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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. Optimized Inversion Recovery Sequences for Quantitative T1 and Magnetization Transfer Imaging

    PubMed Central

    Li, Ke; Zu, Zhongliang; Xu, Junzhong; Janve, Vaibhav A.; Gore, John C.; Does, Mark D.; Gochberg, Daniel F.

    2010-01-01

    Inversion recovery sequences that vary the inversion time (ti) have been employed to determine T1 and, more recently, quantitative magnetization transfer (qMT) parameters. Specifically, in previous work, the inversion recovery pulse sequences varied ti only, while maintaining a constant delay (td) between repetitions. T1 values were determined by fitting to an exponential function, and qMT parameters were then determined by fitting to a bi-exponential function with an approximate solution. In the current study, new protocols are employed, which vary both ti and td and fit the data with minimal approximations. Cramer-Rao lower bounds (CRLB) are calculated to search for acquisition schemes that will maximize the precision efficiencies of T1 and qMT parameters. This approach is supported by Monte Carlo simulations. Measurements on MnCl2 samples verified the optimal T1 schemes. The optimal qMT schemes are confirmed by measurements on a series of cross linked bovine serum albumin (BSA) phantoms of varying concentrations. The effects of varying the number of sampling data points are also explored, and a rapid acquisition scheme is demonstrated in vivo. These new optimized quantitative imaging methods provide an improved means for determining T1 and MT parameter values compared to previous inversion recovery based methods. PMID:20665793

  3. Magnetic resonance imaging in partial epilepsy: additional abnormalities shown with the fluid attenuated inversion recovery (FLAIR) pulse sequence.

    PubMed Central

    Bergin, P S; Fish, D R; Shorvon, S D; Oatridge, A; deSouza, N M; Bydder, G M

    1995-01-01

    Thirty six patients with a history of partial epilepsy had MRI of the brain performed with conventional T1 and T2 weighted pulse sequences as well as the fluid attenuated inversion recovery (FLAIR) sequence. Abnormalities were found in 20 cases (56%), in whom there were 25 lesions or groups of lesions. Twenty four of these lesions were more conspicuous with the FLAIR sequence than with any of the conventional sequences. In 11 of these 20 cases, lesions thought to be of aetiological importance were only seen with the FLAIR sequence. In eight this was a solitary lesion. In the other three, an additional and apparently significant lesion (or lesions) was only seen with the FLAIR sequence when another lesion had been identified with both conventional and FLAIR sequences. The 11 additional lesions or groups of lesions were seen in the hippocampus, amygdala, cortex, or subcortical and periventricular regions. No lesion was found with any pulse sequence in 16 (44%) of the original group of 36 patients. In the eight cases where a lesion was seen only with the FLAIR sequence, localisation was concordant with the electroclinical features. Two of the eight patients with solitary lesions seen only on the FLAIR sequence underwent surgery, after which there was pathological confirmation of the abnormality identified with imaging. In one patient with a congenital cavernoma, the primary lesion was best seen with a contrast enhanced T1 weighted spin echo sequence. In this selected series, the FLAIR sequence increased the yield of MRI examinations of the brain by 30%. Images PMID:7738550

  4. Improved carotid intraplaque hemorrhage imaging using a slab-selective phase-sensitive inversion-recovery (SPI) sequence.

    PubMed

    Wang, Jinnan; Ferguson, Marina S; Balu, Niranjan; Yuan, Chun; Hatsukami, Thomas S; Börnert, Peter

    2010-11-01

    Intraplaque hemorrhage in atherosclerotic plaques has been associated with accelerated plaque growth as well as exacerbation of clinical symptoms. The identification of intraplaque hemorrhage using magnetic resonance imaging primarily relies on the detection of methemoglobin on T(1) weighted images. Current techniques are limited by insufficient intraplaque hemorrhage-wall contrast and poor blood suppression. In this study, a slab-selective phase-sensitive inversion-recovery (SPI) technique is proposed by combining a phase-sensitive reconstruction with a T(1) weighted sequence specifically designed to achieve improved intraplaque hemorrhage imaging. The SPI sequence was optimized and then used on ex vivo plaque specimens for histology based validation and intraplaque hemorrhage-wall contrast-to-noise ratio comparison with magnetization-prepared 3D rapid acquisition gradient echo MP-RAGE. SPI and MP-RAGE were also tested on a group of atherosclerosis patients to compare in vivo intraplaque hemorrhage-wall contrast-to-noise ratio and blood suppression effectiveness. On ex vivo specimens SPI had better intraplaque hemorrhage identification accuracy and a significantly higher intraplaque hemorrhage-wall contrast-to-noise ratio (P = 0.01) than MP-RAGE. Similar results were found in the in vivo test: Slab-selective phase-sensitive inversion-recovery provided a significantly improved intraplaque hemorrhage-wall contrast-to-noise ratio (P < 0.01) and blood suppression efficiency (P < 0.01). In conclusion, SPI is a novel technique optimized for intraplaque hemorrhage detection and validated against histology. It has demonstrated its capability for improved in vivo intraplaque hemorrhage identification and blood suppression in atherosclerosis patients.

  5. The value of the short tau inversion recovery sequence in magnetic resonance imaging of thyroid eye disease.

    PubMed

    Laitt, R D; Hoh, B; Wakeley, C; Kabala, J; Harrad, R; Potts, M; Goddard, P

    1994-03-01

    22 patients with thyroid eye disease were examined with magnetic resonance imaging (MRI) and the results compared with 10 controls. Imaging was performed on a 1.0 T scanner using a head coil. All patients were examined using both T1W and short tau inversion recovery (STIR) sequences. The relative signal intensity (SI) of individual extraocular muscles were quantified by comparison with SI from the adjacent temporalis muscle to give a signal intensity ratio (SIR). The results were compared with clinical disease activity assessed by the Werner grading system. Visual evaluation of muscle size and calculated SIRs showed an increase when compared to normals in 15 of the 22 patients. This difference was significant in patients with high grade (4-6) clinical disease. The known histological changes in this disease suggest that this increase in signal is caused by oedema secondary to acute inflammation. STIR sequences suppress the retro-orbital fat and thus enhance these changes both in the muscles and in the fat itself. The MR findings suggest that the STIR sequence can be used to predict those patients that will respond to anti-inflammatory treatment.

  6. [Optimization of high flip angle for late gadolinium enhancement magnetic resonance imaging by phase-sensitive inversion recovery sequence].

    PubMed

    Yoshizawa, Satoshi; Tsuchihashi, Toshio; Harashina, Satoshi; Yoshimi, Akira; Shimokawa, Kenichi; Matsumura, Yoshio

    2013-04-01

    This study focuses on optimization of the flip angle (FA) of phase-sensitive inversion recovery (PSIR) reconstruction (PSIR-FA) to achieve improved tissue contrast. Intensity normalization removes the larger variations in image intensity caused by falloff, thus improving the visualization of tissue contrast. We evaluated tissue contrast for images in healthy volunteers using the phantom influence of T1 relaxation and FA. T1 relaxation is improved due to the T1(*) effect and enables a high PSIR-FA to be set. The contrast-to-noise ratio (CNR) of the PSIR-FA 20° image is good, since magnetization is almost fully restored to normal. The usefulness of PSIR-FA 20 images was proved statistically. PSIR-FA 20° shows improved tissue contrast as a result of the high accuracy of intensity normalization.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  8. 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…

  9. 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

  10. Multislice and multicoil phase-sensitive inversion-recovery imaging.

    PubMed

    Ma, Jingfei

    2005-04-01

    Phase-sensitive inversion-recovery (PSIR) imaging may provide enhanced T(1) contrast. However, clinical implementation of PSIR imaging is hindered because image reconstruction with this method often lacks robustness and requires manual intervention, particularly for data acquired in multiple slices and with phased-array coils. In this paper, a new algorithm suitable for automatic PSIR image reconstruction of multislice and multicoil data is presented. This algorithm phase corrects by region-growing, employing both the magnitude and the phase information of image pixels. Specifically, phase gradients of the original complex image are first calculated and then used to determine the sequence of the region-growing. The signal direction relating to the phase error for each pixel is then determined during the region-growing using both the magnitude and the phase of the previously determined pixels that are located within a boxcar neighborhood of the pixel. Finally, the intrinsic intercoil and interslice correlation is exploited to ensure consistency in the global polarity of all of the PSIR images. The results are demonstrated with in vivo human brain images acquired at 3 Tesla with an eight-channel phased-array coil.

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

    PubMed

    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.

  12. Sequence-specific, self-reporting hairpin inversion probes.

    PubMed

    Browne, Kenneth A

    2005-02-16

    Sequence-specific probes for detecting target nucleic acids are the cornerstone of the genomics revolution (e.g., microarrays) and of molecular diagnostics. Molecular beacons are self-reporting, nucleic acid probes whose structure includes complementary terminal arm sequences and a loop that is complementary to a target sequence; fluorescence detection is by changes in proximity of fluorophore and quencher pairs attached on opposite arms. However, molecular beacon design is not as simple as attaching arbitrary arm sequences onto previously designed linear probes. The stem arms can also interact with flanking target sequences, changing the hybridization specificity; constantly adapting the arms to avoid such interactions, if not desired, increases design complexity. Herein, I report the use of inversion linkages in probe backbones leading to stem arms of sequence polarity opposite to that of the target-binding region, thereby eliminating potential hybridization of the arms with the target. Using two microbial sequence categories, thermal denaturation and target titration analyses demonstrate that these new hairpin inversion probes retain closed-state stability comparable to that of molecular beacons, contain easily designed arm sequences that do not interact with targets, and, therefore, can be used universally with optimized linear probe sequences.

  13. [An Examination for Uterine Dynamic Study with Phase-sensitive Inversion-recovery].

    PubMed

    Takatsu, Yasuo; Motegi, Shunichi; Miyati, Tosiaki; Yamamura, Kenichirou

    2016-01-01

    The depth of myometrial invasion in patients with endometrial carcinoma is recognized as an important factor that closely correlates with prognosis. Preoperative assessment of myometrial invasion is essential for planning surgery. To enhance the contrast between myometrium and endometrium including myometrial invasion with endometrial carcinoma, we optimized the sequence parameter with phase-sensitive inversion-recovery (PSIR) in gadolinium dynamic study of uterine corpus. On a 1.5-T magnetic resonance imaging (MRI), images were acquired by three-dimensional (3D) T1 -turbo field echo (TFE) with PSIR sequence and gadolinium-diethylenetriamine pentaacetic acid( Gd-DTPA) diluted phantom (0-5 mmol/L) and myometrium model (manganese chloride tetrahydrate+agar). We calculated the null point and the contrast-to-noise ratio (CNR) at multiple TFE inversion delay times, 200 ms-maximum in each combination; flip angles (FAs), 5-35 degrees; TFE factor, 20-40; and shot interval (SI), 500-1000 ms. We assumed that dynamic scanning time was 30 seconds when the sensitivity encoding factor was 2, namely, in this study, the scanning time was 1 minute with no sensitivity encoding. In addition, we compared CNR between optimized PSIR sequence ande-Thrive. We recognized a successful CNR of the 3D PSIR parameter was TFE inversion delay times, 335 ms; FA, 25 degrees; TFE factor, 20; and SI, 500 ms. In each gadolinium-DTPA diluted phantom, the average CNR of the optimized PSIR sequence was approximately 1.7 times (maximum: 3 times) higher than e-Thrive. Optimizing sequence parameter of PSIR is applicable in gadolinium dynamic study of uterine corpus.

  14. 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.

  15. 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.

  16. 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

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

    PubMed

    Harel, Asaff; Ceccarelli, Antonia; 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.

  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. 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

  20. [Improvement of MRI effectiveness in the detection of intracerebral hematoma. Double inversion recovery].

    PubMed

    Burenchev, D V; Skvortsova, V I; Guseva, O I; Shumm, B A; Fomenkov, S A; Prokhorov, A V; Khetchikov, G V; Barkova, L A

    2009-01-01

    A study aimed at developing the pulse consequence, the double inversion recovery (DIR), using low field magnetic tomography, and assessing its effectiveness in the detection of intracerebral hematoma. The research has been conducted at "Ellipse" MR tomograph. The new pulse sequence has been created by the modification of the regular FLAIR, its technical parameters were as follows: the first TI - 90 ms, the second TI - 1300 ms, TR - 4665 ms, echo - 3. Twenty-seven patients have been enrolled in the study. The tissue contrast coefficients on FLAIR and DIR images have been compared. It has been shown that the contrast coefficient of normal brain structures and brain lesions on the DIR images in regard to the white matter are significantly higher than on the FLAIR images. Results of the study revealed that the dynamics of MR symptoms of intracerebral hematoma is faster on the DIR images compared to the FLAIR ones. This finding can be used for detection of intracerebral hematoma in difficult clinical cases.

  1. 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

  2. Phase-sensitive inversion recovery for myocardial T1 mapping with motion correction and parametric fitting.

    PubMed

    Xue, Hui; Greiser, Andreas; Zuehlsdorff, Sven; Jolly, Marie-Pierre; Guehring, Jens; Arai, Andrew E; Kellman, Peter

    2013-05-01

    The assessment of myocardial fibrosis and extracellular volume requires accurate estimation of myocardial T1 s. While image acquisition using the modified Look-Locker inversion recovery technique is clinically feasible for myocardial T1 mapping, respiratory motion can limit its applicability. Moreover, the conventional T1 fitting approach using the magnitude inversion recovery images can lead to less stable T1 estimates and increased computational cost. In this article, we propose a novel T1 mapping scheme that is based on phase-sensitive image reconstruction and the restoration of polarity of the MR signal after inversion. The motion correction is achieved by registering the reconstructed images after background phase removal. The restored signal polarity of the inversion recovery signal helps the T1 fitting resulting in improved quality of the T1 map and reducing the computational cost. Quantitative validation on a data cohort of 45 patients proves the robustness of the proposed method against varying image contrast. Compared to the magnitude T1 fitting, the proposed phase-sensitive method leads to less fluctuation in T1 estimates.

  3. [Development of an Optimizing Program of Scanning Parameters for Double Inversion Recovery MRI].

    PubMed

    Hayashi, Norio; Yarita, Kazuma; Sakata, Kozue; Motegi, Shunichi; Nagase, Hiroyuki; Ujita, Kouichi; Ogura, Akio; Ogura, Toshihiro; Shimada, Takehiro; Tsushima, Yoshito

    2015-06-01

    The purpose of this study was to develop an optimizing program of scanning parameters for double inversion recovery (DIR) MRI. The optimization algorithm consists of the following steps: (1) obtaining the initial parameters (TR, TE, and T1 values of the two attenuated tissues); (2) iterative calculation for minimization of errors; and (3) determination of the optimized TI(1st) and TI(2nd). To evaluate the developed algorithm, we performed the phantom and simulation studies using the phantoms which were imitated T1 values of white and gray matters and cerebrospinal fluid. In addition, white matter attenuated inversion recovery (WAIR) and gray matter attenuated inversion recovery (GAIR) images were obtained by optimized scan parameters in one volunteer. The developed algorithm could calculate the optimized TI(1st) and TI(2nd) values at once. Results of summation of signal intensity (SI) of two attenuated tissues shows that the SI of the two tissues were well-attenuated using the theoretical values which were calculated using the developed algorithm. The correlation coefficient of the SI of the phantom of the gray matter between actual and simulation measurements was r=0.997. The SI obtained by actual measurements well correlated with the SI obtained by the simulation measurements. The WAIR and GAIR images in the volunteer were well enhanced gray or white matters. We thus conclude that it is possible to calculate the optimized parameters for the DIR-MRI using the developed algorithm.

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

    PubMed

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

    2000-03-01

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

  5. 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…

  6. Implications of an inverse branching aftershock sequence model.

    PubMed

    Turcotte, D L; Abaimov, S G; Dobson, I; Rundle, J B

    2009-01-01

    The branching aftershock sequence (BASS) model is a self-similar statistical model for earthquake aftershock sequences. A prescribed parent earthquake generates a first generation of daughter aftershocks. The magnitudes and times of occurrence of the daughters are obtained from statistical distributions. The first generation daughter aftershocks then become parent earthquakes that generate second generation aftershocks. The process is then extended to higher generations. The key parameter in the BASS model is the magnitude difference Deltam* between the parent earthquake and the largest expected daughter earthquake. In the application of the BASS model to aftershocks Deltam* is positive, the largest expected daughter event is smaller than the parent, and the sequence of events (aftershocks) usually dies out, but an exponential growth in the number of events with time is also possible. In this paper we explore this behavior of the BASS model as Deltam* varies, including when Deltam* is negative and the largest expected daughter event is larger than the parent. The applications of this self-similar branching process to biology and other fields are discussed.

  7. 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.

  8. Robust phase sensitive inversion recovery imaging using a Markov random field model.

    PubMed

    Garach, Ravindra M; Ji, Jim X; Ying, Lei; Ma, Jingfei

    2004-01-01

    This paper presents a novel method for phase sensitive inversion recovery (PSIR) imaging for improved T/sub 1/ contrast. This method models the phase of the complex magnetic resonance image using a statistical model based on Markov random fields. A computationally efficient optimization method is developed. Computer simulations and in-vivo brain imaging experiments show that the proposed method can produce PSIR images with enhanced T/sub 1/ contrast and it is robust against high levels of data noise even when rapid phase variations are presented.

  9. Optimal recovery sequencing for critical infrastructure resilience assessment.

    SciTech Connect

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

    2010-09-01

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

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

    PubMed

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

    2012-11-01

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

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

    PubMed

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

    1990-01-01

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

  12. 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.

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

    PubMed

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

    2014-12-01

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

  14. 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

  15. 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

  16. 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

    2016-06-27

    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.

  17. 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

  18. Noncontrast-enhanced renal angiography using multiple inversion recovery and alternating TR balanced steady-state free precession.

    PubMed

    Dong, Hattie Z; Worters, Pauline W; Wu, Holden H; Ingle, R Reeve; Vasanawala, Shreyas S; Nishimura, Dwight G

    2013-08-01

    Noncontrast-enhanced renal angiography techniques based on balanced steady-state free precession avoid external contrast agents, take advantage of high inherent blood signal from the T 2 / T 1 contrast mechanism, and have short steady-state free precession acquisition times. However, background suppression is limited; inflow times are inflexible; labeling region is difficult to define when tagging arterial flow; and scan times are long. To overcome these limitations, we propose the use of multiple inversion recovery preparatory pulses combined with alternating pulse repetition time balanced steady-state free precession to produce renal angiograms. Multiple inversion recovery uses selective spatial saturation followed by four nonselective inversion recovery pulses to concurrently null a wide range of background T 1 species while allowing for adjustable inflow times; alternating pulse repetition time steady-state free precession maintains vessel contrast and provides added fat suppression. The high level of suppression enables imaging in three-dimensional as well as projective two-dimensional formats, the latter of which has a scan time as short as one heartbeat. In vivo studies at 1.5 T demonstrate the superior vessel contrast of this technique.

  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. Constraints in chromosomal inversions in Escherichia coli are not explained by replication pausing at inverted terminator-like sequences.

    PubMed

    François, V; Louarn, J; Patte, J; Rebollo, J E; Louarn, J M

    1990-04-01

    Regions close to the replication terminus of the Escherichia coli chromosome are strongly refractory to genomic inversions. Since these regions also harbour polar replication terminator-like sequences or pause sites, we have investigated the possibility that slowing of replication as a result of pausing at inverted pause sites is responsible for inability to isolate stable inversions affecting these regions. A mutation in the tus gene is known to abolish replication pausing at terminators. We show here that the distribution of invertible and noninvertible segments along the chromosome is not affected by tus mutations. This observation eliminates replication pausing as a cause for the reduced fitness of bacteria harbouring certain chromosomal inversions.

  3. 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

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

    SciTech Connect

    Mark A. Meadows

    2004-11-19

    In the fourth quarter of this DOE NETL project, they have developed an algorithm for generating time-lapse seismic anomalies from changes in fluid properties over time. This forward-modeling algorithm constitutes the first step in the inversion procedure of Phase III of the project. Examples were generated illustrating the flexibility of this approach. Additional activities in this reporting period included a trip by the Principal Investigator to the 7th International Conference on Greenhouse Gas Control Technologies (GHGT-7) in Vancouver, Canada, September 5-9, 2004. In the next quarter, they will work on the second step of the inversion procedure, namely, the inversion of the seismic time-lapse anomalies to obtain changes in fluid properties, and will continue investigating alternative methods for calculating properties of oil/brine/CO{sub 2} and brine/CO{sub 2} systems.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. [Improved visualization of long-axis black-blood imaging of the carotid arteries using phase sensitive inversion recovery combined with 3D IR-T₁TFE].

    PubMed

    Horie, Tomohiko; Kawakata, Mami; Kajihara, Nao; Takano, Hayato; Honda, Masatoshi; Muro, Isao; Ogino, Tetsuo

    2011-01-01

    The purpose of this study was to improve the visualization of long-axis black-blood imaging of the carotid arteries. We experimented on phantom and in-vivo study of 3 dimension (3D) inversion recovery T(1) turbo field echo combined with phase sensitive inversion recovery (PSIR-3D IR-T(1)TFE) at 3.0 Tesla. As a result, the contrast has been improved by calculated images of PSIR-3D IR-T(1)TFE set to inversion time (TI) 350 ms that is shorter than null point of blood. This displays that the contrast between blood and tissues can be improved when the longitudinal magnetization of blood is a negative. Therefore, the visualization of long-axis black-blood imaging of the carotid arteries has been improved by the calculated images of PSIR-3D IR-T(1)TFE set to TI that is shorter than null point of blood.

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

    PubMed

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

    2011-04-01

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

  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.

  13. 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

  14. Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing

    PubMed Central

    2013-01-01

    Background The applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. However, most previous research based on maternal plasma sequencing has been restricted to fetal aneuploidies. To detect specific parentally inherited mutations, invasive approaches to obtain fetal DNA are the current standard in the clinic because of the experimental complexity and resource consumption of previously reported non-invasive approaches. Methods Here, we present a simple and effective non-invasive method for accurate fetal genome recovery-assisted with parental haplotypes. The parental haplotype were firstly inferred using a combination strategy of trio and unrelated individuals. Assisted with the parental haplotype, we then employed a hidden Markov model to non-invasively recover the fetal genome through maternal plasma sequencing. Results Using a sequence depth of approximately 44X against a an approximate 5.69% cff-DNA concentration, we non-invasively inferred fetal genotype and haplotype under different situations of parental heterozygosity. Our data show that 98.57%, 95.37%, and 98.45% of paternal autosome alleles, maternal autosome alleles, and maternal chromosome X in the fetal haplotypes, respectively, were recovered accurately. Additionally, we obtained efficient coverage or strong linkage of 96.65% of reported Mendelian-disorder genes and 98.90% of complex disease-associated markers. Conclusions Our method provides a useful strategy for non-invasive whole fetal genome recovery. PMID:23445748

  15. 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

  16. Sequence of the site-specific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1.

    PubMed Central

    Hiestand-Nauer, R; Iida, S

    1983-01-01

    Inversion of the 4.2-kb C segment flanked by 0.6-kb inverted repeats on the bacteriophage P1 genome is mediated by the P1-encoded site-specific cin recombinase. The cin gene lies adjacent to the C segment and the C inversion cross-over sites cixL and cixR are at the external ends of the inverted repeats. We have sequenced the DNA containing the cin gene and these cix sites. The cin structural gene consists of 561 nucleotides and terminates at the inverted repeat end where the cixL site is located. Only two nucleotides in the cixL region differ from those in the cixR and they are within the cin TAA stop codon. The cin promoter was localized by transposon mutagenesis within a 0.1-kb segment, which contains probable promoter sequences overlapping with a 'pseudo-cix' sequence cixPp. In a particular mutant, integration of an IS1-flanked transposon into the cin control region promoted weak expression of the cin gene. The cin and cix sequences show homology with corresponding, functionally related sequences for H inversion in Salmonella and with cross-over sites for G inversion in phage Mu. Based on a comparison of the DNA sequences and of the gene organizations, a possible evolutionary relationship between these three inversion systems and the possible significance of the cixPp sequence in the cin promoter are discussed. Images Fig. 2. PMID:6315399

  17. [Evaluation of the right internal iliac artery which is anastomosed to transplant renal artery using non-contrast enhanced MR angiography with electrocardiography-gated and 3D True SSFP time-spatial labeling inversion pulse sequence].

    PubMed

    Yoshida, Ayako; Shiratori, Yoko; Suzuki, Makoto; Ozasa, Masaya; Takeyama, Mamoru; Eshima, Mitsuhiro; Shinohara, Maiko; Yamamoto, Takao; Tajima, Tsuyoshi

    2015-05-01

    To evaluate whether electrocardiography-gated is useful in non-contrast-enhanced MRA with time-spatial labeling inversion pulse (Time-SLIP) in renal transplantation patients compared with respiration-triggered free-breathing. Simulation-based analyses of black blood time interval (BBTI) values for spatial selective inversion-recovery pulse and electrocardiography rates were performed, and confirmed on human subjects using a three-dimensional (3D) coherent steady-state free precession (SSFP) sequence on a 1.5 tesla Toshiba MRI scanner. Signal acquisition interval and BBTI values in which signal of a water tissue becomes the null point showed a strong correlation, and successfully suppressed signals from the background and provided better contrast between the arteries and the background. Because electrocardiography-gated non-contrast MRA does not depend on the respiration interval, providing a contrast stable, it was suggested to be an effective screening tool for evaluation of pelvic arteries.

  18. 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

  19. 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

  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. An Inverse Problem Approach to Recovery of In Vivo Nanoparticle Concentrations from Thermal Image Monitoring of MR-Guided Laser Induced Thermal Therapy

    PubMed Central

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

    2012-01-01

    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 nanoparticles 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 nanoparticles selective heating within 5°C of measured MRTI estimations along selected temperature profiles. Results indicate the maximum likelihood 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

  2. 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...

  3. [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

  4. 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.

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

    PubMed

    Messinger-Rapport, B J; Rudy, Y

    1989-11-01

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

  6. 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.

  7. 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.

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

    PubMed

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

    2007-03-01

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

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

  12. 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…

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

    PubMed

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

    2014-01-01

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

  14. Characterization of an inversion on the long arm of chromosome 10 juxtaposing D10S170 and RET and creating the oncogenic sequence RET/PTC.

    PubMed Central

    Pierotti, M A; Santoro, M; Jenkins, R B; Sozzi, G; Bongarzone, I; Grieco, M; Monzini, N; Miozzo, M; Herrmann, M A; Fusco, A

    1992-01-01

    RET/PTC is a transforming sequence created by the fusion of the tyrosine kinase domain of the RET protooncogene with the 5' end of the locus D10S170 designated by probe H4 and is frequently found activated in human papillary thyroid carcinomas. RET and D10S170 have been mapped to contiguous regions of the long arm of chromosome 10: q11.2 and q21, respectively. To identify the mechanism leading to the generation of the oncogenic sequence RET/PTC, a combined cytogenetic and molecular analysis of several cases of papillary thyroid carcinomas was done. In four cases the results indicated that these tumors had RET/PTC activation and a paracentric inversion of the long arm of chromosome 10, inv(10)(q11.2q21), with breakpoints coincident with the regions where RET and D10S170 are located. Therefore, a chromosome 10q inversion provides the structural basis for the D10S170-RET fusion that forms the hybrid transforming sequence RET/PTC. Images PMID:1542652

  15. FAST TRACK PAPER: An advanced slip model for the Umbria-Marche earthquake sequence: coseismic displacements observed by SAR interferometry and model inversion

    NASA Astrophysics Data System (ADS)

    Crippa, B.; Crosetto, M.; Biescas, E.; Troise, C.; Pingue, F.; de Natale, G.

    2006-01-01

    We report an improved slip model for the 1997 September-October Umbria-Marche earthquake sequence in central Italy. The model is based on coseismic displacements estimated by differential synthetic aperture radar (DInSAR) interferometry using an advanced inverse modelling approach that enables the characteristics of the SAR data, especially their dense spatial sampling, to be fully exploited. The paper first looks at DInSAR analysis using the simplest configuration, that is, a single-image pair that temporally covers the earthquake sequence. Yet, given that this DInSAR configuration is often used for coseismic studies and the limited availability of SAR data, we duly consider the limitations of the DInSAR results and discuss the rigorous DInSAR procedure carried out, highlighting key errors associated with such observations. We then focus on the inversion of the estimated DInSAR displacements and on our advanced heterogeneous slip model for this earthquake sequence's main shocks, emphasizing its most significant features.

  16. 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

  17. 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.

  18. Flip angle profile correction for T₁ and T₂ quantification with look-locker inversion recovery 2D steady-state free precession imaging.

    PubMed

    Cooper, Mitchell A; Nguyen, Thanh D; Spincemaille, Pascal; Prince, Martin R; Weinsaft, Jonathan W; Wang, Yi

    2012-11-01

    Fast methods using balanced steady-state free precession have been developed to reduce the scan time of T₁ and T₂ mapping. However, flip angle (FA) profiles created by the short radiofrequency pulses used in steady-state free precession deviate substantially from the ideal rectangular profile, causing T₁ and T₂ mapping errors. The purpose of this study was to develop a FA profile correction for T₁ and T₂ mapping with Look-Locker 2D inversion recovery steady-state free precession and to validate this method using 2D spin echo as a reference standard. Phantom studies showed consistent improvement in T₁ and T₂ accuracy using profile correction at multiple FAs. Over six human calves, profile correction provided muscle T₁ estimates with mean error ranging from excellent (-0.6%) at repetition time/FA = 18 ms/60° to acceptable (6.8%) at repetition time/FA = 4.9 ms/30°, while muscle T₂ estimates were less accurate with mean errors of 31.2% and 47.9%, respectively.

  19. 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.

  20. Acquisition, Extinction, Recovery, and Reversal of Different Response Sequences Under Conditional Control by Nicotine in Rats

    PubMed Central

    Troisi, Joseph R.

    2013-01-01

    Complex voluntary behaviors occur in sequence. Eight rats were trained in an operant procedure that used nicotine and non-drug (saline) states as interoceptive cues that signaled which of two behavioral sequences led to food reward. The distal and proximal responses in the chain were always maintained on variable interval 30-sec and fixed ratio-1 schedules, respectively, and rate differences between the responses were used as the dependent variable. Extinction and reversal training was conducted. Distal response rates were significantly greater than proximal response rates during training, testing, extinction, and reversal learning. These data suggest that (a) nicotine can establish interoceptive control over different response sequences, and (b) extinction of one response sequence may be state-dependent. The clinical relevance of extinction of complex behavioral repertoires such as drug-seeking and drug-taking behavior that are evoked by specific interoceptive cues is addressed in regard to drug abuse treatment and relapse. PMID:24837654

  1. 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

  2. Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.

    PubMed Central

    Kukreti, S; Sun, J S; Loakes, D; Brown, D M; Nguyen, C H; Bisagni, E; Garestier, T; Helene, C

    1998-01-01

    Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a triplex-specific ligand (a benzo[e]pyridoindole derivative, BePI). N6-methoxy-2,6-diaminopurine (K) binds to an A*T base pair better than a T*A, G*C or C*G base pair. Some discrimination is still observed in the presence of BePI and triplex stability is markedly increased. These findings should help in designing BePI-oligonucleotide conjugates to extend the range of DNA sequences available for triplex formation. PMID:9547278

  3. The breakpoint of an inversion of chromosome 14 in a T-cell leukemia: sequences downstream of the immunoglobulin heavy chain locus are implicated in tumorigenesis.

    PubMed

    Baer, R; Heppell, A; Taylor, A M; Rabbitts, P H; Boullier, B; Rabbitts, T H

    1987-12-01

    T-cell tumors are characterized by inversions or translocations of chromosome 14. The breakpoints of these karyotypic abnormalities occur in chromosome bands 14q11 and 14q32--the same bands in which the T-cell receptor (TCR) alpha-chain and immunoglobulin heavy chain genes have been mapped, respectively. Patients with ataxia-telangiectasia are particularly prone to development of T-cell chronic lymphocytic leukemia with such chromosomal abnormalities. We now describe DNA rearrangements of the TCR alpha-chain gene in an ataxia-telangiectasia-associated leukemia containing both a normal and an inverted chromosome 14. The normal chromosome 14 has undergone a productive join of TCR alpha-chain variable (V alpha) and joining (J alpha) gene segments. The other allele of the TCR alpha-chain gene features a DNA rearrangement, about 50 kilobases from the TCR alpha-chain constant (C alpha) gene, that represents the breakpoint of the chromosome 14 inversion; this breakpoint is comprised of a TCR J alpha segment (from 14q11) fused to sequences derived from 14q32 but on the centromeric side of C mu. These results imply that 14q32 sequences located at an undetermined distance downstream of the immunoglobulin C mu locus can contribute to the development of T-cell tumors.

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

    Objectives To assess the utility of the display standardisation of diffusion-weighted MRI (DWI) and to compare the effectiveness of DWI and fluid-attenuated inversion recovery (FLAIR) MRI for the diagnosis of sporadic Creutzfeldt–Jakob disease (sCJD). Design A reliability and agreement study. Setting Thirteen MRI observers comprising eight neurologists and five radiologists at two universities in Japan. Participants Data of 1.5-Tesla DWI and FLAIR were obtained from 29 patients with sCJD and 13 controls. Outcome measures Standardisation of DWI display was performed utilising b0 imaging. The observers participated in standardised DWI, variable DWI (the display adjustment was observer dependent) and FLAIR sessions. The observers independently assessed each MRI for CJD-related lesions, that is, hyperintensity in the cerebral cortex or striatum, using a continuous rating scale. Performance was evaluated by the area under the receiver operating characteristics curve (AUC). Results The mean AUC values were 0.84 (95% CI 0.81 to 0.87) for standardised DWI, 0.85 (95% CI 0.82 to 0.88) for variable DWI and 0.68 (95% CI 0.63 to 0.72) for FLAIR, demonstrating the superiority of DWI (p<0.05). There was a trend for higher intraclass correlations of standardised DWI (0.74, 95% CI 0.66 to 0.83) and variable DWI (0.72, 95% CI 0.62 to 0.81) than that of FLAIR (0.63, 95% CI 0.53 to 0.74), although the differences were not statistically significant. Conclusions Standardised DWI is as reliable as variable DWI, and the two DWI displays are superior to FLAIR for the diagnosis of sCJD. The authors propose that hyperintensity in the cerebral cortex or striatum on 1.5-Tesla DWI but not FLAIR can be a reliable diagnostic marker for sCJD. PMID:22290397

  8. 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

  9. 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

  10. 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.

  11. 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.

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

    PubMed

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

    2015-10-01

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

  13. Feasibility of Coronary Artery Wall Thickening Assessment in Asymptomatic Coronary Artery Disease using Phase-Sensitive Dual Inversion Recovery MRI at 3T

    PubMed Central

    Gharib, Ahmed M.; Zahiri, Homeira; Matta, Jatin; Pettigrew, Roderic I.; Abd-Elmoniem, Khaled Z.

    2013-01-01

    Objectives The purpose of this study is to (1) investigate the image quality of phase-sensitive dual inversion recovery (PS-DIR) coronary wall imaging in healthy subjects and in subjects with known coronary artery disease (CAD) and to (2) investigate the utilization of PS-DIR at 3T in the assessment of coronary artery thickening in subjects with asymptomatic but variable degrees of CAD. Materials and Methods A total of 37 subjects participated in this Institutional Review Board approved and HIPAA-compliant study. These included 21 subjects with known CAD as identified on Multi-Detector CT angiography (MDCT). Sixteen healthy subjects without known history of CAD were included. All subjects were scanned using free-breathing PS-DIR MRI for the assessment of coronary wall thickness at 3T. Lumen-tissue contrast-to-noise ratio (CNR), signal-to-noise (SNR), and quantitative vessel parameters including lumen area and wall thickness were measured. Statistical analyses were performed. Results PS-DIR was successfully completed in 76% of patients and in 88% of the healthy subjects. Phase-sensitive signed magnitude reconstruction, compared to modulus magnitude images, significantly improved lumen-tissue contrast-to-noise ratio (CNR) in both healthy subjects (26.73±11.95 vs. 14.65±9.57, p<0.001) and in patients (21.45±7.61 vs. 16.65±5.85, p<0.001). There was no difference in image CNR and SNR between groups. In arterial segments free of plaques, coronary wall was thicker in patients in comparison to healthy subjects (1.74±0.27mm vs. 1.17±0.14mm, p<0.001) without a change in lumen area (4.51±2.42 mm2 vs. 5.71±3.11 mm2, p=0.25). Conclusions This is the first study to demonstrate the feasibility of successfully obtaining vessel wall images at 3T using PS-DIR in asymptomatic patients with known variable degrees of CAD as detected by MDCT. This was achieved with a fixed subject-invariant planning of blood signal nulling. With that limitation alleviated, PS-DIR coronary wall

  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. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    PubMed Central

    Flynn, Sarah MC; Carr, Steven M

    2007-01-01

    Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA) genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by more than a few percent. The

  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

    2016-07-12

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

  18. 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.

  19. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

    PubMed Central

    Gerritsen, Bram; Pandit, Aridaman; Andeweg, Arno C.; de Boer, Rob J.

    2016-01-01

    Motivation: High Throughput Sequencing (HTS) has enabled researchers to probe the human T cell receptor (TCR) repertoire, which consists of many rare sequences. Distinguishing between true but rare TCR sequences and variants generated by polymerase chain reaction (PCR) and sequencing errors remains a formidable challenge. The conventional approach to handle errors is to remove low quality reads, and/or rare TCR sequences. Such filtering discards a large number of true and often rare TCR sequences. However, accurate identification and quantification of rare TCR sequences is essential for repertoire diversity estimation. Results: We devised a pipeline, called Recover TCR (RTCR), that accurately recovers TCR sequences, including rare TCR sequences, from HTS data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations, we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data, we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines. Availability and Implementation: The RTCR pipeline is implemented in Python (v2.7) and C and is freely available at http://uubram.github.io/RTCR/along with documentation and examples of typical usage. Contact: b.gerritsen@uu.nl PMID:27324198

  20. Ability of a Bacterial Chromosome Segment to Invert Is Dictated by Included Material Rather than Flanking Sequence

    PubMed Central

    Mahan, M. J.; Roth, J. R.

    1991-01-01

    Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the ``permissivity'' of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement. PMID:1783289

  1. Marching-jury backward beam equation and quasi-reversibility methods for hydrologic inversion: Application to contaminant plume spatial distribution recovery

    NASA Astrophysics Data System (ADS)

    Bagtzoglou, Amvrossios C.; Atmadja, Juliana

    2003-02-01

    In this paper, a comparison between the marching-jury backward beam equation (MJBBE) and the quasi-reversibility (QR) methods to perform hydrologic inversion and, more specifically, to reconstruct conservative contaminant plume spatial distributions is presented. The MJBBE, developed by Atmadja and Bagtzoglou [2000, 2001a], was used to recover contaminant spatial distributions in heterogeneous porous media, while the QR method, first applied to groundwater contamination problems by Skaggs and Kabala [1995], was modified to incorporate heterogeneity and explicitly handle the advective term of the transport equation. Spatially uncorrelated and correlated, stationary and nonstationary, heterogeneous dispersion coefficient fields were generated using the Bayesian nearest neighbor method (BNNM). Homogeneous and deterministically heterogeneous cases are also presented for comparison. In addition, contaminant plume initial data with uncertainty were also analyzed using the MJBBE and QR methods. The MJBBE is found to be robust enough to handle highly heterogeneous parameters and is able to preserve the salient features of the initial input data. On the other hand, the QR method is superior in handling cases with homogeneous parameters and with initial data that are plagued by uncertainty but it performs very poorly in cases with heterogeneous media.

  2. Recovery and Phylogenetic Analysis of nifH Sequences from Diazotrophic Bacteria Associated with Dead Aboveground Biomass of Spartina alterniflora

    PubMed Central

    Lovell, Charles R.; Friez, Michael J.; Longshore, John W.; Bagwell, Christopher E.

    2001-01-01

    DNA was extracted from dry standing dead Spartina alterniflora stalks as well as dry Spartina wrack from the North Inlet (South Carolina) and Sapelo Island (Georgia) salt marshes. Partial nifH sequences were PCR amplified, the products were separated by denaturing gradient gel electrophoresis (DGGE), and the prominent DGGE bands were sequenced. Most sequences (109 of 121) clustered with those from α-Proteobacteria, and 4 were very similar (>99%) to that of Azospirillum brasilense. Seven sequences clustered with those from known γ-Proteobacteria and five with those from known anaerobic diazotrophs. The diazotroph assemblages associated with dead Spartina biomass in these two salt marshes were very similar, and relatively few major lineages were represented. PMID:11679360

  3. [Carotid plaque assessment using inversion recovery T1 weighted-3 dimensions variable refocus flip angle turbo spin echo sampling perfection with application optimized contrast using different angle evolutions black blood imaging].

    PubMed

    Inoue, Yuji; Yoneyama, Masami; Nakamura, Masanobu; Ozaki, Satoshi; Ito, Kenjiro; Hiura, Mikio

    2012-01-01

    Vulnerable plaque can be attributed to induction of ischemic symptoms and magnetic resonance imaging of carotid artery is valuable to detect the plaque. Magnetization prepared rapid acquisition with gradient echo (MPRAGE) method could detect hemorrhagic vulnerable plaque as high intensity signal; however, blood flow is not sufficiently masked by this method. The contrast for plaque in T1 weighted image (T1WI) could not be obtained sufficiently with black blood image (BBI) by sampling perfection with application optimized contrast using different angle evolutions (SPACE) method as turbo spin echo (TSE). In addition, an appearance of artifact by slow flow is a problem. Considering these controversial situations in plaque imaging, we examined the modified BBI inversion recovery (IR)-SPACE in which IR was added for SPACE method so that the contrast for plaque in T1WI was optimized. We investigated the application of this method in plaque imaging. As a result of phantom imaging, the contrast for plaque in T1WI was definitely obtained by choosing an appropriate inversion time (TI) for the corresponding repetition time. In clinical cases, blood flow was sufficiently masked by IR-SPACE method and the plaque imaging was clearly obtained in clinical cases to the same extent as MPRAGE method. Since BBI with IR-SPACE method was derived from both IR pulse and flow void effect, this method could obtain the blood flow masking effect definitely. The present study suggested that SPACE method might be applicable to estimate properties of carotid artery plaque.

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

    PubMed

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

    2014-05-01

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

  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. Selective Recovery of 16S rRNA Sequences from Natural Microbial Communities in the Form of cDNA.

    PubMed

    Weller, R; Ward, D M

    1989-07-01

    Cloning of cDNA obtained from 16S rRNA (16S rcDNA) selectively retrieves species-specific sequence information useful for analyzing the composition and structure of natural microbial communities. With this technique we obtained recombinant 16S rcDNA libraries from Escherichia coli and from a model hot-spring cyanobacterial-mat community. The recombinant plasmids contained exclusively 16S rRNA-derived inserts. This selective approach is independent of biasing culture techniques and eliminates the laborious screening required to locate 16S rRNA gene-bearing recombinants in genomic DNA libraries obtained from natural communities. PMID:16347975

  8. Alpha beta T-cell development is not affected by inversion of TCR beta gene enhancer sequences: polar enhancement of gene expression regardless of enhancer orientation.

    PubMed

    Huang, Fang; Cabaud, Olivier; Verthuy, Christophe; Hueber, Anne-Odile; Ferrier, Pierre

    2003-08-01

    V(D)J recombination and expression of the T-cell receptor beta (TCRbeta) gene are required for the development of the alphabeta T lymphocyte lineage. These processes depend on a transcriptional enhancer (Ebeta) which acts preferentially on adjacent upstream sequences, and has little impact on the 5' distal and 3' proximal regions of the TCRbeta locus. Using knock-in mice, we show that alphabeta T-cell differentiation and TCRbeta gene recombination and expression are not sensitive to the orientation of Ebeta sequences. We discuss the implication of these results regarding the mode of enhancer function at this locus during T lymphocyte development.

  9. 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.

  10. 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

  11. 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

  12. 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).

  13. 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

  14. 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.

  15. 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

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

    PubMed

    Branciamore, Sergio; Di Giulio, Massimo

    2012-04-01

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

  18. Cardiac deformation recovery via incompressible transformation decomposition

    NASA Astrophysics Data System (ADS)

    Skrinjar, Oskar; Bistoque, Arnaud

    2005-04-01

    This paper presents a method for automated deformation recovery of the left and right ventricular wall from a time sequence of anatomical images of the heart. The deformation is recovered within the heart wall, i.e. it is not limited only to the epicardium and endocardium. Most of the suggested methods either ignore or approximately model incompressibility of the heart wall. This physical property of the cardiac muscle is mathematically guaranteed to be satisfied by the proposed method. A scheme for decomposition of a complex incompressible geometric transformation into simpler components and its application to cardiac deformation recovery is presented. A general case as well as an application specific solution is discussed. Furthermore, the manipulation of the constructed incompressible transformations, including the computation of the inverse transformation, is computationally inexpensive. The presented method is mathematically guaranteed to generate incompressible transformations which are experimentally shown to be a very good approximation of actual cardiac deformations. The transformation representation has a relatively small number of parameters which leads to a fast deformation recovery. The approach was tested on six sequences of two-dimensional short-axis cardiac MR images. The cardiac deformation was recovered with an average error of 1.1 pixel. The method is directly extendable to three dimensions and to the entire heart.

  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. Inverse anticipating chaos synchronization.

    PubMed

    Shahverdiev, E M; Sivaprakasam, S; Shore, K A

    2002-07-01

    We derive conditions for achieving inverse anticipating synchronization where a driven time-delay chaotic system synchronizes to the inverse future state of the driver. The significance of inverse anticipating chaos in delineating synchronization regimes in time-delay systems is elucidated. The concept is extended to cascaded time-delay systems.

  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. Evaluation of magnetic resonance sequences in imaging mediastinal tumors

    SciTech Connect

    Webb, W.R.; Gamsu, G.; Stark, D.D.; Moon, K.L. Jr.; Moore, E.H.

    1984-10-01

    Ten patients having a mediastinal tumor were studied with magnetic resonance imaging (MRI) using from two to four imaging sequences. Seven had bronchial carcinoma and three had benign lesions. The sequences included the spin-echo technique with repetition time (TR) values of 0.5, 1.0, and 2.0 sec and echo time (TE) values of 28 and 56 msec, and the inversion-recovery technique. The signal-intensity ratios of the mediastinal mass and mediastinal fat, which are a measure of image contrast, were compared for the different imaging sequences. Also signal-to-noise ratios were measured relative to both mediastinal fat and mediastinal mass. With spin-echo imaging, decreasing the TR value resulted in an increase in mass/fat contrast in all patients, making the masses easier to detect, but this also resulted in decreased signal-to-noise ratios. Inversion-recovery imaging with the sequence used resulted in a greatly increased mass/fat contrast, because of a relative decrease in signal from the mass. Spin-echo imaging with both short and long TR values provides good tissue contrast and good signal-to-noise ratios.

  4. 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

  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. Seismic Inversion Methods

    NASA Astrophysics Data System (ADS)

    Jackiewicz, Jason

    2009-09-01

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

  7. 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.

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

    PubMed

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

    2007-01-01

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

  10. 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.

  11. 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

  12. Solar inverse theory

    NASA Astrophysics Data System (ADS)

    Gough, D.

    1984-12-01

    Helioseismological inversion, as with the inversion of any other data, is divided into three phases. The first is the solution of the so-called forward problem: namely, the calculation of the eigenfrequencies of a theoretical equilibrium state. The second is an attempt to understand the results, either empirically by determining how those frequencies vary as chosen parameters defining the equilibrium model are varied, or analytically from asymptotic expansions in limiting cases of high order or degree. The third phase is to pose and solve an inverse problem, which seeks to find a plausible equilibrium model of the Sun whose eigenfrequencies are consistent with observation. The three phases are briefly discussed in this review, and the third, which is not yet widely used in helioseismology, is illustrated with some selected inversions of artificial solar data.

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

    PubMed

    Cirulli, Elizabeth T; Noor, Mohamed A F

    2007-01-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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…

  18. Comparison of different pulse sequences for in vivo determination of T1 relaxation times in the human brain.

    PubMed

    Kjaer, L; Henriksen, O

    1988-01-01

    Quantitative in vivo determination of T1 relaxation times by magnetic resonance imaging (MRI) is hampered by several potential sources of error. This study focused on the influence of the radiofrequency pulse sequences applied with special attention to the significance of the repetition time (TR). T1 measurements were performed on the human brain using a whole body MR scanner operating at 1.5 tesla. Three different pulse sequences were compared including two 6-points inversion recovery (IR) sequences with TR = 2.0 s and 4.0, respectively, and a 12-points partial saturation inversion recovery (PSIR) sequence with TR varying between 0.24 and 8.0 s. The median T1 relaxation times obtained in cortical grey matter and cerebrospinal fluid were significantly shorter in the IR experiments at TR = 2 s than in those carried out at TR = 4 s. Concerning white matter the discrepancy was much less pronounced, but still statistically significant. Supplementary phantom measurements indicated that the higher T1 values are increasingly underestimated when TR is reduced to 2 s. The results suggest that the PSIR sequence or IR sequences with a TR greater than 2 X the T1 level of the tissue type investigated should be employed for accurate T1 determination by MRI in clinical work.

  19. Multifrequency inversion in magnetic resonance elastography.

    PubMed

    Papazoglou, Sebastian; Hirsch, Sebastian; Braun, Jürgen; Sack, Ingolf

    2012-04-21

    Time-harmonic shear wave elastography is capable of measuring viscoelastic parameters in living tissue. However, finite tissue boundaries and waveguide effects give rise to wave interferences which are not accounted for by standard elasticity reconstruction methods. Furthermore, the viscoelasticity of tissue causes dispersion of the complex shear modulus, rendering the recovered moduli frequency dependent. Therefore, we here propose the use of multifrequency wave data from magnetic resonance elastography (MRE) for solving the inverse problem of viscoelasticity reconstruction by an algebraic least-squares solution based on the springpot model. Advantages of the method are twofold: (i) amplitude nulls appearing in single-frequency standing wave patterns are mitigated and (ii) the dispersion of storage and loss modulus with drive frequency is taken into account by the inversion procedure, thereby avoiding subsequent model fitting. As a result, multifrequency inversion produces fewer artifacts in the viscoelastic parameter map than standard single-frequency parameter recovery and may thus support image-based viscoelasticity measurement. The feasibility of the method is demonstrated by simulated wave data and MRE experiments on a phantom and in vivo human brain. Implemented as a clinical method, multifrequency inversion may improve the diagnostic value of time-harmonic MRE in a large variety of applications.

  20. Multifrequency inversion in magnetic resonance elastography

    NASA Astrophysics Data System (ADS)

    Papazoglou, Sebastian; Hirsch, Sebastian; Braun, Jürgen; Sack, Ingolf

    2012-04-01

    Time-harmonic shear wave elastography is capable of measuring viscoelastic parameters in living tissue. However, finite tissue boundaries and waveguide effects give rise to wave interferences which are not accounted for by standard elasticity reconstruction methods. Furthermore, the viscoelasticity of tissue causes dispersion of the complex shear modulus, rendering the recovered moduli frequency dependent. Therefore, we here propose the use of multifrequency wave data from magnetic resonance elastography (MRE) for solving the inverse problem of viscoelasticity reconstruction by an algebraic least-squares solution based on the springpot model. Advantages of the method are twofold: (i) amplitude nulls appearing in single-frequency standing wave patterns are mitigated and (ii) the dispersion of storage and loss modulus with drive frequency is taken into account by the inversion procedure, thereby avoiding subsequent model fitting. As a result, multifrequency inversion produces fewer artifacts in the viscoelastic parameter map than standard single-frequency parameter recovery and may thus support image-based viscoelasticity measurement. The feasibility of the method is demonstrated by simulated wave data and MRE experiments on a phantom and in vivo human brain. Implemented as a clinical method, multifrequency inversion may improve the diagnostic value of time-harmonic MRE in a large variety of applications.

  1. Inversion of triton moments

    NASA Astrophysics Data System (ADS)

    Clare, R. B.; Levinger, J. S.

    1981-02-01

    We use the formalism of hyperspherical harmonics to calculate several moments for the triton photoeffect, for a Volkov spin-independent potential. First, we improve the accuracy of Maleki's calculations of the moments σ2 and σ3 by including more terms in the hyperspherical expansion. We also calculate moments σ0 and σ1 for a Serber mixture. We find reasonable agreement between our moments found by sum rules and those found from the cross sections calculated by Fang et al. and Levinger-Fitzgibbon. We then develop a technique of inversion of a finite number of moments by making the assumption that the cross section can be written as a sum of several Laguerre polynomials multiplied by a decreasing exponential. We test our inversion technique successfully on several model potentials. We then modify it and apply it to the five moments (σ-1 to σ3) for a force without exchange, and find fair agreement with Fang's values of the cross section. Finally, we apply the inversion technique to our three moments (σ-1,σ0,and σ1) for a Serber mixture, and find reasonable agreement with Gorbunov's measurements of the 3He photoeffect. NUCLEAR REACTIONS Triton photoeffects, hyperspherical harmonics, moments of photoeffect, inversion of moments.

  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. Inverse heat conduction problems

    NASA Astrophysics Data System (ADS)

    Orlande, Helcio Rangel Barreto

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

  4. Inverse Functions and their Derivatives.

    ERIC Educational Resources Information Center

    Snapper, Ernst

    1990-01-01

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

  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. Population genomics of inversion polymorphisms in Drosophila melanogaster.

    PubMed

    Corbett-Detig, Russell B; Hartl, Daniel L

    2012-01-01

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

  7. Spontaneous Recovery

    ERIC Educational Resources Information Center

    Rescorla, Robert A.

    2004-01-01

    Spontaneous recovery from extinction is one of the most basic phenomena of Pavlovian conditioning. Although it can be studied by using a variety of designs, some procedures are better than others for identifying the involvement of underlying learning processes. A wide range of different learning mechanisms has been suggested as being engaged by…

  8. Chromosome inversion polymorphisms influence morphological traits in Trimerotropis pallidipennis (Orthoptera).

    PubMed

    Colombo, P C

    2002-04-01

    Trimerotropis pallidipennis is a New World grasshopper whose South-American populations are polymorphic for six pericentric inversions. Previous work has demonstrated that the frequences of these inversions correlate with climatic variables, and hence a possible adaptive pattern was put forward. In the present work we analysed a sample of a natural population of T pallidipennis to ascertain whether the chromosomal inversions have effects on exophenotypes. Two hundred and sixty-eight males coming from a natural population at Uspallata, Mendoza Province, Argentina were analysed, and it was observed that most inversions had significant effects on phenotypes. Furthermore, some body size-related characteristics (such as tegmina length) were correlated with the number of inversions. Individuals from populations at higher altitude or latitude (i.e., at lower minimum temperatures), along with higher frequencies of standard sequences, were significantly smaller, and this coherence between interpopulational with intrapopulational results may indicate that the diminished body size of the standard sequence-carrying individuals may be caused by an effect of the inversions, or genes within the inversions, on body size. We finally put forward the hypothesis that reduced body size in a context of reduced minimum temperature may be a response to shortened development season, and so smaller individuals may be advantageous.

  9. The STIR sequence MRI in the assessment of extraocular muscles in thyroid eye disease.

    PubMed

    Hoh, H B; Laitt, R D; Wakeley, C; Kabala, J; Goddard, P; Potts, M J; Harrad, R A

    1994-01-01

    Nineteen patients with thyroid eye disease were examined with magnetic resonance imaging using the Short Tau Inversion Recovery (STIR) sequence and compared with normal controls. The Signal Intensity Ratio (SIR) of each of the four recti was obtained by comparison with the signal intensity of the adjacent temporalis muscle. The SIR was compared with disease activity assessed using Werner's grading system, a clinical inflammatory score, and the range of extraocular movements. Results show that a high SIR is associated with a high index of disease activity. This technique is likely to prove useful in assessing disease activity and planning the management of thyroid eye disease, particularly with respect to immunosuppression.

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

    PubMed Central

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

    2016-01-01

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

  12. Multiresolution MR elastography using nonlinear inversion

    PubMed Central

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

    2012-01-01

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

  13. Sensitive recovery of recombinant antibody clones after their in silico identification within NGS datasets.

    PubMed

    Spiliotopoulos, Anastasios; Owen, Jonathan P; Maddison, Ben C; Dreveny, Ingrid; Rees, Helen C; Gough, Kevin C

    2015-05-01

    Recently the analytical power of the latest high throughput next generation DNA sequencing platforms has been used to analyse phage that have been selected from the panning of large combinatorial libraries displaying either peptide or antibody ligands. This process, commonly referred to as next generation phage display (NGPD), allows the researcher to determine the identity of specific phage that are being enriched against an antigen target by analysis of the DNA sequence encoding the displayed ligand. This method bypasses several steps in conventional phage panning that include laborious colony picking and functional ligand screening. A downside of this approach is that the only output from such experiments is the DNA sequence information of such enriched phage particles. In the case of peptides, the peptide sequence can be synthesised directly and used for further screening; however this is more difficult with larger antibody fragments such as ScFvs. In the case of ScFvs, their coding sequence would have to be fully elucidated, synthesised and re-cloned before expression. We describe here the application of an inverse PCR-ligation methodology that enables the specific recovery of ScFvs of interest from enriched sub-libraries of phage clones. Phagemid particles are recovered using sequence information derived from their unique heavy chain CDR3/FR4 domains and specific clones can be recovered irrespective of CDR3 size and at levels of abundance that would be refractory to their discovery during conventional phage panning and screening. PMID:25771970

  14. Course of Recovery from Alcoholism

    PubMed Central

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

    2010-01-01

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

  15. 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

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

    PubMed

    Ma, Jianzhong; Amos, Christopher I

    2012-01-01

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

  17. Stress inversion assumptions review

    NASA Astrophysics Data System (ADS)

    Lejri, Mostfa; Maerten, Frantz; Maerten, Laurent; Joonnenkindt, Jean Pierre; Soliva, Roger

    2014-05-01

    Wallace (1951) and Bott (1959) were the first to introduce the idea that the slip on each fault surface has the same direction and sense as the maximum shear stress resolved on that surface. This hypothesis are based on the assumptions that (i) faults are planar, (ii) blocks are rigid, (iii) neither stress perturbations nor block rotations along fault surfaces occur and (iv), the applied stress state is uniform. However, this simplified hypothesis is questionable since complex fault geometries, heterogeneous fault slip directions, evidences of stress perturbations in microstructures and block rotations along fault surfaces were reported in the literature. Earlier numerical geomechanical models confirmed that the striation lines (slip vectors) are not necessarily parallel to the maximum shear stress vector but is consistent with local stress perturbations. This leads us to ask as to what extent the Wallace and Bott simplifications are reliable as a basis hypothesis for stress inversion. In this presentation, a geomechanical multi-parametric study using 3D boundary element method (BEM), covering (i) fault geometries such as intersected faults or corrugated fault surfaces, (ii) the full range of Andersonian state of stress, (iii) fault friction, (iv) half space effect and (v), rock properties, is performed in order to understand the effect of each parameter on the angular misfit between geomechanical slip vectors and the resolved shear stresses. It is shown that significant angular misfits can be found under specific configurations and therefore we conclude that stress inversions based on the Wallace-Bott hypothesis might sometime give results that should be interpreted with care. Major observations are that (i) applying optimum tectonic stress conditions on complex fault geometries can increase the angular misfit, (ii) elastic material properties, combined to half-space effect, can enhance this effect, and (iii) an increase of the sliding friction leads to a

  18. 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

  19. A recurrent inversion on the eutherian X chromosome

    PubMed Central

    Cáceres, Mario; Sullivan, Robert T.; Thomas, James W.

    2007-01-01

    Chromosomal inversions have an important role in evolution, and an increasing number of inversion polymorphisms are being identified in the human population. The evolutionary history of these inversions and the mechanisms by which they arise are therefore of significant interest. Previously, a polymorphic inversion on human chromosome Xq28 that includes the FLNA and EMD loci was discovered and hypothesized to have been the result of nonallelic homologous recombination (NAHR) between near-identical inverted duplications flanking this region. Here, we carried out an in-depth study of the orthologous region in 27 additional eutherians and report that this inversion is not specific to humans, but has occurred independently and repeatedly at least 10 times in multiple eutherian lineages. Moreover, inverted duplications flank the FLNA–EMD region in all 16 species for which high-quality sequence assemblies are available. Based on detailed sequence analyses, we propose a model in which the observed inverted duplications originated from a common duplication event that predates the eutherian radiation. Subsequent gene conversion homogenized the duplications, thereby providing a continuous substrate for NAHR that led to the recurrent inversion of this segment of the genome. These results provide an extreme example in support of the evolutionary breakpoint reusage hypothesis and point out that some near-identical human segmental duplications may, in fact, have originated >100 million years ago. PMID:18003915

  20. 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.

  1. 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.

  2. 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.

  3. Modular theory of inverse systems

    NASA Technical Reports Server (NTRS)

    1979-01-01

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

  4. Inversion exercises inspired by mechanics

    NASA Astrophysics Data System (ADS)

    Groetsch, C. W.

    2016-02-01

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

  5. 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.

  6. 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

  7. Polarization of inverse plasmon scattering

    NASA Technical Reports Server (NTRS)

    Windsor, R. A.; Kellogg, P. J.

    1974-01-01

    The scattering of electrostatic plasma waves by a flux of ultrarelativistic electrons passing through a plasma gives rise to a radiation spectrum which is similar to a synchrotron radiation spectrum. This mechanism, first considered by Gailitis and Tsytovich, is analagous to inverse Compton scattering, and we have named it inverse plasmon scattering. For a power-law electron flux, both inverse plasmon scattering and synchrotron radiation have the same spectral index. In an attempt to distinguish between these mechanisms, we have calculated the polarization level expected from inverse plasmon scattering. The polarization level found is similar to that obtained from a synchrotron radiation source. This means that the radiation produced by two mechanisms, synchrotron radiation and inverse plasmon scattering, is indistinguishable; and this attempt to differentiate between them by polarization effects has been unsuccessful.

  8. 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

  9. 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.

  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. 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…

  12. Stylolite stress inversion

    NASA Astrophysics Data System (ADS)

    Koehn, Daniel; Toussaint, Renaud; Ebner, Marcus; Gomez-Rivas, Enrique; Bons, Paul; Rood, Daisy

    2014-05-01

    Stylolites are localized dissolution seams that can be found in a variety of rocks, and can form due to sediment compaction or tectonic forces. Dissolution of the host-rock next to the stylolite is a function of the applied stress on the stylolite plane. Stylolite teeth indicate the direction of the main compressive stress. Recent advances have shown that the stylolite roughness also shows a stress scaling relation that can be used to calculate magnitudes of stress. Elastic and surface energies produce a different roughness, and the transition between the two is stress dependent and can be quantified. In order to measure the roughness a two or three-dimensional section of a stylolite plane is taken and transferred to a one-dimensional function. The cross-over in the roughness is then picked with the help of an FFT plot. Using this method the burial depth of sedimentary stylolites can be determined. Moreover, tectonic stylolites can be used to determine the full three-dimensional stress tensor if the paleodepth of the tectonic stylolite is known. Stylolites can also be used to find fault offsets and to understand when these faults were active and how the paleotopography looked like at the time the stylolites grew. However, uncertainties remain since Youngs Modulus, Poisson Ratio and surface energy may vary in rocks. In addition, the stylolites record only a snapshot in time, probably the moment when they closed and stopped dissolving. We show examples of the use of stress inversion for stylolite formation conditions in different tectonic settings, and discuss the potential of the method.

  13. Microwave inverse Cerenkov accelerator

    NASA Astrophysics Data System (ADS)

    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 TM01 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 5πmm-mrad. Experiments on sample alumina tubes have been conducted that verify the theoretical dispersion relation for the TM01 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.

  14. 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;…

  15. Temperature inversion in China seas

    NASA Astrophysics Data System (ADS)

    Hao, Jiajia; Chen, Yongli; Wang, Fan

    2010-12-01

    Temperature inversion was reported as a common phenomenon in the areas near the southeastern Chinese coast (region A), west and south of the Korean Peninsula (region B), and north and east of the Shandong Peninsula (region C) during October-May in the present study, based on hydrographic data archived from 1930 through 2001 (319,029 profiles). The inversion was found to be remarkable with obvious temporal and spatial variabilities in both magnitude and coverage, with higher probabilities in region A (up to about 60%) and region C (40%-50%) than in region B (15%-20%). The analysis shows that seasonal variation of the net air-sea heat flux is closely related to the occurrence time of the inversion in the three areas, while the Yangtze and Yellow river freshwater plumes in the surface layer and ocean origin saline water in the subsurface layer maintain stable stratification. It seems that the evaporation/excessive precipitation flux makes little contribution to maintaining the stable inversion. Advection of surface fresh water by the wind-driven coastal currents results in the expansion of inversion in regions A and C. The inversion lasts for the longest period in region A (October-May) sustained by the Taiwan Warm Current carrying the subsurface saline water, while evolution of the inversion in region B is mainly controlled by the Yellow Sea Warm Current.

  16. Givental Graphs and Inversion Symmetry

    NASA Astrophysics Data System (ADS)

    Dunin-Barkowski, Petr; Shadrin, Sergey; Spitz, Loek

    2013-05-01

    Inversion symmetry is a very non-trivial discrete symmetry of Frobenius manifolds. It was obtained by Dubrovin from one of the elementary Schlesinger transformations of a special ODE associated to a Frobenius manifold. In this paper, we review the Givental group action on Frobenius manifolds in terms of Feynman graphs and obtain an interpretation of the inversion symmetry in terms of the action of the Givental group. We also consider the implication of this interpretation of the inversion symmetry for the Schlesinger transformations and for the Hamiltonians of the associated principle hierarchy.

  17. Source Inversion Validation: Quantifying Uncertainties in Earthquake Source Inversions

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    Earthquake source inversions image the spatio-temporal rupture evolution on one or more fault planes using seismic and/or geodetic data. Source inversion methods thus represent an important research tool in seismology to unravel the complexity of earthquake ruptures. Subsequently, source-inversion results are used to study earthquake mechanics, to develop spontaneous dynamic rupture models, to build models for generating rupture realizations for ground-motion simulations, and to perform Coulomb-stress modeling. In all these applications, the underlying finite-source rupture models are treated as “data” (input information), but the uncertainties in these data (i.e. source models obtained from solving an inherently ill-posed inverse problem) are hardly known, and almost always neglected. The Source Inversion Validation (SIV) project attempts to better understand the intra-event variability of earthquake rupture models. We plan to build a long-standing and rigorous testing platform to examine the current state-of-the-art in earthquake source inversion that also facilitates to develop robust approaches to quantify rupture-model uncertainties. Our contribution reviews the current status of the SIV project, recent forward-modeling tests for point and extended sources in layered media, and discusses the strategy of the SIV-project for the coming years.

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

    SciTech Connect

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

    1986-12-01

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

  19. 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 ...

  20. 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.

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

    PubMed Central

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

    2015-01-01

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

  2. 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

  3. 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

  4. Testing earthquake source inversion methodologies

    USGS Publications Warehouse

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

    2011-01-01

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

  5. 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.

  6. Inversion layer MOS solar cells

    NASA Technical Reports Server (NTRS)

    Ho, Fat Duen

    1986-01-01

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

  7. 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)

  8. 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.

  9. Moebius inversion formula and inverting lattice sums

    NASA Astrophysics Data System (ADS)

    Millane, Rick P.

    2000-11-01

    The Mobius inversion formula is an interesting theorem from number theory that has application to a number inverse problems, particularly lattice problems. Specific inverse problems, however, often require related Mobius inversion formulae that can be derived from the fundamental formula. Derivation of such formulae is not easy for the non- specialist, however. Examples of the kinds of inversion formulae that can be derived and their application to inverse lattice problems are described.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. Directional genomic hybridization for chromosomal inversion discovery and detection.

    PubMed

    Ray, F Andrew; Zimmerman, Erin; Robinson, Bruce; Cornforth, Michael N; Bedford, Joel S; Goodwin, Edwin H; Bailey, Susan M

    2013-04-01

    Chromosomal rearrangements are a source of structural variation within the genome that figure prominently in human disease, where the importance of translocations and deletions is well recognized. In principle, inversions-reversals in the orientation of DNA sequences within a chromosome-should have similar detrimental potential. However, the study of inversions has been hampered by traditional approaches used for their detection, which are not particularly robust. Even with significant advances in whole genome approaches, changes in the absolute orientation of DNA remain difficult to detect routinely. Consequently, our understanding of inversions is still surprisingly limited, as is our appreciation for their frequency and involvement in human disease. Here, we introduce the directional genomic hybridization methodology of chromatid painting-a whole new way of looking at structural features of the genome-that can be employed with high resolution on a cell-by-cell basis, and demonstrate its basic capabilities for genome-wide discovery and targeted detection of inversions. Bioinformatics enabled development of sequence- and strand-specific directional probe sets, which when coupled with single-stranded hybridization, greatly improved the resolution and ease of inversion detection. We highlight examples of the far-ranging applicability of this cytogenomics-based approach, which include confirmation of the alignment of the human genome database and evidence that individuals themselves share similar sequence directionality, as well as use in comparative and evolutionary studies for any species whose genome has been sequenced. In addition to applications related to basic mechanistic studies, the information obtainable with strand-specific hybridization strategies may ultimately enable novel gene discovery, thereby benefitting the diagnosis and treatment of a variety of human disease states and disorders including cancer, autism, and idiopathic infertility.

  16. 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.

  17. TR-IA payload recovery system

    NASA Astrophysics Data System (ADS)

    Kochiyama, Jiro; Kinai, Shigeki; Morita, Shinya

    The TR-IA microgravity-experimentation sounding rocket baseline configuration and recovery system are presented. Aerodynamic braking is incorporated through the requisite positioning of the reentry-body center of gravity. The recovery sequence is initiated by baroswitches, which eject the pilot chute. Even in the event of flotation bag malfunction, the structure containing the experiment is watertight. An account is given of the nature and the results of the performance tests conducted to establish the soundness of various materials and components.

  18. 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.

  19. 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

  20. Inversion tectonics in the Maracaibo area, Venezuela

    SciTech Connect

    Roberta, M. ); Duval, B.; Cramez, C.

    1993-02-01

    Sequence stratigraphy and structural interpretation of regional composite seismic lines and new 3D seismic data of Lake Maracaibo lead us to question the old [open quotes]strike-slip fault movement[close quotes] geological paradigm as the major cause of deformation in this area. The pre-Miocene compressional structures of the majority of the oil fields of this area such as Ceuta, Lama, Motatan, etc., are easily and better explained as the result of a Tertiary Tectonic Inversion. Such inversion can be interpreted as a consequence of shortening of [open quotes]depocenters[close quotes] (grabens and half grabens) developed during extensional phases of a back-arc basin. During this shortening, the old faults bordering the [open quotes]depocenters[close quotes] were reactivated with reverse movements creating large compressional structural traps in the hanging wall (old downthrown block). Thin-skinned compressional deformation can occur, locally, outside the major [open quotes]depocenters[close quotes] in the footwall areas between faults of opposite vergence.

  1. 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.

  2. 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.

  3. Inversion strategies for visco-acoustic waveform inversion

    NASA Astrophysics Data System (ADS)

    Kamei, R.; Pratt, R. G.

    2013-08-01

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

  4. Water Recovery Systems for Exploration Missions

    NASA Technical Reports Server (NTRS)

    Pickering, Karen D.

    2007-01-01

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

  5. 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.

  6. Image quality assessment of the right ventricle with three different delayed enhancement sequences in patients suspected of ARVC/D.

    PubMed

    Plaisier, A S; Burgmans, M C; Vonken, E P A; Prakken, N H; Cox, M G P J; Hauer, R N; Velthuis, B K; Cramer, M J M

    2012-03-01

    Histopathologic findings in arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) are replacement of the normal myocardium with fatty and fibrous elements with preferential involvement of the right ventricle. The right ventricular fibrosis can be visualised by post-gadolinium delayed enhancement inversion recovery imaging (DE imaging). We compared the image quality of three different gradient echo MRI sequences for short axis DE imaging of the right ventricle (RV). We retrospectively analysed MRI scans performed between February 2005 and December 2008 in 97 patients (mean age: 41.2 years, 67% men) suspected of ARVC/D. For DE imaging either a 2D Phase Sensitive (PSIR), a 2D (2D) or a 3D (3D) inversion recovery sequence was used in respectively 38, 32 and 27 MRI-examinations. The RV, divided in 10 segments, was assessed for image quality by two radiologists in random sequence. A consensus reading was performed if results differed between the two readings. Image quality was good in 24% of all segments in the 3D group, 66% in the 2D group and 79% in the PSIR group. Poor image quality was observed in 51% (3D), 10% (2D), and 2% (PSIR) of all segments. Exams were considered suitable for clinical use in 7% of exams in the 3D group, 75% of exams in the 2D group and 90% of exams of the PSIR group. Breathing-artifacts occurred in 22% (3D), 59% (2D) and 53% (PSIR). Motion-artifacts occurred in 56% (3D), 28% (2D) and 29% (PSIR). Post-gadolinium imaging using the PSIR sequence results in better and more consistent image quality of the RV compared to the 2D and 3D sequences.

  7. 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.

  8. 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.

  9. Population inversion by chirped pulses

    SciTech Connect

    Lu Tianshi

    2011-09-15

    In this paper, we analyze the condition for complete population inversion by a chirped pulse over a finite duration. The nonadiabatic transition probability is mapped in the two-dimensional parameter space of coupling strength and detuning amplitude. Asymptotic forms of the probability are derived by the interference of nonadiabatic transitions for sinusoidal and triangular pulses. The qualitative difference between the maps for the two types of pulses is accounted for. The map is used for the design of stable inversion pulses under specific accuracy thresholds.

  10. 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.

  11. 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.

  12. PURR-TURBO: a novel pulse sequence for longitudinal relaxographic imaging.

    PubMed

    Lee, J H

    2000-05-01

    A novel pulse sequence based on a segmented phase-encoding scheme for measuring the longitudinal relaxation time (T(1)) value of an NMR signal in an imaging context is introduced. This pulse sequence is a hybrid version of the "single-shot" and "one-shot" inversion recovery (IR) snapshot-FLASH methods. These are also known as "multipoint" IR techniques. The new sequence presented here collects multiple k-space rows at each time point during magnetization recovery, rather than the entire dataset (as in a "single-shot" method) or just one row (as in a "one-shot" method). Thus, it reduces the scanning time without significant sacrifice of the small sampling time advantage of the one-shot IR snapshot-FLASH methods. Furthermore, this approach does not require a high-performance gradient system. Here, we demonstrate that a single slice human brain (1)H(2)O T(1) map with a nominal in-plane resolution of less than (1 mm)2can be obtained at 4 T in about 4 min. Published 2000 Wiley-Liss, Inc.

  13. Inversions. Popular Lectures in Mathematics.

    ERIC Educational Resources Information Center

    Bakel'man, I. Ya

    Inversions are transformations of geometric figures, under which straight lines may be mapped to circles, and conversely. The use of such mapping allows development of a unified method of solution for many of the problems of elementary geometry, especially those concerning constructions and "pencils" of curves. This book discusses the inversion…

  14. 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…

  15. 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.

  16. Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura.

    PubMed

    Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2013-01-01

    Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura--inversion 3 of the O chromosome--in a population sample. The breakpoints could be identified as two rather short fragments (∼300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ∼300-bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double-strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species-group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high-turnover fragment within a long collinear region (∼300 kb).

  17. The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus.

    PubMed

    Szamalek, Justyna M; Goidts, Violaine; Searle, Jeremy B; Cooper, David N; Hameister, Horst; Kehrer-Sawatzki, Hildegard

    2006-01-01

    Seven of nine pericentric inversions that distinguish human (HSA) and chimpanzee karyotypes are chimpanzee-specific. In this study we investigated whether the two extant chimpanzee species, Pan troglodytes (common chimpanzee) and Pan paniscus (bonobo), share exactly the same pericentric inversions. The methods applied were FISH with breakpoint-spanning BAC/PAC clones and PCR analyses of the breakpoint junction sequences. Our findings for the homologues to HSA 4, 5, 9, 12, 16, and 17 confirm for the first time at the sequence level that these pericentric inversions have identical breakpoints in the common chimpanzee and the bonobo. Therefore, these inversions predate the separation of the two chimpanzee species 0.86-2 Mya. Further, the inversions distinguishing human and chimpanzee karyotypes may be regarded as early acquisitions, such that they are likely to have been present at the time of human/chimpanzee divergence. According to the chromosomal speciation theory the inversions themselves could have promoted human speciation.

  18. Applications of inverse pattern projection

    NASA Astrophysics Data System (ADS)

    Li, Wansong; Bothe, Thorsten; Kalms, Michael K.; von Kopylow, Christoph; Jueptner, Werner P. O.

    2003-05-01

    Fast and robust 3D quality control as well as fast deformation measurement is of particular importance for industrial inspection. Additionally a direct response about measured properties is desired. Therefore, robust optical techniques are needed which use as few images as possible for measurement and visualize results in an efficient way. One promising technique for this aim is the inverse pattern projection which has the following advantages: The technique codes the information of a preceding measurement into the projected inverse pattern. Thus, it is possible to do differential measurements using only one camera frame for each state. Additionally, the results are optimized straight fringes for sampling which are independent of the object curvature. The hardware needs are low as just a programmable projector and a standard camera are necessary. The basic idea of inverse pattern projection, necessary algorithms and found optimizations are demonstrated, roughly. Evaluation techniques were found to preserve a high quality phase measurement under imperfect conditions. The different application fields can be sorted out by the type of pattern used for inverse projection. We select two main topics for presentation. One is the incremental (one image per state) deformation measurement which is a promising technique for high speed deformation measurements. A video series of a wavering flag with projected inverse pattern was evaluated to show the complete deformation series. The other application is the optical feature marking (augmented reality) that allows to map any measured result directly onto the object under investigation. Any properties can be visualized directly on the object"s surface which makes inspections easier than with use of a separated indicating device. The general ability to straighten any kind of information on 3D surfaces is shown while preserving an exact mapping of camera image and object parts. In many cases this supersedes an additional monitor to

  19. 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.

  20. Recovery Act Milestones

    ScienceCinema

    Rogers, Matt

    2016-07-12

    Every 100 days, the Department of Energy is held accountable for a progress report on the American Recovery and Reinvestment Act. Update at 200 days, hosted by Matt Rogers, Senior Advisor to Secretary Steven Chu for Recovery Act Implementation.

  1. 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.

  2. MR Imaging with Metal-suppression Sequences for Evaluation of Total Joint Arthroplasty.

    PubMed

    Talbot, Brett S; Weinberg, Eric P

    2016-01-01

    Metallic artifact at orthopedic magnetic resonance (MR) imaging continues to be an important problem, particularly in the realm of total joint arthroplasty. Complications often follow total joint arthroplasty and can be expected for a small percentage of all implanted devices. Postoperative complications involve not only osseous structures but also adjacent soft tissues-a highly problematic area at MR imaging because of artifacts from metallic prostheses. Without special considerations, susceptibility artifacts from ferromagnetic implants can unacceptably degrade image quality. Common artifacts include in-plane distortions (signal loss and signal pileup), poor or absent fat suppression, geometric distortion, and through-section distortion. Basic methods to reduce metallic artifacts include use of spin-echo or fast spin-echo sequences with long echo train lengths, short inversion time inversion-recovery (STIR) sequences for fat suppression, a high bandwidth, thin section selection, and an increased matrix. With care and attention to the alloy type (eg, titanium, cobalt-chromium, stainless steel), orientation of the implant, and magnetic field strength, as well as use of proprietary and nonproprietary metal-suppression techniques, previously nondiagnostic studies can yield key diagnostic information. Specifically, sequences such as the metal artifact reduction sequence (MARS), WARP (Siemens Healthcare, Munich, Germany), slice encoding for metal artifact correction (SEMAC), and multiacquisition with variable-resonance image combination (MAVRIC) can be optimized to reveal pathologic conditions previously hidden by periprosthetic artifacts. Complications of total joint arthroplasty that can be evaluated by using MR imaging with metal-suppression sequences include pseudotumoral conditions such as metallosis and particle disease, infection, aseptic prosthesis loosening, tendon injury, and muscle injury.

  3. 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.

  4. 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…

  5. 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…

  6. Ultrahigh-intensity inverse bremsstrahlung

    NASA Astrophysics Data System (ADS)

    Kostyukov, I. Yu.; Rax, J.-M.

    1999-01-01

    We study inverse bremsstrahlung in the ultrahigh intensity relativistic regime. The fully relativistic ultrahigh intensity absorption (emission) coefficient is derived for an arbitrary scattering potential and small-angle scattering. We find that in the Coulomb field case this absorption (emission) coefficient can be calculated as a function of the quiver energy, drift momentum, and impact parameter in two complementary regimes: (i) for remote collisions when the impact parameter is larger than the amplitude of the quiver motion, and (ii) for instantaneous collisions when the scattering time is shorter than the period of the wave. Both circular and linear polarizations are considered, and this study reveals that in this relativistic regime inverse bremsstrahlung absorption can be viewed as a harmonic Compton resonance heating of the laser-driven electron by the virtual photon of the ion Coulomb field. The relativistic modification of Marcuse's effect [Bell Syst. Tech. J. 41, 1557 (1962)] are also discussed, and relations with previous nonrelativistic results are elucidated.

  7. 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.

  8. Momentum resolution in inverse photoemission.

    PubMed

    Zumbülte, A; Schmidt, A B; Donath, M

    2015-01-01

    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. 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.

  10. 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

  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. Inversions for axisymmetric galactic disks

    NASA Astrophysics Data System (ADS)

    Hiotelis, N.; Patsis, P. A.

    1993-08-01

    We use two models for the distribution function to solve an inverse problem for axisymmetric disks. These systems may be considered - under certain assumptions - as galactic disks. In some cases the solutions of the resulting integral equations are simple, which allows the determination of the kinematic properties of self-consistent models for these systems. These properties for then = 1 Toomre disk are presented in this study.

  13. 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.

  14. Phenomenological description of phase inversion.

    PubMed

    Piela, K; Ooms, G; Sengers, J V

    2009-02-01

    We propose an extended Ginzburg-Landau model for a description of the ambivalence region associated with the phenomenon of phase inversion observed in dispersed water-oil flow through a pipe. In analogy to the classical mean-field theory of phase transitions, it is shown that a good quantitative representation of the ambivalence region is obtained by using the injected phase volume fraction and a friction factor as the appropriate physical parameters.

  15. 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%.

  16. 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.

  17. 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…

  18. Recombination rate predicts inversion size in Diptera.

    PubMed

    Cáceres, M; Barbadilla, A; Ruiz, A

    1999-09-01

    Most species of the Drosophila genus and other Diptera are polymorphic for paracentric inversions. A common observation is that successful inversions are of intermediate size. We test here the hypothesis that the selected property is the recombination length of inversions, not their physical length. If so, physical length of successful inversions should be negatively correlated with recombination rate across species. This prediction was tested by a comprehensive statistical analysis of inversion size and recombination map length in 12 Diptera species for which appropriate data are available. We found that (1) there is a wide variation in recombination map length among species; (2) physical length of successful inversions varies greatly among species and is inversely correlated with the species recombination map length; and (3) neither the among-species variation in inversion length nor the correlation are observed in unsuccessful inversions. The clear differences between successful and unsuccessful inversions point to natural selection as the most likely explanation for our results. Presumably the selective advantage of an inversion increases with its length, but so does its detrimental effect on fertility due to double crossovers. Our analysis provides the strongest and most extensive evidence in favor of the notion that the adaptive value of inversions stems from their effect on recombination.

  19. Recombination rate predicts inversion size in Diptera.

    PubMed Central

    Cáceres, M; Barbadilla, A; Ruiz, A

    1999-01-01

    Most species of the Drosophila genus and other Diptera are polymorphic for paracentric inversions. A common observation is that successful inversions are of intermediate size. We test here the hypothesis that the selected property is the recombination length of inversions, not their physical length. If so, physical length of successful inversions should be negatively correlated with recombination rate across species. This prediction was tested by a comprehensive statistical analysis of inversion size and recombination map length in 12 Diptera species for which appropriate data are available. We found that (1) there is a wide variation in recombination map length among species; (2) physical length of successful inversions varies greatly among species and is inversely correlated with the species recombination map length; and (3) neither the among-species variation in inversion length nor the correlation are observed in unsuccessful inversions. The clear differences between successful and unsuccessful inversions point to natural selection as the most likely explanation for our results. Presumably the selective advantage of an inversion increases with its length, but so does its detrimental effect on fertility due to double crossovers. Our analysis provides the strongest and most extensive evidence in favor of the notion that the adaptive value of inversions stems from their effect on recombination. PMID:10471710

  20. 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.

  1. 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.

  2. A survey of microwave inverse FEL and inverse cerenkov accelerators

    NASA Astrophysics Data System (ADS)

    Marshall, T. C.; Zhang, T. B.

    1997-02-01

    A Microwave Inverse FEL Accelerator (MIFELA) and a Microwave Inverse Cerenkov Accelerator (MICA) are currently under construction at the Yale Beam Physics Laboratory. MIFELA and MICA will share the same injector, a thermionic cathode rf gun that should furnish 5 psec, 6 MeV, 0.2 nC electron pulses spaced by 350 psec, using microwave power of many MW provided from a 2.85 GHz klystron. MIFELA is to operate with ˜4 Mw of 11.4 GHz microwave power in the TE11 mode, with beam injection into each fourth rf cycle; a variable pitch and field undulator together with a guide magnetic field are present as well. MICA will operate at 2.85 GHz using an alumina-lined waveguide driven in the TM01 mode; the phase velocity is just below c, with no guide field. MIFELA produces a beam of spiralling electrons, while MICA makes an axially-directed beam. This is a survey of the operating principles of these smooth-bore "tabletop" accelerators (˜15 MeV) as they are understood prior to operation.

  3. 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.

  4. 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.

  5. Lightcurve Inversion for 65 Cybele

    NASA Astrophysics Data System (ADS)

    Franco, Lorenzo; Pilcher, Frederick

    2015-07-01

    We present a shape and spin axis model for main-belt asteroid 65 Cybele. The model was obtained with lightcurve inversion process, using combined dense photometric data obtained during fifteen apparitions from 1977 to 2014 and sparse data from USNO Flagstaff. Analysis of the resulting data found a sidereal period P = 6.081434 ± 0.000005 hours and two possible pole solutions: (l = 208°, b = -7°) and (l = 27°, b = -14°) with an error of ±15 degrees.

  6. Topography of retinal recovery processes in humans

    PubMed Central

    Mazinani, Babac E; Merx, Elke; Plange, Niklas; Walter, Peter; Roessler, Gernot F

    2014-01-01

    Background The purpose of this study was to examine retinal recovery processes to pographically by the application of three flash sequences with specific interstimulus intervals. Methods Twelve healthy subjects underwent multifocal electroretinography with a light-emitting diode stimulator. Every flash sequence consisted of three flashes with 25 msec between the first and the second flash and 35 msec between the second and the third flash. The interval between the third and the first flash of the next step was 85 msec. The interstimulus interval-dependent amplitude reductions of the multifocal electroretinographic response for these three intervals yielded three data points that were used to determine the complete curve of the recovery kinetics. Results Amplitude reductions were higher with shorter interstimulus intervals. The mean half-life periods of the recovery kinetics for the different concentric rings and all subjects were: ring 1, 29.3±5.9 msec; ring 2, 24.2±6.4 msec; ring 3, 23±4.1 msec; ring 4, 23.1±4.6 msec; and ring 5, 22.3±4.4 msec. The differences between the first and all other rings were statistically significant (P<0.05). Conclusion The kinetics of the amplitude recovery after short interstimulus intervals showed a spatial distribution, with faster recovery toward the macular periphery. PMID:25349472

  7. 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.

  8. Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation.

    PubMed

    Rane, Rahul V; Rako, Lea; Kapun, Martin; Lee, Siu F; Hoffmann, Ary A

    2015-05-01

    Chromosomal inversion polymorphisms are common in animals and plants, and recent models suggest that alternative arrangements spread by capturing different combinations of alleles acting additively or epistatically to favour local adaptation. It is also thought that inversions typically maintain favoured combinations for a long time by suppressing recombination between alternative chromosomal arrangements. Here, we consider patterns of linkage disequilibrium and genetic divergence in an old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known to be associated with climate change adaptation and a recent invasion event into Australia. We extracted, karyotyped and sequenced whole chromosomes from two Australian populations, so that changes in the arrangement of the alleles between geographically separated tropical and temperate areas could be compared. Chromosome-wide linkage disequilibrium (LD) analysis revealed strong LD within the region spanned by In(3R)Payne. This genomic region also showed strong differentiation between the tropical and the temperate populations, but no differentiation between different karyotypes from the same population, after controlling for chromosomal arrangement. Patterns of differentiation across the chromosome arm and in gene ontologies were enhanced by the presence of the inversion. These data support the notion that inversions are strongly selected by bringing together combinations of genes, but it is still not clear if such combinations act additively or epistatically. Our data suggest that climatic adaptation through inversions can be dynamic, reflecting changes in the relative abundance of different forms of an inversion and ongoing evolution of allelic content within an inversion.

  9. Three-dimensional magnetotelluric inversion in practice—the electrical conductivity structure of the San Andreas Fault in Central California

    NASA Astrophysics Data System (ADS)

    Tietze, Kristina; Ritter, Oliver

    2013-10-01

    3-D inversion techniques have become a widely used tool in magnetotelluric (MT) data interpretation. However, with real data sets, many of the controlling factors for the outcome of 3-D inversion are little explored, such as alignment of the coordinate system, handling and influence of data errors and model regularization. Here we present 3-D inversion results of 169 MT sites from the central San Andreas Fault in California. Previous extensive 2-D inversion and 3-D forward modelling of the data set revealed significant along-strike variation of the electrical conductivity structure. 3-D inversion can recover these features but only if the inversion parameters are tuned in accordance with the particularities of the data set. Based on synthetic 3-D data we explore the model space and test the impacts of a wide range of inversion settings. The tests showed that the recovery of a pronounced regional 2-D structure in inversion of the complete impedance tensor depends on the coordinate system. As interdependencies between data components are not considered in standard 3-D MT inversion codes, 2-D subsurface structures can vanish if data are not aligned with the regional strike direction. A priori models and data weighting, that is, how strongly individual components of the impedance tensor and/or vertical magnetic field transfer functions dominate the solution, are crucial controls for the outcome of 3-D inversion. If deviations from a prior model are heavily penalized, regularization is prone to result in erroneous and misleading 3-D inversion models, particularly in the presence of strong conductivity contrasts. A `good' overall rms misfit is often meaningless or misleading as a huge range of 3-D inversion results exist, all with similarly `acceptable' misfits but producing significantly differing images of the conductivity structures. Reliable and meaningful 3-D inversion models can only be recovered if data misfit is assessed systematically in the frequency

  10. 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.

  11. 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.

  12. 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.

  13. Targeted chromosomal deletions and inversions in zebrafish.

    PubMed

    Gupta, Ankit; Hall, Victoria L; Kok, Fatma O; Shin, Masahiro; McNulty, Joseph C; Lawson, Nathan D; Wolfe, Scot A

    2013-06-01

    Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) provide powerful platforms for genome editing in plants and animals. Typically, a single nuclease is sufficient to disrupt the function of protein-coding genes through the introduction of microdeletions or insertions that cause frameshifts within an early coding exon. However, interrogating the function of cis-regulatory modules or noncoding RNAs in many instances requires the excision of this element from the genome. In human cell lines and invertebrates, two nucleases targeting the same chromosome can promote the deletion of intervening genomic segments with modest efficiencies. We have examined the feasibility of using this approach to delete chromosomal segments within the zebrafish genome, which would facilitate the functional study of large noncoding sequences in a vertebrate model of development. Herein, we demonstrate that segmental deletions within the zebrafish genome can be generated at multiple loci and are efficiently transmitted through the germline. Using two nucleases, we have successfully generated deletions of up to 69 kb at rates sufficient for germline transmission (1%-15%) and have excised an entire lincRNA gene and enhancer element. Larger deletions (5.5 Mb) can be generated in somatic cells, but at lower frequency (0.7%). Segmental inversions have also been generated, but the efficiency of these events is lower than the corresponding deletions. The ability to efficiently delete genomic segments in a vertebrate developmental system will facilitate the study of functional noncoding elements on an organismic level.

  14. Multi-Skip Tomographic Inversion

    NASA Astrophysics Data System (ADS)

    Volker, Arno; Bloom, Joost; Lorenz, Maarten

    2011-06-01

    Inspection of corrosion at pipe support locations is difficult because of accessibility limitations. Recently a screening technique has been developed called Multi-Skip ultrasonics. The method utilizes a pitch-catch set-up. Shear waves are transmitted that reflect multiple times in the pipe wall, from which integral wall thickness information is obtained. The method turns out to be very sensitive in detecting the presence of wall loss, but it turns out to be difficult to determine the extent of the wall loss. If the extent is not known, only a conservative estimate of depth can be derived from the Multi-Skip signals, because of the accumulative nature of the change in arrival time due to wall loss. Multi-Skip tomography appears to be a promising method in addition to Multi-Skip screening as a follow-up inspection technique. It uses full wave field inversion to determine a wall thickness profile at a particular location of the pipe on the support. As with the Multi-Skip screening method, Multi-Skip tomography is applied with the transmitter and receiver on both sides of the pipe support location and waves traveling in the axial pipe direction. The wave field inversion consists of a forward modeling step that predicts the measured wave field after which an iterative comparison process with the actually measured wave field results in an estimate of the wall thickness profile under the support.

  15. Sparsity in Bayesian inversion of parametric operator equations

    NASA Astrophysics Data System (ADS)

    Schillings, Cl; Schwab, Ch

    2014-06-01

    We establish posterior sparsity in Bayesian inversion for systems governed by operator equations with distributed parameter uncertainty subject to noisy observation data δ. We generalize the results and algorithms introduced in C Schillings and C Schwab (2013 Inverse Problems 29 065011) for the particular case of scalar diffusion problems with random coefficients to broad classes of forward problems, including general elliptic and parabolic operators with uncertain coefficients, and in random domains. For countably parametric, deterministic representations of uncertain parameters in the forward problem, which belong to a specified sparsity class, we quantify analytic regularity of the likewise countably parametric, deterministic Bayesian posterior density with respect to a uniform prior on the uncertain parameter sequences and prove that the parametric, deterministic density of the Bayesian posterior belongs to the same sparsity class. Generalizing C Schillings and C Schwab (2013 Inverse Problems 29 065011) and C Schwab and A M Stuart (2012 Inverse Problems 28 045003) the forward problems are converted to countably parametric, deterministic operator equations. Computational Bayesian inversion amounts to numerically evaluating expectations of quantities of interest (QoIs) under the Bayesian posterior, conditional on noisy observation data. Our results imply, on the one hand, sparsity of Legendre (generalized) polynomial chaos expansions of the density of the Bayesian posterior with respect to uniform prior and, on the other hand, convergence rates for data-adaptive Smolyak integration algorithms for computational Bayesian estimation, which are independent of the dimension of the parameter space. We prove, mathematically and computationally, that for uncertain inputs with sufficient sparsity convergence rates are, in particular, superior to Markov chain Monte-Carlo sampling of the posterior, in terms of the number N of instances of the parametric forward problem to

  16. Geophysical Inversion through Hierarchical Genetic Algorithm Scheme

    NASA Astrophysics Data System (ADS)

    Furman, Alex; Huisman, Johan A.

    2010-05-01

    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 halts these methods from becoming of more quantitative use. 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. One way to overcome these problems is to combine the advantages of both direct and global inversion methods through hierarchical inversion. That is, starting the inversion with relatively coarse resolution of parameters, achieving good inversion using one of the two inversion schemes (global or direct), and then refining the resolution and applying a combination of global and direct inversion schemes for the whole domain or locally. In this work we explore through synthetic case studies the option of using a global optimization scheme for inversion of electrical resistivity tomography data through hierarchical refinement of the model resolution.

  17. Wideband Arrhythmia-Insensitive-Rapid (AIR) Pulse Sequence for Cardiac T1 mapping without Image Artifacts induced by ICD

    PubMed Central

    Hong, KyungPyo; Jeong, Eun-Kee; Wall, T. Scott; Drakos, Stavros G.; Kim, Daniel

    2015-01-01

    Purpose To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). Methods We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz), in order to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and “wideband” AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5T. Results In 5 phantoms representing native myocardium and blood and post-contrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error >29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error <5%). Similarly, in 11 human subjects, compared with the control T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error >10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error <2.0%). Conclusion This study demonstrates the feasibility of a wideband pulse sequence for cardiac T1 mapping without significant image artifacts induced by ICD. PMID:25975192

  18. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence.

    PubMed

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-03-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  19. Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence

    PubMed Central

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-01-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6–24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  20. Wake Vortex Inverse Model User's Guide

    NASA Technical Reports Server (NTRS)

    Lai, David; Delisi, Donald

    2008-01-01

    NorthWest Research Associates (NWRA) has developed an inverse model for inverting landing aircraft vortex data. The data used for the inversion are the time evolution of the lateral transport position and vertical position of both the port and starboard vortices. The inverse model performs iterative forward model runs using various estimates of vortex parameters, vertical crosswind profiles, and vortex circulation as a function of wake age. Forward model predictions of lateral transport and altitude are then compared with the observed data. Differences between the data and model predictions guide the choice of vortex parameter values, crosswind profile and circulation evolution in the next iteration. Iterations are performed until a user-defined criterion is satisfied. Currently, the inverse model is set to stop when the improvement in the rms deviation between the data and model predictions is less than 1 percent for two consecutive iterations. The forward model used in this inverse model is a modified version of the Shear-APA model. A detailed description of this forward model, the inverse model, and its validation are presented in a different report (Lai, Mellman, Robins, and Delisi, 2007). This document is a User's Guide for the Wake Vortex Inverse Model. Section 2 presents an overview of the inverse model program. Execution of the inverse model is described in Section 3. When executing the inverse model, a user is requested to provide the name of an input file which contains the inverse model parameters, the various datasets, and directories needed for the inversion. A detailed description of the list of parameters in the inversion input file is presented in Section 4. A user has an option to save the inversion results of each lidar track in a mat-file (a condensed data file in Matlab format). These saved mat-files can be used for post-inversion analysis. A description of the contents of the saved files is given in Section 5. An example of an inversion input

  1. Gravity gradiometry and seismic interpretation integration using spatially guided fuzzy c-means clustering inversion

    NASA Astrophysics Data System (ADS)

    Rapstine, Thomas D.

    Gravity gradiometry has been used as a geophysical tool to image salt structure in hydrocarbon exploration. The knowledge of the location, orientation, and spatial extent of salt bodies helps characterize possible petroleum prospects. Imaging around and underneath salt bodies can be challenging given the petrophysical properties and complicated geometry of salt. Methods for imaging beneath salt using seismic data exist but are often iterative and expensive, requiring a refinement of a velocity model at each iteration. Fortunately, the relatively strong density contrast between salt and background density structure pro- vides the opportunity for gravity gradiometry to be useful in exploration, especially when integrated with other geophysical data such as seismic. Quantitatively integrating multiple geophysical data is not trivial, but can improve the recovery of salt body geometry and petrophysical composition using inversion. This thesis provides two options for quantitatively integrating seismic, AGG, and petrophysical data that may aid the imaging of salt bodies. Both methods leverage and expand upon previously developed deterministic inversion methods. The inversion methods leverage seismically derived information, such as horizon slope and salt body interpretation, to constrain the inversion of airborne gravity gradiometry data (AGG) to arrive at a density contrast model. The first method involves constraining a top of salt inversion using slope in a seismic image. The second method expands fuzzy c-means (FCM) clustering inversion to include spatial control on clustering based on a seismically derived salt body interpretation. The effective- ness of the methods are illustrated on a 2D synthetic earth model derived from the SEAM Phase 1 salt model. Both methods show that constraining the inversion of AGG data using information derived from seismic images can improve the recovery of salt.

  2. Energy recovery injectors

    NASA Astrophysics Data System (ADS)

    Volkov, V.; Petrov, V. M.; Atkinson, T.; Matveenko, A.

    2016-10-01

    This article presents a novel design for a superconducting rf electron injector that incorporates energy recovery. This concept relaxes the demands of high power input couplers, improves essential beam parameters and energy efficiency and reduces the overall cost of a compact energy recovery linac machine.

  3. Applications of matrix inversion tomosynthesis

    NASA Astrophysics Data System (ADS)

    Warp, Richard J.; Godfrey, Devon J.; Dobbins, James T., III

    2000-04-01

    The improved image quality and characteristics of new flat- panel x-ray detectors have renewed interest in advanced algorithms such as tomosynthesis. Digital tomosynthesis is a method of acquiring and reconstructing a three-dimensional data set with limited-angle tube movement. Historically, conventional tomosynthesis reconstruction has suffered contamination of the planes of interest by blurred out-of- plane structures. This paper focuses on a Matrix Inversion Tomosynthesis (MITS) algorithm to remove unwanted blur from adjacent planes. The algorithm uses a set of coupled equations to solve for the blurring function in each reconstructed plane. This paper demonstrates the use of the MITS algorithm in three imaging applications: small animal microscopy, chest radiography, and orthopedics. The results of the MITS reconstruction process demonstrate an improved reduction of blur from out-of-plane structures when compared to conventional tomosynthesis. We conclude that the MITS algorithm holds potential in a variety of applications to improve three-dimensional image reconstruction.

  4. Action understanding as inverse planning.

    PubMed

    Baker, Chris L; Saxe, Rebecca; Tenenbaum, Joshua B

    2009-12-01

    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 principle of rationality: the expectation that agents will plan approximately rationally to achieve their goals, given their beliefs about the world. The mental states that caused an agent's behavior are inferred by inverting this model of rational planning using Bayesian inference, integrating the likelihood of the observed actions with the prior over mental states. This approach formalizes in precise probabilistic terms the essence of previous qualitative approaches to action understanding based on an "intentional stance" [Dennett, D. C. (1987). The intentional stance. Cambridge, MA: MIT Press] or a "teleological stance" [Gergely, G., Nádasdy, Z., Csibra, G., & Biró, S. (1995). Taking the intentional stance at 12 months of age. Cognition, 56, 165-193]. In three psychophysical experiments using animated stimuli of agents moving in simple mazes, we assess how well different inverse planning models based on different goal priors can predict human goal inferences. The results provide quantitative evidence for an approximately rational inference mechanism in human goal inference within our simplified stimulus paradigm, and for the flexible nature of goal representations that human observers can adopt. We discuss the implications of our experimental results for human action understanding in real-world contexts, and suggest how our framework might be extended to capture other kinds of mental state inferences, such as inferences about beliefs, or inferring whether an entity is an intentional agent.

  5. Novel mutational mechanism in the thyroglobulin gene: imperfect DNA inversion as a cause for hereditary hypothyroidism.

    PubMed

    Citterio, Cintia E; Rossetti, Liliana C; Souchon, Pierre F; Morales, Cecilia; Thouvard-Viprey, Mathilde; Salmon-Musial, Anne S; Mauran, Pierre L A; Doco-Fenzy, Martine; González-Sarmiento, Rogelio; Rivolta, Carina M; De Brasi, Carlos D; Targovnik, Héctor M

    2013-12-01

    The objective of this study was to perform genetic analysis in three brothers of Turkish origin born from consanguineus parents and affected by congenital hypothyroidism, goiter and low levels of serum TG. The combination of sequencing of DNA, PCR mapping, quantitative real-time PCR, inverse-PCR (I-PCR), multiplex PCR and bioinformatics analysis were used in order to detect TG mutations. We demonstrated that the three affected siblings are homozygous for a DNA inversion of 16,962bp in the TG gene associated with two deleted regions at both sides of the inversion limits. The inversion region includes the first 9bp of exon 48, 1015bp of intron 47, 191bp of exon 47, 1523bp of intron 46, 135bp of exon 46 and the last 14,089bp of intron 45. The proximal deletion corresponds to 27bp of TG intron 45, while the distal deletion spans the last 230bp of TG exon 48 and the first 588bp of intergenic region downstream TG end. The parents were heterozygous carriers of the complex rearrangement. In conclusion, a novel large imperfect DNA inversion within the TG gene was identified by the strategy of I-PCR. This aberration was not detectable by normal sequencing of the exons and exon/intron boundaries. Remarkably, the finding represents the first description of a TG deficiency disease caused by a DNA inversion. PMID:23933148

  6. Constrained resistivity inversion using seismic data

    NASA Astrophysics Data System (ADS)

    Saunders, J. H.; Herwanger, J. V.; Pain, C. C.; Worthington, M. H.; de Oliveira, C. R. E.

    2005-03-01

    In this paper we describe and apply a method for constraining structure in anisotropic electrical resistivity inversion. Structural constraints are routinely used to achieve improved model inversion. Here, a second-order (curvature-based) regularization tensor (model covariance) is used to build structure in the model. This structure could be obtained from other imaging methods such as seismic tomography, core samples or otherwise known structure in the model. Our method allows the incorporation of existing geophysical data into the inversion, in a general form that does not rely on any one-to-one correlation between data sets or material properties. Ambiguities in the resistivity distribution from electrical inversion, and in particular anisotropic inversion, may be reduced with this approach. To demonstrate the approach we invert a synthetic data set, showing the regularization tensor explicitly in different locations. We then apply the method to field data where we have some knowledge of the subsurface from seismic imaging. Our results show that it is possible to achieve a high level of convergence while using spatially varying structural constraints. Common problems associated with resistivity inversion such as source/receiver effects and false imaging of strongly resistive or conductive zones may also be reduced. As part of the inversion method we show how the magnitude of the constraints in the form of penalty parameters appropriate to an inversion may be estimated, reducing the computational expense of resistivity inversion.

  7. Human inversions and their functional consequences

    PubMed Central

    Puig, Marta; Casillas, Sònia; Villatoro, Sergi

    2015-01-01

    Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies. PMID:25998059

  8. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster

    PubMed Central

    Locke, Devin P; Archidiacono, Nicoletta; Misceo, Doriana; Cardone, Maria Francesca; Deschamps, Stephane; Roe, Bruce; Rocchi, Mariano; Eichler, Evan E

    2003-01-01

    Background Pericentric inversions are the most common euchromatic chromosomal differences among humans and the great apes. The human and chimpanzee karyotype differs by nine such events, in addition to several constitutive heterochromatic increases and one chromosomal fusion event. Reproductive isolation and subsequent speciation are thought to be the potential result of pericentric inversions, as reproductive boundaries form as a result of hybrid sterility. Results Here we employed a comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses to narrow the breakpoint interval of a pericentric inversion in chimpanzee involving the orthologous human 15q11-q13 region. We have refined the inversion breakpoint of this chimpanzee-specific rearrangement to a 600 kilobase (kb) interval of the human genome consisting of entirely duplicated material. Detailed analysis of the underlying sequence indicated that this region comprises multiple segmental duplications, including a previously characterized duplication of the alpha7 neuronal nicotinic acetylcholine receptor subunit gene (CHRNA7) in 15q13.3 and several Golgin-linked-to-PML, or LCR15, duplications. Conclusions We conclude that, on the basis of experimental data excluding the CHRNA7 duplicon as the site of inversion, and sequence analysis of regional duplications, the most likely rearrangement site is within a GLP/LCR15 duplicon. This study further exemplifies the genomic plasticity due to the presence of segmental duplications and highlights their importance for a complete understanding of genome evolution. PMID:12914658

  9. Molecular characterization of the breakpoints of an inversion fixed between Drosophila melanogaster and D. subobscura

    SciTech Connect

    Cirera, S.; Martin-Campos, J.M.; Segarra, C.

    1995-01-01

    The two breakpoints of a chromosomal inversion fixed since the split of Drosophila melanogaster and D. subobscura lineages have been isolated and sequenced in both species. The regions spanning the break-points initially were identified by the presence of two signals after interspecific in situ hybridization on polytene chromosomes. Interspecific comparison of the sequenced regions allowed us to delineate the location of the breakpoints. Close to one of these breakpoints a new transcription unit (bcn92) has been identified in both species. The inversion fixed between D. melanogaster and D. subobscura does not seem to have broken any transcription unit. Neither complete nor defective transposable elements were found in the regions encompassing the breakpoints. Short thymine-rich sequences (30-50 hp long) have been found bordering the breakpoint regions. Although alternating Pur-Pyr sequences were detected, these putative target sites for topoisomerase II were not differentially clustered in the breakpoints. 22 refs., 6 figs.

  10. Partial recovery of microbiomes after antibiotic treatment.

    PubMed

    Raymond, Frédéric; Déraspe, Maxime; Boissinot, Maurice; Bergeron, Michel G; Corbeil, Jacques

    2016-09-01

    Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted. PMID:27494088

  11. Fast recovery, high voltage silicon diodes for AC motor controllers

    NASA Technical Reports Server (NTRS)

    Balodis, V.; Berman, A. H.; Gaugh, C.

    1982-01-01

    The fabrication and characterization of a high voltage, high current, fast recovery silicon diode for use in AC motor controllers, originally developed for NASA for use in avionics power supplies, is presented. The diode utilizes a positive bevel PIN mesa structure with glass passivation and has the following characteristics: peak inverse voltage - 1200 volts, forward voltage at 50 amperes - 1.5 volts, reverse recovery time of 200 nanoseconds. Characterization data for the diode, included in a table, show agreement with design concepts developed for power diodes. Circuit diagrams of the diode are also given.

  12. Molecular characterization of the pericentric inversion of chimpanzee chromosome 11 homologous to human chromosome 9.

    PubMed

    Kehrer-Sawatzki, Hildegard; Szamalek, Justyna M; Tänzer, Simone; Platzer, Matthias; Hameister, Horst

    2005-05-01

    In addition to the fusion of human chromosome 2, nine pericentric inversions are the most conspicuous karyotype differences between humans and chimpanzees. In this study we identified the breakpoint regions of the pericentric inversion of chimpanzee chromosome 11 (PTR 11) homologous to human chromosome 9 (HSA 9). The break in homology between PTR 11p and HSA 9p12 maps to pericentromeric segmental duplications, whereas the breakpoint region orthologous to 9q21.33 is located in intergenic single-copy sequences. Close to the inversion breakpoint in PTR 11q, large blocks of alpha satellites are located, which indicate the presence of the centromere. Since G-banding analysis and the comparative BAC analyses performed in this study imply that the inversion breaks occurred in the region homologous to HSA 9q21.33 and 9p12, but not within the centromere, the structure of PTR 11 cannot be explained by a single pericentric inversion. In addition to this pericentric inversion of PTR 11, further events like centromere repositioning or a second smaller inversion must be assumed to explain the structure of PTR 11 compared with HSA 9.

  13. Laterally constrained inversion for CSAMT data interpretation

    NASA Astrophysics Data System (ADS)

    Wang, Ruo; Yin, Changchun; Wang, Miaoyue; Di, Qingyun

    2015-10-01

    Laterally constrained inversion (LCI) has been successfully applied to the inversion of dc resistivity, TEM and airborne EM data. However, it hasn't been yet applied to the interpretation of controlled-source audio-frequency magnetotelluric (CSAMT) data. In this paper, we apply the LCI method for CSAMT data inversion by preconditioning the Jacobian matrix. We apply a weighting matrix to Jacobian to balance the sensitivity of model parameters, so that the resolution with respect to different model parameters becomes more uniform. Numerical experiments confirm that this can improve the convergence of the inversion. We first invert a synthetic dataset with and without noise to investigate the effect of LCI applications to CSAMT data, for the noise free data, the results show that the LCI method can recover the true model better compared to the traditional single-station inversion; and for the noisy data, the true model is recovered even with a noise level of 8%, indicating that LCI inversions are to some extent noise insensitive. Then, we re-invert two CSAMT datasets collected respectively in a watershed and a coal mine area in Northern China and compare our results with those from previous inversions. The comparison with the previous inversion in a coal mine shows that LCI method delivers smoother layer interfaces that well correlate to seismic data, while comparison with a global searching algorithm of simulated annealing (SA) in a watershed shows that though both methods deliver very similar good results, however, LCI algorithm presented in this paper runs much faster. The inversion results for the coal mine CSAMT survey show that a conductive water-bearing zone that was not revealed by the previous inversions has been identified by the LCI. This further demonstrates that the method presented in this paper works for CSAMT data inversion.

  14. Solvent recycle/recovery

    SciTech Connect

    Paffhausen, M.W.; Smith, D.L.; Ugaki, S.N.

    1990-09-01

    This report describes Phase I of the Solvent Recycle/Recovery Task of the DOE Chlorinated Solvent Substitution Program for the US Air Force by the Idaho National Engineering Laboratory, EG G Idaho, Inc., through the US Department of Energy, Idaho Operations Office. The purpose of the task is to identify and test recovery and recycling technologies for proposed substitution solvents identified by the Biodegradable Solvent Substitution Program and the Alternative Solvents/Technologies for Paint Stripping Program with the overall objective of minimizing hazardous wastes. A literature search to identify recycle/recovery technologies and initial distillation studies has been conducted. 4 refs.

  15. Time synchronization and geoacoustic inversion using baleen whale sounds

    NASA Astrophysics Data System (ADS)

    Thode, Aaron; Gerstoft, Peter; Stokes, Dale; Noad, Mike; Burgess, William; Cato, Doug

    2005-09-01

    In 1996 matched-field processing (MFP) and geoacoustic inversion methods were used to invert for range, depth, and source levels of blue whale vocalizations. [A. M. Thode, G. L. D'Spain, and W. A. Kuperman, J. Acoust. Soc. Am. 107, 1286-1300 (2000)]. Humpback whales also produce broadband sequences of sounds that contain significant energy between 50 Hz to over 1 kHz. In Oct. 2003 and 2004 samples of humpback whale song were collected on vertical and titled arrays in 24-m-deep water in conjunction with the Humpback Acoustic Research Collaboration (HARC). The arrays consisted of autonomous recorders attached to a rope, and were time synchronized by extending standard geoacoustic inversion methods to invert for clock offset as well as whale location. The diffuse ambient noise background field was then used to correct for subsequent clock drift. Independent measurements of the local bathymetry and transmission loss were also obtained in the area. Preliminary results are presented for geoacoustic inversions of the ocean floor composition and humpback whale locations and source levels. [Work supported by ONR Ocean Acoustic Entry Level Faculty Award and Marine Mammals Program.

  16. Two hybrid regularization frameworks for solving the electrocardiography inverse problem

    NASA Astrophysics Data System (ADS)

    Jiang, Mingfeng; Xia, Ling; Shou, Guofa; Liu, Feng; Crozier, Stuart

    2008-09-01

    In this paper, two hybrid regularization frameworks, LSQR-Tik and Tik-LSQR, which integrate the properties of the direct regularization method (Tikhonov) and the iterative regularization method (LSQR), have been proposed and investigated for solving ECG inverse problems. The LSQR-Tik method is based on the Lanczos process, which yields a sequence of small bidiagonal systems to approximate the original ill-posed problem and then the Tikhonov regularization method is applied to stabilize the projected problem. The Tik-LSQR method is formulated as an iterative LSQR inverse, augmented with a Tikhonov-like prior information term. The performances of these two hybrid methods are evaluated using a realistic heart-torso model simulation protocol, in which the heart surface source method is employed to calculate the simulated epicardial potentials (EPs) from the action potentials (APs), and then the acquired EPs are used to calculate simulated body surface potentials (BSPs). The results show that the regularized solutions obtained by the LSQR-Tik method are approximate to those of the Tikhonov method, the computational cost of the LSQR-Tik method, however, is much less than that of the Tikhonov method. Moreover, the Tik-LSQR scheme can reconstruct the epcicardial potential distribution more accurately, specifically for the BSPs with large noisy cases. This investigation suggests that hybrid regularization methods may be more effective than separate regularization approaches for ECG inverse problems.

  17. Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus.

    PubMed

    Guijo, M I; Patte, J; del Mar Campos, M; Louarn, J M; Rebollo, J E

    2001-04-01

    The behavior of chromosomal inversions in Escherichia coli depends upon the region they affect. Regions flanking the replication terminus have been termed nondivisible zones (NDZ) because inversions ending in the region were either deleterious or not feasible. This regional phenomenon is further analyzed here. Thirty segments distributed between 23 and 29 min on the chromosome map have been submitted to an inversion test. Twenty-five segments either became deleterious when inverted or were noninvertible, but five segments tolerated inversion. The involvement of polar replication pause sites in this distribution was investigated. The results suggest that the Tus/pause site system may forbid some inversion events, but that other constraints to inversion, unrelated to this system, exist. Our current model for deleterious inversions is that the segments involved carry polar sequences acting in concert with other polar sequences located outside the segments. The observed patchwork of refractory and tolerant segments supports the existence of several NDZs in the 23- to 29-min region. Microscopic observations revealed that deleterious inversions are associated with high frequencies of abnormal nucleoid structure and distribution. Combined with other information, the data suggest that NDZs participate in the organization of the terminal domain of the nucleoid.

  18. Galerkin approximation for inverse problems for nonautonomous nonlinear distributed systems

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Reich, Simeon; Rosen, I. G.

    1988-01-01

    An abstract framework and convergence theory is developed for Galerkin approximation for inverse problems involving the identification of nonautonomous nonlinear distributed parameter systems. A set of relatively easily verified conditions is provided which are sufficient to guarantee the existence of optimal solutions and their approximation by a sequence of solutions to a sequence of approximating finite dimensional identification problems. The approach is based on the theory of monotone operators in Banach spaces and is applicable to a reasonably broad class of nonlinear distributed systems. Operator theoretic and variational techniques are used to establish a fundamental convergence result. An example involving evolution systems with dynamics described by nonstationary quasilinear elliptic operators along with some applications are presented and discussed.

  19. 5-HT1A receptors of the nucleus tractus solitarii facilitate sympathetic recovery following hypotensive hemorrhage in rats

    PubMed Central

    Vantrease, Jaime E.; Dudek, Nichole; DonCarlos, Lydia L.

    2015-01-01

    The role of serotonin in the hemodynamic response to blood loss remains controversial. Caudal raphe serotonin neurons are activated during hypotensive hemorrhage, and their destruction attenuates sympathetic increases following blood loss in unanesthetized rats. Caudal raphe neurons provide serotonin-positive projections to the nucleus tractus solitarii (NTS), and disruption of serotonin-positive nerve terminals in the NTS attenuates sympathetic recovery following hemorrhage. Administration of 5-HT1A-receptor agonists following hemorrhage augments sympathetic-mediated increases in venous tone and tissue hypoxia. These findings led us to hypothesize that severe blood loss promotes activation of 5-HT1A receptors in the NTS, which facilitates sympathetic recovery and peripheral tissue perfusion. Here, we developed an adeno-associated viral vector encoding an efficacious small hairpin RNA sequence targeting the rat 5-HT1A receptor. Unanesthetized rats subjected to NTS injection of the anti-rat 5-HT1A small hairpin RNA-encoding vector 4 wk prior showed normal blood pressure recovery, but an attenuated recovery of renal sympathetic nerve activity (−6.4 ± 12.9 vs. 42.6 ± 15.6% baseline, P < 0.05) 50 min after 21% estimated blood volume withdrawal. The same rats developed increased tissue hypoxia after hemorrhage, as indicated by prolonged elevations in lactate (2.77 ± 0.5 vs. 1.34 ± 0.2 mmol/l, 60 min after start of hemorrhage, P < 0.05). 5-HT1A mRNA levels in the commissural NTS were directly correlated with renal sympathetic nerve activity (P < 0.01) and inversely correlated with lactate (P < 0.05) 60 min after start of hemorrhage. The data suggest that 5-HT1A receptors in the commissural NTS facilitate tissue perfusion after blood loss likely by increasing sympathetic-mediated venous return. PMID:25980022

  20. Monte Carlo uncertainty analyses of a bLS inverse-dispersion technique for measuring gas emissions from livestock operations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The backward Lagrangian stochastic (bLS) inverse-dispersion technique has been used to measure fugitive gas emissions from livestock operations. The accuracy of the bLS technique, as indicated by the percentages of gas recovery in various tracer-release experiments, has generally been within ± 10% o...

  1. Chromosomal and behavioral studies of Mexican Drosophila. III. Inversion polymorphism of D. pseudoobscura.

    PubMed

    Olvera, O; Rockwell, R F; de la Rosa, M E; Gaso, M I; Gonzalez, F; Guzman, J; Levine, L

    1985-01-01

    Four new gene arrangements of chromosome 3 of Drosophila pseudoobscura are reported, as well as an updated phylogenetic sequence of the inversion polymorphism in this species. Evidence that the Tree Line gene arrangement of chromosome 3 was the original form in D. pseudoobscura, and that Central Mexico is the center of distribution of this species is discussed.

  2. An exact inverse method for subsonic flows

    NASA Technical Reports Server (NTRS)

    Daripa, Prabir

    1988-01-01

    A new inverse method for the aerodynamic design of airfoils is presented for subcritical flows. The pressure distribution in this method can be prescribed as a function of the arclength of the still unknown body. It is shown that this inverse problem is mathematically equivalent to solving only one nonlinear boundary value problem subject to known Dirichlet data on the boundary.

  3. Inversion in Mathematical Thinking and Learning

    ERIC Educational Resources Information Center

    Greer, Brian

    2012-01-01

    Inversion is a fundamental relational building block both within mathematics as the study of structures and within people's physical and social experience, linked to many other key elements such as equilibrium, invariance, reversal, compensation, symmetry, and balance. Within purely formal arithmetic, the inverse relationships between addition and…

  4. Iterative method for generating correlated binary sequences

    NASA Astrophysics Data System (ADS)

    Usatenko, O. V.; Melnik, S. S.; Apostolov, S. S.; Makarov, N. M.; Krokhin, A. A.

    2014-11-01

    We propose an efficient iterative method for generating random correlated binary sequences with a prescribed correlation function. The method is based on consecutive linear modulations of an initially uncorrelated sequence into a correlated one. Each step of modulation increases the correlations until the desired level has been reached. The robustness and efficiency of the proposed algorithm are tested by generating sequences with inverse power-law correlations. The substantial increase in the strength of correlation in the iterative method with respect to single-step filtering generation is shown for all studied correlation functions. Our results can be used for design of disordered superlattices, waveguides, and surfaces with selective transport properties.

  5. Light controlled reversible inversion of nanophosphor-stabilized Pickering emulsions for biphasic enantioselective biocatalysis.

    PubMed

    Chen, Zhaowei; Zhou, Li; Bing, Wei; Zhang, Zhijun; Li, Zhenhua; Ren, Jinsong; Qu, Xiaogang

    2014-05-21

    In this work, by utilizing photochromic spiropyrans conjugated upconversion nanophosphors, we have successfully prepared NIR/visible light tuned interfacially active nanoparticles for the formulation of Pickering emulsions with reversible inversion properties. By loading a model enantioselective biocatalytic active bacteria Alcaligenes faecalis ATCC 8750 in the aqueous phase, we demonstrated for the first time that the multifunctional Pickering emulsion not only highly enhanced its catalytic performance but also relieved the substrate inhibition effect. In addition, product recovery, and biocatalysts and colloid emulsifiers recycling could be easily realized based on the inversion ability of the Pickering emulsion. Most importantly, the utilization of NIR/visible light to perform the reversible inversion without any chemical auxiliaries or temperature variation showed little damage toward the biocatalysts, which was highlighted by the high catalytic efficiency and high enantioselectivity even after 10 cycles. The NIR/visible light controlled Pickering emulsion showed promising potential as a powerful technique for biocatalysis in biphasic systems.

  6. RECOVERY OF RUTHENIUM VALUES

    DOEpatents

    Grummitt, W.E.; Hardwick, W.H.

    1961-01-01

    A process is given for the recovery of ruthenium from its aqueous solutions by oxidizing the ruthenium to the octavalent state and subsequently extracting the ruthenium into a halogen-substituted liquid paraffin.

  7. Silver recovery system data

    SciTech Connect

    Boulineau, B.

    1991-08-26

    In August of 1990 the Savannah River Site Photography Group began testing on a different type of silver recovery system. This paper describes the baseline study and the different phases of installation and testing of the system.

  8. Inverse Problem of Vortex Reconstruction

    NASA Astrophysics Data System (ADS)

    Protas, Bartosz; Danaila, Ionut

    2014-11-01

    This study addresses the following question: given incomplete measurements of the velocity field induced by a vortex, can one determine the structure of the vortex? Assuming that the flow is incompressible, inviscid and stationary in the frame of reference moving with the vortex, the ``structure'' of the vortex is uniquely characterized by the functional relation between the streamfunction and vorticity. To focus attention, 3D axisymmetric vortex rings are considered. We show how this inverse problem can be framed as an optimization problem which can then be efficiently solved using variational techniques. More precisely, we use measurements of the tangential velocity on some contour to reconstruct the function defining the streamfunction-vorticity relation in a continuous setting. Two test cases are presented, involving Hill's and Norbury vortices, in which very good reconstructions are obtained. A key result of this study is the application of our approach to obtain an optimal inviscid vortex model in an actual viscous flow problem based on DNS data which leads to a number of nonintuitive findings.

  9. Inverse magnetic/shear catalysis

    NASA Astrophysics Data System (ADS)

    McInnes, Brett

    2016-05-01

    It is well known that very large magnetic fields are generated when the Quark-Gluon Plasma is formed during peripheral heavy-ion collisions. Lattice, holographic, and other studies strongly suggest that these fields may, for observationally relevant field values, induce "inverse magnetic catalysis", signalled by a lowering of the critical temperature for the chiral/deconfinement transition. The theoretical basis of this effect has recently attracted much attention; yet so far these investigations have not included another, equally dramatic consequence of the peripheral collision geometry: the QGP acquires a large angular momentum vector, parallel to the magnetic field. Here we use holographic techniques to argue that the angular momentum can also, independently, have an effect on transition temperatures, and we obtain a rough estimate of the relative effects of the presence of both a magnetic field and an angular momentum density. We find that the shearing angular momentum reinforces the effect of the magnetic field at low values of the baryonic chemical potential, but that it can actually decrease that effect at high chemical potentials.

  10. Package inspection using inverse diffraction

    NASA Astrophysics Data System (ADS)

    McAulay, Alastair D.

    2008-08-01

    More efficient cost-effective hand-held methods of inspecting packages without opening them are in demand for security. Recent new work in TeraHertz sources,1 millimeter waves, presents new possibilities. Millimeter waves pass through cardboard and styrofoam, common packing materials, and also pass through most materials except those with high conductivity like metals which block light and are easily spotted. Estimating refractive index along the path of the beam through the package from observations of the beam passing out of the package provides the necessary information to inspect the package and is a nonlinear problem. So we use a generalized linear inverse technique that we first developed for finding oil by reflection in geophysics.2 The computation assumes parallel slices in the packet of homogeneous material for which the refractive index is estimated. A beam is propagated through this model in a forward computation. The output is compared with the actual observations for the package and an update computed for the refractive indices. The loop is repeated until convergence. The approach can be modified for a reflection system or to include estimation of absorption.

  11. Inversion based on computational simulations

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.

    1998-09-01

    A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal.

  12. A preprocessing strategy for helioseismic inversions

    NASA Astrophysics Data System (ADS)

    Christensen-Dalsgaard, J.; Thompson, M. J.

    1993-05-01

    Helioseismic inversion in general involves considerable computational expense, due to the large number of modes that is typically considered. This is true in particular of the widely used optimally localized averages (OLA) inversion methods, which require the inversion of one or more matrices whose order is the number of modes in the set. However, the number of practically independent pieces of information that a large helioseismic mode set contains is very much less than the number of modes, suggesting that the set might first be reduced before the expensive inversion is performed. We demonstrate with a model problem that by first performing a singular value decomposition the original problem may be transformed into a much smaller one, reducing considerably the cost of the OLA inversion and with no significant loss of information.

  13. Recurrent Neural Network for Computing Outer Inverse.

    PubMed

    Živković, Ivan S; Stanimirović, Predrag S; Wei, Yimin

    2016-05-01

    Two linear recurrent neural networks for generating outer inverses with prescribed range and null space are defined. Each of the proposed recurrent neural networks is based on the matrix-valued differential equation, a generalization of dynamic equations proposed earlier for the nonsingular matrix inversion, the Moore-Penrose inversion, as well as the Drazin inversion, under the condition of zero initial state. The application of the first approach is conditioned by the properties of the spectrum of a certain matrix; the second approach eliminates this drawback, though at the cost of increasing the number of matrix operations. The cases corresponding to the most common generalized inverses are defined. The conditions that ensure stability of the proposed neural network are presented. Illustrative examples present the results of numerical simulations.

  14. Fast wavelet based sparse approximate inverse preconditioner

    SciTech Connect

    Wan, W.L.

    1996-12-31

    Incomplete LU factorization is a robust preconditioner for both general and PDE problems but unfortunately not easy to parallelize. Recent study of Huckle and Grote and Chow and Saad showed that sparse approximate inverse could be a potential alternative while readily parallelizable. However, for special class of matrix A that comes from elliptic PDE problems, their preconditioners are not optimal in the sense that independent of mesh size. A reason may be that no good sparse approximate inverse exists for the dense inverse matrix. Our observation is that for this kind of matrices, its inverse entries typically have piecewise smooth changes. We can take advantage of this fact and use wavelet compression techniques to construct a better sparse approximate inverse preconditioner. We shall show numerically that our approach is effective for this kind of matrices.

  15. Refuse recycling and recovery

    SciTech Connect

    Holmes, J.R.

    1981-01-01

    Sanitary landfill of domestic, commercial, and industrial wastes is the predominant method of waste disposal in the United Kingdom. Although there was various waste disposal processes at various stages of design and test, landfill and incineration are still the only reliable methods of waste processing. Methods of recovery and use of refuse are examined in this book together with various separation processes, waste derived fuels, refuse composting, and glass and metal recovery. (Refs. 39).

  16. Rapid approximate inversion of airborne TEM

    NASA Astrophysics Data System (ADS)

    Fullagar, Peter K.; Pears, Glenn A.; Reid, James E.; Schaa, Ralf

    2015-11-01

    Rapid interpretation of large airborne transient electromagnetic (ATEM) datasets is highly desirable for timely decision-making in exploration. Full solution 3D inversion of entire airborne electromagnetic (AEM) surveys is often still not feasible on current day PCs. Therefore, two algorithms to perform rapid approximate 3D interpretation of AEM have been developed. The loss of rigour may be of little consequence if the objective of the AEM survey is regional reconnaissance. Data coverage is often quasi-2D rather than truly 3D in such cases, belying the need for `exact' 3D inversion. Incorporation of geological constraints reduces the non-uniqueness of 3D AEM inversion. Integrated interpretation can be achieved most readily when inversion is applied to a geological model, attributed with lithology as well as conductivity. Geological models also offer several practical advantages over pure property models during inversion. In particular, they permit adjustment of geological boundaries. In addition, optimal conductivities can be determined for homogeneous units. Both algorithms described here can operate on geological models; however, they can also perform `unconstrained' inversion if the geological context is unknown. VPem1D performs 1D inversion at each ATEM data location above a 3D model. Interpretation of cover thickness is a natural application; this is illustrated via application to Spectrem data from central Australia. VPem3D performs 3D inversion on time-integrated (resistive limit) data. Conversion to resistive limits delivers a massive increase in speed since the TEM inverse problem reduces to a quasi-magnetic problem. The time evolution of the decay is lost during the conversion, but the information can be largely recovered by constructing a starting model from conductivity depth images (CDIs) or 1D inversions combined with geological constraints if available. The efficacy of the approach is demonstrated on Spectrem data from Brazil. Both separately and in

  17. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  18. Intracontinental rifting and inversion: Missour basin and Atlas Mountains, Morocco

    SciTech Connect

    Beauchamp, W.; Barazangi, M.; Demnati, A.; Alji, M.E.

    1996-09-01

    The intracontinental High and Middle Atlas mountain belts in Morocco intersect to form the southern and western margins of the Missour basin, an intermontane basin formed as a result of the uplift and inversion of the Mesozoic Atlas paleorifts. These rifts were areas where the crust was greatly attenuated and more subject to deformation in response to nearby plate boundary tectonics. Data from observations based on seismic reflection profiles and wells over the Missour basin for hydrocarbon exploration and field mapping were used to understand the basin evolution, structural styles, and inversion timing of the nearby Atlas Mountains. Hercynian and Mesozoic normal faults were reactivated into high-angle reverse and thrust faults in the Mesozoic during the Jurassic, Early Cretaceous (early Alpine phase), and the Paleogene (late Alpine phase). The reactivation of synrift normal faults of the paleo-Atlas rifts inverted previous half grabens into anticlinal structures, with the axis of the half graben centered below the axis of the inverted anticline. The resulting inverted fold geometries are controlled by the geometries of the extensional planar or listric faults. The Atlas paleorift system is one of the largest rift systems in Africa. Little hydrocarbon exploration has occurred within the Atlas Mountains and the margins of the paleo-Atlas rift system. Inversion of synrift structures can lead to both the destruction and preservation of synrift traps and the creation of new hydrocarbon traps. The study of the effects of inversion in the Missour basin may lead to the discovery of footwall subthrust hydrocarbon traps in the Mesozoic sedimentary sequence of the Atlas Mountains.

  19. Synthetic inversions for density in the Earth's interior from seismic waveform and geodetic data

    NASA Astrophysics Data System (ADS)

    Blom, N.; Boehm, C.; Fichtner, A.

    2015-12-01

    Density plays an important role in the Earth's interior. On one hand, it is the driving force behind convection; on the other, in imaging efforts, it serves to discriminate between thermal and compositional heterogeneities. Despite its importance, the Earth's 3D density structure remains difficult to infer from surface observations. Gravity measurements, for instance, are sensitive to density but suffer from inherent and strong non-uniqueness. The travel times of seismic body and surface waves are only weakly sensitive to density, and trade-offs with velocity structure are often large. New opportunities for the recovery of density in the Earth may arise from recently developed full-waveform inversion methods that go beyond traditional traveltime tomography. In this study, we assess to which extent, and in which way, full-waveform inversion can be combined with gravity and other geodetic measurements to better constrain global-scale density structure. To this end, we perform synthetic tests in 2D in which we systematically assess the effect on density recovery of different (joint) inversion schemes, types of data used and constraints applied. Our synthetic inversions are based on numerical wave propagation and adjoint techniques to compute seismic Fréchet sensitivity kernels, which are combined with synthetic gravity data to drive gradient-based optimisation schemes. Additional constraints such as a predefined velocity structure, or Earth's mass and inertia tensor, may be imposed using a projected descent scheme.

  20. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  1. Determination of transient fluid temperature using the inverse method

    NASA Astrophysics Data System (ADS)

    Jaremkiewicz, Magdalena

    2014-03-01

    This paper proposes an inverse method to obtain accurate measurements of the transient temperature of fluid. A method for unit step and linear rise of temperature is presented. For this purpose, the thermometer housing is modelled as a full cylindrical element (with no inner hole), divided into four control volumes. Using the control volume method, the heat balance equations can be written for each of the nodes for each of the control volumes. Thus, for a known temperature in the middle of the cylindrical element, the distribution of temperature in three nodes and heat flux at the outer surface were obtained. For a known value of the heat transfer coefficient the temperature of the fluid can be calculated using the boundary condition. Additionally, results of experimental research are presented. The research was carried out during the start-up of an experimental installation, which comprises: a steam generator unit, an installation for boiler feed water treatment, a tray-type deaerator, a blow down flashvessel for heat recovery, a steam pressure reduction station, a boiler control system and a steam header made of martensitic high alloy P91 steel. Based on temperature measurements made in the steam header using the inverse method, accurate measurements of the transient temperature of the steam were obtained. The results of the calculations are compared with the real temperature of the steam, which can be determined for a known pressure and enthalpy.

  2. Support minimized inversion of acoustic and elastic wave scattering

    SciTech Connect

    Safaeinili, A.

    1994-04-24

    This report discusses the following topics on support minimized inversion of acoustic and elastic wave scattering: Minimum support inversion; forward modelling of elastodynamic wave scattering; minimum support linearized acoustic inversion; support minimized nonlinear acoustic inversion without absolute phase; and support minimized nonlinear elastic inversion.

  3. Methodology for determining multilayered temperature inversions

    NASA Astrophysics Data System (ADS)

    Fochesatto, G. J.

    2015-05-01

    Temperature sounding of the atmospheric boundary layer (ABL) and lower troposphere exhibits multilayered temperature inversions specially in high latitudes during extreme winters. These temperature inversion layers are originated based on the combined forcing of local- and large-scale synoptic meteorology. At the local scale, the thermal inversion layer forms near the surface and plays a central role in controlling the surface radiative cooling and air pollution dispersion; however, depending upon the large-scale synoptic meteorological forcing, an upper level thermal inversion can also exist topping the local ABL. In this article a numerical methodology is reported to determine thermal inversion layers present in a given temperature profile and deduce some of their thermodynamic properties. The algorithm extracts from the temperature profile the most important temperature variations defining thermal inversion layers. This is accomplished by a linear interpolation function of variable length that minimizes an error function. The algorithm functionality is demonstrated on actual radiosonde profiles to deduce the multilayered temperature inversion structure with an error fraction set independently.

  4. On the inversion-indel distance

    PubMed Central

    2013-01-01

    Background The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli and Pevzner in 1995. In 2000, El-Mabrouk extended the inversion model to allow the comparison of unichromosomal genomes with unequal contents, thus insertions and deletions of DNA segments besides inversions. However, an exact algorithm was presented only for the case in which we have insertions alone and no deletion (or vice versa), while a heuristic was provided for the symmetric case, that allows both insertions and deletions and is called the inversion-indel distance. In 2005, Yancopoulos, Attie and Friedberg started a new branch of research by introducing the generic double cut and join (DCJ) operation, that can represent several genome rearrangements (including inversions). Among others, the DCJ model gave rise to two important results. First, it has been shown that the inversion distance can be computed in a simpler way with the help of the DCJ operation. Second, the DCJ operation originated the DCJ-indel distance, that allows the comparison of genomes with unequal contents, considering DCJ, insertions and deletions, and can be computed in linear time. Results In the present work we put these two results together to solve an open problem, showing that, when the graph that represents the relation between the two compared genomes has no bad components, the inversion-indel distance is equal to the DCJ-indel distance. We also give a lower and an upper bound for the inversion-indel distance in the presence of bad components. PMID:24564182

  5. Geoacoustic reflectivity inversion: A Bayesian approach

    NASA Astrophysics Data System (ADS)

    Dettmer, Jan

    Propagation and reverberation of acoustic fields in shallow water depend strongly on the spatial variability of seabed geoacoustic parameters; and lack of knowledge of seabed variability is often a limiting factor in acoustic modelling applications. However, direct sampling (e.g., coring) of vertical and lateral variability is expensive and laborious, and matched-field and other long-range inversion methods fail to provide sufficient resolution. This thesis develops a new joint time/frequency domain inversion for high-resolution single-bounce reflection data. The inversion approach has the potential to resolve fine-scale sediment profiles over small seafloor footprints (˜100 m). The approach utilises sequential Bayesian inversion of time- and frequency-domain reflectivity data, employing ray-tracing inversion for reflection travel times and a layer-packet stripping method for spherical-wave reflection coefficient inversion. Rigorous uncertainty estimation is of key importance to yield high quality inversion results. Quantitative geoacoustic uncertainties are provided by a nonlinear Gibbs sampling approach together with full data error covariance estimation (including non-stationary effects). The small footprint of the measurement technique combined with the rigorous inversion of both time and frequency domain data provides a powerful new tool to examine seabed structure on finer scales than heretofore possible. The Bayesian inversion is applied to two data sets collected on the Malta Plateau and the Strait of Sicily during the SCARAB98 experiment. The first application aims to recover multi-layered seabed structure and the second application recovers density and sound velocity gradient structure in the uppermost sediment layer. An interesting new method of deriving reflectivity data from ambient noise measurements is briefly considered in simulation to examine the resolving power and limits of the approach.

  6. Identification of intron/exon boundaries in genomic DNA by inverse PCR.

    PubMed

    Albertsen, H; Thliveris, A

    2001-05-01

    This unit describes identifying intron/exon boundaries in genomic DNA by comparing nucleotide sequences of genomic DNA to cDNA. Cloned genomic DNA is prepared for inverse polymerase chain reaction (PCR) by digesting the DNA with a restriction enzyme and circularizing the restriction fragments by ligation. Diverging primer pairs for each exon are designed on the basis of the cDNA sequence. The circularized restriction fragments are amplified using these diverging primers, the PCR product is sequenced, and the sequence is compared to the cDNA sequence to determine the location of the intron/exon boundaries. The lower complexity of cloned DNA (e.g., YAC, P1, or cosmid DNA) facilitates preparation of good template. This unit describes identifying intron/exon boundaries in genomic DNA by comparing nucleotide sequences of genomic DNA to cDNA. PMID:18428300

  7. Range aliasing in frequency coherent geoacoustic inversion.

    PubMed

    Yardim, Caglar; Gerstoft, Peter; Hodgkiss, William S

    2011-10-01

    This paper discusses the effects of frequency selection on source localization and geoacoustic inversion methods that use frequency coherent objective functions. Matched-field processors based on frequency-coherent objective functions often have rapidly fluctuating range ambiguity surfaces. Insufficient sampling in frequency domain results in range aliasing terms that affect geoacoustic inversion. Range aliasing and its effects on source localization and environmental parameter inversion are demonstrated on data collected during the MAPEX2000 experiment. Guidance for frequency selection to avoid range aliasing is provided.

  8. Population inversion in a stationary recombining plasma

    SciTech Connect

    Otsuka, M.

    1980-12-01

    Population inversion, which occurs in a recombining plasma when a stationary He plasma is brought into contact with a neutral gas, is examined. With hydrogen as a contact gas, noticeable inversion between low-lying levels of H as been found. The overpopulation density is of the order of 10/sup 8/ cm/sup -3/, which is much higher then that (approx. =10/sup 5/ cm/sup -3/) obtained previously with He as a contact gas. Relations between these experimental results and the conditions for population inversion are discussed with the CR model.

  9. An inverse problem in thermal imaging

    NASA Technical Reports Server (NTRS)

    Bryan, Kurt; Caudill, Lester F., Jr.

    1994-01-01

    This paper examines uniqueness and stability results for an inverse problem in thermal imaging. The goal is to identify an unknown boundary of an object by applying a heat flux and measuring the induced temperature on the boundary of the sample. The problem is studied both in the case in which one has data at every point on the boundary of the region and the case in which only finitely many measurements are available. An inversion procedure is developed and used to study the stability of the inverse problem for various experimental configurations.

  10. Inverse Raman effect: applications and detection techniques

    SciTech Connect

    Hughes, L.J. Jr.

    1980-08-01

    The processes underlying the inverse Raman effect are qualitatively described by comparing it to the more familiar phenomena of conventional and stimulated Raman scattering. An experession is derived for the inverse Raman absorption coefficient, and its relationship to the stimulated Raman gain is obtained. The power requirements of the two fields are examined qualitatively and quantitatively. The assumption that the inverse Raman absorption coefficient is constant over the interaction length is examined. Advantages of the technique are discussed and a brief survey of reported studies is presented.

  11. Recovery of Interdependent Networks

    PubMed Central

    Di Muro, M. A.; La Rocca, C. E.; Stanley, H. E.; Havlin, S.; Braunstein, L. A.

    2016-01-01

    Recent network research has focused on the cascading failures in a system of interdependent networks and the necessary preconditions for system collapse. An important question that has not been addressed is how to repair a failing system before it suffers total breakdown. Here we introduce a recovery strategy for nodes and develop an analytic and numerical framework for studying the concurrent failure and recovery of a system of interdependent networks based on an efficient and practically reasonable strategy. Our strategy consists of repairing a fraction of failed nodes, with probability of recovery γ, that are neighbors of the largest connected component of each constituent network. We find that, for a given initial failure of a fraction 1 − p of nodes, there is a critical probability of recovery above which the cascade is halted and the system fully restores to its initial state and below which the system abruptly collapses. As a consequence we find in the plane γ − p of the phase diagram three distinct phases. A phase in which the system never collapses without being restored, another phase in which the recovery strategy avoids the breakdown, and a phase in which even the repairing process cannot prevent system collapse. PMID:26956773

  12. Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

    PubMed Central

    Jacquin, Hugo; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi

    2016-01-01

    Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of ‘true’ LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations. PMID:27177270

  13. BOOK REVIEW: Inverse Problems. Activities for Undergraduates

    NASA Astrophysics Data System (ADS)

    Yamamoto, Masahiro

    2003-06-01

    This book is a valuable introduction to inverse problems. In particular, from the educational point of view, the author addresses the questions of what constitutes an inverse problem and how and why we should study them. Such an approach has been eagerly awaited for a long time. Professor Groetsch, of the University of Cincinnati, is a world-renowned specialist in inverse problems, in particular the theory of regularization. Moreover, he has made a remarkable contribution to educational activities in the field of inverse problems, which was the subject of his previous book (Groetsch C W 1993 Inverse Problems in the Mathematical Sciences (Braunschweig: Vieweg)). For this reason, he is one of the most qualified to write an introductory book on inverse problems. Without question, inverse problems are important, necessary and appear in various aspects. So it is crucial to introduce students to exercises in inverse problems. However, there are not many introductory books which are directly accessible by students in the first two undergraduate years. As a consequence, students often encounter diverse concrete inverse problems before becoming aware of their general principles. The main purpose of this book is to present activities to allow first-year undergraduates to learn inverse theory. To my knowledge, this book is a rare attempt to do this and, in my opinion, a great success. The author emphasizes that it is very important to teach inverse theory in the early years. He writes; `If students consider only the direct problem, they are not looking at the problem from all sides .... The habit of always looking at problems from the direct point of view is intellectually limiting ...' (page 21). The book is very carefully organized so that teachers will be able to use it as a textbook. After an introduction in chapter 1, sucessive chapters deal with inverse problems in precalculus, calculus, differential equations and linear algebra. In order to let one gain some insight

  14. Analysis of Temperature Distributions in Nighttime Inversions

    NASA Astrophysics Data System (ADS)

    Telyak, Oksana; Krasouski, Aliaksandr; Svetashev, Alexander; Turishev, Leonid; Barodka, Siarhei

    2015-04-01

    Adequate prediction of temperature inversion in the atmospheric boundary layer is one of prerequisites for successful forecasting of meteorological parameters and severe weather events. Examples include surface air temperature and precipitation forecasting as well as prediction of fog, frosts and smog with hazardous levels of atmospheric pollution. At the same time, reliable forecasting of temperature inversions remains an unsolved problem. For prediction of nighttime inversions over some specific territory, it is important to study characteristic features of local circulation cells formation and to properly take local factors into account to develop custom modeling techniques for operational use. The present study aims to investigate and analyze vertical temperature distributions in tropospheric inversions (isotherms) over the territory of Belarus. We study several specific cases of formation, evolution and decay of deep nighttime temperature inversions in Belarus by means of mesoscale numerical simulations with WRF model, considering basic mechanisms of isothermal and inverse temperature layers formation in the troposphere and impact of these layers on local circulation cells. Our primary goal is to assess the feasibility of advance prediction of inversions formation with WRF. Modeling results reveal that all cases under consideration have characteristic features of radiative inversions (e.g., their formation times, development phases, inversion intensities, etc). Regions of "blocking" layers formation are extensive and often spread over the entire territory of Belarus. Inversions decay starts from the lowermost (near surface) layer (altitudes of 5 to 50 m). In all cases, one can observe formation of temperature gradients that substantially differ from the basic inversion gradient, i.e. the layer splits into smaller layers, each having a different temperature stratification (isothermal, adiabatic, etc). As opposed to various empirical techniques as well as

  15. Rapid Diagnostics of Onboard Sequences

    NASA Technical Reports Server (NTRS)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  16. Regularized inversion of controlled source audio-frequency magnetotelluric data in horizontally layered transversely isotropic media

    NASA Astrophysics Data System (ADS)

    Zhou, Jianmei; Wang, Jianxun; Shang, Qinglong; Wang, Hongnian; Yin, Changchun

    2014-04-01

    We present an algorithm for inverting controlled source audio-frequency magnetotelluric (CSAMT) data in horizontally layered transversely isotropic (TI) media. The popular inversion method parameterizes the media into a large number of layers which have fixed thickness and only reconstruct the conductivities (e.g. Occam's inversion), which does not enable the recovery of the sharp interfaces between layers. In this paper, we simultaneously reconstruct all the model parameters, including both the horizontal and vertical conductivities and layer depths. Applying the perturbation principle and the dyadic Green's function in TI media, we derive the analytic expression of Fréchet derivatives of CSAMT responses with respect to all the model parameters in the form of Sommerfeld integrals. A regularized iterative inversion method is established to simultaneously reconstruct all the model parameters. Numerical results show that the inverse algorithm, including the depths of the layer interfaces, can significantly improve the inverse results. It can not only reconstruct the sharp interfaces between layers, but also can obtain conductivities close to the true value.

  17. Enhanced coalbed methane recovery

    SciTech Connect

    Mazzotti, M.; Pini, R.; Storti, G.

    2009-01-15

    The recovery of coalbed methane can be enhanced by injecting CO{sub 2} in the coal seam at supercritical conditions. Through an in situ adsorption/desorption process the displaced methane is produced and the adsorbed CO{sub 2} is permanently stored. This is called enhanced coalbed methane recovery (ECBM) and it is a technique under investigation as a possible approach to the geological storage of CO{sub 2} in a carbon dioxide capture and storage system. This work reviews the state of the art on fundamental and practical aspects of the technology and summarizes the results of ECBM field tests. These prove the feasibility of ECBM recovery and highlight substantial opportunities for interdisciplinary research at the interface between earth sciences and chemical engineering.

  18. Recovery from vestibular ototoxicity

    NASA Technical Reports Server (NTRS)

    Black, F. O.; Gianna-Poulin, C.; Pesznecker, S. C.

    2001-01-01

    OBJECTIVE: Determine whether subjects with documented vestibular ototoxicity recover vestibular function and, if so, investigate the recovery dynamics. STUDY DESIGN: Prospective and retrospective reviews and repeated measures. SETTING: Clinical research and technology center. SUBJECTS: Twenty-eight subjects who received vestibulotoxic medications were followed for at least 12 months after initial treatment. CONTROLS: Our subject sample was compared with a published database of normal individuals. INTERVENTIONS: All 28 subjects received systemically administered medications known to be ototoxic. The subjects' treating physicians controlled medication, dosage, and administration schedules. MAIN OUTCOME MEASURES: Tests of horizontal canal vestibulo-ocular function were performed. Subjects' auditory and vestibular symptoms were recorded. RESULTS: Eleven subjects (39%) showed changes in horizontal canal vestibulo-ocular gain constant (GC) and/or time constant (TC) consistent with vestibular ototoxicity. When tested 1 year after ototoxic drug administration, eight of the nine subjects who experienced ototoxic decrease in GC showed a recovery of GC to normal limits. Only one of the eight subjects who experienced ototoxic decrease in TC showed recovery of TC to within normal limits. Ototoxicity onset and recovery were independent of baseline vestibular function, and ototoxicity onset did not correlate with cumulative dose of ototoxic medication. There was no relationship between subjective symptoms and ototoxicity onset. CONCLUSIONS: Recovery of GC after vestibular ototoxicity is more commonly observed than recovery of TC. Because ototoxic changes developed and continued in an unpredictable time and manner in relation to ototoxic drug administration, we propose that once ototoxic changes in vestibulo-ocular reflex are detected, ototoxic medications should be discontinued as soon as possible.

  19. Nanopore sequencing detects structural variants in cancer

    PubMed Central

    Norris, Alexis L.; Workman, Rachael E.; Fan, Yunfan; Eshleman, James R.; Timp, Winston

    2016-01-01

    ABSTRACT Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring. PMID:26787508

  20. Zinc oxide inverse opal enzymatic biosensor

    NASA Astrophysics Data System (ADS)

    You, Xueqiu; Pikul, James H.; King, William P.; Pak, James J.

    2013-06-01

    We report ZnO inverse opal- and nanowire (NW)-based enzymatic glucose biosensors with extended linear detection ranges. The ZnO inverse opal sensors have 0.01-18 mM linear detection range, which is 2.5 times greater than that of ZnO NW sensors and 1.5 times greater than that of other reported ZnO sensors. This larger range is because of reduced glucose diffusivity through the inverse opal geometry. The ZnO inverse opal sensors have an average sensitivity of 22.5 μA/(mM cm2), which diminished by 10% after 35 days, are more stable than ZnO NW sensors whose sensitivity decreased by 10% after 7 days.

  1. Inverse Doppler Effects in Broadband Acoustic Metamaterials.

    PubMed

    Zhai, S L; Zhao, X P; Liu, S; Shen, F L; Li, L L; Luo, C R

    2016-08-31

    The Doppler effect refers to the change in frequency of a wave source as a consequence of the relative motion between the source and an observer. Veselago theoretically predicted that materials with negative refractions can induce inverse Doppler effects. With the development of metamaterials, inverse Doppler effects have been extensively investigated. However, the ideal material parameters prescribed by these metamaterial design approaches are complex and also challenging to obtain experimentally. Here, we demonstrated a method of designing and experimentally characterising arbitrary broadband acoustic metamaterials. These omni-directional, double-negative, acoustic metamaterials are constructed with 'flute-like' acoustic meta-cluster sets with seven double meta-molecules; these metamaterials also overcome the limitations of broadband negative bulk modulus and mass density to provide a region of negative refraction and inverse Doppler effects. It was also shown that inverse Doppler effects can be detected in a flute, which has been popular for thousands of years in Asia and Europe.

  2. Inverse Doppler Effects in Broadband Acoustic Metamaterials.

    PubMed

    Zhai, S L; Zhao, X P; Liu, S; Shen, F L; Li, L L; Luo, C R

    2016-01-01

    The Doppler effect refers to the change in frequency of a wave source as a consequence of the relative motion between the source and an observer. Veselago theoretically predicted that materials with negative refractions can induce inverse Doppler effects. With the development of metamaterials, inverse Doppler effects have been extensively investigated. However, the ideal material parameters prescribed by these metamaterial design approaches are complex and also challenging to obtain experimentally. Here, we demonstrated a method of designing and experimentally characterising arbitrary broadband acoustic metamaterials. These omni-directional, double-negative, acoustic metamaterials are constructed with 'flute-like' acoustic meta-cluster sets with seven double meta-molecules; these metamaterials also overcome the limitations of broadband negative bulk modulus and mass density to provide a region of negative refraction and inverse Doppler effects. It was also shown that inverse Doppler effects can be detected in a flute, which has been popular for thousands of years in Asia and Europe. PMID:27578317

  3. Inverse problem of electro-seismic conversion

    NASA Astrophysics Data System (ADS)

    Chen, Jie; Yang, Yang

    2013-11-01

    When a porous rock is saturated with an electrolyte, electrical fields are coupled with seismic waves via the electro-seismic conversion. Pride (1994 Phys. Rev. B 50 15678-96) derived the governing models, in which Maxwell equations are coupled with Biot's equations through the electro-kinetic mobility parameter. The inverse problem of the linearized electro-seismic conversion consists in two steps, namely the inversion of Biot's equations and the inversion of Maxwell equations. We analyze the reconstruction of conductivity and electro-kinetic mobility parameter in Maxwell equations with internal measurements, while the internal measurements are provided by the results of the inversion of Biot's equations. We show that knowledge of two internal data based on well-chosen boundary conditions uniquely determines these two parameters. Moreover, a Lipschitz-type stability is proved based on the same sets of well-chosen boundary conditions.

  4. Inverse Doppler Effects in Broadband Acoustic Metamaterials

    NASA Astrophysics Data System (ADS)

    Zhai, S. L.; Zhao, X. P.; Liu, S.; Shen, F. L.; Li, L. L.; Luo, C. R.

    2016-08-01

    The Doppler effect refers to the change in frequency of a wave source as a consequence of the relative motion between the source and an observer. Veselago theoretically predicted that materials with negative refractions can induce inverse Doppler effects. With the development of metamaterials, inverse Doppler effects have been extensively investigated. However, the ideal material parameters prescribed by these metamaterial design approaches are complex and also challenging to obtain experimentally. Here, we demonstrated a method of designing and experimentally characterising arbitrary broadband acoustic metamaterials. These omni-directional, double-negative, acoustic metamaterials are constructed with ‘flute-like’ acoustic meta-cluster sets with seven double meta-molecules; these metamaterials also overcome the limitations of broadband negative bulk modulus and mass density to provide a region of negative refraction and inverse Doppler effects. It was also shown that inverse Doppler effects can be detected in a flute, which has been popular for thousands of years in Asia and Europe.

  5. Case of paracentric inversion 19p

    SciTech Connect

    Bettio, D.; Rizzi, N.; Giardino, D.

    1995-09-25

    Paracentric inversions have been described less frequently than pericentric ones. It is not known whether this is due to their rarity or rather to difficulty in detecting intra-arm rearrangements. Paracentric inversions have been noted in all chromosomes except chromosome 19; the short arm was involved in 21 cases and the long arm in 87. We describe the first case of paracentric inversion in chromosome 19. The patient, a 29-year-old man, was referred for cytogenetic investigation because his wife had had 3 spontaneous abortions. No history of subfertility was recorded. Chromosome studies on peripheral blood lymphocytes demonstrated an abnormal QFQ banding pattern in the short arm of one chromosome 19. The comparison between QFQ, GTG and RBA banding led us to suspect a paracentric inversion involving the chromosome 19 short arm. CBG banding resulted in an apparently normal position of the centromere. Parental chromosome studies showed the same anomaly in the patient`s mother. 4 refs.

  6. Magnetostatics of superconductors without an inversion center

    SciTech Connect

    Levitov, L.S.; Nazarov, Y.V.; Eliashberg, G.M.

    1985-05-10

    The penetration of a magnetic field into a London superconductor without an inversion center is analyzed. The magnetization produced in the Meissner layer corresponds to a magnetic-induction jump at the superconductor surface.

  7. Analytic solutions of inverse heat conduction problems

    NASA Astrophysics Data System (ADS)

    Al-Najem, N. M.

    A direct analytic approach is systematically developed for solving inverse heat conduction problems in multi-dimensional finite regions. The inverse problems involve the determination of the surface conditions from the knowledge of the time variation of the temperature at an interior point in the region. In the present approach, the unknown surface temperature is represented by a polynominal in time and a splitting-up procedure is employed to develop a rapidly converging inverse solution. The least square technique is then utilized to estimate the unknown parameters associated with the solution. The method is developed first for the analysis of one-dimensional cases, and then it is generalized to handle two- and three-dimensional situations. It provides an efficient, stable and systematic approach for inverse heat condition problems. The stability and accuracy of the current method of analysis are demonstrated by several numerical examples chosen to provide a very strict test.

  8. Electromagnetic inverse applications for functional brain imaging

    SciTech Connect

    Wood, C.C.

    1997-10-01

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). This project addresses an important mathematical and computational problem in functional brain imaging, namely the electromagnetic {open_quotes}inverse problem.{close_quotes} Electromagnetic brain imaging techniques, magnetoencephalography (MEG) and electroencephalography (EEG), are based on measurements of electrical potentials and magnetic fields at hundreds of locations outside the human head. The inverse problem is the estimation of the locations, magnitudes, and time-sources of electrical currents in the brain from surface measurements. This project extends recent progress on the inverse problem by combining the use of anatomical constraints derived from magnetic resonance imaging (MRI) with Bayesian and other novel algorithmic approaches. The results suggest that we can achieve significant improvements in the accuracy and robustness of inverse solutions by these two approaches.

  9. Psychosocial Recovery and Rehabilitation.

    PubMed

    Antai-Otong, Deborah

    2016-06-01

    This article discusses a psychosocial recovery and rehabilitation recovery model that uses an intensive case management approach. The approach offers an interdisciplinary model that integrates pharmacotherapy, social skills training, cognitive remediation, family involvement, and community integration. This evidence-based plan of care instills hope and nurtures one's capacity to learn and improve function and quality of life. It is cost-effective and offers psychiatric nurses opportunities to facilitate symptomatic remission, facilitate self-efficacy, and improve communication and social cognition skills. Nurses in diverse practice settings must be willing to plan and implement innovative treatment models that provide seamless mental health care across the treatment continuum. PMID:27229282

  10. Rockets for spin recovery

    NASA Technical Reports Server (NTRS)

    Whipple, R. D.

    1980-01-01

    The potential effectiveness of rockets as an auxiliary means for an aircraft to effect recovery from spins was investigated. The advances in rocket technology produced by the space effort suggested that currently available systems might obviate many of the problems encountered in earlier rocket systems. A modern fighter configuration known to exhibit a flat spin mode was selected. An analytical study was made of the thrust requirements for a rocket spin recovery system for the subject configuration. These results were then applied to a preliminary systems study of rocket components appropriate to the problem. Subsequent spin tunnel tests were run to evaluate the analytical results.

  11. JLAB Hurricane recovery

    SciTech Connect

    A. Hutton; D. Arenius; J. Benesch; S. Chattopadhyay; E. F. Daly; O. Garza; R. Kazimi; R. Lauzi; L. Merminga; W. Merz; R. Nelson; W. Oren; M. Poelker; P. Powers; J. Preble; V. Ganni; C. R. Reece; R. Rimmer; M. Spata; S. Suhring

    2004-07-01

    Hurricane Isabel, originally a Category 5 storm, arrived at Jefferson Lab on September 18, 2003 with winds of only 75 mph, creating little direct damage to the infrastructure. However, electric power was lost for four days allowing the superconducting cryomodules to warm up and causing a total loss of the liquid helium. The subsequent recovery of the cryomodules and the impact of the considerable amount of opportunistic preventive maintenance provides important lessons for all accelerator complexes, not only those with superconducting elements. The details of how the recovery process was structured and the resulting improvement in accelerator availability will be discussed in detail.

  12. Wash water recovery system

    NASA Technical Reports Server (NTRS)

    Deckman, G.; Rousseau, J. (Editor)

    1973-01-01

    The Wash Water Recovery System (WWRS) is intended for use in processing shower bath water onboard a spacecraft. The WWRS utilizes flash evaporation, vapor compression, and pyrolytic reaction to process the wash water to allow recovery of potable water. Wash water flashing and foaming characteristics, are evaluated physical properties, of concentrated wash water are determined, and a long term feasibility study on the system is performed. In addition, a computer analysis of the system and a detail design of a 10 lb/hr vortex-type water vapor compressor were completed. The computer analysis also sized remaining system components on the basis of the new vortex compressor design.

  13. Inverse agonism and its therapeutic significance

    PubMed Central

    Khilnani, Gurudas; Khilnani, Ajeet Kumar

    2011-01-01

    A large number of G-protein-coupled receptors (GPCRs) show varying degrees of basal or constitutive activity. This constitutive activity is usually minimal in natural receptors but is markedly observed in wild type and mutated (naturally or induced) receptors. According to conventional two-state drug receptor interaction model, binding of a ligand may initiate activity (agonist with varying degrees of positive intrinsic activity) or prevent the effect of an agonist (antagonist with zero intrinsic activity). Inverse agonists bind with the constitutively active receptors, stabilize them, and thus reduce the activity (negative intrinsic activity). Receptors of many classes (α-and β-adrenergic, histaminergic, GABAergic, serotoninergic, opiate, and angiotensin receptors) have shown basal activity in suitable in vitro models. Several drugs that have been conventionally classified as antagonists (β-blockers, antihistaminics) have shown inverse agonist effects on corresponding constitutively active receptors. Nearly all H1 and H2 antihistaminics (antagonists) have been shown to be inverse agonists. Among the β-blockers, carvedilol and bucindolol demonstrate low level of inverse agonism as compared to propranolol and nadolol. Several antipsychotic drugs (D2 receptors antagonist), antihypertensive (AT1 receptor antagonists), antiserotoninergic drugs and opioid antagonists have significant inverse agonistic activity that contributes partly or wholly to their therapeutic value. Inverse agonism may also help explain the underlying mechanism of beneficial effects of carvedilol in congestive failure, naloxone-induced withdrawal syndrome in opioid dependence, clozapine in psychosis, and candesartan in cardiac hypertrophy. Understanding inverse agonisms has paved a way for newer drug development. It is now possible to develop agents, which have only desired therapeutic value and are devoid of unwanted adverse effect. Pimavanserin (ACP-103), a highly selective 5-HT2A inverse

  14. A fluorophosphate-based inverse Keggin structure

    SciTech Connect

    Fielden, John; Quasdorf, Kyle; Cronin, Leroy; Kogerler, Paul

    2012-07-17

    An unusual PFO(3)(2-)-templated "inverse Keggin" polyanion, [Mo(12)O(46)(PF)(4)](4-), has been isolated from the degradation reaction of an {Mo(132)}-type Keplerate to [PMo(12)O(40)](3-) by [Cu(MeCN)(4)](PF(6)) in acetonitrile. (31)P-NMR studies suggest a structure-directing role for [Cu(MeCN)(4)](+) in the formation of the highly unusual all-inorganic inverse Keggin structure.

  15. Inversion of elastic impedance for unconsolidated sediments

    USGS Publications Warehouse

    Lee, Myung W.

    2006-01-01

    Elastic properties of gas-hydrate-bearing sediments are important for quantifying gas hydrate amounts as well as discriminating the gas hydrate effect on velocity from free gas or pore pressure. This paper presents an elastic inversion method for estimating elastic properties of gas-hydrate-bearing sediments from angle stacks using sequential inversion of P-wave impedance from the zero-offset stack and S-wave impedance from the far-offset stack without assuming velocity ratio.

  16. Inverse compton effect: some consequences for quasars.

    PubMed

    Pfleiderer, J; Grewing, M

    1966-12-16

    The inverse Compton effect can transform enough energy of relativistic electrons into radiation so that an upper limit to the mean energy of the electrons is set. In quasars, the limit is too small to allow the production of any appreciable amount of synchrotron or inverse Compton radiation, unless either the distances are not cosmological or the lifetimes of the relativistic electrons are extremely short, of the order of hours.

  17. Geoacoustic inversion with ships as sources.

    PubMed

    Koch, Robert A; Knobles, David P

    2005-02-01

    Estimation of geoacoustic parameters using acoustic data from a surface ship was performed for a shallow water region in the Gulf of Mexico. The data were recorded from hydrophones in a bottom mounted, horizontal line array (HLA). The techniques developed to produce the geoacoustic inversion are described, and an efficient method for geoacoustic inversion with broadband beam cross-spectral data is demonstrated. The performance of cost functions that involve coherent or incoherent sums over frequency and one or multiple time segments is discussed. Successful inversions for the first sediment layer sound speed and thickness and some of the parameters for the deeper layers were obtained with the surface ship at nominal ranges of 20, 30, or 50 water depths. The data for these inversions were beam cross-spectra from four subapertures of the HLA spanning a little more than two water depths. The subaperture beams included ten frequencies equally spaced in the 120-200 Hz band. The values of the geoacoustic parameters from the inversions are validated by comparisons with geophysical observations and with the parameter values from previous inversions by other invesigators, and by comparing transmission loss (TL) measured in the experiment with modeled TL based on the inverted geoacoustic parameters.

  18. Inverse scattering problems with multi-frequencies

    NASA Astrophysics Data System (ADS)

    Bao, Gang; Li, Peijun; Lin, Junshan; Triki, Faouzi

    2015-09-01

    This paper is concerned with computational approaches and mathematical analysis for solving inverse scattering problems in the frequency domain. The problems arise in a diverse set of scientific areas with significant industrial, medical, and military applications. In addition to nonlinearity, there are two common difficulties associated with the inverse problems: ill-posedness and limited resolution (diffraction limit). Due to the diffraction limit, for a given frequency, only a low spatial frequency part of the desired parameter can be observed from measurements in the far field. The main idea developed here is that if the reconstruction is restricted to only the observable part, then the inversion will become stable. The challenging task is how to design stable numerical methods for solving these inverse scattering problems inspired by the diffraction limit. Recently, novel recursive linearization based algorithms have been presented in an attempt to answer the above question. These methods require multi-frequency scattering data and proceed via a continuation procedure with respect to the frequency from low to high. The objective of this paper is to give a brief review of these methods, their error estimates, and the related mathematical analysis. More attention is paid to the inverse medium and inverse source problems. Numerical experiments are included to illustrate the effectiveness of these methods.

  19. Inverse Bremsstrahlung in Shocked Astrophysical Plasmas

    NASA Technical Reports Server (NTRS)

    Baring, Matthew G.; Jones, Frank C.; Ellison, Donald C.

    2000-01-01

    There has recently been interest in the role of inverse bremsstrahlung, the emission of photons by fast suprathermal ions in collisions with ambient electrons possessing relatively low velocities, in tenuous plasmas in various astrophysical contexts. This follows a long hiatus in the application of suprathermal ion bremsstrahlung to astrophysical models since the early 1970s. The potential importance of inverse bremsstrahlung relative to normal bremsstrahlung, i.e. where ions are at rest, hinges upon the underlying velocity distributions of the interacting species. In this paper, we identify the conditions under which the inverse bremsstrahlung emissivity is significant relative to that for normal bremsstrahlung in shocked astrophysical plasmas. We determine that, since both observational and theoretical evidence favors electron temperatures almost comparable to, and certainly not very deficient relative to proton temperatures in shocked plasmas, these environments generally render inverse bremsstrahlung at best a minor contributor to the overall emission. Hence inverse bremsstrahlung can be safely neglected in most models invoking shock acceleration in discrete sources such as supernova remnants. However, on scales approximately > 100 pc distant from these sources, Coulomb collisional losses can deplete the cosmic ray electrons, rendering inverse bremsstrahlung, and perhaps bremsstrahlung from knock-on electrons, possibly detectable.

  20. On the edge of an inverse cascade.

    PubMed

    Seshasayanan, Kannabiran; Benavides, Santiago Jose; Alexakis, Alexandros

    2014-11-01

    We demonstrate that systems with a parameter-controlled inverse cascade can exhibit critical behavior for which at the critical value of the control parameter the inverse cascade stops. In the vicinity of such a critical point, standard phenomenological estimates for the energy balance will fail since the energy flux towards large length scales becomes zero. We demonstrate this using the computationally tractable model of two-dimensional (2D) magnetohydrodynamics in a periodic box. In the absence of any external magnetic forcing, the system reduces to hydrodynamic fluid turbulence with an inverse energy cascade. In the presence of strong magnetic forcing, the system behaves as 2D magnetohydrodynamic turbulence with forward energy cascade. As the amplitude of the magnetic forcing is varied, a critical value is met for which the energy flux towards the large scales becomes zero. Close to this point, the energy flux scales as a power law with the departure from the critical point and the normalized amplitude of the fluctuations diverges. Similar behavior is observed for the flux of the square vector potential for which no inverse flux is observed for weak magnetic forcing, while a finite inverse flux is observed for magnetic forcing above the critical point. We conjecture that this behavior is generic for systems of variable inverse cascade. PMID:25493730

  1. Sol-gel co-assembly of hollow cylindrical inverse opals and inverse opal columns.

    PubMed

    Haibin, Ni; Ming, Wang; Wei, Chen

    2011-12-19

    A facile approach of fabricating hollow cylindrical inverse opals and inverse opal columns by sol-gel co-assembly method was proposed. Polystyrene (PS) colloidal suspension added with hydrolyzed silicate precursor solution was used to self-assemble composite colloidal crystals which consist of PS colloidal crystal template and infiltrated silica gel in the interstitial of microspheres. Continuous hollow cylindrical composite colloidal crystal films have been produced on capillaries' outside and internal surface. Composite colloidal crystal columns which filling up the interior of a capillary were fabricated by pressure assisted sol-gel co-assembly method. Hollow cylindrical inverse opals and inverse opal columns were obtained after removing PS colloidal crystal from the composite colloidal crystal. Optical properties of the silica hollow cylindrical inverse opals were characterized by transmission spectrum and a stop band was observed. Structure and optical properties of the inverse opal columns were investigated. PMID:22274178

  2. Sol-gel co-assembly of hollow cylindrical inverse opals and inverse opal columns.

    PubMed

    Haibin, Ni; Ming, Wang; Wei, Chen

    2011-12-19

    A facile approach of fabricating hollow cylindrical inverse opals and inverse opal columns by sol-gel co-assembly method was proposed. Polystyrene (PS) colloidal suspension added with hydrolyzed silicate precursor solution was used to self-assemble composite colloidal crystals which consist of PS colloidal crystal template and infiltrated silica gel in the interstitial of microspheres. Continuous hollow cylindrical composite colloidal crystal films have been produced on capillaries' outside and internal surface. Composite colloidal crystal columns which filling up the interior of a capillary were fabricated by pressure assisted sol-gel co-assembly method. Hollow cylindrical inverse opals and inverse opal columns were obtained after removing PS colloidal crystal from the composite colloidal crystal. Optical properties of the silica hollow cylindrical inverse opals were characterized by transmission spectrum and a stop band was observed. Structure and optical properties of the inverse opal columns were investigated.

  3. Recovery of discarded sulfated lead-acid batteries

    NASA Astrophysics Data System (ADS)

    Karami, Hassan; Asadi, Raziyeh

    The aim of this research is to recover discarded sulfated lead-acid batteries. In this work, the effect of two methods (inverse charge and chemical charge) on the reactivation of sulfated active materials was investigated. At the inverse charge, the battery is deeply discharged and the electrolyte of battery is replaced with a new sulfuric acid solution of 1.28 g cm -3. Then, the battery is inversely charged with constant current method (2 A for the battery with the nominal capacity of 40 Ah) for 24 h. At the final stage, the inversely charged battery is directly charged for 48 h. Through these processes, a discarded battery can recover its capacity to more than 80% of a similar fresh and non-sulfated battery. At the chemical charge method, there are some effective parameters that including ammonium persulfate [(NH 4) 2S 2O 8] concentration, recovery temperature and recovery time. The effect of all parameters was optimized by one at a time method. The sulfated battery is deeply discharged and then, its electrolyte was replaced by a 40% ammonium persulfate solution (as oxidant) at temperature of 50 °C. By adding of oxidant solution, the chemical charging of positive and negative plates was performed for optimum time of 1 h. The chemically charged batteries were charged with constant voltage method (2.66 V for the battery with nominal voltage and nominal capacity of 2 V and 10 Ah, respectively) for 24 h. By performing of these processes, a discarded battery can recovers its capacity to more than 84% of the similar fresh and non-sulfated battery. Discharge and cyclelife behaviors of the recovered batteries were investigated and compared with similar healthy battery. The morphology and structure of plates was studied by scanning electron microscopy (SEM) before and after recovery.

  4. Application of the least-squares inversion method: Fourier series versus waveform inversion

    NASA Astrophysics Data System (ADS)

    Min, Dong-Joo; Shin, Jungkyun; Shin, Changsoo

    2015-11-01

    We describe an implicit link between waveform inversion and Fourier series based on inversion methods such as gradient, Gauss-Newton, and full Newton methods. Fourier series have been widely used as a basic concept in studies on seismic data interpretation, and their coefficients are obtained in the classical Fourier analysis. We show that Fourier coefficients can also be obtained by inversion algorithms, and compare the method to seismic waveform inversion algorithms. In that case, Fourier coefficients correspond to model parameters (velocities, density or elastic constants), whereas cosine and sine functions correspond to components of the Jacobian matrix, that is, partial derivative wavefields in seismic inversion. In the classical Fourier analysis, optimal coefficients are determined by the sensitivity of a given function to sine and cosine functions. In the inversion method for Fourier series, Fourier coefficients are obtained by measuring the sensitivity of residuals between given functions and test functions (defined as the sum of weighted cosine and sine functions) to cosine and sine functions. The orthogonal property of cosine and sine functions makes the full or approximate Hessian matrix become a diagonal matrix in the inversion for Fourier series. In seismic waveform inversion, the Hessian matrix may or may not be a diagonal matrix, because partial derivative wavefields correlate with each other to some extent, making them semi-orthogonal. At the high-frequency limits, however, the Hessian matrix can be approximated by either a diagonal matrix or a diagonally-dominant matrix. Since we usually deal with relatively low frequencies in seismic waveform inversion, it is not diagonally dominant and thus it is prohibitively expensive to compute the full or approximate Hessian matrix. By interpreting Fourier series with the inversion algorithms, we note that the Fourier series can be computed at an iteration step using any inversion algorithms such as the

  5. Effects of Inversions on Within- and Between-Species Recombination and Divergence

    PubMed Central

    Stevison, Laurie S.; Hoehn, Kenneth B.; Noor, Mohamed A. F.

    2011-01-01

    Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing-over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and Drosophila persimilis, we detected one double recombinant among 9,739 progeny from F1 hybrids screened, consistent with published double-crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species versus within species. Moreover, we observed strong “interchromosomal effect” (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within versus between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible

  6. A Direct Inversion Scheme For Dc Resistivity Data Using Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Stephen, Jimmy; Manoj, C.; Singh, S. B.

    carried out over Southern Granulite terrain were used. Wide variation of apparent resistivity (102 to 105 Ohm-m) was present in all the three curves. The ANN based inversion resulted in 90% recovery of resistiv- ity parameters and 85% recovery in thickness parameters, as compared to envisaged models. The small discrepancies noticed, however, are well within the resolvability of the resistivity sounding.

  7. ONSITE SOLVENT RECOVERY

    EPA Science Inventory

    This study evaluated the product quality, waste reduction/pollution prevention, and economic aspects of three technologies for onsite solvent recovery. The technologies were (1) atmospheric batch distillation, (2) vacuum heat-pump distillation, and (3) low-emission vapor degreas...

  8. Monkey Able After Recovery

    NASA Technical Reports Server (NTRS)

    1959-01-01

    On May 28, 1959, a Jupiter Intermediate Range Ballistic Missile provided by a U.S. Army team in Redstone Arsenal, Alabama, launched a nose cone carrying Baker, A South American squirrel monkey and Able, An American-born rhesus monkey. This photograph shows Able after recovery of the nose cone of the Jupiter rocket by U.S.S. Kiowa.

  9. Recovery of EUVL substrates

    SciTech Connect

    Vernon, S.P.; Baker, S.L.

    1995-01-19

    Mo/Si multilayers, were removed from superpolished zerodur and fused silica substrates with a dry etching process that, under suitable processing conditions, produces negligible change in either the substrate surface figure or surface roughness. Full recovery of the initial normal incidence extreme ultra-violet (EUV) reflectance response has been demonstrated on reprocessed substrates.

  10. Cost Recovery Through Depreciation.

    ERIC Educational Resources Information Center

    Forrester, Robert T.; Wesolowski, Leonard V.

    1983-01-01

    The approach of adopting depreciation rather than use allowance in order to recover more accurately the cost of college buildings and equipment used on federal projects is considered. It is suggested that depreciation will offer most colleges and universities a higher annual recovery rate, and an opportunity for better facilities planning. For…

  11. Recovery post ICU.

    PubMed

    Jones, Christina

    2014-10-01

    Many ICU patients struggle to recovery following critical illness and may be left with physical, cognitive and psychological problems, which have a negative impact on their quality of life. Gross muscle mass loss and weakness can take some months to recover after the patients' Intensive Care Unit (ICU) discharge, in addition critical illness polyneuropathies can further complicate physical recovery. Psychological problems such as anxiety, depression and post traumatic stress disorder (PTSD) are common and have an negative impact on the patients' ability to engage in rehabilitation after ICU discharge. Finally cognitive deficit affecting memory can be a significant problem. The first step in helping patients to recover from such a devastating illness is to recognise those who have the greatest need and target interventions. Research now suggests that there are interventions that can accelerate physical recovery and reduce the incidence of psychological problems such as anxiety, depression and PTSD. Cognitive rehabilitation, however, is still in its infancy. This review will look at the research into patients' recovery and what can be done to improve this where needed.

  12. The inverse problem in electrocardiography: solutions in terms of epicardial potentials.

    PubMed

    Rudy, Y; Messinger-Rapport, B J

    1988-01-01

    The objective of the inverse problem in electrocardiography is to recover noninvasively regional information about intracardiac electrical events from electrical measurements on the body surface. The choice of epicardial potentials as the solution to the inverse problem is motivated by the availability of a unique epicardial potential solution for each body surface potential distribution, by the ability to verify experimentally the inverse-recovered epicardial potentials, by the proven relationship between epicardial potentials and the details of intracardiac regional events, and by the possibility of using the inverse solution as a supplement or possible replacement to clinical epicardial potential mapping prior to surgical intervention. Although, in principle, the epicardial potential distribution can be recovered from the body surface potential distribution, the inverse problem in terms of potentials is ill-posed, and naive attempts to reconstruct the epicardial potentials result in incorrect solutions which are highly oscillatory. Large deviations from the actual solution may result from inaccuracy of the data measurement, incomplete knowledge of the potential data over the entire torso, and inaccurate description of the inhomogeneous torso volume conductor. This review begins with a mathematical and qualitative description of the inverse problem in terms of epicardial potentials. The ill-posed nature of the problem is demonstrated using a theoretical boundary value problem. Effects of inaccuracies in the body surface potential data (stability estimates) are introduced, and a sensitivity analysis of geometrical and inhomogeneity parameters is presented using an analytical eccentric spheres model. Various computational methods for relating epicardial to body surface potentials, i.e., the computation of the forward transfer matrix, are described and compared. The need for regularization of the inverse recovery of epicardial potentials, resulting from the need to

  13. Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis).

    PubMed

    Huynh, L Y; Maney, D L; Thomas, J W

    2011-04-01

    Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2(m)) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2(m) polymorphism is a complex inversion spanning > 100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2(m) polymorphism, we generated sequence from 8 ZAL2(m) and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2(m), resulting in uniformly high levels of genetic differentiation (F(ST)=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ~104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2(m) homozygotes are exceedingly rare in the population, occurring at a frequency of < 1%, we detected evidence of historical recombination between ZAL2(m) chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.

  14. Source Process of Volcanic Tremor Inferred From Waveform Inversion

    NASA Astrophysics Data System (ADS)

    Garcia-Aristizabal, A.; Kumagai, H.; Nakano, M.

    2004-12-01

    Guagua Pichincha located 12 Km west of Quito, Ecuador, is an active volcano in the Pichincha volcanic complex. Beginning on August 7 1998, Guagua Pichincha activity was characterized by phreatic eruptions, dome growth and collapse, and pyroclastic flows, accompanying volcano-tectonic earthquakes, tremor, and long-period events. In January 2003, after a two-year-long quiescent period, we observed tremor showing harmonic oscillations with a dominant spectral peak at around 2 Hz, which occurred periodically showing well-constrained tremor episodes with active periods of 11 minutes and repose periods of 30 minutes. This type of tremor sequence continued for a few months, and has intermittently occurred until the present. We performed waveform inversions of the tremor to quantify the source process. Since it was recorded only by three seismic stations (three-component seismometers at two stations and a vertical-component seismometer at one station) which are not enough for an accurate description of a moment tensor for the source of tremor, we performed waveform inversions assuming the moment tensors for both horizontal and vertical cracks, and a vertical pipe, which are possible geometries for the source of tremor. We obtained a vertical crack with the strike direction of N80ºE in the northern rim of a dome at a depth nearly 200 m below the caldera floor as the best-fit solution for our inversions. The tremor may be interpreted as the resonance of a vertical crack-like conduit excited during repetitive releases of hot gases which are originating from the contact of hydrothermal water with magma inside the dome.

  15. Control globular structure formation of a copolymer chain through inverse design

    NASA Astrophysics Data System (ADS)

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-01

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  16. Control globular structure formation of a copolymer chain through inverse design.

    PubMed

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-14

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design. PMID:27306020

  17. Inverse bifurcation analysis: application to simple gene systems

    PubMed Central

    Lu, James; Engl, Heinz W; Schuster, Peter

    2006-01-01

    Background Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from parameter space to the space of model behavior, the inverse problem of determining model parameters to result in certain desired properties of the bifurcation diagram provides an attractive methodology for addressing important biological problems. These include understanding how the robustness of qualitative behavior arises from system design as well as providing a way to engineer biological networks with qualitative properties. Results We demonstrate that certain inverse bifurcation problems of biological interest may be cast as optimization problems involving minimal distances of reference parameter sets to bifurcation manifolds. This formulation allows for an iterative solution procedure based on performing a sequence of eigen-system computations and one-parameter continuations of solutions, the latter being a standard capability in existing numerical bifurcation software. As applications of the proposed method, we show that the problem of maximizing regions of a given qualitative behavior as well as the reverse engineering of bistable gene switches can be modelled and efficiently solved. PMID:16859561

  18. Dynamics of the inverse MAPLE nanoparticle deposition process

    NASA Astrophysics Data System (ADS)

    Steiner, Matthew A.; Fitz-Gerald, James M.

    2015-05-01

    Matrix-assisted pulsed laser evaporation (MAPLE) is a processing technique by which laser-sensitive materials are dissolved or placed into colloidal solution with a strongly absorbing sacrificial solvent, which when frozen into a solid target and irradiated under vacuum disperses the undamaged solute material onto a desired substrate. We present an inversion of the original MAPLE process, where the irradiation of metal-based acetate precursors in solution with UV transparent water results in the deposition of inorganic nanoparticles. A theory is forwarded to explain the underlying multiscale sequence of events that control the inverse MAPLE process from acetate decomposition to nanoparticle formation and subsequent ejection. Support for this theory is provided through the analysis of deposited nanoparticles and by novel characterization of MAPLE targets post-irradiation via cryostage scanning electron microscopy. Ejection is shown to proceed through the same phase-explosion mechanism that drives conventional MAPLE, relating the two techniques and advancing the broader understanding of MAPLE deposition processes.

  19. Varying prior information in Bayesian inversion

    NASA Astrophysics Data System (ADS)

    Walker, Matthew; Curtis, Andrew

    2014-06-01

    Bayes' rule is used to combine likelihood and prior probability distributions. The former represents knowledge derived from new data, the latter represents pre-existing knowledge; the Bayesian combination is the so-called posterior distribution, representing the resultant new state of knowledge. While varying the likelihood due to differing data observations is common, there are also situations where the prior distribution must be changed or replaced repeatedly. For example, in mixture density neural network (MDN) inversion, using current methods the neural network employed for inversion needs to be retrained every time prior information changes. We develop a method of prior replacement to vary the prior without re-training the network. Thus the efficiency of MDN inversions can be increased, typically by orders of magnitude when applied to geophysical problems. We demonstrate this for the inversion of seismic attributes in a synthetic subsurface geological reservoir model. We also present results which suggest that prior replacement can be used to control the statistical properties (such as variance) of the final estimate of the posterior in more general (e.g., Monte Carlo based) inverse problem solutions.

  20. Inversion concept of the origin of life.

    PubMed

    Kompanichenko, V N

    2012-06-01

    The essence of the inversion concept of the origin of life can be narrowed down to the following theses: 1) thermodynamic inversion is the key transformation of prebiotic microsystems leading to their transition into primary forms of life; 2) this transformation might occur only in the microsystems oscillating around the bifurcation point under far-from-equilibrium conditions. The transformation consists in the inversion of the balance "free energy contribution / entropy contribution", from negative to positive values. At the inversion moment the microsystem radically reorganizes in accordance with the new negentropy (i.e. biological) way of organization. According to this approach, the origin-of-life process on the early Earth took place in the fluctuating hydrothermal medium. The process occurred in two successive stages: a) spontaneous self-assembly of initial three-dimensional prebiotic microsystems composed mainly of hydrocarbons, lipids and simple amino acids, or their precursors, within the temperature interval of 100-300°C (prebiotic stage); b) non-spontaneous synthesis of sugars, ATP and nucleic acids started at the inversion moment under the temperature 70-100°C (biotic stage). Macro- and microfluctuations of thermodynamic and physico-chemical parameters able to sustain this way of chemical conversion have been detected in several contemporary hydrothermal systems. A minimal self-sufficient unit of life on the early Earth was a community of simplest microorganisms (not a separate microorganism).

  1. The rotation-inversion spectrum of cyanamide

    NASA Astrophysics Data System (ADS)

    Read, W. G.; Cohen, E. A.; Pickett, H. M.

    1986-02-01

    The microwave, millimeter, and submillimeter spectra of cyanamide were studied to better determine the inversion-rotation parameters of the ground and first excited states. A total of 146 transitions including 64 rotation-inversion frequencies between 7 and 500 GHz have been measured at this laboratory. An additional 118 a-type R-branch transitions between 139 and 262 GHz measured by Möller and Winnewisser at Justus Liebig University, Giessen, have also been included in the analysis. The data were fitted to a Hamiltonian which contains a rotation-inversion interaction as an off-diagonal inertial term. The interpretation of the interaction term in terms of the molecular structure and inversion motion is in good agreement with experiment. Higher order rotational effects were handled with a Watson " S" centrifugal distortion Hamiltonian. The inversion splitting, rotational constants, centrifugal distortion constants, nitrogen nuclear quadrupole coupling tensors including χac for the amino nitrogen, and the a and c components of the electric dipole moment are reported.

  2. Speaker independent acoustic-to-articulatory inversion

    NASA Astrophysics Data System (ADS)

    Ji, An

    Acoustic-to-articulatory inversion, the determination of articulatory parameters from acoustic signals, is a difficult but important problem for many speech processing applications, such as automatic speech recognition (ASR) and computer aided pronunciation training (CAPT). In recent years, several approaches have been successfully implemented for speaker dependent models with parallel acoustic and kinematic training data. However, in many practical applications inversion is needed for new speakers for whom no articulatory data is available. In order to address this problem, this dissertation introduces a novel speaker adaptation approach called Parallel Reference Speaker Weighting (PRSW), based on parallel acoustic and articulatory Hidden Markov Models (HMM). This approach uses a robust normalized articulatory space and palate referenced articulatory features combined with speaker-weighted adaptation to form an inversion mapping for new speakers that can accurately estimate articulatory trajectories. The proposed PRSW method is evaluated on the newly collected Marquette electromagnetic articulography -- Mandarin Accented English (EMA-MAE) corpus using 20 native English speakers. Cross-speaker inversion results show that given a good selection of reference speakers with consistent acoustic and articulatory patterns, the PRSW approach gives good speaker independent inversion performance even without kinematic training data.

  3. On the nonuniqueness of receiver function inversions

    SciTech Connect

    Ammon, C.J. ); Randall, G.E. ); Zandt, G. )

    1990-09-10

    To study the resolving power of teleseismic P waveforms for receiver structure, the authors model synthetic waveforms using a time domain waveform inversion scheme beginning with a range of initial models to estimate the range of acceptable velocity structures. To speed up the waveform inversions, they implement Randall's (1989) efficient algorithms for calculating differential seismograms and include a smoothness constraint on all the resulting velocity models utilizing the jumping inversion technique of Shaw and Orcutt (1985). They present the results of more than 235 waveform inversions for one-dimensional velocity structures that indicate that the primary sensitivity of a receiver function is to high wavenumber velocity changes, and a depth-velocity product, not simply velocity. The range of slownesses in a typical receiver function study does not appear to be broad enough to remove the depth-velocity ambiguity; the inclusion of a priori information is necessary. They also present inversion results for station RSCP, located in the Cumberland Plateau, Tennessee. The results are similar to those from a previous study by Owens et al. (1984) and demonstrate the uncertainties in the resulting velocity estimate more clearly.

  4. Structural state testing using eddy current inversion

    NASA Astrophysics Data System (ADS)

    Dolgov, N. Y.; Chernov, L. A.

    2000-05-01

    The inverse eddy current problem can be described as the task of reconstructing an unknown distribution of electrical conductivity from eddy-current probe voltage measurements recorded as function of excitation frequency. Conductivity variation may be a result of surface processing with substances like hydrogen and carbon or surface heating. We developed mathematical reasons and supporting software for inverse conductivity profiling. Inverse problem was solved for layered plane and cylindrical conductors. Because the inverse problem is nonlinear, we propose using an iterative algorithm which can be formalized as the minimization of an error functional related to the difference between the probe voltages theoretically predicted by the direct problem solving and the measured probe voltages. Numerical results were obtained for some models of conductivity distribution. It was shown that inverse problem can be solved exactly in case of correct measurements. Good estimation of the true conductivity distribution takes place also for measurement noise about 2 percent but in the case of 5 percent error, results are worse.

  5. Inversion Concept of the Origin of Life

    NASA Astrophysics Data System (ADS)

    Kompanichenko, V. N.

    2012-06-01

    The essence of the inversion concept of the origin of life can be narrowed down to the following theses: 1) thermodynamic inversion is the key transformation of prebiotic microsystems leading to their transition into primary forms of life; 2) this transformation might occur only in the microsystems oscillating around the bifurcation point under far-from-equilibrium conditions. The transformation consists in the inversion of the balance "free energy contribution / entropy contribution", from negative to positive values. At the inversion moment the microsystem radically reorganizes in accordance with the new negentropy (i.e. biological) way of organization. According to this approach, the origin-of-life process on the early Earth took place in the fluctuating hydrothermal medium. The process occurred in two successive stages: a) spontaneous self-assembly of initial three-dimensional prebiotic microsystems composed mainly of hydrocarbons, lipids and simple amino acids, or their precursors, within the temperature interval of 100-300°C (prebiotic stage); b) non-spontaneous synthesis of sugars, ATP and nucleic acids started at the inversion moment under the temperature 70-100°C (biotic stage). Macro- and microfluctuations of thermodynamic and physico-chemical parameters able to sustain this way of chemical conversion have been detected in several contemporary hydrothermal systems. A minimal self-sufficient unit of life on the early Earth was a community of simplest microorganisms (not a separate microorganism).

  6. Inverse kinematic-based robot control

    NASA Technical Reports Server (NTRS)

    Wolovich, W. A.; Flueckiger, K. F.

    1987-01-01

    A fundamental problem which must be resolved in virtually all non-trivial robotic operations is the well-known inverse kinematic question. More specifically, most of the tasks which robots are called upon to perform are specified in Cartesian (x,y,z) space, such as simple tracking along one or more straight line paths or following a specified surfacer with compliant force sensors and/or visual feedback. In all cases, control is actually implemented through coordinated motion of the various links which comprise the manipulator; i.e., in link space. As a consequence, the control computer of every sophisticated anthropomorphic robot must contain provisions for solving the inverse kinematic problem which, in the case of simple, non-redundant position control, involves the determination of the first three link angles, theta sub 1, theta sub 2, and theta sub 3, which produce a desired wrist origin position P sub xw, P sub yw, and P sub zw at the end of link 3 relative to some fixed base frame. Researchers outline a new inverse kinematic solution and demonstrate its potential via some recent computer simulations. They also compare it to current inverse kinematic methods and outline some of the remaining problems which will be addressed in order to render it fully operational. Also discussed are a number of practical consequences of this technique beyond its obvious use in solving the inverse kinematic question.

  7. O'Sullivan's hydrostatic reduction of an inverted uterus: sonar sequence recorded.

    PubMed

    Ward, H R

    1998-10-01

    A case of acute uterine inversion which was successfully managed with hydrostatic reduction is reported. A sequence of sonograms demonstrating this is presented, as far as we are aware, for the first time.

  8. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

  9. Inverse Cherenkov and inverse FEL accelerator experiments at the Brookhaven Accelerator Test Facility

    SciTech Connect

    Pogorelsky, I.V.; vanSteenbergen, A.; Babzien, M.

    1995-12-31

    Status update on the ongoing inverse Cherenkov acceleration experiment and prospects to its 100 MeV short-term upgrade. The first report on 1 MeV electron acceleration with the 0.5 GW CO{sub 2} laser used in the inverse FEL scheme. (author). 22 refs., 8 figs., 1 tab.

  10. Interplay of Nitrogen-Atom Inversion and Conformational Inversion in Enantiomerization of 1H-1-Benzazepines.

    PubMed

    Ramig, Keith; Subramaniam, Gopal; Karimi, Sasan; Szalda, David J; Ko, Allen; Lam, Aaron; Li, Jeffrey; Coaderaj, Ani; Cavdar, Leyla; Bogdan, Lukasz; Kwon, Kitae; Greer, Edyta M

    2016-04-15

    A series of 2,4-disubstituted 1H-1-benzazepines, 2a-d, 4, and 6, were studied, varying both the substituents at C2 and C4 and at the nitrogen atom. The conformational inversion (ring-flip) and nitrogen-atom inversion (N-inversion) energetics were studied by variable-temperature NMR spectroscopy and computations. The steric bulk of the nitrogen-atom substituent was found to affect both the conformation of the azepine ring and the geometry around the nitrogen atom. Also affected were the Gibbs free energy barriers for the ring-flip and the N-inversion. When the nitrogen-atom substituent was alkyl, as in 2a-c, the geometry of the nitrogen atom was nearly planar and the azepine ring was highly puckered; the result was a relatively high-energy barrier to ring-flip and a low barrier to N-inversion. Conversely, when the nitrogen-atom substituent was a hydrogen atom, as in 2d, 4, and 6, the nitrogen atom was significantly pyramidalized and the azepine ring was less puckered; the result here was a relatively high energy barrier to N-inversion and a low barrier to ring-flip. In these N-unsubstituted compounds, it was found computationally that the lowest-energy stereodynamic process was ring-flip coupled with N-inversion, as N-inversion alone had a much higher energy barrier.

  11. URANIUM RECOVERY PROCESS

    DOEpatents

    Stevenson, J.W.; Werkema, R.G.

    1959-07-28

    The recovery of uranium from magnesium fluoride slag obtained as a by- product in the production of uranium metal by the bomb reduction prccess is presented. Generally the recovery is accomplished by finely grinding the slag, roasting ihe ground slag air, and leaching the roasted slag with a hot, aqueous solution containing an excess of the sodium bicarbonate stoichiometrically required to form soluble uranium carbonate complex. The roasting is preferably carried out at between 425 and 485 deg C for about three hours. The leaching is preferably done at 70 to 90 deg C and under pressure. After leaching and filtration the uranium may be recovered from the clear leach liquor by any desired method.

  12. Gasoline Vapor Recovery

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Gasoline is volatile and some of it evaporates during storage, giving off hydrocarbon vapor. Formerly, the vapor was vented into the atmosphere but anti-pollution regulations have precluded that practice in many localities, so oil companies and storage terminals are installing systems to recover hydrocarbon vapor. Recovery provides an energy conservation bonus in that most of the vapor can be reconverted to gasoline. Two such recovery systems are shown in the accompanying photographs (mid-photo at right and in the foreground below). They are actually two models of the same system, although.configured differently because they are customized to users' needs. They were developed and are being manufactured by Edwards Engineering Corporation, Pompton Plains, New Jersey. NASA technological information proved useful in development of the equipment.

  13. Elemental sulfur recovery process

    DOEpatents

    Flytzani-Stephanopoulos, M.; Zhicheng Hu.

    1993-09-07

    An improved catalytic reduction process for the direct recovery of elemental sulfur from various SO[sub 2]-containing industrial gas streams. The catalytic process provides combined high activity and selectivity for the reduction of SO[sub 2] to elemental sulfur product with carbon monoxide or other reducing gases. The reaction of sulfur dioxide and reducing gas takes place over certain catalyst formulations based on cerium oxide. The process is a single-stage, catalytic sulfur recovery process in conjunction with regenerators, such as those used in dry, regenerative flue gas desulfurization or other processes, involving direct reduction of the SO[sub 2] in the regenerator off gas stream to elemental sulfur in the presence of a catalyst. 4 figures.

  14. Designer drilling increases recovery

    SciTech Connect

    Eck-Olsen, J.; Drevdal, K.E.

    1995-04-01

    Implementation of a new designer-well profile has resulted in increased recovery and production rates. The geologically complex Gullfaks field, located in the Norwegian sector of the North Sea, required a new type of well profile to increase total recovery and production rates from Gullfaks A, B and C platforms. Advances in steerable technology and directional drilling performance enabled a 3-D horizontal, extended-reach well profile, now designated as a designer well, to penetrate multiple targets. This article presents the concept, implementation and conclusions drawn from designer well application. Gullfaks field, in Norwegian North Sea Block 34/10, is the first license ever run by a fully Norwegian joint venture corporation. The license group consists of Statoil (operator), Norsk Hydro and Saga Petroleum. The field currently produces more than 535,000 bopd from three main Jurassic reservoirs.

  15. Elemental sulfur recovery process

    DOEpatents

    Flytzani-Stephanopoulos, Maria; Hu, Zhicheng

    1993-01-01

    An improved catalytic reduction process for the direct recovery of elemental sulfur from various SO.sub.2 -containing industrial gas streams. The catalytic process provides combined high activity and selectivity for the reduction of SO.sub.2 to elemental sulfur product with carbon monoxide or other reducing gases. The reaction of sulfur dioxide and reducing gas takes place over certain catalyst formulations based on cerium oxide. The process is a single-stage, catalytic sulfur recovery process in conjunction with regenerators, such as those used in dry, regenerative flue gas desulfurization or other processes, involving direct reduction of the SO.sub.2 in the regenerator off gas stream to elemental sulfur in the presence of a catalyst.

  16. Children's Understanding of the Arithmetic Concepts of Inversion and Associativity

    ERIC Educational Resources Information Center

    Robinson, Katherine M.; Ninowski, Jerilyn E.; Gray, Melissa L.

    2006-01-01

    Previous studies have shown that even preschoolers can solve inversion problems of the form a + b - b by using the knowledge that addition and subtraction are inverse operations. In this study, a new type of inversion problem of the form d x e [divided by] e was also examined. Grade 6 and 8 students solved inversion problems of both types as well…

  17. The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

    PubMed Central

    Delprat, Alejandra; Ruiz, Alfredo

    2009-01-01

    Background Transposable elements (TEs) are responsible for the generation of chromosomal inversions in several groups of organisms. However, in Drosophila and other Dipterans, where inversions are abundant both as intraspecific polymorphisms and interspecific fixed differences, the evidence for a role of TEs is scarce. Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii. Methodology/Principal Findings To assess the impact of TEs in Drosophila chromosomal evolution and shed light on the mechanism involved, we isolated and sequenced the two breakpoints of another widespread polymorphic inversion from D. buzzatii, 2z3. In the non inverted chromosome, the 2z3 distal breakpoint was located between genes CG2046 and CG10326 whereas the proximal breakpoint lies between two novel genes that we have named Dlh and Mdp. In the inverted chromosome, the analysis of the breakpoint sequences revealed relatively large insertions (2,870-bp and 4,786-bp long) including two copies of the transposon Galileo (subfamily Newton), one at each breakpoint, plus several other TEs. The two Galileo copies: (i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric. Conclusions/Significance Our observations provide the best evidence gathered so far for the role of TEs in the generation of Drosophila inversions. In addition, they show unequivocally that ectopic recombination is the causative mechanism. The fact that the three polymorphic D. buzzatii inversions investigated so far were generated by the same transposon family is remarkable and is conceivably due to Galileo's unusual structure and current (or recent) transpositional activity. PMID:19936241

  18. Recovery, spirituality and psychotherapy.

    PubMed

    Drobin, Frederick

    2014-06-01

    This article concerns the relationship between addiction recovery, spirituality and psychotherapy. Since its founding, members of AA have been encouraged to pursue a spiritual life. They have also sought psychotherapy. A paradox obtains, because 51 % of therapists are atheists. Others have little awareness of the dynamics of the spiritual life. The developmental process of the spiritual life is discussed, and suggestions are made regarding how a therapist might be helpful in this process.

  19. Energy Recovery System

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Cogeneration system is one in which the energy ordinarily wasted in an industrial process is recovered and reused to create a second form of energy. Such an energy recovery system is in use at Crane Company's plant in Ferguson, KY, which manufactures ceramic bathroom fixtures. Crane's system captures hot stack gases from the company's four ceramic kilns and uses them to produce electrical power for plant operations.

  20. Superconducting energy recovery linacs

    NASA Astrophysics Data System (ADS)

    Ben-Zvi, Ilan

    2016-10-01

    High-average-power and high-brightness electron beams from a combination of laser photocathode electron guns and a superconducting energy recovery linac (ERL) is an emerging accelerator science with applications in ERL light sources, high repetition rate free electron lasers , electron cooling, electron ion colliders and more. This paper reviews the accelerator physics issues of superconducting ERLs, discusses major subsystems and provides a few examples of superconducting ERLs.

  1. Genotyping of intron 22 inversion of factor VIII gene for diagnosis of hemophilia A by inverse-shifting polymerase chain reaction and capillary electrophoresis.

    PubMed

    Pan, Tzu-Yu; Wang, Chun-Chi; Shih, Chi-Jen; Wu, Hui-Fen; Chiou, Shyh-Shin; Wu, Shou-Mei

    2014-09-01

    This is the first capillary electrophoresis (CE) analysis for diagnosis of hemophilia A (HA). The intron 22 inversion of factor VIII gene (F8) causes 40-50 % of severe bleeding disorder of HA in all human populations. Consequently, identification of the disease-causing mutations is becoming increasingly important for accurate genetic counseling and prenatal diagnosis. In this study, the key steps of inverse-shifting polymerase chain reaction (IS-PCR) and of short-end injection capillary electrophoresis were used for more specific and rapid genotyping of intron 22 inversion of F8. In IS-PCR, three specific primers were used to amplify 512-bp amplicon for wild type and 584-bp amplicon for patients with intron 22 inversion. The capillary gel electrophoresis (CGE) system was performed using 1× Tris-borate-EDTA (TBE) buffer containing 0.3 % (w/v) polyethylene oxide (PEO). The PCR amplicons were electrokinetically injected at 10 kV for 10 s at a temperature of 25 °C. The optimal short-end injection CGE was applied to detect the F8 gene of HA patients and carriers within 5 min. Intron 22 inversion was indeed found on some HA patients (13/35, 37.1 %). All genotyping results showed good agreement with DNA sequencing method and long-distance polymerase chain reaction (LD-PCR). The IS-PCR combined with short-end injection CGE method was feasible and efficient for intron 22 inversion screening of F8 in the HA populations.

  2. Energy recovery device

    SciTech Connect

    Evans, V.

    1982-08-31

    The energy recovery device includes a housing having a central shaft which is connected to a lever operating a work-load system capable of generating work-load forces. The central shaft is also connected to a disk having four posts generally parallel to the shaft and initially located at positions corresponding to the four major points of a compass. Within each corner of the housing, a helically coiled spring is positioned over a support post. Each spring has two extending arms which contact two respective adjacent posts on the disk so as to maintain the spring under tension. When the lever is at the neutral position, I.E., when no work-load forces are generated, the recovery forces generated by the four springs within the housing are generally balanced. As the lever is displaced from the neutral position by a driving force, the disk rotates whereby the angular displacement between the arms of any spring decreases. Once the disk is displaced, the spring forces aid in continuing displacement of the disk. Simultaneously the work-load system generates forces which oppose any displacement. The springs are preferably configured and dimensioned so that, at any given displacement of the lever from the neutral position, the recovery forces generally counterbalance the work-load forces. Thus the lever will remain at a given displacement when the driving force applied to the lever is removed. Additionally, the counterbalancing of forces permits continued displacement of the lever with a minimal and constant driving force.

  3. Integral inversion to Fraunhofer diffraction for particle sizing.

    PubMed

    Cao, Zhang; Xu, Lijun; Ding, Jie

    2009-09-01

    A new solution to the inversion of Fraunhofer diffraction for particle sizing was introduced. Compared with the well-known Chin-Shifrin inversion, it is an inversion of the form of integral transform and less sensitive to noise. Simulation results with noise-contaminated data were obtained and showed that the new inversion is better than the Chin-Shifrin inversion. Especially when the particle diameter was small, the new inversion still performed well, whereas the Chin-Shifrin inversion did not converge.

  4. Inverse Papular Acrokeratosis of Oswaldo Costa

    PubMed Central

    Marques, Lidiane Pereira; Trope, Beatriz Moritz; Pina, Juliana Carnevale; Cuzzi, Tullia

    2010-01-01

    Acrokeratoelastoidosis of Oswaldo Costa, or inverse papular acrokeratosis, is a rare genodermatosis first described in 1952 by Oswaldo Costa, a Brazilian dermatologist. It is characterized by flesh-colored papules on the lateral aspects of the palms and soles and dorsum of hands. The histological features are hyperkeratosis, hyalinized and homogenous collagen, and a decrease in and fragmentation of the elastic fibers (elastorrhexis). In the absence of elastic fiber fragmentation, a similar clinical presentation is diagnosed as focal acral hyperkeratosis. Many cases of inverse papular acrokeratosis of Oswaldo Costa may have been considered focal acral hyperkeratosis since it can be difficult to find the elastorrhexis. The authors report a case of a 51-year-old woman with inverse papular acrokeratosis of Oswaldo Costa with poor response to topical treatments. PMID:20725552

  5. Error handling strategies in multiphase inverse modeling

    SciTech Connect

    Finsterle, S.; Zhang, Y.

    2010-12-01

    Parameter estimation by inverse modeling involves the repeated evaluation of a function of residuals. These residuals represent both errors in the model and errors in the data. In practical applications of inverse modeling of multiphase flow and transport, the error structure of the final residuals often significantly deviates from the statistical assumptions that underlie standard maximum likelihood estimation using the least-squares method. Large random or systematic errors are likely to lead to convergence problems, biased parameter estimates, misleading uncertainty measures, or poor predictive capabilities of the calibrated model. The multiphase inverse modeling code iTOUGH2 supports strategies that identify and mitigate the impact of systematic or non-normal error structures. We discuss these approaches and provide an overview of the error handling features implemented in iTOUGH2.

  6. Inverse Scattering Approach to Improving Pattern Recognition

    SciTech Connect

    Chapline, G; Fu, C

    2005-02-15

    The Helmholtz machine provides what may be the best existing model for how the mammalian brain recognizes patterns. Based on the observation that the ''wake-sleep'' algorithm for training a Helmholtz machine is similar to the problem of finding the potential for a multi-channel Schrodinger equation, we propose that the construction of a Schrodinger potential using inverse scattering methods can serve as a model for how the mammalian brain learns to extract essential information from sensory data. In particular, inverse scattering theory provides a conceptual framework for imagining how one might use EEG and MEG observations of brain-waves together with sensory feedback to improve human learning and pattern recognition. Longer term, implementation of inverse scattering algorithms on a digital or optical computer could be a step towards mimicking the seamless information fusion of the mammalian brain.

  7. Inverse scattering approach to improving pattern recognition

    NASA Astrophysics Data System (ADS)

    Chapline, George; Fu, Chi-Yung

    2005-05-01

    The Helmholtz machine provides what may be the best existing model for how the mammalian brain recognizes patterns. Based on the observation that the "wake-sleep" algorithm for training a Helmholtz machine is similar to the problem of finding the potential for a multi-channel Schrodinger equation, we propose that the construction of a Schrodinger potential using inverse scattering methods can serve as a model for how the mammalian brain learns to extract essential information from sensory data. In particular, inverse scattering theory provides a conceptual framework for imagining how one might use EEG and MEG observations of brain-waves together with sensory feedback to improve human learning and pattern recognition. Longer term, implementation of inverse scattering algorithms on a digital or optical computer could be a step towards mimicking the seamless information fusion of the mammalian brain.

  8. FAST INVERSION OF SOLAR Ca II SPECTRA

    SciTech Connect

    Beck, C.; Choudhary, D. P.; Rezaei, R.; Louis, R. E.

    2015-01-10

    We present a fast (<<1 s per profile) inversion code for solar Ca II lines. The code uses an archive of spectra that are synthesized prior to the inversion under the assumption of local thermodynamic equilibrium (LTE). We show that it can be successfully applied to spectrograph data or more sparsely sampled spectra from two-dimensional spectrometers. From a comparison to a non-LTE inversion of the same set of spectra, we derive a first-order non-LTE correction to the temperature stratifications derived in the LTE approach. The correction factor is close to unity up to log τ ∼ –3 and increases to values of 2.5 and 4 at log τ = –6 in the quiet Sun and the umbra, respectively.

  9. Optimization and Inverse Design of Pump Impeller

    NASA Astrophysics Data System (ADS)

    Miyauchi, S.; Zhu, B.; Luo, X.; Piao, B.; Matsumoto, H.; Sano, M.; Kassai, N.

    2012-11-01

    As for pump impellers, the meridional flow channel and blade-to-blade flow channel, which are relatively independent of each other but greatly affect performance, are designed in parallel. And the optimization design is used for the former and the inverse design is used for the latter. To verify this new design method, a mixed-flow impeller was made. Next, we use Tani's inverse design method for the blade loading of inverse design. It is useful enough to change a deceleration rate freely and greatly. And it can integrally express the rear blade loading of various methods by NACA, Zangeneh and Stratford. We controlled the deceleration rate by shape parameter m, and its value became almost same with Tani's recommended value of the laminar airfoil.

  10. A new strategy for helioseismic inversions

    NASA Astrophysics Data System (ADS)

    Eff-Darwich, A.; Perez Hernandez, F.

    1997-10-01

    Helioseismic inversion techniques have been revealed as powerful tools for inferring the internal structure and dynamics of the Sun. One of the most popular techniques is Regularized Least Squares. When it is used, it is necessary to define an inversion mesh and a penalty function, without an a priori knowledge of the behaviour of the solution. In addition, this penalty function is weighted by a trade-off parameter that must be fixed in order to obtain the solution. We present here a new technique, developed in order to find the optimal mesh and smoothing function by means of a deep analysis of the basis functions of the inversion problem. We have found that the method is suitable in particular for obtaining the sound speed and density profiles simultaneously, without any reference to the equation of state.

  11. Inverse obstacle scattering for elastic waves

    NASA Astrophysics Data System (ADS)

    Li, Peijun; Wang, Yuliang; Wang, Zewen; Zhao, Yue

    2016-11-01

    Consider the scattering of a time-harmonic plane wave by a rigid obstacle which is embedded in an open space filled with a homogeneous and isotropic elastic medium. An exact transparent boundary condition is introduced to reduce the scattering problem into a boundary value problem in a bounded domain. Given the incident field, the direct problem is to determine the displacement of the wave field from the known obstacle; the inverse problem is to determine the obstacle’s surface from the measurement of the displacement on an artificial boundary enclosing the obstacle. In this paper, we consider both the direct and inverse problems. The direct problem is shown to have a unique weak solution by examining its variational formulation. The domain derivative is derived for the displacement with respect to the variation of the surface. A continuation method with respect to the frequency is developed for the inverse problem. Numerical experiments are presented to demonstrate the effectiveness of the proposed method.

  12. Psycholinguistic Evidence for Inverse Scope in Korean.

    PubMed

    Lee, Sunyoung; O'Grady, William

    2016-08-01

    We use experimental data to shed light on the ongoing question of whether Korean allows inverse scope interpretation in sentences containing an indefinite subject and a universally quantified direct object (e.g., 'Someone bought each loaf of bread at the bakery'). The results of an off-line acceptability judgment task (n = 38) and an online self-paced reading task (n [Formula: see text] 22) indicate that inverse scope interpretations are in fact permitted in Korean as a secondary option, as is also the case in English. We argue that the dispreference for the inverse scope reading reflects processing considerations related to burden on working memory.

  13. Inversion for seismic anisotropy using genetic algorithms

    SciTech Connect

    Horne, S. Univ. of Edinburgh . Dept. of Geology and Geophysics); MacBeth, C. . Dept. of Geology and Geophysics)

    1994-11-01

    A general inversion scheme based on a genetic algorithm is developed to invert seismic observations for anisotropic parameters. The technique is applied to the inversion of shear-wave observations from two azimuthal VSP data sets from the Conoco test site in Oklahoma. Horizontal polarizations and time-delays are inverted for hexagonal and orthorhombic symmetries. The model solutions are consistent with previous studies using trial and error matching of full waveform synthetics. The shear-wave splitting observations suggest the presence of a shear-wave line singularity and are consistent with a dipping fracture system which is known to exist at the test site. Application of the inversion scheme prior to full waveform modeling demonstrates that a considerable saving in time is possible while retaining the same degree of accuracy.

  14. Joint inversion for mapping subsurface hydrologicalparameters

    SciTech Connect

    Tseng, Hung-Wen; Lee, Ki Ha

    2001-03-07

    Using electromagnetic (EM) and seismic travel time data and a least-square criteria, a two-dimensional joint inversion algorithm is under development to assess the feasibility of directly mapping subsurface hydrological properties in a crosswell setup. A simplified Archie's law combined with the time average equation relates the magnetic fields and seismic travel time to two hydrological parameters; rock porosity and pore fluid electrical conductivity. For simplicity, the hydrological parameter distributions are assumed to be two-dimensional. Preliminary results show that joint inversion does have better resolving power for the interpretation than using the EM method alone. Various inversion scenarios have been tested, and it has been found that alternately perturbing just one of the two parameters at each iteration gives the best data fit.

  15. Observation of intrinsic inverse spin Hall effect.

    PubMed

    Werake, Lalani K; Ruzicka, Brian A; Zhao, Hui

    2011-03-11

    We report observation of intrinsic inverse spin Hall effect in undoped GaAs multiple quantum wells with a sample temperature of 10 K. A transient ballistic pure spin current is injected by a pair of laser pulses through quantum interference. By time resolving the dynamics of the pure spin current, the momentum relaxation time is deduced, which sets the lower limit of the scattering time between electrons and holes. The transverse charge current generated by the pure spin current via the inverse spin Hall effect is simultaneously resolved. We find that the charge current is generated well before the first electron-hole scattering event. Generation of the transverse current in the scattering-free ballistic transport regime provides unambiguous evidence for the intrinsic inverse spin Hall effect. PMID:21469830

  16. Reservoir parameter inversion based on weighted statistics

    NASA Astrophysics Data System (ADS)

    Gui, Jin-Yong; Gao, Jian-Hu; Yong, Xue-Shan; Li, Sheng-Jun; Liu, Bin-Yang; Zhao, Wan-Jin

    2015-12-01

    Variation of reservoir physical properties can cause changes in its elastic parameters. However, this is not a simple linear relation. Furthermore, the lack of observations, data overlap, noise interference, and idealized models increases the uncertainties of the inversion result. Thus, we propose an inversion method that is different from traditional statistical rock physics modeling. First, we use deterministic and stochastic rock physics models considering the uncertainties of elastic parameters obtained by prestack seismic inversion and introduce weighting coefficients to establish a weighted statistical relation between reservoir and elastic parameters. Second, based on the weighted statistical relation, we use Markov chain Monte Carlo simulations to generate the random joint distribution space of reservoir and elastic parameters that serves as a sample solution space of an objective function. Finally, we propose a fast solution criterion to maximize the posterior probability density and obtain reservoir parameters. The method has high efficiency and application potential.

  17. Tracer diffusion in silica inverse opals.

    PubMed

    Cherdhirankorn, Thipphaya; Retsch, Markus; Jonas, Ulrich; Butt, Hans-Juergen; Koynov, Kaloian

    2010-06-15

    We employed fluorescence correlation spectroscopy (FCS) to study the diffusion of small fluorescence tracers in liquid filled silica inverse opals. The inverse opals consisted of a nanoporous silica scaffold spanning a hexagonal crystal of spherical voids of 360 nm diameter connected by circular pores of 70 nm diameter. The diffusion of Alexa Fluor 488 in water and of perylene-3,4,9,10-tetracarboxylic diimide (PDI) in toluene was studied. Three diffusion modes could be distinguished: (1) Free diffusion limited by the geometric constraints given by the inverse opal, where, as compared to the free solution, this diffusion is slowed down by a factor of 3-4, (2) slow diffusion inside the nanoporous matrix of the silica scaffold, and (3) diffusion limited by adsorption. On the length scale of the focus of a confocal microscope of roughly 400 nm diffusion was non-Fickian in all cases.

  18. Analytical and experimental studies for space boundary and geometry inverse heat conduction problems

    NASA Astrophysics Data System (ADS)

    Chen, Tzu-Fang

    Inverse Heat Conduction Problems (IHCPs) have been widely used in engineering fields in recent decades. IHCPs are not the same as direct heat conduction problems which are ``well-posed''. IHCPs are made more difficult since they are inherently ``ill-posed'' that is, a small error perturbation will lead to a large error in the solution reconstructed. Prediction of an unknown in an IHCP is not an easy event. An IHCP also handles the desired information from measurements containing noise. A stable and accurate reliable inversion solver shall be studied. This dissertation is split into four parts. The first part describes space boundary IHCPs, and attempts to utilize noisy measurement data to predict unknown surface temperatures or heat fluxes. A new algorithm, using a Kalman Filter to filter the measurement noise combined with an implicit time-marching finite difference scheme, solves a space boundary IHCP. In the second part, errors in reconstruction of the temperature at each boundary of a one-dimensional IHCP can be presented by a simple relation. Each relation contains an unknown coefficient, which can be determined by using one simulation through the inversion solver of a pair of specified sensor locations. This relation can then be used to estimate the other recovery errors at the boundary without using the inverse solver. In the third part, an experimental study of temperature drop between two rough surfaces is conducted. The experimental data are analyzed by utilizing an inversion solver developed in this dissertation. In the fourth part, an IHCP with a melting process using the measured temperature and heat flux at one surface is solved by a new geometry inversion solver with a heat flux limiter to reconstruct the melting front location and the temperature history inside the test domain.

  19. Acquired prosopagnosia abolishes the face inversion effect.

    PubMed

    Busigny, Thomas; Rossion, Bruno

    2010-09-01

    Individual faces are notoriously difficult to recognize when they are presented upside-down. Since acquired prosopagnosia (AP) has been associated with an impairment of expert face processes, a reduced or abolished face inversion effect (FIE) is expected in AP. However, previous studies have incongruently reported apparent normal effects of inversion, a decreased or abolished FIE, but also a surprisingly better performance for inverted faces for some patients. While these discrepant observations may be due to the variability of high-level processes impaired, a careful look at the literature rather suggests that the pattern of FIE in prosopagnosia has been obscured by a selection of patients with associated low-level defects and general visual recognition impairments, as well as trade-offs between accuracy and correct RT measures. Here we conducted an extensive investigation of upright and inverted face processing in a well-characterized case of face-selective AP, PS (Rossion et al., 2003). In 4 individual face discrimination experiments, PS did not present any inversion effect at all, taking into account all dependent measures of performance. However, she showed a small inversion cost for individualizing members of a category of non-face objects (cars), just like normal observers. A fifth experiment with personally familiar faces to recognize confirmed the lack of inversion effect for PS. Following the present report and a survey of the literature, we conclude that the FIE is generally absent, or at least clearly reduced following AP. We also suggest that the paradoxical superior performance for inverted faces observed in rare cases may be due to additional upper visual field defects rather than to high-level competing visual processes. These observations are entirely compatible with the view that AP is associated with a disruption of a process that is also abolished following inversion: the holistic representation of individual exemplars of the face class.

  20. Acoustic Inversion in Optoacoustic Tomography: A Review

    PubMed Central

    Rosenthal, Amir; Ntziachristos, Vasilis; Razansky, Daniel

    2013-01-01

    Optoacoustic tomography enables volumetric imaging with optical contrast in biological tissue at depths beyond the optical mean free path by the use of optical excitation and acoustic detection. The hybrid nature of optoacoustic tomography gives rise to two distinct inverse problems: The optical inverse problem, related to the propagation of the excitation light in tissue, and the acoustic inverse problem, which deals with the propagation and detection of the generated acoustic waves. Since the two inverse problems have different physical underpinnings and are governed by different types of equations, they are often treated independently as unrelated problems. From an imaging standpoint, the acoustic inverse problem relates to forming an image from the measured acoustic data, whereas the optical inverse problem relates to quantifying the formed image. This review focuses on the acoustic aspects of optoacoustic tomography, specifically acoustic reconstruction algorithms and imaging-system practicalities. As these two aspects are intimately linked, and no silver bullet exists in the path towards high-performance imaging, we adopt a holistic approach in our review and discuss the many links between the two aspects. Four classes of reconstruction algorithms are reviewed: time-domain (so called back-projection) formulae, frequency-domain formulae, time-reversal algorithms, and model-based algorithms. These algorithms are discussed in the context of the various acoustic detectors and detection surfaces which are commonly used in experimental studies. We further discuss the effects of non-ideal imaging scenarios on the quality of reconstruction and review methods that can mitigate these effects. Namely, we consider the cases of finite detector aperture, limited-view tomography, spatial under-sampling of the acoustic signals, and acoustic heterogeneities and losses. PMID:24772060

  1. Trimming and procrastination as inversion techniques

    NASA Astrophysics Data System (ADS)

    Backus, George E.

    1996-12-01

    By examining the processes of truncating and approximating the model space (trimming it), and by committing to neither the objectivist nor the subjectivist interpretation of probability (procrastinating), we construct a formal scheme for solving linear and non-linear geophysical inverse problems. The necessary prior information about the correct model xE can be either a collection of inequalities or a probability measure describing where xE was likely to be in the model space X before the data vector y0 was measured. The results of the inversion are (1) a vector z0 that estimates some numerical properties zE of xE; (2) an estimate of the error δz = z0 - zE. As y0 is finite dimensional, so is z0, and hence in principle inversion cannot describe all of xE. The error δz is studied under successively more specialized assumptions about the inverse problem, culminating in a complete analysis of the linear inverse problem with a prior quadratic bound on xE. Our formalism appears to encompass and provide error estimates for many of the inversion schemes current in geomagnetism, and would be equally applicable in geodesy and seismology if adequate prior information were available there. As an idealized example we study the magnetic field at the core-mantle boundary, using satellite measurements of field elements at sites assumed to be almost uniformly distributed on a single spherical surface. Magnetospheric currents are neglected and the crustal field is idealized as a random process with rotationally invariant statistics. We find that an appropriate data compression diagonalizes the variance matrix of the crustal signal and permits an analytic trimming of the idealized problem.

  2. Directional wetting in anisotropic inverse opals.

    PubMed

    Phillips, Katherine R; Vogel, Nicolas; Burgess, Ian B; Perry, Carole C; Aizenberg, Joanna

    2014-07-01

    Porous materials display interesting transport phenomena due to restricted motion of fluids within the nano- to microscale voids. Here, we investigate how liquid wetting in highly ordered inverse opals is affected by anisotropy in pore geometry. We compare samples with different degrees of pore asphericity and find different wetting patterns depending on the pore shape. Highly anisotropic structures are infiltrated more easily than their isotropic counterparts. Further, the wetting of anisotropic inverse opals is directional, with liquids filling from the side more easily. This effect is supported by percolation simulations as well as direct observations of wetting using time-resolved optical microscopy. PMID:24941308

  3. Relative risk regression models with inverse polynomials.

    PubMed

    Ning, Yang; Woodward, Mark

    2013-08-30

    The proportional hazards model assumes that the log hazard ratio is a linear function of parameters. In the current paper, we model the log relative risk as an inverse polynomial, which is particularly suitable for modeling bounded and asymmetric functions. The parameters estimated by maximizing the partial likelihood are consistent and asymptotically normal. The advantages of the inverse polynomial model over the ordinary polynomial model and the fractional polynomial model for fitting various asymmetric log relative risk functions are shown by simulation. The utility of the method is further supported by analyzing two real data sets, addressing the specific question of the location of the minimum risk threshold.

  4. Aneesur Rahman Prize: The Inverse Ising Problem

    NASA Astrophysics Data System (ADS)

    Swendsen, Robert

    2014-03-01

    Many methods are available for carrying out computer simulations of a model Hamiltonian to obtain thermodynamic information by generating a set of configurations. The inverse problem consists of recreating the parameters of the Hamiltonian, given a set of configurations. The problem arises in a variety of contexts, and there has been much interest recently in the inverse Ising problem, in which the configurations consist of Ising spins. I will discuss an efficient method for solving the problem and what it can tell us about the Sherrington-Kirkpatrick model.

  5. Direct and Inverse problems in Electrocardiography

    NASA Astrophysics Data System (ADS)

    Boulakia, M.; Fernández, M. A.; Gerbeau, J. F.; Zemzemi, N.

    2008-09-01

    We present numerical results related to the direct and the inverse problems in electrocardiography. The electrical activity of the heart is described by the bidomain equations. The electrocardiograms (ECGs) recorded in different points on the body surface are obtained by coupling the bidomain equation to a Laplace equation in the torso. The simulated ECGs are quite satisfactory. As regards the inverse problem, our goal is to estimate the parameters of the bidomain-torso model. Here we present some preliminary results of a parameter estimation for the torso model.

  6. 3D geophysical inversion for contact surfaces

    NASA Astrophysics Data System (ADS)

    Lelièvre, Peter; Farquharson, Colin

    2014-05-01

    Geologists' interpretations about the Earth typically involve distinct rock units with contacts (interfaces) between them. In contrast, standard minimum-structure volumetric inversions (performed on meshes of space-filling cells) recover smooth models inconsistent with such interpretations. There are several approaches through which geophysical inversion can help recover models with the desired characteristics. Some authors have developed iterative strategies in which several volumetric inversions are performed with regularization parameters changing to achieve sharper interfaces at automatically determined locations. Another approach is to redesign the regularization to be consistent with the desired model characteristics, e.g. L1-like norms or compactness measures. A few researchers have taken approaches that limit the recovered values to lie within particular ranges, resulting in sharp discontinuities; these include binary inversion, level set methods and clustering strategies. In most of the approaches mentioned above, the model parameterization considers the physical properties in each of the many space-filling cells within the volume of interest. The exception are level set methods, in which a higher dimensional function is parameterized and the contact surface is determined from the zero-level of that function. However, even level-set methods rely on an underlying volumetric mesh. We are researching a fundamentally different type of inversion that parameterizes the Earth in terms of the contact surfaces between rock units. 3D geological Earth models typically comprise wireframe surfaces of tessellated triangles or other polygonal planar facets. This wireframe representation allows for flexible and efficient generation of complicated geological structures. Therefore, a natural approach for representing a geophysical model in an inversion is to parameterize the wireframe contact surfaces as the coordinates of the nodes (facet vertices). The geological and

  7. Bayesian Inference in Satellite Gravity Inversion

    NASA Technical Reports Server (NTRS)

    Kis, K. I.; Taylor, Patrick T.; Wittmann, G.; Kim, Hyung Rae; Torony, B.; Mayer-Guerr, T.

    2005-01-01

    To solve a geophysical inverse problem means applying measurements to determine the parameters of the selected model. The inverse problem is formulated as the Bayesian inference. The Gaussian probability density functions are applied in the Bayes's equation. The CHAMP satellite gravity data are determined at the altitude of 400 kilometer altitude over the South part of the Pannonian basin. The model of interpretation is the right vertical cylinder. The parameters of the model are obtained from the minimum problem solved by the Simplex method.

  8. Aerosol physical properties from satellite horizon inversion

    NASA Technical Reports Server (NTRS)

    Gray, C. R.; Malchow, H. L.; Merritt, D. C.; Var, R. E.; Whitney, C. K.

    1973-01-01

    The feasibility is investigated of determining the physical properties of aerosols globally in the altitude region of 10 to 100 km from a satellite horizon scanning experiment. The investigation utilizes a horizon inversion technique previously developed and extended. Aerosol physical properties such as number density, size distribution, and the real and imaginary components of the index of refraction are demonstrated to be invertible in the aerosol size ranges (0.01-0.1 microns), (0.1-1.0 microns), (1.0-10 microns). Extensions of previously developed radiative transfer models and recursive inversion algorithms are displayed.

  9. Molecular seismology: an inverse problem in nanobiology.

    PubMed

    Hinow, Peter; Boczko, Erik M

    2007-05-01

    The density profile of an elastic fiber like DNA will change in space and time as ligands associate with it. This observation affords a new direction in single molecule studies provided that density profiles can be measured in space and time. In fact, this is precisely the objective of seismology, where the mathematics of inverse problems have been employed with success. We argue that inverse problems in elastic media can be directly applied to biophysical problems of fiber-ligand association, and demonstrate that robust algorithms exist to perform density reconstruction in the condensed phase.

  10. Dispersion analysis with inverse dielectric function modelling.

    PubMed

    Mayerhöfer, Thomas G; Ivanovski, Vladimir; Popp, Jürgen

    2016-11-01

    We investigate how dispersion analysis can profit from the use of a Lorentz-type description of the inverse dielectric function. In particular at higher angles of incidence, reflectance spectra using p-polarized light are dominated by bands from modes that have their transition moments perpendicular to the surface. Accordingly, the spectra increasingly resemble inverse dielectric functions. A corresponding description can therefore eliminate the complex dependencies of the dispersion parameters, allow their determination and facilitate a more accurate description of the optical properties of single crystals.

  11. 3D Electromagnetic inversion using conjugate gradients

    SciTech Connect

    Newman, G.A.; Alumbaugh, D.L.

    1997-06-01

    In large scale 3D EM inverse problems it may not be possible to directly invert a full least-squares system matrix involving model sensitivity elements. Thus iterative methods must be employed. For the inverse problem, we favor either a linear or non-linear (NL) CG scheme, depending on the application. In a NL CG scheme, the gradient of the objective function is required at each relaxation step along with a univariate line search needed to determine the optimum model update. Solution examples based on both approaches will be presented.

  12. Dispersion analysis with inverse dielectric function modelling

    NASA Astrophysics Data System (ADS)

    Mayerhöfer, Thomas G.; Ivanovski, Vladimir; Popp, Jürgen

    2016-11-01

    We investigate how dispersion analysis can profit from the use of a Lorentz-type description of the inverse dielectric function. In particular at higher angles of incidence, reflectance spectra using p-polarized light are dominated by bands from modes that have their transition moments perpendicular to the surface. Accordingly, the spectra increasingly resemble inverse dielectric functions. A corresponding description can therefore eliminate the complex dependencies of the dispersion parameters, allow their determination and facilitate a more accurate description of the optical properties of single crystals.

  13. Inverse source problems for eddy current equations

    NASA Astrophysics Data System (ADS)

    Alonso Rodríguez, Ana; Camaño, Jessika; Valli, Alberto

    2012-01-01

    We study the inverse source problem for the eddy current approximation of Maxwell equations. As for the full system of Maxwell equations, we show that a volume current source cannot be uniquely identified by knowledge of the tangential components of the electromagnetic fields on the boundary, and we characterize the space of non-radiating sources. On the other hand, we prove that the inverse source problem has a unique solution if the source is supported on the boundary of a subdomain or if it is the sum of a finite number of dipoles. We address the applicability of this result for the localization of brain activity from electroencephalography and magnetoencephalography measurements.

  14. Inverse potential scattering in duct acoustics.

    PubMed

    Forbes, Barbara J; Pike, E Roy; Sharp, David B; Aktosun, Tuncay

    2006-01-01

    The inverse problem of the noninvasive measurement of the shape of an acoustical duct in which one-dimensional wave propagation can be assumed is examined within the theoretical framework of the governing Klein-Gordon equation. Previous deterministic methods developed over the last 40 years have all required direct measurement of the reflectance or input impedance but now, by application of the methods of inverse quantum scattering to the acoustical system, it is shown that the reflectance can be algorithmically derived from the radiated wave. The potential and area functions of the duct can subsequently be reconstructed. The results are discussed with particular reference to acoustic pulse reflectometry.

  15. The Inverse Problem in Jet Acoustics

    NASA Technical Reports Server (NTRS)

    Wooddruff, S. L.; Hussaini, M. Y.

    2001-01-01

    The inverse problem for jet acoustics, or the determination of noise sources from far-field pressure information, is proposed as a tool for understanding the generation of noise by turbulence and for the improved prediction of jet noise. An idealized version of the problem is investigated first to establish the extent to which information about the noise sources may be determined from far-field pressure data and to determine how a well-posed inverse problem may be set up. Then a version of the industry-standard MGB code is used to predict a jet noise source spectrum from experimental noise data.

  16. Directional wetting in anisotropic inverse opals.

    PubMed

    Phillips, Katherine R; Vogel, Nicolas; Burgess, Ian B; Perry, Carole C; Aizenberg, Joanna

    2014-07-01

    Porous materials display interesting transport phenomena due to restricted motion of fluids within the nano- to microscale voids. Here, we investigate how liquid wetting in highly ordered inverse opals is affected by anisotropy in pore geometry. We compare samples with different degrees of pore asphericity and find different wetting patterns depending on the pore shape. Highly anisotropic structures are infiltrated more easily than their isotropic counterparts. Further, the wetting of anisotropic inverse opals is directional, with liquids filling from the side more easily. This effect is supported by percolation simulations as well as direct observations of wetting using time-resolved optical microscopy.

  17. [Erythrocyte protoporphyrin during recovery from malnutrition in rats].

    PubMed

    Haydée Langini, S; Río de Gómez del Río, M E; Pita Martín de Portela, M L

    1999-09-01

    Interrelationships between Erythrocyte Protoporphyrin (EP), dietary Iron/Protein ratio (Fe/Prot) and Fe liver content (Feh) were studied during nutritional recovery in an experimental model: weanling female Wistar rats (To) were depleted with a protein-free diet (LP), losing 20% of their initial body weight. Then they were recovered until 45 days of age (T45) with diets containing: casein: 20 g/100 g; Fe (ammonium Fe citrate) (ppm.): 0, 75 or 100 (groups A1, A2 and A3, respectively). Hematocrit, Hemoglobin (Hb) (g/dL). Erythrocyte Protoporphyrin (EP) (microgram/dL Red Blood Cells) and Feh (microgram) were determined at To, LP and T45. Results were compared with control rats (C) fed with 20% of casein and Fe, 50 ppm. EP: a) decreased in C from To to T45 (99 +/- 24; 36 +/- 9; p < 0.01); b) increased in A1 and A2 at T45 (123 +/- 21; 93 +/- 29, respectively, p < 0.01) while A3 did not show significant difference (45 +/- 7) regarding to C: c) correlated inversely with Feh. According to the inverse correlation between EP and Fe/Prot (r = -0.99), we found that 92 ppm was an adequate Fe amount to prevent EP increase. These results confirm that during recovery from undernutrition EP depends on iron liver content, being an adequate indicator of iron nutritional status; therefore, EP would be useful as a predictor of the optimum Fe/Prot ratio for nutritional recovery.

  18. Preserving sequence annotations across reference sequences

    PubMed Central

    2014-01-01

    Background Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. Results As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. Conclusions We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO. PMID:25093075

  19. Riparian vegetation recovery patterns following stream channelization: a geomorphic perspective

    USGS Publications Warehouse

    Hupp, C.R.

    1992-01-01

    Hundreds of kilometres of West Tennessee streams have been channelized since the turn of the century. After a stream is straightened, dredged, or cleared, basin-wide ecologic, hydrologic, and geomorphic processes bring about an integrated, characteristic recovery sequence. The rapid pace of channel responses to channelization provides an opportunity to document and interpret vegetation recovery patterns relative to otherwise long-term, concomitant evolution of river geomorphology. The linkage of channel bed aggradation, woody vegetation establishment, and bank accretion all lead to recovery of the channel. Pioneer species are hardy and fast growing, and can tolerate moderate amounts of slope instability and sediment deposition; these species include river birch (Betula nigra), black willow (Salix nigra), boxelder (Acer negundo), and silver maple (Acer saccharinum). High stem densities and root-mass development appear to enhance bank stability. Tree-ring analyses suggest that on average 65 yr may be required for recovery after channelization. -from Author

  20. Genome‐wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

    PubMed Central

    Lohse, Konrad; Clarke, Magnus; Ritchie, Michael G.; Etges, William J.

    2015-01-01

    Models of speciation‐with‐gene‐flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow. PMID:25824653

  1. Characterization of the breakpoints of a polymorphic inversion complex detects strict and broad breakpoint reuse at the molecular level.

    PubMed

    Puerma, Eva; Orengo, Dorcas J; Salguero, David; Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2014-09-01

    Inversions are an integral part of structural variation within species, and they play a leading role in genome reorganization across species. Work at both the cytological and genome sequence levels has revealed heterogeneity in the distribution of inversion breakpoints, with some regions being recurrently used. Breakpoint reuse at the molecular level has mostly been assessed for fixed inversions through genome sequence comparison, and therefore rather broadly. Here, we have identified and sequenced the breakpoints of two polymorphic inversions-E1 and E2 that share a breakpoint-in the extant Est and E1 + 2 chromosomal arrangements of Drosophila subobscura. The breakpoints are two medium-sized repeated motifs that mediated the inversions by two different mechanisms: E1 via staggered breaks and subsequent repair and E2 via repeat-mediated ectopic recombination. The fine delimitation of the shared breakpoint revealed its strict reuse at the molecular level regardless of which was the intermediate arrangement. The occurrence of other rearrangements in the most proximal and distal extended breakpoint regions reveals the broad reuse of these regions. This differential degree of fragility might be related to their sharing the presence outside the inverted region of snoRNA-encoding genes.

  2. A Stochastic Inversion Method for Potential Field Data: Ant Colony Optimization

    NASA Astrophysics Data System (ADS)

    Liu, Shuang; Hu, Xiangyun; Liu, Tianyou

    2014-07-01

    Simulating natural ants' foraging behavior, the ant colony optimization (ACO) algorithm performs excellently in combinational optimization problems, for example the traveling salesman problem and the quadratic assignment problem. However, the ACO is seldom used to inverted for gravitational and magnetic data. On the basis of the continuous and multi-dimensional objective function for potential field data optimization inversion, we present the node partition strategy ACO (NP-ACO) algorithm for inversion of model variables of fixed shape and recovery of physical property distributions of complicated shape models. We divide the continuous variables into discrete nodes and ants directionally tour the nodes by use of transition probabilities. We update the pheromone trails by use of Gaussian mapping between the objective function value and the quantity of pheromone. It can analyze the search results in real time and promote the rate of convergence and precision of inversion. Traditional mapping, including the ant-cycle system, weaken the differences between ant individuals and lead to premature convergence. We tested our method by use of synthetic data and real data from scenarios involving gravity and magnetic anomalies. The inverted model variables and recovered physical property distributions were in good agreement with the true values. The ACO algorithm for binary representation imaging and full imaging can recover sharper physical property distributions than traditional linear inversion methods. The ACO has good optimization capability and some excellent characteristics, for example robustness, parallel implementation, and portability, compared with other stochastic metaheuristics.

  3. Imaging the Kemaliye geothermal reservoir using three-dimensional magnetotelluric inversion with full distortion correction

    NASA Astrophysics Data System (ADS)

    Moorkamp, M.; Avdeeva, A.

    2015-12-01

    The Gediz Graben in western Anatolia is a well studied tectonic feature and an area of ongoing exploration for geothermal energy. The target of exploration are typically fault damage zones associated with graben bounding normal faults that allow the migration of hot fluids. Within the Kemaliye concession, located at the northern margin of the Gediz Graben, more than 300 MT/AMT stations were acquired in order to image the geometry of the basement and infer the location of major faults. In addition, time-domain electromagnetic (TDEM) measurements were acquired at each site to be able to correct for static-shift. We present 3D inversion results for this dataset using a novel inversion technique that simultaneously inverts for a conductivity model and the four parameters of the full distortion matrix at each site. Using this approach results in a better recovery of structures and less artefacts for the near-surface compared to inversion without any correction. We will demonstrate how this approach works in practice and compare the recovered distortion parameters with the static-shift correction inferred from the TDEM measurements. A comparison with recently drilled boreholes in the area allows us to further verify the accuracy of our inversion results.

  4. Modelling and genetic algorithm based optimisation of inverse supply chain

    NASA Astrophysics Data System (ADS)

    Bányai, T.

    2009-04-01

    The design and control of recycling systems of products with environmental risk have been discussed in the world already for a long time. The main reasons to address this subject are the followings: reduction of waste volume, intensification of recycling of materials, closing the loop, use of less resource, reducing environmental risk [1, 2]. The development of recycling systems is based on the integrated solution of technological and logistic resources and know-how [3]. However the financial conditions of recycling systems is partly based on the recovery, disassembly and remanufacturing options of the used products [4, 5, 6], but the investment and operation costs of recycling systems can be characterised with high logistic costs caused by the geographically wide collection system with more collection level and a high number of operation points of the inverse supply chain. The reduction of these costs is a popular area of the logistics researches. These researches include the design and implementation of comprehensive environmental waste and recycling program to suit business strategies (global system), design and supply all equipment for production line collection (external system), design logistics process to suit the economical and ecological requirements (external system) [7]. To the knowledge of the author, there has been no research work on supply chain design problems that purpose is the logistics oriented optimisation of inverse supply chain in the case of non-linear total cost function consisting not only operation costs but also environmental risk cost. The antecedent of this research is, that the author has taken part in some research projects in the field of closed loop economy ("Closing the loop of electr(on)ic products and domestic appliances from product planning to end-of-life technologies), environmental friendly disassembly (Concept for logistical and environmental disassembly technologies) and design of recycling systems of household appliances

  5. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

    PubMed Central

    Zapata, Luis; Ding, Jia; Willing, Eva-Maria; Hartwig, Benjamin; Bezdan, Daniela; Jiao, Wen-Biao; Patel, Vipul; Velikkakam James, Geo; Koornneef, Maarten; Ossowski, Stephan; Schneeberger, Korbinian

    2016-01-01

    Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods. PMID:27354520

  6. Ecosystem context and historical contingency in apex predator recoveries.

    PubMed

    Stier, Adrian C; Samhouri, Jameal F; Novak, Mark; Marshall, Kristin N; Ward, Eric J; Holt, Robert D; Levin, Phillip S

    2016-05-01

    Habitat loss, overexploitation, and numerous other stressors have caused global declines in apex predators. This "trophic downgrading" has generated widespread concern because of the fundamental role that apex predators can play in ecosystem functioning, disease regulation, and biodiversity maintenance. In attempts to combat declines, managers have conducted reintroductions, imposed stricter harvest regulations, and implemented protected areas. We suggest that full recovery of viable apex predator populations is currently the exception rather than the rule. We argue that, in addition to well-known considerations, such as continued exploitation and slow life histories, there are several underappreciated factors that complicate predator recoveries. These factors include three challenges. First, a priori identification of the suite of trophic interactions, such as resource limitation and competition that will influence recovery can be difficult. Second, defining and accomplishing predator recovery in the context of a dynamic ecosystem requires an appreciation of the timing of recovery, which can determine the relative density of apex predators and other predators and therefore affect competitive outcomes. Third, successful recovery programs require designing adaptive sequences of management strategies that embrace key environmental and species interactions as they emerge. Consideration of recent research on food web modules, alternative stable states, and community assembly offer important insights for predator recovery efforts and restoration ecology more generally. Foremost among these is the importance of a social-ecological perspective in facilitating a long-lasting predator restoration while avoiding unintended consequences. PMID:27386535

  7. Ecosystem context and historical contingency in apex predator recoveries

    PubMed Central

    Stier, Adrian C.; Samhouri, Jameal F.; Novak, Mark; Marshall, Kristin N.; Ward, Eric J.; Holt, Robert D.; Levin, Phillip S.

    2016-01-01

    Habitat loss, overexploitation, and numerous other stressors have caused global declines in apex predators. This “trophic downgrading” has generated widespread concern because of the fundamental role that apex predators can play in ecosystem functioning, disease regulation, and biodiversity maintenance. In attempts to combat declines, managers have conducted reintroductions, imposed stricter harvest regulations, and implemented protected areas. We suggest that full recovery of viable apex predator populations is currently the exception rather than the rule. We argue that, in addition to well-known considerations, such as continued exploitation and slow life histories, there are several underappreciated factors that complicate predator recoveries. These factors include three challenges. First, a priori identification of the suite of trophic interactions, such as resource limitation and competition that will influence recovery can be difficult. Second, defining and accomplishing predator recovery in the context of a dynamic ecosystem requires an appreciation of the timing of recovery, which can determine the relative density of apex predators and other predators and therefore affect competitive outcomes. Third, successful recovery programs require designing adaptive sequences of management strategies that embrace key environmental and species interactions as they emerge. Consideration of recent research on food web modules, alternative stable states, and community assembly offer important insights for predator recovery efforts and restoration ecology more generally. Foremost among these is the importance of a social-ecological perspective in facilitating a long-lasting predator restoration while avoiding unintended consequences. PMID:27386535

  8. Coherent source imaging and dynamic support tracking for inverse scattering using compressive MUSIC

    NASA Astrophysics Data System (ADS)

    Lee, Okkyun; Kim, Jong Min; Yoo, Jaejoon; Jin, Kyunghwan; Ye, Jong Chul

    2011-09-01

    The goal of this paper is to develop novel algorithms for inverse scattering problems such as EEG/MEG, microwave imaging, and/or diffuse optical tomograpahy, and etc. One of the main contributions of this paper is a class of novel non-iterative exact nonlinear inverse scattering theory for coherent source imaging and moving targets. Specifically, the new algorithms guarantee the exact recovery under a very relaxed constraint on the number of source and receivers, under which the conventional methods fail. Such breakthrough was possible thanks to the recent theory of compressive MUSIC and its extension using support correction criterion, where partial support are estimated using the conventional compressed sensing approaches, then the remaining supports are estimated using a novel generalized MUSIC criterion. Numerical results using coherent sources in EEG/MEG and dynamic targets confirm that the new algorithms outperform the conventional ones.

  9. Inverse Doppler Effects in Broadband Acoustic Metamaterials

    PubMed Central

    Zhai, S. L.; Zhao, X. P.; Liu, S.; Shen, F. L.; Li, L. L.; Luo, C. R.

    2016-01-01

    The Doppler effect refers to the change in frequency of a wave source as a consequence of the relative motion between the source and an observer. Veselago theoretically predicted that materials with negative refractions can induce inverse Doppler effects. With the development of metamaterials, inverse Doppler effects have been extensively investigated. However, the ideal material parameters prescribed by these metamaterial design approaches are complex and also challenging to obtain experimentally. Here, we demonstrated a method of designing and experimentally characterising arbitrary broadband acoustic metamaterials. These omni-directional, double-negative, acoustic metamaterials are constructed with ‘flute-like’ acoustic meta-cluster sets with seven double meta-molecules; these metamaterials also overcome the limitations of broadband negative bulk modulus and mass density to provide a region of negative refraction and inverse Doppler effects. It was also shown that inverse Doppler effects can be detected in a flute, which has been popular for thousands of years in Asia and Europe. PMID:27578317

  10. Inversion Symmetry Breaking in Endohedral C_60

    NASA Astrophysics Data System (ADS)

    Clougherty, Dennis; Anderson, Frederick

    1998-03-01

    A pseudo--Jahn--Teller model describing central atom distortions is proposed for endohedral fullerenes of the form A@C_60 where A is either a rare gas or a metal atom. A critical (dimensionless) coupling gc is found, at or below which the symmetric configuration is stable and above which inversion symmetry is broken. Vibronic parameters are given for selected endohedral fullerenes.

  11. [Neural Mechanisms Underlying the Face Inversion Effect].

    PubMed

    Sugase-Miyamoto, Yasuko; Matsumoto, Narihisa; Kawano, Kenji

    2015-10-01

    The ability to recognize faces is reduced with a picture-plane inversion of the faces, known as the face inversion effect. It has been reported that the configuration of facial features, for example, the distance between the eyes and mouth, becomes less perceptible when the face is inverted. In macaque monkeys, designated cortical areas, i.e., face patches, where face images are processed, have been found in the temporal visual cortex along the ventral visual pathway. Neurons in the anterior face patch (anterior part of the inferior temporal cortex) are known to encode view-invariant identity information. Thus, the anterior face patch is believed to be the final processing stage in the face patch system. A recent study showed that the face-inversion decreases the amount of the information about facial identity and facial expression conveyed by neurons, though it did not affect the information about the global category of the stimulus images (monkey versus human versus shape). The anterior face patch may, therefore, serve as the neural basis underlying the face inversion effect. PMID:26450075

  12. The role of nonlinearity in inverse problems

    NASA Astrophysics Data System (ADS)

    Snieder, Roel

    1998-06-01

    In many practical inverse problems, one aims to retrieve a model that has infinitely many degrees of freedom from a finite amount of data. It follows from a simple variable count that this cannot be done in a unique way. Therefore, inversion entails more than estimating a model: any inversion is not complete without a description of the class of models that is consistent with the data; this is called the appraisal problem. Nonlinearity makes the appraisal problem particularly difficult. The first reason for this is that nonlinear error propagation is a difficult problem. The second reason is that for some nonlinear problems the model parameters affect the way in which the model is being interrogated by the data. Two examples are given of this, and it is shown how the nonlinearity may make the problem more ill-posed. Finally, three attempts are shown to carry out the model appraisal for nonlinear inverse problems that are based on an analytical approach, a numerical approach and a common sense approach.

  13. [Sex inversion and epigenetic regulation in Vertebrates].

    PubMed

    Trukhina, A V; Lukina, N A; Nekrasova, A A; Smirnov, A F

    2015-03-01

    This review discusses issues related to the regulation of sex determination and differentiation in various groups of Vertebrates. Special attention was paid to factors of external and internal control for various genetic systems of sex determination, as well as to the epigenetic control of this process. Opportunities for sex inversion in various animals were also discussed.

  14. Using GPU Programming for Inverse Spectroscopy

    SciTech Connect

    David Gerts; N. Fredette; H. Wimberly

    2010-07-01

    The Idaho National Laboratory (INL) has developed a detector that relies heavily on computationally expensive inverse spectroscopy algorithms to determine probabilistic three dimensional mappings of the source and its intensity. This inverse spectroscopy algorithm applies to material accountability due to the potential to determine where nuclear sources are present as a function of time and space. And yet because the novel algorithm can become prohibitively expensive on a standard desktop PC, the INL has incorporated new hardware from the commercial graphics community. General programming for graphics processing units (GPUs) is not a new concept. However, the application of GPUs to evidence theory-based inverse spectroscopy is both novel and particularly apropos. Improvements while using a (slightly upgraded) standard PC are approximately three orders of magnitude, making a ten hour computation in less than four seconds. This significantly changes the concept of prohibitively expensive calculations and makes application to materials accountability possible in near real time. Indeed, the sensor collection time is now expected to dominate the time required to determine the source and its intensity, instead of the inverse spectroscopy method.

  15. Identification of Selective ERRγ Inverse Agonists.

    PubMed

    Kim, Jina; Im, Chun Young; Yoo, Eun Kyung; Ma, Min Jung; Kim, Sang-Bum; Hong, Eunmi; Chin, Jungwook; Hwang, Hayoung; Lee, Sungwoo; Kim, Nam Doo; Jeon, Jae-Han; Lee, In-Kyu; Jeon, Yong Hyun; Choi, Hueng-Sik; Kim, Seong Heon; Cho, Sung Jin

    2016-01-12

    GSK5182 (4) is currently one of the lead compounds for the development of estrogen-related receptor gamma (ERRγ) inverse agonists. Here, we report the design, synthesis, pharmacological and in vitro absorption, distribution, metabolism, excretion, toxicity (ADMET) properties of a series of compounds related to 4. Starting from 4, a series of analogs were structurally modified and their ERRγ inverse agonist activity was measured. A key pharmacophore feature of this novel class of ligands is the introduction of a heterocyclic group for A-ring substitution in the core scaffold. Among the tested compounds, several of them are potent ERRγ inverse agonists as determined by binding and functional assays. The most promising compound, 15g, had excellent binding selectivity over related subtypes (IC50 = 0.44, >10, >10, and 10 μM at the ERRγ, ERRα, ERRβ, and ERα subtypes, respectively). Compound 15g also resulted in 95% transcriptional repression at a concentration of 10 μM, while still maintaining an acceptable in vitro ADMET profile. This novel class of ERRγ inverse agonists shows promise in the development of drugs targeting ERRγ-related diseases.

  16. A Face Inversion Effect without a Face

    ERIC Educational Resources Information Center

    Brandman, Talia; Yovel, Galit

    2012-01-01

    Numerous studies have attributed the face inversion effect (FIE) to configural processing of internal facial features in upright but not inverted faces. Recent findings suggest that face mechanisms can be activated by faceless stimuli presented in the context of a body. Here we asked whether faceless stimuli with or without body context may induce…

  17. Unstructured discontinuous Galerkin for seismic inversion.

    SciTech Connect

    van Bloemen Waanders, Bart Gustaaf; Ober, Curtis Curry; Collis, Samuel Scott

    2010-04-01

    This abstract explores the potential advantages of discontinuous Galerkin (DG) methods for the time-domain inversion of media parameters within the earth's interior. In particular, DG methods enable local polynomial refinement to better capture localized geological features within an area of interest while also allowing the use of unstructured meshes that can accurately capture discontinuous material interfaces. This abstract describes our initial findings when using DG methods combined with Runge-Kutta time integration and adjoint-based optimization algorithms for full-waveform inversion. Our initial results suggest that DG methods allow great flexibility in matching the media characteristics (faults, ocean bottom and salt structures) while also providing higher fidelity representations in target regions. Time-domain inversion using discontinuous Galerkin on unstructured meshes and with local polynomial refinement is shown to better capture localized geological features and accurately capture discontinuous-material interfaces. These approaches provide the ability to surgically refine representations in order to improve predicted models for specific geological features. Our future work will entail automated extensions to directly incorporate local refinement and adaptive unstructured meshes within the inversion process.

  18. Sparse matrix orderings for factorized inverse preconditioners

    SciTech Connect

    Benzi, M.; Tuama, M.

    1998-09-01

    The effect of reorderings on the performance of factorized sparse approximate inverse preconditioners is considered. It is shown that certain reorderings can be very beneficial both in the preconditioner construction phase and in terms of the rate of convergence of the preconditioned iteration.

  19. Inverse-Square Orbits: A Geometric Approach.

    ERIC Educational Resources Information Center

    Rainwater, James C.; Weinstock, Robert

    1979-01-01

    Presents a derivation of Kepler's first law of planetary motion from Newtonian principles. Analogus derivations of the hyperbolic and parabolic orbits of nonreturning comets and the hyperbolic orbit for a particle in a repulsive inverse-square field are also presented. (HM)

  20. Pyrolysis with staged recovery

    DOEpatents

    Green, Norman W.; Duraiswamy, Kandaswamy; Lumpkin, Robert E.; Winter, Bruce L.

    1979-03-20

    In a continuous process for recovery of values contained in a solid carbonaceous material, the carbonaceous material is comminuted and then subjected to flash pyrolysis in the presence of a particulate heat source fed over an overflow weir to form a pyrolysis product stream containing a carbon containing solid residue and volatilized hydrocarbons. After the carbon containing solid residue is separated from the pyrolysis product stream, values are obtained by condensing volatilized hydrocarbons. The particulate source of heat is formed by oxidizing carbon in the solid residue.

  1. The ALEXIS mission recovery

    SciTech Connect

    Bloch, J.; Armstrong, T.; Dingler, B.; Enemark, D.; Holden, D.; Little, C.; Munson, C.; Priedhorsky, B.; Roussel-Dupre, D.; Smith, B.; Warner, R.; Dill, B.; Huffman, G.; McLoughlin, F.; Mills, R.; Miller, R.

    1994-03-01

    The authors report the recovery of the ALEXIS small satellite mission. ALEXIS is a 113-kg satellite that carries an ultrasoft x-ray telescope array and a high-speed VHF receiver/digitizer (BLACKBEARD), supported by a miniature spacecraft bus. It was launched by a Pegasus booster on 1993 April 25, but a solar paddle was damaged during powered flight. Initial attempts to contact ALEXIS were unsuccessful. The satellite finally responded in June, and was soon brought under control. Because the magnetometer had failed, the rescue required the development of new attitude control-techniques. The telemetry system has performed nominally. They discuss the procedures used to recover the ALEXIS mission.

  2. Deepwater pipeline recovery

    SciTech Connect

    McStravick, D.M.; Baugh, B.F.

    1997-07-01

    The paper gives a presentation of the tooling concepts used for the recovery of steel and flexible flowlines in the Gulf of Mexico Shell Tahoe I area in the summer of 1996 in 1,370 ft. of sea water. This offshore operation required a Global Grabber to engage and retrieve 4 1/2-in. steel pipelines, an ROV Pipeline Spear to internally engage the end of the 4 1/2-in. steel pipelines, and a FlexGrip Assembly to wrap and grab 5.566-in. OD flexible pipe. The design of the tooling emphasized the use of API 17D ROV interfaces.

  3. Resource recovery utility

    SciTech Connect

    Jones, R.L.

    1987-02-17

    This patent describes a resource recovery utility comprising: (i) a landfill; (ii) a continuous wall surrounding the perimeter of the landfill; (iii) a containment structure extending completely over the landfill and affixed to the continuous wall; (iv) means for introducing refuse into the landfill; (v) means for compacting the refuse; (vi) means for removing and recovering methane generated by anaerobic bacterial digestion of organic materials contained in the refuse; and (vii) means for removing at least a portion of the compacted refuse from the landfill.

  4. URANIUM RECOVERY PROCESS

    DOEpatents

    Bailes, R.H.; Long, R.S.; Olson, R.S.; Kerlinger, H.O.

    1959-02-10

    A method is described for recovering uranium values from uranium bearing phosphate solutions such as are encountered in the manufacture of phosphate fertilizers. The solution is first treated with a reducing agent to obtain all the uranium in the tetravalent state. Following this reduction, the solution is treated to co-precipitate the rcduced uranium as a fluoride, together with other insoluble fluorides, thereby accomplishing a substantially complete recovery of even trace amounts of uranium from the phosphate solution. This precipitate usually takes the form of a complex fluoride precipitate, and after appropriate pre-treatment, the uranium fluorides are leached from this precipitate and rccovered from the leach solution.

  5. Recovery of organic acids

    DOEpatents

    Verser, Dan W.; Eggeman, Timothy J.

    2011-11-01

    A method is disclosed for the recovery of an organic acid from a dilute salt solution in which the cation of the salt forms an insoluble carbonate salt. A tertiary amine and CO.sub.2 are introduced to the solution to form the insoluble carbonate salt and a complex between the acid and an amine. A water immiscible solvent, such as an alcohol, is added to extract the acid/amine complex from the dilute salt solution to a reaction phase. The reaction phase is continuously dried and a product between the acid and the solvent, such as an ester, is formed.

  6. Recovery of organic acids

    DOEpatents

    Verser, Dan W.; Eggeman, Timothy J.

    2009-10-13

    A method is disclosed for the recovery of an organic acid from a dilute salt solution in which the cation of the salt forms an insoluble carbonate salt. A tertiary amine and CO.sub.2 are introduced to the solution to form the insoluble carbonate salt and a complex between the acid and an amine. A water immiscible solvent, such as an alcohol, is added to extract the acid/amine complex from the dilute salt solution to a reaction phase. The reaction phase is continuously dried and a product between the acid and the solvent, such as an ester, is formed.

  7. Severity of presentation is associated with time to recovery in spinal epidural lipomatosis.

    PubMed

    Praver, Moshe; Kennedy, Benjamin C; Ellis, Jason A; D'Amico, Randy; Mandigo, Christopher E

    2015-08-01

    We present a patient with prednisone-induced spinal epidural lipomatosis (SEL) and relatively acute neurologic deterioration followed by rapid recovery after surgical decompression. SEL is a rare disease characterized by hypertrophy of epidural fat, most commonly associated with exogenous steroid use. To our knowledge, an analysis of the dynamics of steroid dose related to time to onset has never been performed, or of patient presentation features with respect to patient outcome. We retrospectively reviewed the literature for English language series and case reports of SEL associated with prednisone use from 1975-2013. Data were compiled for 41 patients regarding the prescribed dose of prednisone and length of treatment, as well as the severity of symptoms on the Ranawat scale, time to onset, time to recovery, and degree of recovery of neurological symptoms. Fisher's exact test and analysis of variance were used for comparing proportions, and p values <0.05 were considered statistically significant. We found that the mean cumulative dose of prednisone trended towards an association with a lack of recovery (p=0.06) and may be related to rate of recovery. Prescribed prednisone dose varied inversely with the time before onset of neurological symptoms, but failed to reach statistical significance. Higher severity of presenting symptoms on the Ranawat scale were found to be associated with a higher likelihood of delayed recovery (p=0.035). Patients with symptoms lower on the Ranawat scale more frequently experienced complete neurologic recovery, though this did not reach significance. The acuity of neurological deterioration was not related to the time to recovery or ultimate degree of recovery. Severity of presentation on the Ranawat scale is associated with rate of recovery and may be related to degree of recovery in SEL patients. Cumulative dose of prednisone may be related to degree and rate of recovery. Prescribed dose of prednisone may be related to time to onset

  8. Estimating uncertainties in complex joint inverse problems

    NASA Astrophysics Data System (ADS)

    Afonso, Juan Carlos

    2016-04-01

    Sources of uncertainty affecting geophysical inversions can be classified either as reflective (i.e. the practitioner is aware of her/his ignorance) or non-reflective (i.e. the practitioner does not know that she/he does not know!). Although we should be always conscious of the latter, the former are the ones that, in principle, can be estimated either empirically (by making measurements or collecting data) or subjectively (based on the experience of the researchers). For complex parameter estimation problems in geophysics, subjective estimation of uncertainty is the most common type. In this context, probabilistic (aka Bayesian) methods are commonly claimed to offer a natural and realistic platform from which to estimate model uncertainties. This is because in the Bayesian approach, errors (whatever their nature) can be naturally included as part of the global statistical model, the solution of which represents the actual solution to the inverse problem. However, although we agree that probabilistic inversion methods are the most powerful tool for uncertainty estimation, the common claim that they produce "realistic" or "representative" uncertainties is not always justified. Typically, ALL UNCERTAINTY ESTIMATES ARE MODEL DEPENDENT, and therefore, besides a thorough characterization of experimental uncertainties, particular care must be paid to the uncertainty arising from model errors and input uncertainties. We recall here two quotes by G. Box and M. Gunzburger, respectively, of special significance for inversion practitioners and for this session: "…all models are wrong, but some are useful" and "computational results are believed by no one, except the person who wrote the code". In this presentation I will discuss and present examples of some problems associated with the estimation and quantification of uncertainties in complex multi-observable probabilistic inversions, and how to address them. Although the emphasis will be on sources of uncertainty related

  9. Inverse Problems in Classical and Quantum Physics

    NASA Astrophysics Data System (ADS)

    Almasy, Andrea A.

    2009-12-01

    The subject of this thesis is in the area of Applied Mathematics known as Inverse Problems. Inverse problems are those where a set of measured data is analysed in order to get as much information as possible on a model which is assumed to represent a system in the real world. We study two inverse problems in the fields of classical and quantum physics: QCD condensates from tau-decay data and the inverse conductivity problem. We use a functional method which allows us to extract within rather general assumptions phenomenological parameters of QCD (the condensates) from a comparison of the time-like experimental data with asymptotic space-like results from theory. The price to be paid for the generality of assumptions is relatively large errors in the values of the extracted parameters. Although we do not claim that our method is superior to other approaches, we hope that our results lend additional confidence to the numerical results obtained with the help of methods based on QCD sum rules. In this thesis, also two approaches of EIT image reconstruction are proposed. The first is based on reformulating the inverse problem in terms of integral equations. This method uses only a single set of measurements for the reconstruction. The second approach is an algorithm based on linearisation which uses more then one set of measurements. A promising result is that one can qualitatively reconstruct the conductivity inside the cross-section of a human chest. Even though the human volunteer is neither two-dimensional nor circular, such reconstructions can be useful in medical applications: monitoring for lung problems such as accumulating fluid or a collapsed lung and noninvasive monitoring of heart function and blood flow.

  10. Derivation of clones close to met by preparative field inversion gel electrophoresis

    SciTech Connect

    Michiels, F.; Burmeister, M.; Lehrach, H.

    1987-06-05

    The molecular analysis of genes identified by mutations is a major problems in mammalian genetics. As a step toward this goal, preparative field inversion gel electrophoresis (FIGE) was used to selectively isolate clones from the environment of genetically linked markers, and to select a subset of these clones containing sequences next to specific restriction sites rare in mammalian DNA. This approach has been used to generate a library highly enriched in sequences closely linked to the cystic fibrosis marker met. One clone derived from the end of a Not I restriction fragment containing the met sequence was analyzed in detail and localized within a long range map to a position of 300 kilobase pairs 5' of the metD sequence.

  11. Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17.

    PubMed

    Kehrer-Sawatzki, Hildegard; Schreiner, Bettina; Tänzer, Simone; Platzer, Matthias; Müller, Stefan; Hameister, Horst

    2002-08-01

    A comparison of the human genome with that of the chimpanzee is an attractive approach to attempts to understand the specificity of a certain phenotype's development. The two karyotypes differ by one chromosome fusion, nine pericentric inversions, and various additions of heterochromatin to chromosomal telomeres. Only the fusion, which gave rise to human chromosome 2, has been characterized at the sequence level. During the present study, we investigated the pericentric inversion by which chimpanzee chromosome 19 differs from human chromosome 17. Fluorescence in situ hybridization was used to identify breakpoint-spanning bacterial artificial chromosomes (BACs) and plasmid artificial chromosomes (PACs). By sequencing the junction fragments, we localized breakpoints in intergenic regions rich in repetitive elements. Our findings suggest that repeat-mediated nonhomologous recombination has facilitated inversion formation. No addition or deletion of any sequence element was detected at the breakpoints or in the surrounding sequences. Next to the break, at a distance of 10.2-39.1 kb, the following genes were found: NGFR and NXPH3 (on human chromosome 17q21.3) and GUC2D and ALOX15B (on human chromosome 17p13). The inversion affects neither the genomic structure nor the gene-activity state with regard to replication timing of these genes.

  12. Inversion techniques for recovering two-dimensional distributions of auroral emission rates from tomographic rocket photometer measurements

    NASA Technical Reports Server (NTRS)

    Mcdade, Ian. C.; Llewellyn, Edward J.

    1991-01-01

    This paper demonstrates how the spatial distribution of optical emission rates within an auroral arc may be recovered from rocket photometer measurements made in a tomographic spin scan mode. The tomographic inversion procedures required to recover this information and the implementation of two inversion algorithms that are particularly well suited for dealing with the problem of noise in the observational data are described. The performance of the inversion algorithms and the limitations of the rocket tomography technique are assessed using various sets of simulated rocket measurements that were generated from 'known' auroral emission-rate distributions. The simulations are used to investigate how the quality of the tomographic recovery may be influenced by various factors such as noise in the data, rocket penetration of the auroral form, background sources of emission, smearing due to the photometer field of view, and temporal variations in the auroral form.

  13. Neural network tool for rapid recovery of plasma topology

    SciTech Connect

    Tribaldos, V.; van Milligen, B.P.

    1997-01-01

    A general method for the rapid recovery of plasma topology based on a neural network fit of the normalized magnetic flux is presented. We propose a general method for coordinate inversions that is based on a neural network fit of the normalized magnetic flux. The neural network provides a flexible and compact base for representing the plasma topology and allows the evaluation of spatial derivatives by analytic methods (as opposed to finite-difference methods), making it faster than other techniques. We present examples of this technique for both two-dimensional plasmas (tokamak D shaped, X point) and stellarators. {copyright} {ital 1997 American Institute of Physics.}

  14. Stress Recovery and Dynamic Analysis of Functionally Graded Materials

    NASA Astrophysics Data System (ADS)

    Paulino, Rivânia H.; Romero, Juan S.; Menandro, Fernando C. M.

    2008-02-01

    A macroelement recovery technique for the strain field of a functionally graded material (FGM), based on the residual dynamic equilibrium equation for elasticity, is proposed. The derivatives are recovered by solving a local variational problem, using the superconvergence points. The basic idea is to utilize post-processing to achieve a more accurate approximation of the stresses while considering the dynamic nature of the problem. The development includes dynamic modeling of FGM and can be applied to direct and inverse problems. A numerical simulation is presented to better demonstrate the proposed methodology.

  15. New Two-stage Approach For 3d Potential Field Data Inversion

    NASA Astrophysics Data System (ADS)

    Prutkin, I. L.

    into account some additional geological information. Our results have permitted to implement two-stage approach for three-dimensional gravity and magnetic anomalies. The volume model of Kendykty granitoid massif has been constructed according to magnetic data. This case history demonstrates the fa- cilities of our approach in finding a restricted body of arbitrary shape. Since a scale of inverse problem is of no difference for us, we are able to apply our algorithms both to core mantle boundary recovery and for the control over barren rock-ore boundary in mining process.

  16. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  17. SISYPHUS: A high performance seismic inversion factory

    NASA Astrophysics Data System (ADS)

    Gokhberg, Alexey; Simutė, Saulė; Boehm, Christian; Fichtner, Andreas

    2016-04-01

    In the recent years the massively parallel high performance computers became the standard instruments for solving the forward and inverse problems in seismology. The respective software packages dedicated to forward and inverse waveform modelling specially designed for such computers (SPECFEM3D, SES3D) became mature and widely available. These packages achieve significant computational performance and provide researchers with an opportunity to solve problems of bigger size at higher resolution within a shorter time. However, a typical seismic inversion process contains various activities that are beyond the common solver functionality. They include management of information on seismic events and stations, 3D models, observed and synthetic seismograms, pre-processing of the observed signals, computation of misfits and adjoint sources, minimization of misfits, and process workflow management. These activities are time consuming, seldom sufficiently automated, and therefore represent a bottleneck that can substantially offset performance benefits provided by even the most powerful modern supercomputers. Furthermore, a typical system architecture of modern supercomputing platforms is oriented towards the maximum computational performance and provides limited standard facilities for automation of the supporting activities. We present a prototype solution that automates all aspects of the seismic inversion process and is tuned for the modern massively parallel high performance computing systems. We address several major aspects of the solution architecture, which include (1) design of an inversion state database for tracing all relevant aspects of the entire solution process, (2) design of an extensible workflow management framework, (3) integration with wave propagation solvers, (4) integration with optimization packages, (5) computation of misfits and adjoint sources, and (6) process monitoring. The inversion state database represents a hierarchical structure with

  18. Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions.

    PubMed

    Dagilis, Andrius J; Kirkpatrick, Mark

    2016-07-01

    Chromosomal inversions are frequently implicated in isolating species. Models have shown how inversions can evolve in the context of postmating isolation. Inversions are also frequently associated with mating preferences, a topic that has not been studied theoretically. Here, we show how inversions can spread by capturing a mating preference locus and one or more loci involved with epistatic incompatibilities. Inversions can be established under broad conditions ranging from near panmixis to nearly complete speciation. These results provide a hypothesis to explain the growing number of examples of inversions associated with premating isolating mechanisms. PMID:27174252

  19. GENERATING FRACTAL PATTERNS BY USING p-CIRCLE INVERSION

    NASA Astrophysics Data System (ADS)

    Ramírez, José L.; Rubiano, Gustavo N.; Zlobec, Borut Jurčič

    2015-10-01

    In this paper, we introduce the p-circle inversion which generalizes the classical inversion with respect to a circle (p = 2) and the taxicab inversion (p = 1). We study some basic properties and we also show the inversive images of some basic curves. We apply this new transformation to well-known fractals such as Sierpinski triangle, Koch curve, dragon curve, Fibonacci fractal, among others. Then we obtain new fractal patterns. Moreover, we generalize the method called circle inversion fractal be means of the p-circle inversion.

  20. Microwave spectrum of the H2DO+ ion: inversion-rotation transitions and inversion splitting.

    PubMed

    Furuya, Takashi; Saito, Shuji; Araki, Mitsunori

    2007-12-28

    Inversion-rotation spectral lines of the monodeuterated hydronium ion, H(2)DO(+), have been observed by a source-modulation spectrometer in the millimeter- to submillimeter-wave region. The ion was generated by a hollow-cathode discharge in a gas mixture of H(2)O and D(2)O. Nine inversion-rotation lines were measured precisely for the lowest pair of inversion doublets in the frequency region from 210 to 720 GHz. The measured lines were analyzed to derive rotational constants in the inversion-doublet states and inversion splitting. The inversion splitting in the ground state was determined to be 1,215,866(410) MHz, that is, 40.5569(137) cm(-1), where the numbers in parentheses give probable uncertainties estimated from the Jacobian matrix of the assumed centrifugal distortion constants of the inversion-doublet states. The determined inversion splitting is off by -0.58 cm(-1) from the predicted value of 41.14 cm(-1) by Rayamaki et al. using high-order coupled cluster ab initio calculations [J. Chem. Phys. 118, 10929 (2003)], and by 0.039 cm(-1) from the observed value of 40.518(10) cm(-1) by Dong and Nesbitt using high-resolution jet-cooled infrared spectroscopy [J. Chem. Phys. 125, 144311 (2006)] beyond the quoted uncertainty. The most astronomically important transition 0(00)(-)-1(0)(+) for the ortho species was measured at 673,257.024(31) MHz, which could be used as a radioastronomical probe investigating interstellar chemistry of deuterium fractionation in space.

  1. Anaerobic digestion of dairy wastewater by inverse fluidization: the inverse fluidized bed and the inverse turbulent bed reactors.

    PubMed

    Arnaiz, C; Buffiere, P; Elmaleh, S; Lebrato, J; Moletta, R

    2003-11-01

    This paper describes the application of the inverse fluidization technology to the anaerobic digestion of dairy wastewater. Two reactors were investigated: the inverse fluidized bed reactor and the inverse turbulent reactor. In these reactors, a granular floating solid is expanded by a down-flow current of effluent or an up-flow current of gas, respectively. The carrier particles (Extendospheres) were chosen for their large specific surface area (20,000 m2m(-3)) and their low energy requirements for fluidization (gas velocity of 1.5 mm s(-1), 5.4 m h(-1)). Organic load was increased stepwise by reducing hydraulic retention time from more than 60 days to 3 days, while maintaining constant the feed COD concentration. Both reactors achieved more than 90% of COD removal, at an organic loading rate of 10-12 kgCOD m(-3) d(-1), respectively. The performances observed were similar or even higher than that of other previously tested fluidized bed technologies treating the same wastewater. It was found that the main advantages of this system are: low energy requirement, because of the low fluidization velocities required; there is no need of a settling device, because solids accumulate at the bottom of the reactor, so they can be easily drawn out and particles with high-biomass content can be easily recovered. Lipid phosphate concentration has been revealed as a good method for biomass estimation in biofilms since it only includes living biomass.

  2. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  3. A Bayesian method for microseismic source inversion

    NASA Astrophysics Data System (ADS)

    Pugh, D. J.; White, R. S.; Christie, P. A. F.

    2016-08-01

    Earthquake source inversion is highly dependent on location determination and velocity models. Uncertainties in both the model parameters and the observations need to be rigorously incorporated into an inversion approach. Here, we show a probabilistic Bayesian method that allows formal inclusion of the uncertainties in the moment tensor inversion. This method allows the combination of different sets of far-field observations, such as P-wave and S-wave polarities and amplitude ratios, into one inversion. Additional observations can be included by deriving a suitable likelihood function from the uncertainties. This inversion produces samples from the source posterior probability distribution, including a best-fitting solution for the source mechanism and associated probability. The inversion can be constrained to the double-couple space or allowed to explore the gamut of moment tensor solutions, allowing volumetric and other non-double-couple components. The posterior probability of the double-couple and full moment tensor source models can be evaluated from the Bayesian evidence, using samples from the likelihood distributions for the two source models, producing an estimate of whether or not a source is double-couple. Such an approach is ideally suited to microseismic studies where there are many sources of uncertainty and it is often difficult to produce reliability estimates of the source mechanism, although this can be true of many other cases. Using full-waveform synthetic seismograms, we also show the effects of noise, location, network distribution and velocity model uncertainty on the source probability density function. The noise has the largest effect on the results, especially as it can affect other parts of the event processing. This uncertainty can lead to erroneous non-double-couple source probability distributions, even when no other uncertainties exist. Although including amplitude ratios can improve the constraint on the source probability

  4. Uncertainty quantification for ice sheet inverse problems

    NASA Astrophysics Data System (ADS)

    Petra, N.; Ghattas, O.; Stadler, G.; Zhu, H.

    2011-12-01

    Modeling the dynamics of polar ice sheets is critical for projections of future sea level rise. Yet, there remain large uncertainties in the basal boundary conditions and in the non-Newtonian constitutive relations employed within ice sheet models. In this presentation, we consider the problem of estimating uncertainty in the solution of (large-scale) ice sheet inverse problems within the framework of Bayesian inference. Computing the general solution of the inverse problem-i.e., the posterior probability density-is intractable with current methods on today's computers, due to the expense of solving the forward model (3D full Stokes flow with nonlinear rheology) and the high dimensionality of the uncertain parameters (which are discretizations of the basal slipperiness field and the Glen's law exponent field). However, under the assumption of Gaussian noise and prior probability densities, and after linearizing the parameter-to-observable map, the posterior density becomes Gaussian, and can therefore be characterized by its mean and covariance. The mean is given by the solution of a nonlinear least squares optimization problem, which is equivalent to a deterministic inverse problem with appropriate interpretation and weighting of the data misfit and regularization terms. To obtain this mean, we solve a deterministic ice sheet inverse problem; here, we infer parameters arising from discretizations of basal slipperiness and rheological exponent fields. For this purpose, we minimize a regularized misfit functional between observed and modeled surface flow velocities. The resulting least squares minimization problem is solved using an adjoint-based inexact Newton method, which uses first and second derivative information. The posterior covariance matrix is given (in the linear-Gaussian case) by the inverse of the Hessian of the least squares cost functional of the deterministic inverse problem. Direct computation of the Hessian matrix is prohibitive, since it would

  5. Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila.

    PubMed

    Calvete, Oriol; González, Josefa; Betrán, Esther; Ruiz, Alfredo

    2012-07-01

    Chromosomal inversions are usually portrayed as simple two-breakpoint rearrangements changing gene order but not gene number or structure. However, increasing evidence suggests that inversion breakpoints may often have a complex structure and entail gene duplications with potential functional consequences. Here, we used a combination of different techniques to investigate the breakpoint structure and the functional consequences of a complex rearrangement fixed in Drosophila buzzatii and comprising two tandemly arranged inversions sharing the middle breakpoint: 2m and 2n. By comparing the sequence in the breakpoint regions between D. buzzatii (inverted chromosome) and D. mojavensis (noninverted chromosome), we corroborate the breakpoint reuse at the molecular level and infer that inversion 2m was associated with a duplication of a ~13 kb segment and likely generated by staggered breaks plus repair by nonhomologous end joining. The duplicated segment contained the gene CG4673, involved in nuclear transport, and its two nested genes CG5071 and CG5079. Interestingly, we found that other than the inversion and the associated duplication, both breakpoints suffered additional rearrangements, that is, the proximal breakpoint experienced a microinversion event associated at both ends with a 121-bp long duplication that contains a promoter. As a consequence of all these different rearrangements, CG5079 has been lost from the genome, CG5071 is now a single copy nonnested gene, and CG4673 has a transcript ~9 kb shorter and seems to have acquired a more complex gene regulation. Our results illustrate the complex effects of chromosomal rearrangements and highlight the need of complementing genomic approaches with detailed sequence-level and functional analyses of breakpoint regions if we are to fully understand genome structure, function, and evolutionary dynamics.

  6. Introduction to deployable recovery systems

    SciTech Connect

    Meyer, J.

    1985-08-01

    This report provides an introduction to deployable recovery systems for persons with little or no background in parachutes but who are knowledgeable in aerodynamics. A historical review of parachute development is given along with a description of the basic components of most deployable recovery systems. Descriptions are given of the function of each component and of problems that occur if a component fails to perform adequately. Models are presented for deployable recovery systems. Possible directions for future work are suggested in the summary.

  7. A Hebbian learning rule gives rise to mirror neurons and links them to control theoretic inverse models.

    PubMed

    Hanuschkin, A; Ganguli, S; Hahnloser, R H R

    2013-01-01

    Mirror neurons are neurons whose responses to the observation of a motor act resemble responses measured during production of that act. Computationally, mirror neurons have been viewed as evidence for the existence of internal inverse models. Such models, rooted within control theory, map-desired sensory targets onto the motor commands required to generate those targets. To jointly explore both the formation of mirrored responses and their functional contribution to inverse models, we develop a correlation-based theory of interactions between a sensory and a motor area. We show that a simple eligibility-weighted Hebbian learning rule, operating within a sensorimotor loop during motor explorations and stabilized by heterosynaptic competition, naturally gives rise to mirror neurons as well as control theoretic inverse models encoded in the synaptic weights from sensory to motor neurons. Crucially, we find that the correlational structure or stereotypy of the neural code underlying motor explorations determines the nature of the learned inverse model: random motor codes lead to causal inverses that map sensory activity patterns to their motor causes; such inverses are maximally useful, by allowing the imitation of arbitrary sensory target sequences. By contrast, stereotyped motor codes lead to less useful predictive inverses that map sensory activity to future motor actions. Our theory generalizes previous work on inverse models by showing that such models can be learned in a simple Hebbian framework without the need for error signals or backpropagation, and it makes new conceptual connections between the causal nature of inverse models, the statistical structure of motor variability, and the time-lag between sensory and motor responses of mirror neurons. Applied to bird song learning, our theory can account for puzzling aspects of the song system, including necessity of sensorimotor gating and selectivity of auditory responses to bird's own song (BOS) stimuli.

  8. Quasi-3D Waveform Inversion for Velocity Structures and Source Process Analyses Using its Results

    NASA Astrophysics Data System (ADS)

    Hikima, K.; Koketsu, K.

    2007-12-01

    In this study, we propose an efficient waveform inversion method for 2-D velocity structures and 3-D velocity structures are constructed by interpolating the results of the 2-D inversions. We apply these methods to a source process study of the 2003 Miyagi-ken Hokubu earthquake. We will first construct a velocity model, then determine the source processes of this earthquake sequence using the Green's function calculated with the resultant 3-D velocity model. We formulate the inversion procedure in a 2-D cross section. In a 2-D problem, an earthquake is forced to be a line source. Therefore, we introduce approximate transformation from a line source to a point source (Vidale and Helmberger, 1987). We use the 2-D velocity-stress staggered-grid finite difference scheme, so that the source representation is somewhat different from the original 'source box method' and we apply additional corrections to calculated waveforms. The boundary shapes of layers are expressed by connected nodes and we invert observed waveforms for layer thicknesses at the nodes. We perform 2-D velocity inversions along cross sections which involve a medium-size earthquake and observation points. We assemble the results for many stations and interpolated them to construct the 3-D velocity model. Finally, we calculate waveforms from the target earthquake by the 3-D finite difference method with this velocity model to confirm the validity of the model. We next perform waveform inversions for source processes of the 2003 Miyagi-ken Hokubu earthquake sequence using the resultant 3-D velocity model. We divide the fault plane into northern and southern subplanes, so that the southern subplane includes the hypocenter of the mainshock and the largest foreshock. The strike directions of the northern and southern subplanes were N-S and NE-SW, respectively. The Green's functions for these source inversions are calculated using the reciprocal theorem. We determine the slip models using the 3- D structure and

  9. USING SEQUENCING TO IMPROVE OPERATIONAL EFFICIENCY AND RELIABILITY

    SciTech Connect

    D OTTAVIO,T.; NIEDZIELA, J.

    2007-10-15

    Operation of an accelerator requires the efficient and reproducible execution of many different types of procedures. Some procedures, like beam acceleration, magnet quench recovery, and species switching can be quite complex. To improve accelerator reliability and efficiency, automated execution of procedures is required. Creation of a single robust sequencing application permits the streamlining of this process and offers many benefits in sequence creation, editing, and control. In this paper, we present key features of a sequencer application commissioned at the Collider-Accelerator Department of Brookhaven National Laboratory during the 2007 run. Included is a categorization of the different types of sequences in use, a discussion of the features considered desirable in a good sequencer, and a description of the tools created to aid in sequence construction and diagnosis. Finally, highlights from our operational experience are presented, with emphasis on Operations control of the sequencer, and the alignment of sequence construction with existing operational paradigms.

  10. Multimodal sequence learning.

    PubMed

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  11. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  12. Register file soft error recovery

    SciTech Connect

    Fleischer, Bruce M.; Fox, Thomas W.; Wait, Charles D.; Muff, Adam J.; Watson, III, Alfred T.

    2013-10-15

    Register file soft error recovery including a system that includes a first register file and a second register file that mirrors the first register file. The system also includes an arithmetic pipeline for receiving data read from the first register file, and error detection circuitry to detect whether the data read from the first register file includes corrupted data. The system further includes error recovery circuitry to insert an error recovery instruction into the arithmetic pipeline in response to detecting the corrupted data. The inserted error recovery instruction replaces the corrupted data in the first register file with a copy of the data from the second register file.

  13. Hurricane Recovery Report 2004

    NASA Technical Reports Server (NTRS)

    Gordon, Joseph P.

    2005-01-01

    During August and September 2004, four hurricanes tested the mettle of Space Coast residents and the Kennedy Space Center (KSC) leadership and workforce. These threats underscored two important points: the very real vulnerability of KSC and its valuable space program assets to the devastating power of a hurricane, and the planning required to effectively deal with such threats. The damage was significant even though KSC did not experience sustained hurricane-force winds. To better understand and appreciate these points, this report provides an overview of the meteorological history of the Space Coast and what is involved in the planning, preparation, and recovery activities, as well as addressing the impacts of the 2004 hurricane season.

  14. Exercise and cancer recovery.

    PubMed

    Visovsky, Constance; Dvorak, Colleen

    2005-05-01

    Disease and cancer treatment-related side effects such as decreased energy level, muscle weakness, and declines in functional status and body mass have been well documented. There is evidence that exercise, such as low intensity aerobics walking, Tai Chi, or cycling, results in an overall decrease in fatigue levels over the course of cancer treatment. Additionally, there is evidence that regular physical activity or exercise can decrease emotional stress, blood pressure, the duration of neutropenia, thrombocytopenia, and pain. Exercise also has been shown to increase quality of life and improve the maximal oxygen uptake during exertion, sleep patterns, and cognition. However, the majority of studies of exercise and cancer have been conducted with women with early stage breast cancer, limiting the generalizability of these studies to other cancer populations. The purpose of this systematic review is to provide a synthesis of the extant research evidence about th e benefits of exercise related to cancer recovery. PMID:15977980

  15. Speech recovery device

    DOEpatents

    Frankle, Christen M.

    2004-04-20

    There is provided an apparatus and method for assisting speech recovery in people with inability to speak due to aphasia, apraxia or another condition with similar effect. A hollow, rigid, thin-walled tube with semi-circular or semi-elliptical cut out shapes at each open end is positioned such that one end mates with the throat/voice box area of the neck of the assistor and the other end mates with the throat/voice box area of the assisted. The speaking person (assistor) makes sounds that produce standing wave vibrations at the same frequency in the vocal cords of the assisted person. Driving the assisted person's vocal cords with the assisted person being able to hear the correct tone enables the assisted person to speak by simply amplifying the vibration of membranes in their throat.

  16. Face lift postoperative recovery.

    PubMed

    Mottura, A Aldo

    2002-01-01

    The purpose of this paper is to describe what I have studied and experienced, mainly regarding the control and prediction of the postoperative edema; how to achieve an agreeable recovery and give positive support to the patient, who in turn will receive pleasant sensations that neutralize the negative consequences of the surgery.After the skin is lifted, the drainage flow to the flaps is reversed abruptly toward the medial part of the face, where the flap bases are located. The thickness and extension of the flap determines the magnitude of the post-op edema, which is also augmented by medial surgeries (blepharo, rhino) whose trauma obstruct their natural drainage, increasing the congestion and edema. To study the lymphatic drainage, the day before an extended face lift (FL) a woman was infiltrated in the cheek skin with lynfofast (solution of tecmesio) and the absorption was observed by gamma camera. Seven days after the FL she underwent the same study; we observed no absorption by the lymphatic, concluding that a week after surgery, the lymphatic network was still damaged. To study the venous return during surgery, a fine catheter was introduced into the external jugular vein up to the mandibular border to measure the peripheral pressure. Following platysma plication the pressure rose, and again after a simple bandage, but with an elastic bandage it increased even further, diminishing considerably when it was released. Hence, platysma plication and the elastic bandage on the neck augment the venous congestion of the face. There are diseases that produce and can prolong the surgical edema: cardiac, hepatic, and renal insufficiencies, hypothyroidism, malnutrition, etc. According to these factors, the post-op edema can be predicted, the surgeon can choose between a wide dissection or a medial surgery, depending on the social or employment compromises the patient has, or the patient must accept a prolonged recovery if a complex surgery is necessary. Operative

  17. Energy recovery system

    DOEpatents

    Moore, Albert S.; Verhoff, Francis H.

    1980-01-01

    The present invention is directed to an improved wet air oxidation system and method for reducing the chemical oxygen demand (COD) of waste water used from scrubbers of coal gasification plants, with this COD reduction being sufficient to effectively eliminate waste water as an environmental pollutant. The improvement of the present invention is provided by heating the air used in the oxidation process to a temperature substantially equal to the temperature in the oxidation reactor before compressing or pressurizing the air. The compression of the already hot air further heats the air which is then passed in heat exchange with gaseous products of the oxidation reaction for "superheating" the gaseous products prior to the use thereof in turbines as the driving fluid. The superheating of the gaseous products significantly minimizes condensation of gaseous products in the turbine so as to provide a substantially greater recovery of mechanical energy from the process than heretofore achieved.

  18. Integrated oxygen recovery system

    NASA Technical Reports Server (NTRS)

    Lee, M. Gene; Davenport, Ronald J.

    1993-01-01

    Life Systems has conceptualized an innovative Integrated Oxygen Recovery System (IORS) applicable to advanced mission air revitalization. The IORS provides the capability to electrochemically generate metabolic oxygen (O2) and recover O2 from the space habitat atmosphere via a carbon dioxide (CO2) reduction process within a single assembly. To achieve this capability, the IORS utilizes a Solid Metal Cathode (SMC) water electrolysis unit that simultaneously serves as the Sabatier CO2 reduction reactor. The IORS enables two major life support systems currently baselined in closed loop air revitalization systems to be combined into one smaller, less complex system. This concept reduces fluidic and electrical interface requirements and eliminates a hydrogen (H2) interface. Life Systems is performing an evaluation of the IORS process directed at demonstrating performance and quantifying key physical characteristics including power, weight, and volume. The results of the checkout, shakedown, and initial parametric tests are summarized.

  19. Integrated oxygen recovery system

    NASA Technical Reports Server (NTRS)

    Lee, M. Gene; Davenport, Ronald J.

    1993-01-01

    Life Systems has conceptualized an innovative Integrated Oxygen Recovery System (IORS) applicable to advanced mission air revitalization. The IORS provides the capability to electrochemically generate metabolic oxygen (O2) and recover O2 from the space habitat atmosphere via a carbon dioxide (CO2) reduction process within a single assembly. To achieve this capability, the IORS utilizes a Solid Metal Cathode (SMC) water electrolysis unit that simultaneously serves as the Sabatier CO2 reduction reactor. The IORS enables two major life support systems currently baselined in closed loop air revitalization systems to be combined into one smaller, less complex system. This concept reduces fluidic and electrical interface requirements and eliminates a hydrogen (H2) interface. Life Systems is performing an evaluation of the IORS process directed at demonstrating performance and quantifying key physical characteristics including power, weight, and volume. Technical progress achieved during the first two months of the program is summarized.

  20. Speech recovery device

    SciTech Connect

    Frankle, Christen M.

    2000-10-19

    There is provided an apparatus and method for assisting speech recovery in people with inability to speak due to aphasia, apraxia or another condition with similar effect. A hollow, rigid, thin-walled tube with semi-circular or semi-elliptical cut out shapes at each open end is positioned such that one end mates with the throat/voice box area of the neck of the assistor and the other end mates with the throat/voice box area of the assisted. The speaking person (assistor) makes sounds that produce standing wave vibrations at the same frequency in the vocal cords of the assisted person. Driving the assisted person's vocal cords with the assisted person being able to hear the correct tone enables the assisted person to speak by simply amplifying the vibration of membranes in their throat.

  1. Enhanced oil recovery system

    DOEpatents

    Goldsberry, Fred L.

    1989-01-01

    All energy resources available from a geopressured geothermal reservoir are used for the production of pipeline quality gas using a high pressure separator/heat exchanger and a membrane separator, and recovering waste gas from both the membrane separator and a low pressure separator in tandem with the high pressure separator for use in enhanced oil recovery, or in powering a gas engine and turbine set. Liquid hydrocarbons are skimmed off the top of geothermal brine in the low pressure separator. High pressure brine from the geothermal well is used to drive a turbine/generator set before recovering waste gas in the first separator. Another turbine/generator set is provided in a supercritical binary power plant that uses propane as a working fluid in a closed cycle, and uses exhaust heat from the combustion engine and geothermal energy of the brine in the separator/heat exchanger to heat the propane.

  2. Approximate inverse preconditioners for general sparse matrices

    SciTech Connect

    Chow, E.; Saad, Y.

    1994-12-31

    Preconditioned Krylov subspace methods are often very efficient in solving sparse linear matrices that arise from the discretization of elliptic partial differential equations. However, for general sparse indifinite matrices, the usual ILU preconditioners fail, often because of the fact that the resulting factors L and U give rise to unstable forward and backward sweeps. In such cases, alternative preconditioners based on approximate inverses may be attractive. We are currently developing a number of such preconditioners based on iterating on each column to get the approximate inverse. For this approach to be efficient, the iteration must be done in sparse mode, i.e., we must use sparse-matrix by sparse-vector type operatoins. We will discuss a few options and compare their performance on standard problems from the Harwell-Boeing collection.

  3. Bayesian inversion for optical diffraction tomography

    NASA Astrophysics Data System (ADS)

    Ayasso, H.; Duchêne, B.; Mohammad-Djafari, A.

    2010-05-01

    In this paper, optical diffraction tomography is considered as a non-linear inverse scattering problem and tackled within the Bayesian estimation framework. The object under test is a man-made object known to be composed of compact regions made of a finite number of different homogeneous materials. This a priori knowledge is appropriately translated by a Gauss-Markov-Potts prior. Hence, a Gauss-Markov random field is used to model the contrast distribution whereas a hidden Potts-Markov field accounts for the compactness of the regions. First, we express the a posteriori distributions of all the unknowns and then a Gibbs sampling algorithm is used to generate samples and estimate the posterior mean of the unknowns. Some preliminary results, obtained by applying the inversion algorithm to laboratory controlled data, are presented.

  4. Aquifer Structure Identification Using Stochastic Inversion

    SciTech Connect

    Harp, Dylan R; Dai, Zhenxue; Wolfsberg, Andrew V; Vrugt, Jasper A

    2008-01-01

    This study presents a stochastic inverse method for aquifer structure identification using sparse geophysical and hydraulic response data. The method is based on updating structure parameters from a transition probability model to iteratively modify the aquifer structure and parameter zonation. The method is extended to the adaptive parameterization of facies hydraulic parameters by including these parameters as optimization variables. The stochastic nature of the statistical structure parameters leads to nonconvex objective functions. A multi-method genetically adaptive evolutionary approach (AMALGAM-SO) was selected to perform the inversion given its search capabilities. Results are obtained as a probabilistic assessment of facies distribution based on indicator cokriging simulation of the optimized structural parameters. The method is illustrated by estimating the structure and facies hydraulic parameters of a synthetic example with a transient hydraulic response.

  5. Search for the inverse fission of uranium

    NASA Astrophysics Data System (ADS)

    Loveland, W.; Yanez, R.; Beckerman, J.; Leonard, M.; Pettersson, G.; Gross, C. J.; Shapira, D.; Liang, J. F.; Kohley, Z.; Varner, R. L.

    2011-10-01

    A search for the ``inverse fission'' of uranium has been made. Two ``inverse fission'' reactions were studied, the reaction of 124Sn + 100Mo and the reaction of 132Sn + 100Mo. In the former case, evaporation residues were searched for using (a) in-beam α-spectroscopy, (b) post-irradiation α-spectroscopy and (c) in-beam detection of recoiling evaporation residues while in the latter case, the evaporation residue, 230U was searched for using post irradiation radio-analytical techniques. Data acquisition and analysis is on-going with expected upper limits or production cross sections of < 1 microbarn. The implications of these results for determining the fusion probability, PCN, in the collisions of massive nuclei are discussed. This work was supported in part by the USDOE Office of Nuclear Physics under Grant DE-FG06-97ER41026 and Contract No. DE-AC02-06CH11357.

  6. Regularity of mappings inverse to Sobolev mappings

    SciTech Connect

    Vodop'yanov, Sergei K

    2012-10-31

    For homeomorphisms {phi}:{Omega}{yields}{Omega}' on Euclidean domains in R{sup n}, n{>=}2, necessary and sufficient conditions ensuring that the inverse mapping belongs to a Sobolev class are investigated. The result obtained is used to describe a new two-index scale of homeomorphisms in some Sobolev class such that their inverses also form a two-index scale of mappings, in another Sobolev class. This scale involves quasiconformal mappings and also homeomorphisms in the Sobolev class W{sup 1}{sub n-1} such that rankD{phi}(x){<=}n-2 almost everywhere on the zero set of the Jacobian det D{phi}(x). Bibliography: 65 titles.

  7. Space-time inversion and its consequences

    NASA Astrophysics Data System (ADS)

    Chelnokov, M.

    2016-07-01

    The article discusses some new aspects of both the inversion of space and the inversion of time. It is shown that behind the mirror is not symmetric to in front of the mirror. It, in its turn, leads to nonconservation of spatial parity. The same situation takes place in the combined CP-parity. Further, the article shows that from the point of view of different reference systems of the Universe (from the point of view of different galaxies or accumulation of galaxies) time flows not just differently, and, in some cases, in the opposite directions. It leads to major changes in the picture of the Universe. In particular, the concept of the age of the Universe loses its meaning, serious doubts about the idea of the Big Bang and so on.

  8. Linear functional minimization for inverse modeling

    SciTech Connect

    Barajas-Solano, David A.; Wohlberg, Brendt Egon; Vesselinov, Velimir Valentinov; Tartakovsky, Daniel M.

    2015-06-01

    In this paper, we present a novel inverse modeling strategy to estimate spatially distributed parameters of nonlinear models. The maximum a posteriori (MAP) estimators of these parameters are based on a likelihood functional, which contains spatially discrete measurements of the system parameters and spatiotemporally discrete measurements of the transient system states. The piecewise continuity prior for the parameters is expressed via Total Variation (TV) regularization. The MAP estimator is computed by minimizing a nonquadratic objective equipped with the TV operator. We apply this inversion algorithm to estimate hydraulic conductivity of a synthetic confined aquifer from measurements of conductivity and hydraulic head. The synthetic conductivity field is composed of a low-conductivity heterogeneous intrusion into a high-conductivity heterogeneous medium. Our algorithm accurately reconstructs the location, orientation, and extent of the intrusion from the steady-state data only. Finally, addition of transient measurements of hydraulic head improves the parameter estimation, accurately reconstructing the conductivity field in the vicinity of observation locations.

  9. Darwin's “strange inversion of reasoning”

    PubMed Central

    Dennett, Daniel

    2009-01-01

    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

  10. Lasing without inversion in circuit quantum electrodynamics.

    PubMed

    Marthaler, M; Utsumi, Y; Golubev, D S; Shnirman, A; Schön, Gerd

    2011-08-26

    We study the photon generation in a transmission line oscillator coupled to a driven qubit in the presence of a dissipative electromagnetic environment. It has been demonstrated previously that a population inversion in the qubit can lead to a lasing state of the oscillator. Here we show that the circuit can also exhibit the effect of "lasing without inversion." It arises since the coupling to the dissipative environment enhances photon emission as compared to absorption, similar to the recoil effect predicted for atomic systems. While the recoil effect is very weak, and so far elusive, the effect described here should be observable with realistic circuits. We analyze the requirements for system parameters and environment.

  11. Regeneration of stochastic processes: an inverse method

    NASA Astrophysics Data System (ADS)

    Ghasemi, F.; Peinke, J.; Sahimi, M.; Rahimi Tabar, M. R.

    2005-10-01

    We propose a novel inverse method that utilizes a set of data to construct a simple equation that governs the stochastic process for which the data have been measured, hence enabling us to reconstruct the stochastic process. As an example, we analyze the stochasticity in the beat-to-beat fluctuations in the heart rates of healthy subjects as well as those with congestive heart failure. The inverse method provides a novel technique for distinguishing the two classes of subjects in terms of a drift and a diffusion coefficients which behave completely differently for the two classes of subjects, hence potentially providing a novel diagnostic tool for distinguishing healthy subjects from those with congestive heart failure, even at the early stages of the disease development.

  12. New advances in Inverse Cerenkov acceleration

    SciTech Connect

    Kimura, W.D.; Babzien, M.; Cline, D.B.; Fiorito, R.B.; Fontana, J.R.; Gallardo, J.C.; Gottschalk, S.C.; Kusche, K.P. |; Liu, Y.; Pogorelsky, I.V.; Quimby, D.C.; Pantell, R.H.; Rule, D.W.; Skaritka, J.; Sandweiss, J.; van Steenbergen, A.; Yakimenko, V.

    1997-02-01

    Inverse Cerenkov acceleration (ICA) has entered a new phase in its development. The issue of staging and rephasing the optical wave with a microbunched electron beam is now being examined. This ability to accelerate over multiple stages is important for scaling laser accelerator devices to higher energies. An inverse free electron laser (IFEL) will be positioned upstream from the ICA experiment and used to prebunch the electrons. These electrons will then be focused into the ICA interaction region for rephasing and acceleration by the laser beam. Issues that will be examined during these combined ICA/IFEL experiments include rephasing the laser beam with the microbunches, minimizing bunch smearing, and trapping the electrons in an acceleration bucket. {copyright} {ital 1997 American Institute of Physics.}

  13. An efficient method for inverse problems

    NASA Technical Reports Server (NTRS)

    Daripa, Prabir

    1987-01-01

    A new inverse method for aerodynamic design of subcritical airfoils is presented. The pressure distribution in this method can be prescribed in a natural way, i.e. as a function of arclength of the as yet unknown body. This inverse problem is shown to be mathematically equivalent to solving a single nonlinear boundary value problem subject to known Dirichlet data on the boundary. The solution to this problem determines the airfoil, the free stream Mach number M(sub x) and the upstream flow direction theta(sub x). The existence of a solution for any given pressure distribution is discussed. The method is easy to implement and extremely efficient. We present a series of results for which comparisons are made with the known airfoils.

  14. Optical inverse-square displacement sensor

    DOEpatents

    Howe, Robert D.; Kychakoff, George

    1989-01-01

    This invention comprises an optical displacement sensor that uses the inverse-square attenuation of light reflected from a diffused surface to calculate the distance from the sensor to the reflecting surface. Light emerging from an optical fiber or the like is directed onto the surface whose distance is to be measured. The intensity I of reflected light is angle dependent, but within a sufficiently small solid angle it falls off as the inverse square of the distance from the surface. At least a pair of optical detectors are mounted to detect the reflected light within the small solid angle, their ends being at different distances R and R+.DELTA.R from the surface. The distance R can then be found in terms of the ratio of the intensity measurements and the separation length as ##EQU1##

  15. Optical inverse-square displacement sensor

    DOEpatents

    Howe, R.D.; Kychakoff, G.

    1989-09-12

    This invention comprises an optical displacement sensor that uses the inverse-square attenuation of light reflected from a diffused surface to calculate the distance from the sensor to the reflecting surface. Light emerging from an optical fiber or the like is directed onto the surface whose distance is to be measured. The intensity I of reflected light is angle dependent, but within a sufficiently small solid angle it falls off as the inverse square of the distance from the surface. At least a pair of optical detectors are mounted to detect the reflected light within the small solid angle, their ends being at different distances R and R + [Delta]R from the surface. The distance R can then be found in terms of the ratio of the intensity measurements and the separation length as given in an equation. 10 figs.

  16. ORMDIN. 2-D Nonlinear Inverse Heat Conduction

    SciTech Connect

    Bass, B.R.

    1990-05-01

    ORMDIN is a finite-element program developed for two-dimensional nonlinear inverse heat conduction analysis as part of the Oak Ridge National Laboratory Pressurized Water Reactor Blowdown Heat Transfer (BDHT) program. One of the primary objectives of the program was to determine the transient surface temperature and surface heat flux of fuel pin simulators from internal thermocouple signals obtained during a loss-of-coolant accident experiment in the Thermal-Hydraulic Test Facility (THTF). ORMDIN was designed primarily to perform a transient two-dimensional nonlinear inverse heat conduction analysis of the THTF bundle 3 heater rod; however, it can be applied to other cylindrical geometries for which the thermophysical properties are prescribed functions of temperature. The program assumes that discretized temperature histories are provided at three thermocouple locations in the interior of the cylinder. Concurrent with the two-dimensional analysis, ORMDIN also generates one-dimensional solutions for each of the three thermocouple radial planes.

  17. Compression scheme for geophysical electromagnetic inversions

    NASA Astrophysics Data System (ADS)

    Abubakar, A.

    2014-12-01

    We have developed a model-compression scheme for improving the efficiency of the regularized Gauss-Newton inversion algorithm for geophysical electromagnetic applications. In this scheme, the unknown model parameters (the conductivity/resistivity distribution) are represented in terms of a basis such as Fourier and wavelet (Haar and Daubechies). By applying a truncation criterion, the model may then be approximated by a reduced number of basis functions, which is usually much less than the number of the model parameters. Further, because the geophysical electromagnetic measurements have low resolution, it is sufficient for inversion to only keep the low-spatial frequency part of the image. This model-compression scheme accelerates the computational time and also reduces the memory usage of the Gauss-Newton method. We are able to significantly reduce the algorithm computational complexity without compromising the quality of the inverted models.

  18. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  19. Science sequence design

    NASA Technical Reports Server (NTRS)

    Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

    1973-01-01

    The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

  20. Numerical linear algebra for reconstruction inverse problems

    NASA Astrophysics Data System (ADS)

    Nachaoui, Abdeljalil

    2004-01-01

    Our goal in this paper is to discuss various issues we have encountered in trying to find and implement efficient solvers for a boundary integral equation (BIE) formulation of an iterative method for solving a reconstruction problem. We survey some methods from numerical linear algebra, which are relevant for the solution of this class of inverse problems. We motivate the use of our constructing algorithm, discuss its implementation and mention the use of preconditioned Krylov methods.