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Sample records for inversion recovery sequences

  1. Utility of Double Inversion Recovery Sequences in MRI.

    PubMed

    Ryan, Maura E

    2016-04-01

    Investigators from the Mayo Clinic, Rochester Minnesota investigated the utility of three-dimensional (3D) double inversion recovery (DIR) sequences in magnetic resonance imaging (MRI) detection of focal cortical dysplasia (FCD) in children and young adults with epilepsy. PMID:27617491

  2. Fast inversion recovery for myelin suppression (FIRMS). A new magnetic resonance pulse sequence.

    PubMed

    Wolansky, L J; Chiang, P K; Liu, W C; Gonzales, R N; Holodny, A l; Baker, S R

    1997-07-01

    Fast inversion recovery for myelin suppression is a new magnetic resonance sequence with the ability to increase gray-white matter contrast. This can improve the definition of normal anatomical structures. PMID:9237438

  3. Bloch Equations-Based Reconstruction of Myocardium T1 Maps from Modified Look-Locker Inversion Recovery Sequence

    PubMed Central

    Marty, Benjamin; Vignaud, Alexandre; Greiser, Andreas; Robert, Benjamin; de Sousa, Paulo Loureiro; Carlier, Pierre G.

    2015-01-01

    Modified Look-Locker Inversion recovery (MOLLI) sequence is increasingly performed for myocardial T1 mapping but is known to underestimate T1 values. The aim of the study was to quantitatively analyze several sources of errors when T1 maps are derived using standard post-processing of the sequence and to propose a reconstruction approach that takes into account inversion efficacy (η), T2 relaxation during balanced steady-state free-precession readouts and B1+ inhomogeneities. Contributions of the different sources of error were analyzed using Bloch equations simulations of MOLLI sequence. Bloch simulations were then combined with the acquisition of fast B1+ and T2 maps to derive more accurate T1 maps. This novel approach was evaluated on phantoms and on five healthy volunteers. Simulations show that T2 variations, B1+ heterogeneities and inversion efficiency represent major confounders for T1 mapping when MOLLI is processed with standard 3-parameters fitting. In vitro data indicate that T1 values are accurately derived with the simulation approach and in vivo data suggest that myocardium T1 are 15% underestimated when processed with the standard 3-parameters fitting. At the cost of additional acquisitions, this method might be suitable in clinical research protocols for precise tissue characterization as it decorrelates T1 and T2 effects on parametric maps provided by MOLLI sequence and avoids inaccuracies when B1+ is not homogenous throughout the myocardium. PMID:25962182

  4. 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.

  5. Improved Fat Water Separation with Water Selective Inversion Pulse for Inversion Recovery Imaging in Cardiac MRI

    PubMed Central

    Havla, Lukas; Basha, Tamer; Rayatzadeh, Hussein; Shaw, Jaime L.; Manning, Warren J.; Reeder, Scott B.; Kozerke, Sebastian; Nezafat, Reza

    2012-01-01

    Purpose To develop an improved chemical shift-based water-fat separation sequence using a water-selective inversion pulse for inversion-recovery 3D contrast-enhanced cardiac MR. Materials and Methods In inversion-recovery sequences, the fat signal is substantially reduced due to the application of a non-selective inversion pulse. Therefore, for simultaneous visualization of water, fat, and myocardial enhancement in inversion-recovery based sequences such as late Gadolinium enhancement imaging, two separate scans are used. To overcome this, the non-selective inversion pulse is replaced with a water-selective inversion pulse. Imaging was performed in phantoms, 9 healthy subjects and 9 patients with suspected arrhythmogenic right ventricular cardiomyopathy plus 1 patient for tumor/mass imaging. In patients, images with conventional turbo-spin echo (TSE) with and without fat saturation were acquired prior to contrast injection for fat assessment. Subjective image scores (1=poor, 4=excellent) were used for image assessment. Results Phantom experiments showed a fat SNR increase between 1.7 to 5.9 times for inversion times of 150 and 300ms, respectively. The water-selective inversion pulse retains the fat signal in contrast-enhanced cardiac MR, allowing improved visualization of fat in the water-fat separated images of healthy subjects with a score of 3.7 ± 0.6. Patient images acquired with the proposed sequence were scored higher when compared with TSE sequence (3.5 ± 0.7 vs. 2.2 ± 0.5, p<0.05). Conclusion The water-selective inversion pulse retains the fat signal in inversion-recovery based contrast-enhanced cardiac MR, allowing simultaneous visualization of water and fat. PMID:22927327

  6. 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…

  7. 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

  8. Infarct quantification using 3D inversion recovery and 2D phase sensitive inversion recovery; validation in patients and ex vivo

    PubMed Central

    2013-01-01

    Background Cardiovascular-MR (CMR) is the gold standard for quantifying myocardial infarction using late gadolinium enhancement (LGE) technique. Both 2D- and 3D-LGE-sequences are used in clinical practise and in clinical and experimental studies for infarct quantification. Therefore the aim of this study was to investigate if image acquisitions with 2D- and 3D-LGE show the same infarct size in patients and ex vivo. Methods Twenty-six patients with previous myocardial infarction who underwent a CMR scan were included. Images were acquired 10-20 minutes after an injection of 0.2 mmol/kg gadolinium-based contrast agent. Two LGE-sequences, 3D-inversion recovery (IR) and 2D-phase-sensitive (PS) IR, were used in all patients to quantify infarction size. Furthermore, six pigs with reperfused infarction in the left anterior descending artery (40 minutes occlusion and 4 hours of reperfusion) were scanned with 2D- and 3D-LGE ex vivo. A high resolution T1-sequence was used as reference for the infarct quantification ex vivo. Spearman’s rank-order correlation, Wilcoxon matched pairs test and bias according to Bland-Altman was used for comparison of infarct size with different LGE-sequences. Results There was no significant difference between the 2D- and 3D-LGE sequence in left ventricular mass (LVM) (2D: 115 ± 25 g; 3D: 117 ± 24 g: p = 0.35). Infarct size in vivo using 2D- and 3D-LGE showed high correlation and low bias for both LGE-sequences both in absolute volume of infarct (r = 0.97, bias 0.47 ± 2.1 ml) and infarct size as part of LVM (r = 0.94, bias 0.16 ± 2.0%). The 2D- and 3D-LGE-sequences ex vivo correlated well (r = 0.93, bias 0.67 ± 2.4%) for infarct size as part of the LVM. The IR LGE-sequences overestimated infarct size as part of the LVM ex vivo compared to the high resolution T1-sequence (bias 6.7 ± 3.0%, 7.3 ± 2.7% for 2D-PSIR and 3D-IR respectively, p < 0.05 for both). Conclusions Infarct quantification with

  9. Utility of double inversion recovery MRI in paediatric epilepsy.

    PubMed

    Soares, Bruno P; 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

  10. IMPROVED SAMPLE RECOVERY IN THERMOCYCLE SEQUENCING PROTOCOLS

    EPA Science Inventory

    DNA sequencing protocols which utilize multiple cycles of DNA synthesis by Taq DNA polymerase require recovery of small sample volumes from beneath a layer of mineral oil. owever, the small volume of aqueous phase and the high surface tension between the two phases makes complete...

  11. Sodium Inversion Recovery MRI of the Knee Joint In Vivo at 7T

    PubMed Central

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

    2010-01-01

    The loss of proteoglycans in the articular cartilage is an early signature of osteoarthritis. 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 5 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. PMID:20813569

  12. Multiplexed genotyping with sequence-tagged molecular inversion probes.

    PubMed

    Hardenbol, Paul; Banér, Johan; Jain, Maneesh; Nilsson, Mats; Namsaraev, Eugeni A; Karlin-Neumann, George A; Fakhrai-Rad, Hossein; Ronaghi, Mostafa; Willis, Thomas D; Landegren, Ulf; Davis, Ronald W

    2003-06-01

    We report on the development of molecular inversion probe (MIP) genotyping, an efficient technology for large-scale single nucleotide polymorphism (SNP) analysis. This technique uses MIPs to produce inverted sequences, which undergo a unimolecular rearrangement and are then amplified by PCR using common primers and analyzed using universal sequence tag DNA microarrays, resulting in highly specific genotyping. With this technology, multiplex analysis of more than 1,000 probes in a single tube can be done using standard laboratory equipment. Genotypes are generated with a high call rate (95%) and high accuracy (>99%) as determined by independent sequencing. PMID:12730666

  13. 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.

  14. 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.

  15. Phase-Sensitive Inversion-Recovery MRI Improves Longitudinal Cortical Lesion Detection in Progressive MS

    PubMed Central

    Farrell, Colleen; Fabian, Michelle; Howard, Jonathan; Riley, Claire; Miller, Aaron; Lublin, Fred; Inglese, Matilde

    2016-01-01

    Previous studies comparing phase sensitive inversion recovery (PSIR) to double inversion recovery (DIR) have demonstrated that use of PSIR improves cross-sectional in vivo detection of cortical lesions (CL) in multiple sclerosis. We studied the utility of PSIR in detection/characterization of accrual of CL over time in a 1-year longitudinal study in primary progressive multiple sclerosis (PPMS) compared to DIR. PSIR and DIR images were acquired with 3T magnetic resonance imaging (MRI) in 25 patients with PPMS and 19 healthy controls at baseline, and after 1 year in 20 patients with PPMS. CL were classified as intracortical, leucocortical or juxtacortical. Lesion counts and volumes were calculated for both time points from both sequences and compared. Correlations with measures of physical and cognitive disability were determined as well as new CL counts and volumes. Compared to DIR, PSIR led to detection of a higher number of CL involving a larger proportion of patients with PPMS both cross-sectionally (p = 0.006, 88%) and longitudinally (p = 0.007, 95%), and led to the reclassification of a third of CL seen on DIR at each time point. Interestingly, PSIR was more sensitive to new CL accumulation over time compared to DIR. PSIR is a promising technique to monitor cortical damage and disease progression in patients with PPMS over a short-term follow-up. PMID:27002529

  16. 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

  17. 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

  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. Effect of Inversion Recovery Fat Suppression on Hepatic R2* Quantitation in Transfusional Siderosis

    PubMed Central

    Meloni, Antonella; Tyszka, J. Michael; Pepe, Alessia; Wood, John C.

    2016-01-01

    OBJECTIVE The purpose of this study is to evaluate whether the application of spectral presaturation inversion recovery (SPIR) fat suppression in standard multiecho gradient-echo sequences has a significant effect on hepatic R2* quantitation in patients with iron overload syndromes. MATERIALS AND METHODS Eighty patients were scanned with a multiecho gradient-echo sequence without and with the application of SPIR. Six different postprocessing approaches were used to extract R2* values for maximum generality. RESULTS SPIR fat suppression lowered R2* values by 3.9–7.0% (p < 0.0001 in all pairwise comparisons), independently of the postprocessing algorithm. Coefficients of variation for R2* ranged from 4.5% to 10.0%. Regardless of the size of the ROI (area of homogeneous tissue or entire liver profile in the slice), pixelwise approaches combined with an exponential-plus-constant fitting model yielded the lowest coefficients of variation (4.5% and 5.1%), whereas truncated exponential fits of the averaged signals produced the highest coefficients of variation (7.8% and 10%). For R2* values exceeding 200 Hz, a Bland-Altman analysis showed a bias that grew linearly for all postprocessing methods. CONCLUSION SPIR fat suppression resulted in systematically lower hepatic R2* estimates. Because calibration curves were derived using images without fat suppression, these biases should be corrected when reporting liver iron concentrations estimated from fat-suppressed multiecho T2*-weighted images. PMID:25714295

  20. Sodium imaging of the human knee using soft inversion recovery fluid attenuation

    NASA Astrophysics Data System (ADS)

    Feldman, Rebecca E.; Stobbe, Robert; Watts, Alexander; Beaulieu, Christian

    2013-09-01

    Sodium signal strength in MRI is low when compared with 1H. Thus, image voxel volumes must be relatively large in order to produce a sufficient signal-to-noise ratio (SNR). The measurement of sodium in cartilage is hindered by conflation with signal from the adjacent fluid spaces. Inversion recovery can be used to null signal from fluid, but reduces SNR. The purpose of this work was to optimize inversion recovery sodium MRI to enhance cartilage SNR while nulling fluid. Sodium relaxation was first measured for knee cartilage (T1 = 21 ± 1 ms, T2 fast∗=0.8±0.2 ms, T2 slow∗=19.7±0.5 ms) and fluid (T1 = 48 ± 3 ms, T2∗=47±4 ms) in nine healthy subjects at 4.7 T. The rapid relaxation of cartilage in relation to fluid permits the use of a lengthened inversion pulse to preferentially invert the fluid components. Simulations of inversion pulse length were performed to yield a cartilage SNR enhancing combination of parameters that nulled fluid. The simulations were validated in a phantom and then invivo. B0 inhomogeneity was measured and the effect of off-resonance during the soft inversion pulse was assessed with simulation. Soft inversion recovery yielded twice the SNR and much improved sodium images of cartilage in human knee with little confounding signal from fluid.

  1. Magnetization transfer using inversion recovery during off-resonance irradiation

    PubMed Central

    Mangia, Silvia; De Martino, Federico; Liimatainen, Timo; Garwood, Michael; Michaeli, Shalom

    2011-01-01

    Estimation of magnetization transfer (MT) parameters in vivo can be compromised by an inability to drive the magnetization to a steady state using allowable levels of radiofrequency (RF) irradiation, due to safety concerns (tissue heating and specific absorption rate (SAR)). Rather than increasing the RF duration or amplitude, here we propose to circumvent the SAR limitation by sampling the formation of the steady state in separate measurements made with the magnetization initially along the −z and +z axis of the laboratory frame, i.e. with or without an on-resonance inversion pulse prior to the off-resonance irradiation. Results from human brain imaging demonstrate that this choice provides a tremendous benefit in the fitting procedure used to estimate MT parameters. The resulting parametric maps are characterized by notably increased tissue specificity as compared to those obtained with the standard MT acquisition in which magnetization is initially along the +z axis only. PMID:21601405

  2. Magnetization transfer using inversion recovery during off-resonance irradiation.

    PubMed

    Mangia, Silvia; De Martino, Federico; Liimatainen, Timo; Garwood, Michael; Michaeli, Shalom

    2011-12-01

    Estimation of magnetization transfer (MT) parameters in vivo can be compromised by an inability to drive the magnetization to a steady state using allowable levels of radiofrequency (RF) irradiation, due to safety concerns (tissue heating and specific absorption rate (SAR)). Rather than increasing the RF duration or amplitude, here we propose to circumvent the SAR limitation by sampling the formation of the steady state in separate measurements made with the magnetization initially along the -z and +z axis of the laboratory frame, i.e. with or without an on-resonance inversion pulse prior to the off-resonance irradiation. Results from human brain imaging demonstrate that this choice provides a tremendous benefit in the fitting procedure used to estimate MT parameters. The resulting parametric maps are characterized by notably increased tissue specificity as compared to those obtained with the standard MT acquisition in which magnetization is initially along the +z axis only. PMID:21601405

  3. 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

  4. Influence of fat on liver T 1 measurements using modified Look–Locker inversion recovery (MOLLI) methods at 3T

    PubMed Central

    Tunnicliffe, Elizabeth M.; Pavlides, Michael; Robson, Matthew D.

    2016-01-01

    Purpose To characterize the effect of fat on modified Look–Locker inversion recovery (MOLLI) T 1 maps of the liver. The balanced steady‐state free precession (bSSFP) sequence causes water and fat signals to have opposite phase when repetition time (TR) = 2.3 msec at 3T. In voxels that contain both fat and water, the MOLLI T 1 measurement is influenced by the choice of TR. Materials and Methods MOLLI T 1 measurements of the liver were simulated using the Bloch equations while varying the hepatic lipid content (HLC). Phantom scans were performed on margarine phantoms, using both MOLLI and spin echo inversion recovery sequences. MOLLI T 1 at 3T and HLC were determined in patients (n = 8) before and after bariatric surgery. Results At 3T, with HLC in the 0–35% range, higher fat fraction values lead to longer MOLLI T 1 values when TR = 2.3 msec. Patients were found to have higher MOLLI T 1 at elevated HLC (T 1 = 929 ± 97 msec) than at low HLC (T 1 = 870 ± 44 msec). Conclusion At 3T, MOLLI T 1 values are affected by HLC, substantially changing MOLLI T 1 in a clinically relevant range of fat content. J. Magn. Reson. Imaging 2016;44:105–111. PMID:26762615

  5. AIR-SPAMM: alternative inversion recovery spatial modulation of magnetization for myocardial tagging

    NASA Astrophysics Data System (ADS)

    Aletras, Anthony H.; Freidlin, Raisa Z.; Navon, Gil; Arai, Andrew E.

    2004-02-01

    Alternate inversion recovery spatial modulation of magnetization (AIR-SPAMM) can be used either for doubling the number of tags for a given tagging encoding gradient strength or for improving tagging contrast ratio. AIR-SPAMM requires only a single acquisition and utilizes inversion pulses spaced throughout the gradient recalled echo (GRE) cine acquisition to "lock" the recovering magnetization at a desired level. The theory of AIR-SPAMM is presented along with simulations and results from phantoms. AIR-SPAMM can be used either for imaging systole as demonstrated by initial in vivo results or potentially for imaging the entire cardiac cycle in a slice-interleaved manner.

  6. 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.

  7. 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…

  8. 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.

  9. Optimization of Magnetization-Prepared 3-Dimensional Fluid Attenuated Inversion Recovery Imaging for Lesion Detection at 7 T

    PubMed Central

    Saranathan, Manojkumar; Tourdias, Thomas; Kerr, Adam B.; Bernstein, Jeff D.; Kerchner, Geoffrey A.; Han, May H.; Rutt, Brian K.

    2016-01-01

    Purpose The aim of this study was to optimize the 3-dimensional (3D) fluid attenuated inversion recovery (FLAIR) pulse sequence for isotropic high-spatial-resolution imaging of white matter (WM) and cortical lesions at 7 T. Materials and Methods We added a magnetization-prepared (MP) FLAIR module to a Cube 3D fast spin echo sequence and optimized the refocusing flip angle train using extended phase graph simulations, taking into account image contrast, specific absorption rate (SAR), and signal-to-noise ratio (SNR) as well as T1/T2 values of the different species of interest (WM, grey matter, lesions) at 7 T. We also effected improved preparation homogeneity at 7 T by redesigning the refocusing pulse used in the MP segments. Two sets of refocusing flip angle trains—(a) an SNR-optimal and (b) a contrast-optimal set—were derived and used to scan 7 patients with Alzheimer disease/cognitive impairment and 7 patients with multiple sclerosis. Conventional constant refocusing flip MP-FLAIR images were also acquired for comparison. Lesion SNR, contrast, and lesion count were compared between the 2 optimized and the standard FLAIR sequences. Results Whole brain coverage with 0.8 mm3 isotropic spatial resolution in ~5-minute scan times was achieved using the optimized 3D FLAIR sequences at clinically acceptable SAR levels. The SNR efficiency of the SNR-optimal sequence was significantly better than that of conventional constant refocusing flip MP-FLAIR sequence, whereas the scan time was reduced more than 2-fold (~5 vs >10 minutes). The contrast efficiency of the contrast-optimal sequence was comparable with that of the constant refocusing flip sequence. Lesion load ascertained by lesion counting was not significantly different among the sequences. Conclusion Magnetization-prepared FLAIR-Cube with refocusing flip angle trains optimized for SNR and contrast can be used to characterize WM and cortical lesions at 7 Twith 0.8 mm3 isotropic resolution in short scan times and

  10. Cardiovascular magnetic resonance of myocardial edema using a short inversion time inversion recovery (STIR) black-blood technique: Diagnostic accuracy of visual and semi-quantitative assessment

    PubMed Central

    2012-01-01

    Background The short inversion time inversion recovery (STIR) black-blood technique has been used to visualize myocardial edema, and thus to differentiate acute from chronic myocardial lesions. However, some cardiovascular magnetic resonance (CMR) groups have reported variable image quality, and hence the diagnostic value of STIR in routine clinical practice has been put into question. The aim of our study was to analyze image quality and diagnostic performance of STIR using a set of pulse sequence parameters dedicated to edema detection, and to discuss possible factors that influence image quality. We hypothesized that STIR imaging is an accurate and robust way of detecting myocardial edema in non-selected patients with acute myocardial infarction. Methods Forty-six consecutive patients with acute myocardial infarction underwent CMR (day 4.5, +/- 1.6) including STIR for the assessment of myocardial edema and late gadolinium enhancement (LGE) for quantification of myocardial necrosis. Thirty of these patients underwent a follow-up CMR at approximately six months (195 +/- 39 days). Both STIR and LGE images were evaluated separately on a segmental basis for image quality as well as for presence and extent of myocardial hyper-intensity, with both visual and semi-quantitative (threshold-based) analysis. LGE was used as a reference standard for localization and extent of myocardial necrosis (acute) or scar (chronic). Results Image quality of STIR images was rated as diagnostic in 99.5% of cases. At the acute stage, the sensitivity and specificity of STIR to detect infarcted segments on visual assessment was 95% and 78% respectively, and on semi-quantitative assessment was 99% and 83%, respectively. STIR differentiated acutely from chronically infarcted segments with a sensitivity of 95% by both methods and with a specificity of 99% by visual assessment and 97% by semi-quantitative assessment. The extent of hyper-intense areas on acute STIR images was 85% larger than

  11. Improvement of the inverse-gated-decoupling sequence for a faster quantitative analysis of various samples by 13C NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Baguet, Evelyne

    2006-05-01

    The inverse-gated-decoupling sequence enables quantitative 1H decoupled 13C spectra to be obtained. We modified this sequence so as to obtain the same result in less time for molecules containing carbons with various relaxation properties. For that, we determined the optimal 13C longitudinal-magnetization initial value for a faster relaxation while 1H decoupler is stopped. This value can be calculated precisely via the nuclear Overhauser effects, the longitudinal relaxation times, together with the determination of the relaxation rate constants of carbons while 1H are out of equilibrium. A supplementary delay of 1H decoupling and/or a series of selective pulses applied at the beginning of the recovery delay allow an acceleration of 13C longitudinal relaxation. We applied this method to the molecule of vanillin. The simultaneous quantification of all carbons was carried out with a recovery delay divided by two compared to the usual sequence.

  12. Automated Brain Tissue Segmentation Based on Fractional Signal Mapping from Inversion Recovery Look-Locker Acquisition

    PubMed Central

    Shin, Wanyong; Geng, Xiujuan; Gu, Hong; Zhan, Wang; Zou, Qihong; Yang, Yihong

    2010-01-01

    Most current automated segmentation methods are performed on T1- or T2-weighted MR images, relying on relative image intensity that is dependent on other MR parameters and sensitive to B1 magnetic field inhomogeneity. Here, we propose an image segmentation method based on quantitative longitudinal magnetization relaxation time (T1) of brain tissues. Considering the partial volume effect, fractional volume maps of brain tissues (white matter, gray matter, and cerebrospinal fluid) were obtained by fitting the observed signal in an inversion recovery procedure to a linear combination of three exponential functions, which represents the relaxations of each of the tissue types. A Look-Locker acquisition was employed to accelerate the acquisition process. The feasibility and efficacy of this proposed method were evaluated using simulations and experiments. The potential applications of this method in the study of neurological disease as well as normal brain development and aging are discussed. PMID:20452444

  13. 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.

  14. 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

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

    PubMed

    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

  16. On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing

    PubMed Central

    Lucas Lledó, José Ignacio; Cáceres, Mario

    2013-01-01

    One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with low coverage data. However, % of inversions located between segmental duplications are expected to go undetected by the most common sequencing strategies. In general, longer DNA libraries improve the detectability of inversions far better than increments of the coverage depth or the read length. Finally, we review the performance of three algorithms to detect inversions —SVDetect, GRIAL, and VariationHunter—, identify common pitfalls, and reveal important differences in their breakpoint precisions. These results stress the importance of the sequencing strategy for the detection of structural variants, especially inversions, and offer guidelines for the design of future genome sequencing projects. PMID:23637806

  17. 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

  18. 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

  19. 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.

  20. 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

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

    PubMed

    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

  2. A research of 3D gravity inversion based on the recovery of sparse underdetermined linear equations

    NASA Astrophysics Data System (ADS)

    Zhaohai, M.

    2014-12-01

    Because of the properties of gravity data, it is made difficult to solve the problem of multiple solutions. There are two main types of 3D gravity inversion methods:One of two methods is based on the improvement of the instability of the sensitive matrix, solving the problem of multiple solutions and instability in 3D gravity inversion. Another is to join weight function into the 3D gravity inversion iteration. Through constant iteration, it can renewal density values and weight function to achieve the purpose to solve the multiple solutions and instability of the 3D gravity data inversion. Thanks to the sparse nature of the solutions of 3D gravity data inversions, we can transform it into a sparse equation. Then, through solving the sparse equations, we can get perfect 3D gravity inversion results. The main principle is based on zero norm of sparse matrix solution of the equation. Zero norm is mainly to solve the nonzero solution of the sparse matrix. However, the method of this article adopted is same as the principle of zero norm. But the method is the opposite of zero norm to obtain zero value solution. Through the form of a Gaussian fitting solution of the zero norm, we can find the solution by using regularization principle. Moreover, this method has been proved that it had a certain resistance to random noise in the mathematics, and it was more suitable than zero norm for the solution of the geophysical data. 3D gravity which is adopted in this article can well identify abnormal body density distribution characteristics, and it can also recognize the space position of abnormal distribution very well. We can take advantage of the density of the upper and lower limit penalty function to make each rectangular residual density within a reasonable range. Finally, this 3D gravity inversion is applied to a variety of combination model test, such as a single straight three-dimensional model, the adjacent straight three-dimensional model and Y three

  3. 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.

  4. 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.

  5. Noncontrast MR Angiography for Comprehensive Assessment of Abdominopelvic Arteries using Quadruple Inversion-Recovery Preconditioning and 3D balanced Steady-State Free Precession Imaging

    PubMed Central

    Atanasova, Iliyana P.; Kim, Daniel; Lim, Ruth P.; Storey, Pippa; Kim, Sooah; Guo, Hua; Lee, Vivian S.

    2011-01-01

    Purpose To develop a non-contrast MR angiography (MRA) method for comprehensive evaluation of abdominopelvic arteries in a single 3D acquisition. Materials and Methods A non-contrast MRA (NC MRA) pulse sequence was developed using 4 inversion-recovery (IR) pulses and 3D balanced steady-state free precession (b-SSFP) readout to provide arterial imaging from renal to external iliac arteries. Respiratory triggered, high spatial resolution (1.3 × 1.3 × 1.7 mm3) non-contrast angiograms were obtained in seven volunteers and ten patients referred for gadolinium-enhanced MRA (CE MRA). Images were assessed for diagnostic quality by two radiologists. Quantitative measurements of arterial signal contrast were also performed. Results NC MRA imaging was successfully completed in all subjects in 7.0 ± 2.3 minutes. In controls, image quality of NC MRA averaged 2.79 ± 0.39 on a scale of 0 to 3, where 3 is maximum. Image quality of NC MRA (2.65 ± 0.41) was comparable to that of CE MRA (2.9 ± 0.32) in all patients. Contrast ratio measurements in patients demonstrated that NC MRA provides arterial contrast comparable to source CE MRA images with adequate venous and excellent background tissue suppression. Conclusion The proposed non-contrast MRA pulse sequence provides high quality visualization of abdominopelvic arteries within clinically feasible scan times. PMID:21591013

  6. 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.

  7. Non-contrast MRA using an inflow-enhanced, inversion recovery SSFP technique in pediatric abdominal imaging.

    PubMed

    Serai, Suraj; Towbin, Alexander J; Podberesky, Daniel J

    2012-03-01

    Abdominal contrast-enhanced MR angiography (CE-MRA) is routinely performed in children. CE-MRA is challenging in children because of patient motion, difficulty in obtaining intravenous access, and the inability of young patients to perform a breath-hold during imaging. The combination of pediatric-specific difficulties in imaging and the safety concerns regarding the risk of gadolinium-based contrast agents in patients with impaired renal function has renewed interest in the use of non-contrast (NC) MRA techniques. At our institution, we have optimized 3-D NC-MRA techniques for abdominal imaging. The purpose of this work is to demonstrate the utility of an inflow-enhanced, inversion recovery balanced steady-state free precession-based (b-SSFP) NC-MRA technique. PMID:22072071

  8. Homologous recombination among three intragene Alu sequences causes an inversion-deletion resulting in the hereditary bleeding disorder glanzmann thrombasthenia

    SciTech Connect

    Li, L.; Bray, P.F. )

    1993-07-01

    The crucial role of the human platelet fibrinogen receptor in maintaining normal hemostasis is best exemplified by the autosomal recessive bleeding disorder Glanzmann thrombasthenia (GT). The platelet fibrinogen receptor is a heterodimer composed of glycoproteins IIb (GPIIb) and IIIa (GPIIIa). Platelets from patients with GT have a quantitative or qualitative abnormality in GPIIb and GPIIIa and can neither bind fibrinogen nor aggregate. Very few genetic defects have been identified that cause this disorder. The authors describe a kindred with GT in which the affected individuals have a unique inversion-deletion mutation in the gene for GPIIIa. Patient platelets lacked both GPIIIa protein and mRNA. Southern blots of patient genomic DNA probed with an internal 1.0-kb GPIIIa cDNA suggested a large rearrangement of this gene but were normal when probed with small GPIIIa cDNA fragments that were outside the mutation. Cytogenetics and pulsed-field gel analysis of the GPIIIa gene were normal, making a translocation or a very large rearrangement unlikely. Additional Southern analyses suggested that the abnormality was not a small insertion. The authors constructed a patient genomic DNA library and isolated fragments containing the 5' and 3' breakpoints of the mutation. The nucleotide sequence from these genomic clones was determined and revealed that, relative to the normal gene, the mutant allele contained a 1-kb deletion immediately preceding a 15-kb inversion. The DNA breaks occurred in two inverted and one forward Alu sequence within the gene for GPIIIa and in the left, right, and left arms, respectively, of these sequences. There was a 5-bp repeat at the 3 terminus of the inversion. One copy of the repeat remained in the mutant allele breakpoint junction. The alignment and orientation of the different Alu sequences, as well as the position of the breakpoints, suggest that the inversion preceded the deletion in this complex rearrangement. 41 refs., 5 figs.

  9. Effect of iron oxide nanoparticles coating type on the relationship between nanoparticles concentration and signal intensity in inversion recovery T1-weighted MRI

    PubMed Central

    Gharehaghaji, Nahideh; Nazarpoor, Mahmood; Saharkhiz, Hodaiseh

    2015-01-01

    Background: Ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles are used as blood pool contrast agent for magnetic resonance angiography and perfusion imaging. Our aim in this study was to investigate the effect of the two coating types of iron oxide nanoparticles on the relationship between nanoparticles concentration and signal intensity (SI) in T1-weighted MR images. Methods: Different concentrations of the polyethylene glycol (PEG), and carboxydextran-coated iron oxide nanoparticles were imaged using inversion recovery Turbo-FLASH (Turbo fast low-angle shot) pulse sequence with inversion times (TIs) of 300-900 ms (interval of 100 ms). The maximum non-linear and linear relationship between the corrected SI (after non-uniformity correction) and the concentration of the two coated nanoparticles were calculated in T1-weighted images. Results: The maximum non-linear relationship between the corrected SI and the concentration of the PEG, and carboxydextran-coated nanoparticles were obtained at concentrations of 400 and 200 μmol Fe/L at a TI of 900 ms, respectively. In addition, the maximum linear relationship between the corrected SI and the concentration of the PEG, and carboxydextran-coated nanoparticles (R2=0.99) appeared at 228.184 and 205.654 μmolFe/L with a TI of 300 ms, respectively. Conclusion: The maximum non-linear corrected SI of the carboxydextran-coated nanoparticles was slightly higher than that of the PEG-coated nanoparticles at similar TIs. However, the PEG-coated nanoparticles were better than the carboxydextran-coated nanoparticles as a T1 contrast agent for perfusion measurements. PMID:26478869

  10. Segmentation of inversion recovery MR images using neural networks: a study on aging

    NASA Astrophysics Data System (ADS)

    Glass, John O.; Reddick, Wilburn E.; Yo, Virginia S.; Steen, R. G.

    1998-06-01

    Clinicians have long desired early detection of neurological abnormality for treatment of brain malignancies. In attempts to address this concern, there are numerous reports publishing normative databases of age-related changes of the brain in healthy controls, many using magnetic resonance imaging (MRI). However, most of the method used to access tissue volumes were subject to observer variability. We developed a Kohonen self-organizing map to automatically segment MR images for reproducible and accurate identification of tissues. The developed method was applied to quantitatively assess subtle volume differences in normal controls due to maturational and degenerative changes. The volumes calculated in the test population of 73 controls agreed with current hypothesizes concerning age-related changes of the brain as determined by linear regression analysis of segmented tissue to age. Percent gray matter and percent white matter, as well as the ratio of gray matter to white matter were all found to be significantly correlated with age. Percent gray matter and the ratio of gray matter to white matter were inversely proportional to age while percent white matter was directly proportional to age. These results suggest the utility of the developed segmentation technique, as well as the clinical application it may hold.

  11. 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

  12. Importance of contrast-enhanced fluid-attenuated inversion recovery imaging to detect paradoxical expansion of tuberculoma.

    PubMed

    Kim, Hee-Jin

    2014-07-01

    Tuberculosis is a significant public health problem that continues to be a major cause of morbidity and mortality worldwide. Tuberculous meningoencephalitis (TM) is the most common extrapulmonary lesion in tuberculosis. A 41-year-old female was thought to have TM. Tests to confirm the TM diagnosis were initially negative, including tuberculosis PCR and adenosine deaminase level in serum and cerebrospinal fluid (CSF). Anti-tuberculous medication and intravenous steroids were administered to her on the basis of brain imaging and lactate dehydrogenase electrophoresis in CSF, suggestive of the diagnosis of TM. Her neurological problems improved rapidly following treatment. Serologic and CSF markers were positive in PCR and culture after 60 days. Radiological findings are often nonspecific and TM is difficult to diagnose without an increased index of suspicion. The detection of paradoxical expansion of tuberculoma is very important in the maintenance of medication. Magnetic resonance imaging was used to detect paradoxical expansion of the tuberculoma using various methods, such as contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR) imaging. CE-FLAIR imaging conspicuously showed paradoxical expansion of the tuberculoma. If patients present with clear meningitis, without any identified pathogen, there is a need to constantly and scrupulously check for TM, including with the use of CE-FLAIR brain imaging. PMID:24794323

  13. Multicentric/multifocal cerebral lesions: can fluid-attenuated inversion recovery aid the differentiation between glioma and metastases?

    PubMed

    Stuckey, S L; Wijedeera, R

    2008-04-01

    The purpose of the study was to assess whether non-enhancing adjacent cortical signal intensity abnormality detected on fluid-attenuated inversion recovery (FLAIR) can differentiate between multicentric and/or multifocal glioma and non-glioma pathology in patients with multiple enhancing cerebral lesions. Nineteen MR studies were reviewed after a database search and exclusion criteria applied, to detect areas of FLAIR cortex involvement without enhancement. Statistical analysis was carried out using a 2 x 2 contingency table and Fischer's exact ratio. Non-enhancing adjacent cortical T2 signal abnormality was seen in eight of eight multicentric and/or multifocal gliomas and four of 11 of the non-glioma pathologies (10 metastatic disease and 1 lymphoma). The presence of non-enhancing adjacent cortical T2 signal abnormality had a sensitivity of 100% and specificity of 63% for glioma. The positive predictive value was 67% and negative predictive value 100%. Fischer's exact probability test was P = 0.01 when applied to the glioma versus non-glioma categories, indicating a significant difference. Non-enhancing adjacent cortical T2-weighted FLAIR signal appears to be more frequently seen in patients with glioma and multiple enhancing lesions compared with those with glioma and a solitary enhancing cerebral lesion. The absence of this sign favours metastatic disease and the presence suggests that multicentric and/or multifocal glioma should remain a consideration. PMID:18373804

  14. Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and transposases of an unusual family of insertion elements.

    PubMed Central

    Lenich, A G; Glasgow, A C

    1994-01-01

    Deletion analysis of the subcloned DNA inversion region of Moraxella lacunata indicates that Piv is the only M. lacunata-encoded factor required for site-specific inversion of the tfpQ/tfpI pilin segment. The predicted amino acid sequence of Piv shows significant homology solely with the transposases/integrases of a family of insertion sequence elements, suggesting that Piv is a novel site-specific recombinase. Images PMID:8021196

  15. Bone metastases from prostate, breast and multiple myeloma: differences in lesion conspicuity at short-tau inversion recovery and diffusion-weighted MRI

    PubMed Central

    Pearce, T; Philip, S; Brown, J; Koh, D M; Burn, P R

    2012-01-01

    Objectives The objective of this study was to compare the relative conspicuity of bone metastases on short-tau inversion recovery (STIR) and diffusion-weighted MRI (DWI) whole-body MR sequences for breast, prostate and myeloma malignancies. Methods 44 whole-body MRI scans were reviewed retrospectively (coronal T1 weighted, STIR and DWI with b=800). On each scan, up to four of the largest bone lesions were identified on T1 weighting, and the region of interest signal intensity was measured on STIR and DWI, as well as the background signal intensity. The mean lesion signal to background ratio was calculated for each patient and then for each malignancy group. Results In prostate cancer patients, the DWI signal/background ratio was greater than that of STIR in 22 out of 24 patients (mean DWI lesion/background ratio 3.91, mean STIR lesion/background ratio 2.31; p=0.0001). In multiple myeloma, the DWI ratio was higher in 6/7 patients (DWI group mean ratio 7.59, STIR group mean ratio 3.7; p=0.0366). In 13 breast cancer patients, mean STIR and DWI signal/background were similar (DWI group mean ratio 4.13, group mean STIR ratio 4.26; p=0.8587). Conclusion Bone lesion conspicuity measured by lesion/background signal intensity was higher on DWI b=800 than on STIR in patients with prostate cancer and multiple myeloma. DWI should be used in whole-body MR oncology protocols in these conditions to maximise lesion detection. PMID:22457319

  16. 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

  17. 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

  18. 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

  19. 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…

  20. Direct reconstruction of T1 from k-space using a radial saturation-recovery sequence

    NASA Astrophysics Data System (ADS)

    Chen, Liyong; DiBella, Edward V. R.

    2011-03-01

    Contrast agent concentration ([CA]) must be known accurately to quantify dynamic contrast-enhanced (DCE) MR imaging. Accurate concentrations can be obtained if the longitudinal relaxation rate constant T1 is known both pre- and post-contrast injection. Post-contrast signal intensity in the images is often saturated and an approximation to T1 can be difficult to obtain. One method that has been proposed for accurate T1 estimation effectively acquires multiple images with different effective saturation recovery times (eSRTs) and fits the images to the equation for T1 recovery to obtain T1 values. This was done with a radial saturation-recovery sequence for 2D imaging of myocardial perfusion with DCE MRI. This multi-SRT method assumes that the signal intensity is constant for different readouts in each image. Here this assumption is not necessary as a model-based reconstruction method is proposed that directly reconstructs an image of T1 values from k-space. The magnetization for each ray at each readout pulse is modeled in the reconstruction with Bloch equations. Computer simulations based on a 72 ray cardiac DCE MRI acquisition were used to test the method. The direct model-based reconstruction gave accurate T1 values and was slightly more accurate than the multi-SRT method that used three sub-images.

  1. 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

  2. On the integral inversion of satellite-to-satellite velocity differences for local gravity field recovery: a theoretical study

    NASA Astrophysics Data System (ADS)

    Eshagh, Mehdi; Šprlák, Michal

    2016-02-01

    The gravity field can be recovered locally from the satellite-to-satellite velocity differences (VDs) between twin-satellites moving in the same orbit. To do so, three different integral formulae are derived in this paper to recover geoid height, radial component of gravity anomaly and gravity disturbance at sea level. Their kernel functions contain the product of two Legendre polynomials with different arguments. Such kernels are relatively complicated and it may be impossible to find their closed-forms. However, we could find the one related to recovering the geoid height from the VD data. The use of spectral forms of the kernels is possible and one does not have to generate them to very high degrees. The kernel functions are well-behaving meaning that they reduce the contribution of far-zone data and for example a cap margin of 7° is enough for recovering gravity anomalies. This means that the inversion area should be larger by 7° from all directions than the desired area to reduce the effect of spatial truncation error of the integral formula. Numerical studies using simulated data over Fennoscandia showed that when the distance between the twin-satellites is small, higher frequencies of the anomalies can be recovered from the VD data. In the ideal case of having short distance between the satellites flying at 250 km level, recovering radial component of gravity anomaly with an accuracy of 7 mGal is possible over Fennoscandia, if the VD data is contaminated only with the spatial truncation error, which is an ideal assumption. However, the problem is that the power of VD signal is very low when the satellites are close and it is very difficult to recognise the signal amongst the noise of the VD data. We also show that for a successful determination of gravity anomalies at sea level from an altitude of 250 km mean VDs with better accuracy than 0.01 mm/s are required. When coloured noise at this level is used for the VDs at 250 km with separation of 300 km, the

  3. 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. PMID:22918665

  4. Recovery

    NASA Video Gallery

    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...

  5. [Recovery].

    PubMed

    Estingoy, Pierrette; Gilliot, Élodie; Parisot, Clément

    2015-01-01

    The historical fatalism of the impossibility of recovering from psychosis eased from the 1970s with the shaping of the idea of a possible recovery. Recovery is today the objective for the patient and caregivers. The key to achieving this lies in the encounter with Others. A collective approach, on the level of the institution, must be established. The aim is to create opportunities for the patient to express their doubts and feelings. PMID:26363659

  6. 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.

  7. Herpesvirus-dependent amplification and inversion of cell-associated viral thymidine kinase gene flanked by viral a sequences and linked to an origin of viral DNA replication.

    PubMed Central

    Mocarski, E S; Roizman, B

    1982-01-01

    The genome of herpes simplex virus 1 or 2 consists of two components, L and S, which invert relative to each other during infection. As a result, viral DNA consists of four equimolar populations of molecules differing solely in the relative orientations of the L and S components. Previous studies have shown that the a sequences, located in the same orientation at the genomic termini and in inverted orientation at the L-S junction, play a key role in the inversion of L and S components. In this report we describe a virus-dependent system designed to allow identification of the viral genes capable of acting in trans to invert DNA flanked by inverted copies of a sequences. In this system, cells are converted to the thymidine kinase-positive phenotype with a chimeric plasmid carrying the thymidine kinase gene flanked by inverted copies of the a sequence and linked to an origin of viral DNA replication derived from the S component. The DNA introduced into the cells is retained and propagated in its original sequence arrangement as head-to-tail concatemers. Infection of these cells with herpes simplex virus 1 or 2 results in as much as 100-fold amplification of the plasmid sequences and inversion of the DNA flanked by copies of the a sequence. In infected cells, the amplified resident DNA accumulates in head-to-tail concatemers and no rearrangement other than the inversions could be detected. These results suggest that the a sequence-dependent inversions required trans-acting viral gene products. Images PMID:6291055

  8. 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.

  9. 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.

  10. A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17

    PubMed Central

    Forman, Oliver P.; Pettitt, Louise; Komáromy, András M.; Bedford, Peter; Mellersh, Cathryn

    2015-01-01

    Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant. PMID:26683476

  11. A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17.

    PubMed

    Forman, Oliver P; Pettitt, Louise; Komáromy, András M; Bedford, Peter; Mellersh, Cathryn

    2015-01-01

    Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant. PMID:26683476

  12. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

    PubMed Central

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

    2015-01-01

    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. PMID:26039588

  13. 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

    2015-01-01

    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. PMID:26039588

  14. 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. PMID:25086366

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

    PubMed

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

    2015-06-01

    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. PMID:24117189

  16. 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.

  17. 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. PMID:18979765

  18. Age, Gender and Normalization Covariates for Spinal Cord Gray Matter and Total Cross-Sectional Areas at Cervical and Thoracic Levels: A 2D Phase Sensitive Inversion Recovery Imaging Study

    PubMed Central

    Papinutto, Nico; Schlaeger, Regina; Panara, Valentina; Zhu, Alyssa H.; Caverzasi, Eduardo; Stern, William A.; Hauser, Stephen L.; Henry, Roland G.

    2015-01-01

    The source of inter-subject variability and the influence of age and gender on morphometric characteristics of the spinal cord, such as the total cross-sectional area (TCA), the gray matter (GM) and white matter (WM) areas, currently remain under investigation. Understanding the effect of covariates such as age, gender, brain volumes, and skull- and vertebra-derived metrics on cervical and thoracic spinal cord TCA and GM areas in healthy subjects would be fundamental for exploring compartment specific changes in neurological diseases affecting the spinal cord. Using Magnetic Resonance Imaging at 3T we investigated 32 healthy subjects using a 2D phase sensitive inversion recovery sequence and we measured TCA, GM and WM areas at 4 cervical and thoracic levels of the spinal cord. We assessed age and gender relationships of cord measures and explored associations between cord measures and a) brain volumes and b) skull- and vertebra-derived metrics. Age and gender had a significant effect on TCA, WM and GM areas (with women and elderly having smaller values than men and younger people respectively), but not on the GM area/TCA ratio. The total intracranial volume and C3 vertebra dimensions showed the highest correlations with cord measures. When used in multi-regression models, they reduced cord areas group variability by approximately a third. Age and gender influences on cord measures and normalization strategies here presented might be of use in the study of compartment specific changes in various neurological diseases affecting the spinal cord. PMID:25781178

  19. 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.

  20. 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…

  1. 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

  2. Inversion of Moraxella lacunata type 4 pilin gene sequences by a Neisseria gonorrhoeae site-specific recombinase.

    PubMed Central

    Rozsa, F W; Meyer, T F; Fussenegger, M

    1997-01-01

    A plasmid library of Neisseria gonorrhoeae sequences was screened for the ability to mediate recombinations on a sequence containing the Moraxella lacunata type 4 pilin gene invertible region in Escherichia coli. A plasmid containing the N. gonorrhoeae sequence encoding the putative recombinase (gcr) was identified and sequenced. Plasmids containing gcr were able to mediate site-specific recombinations despite a weak amino acid homology to Piv, the native M. lacunata pilin gene invertase. The gcr gene is present only in pathogenic strains of Neisseria tested; however, in our assays gene knockouts of gcr did not alter the variation of surface features that play a role in the pathogenesis of N. gonorrhoeae. PMID:9079926

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

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

    PubMed

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

    2015-11-01

    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. PMID:26370781

  9. 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.

  10. Contrast-enhanced magnetic resonance pancreatography with gadoteridol by heavily T2-weighted three-dimensional fluid-attenuated inversion recovery: preliminary results in healthy subjects

    PubMed Central

    Suzuki, Kojiro; Naganawa, Shinji; Furuhashi, Naohiro; Yamazaki, Masahiro; Ogawa, Hiroshi; Kawai, Hisashi

    2016-01-01

    ABSTRACT The purpose of this study was to investigate the feasibility of contrast-enhanced magnetic resonance (MR) pancreatography with intravenously administered gadolinium-based contrast material (GBCM) in healthy subjects. Eight healthy male subjects (age: 29–53 years old, median: 37 years old) were enrolled. Contrast-enhanced MR pancreatography was scanned with heavily T2-weighted three-dimensional fluid-attenuated inversion recovery (hT2W-3D-FLAIR) before and after intravenous GBCM administration. Two radiologists evaluated the images, referring to three-dimensional MR pancreatography by consensus. Scanning was performed five times at 1.5-h intervals (at 0.5, 2, 3.5, 5, and 6.5 h) after GBCM administration. In all subjects, pre-contrast-enhanced hT2W-3D-FLAIR images demonstrated no visualization of the main pancreatic duct. After GBCM administration, the main pancreatic duct was visualized in all subjects at 0.5 h (n=4, 50%) and/or 2 h (n=7, 88%). The mean signal intensity of the main pancreatic duct was 3.17 ± 0.78 at pre-contrast enhancement, 7.96 ± 4.60 at 0.5 h, and 8.08 ± 4.64 at 2 h. The signal intensity ratio of the main pancreatic duct against the pancreatic parenchyma was statistically higher (P < 0.01) at the 0.5-h and 2-h scans than that of pre-contrast-enhanced scan. Intravenously administered GBCM seeped into the pancreatic duct in sufficient concentration to alter the appearance of the main pancreatic duct by hT2W-3D-FLAIR in healthy subjects. PMID:27303104

  11. 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. PMID:27272187

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

    PubMed Central

    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. PMID:27272187

  13. 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.

  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. PMID:23078018

  15. The treatment of solvent recovery raffinate by aerobic granular sludge in a pilot-scale sequencing batch reactor.

    PubMed

    Long, Bei; Yang, Chang-zhu; Pu, Wen-hong; Yang, Jia-kuan; Jiang, Guo-sheng; Dan, Jing-feng; Zhang, Jing; Zhang, Li

    2015-09-01

    Mature aerobic granular sludge (AGS) was inoculated for the start-up of a pilot-scale sequencing batch reactor for the treatment of high concentration solvent recovery raffinate (SRR). The proportion of simulated wastewater (SW) (w/w) in the influent gradually decreased to zero during the operation, while volume of SRR gradually increased from zero to 10.84 L. AGS was successfully domesticated after 48 days, which maintained its structure during the operation. The domesticated AGS was orange, irregular, smooth and compact. Sludge volume index (SVI), SV30/SV5, mixed liquor volatile suspended solids/mixed liquor suspended solids (MLVSS/MLSS), extracellular polymeric substances, proteins/polysaccharides, average particle size, granulation rate, specific oxygen utilization rates (SOUR)H and (SOUR)N of AGS were about 38 mL/g, 0.97, 0.52, 39.73 mg/g MLVSS, 1.17, 1.51 mm, 96.66%, 47.40 mg O2/h g volatile suspended solids (VSS) and 8.96 mg O2/h g VSS, respectively. Good removal effect was achieved by the reactor. Finally, the removal rates of chemical oxygen demand (COD), total inorganic nitrogen (TIN), NH4+-N and total phosphorus (TP) were more than 98%, 96%, 97% and 97%, respectively. The result indicated gradually increasing the proportion of real wastewater in influent was a useful domestication method, and the feasibility of AGS for treatment of high C/N ratio industrial wastewater. PMID:26322760

  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)

    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.

  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)

    ScienceCinema

    Peng, Ze [DOE JGI

    2013-01-25

    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. An episode of fault-valve behaviour during compressional inversion? — The 2004 MJ6.8 Mid-Niigata Prefecture, Japan, earthquake sequence

    NASA Astrophysics Data System (ADS)

    Sibson, Richard H.

    2007-05-01

    Principal ruptures of the 2004 Mid-Niigata Prefecture sequence involved close-to-pure reverse slip on a 50-60° WNW dipping fault system uplifting a Miocene rift basin on its hanging wall, consistent with geological evidence for ongoing compressional inversion in the region since the Late Pliocene. The MJ6.8 mainshock was followed by four other MJ > 6 shocks (all with hypocentres in the 7-12 km depth range) and a rich aftershock sequence defined a criss-crossing network of reverse-slip rupture planes dipping 50-60° WNW and 25-35° ESE. The steep rupture planes dip close to the maximum for reverse-fault earthquakes and are poorly oriented for frictional reactivation assuming horizontal maximum compressive stress. In contrast, the subsidiary ESE-dipping thrusts appear optimally oriented in the stress field. The combined reactivation of existing, unfavourably oriented reverse faults and optimally oriented thrusts requires high but probably variable fluid-overpressuring within the rock-mass. Evidence for overpressures in and around the seismogenic fault system comes from borehole measurements in the hanging-wall sedimentary basin plus a range of anomalous seismological and electrical characteristics which also suggest an overpressured mid-crust below the seismogenic zone. Minor postseismic effusion of anomalously warm, saline formation fluids was recorded from the aftershock area: similar discharges characterize the epicentral areas of historic earthquakes in the Niigata region. The rupturing of unfavourably oriented faults in a fluid-overpressured compressional regime - together with the swarm-like character of the aftershock activity and the evidence of postseismic discharge - are all suggestive of a 'fault-valve' episode involving upwards migration of fluids from compartmentalized fluid-overpressures within the seismogenic zone.

  19. Reassessment of the source of the 1976 Friuli, NE Italy, earthquake sequence from the joint inversion of high-precision levelling and triangulation data

    NASA Astrophysics Data System (ADS)

    Cheloni, D.; D'Agostino, N.; D'Anastasio, E.; Selvaggi, G.

    2012-08-01

    In this study, we revisit the mechanism of the 1976 Friuli (NE Italy) earthquake sequence (main shocks Mw 6.4, 5.9 and 6.0). We present a new source model that simultaneously fits all the available geodetic measurements of the observed deformation. We integrate triangulation measurements, which have never been previously used in the source modelling of this sequence, with high-precision levelling that covers the epicentral area. We adopt a mixed linear/non-linear optimization scheme, in which we iteratively search for the best-fitting solution by performing several linear slip inversions while varying fault location using a grid search method. Our preferred solution consists of a shallow north-dipping fault plane with assumed azimuth of 282° and accommodating a reverse dextral slip of about 1 m. The estimated geodetic moment is 6.6 × 1018 Nm (Mw 6.5), in agreement with seismological estimates. Yet, our preferred model shows that the geodetic solution is consistent with the activation of a single fault system during the entire sequence, the surface expression of which could be associated with the Buia blind thrust, supporting the hypothesis that the main activity of the Eastern Alps occurs close to the relief margin, as observed in other mountain belts. The retrieved slip pattern consists of a main coseismic patch located 3-5 km depth, in good agreement with the distribution of the main shocks. Additional slip is required in the shallower portions of the fault to reproduce the local uplift observed in the region characterized by Quaternary active folding. We tentatively interpret this patch as postseismic deformation (afterslip) occurring at the edge of the main coseismic patch. Finally, our rupture plane spatially correlates with the area of the locked fault determined from interseismic measurements, supporting the hypothesis that interseismic slip on the creeping dislocation causes strain to accumulate on the shallow (above ˜10 km depth) locked section

  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. An Episode of Fault-Valve Behavior During Compressional Inversion - the 2004 MJ 6.8 Niigata-ken Chuetsu Earthquake Sequence

    NASA Astrophysics Data System (ADS)

    Sibson, R. H.

    2006-12-01

    Principal ruptures of the 2004 Niigata-ken Chuetsu sequence involved close-to-pure reverse slip on a 50- 60° WNW dipping fault system uplifting a Miocene rift basin on its hanging wall, consistent with geological evidence for ongoing compressional inversion in the region since the Late Pliocene. The MJ6.8 mainshock was followed by four other MJ>6 shocks (all with hypocenters in the 7-12 km depth range) and a rich aftershock sequence defined a criss-crossing network of reverse-slip rupture planes dipping 50- 60° WNW and 25-35° ESE. The steep rupture planes dip close to the maximum for reverse-fault earthquakes. Assuming horizontal maximum compressive stress, they are poorly oriented for frictional reactivation (50-60° to σ1), lying close to the lock-up angle for standard coefficients of rock friction. In contrast, subsidiary ESE-dipping thrusts (25-35° to σ1) appear optimally oriented for reactivation. Reactivation of existing, unfavorably oriented reverse faults is thus competing with slip on optimally oriented thrusts, requiring high but probably variable fluid-overpressuring within the rock-mass. Supporting evidence for fluid-overpressures around the seismogenic structures includes direct measurements of overpressures in oil/gas boreholes within the >6 km thick sedimentary basin on the hanging-wall of the main fault, plus a range of geophysical measurements consistent with local overpressuring in and around the fault system. Minor postseismic effusion of anomalously warm, saline formation fluids was recorded from the aftershock area of this earthquake: similar discharges occur in the epicentral areas of previous earthquakes in the Niigata region. Compressional stress in the upper crust helps to contain overpressured fluids which may, in part, be derived from beneath the seismogenic zone where anomalous electrical and seismological characteristics also suggest distributed overpressuring in the mid-crust. The rupturing of unfavorably oriented faults in a

  2. 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

  3. Virus recovery and full-length sequence analysis of atypical bovine pestivirus Th/04_KhonKaen.

    PubMed

    Liu, Lihong; Kampa, Jaruwan; Belák, Sándor; Baule, Claudia

    2009-07-01

    Phylogenetic analysis of recently identified "atypical" bovine pestiviruses, performed based on different gene regions, has revealed unclear relationships with other established species, therefore, their phylogenetic position could not be determined so far. In this study, the atypical pestivirus Th/04_KhonKaen was recovered from serum of a naturally infected calf and the complete genome sequence was determined and analysed, as means to define its position. The viral genome is 12,337 nucleotides (nt) long, and comprises a 5'-UTR of 383 nt, a 3'-UTR of 254 nt and an open reading frame of 11,700 nt, without duplication of viral sequences or insertions of cellular sequences. The phylogenetic analyses of the full-length sequence, performed by Neighbor-joining, Maximum likelihood, and the Bayesian approach, unanimously placed Th/04_KhonKaen in a single lineage, distinct from the established pestivirus species, and close to bovine viral diarrhea virus types 1 and 2. Furthermore, Th/04_KhonKaen and two previously reported atypical pestiviruses D32/00_'HoBi' and CH-KaHo/cont formed a well-supported monophyletic clade in trees based on the complete N(pro) and E2 gene regions. The finding provides conclusive classification of the Th/04_KhonKaen virus and confirms the standing of the "atypical" bovine pestiviruses as a novel pestivirus species. PMID:19349128

  4. 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.

  5. 3-T Breast Diffusion-Weighted MRI by Echo-Planar Imaging with Spectral Spatial Excitation or with Additional Spectral Inversion Recovery: An In Vivo Comparison of Image Quality

    PubMed Central

    Jacobsen, Megan C.; Dogan, Basak E.; Adrada, Beatriz E.; Plaxco, Jeri Sue; Wei, Wei; Son, Jong Bum; Hazle, John D.; Ma, Jingfei

    2015-01-01

    Objective To compare conventional DWI with spectral spatial excitation (cDWI) and an enhanced DWI with additional adiabatic spectral inversion recovery (eDWI) for 3T breast MRI. Methods Twenty-four patients were enrolled in the study with both cDWI and eDWI. Three breast radiologists scored cDWI and eDWI images of each patient for fat-suppression quality, geometric distortion, visibility of normal structure and biopsy-proven lesions, and overall image quality. SNR, CNR and ADC for evaluable tissues were measured. Statistical tests were performed for qualitative and quantitative comparisons. Results eDWI yielded significantly higher CNR and SNR on a lesion and higher glandular CNR and SNR, and muscle SNR on a patient basis. eDWI also yielded significantly higher qualitative scores in all categories. No significant difference was found in ADC values. Conclusion eDWI provided superior image quality and higher CNR and SNR on a lesion basis. eDWI can replace cDWI for 3T breast DWI. PMID:25695868

  6. 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.

  7. Advanced space recovery systems

    NASA Technical Reports Server (NTRS)

    Wailes, William K.

    1989-01-01

    The design evolution of a space recovery system designed by a NASA-contracted study is described, with particular attention given to the design of a recovery system for a propulsion/avionics module (P/AM), which weighs 60,000 lb at the recovery initiation and achieves subsonic terminal descent at or above 50,000 ft msl. The components of the recovery system concept are described together with the operational sequences of the recovery. The recovery system concept offers low cost, low weight, good performance, a potential for pinpoint landing, and an operational flexibility.

  8. 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.

  9. Sustainable nutrients recovery and recycling by optimizing the chemical addition sequence for struvite precipitation from raw swine slurries.

    PubMed

    Taddeo, Raffaele; Kolppo, Kari; Lepistö, Raghida

    2016-09-15

    Livestock farming contributes heavily to nitrogen (N) and phosphorus (P) flows into the environment, a major cause of eutrophication of coastal and freshwater systems. Furthermore, the growing demand for N-P fertilizers is increasing the emission of anthropogenic reactive N into the atmosphere and the depletion of the current P reserves. Therefore, it is essential to minimize the anthropogenic impact on the environment and recycle the wasted N-P for agricultural reuse. This study focused on enhancing struvite (MgNH4PO4*6H2O) precipitation from raw swine slurries in batch and laboratory-scale reactors. Different chemical addition sequences were evaluated, and the best removal efficiency (E%) was obtained when the chemicals were mixed before the precipitation process. Struvite was detected at a pH as low as 6 (E%N-P∼50%), and high E%N-P was found at pH 7-9.5 (80-95%). Furthermore, air stripping was used in place of NaOH to adjust pH, returning the same efficiency as if only alkali had been used. XRD and FE-SEM analysis of the precipitate showed that the recovered struvite was of high purity with orthorhombic crystalline structure and only trace amounts of impurities from matrix organics, co-precipitation products (CaO and amorphous calcium-phosphates), and residuals of added chemicals (MgO). PMID:27208994

  10. Associating approximate paths and temporal sequences of noisy detections: Application to the recovery of spatio-temporal cancer cell trajectories.

    PubMed

    Dorfer, Matthias; Kazmar, Tomáš; Šmíd, Matěj; Sing, Sanchit; Kneißl, Julia; Keller, Simone; Debeir, Olivier; Luber, Birgit; Mattes, Julian

    2016-01-01

    In this paper we address the problem of recovering spatio-temporal trajectories of cancer cells in phase contrast video-microscopy where the user provides the paths on which the cells are moving. The paths are purely spatial, without temporal information. To recover the temporal information associated to a given path we propose an approach based on automatic cell detection and on a graph-based shortest path search. The nodes in the graph consist of the projections of the cell detections onto the geometrical cell path. The edges relate nodes which correspond to different frames of the sequence and potentially to the same cell and trajectory. In this directed graph we search for the shortest path and use it to define a temporal parametrization of the corresponding geometrical cell path. An evaluation based on 286 paths of 7 phase contrast microscopy videos shows that our algorithm allows to recover 92% of trajectory points with respect to the associated ground truth. We compare our method with a state-of-the-art algorithm for semi-automated cell tracking in phase contrast microscopy which requires interactively placed starting points for the cells to track. The comparison shows that supporting geometrical paths in combination with our algorithm allow us to obtain more reliable cell trajectories. PMID:25987193

  11. Reduced Scan Time 3D FLAIR using Modulated Inversion and Repetition Time

    PubMed Central

    Gai, Neville D.; Butman, John A.

    2014-01-01

    Purpose To design and evaluate a new reduced scan time 3D FLuid Attenuated Inversion Recovery (FLAIR) sequence. Materials and Methods The 3D FLAIR sequence was modified so that the repetition time was modulated in a predetermined smooth fashion (3D mFLAIR). Inversion times were adjusted accordingly to maintain CSF suppression. Simulations were performed to determine SNR for gray matter (GM), white matter (WM) and CSF. Fourteen volunteers were imaged using the modified and product sequence. SNR measurements were performed in GM, WM and CSF. Mean value and the 95% confidence interval ([CI]) were assessed. Scan time for the 3D FLAIR and 3D mFLAIR sequences was measured. Results There was no statistically significant difference in the SNR measured in GM (P value = 0.5; mean SNR = 42.8 [CI]: 38.2-45.5 vs 42.2 [CI]: 38.3-46.1 for 3D FLAIR and 3D mFLAIR, respectively) and WM (P value = 0.25; mean SNR = 32.1 [CI]: 30.3-33.8 vs 32.9 [CI]: 31.1-34.7). Scan time reduction greater than 30% was achieved for the given parameter set with the 3D mFLAIR sequence. Conclusion Scan time for 3D FLAIR can be effectively reduced by modulating repetition and inversion time in a predetermined fashion while maintaining the SNR and CNR of a constant TR sequence. PMID:24979311

  12. Endolymphatic Hydrops Detected by 3-Dimensional Fluid-Attenuated Inversion Recovery MRI following Intratympanic Injection of Gadolinium in the Asymptomatic Contralateral Ears of Patients with Unilateral Ménière’s Disease

    PubMed Central

    Liu, Yupeng; Jia, Huan; Shi, Jun; Zheng, Hui; Li, Yuhua; Yang, Jun; Wu, Hao

    2015-01-01

    Background The aim of this study was to identify the incidence of endolymphatic hydrops using 3-dimensional fluid-attenuated inversion recovery (3D-FLAIR) magnetic resonance imaging (MRI) in the contralateral ear in patients with unilateral Ménière’s disease (MD). Material/Methods This was a prospective study. 3D-FLAIR MRI was performed with a 3 Tesla (3 T) unit 24 h after the intratympanic administration of gadolinium (Gd) in 30 unilateral MD patients with an asymptomatic contralateral ear. The incidence of contralateral involvement in unilateral MD patients and the potential correlations between the affected and contralateral ears were analyzed. Results Endolymphatic hydrops was observed in 7 of the 30 (23.3%) asymptomatic ears. The mean PTA of the asymptomatic ears in the contralateral hydrops patients (33.0±6.1 dB) was significantly higher compared with the non-hydrops patients (17.8±5.7 dB). The patients with observed contralateral hydrops exhibited a significantly longer duration of the disease compared with the non-hydrops patients (6.7±6.3 vs. 2.9±3.1 years, respectively). Furthermore, the patients with contralateral hydrops had a worse hearing level in the affected ears compared with the non-hydrops patients (70.3±7.4 vs. 52.5±3.8 dB, respectively). Conclusions Endolymphatic hydrops is closely related to hearing loss but does not necessarily result in Ménière’s symptoms. Patients with a long history of MD and severe hearing loss in the affected ear are more likely to exhibit endolymphatic hydrops in the asymptomatic contralateral ear. Adequate attention should focus on unilateral MD patients with contralateral ear hydrops because of the potential to develop bilateral MD. PMID:25742875

  13. Deformation along the western Indian plate boundary: new constraints from differential and multi-aperture InSAR data inversion for the 2008, Baluchistan (Western Pakistan) seismic sequence.

    NASA Astrophysics Data System (ADS)

    Pezzo, Giuseppe; Merryman Boncori, John Peter; Atzori, Simone; Antonioli, Andrea; Salvi, Stefano

    2014-05-01

    We use Synthetic Aperture Radar Differential Interferometry (DInSAR) and Multi-Aperture Interferometry (MAI) to constrain the sources of the three largest events of the 2008 Baluchistan (western Pakistan) seismic sequence, namely two Mw 6.4 events only 12 hours apart and an Mw 5.7event occurred 40 days later. The sequence took place in the Quetta Syntaxis, the most seismically active region of Baluchistan, tectonically located between the colliding Indian Plate and the Afghan block of the Eurasian Plate. Elastic dislocation modelling of the surface displacements, derived from ascending and descending ENVISAT ASAR acquisitions, yields slip distributions with peak values of 80 cm and 70 cm for the two main events on a pair of strike-slip near-vertical faults, and values up to 50 cm for the largest aftershock on a NE-SW strike-slip fault. The MAI measurements, with their high sensitivity to the north-south motion component, are crucial in this area to resolve the fault plane ambiguity of moment tensors. We also studied the relationships between the largest earthquakes of the sequence by means of the Coulomb Failure Function to verify the agreement of our source modelling with the stress variations induced by the October 28 earthquake on the October 29 fault plane, and the stress variations induced by the two mainshocks on the December 09 fault plane. Our results provide insight into the deformation style of the Quetta Syntaxis, suggesting that right-lateral slip released at intermediate depths on large NW fault planes is compatible with contemporaneous left-lateral activation on NE-SW minor faults at shallower depths, in agreement with a bookshelf deformation mechanism.

  14. 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. Supplementary Information - Fig S2. Map of Greece showing seismic stations (green triangles) used in moment tensor analysis. Yellow stars show epicenter of mainshocks. Supplementary Fig. S3. a: Moment tensor solution of the 12 November 2013 (18:09 UTC) earthquake. To the left observed and synthetic displacement waveforms (continuous and dotted lines respectively) are shown, at the inverted stations for the radial, tangential and vertical components. At the right part of the figure the summary of the

  15. Deformation of the western Indian Plate boundary: insights from differential and multi-aperture InSAR data inversion for the 2008 Baluchistan (Western Pakistan) seismic sequence

    NASA Astrophysics Data System (ADS)

    Pezzo, Giuseppe; Merryman Boncori, John Peter; Atzori, Simone; Antonioli, Andrea; Salvi, Stefano

    2014-07-01

    In this study, we use Differential Synthetic Aperture Radar Interferometry (DInSAR) and multi-aperture interferometry (MAI) to constrain the sources of the three largest events of the 2008 Baluchistan (western Pakistan) seismic sequence, namely two Mw 6.4 events only 12 hr apart and an Mw 5.7 event that occurred 40 d later. The sequence took place in the Quetta Syntaxis, the most seismically active region of Baluchistan, tectonically located between the colliding Indian Plate and the Afghan Block of the Eurasian Plate. Surface displacements estimated from ascending and descending ENVISAT ASAR acquisitions were used to derive elastic dislocation models for the sources of the two main events. The estimated slip distributions have peak values of 120 and 130 cm on a pair of almost parallel and near-vertical faults striking NW-SE, and of 50 cm and 60 cm on two high-angle faults striking NE-SW. Values up to 50 cm were found for the largest aftershock on an NE-SW fault located between the sources of the main shocks. The MAI measurements, with their high sensitivity to the north-south motion component, are crucial in this area to accurately describe the coseismic displacement field. Our results provide insight into the deformation style of the Quetta Syntaxis, suggesting that right-lateral slip released at shallow depths on large NW fault planes is compatible with left-lateral activation on smaller NE-SW faults.

  16. 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.

  17. [Biological and clinical safety of nomegestrol acetate administered alone then associated in inverse sequence with transdermal 17 beta estradiol, in women at risk of dyslipoproteinemia type IIa].

    PubMed

    Zartarian, M; Chevallier, T; Micheletti, M C; Leber, C; Jamin, C

    1998-12-01

    In this study including 26 patients with dyslipoproteinemia classified IIa, we evaluated biochemical and clinical safety of Nomegestrol acetate (Lutenyl) used for its antigonadotrophin property. It was administered alone, during 3 cycles at the dose of 5 mg/d for 21 days by cycle and then it was associated (at the same sequence and dose), without any wash out, for the next 6 cycles, with a 17 beta estradiol patch (Estraderm TTS 50), 50 micrograms/d from the 11th to the 21st day of each cycle. Nomegestrol acetate, alone, had no significant effect on glycemia, antithrombin III, triglycerides, total cholesterol, apoprotein A1, and LpA1 values compared to those at baseline but apoprotein B and Lp (a) values tended to decrease slightly. Serum progesterone levels were collapsed, and FSH values were low. Weight and blood pressure remained constant. Adding 17 beta estradiol enabled to significantly decrease and normalize the apoprotein B values after the first 3 cycles compared to the baseline values, then these values remained constant during the next 3 cycles. There was no effect on the other parameters (except for a significant increase in plasmatic estradiol values) on the antigonadotrophin property of Nomegestrol acetate, nor on weight and blood pressure which remained constant. Moreover, we observed an important decrease in the rate of amenorrheic cycles compared to those with Nomegestrol acetate alone. PMID:9949893

  18. The multicopy appearance of a large inverted duplication and the sequence at the inversion joint suggest a new model for gene amplification.

    PubMed Central

    Hyrien, O; Debatisse, M; Buttin, G; de Saint Vincent, B R

    1988-01-01

    The amplified DNA of HC50474, a Chinese hamster fibroblast cell line selected in three steps for high resistance to coformycin, consists chiefly of 150 copies of a large inverted duplication including the adenylate deaminase gene. Most if not all of these units are more than 2 x 120 kb long. The inverted duplication was first detected in the cells recovered from the second selection step, at the same chromosomal location as the first step amplified units. Its formation and amplification appear to be coupled since the second step cell line already contained 40 copies of this novel structure. Reamplification of the inverted duplication occurred at the third step of selection concomitant with the loss of amplified DNA acquired during the first step. The head-to-head junction has been formed by recombination within a recombinational hotspot described previously [Hyrien, O., Debatisse, M., Buttin, G. and Robert de Saint Vincent, B. (1987) EMBO J., 6, 2401-2408]. Sequences at the joint and in the corresponding wild-type region reveal that the crossover sites, one of which occurs in the putative promoter region of B2 repeat, are located at the top of significant stem-loop structures and that patchy homologies between the parental molecules on one side of the breakpoints allow alignment of these crossover sites. We present a model which explains the formation and amplification of this and other large inverted duplications by errors in DNA replication. Images PMID:3366118

  19. Multidimensional NMR inversion without Kronecker products: Multilinear inversion.

    PubMed

    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. PMID:27209370

  20. 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.

  1. Appropriate selection of MRI sequences for common scenarios in clinical practice.

    PubMed

    Chavhan, Govind B

    2016-05-01

    Knowledge about sequence properties is essential to plan and acquire a diagnostic MRI examination. The broad four categories of sequences include spin echo (SE), gradient echo (GRE), inversion recovery (IR) and echoplanar imaging (EPI). Varieties of sequences from these four categories are available for clinical application. They have different contrast mechanisms, spatial and contrast resolution and speed of acquisition. Choice of sequence differs in various scenarios in clinical practice such as solid organ imaging, moving target imaging, bone and bone marrow imaging, cartilage imaging and vessel imaging, taking into consideration properties of sequences to answer the clinical question. Broad classification of sequences and differences in their contrast, spatial and contrast resolution, and speed of acquisition are discussed in this review. A few common clinical scenarios of MRI imaging are illustrated, along with reasons for the given sequence choices. PMID:27229493

  2. 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. Compton); "Reading Recovery in Arizona--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 Central

    2009-01-01

    Background 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. Results 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. Conclusion 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. PMID:19698121

  4. 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." PMID:15177788

  5. 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

  6. Recovery as a psychological construct.

    PubMed

    Corrigan, P W; Giffort, D; Rashid, F; Leary, M; Okeke, I

    1999-06-01

    Mental health advocates have proposed recovery as a vision for severe mental illness. The purpose of this study is to examine psychometric characteristics of a measure of the psychological construct. Thirty-five participants in a partial hospitalization program were administered the Recovery Scale and measures of quality of life, social support, self-esteem, consumer empowerment, psychiatric symptoms, needs and resources, global functioning, and verbal intelligence. Results showed the scale to have satisfactory test-retest reliability and internal consistency. Analysis of the concurrent validity of the Recovery Scale showed recovery to be positively associated with self-esteem, empowerment, social support, and quality of life. It was inversely associated with psychiatric symptoms and age. Implications of these findings for a psychological model of recovery are discussed. PMID:10401893

  7. Completion of Kunjin virus RNA sequence and recovery of an infectious RNA transcribed from stably cloned full-length cDNA.

    PubMed Central

    Khromykh, A A; Westaway, E G

    1994-01-01

    Completion of the Kunjin virus (KUN) RNA sequence showed that it is the longest flavivirus sequence reported (11,022 bases), commencing with a 5' noncoding region of 96 bases. The 3' noncoding sequence of 624 nucleotides included a unique insertion sequence of 46 bases adjacent to the stop codon, but otherwise it had properties similar to those of RNAs of closely related flaviviruses. A full-length KUN cDNA clone which could be stably propagated in Escherichia coli DH5 alpha was constructed; SP6 polymerase RNA transcripts from amplified cDNA were infectious when transfected into BHK-21 cells. A mutational change abolishing the BamHI restriction site at position 4049, leading to a conservative amino acid change of Arg-175 to Lys in the NS2A protein, was introduced into the cDNA during construction and was retained in the recovered virus. Extra terminal nucleotides introduced during cloning of the cDNA were shown to be present in the in vitro RNA transcripts but absent in the RNA of recovered virus. Although recovered virus differed from the parental KUN by a smaller plaque phenotype and delayed growth rate in BHK-21 cells and mice, it was very similar as assessed by several other criteria, such as peak titer during growth in cells, infectivity titer in cells and in mice, rate of adsorption and penetration in cells, replication at 39 degrees C, and neurovirulence after intraperitoneal injection in mice. The KUN stably cloned cDNA will provide a useful basis for future studies in defining and characterizing functional roles of all the gene products. Images PMID:8207832

  8. 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…

  9. 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.

  10. Inverse structure functions

    SciTech Connect

    Pearson, Bruce R.; Water, Willem van de

    2005-03-01

    While the ordinary structure function in turbulence is concerned with the statistical moments of the velocity increment {delta}u measured over a distance r, the inverse structure function is related to the distance r where the turbulent velocity exits the interval {delta}u. We study inverse structure functions of wind-tunnel turbulence which covers a range of Reynolds numbers Re{sub {lambda}}=400-1100. We test a recently proposed relation between the scaling exponents of the ordinary structure functions and those of the inverse structure functions [S. Roux and M. H. Jensen, Phys. Rev. E 69, 16309 (2004)]. The relatively large range of Reynolds numbers in our experiment also enables us to address the scaling with Reynolds number that is expected to highlight the intermediate dissipative range. While we firmly establish the (relative) scaling of inverse structure functions, our experimental results fail both predictions. Therefore, the question of the significance of inverse structure functions remains open.

  11. Genomic Phenotyping by Barcode Sequencing Broadly Distinguishes between Alkylating Agents, Oxidizing Agents, and Non-Genotoxic Agents, and Reveals a Role for Aromatic Amino Acids in Cellular Recovery after Quinone Exposure

    PubMed Central

    Svensson, J. Peter; Quirós Pesudo, Laia; McRee, Siobhan K.; Adeleye, Yeyejide; Carmichael, Paul; Samson, Leona D.

    2013-01-01

    Toxicity screening of compounds provides a means to identify compounds harmful for human health and the environment. Here, we further develop the technique of genomic phenotyping to improve throughput while maintaining specificity. We exposed cells to eight different compounds that rely on different modes of action: four genotoxic alkylating (methyl methanesulfonate (MMS), N-Methyl-N-nitrosourea (MNU), N,N′-bis(2-chloroethyl)-N-nitroso-urea (BCNU), N-ethylnitrosourea (ENU)), two oxidizing (2-methylnaphthalene-1,4-dione (menadione, MEN), benzene-1,4-diol (hydroquinone, HYQ)), and two non-genotoxic (methyl carbamate (MC) and dimethyl sulfoxide (DMSO)) compounds. A library of S. cerevisiae 4,852 deletion strains, each identifiable by a unique genetic ‘barcode’, were grown in competition; at different time points the ratio between the strains was assessed by quantitative high throughput ‘barcode’ sequencing. The method was validated by comparison to previous genomic phenotyping studies and 90% of the strains identified as MMS-sensitive here were also identified as MMS-sensitive in a much lower throughput solid agar screen. The data provide profiles of proteins and pathways needed for recovery after both genotoxic and non-genotoxic compounds. In addition, a novel role for aromatic amino acids in the recovery after treatment with oxidizing agents was suggested. The role of aromatic acids was further validated; the quinone subgroup of oxidizing agents were extremely toxic in cells where tryptophan biosynthesis was compromised. PMID:24040048

  12. Comparison of two fat-suppressed magnetic resonance imaging pulse sequences to standard t2-weighted images for brain parenchymal contrast and lesion detection in dogs with inflammatory intracranial disease.

    PubMed

    Young, Benjamin D; Mankin, Joseph M; Griffin, John F; Fosgate, Geoffrey T; Fowler, Jennifer L; Levine, Jonathan M

    2015-01-01

    T2-weighted (T2w) sequences are commonly relied upon in magnetic resonance imaging protocols for the detection of brain lesions in dogs. Previously, the effect of fluid suppression via fluid-attenuated inversion recovery (FLAIR) has been compared to T2-weighting with mixed results. Short tau inversion recovery (STIR) has been reported to increase the detection of some CNS lesions in people. The purpose of the current study was to evaluate the effect of fat suppression on brain parenchymal contrast resolution and lesion detection in dogs. We compared three sequences: T2w images, STIR, and T2w FLAIR with chemical fat suppression (T2-FLAIR-FS) in dogs with meningoencephalitis. Dogs with meningoencephalitis and dogs with idiopathic epilepsy were retrospectively identified and anonymized. Evaluators recorded the presence or absence of lesions within 12 predetermined brain regions on randomized sequences, viewing and scoring each sequence individually. Additionally, signal-to-noise ratios, contrast-to-noise ratios, and relative contrast (RC) were measured in a reference population. Short tau inversion recovery sequences had the highest RC between gray and white matter. While descriptively more lesions were identified by evaluators on T2-FLAIR-FS images, there was no statistical difference in the relative sensitivity of lesion detection between the sequences. Nor was there a statistical difference in false lesion detection within our reference population. Short tau inversion recovery may be favored for enhanced anatomic contrast depiction in brain imaging. No benefit of the inclusion of a fat-suppressed T2-FLAIR sequence was found. PMID:25395066

  13. Plasma inverse transition acceleration

    SciTech Connect

    Xie, Ming

    2001-06-18

    It can be proved fundamentally from the reciprocity theorem with which the electromagnetism is endowed that corresponding to each spontaneous process of radiation by a charged particle there is an inverse process which defines a unique acceleration mechanism, from Cherenkov radiation to inverse Cherenkov acceleration (ICA) [1], from Smith-Purcell radiation to inverse Smith-Purcell acceleration (ISPA) [2], and from undulator radiation to inverse undulator acceleration (IUA) [3]. There is no exception. Yet, for nearly 30 years after each of the aforementioned inverse processes has been clarified for laser acceleration, inverse transition acceleration (ITA), despite speculation [4], has remained the least understood, and above all, no practical implementation of ITA has been found, until now. Unlike all its counterparts in which phase synchronism is established one way or the other such that a particle can continuously gain energy from an acceleration wave, the ITA to be discussed here, termed plasma inverse transition acceleration (PITA), operates under fundamentally different principle. As a result, the discovery of PITA has been delayed for decades, waiting for a conceptual breakthrough in accelerator physics: the principle of alternating gradient acceleration [5, 6, 7, 8, 9, 10]. In fact, PITA was invented [7, 8] as one of several realizations of the new principle.

  14. One-Step Recovery of scFv Clones from High-Throughput Sequencing-Based Screening of Phage Display Libraries Challenged to Cells Expressing Native Claudin-1

    PubMed Central

    Sasso, Emanuele; Paciello, Rolando; D'Auria, Francesco; Riccio, Gennaro; Froechlich, Guendalina; Cortese, Riccardo; Nicosia, Alfredo; De Lorenzo, Claudia; Zambrano, Nicola

    2015-01-01

    Expanding the availability of monoclonal antibodies interfering with hepatitis C virus infection of hepatocytes is an active field of investigation within medical biotechnologies, to prevent graft reinfection in patients subjected to liver transplantation and to overcome resistances elicited by novel antiviral drugs. In this paper, we describe a complete pipeline for screening of phage display libraries of human scFvs against native Claudin-1, a tight-junction protein involved in hepatitis C virus infection, expressed on the cell surface of human hepatocytes. To this aim, we implemented a high-throughput sequencing approach for library screening, followed by a simple and effective strategy to recover active binder clones from enriched sublibraries. The recovered clones were successfully converted to active immunoglobulins, thus demonstrating the effectiveness of the whole procedure. This novel approach can guarantee rapid and cheap isolation of antibodies for virtually any native antigen involved in human diseases, for therapeutic and/or diagnostic applications. PMID:26649313

  15. 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…

  16. Inversion of electromagnetic data: An overview of new techniques

    NASA Astrophysics Data System (ADS)

    Oldenburg, Doug

    1990-09-01

    This paper explores some of the newer techniques for acquiring and inverting electromagnetic data. Attention is confined primarily to the 2d magnetotelluric (MT) problem but the inverse methods are applicable to all areas of EM induction. The basis of the EMAP technique of Bostick is presented along with examples to illustrate the efficacy of that method in structural imaging and in overcoming the deleterious effects of near-surface distortions of the electric field. Reflectivity imaging methods and the application of seismic migration techniques to EM problems are also explored as imaging tools. Two new approaches to the solution of the inverse problem are presented. The AIM (Approximate Inverse Mapping) inversion of Oldenburg and Ellis uses a new way to estimate a perturbation in an iterative solution which does not involve linearization of the equations. The RRI (Rapid Relaxation Inverse) of Smith and Booker shows how approximate Fréchet derivatives and sequences of 1d inversions can be used to develop a practical inversion algorithm. The overview is structured to provide insight about the latest inversion techniques and also to touch upon most areas of the inverse problem that must be considered to carry out a practical inversion. These include model parameterization, methods of calculating first order sensitivities, and methods for setting up a linearized inversion.

  17. Generalized emissivity inverse problem.

    PubMed

    Ming, DengMing; Wen, Tao; Dai, XianXi; Dai, JiXin; Evenson, William E

    2002-04-01

    Inverse problems have recently drawn considerable attention from the physics community due to of potential widespread applications [K. Chadan and P. C. Sabatier, Inverse Problems in Quantum Scattering Theory, 2nd ed. (Springer Verlag, Berlin, 1989)]. An inverse emissivity problem that determines the emissivity g(nu) from measurements of only the total radiated power J(T) has recently been studied [Tao Wen, DengMing Ming, Xianxi Dai, Jixin Dai, and William E. Evenson, Phys. Rev. E 63, 045601(R) (2001)]. In this paper, a new type of generalized emissivity and transmissivity inverse (GETI) problem is proposed. The present problem differs from our previous work on inverse problems by allowing the unknown (emissivity) function g(nu) to be temperature dependent as well as frequency dependent. Based on published experimental information, we have developed an exact solution formula for this GETI problem. A universal function set suggested for numerical calculation is shown to be robust, making this inversion method practical and convenient for realistic calculations. PMID:12005916

  18. 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.

  19. Direct and indirect inversions

    NASA Astrophysics Data System (ADS)

    Virieux, Jean; Brossier, Romain; Métivier, Ludovic; Operto, Stéphane; Ribodetti, Alessandra

    2016-06-01

    A bridge is highlighted between the direct inversion and the indirect inversion. They are based on fundamental different approaches: one is looking after a projection from the data space to the model space while the other one is reducing a misfit between observed data and synthetic data obtained from a given model. However, it is possible to obtain similar structures for model perturbation, and we shall focus on P-wave velocity reconstruction. This bridge is built up through the Born approximation linearizing the forward problem with respect to model perturbation and through asymptotic approximations of the Green functions of the wave propagation equation. We first describe the direct inversion and its ingredients and then we focus on a specific misfit function design leading to a indirect inversion. Finally, we shall compare this indirect inversion with more standard least-squares inversion as the FWI, enabling the focus on small weak velocity perturbations on one side and the speed-up of the velocity perturbation reconstruction on the other side. This bridge has been proposed by the group led by Raul Madariaga in the early nineties, emphasizing his leading role in efficient imaging workflows for seismic velocity reconstruction, a drastic requirement at that time.

  20. Electromagnetic inverse scattering

    NASA Technical Reports Server (NTRS)

    Bojarski, N. N.

    1972-01-01

    A three-dimensional electromagnetic inverse scattering identity, based on the physical optics approximation, is developed for the monostatic scattered far field cross section of perfect conductors. Uniqueness of this inverse identity is proven. This identity requires complete scattering information for all frequencies and aspect angles. A nonsingular integral equation is developed for the arbitrary case of incomplete frequence and/or aspect angle scattering information. A general closed-form solution to this integral equation is developed, which yields the shape of the scatterer from such incomplete information. A specific practical radar solution is presented. The resolution of this solution is developed, yielding short-pulse target resolution radar system parameter equations. The special cases of two- and one-dimensional inverse scattering and the special case of a priori knowledge of scatterer symmetry are treated in some detail. The merits of this solution over the conventional radar imaging technique are discussed.

  1. Inverse temperature in Superstatistics

    NASA Astrophysics Data System (ADS)

    Loguercio, Humberto; Davis, Sergio

    2016-05-01

    In this work, it is shown that there are (at least) three alternative definitions of the inverse temperature for a non-canonical ensemble. These definitions coincide in expectation but, in general, not in their higher moments. We explore in detail the application to the recent formalism of Superstatistics (C. Beck, 2003), and, in particular, to the configurational probability distribution in the microcanonical ensemble.

  2. AVO inversion based on inverse operator estimation in trust region

    NASA Astrophysics Data System (ADS)

    Yin, Xing-Yao; Deng, Wei; Zong, Zhao-Yun

    2016-04-01

    Amplitude variation with offset (AVO) inversion is widely utilized in exploration geophysics, especially for reservoir prediction and fluid identification. Inverse operator estimation in the trust region algorithm is applied for solving AVO inversion problems in which optimization and inversion directly are integrated. The L1 norm constraint is considered on the basis of reasonable initial model in order to improve effciency and stability during the AVO inversion process. In this study, high-order Zoeppritz approximation is utilized to establish the inversion objective function in which variation of {{v}\\text{p}}/{{v}\\text{s}} with time is taken into consideration. A model test indicates that the algorithm has a relatively higher stability and accuracy than the damp least-squares algorithm. Seismic data inversion is feasible and inversion values of three parameters ({{v}\\text{p}},{{v}\\text{s}},ρ ) maintain good consistency with logging curves.

  3. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  4. Silk inverse opals

    NASA Astrophysics Data System (ADS)

    Kim, Sunghwan; Mitropoulos, Alexander N.; Spitzberg, Joshua D.; Tao, Hu; Kaplan, David L.; Omenetto, Fiorenzo G.

    2012-12-01

    Periodic nanostructures provide the facility to control and manipulate the flow of light through their lattices. Three-dimensional photonic crystals enable the controlled design of structural colour, which can be varied by infiltrating the structure with different (typically liquid) fillers. Here, we report three-dimensional photonic crystals composed entirely of a purified natural protein (silk fibroin). The biocompatibility of this protein, as well as its favourable material properties and ease of biological functionalization, present opportunities for otherwise unattainable device applications such as bioresorbable integration of structural colour within living tissue or lattice functionalization by means of organic and inorganic material doping. We present a silk inverse opal that demonstrates a pseudo-photonic bandgap in the visible spectrum and show its associated structural colour beneath biological tissue. We also leverage silk's facile dopability to manufacture a gold nanoparticle silk inverse opal and demonstrate patterned heating mediated by enhancement of nanoparticle absorption at the band-edge frequency of the photonic crystal.

  5. 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.

  6. Multislice perfusion imaging in human brain using the C-FOCI inversion pulse: comparison with hyperbolic secant.

    PubMed

    Yongbi, M N; Yang, Y; Frank, J A; Duyn, J H

    1999-12-01

    Perfusion studies based on pulsed arterial spin labeling have primarily applied hyperbolic secant (HS) pulses for spin inversion. To optimize perfusion sensitivity, it is highly desirable to implement the HS pulse with the same slice width as the width of the imaging pulse. Unfortunately, this approach causes interactions between the slice profiles and manifests as residual signal from static tissue in the resultant perfusion image. This problem is currently overcome by increasing the selective HS width relative to the imaging slice width. However, this solution increases the time for the labeled blood to reach the imaging slice (transit time), causing loss of perfusion sensitivity as a result of T(1) relaxation effects. In this study, we demonstrate that the preceding problems can be largely overcome by use of the C-shaped frequency offset corrected inversion (FOCI) pulse [Ordidge et al., Magn Reson Med 1996;36:562]. The implementation of this pulse for multislice perfusion imaging on the cerebrum is presented, showing substantial improvement in slice definition in vivo compared with the HS pulse. The sharper FOCI profile is shown to reduce the physical gap (or "safety margin") between the inversion and imaging slabs, resulting in a significant increase in perfusion signal without residual contamination from static tissue. The mean +/- SE (n = 6) gray matter perfusion-weighted signal (DeltaM/M(o)) without the application of vascular signal suppression gradients were 1.19 +/- 0. 10% (HS-flow-sensitive alternating inversion recovery [FAIR]), and 1. 51 +/- 0.11% for the FOCI-FAIR sequence. The corresponding values with vascular signal suppression were 0.64 +/- 0.14%, and 0.91 +/- 0. 08% using the HS- and FOCI-FAIR sequences, respectively. Compared with the HS-based data, the FOCI-FAIR results correspond to an average increase in perfusion signal of up to between 26%-30%. Magn Reson Med 42:1098-1105, 1999. PMID:10571931

  7. Inverse avalanches on Abelian sandpiles

    SciTech Connect

    Chau, H.F. Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801-3080 )

    1994-11-01

    A simple and computationally efficient way of finding inverse avalanches for Abelian sandpiles, called the inverse particle addition operator, is presented. In addition, the method is shown to be optimal in the sense that it requires the minimum amount of computation among methods of the same kind. The method is also conceptually succinct because avalanche and inverse avalanche are placed in the same footing.

  8. Measuring spin relaxation with standard pulse sequences in the singlet-triplet basis

    NASA Astrophysics Data System (ADS)

    Keevers, T. L.; McCamey, D. R.

    2015-08-01

    Pulsed electrically and optically-detected magnetic resonance are extremely sensitive to changes in the permutation symmetry of weakly-coupled spin pairs, and are well-suited for investigating devices with a small number of spins. However, the change in observable from conventional electron spin resonance modifies the results of standard inductively-detected pulse sequences which are routinely used to obtain phase coherence and lifetimes. Whilst these effects have been discussed for single-pulse experiments, their role in multi-pulse sequences is less clear. Here, we investigate this effect in Hahn echo and inversion-recovery sequences, and show a second set of narrower echoes are produced that distort measurement outcomes. We demonstrate that phase cycling is able to deconvolve the additional echo signals, allowing spin relaxation times to be reliably extracted.

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

    PubMed

    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. PMID:25828242

  10. 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.

  11. Comparison of Pulse Sequences for R1–based Electron Paramagnetic Resonance Oxygen Imaging

    PubMed Central

    Epel, Boris; Halpern, Howard J.

    2015-01-01

    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. PMID:25828242

  12. Multiscale full waveform inversion

    NASA Astrophysics Data System (ADS)

    Fichtner, Andreas; Trampert, Jeannot; Cupillard, Paul; Saygin, Erdinc; Taymaz, Tuncay; Capdeville, Yann; Villaseñor, Antonio

    2013-07-01

    We develop and apply a full waveform inversion method that incorporates seismic data on a wide range of spatio-temporal scales, thereby constraining the details of both crustal and upper-mantle structure. This is intended to further our understanding of crust-mantle interactions that shape the nature of plate tectonics, and to be a step towards improved tomographic models of strongly scale-dependent earth properties, such as attenuation and anisotropy. The inversion for detailed regional earth structure consistently embedded within a large-scale model requires locally refined numerical meshes that allow us to (1) model regional wave propagation at high frequencies, and (2) capture the inferred fine-scale heterogeneities. The smallest local grid spacing sets the upper bound of the largest possible time step used to iteratively advance the seismic wave field. This limitation leads to extreme computational costs in the presence of fine-scale structure, and it inhibits the construction of full waveform tomographic models that describe earth structure on multiple scales. To reduce computational requirements to a feasible level, we design a multigrid approach based on the decomposition of a multiscale earth model with widely varying grid spacings into a family of single-scale models where the grid spacing is approximately uniform. Each of the single-scale models contains a tractable number of grid points, which ensures computational efficiency. The multi-to-single-scale decomposition is the foundation of iterative, gradient-based optimization schemes that simultaneously and consistently invert data on all scales for one multi-scale model. We demonstrate the applicability of our method in a full waveform inversion for Eurasia, with a special focus on Anatolia where coverage is particularly dense. Continental-scale structure is constrained by complete seismic waveforms in the 30-200 s period range. In addition to the well-known structural elements of the Eurasian mantle

  13. Neighborhood inverse consistency preprocessing

    SciTech Connect

    Freuder, E.C.; Elfe, C.D.

    1996-12-31

    Constraint satisfaction consistency preprocessing methods are used to reduce search effort. Time and especially space costs limit the amount of preprocessing that will be cost effective. A new form of consistency preprocessing, neighborhood inverse consistency, can achieve more problem pruning than the usual arc consistency preprocessing in a cost effective manner. There are two basic ideas: (1) Common forms of consistency enforcement basically operate by identifying and remembering solutions to subproblems for which a consistent value cannot be found for some additional problem variable. The space required for this memory can quickly become prohibitive. Inverse consistency basically operates by removing values for variables that are not consistent with any solution to some subproblem involving additional variables. The space requirement is at worst linear. (2) Typically consistency preprocessing achieves some level of consistency uniformly throughout the problem. A subproblem solution will be tested against each additional variable that constrains any subproblem variable. Neighborhood consistency focuses attention on the subproblem formed by the variables that are all constrained by the value in question. By targeting highly relevant subproblems we hope to {open_quotes}skim the cream{close_quotes}, obtaining a high payoff for a limited cost.

  14. 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

  15. Molecular Characterization of Hobo-Mediated Inversions in Drosophila Melanogaster

    PubMed Central

    Eggleston, W. B.; Rim, N. R.; Lim, J. K.

    1996-01-01

    The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation. PMID:8889527

  16. 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.

  17. Inverse magnetorheological fluids.

    PubMed

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

    2014-09-01

    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. PMID:25022363

  18. 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.

  19. Inverse problem for Bremsstrahlung radiation

    SciTech Connect

    Voss, K.E.; Fisch, N.J.

    1991-10-01

    For certain predominantly one-dimensional distribution functions, an analytic inversion has been found which yields the velocity distribution of superthermal electrons given their Bremsstrahlung radiation. 5 refs.

  20. 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

  1. 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

  2. On nonsingular potentials of Cox-Thompson inversion scheme

    NASA Astrophysics Data System (ADS)

    Pálmai, Tamás; Apagyi, Barnabás

    2010-02-01

    We establish a condition for obtaining nonsingular potentials using the Cox-Thompson inverse scattering method with one phase shift. The anomalous singularities of the potentials are avoided by maintaining unique solutions of the underlying Regge-Newton integral equation for the transformation kernel. As a by-product, new inequality sequences of zeros of Bessel functions are discovered.

  3. On nonsingular potentials of Cox-Thompson inversion scheme

    SciTech Connect

    Palmai, Tamas; Apagyi, Barnabas

    2010-02-15

    We establish a condition for obtaining nonsingular potentials using the Cox-Thompson inverse scattering method with one phase shift. The anomalous singularities of the potentials are avoided by maintaining unique solutions of the underlying Regge-Newton integral equation for the transformation kernel. As a by-product, new inequality sequences of zeros of Bessel functions are discovered.

  4. Inverse Problems of Thermoelectricity

    NASA Astrophysics Data System (ADS)

    Anatychuk, L. I.; Luste, O. J.; Kuz, R. V.; Strutinsky, M. N.

    2011-05-01

    Classical thermoelectricity is based on the use of the Seebeck and Thomson effects that occur in the near-contact areas between n- and p-type materials. A conceptually different approach to thermoelectric power converter design that is based on the law of thermoelectric induction of currents is also known. The efficiency of this approach has already been demonstrated by its first applications. More than 10 basically new types of thermoelements were discovered with properties that cannot be achieved by thermocouple power converters. Therefore, further development of this concept is of practical interest. This paper provides a classification and theory for solving the inverse problems of thermoelectricity that form the basis for devising new thermoelement types. Computer methods for their solution for anisotropic and inhomogeneous media are elaborated. Regularities related to thermoelectric current excitation in anisotropic and inhomogeneous media are established. The possibility of obtaining eddy currents of a particular configuration through control of the temperature field and material parameters for the creation of new thermo- element types is demonstrated for three-dimensional (3D) models of anisotropic and inhomogeneous media.

  5. 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

  6. 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. PMID:24266232

  7. Earthquake source inversion with dense networks

    NASA Astrophysics Data System (ADS)

    Somala, S.; Ampuero, J. P.; Lapusta, N.

    2012-12-01

    (since the bulk properties are not known at higher frequencies), add noise of the desired level, and then apply our inversion approach. The results indicate that dense networks (e.g., 1-km spacing) produce sharper images of the considered sources than sparse networks (e.g., 10-20 km spacing), with better amplitude recovery and better resolution with depth. This is true even when noiseless sparse networks are compared with noisy dense networks, provided that the standard deviations of noise do not exceed ~1% of the maximum earthquake source amplitude (e.g., 1 cm/s noise for 1 m/s Haskell source). Substantial qualitative improvements arise when features of relatively narrow spatial extent are included in the source, in which case the dense networks can reproduce the features whereas the sparse networks cannot. We will report on our current efforts to mathematically quantify the differences between the inversions of sparse and dense data and to incorporate the effect of errors in the bulk velocity model.

  8. Reading Recovery. [Fact Sheets].

    ERIC Educational Resources Information Center

    Reading Recovery Council of North America, Columbus, OH.

    This set of 10 fact sheets (each 2 to 4 pages long) addresses aspects of Reading Recovery, a program that helps children to be proficient readers and writers by the end of the first grade. It discusses the basic facts of Reading Recovery; Reading Recovery for Spanish literacy; Reading Recovery lessons; Reading Recovery professional development;…

  9. 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…

  10. 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...

  11. 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. PMID:26327445

  12. Earthquake source inversion of tsunami runup prediction

    NASA Astrophysics Data System (ADS)

    Sekar, Anusha

    Our goal is to study two inverse problems: using seismic data to invert for earthquake parameters and using tide gauge data to invert for earthquake parameters. We focus on the feasibility of using a combination of these inverse problems to improve tsunami runup prediction. A considerable part of the thesis is devoted to studying the seismic forward operator and its modeling using immersed interface methods. We develop an immersed interface method for solving the variable coefficient advection equation in one dimension with a propagating singularity and prove a convergence result for this method. We also prove a convergence result for the one-dimensional acoustic system of partial differential equations solved using immersed interface methods with internal boundary conditions. Such systems form the building blocks of the numerical model for the earthquake. For a simple earthquake-tsunami model, we observe a variety of possibilities in the recovery of the earthquake parameters and tsunami runup prediction. In some cases the data are insufficient either to invert for the earthquake parameters or to predict the runup. When more data are added, we are able to resolve the earthquake parameters with enough accuracy to predict the runup. We expect that this variety will be true in a real world three dimensional geometry as well.

  13. Microwave inverse Cerenkov accelerator

    SciTech Connect

    Zhang, T.B.; Marshall, T.C.; LaPointe, M.A.; Hirshfield, J.L.

    1997-03-01

    A Microwave Inverse Cerenkov Accelerator (MICA) is currently under construction at the Yale Beam Physics Laboratory. The accelerating structure in MICA consists of an axisymmetric dielectrically lined waveguide. For the injection of 6 MeV microbunches from a 2.856 GHz RF gun, and subsequent acceleration by the TM{sub 01} fields, particle simulation studies predict that an acceleration gradient of 6.3 MV/m can be achieved with a traveling-wave power of 15 MW applied to the structure. Synchronous injection into a narrow phase window is shown to allow trapping of all injected particles. The RF fields of the accelerating structure are shown to provide radial focusing, so that longitudinal and transverse emittance growth during acceleration is small, and that no external magnetic fields are required for focusing. For 0.16 nC, 5 psec microbunches, the normalized emittance of the accelerated beam is predicted to be less than 5{pi}mm-mrad. Experiments on sample alumina tubes have been conducted that verify the theoretical dispersion relation for the TM{sub 01} mode over a two-to-one range in frequency. No excitation of axisymmetric or non-axisymmetric competing waveguide modes was observed. High power tests showed that tangential electric fields at the inner surface of an uncoated sample of alumina pipe could be sustained up to at least 8.4 MV/m without breakdown. These considerations suggest that a MICA test accelerator can be built to examine these predictions using an available RF power source, 6 MeV RF gun and associated beam line. {copyright} {ital 1997 American Institute of Physics.}

  14. Heart Attack Recovery FAQs

    MedlinePlus

    ... Pressure High Blood Pressure Tools & Resources Stroke More Heart Attack Recovery FAQs Updated:Aug 24,2016 Most people ... recovery. View an animation of a heart attack . Heart Attack Recovery Questions and Answers What treatments will I ...

  15. 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

  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

    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 generalized inversion method: Simultaneous source localization and environmental inversion

    NASA Astrophysics Data System (ADS)

    Neilsen, Tracianne B.; Knobles, David P.

    2002-05-01

    The problem of localizing and tracking a source in the shallow ocean is often complicated by uncertainty in the environmental parameters. Likewise, the estimates of environmental parameters in the shallow ocean obtained by inversion methods can be degraded by incorrect information about the source location. To overcome both these common obstacles-environmental mismatch in matched field processing and incorrect source location in geoacoustic inversions-a generalized inversion scheme is developed that includes both source and environmental parameters as unknowns in the inversion. The new technique called systematic decoupling using rotated coordinates (SDRC) expands the original idea of rotated coordinates [M. D. Collins and L. Fishman, J. Acoust. Soc. Am. 98, 1637-1644 (1995)] by using multiple sets of coherent broadband rotated coordinates, each corresponding to a different set of bounds, to systematically decouple the unknowns in a series of simulated annealing inversions. The results of applying the SDRC inversion method to data from the Area Characterization Test II experiment performed on the New Jersey continental shelf are presented. [Work supported by ONR.

  19. 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. PMID:25712227

  20. 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.

  1. 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.

  2. 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)

  3. 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.

  4. 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.

  5. Uterine Inversion; A case report.

    PubMed

    Bouchikhi, C; Saadi, H; Fakhir, B; Chaara, H; Bouguern, H; Banani, A; Melhouf, Ma

    2008-01-01

    The puerperal uterine inversion is a rare and severe complication occurring in the third stage of labour. The mechanisms are not completely known. However, extrinsic factors such as oxytocic arrests after a prolonged labour, umbilical cord traction or abdominal expression are pointed. Other intrinsic factors such as primiparity, uterine hypotonia, various placental localizations, fundic myoma or short umbilical cord were also reported. The diagnosis of the uterine inversion is mainly supported by clinical symptoms. It is based on three elements: haemorrhage, shock and a strong pelvic pain. The immediate treatment of the uterine inversion is required. It is based on a medical reanimation associated with firstly a manual reduction then surgical treatment using various techniques. We report an observation of a 25 years old grand multiparous patient with a subacute uterine inversion after delivery at home. PMID:21516244

  6. Uterine Inversion; A case report

    PubMed Central

    Bouchikhi, C; Saadi, H; Fakhir, B; Chaara, H; Bouguern, H; Banani, A; Melhouf, MA

    2008-01-01

    The puerperal uterine inversion is a rare and severe complication occurring in the third stage of labour. The mechanisms are not completely known. However, extrinsic factors such as oxytocic arrests after a prolonged labour, umbilical cord traction or abdominal expression are pointed. Other intrinsic factors such as primiparity, uterine hypotonia, various placental localizations, fundic myoma or short umbilical cord were also reported. The diagnosis of the uterine inversion is mainly supported by clinical symptoms. It is based on three elements: haemorrhage, shock and a strong pelvic pain. The immediate treatment of the uterine inversion is required. It is based on a medical reanimation associated with firstly a manual reduction then surgical treatment using various techniques. We report an observation of a 25 years old grand multiparous patient with a subacute uterine inversion after delivery at home. PMID:21516244

  7. 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

  8. Computation of inverse magnetic cascades

    SciTech Connect

    Montgomery, D.

    1981-10-01

    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.

  9. 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.

  10. 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.

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

    PubMed

    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

  12. 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

  13. Magnetic resonance imaging of myelin using ultrashort Echo time (UTE) pulse sequences: Phantom, specimen, volunteer and multiple sclerosis patient studies.

    PubMed

    Sheth, Vipul; Shao, Hongda; Chen, Jun; Vandenberg, Scott; Corey-Bloom, Jody; Bydder, Graeme M; Du, Jiang

    2016-08-01

    Clinical magnetic resonance imaging of multiple sclerosis (MS) has focused on indirect imaging of myelin in white matter by detecting signal from protons in the water associated with myelin. Here we show that protons in myelin can be directly imaged using ultrashort echo time (UTE) free induction decay (FID) and imaging sequences on a clinical 3T MR scanner. An adiabatic inversion recovery UTE (IR-UTE) sequence was used to detect signal from myelin and simultaneously suppress signal from water protons. Validation studies were performed on myelin lipid and myelin basic protein (MBP) phantoms in the forms of lyophilized powders as well as suspensions in D2O and H2O. IR-UTE sequences were then used to image MS brain specimens, healthy volunteers, and patients. The T2* of myelin was measured using a UTE FID sequence, as well as UTE and IR-UTE sequences at different TEs. T2* values of ~110-330μs were measured with UTE FID, as well as with UTE and IR-UTE sequences for myelin powders, myelin-D2O and myelin-H2O phantoms, consistent with selective imaging of myelin protons with IR-UTE sequences. Our studies showed myelin selective imaging of white matter in the brains in vitro and in vivo. Complete or partial signal loss was observed in specimens in areas of the brain with histopathologic evidence of myelin loss, and in the brain of patients with MS. PMID:27155128

  14. 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.

  15. Global inversion for anisotropy during full-waveform inversion

    NASA Astrophysics Data System (ADS)

    Debens, H. A.; Warner, M.; Umpleby, A.

    2015-12-01

    Full-waveform inversion (FWI) is a powerful tool for quantitative estimation of high-resolution high-fidelity models of subsurface seismic parameters, typically P-wave velocity. The solution to FWI's posed nonlinear inverse problem is obtained via an iterative series of linearized local updates to a start model, assuming this model lies within the basin of attraction to the global minimum. Thanks to many successful published applications to three-dimensional (3D) field datasets, its advance has been rapid and driven in large-part by the oil and gas industry. The consideration of seismic anisotropy during FWI is of vital importance, as it holds influence over both the kinematics and dynamics of seismic waveforms. If not appropriately taken into account then inadequacies in the anisotropy model are likely to manifest as significant error in the recovered velocity model. Conventionally, anisotropic FWI employs either an a priori anisotropy model, held fixed during FWI, or it uses a multi-parameter local inversion scheme to recover the anisotropy as part of the FWI; both of these methods can be problematic. Constructing an anisotropy model prior to FWI often involves intensive (and hence expensive) iterative procedures, such as travel-time tomography or moveout velocity analysis. On the other hand, introducing multiple parameters to FWI itself increases the complexity of what is already an underdetermined inverse problem. We propose that global rather than local FWI can be used to recover the long-wavelength acoustic anisotropy model, and that this can then be followed by more-conventional local FWI to recover the detailed model. We validate this approach using a full 3D field dataset, demonstrating that it avoids problems associated to crosstalk that can bedevil local inversion schemes, and reconciles well with in situ borehole measurements. Although our approach includes a global inversion for anisotropy, it is nonetheless affordable and practical for 3D field data.

  16. Inversion by P4: polarization-picture post-processing.

    PubMed

    Schechner, Yoav Y

    2011-03-12

    Polarization may be sensed by imaging modules. This is done in various engineering systems as well as in biological systems, specifically by insects and some marine species. However, polarization per pixel is usually not the direct variable of interest. Rather, polarization-related data serve as a cue for recovering task-specific scene information. How should polarization-picture post-processing (P(4)) be done for the best scene understanding? Answering this question is not only helpful for advanced engineering (computer vision), but also to prompt hypotheses as to the processing occurring within biological systems. In various important cases, the answer is found by a principled expression of scene recovery as an inverse problem. Such an expression relies directly on a physics-based model of effects in the scene. The model includes analysis that depends on the different polarization components, thus facilitating the use of these components during the inversion, in a proper, even if non-trivial, manner. We describe several examples for this approach. These include automatic removal of path radiance in haze or underwater, overcoming partial semireflections and visual reverberations; three-dimensional recovery and distance-adaptive denoising. The resulting inversion algorithms rely on signal-processing methods, such as independent component analysis, deconvolution and optimization. PMID:21282167

  17. Geophysical Inversion Through Hierarchical Scheme

    NASA Astrophysics Data System (ADS)

    Furman, A.; Huisman, J. A.

    2010-12-01

    Geophysical investigation is a powerful tool that allows non-invasive and non-destructive mapping of subsurface states and properties. However, non-uniqueness associated with the inversion process prevents the quantitative use of these methods. One major direction researchers are going is constraining the inverse problem by hydrological observations and models. An alternative to the commonly used direct inversion methods are global optimization schemes (such as genetic algorithms and Monte Carlo Markov Chain methods). However, the major limitation here is the desired high resolution of the tomographic image, which leads to a large number of parameters and an unreasonably high computational effort when using global optimization schemes. Two innovative schemes are presented here. First, a hierarchical approach is used to reduce the computational effort for the global optimization. Solution is achieved for coarse spatial resolution, and this solution is used as the starting point for finer scheme. We show that the computational effort is reduced in this way dramatically. Second, we use a direct ERT inversion as the starting point for global optimization. In this case preliminary results show that the outcome is not necessarily beneficial, probably because of spatial mismatch between the results of the direct inversion and the true resistivity field.

  18. 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.

  19. 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

  20. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  1. Influence of food colorant and initial COD concentration on the efficiencies of micro-aerobic sequencing batch reactor (micro-aerobic SBR) for casein recovery under non-sterile condition by Lactobacillus casei TISTR 1500.

    PubMed

    Seesuriyachan, Phisit; Chaiyaso, Thanongsak; Sasaki, Ken; Techapun, Charin

    2009-09-01

    The acid biocoagulants produced from non-sterile lactic acid fermentation by Lactobacillus casei TISTR 1500 were used to settle colloidal protein, mainly casein, at the isoelectric point in dairy effluent prior to secondary treatment. High concentration of azo dye (Ponceau 4R) in the dairy wastewater and the stress of starvation decreased the efficiencies of the micro-aerobic SBR. Consequently, low casein recovery obtained and organic removal suffered a decline. The number of lactic acid bacteria (LAB) also declined from log 7.4 to log 5.30 in the system fed with 400 mg L(-1) of the dye containing wastewater. The recovery of the system, however, showed that 25,000 mg COD L(-1) influent with 200 mg L(-1) of the dye maintained the growth of LAB in the range of log 7.74-8.12, with lactic and acetic production (2597 and 197 mg L(-1)) and 83% protein removal. The results in this study suggested that the inhibitory effects were compensated with high organic content feeding. PMID:19423333

  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. 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.

  4. Darwin's "strange inversion of reasoning".

    PubMed

    Dennett, Daniel

    2009-06-16

    Darwin's theory of evolution by natural selection unifies the world of physics with the world of meaning and purpose by proposing a deeply counterintuitive "inversion of reasoning" (according to a 19th century critic): "to make a perfect and beautiful machine, it is not requisite to know how to make it" [MacKenzie RB (1868) (Nisbet & Co., London)]. Turing proposed a similar inversion: to be a perfect and beautiful computing machine, it is not requisite to know what arithmetic is. Together, these ideas help to explain how we human intelligences came to be able to discern the reasons for all of the adaptations of life, including our own. PMID:19528651

  5. 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.

  6. 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.

  7. IS50-mediated inverse transposition: specificity and precision.

    PubMed

    Nag, D K; DasGupta, U; Adelt, G; Berg, D E

    1985-01-01

    The IS50 elements, which are present as inverted repeats in the kanamycin-resistance transposon, Tn5, can move in unison carrying with them any interstitial DNA segment. In consequence, DNA molecules such as a lambda::Tn5 phage genome are composed of two overlapping transposons - the kan segment bracketed by IS50 elements (Tn5), and lambda bracketed by IS50 elements. During direct transposition, mediated by IS50 "O" (outside) ends, the kan gene is moved and the lambda vector is left behind. During inverse transposition, mediated by the "I" (inside) ends of the IS50 elements, the lambda vector segment is moved and the kan gene is left behind. Direct transposition is several orders of magnitude more frequent than inverse transposition (Isberg and Syvanen, 1981; Sasakawa and Berg, 1982). We assessed the specificity and precision of the rare events mediated by pairs of I ends by mapping and sequencing independent inverse transpositions from a lambda::Tn5 phage into the amp and tet genes of plasmid pBR322. Using restriction analyses, 32 and 40 distinct sites of insertion were found among 46 and 72 independent inverse transpositions into the amp and tet genes, respectively. Eleven sites were used in two or more insertion events, and the two sites in tet used most frequently corresponded to major hotspots for the insertion of the Tn5 (by direct transposition). The sequences of 22 sites of inverse transposition (including each of the sites used more than once) were determined, in eleven cases by analyzing both pBR322-IS50 junctions, and in eleven others by sequencing one junction. The sequence of the "I" end of IS50 was preserved and 9-bp target sequence duplications were present in every case analyzed. GC pairs were found at each end of the target sequence duplication in ten of the eleven sites used more than once, and also in seven of the other eleven sites. Our data indicate that transposition mediated by pairs of "I" ends is similar in its specificity and precision to

  8. 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.

  9. Double obstacle phase field approach to an inverse problem for a discontinuous diffusion coefficient

    NASA Astrophysics Data System (ADS)

    Deckelnick, Klaus; Elliott, Charles M.; Styles, Vanessa

    2016-04-01

    We propose a double obstacle phase field approach to the recovery of piece-wise constant diffusion coefficients for elliptic partial differential equations. The approach to this inverse problem is that of optimal control in which we have a quadratic fidelity term to which we add a perimeter regularization weighted by a parameter σ. This yields a functional which is optimized over a set of diffusion coefficients subject to a state equation which is the underlying elliptic PDE. In order to derive a problem which is amenable to computation the perimeter functional is relaxed using a gradient energy functional together with an obstacle potential in which there is an interface parameter ɛ. This phase field approach is justified by proving {{Γ }}- convergence to the functional with perimeter regularization as ε \\to 0. The computational approach is based on a finite element approximation. This discretization is shown to converge in an appropriate way to the solution of the phase field problem. We derive an iterative method which is shown to yield an energy decreasing sequence converging to a discrete critical point. The efficacy of the approach is illustrated with numerical experiments.

  10. Inverse free electron laser accelerator

    SciTech Connect

    Fisher, A.; Gallardo, J.; Sandweiss, J.; van Steenbergen, A. )

    1992-07-01

    The study of the INVERSE FREE ELECTRON LASER, as a potential mode of electron acceleration, is being pursued at Brookhaven National Laboratory. Recent studies have focussed on the development of a low energy, high gradient, multi stage linear accelerator. The elementary ingredients for the IFEL interaction are the 50 MeV Linac e[sup [minus

  11. Inverse Free Electron Laser accelerator

    SciTech Connect

    Fisher, A.; Gallardo, J.; van Steenbergen, A. ); Sandweiss, J. )

    1992-09-01

    The study of the INVERSE FREE ELECTRON LASER, as a potential mode of electron acceleration, is being pursued at Brookhaven National Laboratory. Recent studies have focussed on the development of a low energy, high gradient, multi stage linear accelerator. The elementary ingredients for the IFEL interaction are the 50 MeV Linac e[sup [minus

  12. 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…

  13. 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.

  14. Disaster Recovery Planning.

    ERIC Educational Resources Information Center

    Wilkins, Jeannine W.

    1985-01-01

    Every school needs an effective disaster recovery plan that is flexible, comprehensive and designed to take into account unexpected disasters. Presents guidelines for preparing such a plan, with immediate and long-range recovery procedures. (MD)

  15. Recovery Act Milestones

    ScienceCinema

    Rogers, Matt

    2013-05-29

    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.

  16. 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%.

  17. 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.

  18. 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…

  19. 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…

  20. Seismic full waveform inversion from compressive measurements

    NASA Astrophysics Data System (ADS)

    Ramirez, Ana; Arce, Gonzalo R.

    2015-05-01

    Traditional methods in seismic acquisition require sources and geophones that are uniformly located along a spatial line, using the Nyquist sampling rate. Depending on the area to be explored, it can be necessary to use seismic surveys with large offsets, or decrease the separation between adjacent geophones to improve the resolution, which generates very high volumes of data. It makes the exploration process more difficult and particularly expensive. This work presents the reconstruction of a compressive set of seismic traces acquired using the compressive sensing paradigm where the pair of sources and geophones are randomly located along the spatial line. The recovery of the wavefield from compressive measurements is feasible due to the capabilities of Curvelets on representing wave propagators with only a small set of coefficients. The method first uses the compressive samples to find a sparse vector representation of each pixel in a 2-D Curvelet dictionary. The sparse vector representation is estimated by solving a sparsity constrained optimization problem using the Gradient Projection for Sparse Reconstruction (GPSR) method. The estimated vector is then used to compute the seismic velocity profiles via acoustic Full Waveform Inversion (FWI). Simulations of the reconstructed image gathers and the resulting seismic velocity profiles illustrate the performance of the method. An improvement in the resulting images is obtained in comparison with traditional F-K filtering used in seismic data processing when traces are missing.

  1. 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.

  2. 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.

  3. 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. PMID:23862809

  4. Southern California Adjoint Source Inversions

    NASA Astrophysics Data System (ADS)

    Tromp, J.; Kim, Y.

    2007-12-01

    Southern California Centroid-Moment Tensor (CMT) solutions with 9 components (6 moment tensor elements, latitude, longitude, and depth) are sought to minimize a misfit function computed from waveform differences. The gradient of a misfit function is obtained based upon two numerical simulations for each earthquake: one forward calculation for the southern California model, and an adjoint calculation that uses time-reversed signals at the receivers. Conjugate gradient and square-root variable metric methods are used to iteratively improve the earthquake source model while reducing the misfit function. The square-root variable metric algorithm has the advantage of providing a direct approximation to the posterior covariance operator. We test the inversion procedure by perturbing each component of the CMT solution, and see how the algorithm converges. Finally, we demonstrate full inversion capabilities using data for real Southern California earthquakes.

  5. 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.

  6. 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.

  7. Techniques in Doppler gravity inversion

    NASA Technical Reports Server (NTRS)

    Phillips, R. J.

    1974-01-01

    The types of Doppler gravity data available for local as opposed to planetwide geophysical modeling are reviewed. Those gravity fields that are determined dynamically in orbit determination programs yield a smoothed representation of the local gravity field that may be used for quantitative modeling. An estimate of the difference between smoothed and true fields can be considered as a noise limitation in generating local gravity models. A nonlinear inversion for the geometry, depth, and density of the Mare Serenitatis mascon using an ellipsoidal model yielded a global least squares minimum in horizontal dimensions, depth, and thickness-density contrast product. It was subsequently found, by using a linear model, that there were an infinite number of solutions corresponding to various combinations of depth and lateral inhomogeneity. Linear modeling was performed by means of generalized inverse theory.

  8. 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.

  9. Inverse psoriasis treated with ustekinumab.

    PubMed

    Campos, Manuel António; Varela, Paulo; Baptista, Armando; Moreira, Ana Isabel

    2016-01-01

    Inverse psoriasis is characterised by the involvement of flexural skin folds. This form of psoriasis has distinct clinical and therapeutic features. This report refers to the case of a 48-year-old Caucasian man who was observed in our department, with a clinically and biopsy proven diagnosis of inverse psoriasis. For 2 years, the patient was treated with different combinations of corticosteroids, vitamin D analogues and methotrexate, with no satisfactory response. Given the lack of a clinical response and comorbidities, latent tuberculosis was excluded, and we started treatment with ustekinumab. We chose this biological agent because the patient was a long-distance truck driver and refused the possibility of autoinjections. The patient underwent three ustekinumab injections, which resulted in significant improvement of pruritus, erythaematous lesions and quality of life. PMID:27222277

  10. Pyramidal inversion domain boundaries revisited

    SciTech Connect

    Remmele, T.; Albrecht, M.; Irmscher, K.; Fornari, R.; Strassburg, M.

    2011-10-03

    The structure of pyramidal inversion domain boundaries in GaN:Mg was investigated by aberration corrected transmission electron microscopy. The analysis shows the upper (0001) boundary to consist of a single Mg layer inserted between polarity inverted GaN layers in an abcab stacking. The Mg bound in these defects is at least one order of magnitude lower than the chemical Mg concentration. Temperature dependent Hall effect measurements show that up to 27% of the Mg acceptors is electrically compensated.

  11. Stochastic inversion by ray continuation

    SciTech Connect

    Haas, A.; Viallix

    1989-05-01

    The conventional tomographic inversion consists in minimizing residuals between measured and modelled traveltimes. The process tends to be unstable and some additional constraints are required to stabilize it. The stochastic formulation generalizes the technique and sets it on firmer theoretical bases. The Stochastic Inversion by Ray Continuation (SIRC) is a probabilistic approach, which takes a priori geological information into account and uses probability distributions to characterize data correlations and errors. It makes it possible to tie uncertainties to the results. The estimated parameters are interval velocities and B-spline coefficients used to represent smoothed interfaces. Ray tracing is done by a continuation technique between source and receives. The ray coordinates are computed from one path to the next by solving a linear system derived from Fermat's principle. The main advantages are fast computations, accurate traveltimes and derivatives. The seismic traces are gathered in CMPs. For a particular CMP, several reflecting elements are characterized by their time gradient measured on the stacked section, and related to a mean emergence direction. The program capabilities are tested on a synthetic example as well as on a field example. The strategy consists in inverting the parameters for one layer, then for the next one down. An inversion step is divided in two parts. First the parameters for the layer concerned are inverted, while the parameters for the upper layers remain fixed. Then all the parameters are reinverted. The velocity-depth section computed by the program together with the corresponding errors can be used directly for the interpretation, as an initial model for depth migration or for the complete inversion program under development.

  12. Heat shock protein hsp70 accelerates the recovery of heat-shocked mammalian cells through its modulation of heat shock transcription factor HSF1.

    PubMed Central

    Kim, D; Ouyang, H; Li, G C

    1995-01-01

    The role of mammalian 70-kDa heat shock protein (hsp70) in regulating cellular response to heat shock was examined by using three closely related rat cells: control Rat-1 cells, thermotolerant Rat-1 (TT Rat-1) cells, and heat-resistant M21 cells, a derivative of Rat-1 cells that constitutively overexpress human hsp70. In all these cells, after a prescribed heat shock, the level of the phosphorylated form of heat shock transcription factor HSF1 and that of HSF1 capable of binding to its cognitive DNA sequence heat shock element (HSE) exhibit similar time dependence. The amount of a constitutive HSE-binding activity (CHBA), on the other hand, inversely correlates with those of the two aforementioned forms of HSF1. The recovery kinetics from heat shock are different for the three cell lines, with the thermal-resistant TT Rat-1 and M21 cells showing faster recovery in terms of the state of phosphorylation of HSF1 and its ability to bind HSE or in terms of the reappearance of CHBA. Treatment with okadaic acid, a serine/threonine phosphatase inhibitor, delays the recovery kinetics of Rat-1 cells but not that of thermal-resistant M21 cells. These results are interpreted in terms of a role for hsp70 in the recovery of heat-shocked mammalian cells. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:7892235

  13. Synthesis and characterization of FE colloid catalysts in inverse micelle solutions

    SciTech Connect

    Martino, A.; Sault, A.G.; Kawola, J.S.; Stoker, M.; Hicks, M.; Bartholomew, C.H.

    1995-02-01

    Formation of Fe clusters in inverse micelles was studied. Iron salts are solubilized within the polar interior of inverse micelles, and addition of LiBH{sub 4} initiates reduction to produce monodisperse, nanometer-sized Fe based particles. The reaction sequence is sustained by material exchange between inverse micelles. Surfactant interface provides a spatial constraint on reaction volume, and reactions carried out in these micro-heterogeneous solutions produce colloidal sized particles (10--100 {Angstrom}) stabilized in solution against flocculation by surfactant. In this paper, the clusters were characterized using TEM, Moessbauer spectroscopy, electron diffraction, and x-ray photoelectron spectroscopy.

  14. 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…

  15. 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.

  16. 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.

  17. 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.

  18. 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. PMID:26767379

  19. 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.

  20. 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.

  1. 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.

  2. [Aspects of FLAIR sequences, 3D-CISS and diffusion-weight MR imaging of intracranial epidermoid cysts].

    PubMed

    Doll, A; Abu Eid, M; Kehrli, P; Esposito, P; Gillis, C; Bogorin, A; Jacques, C; Dietemann, J L

    2000-06-01

    We propose to assess the usefulness of diffusion-weighted MR Imaging (DWI), fluid-attenuated inversion recovery (FLAIR) and constructive interference in steady state (CISS) sequences in depicting epidermoid cysts (EC). FLAIR, CISS and DWI were obtained in 7 patients among 22. All patients were studied with T1 and T2 sequences. On Spin Echo images, EC demonstrate signal similar to LCS, which may lead to difficult differentiation between EC and arachnoid cyst (AC), specially for inexperienced radiologists. EC appear with a heterogeneous signal on T1 images (32%), irregular limits (91%) and with extension through foramen of Pacchioni in 18% of cases. On FLAIR sequence, the tumors were heterogeneous, different from void signal of CSF in 86% of cases. On CISS sequence, the tumors appear heterogeneous, hyperintense but less than LCS and with irregular limits in all cases. Some more, CISS images allowed to appreciate exact tumor extension and their relations with nerves and vessels. On DWI images, signal is hyperintense in all cases. Our study exhibited the great usefulness of DWI, CISS and FLAIR sequences in diagnosis of EC and in differentiating EC from AC. PMID:10970961

  3. The continuation inverse problem revisited

    NASA Astrophysics Data System (ADS)

    Huestis, Stephen P.

    1998-06-01

    The non-uniqueness of the continuation of a finite collection of harmonic potential field data to a level surface in the source-free region forces its treatment as an inverse problem. A formalism is proposed for the construction of continuation functions which are extremal by various measures. The problem is cast in such a form that the inverse problem solution is the potential function on the lowest horizontal surface above all sources, serving as the boundary function for the Dirichlet problem in the upper half-plane. The desired continuation, at the higher level of interest, must then be in the range of the upward continuation operator acting on this boundary function, rather than being allowed the full freedom of itself being part of a Dirichlet problem boundary function. Extremal solutions minimize non-linear functionals of the continuation function, which are re-expressed as different functionals of the boundary function. A crux of the method is that there is no essential distinction between the upward and downward continuation inverse problems to levels above or below data locations. Casting the optimization as a Lagrange multiplier problem leads to an integral equation for the boundary function, which is readily solved in the Fourier domain for a certain class of functionals. The desired extremal continuation is then given by upward continuation. It is found that for some functionals, application of the Lagrange multiplier theorem requires a further restriction on the set of allowable boundary functions: bandlimitedness is a natural choice for the continuation problem. With this imposition, the theory is developed in detail for semi-norm functionals penalizing departure from a constant potential, in the 2-norm and Sobelev norm senses, and illustrated by application for a small synthetic Deep Tow magnetic field data set.

  4. High resolution 3D nonlinear integrated inversion

    NASA Astrophysics Data System (ADS)

    Li, Yong; Wang, Xuben; Li, Zhirong; Li, Qiong; Li, Zhengwen

    2009-06-01

    The high resolution 3D nonlinear integrated inversion method is based on nonlinear theory. Under layer control, the log data from several wells (or all wells) in the study area and seismic trace data adjacent to the wells are input to a network with multiple inputs and outputs and are integratedly trained to obtain an adaptive weight function of the entire study area. Integrated nonlinear mapping relationships are built and updated by the lateral and vertical geologic variations of the reservoirs. Therefore, the inversion process and its inversion results can be constrained and controlled and a stable seismic inversion section with high resolution with velocity inversion, impedance inversion, and density inversion sections, can be gained. Good geologic effects have been obtained in model computation tests and real data processing, which verified that this method has high precision, good practicality, and can be used for quantitative reservoir analysis.

  5. Planetary radar data inversion techniques improvement

    NASA Astrophysics Data System (ADS)

    Picardi, G.; Masdea, A.; Mastrogiuseppe, M.; Restano, M.; Seu, R.

    2012-04-01

    The planetary radar (e.g. MARSIS) data inversion is based on the selection of groups of stationary frames, within the area under investigation, that shall be statistically analyzed after suitable correction. The selection step includes the recovery of bad/poor data and the estimation of the geometrical surface and subsurface features; these feature shall be utilized in order to obtain data that are only dependent by the material nature of the inclusion, within the layer, and of the interface. This paper is addressed to the techniques used for the frames selection, recovery and their geometric estimation content. As first step, frames have been selected in Mars areas where the surface and subsurface have a physical optics behavior (i.e. quite flat); the surface flatness has been estimated according to a simulator based on MOLA (Mars Orbiter Laser Altimeter) data while the subsurface has been estimated taking into account the Doppler filters content (i.e. filter 0, +1, -1). Being the surface and subsurface quite flat only small geometric contribution have been estimated and used for correction of the received echoes. To perform this task surface and subsurface models have been developed, under the Kirchhoff approximation hypothesis, to be compared with the experimental data. A figure showing the different material nature of different areas of the Mars South Pole has been drawn. The discovery of areas with an high dielectric constant led geologists to analyze those areas with other instrument to confirm the results obtained by MARSIS. This paper outlines also the way out for future works in order to analyze more complex surface and subsurface scenarios where conditions for geometric optics or fractal can be present. In this case, it will be mandatory to develop a clutter cancellation technique to avoid the presence of false subsurface echoes generated by surface and subsurface features not immediately below the nadir direction of observation. It will be also necessary

  6. Parallel inverse iteration with reorthogonalization

    SciTech Connect

    Fann, G.I.; Littlefield, R.J.

    1993-03-01

    A parallel method for finding orthogonal eigenvectors of real symmetric tridiagonal is described. The method uses inverse iteration with repeated Modified Gram-Schmidt (MGS) reorthogonalization of the unconverged iterates for clustered eigenvalues. This approach is more parallelizable than reorthogonalizing against fully converged eigenvectors, as is done by LAPACK's current DSTEIN routine. The new method is found to provide accuracy and speed comparable to DSTEIN's and to have good parallel scalability even for matrices with large clusters of eigenvalues. We present al results for residual and orthogonality tests, plus timings on IBM RS/6000 (sequential) and Intel Touchstone DELTA (parallel) computers.

  7. Parallel inverse iteration with reorthogonalization

    SciTech Connect

    Fann, G.I.; Littlefield, R.J.

    1993-03-01

    A parallel method for finding orthogonal eigenvectors of real symmetric tridiagonal is described. The method uses inverse iteration with repeated Modified Gram-Schmidt (MGS) reorthogonalization of the unconverged iterates for clustered eigenvalues. This approach is more parallelizable than reorthogonalizing against fully converged eigenvectors, as is done by LAPACK`s current DSTEIN routine. The new method is found to provide accuracy and speed comparable to DSTEIN`s and to have good parallel scalability even for matrices with large clusters of eigenvalues. We present al results for residual and orthogonality tests, plus timings on IBM RS/6000 (sequential) and Intel Touchstone DELTA (parallel) computers.

  8. 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.

  9. Direct and inverse modeling of multiphase flow systems

    SciTech Connect

    Finsterle, S.

    1995-10-01

    A modeling study is presented which demonstrates how the combination of simulation and optimization techniques can be used to improve the design of a multi-component remediation system. A series of computer codes has been developed at the Lawrence Berkeley National Laboratory to solve forward and inverse problems in groundwater hydrology. Simulations of non-isothermal, three-phase flow of volatile organic compounds in three-dimensional heterogeneous media were performed. Inverse modeling capabilities have been developed which can be used for both automatic model calibration and optimization of remediation schemes. In this study, we discuss a sequence of simulations to demonstrate the potential use of numerical models to design and analyze cleanup of a contaminated aquifer.

  10. Parallel computation of manipulator inverse dynamics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Bejczy, Antal K.

    1991-01-01

    In this article, parallel computation of manipulator inverse dynamics is investigated. A hierarchical graph-based mapping approach is devised to analyze the inherent parallelism in the Newton-Euler formulation at several computational levels, and to derive the features of an abstract architecture for exploitation of parallelism. At each level, a parallel algorithm represents the application of a parallel model of computation that transforms the computation into a graph whose structure defines the features of an abstract architecture, i.e., number of processors, communication structure, etc. Data-flow analysis is employed to derive the time lower bound in the computation as well as the sequencing of the abstract architecture. The features of the target architecture are defined by optimization of the abstract architecture to exploit maximum parallelism while minimizing architectural complexity. An architecture is designed and implemented that is capable of efficient exploitation of parallelism at several computational levels. The computation time of the Newton-Euler formulation for a 6-degree-of-freedom (dof) general manipulator is measured as 187 microsec. The increase in computation time for each additional dof is 23 microsec, which leads to a computation time of less than 500 microsec, even for a 12-dof redundant arm.