints of balancer chromosomes and characterizing the mutant alleles carried by them. PMID:27172211

  9. Inverse Ising inference with correlated samples

    NASA Astrophysics Data System (ADS)

    Obermayer, Benedikt; Levine, Erel

    2014-12-01

    Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially, the parameters of the least constrained statistical model are learned from the observed correlations such that direct interactions can be separated from indirect correlations. Among many other applications, this approach has been helpful for protein structure prediction, because residues which interact in the 3D structure often show correlated substitutions in a multiple sequence alignment. In this context, samples used for inference are not independent but share an evolutionary history on a phylogenetic tree. Here, we discuss the effects of correlations between samples on global inference. Such correlations could arise due to phylogeny but also via other slow dynamical processes. We present a simple analytical model to address the resulting inference biases, and develop an exact method accounting for background correlations in alignment data by combining phylogenetic modeling with an adaptive cluster expansion algorithm. We find that popular reweighting schemes are only marginally effective at removing phylogenetic bias, suggest a rescaling strategy that yields better results, and provide evidence that our conclusions carry over to the frequently used mean-field approach to the inverse Ising problem.

  10. Inversion strategies for visco-acoustic waveform inversion

    NASA Astrophysics Data System (ADS)

    Kamei, R.; Pratt, R. G.

    2013-08-01

    Visco-acoustic waveform inversion can potentially yield quantitative images of the distribution of both velocity and the attenuation parameters from seismic data. Intrinsic P-wave attenuation has been of particular interest, but has also proven challenging. Frequency-domain inversion allows attenuation and velocity relations to be easily incorporated, and allows a natural multiscale approach. The Laplace-Fourier approach extends this to allow the natural damping of waveforms to enhance early arrivals. Nevertheless, simultaneous inversion of velocity and attenuation leads to significant `cross-talk' between the resulting images, reflecting a lack of parameter resolution and indicating the need for pre-conditioning and regularization of the inverse problem. We analyse the cross-talk issue by partitioning the inversion parameters into two classes; the velocity parameter class, and the attenuation parameter class. Both parameters are defined at a reference frequency, and a dispersion relation is assumed that describes these parameters at any other frequency. We formulate the model gradients at a forward modelling frequency, and convert them to the reference frequency by employing the Jacobian of the coordinate change represented by the dispersion relation. We show that at a given modelling frequency, the Fréchet derivatives corresponding to these two parameter classes differ only by a 90° phase shift, meaning that the magnitudes of resulting model updates will be unscaled, and will not reflect the expected magnitudes in realistic (Q-1 ≪ 1) media. Due to the lack of scaling, cross-talk will be enhanced by poor subsurface illumination, by errors in kinematics, and by data noise. To solve these issues, we introduce an attenuation scaling term (the inverse of a penalty term) that is used to pre-condition the gradient by controlling the magnitudes of the updates to the attenuation parameters. Initial results from a suite of synthetic cross-hole tests using a three

  11. Inversions between ribosomal RNA genes of Escherichia coli.

    PubMed Central

    Hill, C W; Harnish, B W

    1981-01-01

    It might be anticipated that the presence of redundant but oppositely oriented sequences in a chromosome could allow inversion of the intervening material through homologous recombination. For example, the ribosomal RNA gene rrnD of Escherichia coli has the opposite orientation fro rrnB and rrnE and is separated from these genes by roughly 20% of the chromosome. Starting with a derivative of Cavalli Hfr, we have constructed mutants that have an inversion of the segment between rrnD and either rrnB or rrnE. These mutants are generally quite viable but do exhibit a slight reduction in growth rate relative to the parental strain. A major line of laboratory E. coli, W3110 and its derivatives, also has an inversion between rrnD and rrnE, probably created directly by a recombinational event between these highly homologous genes. Images PMID:6273909

  12. Some Phenomena on Negative Inversion Constructions

    ERIC Educational Resources Information Center

    Sung, Tae-Soo

    2013-01-01

    We examine the characteristics of NDI (negative degree inversion) and its relation with other inversion phenomena such as SVI (subject-verb inversion) and SAI (subject-auxiliary inversion). The negative element in the NDI construction may be" not," a negative adverbial, or a negative verb. In this respect, NDI has similar licensing…

  13. The representation and computation of generalized inverse

    NASA Astrophysics Data System (ADS)

    Sheng, Xingping; Chen, Guoliang; Gong, Yi

    2008-03-01

    This paper presents a novel representation for the generalized inverse . Based on this, we give an algorithm to compute this generalized inverse. As an application, we use Gauss-Jordan elimination to compute the weighted Moore-Penrose inverse and the Drazin inverse Ad.

  14. Optimization and geophysical inverse problems

    SciTech Connect

    Barhen, J.; Berryman, J.G.; Borcea, L.; Dennis, J.; de Groot-Hedlin, C.; Gilbert, F.; Gill, P.; Heinkenschloss, M.; Johnson, L.; McEvilly, T.; More, J.; Newman, G.; Oldenburg, D.; Parker, P.; Porto, B.; Sen, M.; Torczon, V.; Vasco, D.; Woodward, N.B.

    2000-10-01

    A fundamental part of geophysics is to make inferences about the interior of the earth on the basis of data collected at or near the surface of the earth. In almost all cases these measured data are only indirectly related to the properties of the earth that are of interest, so an inverse problem must be solved in order to obtain estimates of the physical properties within the earth. In February of 1999 the U.S. Department of Energy sponsored a workshop that was intended to examine the methods currently being used to solve geophysical inverse problems and to consider what new approaches should be explored in the future. The interdisciplinary area between inverse problems in geophysics and optimization methods in mathematics was specifically targeted as one where an interchange of ideas was likely to be fruitful. Thus about half of the participants were actively involved in solving geophysical inverse problems and about half were actively involved in research on general optimization methods. This report presents some of the topics that were explored at the workshop and the conclusions that were reached. In general, the objective of a geophysical inverse problem is to find an earth model, described by a set of physical parameters, that is consistent with the observational data. It is usually assumed that the forward problem, that of calculating simulated data for an earth model, is well enough understood so that reasonably accurate synthetic data can be generated for an arbitrary model. The inverse problem is then posed as an optimization problem, where the function to be optimized is variously called the objective function, misfit function, or fitness function. The objective function is typically some measure of the difference between observational data and synthetic data calculated for a trial model. However, because of incomplete and inaccurate data, the objective function often incorporates some additional form of regularization, such as a measure of smoothness

  15. Geochron Inversion of Magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Craven, J. A.; Roots, E.; Rainbird, R.

    2016-12-01

    A new constrained inversion scheme is proposed whereby model smoothness is evaluated in a time stratigraphic approach. In a standard inversion scheme, the model space is parameterized such that the three dimensions represent spatial dimensions. In time stratigraphy, or more specifically within its mathematical formulation termed the Geo-Chronological (aka GeoChron) space, the model consists of two horizontal dimension coupled with a vertical time dimension. In Geochron space, the model is constrained such that units are smooth in the horizontal directions at the time of their deposition if subsequent tectonic movement is removed. We have modified Occam 2d to work in Geochron space and present tests using 1) synthetic magnetotelluric data from a range of simple test scenarios and and 2) real data collected in sedimentary basin in northern Canada. The results are promising and provide a new framework to guide the incorporation of stratigraphic data into an inversion.

  16. Seismic constraints in magnetotelluric inversion

    NASA Astrophysics Data System (ADS)

    Mandolesi, E.; Jones, A. G.

    2010-12-01

    Non-uniqueness is one of the least governable features in inversion of geophysical data, and magnetotelluric models obtained from inversion are dramatically affected by problems of non-uniqueness. In order to reduce the dimension of acceptable model space in which the inversion model is selected, several solutions have been proposed with different degree of success, usually by introducing some regularization terms in the defined objective function. In our present scheme, information from a seismic inversion is integrated in the inversion process in order to reduce non-uniqueness of solutions and to improve the robustness of the inversion results. The inversion scheme is implemented by including in the objective function a term that maximizes the mutual information between the reference (in this case seismic) model and the electromagnetic model, so that it is possible to plot an empirical histogram that maps phase velocity in electrical conductivity in the considered profile. In probability and information theory the mutual information of two random variables is a quantity that measures their mutual dependence. Given a reference image, in this work a seismic profile, and a second image which needs to be put in the same coordinate system as the reference image, this image is deformed until the mutual information between it and the reference image is maximized. In this way the inversion scheme is driven to fit magnetotelluric data and to take the most possible advantage from seismic information available from the profile. Using this approach it is possible to use a linearized inversion scheme to invert data from a highly non-linear problem like magnetotellurics, keeping it in its whole complexity and obtaining results that allows appreciation of the empirical coupling between the reference image and the obtained (MT) model. Any reference model can be used in our approach during the inversion process, making this scheme suitable to use a reference model produced by a

  17. Stochastic inverse problems: Models and metrics

    SciTech Connect

    Sabbagh, Elias H.; Sabbagh, Harold A.; Murphy, R. Kim; Aldrin, John C.; Annis, Charles; Knopp, Jeremy S.

    2015-03-31

    In past work, we introduced model-based inverse methods, and applied them to problems in which the anomaly could be reasonably modeled by simple canonical shapes, such as rectangular solids. In these cases the parameters to be inverted would be length, width and height, as well as the occasional probe lift-off or rotation. We are now developing a formulation that allows more flexibility in modeling complex flaws. The idea consists of expanding the flaw in a sequence of basis functions, and then solving for the expansion coefficients of this sequence, which are modeled as independent random variables, uniformly distributed over their range of values. There are a number of applications of such modeling: 1. Connected cracks and multiple half-moons, which we have noted in a POD set. Ideally we would like to distinguish connected cracks from one long shallow crack. 2. Cracks of irregular profile and shape which have appeared in cold work holes during bolt-hole eddy-current inspection. One side of such cracks is much deeper than other. 3. L or C shaped crack profiles at the surface, examples of which have been seen in bolt-hole cracks. By formulating problems in a stochastic sense, we are able to leverage the stochastic global optimization algorithms in NLSE, which is resident in VIC-3D®, to answer questions of global minimization and to compute confidence bounds using the sensitivity coefficient that we get from NLSE. We will also address the issue of surrogate functions which are used during the inversion process, and how they contribute to the quality of the estimation of the bounds.

  18. An inverse shock response spectrum

    NASA Astrophysics Data System (ADS)

    Brake, M. R.

    2011-10-01

    The shock response spectrum (SRS) is a tool commonly used by application engineers that characterizes the severity of a transient acceleration. Due to the definition of the SRS, neither an analytical nor a unique inverse exists for an arbitrary function. An SRS presented without any temporal information makes creating a corresponding acceleration time history for an experimental or numerical study prohibitively difficult without a rigorous method to determine an inverse of the SRS (a corresponding time history). The present work develops a method to calculate an inverse of an arbitrary SRS using three sets of well characterized basis functions: an impulse function, a sine function/damped sine function, and a modified Morlet wavelet. These three basis functions are specifically chosen for the properties of their transformations: the impulse introduces a constant increase to the SRS above a given frequency, the sine wave introduces a narrow peak at a given frequency, and the Morlet wavelet introduces a plateau with an adjustable width and relative height. Using the definition of the SRS, the transformations of the basis functions are calculated and these expressions are used to derive a methodology for calculating an inverse SRS. The effectiveness of the method is demonstrated by several examples. The quality of an inverse SRS is evaluated by comparing the SRS of the inverse to the target SRS. This method is developed in order to provide a quick estimate of a corresponding time history; in applications where a higher fidelity representation of the SRS is needed than can be provided by the method developed, a genetic algorithm is used to optimize the coefficients of the basis functions. Given a sufficient number of basis functions for the optimization, the resulting SRS can almost exactly match a randomly generated target SRS that is nonzero over the frequency range considered. For applications in which the permissable basis functions are limited (such as for an

  19. Recovery Act Milestones

    SciTech Connect

    Rogers, Matt

    2009-01-01

    Every 100 days, the Department of Energy is held accountable for a progress report on the American Recovery and Reinvestment Act. Update at 200 days, hosted by Matt Rogers, Senior Advisor to Secretary Steven Chu for Recovery Act Implementation.

  20. Recovery Act Milestones

    ScienceCinema

    Rogers, Matt

    2016-07-12

    Every 100 days, the Department of Energy is held accountable for a progress report on the American Recovery and Reinvestment Act. Update at 200 days, hosted by Matt Rogers, Senior Advisor to Secretary Steven Chu for Recovery Act Implementation.

  1. Population inversion by chirped pulses

    SciTech Connect

    Lu Tianshi

    2011-09-15

    In this paper, we analyze the condition for complete population inversion by a chirped pulse over a finite duration. The nonadiabatic transition probability is mapped in the two-dimensional parameter space of coupling strength and detuning amplitude. Asymptotic forms of the probability are derived by the interference of nonadiabatic transitions for sinusoidal and triangular pulses. The qualitative difference between the maps for the two types of pulses is accounted for. The map is used for the design of stable inversion pulses under specific accuracy thresholds.

  2. Multiphase inverse modeling: An Overview

    SciTech Connect

    Finsterle, S.

    1998-03-01

    Inverse modeling is a technique to derive model-related parameters from a variety of observations made on hydrogeologic systems, from small-scale laboratory experiments to field tests to long-term geothermal reservoir responses. If properly chosen, these observations contain information about the system behavior that is relevant to the performance of a geothermal field. Estimating model-related parameters and reducing their uncertainty is an important step in model development, because errors in the parameters constitute a major source of prediction errors. This paper contains an overview of inverse modeling applications using the ITOUGH2 code, demonstrating the possibilities and limitations of a formalized approach to the parameter estimation problem.

  3. Low Frequency Geoacoustic Inversion Method

    DTIC Science & Technology

    2010-01-01

    Inversion Method A. Tolstoy 1538 Hampton Hill Circle, McLean VA 22101 phone: (703) 760-0881 email: atolstoy@ieee.org Award Number: N00014-10-C...inversion method ( Tolstoy , ’10) with extension to slightly higher frequencies (up to 100Hz) and longer ranges (up 5km); � to apply the new LF...correlation value (see Tolstoy , ’93). A new feature for this effort includes software to check if the sampling has been fine enough to catch the “true

  4. Damage identification using inverse methods.

    PubMed

    Friswell, Michael I

    2007-02-15

    This paper gives an overview of the use of inverse methods in damage detection and location, using measured vibration data. Inverse problems require the use of a model and the identification of uncertain parameters of this model. Damage is often local in nature and although the effect of the loss of stiffness may require only a small number of parameters, the lack of knowledge of the location means that a large number of candidate parameters must be included. This paper discusses a number of problems that exist with this approach to health monitoring, including modelling error, environmental effects, damage localization and regularization.

  5. Chemical Shift Anisotropy Selective Inversion*

    PubMed Central

    Caporini, Marc. A.; Turner, Christopher. J.; Bielecki, Anthony; Griffin, Robert G.

    2009-01-01

    Magic Angle Spinning (MAS) is used in solid-state NMR to remove the broadening effects of the chemical shift anisotropy (CSA). In this work we investigate a technique that can reintroduce the CSA in order to selectively invert transverse magnetization. The technique involves an amplitude sweep of the radio frequency field through a multiple of the spinning frequency. The selectivity of this inversion mechanism is determined by the size of the CSA. We develop a theoretical framework to describe this process and demonstrate the CSA selective inversion with numerical simulations and experimental data. We combine this approach with cross polarization (CP) for potential applications in multi-dimensional MAS NMR. PMID:19648036

  6. Probabilistic inversion: a preliminary discussion

    NASA Astrophysics Data System (ADS)

    Battista Rossi, Giovanni; Crenna, Francesco

    2015-02-01

    We continue the discussion on the possibility of interpreting probability as a logic, that we have started in the previous IMEKO TC1-TC7-TC13 Symposium. We show here how a probabilistic logic can be extended up to including direct and inverse functions. We also discuss the relationship between this framework and the Bayes-Laplace rule, showing how the latter can be formally interpreted as a probabilistic inversion device. We suggest that these findings open a new perspective in the evaluation of measurement uncertainty.

  7. Statistical inference for inverse problems

    NASA Astrophysics Data System (ADS)

    Bissantz, Nicolai; Holzmann, Hajo

    2008-06-01

    In this paper we study statistical inference for certain inverse problems. We go beyond mere estimation purposes and review and develop the construction of confidence intervals and confidence bands in some inverse problems, including deconvolution and the backward heat equation. Further, we discuss the construction of certain hypothesis tests, in particular concerning the number of local maxima of the unknown function. The methods are illustrated in a case study, where we analyze the distribution of heliocentric escape velocities of galaxies in the Centaurus galaxy cluster, and provide statistical evidence for its bimodality.

  8. Thermoelectric properties of inverse opals

    NASA Astrophysics Data System (ADS)

    Mahan, G. D.; Poilvert, N.; Crespi, V. H.

    2016-02-01

    Rayleigh's method [Philos. Mag. Ser. 5 34, 481 (1892)] is used to solve for the classical thermoelectric equations in inverse opals. His theory predicts that in an inverse opal, with periodic holes, the Seebeck coefficient and the figure of merit are identical to that of the bulk material. We also provide a major revision to Rayleigh's method, in using the electrochemical potential as an important variable, instead of the electrostatic potential. We also show that in some cases, the thermal boundary resistance is important in the effective thermal conductivity.

  9. What Is "No Recovery?"

    ERIC Educational Resources Information Center

    Kauffman, Jeffrey

    2008-01-01

    Thanatologists, as Balk recently commented (Balk, 2004), have been saying that there is no recovery from bereavement, or that we should not speak of bereavement as leading to a recovery. The term recovery has a high level of plasticity and can be shaped to fit diverse meanings, including contradictory meanings. We will sort our way through some of…

  10. Enhanced oil recovery update

    SciTech Connect

    Smith, R.V

    1989-03-01

    Technology continues to grow in the realm of enhanced oil recovery. Since 1950 several processes have proven economic for oil recovery. Others are still in their infancy and must be custom designed for each reservoir. This paper gives a general overview of these processes. The author focuses on the latest technology and the outlook for enhanced oil recovery operations.

  11. What Is "No Recovery?"

    ERIC Educational Resources Information Center

    Kauffman, Jeffrey

    2008-01-01

    Thanatologists, as Balk recently commented (Balk, 2004), have been saying that there is no recovery from bereavement, or that we should not speak of bereavement as leading to a recovery. The term recovery has a high level of plasticity and can be shaped to fit diverse meanings, including contradictory meanings. We will sort our way through some of…

  12. Youth in Recovery

    ERIC Educational Resources Information Center

    de Miranda, John; Williams, Greg

    2011-01-01

    Young people are entering long-term recovery probably in greater numbers than ever before. A key word here is "probably" because we know precious little about the phenomenon of young people who recover from alcohol and drug addition. This article is a preliminary exploration of youth in recovery. It reviews several types of recovery support…

  13. Youth in Recovery

    ERIC Educational Resources Information Center

    de Miranda, John; Williams, Greg

    2011-01-01

    Young people are entering long-term recovery probably in greater numbers than ever before. A key word here is "probably" because we know precious little about the phenomenon of young people who recover from alcohol and drug addition. This article is a preliminary exploration of youth in recovery. It reviews several types of recovery support…

  14. Resistivity inversion in 2-D anisotropic media: numerical experiments

    NASA Astrophysics Data System (ADS)

    Wiese, Timothy; Greenhalgh, Stewart; Zhou, Bing; Greenhalgh, Mark; Marescot, Laurent

    2015-04-01

    Many rocks and layered/fractured sequences have a clearly expressed electrical anisotropy although it is rare in practice to incorporate anisotropy into resistivity inversion. In this contribution, we present a series of 2.5-D synthetic inversion experiments for various electrode configurations and 2-D anisotropic models. We examine and compare the image reconstructions obtained using the correct anisotropic inversion code with those obtained using the false but widely used isotropic assumption. Superior reconstruction in terms of reduced data misfit, true anomaly shape and position, and anisotropic background parameters were obtained when the correct anisotropic assumption was employed for medium to high coefficients of anisotropy. However, for low coefficient values the isotropic assumption produced better-quality results. When an erroneous isotropic inversion is performed on medium to high level anisotropic data, the images are dominated by patterns of banded artefacts and high data misfits. Various pole-pole, pole-dipole and dipole-dipole data sets were investigated and evaluated for the accuracy of the inversion result. The eigenvalue spectra of the pseudo-Hessian matrix and the formal resolution matrix were also computed to determine the information content and goodness of the results. We also present a data selection strategy based on high sensitivity measurements which drastically reduces the number of data to be inverted but still produces comparable results to that of the comprehensive data set. Inversion was carried out using transversely isotropic model parameters described in two different co-ordinate frames for the conductivity tensor, namely Cartesian versus natural or eigenframe. The Cartesian frame provided a more stable inversion product. This can be simply explained from inspection of the eigenspectra of the pseudo-Hessian matrix for the two model descriptions.

  15. Inverse boundary-layer technique for airfoil design

    NASA Technical Reports Server (NTRS)

    Henderson, M. L.

    1979-01-01

    A description is presented of a technique for the optimization of airfoil pressure distributions using an interactive inverse boundary-layer program. This program allows the user to determine quickly a near-optimum subsonic pressure distribution which meets his requirements for lift, drag, and pitching moment at the desired flow conditions. The method employs an inverse turbulent boundary-layer scheme for definition of the turbulent recovery portion of the pressure distribution. Two levels of pressure-distribution architecture are used - a simple roof top for preliminary studies and a more complex four-region architecture for a more refined design. A technique is employed to avoid the specification of pressure distributions which result in unrealistic airfoils, that is, those with negative thickness. The program allows rapid evaluation of a designed pressure distribution off-design in Reynolds number, transition location, and angle of attack, and will compute an airfoil contour for the designed pressure distribution using linear theory.

  16. Geoacoustic Inversion in Shallow Water

    DTIC Science & Technology

    2013-09-30

    sound speed profiles in the bottom sediment materials ( Tolstoy et al., 1998; Chapman et al., 2003). However, there has not been a benchmark comparison...EL115, (2008). Tolstoy , A., N.R. Chapman and G. Brooke, Workshop ’97: Benchmarking for Geoacoustic Inversion in Shallow Water, J. Comp. Acoustics, 6, 1

  17. Geoacoustic Inversion in Shallow Water

    DTIC Science & Technology

    2012-09-30

    The inversion performance has been assessed previously in ONR Benchmarking workshops ( Tolstoy et al., 1998; Chapman et al., 2003) that used simulated...Transmission loss measurements and geoacoustic sensitivity modeling at 1.2 kHz, J. Acoust. Soc. Am., 124, EL110-EL115, (2008). Tolstoy , A., N.R

  18. Wave-equation dispersion inversion

    NASA Astrophysics Data System (ADS)

    Li, Jing; Feng, Zongcai; Schuster, Gerard

    2017-03-01

    We present the theory for wave-equation inversion of dispersion curves, where the misfit function is the sum of the squared differences between the wavenumbers along the predicted and observed dispersion curves. The dispersion curves are obtained from Rayleigh waves recorded by vertical-component geophones. Similar to wave-equation traveltime tomography, the complicated surface wave arrivals in traces are skeletonized as simpler data, namely the picked dispersion curves in the phase-velocity and frequency domains. Solutions to the elastic wave equation and an iterative optimization method are then used to invert these curves for 2-D or 3-D S-wave velocity models. This procedure, denoted as wave-equation dispersion inversion (WD), does not require the assumption of a layered model and is significantly less prone to the cycle-skipping problems of full waveform inversion. The synthetic and field data examples demonstrate that WD can approximately reconstruct the S-wave velocity distributions in laterally heterogeneous media if the dispersion curves can be identified and picked. The WD method is easily extended to anisotropic data and the inversion of dispersion curves associated with Love waves.

  19. Inversions. Popular Lectures in Mathematics.

    ERIC Educational Resources Information Center

    Bakel'man, I. Ya

    Inversions are transformations of geometric figures, under which straight lines may be mapped to circles, and conversely. The use of such mapping allows development of a unified method of solution for many of the problems of elementary geometry, especially those concerning constructions and "pencils" of curves. This book discusses the inversion…

  20. Cascade sample matrix inversion arrays

    NASA Astrophysics Data System (ADS)

    Hanson, Timothy; Essman, Joseph

    It is shown that if a narrowband adaptive array is partitioned and processed as a cascade of adaptive arrays, computational complexity is reduced and performance is only slightly degraded. The sample matrix inversion (SMI) and covariance matrix estimation are discussed. Cascade SMI complexity is examined. Simulation results are presented.

  1. Action Understanding as Inverse Planning

    ERIC Educational Resources Information Center

    Baker, Chris L.; Saxe, Rebecca; Tenenbaum, Joshua B.

    2009-01-01

    Humans are adept at inferring the mental states underlying other agents' actions, such as goals, beliefs, desires, emotions and other thoughts. We propose a computational framework based on Bayesian inverse planning for modeling human action understanding. The framework represents an intuitive theory of intentional agents' behavior based on the…

  2. Action Understanding as Inverse Planning

    ERIC Educational Resources Information Center

    Baker, Chris L.; Saxe, Rebecca; Tenenbaum, Joshua B.

    2009-01-01

    Humans are adept at inferring the mental states underlying other agents' actions, such as goals, beliefs, desires, emotions and other thoughts. We propose a computational framework based on Bayesian inverse planning for modeling human action understanding. The framework represents an intuitive theory of intentional agents' behavior based on the…

  3. Workflows for Full Waveform Inversions

    NASA Astrophysics Data System (ADS)

    Boehm, Christian; Krischer, Lion; Afanasiev, Michael; van Driel, Martin; May, Dave A.; Rietmann, Max; Fichtner, Andreas

    2017-04-01

    Despite many theoretical advances and the increasing availability of high-performance computing clusters, full seismic waveform inversions still face considerable challenges regarding data and workflow management. While the community has access to solvers which can harness modern heterogeneous computing architectures, the computational bottleneck has fallen to these often manpower-bounded issues that need to be overcome to facilitate further progress. Modern inversions involve huge amounts of data and require a tight integration between numerical PDE solvers, data acquisition and processing systems, nonlinear optimization libraries, and job orchestration frameworks. To this end we created a set of libraries and applications revolving around Salvus (http://salvus.io), a novel software package designed to solve large-scale full waveform inverse problems. This presentation focuses on solving passive source seismic full waveform inversions from local to global scales with Salvus. We discuss (i) design choices for the aforementioned components required for full waveform modeling and inversion, (ii) their implementation in the Salvus framework, and (iii) how it is all tied together by a usable workflow system. We combine state-of-the-art algorithms ranging from high-order finite-element solutions of the wave equation to quasi-Newton optimization algorithms using trust-region methods that can handle inexact derivatives. All is steered by an automated interactive graph-based workflow framework capable of orchestrating all necessary pieces. This naturally facilitates the creation of new Earth models and hopefully sparks new scientific insights. Additionally, and even more importantly, it enhances reproducibility and reliability of the final results.

  4. Temporally resolved parametric assessment of Z-magnetization recovery (TOPAZ): Dynamic myocardial T1 mapping using a cine steady-state look-locker approach.

    PubMed

    Weingärtner, Sebastian; Shenoy, Chetan; Rieger, Benedikt; Schad, Lothar R; Schulz-Menger, Jeanette; Akçakaya, Mehmet

    2017-08-30

    To develop and evaluate a cardiac phase-resolved myocardial T1 mapping sequence. The proposed method for temporally resolved parametric assessment of Z-magnetization recovery (TOPAZ) is based on contiguous fast low-angle shot imaging readout after magnetization inversion from the pulsed steady state. Thereby, segmented k-space data are acquired over multiple heartbeats, before reaching steady state. This results in sampling of the inversion-recovery curve for each heart phase at multiple points separated by an R-R interval. Joint T1 and B1+ estimation is performed for reconstruction of cardiac phase-resolved T1 and B1+ maps. Sequence parameters are optimized using numerical simulations. Phantom and in vivo imaging are performed to compare the proposed sequence to a spin-echo reference and saturation pulse prepared heart rate-independent inversion-recovery (SAPPHIRE) T1 mapping sequence in terms of accuracy and precision. In phantom, TOPAZ T1 values with integrated B1+ correction are in good agreement with spin-echo T1 values (normalized root mean square error = 4.2%) and consistent across the cardiac cycle (coefficient of variation = 1.4 ± 0.78%) and different heart rates (coefficient of variation = 1.2 ± 1.9%). In vivo imaging shows no significant difference in TOPAZ T1 times between the cardiac phases (analysis of variance: P = 0.14, coefficient of variation = 3.2 ± 0.8%), but underestimation compared with SAPPHIRE (T1 time ± precision: 1431 ± 56 ms versus 1569 ± 65 ms). In vivo precision is comparable to SAPPHIRE T1 mapping until middiastole (P > 0.07), but deteriorates in the later phases. The proposed sequence allows cardiac phase-resolved T1 mapping with integrated B1+ assessment at a temporal resolution of 40 ms. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  5. Value of non-contrast sequences in magnetic resonance angiography of hepatic arterial vasculature.

    PubMed

    Kalra, Vivek B; Gilbert, John W; Krishnamoorthy, Saravanan; Cornfeld, Daniel

    2014-06-01

    To evaluate value of adding non-contrast MR angiographic sequence (In-Flow Inversion Recovery [IFIR]) to standard fat-suppressed T1-weighted postcontrast sequence (3D spoiled gradient echo [3D-GRE]) for evaluating hepatic arterial anatomy. Retrospective evaluation of 30 consecutive patients undergoing multiphase liver MRI. Individual vessels for IFIR/3D-GRE sequences were evaluated by two blinded readers using a four-point scale. Statistical analysis was performed using the Wilcoxon signed-rank test for vessel conspicuity between IFIR/3D-GRE sequences. IFIR alone diagnostically imaged 8.1% of vessels, 3D-GRE alone 25.8%, 55.8% by both 3D-GRE/IFIR, and 10.3% of vessels by neither. Two patients with variant vascular anatomy were visualized with both sequences. Addition of IFIR to 3D-GRE resulted in statistically significant increase in arterial visualization (p<0.001), 10% relative increase in identified vessels, and 3-5 mi increase in acquisition time for total scan time of 30-35 min. IFIR may be a useful adjunct to 3D-GRE in hepatic angiography without adding considerably to scan time. 10% more hepatic arteries were seen when combining information from IFIR/3D-GRE vs. 3D-GRE alone. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  6. Battleground Energy Recovery Project

    SciTech Connect

    Bullock, Daniel

    2011-12-31

    In October 2009, the project partners began a 36-month effort to develop an innovative, commercial-scale demonstration project incorporating state-of-the-art waste heat recovery technology at Clean Harbors, Inc., a large hazardous waste incinerator site located in Deer Park, Texas. With financial support provided by the U.S. Department of Energy, the Battleground Energy Recovery Project was launched to advance waste heat recovery solutions into the hazardous waste incineration market, an area that has seen little adoption of heat recovery in the United States. The goal of the project was to accelerate the use of energy-efficient, waste heat recovery technology as an alternative means to produce steam for industrial processes. The project had three main engineering and business objectives: Prove Feasibility of Waste Heat Recovery Technology at a Hazardous Waste Incinerator Complex; Provide Low-cost Steam to a Major Polypropylene Plant Using Waste Heat; and Create a Showcase Waste Heat Recovery Demonstration Project.

  7. Seismic inversion with generalized Radon transform based on local second-order approximation of scattered field in acoustic media

    NASA Astrophysics Data System (ADS)

    Ouyang, Wei; Mao, Weijian; Li, Xuelei; Li, Wuqun

    2014-08-01

    Sound velocity inversion problem based on scattering theory is formulated in terms of a nonlinear integral equation associated with scattered field. Because of its nonlinearity, in practice, linearization algorisms (Born/single scattering approximation) are widely used to obtain an approximate inversion solution. However, the linearized strategy is not congruent with seismic wave propagation mechanics in strong perturbation (heterogeneous) medium. In order to partially dispense with the weak perturbation assumption of the Born approximation, we present a new approach from the following two steps: firstly, to handle the forward scattering by taking into account the second-order Born approximation, which is related to generalized Radon transform (GRT) about quadratic scattering potential; then to derive a nonlinear quadratic inversion formula by resorting to inverse GRT. In our formulation, there is a significant quadratic term regarding scattering potential, and it can provide an amplitude correction for inversion results beyond standard linear inversion. The numerical experiments demonstrate that the linear single scattering inversion is only good in amplitude for relative velocity perturbation () of background media up to 10 %, and its inversion errors are unacceptable for the perturbation beyond 10 %. In contrast, the quadratic inversion can give more accurate amplitude-preserved recovery for the perturbation up to 40 %. Our inversion scheme is able to manage double scattering effects by estimating a transmission factor from an integral over a small area, and therefore, only a small portion of computational time is added to the original linear migration/inversion process.

  8. T2-weighted cardiac MR assessment of the myocardial area-at-risk and salvage area in acute reperfused myocardial infarction: comparison of state-of-the-art dark blood and bright blood T2-weighted sequences.

    PubMed

    Viallon, Magalie; Mewton, Nathan; Thuny, Franck; Guehring, Jens; O'Donnell, Thomas; Stemmer, Alto; Bi, Xiaoming; Rapacchi, Stanislas; Zuehlsdorff, Sven; Revel, Didier; Croisille, Pierre

    2012-02-01

    To compare different state-of-the-art T2-weighted (T2w) imaging sequences combined with late gadolinium enhancement (LGE) for myocardial salvage area (MSA) assessment by cardiac magnetic resonance (CMR). T2w imaging has been used to assess the myocardial area at risk (AAR) in acute myocardial infarction (AMI) patients, but its clinical application is challenging due to technical and physical limitations. Thirty patients with reperfused AMI underwent complete CMR imaging 2-5 days after hospital admission. Myocardial AAR and MSA were quantified on four different T2w sequences: (a) free-breathing T2-prepared single-shot balanced steady-state free precession (T2p_ssbSSFP); (b) breathhold T2-weighted acquisition for cardiac unified T2 edema (ACUTE); (c) breathhold T2w dark-blood inversion recovery turbo-spin echo (IR-TSE) (short-term inversion recovery: STIR); and (d) free-breathing high-resolution T2 dark-blood navigated BLADE. The diagnostic performance of each technique was also assessed. Quantitative analysis showed significant differences in myocardial AAR extent as quantified by the four T2w sequences (P < 0.05). There were also significant differences in sensitivity, specificity and overall diagnostic performance. Detection and quantification of AAR, and thus of MSA, by T2wCMR in reperfused AMI patients varied significantly between different T2w sequences in the same clinical setting. Copyright © 2011 Wiley Periodicals, Inc.

  9. Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura.

    PubMed

    Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2013-01-01

    Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura--inversion 3 of the O chromosome--in a population sample. The breakpoints could be identified as two rather short fragments (∼300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ∼300-bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double-strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species-group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high-turnover fragment within a long collinear region (∼300 kb).

  10. Phosphoric acid enhances the performance of Fe(III) affinity chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for recovery, detection and sequencing of phosphopeptides.

    PubMed

    Stensballe, Allan; Jensen, Ole Nørregaard

    2004-01-01

    An integrated analytical strategy for enrichment, detection and sequencing of phosphorylated peptides by matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) is reported. o-Phosphoric acid was found to enhance phosphopeptide ion signals in MALDI-MS when used as the acid dopant in 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. The effect was largest for multiply phosphorylated peptides, which exhibited an up to ten-fold increase in ion intensity as compared with standard sample preparation methods. The enhanced phosphopeptide response was observed during MALDI-MS analysis of several peptide mixtures derived by proteolytic digestion of phosphoproteins. Furthermore, the mixture of 2,5-DHB and o-phosphoric acid was an excellent eluant for immobilized metal affinity chromatography (IMAC). Singly and multiply phosphorylated peptide species were efficiently recovered from Fe(III)-IMAC columns, reducing sample handling for phosphopeptide mapping by MALDI-MS and subsequent phosphopeptide sequencing by MALDI-MS/MS. The enhanced response of phosphopeptide ions in MALDI facilitates MS/MS of large (>3 kDa) multiply phosphorylated peptide species and reduces the amount of analyte needed for complete characterization of phosphoproteins.

  11. The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus.

    PubMed

    Szamalek, Justyna M; Goidts, Violaine; Searle, Jeremy B; Cooper, David N; Hameister, Horst; Kehrer-Sawatzki, Hildegard

    2006-01-01

    Seven of nine pericentric inversions that distinguish human (HSA) and chimpanzee karyotypes are chimpanzee-specific. In this study we investigated whether the two extant chimpanzee species, Pan troglodytes (common chimpanzee) and Pan paniscus (bonobo), share exactly the same pericentric inversions. The methods applied were FISH with breakpoint-spanning BAC/PAC clones and PCR analyses of the breakpoint junction sequences. Our findings for the homologues to HSA 4, 5, 9, 12, 16, and 17 confirm for the first time at the sequence level that these pericentric inversions have identical breakpoints in the common chimpanzee and the bonobo. Therefore, these inversions predate the separation of the two chimpanzee species 0.86-2 Mya. Further, the inversions distinguishing human and chimpanzee karyotypes may be regarded as early acquisitions, such that they are likely to have been present at the time of human/chimpanzee divergence. According to the chromosomal speciation theory the inversions themselves could have promoted human speciation.

  12. MR Imaging with Metal-suppression Sequences for Evaluation of Total Joint Arthroplasty.

    PubMed

    Talbot, Brett S; Weinberg, Eric P

    2016-01-01

    Metallic artifact at orthopedic magnetic resonance (MR) imaging continues to be an important problem, particularly in the realm of total joint arthroplasty. Complications often follow total joint arthroplasty and can be expected for a small percentage of all implanted devices. Postoperative complications involve not only osseous structures but also adjacent soft tissues-a highly problematic area at MR imaging because of artifacts from metallic prostheses. Without special considerations, susceptibility artifacts from ferromagnetic implants can unacceptably degrade image quality. Common artifacts include in-plane distortions (signal loss and signal pileup), poor or absent fat suppression, geometric distortion, and through-section distortion. Basic methods to reduce metallic artifacts include use of spin-echo or fast spin-echo sequences with long echo train lengths, short inversion time inversion-recovery (STIR) sequences for fat suppression, a high bandwidth, thin section selection, and an increased matrix. With care and attention to the alloy type (eg, titanium, cobalt-chromium, stainless steel), orientation of the implant, and magnetic field strength, as well as use of proprietary and nonproprietary metal-suppression techniques, previously nondiagnostic studies can yield key diagnostic information. Specifically, sequences such as the metal artifact reduction sequence (MARS), WARP (Siemens Healthcare, Munich, Germany), slice encoding for metal artifact correction (SEMAC), and multiacquisition with variable-resonance image combination (MAVRIC) can be optimized to reveal pathologic conditions previously hidden by periprosthetic artifacts. Complications of total joint arthroplasty that can be evaluated by using MR imaging with metal-suppression sequences include pseudotumoral conditions such as metallosis and particle disease, infection, aseptic prosthesis loosening, tendon injury, and muscle injury. ©RSNA, 2015.

  13. Measurement of bound and pore water T1 relaxation times in cortical bone using three-dimensional ultrashort echo time cones sequences.

    PubMed

    Chen, Jun; Chang, Eric Y; Carl, Michael; Ma, Yajun; Shao, Hongda; Chen, Bimin; Wu, Zhihong; Du, Jiang

    2017-06-01

    We present three-dimensional ultrashort echo time Cones (3D UTE Cones) techniques for quantification of total water T1 ( T1TW), bound water T1 ( T1BW), and pore water T1 ( T1PW) in vitro and in vivo using a 3 Tesla (T) scanner. T1TW, T1BW, and T1PW were measured with three-dimensional (3D) Cones and adiabatic inversion recovery Cone (IR-Cone) sequences. Two-dimensional (2D) nonselective ultrashort echo time (UTE) techniques, including saturation recovery, variable repetition times (TRs), and inversion recovery (IR) preparation approaches were compared with 3D-Cones techniques on bovine cortical bone samples (n = 8). The 3D Cones sequences were used to measure T1TW, T1BW, and T1PW in the tibial midshaft of healthy volunteers (n = 8). Comparable T1 images were achieved for cortical bone between 3D Cones and 2D UTE techniques as well as those published in the literature. The 3D Cones sequences showed a mean T1TW of 208 ± 22 ms, a mean T1PW of 545 ± 28 ms, and a mean T1BW of 131 ± 12 ms for bovine cortical bone; and a mean T1TW of 246 ± 32 ms, a mean T1PW of 524 ± 46 ms, and a mean T1BW of 134 ± 11 ms for the tibial midshaft of healthy volunteers. The 3D Cones sequences can be used for fast volumetric assessment of bound and pore water T1 images in vitro and in vivo. Magn Reson Med 77:2136-2145, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  14. EPA Recovery Mapper

    EPA Pesticide Factsheets

    The EPA Recovery Mapper is an Internet interactive mapping application that allows users to discover information about every American Recovery and Reinvestment Act (ARRA) award that EPA has funded for six programs. By integrating data reported by the recipients of Recovery Act funding and data created by EPA, this application delivers a level of transparency and public accessibility to users interested in EPA's use of Recovery Act monies. The application is relatively easy to use and builds on the same mapping model as Google, Bing, MapQuest and other commonly used mapping interfaces. EPA Recovery Mapper tracks each award made by each program and gives basic Quick Facts information for each award including award name, location, award date, dollar amounts and more. Data Summaries for each EPA program or for each state are provided displaying dollars for Total Awarded, Total Received (Paid), and Total Jobs This Quarter by Recovery for the latest quarter of data released by Recovery.gov. The data are reported to the government and EPA four times a year by the award recipients. The latest quarterly report will always be displayed in the EPA Recovery Mapper. In addition, the application provides many details about each award. Users will learn more about how to access and interpret these data later in this document. Data shown in the EPA Recovery Mapper are derived from information reported back to FederalReporting.gov from the recipients of Recovery Act funding. EPA

  15. 3-D joint inversion of the magnetotelluric phase tensor and vertical magnetic transfer functions

    NASA Astrophysics Data System (ADS)

    Tietze, Kristina; Ritter, Oliver; Egbert, Gary D.

    2015-11-01

    With advancing computational resources, 3-D inversion techniques have become feasible in recent years and are now a more widely used tool for magnetotelluric (MT) data interpretation. Galvanic distortion caused by small-scale near-surface inhomogeneities remains an obstacle for 3-D MT inversion which so far has experienced little attention. If not considered properly, the effect on 3-D inversion can be immense and result in erroneous subsurface models and interpretations. To tackle the problem we implemented inversion of the distortion-free phase tensor into the ModEM inversion package. The dimensionless phase tensor components describe only variations of the conductivity structure. When inverting these data, particular care has to be taken of the conductivity structure in the a priori model, which provides the reference frame when transferring the information from phase tensors into absolute conductivity values. Our results obtained with synthetic data show that phase tensor inversion can recover the regional conductivity structure in presence of galvanic distortion if the a priori model provides a reasonable assumption for the regional resistivity average. Joint inversion of phase tensor data and vertical magnetic transfer functions improves recovery of the absolute resistivity structure and is less dependent on the prior model. We also used phase tensor inversion for a data set of more than 250 MT sites from the central San Andreas fault, California, where a number of sites showed significant galvanic distortion. We find the regional structure of the phase tensor inversion results compatible with previously obtained models from impedance inversion. In the vicinity of distorted sites, phase tensor inversion models exhibit more homogeneous/smoother conductivity structures.

  16. Sequence landscapes.

    PubMed Central

    Clift, B; Haussler, D; McConnell, R; Schneider, T D; Stormo, G D

    1986-01-01

    We describe a method for representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain is written the number of times that the subsequence appears. A data structure called a DAWG, which can be built in time proportional to the length of the sequence, is used to construct the landscape. For the 40 thousand bases of bacteriophage T7, the DAWG can be built in 30 seconds. The time to display any portion of the landscape is less than a second. Using sequence landscapes, one can quickly locate significant repeats. PMID:3753762

  17. Momentum resolution in inverse photoemission

    SciTech Connect

    Zumbülte, A.; Schmidt, A. B.; Donath, M.

    2015-01-15

    We present a method to determine the electron beam divergence, and thus the momentum resolution, of an inverse-photoemission setup directly from a series of spectra measured on Cu(111). Simulating these spectra with different beam divergences shows a distinct influence of the divergence on the appearance of the Shockley surface state. Upon crossing the Fermi level, its rise in intensity can be directly linked with the beam divergence. A comparison of measurement and simulation enables us to quantify the momentum resolution independent of surface quality, energy resolution, and experimental geometry. With spin resolution, a single spectrum taken around the Fermi momentum of a spin-split surface state, e.g., on Au(111), is sufficient to derive the momentum resolution of an inverse-photoemission setup.

  18. Simplified, inverse, ejector design tool

    NASA Technical Reports Server (NTRS)

    Dechant, Lawrence J.

    1993-01-01

    A simple lumped parameter based inverse design tool has been developed which provides flow path geometry and entrainment estimates subject to operational, acoustic, and design constraints. These constraints are manifested through specification of primary mass flow rate or ejector thrust, fully-mixed exit velocity, and static pressure matching. Fundamentally, integral forms of the conservation equations coupled with the specified design constraints are combined to yield an easily invertible linear system in terms of the flow path cross-sectional areas. Entrainment is computed by back substitution. Initial comparison with experimental and analogous one-dimensional methods show good agreement. Thus, this simple inverse design code provides an analytically based, preliminary design tool with direct application to High Speed Civil Transport (HSCT) design studies.

  19. Broadband synthetic aperture geoacoustic inversion.

    PubMed

    Tan, Bien Aik; Gerstoft, Peter; Yardim, Caglar; Hodgkiss, William S

    2013-07-01

    A typical geoacoustic inversion procedure involves powerful source transmissions received on a large-aperture receiver array. A more practical approach is to use a single moving source and/or receiver in a low signal to noise ratio (SNR) setting. This paper uses single-receiver, broadband, frequency coherent matched-field inversion and exploits coherently repeated transmissions to improve estimation of the geoacoustic parameters. The long observation time creates a synthetic aperture due to relative source-receiver motion. This approach is illustrated by studying the transmission of multiple linear frequency modulated (LFM) pulses which results in a multi-tonal comb spectrum that is Doppler sensitive. To correlate well with the measured field across a receiver trajectory and to incorporate transmission from a source trajectory, waveguide Doppler and normal mode theory is applied. The method is demonstrated with low SNR, 100-900 Hz LFM pulse data from the Shallow Water 2006 experiment.

  20. Analysis of RAE-1 inversion

    NASA Technical Reports Server (NTRS)

    Hedland, D. A.; Degonia, P. K.

    1974-01-01

    The RAE-1 spacecraft inversion performed October 31, 1972 is described based upon the in-orbit dynamical data in conjunction with results obtained from previously developed computer simulation models. The computer simulations used are predictive of the satellite dynamics, including boom flexing, and are applicable during boom deployment and retraction, inter-phase coast periods, and post-deployment operations. Attitude data, as well as boom tip data, were analyzed in order to obtain a detailed description of the dynamical behavior of the spacecraft during and after the inversion. Runs were made using the computer model and the results were analyzed and compared with the real time data. Close agreement between the actual recorded spacecraft attitude and the computer simulation results was obtained.

  1. RTM-based waveform inversion

    NASA Astrophysics Data System (ADS)

    Zhou, Hongbo; Zhang, Guanquan; Ortigosa, Francisco

    2010-05-01

    Waveform inversion that determines the subsurface velocity structures can be implemented in either data domain, which compares the differences between the real data and the simulated data (Tarantola, 2005), or in image domain, which checks the coherency of the events in the CIGs (Common Image Gathers) (Symes and Kern, 1994; Chavent and Jacewitz, 1995). In the past, classic waveform inversion, as a data-domain approach, has little success in the field data experiments. We believe that one of the problems is the unknown simulation equations. The real waves will likely propagate with different kinds of wave equations at different subsurface areas. This implies that no single simulation equation can adequately describe the wave propagations underneath the earth. Because of the uncertainty of amplitudes of the waves, the objective function for classic waveform inversion that tries to compare the differences between the observed data and the simulated data will definitely hurt than help inversions. Fortunately, although waves propagate in various forms, only the amplitudes of the waves vary. The traveltime for these various forms of wave equations that are determined by the eikonal equations are more or less the same. In other words, traveltime can provide more reliable information than amplitudes. This suggests that an effective waveform inversion should emphasize on the events' traveltime or phase information and downplay the role of amplitude information. Following Chavent and Jacewitz (1995), we propose an image-domain approach that is based on the criteria that seismic data must be geometrically coherent after prestack depth migration. When the velocity is correct, the events at CIGs should be flat and therefore have maximum stack power for redundant shots. This image-domain approach relies on event coherency (traveltime) and has the effect of emphasizing more on the reliable traveltime information instead of unreliable amplitudes. Here we choose RTM (Reverse

  2. Ultrahigh-intensity inverse bremsstrahlung

    NASA Astrophysics Data System (ADS)

    Kostyukov, I. Yu.; Rax, J.-M.

    1999-01-01

    We study inverse bremsstrahlung in the ultrahigh intensity relativistic regime. The fully relativistic ultrahigh intensity absorption (emission) coefficient is derived for an arbitrary scattering potential and small-angle scattering. We find that in the Coulomb field case this absorption (emission) coefficient can be calculated as a function of the quiver energy, drift momentum, and impact parameter in two complementary regimes: (i) for remote collisions when the impact parameter is larger than the amplitude of the quiver motion, and (ii) for instantaneous collisions when the scattering time is shorter than the period of the wave. Both circular and linear polarizations are considered, and this study reveals that in this relativistic regime inverse bremsstrahlung absorption can be viewed as a harmonic Compton resonance heating of the laser-driven electron by the virtual photon of the ion Coulomb field. The relativistic modification of Marcuse's effect [Bell Syst. Tech. J. 41, 1557 (1962)] are also discussed, and relations with previous nonrelativistic results are elucidated.

  3. Inverse statistics and information content

    NASA Astrophysics Data System (ADS)

    Ebadi, H.; Bolgorian, Meysam; Jafari, G. R.

    2010-12-01

    Inverse statistics analysis studies the distribution of investment horizons to achieve a predefined level of return. This distribution provides a maximum investment horizon which determines the most likely horizon for gaining a specific return. There exists a significant difference between inverse statistics of financial market data and a fractional Brownian motion (fBm) as an uncorrelated time-series, which is a suitable criteria to measure information content in financial data. In this paper we perform this analysis for the DJIA and S&P500 as two developed markets and Tehran price index (TEPIX) as an emerging market. We also compare these probability distributions with fBm probability, to detect when the behavior of the stocks are the same as fBm.

  4. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

    PubMed Central

    2010-01-01

    Background Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools. PMID:20974007

  5. Nonlinear Waves and Inverse Scattering

    DTIC Science & Technology

    1990-09-18

    problems. Research is really two pronged. It is necessary for us to understand and effectively solve both classical and new direct and inverse scattering... descoveries employed IST in one spatial dimension, we have developed effective procedures to carry forth the method for multidimensional problems. In one...Employing IST we have been able to find new solutions to physically interesting multidimensional nonlinear wave equations. The method requires a

  6. Low Frequency Geoacoustic Inversion Method

    DTIC Science & Technology

    2011-09-01

    DISTRIBUTION STATEMENT A: Distribution approved for public release, distribution is unlimited Low Frequency Geoacoustic Inversion Method A. Tolstoy ... Tolstoy , ’10), particularly the investigation of a new broadband method (the minimization method; see Tolstoy , ’12); � to apply the LF G.I. method...ADDRESS(ES) A. Tolstoy ,1538 Hampton Hill Circle,McLean,VA,22101 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND

  7. Low Frequency Geoacoustic Inversion Method

    DTIC Science & Technology

    2012-09-30

    DISTRIBUTION STATEMENT A: Distribution approved for public release, distribution is unlimited Low Frequency Geoacoustic Inversion Method A. Tolstoy ...recently featuring the minimization processor ( Tolstoy , ’10 and ’12); demonstration that horizontal arrays can be successfully used for G.I. with the...over twenty years, particularly for the suppression of sidelobes ( Tolstoy , ’93). For each the MFP values at sidelobes (non-true parameter values

  8. Inverse Gibbs-Thomson effect

    NASA Astrophysics Data System (ADS)

    Gershanov, V. Yu.; Garmashov, S. I.

    2015-01-01

    We prove the existence of an effect inverse to the Gibbs-Thomson effect for mass transfer in systems consisting of a solid phase and the solution of the solid phase material in a certain solvent. The effect involves a change in the shape of the interface due to a variation of the equilibrium concentrations under it, which is induced by external conditions, and exists in the presence of a negative feedback for mass transfer associated with capillary effects.

  9. Viscoacoustic anisotropic full waveform inversion

    NASA Astrophysics Data System (ADS)

    Qu, Yingming; Li, Zhenchun; Huang, Jianping; Li, Jinli

    2017-01-01

    A viscoacoustic vertical transverse isotropic (VTI) quasi-differential wave equation, which takes account for both the viscosity and anisotropy of media, is proposed for wavefield simulation in this study. The finite difference method is used to solve the equations, for which the attenuation terms are solved in the wavenumber domain, and all remaining terms in the time-space domain. To stabilize the adjoint wavefield, robust regularization operators are applied to the wave equation to eliminate the high-frequency component of the numerical noise produced during the backward propagation of the viscoacoustic wavefield. Based on these strategies, we derive the corresponding gradient formula and implement a viscoacoustic VTI full waveform inversion (FWI). Numerical tests verify that our proposed viscoacoustic VTI FWI can produce accurate and stable inversion results for viscoacoustic VTI data sets. In addition, we test our method's sensitivity to velocity, Q, and anisotropic parameters. Our results show that the sensitivity to velocity is much higher than that to Q and anisotropic parameters. As such, our proposed method can produce acceptable inversion results as long as the Q and anisotropic parameters are within predefined thresholds.

  10. Sequencing technologies and genome sequencing.

    PubMed

    Pareek, Chandra Shekhar; Smoczynski, Rafal; Tretyn, Andrzej

    2011-11-01

    The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

  11. Supervised classification of brain tissues through local multi-scale texture analysis by coupling DIR and FLAIR MR sequences

    NASA Astrophysics Data System (ADS)

    Poletti, Enea; Veronese, Elisa; Calabrese, Massimiliano; Bertoldo, Alessandra; Grisan, Enrico

    2012-02-01

    The automatic segmentation of brain tissues in magnetic resonance (MR) is usually performed on T1-weighted images, due to their high spatial resolution. T1w sequence, however, has some major downsides when brain lesions are present: the altered appearance of diseased tissues causes errors in tissues classification. In order to overcome these drawbacks, we employed two different MR sequences: fluid attenuated inversion recovery (FLAIR) and double inversion recovery (DIR). The former highlights both gray matter (GM) and white matter (WM), the latter highlights GM alone. We propose here a supervised classification scheme that does not require any anatomical a priori information to identify the 3 classes, "GM", "WM", and "background". Features are extracted by means of a local multi-scale texture analysis, computed for each pixel of the DIR and FLAIR sequences. The 9 textures considered are average, standard deviation, kurtosis, entropy, contrast, correlation, energy, homogeneity, and skewness, evaluated on a neighborhood of 3x3, 5x5, and 7x7 pixels. Hence, the total number of features associated to a pixel is 56 (9 textures x3 scales x2 sequences +2 original pixel values). The classifier employed is a Support Vector Machine with Radial Basis Function as kernel. From each of the 4 brain volumes evaluated, a DIR and a FLAIR slice have been selected and manually segmented by 2 expert neurologists, providing 1st and 2nd human reference observations which agree with an average accuracy of 99.03%. SVM performances have been assessed with a 4-fold cross-validation, yielding an average classification accuracy of 98.79%.

  12. Recovery and Money Management

    PubMed Central

    Rowe, Michael; Serowik, Kristin L.; Ablondi, Karen; Wilbur, Charles; Rosen, Marc I.

    2014-01-01

    Objective Social recovery and external money management are important approaches in contemporary mental health care, but little research has been done on the relationship between the two or on application of recovery principles to money management for people at risk of being assigned a representative payee or conservator. Methods Twenty-five transcripts out of forty-nine total qualitative interviews with persons receiving SSI or SSDI who were at risk of being assigned a money manager were analyzed to assess the presence of recognized recovery themes. Results The recovery principles of self-direction and responsibility were strong themes in participant comments related to money management. Conclusions and Implications for Practice Money management interventions should incorporate peoples’ recovery-related motivations to acquire financial management skills as a means to direct and assume responsibility for one’s finances. Staff involved in money management should receive training to support client’s recovery-related goals. PMID:23750764

  13. Recovery and money management.

    PubMed

    Rowe, Michael; Serowik, Kristin L; Ablondi, Karen; Wilber, Charles; Rosen, Marc I

    2013-06-01

    Social recovery and external money management are important approaches in contemporary mental health care, but little research has been done on the relationship between the two or on application of recovery principles to money management for people at risk of being assigned a representative payee or conservator. Out of 49 total qualitative interviews, 25 transcripts with persons receiving Social Security insurance or Social Security disability insurance who were at risk of being assigned a money manager were analyzed to assess the presence of recognized recovery themes. The recovery principles of self-direction and responsibility were strong themes in participant comments related to money management. Money management interventions should incorporate peoples' recovery-related motivations to acquire financial management skills as a means to direct and assume responsibility for one's finances. Staff involved in money management should receive training to support client's recovery-related goals. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  14. Evolutionary Toggling of the MAPT 17q21.31 Inversion Region

    PubMed Central

    Zody, Michael C.; Jiang, Zhaoshi; Fung, Hon-Chung; Antonacci, Francesca; Hillier, LaDeana W.; Cardone, Maria Francesca; Graves, Tina A.; Kidd, Jeffrey M.; Cheng, Ze; Abouelleil, Amr; Chen, Lin; Wallis, John; Glasscock, Jarret; Wilson, Richard K.; Reily, Amy Denise; Duckworth, Jaime; Ventura, Mario; Hardy, John; Warren, Wesley C.; Eichler, Evan E.

    2008-01-01

    Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and contrast it with the sequence structure and genetic variation of the corresponding 1.5 Mb region for the non-inverted H1 human haplotype and that of chimpanzee and orangutan. We find that inversion of the MAPT region is similarly polymorphic in other great ape species and present evidence that the inversions have occurred independently in both chimpanzee and humans. In humans, the inversion breakpoints correspond to core duplications encoding the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape/human ancestral state with inversion recurrences during primate evolution. We demonstrate that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its preference to undergo microdeletion associated with mental retardation in European populations. PMID:19165922

  15. Inversion Therapy: Can It Relieve Back Pain?

    MedlinePlus

    ... pain Does inversion therapy relieve back pain? Is it safe? Answers from Edward R. Laskowski, M.D. ... t provide lasting relief from back pain, and it's not safe for everyone. Inversion therapy involves hanging ...

  16. Sequential Geoacoustic Filtering and Geoacoustic Inversion

    DTIC Science & Technology

    2015-09-30

    nesses, sound speed profiles, density and attenuation values. Here we introduce a passive geoacoustic inversion algorithm for use with drifting ...Am, 131, 3633-3641, [Published, refereed] Yardim, Gerstoft, Hodgkiss (2012), Sequential geoacoustic inversion at the continental shelfbreak, J

  17. Recovery Systems Design Guide

    DTIC Science & Technology

    1978-12-01

    APPLICATIONS 2....................................................2 VEHICLE RECOVERY............................................... 2 Recovery of Target Drones ...approach to parachute of target drones and missile components. The cluster- design and performance prediction. The Germans ing of parachutes of all sizes and...availability of data to the authors and the technical compunity In genera. 1] VEHICLE RECOVERY KD2R-5 and MOM-74C Target Drones . The first target drone of the

  18. Intermediate water recovery system

    NASA Technical Reports Server (NTRS)

    Deckman, G.; Anderson, A. R. (Editor)

    1973-01-01

    A water recovery system for collecting, storing, and processing urine, wash water, and humidity condensates from a crew of three aboard a spacecraft is described. The results of a 30-day test performed on a breadboard system are presented. The intermediate water recovery system produced clear, sterile, water with a 96.4 percent recovery rate from the processed urine. Recommendations for improving the system are included.

  19. Efficient trans-dimensional Bayesian inversion for geoacoustic profile estimation

    NASA Astrophysics Data System (ADS)

    Dosso, Stan E.; Dettmer, Jan; Steininger, Gavin; Holland, Charles W.

    2014-11-01

    This paper considers the efficiency of trans-dimensional (trans-D) Bayesian inversion based on reversible-jump Markov-chain Monte Carlo (rjMCMC) sampling, with application to geophysical inverse problems for a depth-dependent earth or seabed model of an unknown number of layers (seabed acoustic reflectivity inversion is the specific example). Trans-D inversion is applied to sample the posterior probability density over geoacoustic/geophysical parameters for a variable number of layers, providing profile estimates with uncertainties that include the uncertainty in the model parameterization. However, the approach is computationally intensive. The efficiency of rjMCMC sampling is largely determined by the proposal schemes which are applied to generate perturbed values for existing parameters and new values for parameters assigned to layers added to the model. Several proposal schemes are considered here, some of which appear new for trans-D geophysical inversion. Perturbations of existing parameters are considered in a principal-component space based on an eigen-decomposition of the unit-lag parameter covariance matrix (computed from successive models along the Markov chain, a diminishing adaptation). The relative efficiency of proposing new parameters from the prior versus a Gaussian distribution focused near existing values is examined. Parallel tempering, which employs a sequence of interacting Markov chains in which the likelihood function is successively relaxed, is also considered as a means to increase the acceptance rate of new layers. The relative efficiency of various proposal schemes is compared through repeated inversions with a pragmatic convergence criterion.

  20. Comparison amongst pulse sequences for enhanced contrast to noise ratio in magnetic resonance imaging.

    PubMed

    Amin, Naima; Afzal, Rao Muhammad; Yousaf, Muhammad; Javid, Muhammad Arshad

    2017-02-01

    To provide optimised pulse sequence and imaging protocols for contrast-to-noise ratio and for tissues that have different signal intensities in magnetic resonance imaging. A tissue equivalent material, ferrous benzoic xylenol orange gel, was prepared using gelatine, ferrous ammonium sulfate, sulfuric acid, xylenol orange tetrasodium salt and benzoic acid. The gel was irradiated using 6MV photons from a Varian Clinac 600C linear accelerator, with a dose of 5, 10, 15, 20 and 25 gray. Experimental variations in imaging parameters were performed in echo time and repetition time. The quantitative analysis consisted of contrast-to-noise ratio. Conventional spin echo and fast spin echo were equivalent for the tissues of comparable signal intensities and for entities moderate difference between signal intensities. Conventional spin echo provided remarkable contrast for tissues where signal intensity difference was extremely high in T1, T2-weighted study. An appropriate inversion time of fast fluid attenuated inversion recovery made it significant to measure contrast between tissues where signal intensity difference was the smallest and ordinary. Choice of pulse sequence and parameters played a vital role in developing fine image contrast.

  1. Topography of retinal recovery processes in humans

    PubMed Central

    Mazinani, Babac E; Merx, Elke; Plange, Niklas; Walter, Peter; Roessler, Gernot F

    2014-01-01

    Background The purpose of this study was to examine retinal recovery processes to pographically by the application of three flash sequences with specific interstimulus intervals. Methods Twelve healthy subjects underwent multifocal electroretinography with a light-emitting diode stimulator. Every flash sequence consisted of three flashes with 25 msec between the first and the second flash and 35 msec between the second and the third flash. The interval between the third and the first flash of the next step was 85 msec. The interstimulus interval-dependent amplitude reductions of the multifocal electroretinographic response for these three intervals yielded three data points that were used to determine the complete curve of the recovery kinetics. Results Amplitude reductions were higher with shorter interstimulus intervals. The mean half-life periods of the recovery kinetics for the different concentric rings and all subjects were: ring 1, 29.3±5.9 msec; ring 2, 24.2±6.4 msec; ring 3, 23±4.1 msec; ring 4, 23.1±4.6 msec; and ring 5, 22.3±4.4 msec. The differences between the first and all other rings were statistically significant (P<0.05). Conclusion The kinetics of the amplitude recovery after short interstimulus intervals showed a spatial distribution, with faster recovery toward the macular periphery. PMID:25349472

  2. Hospital service recovery.

    PubMed

    Gutbezahl, Cary; Haan, Perry

    2006-01-01

    An organization's ability to correct service errors is an important factor in achieving success in today's service economy. This paper examines service recovery in hospitals in the U.S. First is a general review of service recovery theories. Next is a discussion of specific service issues related to the hospital environment. The literature on service recovery is used to make specific recommendations to hospitals for ways to improve their ability to remedy service errors when they occur. Suggestions for future research in the field of service recovery are also made.

  3. Apollo Recovery Operations

    NASA Technical Reports Server (NTRS)

    Interbartolo, Michael

    2009-01-01

    Objectives include: a) Describe the organization of recovery force command and control and landing areas; b) Describe the function and timeline use of the Earth Landing System (ELS); c) Describe Stable 1 vs Stable 2 landing configurations and the function of the Command Module Uprighting System; d) Explain the activities of the helicopter and swimmer teams in egress and recovery of the crew; e)Explain the activities of the swimmer teams and primary recovery ship in recovery of the Command Module; and f) Describe several landing incidents that occurred during Apollo.

  4. APOLLO 10 RECOVERY

    NASA Image and Video Library

    1969-05-26

    S69-20638 (26 May 1969) --- Astronaut Eugene A. Cernan, lunar module pilot, egresses the Apollo 10 spacecraft during recovery operations in the South Pacific. U.S. Navy underwater demolition team swimmers assist in the recovery operations. Already in life raft are astronauts Thomas P. Stafford (left), commander; and John W. Young, command module pilot. The three crewmen were picked up by helicopter and flown to the prime recovery ship, USS Princeton. Splashdown occurred at 11:53 a.m. (CDT), May 26, 1969, about 400 miles east of American Samoa, and about four miles from the recovery ship, to conclude a successful eight-day lunar orbit mission.

  5. Resource Recovery Guide

    SciTech Connect

    Abert, J.G.

    1983-01-01

    Resource Recovery Guides is a collection of articles orignally published between 1975 and 1981. Many of these articles were not easily available to interested readers. Subjects discussed include newspaper recycling, aluminum recovery, codisposal of solid waste and dry sewage sludge, and the recovery of glass from urban refuse. Includes a combined author and subject index. Contents: National concerns for recycling and resource recovery of municipal waste: policy perspectives. Planning, procurement, marketing, economics, and finance. Waste as a source of raw materials. Waste as an energy source.

  6. On the Magic Square and Inverse

    ERIC Educational Resources Information Center

    Elzaidi, S. M.

    2005-01-01

    In this note, we give a method for finding the inverse of a three by three magic square matrix without using the usual methods for finding the inverse of a matrix. Also we give a method for finding the inverse of a three by three magic square matrix whose entries are also matrices. By using these ideas, we can construct large matrices whose…

  7. On the Magic Square and Inverse

    ERIC Educational Resources Information Center

    Elzaidi, S. M.

    2005-01-01

    In this note, we give a method for finding the inverse of a three by three magic square matrix without using the usual methods for finding the inverse of a matrix. Also we give a method for finding the inverse of a three by three magic square matrix whose entries are also matrices. By using these ideas, we can construct large matrices whose…

  8. Inversion: A Most Useful Kind of Transformation.

    ERIC Educational Resources Information Center

    Dubrovsky, Vladimir

    1992-01-01

    The transformation assigning to every point its inverse with respect to a circle with given radius and center is called an inversion. Discusses inversion with respect to points, circles, angles, distances, space, and the parallel postulate. Exercises related to these topics are included. (MDH)

  9. Fast Computation of the Inverse CMH Model

    NASA Technical Reports Server (NTRS)

    Patel, Umesh D.; Torre, Edward Della; Day, John H. (Technical Monitor)

    2001-01-01

    A fast computational method based on differential equation approach for inverse DOK model has been extended for the inverse CMH model. Also, a cobweb technique for calculating the inverse CMH model is also presented. The two techniques are differed from the point of view of flexibility and computation time.

  10. Recombination rate predicts inversion size in Diptera.

    PubMed Central

    Cáceres, M; Barbadilla, A; Ruiz, A

    1999-01-01

    Most species of the Drosophila genus and other Diptera are polymorphic for paracentric inversions. A common observation is that successful inversions are of intermediate size. We test here the hypothesis that the selected property is the recombination length of inversions, not their physical length. If so, physical length of successful inversions should be negatively correlated with recombination rate across species. This prediction was tested by a comprehensive statistical analysis of inversion size and recombination map length in 12 Diptera species for which appropriate data are available. We found that (1) there is a wide variation in recombination map length among species; (2) physical length of successful inversions varies greatly among species and is inversely correlated with the species recombination map length; and (3) neither the among-species variation in inversion length nor the correlation are observed in unsuccessful inversions. The clear differences between successful and unsuccessful inversions point to natural selection as the most likely explanation for our results. Presumably the selective advantage of an inversion increases with its length, but so does its detrimental effect on fertility due to double crossovers. Our analysis provides the strongest and most extensive evidence in favor of the notion that the adaptive value of inversions stems from their effect on recombination. PMID:10471710

  11. Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication

    PubMed Central

    Kong, Sing-Guan; Fan, Wen-Lang; Chen, Hong-Da; Hsu, Zi-Ting; Zhou, Nengji; Zheng, Bo; Lee, Hoong-Chien

    2009-01-01

    The cause of symmetry is usually subtle, and its study often leads to a deeper understanding of the bearer of the symmetry. To gain insight into the dynamics driving the growth and evolution of genomes, we conducted a comprehensive study of textual symmetries in 786 complete chromosomes. We focused on symmetry based on our belief that, in spite of their extreme diversity, genomes must share common dynamical principles and mechanisms that drive their growth and evolution, and that the most robust footprints of such dynamics are symmetry related. We found that while complement and reverse symmetries are essentially absent in genomic sequences, inverse–complement plus reverse–symmetry is prevalent in complex patterns in most chromosomes, a vast majority of which have near maximum global inverse symmetry. We also discovered relations that can quantitatively account for the long observed but unexplained phenomenon of -mer skews in genomes. Our results suggest segmental and whole-genome inverse duplications are important mechanisms in genome growth and evolution, probably because they are efficient means by which the genome can exploit its double-stranded structure to enrich its code-inventory. PMID:19898631

  12. Isotropic probability measures in infinite dimensional spaces: Inverse problems/prior information/stochastic inversion

    NASA Technical Reports Server (NTRS)

    Backus, George

    1987-01-01

    Let R be the real numbers, R(n) the linear space of all real n-tuples, and R(infinity) the linear space of all infinite real sequences x = (x sub 1, x sub 2,...). Let P sub n :R(infinity) approaches R(n) be the projection operator with P sub n (x) = (x sub 1,...,x sub n). Let p(infinity) be a probability measure on the smallest sigma-ring of subsets of R(infinity) which includes all of the cylinder sets P sub n(-1) (B sub n), where B sub n is an arbitrary Borel subset of R(n). Let p sub n be the marginal distribution of p(infinity) on R(n), so p sub n(B sub n) = p(infinity)(P sub n to the -1(B sub n)) for each B sub n. A measure on R(n) is isotropic if it is invariant under all orthogonal transformations of R(n). All members of the set of all isotropic probability distributions on R(n) are described. The result calls into question both stochastic inversion and Bayesian inference, as currently used in many geophysical inverse problems.

  13. MR imaging of the knee in patients with medial unicompartmental arthroplasty: comparison among sequences at 1.5 T.

    PubMed

    Aliprandi, A; Perona, F; Bandirali, M; Randelli, P; Cabitza, P; Sardanelli, F

    2009-03-01

    This study was done to test a series of magnetic resonance (MR) imaging sequences of the knee after medial unicompartmental arthroplasty. Four patients who had undergone Oxford III medial unicompartmental arthroplasty underwent 1.5-T MR imaging of the operated knee using coronal sequences: T1-weighted spin-echo (SE), T1-weighted turbo SE (TSE), proton-density (PD)- and T2-weighted TSE, T1-weighted gradient echo (GE), short-tau inversion recovery (STIR), multi echo data image combination (MEDIC), T2*-weighted GE, volumetric interpolated breath-hold examination (VIBE), and dual-echo steady state (DESS). For each sequence, we evaluated the visibility of the anatomical structures of the central pivot, lateral compartment, and anterior compartment using a semiquantitative score (0=total masking; 1=insufficient visibility; 2=sufficient visibility; 3=optimal visibility). The sum of the scores given to each sequence was divided by the maximal sum, obtaining a percentage visibility index. Friedman and sign tests were used for statistical analysis. MR examination time was 30-32 min. No patients reported pain, heat or other local discomfort. The visibility index ranged between 83% and 89% for the first four sequences without significant differences among them, 58% for STIR and 11%-36% for the last five sequences. Significant differences were found between each of the four first sequences and the remaining sequences (p<0.004) and between STIR and the last five sequences (p<0.008). MR imaging of the knee after medial unicompartmental arthroplasty was not associated with adverse events. An imaging protocol including SE, TSE and STIR sequences could be used to study the knee with unicompartmental arthroplasty.

  14. Dynamic data integration and stochastic inversion of a confined aquifer

    NASA Astrophysics Data System (ADS)

    Wang, D.; Zhang, Y.; Irsa, J.; Huang, H.; Wang, L.

    2013-12-01

    and coarsening and therefore reducing the associated estimation uncertainty), a parallel LSQR solver was written and verified. For the 50×50 grid, the parallel solver sped up the serial solution time by 14X using 4 CPUs (research on parallel performance and scaling is ongoing). A sensitivity analysis was conducted to examine the relation between the observed data and the inversion outcomes, where measurement errors of increasing magnitudes (i.e., ×1, 2, 5, 10% of the total head variation and up to ×2% of the total flux variation) were imposed on the observed data. Inversion results were stable but the accuracy of Ks and boundary estimation degraded with increasing errors, as expected. In particular, quality of the observed heads is critical to hydraulic head recovery, while quality of the observed fluxes plays a dominant role in K estimation. References: Wang, D., Y. Zhang, J. Irsa, H. Huang, and L. Wang (2013), Data integration and stochastic inversion of a confined aquifer with high performance computing, Advances in Water Resources, in preparation. Paige, C. C., and M. A. Saunders (1982), LSQR: an algorithm for sparse linear equations and sparse least squares, ACM Transactions on Mathematical Software, 8(1), 43-71.

  15. Sample sequencing

    SciTech Connect

    Prange, C.

    1994-04-01

    The goal of the Human Genome Project is to sequence all 3 billion basepairs of human DNA. At Lawrence Livermore Lab, attention is focused on Chromosome 19, which has been estimated to contain approximately 2000 genes. So far, only 200 have been mapped to specific areas on the chromosome. For this reason, a simple method is needed to predict the most likely locations of the coding regions in the DNA. In addition, there is also a need for unique market sites (STS`s) along the chromosome. Sample sequencing uses standard cloning techniques to prepare DNA for sequencing. Once sequence is obtained, it is analyzed using databases to predict the regions most likely to contain genes. All sequences may also be used to generate STS`s. So far, 21 fragments from five different clones have been completely sequenced, with fragments from eight more clones in progress. Constant improvement of methods to increase efficiency and accuracy combined with utilization of the most current databases available make sample sequencing a useful tool for reaching the goals of the Human Genome Project.

  16. Cardiovascular magnetic resonance in patients with magnetic resonance conditional pacemaker systems at 1.5 T: influence of pacemaker related artifacts on image quality including first pass perfusion, aortic and mitral valve assessment, flow measurement, short tau inversion recovery and T1-weighted imaging.

    PubMed

    Klein-Wiele, Oliver; Garmer, Marietta; Busch, Martin; Mateiescu, Serban; Urbien, Rhyan; Barbone, Gianluca; Kara, Kaffer; Schulte-Hermes, Michael; Metz, Frauke; Hailer, Birgit; Grönemeyer, Dietrich

    2017-03-01

    There are only limited data on the impact of device-related artifacts on image quality in cardiovascular magnetic resonance imaging (CMR) in patients with pacemakers (PM). Adenosine stress perfusion, T1-weighted imaging and flow measurement as well as valve characterization have not been evaluated previously concerning artifact burden. We aimed to assess image quality in all routinely used CMR sequences. We analyzed 2623 myocardial segments in CMR scans of 61 patients with MR conditional PM (mean age 72.1 ± 11.5 years), 23 (37.7%) with right sided, 38 (62.3%) with left-sided devices. There were no relevant artifacts in patients with right-sided devices irrespective of the imaging sequence. In left-sided implants no PM-induced artifacts were found in first pass perfusion sequence, flow analysis and T1 weighted imaging. Only few patients with left-sided devices showed significant PM-artifacts in aortic (3/38, 7.9%)/mitral (n = 2/38, 5.3%) valve imaging and STIR (n = 3/35, 8.6%). In STIR only 14/805 (1.7%) segments were involved. In left-sided PM SSFP cine sequences had more artifact burden than LGE with 377/1505 (25.0%) vs. 162/1505 (10.8%) myocardial segments involved by relevant artifacts respectively (p < 0.001). Apart from cine and LGE imaging in anterior myocardial segments with left-sided implants presence of MRI conditional pacemakers does not affect CMR image quality in multimodal CMR examinations to a significant extent. Our data supports evidence that reduced image quality does not need to be a major concern in PM patients undergoing CMR.

  17. Dynamically consistent Jacobian inverse for mobile manipulators

    NASA Astrophysics Data System (ADS)

    Ratajczak, Joanna; Tchoń, Krzysztof

    2016-06-01

    By analogy to the definition of the dynamically consistent Jacobian inverse for robotic manipulators, we have designed a dynamically consistent Jacobian inverse for mobile manipulators built of a non-holonomic mobile platform and a holonomic on-board manipulator. The endogenous configuration space approach has been exploited as a source of conceptual guidelines. The new inverse guarantees a decoupling of the motion in the operational space from the forces exerted in the endogenous configuration space and annihilated by the dual Jacobian inverse. A performance study of the new Jacobian inverse as a tool for motion planning is presented.

  18. An algorithm for constructing minimal order inverses

    NASA Technical Reports Server (NTRS)

    Patel, R. V.

    1976-01-01

    In this paper an algorithm is presented for constructing minimal order inverses of linear, time invariant, controllable and observable, multivariable systems. By means of simple matrix operations, a 'state-overdescribed' system is first constructed which is an inverse of the given multivariable system. A simple Gauss-Jordan type reduction procedure is then used to remove the redundancy in the state vector of the inverse system to obtain a minimal order inverse. When the given multivariable system is not invertible, the algorithm enables a minimal order inverse of an invertible subsystem to be constructed. Numerical examples are given to illustrate the use of the algorithm.

  19. Energy recovery injectors

    NASA Astrophysics Data System (ADS)

    Volkov, V.; Petrov, V. M.; Atkinson, T.; Matveenko, A.

    2016-10-01

    This article presents a novel design for a superconducting rf electron injector that incorporates energy recovery. This concept relaxes the demands of high power input couplers, improves essential beam parameters and energy efficiency and reduces the overall cost of a compact energy recovery linac machine.

  20. "Sizing Up" Codependency Recovery.

    ERIC Educational Resources Information Center

    Messner, Beth A.

    1996-01-01

    Analyzes codependency related, self-help literature with a dramatistic lens to explore M. Beattie's bibliotherapeutic portrayal of codependency and codependency recovery. Depicts Beattie's "stylistic medicine" for codependency recovery as a three-step, rebirth experience: (1) recognize the codependent pollution within; (2) engage in…

  1. "Sizing Up" Codependency Recovery.

    ERIC Educational Resources Information Center

    Messner, Beth A.

    1996-01-01

    Analyzes codependency related, self-help literature with a dramatistic lens to explore M. Beattie's bibliotherapeutic portrayal of codependency and codependency recovery. Depicts Beattie's "stylistic medicine" for codependency recovery as a three-step, rebirth experience: (1) recognize the codependent pollution within; (2) engage in…

  2. Interpid, Carpenter recovery

    NASA Image and Video Library

    1962-05-24

    S62-04027 (24 May 1962) --- Astronaut M. Scott Carpenter, prime pilot for the Mercury-Atlas 7 (MA-7) mission, arrives aboard the prime recovery ship, USS Intrepid, during recovery operations following his Earth-orbital mission. Photo credit: NASA

  3. Interpid, Carpenter recovery

    NASA Image and Video Library

    1962-01-01

    S62-04058 (24 May 1962) --- Astronaut M. Scott Carpenter, prime pilot for the Mercury-Atlas 7 (MA-7) mission, arrives aboard the prime recovery ship, USS Intrepid, during recovery operations following his Earth-orbital mission. Photo credit: NASA

  4. Sparsity constrained contrast source inversion.

    PubMed

    Ramirez, Ana B; van Dongen, Koen W A

    2016-09-01

    Ultrasound imaging is used for detecting and characterizing breast lesions. A state of the art imaging method is the contrast source inversion (CSI), which solves the full wave nonlinear inverse problem. However, when the measurements are acquired in noisy environments, CSI can diverge from the correct solution after several iterations. Problems associated with noisy data were originally solved by including total variation (TV) regularization. Unfortunately, for very noisy data, TV regularization alone is not sufficient. In this work, compressed sensing ideas are used to regularize the inversion process by restricting the solution of the CSI method to be sparse in a transformation domain. The proposed method estimates the contrast source and contrast function by minimizing the mean squared error between the measured and modeled data. An extra penalty term is added to measure sparsity in the transformation domain. A second method that combines sparsity of the contrast source and minimal TV in the contrast function is also presented. The proposed methods are tested on noise-free and noisy synthetic data sets representing a scan of a cancerous breast. Numerical experiments show that, for measurements contaminated with 1% noise, the sparsity constrained CSI improves the normalized mean squared error of the reconstructed speed-of-sound profiles up to 36% in comparison with traditional CSI. Also, for measurements contaminated with 5% noise, the proposed methods improve the quality of the reconstruction up to 70% in comparison with the traditional CSI method. Experimental results also show that the methods remain convergent to the correct speed-of-sound profile as the number of iterations increases.

  5. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  6. GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution?

    PubMed

    Bridi, L C; Rafael, M S

    2016-02-01

    Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi.

  7. Rotation and inversion in nitrosamines

    NASA Astrophysics Data System (ADS)

    Kirste, Karl; Rademacher, Paul

    1981-04-01

    Geometry optimizations of the ground states as well as of the transition states for internal rotation and inversion have been performed by the semiempirical MNDO method for dimethyl nitrosamine (1), perfluordimethyl nitrosamine (2), N-nitroso aziridine (3), and N-nitroso azetidine (4). It was found that the potential barrier to internal rotation about the N-N bond is always of lower energy than that to inversion on the nitroso nitrogen. While the ground states tend to adopt structures which enable mesomerism, the lowest transition state is characterized by a pyramidal sp3-hybridized amino nitrogen. In accordance with experimental results the low barriers to rotation of 2 (7.96 kcal mol -1), 3 (3.38 kcal mol -1) and 4 (9.97 kcal mol -1) in comparison with 1 (12.54 kcal mol -1) indicate that in donor-acceptor molecules the transfer of charge can be limited by electronic and stereochemical effects. In particular, the equivalence of the α-methylene hydrogens which was observed in the NMR-spectrum of 3 is due to unhindered rotation and ring inveirsion.

  8. Uncertainty Quantification and Transdimensional Inversion

    NASA Astrophysics Data System (ADS)

    Sambridge, M.; Hawkins, R.

    2014-12-01

    Over recent years transdimensional inference methods have grown in popularity and found applications in fields ranging from Solid Earth Geophysics, to Geochemistry. In all applications of inversion assumptions are made about the nature of the model parametrisation, complexity and data noise characteristics, and results can be significantly dependent on those assumptions. Often these are in the form of fixed choices imposed a priori, e.g. in the grid size of the model or noise level in the data. A transdimensional approach allows these assumptions to be relaxed by incorporating relevant parameters as unknowns in the inference problem, e.g. the number of model parameters becomes a variable as does the form of basis functions and the variance of the data noise. In this way uncertainty due to parameterisation effects or data noise choices may be incorporated into the inference process. Probabilistic sampling techniques such as Birth-Death Markov chain Monte Carlo and the Reversible jump algorithm, allow sampling over complex posterior probability density functions providing information on constraint, trade-offs and uncertainty in the unknowns. This talk will present a review of trans-dimensional inference and its application in geophysical inversion, and highlight some emerging trends such as Multi-scale McMC, Parallel Tempering and Sequential McMC which hold the promise of further extending the range of problems where these methods are practical.

  9. MOSES Inversions using Multiresolution SMART

    NASA Astrophysics Data System (ADS)

    Rust, Thomas; Fox, Lewis; Kankelborg, Charles; Courrier, Hans; Plovanic, Jacob

    2014-06-01

    We present improvements to the SMART inversion algorithm for the MOSES imaging spectrograph. MOSES, the Multi-Order Solar EUV Spectrograph, is a slitless extreme ultraviolet spectrograph designed to measure cotemporal narrowband spectra over a wide field of view via tomographic inversion of images taken at three orders of a concave diffraction grating. SMART, the Smooth Multiplicative Algebraic Reconstruction Technique, relies on a global chi squared goodness of fit criterion, which enables overfit and underfit regions to "balance out" when judging fit quality. "Good" reconstructions show poor fits at some positions and length scales. Here we take a multiresolution approach to SMART, applying corrections to the reconstruction at positions and scales where correction is warranted based on the noise. The result is improved fit residuals that more closely resemble the expected noise in the images. Within the multiresolution framework it is also easy to include a regularized deconvolution of the instrument point spread functions, which we do. Different point spread functions among MOSES spectral orders results in spurious doppler shifts in the reconstructions, most notable near bright compact emission. We estimate the point spread funtions from the data. Deconvolution is done using the Richardson-Lucy method, which is algorithmically similar to SMART. Regularization results from only correcting the reconstruction at positions and scales where correction is warranted based on the noise. We expect the point spread function deconvolution to increase signal to noise and reduce systematic error in MOSES reconstructions.

  10. Neural network explanation using inversion.

    PubMed

    Saad, Emad W; Wunsch, Donald C

    2007-01-01

    An important drawback of many artificial neural networks (ANN) is their lack of explanation capability [Andrews, R., Diederich, J., & Tickle, A. B. (1996). A survey and critique of techniques for extracting rules from trained artificial neural networks. Knowledge-Based Systems, 8, 373-389]. This paper starts with a survey of algorithms which attempt to explain the ANN output. We then present HYPINV, a new explanation algorithm which relies on network inversion; i.e. calculating the ANN input which produces a desired output. HYPINV is a pedagogical algorithm, that extracts rules, in the form of hyperplanes. It is able to generate rules with arbitrarily desired fidelity, maintaining a fidelity-complexity tradeoff. To our knowledge, HYPINV is the only pedagogical rule extraction method, which extracts hyperplane rules from continuous or binary attribute neural networks. Different network inversion techniques, involving gradient descent as well as an evolutionary algorithm, are presented. An information theoretic treatment of rule extraction is presented. HYPINV is applied to example synthetic problems, to a real aerospace problem, and compared with similar algorithms using benchmark problems.

  11. Targeted chromosomal deletions and inversions in zebrafish.

    PubMed

    Gupta, Ankit; Hall, Victoria L; Kok, Fatma O; Shin, Masahiro; McNulty, Joseph C; Lawson, Nathan D; Wolfe, Scot A

    2013-06-01

    Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) provide powerful platforms for genome editing in plants and animals. Typically, a single nuclease is sufficient to disrupt the function of protein-coding genes through the introduction of microdeletions or insertions that cause frameshifts within an early coding exon. However, interrogating the function of cis-regulatory modules or noncoding RNAs in many instances requires the excision of this element from the genome. In human cell lines and invertebrates, two nucleases targeting the same chromosome can promote the deletion of intervening genomic segments with modest efficiencies. We have examined the feasibility of using this approach to delete chromosomal segments within the zebrafish genome, which would facilitate the functional study of large noncoding sequences in a vertebrate model of development. Herein, we demonstrate that segmental deletions within the zebrafish genome can be generated at multiple loci and are efficiently transmitted through the germline. Using two nucleases, we have successfully generated deletions of up to 69 kb at rates sufficient for germline transmission (1%-15%) and have excised an entire lincRNA gene and enhancer element. Larger deletions (5.5 Mb) can be generated in somatic cells, but at lower frequency (0.7%). Segmental inversions have also been generated, but the efficiency of these events is lower than the corresponding deletions. The ability to efficiently delete genomic segments in a vertebrate developmental system will facilitate the study of functional noncoding elements on an organismic level.

  12. Three-dimensional magnetotelluric inversion in practice—the electrical conductivity structure of the San Andreas Fault in Central California

    NASA Astrophysics Data System (ADS)

    Tietze, Kristina; Ritter, Oliver

    2013-10-01

    3-D inversion techniques have become a widely used tool in magnetotelluric (MT) data interpretation. However, with real data sets, many of the controlling factors for the outcome of 3-D inversion are little explored, such as alignment of the coordinate system, handling and influence of data errors and model regularization. Here we present 3-D inversion results of 169 MT sites from the central San Andreas Fault in California. Previous extensive 2-D inversion and 3-D forward modelling of the data set revealed significant along-strike variation of the electrical conductivity structure. 3-D inversion can recover these features but only if the inversion parameters are tuned in accordance with the particularities of the data set. Based on synthetic 3-D data we explore the model space and test the impacts of a wide range of inversion settings. The tests showed that the recovery of a pronounced regional 2-D structure in inversion of the complete impedance tensor depends on the coordinate system. As interdependencies between data components are not considered in standard 3-D MT inversion codes, 2-D subsurface structures can vanish if data are not aligned with the regional strike direction. A priori models and data weighting, that is, how strongly individual components of the impedance tensor and/or vertical magnetic field transfer functions dominate the solution, are crucial controls for the outcome of 3-D inversion. If deviations from a prior model are heavily penalized, regularization is prone to result in erroneous and misleading 3-D inversion models, particularly in the presence of strong conductivity contrasts. A `good' overall rms misfit is often meaningless or misleading as a huge range of 3-D inversion results exist, all with similarly `acceptable' misfits but producing significantly differing images of the conductivity structures. Reliable and meaningful 3-D inversion models can only be recovered if data misfit is assessed systematically in the frequency

  13. Chloroplast DNA inversions and the origin of the grass family (Poaceae).

    PubMed Central

    Doyle, J J; Davis, J I; Soreng, R J; Garvin, D; Anderson, M J

    1992-01-01

    The phylogenetic affinities of the grass family (Poaceae) have long been debated. The chloroplast genomes of at least some grasses have been known to possess three inversions relative to the typical gene arrangement found in most flowering plants. We have surveyed for the presence of these inversions in grasses and other monocots by polymerase chain reaction amplification with primers constructed from sequences flanking the inversion end points. Amplification phenotypes diagnostic for the largest inversion (28 kilobase pairs) were found in genera representing all grass subfamilies, and in the nongrass families Restionaceae, Ecdeiocoleaceae, and Joinvilleaceae, but not in any other monocots--notably, Flagellariaceae, Anarthriaceae, Cyperaceae, or Juncaceae. This finding is consistent with one of the two principal views of grass phylogeny in suggesting that Poaceae and Cyperaceae (sedges) are not closest relatives. A second (approximately 6 kilobases) inversion appears to occur in a subset of the families possessing the 28-kilobase inversion and links Joinvilleaceae and Poaceae, while the smallest inversion appears unique to grasses. These inversions thus provide a nested set of phylogenetic characters, indicating a hierarchy of relationships in the grasses and allies, with Joinvilleaceae identified as the likely sister group to the Poaceae. Images PMID:1502190

  14. Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation.

    PubMed

    Rane, Rahul V; Rako, Lea; Kapun, Martin; Lee, Siu F; Hoffmann, Ary A

    2015-05-01

    Chromosomal inversion polymorphisms are common in animals and plants, and recent models suggest that alternative arrangements spread by capturing different combinations of alleles acting additively or epistatically to favour local adaptation. It is also thought that inversions typically maintain favoured combinations for a long time by suppressing recombination between alternative chromosomal arrangements. Here, we consider patterns of linkage disequilibrium and genetic divergence in an old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known to be associated with climate change adaptation and a recent invasion event into Australia. We extracted, karyotyped and sequenced whole chromosomes from two Australian populations, so that changes in the arrangement of the alleles between geographically separated tropical and temperate areas could be compared. Chromosome-wide linkage disequilibrium (LD) analysis revealed strong LD within the region spanned by In(3R)Payne. This genomic region also showed strong differentiation between the tropical and the temperate populations, but no differentiation between different karyotypes from the same population, after controlling for chromosomal arrangement. Patterns of differentiation across the chromosome arm and in gene ontologies were enhanced by the presence of the inversion. These data support the notion that inversions are strongly selected by bringing together combinations of genes, but it is still not clear if such combinations act additively or epistatically. Our data suggest that climatic adaptation through inversions can be dynamic, reflecting changes in the relative abundance of different forms of an inversion and ongoing evolution of allelic content within an inversion.

  15. Comparative study of inversion methods of three-dimensional NMR and sensitivity to fluids

    NASA Astrophysics Data System (ADS)

    Tan, Maojin; Wang, Peng; Mao, Keyu

    2014-04-01

    Three-dimensional nuclear magnetic resonance (3D NMR) logging can simultaneously measure transverse relaxation time (T2), longitudinal relaxation time (T1), and diffusion coefficient (D). These parameters can be used to distinguish fluids in the porous reservoirs. For 3D NMR logging, the relaxation mechanism and mathematical model, Fredholm equation, are introduced, and the inversion methods including Singular Value Decomposition (SVD), Butler-Reeds-Dawson (BRD), and Global Inversion (GI) methods are studied in detail, respectively. During one simulation test, multi-echo CPMG sequence activation is designed firstly, echo trains of the ideal fluid models are synthesized, then an inversion algorithm is carried on these synthetic echo trains, and finally T2-T1-D map is built. Futhermore, SVD, BRD, and GI methods are respectively applied into a same fluid model, and the computing speed and inversion accuracy are compared and analyzed. When the optimal inversion method and matrix dimention are applied, the inversion results are in good aggreement with the supposed fluid model, which indicates that the inversion method of 3D NMR is applieable for fluid typing of oil and gas reservoirs. Additionally, the forward modeling and inversion tests are made in oil-water and gas-water models, respectively, the sensitivity to the fluids in different magnetic field gradients is also examined in detail. The effect of magnetic gradient on fluid typing in 3D NMR logging is stuied and the optimal manetic gradient is choosen.

  16. Design of RNAs: comparing programs for inverse RNA folding.

    PubMed

    Churkin, Alexander; Retwitzer, Matan Drory; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2017-01-03

    Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.

  17. An approximate factorization method for inverse medium scattering with unknown buried objects

    NASA Astrophysics Data System (ADS)

    Qu, Fenglong; Yang, Jiaqing; Zhang, Bo

    2017-03-01

    This paper is concerned with the inverse problem of scattering of time-harmonic acoustic waves by an inhomogeneous medium with different kinds of unknown buried objects inside. By constructing a sequence of operators which are small perturbations of the far-field operator in a suitable way, we prove that each operator in this sequence has a factorization satisfying the Range Identity. We then develop an approximate factorization method for recovering the support of the inhomogeneous medium from the far-field data. Finally, numerical examples are provided to illustrate the practicability of the inversion algorithm.

  18. Strategies for efficient resolution analysis in full-waveform inversion

    NASA Astrophysics Data System (ADS)

    Fichtner, A.; van Leeuwen, T.; Trampert, J.

    2016-12-01

    Full-waveform inversion is developing into a standard method in the seismological toolbox. It combines numerical wave propagation for heterogeneous media with adjoint techniques in order to improve tomographic resolution. However, resolution becomes increasingly difficult to quantify because of the enormous computational requirements. Here we present two families of methods that can be used for efficient resolution analysis in full-waveform inversion. They are based on the targeted extraction of resolution proxies from the Hessian matrix, which is too large to store and to compute explicitly. Fourier methods rest on the application of the Hessian to Earth models with harmonic oscillations. This yields the Fourier spectrum of the Hessian for few selected wave numbers, from which we can extract properties of the tomographic point-spread function for any point in space. Random probing methods use uncorrelated, random test models instead of harmonic oscillations. Auto-correlating the Hessian-model applications for sufficiently many test models also characterises the point-spread function. Both Fourier and random probing methods provide a rich collection of resolution proxies. These include position- and direction-dependent resolution lengths, and the volume of point-spread functions as indicator of amplitude recovery and inter-parameter trade-offs. The computational requirements of these methods are equivalent to approximately 7 conjugate-gradient iterations in full-waveform inversion. This is significantly less than the optimisation itself, which may require tens to hundreds of iterations to reach convergence. In addition to the theoretical foundations of the Fourier and random probing methods, we show various illustrative examples from real-data full-waveform inversion for crustal and mantle structure.

  19. Constrained and joint inversion on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Doetsch, J.; Jordi, C.; Rieckh, V.; Guenther, T.; Schmelzbach, C.

    2015-12-01

    Unstructured meshes allow for inclusion of arbitrary surface topography, complex acquisition geometry and undulating geological interfaces in the inversion of geophysical data. This flexibility opens new opportunities for coupling different geophysical and hydrological data sets in constrained and joint inversions. For example, incorporating geological interfaces that have been derived from high-resolution geophysical data (e.g., ground penetrating radar) can add geological constraints to inversions of electrical resistivity data. These constraints can be critical for a hydrogeological interpretation of the inversion results. For time-lapse inversions of geophysical data, constraints can be derived from hydrological point measurements in boreholes, but it is difficult to include these hard constraints in the inversion of electrical resistivity monitoring data. Especially mesh density and the regularization footprint around the hydrological point measurements are important for an improved inversion compared to the unconstrained case. With the help of synthetic and field examples, we analyze how regularization and coupling operators should be chosen for time-lapse inversions constrained by point measurements and for joint inversions of geophysical data in order to take full advantage of the flexibility of unstructured meshes. For the case of constraining to point measurements, it is important to choose a regularization operator that extends beyond the neighboring cells and the uncertainty in the point measurements needs to be accounted for. For joint inversion, the choice of the regularization depends on the expected subsurface heterogeneity and the cell size of the parameter mesh.

  20. Solvent recycle/recovery

    SciTech Connect

    Paffhausen, M.W.; Smith, D.L.; Ugaki, S.N.

    1990-09-01

    This report describes Phase I of the Solvent Recycle/Recovery Task of the DOE Chlorinated Solvent Substitution Program for the US Air Force by the Idaho National Engineering Laboratory, EG G Idaho, Inc., through the US Department of Energy, Idaho Operations Office. The purpose of the task is to identify and test recovery and recycling technologies for proposed substitution solvents identified by the Biodegradable Solvent Substitution Program and the Alternative Solvents/Technologies for Paint Stripping Program with the overall objective of minimizing hazardous wastes. A literature search to identify recycle/recovery technologies and initial distillation studies has been conducted. 4 refs.

  1. Distribution and Phylogenetic Significance of the 71-kb Inversion in the Plastid Genome in Funariidae (Bryophyta)

    PubMed Central

    Goffinet, Bernard; Wickett, Norman J.; Werner, Olaf; Ros, Rosa Maria; Shaw, A. Jonathan; Cox, Cymon J.

    2007-01-01

    Background and Aims The recent assembly of the complete sequence of the plastid genome of the model taxon Physcomitrella patens (Funariaceae, Bryophyta) revealed that a 71-kb fragment, encompassing much of the large single copy region, is inverted. This inversion of 57% of the genome is the largest rearrangement detected in the plastid genomes of plants to date. Although initially considered diagnostic of Physcomitrella patens, the inversion was recently shown to characterize the plastid genome of two species from related genera within Funariaceae, but was lacking in another member of Funariidae. The phylogenetic significance of the inversion has remained ambiguous. Methods Exemplars of all families included in Funariidae were surveyed. DNA sequences spanning the inversion break ends were amplified, using primers that anneal to genes on either side of the putative end points of the inversion. Primer combinations were designed to yield a product for either the inverted or the non-inverted architecture. Key Results The survey reveals that exemplars of eight genera of Funariaceae, the sole species of Disceliaceae and three generic representatives of Encalyptales all share the 71-kb inversion in the large single copy of the plastid genome. By contrast, the plastid genome of Gigaspermaceae (Funariales) is characterized by a gene order congruent with that described for other mosses, liverworts and hornworts, and hence it does not possess this inversion. Conclusions The phylogenetic distribution of the inversion in the gene order supports a hypothesis only weakly supported by inferences from sequence data whereby Funariales are paraphyletic, with Funariaceae and Disceliaceae sharing a common ancestor with Encalyptales, and Gigaspermaceae sister to this combined clade. To reflect these relationships, Gigaspermaceae are excluded from Funariales and accommodated in their own order, Gigaspermales order nov., within Funariideae. PMID:17337480

  2. Wideband Arrhythmia-Insensitive-Rapid (AIR) Pulse Sequence for Cardiac T1 mapping without Image Artifacts induced by ICD

    PubMed Central

    Hong, KyungPyo; Jeong, Eun-Kee; Wall, T. Scott; Drakos, Stavros G.; Kim, Daniel

    2015-01-01

    Purpose To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). Methods We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz), in order to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and “wideband” AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5T. Results In 5 phantoms representing native myocardium and blood and post-contrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error >29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error <5%). Similarly, in 11 human subjects, compared with the control T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error >10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error <2.0%). Conclusion This study demonstrates the feasibility of a wideband pulse sequence for cardiac T1 mapping without significant image artifacts induced by ICD. PMID:25975192

  3. Direct magnitude and phase imaging of myelin using ultrashort echo time (UTE) pulse sequences: A feasibility study.

    PubMed

    He, Qun; Ma, Yajun; Fan, Shujuan; Shao, Hongda; Sheth, Vipul; Bydder, Graeme M; Du, Jiang

    2017-02-20

    In this paper, we aimed to investigate the feasibility of direct visualization of myelin, including myelin lipid and myelin basic protein (MBP), using two-dimensional ultrashort echo time (2D UTE) sequences and utilize phase information as a contrast mechanism in phantoms and in volunteers. The standard UTE sequence was used to detect both myelin and long T2 signal. An adiabatic inversion recovery UTE (IR-UTE) sequence was used to selectively detect myelin by suppressing signal from long T2 water protons. Magnitude and phase imaging and T2* were investigated on myelin lipid and MBP in the forms of lyophilized powders as well as paste-like phantoms with the powder mixed with D2O, and rubber phantoms as well as healthy volunteers. Contrast to noise ratio (CNR) between white and gray matter was measured. Both magnitude and phase images were generated for myelin and rubber phantoms as well white matter in vivo using the IR-UTE sequence. T2* values of ~300μs were comparable for myelin paste phantoms and the short T2* component in white matter of the brain in vivo. Mean CNR between white and gray matter in IR-UTE imaging was increased from -7.3 for the magnitude images to 57.4 for the phase images. The preliminary results suggest that the IR-UTE sequence allows simultaneous magnitude and phase imaging of myelin in vitro and in vivo.

  4. Wake Vortex Inverse Model User's Guide

    NASA Technical Reports Server (NTRS)

    Lai, David; Delisi, Donald

    2008-01-01

    NorthWest Research Associates (NWRA) has developed an inverse model for inverting landing aircraft vortex data. The data used for the inversion are the time evolution of the lateral transport position and vertical position of both the port and starboard vortices. The inverse model performs iterative forward model runs using various estimates of vortex parameters, vertical crosswind profiles, and vortex circulation as a function of wake age. Forward model predictions of lateral transport and altitude are then compared with the observed data. Differences between the data and model predictions guide the choice of vortex parameter values, crosswind profile and circulation evolution in the next iteration. Iterations are performed until a user-defined criterion is satisfied. Currently, the inverse model is set to stop when the improvement in the rms deviation between the data and model predictions is less than 1 percent for two consecutive iterations. The forward model used in this inverse model is a modified version of the Shear-APA model. A detailed description of this forward model, the inverse model, and its validation are presented in a different report (Lai, Mellman, Robins, and Delisi, 2007). This document is a User's Guide for the Wake Vortex Inverse Model. Section 2 presents an overview of the inverse model program. Execution of the inverse model is described in Section 3. When executing the inverse model, a user is requested to provide the name of an input file which contains the inverse model parameters, the various datasets, and directories needed for the inversion. A detailed description of the list of parameters in the inversion input file is presented in Section 4. A user has an option to save the inversion results of each lidar track in a mat-file (a condensed data file in Matlab format). These saved mat-files can be used for post-inversion analysis. A description of the contents of the saved files is given in Section 5. An example of an inversion input

  5. Fast recovery, high voltage silicon diodes for AC motor controllers

    NASA Technical Reports Server (NTRS)

    Balodis, V.; Berman, A. H.; Gaugh, C.

    1982-01-01

    The fabrication and characterization of a high voltage, high current, fast recovery silicon diode for use in AC motor controllers, originally developed for NASA for use in avionics power supplies, is presented. The diode utilizes a positive bevel PIN mesa structure with glass passivation and has the following characteristics: peak inverse voltage - 1200 volts, forward voltage at 50 amperes - 1.5 volts, reverse recovery time of 200 nanoseconds. Characterization data for the diode, included in a table, show agreement with design concepts developed for power diodes. Circuit diagrams of the diode are also given.

  6. Applications of matrix inversion tomosynthesis

    NASA Astrophysics Data System (ADS)

    Warp, Richard J.; Godfrey, Devon J.; Dobbins, James T., III

    2000-04-01

    The improved image quality and characteristics of new flat- panel x-ray detectors have renewed interest in advanced algorithms such as tomosynthesis. Digital tomosynthesis is a method of acquiring and reconstructing a three-dimensional data set with limited-angle tube movement. Historically, conventional tomosynthesis reconstruction has suffered contamination of the planes of interest by blurred out-of- plane structures. This paper focuses on a Matrix Inversion Tomosynthesis (MITS) algorithm to remove unwanted blur from adjacent planes. The algorithm uses a set of coupled equations to solve for the blurring function in each reconstructed plane. This paper demonstrates the use of the MITS algorithm in three imaging applications: small animal microscopy, chest radiography, and orthopedics. The results of the MITS reconstruction process demonstrate an improved reduction of blur from out-of-plane structures when compared to conventional tomosynthesis. We conclude that the MITS algorithm holds potential in a variety of applications to improve three-dimensional image reconstruction.

  7. Inverse planning incorporating organ motion.

    PubMed

    Li, J G; Xing, L

    2000-07-01

    Accurate targeting is important in intensity-modulated radiation therapy (IMRT). The positional uncertainties of structures with respect to the external beams arise in part from random organ motion and patient setup errors. While it is important to improve immobilization and reduce the influence of organ motion, the residual effects should be included in the IMRT plan design. Current inverse planning algorithms follow the conventional approach and include uncertainties by assuming population-based margins to the target and sensitive structures. Margin around a structure represents a "hard boundary" and the fact that a structure has a spatial probability distribution has been completely ignored. With increasing understanding of spatial uncertainties of structures and the technical capability of fine-tuning the dose distribution on an individual beamlet level in IMRT, it seems timely and important to fully utilize the information in the planning process. This will reduce the "effective" margins of the structures and facilitate dose escalation. Instead of specifying a "hard margin," we describe an inverse planning algorithm which takes into consideration positional uncertainty in terms of spatial probability distribution. The algorithm was demonstrated by assuming that the random organ motion can be represented by a three-dimensional Gaussian distribution function. Other probability distributions can be dealt with similarly. In particular, the commonly used "hard margin" is a special case of the current approach with a uniform probability distribution within a specified range. The algorithm was applied to plan treatment for a prostate case and a pancreatic case. The results were compared with those obtained by adding a margin to the clinical target volume. Better sparing of the sensitive structures were obtained in both cases using the proposed method for approximately the same target coverage.

  8. RECOVERY OF RUTHENIUM VALUES

    DOEpatents

    Grummitt, W.E.; Hardwick, W.H.

    1961-01-01

    A process is given for the recovery of ruthenium from its aqueous solutions by oxidizing the ruthenium to the octavalent state and subsequently extracting the ruthenium into a halogen-substituted liquid paraffin.

  9. CEBAF Energy Recovery Experiment

    SciTech Connect

    Bogacz, Alex; Bogacz, Slawomir; Bogacz, Alex; Bogacz, Slawomir; Beard, Kevin; Bengtsson, Johan; Butler, Corey; Chao, Yu-Chiu; Chattopadhyay, Swapan; Dong, Hai; Douglas, David; Freyberger, Arne; Guerra, Al; Hicks, William; Hofler, Alicia; Hovater, J.; Hutton, Andrew; Lauze, Ronald; Merminga, Nikolitsa; Plawski, Tomasz; Roblin, Yves; Spata, Michael; Tennant, Christopher; Tiefenback, Michael; Bernard, A.; Toyokawa, Hiroyuki

    2003-05-01

    A successful GeV scale energy recovery demonstration with high ratio of accelerated-to-recovered energies (50:1) was recently carried out on the CEBAF recirculating linear accelerator. Future high energy (multi-GeV), high current (hundreds of milli-Amperes) beams would require gigaWatt-class RF systems in conventional linacs - a prohibitively expensive proposition. However, invoking energy recovery [1] alleviates extreme RF power demands; required RF power becomes nearly independent of beam current, which improves linac efficiency and increases cost effectiveness. Furthermore, energy recovering linacs promise efficiencies of storage rings, while maintaining beam quality of linacs: superior emittance and energy spread and short bunches (sub-pico sec.). Finally, energy recovery alleviates shielding, if the beam is dumped below the neutron production threshold. Jefferson Lab has demonstrated its expertise in the field of Energy Recovery Linacs (ERLs) with the successful operation of the

  10. Heart Attack Recovery FAQs

    MedlinePlus

    ... a Heart Attack Treatment of a Heart Attack Life After a Heart Attack Heart Failure About Heart Failure ... a Heart Attack • Treatment of a Heart Attack • Life After a Heart Attack Lifestyle Changes Recovery FAQs • Heart ...

  11. Silver recovery system data

    SciTech Connect

    Boulineau, B.

    1991-08-26

    In August of 1990 the Savannah River Site Photography Group began testing on a different type of silver recovery system. This paper describes the baseline study and the different phases of installation and testing of the system.

  12. Disaster Recovery Guide

    MedlinePlus

    ... Cross Store Home Get Help Prepare for Emergencies Disaster Recovery Guide When the immediate emergency is over, ... local Red Cross chapter . Staying Safe After a Disaster Learn the steps to take during and after ...

  13. A Bayesian approach to nonlinear inversion

    NASA Technical Reports Server (NTRS)

    Jackson, D. D.; Matsuura, M.

    1985-01-01

    Powerful methods are now available for solving linear parametric inverse problems. However, many inverse problems which arise in geohysics are nonlinear. Fortunately, it is possible to treat most of these with the air of linear perturbation theory and liner inversion. But a convenient method is needed for assessing the importance of nonlinearity in these quasi-linear problems. The present paper provides such a method. Matsu'ura and Jackson (1984) have presented a simple algorithm for evaluating the asymptotic covariance matrix fo estimation errors. In the present investigation, aspects of linear inversion are discussed, taking into account linear parametric inverse problems, nonuniqueness, prior information, confidence limits, conditional and marginal statistics, the relative importance of the prior and observational data, and standardized variables. Attention is also given to nonlinear inversion, and the application of the considered approaches to a number of examples.

  14. Refuse recycling and recovery

    SciTech Connect

    Holmes, J.R.

    1981-01-01

    Sanitary landfill of domestic, commercial, and industrial wastes is the predominant method of waste disposal in the United Kingdom. Although there was various waste disposal processes at various stages of design and test, landfill and incineration are still the only reliable methods of waste processing. Methods of recovery and use of refuse are examined in this book together with various separation processes, waste derived fuels, refuse composting, and glass and metal recovery. (Refs. 39).

  15. Apollo 8 Recovery

    NASA Technical Reports Server (NTRS)

    1968-01-01

    A team of U.S. Navy underwater demolition swimmers prepares the Apollo 8 command module for being hoisted aboard the carrier U.S.S. Yorktown, prime recovery vessel for the initial manned lunar orbital mission. The crew members - astronauts Frank Borman, James A. Lovell, Jr., and William A. Anders - had already egressed the spacecraft and were aboard the recovery ship at the time of this photo.

  16. Postattack Recovery Strategies.

    DTIC Science & Technology

    1980-11-01

    relocation conditions --problems that range from financing and the stockpiling of needed resources to providing information about how, where, and with...sustain their health, improve economic and social conditions and start rebuilding for the long-term recovery. The types of information that would be...Postattack Economic Conditions One of the important federal roles for aiding postattack economic recovery will be that of supplying information on

  17. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

    USDA-ARS?s Scientific Manuscript database

    Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combinat...

  18. Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence

    PubMed Central

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-01-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6–24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  19. Inversion methods for interpretation of asteroid lightcurves

    NASA Technical Reports Server (NTRS)

    Kaasalainen, Mikko; Lamberg, L.; Lumme, K.

    1992-01-01

    We have developed methods of inversion that can be used in the determination of the three-dimensional shape or the albedo distribution of the surface of a body from disk-integrated photometry, assuming the shape to be strictly convex. In addition to the theory of inversion methods, we have studied the practical aspects of the inversion problem and applied our methods to lightcurve data of 39 Laetitia and 16 Psyche.

  20. Forward model nonlinearity versus inverse model nonlinearity

    USGS Publications Warehouse

    Mehl, S.

    2007-01-01

    The issue of concern is the impact of forward model nonlinearity on the nonlinearity of the inverse model. The question posed is, "Does increased nonlinearity in the head solution (forward model) always result in increased nonlinearity in the inverse solution (estimation of hydraulic conductivity)?" It is shown that the two nonlinearities are separate, and it is not universally true that increased forward model nonlinearity increases inverse model nonlinearity. ?? 2007 National Ground Water Association.

  1. NICOLE: NLTE Stokes Synthesis/Inversion Code

    NASA Astrophysics Data System (ADS)

    Socas-Navarro, H.

    2015-08-01

    NICOLE, written in Fortran 90, seeks the model atmosphere that provides the best fit to the Stokes profiles (in a least-squares sense) of an arbitrary number of simultaneously-observes spectral lines from solar/stellar atmospheres. The inversion core used for the development of NICOLE is the LORIEN engine (the Lovely Reusable Inversion ENgine), which combines the SVD technique with the Levenberg-Marquardt minimization method to solve the inverse problem.

  2. Matched Field Tomographic Inversion for Geoacoustic Properties

    DTIC Science & Technology

    2016-06-07

    Matched Field Tomographic Inversion for Geoacoustic Properties N.Ross Chapman School of Earth and Ocean Sciences University of Victoria PO Box 3055...sound propagation in shallow water. The long term goal of this work is to develop a new tomographic inversion method based on matched field processing of...broadband data for estimating geoacoustic properties over an extended region of the ocean bottom. OBJECTIVES Matched field tomographic inversion is a

  3. Time-reversal and Bayesian inversion

    NASA Astrophysics Data System (ADS)

    Debski, Wojciech

    2017-04-01

    Probabilistic inversion technique is superior to the classical optimization-based approach in all but one aspects. It requires quite exhaustive computations which prohibit its use in huge size inverse problems like global seismic tomography or waveform inversion to name a few. The advantages of the approach are, however, so appealing that there is an ongoing continuous afford to make the large inverse task as mentioned above manageable with the probabilistic inverse approach. One of the perspective possibility to achieve this goal relays on exploring the internal symmetry of the seismological modeling problems in hand - a time reversal and reciprocity invariance. This two basic properties of the elastic wave equation when incorporating into the probabilistic inversion schemata open a new horizons for Bayesian inversion. In this presentation we discuss the time reversal symmetry property, its mathematical aspects and propose how to combine it with the probabilistic inverse theory into a compact, fast inversion algorithm. We illustrate the proposed idea with the newly developed location algorithm TRMLOC and discuss its efficiency when applied to mining induced seismic data.

  4. Adaptation through chromosomal inversions in Anopheles

    PubMed Central

    Ayala, Diego; Ullastres, Anna; González, Josefa

    2014-01-01

    Chromosomal inversions have been repeatedly involved in local adaptation in a large number of animals and plants. The ecological and behavioral plasticity of Anopheles species—human malaria vectors—is mirrored by high amounts of polymorphic inversions. The adaptive significance of chromosomal inversions has been consistently attested by strong and significant correlations between their frequencies and a number of phenotypic traits. Here, we provide an extensive literature review of the different adaptive traits associated with chromosomal inversions in the genus Anopheles. Traits having important consequences for the success of present and future vector control measures, such as insecticide resistance and behavioral changes, are discussed. PMID:24904633

  5. Human inversions and their functional consequences

    PubMed Central

    Puig, Marta; Casillas, Sònia; Villatoro, Sergi

    2015-01-01

    Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies. PMID:25998059

  6. Inverse Problem;Litho_Inversion; Geology and Geophysics

    NASA Astrophysics Data System (ADS)

    Antonio, Guillen; Gabriel, Courrioux; Bernard, Bourgine

    2015-04-01

    Subsurface modeling is a key tool to describe, understand and quantify geological processes. As the subsurface is inaccessible and its observation is limited by acquisition methods, 3D models of the subsurface are usually built from the interpretation of sparse data with limited resolution. Therefore, uncertainties occur during the model building process, due to possible cognitive human biais, natural variability of geological objects and intrinsic uncertainties of data. In such context, the predictibility of models is limited by uncertainties, which must be assessed in order to reduce economical and human risks linked to the use of models. This work focuses more specifically on uncertainties about geological structures. In this context, a stochastic method is developed for generating structural models with various fault and horizon geometries as well as fault connections. Realistic geological objects are obtained using implicit modeling that represents a surface by an equipotential of a volumetric scalar field. Faults have also been described by a reduced set of uncertain parameters, which opens the way to the inversion of structural objects using geophysical data by baysian methods.

  7. Are chromosomal inversions induced by transposable elements? A paradigm from the malaria mosquito Anopheles gambiae.

    PubMed

    Mathiopoulos, K D; della Torre, A; Santolamazza, F; Predazzi, V; Petrarca, V; Coluzzi, M

    1999-09-01

    Chromosomal rearrangements abound in nature and can be studied in detail in organisms with polytene chromosomes. In Drosophila and in Anopheline mosquitoes most speciation processes seem to be associated with the establishment of chromosomal rearrangements, particularly of paracentric inversions. It is not known what triggers inversions in natural populations. In the laboratory inversions are commonly generated by X-rays, mutagens or after the activity of certain transposable elements (TEs). The Anopheles gambiae complex is comprised of six sibling species, each one characterized by the presence of fixed paracentric inversions on their chromosomes. Two of these, An. gambiae s.s. and An. arabiensis, are the most important vectors of human malaria and are structured into sub-populations, each carrying a characteristic set of polymorphic chromosomal inversions. We have cloned the breakpoints of the naturally occurring polymorphic inversion In(2R)d' of An. arabiensis. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a transposable element that we called Odysseus. Characteristics of Odysseus' terminal region and its cytological distribution in different strains as well as within the same strain indicate that Odysseus is an actively transposing element. The presence of Odysseus at the junction of the naturally occurring inversion In(2R)d' suggests that the inversion may be the result of the TEs activity. Cytological evidence from Drosophila melanogaster has also implicated the hobo transposable element in the generation of certain Hawaiian endemic inversions. This picture supports the hypothesis of the important role of TEs in generating natural inversions.

  8. Molecular characterization of the breakpoints of an inversion fixed between Drosophila melanogaster and D. subobscura

    SciTech Connect

    Cirera, S.; Martin-Campos, J.M.; Segarra, C.

    1995-01-01

    The two breakpoints of a chromosomal inversion fixed since the split of Drosophila melanogaster and D. subobscura lineages have been isolated and sequenced in both species. The regions spanning the break-points initially were identified by the presence of two signals after interspecific in situ hybridization on polytene chromosomes. Interspecific comparison of the sequenced regions allowed us to delineate the location of the breakpoints. Close to one of these breakpoints a new transcription unit (bcn92) has been identified in both species. The inversion fixed between D. melanogaster and D. subobscura does not seem to have broken any transcription unit. Neither complete nor defective transposable elements were found in the regions encompassing the breakpoints. Short thymine-rich sequences (30-50 hp long) have been found bordering the breakpoint regions. Although alternating Pur-Pyr sequences were detected, these putative target sites for topoisomerase II were not differentially clustered in the breakpoints. 22 refs., 6 figs.

  9. Laterally constrained inversion for CSAMT data interpretation

    NASA Astrophysics Data System (ADS)

    Wang, Ruo; Yin, Changchun; Wang, Miaoyue; Di, Qingyun

    2015-10-01

    Laterally constrained inversion (LCI) has been successfully applied to the inversion of dc resistivity, TEM and airborne EM data. However, it hasn't been yet applied to the interpretation of controlled-source audio-frequency magnetotelluric (CSAMT) data. In this paper, we apply the LCI method for CSAMT data inversion by preconditioning the Jacobian matrix. We apply a weighting matrix to Jacobian to balance the sensitivity of model parameters, so that the resolution with respect to different model parameters becomes more uniform. Numerical experiments confirm that this can improve the convergence of the inversion. We first invert a synthetic dataset with and without noise to investigate the effect of LCI applications to CSAMT data, for the noise free data, the results show that the LCI method can recover the true model better compared to the traditional single-station inversion; and for the noisy data, the true model is recovered even with a noise level of 8%, indicating that LCI inversions are to some extent noise insensitive. Then, we re-invert two CSAMT datasets collected respectively in a watershed and a coal mine area in Northern China and compare our results with those from previous inversions. The comparison with the previous inversion in a coal mine shows that LCI method delivers smoother layer interfaces that well correlate to seismic data, while comparison with a global searching algorithm of simulated annealing (SA) in a watershed shows that though both methods deliver very similar good results, however, LCI algorithm presented in this paper runs much faster. The inversion results for the coal mine CSAMT survey show that a conductive water-bearing zone that was not revealed by the previous inversions has been identified by the LCI. This further demonstrates that the method presented in this paper works for CSAMT data inversion.

  10. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  11. Two hybrid regularization frameworks for solving the electrocardiography inverse problem.

    PubMed

    Jiang, Mingfeng; Xia, Ling; Shou, Guofa; Liu, Feng; Crozier, Stuart

    2008-09-21

    In this paper, two hybrid regularization frameworks, LSQR-Tik and Tik-LSQR, which integrate the properties of the direct regularization method (Tikhonov) and the iterative regularization method (LSQR), have been proposed and investigated for solving ECG inverse problems. The LSQR-Tik method is based on the Lanczos process, which yields a sequence of small bidiagonal systems to approximate the original ill-posed problem and then the Tikhonov regularization method is applied to stabilize the projected problem. The Tik-LSQR method is formulated as an iterative LSQR inverse, augmented with a Tikhonov-like prior information term. The performances of these two hybrid methods are evaluated using a realistic heart-torso model simulation protocol, in which the heart surface source method is employed to calculate the simulated epicardial potentials (EPs) from the action potentials (APs), and then the acquired EPs are used to calculate simulated body surface potentials (BSPs). The results show that the regularized solutions obtained by the LSQR-Tik method are approximate to those of the Tikhonov method, the computational cost of the LSQR-Tik method, however, is much less than that of the Tikhonov method. Moreover, the Tik-LSQR scheme can reconstruct the epcicardial potential distribution more accurately, specifically for the BSPs with large noisy cases. This investigation suggests that hybrid regularization methods may be more effective than separate regularization approaches for ECG inverse problems.

  12. Strategies for source space limitation in tomographic inverse procedures

    SciTech Connect

    George, J.S.; Lewis, P.S.; Schlitt, H.A.; Kaplan, L.; Gorodnitsky, I.; Wood, C.C.

    1994-02-01

    The use of magnetic recordings for localization of neural activity requires the solution of an ill-posed inverse problem: i.e. the determination of the spatial configuration, orientation, and timecourse of the currents that give rise to a particular observed field distribution. In its general form, this inverse problem has no unique solution; due to superposition and the existence of silent source configurations, a particular magnetic field distribution at the head surface could be produced by any number of possible source configurations. However, by making assumptions concerning the number and properties of neural sources, it is possible to use numerical minimization techniques to determine the source model parameters that best account for the experimental observations while satisfying numerical or physical criteria. In this paper the authors describe progress on the development and validation of inverse procedures that produce distributed estimates of neuronal currents. The goal is to produce a temporal sequence of 3-D tomographic reconstructions of the spatial patterns of neural activation. Such approaches have a number of advantages, in principle. Because they do not require estimates of model order and parameter values (beyond specification of the source space), they minimize the influence of investigator decisions and are suitable for automated analyses. These techniques also allow localization of sources that are not point-like; experimental studies of cognitive processes and of spontaneous brain activity are likely to require distributed source models.

  13. Time synchronization and geoacoustic inversion using baleen whale sounds

    NASA Astrophysics Data System (ADS)

    Thode, Aaron; Gerstoft, Peter; Stokes, Dale; Noad, Mike; Burgess, William; Cato, Doug

    2005-09-01

    In 1996 matched-field processing (MFP) and geoacoustic inversion methods were used to invert for range, depth, and source levels of blue whale vocalizations. [A. M. Thode, G. L. D'Spain, and W. A. Kuperman, J. Acoust. Soc. Am. 107, 1286-1300 (2000)]. Humpback whales also produce broadband sequences of sounds that contain significant energy between 50 Hz to over 1 kHz. In Oct. 2003 and 2004 samples of humpback whale song were collected on vertical and titled arrays in 24-m-deep water in conjunction with the Humpback Acoustic Research Collaboration (HARC). The arrays consisted of autonomous recorders attached to a rope, and were time synchronized by extending standard geoacoustic inversion methods to invert for clock offset as well as whale location. The diffuse ambient noise background field was then used to correct for subsequent clock drift. Independent measurements of the local bathymetry and transmission loss were also obtained in the area. Preliminary results are presented for geoacoustic inversions of the ocean floor composition and humpback whale locations and source levels. [Work supported by ONR Ocean Acoustic Entry Level Faculty Award and Marine Mammals Program.

  14. A generalized smoothness criterion for acoustic-to-articulatory inversion

    PubMed Central

    Ghosh, Prasanta Kumar; Narayanan, Shrikanth

    2010-01-01

    The many-to-one mapping from representations in the speech articulatory space to acoustic space renders the associated acoustic-to-articulatory inverse mapping non-unique. Among various techniques, imposing smoothness constraints on the articulator trajectories is one of the common approaches to handle the non-uniqueness in the acoustic-to-articulatory inversion problem. This is because, articulators typically move smoothly during speech production. A standard smoothness constraint is to minimize the energy of the difference of the articulatory position sequence so that the articulator trajectory is smooth and low-pass in nature. Such a fixed definition of smoothness is not always realistic or adequate for all articulators because different articulators have different degrees of smoothness. In this paper, an optimization formulation is proposed for the inversion problem, which includes a generalized smoothness criterion. Under such generalized smoothness settings, the smoothness parameter can be chosen depending on the specific articulator in a data-driven fashion. In addition, this formulation allows estimation of articulatory positions recursively over time without any loss in performance. Experiments with the MOCHA TIMIT database show that the estimated articulator trajectories obtained using such a generalized smoothness criterion have lower RMS error and higher correlation with the actual measured trajectories compared to those obtained using a fixed smoothness constraint. PMID:20968386

  15. Recovery of Interdependent Networks

    NASA Astrophysics Data System (ADS)

    di Muro, M. A.; La Rocca, C. E.; Stanley, H. E.; Havlin, S.; Braunstein, L. A.

    2016-03-01

    Recent network research has focused on the cascading failures in a system of interdependent networks and the necessary preconditions for system collapse. An important question that has not been addressed is how to repair a failing system before it suffers total breakdown. Here we introduce a recovery strategy for nodes and develop an analytic and numerical framework for studying the concurrent failure and recovery of a system of interdependent networks based on an efficient and practically reasonable strategy. Our strategy consists of repairing a fraction of failed nodes, with probability of recovery γ, that are neighbors of the largest connected component of each constituent network. We find that, for a given initial failure of a fraction 1 ‑ p of nodes, there is a critical probability of recovery above which the cascade is halted and the system fully restores to its initial state and below which the system abruptly collapses. As a consequence we find in the plane γ ‑ p of the phase diagram three distinct phases. A phase in which the system never collapses without being restored, another phase in which the recovery strategy avoids the breakdown, and a phase in which even the repairing process cannot prevent system collapse.

  16. Recovery of Interdependent Networks.

    PubMed

    Di Muro, M A; La Rocca, C E; Stanley, H E; Havlin, S; Braunstein, L A

    2016-03-09

    Recent network research has focused on the cascading failures in a system of interdependent networks and the necessary preconditions for system collapse. An important question that has not been addressed is how to repair a failing system before it suffers total breakdown. Here we introduce a recovery strategy for nodes and develop an analytic and numerical framework for studying the concurrent failure and recovery of a system of interdependent networks based on an efficient and practically reasonable strategy. Our strategy consists of repairing a fraction of failed nodes, with probability of recovery γ, that are neighbors of the largest connected component of each constituent network. We find that, for a given initial failure of a fraction 1 - p of nodes, there is a critical probability of recovery above which the cascade is halted and the system fully restores to its initial state and below which the system abruptly collapses. As a consequence we find in the plane γ - p of the phase diagram three distinct phases. A phase in which the system never collapses without being restored, another phase in which the recovery strategy avoids the breakdown, and a phase in which even the repairing process cannot prevent system collapse.

  17. Recovery of Interdependent Networks

    PubMed Central

    Di Muro, M. A.; La Rocca, C. E.; Stanley, H. E.; Havlin, S.; Braunstein, L. A.

    2016-01-01

    Recent network research has focused on the cascading failures in a system of interdependent networks and the necessary preconditions for system collapse. An important question that has not been addressed is how to repair a failing system before it suffers total breakdown. Here we introduce a recovery strategy for nodes and develop an analytic and numerical framework for studying the concurrent failure and recovery of a system of interdependent networks based on an efficient and practically reasonable strategy. Our strategy consists of repairing a fraction of failed nodes, with probability of recovery γ, that are neighbors of the largest connected component of each constituent network. We find that, for a given initial failure of a fraction 1 − p of nodes, there is a critical probability of recovery above which the cascade is halted and the system fully restores to its initial state and below which the system abruptly collapses. As a consequence we find in the plane γ − p of the phase diagram three distinct phases. A phase in which the system never collapses without being restored, another phase in which the recovery strategy avoids the breakdown, and a phase in which even the repairing process cannot prevent system collapse. PMID:26956773

  18. Monte Carlo uncertainty analyses of a bLS inverse-dispersion technique for measuring gas emissions from livestock operations

    USDA-ARS?s Scientific Manuscript database

    The backward Lagrangian stochastic (bLS) inverse-dispersion technique has been used to measure fugitive gas emissions from livestock operations. The accuracy of the bLS technique, as indicated by the percentages of gas recovery in various tracer-release experiments, has generally been within ± 10% o...

  19. Inverse problem in radionuclide transport

    SciTech Connect

    Yu, C.

    1988-01-01

    The disposal of radioactive waste must comply with the performance objectives set forth in 10 CFR 61 for low-level waste (LLW) and 10 CFR 60 for high-level waste (HLW). To determine probable compliance, the proposed disposal system can be modeled to predict its performance. One of the difficulties encountered in such a study is modeling the migration of radionuclides through a complex geologic medium for the long term. Although many radionuclide transport models exist in the literature, the accuracy of the model prediction is highly dependent on the model parameters used. The problem of using known parameters in a radionuclide transport model to predict radionuclide concentrations is a direct problem (DP); whereas the reverse of DP, i.e., the parameter identification problem of determining model parameters from known radionuclide concentrations, is called the inverse problem (IP). In this study, a procedure to solve IP is tested, using the regression technique. Several nonlinear regression programs are examined, and the best one is recommended. 13 refs., 1 tab.

  20. Inverse magnetic/shear catalysis

    NASA Astrophysics Data System (ADS)

    McInnes, Brett

    2016-05-01

    It is well known that very large magnetic fields are generated when the Quark-Gluon Plasma is formed during peripheral heavy-ion collisions. Lattice, holographic, and other studies strongly suggest that these fields may, for observationally relevant field values, induce ;inverse magnetic catalysis;, signalled by a lowering of the critical temperature for the chiral/deconfinement transition. The theoretical basis of this effect has recently attracted much attention; yet so far these investigations have not included another, equally dramatic consequence of the peripheral collision geometry: the QGP acquires a large angular momentum vector, parallel to the magnetic field. Here we use holographic techniques to argue that the angular momentum can also, independently, have an effect on transition temperatures, and we obtain a rough estimate of the relative effects of the presence of both a magnetic field and an angular momentum density. We find that the shearing angular momentum reinforces the effect of the magnetic field at low values of the baryonic chemical potential, but that it can actually decrease that effect at high chemical potentials.

  1. Inversion based on computational simulations

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.

    1998-09-01

    A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal.

  2. MODEL SELECTION FOR SPECTROPOLARIMETRIC INVERSIONS

    SciTech Connect

    Asensio Ramos, A.; Manso Sainz, R.; Martinez Gonzalez, M. J.; Socas-Navarro, H.; Viticchie, B.

    2012-04-01

    Inferring magnetic and thermodynamic information from spectropolarimetric observations relies on the assumption of a parameterized model atmosphere whose parameters are tuned by comparison with observations. Often, the choice of the underlying atmospheric model is based on subjective reasons. In other cases, complex models are chosen based on objective reasons (for instance, the necessity to explain asymmetries in the Stokes profiles) but it is not clear what degree of complexity is needed. The lack of an objective way of comparing models has, sometimes, led to opposing views of the solar magnetism because the inferred physical scenarios are essentially different. We present the first quantitative model comparison based on the computation of the Bayesian evidence ratios for spectropolarimetric observations. Our results show that there is not a single model appropriate for all profiles simultaneously. Data with moderate signal-to-noise ratios (S/Ns) favor models without gradients along the line of sight. If the observations show clear circular and linear polarization signals above the noise level, models with gradients along the line are preferred. As a general rule, observations with large S/Ns favor more complex models. We demonstrate that the evidence ratios correlate well with simple proxies. Therefore, we propose to calculate these proxies when carrying out standard least-squares inversions to allow for model comparison in the future.

  3. Inversion of SPECTREM airborne electromagnetic data for groundwater assessment in outback Australia

    NASA Astrophysics Data System (ADS)

    Ley-Cooper, A. Y.; Munday, T. J.

    2012-12-01

    Inversion methods based on 1D forward model responses accurately honour flat laying layered environments and they have a valuable role in extracting hydrogeological information from a range of AEM systems. The conversion of a non-linear EM response to accurate estimates of ground conductivity is essential for groundwater assessment and aquifer characterisation. It is critical to ensure the forward response accurately models the system transfer function used in the inversion. The weathered conductive nature of the Australian overburden, presents a challenge for all EM induction techniques. Target geometry can be modelled for each system, but field conditions add complexity. We examine effects arising from applying a 1D inversion on SPECTREM2000 AEM data in areas with 3D anisotropy, and consider its suitability for regional surveys in outback Australia. The accurate recovery of conductivity models from AEM systems normally considered as targeting tools, has become particularly important where their conjunctive use for mineral exploration and groundwater assessment is now being canvassed. SPECTREM is a fixed wing, time domain EM system that employs a bipolar full cycle square current waveform operating with a variable base frequency from 25Hz upwards. Its rms transmitter dipole moment is 400 000 A.m2 , and flies at a nominal height of 90m above the ground with the 'bird' towed approximately 131m behind and 40m below the aircraft. Both X and Z component data are recorded and then processed to produce a step response at each fiducial. Through a consideration of approaches to primary field removal, data normalisation, and an understanding of transmitter(TX) - receiver(RX) geometry we have a procedure to model and invert data from this system. Relative separations of TX and RX are not monitored in flight, requiring they be estimated afterwards. The challenge, with this system having a transmitter always active, is to separate the measured total field into the transmitted

  4. Iterative method for generating correlated binary sequences

    NASA Astrophysics Data System (ADS)

    Usatenko, O. V.; Melnik, S. S.; Apostolov, S. S.; Makarov, N. M.; Krokhin, A. A.

    2014-11-01

    We propose an efficient iterative method for generating random correlated binary sequences with a prescribed correlation function. The method is based on consecutive linear modulations of an initially uncorrelated sequence into a correlated one. Each step of modulation increases the correlations until the desired level has been reached. The robustness and efficiency of the proposed algorithm are tested by generating sequences with inverse power-law correlations. The substantial increase in the strength of correlation in the iterative method with respect to single-step filtering generation is shown for all studied correlation functions. Our results can be used for design of disordered superlattices, waveguides, and surfaces with selective transport properties.

  5. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  6. Inversion and approximation of Laplace transforms

    NASA Technical Reports Server (NTRS)

    Lear, W. M.

    1980-01-01

    A method of inverting Laplace transforms by using a set of orthonormal functions is reported. As a byproduct of the inversion, approximation of complicated Laplace transforms by a transform with a series of simple poles along the left half plane real axis is shown. The inversion and approximation process is simple enough to be put on a programmable hand calculator.

  7. An exact inverse method for subsonic flows

    NASA Technical Reports Server (NTRS)

    Daripa, Prabir

    1988-01-01

    A new inverse method for the aerodynamic design of airfoils is presented for subcritical flows. The pressure distribution in this method can be prescribed as a function of the arclength of the still unknown body. It is shown that this inverse problem is mathematically equivalent to solving only one nonlinear boundary value problem subject to known Dirichlet data on the boundary.

  8. Essential right inverses and system zeros

    NASA Technical Reports Server (NTRS)

    Wyman, B. F.; Sain, M. K.

    1979-01-01

    A module-theoretic definition of right inverse systems for epic functions is presented to developing a theory for inverse systems. Examples are given which illustrate the basic conceptual issues of the approach. The theory provides a way to better understanding of multivariable zeros.

  9. Inversion in Mathematical Thinking and Learning

    ERIC Educational Resources Information Center

    Greer, Brian

    2012-01-01

    Inversion is a fundamental relational building block both within mathematics as the study of structures and within people's physical and social experience, linked to many other key elements such as equilibrium, invariance, reversal, compensation, symmetry, and balance. Within purely formal arithmetic, the inverse relationships between addition and…

  10. Inversion in Mathematical Thinking and Learning

    ERIC Educational Resources Information Center

    Greer, Brian

    2012-01-01

    Inversion is a fundamental relational building block both within mathematics as the study of structures and within people's physical and social experience, linked to many other key elements such as equilibrium, invariance, reversal, compensation, symmetry, and balance. Within purely formal arithmetic, the inverse relationships between addition and…

  11. Prestack seismic inversion and reservoir property prediction

    NASA Astrophysics Data System (ADS)

    Chi, Xingang

    In this dissertation, I have applied the method of prestack seismic inversion with uncertainty analysis. Also, I have developed the methods of the rock physics template analysis, the fluid modulus inversion and the reservoir property inversion from AVO attributes with and without constraint to improve the technique of reservoir characterization. I use the prestack seismic inversion to invert the elastic properties and use the statistical method to derive the posterior probability of the inverted elastic properties for the uncertainty analysis. I use the rock physics template drawn in the cross-plot of the inverted elastic properties to analyze the lithology and fluid property in the target reservoir. I develop the fluid modulus inversion method based on the simplified Gassmann's equation and the empirical rock physics relationship. Using the inverted fluid modulus, I estimate the gas saturation of the target reservoir before drilling. The reservoir property inversion is to predict the porosity, shale volume and water saturation of the reservoir from AVO attributes to enhance the reservoir interpretation and characterization. I apply this method with the statistical analysis together to execute the uncertainty analysis for the inversion results. Two methods of reservoir property inversion from AVO attributes are attempted in this dissertation: one is performed without constraint and the other is performed with the constrained relationship of the porosity and shale volume.

  12. Galerkin approximation for inverse problems for nonautonomous nonlinear distributed systems

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Reich, Simeon; Rosen, I. G.

    1988-01-01

    An abstract framework and convergence theory is developed for Galerkin approximation for inverse problems involving the identification of nonautonomous nonlinear distributed parameter systems. A set of relatively easily verified conditions is provided which are sufficient to guarantee the existence of optimal solutions and their approximation by a sequence of solutions to a sequence of approximating finite dimensional identification problems. The approach is based on the theory of monotone operators in Banach spaces and is applicable to a reasonably broad class of nonlinear distributed systems. Operator theoretic and variational techniques are used to establish a fundamental convergence result. An example involving evolution systems with dynamics described by nonstationary quasilinear elliptic operators along with some applications are presented and discussed.

  13. Analysis, Control and Inverse Theory of Fluids,Waves, Materials Structures, and theirInteractions

    DTIC Science & Technology

    2015-07-06

    dimensional problem) C) Area concerning Inverse Theory of Partial Differential Equations ; more precisely, coefficient recovery via just one boundary...stability of a wave equation with strong damping and dynamic boundary conditions, Evolution Equations and Control Theory , Vol 2, Nr 4, pp 631-667, 2013...specialization of the known optimal control or min-max game theory of parabolic problems of the literature B) Area concerning flow-structure interaction

  14. Kalman filtering, smoothing and recursive robot arm forward and inverse dynamics

    NASA Technical Reports Server (NTRS)

    Rodriguez, G.

    1986-01-01

    The inverse and forward dynamics problems for multi-link serial manipulators are solved by using recursive techniques from linear filtering and smoothing theory. The pivotal step is to cast the system dynamics and kinematics as a two-point boundary-value problem. Solution of this problem leads to filtering and smoothing techniques identical to the equations of Kalman filtering and Bryson-Frazier fixed time-interval smoothing. The solutions prescribe an inward filtering recursion to compute a sequence of constraint moments and forces followed by an outward recursion to determine a corresponding sequence of angular and linear accelerations. In addition to providing techniques to compute joint accelerations from applied joint moments (and vice versa), the report provides an approach to evaluate recursively the composite multi-link system inertia matrix and its inverse. The report lays the foundation for the potential use of filtering and smoothing techniques in robot inverse and forward dynamics and in robot control design.

  15. Learning Inverse Rig Mappings by Nonlinear Regression.

    PubMed

    Holden, Daniel; Saito, Jun; Komura, Taku

    2016-11-11

    We present a framework to design inverse rig-functions - functions that map low level representations of a character's pose such as joint positions or surface geometry to the representation used by animators called the animation rig. Animators design scenes using an animation rig, a framework widely adopted in animation production which allows animators to design character poses and geometry via intuitive parameters and interfaces. Yet most state-of-the-art computer animation techniques control characters through raw, low level representations such as joint angles, joint positions, or vertex coordinates. This difference often stops the adoption of state-of-the-art techniques in animation production. Our framework solves this issue by learning a mapping between the low level representations of the pose and the animation rig. We use nonlinear regression techniques, learning from example animation sequences designed by the animators. When new motions are provided in the skeleton space, the learned mapping is used to estimate the rig controls that reproduce such a motion. We introduce two nonlinear functions for producing such a mapping: Gaussian process regression and feedforward neural networks. The appropriate solution depends on the nature of the rig and the amount of data available for training. We show our framework applied to various examples including articulated biped characters, quadruped characters, facial animation rigs, and deformable characters. With our system, animators have the freedom to apply any motion synthesis algorithm to arbitrary rigging and animation pipelines for immediate editing. This greatly improves the productivity of 3D animation, while retaining the flexibility and creativity of artistic input.

  16. Nonlinear inversion for arbitrarily-oriented anisotropic models: Synthetic testing

    NASA Astrophysics Data System (ADS)

    Bremner, P. M.; Panning, M. P.

    2010-12-01

    We present an implementation of new 3-D finite-frequency kernels, based on the Born approximation, for inversion of a synthetic surface wave dataset. The kernels are formulated based on a hexagonal symmetry with an arbitrary orientation. Numerical tests are performed to achieve a robust inversion scheme. Nonlinear inversion schemes are examined for adequate recovery of three input models to include: isotropic, anisotropic, and both anisotropic and isotropic input models. Output models from inversions of calculated synthetic data are compared against these input models to test for accurate reproduction of input model features, and the resolution of those features. The focus of this study is on inverting for structure beneath western North America. The synthetic dataset consists of collected seismic waveforms of 128 earthquake mechanisms, of magnitude 6-7 from Dec 2006 to Feb 2009, from the IRIS database. Events were selected to correlate with USArray deployments, and to have as complete an azimuthal coverage as possible. The events occurred within a circular region of radius 150° centered about 44° lat, -110° lon (an arbitrary location within USArray coverage). The seismograms have been calculated within a simplified version of PREM in which the crust and 220 km discontinuity have been removed, dubbed PREM LIGHT, utilizing a spectral element code (SEM) coupled to a normal mode solution. The mesh consists of a 3-D heterogeneous outer shell, representing the upper mantle above 400 km depth, coupled to a spherically symmetric inner sphere. The SEM solves the weak formulation of the seismic wave equation in the outer shell, and uses normal mode summation methods for the inner sphere. To validate the results of the SEM, seismograms are benchmarked against seismograms calculated with a 1-D normal mode summation. From the synthetic dataset, multi-taper fundamental mode surface wave phase delay measurements are taken. The orthogonal 2.5π spheroidal wave function

  17. Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus.

    PubMed Central

    Guijo, M I; Patte, J; del Mar Campos, M; Louarn, J M; Rebollo, J E

    2001-01-01

    The behavior of chromosomal inversions in Escherichia coli depends upon the region they affect. Regions flanking the replication terminus have been termed nondivisible zones (NDZ) because inversions ending in the region were either deleterious or not feasible. This regional phenomenon is further analyzed here. Thirty segments distributed between 23 and 29 min on the chromosome map have been submitted to an inversion test. Twenty-five segments either became deleterious when inverted or were noninvertible, but five segments tolerated inversion. The involvement of polar replication pause sites in this distribution was investigated. The results suggest that the Tus/pause site system may forbid some inversion events, but that other constraints to inversion, unrelated to this system, exist. Our current model for deleterious inversions is that the segments involved carry polar sequences acting in concert with other polar sequences located outside the segments. The observed patchwork of refractory and tolerant segments supports the existence of several NDZs in the 23- to 29-min region. Microscopic observations revealed that deleterious inversions are associated with high frequencies of abnormal nucleoid structure and distribution. Combined with other information, the data suggest that NDZs participate in the organization of the terminal domain of the nucleoid. PMID:11290700

  18. Light controlled reversible inversion of nanophosphor-stabilized Pickering emulsions for biphasic enantioselective biocatalysis.

    PubMed

    Chen, Zhaowei; Zhou, Li; Bing, Wei; Zhang, Zhijun; Li, Zhenhua; Ren, Jinsong; Qu, Xiaogang

    2014-05-21

    In this work, by utilizing photochromic spiropyrans conjugated upconversion nanophosphors, we have successfully prepared NIR/visible light tuned interfacially active nanoparticles for the formulation of Pickering emulsions with reversible inversion properties. By loading a model enantioselective biocatalytic active bacteria Alcaligenes faecalis ATCC 8750 in the aqueous phase, we demonstrated for the first time that the multifunctional Pickering emulsion not only highly enhanced its catalytic performance but also relieved the substrate inhibition effect. In addition, product recovery, and biocatalysts and colloid emulsifiers recycling could be easily realized based on the inversion ability of the Pickering emulsion. Most importantly, the utilization of NIR/visible light to perform the reversible inversion without any chemical auxiliaries or temperature variation showed little damage toward the biocatalysts, which was highlighted by the high catalytic efficiency and high enantioselectivity even after 10 cycles. The NIR/visible light controlled Pickering emulsion showed promising potential as a powerful technique for biocatalysis in biphasic systems.

  19. Fast wavelet based sparse approximate inverse preconditioner

    SciTech Connect

    Wan, W.L.

    1996-12-31

    Incomplete LU factorization is a robust preconditioner for both general and PDE problems but unfortunately not easy to parallelize. Recent study of Huckle and Grote and Chow and Saad showed that sparse approximate inverse could be a potential alternative while readily parallelizable. However, for special class of matrix A that comes from elliptic PDE problems, their preconditioners are not optimal in the sense that independent of mesh size. A reason may be that no good sparse approximate inverse exists for the dense inverse matrix. Our observation is that for this kind of matrices, its inverse entries typically have piecewise smooth changes. We can take advantage of this fact and use wavelet compression techniques to construct a better sparse approximate inverse preconditioner. We shall show numerically that our approach is effective for this kind of matrices.

  20. GT-7 RECOVERY

    NASA Image and Video Library

    1965-12-18

    S65-61830 (18 Dec. 1965) --- Astronauts James A. Lovell Jr. (left), Gemini-7 pilot, and Frank Borman, command pilot, are shown just after they arrived aboard the aircraft carrier USS Wasp. Greeting the astronauts are Donald Stullken (at Lovell's right), Recovery Operations Branch, Landing and Recovery Division, Dr. Howard Minners (standing beside Borman), Flight Medicine Branch, Center Medical Office, Manned Spacecraft Center, and Bennett James (standing behind Borman), a NASA Public Affairs Officer. The National Aeronautics and Space Administration's Gemini-7 spacecraft splashed down in the western Atlantic recovery area at 9:05 a.m. (EST), Dec. 18, 1965, to conclude a record-breaking 14-day mission in space. Photo credit: NASA