Breast density quantification using magnetic resonance imaging (MRI) with bias field correction: A postmortem study

PubMed Central

Ding, Huanjun; Johnson, Travis; Lin, Muqing; Le, Huy Q.; Ducote, Justin L.; Su, Min-Ying; Molloi, Sabee

2013-01-01

Purpose: Quantification of breast density based on three-dimensional breast MRI may provide useful information for the early detection of breast cancer. However, the field inhomogeneity can severely challenge the computerized image segmentation process. In this work, the effect of the bias field in breast density quantification has been investigated with a postmortem study. Methods: T1-weighted images of 20 pairs of postmortem breasts were acquired on a 1.5 T breast MRI scanner. Two computer-assisted algorithms were used to quantify the volumetric breast density. First, standard fuzzy c-means (FCM) clustering was used on raw images with the bias field present. Then, the coherent local intensity clustering (CLIC) method estimated and corrected the bias field during the iterative tissue segmentation process. Finally, FCM clustering was performed on the bias-field-corrected images produced by CLIC method. The left–right correlation for breasts in the same pair was studied for both segmentation algorithms to evaluate the precision of the tissue classification. Finally, the breast densities measured with the three methods were compared to the gold standard tissue compositions obtained from chemical analysis. The linear correlation coefficient, Pearson's r, was used to evaluate the two image segmentation algorithms and the effect of bias field. Results: The CLIC method successfully corrected the intensity inhomogeneity induced by the bias field. In left–right comparisons, the CLIC method significantly improved the slope and the correlation coefficient of the linear fitting for the glandular volume estimation. The left–right breast density correlation was also increased from 0.93 to 0.98. When compared with the percent fibroglandular volume (%FGV) from chemical analysis, results after bias field correction from both the CLIC the FCM algorithms showed improved linear correlation. As a result, the Pearson's r increased from 0.86 to 0.92 with the bias field correction. Conclusions: The investigated CLIC method significantly increased the precision and accuracy of breast density quantification using breast MRI images by effectively correcting the bias field. It is expected that a fully automated computerized algorithm for breast density quantification may have great potential in clinical MRI applications. PMID:24320536

Breast density quantification using magnetic resonance imaging (MRI) with bias field correction: a postmortem study.

PubMed

Ding, Huanjun; Johnson, Travis; Lin, Muqing; Le, Huy Q; Ducote, Justin L; Su, Min-Ying; Molloi, Sabee

2013-12-01

Quantification of breast density based on three-dimensional breast MRI may provide useful information for the early detection of breast cancer. However, the field inhomogeneity can severely challenge the computerized image segmentation process. In this work, the effect of the bias field in breast density quantification has been investigated with a postmortem study. T1-weighted images of 20 pairs of postmortem breasts were acquired on a 1.5 T breast MRI scanner. Two computer-assisted algorithms were used to quantify the volumetric breast density. First, standard fuzzy c-means (FCM) clustering was used on raw images with the bias field present. Then, the coherent local intensity clustering (CLIC) method estimated and corrected the bias field during the iterative tissue segmentation process. Finally, FCM clustering was performed on the bias-field-corrected images produced by CLIC method. The left-right correlation for breasts in the same pair was studied for both segmentation algorithms to evaluate the precision of the tissue classification. Finally, the breast densities measured with the three methods were compared to the gold standard tissue compositions obtained from chemical analysis. The linear correlation coefficient, Pearson's r, was used to evaluate the two image segmentation algorithms and the effect of bias field. The CLIC method successfully corrected the intensity inhomogeneity induced by the bias field. In left-right comparisons, the CLIC method significantly improved the slope and the correlation coefficient of the linear fitting for the glandular volume estimation. The left-right breast density correlation was also increased from 0.93 to 0.98. When compared with the percent fibroglandular volume (%FGV) from chemical analysis, results after bias field correction from both the CLIC the FCM algorithms showed improved linear correlation. As a result, the Pearson's r increased from 0.86 to 0.92 with the bias field correction. The investigated CLIC method significantly increased the precision and accuracy of breast density quantification using breast MRI images by effectively correcting the bias field. It is expected that a fully automated computerized algorithm for breast density quantification may have great potential in clinical MRI applications.

Direct estimation of 17 O MR images (DIESIS) for quantification of oxygen metabolism in the human brain with partial volume correction.

PubMed

Kurzhunov, Dmitry; Borowiak, Robert; Reisert, Marco; Özen, Ali Caglar; Bock, Michael

2018-05-16

To provide a data post-processing method that corrects for partial volume effects (PVE) and fast T2* decay in dynamic 17 O MRI for the mapping of cerebral metabolic rates of oxygen consumption (CMRO 2 ). CMRO 2 is altered in neurodegenerative diseases and tumors and can be measured after 17 O gas inhalation using dynamic 17 O MRI. CMRO 2 quantification is difficult because of PVE. To correct for PVE, a direct estimation of the MR images (DIESIS) method is proposed and used in 4 dynamic 17 O MRI data sets of a healthy volunteer acquired on a 3T MRI system. With DIESIS, 17 O MR signal time curves in selected regions were directly estimated based on parcellation of a coregistered 1 H MPRAGE image. Profile likelihood analysis of the DIESIS method showed identifiability of CMRO 2 . In white matter (WM), DIESES reduced CMRO 2 from 0.97 ± 0.25 µmol/g tissue /min with Kaiser-Bessel gridding reconstruction to 0.85 ± 0.21 µmol/g tissue /min, whereas in gray matter (GM) it increases from 1.3 ± 0.31 µmol/g tissue /min to 1.86 ± 0.36 µmol/g tissue /min; both values are closer to the literature values from the 15 O-PET studies. DIESIS provided an increased separation of CMRO 2 values in GM and WM brain regions and corrected for partial volume effects in 17 O-MRI inhalation experiments. DIESIS could also be applied to more heterogeneous tissues such as glioblastomas if subregions of the tumor can be represented as additional parcels. © 2018 International Society for Magnetic Resonance in Medicine.

MR/PET quantification tools: Registration, segmentation, classification, and MR-based attenuation correction

PubMed Central

Fei, Baowei; Yang, Xiaofeng; Nye, Jonathon A.; Aarsvold, John N.; Raghunath, Nivedita; Cervo, Morgan; Stark, Rebecca; Meltzer, Carolyn C.; Votaw, John R.

2012-01-01

Purpose: Combined MR/PET is a relatively new, hybrid imaging modality. A human MR/PET prototype system consisting of a Siemens 3T Trio MR and brain PET insert was installed and tested at our institution. Its present design does not offer measured attenuation correction (AC) using traditional transmission imaging. This study is the development of quantification tools including MR-based AC for quantification in combined MR/PET for brain imaging. Methods: The developed quantification tools include image registration, segmentation, classification, and MR-based AC. These components were integrated into a single scheme for processing MR/PET data. The segmentation method is multiscale and based on the Radon transform of brain MR images. It was developed to segment the skull on T1-weighted MR images. A modified fuzzy C-means classification scheme was developed to classify brain tissue into gray matter, white matter, and cerebrospinal fluid. Classified tissue is assigned an attenuation coefficient so that AC factors can be generated. PET emission data are then reconstructed using a three-dimensional ordered sets expectation maximization method with the MR-based AC map. Ten subjects had separate MR and PET scans. The PET with [11C]PIB was acquired using a high-resolution research tomography (HRRT) PET. MR-based AC was compared with transmission (TX)-based AC on the HRRT. Seventeen volumes of interest were drawn manually on each subject image to compare the PET activities between the MR-based and TX-based AC methods. Results: For skull segmentation, the overlap ratio between our segmented results and the ground truth is 85.2 ± 2.6%. Attenuation correction results from the ten subjects show that the difference between the MR and TX-based methods was <6.5%. Conclusions: MR-based AC compared favorably with conventional transmission-based AC. Quantitative tools including registration, segmentation, classification, and MR-based AC have been developed for use in combined MR/PET. PMID:23039679

Magnetic Resonance Fingerprinting of Adult Brain Tumors: Initial Experience

PubMed Central

Badve, Chaitra; Yu, Alice; Dastmalchian, Sara; Rogers, Matthew; Ma, Dan; Jiang, Yun; Margevicius, Seunghee; Pahwa, Shivani; Lu, Ziang; Schluchter, Mark; Sunshine, Jeffrey; Griswold, Mark; Sloan, Andrew; Gulani, Vikas

2016-01-01

Background Magnetic resonance fingerprinting (MRF) allows rapid simultaneous quantification of T1 and T2 relaxation times. This study assesses the utility of MRF in differentiating between common types of adult intra-axial brain tumors. Methods MRF acquisition was performed in 31 patients with untreated intra-axial brain tumors: 17 glioblastomas, 6 WHO grade II lower-grade gliomas and 8 metastases. T1, T2 of the solid tumor (ST), immediate peritumoral white matter (PW), and contralateral white matter (CW) were summarized within each region of interest. Statistical comparisons on mean, standard deviation, skewness and kurtosis were performed using univariate Wilcoxon rank sum test across various tumor types. Bonferroni correction was used to correct for multiple comparisons testing. Multivariable logistic regression analysis was performed for discrimination between glioblastomas and metastases and area under the receiver operator curve (AUC) was calculated. Results Mean T2 values could differentiate solid tumor regions of lower-grade gliomas from metastases (mean±sd: 172±53ms and 105±27ms respectively, p =0.004, significant after Bonferroni correction). Mean T1 of PW surrounding lower-grade gliomas differed from PW around glioblastomas (mean±sd: 1066±218ms and 1578±331ms respectively, p=0.004, significant after Bonferroni correction). Logistic regression analysis revealed that mean T2 of ST offered best separation between glioblastomas and metastases with AUC of 0.86 (95% CI 0.69–1.00, p<0.0001). Conclusion MRF allows rapid simultaneous T1, T2 measurement in brain tumors and surrounding tissues. MRF based relaxometry can identify quantitative differences between solid-tumor regions of lower grade gliomas and metastases and between peritumoral regions of glioblastomas and lower grade gliomas. PMID:28034994

MR Fingerprinting of Adult Brain Tumors: Initial Experience.

PubMed

Badve, C; Yu, A; Dastmalchian, S; Rogers, M; Ma, D; Jiang, Y; Margevicius, S; Pahwa, S; Lu, Z; Schluchter, M; Sunshine, J; Griswold, M; Sloan, A; Gulani, V

2017-03-01

MR fingerprinting allows rapid simultaneous quantification of T1 and T2 relaxation times. This study assessed the utility of MR fingerprinting in differentiating common types of adult intra-axial brain tumors. MR fingerprinting acquisition was performed in 31 patients with untreated intra-axial brain tumors: 17 glioblastomas, 6 World Health Organization grade II lower grade gliomas, and 8 metastases. T1, T2 of the solid tumor, immediate peritumoral white matter, and contralateral white matter were summarized within each ROI. Statistical comparisons on mean, SD, skewness, and kurtosis were performed by using the univariate Wilcoxon rank sum test across various tumor types. Bonferroni correction was used to correct for multiple-comparison testing. Multivariable logistic regression analysis was performed for discrimination between glioblastomas and metastases, and area under the receiver operator curve was calculated. Mean T2 values could differentiate solid tumor regions of lower grade gliomas from metastases (mean, 172 ± 53 ms, and 105 ± 27 ms, respectively; P = .004, significant after Bonferroni correction). The mean T1 of peritumoral white matter surrounding lower grade gliomas differed from peritumoral white matter around glioblastomas (mean, 1066 ± 218 ms, and 1578 ± 331 ms, respectively; P = .004, significant after Bonferroni correction). Logistic regression analysis revealed that the mean T2 of solid tumor offered the best separation between glioblastomas and metastases with an area under the curve of 0.86 (95% CI, 0.69-1.00; P < .0001). MR fingerprinting allows rapid simultaneous T1 and T2 measurement in brain tumors and surrounding tissues. MR fingerprinting-based relaxometry can identify quantitative differences between solid tumor regions of lower grade gliomas and metastases and between peritumoral regions of glioblastomas and lower grade gliomas. © 2017 by American Journal of Neuroradiology.

Effect of PRESS and STEAM sequences on magnetic resonance spectroscopic liver fat quantification.

PubMed

Hamilton, Gavin; Middleton, Michael S; Bydder, Mark; Yokoo, Takeshi; Schwimmer, Jeffrey B; Kono, Yuko; Patton, Heather M; Lavine, Joel E; Sirlin, Claude B

2009-07-01

To compare PRESS and STEAM MR spectroscopy for assessment of liver fat in human subjects. Single-voxel (20 x 20 x 20 mm) PRESS and STEAM spectra were obtained at 1.5T in 49 human subjects with known or suspected fatty liver disease. PRESS and STEAM sequences were obtained with fixed TR (1500 msec) and different TE (five PRESS spectra between TE 30-70 msec, five STEAM spectra between TE 20-60 msec). Spectra were quantified and T2 and T2-corrected peak area were calculated by different techniques. The values were compared for PRESS and STEAM. Water T2 values from PRESS and STEAM were not significantly different (P = 0.33). Fat peak T2s were 25%-50% shorter on PRESS than on STEAM (P < 0.02 for all comparisons) and there was no correlation between T2s of individual peaks. PRESS systematically overestimated the relative fat peak areas (by 7%-263%) compared to STEAM (P < 0.005 for all comparisons). The peak area given by PRESS was more dependent on the T2-correction technique than STEAM. Measured liver fat depends on the MRS sequence used. Compared to STEAM, PRESS underestimates T2 values of fat, overestimates fat fraction, and provides a less consistent fat fraction estimate, probably due to J coupling effects. (c) 2009 Wiley-Liss, Inc.

Extension of the International Atomic Energy Agency phantom study in image quantification: results of multicentre evaluation in Croatia.

PubMed

Grošev, Darko; Gregov, Marin; Wolfl, Miroslava Radić; Krstonošić, Branislav; Debeljuh, Dea Dundara

2018-06-07

To make quantitative methods of nuclear medicine more available, four centres in Croatia participated in the national intercomparison study, following the materials and methods used in the previous international study organized by the International Atomic Energy Agency (IAEA). The study task was to calculate the activities of four Ba sources (T1/2=10.54 years; Eγ=356 keV) using planar and single-photon emission computed tomography (SPECT) or SPECT/CT acquisitions of the sources inside a water-filled cylindrical phantom. The sources were previously calibrated by the US National Institute of Standards and Technology. Triple-energy window was utilized for scatter correction. Planar studies were corrected for attenuation correction (AC) using the conjugate-view method. For SPECT/CT studies, data from X-ray computed tomography were used for attenuation correction (CT-AC), whereas for SPECT-only acquisition, the Chang-AC method was applied. Using the lessons learned from the IAEA study, data were acquired according to the harmonized data acquisition protocol, and the acquired images were then processed using centralized data analysis. The accuracy of the activity quantification was evaluated as the ratio R between the calculated activity and the value obtained from National Institute of Standards and Technology. For planar studies, R=1.06±0.08; for SPECT/CT study using CT-AC, R=1.00±0.08; and for Chang-AC, R=0.89±0.12. The results are in accordance with those obtained within the larger IAEA study and confirm that SPECT/CT method is the most appropriate for accurate activity quantification.

Isotropic resolution diffusion tensor imaging of lumbosacral and sciatic nerves using a phase‐corrected diffusion‐prepared 3D turbo spin echo

PubMed Central

Van, Anh T.; Weidlich, Dominik; Kooijman, Hendrick; Hock, Andreas; Rummeny, Ernst J.; Gersing, Alexandra; Kirschke, Jan S.; Karampinos, Dimitrios C.

2018-01-01

Purpose To perform in vivo isotropic‐resolution diffusion tensor imaging (DTI) of lumbosacral and sciatic nerves with a phase‐navigated diffusion‐prepared (DP) 3D turbo spin echo (TSE) acquisition and modified reconstruction incorporating intershot phase‐error correction and to investigate the improvement on image quality and diffusion quantification with the proposed phase correction. Methods Phase‐navigated DP 3D TSE included magnitude stabilizers to minimize motion and eddy‐current effects on the signal magnitude. Phase navigation of motion‐induced phase errors was introduced before readout in 3D TSE. DTI of lower back nerves was performed in vivo using 3D TSE and single‐shot echo planar imaging (ss‐EPI) in 13 subjects. Diffusion data were phase‐corrected per k z plane with respect to T2‐weighted data. The effects of motion‐induced phase errors on DTI quantification was assessed for 3D TSE and compared with ss‐EPI. Results Non–phase‐corrected 3D TSE resulted in artifacts in diffusion‐weighted images and overestimated DTI parameters in the sciatic nerve (mean diffusivity [MD] = 2.06 ± 0.45). Phase correction of 3D TSE DTI data resulted in reductions in all DTI parameters (MD = 1.73 ± 0.26) of statistical significance (P ≤ 0.001) and in closer agreement with ss‐EPI DTI parameters (MD = 1.62 ± 0.21). Conclusion DP 3D TSE with phase correction allows distortion‐free isotropic diffusion imaging of lower back nerves with robustness to motion‐induced artifacts and DTI quantification errors. Magn Reson Med 80:609–618, 2018. © 2018 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. PMID:29380414

Correlated displacement-T2 MRI by means of a Pulsed Field Gradient-Multi Spin Echo Method.

PubMed

Windt, Carel W; Vergeldt, Frank J; Van As, Henk

2007-04-01

A method for correlated displacement-T2 imaging is presented. A Pulsed Field Gradient-Multi Spin Echo (PFG-MSE) sequence is used to record T2 resolved propagators on a voxel-by-voxel basis, making it possible to perform single voxel correlated displacement-T2 analyses. In spatially heterogeneous media the method thus gives access to sub-voxel information about displacement and T2 relaxation. The sequence is demonstrated using a number of flow conducting model systems: a tube with flowing water of variable intrinsic T2's, mixing fluids of different T2's in an "X"-shaped connector, and an intact living plant. PFG-MSE can be applied to yield information about the relation between flow, pore size and exchange behavior, and can aid volume flow quantification by making it possible to correct for T2 relaxation during the displacement labeling period Delta in PFG displacement imaging methods. Correlated displacement-T2 imaging can be of special interest for a number of research subjects, such as the flow of liquids and mixtures of liquids or liquids and solids moving through microscopic conduits of different sizes (e.g., plants, porous media, bioreactors, biomats).

Motion corrected DWI with integrated T2-mapping for simultaneous estimation of ADC, T2-relaxation and perfusion in prostate cancer.

PubMed

Skorpil, M; Brynolfsson, P; Engström, M

2017-06-01

Multiparametric magnetic resonance imaging (MRI) and PI-RADS (Prostate Imaging - Reporting and Data System) has become the standard to determine a probability score for a lesion being a clinically significant prostate cancer. T2-weighted and diffusion-weighted imaging (DWI) are essential in PI-RADS, depending partly on visual assessment of signal intensity, while dynamic-contrast enhanced imaging is less important. To decrease inter-rater variability and further standardize image evaluation, complementary objective measures are in need. We here demonstrate a sequence enabling simultaneous quantification of apparent diffusion coefficient (ADC) and T2-relaxation, as well as calculation of the perfusion fraction f from low b-value intravoxel incoherent motion data. Expandable wait pulses were added to a FOCUS DW SE-EPI sequence, allowing the effective echo time to change at run time. To calculate both ADC and f, b-values 200s/mm 2 and 600s/mm 2 were chosen, and for T2-estimation 6 echo times between 64.9ms and 114.9ms were used. Three patients with prostate cancer were examined and all had significantly decreased ADC and T2-values, while f was significantly increased in 2 of 3 tumors. T2 maps obtained in phantom measurements and in a healthy volunteer were compared to T2 maps from a SE sequence with consecutive scans, showing good agreement. In addition, a motion correction procedure was implemented to reduce the effects of prostate motion, which improved T2-estimation. This sequence could potentially enable more objective tumor grading, and decrease the inter-rater variability in the PI-RADS classification. Copyright © 2017 Elsevier Inc. All rights reserved.

Impact of sequential proton density fat fraction for quantification of hepatic steatosis in nonalcoholic fatty liver disease.

PubMed

Idilman, Ilkay S; Keskin, Onur; Elhan, Atilla Halil; Idilman, Ramazan; Karcaaltincaba, Musturay

2014-05-01

To determine the utility of sequential MRI-estimated proton density fat fraction (MRI-PDFF) for quantification of the longitudinal changes in liver fat content in individuals with nonalcoholic fatty liver disease (NAFLD). A total of 18 consecutive individuals (M/F: 10/8, mean age: 47.7±9.8 years) diagnosed with NAFLD, who underwent sequential PDFF calculations for the quantification of hepatic steatosis at two different time points, were included in the study. All patients underwent T1-independent volumetric multi-echo gradient-echo imaging with T2* correction and spectral fat modeling. A close correlation for quantification of hepatic steatosis between the initial MRI-PDFF and liver biopsy was observed (rs=0.758, p<0.001). The median interval between two sequential MRI-PDFF measurements was 184 days. From baseline to the end of the follow-up period, serum GGT level and homeostasis model assessment score were significantly improved (p=0.015, p=0.006, respectively), whereas BMI, serum AST, and ALT levels were slightly decreased. MRI-PDFFs were significantly improved (p=0.004). A good correlation between two sequential MRI-PDFF calculations was observed (rs=0.714, p=0.001). With linear regression analyses, only delta serum ALT levels had a significant effect on delta MRI-PDFF calculations (r2=38.6%, p=0.006). At least 5.9% improvement in MRI-PDFF is needed to achieve a normalized abnormal ALT level. The improvement of MRI-PDFF score was associated with the improvement of biochemical parameters in patients who had improvement in delta MRI-PDFF (p<0.05). MRI-PDFF can be used for the quantification of the longitudinal changes of hepatic steatosis. The changes in serum ALT levels significantly reflected changes in MRI-PDFF in patients with NAFLD.

A comparison of liver fat content as determined by magnetic resonance imaging-proton density fat fraction and MRS versus liver histology in non-alcoholic fatty liver disease.

PubMed

Idilman, Ilkay S; Keskin, Onur; Celik, Azim; Savas, Berna; Elhan, Atilla Halil; Idilman, Ramazan; Karcaaltincaba, Musturay

2016-03-01

Many imaging methods have been defined for quantification of hepatic steatosis in non-alcoholic fatty liver disease (NAFLD). However, studies comparing the efficiency of magnetic resonance imaging-proton density fat fraction (MRI-PDFF), magnetic resonance spectroscopy (MRS), and liver histology for quantification of liver fat content are limited. To compare the efficiency of MRI-PDFF and MRS in the quantification of liver fat content in individuals with NAFLD. A total of 19 NAFLD patients underwent MRI-PDFF, MRS, and liver biopsy for quantification of liver fat content. The MR examinations were performed on a 1.5 HDx MRI system. The MRI protocol included T1-independent volumetric multi-echo gradient-echo imaging with T2* correction and spectral fat modeling and MRS with STEAM technique. A close correlation was observed between liver MRI-PDFF- and histology- determined steatosis (r = 0.743, P < 0.001) and between liver MRS- and histology-determined steatosis (r = 0.712, P < 0.001), with no superiority between them (ƶ = 0.19, P = 0.849). For quantification of hepatic steatosis, a high correlation was observed between the two MRI methods (r = 0.986, P < 0.001). MRI-PDFF and MRS accurately differentiated moderate/severe steatosis from mild/no hepatic steatosis (P = 0.007 and 0.013, respectively), with no superiority between them (AUCMRI-PDFF = 0.881 ± 0.0856 versus AUCMRS = 0.857 ± 0.0924, P = 0.461). Both MRI-PDFF and MRS can be used for accurate quantification of hepatic steatosis. © The Foundation Acta Radiologica 2015.

A computerized MRI biomarker quantification scheme for a canine model of Duchenne muscular dystrophy

PubMed Central

Wang, Jiahui; Fan, Zheng; Vandenborne, Krista; Walter, Glenn; Shiloh-Malawsky, Yael; An, Hongyu; Kornegay, Joe N.; Styner, Martin A.

2015-01-01

Purpose Golden retriever muscular dystrophy (GRMD) is a widely used canine model of Duchenne muscular dystrophy (DMD). Recent studies have shown that magnetic resonance imaging (MRI) can be used to non-invasively detect consistent changes in both DMD and GRMD. In this paper, we propose a semi-automated system to quantify MRI biomarkers of GRMD. Methods Our system was applied to a database of 45 MRI scans from 8 normal and 10 GRMD dogs in a longitudinal natural history study. We first segmented six proximal pelvic limb muscles using two competing schemes: 1) standard, limited muscle range segmentation and 2) semi-automatic full muscle segmentation. We then performed pre-processing, including: intensity inhomogeneity correction, spatial registration of different image sequences, intensity calibration of T2-weighted (T2w) and T2-weighted fat suppressed (T2fs) images, and calculation of MRI biomarker maps. Finally, for each of the segmented muscles, we automatically measured MRI biomarkers of muscle volume and intensity statistics over MRI biomarker maps, and statistical image texture features. Results The muscle volume and the mean intensities in T2 value, fat, and water maps showed group differences between normal and GRMD dogs. For the statistical texture biomarkers, both the histogram and run-length matrix features showed obvious group differences between normal and GRMD dogs. The full muscle segmentation shows significantly less error and variability in the proposed biomarkers when compared to the standard, limited muscle range segmentation. Conclusion The experimental results demonstrated that this quantification tool can reliably quantify MRI biomarkers in GRMD dogs, suggesting that it would also be useful for quantifying disease progression and measuring therapeutic effect in DMD patients. PMID:23299128

Quantification of glutathione transverse relaxation time T2 using echo time extension with variable refocusing selectivity and symmetry in the human brain at 7 Tesla

NASA Astrophysics Data System (ADS)

Swanberg, Kelley M.; Prinsen, Hetty; Coman, Daniel; de Graaf, Robin A.; Juchem, Christoph

2018-05-01

Glutathione (GSH) is an endogenous antioxidant implicated in numerous biological processes, including those associated with multiple sclerosis, aging, and cancer. Spectral editing techniques have greatly facilitated the acquisition of glutathione signal in living humans via proton magnetic resonance spectroscopy, but signal quantification at 7 Tesla is still hampered by uncertainty about the glutathione transverse decay rate T2 relative to those of commonly employed quantitative references like N-acetyl aspartate (NAA), total creatine, or water. While the T2 of uncoupled singlets can be derived in a straightforward manner from exponential signal decay as a function of echo time, similar estimation of signal decay in GSH is complicated by a spin system that involves both weak and strong J-couplings as well as resonances that overlap those of several other metabolites and macromolecules. Here, we extend a previously published method for quantifying the T2 of GABA, a weakly coupled system, to quantify T2 of the strongly coupled spin system glutathione in the human brain at 7 Tesla. Using full density matrix simulation of glutathione signal behavior, we selected an array of eight optimized echo times between 72 and 322 ms for glutathione signal acquisition by J-difference editing (JDE). We varied the selectivity and symmetry parameters of the inversion pulses used for echo time extension to further optimize the intensity, simplicity, and distinctiveness of glutathione signals at chosen echo times. Pairs of selective adiabatic inversion pulses replaced nonselective pulses at three extended echo times, and symmetry of the time intervals between the two extension pulses was adjusted at one extended echo time to compensate for J-modulation, thereby resulting in appreciable signal-to-noise ratio and quantifiable signal shapes at all measured points. Glutathione signal across all echo times fit smooth monoexponential curves over ten scans of occipital cortex voxels in nine subjects. The T2 of glutathione was calculated to be 145.0 ± 20.1 ms (mean ± standard deviation); this result was robust within one standard deviation to changes in metabolite fitting baseline corrections and removal of individual data points on the signal decay curve. The measured T2 of NAA (222.1 ± 24.7 ms) and total creatine (153.0 ± 19.9 ms) were both higher than that calculated for GSH. Apparent glutathione concentration quantified relative to both reference metabolites increased by up to 32% and 6%, respectively, upon correction with calculated T2 values, emphasizing the importance of considering T2 relaxation differences in the spectroscopic measurement of these metabolites, especially at longer echo times.

Quantification of glutathione transverse relaxation time T2 using echo time extension with variable refocusing selectivity and symmetry in the human brain at 7 Tesla.

PubMed

Swanberg, Kelley M; Prinsen, Hetty; Coman, Daniel; de Graaf, Robin A; Juchem, Christoph

2018-05-01

Glutathione (GSH) is an endogenous antioxidant implicated in numerous biological processes, including those associated with multiple sclerosis, aging, and cancer. Spectral editing techniques have greatly facilitated the acquisition of glutathione signal in living humans via proton magnetic resonance spectroscopy, but signal quantification at 7 Tesla is still hampered by uncertainty about the glutathione transverse decay rate T 2 relative to those of commonly employed quantitative references like N-acetyl aspartate (NAA), total creatine, or water. While the T 2 of uncoupled singlets can be derived in a straightforward manner from exponential signal decay as a function of echo time, similar estimation of signal decay in GSH is complicated by a spin system that involves both weak and strong J-couplings as well as resonances that overlap those of several other metabolites and macromolecules. Here, we extend a previously published method for quantifying the T 2 of GABA, a weakly coupled system, to quantify T 2 of the strongly coupled spin system glutathione in the human brain at 7 Tesla. Using full density matrix simulation of glutathione signal behavior, we selected an array of eight optimized echo times between 72 and 322 ms for glutathione signal acquisition by J-difference editing (JDE). We varied the selectivity and symmetry parameters of the inversion pulses used for echo time extension to further optimize the intensity, simplicity, and distinctiveness of glutathione signals at chosen echo times. Pairs of selective adiabatic inversion pulses replaced nonselective pulses at three extended echo times, and symmetry of the time intervals between the two extension pulses was adjusted at one extended echo time to compensate for J-modulation, thereby resulting in appreciable signal-to-noise ratio and quantifiable signal shapes at all measured points. Glutathione signal across all echo times fit smooth monoexponential curves over ten scans of occipital cortex voxels in nine subjects. The T 2 of glutathione was calculated to be 145.0 ± 20.1 ms (mean ± standard deviation); this result was robust within one standard deviation to changes in metabolite fitting baseline corrections and removal of individual data points on the signal decay curve. The measured T 2 of NAA (222.1 ± 24.7 ms) and total creatine (153.0 ± 19.9 ms) were both higher than that calculated for GSH. Apparent glutathione concentration quantified relative to both reference metabolites increased by up to 32% and 6%, respectively, upon correction with calculated T 2 values, emphasizing the importance of considering T 2 relaxation differences in the spectroscopic measurement of these metabolites, especially at longer echo times. Copyright © 2018 Elsevier Inc. All rights reserved.

Zero-Echo-Time and Dixon Deep Pseudo-CT (ZeDD CT): Direct Generation of Pseudo-CT Images for Pelvic PET/MRI Attenuation Correction Using Deep Convolutional Neural Networks with Multiparametric MRI.

PubMed

Leynes, Andrew P; Yang, Jaewon; Wiesinger, Florian; Kaushik, Sandeep S; Shanbhag, Dattesh D; Seo, Youngho; Hope, Thomas A; Larson, Peder E Z

2018-05-01

Accurate quantification of uptake on PET images depends on accurate attenuation correction in reconstruction. Current MR-based attenuation correction methods for body PET use a fat and water map derived from a 2-echo Dixon MRI sequence in which bone is neglected. Ultrashort-echo-time or zero-echo-time (ZTE) pulse sequences can capture bone information. We propose the use of patient-specific multiparametric MRI consisting of Dixon MRI and proton-density-weighted ZTE MRI to directly synthesize pseudo-CT images with a deep learning model: we call this method ZTE and Dixon deep pseudo-CT (ZeDD CT). Methods: Twenty-six patients were scanned using an integrated 3-T time-of-flight PET/MRI system. Helical CT images of the patients were acquired separately. A deep convolutional neural network was trained to transform ZTE and Dixon MR images into pseudo-CT images. Ten patients were used for model training, and 16 patients were used for evaluation. Bone and soft-tissue lesions were identified, and the SUV max was measured. The root-mean-squared error (RMSE) was used to compare the MR-based attenuation correction with the ground-truth CT attenuation correction. Results: In total, 30 bone lesions and 60 soft-tissue lesions were evaluated. The RMSE in PET quantification was reduced by a factor of 4 for bone lesions (10.24% for Dixon PET and 2.68% for ZeDD PET) and by a factor of 1.5 for soft-tissue lesions (6.24% for Dixon PET and 4.07% for ZeDD PET). Conclusion: ZeDD CT produces natural-looking and quantitatively accurate pseudo-CT images and reduces error in pelvic PET/MRI attenuation correction compared with standard methods. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Quantitative magnetic resonance spectroscopy at 3T based on the principle of reciprocity.

PubMed

Zoelch, Niklaus; Hock, Andreas; Henning, Anke

2018-05-01

Quantification of magnetic resonance spectroscopy signals using the phantom replacement method requires an adequate correction of differences between the acquisition of the reference signal in the phantom and the measurement in vivo. Applying the principle of reciprocity, sensitivity differences can be corrected at low field strength by measuring the RF transmitter gain needed to obtain a certain flip angle in the measured volume. However, at higher field strength the transmit sensitivity may vary from the reception sensitivity, which leads to wrongly estimated concentrations. To address this issue, a quantification approach based on the principle of reciprocity for use at 3T is proposed and validated thoroughly. In this approach, the RF transmitter gain is determined automatically using a volume-selective power optimization and complemented with information from relative reception sensitivity maps derived from contrast-minimized images to correct differences in transmission and reception sensitivity. In this way, a reliable measure of the local sensitivity was obtained. The proposed method is used to derive in vivo concentrations of brain metabolites and tissue water in two studies with different coil sets in a total of 40 healthy volunteers. Resulting molar concentrations are compared with results using internal water referencing (IWR) and Electric REference To access In vivo Concentrations (ERETIC). With the proposed method, changes in coil loading and regional sensitivity due to B 1 inhomogeneities are successfully corrected, as demonstrated in phantom and in vivo measurements. For the tissue water content, coefficients of variation between 2% and 3.5% were obtained (0.6-1.4% in a single subject). The coefficients of variation of the three major metabolites ranged from 3.4-14.5%. In general, the derived concentrations agree well with values estimated with IWR. Hence, the presented method is a valuable alternative for IWR, without the need for additional hardware such as ERETIC and with potential advantages in diseased tissue. Copyright © 2018 John Wiley & Sons, Ltd.

Relaxivity-iron calibration in hepatic iron overload: Probing underlying biophysical mechanisms using a Monte Carlo model

PubMed Central

Ghugre, Nilesh R.; Wood, John C.

2010-01-01

Iron overload is a serious condition for patients with β-thalassemia, transfusion-dependent sickle cell anemia and inherited disorders of iron metabolism. MRI is becoming increasingly important in non-invasive quantification of tissue iron, overcoming the drawbacks of traditional techniques (liver biopsy). R2*(1/T2*) rises linearly with iron while R2(1/T2) has a curvilinear relationship in human liver. Although recent work has demonstrated clinically-valid estimates of human liver iron, the calibration varies with MRI sequence, field strength, iron chelation therapy and organ imaged, forcing recalibration in patients. To understand and correct these limitations, a thorough understanding of the underlying biophysics is of critical importance. Toward this end, a Monte Carlo based approach, using human liver as a ‘model’ tissue system, was employed to determine the contribution of particle size and distribution on MRI signal relaxation. Relaxivities were determined for hepatic iron concentrations (HIC) ranging from 0.5–40 mg iron/ g dry tissue weight. Model predictions captured the linear and curvilinear relationship of R2* and R2 with HIC respectively and were within in vivo confidence bounds; contact or chemical exchange mechanisms were not necessary. A validated and optimized model will aid understanding and quantification of iron-mediated relaxivity in tissues where biopsy is not feasible (heart, spleen). PMID:21337413

MR Fingerprinting for Rapid Quantitative Abdominal Imaging

PubMed Central

Chen, Yong; Jiang, Yun; Pahwa, Shivani; Ma, Dan; Lu, Lan; Twieg, Michael D.; Wright, Katherine L.; Seiberlich, Nicole; Griswold, Mark A.

2016-01-01

Purpose To develop a magnetic resonance (MR) “fingerprinting” technique for quantitative abdominal imaging. Materials and Methods This HIPAA-compliant study had institutional review board approval, and informed consent was obtained from all subjects. To achieve accurate quantification in the presence of marked B0 and B1 field inhomogeneities, the MR fingerprinting framework was extended by using a two-dimensional fast imaging with steady-state free precession, or FISP, acquisition and a Bloch-Siegert B1 mapping method. The accuracy of the proposed technique was validated by using agarose phantoms. Quantitative measurements were performed in eight asymptomatic subjects and in six patients with 20 focal liver lesions. A two-tailed Student t test was used to compare the T1 and T2 results in metastatic adenocarcinoma with those in surrounding liver parenchyma and healthy subjects. Results Phantom experiments showed good agreement with standard methods in T1 and T2 after B1 correction. In vivo studies demonstrated that quantitative T1, T2, and B1 maps can be acquired within a breath hold of approximately 19 seconds. T1 and T2 measurements were compatible with those in the literature. Representative values included the following: liver, 745 msec ± 65 (standard deviation) and 31 msec ± 6; renal medulla, 1702 msec ± 205 and 60 msec ± 21; renal cortex, 1314 msec ± 77 and 47 msec ± 10; spleen, 1232 msec ± 92 and 60 msec ± 19; skeletal muscle, 1100 msec ± 59 and 44 msec ± 9; and fat, 253 msec ± 42 and 77 msec ± 16, respectively. T1 and T2 in metastatic adenocarcinoma were 1673 msec ± 331 and 43 msec ± 13, respectively, significantly different from surrounding liver parenchyma relaxation times of 840 msec ± 113 and 28 msec ± 3 (P < .0001 and P < .01) and those in hepatic parenchyma in healthy volunteers (745 msec ± 65 and 31 msec ± 6, P < .0001 and P = .021, respectively). Conclusion A rapid technique for quantitative abdominal imaging was developed that allows simultaneous quantification of multiple tissue properties within one 19-second breath hold, with measurements comparable to those in published literature. © RSNA, 2016 PMID:26794935

MR Fingerprinting for Rapid Quantitative Abdominal Imaging.

PubMed

Chen, Yong; Jiang, Yun; Pahwa, Shivani; Ma, Dan; Lu, Lan; Twieg, Michael D; Wright, Katherine L; Seiberlich, Nicole; Griswold, Mark A; Gulani, Vikas

2016-04-01

To develop a magnetic resonance (MR) "fingerprinting" technique for quantitative abdominal imaging. This HIPAA-compliant study had institutional review board approval, and informed consent was obtained from all subjects. To achieve accurate quantification in the presence of marked B0 and B1 field inhomogeneities, the MR fingerprinting framework was extended by using a two-dimensional fast imaging with steady-state free precession, or FISP, acquisition and a Bloch-Siegert B1 mapping method. The accuracy of the proposed technique was validated by using agarose phantoms. Quantitative measurements were performed in eight asymptomatic subjects and in six patients with 20 focal liver lesions. A two-tailed Student t test was used to compare the T1 and T2 results in metastatic adenocarcinoma with those in surrounding liver parenchyma and healthy subjects. Phantom experiments showed good agreement with standard methods in T1 and T2 after B1 correction. In vivo studies demonstrated that quantitative T1, T2, and B1 maps can be acquired within a breath hold of approximately 19 seconds. T1 and T2 measurements were compatible with those in the literature. Representative values included the following: liver, 745 msec ± 65 (standard deviation) and 31 msec ± 6; renal medulla, 1702 msec ± 205 and 60 msec ± 21; renal cortex, 1314 msec ± 77 and 47 msec ± 10; spleen, 1232 msec ± 92 and 60 msec ± 19; skeletal muscle, 1100 msec ± 59 and 44 msec ± 9; and fat, 253 msec ± 42 and 77 msec ± 16, respectively. T1 and T2 in metastatic adenocarcinoma were 1673 msec ± 331 and 43 msec ± 13, respectively, significantly different from surrounding liver parenchyma relaxation times of 840 msec ± 113 and 28 msec ± 3 (P < .0001 and P < .01) and those in hepatic parenchyma in healthy volunteers (745 msec ± 65 and 31 msec ± 6, P < .0001 and P = .021, respectively). A rapid technique for quantitative abdominal imaging was developed that allows simultaneous quantification of multiple tissue properties within one 19-second breath hold, with measurements comparable to those in published literature.

Quantification of adipose tissue in a rodent model of obesity

NASA Astrophysics Data System (ADS)

Johnson, David H.; Flask, Chris; Wan, Dinah; Ernsberger, Paul; Wilson, David L.

2006-03-01

Obesity is a global epidemic and a comorbidity for many diseases. We are using MRI to characterize obesity in rodents, especially with regard to visceral fat. Rats were scanned on a 1.5T clinical scanner, and a T1W, water-spoiled image (fat only) was divided by a matched T1W image (fat + water) to yield a ratio image related to the lipid content in each voxel. The ratio eliminated coil sensitivity inhomogeneity and gave flat values across a fat pad, except for outlier voxels (> 1.0) due to motion. Following sacrifice, fat pad volumes were dissected and measured by displacement in canola oil. In our study of 6 lean (SHR), 6 dietary obese (SHR-DO), and 9 genetically obese rats (SHROB), significant differences in visceral fat volume was observed with an average of 29+/-16 ml increase due to diet and 84+/-44 ml increase due to genetics relative to lean control with a volume of 11+/-4 ml. Subcutaneous fat increased 14+/-8 ml due to diet and 198+/-105 ml due to genetics relative to the lean control with 7+/-3 ml. Visceral fat strongly correlated between MRI and dissection (R2 = 0.94), but MRI detected over five times the subcutaneous fat found with error-prone dissection. Using a semi-automated images segmentation method on the ratio images, intra-subject variation was very low. Fat pad composition as estimated from ratio images consistently differentiated the strains with SHROB having a greater lipid concentration in adipose tissues. Future work will include in vivo studies of diet versus genetics, identification of new phenotypes, and corrective measures for obesity; technical efforts will focus on correction for motion and automation in quantification.

A novel quadruplex real-time PCR method for simultaneous detection of Cry2Ae and two genetically modified cotton events (GHB119 and T304-40).

PubMed

Li, Xiang; Wang, Xiuxiu; Yang, Jielin; Liu, Yueming; He, Yuping; Pan, Liangwen

2014-05-16

To date, over 150 genetically modified (GM) crops are widely cultivated. To comply with regulations developed for genetically modified organisms (GMOs), including labeling policies, many detection methods for GMO identification and quantification have been developed. To detect the entrance and exit of unauthorized GM crop events in China, we developed a novel quadruplex real-time PCR method for simultaneous detection and quantification of GM cotton events GHB119 and T304-40 in cotton-derived products (based on the 5'-flanking sequence) and the insect-resistance gene Cry2Ae. The limit of detection was 10 copies for GHB119 and Cry2Ae and 25 copies for T304-40. The limit of quantification was 25 copies for GHB119 and Cry2Ae and 50 copies for T304-40. Moreover, low bias and acceptable standard deviation and relative standard deviation values were obtained in quantification analysis of six blind samples containing different GHB119 and T304-40 ingredients. The developed quadruplex quantitative method could be used for quantitative detection of two GM cotton events (GHB119 and T304-40) and Cry2Ae gene ingredient in cotton derived products.

A novel quadruplex real-time PCR method for simultaneous detection of Cry2Ae and two genetically modified cotton events (GHB119 and T304-40)

PubMed Central

2014-01-01

Background To date, over 150 genetically modified (GM) crops are widely cultivated. To comply with regulations developed for genetically modified organisms (GMOs), including labeling policies, many detection methods for GMO identification and quantification have been developed. Results To detect the entrance and exit of unauthorized GM crop events in China, we developed a novel quadruplex real-time PCR method for simultaneous detection and quantification of GM cotton events GHB119 and T304-40 in cotton-derived products (based on the 5′-flanking sequence) and the insect-resistance gene Cry2Ae. The limit of detection was 10 copies for GHB119 and Cry2Ae and 25 copies for T304-40. The limit of quantification was 25 copies for GHB119 and Cry2Ae and 50 copies for T304-40. Moreover, low bias and acceptable standard deviation and relative standard deviation values were obtained in quantification analysis of six blind samples containing different GHB119 and T304-40 ingredients. Conclusions The developed quadruplex quantitative method could be used for quantitative detection of two GM cotton events (GHB119 and T304-40) and Cry2Ae gene ingredient in cotton derived products. PMID:24884946

Noninvasive quantification of T2 and concentrations of ascorbate and glutathione in the human brain from the same double-edited spectra.

PubMed

Emir, Uzay E; Deelchand, Dinesh; Henry, Pierre-Gilles; Terpstra, Melissa

2011-04-01

The transverse relaxation times (T(2)) and concentrations of Ascorbate (Asc) and glutathione (GSH) were measured from a single dataset of double-edited spectra that were acquired at several TEs at 4 T in the human brain. Six TEs between 102 and 152  ms were utilized to calculate T(2) for the group of 12 subjects scanned five times each. Spectra measured at all six TEs were summed to quantify the concentration in each individual scan. LCModel fitting was optimized for the quantification of the Asc and GSH double-edited spectra. When the fitted baseline was constrained to be flat, T(2) was found to be 67  ms (95% confidence interval, 50-83  ms) for GSH and ≤115  ms for Asc using the sum of spectra measured over 60 scans. The Asc and GSH concentrations quantified in each of the 60 scans were 0.62 ± 0.08 and 0.81 ± 0.11  µmol/g [mean ± standard deviation (SD), n = 60], respectively, using 10  µmol/g N-acetylaspartate as an internal reference and assuming a constant influence of N-acetylaspartate and antioxidant T(2) relaxation in the reference solution and in vivo. The T(2) value of GSH was measured for the first time in the human brain. The data are consistent with short T(2) for both antioxidants. These T(2) values are essential for the absolute quantification of Asc and GSH concentrations measured at long TE, and provide a critical step towards addressing assumptions about T(2), and therefore towards the quantification of concentrations without the possibility of systematic bias. Copyright © 2010 John Wiley & Sons, Ltd.

Geometric distortion correction in prostate diffusion-weighted MRI and its effect on quantitative apparent diffusion coefficient analysis.

PubMed

Nketiah, Gabriel; Selnaes, Kirsten M; Sandsmark, Elise; Teruel, Jose R; Krüger-Stokke, Brage; Bertilsson, Helena; Bathen, Tone F; Elschot, Mattijs

2018-05-01

To evaluate the effect of correction for B 0 inhomogeneity-induced geometric distortion in echo-planar diffusion-weighted imaging on quantitative apparent diffusion coefficient (ADC) analysis in multiparametric prostate MRI. Geometric distortion correction was performed in echo-planar diffusion-weighted images (b = 0, 50, 400, 800 s/mm 2 ) of 28 patients, using two b 0 scans with opposing phase-encoding polarities. Histology-matched tumor and healthy tissue volumes of interest delineated on T 2 -weighted images were mapped to the nondistortion-corrected and distortion-corrected data sets by resampling with and without spatial coregistration. The ADC values were calculated on the volume and voxel level. The effect of distortion correction on ADC quantification and tissue classification was evaluated using linear-mixed models and logistic regression, respectively. Without coregistration, the absolute differences in tumor ADC (range: 0.0002-0.189 mm 2 /s×10 -3 (volume level); 0.014-0.493 mm 2 /s×10 -3 (voxel level)) between the nondistortion-corrected and distortion-corrected were significantly associated (P < 0.05) with distortion distance (mean: 1.4 ± 1.3 mm; range: 0.3-5.3 mm). No significant associations were found upon coregistration; however, in patients with high rectal gas residue, distortion correction resulted in improved spatial representation and significantly better classification of healthy versus tumor voxels (P < 0.05). Geometric distortion correction in DWI could improve quantitative ADC analysis in multiparametric prostate MRI. Magn Reson Med 79:2524-2532, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

An online open-source tool for automated quantification of liver and myocardial iron concentrations by T2* magnetic resonance imaging.

PubMed

Git, K-A; Fioravante, L A B; Fernandes, J L

2015-09-01

To assess whether an online open-source tool would provide accurate calculations of T2(*) values for iron concentrations in the liver and heart compared with a standard reference software. An online open-source tool, written in pure HTML5/Javascript, was tested in 50 patients (age 26.0 ± 18.9 years, 46% males) who underwent T2(*) MRI of the liver and heart for iron overload assessment as part of their routine workup. Automated truncation correction was the default with optional manual adjustment provided if needed. The results were compared against a standard reference measurement using commercial software with manual truncation (CVI(42)(®) v. 5.1; Circle Cardiovascular Imaging; Calgary, AB). The mean liver T2(*) values calculated with the automated tool was 4.3 ms [95% confidence interval (CI) 3.1 to 5.5 ms] vs 4.26 ms using the reference software (95% CI 3.1 to 5.4 ms) without any significant differences (p = 0.71). In the liver, the mean difference was 0.036 ms (95% CI -0.1609 to 0.2329 ms) with a regression correlation coefficient of 0.97. For the heart, the automated T2(*) value was 26.0 ms (95% CI 22.9 to 29.0 ms) vs 25.3 ms (95% CI 22.3 to 28.3 ms), p = 0.28. The mean difference was 0.72 ms (95% CI 0.08191 to 1.3621 ms) with a correlation coefficient of 0.96. The automated online tool provides similar T2(*) values for the liver and myocardial iron concentrations as compared with a standard reference software. The online program provides an open-source tool for the calculation of T2(*) values, incorporating an automated correction algorithm in a simple and easy-to-use interface.

Exploiting multicompartment effects in triple-echo steady-state T2 mapping for fat fraction quantification.

PubMed

Liu, Dian; Steingoetter, Andreas; Curcic, Jelena; Kozerke, Sebastian

2018-01-01

To investigate and exploit the effect of intravoxel off-resonance compartments in the triple-echo steady-state (TESS) sequence without fat suppression for T 2 mapping and to leverage the results for fat fraction quantification. In multicompartment tissue, where at least one compartment is excited off-resonance, the total signal exhibits periodic modulations as a function of echo time (TE). Simulated multicompartment TESS signals were synthesized at various TEs. Fat emulsion phantoms were prepared and scanned at the same TE combinations using TESS. In vivo knee data were obtained with TESS to validate the simulations. The multicompartment effect was exploited for fat fraction quantification in the stomach by acquiring TESS signals at two TE combinations. Simulated and measured multicompartment signal intensities were in good agreement. Multicompartment effects caused erroneous T 2 offsets, even at low water-fat ratios. The choice of TE caused T 2 variations of as much as 28% in cartilage. The feasibility of fat fraction quantification to monitor the decrease of fat content in the stomach during digestion is demonstrated. Intravoxel off-resonance compartments are a confounding factor for T 2 quantification using TESS, causing errors that are dependent on the TE. At the same time, off-resonance effects may allow for efficient fat fraction mapping using steady-state imaging. Magn Reson Med 79:423-429, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

MR-based measurements and simulations of the magnetic field created by a realistic transcranial magnetic stimulation (TMS) coil and stimulator.

PubMed

Mandija, Stefano; Petrov, Petar I; Neggers, Sebastian F W; Luijten, Peter R; van den Berg, Cornelis A T

2016-11-01

Transcranial magnetic stimulation (TMS) is an emerging technique that allows non-invasive neurostimulation. However, the correct validation of electromagnetic models of typical TMS coils and the correct assessment of the incident TMS field (B TMS ) produced by standard TMS stimulators are still lacking. Such a validation can be performed by mapping B TMS produced by a realistic TMS setup. In this study, we show that MRI can provide precise quantification of the magnetic field produced by a realistic TMS coil and a clinically used TMS stimulator in the region in which neurostimulation occurs. Measurements of the phase accumulation created by TMS pulses applied during a tailored MR sequence were performed in a phantom. Dedicated hardware was developed to synchronize a typical, clinically used, TMS setup with a 3-T MR scanner. For comparison purposes, electromagnetic simulations of B TMS were performed. MR-based measurements allow the mapping and quantification of B TMS starting 2.5 cm from the TMS coil. For closer regions, the intra-voxel dephasing induced by B TMS prohibits TMS field measurements. For 1% TMS output, the maximum measured value was ~0.1 mT. Simulations reflect quantitatively the experimental data. These measurements can be used to validate electromagnetic models of TMS coils, to guide TMS coil positioning, and for dosimetry and quality assessment of concurrent TMS-MRI studies without the need for crude methods, such as motor threshold, for stimulation dose determination. Copyright © 2016 John Wiley & Sons, Ltd.

Quantification of regional myocardial blood flow estimation with three-dimensional dynamic rubidium-82 PET and modified spillover correction model.

PubMed

Katoh, Chietsugu; Yoshinaga, Keiichiro; Klein, Ran; Kasai, Katsuhiko; Tomiyama, Yuuki; Manabe, Osamu; Naya, Masanao; Sakakibara, Mamoru; Tsutsui, Hiroyuki; deKemp, Robert A; Tamaki, Nagara

2012-08-01

Myocardial blood flow (MBF) estimation with (82)Rubidium ((82)Rb) positron emission tomography (PET) is technically difficult because of the high spillover between regions of interest, especially due to the long positron range. We sought to develop a new algorithm to reduce the spillover in image-derived blood activity curves, using non-uniform weighted least-squares fitting. Fourteen volunteers underwent imaging with both 3-dimensional (3D) (82)Rb and (15)O-water PET at rest and during pharmacological stress. Whole left ventricular (LV) (82)Rb MBF was estimated using a one-compartment model, including a myocardium-to-blood spillover correction to estimate the corresponding blood input function Ca(t)(whole). Regional K1 values were calculated using this uniform global input function, which simplifies equations and enables robust estimation of MBF. To assess the robustness of the modified algorithm, inter-operator repeatability of 3D (82)Rb MBF was compared with a previously established method. Whole LV correlation of (82)Rb MBF with (15)O-water MBF was better (P < .01) with the modified spillover correction method (r = 0.92 vs r = 0.60). The modified method also yielded significantly improved inter-operator repeatability of regional MBF quantification (r = 0.89) versus the established method (r = 0.82) (P < .01). A uniform global input function can suppress LV spillover into the image-derived blood input function, resulting in improved precision for MBF quantification with 3D (82)Rb PET.

Evaluation of MR imaging with T1 and T2* mapping for the determination of hepatic iron overload.

PubMed

Henninger, B; Kremser, C; Rauch, S; Eder, R; Zoller, H; Finkenstedt, A; Michaely, H J; Schocke, M

2012-11-01

To evaluate MRI using T1 and T2* mapping sequences in patients with suspected hepatic iron overload (HIO). Twenty-five consecutive patients with clinically suspected HIO were retrospectively studied. All underwent MRI and liver biopsy. For the quantification of liver T2* values we used a fat-saturated multi-echo gradient echo sequence with 12 echoes (TR = 200 ms, TE = 0.99 ms +  n × 1.41 ms, flip angle 20°). T1 values were obtained using a fast T1 mapping sequence based on an inversion recovery snapshot FLASH sequence. Parameter maps were analysed using regions of interest. ROC analysis calculated cut-off points at 10.07 ms and 15.47 ms for T2* in the determination of HIO with accuracy 88 %/88 %, sensitivity 84 %/89.5 % and specificity 100 %/83 %. MRI correctly classified 20 patients (80 %). All patients with HIO only had decreased T1 and T2* relaxation times. There was a significant difference in T1 between patients with HIO only and patients with HIO and steatohepatitis (P = 0.018). MRI-based T2* relaxation diagnoses HIO very accurately, even at low iron concentrations. Important additional information may be obtained by the combination of T1 and T2* mapping. It is a rapid, non-invasive, accurate and reproducible technique for validating the evidence of even low hepatic iron concentrations. • Hepatic iron overload causes fibrosis, cirrhosis and increases hepatocellular carcinoma risk. • MRI detects iron because of the field heterogeneity generated by haemosiderin. • T2* relaxation is very accurate in diagnosing hepatic iron overload. • Additional information may be obtained by T1 and T2* mapping.

Characterization of macromolecular baseline of human brain using metabolite cycled semi-LASER at 9.4T.

PubMed

Giapitzakis, Ioannis-Angelos; Avdievich, Nikolai; Henning, Anke

2018-08-01

Macromolecular resonances (MM) arise mainly from cytosolic proteins and overlap with metabolites, influencing metabolite quantification. Macromolecules can serve as valuable biomarkers for diseases and pathologies. The objectives of this study were to characterize MM at 9.4T in the human brain (occipital and left parietal lobe) and to describe the RF coil setup used for MM acquisition in the two regions. An adiabatic inversion pulse was optimised for metabolite nulling at 9.4T using double inversion recovery and was combined for the first time with metabolite cycled (MC) semi-LASER and appropriate coil configuration. MM spectra (seven volunteers) from two brain locations were averaged and smoothed creating MM templates, which were then parametrized using simulated Voigt-shaped lines within LCModel. Quantification was performed on individual data sets, including corrections for different tissue composition and the T 1 and T 2 relaxation of water. Our coil configuration method resulted in efficient B1+ (>30 T/√kW) for both brain regions. The 15 MM components were detected and quantified in MM baselines of the two brain areas. No significant differences in concentration levels of MM between different regions were found. Two new MM peaks were reported (M7 & M8). Double inversion, which was combined with MC semi-LASER, enabled the acquisition of high spectral resolution MM spectra for both brain regions at 9.4T. The 15 MM components were detected and quantified. Two new MM peaks were reported for the first time (M7 & M8) and preliminarily assigned to β-methylene protons of aspartyl-groups. Magn Reson Med 80:462-473, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

A computerized MRI biomarker quantification scheme for a canine model of Duchenne muscular dystrophy.

PubMed

Wang, Jiahui; Fan, Zheng; Vandenborne, Krista; Walter, Glenn; Shiloh-Malawsky, Yael; An, Hongyu; Kornegay, Joe N; Styner, Martin A

2013-09-01

Golden retriever muscular dystrophy (GRMD) is a widely used canine model of Duchenne muscular dystrophy (DMD). Recent studies have shown that magnetic resonance imaging (MRI) can be used to non-invasively detect consistent changes in both DMD and GRMD. In this paper, we propose a semiautomated system to quantify MRI biomarkers of GRMD. Our system was applied to a database of 45 MRI scans from 8 normal and 10 GRMD dogs in a longitudinal natural history study. We first segmented six proximal pelvic limb muscles using a semiautomated full muscle segmentation method. We then performed preprocessing, including intensity inhomogeneity correction, spatial registration of different image sequences, intensity calibration of T2-weighted and T2-weighted fat-suppressed images, and calculation of MRI biomarker maps. Finally, for each of the segmented muscles, we automatically measured MRI biomarkers of muscle volume, intensity statistics over MRI biomarker maps, and statistical image texture features. The muscle volume and the mean intensities in T2 value, fat, and water maps showed group differences between normal and GRMD dogs. For the statistical texture biomarkers, both the histogram and run-length matrix features showed obvious group differences between normal and GRMD dogs. The full muscle segmentation showed significantly less error and variability in the proposed biomarkers when compared to the standard, limited muscle range segmentation. The experimental results demonstrated that this quantification tool could reliably quantify MRI biomarkers in GRMD dogs, suggesting that it would also be useful for quantifying disease progression and measuring therapeutic effect in DMD patients.

Early postnatal myelin content estimate of white matter via T1w/T2w ratio

NASA Astrophysics Data System (ADS)

Lee, Kevin; Cherel, Marie; Budin, Francois; Gilmore, John; Zaldarriaga Consing, Kirsten; Rasmussen, Jerod; Wadhwa, Pathik D.; Entringer, Sonja; Glasser, Matthew F.; Van Essen, David C.; Buss, Claudia; Styner, Martin

2015-03-01

To develop and evaluate a novel processing framework for the relative quantification of myelin content in cerebral white matter (WM) regions from brain MRI data via a computed ratio of T1 to T2 weighted intensity values. We employed high resolution (1mm3 isotropic) T1 and T2 weighted MRI from 46 (28 male, 18 female) neonate subjects (typically developing controls) scanned on a Siemens Tim Trio 3T at UC Irvine. We developed a novel, yet relatively straightforward image processing framework for WM myelin content estimation based on earlier work by Glasser, et al. We first co-register the structural MRI data to correct for motion. Then, background areas are masked out via a joint T1w and T2 foreground mask computed. Raw T1w/T2w-ratios images are computed next. For purpose of calibration across subjects, we first coarsely segment the fat-rich facial regions via an atlas co-registration. Linear intensity rescaling based on median T1w/T2w-ratio values in those facial regions yields calibrated T1w/T2wratio images. Mean values in lobar regions are evaluated using standard statistical analysis to investigate their interaction with age at scan. Several lobes have strongly positive significant interactions of age at scan with the computed T1w/T2w-ratio. Most regions do not show sex effects. A few regions show no measurable effects of change in myelin content change within the first few weeks of postnatal development, such as cingulate and CC areas, which we attribute to sample size and measurement variability. We developed and evaluated a novel way to estimate white matter myelin content for use in studies of brain white matter development.

Sensitivity of Chemical Shift-Encoded Fat Quantification to Calibration of Fat MR Spectrum

PubMed Central

Wang, Xiaoke; Hernando, Diego; Reeder, Scott B.

2015-01-01

Purpose To evaluate the impact of different fat spectral models on proton density fat-fraction (PDFF) quantification using chemical shift-encoded (CSE) MRI. Material and Methods Simulations and in vivo imaging were performed. In a simulation study, spectral models of fat were compared pairwise. Comparison of magnitude fitting and mixed fitting was performed over a range of echo times and fat fractions. In vivo acquisitions from 41 patients were reconstructed using 7 published spectral models of fat. T2-corrected STEAM-MRS was used as reference. Results Simulations demonstrate that imperfectly calibrated spectral models of fat result in biases that depend on echo times and fat fraction. Mixed fitting is more robust against this bias than magnitude fitting. Multi-peak spectral models showed much smaller differences among themselves than when compared to the single-peak spectral model. In vivo studies show all multi-peak models agree better (for mixed fitting, slope ranged from 0.967–1.045 using linear regression) with reference standard than the single-peak model (for mixed fitting, slope=0.76). Conclusion It is essential to use a multi-peak fat model for accurate quantification of fat with CSE-MRI. Further, fat quantification techniques using multi-peak fat models are comparable and no specific choice of spectral model is shown to be superior to the rest. PMID:25845713

Towards high-resolution 4D flow MRI in the human aorta using kt-GRAPPA and B1+ shimming at 7T.

PubMed

Schmitter, Sebastian; Schnell, Susanne; Uğurbil, Kâmil; Markl, Michael; Van de Moortele, Pierre-François

2016-08-01

To evaluate the feasibility of aortic 4D flow magnetic resonance imaging (MRI) at 7T with improved spatial resolution using kt-GRAPPA acceleration while restricting acquisition time and to address radiofrequency (RF) excitation heterogeneities with B1+ shimming. 4D flow MRI data were obtained in the aorta of eight subjects using a 16-channel transmit/receive coil array at 7T. Flow quantification and acquisition time were compared for a kt-GRAPPA accelerated (R = 5) and a standard GRAPPA (R = 2) accelerated protocol. The impact of different dynamic B1+ shimming strategies on flow quantification was investigated. Two kt-GRAPPA accelerated protocols with 1.2 × 1.2 × 1.2 mm(3) and 1.8 × 1.8 × 2.4 mm(3) spatial resolution were compared. Using kt-GRAPPA, we achieved a 4.3-fold reduction in net acquisition time resulting in scan times of about 10 minutes. No significant effect on flow quantification was observed compared to standard GRAPPA with R = 2. Optimizing the B1+ fields for the aorta impacted significantly (P <  0.05) the flow quantification while specific B1+ settings were required for respiration navigators. The high-resolution protocol yielded similar flow quantification, but allowed the depiction of branching vessels. 7T in combination with B1+ shimming allows for high-resolution 4D flow MRI acquisitions in the human aorta, while kt-GRAPPA limits total scan times without affecting flow quantification. J. Magn. Reson. Imaging 2016;44:486-499. © 2016 Wiley Periodicals, Inc.

Reproducibility of MR-Based Liver Fat Quantification Across Field Strength: Same-Day Comparison Between 1.5T and 3T in Obese Subjects

PubMed Central

Artz, Nathan S.; Haufe, William M.; Hooker, Catherine A.; Hamilton, Gavin; Wolfson, Tanya; Campos, Guilherme M.; Gamst, Anthony C.; Schwimmer, Jeffrey B.; Sirlin, Claude B.; Reeder, Scott B.

2016-01-01

Purpose To examine the reproducibility of quantitative magnetic resonance (MR) methods to estimate hepatic proton density fat-fraction (PDFF) at different magnetic field strengths. Materials and Methods This Health Insurance Portability and Accountability Act (HIPAA)-compliant study was approved by the Institutional Review Board. Following informed consent, 25 severely obese subjects (mean body mass index [BMI]: 45 ± 4, range: 38–53 kg/m2) were scanned at 1.5T and 3T on the same day. Two confounder-corrected multiecho chemical shift-encoded gradient-echo-based imaging methods were acquired to estimate PDFF over the entire liver: 3D complex-based (MRI-C) and 2D magnitude-based (MRI-M) MRI. Single-voxel MR spectroscopy (MRS) was performed in the right liver lobe. Using linear regression, pairwise comparisons of estimated PDFF were made between methods (MRI-C, MRI-M, MRS) at each field strength and for each method across field strengths. Results 1.5T vs. 3T regression analyses for MRI-C, MRI-M, and MRS PDFF measurements yielded R2 values of 0.99, 0.97, and 0.90, respectively. The best-fit line was near unity (slope(m) = 1, intercept(b) = 0), indicating excellent agreement for each case: MRI-C (m = 0.92 [0.87, 0.99], b = 1.4 [0.7, 1.8]); MRI-M (m = 1.0 [0.90, 1.08], b = −1.4 [−2.4, −0.5]); MRS (m = 0.98 [0.82, 1.15], b = 1.2 [−0.2, 3.0]). Comparing MRI-C and MRI-M yielded an R2 = 0.98 (m = 1.1 [1.02, 1.16], b = −1.8 [−2.8, −1.1]) at 1.5T, and R2 = 0.99 (m = 0.98 [0.93, 1.03], b = 1.2 [0.7, 1.7]) at 3T. Conclusion This study demonstrates that PDFF estimation is reproducible across field strengths and across two confounder-corrected MR-based methods. PMID:25620624

Reproducibility of MR-based liver fat quantification across field strength: Same-day comparison between 1.5T and 3T in obese subjects.

PubMed

Artz, Nathan S; Haufe, William M; Hooker, Catherine A; Hamilton, Gavin; Wolfson, Tanya; Campos, Guilherme M; Gamst, Anthony C; Schwimmer, Jeffrey B; Sirlin, Claude B; Reeder, Scott B

2015-09-01

To examine the reproducibility of quantitative magnetic resonance (MR) methods to estimate hepatic proton density fat-fraction (PDFF) at different magnetic field strengths. This Health Insurance Portability and Accountability Act (HIPAA)-compliant study was approved by the Institutional Review Board. Following informed consent, 25 severely obese subjects (mean body mass index [BMI]: 45 ± 4, range: 38-53 kg/m(2) ) were scanned at 1.5T and 3T on the same day. Two confounder-corrected multiecho chemical shift-encoded gradient-echo-based imaging methods were acquired to estimate PDFF over the entire liver: 3D complex-based (MRI-C) and 2D magnitude-based (MRI-M) MRI. Single-voxel MR spectroscopy (MRS) was performed in the right liver lobe. Using linear regression, pairwise comparisons of estimated PDFF were made between methods (MRI-C, MRI-M, MRS) at each field strength and for each method across field strengths. 1.5T vs. 3T regression analyses for MRI-C, MRI-M, and MRS PDFF measurements yielded R(2) values of 0.99, 0.97, and 0.90, respectively. The best-fit line was near unity (slope(m) = 1, intercept(b) = 0), indicating excellent agreement for each case: MRI-C (m = 0.92 [0.87, 0.99], b = 1.4 [0.7, 1.8]); MRI-M (m = 1.0 [0.90, 1.08], b = -1.4 [-2.4, -0.5]); MRS (m = 0.98 [0.82, 1.15], b = 1.2 [-0.2, 3.0]). Comparing MRI-C and MRI-M yielded an R(2)  = 0.98 (m = 1.1 [1.02, 1.16], b = -1.8 [-2.8, -1.1]) at 1.5T, and R(2)  = 0.99 (m = 0.98 [0.93, 1.03], b = 1.2 [0.7, 1.7]) at 3T. This study demonstrates that PDFF estimation is reproducible across field strengths and across two confounder-corrected MR-based methods. © 2015 Wiley Periodicals, Inc.

On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

PubMed Central

Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

2014-01-01

Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

A simple and low cost dual-wavelength β-correction spectrophotometric determination and speciation of mercury(II) in water using chromogenic reagent 4-(2-thiazolylazo) resorcinol

NASA Astrophysics Data System (ADS)

Al-Bagawi, A. H.; Ahmad, W.; Saigl, Z. M.; Alwael, H.; Al-Harbi, E. A.; El-Shahawi, M. S.

2017-12-01

The most common problems in spectrophotometric determination of various complex species originate from the background spectral interference. Thus, the present study aimed to overcome the spectral matrix interference for the precise analysis and speciation of mercury(II) in water by dual-wavelength β-correction spectrophotometry using 4-(2-thiazolylazo) resorcinol (TAR) as chromogenic reagent. The principle was based on measuring the correct absorbance for the formed complex of mercury(II) ions with TAR reagent at 547 nm (lambda max). Under optimized conditions, a linear dynamic range of 0.1-2.0 μg mL- 1 with correlation coefficient (R2) of 0.997 were obtained with lower limits of detection (LOD) of 0.024 μg mL- 1 and limit of quantification (LOQ) of 0.081 μg mL- 1. The values of RSD and relative error (RE) obtained for β-correction method and single wavelength spectrophotometry were 1.3, 1.32% and 4.7, 5.9%, respectively. The method was validated in tap and sea water in terms of the data obtained from inductively coupled plasma-optical emission spectrometry (ICP-OES) using student's t and F tests. The developed methodology satisfactorily overcomes the spectral interference in trace determination and speciation of mercury(II) ions in water.

Evaluation of liver fat in the presence of iron with MRI using T2* correction: a clinical approach.

PubMed

Henninger, Benjamin; Benjamin, Henninger; Kremser, Christian; Christian, Kremser; Rauch, Stefan; Stefan, Rauch; Eder, Robert; Robert, Eder; Judmaier, Werner; Werner, Judmaier; Zoller, Heinz; Heinz, Zoller; Michaely, Henrik; Henrik, Michaely; Schocke, Michael; Michael, Schocke

2013-06-01

To assess magnetic resonance imaging (MRI) with conventional chemical shift-based sequences with and without T2* correction for the evaluation of steatosis hepatitis (SH) in the presence of iron. Thirty-one patients who underwent MRI and liver biopsy because of clinically suspected diffuse liver disease were retrospectively analysed. The signal intensity (SI) was calculated in co-localised regions of interest (ROIs) using conventional spoiled gradient-echo T1 FLASH in-phase and opposed-phase (IP/OP). T2* relaxation time was recorded in a fat-saturated multi-echo-gradient-echo sequence. The fat fraction (FF) was calculated with non-corrected and T2*-corrected SIs. Results were correlated with liver biopsy. There was significant difference (P < 0.001) between uncorrected and T2* corrected FF in patients with SH and concomitant hepatic iron overload (HIO). Using 5 % as a threshold resulted in eight false negative results with uncorrected FF whereas T2* corrected FF lead to true positive results in 5/8 patients. ROC analysis calculated three threshold values (8.97 %, 5.3 % and 3.92 %) for T2* corrected FF with accuracy 84 %, sensitivity 83-91 % and specificity 63-88 %. FF with T2* correction is accurate for the diagnosis of hepatic fat in the presence of HIO. Findings of our study suggest the use of IP/OP imaging in combination with T2* correction. • Magnetic resonance helps quantify both iron and fat content within the liver • T2* correction helps to predict the correct diagnosis of steatosis hepatitis • "Fat fraction" from T2*-corrected chemical shift-based sequences accurately quantifies hepatic fat • "Fat fraction" without T2* correction underestimates hepatic fat with iron overload.

Impact of reconstruction parameters on quantitative I-131 SPECT

NASA Astrophysics Data System (ADS)

van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.

2016-07-01

Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR modelling is the most robust and reliable method to reconstruct accurate quantitative iodine-131 SPECT images.

SU-D-207A-04: Use of Gradient Echo Plural Contrast Imaging (GEPCI) in MR-Guided Radiation Therapy: A Feasibility Study Targeting Brain Treatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, B; Rao, Y; Tsien, C

Purpose: To implement the Gradient Echo Plural Contrast Imaging(GEPCI) technique in MRI-simulation for radiation therapy and assess the feasibility of using GEPCI images with advanced inhomogeneity correction in MRI-guided radiotherapy for brain treatment. Methods: An optimized multigradient-echo GRE sequence (TR=50ms;TE1=4ms;delta-TE=4ms;flip angle=300,11 Echoes) was developed to generate both structural (T1w and T2*w) and functional MRIs (field and susceptibility maps) from a single acquisition. One healthy subject (Subject1) and one post-surgical brain cancer patient (Subject2) were scanned on a Philips Ingenia 1.5T MRI used for radiation therapy simulation. Another healthy subject (Subject3) was scanned on a 0.35T MRI-guided radiotherapy (MR-IGRT) system (ViewRay).more » A voxel spread function (VSF) was used to correct the B0 inhomogeneities caused by surgical cavities and edema for Subject2. GEPCI images and standard radiotherapy planning MRIs for this patient were compared focusing the delineation of radiotherapy target region. Results: GEPCI brain images were successfully derived from all three subjects with scan times of <7 minutes. The images derived for Subjects1&2 demonstrated that GEPCI can be applied and combined into radiotherapy MRI simulation. Despite low field, T1-weighted and R2* images were successfully reconstructed for Subject3 and were satisfactory for contour and target delineation. The R2* distribution of grey matter (center=12,FWHM=4.5) and white matter (center=14.6, FWHM=2) demonstrated the feasibility for tissue segmentation and quantification. The voxel spread function(VSF) corrected surgical site related inhomogeneities for Subject2. R2* and quantitative susceptibility map(QSM) images for Subject2 can be used to quantitatively assess the brain structure response to radiation over the treatment course. Conclusion: We implemented the GEPCI technique in MRI-simulation and in MR-IGRT system for radiation therapy. The images demonstrated that it is feasible to adopt this technique in radiotherapy for structural delineation. The preliminary data also enable the opportunity for quantitative assessment of radiation response of the target region and normal tissue.« less

Influence of Co-57 and CT Transmission Measurements on the Quantification Accuracy and Partial Volume Effect of a Small Animal PET Scanner.

PubMed

Mannheim, Julia G; Schmid, Andreas M; Pichler, Bernd J

2017-12-01

Non-invasive in vivo positron emission tomography (PET) provides high detection sensitivity in the nano- to picomolar range and in addition to other advantages, the possibility to absolutely quantify the acquired data. The present study focuses on the comparison of transmission data acquired with an X-ray computed tomography (CT) scanner or a Co-57 source for the Inveon small animal PET scanner (Siemens Healthcare, Knoxville, TN, USA), as well as determines their influences on the quantification accuracy and partial volume effect (PVE). A special focus included the impact of the performed calibration on the quantification accuracy. Phantom measurements were carried out to determine the quantification accuracy, the influence of the object size on the quantification, and the PVE for different sphere sizes, along the field of view and for different contrast ratios. An influence of the emission activity on the Co-57 transmission measurements was discovered (deviations up to 24.06 % measured to true activity), whereas no influence of the emission activity on the CT attenuation correction was identified (deviations <3 % for measured to true activity). The quantification accuracy was substantially influenced by the applied calibration factor and by the object size. The PVE demonstrated a dependency on the sphere size, the position within the field of view, the reconstruction and correction algorithms and the count statistics. Depending on the reconstruction algorithm, only ∼30-40 % of the true activity within a small sphere could be resolved. The iterative 3D reconstruction algorithms uncovered substantially increased recovery values compared to the analytical and 2D iterative reconstruction algorithms (up to 70.46 % and 80.82 % recovery for the smallest and largest sphere using iterative 3D reconstruction algorithms). The transmission measurement (CT or Co-57 source) to correct for attenuation did not severely influence the PVE. The analysis of the quantification accuracy and the PVE revealed an influence of the object size, the reconstruction algorithm and the applied corrections. Particularly, the influence of the emission activity during the transmission measurement performed with a Co-57 source must be considered. To receive comparable results, also among different scanner configurations, standardization of the acquisition (imaging parameters, as well as applied reconstruction and correction protocols) is necessary.

Validation of a T1 and T2* leakage correction method based on multi-echo DSC-MRI using MION as a reference standard

PubMed Central

Stokes, Ashley M.; Semmineh, Natenael; Quarles, C. Chad

2015-01-01

Purpose A combined biophysical- and pharmacokinetic-based method is proposed to separate, quantify, and correct for both T1 and T2* leakage effects using dual-echo DSC acquisitions to provide more accurate hemodynamic measures, as validated by a reference intravascular contrast agent (CA). Methods Dual-echo DSC-MRI data were acquired in two rodent glioma models. The T1 leakage effects were removed and also quantified in order to subsequently correct for the remaining T2* leakage effects. Pharmacokinetic, biophysical, and combined biophysical and pharmacokinetic models were used to obtain corrected cerebral blood volume (CBV) and cerebral blood flow (CBF), and these were compared with CBV and CBF from an intravascular CA. Results T1-corrected CBV was significantly overestimated compared to MION CBV, while T1+T2*-correction yielded CBV values closer to the reference values. The pharmacokinetic and simplified biophysical methods showed similar results and underestimated CBV in tumors exhibiting strong T2* leakage effects. The combined method was effective for correcting T1 and T2* leakage effects across tumor types. Conclusions Correcting for both T1 and T2* leakage effects yielded more accurate measures of CBV. The combined correction method yields more reliable CBV measures than either correction method alone, but for certain brain tumor types (e.g., gliomas) the simplified biophysical method may provide a robust and computationally efficient alternative. PMID:26362714

Quantifying iron content in magnetic resonance imaging.

PubMed

Ghassaban, Kiarash; Liu, Saifeng; Jiang, Caihong; Haacke, E Mark

2018-04-25

Measuring iron content has practical clinical indications in the study of diseases such as Parkinson's disease, Huntington's disease, ferritinopathies and multiple sclerosis as well as in the quantification of iron content in microbleeds and oxygen saturation in veins. In this work, we review the basic concepts behind imaging iron using T2, T2*, T2', phase and quantitative susceptibility mapping in the human brain, liver and heart, followed by the applications of in vivo iron quantification in neurodegenerative diseases, iron tagged cells and ultra-small superparamagnetic iron oxide (USPIO) nanoparticles. Copyright © 2018 Elsevier Inc. All rights reserved.

Accelerated T1ρ acquisition for knee cartilage quantification using compressed sensing and data-driven parallel imaging: A feasibility study.

PubMed

Pandit, Prachi; Rivoire, Julien; King, Kevin; Li, Xiaojuan

2016-03-01

Quantitative T1ρ imaging is beneficial for early detection for osteoarthritis but has seen limited clinical use due to long scan times. In this study, we evaluated the feasibility of accelerated T1ρ mapping for knee cartilage quantification using a combination of compressed sensing (CS) and data-driven parallel imaging (ARC-Autocalibrating Reconstruction for Cartesian sampling). A sequential combination of ARC and CS, both during data acquisition and reconstruction, was used to accelerate the acquisition of T1ρ maps. Phantom, ex vivo (porcine knee), and in vivo (human knee) imaging was performed on a GE 3T MR750 scanner. T1ρ quantification after CS-accelerated acquisition was compared with non CS-accelerated acquisition for various cartilage compartments. Accelerating image acquisition using CS did not introduce major deviations in quantification. The coefficient of variation for the root mean squared error increased with increasing acceleration, but for in vivo measurements, it stayed under 5% for a net acceleration factor up to 2, where the acquisition was 25% faster than the reference (only ARC). To the best of our knowledge, this is the first implementation of CS for in vivo T1ρ quantification. These early results show that this technique holds great promise in making quantitative imaging techniques more accessible for clinical applications. © 2015 Wiley Periodicals, Inc.

Stable-isotope-labeled Histone Peptide Library for Histone Post-translational Modification and Variant Quantification by Mass Spectrometry *

PubMed Central

Lin, Shu; Wein, Samuel; Gonzales-Cope, Michelle; Otte, Gabriel L.; Yuan, Zuo-Fei; Afjehi-Sadat, Leila; Maile, Tobias; Berger, Shelley L.; Rush, John; Lill, Jennie R.; Arnott, David; Garcia, Benjamin A.

2014-01-01

To facilitate accurate histone variant and post-translational modification (PTM) quantification via mass spectrometry, we present a library of 93 synthetic peptides using Protein-Aqua™ technology. The library contains 55 peptides representing different modified forms from histone H3 peptides, 23 peptides representing H4 peptides, 5 peptides representing canonical H2A peptides, 8 peptides representing H2A.Z peptides, and peptides for both macroH2A and H2A.X. The PTMs on these peptides include lysine mono- (me1), di- (me2), and tri-methylation (me3); lysine acetylation; arginine me1; serine/threonine phosphorylation; and N-terminal acetylation. The library was subjected to chemical derivatization with propionic anhydride, a widely employed protocol for histone peptide quantification. Subsequently, the detection efficiencies were quantified using mass spectrometry extracted ion chromatograms. The library yields a wide spectrum of detection efficiencies, with more than 1700-fold difference between the peptides with the lowest and highest efficiencies. In this paper, we describe the impact of different modifications on peptide detection efficiencies and provide a resource to correct for detection biases among the 93 histone peptides. In brief, there is no correlation between detection efficiency and molecular weight, hydrophobicity, basicity, or modification type. The same types of modifications may have very different effects on detection efficiencies depending on their positions within a peptide. We also observed antagonistic effects between modifications. In a study of mouse trophoblast stem cells, we utilized the detection efficiencies of the peptide library to correct for histone PTM/variant quantification. For most histone peptides examined, the corrected data did not change the biological conclusions but did alter the relative abundance of these peptides. For a low-abundant histone H2A variant, macroH2A, the corrected data led to a different conclusion than the uncorrected data. The peptide library and detection efficiencies presented here may serve as a resource to facilitate studies in the epigenetics and proteomics fields. PMID:25000943

Influence of the way of reporting alpha-Amylase values in saliva in different naturalistic situations: A pilot study

PubMed Central

Contreras-Aguilar, María Dolores; Escribano, Damián; Martínez-Subiela, Silvia; Martínez-Miró, Silvia; Rubio, Mónica; Tvarijonaviciute, Asta; Tecles, Fernando; Cerón, Jose J.

2017-01-01

The objective of this pilot study was to compare the different ways of measuring salivary alpha-amylase (sAA, enzymatic vs. concentration) and to evaluate the influence that the different ways of reporting the results can have in sAA interpretation. For this purpose, sAA was measured by direct quantification and also by an enzymatic assay in three different naturalistic situations, a physical stressor (situation 1) and two mental stressors of different intensity (situations 2 and 3). The results were expressed in three different ways (without correction, multiplied by flow rate and divided by protein concentration). sAA concentration and activity increased just after situations 1 and 3. When values were multiplied by the flow rate, significant changes after situation 1 were detected only for sAA activity but not for sAA concentration, being these changes of lower significance and magnitude that those observed for sAA activity without any correction. In addition, a significant increase in sAA activity was found at T+15 in situation 2. In situation 3 the significant decrease in sAA at T+15 disappeared. When values were divided by protein concentration, there were no significant changes in situations 1 or 3, but a decrease in situation 2 at T+0 and an increase at T+15. sAA activity and concentration showed a significant correlation in all situations. This pilot study points out that the way of expressing sAA can influence the results obtained in different stress models and also their interpretation. Therefore, how sAA is reported and the factors involved in the different ways of expressing sAA, should be taken into consideration for an objective interpretation of sAA values. PMID:28654668

Influence of the way of reporting alpha-Amylase values in saliva in different naturalistic situations: A pilot study.

PubMed

Contreras-Aguilar, María Dolores; Escribano, Damián; Martínez-Subiela, Silvia; Martínez-Miró, Silvia; Rubio, Mónica; Tvarijonaviciute, Asta; Tecles, Fernando; Cerón, Jose J

2017-01-01

The objective of this pilot study was to compare the different ways of measuring salivary alpha-amylase (sAA, enzymatic vs. concentration) and to evaluate the influence that the different ways of reporting the results can have in sAA interpretation. For this purpose, sAA was measured by direct quantification and also by an enzymatic assay in three different naturalistic situations, a physical stressor (situation 1) and two mental stressors of different intensity (situations 2 and 3). The results were expressed in three different ways (without correction, multiplied by flow rate and divided by protein concentration). sAA concentration and activity increased just after situations 1 and 3. When values were multiplied by the flow rate, significant changes after situation 1 were detected only for sAA activity but not for sAA concentration, being these changes of lower significance and magnitude that those observed for sAA activity without any correction. In addition, a significant increase in sAA activity was found at T+15 in situation 2. In situation 3 the significant decrease in sAA at T+15 disappeared. When values were divided by protein concentration, there were no significant changes in situations 1 or 3, but a decrease in situation 2 at T+0 and an increase at T+15. sAA activity and concentration showed a significant correlation in all situations. This pilot study points out that the way of expressing sAA can influence the results obtained in different stress models and also their interpretation. Therefore, how sAA is reported and the factors involved in the different ways of expressing sAA, should be taken into consideration for an objective interpretation of sAA values.

MRI-based methods for quantification of the cerebral metabolic rate of oxygen

PubMed Central

Rodgers, Zachary B; Detre, John A

2016-01-01

The brain depends almost entirely on oxidative metabolism to meet its significant energy requirements. As such, the cerebral metabolic rate of oxygen (CMRO2) represents a key measure of brain function. Quantification of CMRO2 has helped elucidate brain functional physiology and holds potential as a clinical tool for evaluating neurological disorders including stroke, brain tumors, Alzheimer’s disease, and obstructive sleep apnea. In recent years, a variety of magnetic resonance imaging (MRI)-based CMRO2 quantification methods have emerged. Unlike positron emission tomography – the current “gold standard” for measurement and mapping of CMRO2 – MRI is non-invasive, relatively inexpensive, and ubiquitously available in modern medical centers. All MRI-based CMRO2 methods are based on modeling the effect of paramagnetic deoxyhemoglobin on the magnetic resonance signal. The various methods can be classified in terms of the MRI contrast mechanism used to quantify CMRO2: T2*, T2′, T2, or magnetic susceptibility. This review article provides an overview of MRI-based CMRO2 quantification techniques. After a brief historical discussion motivating the need for improved CMRO2 methodology, current state-of-the-art MRI-based methods are critically appraised in terms of their respective tradeoffs between spatial resolution, temporal resolution, and robustness, all of critical importance given the spatially heterogeneous and temporally dynamic nature of brain energy requirements. PMID:27089912

Consistency of flow quantifications in tridirectional phase-contrast MRI

NASA Astrophysics Data System (ADS)

Unterhinninghofen, R.; Ley, S.; Dillmann, R.

2009-02-01

Tridirectionally encoded phase-contrast MRI is a technique to non-invasively acquire time-resolved velocity vector fields of blood flow. These may not only be used to analyze pathological flow patterns, but also to quantify flow at arbitrary positions within the acquired volume. In this paper we examine the validity of this approach by analyzing the consistency of related quantifications instead of comparing it with an external reference measurement. Datasets of the thoracic aorta were acquired from 6 pigs, 1 healthy volunteer and 3 patients with artificial aortic valves. Using in-house software an elliptical flow quantification plane was placed manually at 6 positions along the descending aorta where it was rotated to 5 different angles. For each configuration flow was computed based on the original data and data that had been corrected for phase offsets. Results reveal that quantifications are more dependent on changes in position than on changes in angle. Phase offset correction considerably reduces this dependency. Overall consistency is good with a maximum variation coefficient of 9.9% and a mean variation coefficient of 7.2%.

Impact of time-of-flight PET on quantification errors in MR imaging-based attenuation correction.

PubMed

Mehranian, Abolfazl; Zaidi, Habib

2015-04-01

Time-of-flight (TOF) PET/MR imaging is an emerging imaging technology with great capabilities offered by TOF to improve image quality and lesion detectability. We assessed, for the first time, the impact of TOF image reconstruction on PET quantification errors induced by MR imaging-based attenuation correction (MRAC) using simulation and clinical PET/CT studies. Standard 4-class attenuation maps were derived by segmentation of CT images of 27 patients undergoing PET/CT examinations into background air, lung, soft-tissue, and fat tissue classes, followed by the assignment of predefined attenuation coefficients to each class. For each patient, 4 PET images were reconstructed: non-TOF and TOF both corrected for attenuation using reference CT-based attenuation correction and the resulting 4-class MRAC maps. The relative errors between non-TOF and TOF MRAC reconstructions were compared with their reference CT-based attenuation correction reconstructions. The bias was locally and globally evaluated using volumes of interest (VOIs) defined on lesions and normal tissues and CT-derived tissue classes containing all voxels in a given tissue, respectively. The impact of TOF on reducing the errors induced by metal-susceptibility and respiratory-phase mismatch artifacts was also evaluated using clinical and simulation studies. Our results show that TOF PET can remarkably reduce attenuation correction artifacts and quantification errors in the lungs and bone tissues. Using classwise analysis, it was found that the non-TOF MRAC method results in an error of -3.4% ± 11.5% in the lungs and -21.8% ± 2.9% in bones, whereas its TOF counterpart reduced the errors to -2.9% ± 7.1% and -15.3% ± 2.3%, respectively. The VOI-based analysis revealed that the non-TOF and TOF methods resulted in an average overestimation of 7.5% and 3.9% in or near lung lesions (n = 23) and underestimation of less than 5% for soft tissue and in or near bone lesions (n = 91). Simulation results showed that as TOF resolution improves, artifacts and quantification errors are substantially reduced. TOF PET substantially reduces artifacts and improves significantly the quantitative accuracy of standard MRAC methods. Therefore, MRAC should be less of a concern on future TOF PET/MR scanners with improved timing resolution. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Occurrence of a Sequence in Marine Cyanophages Similar to That of T4 g20 and Its Application to PCR-Based Detection and Quantification Techniques†

PubMed Central

Fuller, Nicholas J.; Wilson, William H.; Joint, Ian R.; Mann, Nicholas H.

1998-01-01

Viruses are ubiquitous components of marine ecosystems and are known to infect unicellular phycoerythrin-containing cyanobacteria belonging to the genus Synechococcus. A conserved region from the cyanophage genome was identified in three genetically distinct cyanomyoviruses, and a sequence analysis revealed that this region exhibited significant similarity to a gene encoding a capsid assembly protein (gp20) from the enteric coliphage T4. The results of a comparison of gene 20 sequences from three cyanomyoviruses and T4 allowed us to design two degenerate PCR primers, CPS1 and CPS2, which specifically amplified a 165-bp region from the majority of cyanomyoviruses tested. A competitive PCR (cPCR) analysis revealed that cyanomyovirus strains could be accurately enumerated, and it was demonstrated that quantification was log-linear over ca. 3 orders of magnitude. Different calibration curves were obtained for each of the three cyanomyovirus strains tested; consequently, cPCR performed with primers CPS1 and CPS2 could lead to substantial inaccuracies in estimates of phage abundance in natural assemblages. Further sequence analysis of cyanomyovirus gene 20 homologs would be necessary in order to design primers which do not exhibit phage-to-phage variability in priming efficiency. It was demonstrated that PCR products of the correct size could be amplified from seawater samples following 100× concentration and even directly without any prior concentration. Hence, the use of degenerate primers in PCR analyses of cyanophage populations should provide valuable data on the diversity of cyanophages in natural assemblages. Further optimization of procedures may ultimately lead to a sensitive assay which can be used to analyze natural cyanophage populations both quantitatively (by cPCR) and qualitatively following phylogenetic analysis of amplified products. PMID:9603813

Analyte quantification with comprehensive two-dimensional gas chromatography: assessment of methods for baseline correction, peak delineation, and matrix effect elimination for real samples.

PubMed

Samanipour, Saer; Dimitriou-Christidis, Petros; Gros, Jonas; Grange, Aureline; Samuel Arey, J

2015-01-02

Comprehensive two-dimensional gas chromatography (GC×GC) is used widely to separate and measure organic chemicals in complex mixtures. However, approaches to quantify analytes in real, complex samples have not been critically assessed. We quantified 7 PAHs in a certified diesel fuel using GC×GC coupled to flame ionization detector (FID), and we quantified 11 target chlorinated hydrocarbons in a lake water extract using GC×GC with electron capture detector (μECD), further confirmed qualitatively by GC×GC with electron capture negative chemical ionization time-of-flight mass spectrometer (ENCI-TOFMS). Target analyte peak volumes were determined using several existing baseline correction algorithms and peak delineation algorithms. Analyte quantifications were conducted using external standards and also using standard additions, enabling us to diagnose matrix effects. We then applied several chemometric tests to these data. We find that the choice of baseline correction algorithm and peak delineation algorithm strongly influence the reproducibility of analyte signal, error of the calibration offset, proportionality of integrated signal response, and accuracy of quantifications. Additionally, the choice of baseline correction and the peak delineation algorithm are essential for correctly discriminating analyte signal from unresolved complex mixture signal, and this is the chief consideration for controlling matrix effects during quantification. The diagnostic approaches presented here provide guidance for analyte quantification using GC×GC. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Multicenter evaluation of stress-first myocardial perfusion image triage by nuclear technologists and automated quantification.

PubMed

Chaudhry, Waseem; Hussain, Nasir; Ahlberg, Alan W; Croft, Lori B; Fernandez, Antonio B; Parker, Mathew W; Swales, Heather H; Slomka, Piotr J; Henzlova, Milena J; Duvall, W Lane

2017-06-01

A stress-first myocardial perfusion imaging (MPI) protocol saves time, is cost effective, and decreases radiation exposure. A limitation of this protocol is the requirement for physician review of the stress images to determine the need for rest images. This hurdle could be eliminated if an experienced technologist and/or automated computer quantification could make this determination. Images from consecutive patients who were undergoing a stress-first MPI with attenuation correction at two tertiary care medical centers were prospectively reviewed independently by a technologist and cardiologist blinded to clinical and stress test data. Their decision on the need for rest imaging along with automated computer quantification of perfusion results was compared with the clinical reference standard of an assessment of perfusion images by a board-certified nuclear cardiologist that included clinical and stress test data. A total of 250 patients (mean age 61 years and 55% female) who underwent a stress-first MPI were studied. According to the clinical reference standard, 42 (16.8%) and 208 (83.2%) stress-first images were interpreted as "needing" and "not needing" rest images, respectively. The technologists correctly classified 229 (91.6%) stress-first images as either "needing" (n = 28) or "not needing" (n = 201) rest images. Their sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 66.7%, 96.6%, 80.0%, and 93.5%, respectively. An automated stress TPD score ≥1.2 was associated with optimal sensitivity and specificity and correctly classified 179 (71.6%) stress-first images as either "needing" (n = 31) or "not needing" (n = 148) rest images. Its sensitivity, specificity, PPV, and NPV were 73.8%, 71.2%, 34.1%, and 93.1%, respectively. In a model whereby the computer or technologist could correct for the other's incorrect classification, 242 (96.8%) stress-first images were correctly classified. The composite sensitivity, specificity, PPV, and NPV were 83.3%, 99.5%, 97.2%, and 96.7%, respectively. Technologists and automated quantification software had a high degree of agreement with the clinical reference standard for determining the need for rest images in a stress-first imaging protocol. Utilizing an experienced technologist and automated systems to screen stress-first images could expand the use of stress-first MPI to sites where the cardiologist is not immediately available for interpretation.

Multimodal partial volume correction: Application to [11C]PIB PET/MRI myelin imaging in multiple sclerosis.

PubMed

Grecchi, Elisabetta; Veronese, Mattia; Bodini, Benedetta; García-Lorenzo, Daniel; Battaglini, Marco; Stankoff, Bruno; Turkheimer, Federico E

2017-12-01

The [ 11 C]PIB PET tracer, originally developed for amyloid imaging, has been recently repurposed to quantify demyelination and remyelination in multiple sclerosis (MS). Myelin PET imaging, however, is limited by its low resolution that deteriorates the quantification accuracy of white matter (WM) lesions. Here, we introduce a novel partial volume correction (PVC) method called Multiresolution-Multimodal Resolution-Recovery (MM-RR), which uses the wavelet transform and a synergistic statistical model to exploit MRI structural images to improve the resolution of [ 11 C]PIB PET myelin imaging. MM-RR performance was tested on a phantom acquisition and in a dataset comprising [ 11 C]PIB PET and MR T1- and T2-weighted images of 8 healthy controls and 20 MS patients. For the control group, the MM-RR PET images showed an average increase of 5.7% in WM uptake while the grey-matter (GM) uptake remained constant, resulting in +31% WM/GM contrast. Furthermore, MM-RR PET binding maps correlated significantly with the mRNA expressions of the most represented proteins in the myelin sheath (R 2  = 0.57 ± 0.09). In the patient group, MM-RR PET images showed sharper lesion contours and significant improvement in normal-appearing tissue/WM-lesion contrast compared to standard PET (contrast improvement > +40%). These results were consistent with MM-RR performances in phantom experiments.

Quantification of 11C-Laniquidar Kinetics in the Brain.

PubMed

Froklage, Femke E; Boellaard, Ronald; Bakker, Esther; Hendrikse, N Harry; Reijneveld, Jaap C; Schuit, Robert C; Windhorst, Albert D; Schober, Patrick; van Berckel, Bart N M; Lammertsma, Adriaan A; Postnov, Andrey

2015-11-01

Overexpression of the multidrug efflux transport P-glycoprotein may play an important role in pharmacoresistance. (11)C-laniquidar is a newly developed tracer of P-glycoprotein expression. The aim of this study was to develop a pharmacokinetic model for quantification of (11)C-laniquidar uptake and to assess its test-retest variability. Two (test-retest) dynamic (11)C-laniquidar PET scans were obtained in 8 healthy subjects. Plasma input functions were obtained using online arterial blood sampling with metabolite corrections derived from manual samples. Coregistered T1 MR images were used for region-of-interest definition. Time-activity curves were analyzed using various plasma input compartmental models. (11)C-laniquidar was metabolized rapidly, with a parent plasma fraction of 50% at 10 min after tracer injection. In addition, the first-pass extraction of (11)C-laniquidar was low. (11)C-laniquidar time-activity curves were best fitted to an irreversible single-tissue compartment (1T1K) model using conventional models. Nevertheless, significantly better fits were obtained using 2 parallel single-tissue compartments, one for parent tracer and the other for labeled metabolites (dual-input model). Robust K1 results were also obtained by fitting the first 5 min of PET data to the 1T1K model, at least when 60-min plasma input data were used. For both models, the test-retest variability of (11)C-laniquidar rate constant for transfer from arterial plasma to tissue (K1) was approximately 19%. The accurate quantification of (11)C-laniquidar kinetics in the brain is hampered by its fast metabolism and the likelihood that labeled metabolites enter the brain. Best fits for the entire 60 min of data were obtained using a dual-input model, accounting for uptake of (11)C-laniquidar and its labeled metabolites. Alternatively, K1 could be obtained from a 5-min scan using a standard 1T1K model. In both cases, the test-retest variability of K1 was approximately 19%. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Quantification of myocardial oxygenation in heart failure using blood-oxygen-level-dependent T2* magnetic resonance imaging: Comparison with cardiopulmonary exercise test.

PubMed

Nagao, Michinobu; Yamasaki, Yuzo; Kawanami, Satoshi; Kamitani, Takeshi; Sagiyama, Koji; Higo, Taiki; Ide, Tomomi; Takemura, Atsushi; Ishizaki, Umiko; Fukushima, Kenji; Watanabe, Yuji; Honda, Hiroshi

2017-06-01

Quantification of myocardial oxygenation (MO) in heart failure (HF) has been less than satisfactory. This has necessitated the use of invasive techniques to measure MO directly or to determine the oxygen demand during exercise using the cardiopulmonary exercise (CPX) test. We propose a new quantification method for MO using blood-oxygen-level-dependent (BOLD) myocardial T2* magnetic resonance imaging (M-T2* MRI), and investigate its correlation with CPX results. Thirty patients with refractory HF who underwent cardiac MRI and CPX test for heart transplantation, and 24 healthy, age-matched volunteers as controls were enrolled. M-T2* imaging was performed using a 3-Tesla and multi-echo gradient-echo sequence. M-T2* was calculated by fitting the signal intensity data for the mid-left ventricular septum to a decay curve. M-T2* was measured under room-air (T2*-air) and after inhalation of oxygen for 10min at a flow rate of 10L/min (T2*-oxy). MO was defined as the difference between the two values (ΔT2*). Changes in M-T2* at the two conditions and ΔT2* between the two groups were compared. Correlation between ΔT2* and CPX results was analyzed using the Pearson coefficient. T2*-oxy was significantly greater than T2*-air in patients with HF (29.9±7.3ms vs. 26.7±6.0ms, p<0.001), whereas no such difference was observed in controls (25.5±4.0ms vs. 25.4±4.4ms). ΔT2* was significantly greater for patients with HF than for controls (3.2±4.5ms vs. -0.1±1.3ms, p<0.001). A significant correlation between ΔT2* and CPX results (peak VO 2 , r=-0.46, p<0.05; O 2 pulse, r=-0.54, p<0.005) was observed. ΔT2* is increased T2*-oxy is greater in patients with HF, and is correlated with oxygen metabolism during exercise as measured by the CPX test. Hence, ΔT2* can be used as a surrogate marker of MO instead of CPX test. Copyright © 2017 Elsevier Inc. All rights reserved.

A universal real-time PCR assay for the quantification of group-M HIV-1 proviral load.

PubMed

Malnati, Mauro S; Scarlatti, Gabriella; Gatto, Francesca; Salvatori, Francesca; Cassina, Giulia; Rutigliano, Teresa; Volpi, Rosy; Lusso, Paolo

2008-01-01

Quantification of human immunodeficiency virus type-1 (HIV-1) proviral DNA is increasingly used to measure the HIV-1 cellular reservoirs, a helpful marker to evaluate the efficacy of antiretroviral therapeutic regimens in HIV-1-infected individuals. Furthermore, the proviral DNA load represents a specific marker for the early diagnosis of perinatal HIV-1 infection and might be predictive of HIV-1 disease progression independently of plasma HIV-1 RNA levels and CD4(+) T-cell counts. The high degree of genetic variability of HIV-1 poses a serious challenge for the design of a universal quantitative assay capable of detecting all the genetic subtypes within the main (M) HIV-1 group with similar efficiency. Here, we describe a highly sensitive real-time PCR protocol that allows for the correct quantification of virtually all group-M HIV-1 strains with a higher degree of accuracy compared with other methods. The protocol involves three stages, namely DNA extraction/lysis, cellular DNA quantification and HIV-1 proviral load assessment. Owing to the robustness of the PCR design, this assay can be performed on crude cellular extracts, and therefore it may be suitable for the routine analysis of clinical samples even in developing countries. An accurate quantification of the HIV-1 proviral load can be achieved within 1 d from blood withdrawal.

X-ray fluorescence at nanoscale resolution for multicomponent layered structures: A solar cell case study

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, Bradley M.; Stuckelberger, Michael; Jeffries, April

The study of a multilayered and multicomponent system by spatially resolved X-ray fluorescence microscopy poses unique challenges in achieving accurate quantification of elemental distributions. This is particularly true for the quantification of materials with high X-ray attenuation coefficients, depth-dependent composition variations and thickness variations. A widely applicable procedure for use after spectrum fitting and quantification is described. This procedure corrects the elemental distribution from the measured fluorescence signal, taking into account attenuation of the incident beam and generated fluorescence from multiple layers, and accounts for sample thickness variations. Deriving from Beer–Lambert's law, formulae are presented in a general integral formmore » and numerically applicable framework. Here, the procedure is applied using experimental data from a solar cell with a Cu(In,Ga)Se 2 absorber layer, measured at two separate synchrotron beamlines with varied measurement geometries. This example shows the importance of these corrections in real material systems, which can change the interpretation of the measured distributions dramatically.« less

X-ray fluorescence at nanoscale resolution for multicomponent layered structures: A solar cell case study

DOE PAGES

West, Bradley M.; Stuckelberger, Michael; Jeffries, April; ...

2017-01-01

The study of a multilayered and multicomponent system by spatially resolved X-ray fluorescence microscopy poses unique challenges in achieving accurate quantification of elemental distributions. This is particularly true for the quantification of materials with high X-ray attenuation coefficients, depth-dependent composition variations and thickness variations. A widely applicable procedure for use after spectrum fitting and quantification is described. This procedure corrects the elemental distribution from the measured fluorescence signal, taking into account attenuation of the incident beam and generated fluorescence from multiple layers, and accounts for sample thickness variations. Deriving from Beer–Lambert's law, formulae are presented in a general integral formmore » and numerically applicable framework. Here, the procedure is applied using experimental data from a solar cell with a Cu(In,Ga)Se 2 absorber layer, measured at two separate synchrotron beamlines with varied measurement geometries. This example shows the importance of these corrections in real material systems, which can change the interpretation of the measured distributions dramatically.« less

Segmentation And Quantification Of Black Holes In Multiple Sclerosis

PubMed Central

Datta, Sushmita; Sajja, Balasrinivasa Rao; He, Renjie; Wolinsky, Jerry S.; Gupta, Rakesh K.; Narayana, Ponnada A.

2006-01-01

A technique that involves minimal operator intervention was developed and implemented for identification and quantification of black holes on T1- weighted magnetic resonance images (T1 images) in multiple sclerosis (MS). Black holes were segmented on T1 images based on grayscale morphological operations. False classification of black holes was minimized by masking the segmented images with images obtained from the orthogonalization of T2-weighted and T1 images. Enhancing lesion voxels on postcontrast images were automatically identified and eliminated from being included in the black hole volume. Fuzzy connectivity was used for the delineation of black holes. The performance of this algorithm was quantitatively evaluated on 14 MS patients. PMID:16126416

Effects of RF pulse profile and intra-voxel phase dispersion on MR fingerprinting with balanced SSFP readout.

PubMed

Chiu, Su-Chin; Lin, Te-Ming; Lin, Jyh-Miin; Chung, Hsiao-Wen; Ko, Cheng-Wen; Büchert, Martin; Bock, Michael

2017-09-01

To investigate possible errors in T1 and T2 quantification via MR fingerprinting with balanced steady-state free precession readout in the presence of intra-voxel phase dispersion and RF pulse profile imperfections, using computer simulations based on Bloch equations. A pulse sequence with TR changing in a Perlin noise pattern and a nearly sinusoidal pattern of flip angle following an initial 180-degree inversion pulse was employed. Gaussian distributions of off-resonance frequency were assumed for intra-voxel phase dispersion effects. Slice profiles of sinc-shaped RF pulses were computed to investigate flip angle profile influences. Following identification of the best fit between the acquisition signals and those established in the dictionary based on known parameters, estimation errors were reported. In vivo experiments were performed at 3T to examine the results. Slight intra-voxel phase dispersion with standard deviations from 1 to 3Hz resulted in prominent T2 under-estimations, particularly at large T2 values. T1 and off-resonance frequencies were relatively unaffected. Slice profile imperfections led to under-estimations of T1, which became greater as regional off-resonance frequencies increased, but could be corrected by including slice profile effects in the dictionary. Results from brain imaging experiments in vivo agreed with the simulation results qualitatively. MR fingerprinting using balanced SSFP readout in the presence of intra-voxel phase dispersion and imperfect slice profile leads to inaccuracies in quantitative estimations of the relaxation times. Copyright © 2017 Elsevier Inc. All rights reserved.

76 FR 78182 - Application of the Segregation Rules to Small Shareholders; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-16

... CONTACT: Concerning the proposed regulations, Stephen R. Cleary, (202) 622-7750 (not a toll-free number... ``regard to Sec. 1.382-2T(h)(i)(A)) or a first'' is corrected to read ``regard to Sec. 1.382-2T(h)(2)(i)(A.... Clarification of Sec. 1.382-2T(j)(3)'', last line of the paragraph, the language ``2T(h)(i)(A).'' is corrected...

Magnetic Susceptibility as a B0 Field Strength Independent MRI Biomarker of Liver Iron Overload

PubMed Central

Hernando, Diego; Cook, Rachel J.; Diamond, Carol; Reeder, Scott B.

2013-01-01

Purpose MR-based quantification of liver magnetic susceptibility may enable field strength-independent measurement of liver iron concentration (LIC). However, susceptibility quantification is challenging, due to non-local effects of susceptibility on the B0 field. The purpose of this work is to demonstrate feasibility of susceptibility-based LIC quantification using a fat-referenced approach. Methods Phantoms consisting of vials with increasing iron concentrations immersed between oil/water layers, and twenty-seven subjects (9 controls/18 subjects with liver iron overload) were scanned. Ferriscan (1.5T) provided R2-based reference LIC. Multi-echo 3D-SPGR (1.5T/3T) enabled fat-water, B0- and R2*-mapping. Phantom iron concentration (mg Fe/l) was estimated from B0 differences (ΔB0) between vials and neighboring oil. Liver susceptibility and LIC (mg Fe/g dry tissue) was estimated from ΔB0 between the lateral right lobe of the liver and adjacent subcutaneous adipose tissue (SAT). Results Estimated phantom iron concentrations had good correlation with true iron concentrations (1.5T:slope=0.86, intercept=0.72, r2=0.98; 3T:slope=0.85, intercept=1.73, r2=0.98). In liver, ΔB0 correlated strongly with R2* (1.5T:r2=0.86; 3T:r2=0.93) and B0-LIC had good agreement with Ferriscan-LIC (slopes/intercepts nearly 1.0/0.0, 1.5T:r2=0.67, slope=0.93±0.13, p≈0.50, intercept=1.93±0.78, p≈0.02; 3T:r2=0.84, slope=1.01±0.09, p≈0.90, intercept=0.23±0.52, p≈0.68). Discussion Fat-referenced, susceptibility-based LIC estimation is feasible at both field strengths. This approach may enable improved susceptibility mapping in the abdomen. PMID:23801540

New approach for the quantification of processed animal proteins in feed using light microscopy.

PubMed

Veys, P; Baeten, V

2010-07-01

A revision of European Union's total feed ban on animal proteins in feed will need robust quantification methods, especially for control analyses, if tolerance levels are to be introduced, as for fishmeal in ruminant feed. In 2006, a study conducted by the Community Reference Laboratory for Animal Proteins in feedstuffs (CRL-AP) demonstrated the deficiency of the official quantification method based on light microscopy. The study concluded that the method had to be revised. This paper puts forward an improved quantification method based on three elements: (1) the preparation of permanent slides with an optical adhesive preserving all morphological markers of bones necessary for accurate identification and precision counting; (2) the use of a counting grid eyepiece reticle; and (3) new definitions for correction factors for the estimated portions of animal particles in the sediment. This revised quantification method was tested on feeds adulterated at different levels with bovine meat and bone meal (MBM) and fishmeal, and it proved to be effortless to apply. The results obtained were very close to the expected values of contamination levels for both types of adulteration (MBM or fishmeal). Calculated values were not only replicable, but also reproducible. The advantages of the new approach, including the benefits of the optical adhesive used for permanent slide mounting and the experimental conditions that need to be met to implement the new method correctly, are discussed.

Assessment of spill flow emissions on the basis of measured precipitation and waste water data

NASA Astrophysics Data System (ADS)

Hochedlinger, Martin; Gruber, Günter; Kainz, Harald

2005-09-01

Combined sewer overflows (CSOs) are substantial contributors to the total emissions into surface water bodies. The emitted pollution results from dry-weather waste water loads, surface runoff pollution and from the remobilisation of sewer deposits and sewer slime during storm events. One possibility to estimate overflow loads is a calculation with load quantification models. Input data for these models are pollution concentrations, e.g. Total Chemical Oxygen Demand (COD tot), Total Suspended Solids (TSS) or Soluble Chemical Oxygen Demand (COD sol), rainfall series and flow measurements for model calibration and validation. It is important for the result of overflow loads to model with reliable input data, otherwise this inevitably leads to bad results. In this paper the correction of precipitation measurements and the sewer online-measurements are presented to satisfy the load quantification model requirements already described. The main focus is on tipping bucket gauge measurements and their corrections. The results evidence the importance of their corrections due the effects on load quantification modelling and show the difference between corrected and not corrected data of storm events with high rain intensities.

Development, optimization, and single laboratory validation of an event-specific real-time PCR method for the detection and quantification of Golden Rice 2 using a novel taxon-specific assay.

PubMed

Jacchia, Sara; Nardini, Elena; Savini, Christian; Petrillo, Mauro; Angers-Loustau, Alexandre; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

2015-02-18

In this study, we developed, optimized, and in-house validated a real-time PCR method for the event-specific detection and quantification of Golden Rice 2, a genetically modified rice with provitamin A in the grain. We optimized and evaluated the performance of the taxon (targeting rice Phospholipase D α2 gene)- and event (targeting the 3' insert-to-plant DNA junction)-specific assays that compose the method as independent modules, using haploid genome equivalents as unit of measurement. We verified the specificity of the two real-time PCR assays and determined their dynamic range, limit of quantification, limit of detection, and robustness. We also confirmed that the taxon-specific DNA sequence is present in single copy in the rice genome and verified its stability of amplification across 132 rice varieties. A relative quantification experiment evidenced the correct performance of the two assays when used in combination.

Ultrasensitive Quantification of Hepatitis B Virus A1762T/G1764A Mutant by a SimpleProbe PCR Using a Wild-Type-Selective PCR Blocker and a Primer-Blocker-Probe Partial-Overlap Approach ▿

PubMed Central

Nie, Hui; Evans, Alison A.; London, W. Thomas; Block, Timothy M.; Ren, Xiangdong David

2011-01-01

Hepatitis B virus (HBV) carrying the A1762T/G1764A double mutation in the basal core promoter (BCP) region is associated with HBe antigen seroconversion and increased risk of liver cirrhosis and hepatocellular carcinoma (HCC). Quantification of the mutant viruses may help in predicting the risk of HCC. However, the viral genome tends to have nucleotide polymorphism, which makes it difficult to design hybridization-based assays including real-time PCR. Ultrasensitive quantification of the mutant viruses at the early developmental stage is even more challenging, as the mutant is masked by excessive amounts of the wild-type (WT) viruses. In this study, we developed a selective inhibitory PCR (siPCR) using a locked nucleic acid-based PCR blocker to selectively inhibit the amplification of the WT viral DNA but not the mutant DNA. At the end of siPCR, the proportion of the mutant could be increased by about 10,000-fold, making the mutant more readily detectable by downstream applications such as real-time PCR and DNA sequencing. We also describe a primer-probe partial overlap approach which significantly simplified the melting curve patterns and minimized the influence of viral genome polymorphism on assay accuracy. Analysis of 62 patient samples showed a complete match of the melting curve patterns with the sequencing results. More than 97% of HBV BCP sequences in the GenBank database can be correctly identified by the melting curve analysis. The combination of siPCR and the SimpleProbe real-time PCR enabled mutant quantification in the presence of a 100,000-fold excess of the WT DNA. PMID:21562108

A 3D MR-acquisition scheme for nonrigid bulk motion correction in simultaneous PET-MR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolbitsch, Christoph, E-mail: christoph.1.kolbitsch@kcl.ac.uk; Prieto, Claudia; Schaeffter, Tobias

Purpose: Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET-MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracermore » uptake quantification. A 3D MR-acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET-MR data. Methods: A respiratory navigated three dimensional (3D) MR-acquisition with Radial Phase Encoding (RPE) is used to obtain T1- and T2-weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters. Results: Six respiratory gated 3D data sets with T1- and T2-weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than 10% with the proposed motion compensation approach. Conclusions: A MR acquisition scheme which yields both high resolution 3D anatomical data and highly accurate nonrigid motion information without an increase in scan time is presented. The proposed method leads to a strong improvement in both MR and PET image quality and ensures an accurate assessment of tracer uptake.« less

MR-assisted PET motion correction in simultaneous PET/MRI studies of dementia subjects.

PubMed

Chen, Kevin T; Salcedo, Stephanie; Chonde, Daniel B; Izquierdo-Garcia, David; Levine, Michael A; Price, Julie C; Dickerson, Bradford C; Catana, Ciprian

2018-03-08

Subject motion in positron emission tomography (PET) studies leads to image blurring and artifacts; simultaneously acquired magnetic resonance imaging (MRI) data provides a means for motion correction (MC) in integrated PET/MRI scanners. To assess the effect of realistic head motion and MR-based MC on static [ 18 F]-fluorodeoxyglucose (FDG) PET images in dementia patients. Observational study. Thirty dementia subjects were recruited. 3T hybrid PET/MR scanner where EPI-based and T 1 -weighted sequences were acquired simultaneously with the PET data. Head motion parameters estimated from high temporal resolution MR volumes were used for PET MC. The MR-based MC method was compared to PET frame-based MC methods in which motion parameters were estimated by coregistering 5-minute frames before and after accounting for the attenuation-emission mismatch. The relative changes in standardized uptake value ratios (SUVRs) between the PET volumes processed with the various MC methods, without MC, and the PET volumes with simulated motion were compared in relevant brain regions. The absolute value of the regional SUVR relative change was assessed with pairwise paired t-tests testing at the P = 0.05 level, comparing the values obtained through different MR-based MC processing methods as well as across different motion groups. The intraregion voxelwise variability of regional SUVRs obtained through different MR-based MC processing methods was also assessed with pairwise paired t-tests testing at the P = 0.05 level. MC had a greater impact on PET data quantification in subjects with larger amplitude motion (higher than 18% in the medial orbitofrontal cortex) and greater changes were generally observed for the MR-based MC method compared to the frame-based methods. Furthermore, a mean relative change of ∼4% was observed after MC even at the group level, suggesting the importance of routinely applying this correction. The intraregion voxelwise variability of regional SUVRs was also decreased using MR-based MC. All comparisons were significant at the P = 0.05 level. Incorporating temporally correlated MR data to account for intraframe motion has a positive impact on the FDG PET image quality and data quantification in dementia patients. 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Multicenter evaluation of stress-first myocardial perfusion image triage by nuclear technologists and automated quantification

PubMed Central

Chaudhry, Waseem; Hussain, Nasir; Ahlberg, Alan W.; Croft, Lori B.; Fernandez, Antonio B.; Parker, Mathew W.; Swales, Heather H.; Slomka, Piotr J.; Henzlova, Milena J.; Duvall, W. Lane

2016-01-01

Background A stress-first myocardial perfusion imaging (MPI) protocol saves time, is cost effective, and decreases radiation exposure. A limitation of this protocol is the requirement for physician review of the stress images to determine the need for rest images. This hurdle could be eliminated if an experienced technologist and/or automated computer quantification could make this determination. Methods Images from consecutive patients who were undergoing a stress-first MPI with attenuation correction at two tertiary care medical centers were prospectively reviewed independently by a technologist and cardiologist blinded to clinical and stress test data. Their decision on the need for rest imaging along with automated computer quantification of perfusion results was compared with the clinical reference standard of an assessment of perfusion images by a board-certified nuclear cardiologist that included clinical and stress test data. Results A total of 250 patients (mean age 61 years and 55% female) who underwent a stress-first MPI were studied. According to the clinical reference standard, 42 (16.8%) and 208 (83.2%) stress-first images were interpreted as “needing” and “not needing” rest images, respectively. The technologists correctly classified 229 (91.6%) stress-first images as either “needing” (n = 28) or “not needing” (n = 201) rest images. Their sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 66.7%, 96.6%, 80.0%, and 93.5%, respectively. An automated stress TPD score ≥1.2 was associated with optimal sensitivity and specificity and correctly classified 179 (71.6%) stress-first images as either “needing” (n = 31) or “not needing” (n = 148) rest images. Its sensitivity, specificity, PPV, and NPV were 73.8%, 71.2%, 34.1%, and 93.1%, respectively. In a model whereby the computer or technologist could correct for the other's incorrect classification, 242 (96.8%) stress-first images were correctly classified. The composite sensitivity, specificity, PPV, and NPV were 83.3%, 99.5%, 97.2%, and 96.7%, respectively. Conclusion Technologists and automated quantification software had a high degree of agreement with the clinical reference standard for determining the need for rest images in a stress-first imaging protocol. Utilizing an experienced technologist and automated systems to screen stress-first images could expand the use of stress-first MPI to sites where the cardiologist is not immediately available for interpretation. PMID:26566774

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates.

PubMed

Tuerk, Andreas; Wiktorin, Gregor; Güler, Serhat

2017-05-01

Accuracy of transcript quantification with RNA-Seq is negatively affected by positional fragment bias. This article introduces Mix2 (rd. "mixquare"), a transcript quantification method which uses a mixture of probability distributions to model and thereby neutralize the effects of positional fragment bias. The parameters of Mix2 are trained by Expectation Maximization resulting in simultaneous transcript abundance and bias estimates. We compare Mix2 to Cufflinks, RSEM, eXpress and PennSeq; state-of-the-art quantification methods implementing some form of bias correction. On four synthetic biases we show that the accuracy of Mix2 overall exceeds the accuracy of the other methods and that its bias estimates converge to the correct solution. We further evaluate Mix2 on real RNA-Seq data from the Microarray and Sequencing Quality Control (MAQC, SEQC) Consortia. On MAQC data, Mix2 achieves improved correlation to qPCR measurements with a relative increase in R2 between 4% and 50%. Mix2 also yields repeatable concentration estimates across technical replicates with a relative increase in R2 between 8% and 47% and reduced standard deviation across the full concentration range. We further observe more accurate detection of differential expression with a relative increase in true positives between 74% and 378% for 5% false positives. In addition, Mix2 reveals 5 dominant biases in MAQC data deviating from the common assumption of a uniform fragment distribution. On SEQC data, Mix2 yields higher consistency between measured and predicted concentration ratios. A relative error of 20% or less is obtained for 51% of transcripts by Mix2, 40% of transcripts by Cufflinks and RSEM and 30% by eXpress. Titration order consistency is correct for 47% of transcripts for Mix2, 41% for Cufflinks and RSEM and 34% for eXpress. We, further, observe improved repeatability across laboratory sites with a relative increase in R2 between 8% and 44% and reduced standard deviation.

Transcript Quantification of Genes Involved in Steviol Glycoside Biosynthesis in Stevia rebaudiana Bertoni by Real-Time Polymerase Chain Reaction (RT-PCR).

PubMed

Modi, Arpan; Kumar, Nitish; Narayanan, Subhash

2016-01-01

Stevia (Stevia rebaudiana Bertoni) is a medicinal plant having sweet, diterpenoid glycosides known as steviol glycosides which are 200-300 times sweeter than sucrose (0.4 % solution). They are synthesized mainly in the leaves via plastid localized 2-C-methyl-D-erythrose-4-phosphate pathway (MEP pathway). Fifteen genes are involved in the formation of these glycosides. In the present protocol, a method for the quantification of transcripts of these genes is shown. The work involves RNA extraction and cDNA preparation, and therefore, procedures for the confirmation of DNA-free cDNA preparation have also been illustrated. Moreover, details of plant treatments are not mentioned as this protocol may apply to relative gene expression profile in any medicinal plant with any treatment. The treatments are numbered as T0 (Control), T1, T2, T3, and T4.

Vascular input function correction of inflow enhancement for improved pharmacokinetic modeling of liver DCE-MRI.

PubMed

Ning, Jia; Schubert, Tilman; Johnson, Kevin M; Roldán-Alzate, Alejandro; Chen, Huijun; Yuan, Chun; Reeder, Scott B

2018-06-01

To propose a simple method to correct vascular input function (VIF) due to inflow effects and to test whether the proposed method can provide more accurate VIFs for improved pharmacokinetic modeling. A spoiled gradient echo sequence-based inflow quantification and contrast agent concentration correction method was proposed. Simulations were conducted to illustrate improvement in the accuracy of VIF estimation and pharmacokinetic fitting. Animal studies with dynamic contrast-enhanced MR scans were conducted before, 1 week after, and 2 weeks after portal vein embolization (PVE) was performed in the left portal circulation of pigs. The proposed method was applied to correct the VIFs for model fitting. Pharmacokinetic parameters fitted using corrected and uncorrected VIFs were compared between different lobes and visits. Simulation results demonstrated that the proposed method can improve accuracy of VIF estimation and pharmacokinetic fitting. In animal study results, pharmacokinetic fitting using corrected VIFs demonstrated changes in perfusion consistent with changes expected after PVE, whereas the perfusion estimates derived by uncorrected VIFs showed no significant changes. The proposed correction method improves accuracy of VIFs and therefore provides more precise pharmacokinetic fitting. This method may be promising in improving the reliability of perfusion quantification. Magn Reson Med 79:3093-3102, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Toward computer-aided emphysema quantification on ultralow-dose CT: reproducibility of ventrodorsal gravity effect measurement and correction

NASA Astrophysics Data System (ADS)

Wiemker, Rafael; Opfer, Roland; Bülow, Thomas; Rogalla, Patrik; Steinberg, Amnon; Dharaiya, Ekta; Subramanyan, Krishna

2007-03-01

Computer aided quantification of emphysema in high resolution CT data is based on identifying low attenuation areas below clinically determined Hounsfield thresholds. However, the emphysema quantification is prone to error since a gravity effect can influence the mean attenuation of healthy lung parenchyma up to +/- 50 HU between ventral and dorsal lung areas. Comparing ultra-low-dose (7 mAs) and standard-dose (70 mAs) CT scans of each patient we show that measurement of the ventrodorsal gravity effect is patient specific but reproducible. It can be measured and corrected in an unsupervised way using robust fitting of a linear function.

Quantitative ultrashort echo time imaging for assessment of massive iron overload at 1.5 and 3 Tesla.

PubMed

Krafft, Axel J; Loeffler, Ralf B; Song, Ruitian; Tipirneni-Sajja, Aaryani; McCarville, M Beth; Robson, Matthew D; Hankins, Jane S; Hillenbrand, Claudia M

2017-11-01

Hepatic iron content (HIC) quantification via transverse relaxation rate (R2*)-MRI using multi-gradient echo (mGRE) imaging is compromised toward high HIC or at higher fields due to the rapid signal decay. Our study aims at presenting an optimized 2D ultrashort echo time (UTE) sequence for R2* quantification to overcome these limitations. Two-dimensional UTE imaging was realized via half-pulse excitation and radial center-out sampling. The sequence includes chemically selective saturation pulses to reduce streaking artifacts from subcutaneous fat, and spatial saturation (sSAT) bands to suppress out-of-slice signals. The sequence employs interleaved multi-echo readout trains to achieve dense temporal sampling of rapid signal decays. Evaluation was done at 1.5 Tesla (T) and 3T in phantoms, and clinical applicability was demonstrated in five patients with biopsy-confirmed massively high HIC levels (>25 mg Fe/g dry weight liver tissue). In phantoms, the sSAT pulses were found to remove out-of-slice contamination, and R2* results were in excellent agreement to reference mGRE R2* results (slope of linear regression: 1.02/1.00 for 1.5/3T). UTE-based R2* quantification in patients with massive iron overload proved successful at both field strengths and was consistent with biopsy HIC values. The UTE sequence provides a means to measure R2* in patients with massive iron overload, both at 1.5T and 3T. Magn Reson Med 78:1839-1851, 2017. © 2017 Wiley Periodicals, Inc. © 2017 International Society for Magnetic Resonance in Medicine.

MR fingerprinting for rapid quantification of myocardial T1 , T2 , and proton spin density.

PubMed

Hamilton, Jesse I; Jiang, Yun; Chen, Yong; Ma, Dan; Lo, Wei-Ching; Griswold, Mark; Seiberlich, Nicole

2017-04-01

To introduce a two-dimensional MR fingerprinting (MRF) technique for quantification of T 1 , T 2 , and M 0 in myocardium. An electrocardiograph-triggered MRF method is introduced for mapping myocardial T 1 , T 2 , and M 0 during a single breath-hold in as short as four heartbeats. The pulse sequence uses variable flip angles, repetition times, inversion recovery times, and T 2 preparation dephasing times. A dictionary of possible signal evolutions is simulated for each scan that incorporates the subject's unique variations in heart rate. Aspects of the sequence design were explored in simulations, and the accuracy and precision of cardiac MRF were assessed in a phantom study. In vivo imaging was performed at 3 Tesla in 11 volunteers to generate native parametric maps. T 1 and T 2 measurements from the proposed cardiac MRF sequence correlated well with standard spin echo measurements in the phantom study (R 2  > 0.99). A Bland-Altman analysis revealed good agreement for myocardial T 1 measurements between MRF and MOLLI (bias 1 ms, 95% limits of agreement -72 to 72 ms) and T 2 measurements between MRF and T 2 -prepared balanced steady-state free precession (bias, -2.6 ms; 95% limits of agreement, -8.5 to 3.3 ms). MRF can provide quantitative single slice T 1 , T 2 , and M 0 maps in the heart within a single breath-hold. Magn Reson Med 77:1446-1458, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Validation of a DIXON-based fat quantification technique for the measurement of visceral fat using a CT-based reference standard.

PubMed

Heckman, Katherine M; Otemuyiwa, Bamidele; Chenevert, Thomas L; Malyarenko, Dariya; Derstine, Brian A; Wang, Stewart C; Davenport, Matthew S

2018-06-27

The purpose of the study is to determine whether a novel semi-automated DIXON-based fat quantification algorithm can reliably quantify visceral fat using a CT-based reference standard. This was an IRB-approved retrospective cohort study of 27 subjects who underwent abdominopelvic CT within 7 days of proton density fat fraction (PDFF) mapping on a 1.5T MRI. Cross-sectional visceral fat area per slice (cm 2 ) was measured in blinded fashion in each modality at intervertebral disc levels from T12 to L4. CT estimates were obtained using a previously published semi-automated computational image processing system that sums pixels with attenuation - 205 to - 51 HU. MR estimates were obtained using two novel semi-automated DIXON-based fat quantification algorithms that measure visceral fat area by spatially regularizing non-uniform fat-only signal intensity or de-speckling PDFF 2D images and summing pixels with PDFF ≥ 50%. Pearson's correlations and Bland-Altman analyses were performed. Visceral fat area per slice ranged from 9.2 to 429.8 cm 2 for MR and from 1.6 to 405.5 cm 2 for CT. There was a strong correlation between CT and MR methods in measured visceral fat area across all studied vertebral body levels (r = 0.97; n = 101 observations); the least (r = 0.93) correlation was at T12. Bland-Altman analysis revealed a bias of 31.7 cm 2 (95% CI [- 27.1]-90.4 cm 2 ), indicating modestly higher visceral fat assessed by MR. MR- and CT-based visceral fat quantification are highly correlated and have good cross-modality reliability, indicating that visceral fat quantification by either method can yield a stable and reliable biomarker.

Assessment of MR-based R2* and quantitative susceptibility mapping for the quantification of liver iron concentration in a mouse model at 7T.

PubMed

Simchick, Gregory; Liu, Zhi; Nagy, Tamas; Xiong, May; Zhao, Qun

2018-03-25

To assess the feasibility of quantifying liver iron concentration (LIC) using R2* and quantitative susceptibility mapping (QSM) at a high field strength of 7 Tesla (T). Five different concentrations of Fe-dextran were injected into 12 mice to produce various degrees of liver iron overload. After mice were sacrificed, blood and liver samples were harvested. Ferritin enzyme-linked immunosorbent assay (ELISA) and inductively coupled plasma mass spectrometry were performed to quantify serum ferritin concentration and LIC. Multiecho gradient echo MRI was conducted to estimate R2* and the magnetic susceptibility of each liver sample through complex nonlinear least squares fitting and a morphology enabled dipole inversion method, respectively. Average estimates of serum ferritin concentration, LIC, R2*, and susceptibility all show good linear correlations with injected Fe-dextran concentration; however, the standard deviations in the estimates of R2* and susceptibility increase with injected Fe-dextran concentration. Both R2* and susceptibility measurements also show good linear correlations with LIC (R 2  = 0.78 and R 2  = 0.91, respectively), and a susceptibility-to-LIC conversion factor of 0.829 ppm/(mg/g wet) is derived. The feasibility of quantifying LIC using MR-based  R2* and QSM at a high field strength of 7T is demonstrated. Susceptibility quantification, which is an intrinsic property of tissues and benefits from being field-strength independent, is more robust than R2* quantification in this ex vivo study. A susceptibility-to-LIC conversion factor is presented that agrees relatively well with previously published QSM derived results obtained at 1.5T and 3T. © 2018 International Society for Magnetic Resonance in Medicine.

Evaluation of the potential use of hybrid LC-MS/MS for active drug quantification applying the 'free analyte QC concept'.

PubMed

Jordan, Gregor; Onami, Ichio; Heinrich, Julia; Staack, Roland F

2017-11-01

Assessment of active drug exposure of biologics may be crucial for drug development. Typically, ligand-binding assay methods are used to provide free/active drug concentrations. To what extent hybrid LC-MS/MS procedures enable correct 'active' drug quantification is currently under consideration. Experimental & results: The relevance of appropriate extraction condition was evaluated by a hybrid target capture immuno-affinity LC-MS/MS method using total and free/active quality controls (QCs). The rapid extraction (10 min) provided correct results, whereas overnight incubation resulted in significant overestimation of the free/active drug (monclonal antibody) concentration. Conventional total QCs were inappropriate to determine optimal method conditions in contrast to free/active QCs. The 'free/active analyte QC concept' enables development of appropriate extraction conditions for correct active drug quantification by hybrid LC-MS/MS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoff, M; Rane-Levandovsky, S; Andre, J

Purpose: Traditional arterial spin labeling (ASL) acquisitions with echo planar imaging (EPI) readouts suffer from image distortion due to susceptibility effects, compromising ASL’s ability to accurately quantify cerebral blood flow (CBF) and assess disease-specific patterns associated with CBF abnormalities. Phase labeling for additional coordinate encoding (PLACE) can remove image distortion; our goal is to apply PLACE to improve the quantitative accuracy of ASL CBF in humans. Methods: Four subjects were imaged on a 3T Philips Ingenia scanner using a 16-channel receive coil with a 21/21/10cm (frequency/phase/slice direction) field-of-view. An ASL sequence with a pseudo-continuous ASL (pCASL) labeling scheme was employedmore » to acquire thirty dynamics of single-shot EPI data, with control and label datasets for all dynamics, and PLACE gradients applied on odd dynamics. Parameters included a post-labeling delay = 2s, label duration = 1.8s, flip angle = 90°, TR/TE = 5000/23.5ms, and 2.9/2.9/5.0mm (frequency/phase/slice direction) voxel size. “M0” EPI-reference images and T1-weighted spin-echo images with 0.8/1.0/3.3mm (frequency/phase/slice directions) voxel size were also acquired. Complex conjugate image products of pCASL odd and even dynamics were formed, a linear phase ramp applied, and data expanded and smoothed. Data phase was extracted to map control, label, and M0 magnitude image pixels to their undistorted locations, and images were rebinned to original size. All images were corrected for motion artifacts in FSL 5.0. pCASL images were registered to M0 images, and control and label images were subtracted to compute quantitative CBF maps. Results: pCASL image and CBF map distortions were removed by PLACE in all subjects. Corrected images conformed well to the anatomical T1-weighted reference image, and deviations in corrected CBF maps were evident. Conclusion: Eliminating pCASL distortion with PLACE can improve CBF quantification accuracy using minimal pulse sequence modifications and no additional scan time, improving ASL’s clinical applicability.« less

Bladder cancer staging in CT urography: effect of stage labels on statistical modeling of a decision support system

NASA Astrophysics Data System (ADS)

Gandikota, Dhanuj; Hadjiiski, Lubomir; Cha, Kenny H.; Chan, Heang-Ping; Caoili, Elaine M.; Cohan, Richard H.; Weizer, Alon; Alva, Ajjai; Paramagul, Chintana; Wei, Jun; Zhou, Chuan

2018-02-01

In bladder cancer, stage T2 is an important threshold in the decision of administering neoadjuvant chemotherapy. Our long-term goal is to develop a quantitative computerized decision support system (CDSS-S) to aid clinicians in accurate staging. In this study, we examined the effect of stage labels of the training samples on modeling such a system. We used a data set of 84 bladder cancers imaged with CT Urography (CTU). At clinical staging prior to treatment, 43 lesions were staged as below stage T2 and 41 were stage T2 or above. After cystectomy and pathological staging that is considered the gold standard, 10 of the lesions were upstaged to stage T2 or above. After correcting the stage labels, 33 lesions were below stage T2, and 51 were stage T2 or above. For the CDSS-S, the lesions were segmented using our AI-CALS method and radiomic features were extracted. We trained a linear discriminant analysis (LDA) classifier with leave-one-case-out cross validation to distinguish between bladder lesions of stage T2 or above and those below stage T2. The CDSS-S was trained and tested with the corrected post-cystectomy labels, and as a comparison, CDSS-S was also trained with understaged pre-treatment labels and tested on lesions with corrected labels. The test AUC for the CDSS-S trained with corrected labels was 0.89 +/- 0.04. For the CDSS-S trained with understaged pre-treatment labels and tested on the lesions with corrected labels, the test AUC was 0.86 +/- 0.04. The likelihood of stage T2 or above for 9 out of the 10 understaged lesions was correctly increased for the CDSS-S trained with corrected labels. The CDSS-S is sensitive to the accuracy of stage labeling. The CDSS-S trained with correct labels shows promise in prediction of the bladder cancer stage.

Quantitative analysis of hepatic iron in patients suspected of coexisting iron overload and steatosis using multi-echo single-voxel magnetic resonance spectroscopy: Comparison with fat-saturated multi-echo gradient echo sequence.

PubMed

Lin, Huimin; Fu, Caixia; Kannengiesser, Stephan; Cheng, Shu; Shen, Jun; Dong, Haipeng; Yan, Fuhua

2018-03-07

The coexistence of hepatic iron and fat is common in patients with hyperferritinemia, which plays an interactive and aggressive role in the progression of diseases (fibrosis, cirrhosis, and hepatocellular carcinomas). To evaluate a modified high-speed T 2 -corrected multi-echo, single voxel spectroscopy sequence (HISTOV) for liver iron concentration (LIC) quantification in patients with hyperferritinemia, with simultaneous fat fraction (FF) estimation. Retrospective cohort study. Thirty-eight patients with hyperferritinemia were enrolled. HISTOV, a fat-saturated multi-echo gradient echo (GRE) sequence, and a spin echo sequence (FerriScan) were performed at 1.5T. R 2 of the water signal and FF were calculated with HISTOV, and R2* values were derived from the GRE sequence, with R 2 and LIC from FerriScan serving as the references. Linear regression, correlation analyses, receiver operating characteristic analyses, and Bland-Altman analyses were conducted. Abnormal hepatic iron load was detected in 32/38 patients, of whom 10/32 had coexisting steatosis. Strong correlation was found between R2* and FerriScan-LIC (R 2 = 0.861), and between HISTOV-R 2_ water and FerriScan-R 2 (R 2  = 0.889). Furthermore, HISTOV-R 2_ water was not correlated with HISTOV-FF. The area under the curve (AUC) for HISTOV-R 2_ water was 0.974, 0.971, and 1, corresponding to clinical FerriScan-LIC thresholds of 1.8, 3.2, and 7.0 mg/g dw, respectively. No significant difference in the AUC was found between HISTOV-R 2_ water and R2* at any of the LIC thresholds, with P-values of 0.42, 0.37, and 1, respectively. HISTOV-LIC showed excellent agreement with FerriScan-LIC, with a mean bias of 0.00 ± 1.18 mg/g dw, whereas the mean bias between GRE-LIC and FerriScan-LIC was 0.53 ± 1.49 mg/g dw. HISTOV is useful for the quantification and grading of liver iron overload in patients with hyperferritinemia, particularly in cases with coexisting steatosis. HISTOV-LIC showed no systematic bias compared with FerriScan-LIC, making it a promising alternative for iron quantification. 3 Technical Efficacy Stage 2 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Comparison of NIR chemical imaging with conventional NIR, Raman and ATR-IR spectroscopy for quantification of furosemide crystal polymorphs in ternary powder mixtures.

PubMed

Schönbichler, S A; Bittner, L K H; Weiss, A K H; Griesser, U J; Pallua, J D; Huck, C W

2013-08-01

The aim of this study was to evaluate the ability of near-infrared chemical imaging (NIR-CI), near-infrared (NIR), Raman and attenuated-total-reflectance infrared (ATR-IR) spectroscopy to quantify three polymorphic forms (I, II, III) of furosemide in ternary powder mixtures. For this purpose, partial least-squares (PLS) regression models were developed, and different data preprocessing algorithms such as normalization, standard normal variate (SNV), multiplicative scatter correction (MSC) and 1st to 3rd derivatives were applied to reduce the influence of systematic disturbances. The performance of the methods was evaluated by comparison of the standard error of cross-validation (SECV), R(2), and the ratio performance deviation (RPD). Limits of detection (LOD) and limits of quantification (LOQ) of all methods were determined. For NIR-CI, a SECVcorr-spec and a SECVsingle-pixel corrected were calculated to assess the loss of accuracy by taking advantage of the spatial information. NIR-CI showed a SECVcorr-spec (SECVsingle-pixel corrected) of 2.82% (3.71%), 3.49% (4.65%), and 4.10% (5.06%) for form I, II, III. NIR had a SECV of 2.98%, 3.62%, and 2.75%, and Raman reached 3.25%, 3.08%, and 3.18%. The SECV of the ATR-IR models were 7.46%, 7.18%, and 12.08%. This study proves that NIR-CI, NIR, and Raman are well suited to quantify forms I-III of furosemide in ternary mixtures. Because of the pressure-dependent conversion of form II to form I, ATR-IR was found to be less appropriate for an accurate quantification of the mixtures. In this study, the capability of NIR-CI for the quantification of polymorphic ternary mixtures was compared with conventional spectroscopic techniques for the first time. For this purpose, a new way of spectra selection was chosen, and two kinds of SECVs were calculated to achieve a better comparability of NIR-CI to NIR, Raman, and ATR-IR. Copyright © 2013 Elsevier B.V. All rights reserved.

77 FR 9844 - Allocation and Apportionment of Interest Expense; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-21

... [Corrected] 0 Par. 2. Section 1.861-9T is amended by revising paragraph (l) to read as follows: Sec. 1.861-9T... applicability date of paragraphs (e)(2), (e)(3), and (h)(4) expires on January 13, 2015. Sec. 1.861-11T [Corrected] 0 Par. 3. Section 1.861-11T is amended by revising paragraph (i) to read as follows: Sec. 1.861...

Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR

NASA Astrophysics Data System (ADS)

Mérida, Inés; Reilhac, Anthonin; Redouté, Jérôme; Heckemann, Rolf A.; Costes, Nicolas; Hammers, Alexander

2017-04-01

In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to  +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the attenuation maps. This work demonstrates that inaccuracies in attenuation maps can induce bias in dynamic brain PET studies. Multi-atlas attenuation correction with MaxProb enables quantification on hybrid PET-MR scanners, eschewing the need for CT.

Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR.

PubMed

Mérida, Inés; Reilhac, Anthonin; Redouté, Jérôme; Heckemann, Rolf A; Costes, Nicolas; Hammers, Alexander

2017-04-07

In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [ 18 F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [ 18 F]MPPF. A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BP ND ). On static [ 18 F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [ 18 F]MPPF, most regional errors on BP ND ranged from -1 to  +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the attenuation maps. This work demonstrates that inaccuracies in attenuation maps can induce bias in dynamic brain PET studies. Multi-atlas attenuation correction with MaxProb enables quantification on hybrid PET-MR scanners, eschewing the need for CT.

Absolute cerebral blood flow quantification with pulsed arterial spin labeling during hyperoxia corrected with the simultaneous measurement of the longitudinal relaxation time of arterial blood.

PubMed

Pilkinton, David T; Hiraki, Teruyuki; Detre, John A; Greenberg, Joel H; Reddy, Ravinder

2012-06-01

Quantitative arterial spin labeling (ASL) estimates of cerebral blood flow (CBF) during oxygen inhalation are important in several contexts, including functional experiments calibrated with hyperoxia and studies investigating the effect of hyperoxia on regional CBF. However, ASL measurements of CBF during hyperoxia are confounded by the reduction in the longitudinal relaxation time of arterial blood (T(1a) ) from paramagnetic molecular oxygen dissolved in blood plasma. The aim of this study is to accurately quantify the effect of arbitrary levels of hyperoxia on T(1a) and correct ASL measurements of CBF during hyperoxia on a per-subject basis. To mitigate artifacts, including the inflow of fresh spins, partial voluming, pulsatility, and motion, a pulsed ASL approach was implemented for in vivo measurements of T(1a) in the rat brain at 3 Tesla. After accounting for the effect of deoxyhemoglobin dilution, the relaxivity of oxygen on blood was found to closely match phantom measurements. The results of this study suggest that the measured ASL signal changes are dominated by reductions in T(1a) for brief hyperoxic inhalation epochs, while the physiologic effects of oxygen on the vasculature account for most of the measured reduction in CBF for longer hyperoxic exposures. Copyright © 2011 Wiley-Liss, Inc.

Quantification of γ-aminobutyric acid (GABA) in 1 H MRS volumes composed heterogeneously of grey and white matter.

PubMed

Mikkelsen, Mark; Singh, Krish D; Brealy, Jennifer A; Linden, David E J; Evans, C John

2016-11-01

The quantification of γ-aminobutyric acid (GABA) concentration using localised MRS suffers from partial volume effects related to differences in the intrinsic concentration of GABA in grey (GM) and white (WM) matter. These differences can be represented as a ratio between intrinsic GABA in GM and WM: r M . Individual differences in GM tissue volume can therefore potentially drive apparent concentration differences. Here, a quantification method that corrects for these effects is formulated and empirically validated. Quantification using tissue water as an internal concentration reference has been described previously. Partial volume effects attributed to r M can be accounted for by incorporating into this established method an additional multiplicative correction factor based on measured or literature values of r M weighted by the proportion of GM and WM within tissue-segmented MRS volumes. Simulations were performed to test the sensitivity of this correction using different assumptions of r M taken from previous studies. The tissue correction method was then validated by applying it to an independent dataset of in vivo GABA measurements using an empirically measured value of r M . It was shown that incorrect assumptions of r M can lead to overcorrection and inflation of GABA concentration measurements quantified in volumes composed predominantly of WM. For the independent dataset, GABA concentration was linearly related to GM tissue volume when only the water signal was corrected for partial volume effects. Performing a full correction that additionally accounts for partial volume effects ascribed to r M successfully removed this dependence. With an appropriate assumption of the ratio of intrinsic GABA concentration in GM and WM, GABA measurements can be corrected for partial volume effects, potentially leading to a reduction in between-participant variance, increased power in statistical tests and better discriminability of true effects. Copyright © 2016 John Wiley & Sons, Ltd.

Patient motion effects on the quantification of regional myocardial blood flow with dynamic PET imaging.

PubMed

Hunter, Chad R R N; Klein, Ran; Beanlands, Rob S; deKemp, Robert A

2016-04-01

Patient motion is a common problem during dynamic positron emission tomography (PET) scans for quantification of myocardial blood flow (MBF). The purpose of this study was to quantify the prevalence of body motion in a clinical setting and evaluate with realistic phantoms the effects of motion on blood flow quantification, including CT attenuation correction (CTAC) artifacts that result from PET-CT misalignment. A cohort of 236 sequential patients was analyzed for patient motion under resting and peak stress conditions by two independent observers. The presence of motion, affected time-frames, and direction of motion was recorded; discrepancy between observers was resolved by consensus review. Based on these results, patient body motion effects on MBF quantification were characterized using the digital NURBS-based cardiac-torso phantom, with characteristic time activity curves (TACs) assigned to the heart wall (myocardium) and blood regions. Simulated projection data were corrected for attenuation and reconstructed using filtered back-projection. All simulations were performed without noise added, and a single CT image was used for attenuation correction and aligned to the early- or late-frame PET images. In the patient cohort, mild motion of 0.5 ± 0.1 cm occurred in 24% and moderate motion of 1.0 ± 0.3 cm occurred in 38% of patients. Motion in the superior/inferior direction accounted for 45% of all detected motion, with 30% in the superior direction. Anterior/posterior motion was predominant (29%) in the posterior direction. Left/right motion occurred in 24% of cases, with similar proportions in the left and right directions. Computer simulation studies indicated that errors in MBF can approach 500% for scans with severe patient motion (up to 2 cm). The largest errors occurred when the heart wall was shifted left toward the adjacent lung region, resulting in a severe undercorrection for attenuation of the heart wall. Simulations also indicated that the magnitude of MBF errors resulting from motion in the superior/inferior and anterior/posterior directions was similar (up to 250%). Body motion effects were more detrimental for higher resolution PET imaging (2 vs 10 mm full-width at half-maximum), and for motion occurring during the mid-to-late time-frames. Motion correction of the reconstructed dynamic image series resulted in significant reduction in MBF errors, but did not account for the residual PET-CTAC misalignment artifacts. MBF bias was reduced further using global partial-volume correction, and using dynamic alignment of the PET projection data to the CT scan for accurate attenuation correction during image reconstruction. Patient body motion can produce MBF estimation errors up to 500%. To reduce these errors, new motion correction algorithms must be effective in identifying motion in the left/right direction, and in the mid-to-late time-frames, since these conditions produce the largest errors in MBF, particularly for high resolution PET imaging. Ideally, motion correction should be done before or during image reconstruction to eliminate PET-CTAC misalignment artifacts.

Reference-tissue correction of T2-weighted signal intensity for prostate cancer detection

NASA Astrophysics Data System (ADS)

Peng, Yahui; Jiang, Yulei; Oto, Aytekin

2014-03-01

The purpose of this study was to investigate whether correction with respect to reference tissue of T2-weighted MRimage signal intensity (SI) improves its effectiveness for classification of regions of interest (ROIs) as prostate cancer (PCa) or normal prostatic tissue. Two image datasets collected retrospectively were used in this study: 71 cases acquired with GE scanners (dataset A), and 59 cases acquired with Philips scanners (dataset B). Through a consensus histology- MR correlation review, 175 PCa and 108 normal-tissue ROIs were identified and drawn manually. Reference-tissue ROIs were selected in each case from the levator ani muscle, urinary bladder, and pubic bone. T2-weighted image SI was corrected as the ratio of the average T2-weighted image SI within an ROI to that of a reference-tissue ROI. Area under the receiver operating characteristic curve (AUC) was used to evaluate the effectiveness of T2-weighted image SIs for differentiation of PCa from normal-tissue ROIs. AUC (+/- standard error) for uncorrected T2-weighted image SIs was 0.78+/-0.04 (datasets A) and 0.65+/-0.05 (datasets B). AUC for corrected T2-weighted image SIs with respect to muscle, bladder, and bone reference was 0.77+/-0.04 (p=1.0), 0.77+/-0.04 (p=1.0), and 0.75+/-0.04 (p=0.8), respectively, for dataset A; and 0.81+/-0.04 (p=0.002), 0.78+/-0.04 (p<0.001), and 0.79+/-0.04 (p<0.001), respectively, for dataset B. Correction in reference to the levator ani muscle yielded the most consistent results between GE and Phillips images. Correction of T2-weighted image SI in reference to three types of extra-prostatic tissue can improve its effectiveness for differentiation of PCa from normal-tissue ROIs, and correction in reference to the levator ani muscle produces consistent T2-weighted image SIs between GE and Phillips MR images.

Effect of gauge-field interaction on fermion transport in two dimensions: Hartree conductivity correction and dephasing

NASA Astrophysics Data System (ADS)

Ludwig, T.; Gornyi, I. V.; Mirlin, A. D.; Wölfle, P.

2008-06-01

We consider the quantum corrections to the conductivity of fermions interacting via a Chern Simons gauge field and concentrate on the Hartree-type contributions. The first-order Hartree approximation is only valid in the limit of weak coupling λ≪g-1/2 to the gauge field ( g≫1 is the dimensionless conductance) and results in an antilocalizing conductivity correction ˜λ2gln2T . In the case of strong coupling, an infinite summation of higher-order terms is necessary, which includes both the virtual (renormalization of the frequency) and real (dephasing) processes. At intermediate temperatures, T0≪T≪gT0 , where T0˜1/g2τ and τ is the elastic scattering time, the T dependence of the conductivity is determined by the Hartree correction, δσH(T)-δσH(gT0)∝g1/2-(T/T0)1/2[1+ln(gT0/T)1/2] , so that σ(T) increases with lowering T . At low temperatures, T≪T0 , the temperature-dependent part of the Hartree correction assumes a logarithmic form with a coefficient of order unity, δσH∝ln(1/T) . As a result, the negative exchange contribution δσex∝-lngln(1/T) becomes dominant, which yields localization in the limit of T→0 . We further discuss dephasing at strong coupling and show that the dephasing rates are of the order of T , owing to the interplay of inelastic scattering and renormalization. On the other hand, the dephasing length is anomalously short, Lφ≪LT , where LT is the thermal length. For the case of composite fermions with long-range Coulomb interaction, the gauge-field propagator is less singular. The resulting Hartree correction has the usual sign and temperature dependence, δσH∝lngln(1/T) , and for realistic g is overcompensated by the negative exchange contribution due to the gauge-boson and scalar parts of the interaction. In this case, the dephasing length Lφ is of the order of LT for not too low temperatures and exceeds LT for T≲gT0 .

T1- and T2*-dominant extravasation correction in DSC-MRI: Part I—theoretical considerations and implications for assessment of tumor hemodynamic properties

PubMed Central

Bjornerud, Atle; Sorensen, A Gregory; Mouridsen, Kim; Emblem, Kyrre E

2011-01-01

We present a novel contrast agent (CA) extravasation-correction method based on analysis of the tissue residue function for assessment of multiple hemodynamic parameters. The method enables semiquantitative determination of the transfer constant and can be used to distinguish between T1- and T2*-dominant extravasation effects, while being insensitive to variations in tissue mean transit time (MTT). Results in 101 patients with confirmed glioma suggest that leakage-corrected absolute cerebral blood volume (CBV) values obtained with the proposed method provide improved overall survival prediction compared with normalized CBV values combined with an established leakage-correction method. Using a standard gradient-echo echo-planar imaging sequence, ∼60% and 10% of tumors with detectable CA extravasation mainly exhibited T1- and T2*-dominant leakage effects, respectively. The remaining 30% of leaky tumors had mixed T1- and T2*-dominant effects. Using an MTT-sensitive correction method, our results show that CBV is underestimated when tumor MTT is significantly longer than MTT in the reference tissue. Furthermore, results from our simulations suggest that the relative contribution of T1- versus T2*-dominant extravasation effects is strongly dependent on the effective transverse relaxivity in the extravascular space and may thus be a potential marker for cellular integrity and tissue structure. PMID:21505483

The Safe Correction Angle of Osteotomy at T12 and L1 for Ankylosing Spondylitis Kyphosis: Patients With 2-level Osteotomy.

PubMed

Liu, Chao; Yu, Wen; Zheng, Guoquan; Guo, Yue; Song, Kai; Tang, Xiangyu; Wang, Zheng; Wang, Yan; Zhang, Yonggang

2017-08-01

This is a retrospective clinical study. To investigate the correction angle and safety of the spinal osteotomy at the T12 or L1 vertebra. Monosegment subtraction osteotomy cannot effectively correct severe kyphosis in ankylosing spondylitis (AS), generally 2-level spinal osteotomy was taken for achieving expected correction. According to literature, the T12 or L1 were usually taken as the upper spinal osteotomy vertebra. Because of the canalis vertebralis at the T12 and L1 were spinal cord and medullary cone, so the spinal osteotomy at the T12 or L1 vertebra were more dangerous than at lower level. The correction angle and safety of the spinal osteotomy at the T12 or L1 vertebra have not yet been reported. From July 2009 to 2014, 33 patients in our department with severe AS kyphosis underwent 2-level pedicle subtraction osteotomy were studied. Preoperative and postoperative relevant parameters and complications were recorded. The upper spinal osteotomy was taken at the T12 vertebra for 10 patients. The upper spinal osteotomy was taken at the L1 vertebra for 23 patients. The mean amount of correction of T12 and L1 was 26.230 and 27.952 degrees, respectively. All patients could walk with orthophoria and lie horizontally postoperatively. No deadly vascular and neurological lesion occurred. Performing pedicle subtraction osteotomy at T12 and L1 can safely achieve a mean correction of 26.230 and 27.952 degrees, respectively. Two-level osteotomy was safely and advocated for correcting severe AS kyphosis. Level III.

Combining image-derived and venous input functions enables quantification of serotonin-1A receptors with [carbonyl-11C]WAY-100635 independent of arterial sampling.

PubMed

Hahn, Andreas; Nics, Lukas; Baldinger, Pia; Ungersböck, Johanna; Dolliner, Peter; Frey, Richard; Birkfellner, Wolfgang; Mitterhauser, Markus; Wadsak, Wolfgang; Karanikas, Georgios; Kasper, Siegfried; Lanzenberger, Rupert

2012-08-01

image- derived input functions (IDIFs) represent a promising technique for a simpler and less invasive quantification of PET studies as compared to arterial cannulation. However, a number of limitations complicate the routine use of IDIFs in clinical research protocols and the full substitution of manual arterial samples by venous ones has hardly been evaluated. This study aims for a direct validation of IDIFs and venous data for the quantification of serotonin-1A receptor binding (5-HT(1A)) with [carbonyl-(11)C]WAY-100635 before and after hormone treatment. Fifteen PET measurements with arterial and venous blood sampling were obtained from 10 healthy women, 8 scans before and 7 after eight weeks of hormone replacement therapy. Image-derived input functions were derived automatically from cerebral blood vessels, corrected for partial volume effects and combined with venous manual samples from 10 min onward (IDIF+VIF). Corrections for plasma/whole-blood ratio and metabolites were done separately with arterial and venous samples. 5-HT(1A) receptor quantification was achieved with arterial input functions (AIF) and IDIF+VIF using a two-tissue compartment model. Comparison between arterial and venous manual blood samples yielded excellent reproducibility. Variability (VAR) was less than 10% for whole-blood activity (p>0.4) and below 2% for plasma to whole-blood ratios (p>0.4). Variability was slightly higher for parent fractions (VARmax=24% at 5 min, p<0.05 and VAR<13% after 20 min, p>0.1) but still within previously reported values. IDIFs after partial volume correction had peak values comparable to AIFs (mean difference Δ=-7.6 ± 16.9 kBq/ml, p>0.1), whereas AIFs exhibited a delay (Δ=4 ± 6.4s, p<0.05) and higher peak width (Δ=15.9 ± 5.2s, p<0.001). Linear regression analysis showed strong agreement for 5-HT(1A) binding as obtained with AIF and IDIF+VIF at baseline (R(2)=0.95), after treatment (R(2)=0.93) and when pooling all scans (R(2)=0.93), with slopes and intercepts in the range of 0.97 to 1.07 and -0.05 to 0.16, respectively. In addition to the region of interest analysis, the approach yielded virtually identical results for voxel-wise quantification as compared to the AIF. Despite the fast metabolism of the radioligand, manual arterial blood samples can be substituted by venous ones for parent fractions and plasma to whole-blood ratios. Moreover, the combination of image-derived and venous input functions provides a reliable quantification of 5-HT(1A) receptors. This holds true for 5-HT(1A) binding estimates before and after treatment for both regions of interest-based and voxel-wise modeling. Taken together, the approach provides less invasive receptor quantification by full independence of arterial cannulation. This offers great potential for the routine use in clinical research protocols and encourages further investigation for other radioligands with different kinetic characteristics. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantitative Evaluation of 2 Scatter-Correction Techniques for 18F-FDG Brain PET/MRI in Regard to MR-Based Attenuation Correction.

PubMed

Teuho, Jarmo; Saunavaara, Virva; Tolvanen, Tuula; Tuokkola, Terhi; Karlsson, Antti; Tuisku, Jouni; Teräs, Mika

2017-10-01

In PET, corrections for photon scatter and attenuation are essential for visual and quantitative consistency. MR attenuation correction (MRAC) is generally conducted by image segmentation and assignment of discrete attenuation coefficients, which offer limited accuracy compared with CT attenuation correction. Potential inaccuracies in MRAC may affect scatter correction, because the attenuation image (μ-map) is used in single scatter simulation (SSS) to calculate the scatter estimate. We assessed the impact of MRAC to scatter correction using 2 scatter-correction techniques and 3 μ-maps for MRAC. Methods: The tail-fitted SSS (TF-SSS) and a Monte Carlo-based single scatter simulation (MC-SSS) algorithm implementations on the Philips Ingenuity TF PET/MR were used with 1 CT-based and 2 MR-based μ-maps. Data from 7 subjects were used in the clinical evaluation, and a phantom study using an anatomic brain phantom was conducted. Scatter-correction sinograms were evaluated for each scatter correction method and μ-map. Absolute image quantification was investigated with the phantom data. Quantitative assessment of PET images was performed by volume-of-interest and ratio image analysis. Results: MRAC did not result in large differences in scatter algorithm performance, especially with TF-SSS. Scatter sinograms and scatter fractions did not reveal large differences regardless of the μ-map used. TF-SSS showed slightly higher absolute quantification. The differences in volume-of-interest analysis between TF-SSS and MC-SSS were 3% at maximum in the phantom and 4% in the patient study. Both algorithms showed excellent correlation with each other with no visual differences between PET images. MC-SSS showed a slight dependency on the μ-map used, with a difference of 2% on average and 4% at maximum when a μ-map without bone was used. Conclusion: The effect of different MR-based μ-maps on the performance of scatter correction was minimal in non-time-of-flight 18 F-FDG PET/MR brain imaging. The SSS algorithm was not affected significantly by MRAC. The performance of the MC-SSS algorithm is comparable but not superior to TF-SSS, warranting further investigations of algorithm optimization and performance with different radiotracers and time-of-flight imaging. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Quantitative (23) Na MRI of human knee cartilage using dual-tuned (1) H/(23) Na transceiver array radiofrequency coil at 7 tesla.

PubMed

Moon, Chan Hong; Kim, Jung-Hwan; Zhao, Tiejun; Bae, Kyongtae Ty

2013-11-01

To develop quantitative dual-tuned (DT) (1) H/(23) Na MRI of human knee cartilage in vivo at 7 Tesla (T). A sensitive (23) Na transceiver array RF coil was developed at 7T. B1 fields generated by the transceiver array coil were characterized and corrected in the (23) Na images. Point spread function (PSF) of the (23) Na images was measured, and the signal decrease due to partial-volume-effect was compensated in [(23) Na] quantification of knee cartilage. SNR and [(23) Na] in anterior femoral cartilage were measured from seven healthy subjects. SNR of (23) Na image with the transceiver array coil was higher than that of birdcage coil. SNR in the cartilage at 2-mm isotropic resolution was 26.80 ± 3.69 (n = 7). B1 transmission and reception fields produced by the DT coil at 7T were similar to each other. Effective full-width-half-maximum of (23) Na image was ∼5 mm at 2-mm resolution. Mean [(23) Na] was 288.13 ± 29.50 mM (n = 7) in the anterior femoral cartilage of normal subjects. We developed a new high-sensitivity (23) Na RF coil for knee MRI at 7T. Our (1) H/(23) Na MRI allowed quantitative measurement of [(23) Na] in knee cartilage by measuring PSF and cartilage thickness from (23) Na and (1) H image, respectively. Copyright © 2013 Wiley Periodicals, Inc.

Impact of motion and partial volume effects correction on PET myocardial perfusion imaging using simultaneous PET-MR

NASA Astrophysics Data System (ADS)

Petibon, Yoann; Guehl, Nicolas J.; Reese, Timothy G.; Ebrahimi, Behzad; Normandin, Marc D.; Shoup, Timothy M.; Alpert, Nathaniel M.; El Fakhri, Georges; Ouyang, Jinsong

2017-01-01

PET is an established modality for myocardial perfusion imaging (MPI) which enables quantification of absolute myocardial blood flow (MBF) using dynamic imaging and kinetic modeling. However, heart motion and partial volume effects (PVE) significantly limit the spatial resolution and quantitative accuracy of PET MPI. Simultaneous PET-MR offers a solution to the motion problem in PET by enabling MR-based motion correction of PET data. The aim of this study was to develop a motion and PVE correction methodology for PET MPI using simultaneous PET-MR, and to assess its impact on both static and dynamic PET MPI using 18F-Flurpiridaz, a novel 18F-labeled perfusion tracer. Two dynamic 18F-Flurpiridaz MPI scans were performed on healthy pigs using a PET-MR scanner. Cardiac motion was tracked using a dedicated tagged-MRI (tMR) sequence. Motion fields were estimated using non-rigid registration of tMR images and used to calculate motion-dependent attenuation maps. Motion correction of PET data was achieved by incorporating tMR-based motion fields and motion-dependent attenuation coefficients into image reconstruction. Dynamic and static PET datasets were created for each scan. Each dataset was reconstructed as (i) Ungated, (ii) Gated (end-diastolic phase), and (iii) Motion-Corrected (MoCo), each without and with point spread function (PSF) modeling for PVE correction. Myocardium-to-blood concentration ratios (MBR) and apparent wall thickness were calculated to assess image quality for static MPI. For dynamic MPI, segment- and voxel-wise MBF values were estimated by non-linear fitting of a 2-tissue compartment model to tissue time-activity-curves. MoCo and Gating respectively decreased mean apparent wall thickness by 15.1% and 14.4% and increased MBR by 20.3% and 13.6% compared to Ungated images (P  <  0.01). Combined motion and PSF correction (MoCo-PSF) yielded 30.9% (15.7%) lower wall thickness and 82.2% (20.5%) higher MBR compared to Ungated data reconstructed without (with) PSF modeling (P  <  0.01). For dynamic PET, mean MBF across all segments were comparable for MoCo (0.72  ±  0.21 ml/min/ml) and Gating (0.69  ±  0.18 ml/min/ml). Ungated data yielded significantly lower mean MBF (0.59  ±  0.16 ml/min/ml). Mean MBF for MoCo-PSF was 0.80  ±  0.22 ml/min/ml, which was 37.9% (25.0%) higher than that obtained from Ungated data without (with) PSF correction (P  <  0.01). The developed methodology holds promise to improve the image quality and sensitivity of PET MPI studies performed using PET-MR.

Improved workflow for quantification of left ventricular volumes and mass using free-breathing motion corrected cine imaging.

PubMed

Cross, Russell; Olivieri, Laura; O'Brien, Kendall; Kellman, Peter; Xue, Hui; Hansen, Michael

2016-02-25

Traditional cine imaging for cardiac functional assessment requires breath-holding, which can be problematic in some situations. Free-breathing techniques have relied on multiple averages or real-time imaging, producing images that can be spatially and/or temporally blurred. To overcome this, methods have been developed to acquire real-time images over multiple cardiac cycles, which are subsequently motion corrected and reformatted to yield a single image series displaying one cardiac cycle with high temporal and spatial resolution. Application of these algorithms has required significant additional reconstruction time. The use of distributed computing was recently proposed as a way to improve clinical workflow with such algorithms. In this study, we have deployed a distributed computing version of motion corrected re-binning reconstruction for free-breathing evaluation of cardiac function. Twenty five patients and 25 volunteers underwent cardiovascular magnetic resonance (CMR) for evaluation of left ventricular end-systolic volume (ESV), end-diastolic volume (EDV), and end-diastolic mass. Measurements using motion corrected re-binning were compared to those using breath-held SSFP and to free-breathing SSFP with multiple averages, and were performed by two independent observers. Pearson correlation coefficients and Bland-Altman plots tested agreement across techniques. Concordance correlation coefficient and Bland-Altman analysis tested inter-observer variability. Total scan plus reconstruction times were tested for significant differences using paired t-test. Measured volumes and mass obtained by motion corrected re-binning and by averaged free-breathing SSFP compared favorably to those obtained by breath-held SSFP (r = 0.9863/0.9813 for EDV, 0.9550/0.9685 for ESV, 0.9952/0.9771 for mass). Inter-observer variability was good with concordance correlation coefficients between observers across all acquisition types suggesting substantial agreement. Both motion corrected re-binning and averaged free-breathing SSFP acquisition and reconstruction times were shorter than breath-held SSFP techniques (p < 0.0001). On average, motion corrected re-binning required 3 min less than breath-held SSFP imaging, a 37% reduction in acquisition and reconstruction time. The motion corrected re-binning image reconstruction technique provides robust cardiac imaging that can be used for quantification that compares favorably to breath-held SSFP as well as multiple average free-breathing SSFP, but can be obtained in a fraction of the time when using cloud-based distributed computing reconstruction.

A New Strategy for Fast MRI-Based Quantification of the Myelin Water Fraction: Application to Brain Imaging in Infants

PubMed Central

Kulikova, Sofya; Hertz-Pannier, Lucie; Dehaene-Lambertz, Ghislaine

2016-01-01

The volume fraction of water related to myelin (fmy) is a promising MRI index for in vivo assessment of brain myelination, that can be derived from multi-component analysis of T1 and T2 relaxometry signals. However, existing quantification methods require rather long acquisition and/or post-processing times, making implementation difficult both in research studies on healthy unsedated children and in clinical examinations. The goal of this work was to propose a novel strategy for fmy quantification within acceptable acquisition and post-processing times. Our approach is based on a 3-compartment model (myelin-related water, intra/extra-cellular water and unrestricted water), and uses calibrated values of inherent relaxation times (T1c and T2c) for each compartment c. Calibration was first performed on adult relaxometry datasets (N = 3) acquired with large numbers of inversion times (TI) and echo times (TE), using an original combination of a region contraction approach and a non-negative least-square (NNLS) algorithm. This strategy was compared with voxel-wise fitting, and showed robust estimation of T1c and T2c. The accuracy of fmy calculations depending on multiple factors was investigated using simulated data. In the testing stage, our strategy enabled fast fmy mapping, based on relaxometry datasets acquired with reduced TI and TE numbers (acquisition <6 min), and analyzed with NNLS algorithm (post-processing <5min). In adults (N = 13, mean age 22.4±1.6 years), fmy maps showed variability across white matter regions, in agreement with previous studies. In healthy infants (N = 18, aged 3 to 34 weeks), asynchronous changes in fmy values were demonstrated across bundles, confirming the well-known progression of myelination. PMID:27736872

Large NLO corrections in t\\overline{t}{W}^{± } and t\\overline{t}t\\overline{t} hadroproduction from supposedly subleading EW contributions

NASA Astrophysics Data System (ADS)

Frederix, Rikkert; Pagani, Davide; Zaro, Marco

2018-02-01

We calculate the complete-NLO predictions for t\\overline{t}{W}^{± } and t\\overline{t}t\\overline{t} production in proton-proton collisions at 13 and 100 TeV. All the non-vanishing contributions of O({α}_s^i{α}^j) with i + j = 3 , 4 for t\\overline{t}{W}^{± } and i + j = 4 , 5 for t\\overline{t}t\\overline{t} are evaluated without any approximation. For t\\overline{t}{W}^{± } we find that, due to the presence of tW → tW scattering, at 13(100) TeV the O({α}_s{α}^3) contribution is about 12(70)% of the LO, i.e., it is larger than the so-called NLO EW corrections (the O({α}_s^2{α}^2) terms) and has opposite sign. In the case of t\\overline{t}t\\overline{t} production, large contributions from electroweak tt → tt scattering are already present at LO in the O({α}_s^3α ) and O({α}_s^2{α}^2) terms. For the same reason we find that both NLO terms of O({α}_s^4α ) , i.e., the NLO EW corrections, and O({α}_s^3{α}^2) are large (±15% of the LO) and their relative contributions strongly depend on the values of the renormalisation and factorisation scales. However, large accidental cancellations are present (away from the threshold region) between these two contributions. Moreover, the NLO corrections strongly depend on the kinematics and are particularly large at the threshold, where even the relative contribution from O({α}_s^2{α}^3) terms amounts to tens of percents.

dAcquisition setting optimization and quantitative imaging for 124I studies with the Inveon microPET-CT system.

PubMed

Anizan, Nadège; Carlier, Thomas; Hindorf, Cecilia; Barbet, Jacques; Bardiès, Manuel

2012-02-13

Noninvasive multimodality imaging is essential for preclinical evaluation of the biodistribution and pharmacokinetics of radionuclide therapy and for monitoring tumor response. Imaging with nonstandard positron-emission tomography [PET] isotopes such as 124I is promising in that context but requires accurate activity quantification. The decay scheme of 124I implies an optimization of both acquisition settings and correction processing. The PET scanner investigated in this study was the Inveon PET/CT system dedicated to small animal imaging. The noise equivalent count rate [NECR], the scatter fraction [SF], and the gamma-prompt fraction [GF] were used to determine the best acquisition parameters for mouse- and rat-sized phantoms filled with 124I. An image-quality phantom as specified by the National Electrical Manufacturers Association NU 4-2008 protocol was acquired and reconstructed with two-dimensional filtered back projection, 2D ordered-subset expectation maximization [2DOSEM], and 3DOSEM with maximum a posteriori [3DOSEM/MAP] algorithms, with and without attenuation correction, scatter correction, and gamma-prompt correction (weighted uniform distribution subtraction). Optimal energy windows were established for the rat phantom (390 to 550 keV) and the mouse phantom (400 to 590 keV) by combining the NECR, SF, and GF results. The coincidence time window had no significant impact regarding the NECR curve variation. Activity concentration of 124I measured in the uniform region of an image-quality phantom was underestimated by 9.9% for the 3DOSEM/MAP algorithm with attenuation and scatter corrections, and by 23% with the gamma-prompt correction. Attenuation, scatter, and gamma-prompt corrections decreased the residual signal in the cold insert. The optimal energy windows were chosen with the NECR, SF, and GF evaluation. Nevertheless, an image quality and an activity quantification assessment were required to establish the most suitable reconstruction algorithm and corrections for 124I small animal imaging.

Distortion correction of echo-planar diffusion-weighted images of uterine cervix.

PubMed

deSouza, Nandita M; Orton, Matthew; Downey, Kate; Morgan, Veronica A; Collins, David J; Giles, Sharon L; Payne, Geoffrey S

2016-05-01

To investigate the clinical utility of the reverse gradient algorithm in correcting distortions in diffusion-weighted images of the cervix and for increasing diagnostic performance. Forty-one patients ages 25-72 years (mean 40 ± 11 years) with suspected or early stage cervical cancer were imaged at 3T using an endovaginal coil. T2 -weighted (W) and diffusion-weighted images with right and left phase-encode gradient directions were obtained coronal to the cervix (b = 0, 100, 300, 500, 800 s mm(-2) ). Differences in angle of the endocervical canal to the x-axis between T2 W and right-gradient, left-gradient, and corrected images were measured. Uncorrected and corrected images were assessed for diagnostic performance when viewed together with T2 W images by two independent observers against subsequent histology. The angles of the endocervical canal relative to the x-axis were significantly different between the T2 W images and the right-gradient images (P = 0.007), approached significance for left-gradient images (P = 0.055), and were not significantly different after correction (P = 0.95). Corrected images enabled a definitive diagnosis in 34% (n = 14) of patients classified as equivocal on uncorrected images. Tumor volume in this subset was 0.18 ± 0.44 cm(3) (mean ± SD; sensitivity of detection 100% [8/8], specificity 50% [3/6] for an experienced observer). Correction did not improve diagnostic performance for the less-experienced observer. Distortion-corrected diffusion-weighted images improved correspondence with T2 W images and diagnostic performance in a third of cases. © 2015 The Authors Journal of Magnetic Resonance Imaging published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Corrective Action Decision Document/Closure Report for Corrective Action Unit 105: Area 2 Yucca Flat Atmospheric Test Sites, Nevada National Security Site, Nevada, Revision 0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthews, Patrick

2013-09-01

This Corrective Action Decision Document/Closure Report presents information supporting the closure of Corrective Action Unit (CAU) 105: Area 2 Yucca Flat Atmospheric Test Sites, Nevada National Security Site, Nevada. CAU 105 comprises the following five corrective action sites (CASs): -02-23-04 Atmospheric Test Site - Whitney Closure In Place -02-23-05 Atmospheric Test Site T-2A Closure In Place -02-23-06 Atmospheric Test Site T-2B Clean Closure -02-23-08 Atmospheric Test Site T-2 Closure In Place -02-23-09 Atmospheric Test Site - Turk Closure In Place The purpose of this Corrective Action Decision Document/Closure Report is to provide justification and documentation supporting the recommendation that nomore » further corrective action is needed for CAU 105 based on the implementation of the corrective actions. Corrective action investigation (CAI) activities were performed from October 22, 2012, through May 23, 2013, as set forth in the Corrective Action Investigation Plan for Corrective Action Unit 105: Area 2 Yucca Flat Atmospheric Test Sites; and in accordance with the Soils Activity Quality Assurance Plan, which establishes requirements, technical planning, and general quality practices.« less

Automated PET-only quantification of amyloid deposition with adaptive template and empirically pre-defined ROI

NASA Astrophysics Data System (ADS)

Akamatsu, G.; Ikari, Y.; Ohnishi, A.; Nishida, H.; Aita, K.; Sasaki, M.; Yamamoto, Y.; Sasaki, M.; Senda, M.

2016-08-01

Amyloid PET is useful for early and/or differential diagnosis of Alzheimer’s disease (AD). Quantification of amyloid deposition using PET has been employed to improve diagnosis and to monitor AD therapy, particularly in research. Although MRI is often used for segmentation of gray matter and for spatial normalization into standard Montreal Neurological Institute (MNI) space where region-of-interest (ROI) template is defined, 3D MRI is not always available in clinical practice. The purpose of this study was to examine the feasibility of PET-only amyloid quantification with an adaptive template and a pre-defined standard ROI template that has been empirically generated from typical cases. A total of 68 subjects who underwent brain 11C-PiB PET were examined. The 11C-PiB images were non-linearly spatially normalized to the standard MNI T1 atlas using the same transformation parameters of MRI-based normalization. The automatic-anatomical-labeling-ROI (AAL-ROI) template was applied to the PET images. All voxel values were normalized by the mean value of cerebellar cortex to generate the SUVR-scaled images. Eleven typical positive images and eight typical negative images were normalized and averaged, respectively, and were used as the positive and negative template. Positive and negative masks which consist of voxels with SUVR  ⩾1.7 were extracted from both templates. Empirical PiB-prone ROI (EPP-ROI) was generated by subtracting the negative mask from the positive mask. The 11C-PiB image of each subject was non-rigidly normalized to the positive and negative template, respectively, and the one with higher cross-correlation was adopted. The EPP-ROI was then inversely transformed to individual PET images. We evaluated differences of SUVR between standard MRI-based method and PET-only method. We additionally evaluated whether the PET-only method would correctly categorize 11C-PiB scans as positive or negative. Significant correlation was observed between the SUVRs obtained with AAL-ROI and those with EPP-ROI when MRI-based normalization was used, the latter providing higher SUVR. When EPP-ROI was used, MRI-based method and PET-only method provided almost identical SUVR. All 11C-PiB scans were correctly categorized into positive and negative using a cutoff value of 1.7 as compared to visual interpretation. The 11C-PiB SUVR were 2.30  ±  0.24 and 1.25  ±  0.11 for the positive and negative images. PET-only amyloid quantification method with adaptive templates and EPP-ROI can provide accurate, robust and simple amyloid quantification without MRI.

Issues in quantification of registered respiratory gated PET/CT in the lung.

PubMed

Cuplov, Vesna; Holman, Beverley F; McClelland, Jamie; Modat, Marc; Hutton, Brian F; Thielemans, Kris

2017-12-14

PET/CT quantification of lung tissue is limited by several difficulties: the lung density and local volume changes during respiration, the anatomical mismatch between PET and CT and the relative contributions of tissue, air and blood to the PET signal (the tissue fraction effect). Air fraction correction (AFC) has been shown to improve PET image quantification in the lungs. Methods to correct for the movement and anatomical mismatch involve respiratory gating and image registration techniques. While conventional registration methods only account for spatial mismatch, the Jacobian determinant of the deformable registration transformation field can be used to estimate local volume changes and could therefore potentially be used to correct (i.e. Jacobian Correction, JC) the PET signal for changes in concentration due to local volume changes. This work aims to investigate the relationship between variations in the lung due to respiration, specifically density, tracer concentration and local volume changes. In particular, we study the effect of AFC and JC on PET quantitation after registration of respiratory gated PET/CT patient data. Six patients suffering from lung cancer with solitary pulmonary nodules underwent [Formula: see text]F-FDG PET/cine-CT. The PET data were gated into six respiratory gates using displacement gating based on a real-time position management (RPM) signal and reconstructed with matched gated CT. The PET tracer concentration and tissue density were extracted from registered gated PET and CT images before and after corrections (AFC or JC) and compared to the values from the reference images. Before correction, we observed a linear correlation between the PET tracer concentration values and density. Across all gates and patients, the maximum relative change in PET tracer concentration before (after) AFC was found to be 16.2% (4.1%) and the maximum relative change in tissue density and PET tracer concentration before (after) JC was found to be 17.1% (5.5%) and 16.2% (6.8%) respectively. Overall our results show that both AFC or JC largely explain the observed changes in PET tracer activity over the respiratory cycle. We also speculate that a second order effect is related to change in fluid content but this needs further investigation. Consequently, either AFC or JC is recommended when combining lung PET images from different gates to reduce noise.

Issues in quantification of registered respiratory gated PET/CT in the lung

NASA Astrophysics Data System (ADS)

Cuplov, Vesna; Holman, Beverley F.; McClelland, Jamie; Modat, Marc; Hutton, Brian F.; Thielemans, Kris

2018-01-01

PET/CT quantification of lung tissue is limited by several difficulties: the lung density and local volume changes during respiration, the anatomical mismatch between PET and CT and the relative contributions of tissue, air and blood to the PET signal (the tissue fraction effect). Air fraction correction (AFC) has been shown to improve PET image quantification in the lungs. Methods to correct for the movement and anatomical mismatch involve respiratory gating and image registration techniques. While conventional registration methods only account for spatial mismatch, the Jacobian determinant of the deformable registration transformation field can be used to estimate local volume changes and could therefore potentially be used to correct (i.e. Jacobian Correction, JC) the PET signal for changes in concentration due to local volume changes. This work aims to investigate the relationship between variations in the lung due to respiration, specifically density, tracer concentration and local volume changes. In particular, we study the effect of AFC and JC on PET quantitation after registration of respiratory gated PET/CT patient data. Six patients suffering from lung cancer with solitary pulmonary nodules underwent 18 F-FDG PET/cine-CT. The PET data were gated into six respiratory gates using displacement gating based on a real-time position management (RPM) signal and reconstructed with matched gated CT. The PET tracer concentration and tissue density were extracted from registered gated PET and CT images before and after corrections (AFC or JC) and compared to the values from the reference images. Before correction, we observed a linear correlation between the PET tracer concentration values and density. Across all gates and patients, the maximum relative change in PET tracer concentration before (after) AFC was found to be 16.2% (4.1%) and the maximum relative change in tissue density and PET tracer concentration before (after) JC was found to be 17.1% (5.5%) and 16.2% (6.8%) respectively. Overall our results show that both AFC or JC largely explain the observed changes in PET tracer activity over the respiratory cycle. We also speculate that a second order effect is related to change in fluid content but this needs further investigation. Consequently, either AFC or JC is recommended when combining lung PET images from different gates to reduce noise.

Simultaneous quantification of T4, T3, rT3, 3,5-T2 and 3,3'-T2 in larval zebrafish (Danio rerio) as a model to study exposure to polychlorinated biphenyls.

PubMed

Chen, Xiaopeng; Walter, Kyla M; Miller, Galen W; Lein, Pamela J; Puschner, Birgit

2018-06-01

Environmental toxicants that interfere with thyroid hormone (TH) signaling can impact growth and development in animals and humans. Zebrafish represent a model to study chemically induced TH disruption, prompting the need for sensitive detection of THs. Simultaneous quantification of 3,3',5-triiodo-l-thyronine (T3), thyroxine (T4), 3,3',5'-triiodo-l-thyronine (rT3), 3,5-diiodo-l-thyronine (3,5-T2) and 3,3'-diiodo-l-thyronine (3,3'-T2) in zebrafish larvae was achieved by ultra-performance liquid chromatography-tandem mass spectrometry in positive ion mode. Solid-phase extraction with SampliQ cartridges and derivatization with 3 m hydrochloric acid in n-butanol reduced matrix effects. Derivatized compounds were separated on an Acquity UPLC BEH C 18 column with mobile phases consisting of 0.1% acetic acid in deionized water and 0.1% acetic acid in methanol. The limits of detection ranged from 0.5 to 0.6 pg injected on column. The method was validated by evaluating recovery (77.1-117.2%), accuracy (87.3-123.9%) and precision (0.5-12.4%) using diluted homogenized zebrafish embryos spiked with all target compounds. This method was then applied to zebrafish larvae collected after 114 h of exposure to polychlorinated biphenyls (PCBs), including PCB 28, PCB 66 and PCB 95, or the technical mixture Aroclor 1254. Exposure to PCB 28 and PCB 95 increased the T4:T3 ratio and decreased the T3:rT3 ratio, demonstrating that this method can effectively detect PCB-induced alterations in THs. Copyright © 2018 John Wiley & Sons, Ltd.

Validation and quantification of [18F]altanserin binding in the rat brain using blood input and reference tissue modeling

PubMed Central

Riss, Patrick J; Hong, Young T; Williamson, David; Caprioli, Daniele; Sitnikov, Sergey; Ferrari, Valentina; Sawiak, Steve J; Baron, Jean-Claude; Dalley, Jeffrey W; Fryer, Tim D; Aigbirhio, Franklin I

2011-01-01

The 5-hydroxytryptamine type 2a (5-HT2A) selective radiotracer [18F]altanserin has been subjected to a quantitative micro-positron emission tomography study in Lister Hooded rats. Metabolite-corrected plasma input modeling was compared with reference tissue modeling using the cerebellum as reference tissue. [18F]altanserin showed sufficient brain uptake in a distribution pattern consistent with the known distribution of 5-HT2A receptors. Full binding saturation and displacement was documented, and no significant uptake of radioactive metabolites was detected in the brain. Blood input as well as reference tissue models were equally appropriate to describe the radiotracer kinetics. [18F]altanserin is suitable for quantification of 5-HT2A receptor availability in rats. PMID:21750562

Patient motion effects on the quantification of regional myocardial blood flow with dynamic PET imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunter, Chad R. R. N.; Kemp, Robert A. de, E-mail: RAdeKemp@ottawaheart.ca; Klein, Ran

Purpose: Patient motion is a common problem during dynamic positron emission tomography (PET) scans for quantification of myocardial blood flow (MBF). The purpose of this study was to quantify the prevalence of body motion in a clinical setting and evaluate with realistic phantoms the effects of motion on blood flow quantification, including CT attenuation correction (CTAC) artifacts that result from PET–CT misalignment. Methods: A cohort of 236 sequential patients was analyzed for patient motion under resting and peak stress conditions by two independent observers. The presence of motion, affected time-frames, and direction of motion was recorded; discrepancy between observers wasmore » resolved by consensus review. Based on these results, patient body motion effects on MBF quantification were characterized using the digital NURBS-based cardiac-torso phantom, with characteristic time activity curves (TACs) assigned to the heart wall (myocardium) and blood regions. Simulated projection data were corrected for attenuation and reconstructed using filtered back-projection. All simulations were performed without noise added, and a single CT image was used for attenuation correction and aligned to the early- or late-frame PET images. Results: In the patient cohort, mild motion of 0.5 ± 0.1 cm occurred in 24% and moderate motion of 1.0 ± 0.3 cm occurred in 38% of patients. Motion in the superior/inferior direction accounted for 45% of all detected motion, with 30% in the superior direction. Anterior/posterior motion was predominant (29%) in the posterior direction. Left/right motion occurred in 24% of cases, with similar proportions in the left and right directions. Computer simulation studies indicated that errors in MBF can approach 500% for scans with severe patient motion (up to 2 cm). The largest errors occurred when the heart wall was shifted left toward the adjacent lung region, resulting in a severe undercorrection for attenuation of the heart wall. Simulations also indicated that the magnitude of MBF errors resulting from motion in the superior/inferior and anterior/posterior directions was similar (up to 250%). Body motion effects were more detrimental for higher resolution PET imaging (2 vs 10 mm full-width at half-maximum), and for motion occurring during the mid-to-late time-frames. Motion correction of the reconstructed dynamic image series resulted in significant reduction in MBF errors, but did not account for the residual PET–CTAC misalignment artifacts. MBF bias was reduced further using global partial-volume correction, and using dynamic alignment of the PET projection data to the CT scan for accurate attenuation correction during image reconstruction. Conclusions: Patient body motion can produce MBF estimation errors up to 500%. To reduce these errors, new motion correction algorithms must be effective in identifying motion in the left/right direction, and in the mid-to-late time-frames, since these conditions produce the largest errors in MBF, particularly for high resolution PET imaging. Ideally, motion correction should be done before or during image reconstruction to eliminate PET-CTAC misalignment artifacts.« less

Corrective Action Decision Document/Closure Report for Corrective Action Unit 569: Area 3 Yucca Flat Atmospheric Test Sites Nevada National Security Site, Nevada with ROTC 1, Revision 0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sloop, Christy

2013-04-01

This Corrective Action Decision Document/Closure Report presents information supporting the closure of Corrective Action Unit (CAU) 569: Area 3 Yucca Flat Atmospheric Test Sites, Nevada National Security Site, Nevada. CAU 569 comprises the following nine corrective action sites (CASs): • 03-23-09, T-3 Contamination Area • 03-23-10, T-3A Contamination Area • 03-23-11, T-3B Contamination Area • 03-23-12, T-3S Contamination Area • 03-23-13, T-3T Contamination Area • 03-23-14, T-3V Contamination Area • 03-23-15, S-3G Contamination Area • 03-23-16, S-3H Contamination Area • 03-23-21, Pike Contamination Area The purpose of this Corrective Action Decision Document/Closure Report is to provide justification and documentation supportingmore » the recommendation that no further corrective action is needed for CAU 569 based on the implementation of the corrective actions listed in Table ES-2.« less

High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

PubMed Central

Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

2017-01-01

Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P < 0.001; and 0.94 for magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

An experimental phantom study of the effect of gadolinium-based MR contrast agents on PET attenuation coefficients and PET quantification in PET-MR imaging: application to cardiac studies.

PubMed

O' Doherty, Jim; Schleyer, Paul

2017-12-01

Simultaneous cardiac perfusion studies are an increasing trend in PET-MR imaging. During dynamic PET imaging, the introduction of gadolinium-based MR contrast agents (GBCA) at high concentrations during a dual injection of GBCA and PET radiotracer may cause increased attenuation effects of the PET signal, and thus errors in quantification of PET images. We thus aimed to calculate the change in linear attenuation coefficient (LAC) of a mixture of PET radiotracer and increasing concentrations of GBCA in solution and furthermore, to investigate if this change in LAC produced a measurable effect on the image-based PET activity concentration when attenuation corrected by three different AC strategies. We performed simultaneous PET-MR imaging of a phantom in a static scenario using a fixed activity of 40 MBq [18 F]-NaF, water, and an increasing GBCA concentration from 0 to 66 mM (based on an assumed maximum possible concentration of GBCA in the left ventricle in a clinical study). This simulated a range of clinical concentrations of GBCA. We investigated two methods to calculate the LAC of the solution mixture at 511 keV: (1) a mathematical mixture rule and (2) CT imaging of each concentration step and subsequent conversion to LAC at 511 keV. This comparison showed that the ranges of LAC produced by both methods are equivalent with an increase in LAC of the mixed solution of approximately 2% over the range of 0-66 mM. We then employed three different attenuation correction methods to the PET data: (1) each PET scan at a specific millimolar concentration of GBCA corrected by its corresponding CT scan, (2) each PET scan corrected by a CT scan with no GBCA present (i.e., at 0 mM GBCA), and (3) a manually generated attenuation map, whereby all CT voxels in the phantom at 0 mM were replaced by LAC = 0.1 cm -1 . All attenuation correction methods (1-3) were accurate to the true measured activity concentration within 5%, and there were no trends in image-based activity concentrations upon increasing the GBCA concentration of the solution. The presence of high GBCA concentration (representing a worst-case scenario in dynamic cardiac studies) in solution with PET radiotracer produces a minimal effect on attenuation-corrected PET quantification.

Accurate Quantification of T Cells by Measuring Loss of Germline T-Cell Receptor Loci with Generic Single Duplex Droplet Digital PCR Assays.

PubMed

Zoutman, Willem H; Nell, Rogier J; Versluis, Mieke; van Steenderen, Debby; Lalai, Rajshri N; Out-Luiting, Jacoba J; de Lange, Mark J; Vermeer, Maarten H; Langerak, Anton W; van der Velden, Pieter A

2017-03-01

Quantifying T cells accurately in a variety of tissues of benign, inflammatory, or malignant origin can be of great importance in a variety of clinical applications. Flow cytometry and immunohistochemistry are considered to be gold-standard methods for T-cell quantification. However, these methods require fresh, frozen, or fixated cells and tissue of a certain quality. In addition, conventional and droplet digital PCR (ddPCR), whether followed by deep sequencing techniques, have been used to elucidate T-cell content by focusing on rearranged T-cell receptor (TCR) genes. These approaches typically target the whole TCR repertoire, thereby supplying additional information about TCR use. We alternatively developed and validated two novel generic single duplex ddPCR assays to quantify T cells accurately by measuring loss of specific germline TCR loci and compared them with flow cytometry-based quantification. These assays target sequences between the Dδ2 and Dδ3 genes (TRD locus) and Dβ1 and Jβ1.1 genes (TRB locus) that become deleted systematically early during lymphoid differentiation. Because these ddPCR assays require small amounts of DNA instead of freshly isolated, frozen, or fixated material, initially unanalyzable (scarce) specimens can be assayed from now on, supplying valuable information about T-cell content. Our ddPCR method provides a novel and sensitive way for quantifying T cells relatively fast, accurate, and independent of the cellular context. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Nonbinary quantification technique accounting for myocardial infarct heterogeneity: Feasibility of applying percent infarct mapping in patients.

PubMed

Mastrodicasa, Domenico; Elgavish, Gabriel A; Schoepf, U Joseph; Suranyi, Pal; van Assen, Marly; Albrecht, Moritz H; De Cecco, Carlo N; van der Geest, Rob J; Hardy, Rayphael; Mantini, Cesare; Griffith, L Parkwood; Ruzsics, Balazs; Varga-Szemes, Akos

2018-02-15

Binary threshold-based quantification techniques ignore myocardial infarct (MI) heterogeneity, yielding substantial misquantification of MI. To assess the technical feasibility of MI quantification using percent infarct mapping (PIM), a prototype nonbinary algorithm, in patients with suspected MI. Prospective cohort POPULATION: Patients (n = 171) with suspected MI referred for cardiac MRI. Inversion recovery balanced steady-state free-precession for late gadolinium enhancement (LGE) and modified Look-Locker inversion recovery (MOLLI) T 1 -mapping on a 1.5T system. Infarct volume (IV) and infarct fraction (IF) were quantified by two observers based on manual delineation, binary approaches (2-5 standard deviations [SD] and full-width at half-maximum [FWHM] thresholds) in LGE images, and by applying the PIM algorithm in T 1 and LGE images (PIM T1 ; PIM LGE ). IV and IF were analyzed using repeated measures analysis of variance (ANOVA). Agreement between the approaches was determined with Bland-Altman analysis. Interobserver agreement was assessed by intraclass correlation coefficient (ICC) analysis. MI was observed in 89 (54.9%) patients, and 185 (38%) short-axis slices. IF with 2, 3, 4, 5SDs and FWHM techniques were 15.7 ± 6.6, 13.4 ± 5.6, 11.6 ± 5.0, 10.8 ± 5.2, and 10.0 ± 5.2%, respectively. The 5SD and FWHM techniques had the best agreement with manual IF (9.9 ± 4.8%) determination (bias 1.0 and 0.2%; P = 0.1426 and P = 0.8094, respectively). The 2SD and 3SD algorithms significantly overestimated manual IF (9.9 ± 4.8%; both P < 0.0001). PIM LGE measured significantly lower IF (7.8 ± 3.7%) compared to manual values (P < 0.0001). PIM LGE , however, showed the best agreement with the PIM T1 reference (7.6 ± 3.6%, P = 0.3156). Interobserver agreement was rated good to excellent for IV (ICCs between 0.727-0.820) and fair to good for IF (0.589-0.736). The application of the PIM LGE technique for MI quantification in patients is feasible. PIM LGE , with its ability to account for voxelwise MI content, provides significantly smaller IF than any thresholding technique and shows excellent agreement with the T 1 -based reference. 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Tujin; Gao, Yuqian; Gaffrey, Matthew J.

2014-12-17

Mass spectrometry-based targeted quantification is a promising technology for site-specific quantification of posttranslational modifications (PTMs). However, a major constraint of most targeted MS approaches is the limited sensitivity for quantifying low-abundance PTMs, requiring the use of affinity reagents to enrich specific PTMs. Herein, we demonstrate the direct site-specific quantification of ERK phosphorylation isoforms (pT, pY, pTpY) and their relative stoichiometries using a highly sensitive targeted MS approach termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM). PRISM provides effective enrichment of target peptides within a given fraction from complex biological matrix with minimal sample losses, followed by selected reactionmore » monitoring (SRM) quantification. The PRISM-SRM approach enabled direct quantification of ERK phosphorylation in human mammary epithelial cells (HMEC) from as little as 25 µg tryptic peptides from whole cell lysates. Compared to immobilized metal-ion affinity chromatography, PRISM provided >10-fold improvement in signal intensities, presumably due to the better peptide recovery of PRISM for handling small size samples. This approach was applied to quantify ERK phosphorylation dynamics in HMEC treated by different doses of EGF at both the peak activation (10 min) and steady state (2 h). At 10 min, the maximal ERK activation was observed with 0.3 ng/mL dose, whereas the maximal steady state level of ERK activation at 2 h was at 3 ng/ml dose, corresponding to 1200 and 9000 occupied receptors, respectively. At 10 min, the maximally activated pTpY isoform represented ~40% of total ERK, falling to less than 10% at 2 h. The time course and dose-response profiles of individual phosphorylated ERK isoforms indicated that singly phosphorylated pT-ERK never increases significantly, while the increase of pY-ERK paralleled that of pTpY-ERK. This data supports for a processive, rather than distributed, model of ERK phosphorylation. The PRISM-SRM quantification of protein phosphorylation illustrates the potential for simultaneous quantification of multiple PTMs.« less

Quantification of the xenoestrogens 4-tert.-octylphenol and bisphenol A in water and in fish tissue based on microwave assisted extraction, solid-phase extraction and liquid chromatography-mass spectrometry.

PubMed

Pedersen, S N; Lindholst, C

1999-12-09

Extraction methods were developed for quantification of the xenoestrogens 4-tert.-octylphenol (tOP) and bisphenol A (BPA) in water and in liver and muscle tissue from the rainbow trout (Oncorhynchus mykiss). The extraction of tOP and BPA from tissue samples was carried out using microwave-assisted solvent extraction (MASE) followed by solid-phase extraction (SPE). Water samples were extracted using only SPE. For the quantification of tOP and BPA, liquid chromatography mass spectrometry (LC-MS) equipped with an atmospheric pressure chemical ionisation interface (APCI) was applied. The combined methods for tissue extraction allow the use of small sample amounts of liver or muscle (typically 1 g), low volumes of solvent (20 ml), and short extraction times (25 min). Limits of quantification of tOP in tissue samples were found to be approximately 10 ng/g in muscle and 50 ng/g in liver (both based on 1 g of fresh tissue). The corresponding values for BPA were approximately 50 ng/g in both muscle and liver tissue. In water, the limit of quantification for tOP and BPA was approximately 0.1 microg/l (based on 100 ml sample size).

13C-NMR spectra and contact time experiment for Skjervatjern fulvic and humic acids

USGS Publications Warehouse

Malcolm, R.L.

1992-01-01

The T(CP) and T(1p) time constants for Skjervatjern fulvic and humic acids were determined to be short with T(CP) values ranging from 0.14 ms to 0.53 ms and T(1p) values ranging from 3.3 ms to 5.9 ms. T(CP) or T(1p) time constants at a contact time of 1 ms are favorable for quantification of 13C-NMR spectra. Because of the short T(CP) values, correction factors for signal intensity for various regions of the 13C-NMR spectra would be necessary at contact times greater than 1.1 ms or less than 0.9 ms. T(CP) and T(1p) values have a limited non-homogeneity within Skjervatjern fulvic and humic acids. A pulse delay or repeat time of 700 ms is more than adequate for quantification of these 13C-NMR spectra. Paramagnetic effects in these humic substances are precluded due to low inorganic ash contents, low contents of Fe, Mn, and Co, and low organic free-radical contents. The observed T(CP) values suggest that all the carbon types in Skjervatjern fulvic and humic acids are fully cross-polarized before significant proton relaxation occurs. The 13C-NMR spectra for Skjervatjern fulvic acid is similar to most aquatic fulvic acids as it is predominantly aliphatic, low in aromaticity (fa1 = 24), low in phenolic content, high in carboxyl content, and has no resolution of a methoxyl peak. The 13C-NMR spectra for Skjervatjern humic acid is also similar to most other aquatic humic acids in that it is also predominantly aliphatic, high in aromaticity (fa1 = 38), moderate in phenolic content, moderate in carboxyl content, and has a clear resolution of a methoxyl carbon region. After the consideration of the necessary 13C-NMR experimental conditions, these spectra are considered to be quantitative. With careful consideration of the previously determined 13C-NMR experimental conditions, quantitative spectra can be obtained for humic substances in the future from the HUMEX site. Possible changes in humic substances due to acidification should be determined from 13C-NMR data.

In vivo metabolism and partitioning of 6-[18F]fluoro-L-meta-tyrosine in whole blood: a unified compartment model

NASA Astrophysics Data System (ADS)

Asselin, Marie-Claude; Wahl, Lindi M.; Cunningham, Vincent J.; Amano, Shigeko; Nahmias, Claude

2002-06-01

Physiological quantification of dynamic PET data requires the determination of an input function, preferably from plasma. A compartmental model relating a parent radiotracer, its radiolabelled metabolites and their exchange between plasma and erythrocytes is presented. This model allows for the time course of radioactivity measured in whole blood to be transformed into the time course of the radiotracer in plasma. The utility of this approach is illustrated with blood data collected on 30 human subjects injected with 6-[18F]fluoro-L-meta-tyrosine (FmT), a pre-synaptic dopaminergic radiotracer. A three-compartment four-parameter model is shown to yield significantly better fits to the blood data than related lower and higher order models. This model is found to be robust to measurement noise, and yet sensitive to metabolic changes induced by pretreatment with carbidopa. For FmT, the between-subject variations are shown to be small enough to warrant the use of a population-based correction;; tissue time-activity curves were simulated to verify that this correction does not significantly affect the precision and accuracy of the derived rate constants. The unified blood model can be adapted for radiotracers other than FmT as long as the blood partition ratio of the parent radiotracer differs from that of its metabolites and/or the rate at which they equilibrate between plasma and erythrocytes is different.

Slice profile and B1 corrections in 2D magnetic resonance fingerprinting.

PubMed

Ma, Dan; Coppo, Simone; Chen, Yong; McGivney, Debra F; Jiang, Yun; Pahwa, Shivani; Gulani, Vikas; Griswold, Mark A

2017-11-01

The goal of this study is to characterize and improve the accuracy of 2D magnetic resonance fingerprinting (MRF) scans in the presence of slice profile (SP) and B 1 imperfections, which are two main factors that affect quantitative results in MRF. The SP and B 1 imperfections are characterized and corrected separately. The SP effect is corrected by simulating the radiofrequency pulse in the dictionary, and the B 1 is corrected by acquiring a B 1 map using the Bloch-Siegert method before each scan. The accuracy, precision, and repeatability of the proposed method are evaluated in phantom studies. The effects of both SP and B 1 imperfections are also illustrated and corrected in the in vivo studies. The SP and B 1 corrections improve the accuracy of the T 1 and T 2 values, independent of the shape of the radiofrequency pulse. The T 1 and T 2 values obtained from different excitation patterns become more consistent after corrections, which leads to an improvement of the robustness of the MRF design. This study demonstrates that MRF is sensitive to both SP and B 1 effects, and that corrections can be made to improve the accuracy of MRF with only a 2-s increase in acquisition time. Magn Reson Med 78:1781-1789, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

The Combined Quantification and Interpretation of Multiple Quantitative Magnetic Resonance Imaging Metrics Enlightens Longitudinal Changes Compatible with Brain Repair in Relapsing-Remitting Multiple Sclerosis Patients.

PubMed

Bonnier, Guillaume; Maréchal, Benedicte; Fartaria, Mário João; Falkowskiy, Pavel; Marques, José P; Simioni, Samanta; Schluep, Myriam; Du Pasquier, Renaud; Thiran, Jean-Philippe; Krueger, Gunnar; Granziera, Cristina

2017-01-01

Quantitative and semi-quantitative MRI (qMRI) metrics provide complementary specificity and differential sensitivity to pathological brain changes compatible with brain inflammation, degeneration, and repair. Moreover, advanced magnetic resonance imaging (MRI) metrics with overlapping elements amplify the true tissue-related information and limit measurement noise. In this work, we combined multiple advanced MRI parameters to assess focal and diffuse brain changes over 2 years in a group of early-stage relapsing-remitting MS patients. Thirty relapsing-remitting MS patients with less than 5 years disease duration and nine healthy subjects underwent 3T MRI at baseline and after 2 years including T1, T2, T2* relaxometry, and magnetization transfer imaging. To assess longitudinal changes in normal-appearing (NA) tissue and lesions, we used analyses of variance and Bonferroni correction for multiple comparisons. Multivariate linear regression was used to assess the correlation between clinical outcome and multiparametric MRI changes in lesions and NA tissue. In patients, we measured a significant longitudinal decrease of mean T2 relaxation times in NA white matter ( p  = 0.005) and a decrease of T1 relaxation times in the pallidum ( p  < 0.05), which are compatible with edema reabsorption and/or iron deposition. No longitudinal changes in qMRI metrics were observed in controls. In MS lesions, we measured a decrease in T1 relaxation time ( p -value < 2.2e-16) and a significant increase in MTR ( p -value < 1e-6), suggesting repair mechanisms, such as remyelination, increased axonal density, and/or a gliosis. Last, the evolution of advanced MRI metrics-and not changes in lesions or brain volume-were correlated to motor and cognitive tests scores evolution (Adj- R 2  > 0.4, p  < 0.05). In summary, the combination of multiple advanced MRI provided evidence of changes compatible with focal and diffuse brain repair at early MS stages as suggested by histopathological studies.

Quantitative MRI for hepatic fat fraction and T2* measurement in pediatric patients with non-alcoholic fatty liver disease.

PubMed

Deng, Jie; Fishbein, Mark H; Rigsby, Cynthia K; Zhang, Gang; Schoeneman, Samantha E; Donaldson, James S

2014-11-01

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in children. The gold standard for diagnosis is liver biopsy. MRI is a non-invasive imaging method to provide quantitative measurement of hepatic fat content. The methodology is particularly appealing for the pediatric population because of its rapidity and radiation-free imaging techniques. To develop a multi-point Dixon MRI method with multi-interference models (multi-fat-peak modeling and bi-exponential T2* correction) for accurate hepatic fat fraction (FF) and T2* measurements in pediatric patients with NAFLD. A phantom study was first performed to validate the accuracy of the MRI fat fraction measurement by comparing it with the chemical fat composition of the ex-vivo pork liver-fat homogenate. The most accurate model determined from the phantom study was used for fat fraction and T2* measurements in 52 children and young adults referred from the pediatric hepatology clinic with suspected or identified NAFLD. Separate T2* values of water (T2*W) and fat (T2*F) components derived from the bi-exponential fitting were evaluated and plotted as a function of fat fraction. In ten patients undergoing liver biopsy, we compared histological analysis of liver fat fraction with MRI fat fraction. In the phantom study the 6-point Dixon with 5-fat-peak, bi-exponential T2* modeling demonstrated the best precision and accuracy in fat fraction measurements compared with other methods. This model was further calibrated with chemical fat fraction and applied in patients, where similar patterns were observed as in the phantom study that conventional 2-point and 3-point Dixon methods underestimated fat fraction compared to the calibrated 6-point 5-fat-peak bi-exponential model (P < 0.0001). With increasing fat fraction, T2*W (27.9 ± 3.5 ms) decreased, whereas T2*F (20.3 ± 5.5 ms) increased; and T2*W and T2*F became increasingly more similar when fat fraction was higher than 15-20%. Histological fat fraction measurements in ten patients were highly correlated with calibrated MRI fat fraction measurements (Pearson correlation coefficient r = 0.90 with P = 0.0004). Liver MRI using multi-point Dixon with multi-fat-peak and bi-exponential T2* modeling provided accurate fat quantification in children and young adults with non-alcoholic fatty liver disease and may be used to screen at-risk or affected individuals and to monitor disease progress noninvasively.

Effect of hydrocarbon to nuclear magnetic resonance (NMR) logging in tight sandstone reservoirs and method for hydrocarbon correction

NASA Astrophysics Data System (ADS)

Xiao, Liang; Mao, Zhi-qiang; Xie, Xiu-hong

2017-04-01

It is crucial to understand the behavior of the T2 distribution in the presence of hydrocarbon to properly interpret pore size distribution from NMR logging. The NMR T2 spectrum is associated with pore throat radius distribution under fully brine saturated. However, when the pore space occupied by hydrocarbon, the shape of NMR spectrum is changed due to the bulk relaxation of hydrocarbon. In this study, to understand the effect of hydrocarbon to NMR logging, the kerosene and transformer oil are used to simulate borehole crude oils with different viscosity. 20 core samples, which were separately drilled from conventional, medium porosity and permeability and tight sands are saturated with four conditions of irreducible water saturation, fully saturated with brine, hydrocarbon-bearing condition and residual oil saturation, and the corresponding NMR experiments are applied to acquire NMR measurements. The residual oil saturation is used to simulate field NMR logging due to the shallow investigation depth of NMR logging. The NMR spectra with these conditions are compared, the results illustrate that for core samples drilled from tight sandstone reservoirs, the shape of NMR spectra have much change once they pore space occupied by hydrocarbon. The T2 distributions are wide, and they are bimodal due to the effect of bulk relaxation of hydrocarbon, even though the NMR spectra are unimodal under fully brine saturated. The location of the first peaks are similar with those of the irreducible water, and the second peaks are close to the bulk relaxation of viscosity oils. While for core samples drilled from conventional formations, the shape of T2 spectra have little changes. The T2 distributions overlap with each other under these three conditions of fully brine saturated, hydrocarbon-bearing and residual oil. Hence, in tight sandstone reservoirs, the shape of NMR logging should be corrected. In this study, based on the lab experiments, seven T2 times of 1ms, 3ms, 10ms, 33ms, 100ms, 300ms and 1000ms are first used to separate the T2 distributions of the residual oil saturation as 8 parts, and 8 pore components percentage compositions are calculated, second, an optimal T2 cutoff is determined to cut the T2 spectra of fully brine saturated conditions into two parts, the left parts (with short T2 time) represent to the irreducible water, and they do not need to be corrected, only the shape for the right parts of the T2 spectra needed to be corrected. Third the relationships among the amplitudes corresponding to the T2 times large than the optimal T2 cut off and 8 pore components percentage compositions are established, and they are used to predict corrected T2 amplitudes from NMR logging under residual oil saturation. Finally, the amplitudes corresponding to the left parts and the estimated amplitudes are spliced as the corrected NMR amplitudes, and a corrected T2 spectrum can be obtained. The reliability of this method is verified by comparing the corrected results and the experimental measurements. This method is extended to field application, fully water saturated T2 distributions are extracted from field NMR logging, and they are used to precisely evaluate hydrocarbon-bearing formations pore structure.

Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations.

PubMed

Schryvers, D; Salje, E K H; Nishida, M; De Backer, A; Idrissi, H; Van Aert, S

2017-05-01

The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective materials. Copyright © 2017 Elsevier B.V. All rights reserved.

Comprehensive Analysis of Mandibular Residual Asymmetry after Bilateral Sagittal Split Ramus Osteotomy Correction of Menton Point Deviation

PubMed Central

Lin, Qiuping; Huang, Xiaoqiong; Xu, Yue; Yang, Xiaoping

2016-01-01

Purpose Facial asymmetry often persists even after mandibular deviation corrected by the bilateral sagittal split ramus osteotomy (BSSRO) operation, since the reference facial sagittal plane for the asymmetry analysis is usually set up before the mandibular menton (Me) point correction. Our aim is to develop a predictive and quantitative method to assess the true asymmetry of the mandible after a midline correction performed by a virtual BSSRO, and to verify its availability by evaluation of the post-surgical improvement. Patients and Methods A retrospective cohort study was conducted at the Hospital of Stomatology, Sun Yat-sen University (China) of patients with pure hemi-mandibular elongation (HE) from September 2010 through May 2014. Mandibular models were reconstructed from CBCT images of patients with pre-surgical orthodontic treatment. After mandibular de-rotation and midline alignment with virtual BSSRO, the elongation hemi-mandible was virtually mirrored along the facial sagittal plane. The residual asymmetry, defined as the superimposition and boolean operation of the mirrored elongation side on the normal side, was calculated, including the volumetric differences and the length of transversal and vertical asymmetry discrepancy. For more specific evaluation, both sides of the hemi-mandible were divided into the symphysis and parasymphysis (SP), mandibular body (MB), and mandibular angle (MA) regions. Other clinical variables include deviation of Me point, dental midline and molar relationship. The measurement of volumetric discrepancy between the two sides of post-surgical hemi-mandible were also calculated to verify the availability of virtual surgery. Paired t-tests were computed and the P value was set at .05. Results This study included 45 patients. The volume differences were 407.8±64.8 mm3, 2139.1±72.5 mm3, and 422.5±36.9 mm3; residual average transversal discrepancy, 1.9 mm, 1.0 mm, and 2.2 mm; average vertical discrepancy, 1.1 mm, 2.2 mm, and 2.2 mm (before virtual surgery). The post-surgical volumetric measurement showed no statistical differences between bilateral mandibular regions. Conclusions Mandibular asymmetry persists after Me point correction. A 3D quantification of mandibular residual asymmetry after Me point correction and mandible de-rotation with virtual BSSRO sets up a true reference mirror plane for comprehensive asymmetry assessment of bilateral mandibular structure, thereby providing an accurate guidance for orthognathic surgical planning. PMID:27571364

Comprehensive Analysis of Mandibular Residual Asymmetry after Bilateral Sagittal Split Ramus Osteotomy Correction of Menton Point Deviation.

PubMed

Lin, Han; Zhu, Ping; Lin, Qiuping; Huang, Xiaoqiong; Xu, Yue; Yang, Xiaoping

2016-01-01

Facial asymmetry often persists even after mandibular deviation corrected by the bilateral sagittal split ramus osteotomy (BSSRO) operation, since the reference facial sagittal plane for the asymmetry analysis is usually set up before the mandibular menton (Me) point correction. Our aim is to develop a predictive and quantitative method to assess the true asymmetry of the mandible after a midline correction performed by a virtual BSSRO, and to verify its availability by evaluation of the post-surgical improvement. A retrospective cohort study was conducted at the Hospital of Stomatology, Sun Yat-sen University (China) of patients with pure hemi-mandibular elongation (HE) from September 2010 through May 2014. Mandibular models were reconstructed from CBCT images of patients with pre-surgical orthodontic treatment. After mandibular de-rotation and midline alignment with virtual BSSRO, the elongation hemi-mandible was virtually mirrored along the facial sagittal plane. The residual asymmetry, defined as the superimposition and boolean operation of the mirrored elongation side on the normal side, was calculated, including the volumetric differences and the length of transversal and vertical asymmetry discrepancy. For more specific evaluation, both sides of the hemi-mandible were divided into the symphysis and parasymphysis (SP), mandibular body (MB), and mandibular angle (MA) regions. Other clinical variables include deviation of Me point, dental midline and molar relationship. The measurement of volumetric discrepancy between the two sides of post-surgical hemi-mandible were also calculated to verify the availability of virtual surgery. Paired t-tests were computed and the P value was set at .05. This study included 45 patients. The volume differences were 407.8±64.8 mm3, 2139.1±72.5 mm3, and 422.5±36.9 mm3; residual average transversal discrepancy, 1.9 mm, 1.0 mm, and 2.2 mm; average vertical discrepancy, 1.1 mm, 2.2 mm, and 2.2 mm (before virtual surgery). The post-surgical volumetric measurement showed no statistical differences between bilateral mandibular regions. Mandibular asymmetry persists after Me point correction. A 3D quantification of mandibular residual asymmetry after Me point correction and mandible de-rotation with virtual BSSRO sets up a true reference mirror plane for comprehensive asymmetry assessment of bilateral mandibular structure, thereby providing an accurate guidance for orthognathic surgical planning.

Fully automated system for the quantification of human osteoarthritic knee joint effusion volume using magnetic resonance imaging.

PubMed

Li, Wei; Abram, François; Pelletier, Jean-Pierre; Raynauld, Jean-Pierre; Dorais, Marc; d'Anjou, Marc-André; Martel-Pelletier, Johanne

2010-01-01

Joint effusion is frequently associated with osteoarthritis (OA) flare-up and is an important marker of therapeutic response. This study aimed at developing and validating a fully automated system based on magnetic resonance imaging (MRI) for the quantification of joint effusion volume in knee OA patients. MRI examinations consisted of two axial sequences: a T2-weighted true fast imaging with steady-state precession and a T1-weighted gradient echo. An automated joint effusion volume quantification system using MRI was developed and validated (a) with calibrated phantoms (cylinder and sphere) and effusion from knee OA patients; (b) with assessment by manual quantification; and (c) by direct aspiration. Twenty-five knee OA patients with joint effusion were included in the study. The automated joint effusion volume quantification was developed as a four stage sequencing process: bone segmentation, filtering of unrelated structures, segmentation of joint effusion, and subvoxel volume calculation. Validation experiments revealed excellent coefficients of variation with the calibrated cylinder (1.4%) and sphere (0.8%) phantoms. Comparison of the OA knee joint effusion volume assessed by the developed automated system and by manual quantification was also excellent (r = 0.98; P < 0.0001), as was the comparison with direct aspiration (r = 0.88; P = 0.0008). The newly developed fully automated MRI-based system provided precise quantification of OA knee joint effusion volume with excellent correlation with data from phantoms, a manual system, and joint aspiration. Such an automated system will be instrumental in improving the reproducibility/reliability of the evaluation of this marker in clinical application.

Simultaneous MR quantification of hepatic fat content, fatty acid composition, transverse relaxation time and magnetic susceptibility for the diagnosis of non-alcoholic steatohepatitis.

PubMed

Leporq, B; Lambert, S A; Ronot, M; Vilgrain, V; Van Beers, B E

2017-10-01

Non-alcoholic steatohepatitis (NASH) is characterized at histology by steatosis, hepatocyte ballooning and inflammatory infiltrates, with or without fibrosis. Although diamagnetic material in fibrosis and inflammation can be detected with quantitative susceptibility imaging, fatty acid composition changes in NASH relative to simple steatosis have also been reported. Therefore, our aim was to develop a single magnetic resonance (MR) acquisition and post-processing scheme for the diagnosis of steatohepatitis by the simultaneous quantification of hepatic fat content, fatty acid composition, T 2 * transverse relaxation time and magnetic susceptibility in patients with non-alcoholic fatty liver disease. MR acquisition was performed at 3.0 T using a three-dimensional, multi-echo, spoiled gradient echo sequence. Phase images were unwrapped to compute the B 0 field inhomogeneity (ΔB 0 ) map. The ΔB 0 -demodulated real part images were used for fat-water separation, T 2 * and fatty acid composition quantification. The external and internal fields were separated with the projection onto dipole field method. Susceptibility maps were obtained after dipole inversion from the internal field map with single-orientation Bayesian regularization including spatial priors. Method validation was performed in 32 patients with biopsy-proven, non-alcoholic fatty liver disease from which 12 had simple steatosis and 20 NASH. Liver fat fraction and T 2 * did not change significantly between patients with simple steatosis and NASH. In contrast, the saturated fatty acid fraction increased in patients with NASH relative to patients with simple steatosis (48 ± 2% versus 44 ± 4%; p < 0.05) and the magnetic susceptibility decreased (-0.30 ± 0.27 ppm versus 0.10 ± 0.14 ppm; p < 0.001). The area under the receiver operating characteristic curve for magnetic susceptibility as NASH marker was 0.91 (95% CI: 0.79-1.0). Simultaneous MR quantification of fat content, fatty acid composition, T 2 * and magnetic susceptibility is feasible in the liver. Our preliminary results suggest that quantitative susceptibility imaging has a high diagnostic performance for the diagnosis of NASH. Copyright © 2017 John Wiley & Sons, Ltd.

Evaluation and automatic correction of metal-implant-induced artifacts in MR-based attenuation correction in whole-body PET/MR imaging

NASA Astrophysics Data System (ADS)

Schramm, G.; Maus, J.; Hofheinz, F.; Petr, J.; Lougovski, A.; Beuthien-Baumann, B.; Platzek, I.; van den Hoff, J.

2014-06-01

The aim of this paper is to describe a new automatic method for compensation of metal-implant-induced segmentation errors in MR-based attenuation maps (MRMaps) and to evaluate the quantitative influence of those artifacts on the reconstructed PET activity concentration. The developed method uses a PET-based delineation of the patient contour to compensate metal-implant-caused signal voids in the MR scan that is segmented for PET attenuation correction. PET emission data of 13 patients with metal implants examined in a Philips Ingenuity PET/MR were reconstructed with the vendor-provided method for attenuation correction (MRMaporig, PETorig) and additionally with a method for attenuation correction (MRMapcor, PETcor) developed by our group. MRMaps produced by both methods were visually inspected for segmentation errors. The segmentation errors in MRMaporig were classified into four classes (L1 and L2 artifacts inside the lung and B1 and B2 artifacts inside the remaining body depending on the assigned attenuation coefficients). The average relative SUV differences (\\varepsilon _{rel}^{av}) between PETorig and PETcor of all regions showing wrong attenuation coefficients in MRMaporig were calculated. Additionally, relative SUVmean differences (ɛrel) of tracer accumulations in hot focal structures inside or in the vicinity of these regions were evaluated. MRMaporig showed erroneous attenuation coefficients inside the regions affected by metal artifacts and inside the patients' lung in all 13 cases. In MRMapcor, all regions with metal artifacts, except for the sternum, were filled with the soft-tissue attenuation coefficient and the lung was correctly segmented in all patients. MRMapcor only showed small residual segmentation errors in eight patients. \\varepsilon _{rel}^{av} (mean ± standard deviation) were: ( - 56 ± 3)% for B1, ( - 43 ± 4)% for B2, (21 ± 18)% for L1, (120 ± 47)% for L2 regions. ɛrel (mean ± standard deviation) of hot focal structures were: ( - 52 ± 12)% in B1, ( - 45 ± 13)% in B2, (19 ± 19)% in L1, (51 ± 31)% in L2 regions. Consequently, metal-implant-induced artifacts severely disturb MR-based attenuation correction and SUV quantification in PET/MR. The developed algorithm is able to compensate for these artifacts and improves SUV quantification accuracy distinctly.

Direct T2 Quantification of Myocardial Edema in Acute Ischemic Injury

PubMed Central

Verhaert, David; Thavendiranathan, Paaladinesh; Giri, Shivraman; Mihai, Georgeta; Rajagopalan, Sanjay; Simonetti, Orlando P.; Raman, Subha V.

2014-01-01

OBJECTIVES To evaluate the utility of rapid, quantitative T2 mapping compared with conventional T2-weighted imaging in patients presenting with various forms of acute myocardial infarction. BACKGROUND T2-weighted cardiac magnetic resonance (CMR) identifies myocardial edema before the onset of irreversible ischemic injury and has shown value in risk-stratifying patients with chest pain. Clinical acceptance of T2-weighted CMR has, however, been limited by well-known technical problems associated with existing techniques. T2 quantification has recently been shown to overcome these problems; we hypothesized that T2 measurement in infarcted myocardium versus remote regions versus zones of microvascular obstruction in acute myocardial infarction patients could help reduce uncertainty in interpretation of T2-weighted images. METHODS T2 values using a novel mapping technique were prospectively recorded in 16 myocardial segments in 27 patients admitted with acute myocardial infarction. Regional T2 values were averaged in the infarct zone and remote myocardium, both defined by a reviewer blinded to the results of T2 mapping. Myocardial T2 was also measured in a group of 21 healthy volunteers. RESULTS T2 of the infarct zone was 69 ± 6 ms compared with 56 ± 3.4 ms for remote myocardium (p < 0.0001). No difference in T2 was observed between remote myocardium and myocardium of healthy volunteers (56 ± 3.4 ms and 55.5 ± 2.3 ms, respectively, p = NS). T2 mapping allowed for the detection of edematous myocardium in 26 of 27 patients; by comparison, segmented breath-hold T2-weighted short tau inversion recovery images were negative in 7 and uninterpretable in another 2 due to breathing artifacts. Within the infarct zone, areas of microvascular obstruction were characterized by a lower T2 value (59 ± 6 ms) compared with areas with no microvascular obstruction (71.6 ± 10 ms, p < 0.0001). T2 mapping provided consistent high-quality results in patients unable to breath-hold and in those with irregular heart rhythms, in whom short tau inversion recovery often yielded inadequate imaging. CONCLUSIONS Quantitative T2 mapping reliably identifies myocardial edema without the limitations encountered by T2-weighted short tau inversion recovery imaging, and may therefore be clinically more robust in showing acute ischemic injury. PMID:21414575

TH-CD-206-01: Expectation-Maximization Algorithm-Based Tissue Mixture Quantification for Perfusion MRI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, H; Xing, L; Liang, Z

Purpose: To investigate the feasibility of estimating the tissue mixture perfusions and quantifying cerebral blood flow change in arterial spin labeled (ASL) perfusion MR images. Methods: The proposed perfusion MR image analysis framework consists of 5 steps: (1) Inhomogeneity correction was performed on the T1- and T2-weighted images, which are available for each studied perfusion MR dataset. (2) We used the publicly available FSL toolbox to strip off the non-brain structures from the T1- and T2-weighted MR images. (3) We applied a multi-spectral tissue-mixture segmentation algorithm on both T1- and T2-structural MR images to roughly estimate the fraction of eachmore » tissue type - white matter, grey matter and cerebral spinal fluid inside each image voxel. (4) The distributions of the three tissue types or tissue mixture across the structural image array are down-sampled and mapped onto the ASL voxel array via a co-registration operation. (5) The presented 4-dimensional expectation-maximization (4D-EM) algorithm takes the down-sampled three tissue type distributions on perfusion image data to generate the perfusion mean, variance and percentage images for each tissue type of interest. Results: Experimental results on three volunteer datasets demonstrated that the multi-spectral tissue-mixture segmentation algorithm was effective to initialize tissue mixtures from T1- and T2-weighted MR images. Compared with the conventional ASL image processing toolbox, the proposed 4D-EM algorithm not only generated comparable perfusion mean images, but also produced perfusion variance and percentage images, which the ASL toolbox cannot obtain. It is observed that the perfusion contribution percentages may not be the same as the corresponding tissue mixture volume fractions estimated in the structural images. Conclusion: A specific application to brain ASL images showed that the presented perfusion image analysis method is promising for detecting subtle changes in tissue perfusions, which is valuable for the early diagnosis of certain brain diseases, e.g. multiple sclerosis.« less

Patch Based Synthesis of Whole Head MR Images: Application to EPI Distortion Correction.

PubMed

Roy, Snehashis; Chou, Yi-Yu; Jog, Amod; Butman, John A; Pham, Dzung L

2016-10-01

Different magnetic resonance imaging pulse sequences are used to generate image contrasts based on physical properties of tissues, which provide different and often complementary information about them. Therefore multiple image contrasts are useful for multimodal analysis of medical images. Often, medical image processing algorithms are optimized for particular image contrasts. If a desirable contrast is unavailable, contrast synthesis (or modality synthesis) methods try to "synthesize" the unavailable constrasts from the available ones. Most of the recent image synthesis methods generate synthetic brain images, while whole head magnetic resonance (MR) images can also be useful for many applications. We propose an atlas based patch matching algorithm to synthesize T 2 -w whole head (including brain, skull, eyes etc) images from T 1 -w images for the purpose of distortion correction of diffusion weighted MR images. The geometric distortion in diffusion MR images due to in-homogeneous B 0 magnetic field are often corrected by non-linearly registering the corresponding b = 0 image with zero diffusion gradient to an undistorted T 2 -w image. We show that our synthetic T 2 -w images can be used as a template in absence of a real T 2 -w image. Our patch based method requires multiple atlases with T 1 and T 2 to be registeLowRes to a given target T 1 . Then for every patch on the target, multiple similar looking matching patches are found on the atlas T 1 images and corresponding patches on the atlas T 2 images are combined to generate a synthetic T 2 of the target. We experimented on image data obtained from 44 patients with traumatic brain injury (TBI), and showed that our synthesized T 2 images produce more accurate distortion correction than a state-of-the-art registration based image synthesis method.

Pure hydroxyapatite phantoms for the calibration of in vivo X-ray fluorescence systems of bone lead and strontium quantification.

PubMed

Da Silva, Eric; Kirkham, Brian; Heyd, Darrick V; Pejović-Milić, Ana

2013-10-01

Plaster of Paris [poP, CaSO4·(1)/(2) H2O] is the standard phantom material used for the calibration of in vivo X-ray fluorescence (IVXRF)-based systems of bone metal quantification (i.e bone strontium and lead). Calibration of IVXRF systems of bone metal quantification employs the use of a coherent normalization procedure which requires the application of a coherent correction factor (CCF) to the data, calculated as the ratio of the relativistic form factors of the phantom material and bone mineral. Various issues have been raised as to the suitability of poP for the calibration of IVXRF systems of bone metal quantification which include its chemical purity and its chemical difference from bone mineral (a calcium phosphate). This work describes the preparation of a chemically pure hydroxyapatite phantom material, of known composition and stoichiometry, proposed for the purpose of calibrating IVXRF systems of bone strontium and lead quantification as a replacement for poP. The issue with contamination by the analyte was resolved by preparing pure Ca(OH)2 by hydroxide precipitation, which was found to bring strontium and lead levels to <0.7 and <0.3 μg/g Ca, respectively. HAp phantoms were prepared from known quantities of chemically pure Ca(OH)2, CaHPO4·2H2O prepared from pure Ca(OH)2, the analyte, and a HPO4(2-) containing setting solution. The final crystal structure of the material was found to be similar to that of the bone mineral component of NIST SRM 1486 (bone meal), as determined by powder X-ray diffraction spectrometry.

Quantification of Noise Sources in EMI Surveys

DTIC Science & Technology

2012-04-09

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/ 6110 --12-9400 Quantification of Noise Sources in EMI Surveys ESTCP MR-0508 Final Guidance...NUMBER 2 . REPORT TYPE1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 6. AUTHOR(S) 8. PERFORMING ORGANIZATION REPORT NUMBER 7. PERFORMING...Barrow,‡ Jonathan T. Miller,‡ and Thomas H. Bell,‡ Naval Research Laboratory, Code 6110 4555 Overlook Avenue, SW Washington, DC 20375-5320 NRL/MR

Accuracy of Area at Risk Quantification by Cardiac Magnetic Resonance According to the Myocardial Infarction Territory.

PubMed

Fernández-Friera, Leticia; García-Ruiz, José Manuel; García-Álvarez, Ana; Fernández-Jiménez, Rodrigo; Sánchez-González, Javier; Rossello, Xavier; Gómez-Talavera, Sandra; López-Martín, Gonzalo J; Pizarro, Gonzalo; Fuster, Valentín; Ibáñez, Borja

2017-05-01

Area at risk (AAR) quantification is important to evaluate the efficacy of cardioprotective therapies. However, postinfarction AAR assessment could be influenced by the infarcted coronary territory. Our aim was to determine the accuracy of T 2 -weighted short tau triple-inversion recovery (T 2 W-STIR) cardiac magnetic resonance (CMR) imaging for accurate AAR quantification in anterior, lateral, and inferior myocardial infarctions. Acute reperfused myocardial infarction was experimentally induced in 12 pigs, with 40-minute occlusion of the left anterior descending (n = 4), left circumflex (n = 4), and right coronary arteries (n = 4). Perfusion CMR was performed during selective intracoronary gadolinium injection at the coronary occlusion site (in vivo criterion standard) and, additionally, a 7-day CMR, including T 2 W-STIR sequences, was performed. Finally, all animals were sacrificed and underwent postmortem Evans blue staining (classic criterion standard). The concordance between the CMR-based criterion standard and T 2 W-STIR to quantify AAR was high for anterior and inferior infarctions (r = 0.73; P = .001; mean error = 0.50%; limits = -12.68%-13.68% and r = 0.87; P = .001; mean error = -1.5%; limits = -8.0%-5.8%, respectively). Conversely, the correlation for the circumflex territories was poor (r = 0.21, P = .37), showing a higher mean error and wider limits of agreement. A strong correlation between pathology and the CMR-based criterion standard was observed (r = 0.84, P < .001; mean error = 0.91%; limits = -7.55%-9.37%). T 2 W-STIR CMR sequences are accurate to determine the AAR for anterior and inferior infarctions; however, their accuracy for lateral infarctions is poor. These findings may have important implications for the design and interpretation of clinical trials evaluating the effectiveness of cardioprotective therapies. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Quantification of viable bacterial starter cultures of Virgibacillus sp. and Tetragenococcus halophilus in fish sauce fermentation by real-time quantitative PCR.

PubMed

Udomsil, Natteewan; Chen, Shu; Rodtong, Sureelak; Yongsawatdigul, Jirawat

2016-08-01

Real-time quantitative polymerase chain reaction (qPCR) methods were developed for the quantification of Virgibacillus sp. SK37 and Tetragenococcus halophilus MS33, which were added as starter cultures in fish sauce fermentation. The PCR assays were coupled with propidium monoazide (PMA) treatment of samples to selectively quantify viable cells and integrated with exogenous recombinant Escherichia coli cells to control variabilities in analysis procedures. The qPCR methods showed species-specificity for both Virgibacillus halodenitrificans and T. halophilus as evaluated using 6 reference strains and 28 strains of bacteria isolated from fish sauce fermentation. The qPCR efficiencies were 101.1% for V. halodenitrificans and 90.2% for T. halophilus. The quantification limits of the assays were 10(3) CFU/mL and 10(2) CFU/mL in fish sauce samples with linear correlations over 4 Logs for V. halodenitrificans and T. halophilus, respectively. The matrix effect was not observed when evaluated using fish sauce samples fermented for 1-6 months. The developed PMA-qPCR methods were successfully applied to monitor changes of Virgibacillus sp. SK37 and T. halophilus MS33 in a mackerel fish sauce fermentation model where culture-dependent techniques failed to quantify the starter cultures. The results demonstrated the usability of the methods as practical tools for monitoring the starter cultures in fish sauce fermentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Calibration transfer of a Raman spectroscopic quantification method for the assessment of liquid detergent compositions from at-line laboratory to in-line industrial scale.

PubMed

Brouckaert, D; Uyttersprot, J-S; Broeckx, W; De Beer, T

2018-03-01

Calibration transfer or standardisation aims at creating a uniform spectral response on different spectroscopic instruments or under varying conditions, without requiring a full recalibration for each situation. In the current study, this strategy is applied to construct at-line multivariate calibration models and consequently employ them in-line in a continuous industrial production line, using the same spectrometer. Firstly, quantitative multivariate models are constructed at-line at laboratory scale for predicting the concentration of two main ingredients in hard surface cleaners. By regressing the Raman spectra of a set of small-scale calibration samples against their reference concentration values, partial least squares (PLS) models are developed to quantify the surfactant levels in the liquid detergent compositions under investigation. After evaluating the models performance with a set of independent validation samples, a univariate slope/bias correction is applied in view of transporting these at-line calibration models to an in-line manufacturing set-up. This standardisation technique allows a fast and easy transfer of the PLS regression models, by simply correcting the model predictions on the in-line set-up, without adjusting anything to the original multivariate calibration models. An extensive statistical analysis is performed in order to assess the predictive quality of the transferred regression models. Before and after transfer, the R 2 and RMSEP of both models is compared for evaluating if their magnitude is similar. T-tests are then performed to investigate whether the slope and intercept of the transferred regression line are not statistically different from 1 and 0, respectively. Furthermore, it is inspected whether no significant bias can be noted. F-tests are executed as well, for assessing the linearity of the transfer regression line and for investigating the statistical coincidence of the transfer and validation regression line. Finally, a paired t-test is performed to compare the original at-line model to the slope/bias corrected in-line model, using interval hypotheses. It is shown that the calibration models of Surfactant 1 and Surfactant 2 yield satisfactory in-line predictions after slope/bias correction. While Surfactant 1 passes seven out of eight statistical tests, the recommended validation parameters are 100% successful for Surfactant 2. It is hence concluded that the proposed strategy for transferring at-line calibration models to an in-line industrial environment via a univariate slope/bias correction of the predicted values offers a successful standardisation approach. Copyright © 2017 Elsevier B.V. All rights reserved.

MR-based attenuation correction methods for improved PET quantification in lesions within bone and susceptibility artifact regions.

PubMed

Bezrukov, Ilja; Schmidt, Holger; Mantlik, Frédéric; Schwenzer, Nina; Brendle, Cornelia; Schölkopf, Bernhard; Pichler, Bernd J

2013-10-01

Hybrid PET/MR systems have recently entered clinical practice. Thus, the accuracy of MR-based attenuation correction in simultaneously acquired data can now be investigated. We assessed the accuracy of 4 methods of MR-based attenuation correction in lesions within soft tissue, bone, and MR susceptibility artifacts: 2 segmentation-based methods (SEG1, provided by the manufacturer, and SEG2, a method with atlas-based susceptibility artifact correction); an atlas- and pattern recognition-based method (AT&PR), which also used artifact correction; and a new method combining AT&PR and SEG2 (SEG2wBONE). Attenuation maps were calculated for the PET/MR datasets of 10 patients acquired on a whole-body PET/MR system, allowing for simultaneous acquisition of PET and MR data. Eighty percent iso-contour volumes of interest were placed on lesions in soft tissue (n = 21), in bone (n = 20), near bone (n = 19), and within or near MR susceptibility artifacts (n = 9). Relative mean volume-of-interest differences were calculated with CT-based attenuation correction as a reference. For soft-tissue lesions, none of the methods revealed a significant difference in PET standardized uptake value relative to CT-based attenuation correction (SEG1, -2.6% ± 5.8%; SEG2, -1.6% ± 4.9%; AT&PR, -4.7% ± 6.5%; SEG2wBONE, 0.2% ± 5.3%). For bone lesions, underestimation of PET standardized uptake values was found for all methods, with minimized error for the atlas-based approaches (SEG1, -16.1% ± 9.7%; SEG2, -11.0% ± 6.7%; AT&PR, -6.6% ± 5.0%; SEG2wBONE, -4.7% ± 4.4%). For lesions near bone, underestimations of lower magnitude were observed (SEG1, -12.0% ± 7.4%; SEG2, -9.2% ± 6.5%; AT&PR, -4.6% ± 7.8%; SEG2wBONE, -4.2% ± 6.2%). For lesions affected by MR susceptibility artifacts, quantification errors could be reduced using the atlas-based artifact correction (SEG1, -54.0% ± 38.4%; SEG2, -15.0% ± 12.2%; AT&PR, -4.1% ± 11.2%; SEG2wBONE, 0.6% ± 11.1%). For soft-tissue lesions, none of the evaluated methods showed statistically significant errors. For bone lesions, significant underestimations of -16% and -11% occurred for methods in which bone tissue was ignored (SEG1 and SEG2). In the present attenuation correction schemes, uncorrected MR susceptibility artifacts typically result in reduced attenuation values, potentially leading to highly reduced PET standardized uptake values, rendering lesions indistinguishable from background. While AT&PR and SEG2wBONE show accurate results in both soft tissue and bone, SEG2wBONE uses a two-step approach for tissue classification, which increases the robustness of prediction and can be applied retrospectively if more precision in bone areas is needed.

Roundness variation in JPEG images affects the automated process of nuclear immunohistochemical quantification: correction with a linear regression model.

PubMed

López, Carlos; Jaén Martinez, Joaquín; Lejeune, Marylène; Escrivà, Patricia; Salvadó, Maria T; Pons, Lluis E; Alvaro, Tomás; Baucells, Jordi; García-Rojo, Marcial; Cugat, Xavier; Bosch, Ramón

2009-10-01

The volume of digital image (DI) storage continues to be an important problem in computer-assisted pathology. DI compression enables the size of files to be reduced but with the disadvantage of loss of quality. Previous results indicated that the efficiency of computer-assisted quantification of immunohistochemically stained cell nuclei may be significantly reduced when compressed DIs are used. This study attempts to show, with respect to immunohistochemically stained nuclei, which morphometric parameters may be altered by the different levels of JPEG compression, and the implications of these alterations for automated nuclear counts, and further, develops a method for correcting this discrepancy in the nuclear count. For this purpose, 47 DIs from different tissues were captured in uncompressed TIFF format and converted to 1:3, 1:23 and 1:46 compression JPEG images. Sixty-five positive objects were selected from these images, and six morphological parameters were measured and compared for each object in TIFF images and those of the different compression levels using a set of previously developed and tested macros. Roundness proved to be the only morphological parameter that was significantly affected by image compression. Factors to correct the discrepancy in the roundness estimate were derived from linear regression models for each compression level, thereby eliminating the statistically significant differences between measurements in the equivalent images. These correction factors were incorporated in the automated macros, where they reduced the nuclear quantification differences arising from image compression. Our results demonstrate that it is possible to carry out unbiased automated immunohistochemical nuclear quantification in compressed DIs with a methodology that could be easily incorporated in different systems of digital image analysis.

Accuracy of Rhenium-188 SPECT/CT activity quantification for applications in radionuclide therapy using clinical reconstruction methods.

PubMed

Esquinas, Pedro L; Uribe, Carlos F; Gonzalez, M; Rodríguez-Rodríguez, Cristina; Häfeli, Urs O; Celler, Anna

2017-07-20

The main applications of 188 Re in radionuclide therapies include trans-arterial liver radioembolization and palliation of painful bone-metastases. In order to optimize 188 Re therapies, the accurate determination of radiation dose delivered to tumors and organs at risk is required. Single photon emission computed tomography (SPECT) can be used to perform such dosimetry calculations. However, the accuracy of dosimetry estimates strongly depends on the accuracy of activity quantification in 188 Re images. In this study, we performed a series of phantom experiments aiming to investigate the accuracy of activity quantification for 188 Re SPECT using high-energy and medium-energy collimators. Objects of different shapes and sizes were scanned in Air, non-radioactive water (Cold-water) and water with activity (Hot-water). The ordered subset expectation maximization algorithm with clinically available corrections (CT-based attenuation, triple-energy window (TEW) scatter and resolution recovery was used). For high activities, the dead-time corrections were applied. The accuracy of activity quantification was evaluated using the ratio of the reconstructed activity in each object to this object's true activity. Each object's activity was determined with three segmentation methods: a 1% fixed threshold (for cold background), a 40% fixed threshold and a CT-based segmentation. Additionally, the activity recovered in the entire phantom, as well as the average activity concentration of the phantom background were compared to their true values. Finally, Monte-Carlo simulations of a commercial [Formula: see text]-camera were performed to investigate the accuracy of the TEW method. Good quantification accuracy (errors  <10%) was achieved for the entire phantom, the hot-background activity concentration and for objects in cold background segmented with a 1% threshold. However, the accuracy of activity quantification for objects segmented with 40% threshold or CT-based methods decreased (errors  >15%), mostly due to partial-volume effects. The Monte-Carlo simulations confirmed that TEW-scatter correction applied to 188 Re, although practical, yields only approximate estimates of the true scatter.

Comparison of magnetic resonance spectroscopy, proton density fat fraction and histological analysis in the quantification of liver steatosis in children and adolescents

PubMed Central

Di Martino, Michele; Pacifico, Lucia; Bezzi, Mario; Di Miscio, Rossella; Sacconi, Beatrice; Chiesa, Claudio; Catalano, Carlo

2016-01-01

AIM To establish a threshold value for liver fat content between healthy children and those with non-alcoholic fatty liver disease (NAFLD) by using magnetic resonance imaging (MRI), with liver biopsy serving as a reference standard. METHODS The study was approved by the local ethics committee, and written informed consent was obtained from all participants and their legal guardians before the study began. Twenty-seven children with NAFLD underwent liver biopsy to assess the presence of nonalcoholic steatohepatitis. The assessment of liver fat fraction was performed using MRI, with a high field magnet and 2D gradient-echo and multiple-echo T1-weighted sequence with low flip angle and single-voxel point-resolved ¹H MR-Spectroscopy (¹H-MRS), corrected for T1 and T2* decays. Receiver operating characteristic curve analysis was used to determine the best cut-off value. Lin coefficient test was used to evaluate the correlation between histology, MRS and MRI-PDFF. A Mann-Whitney U-test and multivariate analysis were performed to analyze the continuous variables. RESULTS According to MRS, the threshold value between healthy children and those with NAFLD is 6%; using MRI-PDFF, a cut-off value of 3.5% is suggested. The Lin analysis revealed a good fit between the histology and MRS as well as MRI-PDFF. CONCLUSION MRS is an accurate and precise method for detecting NAFLD in children. PMID:27818597

Detection and differentiation of early acute and following age stages of myocardial infarction with quantitative post-mortem cardiac 1.5T MR.

PubMed

Schwendener, Nicole; Jackowski, Christian; Persson, Anders; Warntjes, Marcel J; Schuster, Frederick; Riva, Fabiano; Zech, Wolf-Dieter

2017-01-01

Recently, quantitative MR sequences have started being used in post-mortem imaging. The goal of the present study was to evaluate if early acute and following age stages of myocardial infarction can be detected and discerned by quantitative 1.5T post-mortem cardiac magnetic resonance (PMCMR) based on quantitative T1, T2 and PD values. In 80 deceased individuals (25 female, 55 male), a cardiac MR quantification sequence was performed prior to cardiac dissection at autopsy in a prospective study. Focal myocardial signal alterations detected in synthetically generated MR images were MR quantified for their T1, T2 and PD values. The locations of signal alteration measurements in PMCMR were targeted at autopsy heart dissection and cardiac tissue specimens were taken for histologic examinations. Quantified signal alterations in PMCMR were correlated to their according histologic age stage of myocardial infarction. In PMCMR seventy-three focal myocardial signal alterations were detected in 49 of 80 investigated hearts. These signal alterations were diagnosed histologically as early acute (n=39), acute (n=14), subacute (n=10) and chronic (n=10) age stages of myocardial infarction. Statistical analysis revealed that based on their quantitative T1, T2 and PD values, a significant difference between all defined age groups of myocardial infarction can be determined. It can be concluded that quantitative 1.5T PMCMR quantification based on quantitative T1, T2 and PD values is feasible for characterization and differentiation of early acute and following age stages of myocardial infarction. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The impact of direct vertebral rotation (DVR) on radiographic outcome in surgical correction of idiopathic scoliosis.

PubMed

Urbanski, Wiktor; Wolanczyk, Michal J; Jurasz, Wojciech; Kulej, Miroslaw; Morasiewicz, Piotr; Dragan, Szymon Lukasz; Sasiadek, Marek; Dragan, Szymon Feliks

2017-07-01

Recent developments of spinal instruments allow to address nearly all components of idiopathic scoliosis. Direct vertebral rotation (DVR) maneuver was introduced to correct apical axial vertebral rotation. It is however still not well established how efficiently DVR affects results of scoliosis correction. The object of the study was to evaluate en bloc apical vertebral rotation (DVR) and its impact on coronal and sagittal correction of the spine in patients undergoing surgical scoliosis treatment. Thirty-six consecutive patients who underwent posterior spinal fusion with pedicle screws only constructs for idiopathic scoliosis. Fifteen patients (20 curves) were corrected by rod derotation only and 21 patients (26 curves) had both rod derotation and DVR. Curve measurements were performed on x-rays obtained before and postoperatively-coronal curves, kyphosis (T2-T12, T5-T12). Spine flexibility was assessed on prone bending x-rays. Apical axial rotation was determined on CT scans obtained intraoperatively and postoperatively. Rotation angle (RAsag) was measured according to Aaro and Dahlborn. We observed reduction of RAsag in all patients; however, in DVR group, decrease was greater, by 31.8% comparing to non-DVR group, by 8.6% (p = 0.0003). Mean coronal correction in DVR group was 68.8% and in rod derotation group without DVR 55% (p = 0.002). No significant correlation was found between degree of derotation obtained and coronal correction. In DVR group T2-T12 kyphosis has increased in 28 (65%) patients whereas in non-DVR group in 31 (69%) cases. Mean value of T2-T12 kyphosis growth was 16.7% in DVR and 22.1% in non-DVR group. These differences however did not occur statistically significant. Direct vertebral rotation (DVR) maneuver reduces significantly apical rotation of the spine, enhances ability of coronal correction, and it does not reduce thoracic kyphosis.

Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography.

PubMed

Croft, Daniel E; van Hemert, Jano; Wykoff, Charles C; Clifton, David; Verhoek, Michael; Fleming, Alan; Brown, David M

2014-01-01

Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. Copyright 2014, SLACK Incorporated.

Non-water-suppressed short-echo-time magnetic resonance spectroscopic imaging using a concentric ring k-space trajectory.

PubMed

Emir, Uzay E; Burns, Brian; Chiew, Mark; Jezzard, Peter; Thomas, M Albert

2017-07-01

Water-suppressed MRS acquisition techniques have been the standard MRS approach used in research and for clinical scanning to date. The acquisition of a non-water-suppressed MRS spectrum is used for artefact correction, reconstruction of phased-array coil data and metabolite quantification. Here, a two-scan metabolite-cycling magnetic resonance spectroscopic imaging (MRSI) scheme that does not use water suppression is demonstrated and evaluated. Specifically, the feasibility of acquiring and quantifying short-echo (T E  = 14 ms), two-dimensional stimulated echo acquisition mode (STEAM) MRSI spectra in the motor cortex is demonstrated on a 3 T MRI system. The increase in measurement time from the metabolite-cycling is counterbalanced by a time-efficient concentric ring k-space trajectory. To validate the technique, water-suppressed MRSI acquisitions were also performed for comparison. The proposed non-water-suppressed metabolite-cycling MRSI technique was tested for detection and correction of resonance frequency drifts due to subject motion and/or hardware instability, and the feasibility of high-resolution metabolic mapping over a whole brain slice was assessed. Our results show that the metabolite spectra and estimated concentrations are in agreement between non-water-suppressed and water-suppressed techniques. The achieved spectral quality, signal-to-noise ratio (SNR) > 20 and linewidth <7 Hz allowed reliable metabolic mapping of five major brain metabolites in the motor cortex with an in-plane resolution of 10 × 10 mm 2 in 8 min and with a Cramér-Rao lower bound of less than 20% using LCModel analysis. In addition, the high SNR of the water peak of the non-water-suppressed technique enabled voxel-wise single-scan frequency, phase and eddy current correction. These findings demonstrate that our non-water-suppressed metabolite-cycling MRSI technique can perform robustly on 3 T MRI systems and within a clinically feasible acquisition time. © 2017 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Does fat suppression via chemically selective saturation affect R2*-MRI for transfusional iron overload assessment? A clinical evaluation at 1.5T and 3T.

PubMed

Krafft, Axel J; Loeffler, Ralf B; Song, Ruitian; Bian, Xiao; McCarville, M Beth; Hankins, Jane S; Hillenbrand, Claudia M

2016-08-01

Fat suppression (FS) via chemically selective saturation (CHESS) eliminates fat-water oscillations in multiecho gradient echo (mGRE) R2*-MRI. However, for increasing R2* values as seen with increasing liver iron content (LIC), the water signal spectrally overlaps with the CHESS band, which may alter R2*. We investigated the effect of CHESS on R2* and developed a heuristic correction for the observed CHESS-induced R2* changes. Eighty patients [female, n = 49; male, n = 31; mean age (± standard deviation), 18.3 ± 11.7 y] with iron overload were scanned with a non-FS and a CHESS-FS mGRE sequence at 1.5T and 3T. Mean liver R2* values were evaluated using three published fitting approaches. Measured and model-corrected R2* values were compared and statistically analyzed. At 1.5T, CHESS led to a systematic R2* reduction (P < 0.001 for all fitting algorithms) especially toward higher R2*. Our model described the observed changes well and reduced the CHESS-induced R2* bias after correction (linear regression slopes: 1.032/0.927/0.981). No CHESS-induced R2* reductions were found at 3T. The CHESS-induced R2* bias at 1.5T needs to be considered when applying R2*-LIC biopsy calibrations for clinical LIC assessment, which were established without FS at 1.5T. The proposed model corrects the R2* bias and could therefore improve clinical iron overload assessment based on linear R2*-LIC calibrations. Magn Reson Med 76:591-601, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Model-independent analyses of non-Gaussianity in Planck CMB maps using Minkowski functionals

NASA Astrophysics Data System (ADS)

Buchert, Thomas; France, Martin J.; Steiner, Frank

2017-05-01

Despite the wealth of Planck results, there are difficulties in disentangling the primordial non-Gaussianity of the Cosmic Microwave Background (CMB) from the secondary and the foreground non-Gaussianity (NG). For each of these forms of NG the lack of complete data introduces model-dependences. Aiming at detecting the NGs of the CMB temperature anisotropy δ T , while paying particular attention to a model-independent quantification of NGs, our analysis is based upon statistical and morphological univariate descriptors, respectively: the probability density function P(δ T) , related to v0, the first Minkowski Functional (MF), and the two other MFs, v1 and v2. From their analytical Gaussian predictions we build the discrepancy functions {{ Δ }k} (k  =  P, 0, 1, 2) which are applied to an ensemble of 105 CMB realization maps of the Λ CDM model and to the Planck CMB maps. In our analysis we use general Hermite expansions of the {{ Δ }k} up to the 12th order, where the coefficients are explicitly given in terms of cumulants. Assuming hierarchical ordering of the cumulants, we obtain the perturbative expansions generalizing the second order expansions of Matsubara to arbitrary order in the standard deviation {σ0} for P(δ T) and v0, where the perturbative expansion coefficients are explicitly given in terms of complete Bell polynomials. The comparison of the Hermite expansions and the perturbative expansions is performed for the Λ CDM map sample and the Planck data. We confirm the weak level of non-Gaussianity (1-2)σ of the foreground corrected masked Planck 2015 maps.

Magnetic Resonance Spectroscopy: An Objective Technique for the Quantification of Prostate Cancer Pathologies

DTIC Science & Technology

2005-02-01

Holshouser BA, Burley T, Ashwal S . Predicting neuropsychologic outcome after traumatic brain injury in children . Pediatr Neurol 2003;28(2):104-114. 5...breast cancer tissue. NMR Biomed 2002;15(5):327-337. 25. Ala- Korpela M, Posio P, Mattila S , Korhonen A, Williams SR. Absolute quantification of...STATEMENT: Approved for Public Release; Distribution Unlimited The views, opinions and/or findings contained in this report are those of the author( s ) and

Improved algorithm for computerized detection and quantification of pulmonary emphysema at high-resolution computed tomography (HRCT)

NASA Astrophysics Data System (ADS)

Tylen, Ulf; Friman, Ola; Borga, Magnus; Angelhed, Jan-Erik

2001-05-01

Emphysema is characterized by destruction of lung tissue with development of small or large holes within the lung. These areas will have Hounsfield values (HU) approaching -1000. It is possible to detect and quantificate such areas using simple density mask technique. The edge enhancement reconstruction algorithm, gravity and motion of the heart and vessels during scanning causes artefacts, however. The purpose of our work was to construct an algorithm that detects such image artefacts and corrects them. The first step is to apply inverse filtering to the image removing much of the effect of the edge enhancement reconstruction algorithm. The next step implies computation of the antero-posterior density gradient caused by gravity and correction for that. Motion artefacts are in a third step corrected for by use of normalized averaging, thresholding and region growing. Twenty healthy volunteers were investigated, 10 with slight emphysema and 10 without. Using simple density mask technique it was not possible to separate persons with disease from those without. Our algorithm improved separation of the two groups considerably. Our algorithm needs further refinement, but may form a basis for further development of methods for computerized diagnosis and quantification of emphysema by HRCT.

SU-F-R-28: Correction of FCh-PET Bladder Uptake Using Virtual Sinograms and Investigation of Its Impact On the Quantification of Prostate Textural Characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laberge, S; Beauregard, J; Archambault, L

2016-06-15

Purpose: Textural biomarkers as a tool for quantifying intratumoral heterogeneity hold great promise for diagnosis and early assessment of treatment response in prostate cancer. However, spill-in counts from the bladder uptake are suspected to have an impact on the textural measurements of the prostate volume. This work proposes a correction method for the FCh-PET bladder uptake and investigates its impact on intraprostatic textural properties. Methods: Two patients with PC received pre-treatment dynamic FCh-PET scans reconstructed at four time points (interval: 2 min), for which prostate and bladder contours were obtained. Projection bins affected by bladder uptake were determined by forward-projection.more » For each time point and axial position, virtual sinograms were obtained and affected bins replaced by a weighted combination of original values and values interpolated using cubic spline from non-affected bins of the current and adjacent projection angles. The process was optimized using a genetic algorithm in terms of minimization of the root-mean-square error (RMSE) within the bladder between the corrected dynamic time point volume and a reference initial uptake volume. Finally, the impact of the bladder uptake correction on the prostate region was investigated using two standard SUV metrics (1) and three texture metrics (2): 1) SUVmax, SUVmean; 2) Contrast, Homogeneity, Coarseness. Results: Without bladder uptake correction, SUVmax and SUVmean were on average overestimated in the prostate by 0%, 0%, 33.2%, 51.2%, and 3.6%, 6.0%, 2.9%, 3.2%, for each time point respectively. Contrast varied by −9.1%, −6.7%, +40.4%, +107.7%, and Homogeneity and Coarseness by +4.5%, +1.8%, −8.8%, −14.8% and +1.0%, +0.5%, −9.5%, +0.9%. Conclusion: We proposed a method for FCh-PET bladder uptake correction and showed an impact on the quantification of the prostate signal. This method achieved a large reduction of intra-prostatic SUVmax while minimizing the impact on SUVmean. Further investigation is necessary to interpret changes in textural features. SL acknowledges partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council (Grant number: 432290).« less

Gaussian signal relaxation around spin echoes: Implications for precise reversible transverse relaxation quantification of pulmonary tissue at 1.5 and 3 Tesla.

PubMed

Zapp, Jascha; Domsch, Sebastian; Weingärtner, Sebastian; Schad, Lothar R

2017-05-01

To characterize the reversible transverse relaxation in pulmonary tissue and to study the benefit of a quadratic exponential (Gaussian) model over the commonly used linear exponential model for increased quantification precision. A point-resolved spectroscopy sequence was used for comprehensive sampling of the relaxation around spin echoes. Measurements were performed in an ex vivo tissue sample and in healthy volunteers at 1.5 Tesla (T) and 3 T. The goodness of fit using χred2 and the precision of the fitted relaxation time by means of its confidence interval were compared between the two relaxation models. The Gaussian model provides enhanced descriptions of pulmonary relaxation with lower χred2 by average factors of 4 ex vivo and 3 in volunteers. The Gaussian model indicates higher sensitivity to tissue structure alteration with increased precision of reversible transverse relaxation time measurements also by average factors of 4 ex vivo and 3 in volunteers. The mean relaxation times of the Gaussian model in volunteers are T2,G' = (1.97 ± 0.27) msec at 1.5 T and T2,G' = (0.83 ± 0.21) msec at 3 T. Pulmonary signal relaxation was found to be accurately modeled as Gaussian, providing a potential biomarker T2,G' with high sensitivity. Magn Reson Med 77:1938-1945, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Fully automated system for the quantification of human osteoarthritic knee joint effusion volume using magnetic resonance imaging

PubMed Central

2010-01-01

Introduction Joint effusion is frequently associated with osteoarthritis (OA) flare-up and is an important marker of therapeutic response. This study aimed at developing and validating a fully automated system based on magnetic resonance imaging (MRI) for the quantification of joint effusion volume in knee OA patients. Methods MRI examinations consisted of two axial sequences: a T2-weighted true fast imaging with steady-state precession and a T1-weighted gradient echo. An automated joint effusion volume quantification system using MRI was developed and validated (a) with calibrated phantoms (cylinder and sphere) and effusion from knee OA patients; (b) with assessment by manual quantification; and (c) by direct aspiration. Twenty-five knee OA patients with joint effusion were included in the study. Results The automated joint effusion volume quantification was developed as a four stage sequencing process: bone segmentation, filtering of unrelated structures, segmentation of joint effusion, and subvoxel volume calculation. Validation experiments revealed excellent coefficients of variation with the calibrated cylinder (1.4%) and sphere (0.8%) phantoms. Comparison of the OA knee joint effusion volume assessed by the developed automated system and by manual quantification was also excellent (r = 0.98; P < 0.0001), as was the comparison with direct aspiration (r = 0.88; P = 0.0008). Conclusions The newly developed fully automated MRI-based system provided precise quantification of OA knee joint effusion volume with excellent correlation with data from phantoms, a manual system, and joint aspiration. Such an automated system will be instrumental in improving the reproducibility/reliability of the evaluation of this marker in clinical application. PMID:20846392

Using RT-PCR and bDNA assays to measure non-clade B HIV-1 subtype RNA.

PubMed

Pasquier, C; Sandres, K; Salama, G; Puel, J; Izopet, J

1999-08-01

The performance of the new version of RT-PCR assay (Amplicor HIV-1 Monitor v1.5) was assessed. The quantification of non-B subtype HIV-1 plasma RNA (30A, 1C, 1D, 3E, 2F, 3G) obtained using Monitor v1.5 was compared to the former version of this assay (Monitor v1.0) and to the Quantiplex v2.0 bDNA assay. The new primers used in Monitor v1.5 were similar to the former version in both specificity and sensitivity. The new primers corrected the detection and quantification defect observed previously for HIV-1 non-B subtypes and gave slightly higher RNA concentrations than those measured using the bDNA assay (+0.39 log copies/ml).

Quantification of hepatic macrosteatosis in living, related liver donors using T1-independent, T2*-corrected chemical shift MRI.

PubMed

Joe, Eugene; Lee, Jeong Min; Kim, Kyung Won; Lee, Kyung Bun; Kim, Soo Jin; Baek, Jee Hyun; Shin, Cheong Il; Suh, Kyung Suk; Yi, Nam Joon; Han, Joon Koo; Choi, Byung Ihn

2012-11-01

To evaluate the diagnostic implications of the iterative decomposition of water and fat using echo-asymmetry and the least-squares estimation (IDEAL) technique to detect hepatic steatosis (HS) in potential liver donors using histopathology as the reference standard. Forty-nine potential liver donors (32 male, 17 female; mean age, 31.7 years) were included. All patients were imaged using the in- and out-of-phase (IOP) gradient-echo (GRE) and IDEAL techniques on a 1.5 T MR scanner. To estimate the hepatic fat fraction (FF), two reviewers performed regions-of-interest measurement in 15 areas of the liver seen on the IOP images and on the IDEAL-FF images. The magnetic resonance imaging (MRI) and pathology values of macrosteatosis were correlated using the Pearson correlation coefficient. We analyzed the diagnostic performance of IOP imaging and IDEAL for detecting HS. The results of the hepatic-FF estimated on IDEAL were well correlated with the histologic degree of macrosteatosis (γ = 0.902, P < 0.001). IDEAL showed 100% sensitivity and 91% specificity for detecting HS, and IOP imaging showed 87.5% sensitivity and 97% specificity, respectively. IDEAL is a useful tool for the preoperative diagnosis of HS in potential living liver donors; it can also help to avoid unnecessary biopsies in these patients. Copyright © 2012 Wiley Periodicals, Inc.

Multi-jet merged top-pair production including electroweak corrections

NASA Astrophysics Data System (ADS)

Gütschow, Christian; Lindert, Jonas M.; Schönherr, Marek

2018-04-01

We present theoretical predictions for the production of top-quark pairs in association with jets at the LHC including electroweak (EW) corrections. First, we present and compare differential predictions at the fixed-order level for t\\bar{t} and t\\bar{t}+ {jet} production at the LHC considering the dominant NLO EW corrections of order O(α_{s}^2 α ) and O(α_{s}^3 α ) respectively together with all additional subleading Born and one-loop contributions. The NLO EW corrections are enhanced at large energies and in particular alter the shape of the top transverse momentum distribution, whose reliable modelling is crucial for many searches for new physics at the energy frontier. Based on the fixed-order results we motivate an approximation of the EW corrections valid at the percent level, that allows us to readily incorporate the EW corrections in the MePs@Nlo framework of Sherpa combined with OpenLoops. Subsequently, we present multi-jet merged parton-level predictions for inclusive top-pair production incorporating NLO QCD + EW corrections to t\\bar{t} and t\\bar{t}+ {jet}. Finally, we compare at the particle-level against a recent 8 TeV measurement of the top transverse momentum distribution performed by ATLAS in the lepton + jet channel. We find very good agreement between the Monte Carlo prediction and the data when the EW corrections are included.

Quantification of in vivo short echo-time proton magnetic resonance spectra at 14.1 T using two different approaches of modelling the macromolecule spectrum

NASA Astrophysics Data System (ADS)

Cudalbu, C.; Mlynárik, V.; Xin, L.; Gruetter, Rolf

2009-10-01

Reliable quantification of the macromolecule signals in short echo-time 1H MRS spectra is particularly important at high magnetic fields for an accurate quantification of metabolite concentrations (the neurochemical profile) due to effectively increased spectral resolution of the macromolecule components. The purpose of the present study was to assess two approaches of quantification, which take the contribution of macromolecules into account in the quantification step. 1H spectra were acquired on a 14.1 T/26 cm horizontal scanner on five rats using the ultra-short echo-time SPECIAL (spin echo full intensity acquired localization) spectroscopy sequence. Metabolite concentrations were estimated using LCModel, combined with a simulated basis set of metabolites using published spectral parameters and either the spectrum of macromolecules measured in vivo, using an inversion recovery technique, or baseline simulated by the built-in spline function. The fitted spline function resulted in a smooth approximation of the in vivo macromolecules, but in accordance with previous studies using Subtract-QUEST could not reproduce completely all features of the in vivo spectrum of macromolecules at 14.1 T. As a consequence, the measured macromolecular 'baseline' led to a more accurate and reliable quantification at higher field strengths.

Defective aquaporin-2 trafficking in nephrogenic diabetes insipidus and correction by chemical chaperones.

PubMed Central

Tamarappoo, B K; Verkman, A S

1998-01-01

Five single-point aquaporin-2 (AQP2) mutations that cause non-X-linked nephrogenic diabetes insipidus (NDI) were characterized to establish the cellular defect and to develop therapeutic strategies. In Xenopus oocytes expressing AQP2 cRNAs, single-channel water permeabilities of mutants L22V, T126M, and A147T were similar to that of wild-type AQP2, whereas R187C and C181W were nonfunctional. In [35S]methionine pulse-chase experiments in transiently transfected CHO cells, half-times for AQP2 degradation were approximately 4 h for wild-type AQP2 and L22V, and mildly decreased for T126M (2.7 h), C181W (2.4 h), R187C (2.0 h), and A147T (1.8 h). Immunofluorescence showed three distinct AQP2-staining patterns: plasma membrane and endosomal staining (wild-type, L22V), endoplasmic reticulum (ER) staining (T126M > A147T approximately R187C), or a mixed pattern of reticular and perinuclear vesicular staining. Immunoblot of fractionated vesicles confirmed primary ER localization of T126M, R187C, and A147T. To determine if the AQP2-trafficking defect is correctable, cells were incubated with the "chemical chaperone" glycerol for 48 h. Immunoblot showed that glycerol produced a nearly complete redistribution of AQP2 (T126M, A147T, and R187C) from ER to membrane/endosome fractions. Immunofluorescence confirmed the cellular redistribution. Redistribution of AQP2 mutants was also demonstrated in transfected MDCK cells, and using the chaperones TMAO and DMSO in place of glycerol in CHO cells. Water permeability measurements indicated that functional correction was achieved. These results indicate defective mammalian cell processing of mutant AQP2 water channels in NDI, and provide evidence for pharmacological correction of the processing defect by chemical chaperones. PMID:9593782

Simultaneous quantification of hepatic MRI-PDFF and R2* in a rabbit model with nonalcoholic fatty liver disease.

PubMed

Wang, Xiaomin; Zhang, Xiaojing; Ma, Lin; Li, Shengli

2018-06-20

Quantification of hepatic fat and iron content is important for early detection and monitoring of nonalcoholic fatty liver disease (NAFLD) patients. This study evaluated quantification efficiency of hepatic proton density fat fraction (PDFF) by MRI using NAFLD rabbits. R2* was also measured to investigate whether it correlates with fat levels in NAFLD. NAFLD rabbit model was successfully established by high fat and cholesterol diet. Rabbits underwent MRI examination for fat and iron analyses, compared with liver histological findings. MR examinations were performed on a 3.0T MR system using multi-echo 3D gradient recalled echo (GRE) sequence. MRI-PDFF showed significant differences between different steatosis grades with medians of 3.72% (normal), 5.43% (mild), 9.11% (moderate) and 11.17% (severe), whereas this was not observed in R2*. Close correlation between MRI-PDFF and histological steatosis was observed (r=0.78, P=0.000). Hepatic iron deposit was not found in any rabbits. There was no correlation between R2* and either liver MRI-PDFF or histological steatosis. MR measuring MRI-PDFF and R2* simultaneously provides promising quantification of steatosis and iron. Rabbit NAFLD model confirmed accuracy of MRI-PDFF for liver fat quantification. R2* measurement and relationship between fat and iron of NAFLD liver need further experimental investigation.

Improved Strategies and Optimization of Calibration Models for Real-time PCR Absolute Quantification

EPA Science Inventory

Real-time PCR absolute quantification applications rely on the use of standard curves to make estimates of DNA target concentrations in unknown samples. Traditional absolute quantification approaches dictate that a standard curve must accompany each experimental run. However, t...

Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis

PubMed Central

Masvidal, Laia; Igreja, Susana; Ramos, Maria D; Alvarez, Antoni; de Gracia, Javier; Ramalho, Anabela; Amaral, Margarida D; Larriba, Sara; Casals, Teresa

2014-01-01

The major purpose of the present study was to quantify correctly spliced CFTR transcripts in human nasal epithelial cells from cystic fibrosis (CF) patients carrying the splicing mutations c.580-1G>T (712-1G>T) and c.2657+5G>A (2789+5G>A) and to assess the applicability of this model in CFTR therapeutic approaches. We performed the relative quantification of CFTR mRNA by reverse transcription quantitative PCR (RT-qPCR) of these splicing mutations in four groups (wild type, CF-F508del controls, CF patients and CF carriers) of individuals. In addition, in vitro assays using minigene constructs were performed to evaluate the effect of a new CF complex allele c.[2657+5G>A; 2562T>G]. Ex vivo qPCR data show that the primary consequence of both mutations at the RNA level is the skipping of their neighboring exon (6 and 16, respectively). The CFTR minigenes results mimicked the ex vivo data, as exon 16 skipping is the main aberrant transcript, and the correctly spliced transcript level was observed in a similar proportion when the c.2657+5G>A mutation is present. In summary, we provide evidence that ex vivo quantitative transcripts analysis using RT/qPCR is a robust technology that could be useful for measuring the efficacy of therapeutic approaches that attempt to achieve an increase in CFTR gene expression. PMID:24129438

CO2 flux from Javanese mud volcanism

NASA Astrophysics Data System (ADS)

Queißer, M.; Burton, M. R.; Arzilli, F.; Chiarugi, A.; Marliyani, G. I.; Anggara, F.; Harijoko, A.

2017-06-01

Studying the quantity and origin of CO2 emitted by back-arc mud volcanoes is critical to correctly model fluid-dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO2 with a volume fraction of at least 16 vol %. A lower limit CO2 flux of 1.4 kg s-1 (117 t d-1) was determined, in line with the CO2 flux from the Javanese mud volcano LUSI. Extrapolating these results to mud volcanism from the whole of Java suggests an order of magnitude total CO2 flux of 3 kt d-1, comparable with the expected back-arc efflux of magmatic CO2. After discussing geochemical, geological, and geophysical evidence we conclude that the source of CO2 observed at Bledug Kuwu is likely a mixture of thermogenic, biogenic, and magmatic CO2, with faulting controlling potential pathways for magmatic fluids. This study further demonstrates the merit of man-portable active remote sensing instruments for probing natural gas releases, enabling bottom-up quantification of CO2 fluxes.

Detection and simultaneous quantification of three smoking-related ethylthymidine adducts in human salivary DNA by liquid chromatography tandem mass spectrometry.

PubMed

Chen, Hauh-Jyun Candy; Lee, Chin-Ron

2014-01-03

Smoking cigarette increases levels of certain ethylated DNA adducts in certain tissues and urine. Cigarette smoking is a major risk factor of various cancers and DNA ethylation is involved in smoking-related carcinogenesis. Among the ethylated DNA adducts, O(2)-ethylthymidine (O(2)-edT) and the promutagenic O(4)-ethylthymidine (O(4)-edT) are poorly repaired and they can accumulate in vivo. Using an accurate, highly sensitive, and quantitative assay based on stable isotope dilution nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS), O(2)-edT, N(3)-edT (N(3)-ethylthymidine), and O(4)-edT adducts in human salivary DNA were simultaneous detected and quantified. Saliva is easily accessible and available and it can be a potential target in searching for noninvasive biomarkers. Under the highly selected reaction monitoring (H-SRM) mode, salivary samples from 20 smokers and 13 nonsmokers were analyzed. Starting with 50 μg of DNA isolated from about 3.5 mL of saliva, levels of O(2)-edT, N(3)-edT, and O(4)-edT in 20 smokers' salivary DNA samples were 5.3±6.2, 4.5±5.7, 4.2±8.0 in 10(8) normal nucleotides, respectively, while those in 13 nonsmokers were non-detectable. In addition, statistically significant correlations (p<0.0001) were observed between levels of O(2)-edT and N(3)-edT (γ=0.7388), between levels of O(2)-edT and O(4)-edT (γ=0.8839), and between levels of N(3)-edT, and O(4)-edT (γ=0.7835). To the best of our knowledge, this is the first report of detection and quantification of these three ethylthymidine adducts in human salivary DNA, which might be potential biomarkers for exposure to ethylating agents and possibly for cancer risk assessment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Experimental artefacts occurring during atom probe tomography analysis of oxide nanoparticles in metallic matrix: Quantification and correction

NASA Astrophysics Data System (ADS)

Hatzoglou, C.; Radiguet, B.; Pareige, P.

2017-08-01

Oxide Dispersion Strengthened (ODS) steels are promising candidates for future nuclear reactors, partly due to the fine dispersion of the nanoparticles they contain. Until now, there was no consensus as to the nature of the nanoparticles because their analysis pushed the techniques to their limits and in consequence, introduced some artefacts. In this study, the artefacts that occur during atom probe tomography analysis are quantified. The artefacts quantification reveals that the particles morphology, chemical composition and atomic density are biased. A model is suggested to correct these artefacts in order to obtain a fine and accurate characterization of the nanoparticles. This model is based on volume fraction calculation and an analytical expression of the atomic density. Then, the studied ODS steel reveals nanoparticles, pure in Y, Ti and O, with a core/shell structure. The shell is rich in Cr. The Cr content of the shell is dependent on that of the matrix by a factor of 1.5. This study also shows that 15% of the atoms that were initially in the particles are not detected during the analysis. This only affects O atoms. The particle stoichiometry evolves from YTiO2 for the smallest observed (<2 nm) to Y2TiO5 for the biggest (>8 nm).

Quantitative proton magnetic resonance spectroscopy without water suppression

NASA Astrophysics Data System (ADS)

Özdemir, M. S.; DeDeene, Y.; Fieremans, E.; Lemahieu, I.

2009-06-01

The suppression of the abundant water signal has been traditionally employed to decrease the dynamic range of the NMR signal in proton MRS (1H MRS) in vivo. When using this approach, if the intent is to utilize the water signal as an internal reference for the absolute quantification of metabolites, additional measurements are required for the acquisition of the water signal. This can be prohibitively time-consuming and is not desired clinically. Additionally, traditional water suppression can lead to metabolite alterations. This can be overcome by performing quantitative 1H MRS without water suppression. However, the non-water-suppressed spectra suffer from gradient-induced frequency modulations, resulting in sidebands in the spectrum. Sidebands may overlap with the metabolites, which renders the spectral analysis and quantification problematic. In this paper, we performed absolute quantification of metabolites without water suppression. Sidebands were removed by utilizing the phase of an external reference signal of single resonance to observe the time-varying the static field fluctuations induced by gradient-vibration and deconvolving this phase contamination from the desired NMR signal. The quantification of metabolites was determined after sideband correction by calibrating the metabolite signal intensities against the recorded water signal. The method was evaluated by phantom and in vivo measurements in human brain. The maximum systematic error for the quantified metabolite concentrations was found to be 10.8%, showing the feasibility of the quantification after sideband correction.

Vanishing Corrections for the Position in a Linear Model of FKPP Fronts

NASA Astrophysics Data System (ADS)

Berestycki, Julien; Brunet, Éric; Harris, Simon C.; Roberts, Matt

2017-02-01

Take the linearised FKPP equation {partialth = partial2xh + h} with boundary condition h( m( t), t) = 0. Depending on the behaviour of the initial condition h 0( x) = h( x, 0) we obtain the asymptotics—up to a o(1) term r( t)—of the absorbing boundary m( t) such that {ω(x) := lim_{tto∞} h(x + m(t) ,t)} exists and is non-trivial. In particular, as in Bramson's results for the non-linear FKPP equation, we recover the celebrated {-3/2 log t} correction for initial conditions decaying faster than {x^{ν}e^{-x}} for some {ν < -2}. Furthermore, when we are in this regime, the main result of the present work is the identification (to first order) of the r( t) term, which ensures the fastest convergence to {ω(x)}. When h 0( x) decays faster than {x^{ν}e^{-x}} for some {ν < -3}, we show that r( t) must be chosen to be {-3√{π/t}}, which is precisely the term predicted heuristically by Ebert-van Saarloos (Phys. D Nonlin. Phenom. 146(1): 1-99, 2000) in the non-linear case (see also Mueller and Munier Phys Rev E 90(4):042143, 2014, Henderson, Commun Math Sci 14(4):973-985, 2016, Brunet and Derrida Stat Phys 1-20, 2015). When the initial condition decays as {x^{ν}e^{-x}} for some {ν in [-3, -2)}, we show that even though we are still in the regime where Bramson's correction is {-3/2 log t}, the Ebert-van Saarloos correction has to be modified. Similar results were recently obtained by Henderson CommunMath Sci 14(4):973-985, 2016 using an analytical approach and only for compactly supported initial conditions.

Measurement of fat fraction in the human thymus by localized NMR and three-point Dixon MRI techniques.

PubMed

Fishbein, Kenneth W; Makrogiannis, Sokratis K; Lukas, Vanessa A; Okine, Marilyn; Ramachandran, Ramona; Ferrucci, Luigi; Egan, Josephine M; Chia, Chee W; Spencer, Richard G

2018-07-01

To develop a protocol to non-invasively measure and map fat fraction, fat/(fat+water), as a function of age in the adult thymus for future studies monitoring the effects of interventions aimed at promoting thymic rejuvenation and preservation of immunity in older adults. Three-dimensional spoiled gradient echo 3T MRI with 3-point Dixon fat-water separation was performed at full inspiration for thymus conspicuity in 36 volunteers 19 to 56 years old. Reproducible breath-holding was facilitated by real-time pressure recording external to the console. The MRI method was validated against localized spectroscopy in vivo, with ECG triggering to compensate for stretching during the cardiac cycle. Fat fractions were corrected for T 1 and T 2 bias using relaxation times measured using inversion recovery-prepared PRESS with incremented echo time. In thymus at 3 T, T 1water  = 978 ± 75 ms, T 1fat  = 323 ± 37 ms, T 2water  = 43.4 ± 9.7 ms and T 2fat  = 52.1 ± 7.6 ms were measured. Mean T 1 -corrected MRI fat fractions varied from 0.2 to 0.8 and were positively correlated with age, weight and body mass index (BMI). In subjects with matching MRI and MRS fat fraction measurements, the difference between these measurements exhibited a mean of -0.008 with a 95% confidence interval of (0.123, -0.138). 3-point Dixon MRI of the thymus with T 1 bias correction produces quantitative fat fraction maps that correlate with T 2 -corrected MRS measurements and show age trends consistent with thymic involution. Published by Elsevier Inc.

Empirical Correction to the Likelihood Ratio Statistic for Structural Equation Modeling with Many Variables.

PubMed

Yuan, Ke-Hai; Tian, Yubin; Yanagihara, Hirokazu

2015-06-01

Survey data typically contain many variables. Structural equation modeling (SEM) is commonly used in analyzing such data. The most widely used statistic for evaluating the adequacy of a SEM model is T ML, a slight modification to the likelihood ratio statistic. Under normality assumption, T ML approximately follows a chi-square distribution when the number of observations (N) is large and the number of items or variables (p) is small. However, in practice, p can be rather large while N is always limited due to not having enough participants. Even with a relatively large N, empirical results show that T ML rejects the correct model too often when p is not too small. Various corrections to T ML have been proposed, but they are mostly heuristic. Following the principle of the Bartlett correction, this paper proposes an empirical approach to correct T ML so that the mean of the resulting statistic approximately equals the degrees of freedom of the nominal chi-square distribution. Results show that empirically corrected statistics follow the nominal chi-square distribution much more closely than previously proposed corrections to T ML, and they control type I errors reasonably well whenever N ≥ max(50,2p). The formulations of the empirically corrected statistics are further used to predict type I errors of T ML as reported in the literature, and they perform well.

Accuracy of 1H magnetic resonance spectroscopy for quantification of 2-hydroxyglutarate using linear combination and J-difference editing at 9.4T.

PubMed

Neuberger, Ulf; Kickingereder, Philipp; Helluy, Xavier; Fischer, Manuel; Bendszus, Martin; Heiland, Sabine

2017-12-01

Non-invasive detection of 2-hydroxyglutarate (2HG) by magnetic resonance spectroscopy is attractive since it is related to tumor metabolism. Here, we compare the detection accuracy of 2HG in a controlled phantom setting via widely used localized spectroscopy sequences quantified by linear combination of metabolite signals vs. a more complex approach applying a J-difference editing technique at 9.4T. Different phantoms, comprised out of a concentration series of 2HG and overlapping brain metabolites, were measured with an optimized point-resolved-spectroscopy sequence (PRESS) and an in-house developed J-difference editing sequence. The acquired spectra were post-processed with LCModel and a simulated metabolite set (PRESS) or with a quantification formula for J-difference editing. Linear regression analysis demonstrated a high correlation of real 2HG values with those measured with the PRESS method (adjusted R-squared: 0.700, p<0.001) as well as with those measured with the J-difference editing method (adjusted R-squared: 0.908, p<0.001). The regression model with the J-difference editing method however had a significantly higher explanatory value over the regression model with the PRESS method (p<0.0001). Moreover, with J-difference editing 2HG was discernible down to 1mM, whereas with the PRESS method 2HG values were not discernable below 2mM and with higher systematic errors, particularly in phantoms with high concentrations of N-acetyl-asparate (NAA) and glutamate (Glu). In summary, quantification of 2HG with linear combination of metabolite signals shows high systematic errors particularly at low 2HG concentration and high concentration of confounding metabolites such as NAA and Glu. In contrast, J-difference editing offers a more accurate quantification even at low 2HG concentrations, which outweighs the downsides of longer measurement time and more complex postprocessing. Copyright © 2017. Published by Elsevier GmbH.

Correction of hypokyphosis in thoracic adolescent idiopathic scoliosis using sublaminar bands: a 3D multicenter study.

PubMed

Ilharreborde, Brice; Pesenti, Sébastien; Ferrero, Emmanuelle; Accadbled, Franck; Jouve, Jean-Luc; De Gauzy, Jérôme Sales; Mazda, Keyvan

2018-02-01

The comparison of implants and correction methods remain controversial in AIS. Excellent frontal and axial correction rates have been reported with all-screw constructs, but at the expense of sagittal alignment, which has a tendency to flatten postoperatively. Posteromedial translation using hybrid constructs seems to preserve and improve thoracic kyphosis (TK), but no series exist to date with a significant number of hypokyphotic patients. In addition, the measures of TK in 2D are often wrong in severe AIS due to axial rotation. The goals of this study were therefore to analyze the 3D radiological outcomes of a group of hypokyphotic AIS patients operated with sublaminar bands. 35 consecutive AIS hypokyphotic patients (T4T12 <15°) operated in three centers were included, with a minimum 2-year follow-up. The surgical technique was similar in all centers, associating lumbar pedicle screws and thoracic sublaminar bands. Posteromedial translation was the main correction technique, and no patient underwent prior anterior release. 3D spinal reconstructions were performed preoperatively, postoperatively and at the latest follow-up by an independent observer using SterEOS (EOS imaging, Paris, France), and 2D and 3D measurements were compared. In addition, a new 3D parameter [sagittal shift of the apical vertebra (SSAV)], reflecting the translation of the apical vertebra of the main curve in the patient sagittal plane, was described and reported. The age of the cohort was 16 years and the number of sublaminar bands used for correction averaged 6 (±1.5). T1T12 and T4T12 sagittal Cobb angles appeared to be overestimated on 2D postoperatively (3°, p = 0.002 and 4°, p < 0.001, respectively). Hence, only 3D measurements were kept for the quantitative analysis of the postoperative correction. T4T12 TK significantly increased after surgery (average 8° ± 7°, p < 0.001), but 11 patients (31.4%) remained hypokyphotic. Seven out of the eight patients (87.5%) who presented a thoracic lordosis (i.e., T4T12 <0°) preoperatively were corrected after surgery (mean gain 16° ± 4°). A posterior shift (positive SSAV) of the apical vertebra was reported in 24 patients (68.6%). In this subgroup, the mean SSAV was +2 cm (±1). Good correlation was found between the SSAV and the postoperative change in 3D T4T12 kyphosis (r = 0.62). Measures in 2D tend to overestimate sagittal alignment and are not sufficient to evaluate postoperative correction. SSAV is a new 3D parameter reflecting the TK change that needs to be further investigated and used in the future. This series confirms that sublaminar bands should be considered in hypokyphotic patients, since thoracic sagittal alignment was restored in 68.6% of the cases.

Bone marrow fat quantification in the presence of trabecular bone: initial comparison between water-fat imaging and single-voxel MRS

PubMed Central

Karampinos, Dimitrios C.; Melkus, Gerd; Baum, Thomas; Bauer, Jan S.; Rummeny, Ernst J.; Krug, Roland

2013-01-01

Purpose The purpose of the present study was to test the relative performance of chemical shift-based water-fat imaging in measuring bone marrow fat fraction in the presence of trabecular bone, having as reference standard the single-voxel magnetic resonance spectroscopy (MRS). Methods Six-echo gradient echo imaging and single-voxel MRS measurements were performed on the proximal femur of seven healthy volunteers. The bone marrow fat spectrum was characterized based on the magnitude of measurable fat peaks and an a priori knowledge of the chemical structure of triglycerides, in order to accurately extract the water peak from the overlapping broad fat peaks in MRS. The imaging-based fat fraction results were then compared to the MRS-based results both without and with taking into consideration the presence of short T2* water components in MRS. Results There was a significant underestimation of the fat fraction using the MRS model not accounting for short T2* species with respect to the imaging-based water fraction. A good equivalency was observed between the fat fraction using the MRS model accounting for short T2* species and the imaging-based fat fraction (R2=0.87). Conclusion The consideration of the short T2* water species effect on bone marrow fat quantification is essential when comparing MRS-based and imaging-based fat fraction results. PMID:23657998

Magnetic resonance measurement of muscle T2, fat-corrected T2 and fat fraction in the assessment of idiopathic inflammatory myopathies

PubMed Central

Yao, Lawrence; Yip, Adrienne L.; Shrader, Joseph A.; Mesdaghinia, Sepehr; Volochayev, Rita; Jansen, Anna V.; Miller, Frederick W.

2016-01-01

Objective. This study examines the utility of MRI, including T2 maps and T2 maps corrected for muscle fat content, in evaluating patients with idiopathic inflammatory myopathy. Methods. A total of 44 patients with idiopathic inflammatory myopathy, 18 of whom were evaluated after treatment with rituximab, underwent MRI of the thighs and detailed clinical assessment. T2, fat fraction (FF) and fat corrected T2 (fc-T2) maps were generated from standardized MRI scans, and compared with semi-quantitative scoring of short tau inversion recovery (STIR) and T1-weighted sequences, as well as various myositis disease metrics, including the Physician Global Activity, the modified Childhood Myositis Assessment Scale and the muscle domain of the Myositis Disease Activity Assessment Tool-muscle (MDAAT-muscle). Results. Mean T2 and mean fc-T2 correlated similarly with STIR scores (Spearman rs = 0.64 and 0.64, P < 0.01), while mean FF correlated with T1 damage scores (rs = 0.69, P < 0.001). Baseline T2, fc-T2 and STIR scores correlated significantly with the Physician Global Activity, modified Childhood Myositis Assessment Scale and MDAAT-muscle (rs range = 0.41–0.74, P < 0.01). The response of MRI measures to rituximab was variable, and did not significantly agree with a standardized clinical definition of improvement. Standardized response means for the MRI measures were similar. Conclusion. Muscle T2, fc-T2 and FF measurements exhibit content validity with reference to semi-quantitative scoring of STIR and T1 MRI, and also exhibit construct validity with reference to several myositis activity and damage measures. T2 was as responsive as fc-T2 and STIR scoring, although progression of muscle damage was negligible during the study. PMID:26412808

Modeling Data Containing Outliers using ARIMA Additive Outlier (ARIMA-AO)

NASA Astrophysics Data System (ADS)

Saleh Ahmar, Ansari; Guritno, Suryo; Abdurakhman; Rahman, Abdul; Awi; Alimuddin; Minggi, Ilham; Arif Tiro, M.; Kasim Aidid, M.; Annas, Suwardi; Utami Sutiksno, Dian; Ahmar, Dewi S.; Ahmar, Kurniawan H.; Abqary Ahmar, A.; Zaki, Ahmad; Abdullah, Dahlan; Rahim, Robbi; Nurdiyanto, Heri; Hidayat, Rahmat; Napitupulu, Darmawan; Simarmata, Janner; Kurniasih, Nuning; Andretti Abdillah, Leon; Pranolo, Andri; Haviluddin; Albra, Wahyudin; Arifin, A. Nurani M.

2018-01-01

The aim this study is discussed on the detection and correction of data containing the additive outlier (AO) on the model ARIMA (p, d, q). The process of detection and correction of data using an iterative procedure popularized by Box, Jenkins, and Reinsel (1994). By using this method we obtained an ARIMA models were fit to the data containing AO, this model is added to the original model of ARIMA coefficients obtained from the iteration process using regression methods. In the simulation data is obtained that the data contained AO initial models are ARIMA (2,0,0) with MSE = 36,780, after the detection and correction of data obtained by the iteration of the model ARIMA (2,0,0) with the coefficients obtained from the regression Zt = 0,106+0,204Z t-1+0,401Z t-2-329X 1(t)+115X 2(t)+35,9X 3(t) and MSE = 19,365. This shows that there is an improvement of forecasting error rate data.

TU-AB-201-11: A Novel Theoretical Framework for MRI-Only Image Guided LDR Prostate and Breast Brachytherapy Implant Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soliman, A; Elzibak, A; Fatemi, A

Purpose: To propose a novel framework for accurate model-based dose calculations using only MR images for LDR prostate and breast seed implant brachytherapy. Methods: Model-based dose calculation methodologies recommended by TG-186 require further knowledge about specific tissue composition, which is challenging with MRI. However, relying on MRI-only for implant dosimetry would reduce the soft tissue delineation uncertainty, costs, and uncertainties associated with multi-modality registration and fusion processes. We propose a novel framework to address this problem using quantitative MRI acquisitions and reconstruction techniques. The framework includes three steps: (1) Identify the locations of seeds(2) Identify the presence (or absence) ofmore » calcification(s)(3) Quantify the water and fat content in the underlying tissueSteps (1) and (2) consider the sources that limit patient dosimetry, particularly the inter-seed attenuation and the calcified regions; while step (3) targets the quantification of the tissue composition to consider the heterogeneities in the medium. Our preliminary work has shown that the seeds and the calcifications can be identified with MRI using both the magnitude and the phase images. By employing susceptibility-weighted imaging with specific post-processing techniques, the phase images can be further explored to distinguish the seeds from the calcifications. Absolute quantification of tissue, water, and fat content is feasible and was previously demonstrated in phantoms and in-vivo applications, particularly for brain diseases. The approach relies on the proportionality of the MR signal to the number of protons in an image volume. By employing appropriate correction algorithms for T1 - and T2*-related biases, B1 transmit and receive field inhomogeneities, absolute water/fat content can be determined. Results: By considering calcification and interseed attenuation, and through the knowledge of water and fat mass density, accurate patient-specific implant dosimetry can be achieved with MRI-only. Conclusion: The proposed framework showed that model-based dose calculation is feasible using MRI-only state-of-the-art techniques.« less

High-speed multislice T1 mapping using inversion-recovery echo-planar imaging.

PubMed

Ordidge, R J; Gibbs, P; Chapman, B; Stehling, M K; Mansfield, P

1990-11-01

Tissue contrast in MR images is a strong function of spin-lattice (T1) and spin-spin (T2) relaxation times. However, the T1 relaxation time is rarely quantified because of the long scan time required to produce an accurate T1 map of the subject. In a standard 2D FT technique, this procedure may take up to 30 min. Modifications of the echo-planar imaging (EPI) technique which incorporate the principle of inversion recovery (IR) enable multislice T1 maps to be produced in total scan times varying from a few seconds up to a minute. Using IR-EPI, rapid quantification of T1 values may thus lead to better discrimination between tissue types in an acceptable scan time.

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 1 Report for Beale AFB, Marysville, California. Volume 2.

DTIC Science & Technology

1987-05-01

Maintarer.e ground water 2 scil borinF 8 hand auger 12 Disna:-e Area No. 10 (DA-10) - Entomology Bldg UO soil boring 6 13 Landfil: Nc. 1 (LF-1) ground...l’JSZIL I ’ SCIL SO V ; 7 ILill ( oi[ ;Q0 SO IL. $;I 60 . *O (3 .1 *, W i ; Q,. t.t WLi it hI OX aoPit IV 3 ’ Table F-1 (Cont.) 6OIOOtO LAB WPLIAT

Spinal focal lesion detection in multiple myeloma using multimodal image features

NASA Astrophysics Data System (ADS)

Fränzle, Andrea; Hillengass, Jens; Bendl, Rolf

2015-03-01

Multiple myeloma is a tumor disease in the bone marrow that affects the skeleton systemically, i.e. multiple lesions can occur in different sites in the skeleton. To quantify overall tumor mass for determining degree of disease and for analysis of therapy response, volumetry of all lesions is needed. Since the large amount of lesions in one patient impedes manual segmentation of all lesions, quantification of overall tumor volume is not possible until now. Therefore development of automatic lesion detection and segmentation methods is necessary. Since focal tumors in multiple myeloma show different characteristics in different modalities (changes in bone structure in CT images, hypointensity in T1 weighted MR images and hyperintensity in T2 weighted MR images), multimodal image analysis is necessary for the detection of focal tumors. In this paper a pattern recognition approach is presented that identifies focal lesions in lumbar vertebrae based on features from T1 and T2 weighted MR images. Image voxels within bone are classified using random forests based on plain intensities and intensity value derived features (maximum, minimum, mean, median) in a 5 x 5 neighborhood around a voxel from both T1 and T2 weighted MR images. A test data sample of lesions in 8 lumbar vertebrae from 4 multiple myeloma patients can be classified at an accuracy of 95% (using a leave-one-patient-out test). The approach provides a reasonable delineation of the example lesions. This is an important step towards automatic tumor volume quantification in multiple myeloma.

Determination of thyroid hormones in placenta using isotope-dilution liquid chromatography quadrupole time-of-flight mass spectrometry.

PubMed

Li, Zhong-Min; Giesert, Florian; Vogt-Weisenhorn, Daniela; Main, Katharina Maria; Skakkebæk, Niels Erik; Kiviranta, Hannu; Toppari, Jorma; Feldt-Rasmussen, Ulla; Shen, Heqing; Schramm, Karl-Werner; De Angelis, Meri

2018-01-26

The transplacental passage of thyroid hormones (THs) is of great significance since the maternal THs are vitally important in ensuring the normal fetal development. In this paper, we determined the concentrations of seven THs, viz. L-thyroxine (T 4 ), 3,3',5-triiodo-l-thyronine (T 3 ), 3,3',5'-triiodo-l-thyronine (rT 3 ), 3,3'-diiodo-l-thyronine (T 2 ), 3,5-diiodo-l-thyronine (rT 2 ), 3-iodo-l-thyronine (T 1 ) and 3-iodothyronamine (T 1 AM), in placenta using isotope dilution liquid chromatography quadrupole time-of-flight mass spectrometry. We optimized the method using isotopically labeled quantification standards ( 13 C 6 -T 4 , 13 C 6 -T 3 , 13 C 6 -rT 3 and 13 C 6 -T 2 ) and recovery standard ( 13 C 12 -T 4 ) in combination with solid-liquid extraction, liquid-liquid extraction and solid phase extraction. The linearity was obtained in the range of 0.5-150 pg uL -1 with R 2 values >0.99. The method detection limits (MDLs) ranged from 0.01 ng g -1 to 0.2 ng g -1 , while the method quantification limits (MQLs) were between 0.04 ng g -1 and 0.7 ng g -1 . The spike-recoveries for THs (except for T 1 and T 1 AM) were in the range of 81.0%-112%, with a coefficient of variation (CV) of 0.5-6.2%. The intra-day CVs and inter-day CVs were 0.5%-10.3% and 1.19%-8.88%, respectively. Concentrations of the THs were 22.9-35.0 ng g -1  T 4 , 0.32-0.46 ng g -1  T 3 , 2.86-3.69 ng g -1 rT 3 , 0.16-0.26 ng g -1  T 2 , and < MDL for other THs in five human placentas, and 2.05-3.51 ng g -1  T 4 , 0.37-0.62 ng g -1  T 3 , 0.96-1.3 ng g -1 rT 3 , 0.07-0.13 ng g -1  T 2 and < MDL for other THs in five mouse placentas. The presence of T 2 was tracked in placenta for the first time. This method with improved selectivity and sensitivity allows comprehensive evaluation of TH homeostasis in research of metabolism and effects of environmental contaminant exposures. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of tumor mobility during the breathing cycle using 3D dynamic MRI

NASA Astrophysics Data System (ADS)

Schoebinger, Max; Plathow, Christian; Wolf, Ivo; Kauczor, Hans-Ulrich; Meinzer, Hans-Peter

2006-03-01

Respiration causes movement and shape changes in thoracic tumors, which has a direct influence on the radio-therapy planning process. Current methods for the estimation of tumor mobility are either two-dimensional (fluoroscopy, 2D dynamic MRI) or based on radiation (3D (+t) CT, implanted gold markers). With current advances in dynamic MRI acquisition, 3D+t image sequences of the thorax can be acquired covering the thorax over the whole breathing cycle. In this work, methods are presented for the interactive segmentation of tumors in dynamic images, the calculation of tumor trajectories, dynamic tumor volumetry and dynamic tumor rotation/deformation based on 3D dynamic MRI. For volumetry calculation, a set of 21 related partial volume correcting volumetry algorithms has been evaluated based on tumor surrogates. Conventional volumetry based on voxel counting yielded a root mean square error of 29% compared to a root mean square error of 11% achieved by the algorithm performing best among the different volumetry methods. The new workflow has been applied to a set of 26 patients. Preliminary results indicate, that 3D dynamic MRI reveals important aspects of tumor behavior during the breathing cycle. This might imply the possibility to further improve high-precision radiotherapy techniques.

Metabolite ratios to assumed stable creatine level may confound the quantification of proton brain MR spectroscopy.

PubMed

Li, Belinda S Y; Wang, Hao; Gonen, Oded

2003-10-01

In localized brain proton MR spectroscopy ((1)H-MRS), metabolites' levels are often expressed as ratios, rather than as absolute concentrations. Frequently, their denominator is the creatine [Cr], which level is explicitly assumed to be stable in normal as well as in many pathologic states. The rationale is that ratios self-correct for imager and localization method differences, gain instabilities, regional susceptibility variations and partial volume effects. The implicit assumption is that these benefits are worth their cost(w)-(w) propagation of the individual variation of each of the ratio's components. To test this hypothesis, absolute levels of N-acetylaspartate [NAA], choline [Cho] and [Cr] were quantified in various regions of the brains of 8 volunteers, using 3-dimensional (3D) (1)H-MRS at 1.5 T. The results show that in over 50% of approximately 2000 voxels examined, [NAA]/[Cr] and [Cho]/[Cr] exhibited higher coefficients of variations (CV) than [NAA] and [Cho] individually. Furthermore, in approximately 33% of these voxels, the ratios' CVs exceeded even the combined constituents' CVs. Consequently, basing metabolite quantification on ratios and assuming stable [Cr] introduces more variability into (1)H-MRS than it prevents. Therefore, its cost exceeds the benefit.

Myocardial Mapping With Cardiac Magnetic Resonance: The Diagnostic Value of Novel Sequences.

PubMed

Sanz, Javier; LaRocca, Gina; Mirelis, Jesús G

2016-09-01

Cardiac magnetic resonance has evolved into a crucial modality for the evaluation of cardiomyopathy due to its ability to characterize myocardial structure and function. In the last few years, interest has increased in the potential of "mapping" techniques that provide direct and objective quantification of myocardial properties such as T1, T2, and T2* times. These approaches enable the detection of abnormalities that affect the myocardium in a diffuse fashion and/or may be too subtle for visual recognition. This article reviews the current state of myocardial T1 and T2-mapping in both health and disease. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Technical Note: Deep learning based MRAC using rapid ultra-short echo time imaging.

PubMed

Jang, Hyungseok; Liu, Fang; Zhao, Gengyan; Bradshaw, Tyler; McMillan, Alan B

2018-05-15

In this study, we explore the feasibility of a novel framework for MR-based attenuation correction for PET/MR imaging based on deep learning via convolutional neural networks, which enables fully automated and robust estimation of a pseudo CT image based on ultrashort echo time (UTE), fat, and water images obtained by a rapid MR acquisition. MR images for MRAC are acquired using dual echo ramped hybrid encoding (dRHE), where both UTE and out-of-phase echo images are obtained within a short single acquisition (35 sec). Tissue labeling of air, soft tissue, and bone in the UTE image is accomplished via a deep learning network that was pre-trained with T1-weighted MR images. UTE images are used as input to the network, which was trained using labels derived from co-registered CT images. The tissue labels estimated by deep learning are refined by a conditional random field based correction. The soft tissue labels are further separated into fat and water components using the two-point Dixon method. The estimated bone, air, fat, and water images are then assigned appropriate Hounsfield units, resulting in a pseudo CT image for PET attenuation correction. To evaluate the proposed MRAC method, PET/MR imaging of the head was performed on 8 human subjects, where Dice similarity coefficients of the estimated tissue labels and relative PET errors were evaluated through comparison to a registered CT image. Dice coefficients for air (within the head), soft tissue, and bone labels were 0.76±0.03, 0.96±0.006, and 0.88±0.01. In PET quantification, the proposed MRAC method produced relative PET errors less than 1% within most brain regions. The proposed MRAC method utilizing deep learning with transfer learning and an efficient dRHE acquisition enables reliable PET quantification with accurate and rapid pseudo CT generation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows

NASA Astrophysics Data System (ADS)

Gokce, Emine; Shuford, Christopher M.; Franck, William L.; Dean, Ralph A.; Muddiman, David C.

2011-12-01

Normalization of spectral counts (SpCs) in label-free shotgun proteomic approaches is important to achieve reliable relative quantification. Three different SpC normalization methods, total spectral count (TSpC) normalization, normalized spectral abundance factor (NSAF) normalization, and normalization to selected proteins (NSP) were evaluated based on their ability to correct for day-to-day variation between gel-based sample preparation and chromatographic performance. Three spectral counting data sets obtained from the same biological conidia sample of the rice blast fungus Magnaporthe oryzae were analyzed by 1D gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Equine myoglobin and chicken ovalbumin were spiked into the protein extracts prior to 1D-SDS- PAGE as internal protein standards for NSP. The correlation between SpCs of the same proteins across the different data sets was investigated. We report that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpC plots, while NSP did not afford effective corrections of the unnormalized data. Furthermore, when utilizing TSpC normalization prior to relative protein quantification, t-testing and fold-change revealed the cutoff limits for determining real biological change to be a function of the absolute number of SpCs. For instance, we observed the variance decreased as the number of SpCs increased, which resulted in a higher propensity for detecting statistically significant, yet artificial, change for highly abundant proteins. Thus, we suggest applying higher confidence level and lower fold-change cutoffs for proteins with higher SpCs, rather than using a single criterion for the entire data set. By choosing appropriate cutoff values to maintain a constant false positive rate across different protein levels (i.e., SpC levels), it is expected this will reduce the overall false negative rate, particularly for proteins with higher SpCs.

Hepatic fat quantification using the two-point Dixon method and fat color maps based on non-alcoholic fatty liver disease activity score.

PubMed

Hayashi, Tatsuya; Saitoh, Satoshi; Takahashi, Junji; Tsuji, Yoshinori; Ikeda, Kenji; Kobayashi, Masahiro; Kawamura, Yusuke; Fujii, Takeshi; Inoue, Masafumi; Miyati, Tosiaki; Kumada, Hiromitsu

2017-04-01

The two-point Dixon method for magnetic resonance imaging (MRI) is commonly used to non-invasively measure fat deposition in the liver. The aim of the present study was to assess the usefulness of MRI-fat fraction (MRI-FF) using the two-point Dixon method based on the non-alcoholic fatty liver disease activity score. This retrospective study included 106 patients who underwent liver MRI and MR spectroscopy, and 201 patients who underwent liver MRI and histological assessment. The relationship between MRI-FF and MR spectroscopy-fat fraction was used to estimate the corrected MRI-FF for hepatic multi-peaks of fat. Then, a color FF map was generated with the corrected MRI-FF based on the non-alcoholic fatty liver disease activity score. We defined FF variability as the standard deviation of FF in regions of interest. Uniformity of hepatic fat was visually graded on a three-point scale using both gray-scale and color FF maps. Confounding effects of histology (iron, inflammation and fibrosis) on corrected MRI-FF were assessed by multiple linear regression. The linear correlations between MRI-FF and MR spectroscopy-fat fraction, and between corrected MRI-FF and histological steatosis were strong (R 2  = 0.90 and R 2  = 0.88, respectively). Liver fat variability significantly increased with visual fat uniformity grade using both of the maps (ρ = 0.67-0.69, both P < 0.001). Hepatic iron, inflammation and fibrosis had no significant confounding effects on the corrected MRI-FF (all P > 0.05). The two-point Dixon method and the gray-scale or color FF maps based on the non-alcoholic fatty liver disease activity score were useful for fat quantification in the liver of patients without severe iron deposition. © 2016 The Japan Society of Hepatology.

Does Fat Suppression via Chemically Selective Saturation (CHESS) Affect R2*-MRI for Transfusional Iron Overload Assessment? A Clinical Evaluation at 1.5 and 3 Tesla

PubMed Central

Krafft, Axel J.; Loeffler, Ralf B.; Song, Ruitian; Bian, Xiao; McCarville, M. Beth; Hankins, Jane S.; Hillenbrand, Claudia M.

2015-01-01

Purpose Fat suppression (FS) via chemically selective saturation (CHESS) eliminates fat-water oscillations in multi-echo gradient echo (mGRE) R2*-MRI. However, for increasing R2* values as seen with increasing liver iron content (LIC), the water signal spectrally overlaps with the CHESS band, which may alter R2*. Here, we investigate the effect of CHESS on R2* and describe a heuristic correction for the observed CHESS-induced R2* changes. Methods Eighty patients (49/31 female/male, mean age: 18.3±11.7 years) with iron overload were scanned with a non-FS and a CHESS-FS mGRE sequence at 1.5T and 3T. Mean liver R2* values were evaluated using 3 published fitting approaches. Measured and model-corrected R2* values were compared and statistically analyzed. Results At 1.5T, CHESS led to a systematic R2* reduction (P<0.001 for all fitting algorithms) especially toward higher R2*. Our model described the observed changes well and reduced the CHESS-induced R2* bias after correction (linear regression slopes: 1.032/0.927/0.981). No CHESS-induced R2* reductions were found at 3T. Conclusion The CHESS-induced R2* bias at 1.5T needs to be considered when applying R2*-LIC biopsy calibrations for clinical LIC assessment which were established without FS at 1.5T. The proposed model corrects the R2* bias and could therefore improve clinical iron overload assessment based on linear R2*-LIC calibrations. PMID:26308155

Wind Tunnel Corrections for High Angle of Attack Models,

DTIC Science & Technology

1981-02-01

MAQUETTES EN SOUFFLERIE par X.Vaucheret GERMA * J ACTIVITIES ON WIND TUNNEL CORRECTIONS byH.HoIst A REVIEW OF RESEARCH AT NLR ON WIND TUNNEL...1-10 Ro - ,2.13M106 M - 0.230 ° BALANCE — corrected -T unoorreoted •r r^a—Q * o n ...8217 n * t ?’ A *i o o 1 1 -0.70 -0.65 -0.60 -0.S5 -0.50 -0.45 -0.40 Fig.l 1 Corrected

QR in Child Grammar: Evidence from Antecedent-Contained Deletion

ERIC Educational Resources Information Center

Syrett, Kristen; Lidz, Jeffrey

2009-01-01

We show that 4-year-olds assign the correct interpretation to antecedent-contained deletion (ACD) sentences because they have the correct representation of these structures. This representation involves Quantifier Raising (QR) of a Quantificational Noun Phrase (QNP) that must move out of the site of the verb phrase in which it is contained to…

On Neglecting Chemical Exchange Effects When Correcting in Vivo 31P MRS Data for Partial Saturation

NASA Astrophysics Data System (ADS)

Ouwerkerk, Ronald; Bottomley, Paul A.

2001-02-01

Signal acquisition in most MRS experiments requires a correction for partial saturation that is commonly based on a single exponential model for T1 that ignores effects of chemical exchange. We evaluated the errors in 31P MRS measurements introduced by this approximation in two-, three-, and four-site chemical exchange models under a range of flip-angles and pulse sequence repetition times (TR) that provide near-optimum signal-to-noise ratio (SNR). In two-site exchange, such as the creatine-kinase reaction involving phosphocreatine (PCr) and γ-ATP in human skeletal and cardiac muscle, errors in saturation factors were determined for the progressive saturation method and the dual-angle method of measuring T1. The analysis shows that these errors are negligible for the progressive saturation method if the observed T1 is derived from a three-parameter fit of the data. When T1 is measured with the dual-angle method, errors in saturation factors are less than 5% for all conceivable values of the chemical exchange rate and flip-angles that deliver useful SNR per unit time over the range T1/5 ≤ TR ≤ 2T1. Errors are also less than 5% for three- and four-site exchange when TR ≥ T1*/2, the so-called "intrinsic" T1's of the metabolites. The effect of changing metabolite concentrations and chemical exchange rates on observed T1's and saturation corrections was also examined with a three-site chemical exchange model involving ATP, PCr, and inorganic phosphate in skeletal muscle undergoing up to 95% PCr depletion. Although the observed T1's were dependent on metabolite concentrations, errors in saturation corrections for TR = 2 s could be kept within 5% for all exchanging metabolites using a simple interpolation of two dual-angle T1 measurements performed at the start and end of the experiment. Thus, the single-exponential model appears to be reasonably accurate for correcting 31P MRS data for partial saturation in the presence of chemical exchange. Even in systems where metabolite concentrations change, accurate saturation corrections are possible without much loss in SNR.

Brain extraction in partial volumes T2*@7T by using a quasi-anatomic segmentation with bias field correction.

PubMed

Valente, João; Vieira, Pedro M; Couto, Carlos; Lima, Carlos S

2018-02-01

Poor brain extraction in Magnetic Resonance Imaging (MRI) has negative consequences in several types of brain post-extraction such as tissue segmentation and related statistical measures or pattern recognition algorithms. Current state of the art algorithms for brain extraction work on weighted T1 and T2, being not adequate for non-whole brain images such as the case of T2*FLASH@7T partial volumes. This paper proposes two new methods that work directly in T2*FLASH@7T partial volumes. The first is an improvement of the semi-automatic threshold-with-morphology approach adapted to incomplete volumes. The second method uses an improved version of a current implementation of the fuzzy c-means algorithm with bias correction for brain segmentation. Under high inhomogeneity conditions the performance of the first method degrades, requiring user intervention which is unacceptable. The second method performed well for all volumes, being entirely automatic. State of the art algorithms for brain extraction are mainly semi-automatic, requiring a correct initialization by the user and knowledge of the software. These methods can't deal with partial volumes and/or need information from atlas which is not available in T2*FLASH@7T. Also, combined volumes suffer from manipulations such as re-sampling which deteriorates significantly voxel intensity structures making segmentation tasks difficult. The proposed method can overcome all these difficulties, reaching good results for brain extraction using only T2*FLASH@7T volumes. The development of this work will lead to an improvement of automatic brain lesions segmentation in T2*FLASH@7T volumes, becoming more important when lesions such as cortical Multiple-Sclerosis need to be detected. Copyright © 2017 Elsevier B.V. All rights reserved.

Test-retest reliability of automated whole body and compartmental muscle volume measurements on a wide bore 3T MR system.

PubMed

Thomas, Marianna S; Newman, David; Leinhard, Olof Dahlqvist; Kasmai, Bahman; Greenwood, Richard; Malcolm, Paul N; Karlsson, Anette; Rosander, Johannes; Borga, Magnus; Toms, Andoni P

2014-09-01

To measure the test-retest reproducibility of an automated system for quantifying whole body and compartmental muscle volumes using wide bore 3 T MRI. Thirty volunteers stratified by body mass index underwent whole body 3 T MRI, two-point Dixon sequences, on two separate occasions. Water-fat separation was performed, with automated segmentation of whole body, torso, upper and lower leg volumes, and manually segmented lower leg muscle volumes. Mean automated total body muscle volume was 19·32 L (SD9·1) and 19·28 L (SD9·12) for first and second acquisitions (Intraclass correlation coefficient (ICC) = 1·0, 95% level of agreement -0·32-0·2 L). ICC for all automated test-retest muscle volumes were almost perfect (0·99-1·0) with 95% levels of agreement 1.8-6.6% of mean volume. Automated muscle volume measurements correlate closely with manual quantification (right lower leg: manual 1·68 L (2SD0·6) compared to automated 1·64 L (2SD 0·6), left lower leg: manual 1·69 L (2SD 0·64) compared to automated 1·63 L (SD0·61), correlation coefficients for automated and manual segmentation were 0·94-0·96). Fully automated whole body and compartmental muscle volume quantification can be achieved rapidly on a 3 T wide bore system with very low margins of error, excellent test-retest reliability and excellent correlation to manual segmentation in the lower leg. Sarcopaenia is an important reversible complication of a number of diseases. Manual quantification of muscle volume is time-consuming and expensive. Muscles can be imaged using in and out of phase MRI. Automated atlas-based segmentation can identify muscle groups. Automated muscle volume segmentation is reproducible and can replace manual measurements.

Quantification of Triacylglycerol Molecular Species in Edible Fats and Oils by Gas Chromatography-Flame Ionization Detector Using Correction Factors.

PubMed

Yoshinaga, Kazuaki; Obi, Junji; Nagai, Toshiharu; Iioka, Hiroyuki; Yoshida, Akihiko; Beppu, Fumiaki; Gotoh, Naohiro

2017-03-01

In the present study, the resolution parameters and correction factors (CFs) of triacylglycerol (TAG) standards were estimated by gas chromatography-flame ionization detector (GC-FID) to achieve the precise quantification of the TAG composition in edible fats and oils. Forty seven TAG standards comprising capric acid, lauric acid, myristic acid, pentadecanoic acid, palmitic acid, palmitoleic acid, stearic acid, oleic acid, linoleic acid, and/or linolenic acid were analyzed, and the CFs of these TAGs were obtained against tripentadecanoyl glycerol as the internal standard. The capillary column was Ultra ALLOY + -65 (30 m × 0.25 mm i.d., 0.10 μm thickness) and the column temperature was programmed to rise from 250°C to 360°C at 4°C/min and then hold for 25 min. The limit of detection (LOD) and limit of quantification (LOQ) values of the TAG standards were > 0.10 mg and > 0.32 mg per 100 mg fat and oil, respectively, except for LnLnLn, and the LOD and LOQ values of LnLnLn were 0.55 mg and 1.84 mg per 100 mg fat and oil, respectively. The CFs of TAG standards decreased with increasing total acyl carbon number and degree of desaturation of TAG molecules. Also, there were no remarkable differences in the CFs between TAG positional isomers such as 1-palmitoyl-2-oleoyl-3-stearoyl-rac-glycerol, 1-stearoyl-2-palmitoyl-3-oleoyl-rac-glycerol, and 1-palmitoyl-2-stearoyl-3-oleoyl-rac-glycerol, which cannot be separated by GC-FID. Furthermore, this method was able to predict the CFs of heterogeneous (AAB- and ABC-type) TAGs from the CFs of homogenous (AAA-, BBB-, and CCC-type) TAGs. In addition, the TAG composition in cocoa butter, palm oil, and canola oil was determined using CFs, and the results were found to be in good agreement with those reported in the literature. Therefore, the GC-FID method using CFs can be successfully used for the quantification of TAG molecular species in natural fats and oils.

Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

PubMed

Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

2004-03-01

Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

Quantification of Superparamagnetic Iron Oxide (SPIO)-labeled Cells Using MRI

PubMed Central

Rad, Ali M; Arbab, Ali S; Iskander, ASM; Jiang, Quan; Soltanian-Zadeh, Hamid

2015-01-01

Purpose To show the feasibility of using magnetic resonance imaging (MRI) to quantify superparamagnetic iron oxide (SPIO)-labeled cells. Materials and Methods Lymphocytes and 9L rat gliosarcoma cells were labeled with Ferumoxides-Protamine Sulfate complex (FE-PRO). Cells were labeled efficiently (more than 95%) and iron concentration inside each cell was measured by spectrophotometry (4.77-30.21 picograms). Phantom tubes containing different number of labeled or unlabeled cells as well as different concentrations of FE-PRO were made. In addition, labeled and unlabeled cells were injected into fresh and fixed rat brains. Results Cellular viability and proliferation of labeled and unlabeled cells were shown to be similar. T2-weighted images were acquired using 7 T and 3 T MRI systems and R2 maps of the tubes containing cells, free FE-PRO, and brains were made. There was a strong linear correlation between R2 values and labeled cell numbers but the regression lines were different for the lymphocytes and gliosarcoma cells. Similarly, there was strong correlation between R2 values and free iron. However, free iron had higher R2 values than the labeled cells for the same concentration of iron. Conclusion Our data indicated that in vivo quantification of labeled cells can be done by careful consideration of different factors and specific control groups. PMID:17623892

Magnetic Resonance T1 Relaxation Time of Venous Thrombus Is Determined by Iron Processing and Predicts Susceptibility to Lysis

PubMed Central

Modarai, Bijan; Blume, Ulrike; Humphries, Julia; Patel, Ashish S.; Phinikaridou, Alkystis; Evans, Colin E.; Mattock, Katherine; Grover, Steven P.; Ahmad, Anwar; Lyons, Oliver T.; Attia, Rizwan Q.; Renné, Thomas; Premaratne, Sobath; Wiethoff, Andrea J.; Botnar, René M.; Schaeffter, Tobias; Waltham, Matthew; Smith, Alberto

2014-01-01

Background The magnetic resonance longitudinal relaxation time (T1) changes with thrombus age in humans. In this study, we investigate the possible mechanisms that give rise to the T1 signal in venous thrombi and whether changes in T1 relaxation time are informative of the susceptibility to lysis. Methods and Results Venous thrombosis was induced in the vena cava of BALB/C mice, and temporal changes in T1 relaxation time correlated with thrombus composition. The mean T1 relaxation time of thrombus was shortest at 7days following thrombus induction and returned to that of blood as the thrombus resolved. T1 relaxation time was related to thrombus methemoglobin formation and further processing. Studies in inducible nitric oxide synthase (iNOS−/−)–deficient mice revealed that inducible nitric oxide synthase mediates oxidation of erythrocyte lysis–derived iron to paramagnetic Fe3+, which causes thrombus T1 relaxation time shortening. Studies using chemokine receptor-2–deficient mice (Ccr2−/−) revealed that the return of the T1 signal to that of blood is regulated by removal of Fe3+ by macrophages that accumulate in the thrombus during its resolution. Quantification of T1 relaxation time was a good predictor of successful thrombolysis with a cutoff point of <747 ms having a sensitivity and specificity to predict successful lysis of 83% and 94%, respectively. Conclusions The source of the T1 signal in the thrombus results from the oxidation of iron (released from the lysis of trapped erythrocytes in the thrombus) to its paramagnetic Fe3+ form. Quantification of T1 relaxation time appears to be a good predictor of the success of thrombolysis. PMID:23820077

Bidirectional Contrast agent leakage correction of dynamic susceptibility contrast (DSC)-MRI improves cerebral blood volume estimation and survival prediction in recurrent glioblastoma treated with bevacizumab.

PubMed

Leu, Kevin; Boxerman, Jerrold L; Lai, Albert; Nghiemphu, Phioanh L; Pope, Whitney B; Cloughesy, Timothy F; Ellingson, Benjamin M

2016-11-01

To evaluate a leakage correction algorithm for T 1 and T2* artifacts arising from contrast agent extravasation in dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) that accounts for bidirectional contrast agent flux and compare relative cerebral blood volume (CBV) estimates and overall survival (OS) stratification from this model to those made with the unidirectional and uncorrected models in patients with recurrent glioblastoma (GBM). We determined median rCBV within contrast-enhancing tumor before and after bevacizumab treatment in patients (75 scans on 1.5T, 19 scans on 3.0T) with recurrent GBM without leakage correction and with application of the unidirectional and bidirectional leakage correction algorithms to determine whether rCBV stratifies OS. Decreased post-bevacizumab rCBV from baseline using the bidirectional leakage correction algorithm significantly correlated with longer OS (Cox, P = 0.01), whereas rCBV change using the unidirectional model (P = 0.43) or the uncorrected rCBV values (P = 0.28) did not. Estimates of rCBV computed with the two leakage correction algorithms differed on average by 14.9%. Accounting for T 1 and T2* leakage contamination in DSC-MRI using a two-compartment, bidirectional rather than unidirectional exchange model might improve post-bevacizumab survival stratification in patients with recurrent GBM. J. Magn. Reson. Imaging 2016;44:1229-1237. © 2016 International Society for Magnetic Resonance in Medicine.

Power corrections to the HTL effective Lagrangian of QED

NASA Astrophysics Data System (ADS)

Carignano, Stefano; Manuel, Cristina; Soto, Joan

2018-05-01

We present compact expressions for the power corrections to the hard thermal loop (HTL) Lagrangian of QED in d space dimensions. These are corrections of order (L / T) 2, valid for momenta L ≪ T, where T is the temperature. In the limit d → 3 we achieve a consistent regularization of both infrared and ultraviolet divergences, which respects the gauge symmetry of the theory. Dimensional regularization also allows us to witness subtle cancellations of infrared divergences. We also discuss how to generalize our results in the presence of a chemical potential, so as to obtain the power corrections to the hard dense loop (HDL) Lagrangian.

Semi-automatic segmentation of myocardium at risk in T2-weighted cardiovascular magnetic resonance.

PubMed

Sjögren, Jane; Ubachs, Joey F A; Engblom, Henrik; Carlsson, Marcus; Arheden, Håkan; Heiberg, Einar

2012-01-31

T2-weighted cardiovascular magnetic resonance (CMR) has been shown to be a promising technique for determination of ischemic myocardium, referred to as myocardium at risk (MaR), after an acute coronary event. Quantification of MaR in T2-weighted CMR has been proposed to be performed by manual delineation or the threshold methods of two standard deviations from remote (2SD), full width half maximum intensity (FWHM) or Otsu. However, manual delineation is subjective and threshold methods have inherent limitations related to threshold definition and lack of a priori information about cardiac anatomy and physiology. Therefore, the aim of this study was to develop an automatic segmentation algorithm for quantification of MaR using anatomical a priori information. Forty-seven patients with first-time acute ST-elevation myocardial infarction underwent T2-weighted CMR within 1 week after admission. Endocardial and epicardial borders of the left ventricle, as well as the hyper enhanced MaR regions were manually delineated by experienced observers and used as reference method. A new automatic segmentation algorithm, called Segment MaR, defines the MaR region as the continuous region most probable of being MaR, by estimating the intensities of normal myocardium and MaR with an expectation maximization algorithm and restricting the MaR region by an a priori model of the maximal extent for the user defined culprit artery. The segmentation by Segment MaR was compared against inter observer variability of manual delineation and the threshold methods of 2SD, FWHM and Otsu. MaR was 32.9 ± 10.9% of left ventricular mass (LVM) when assessed by the reference observer and 31.0 ± 8.8% of LVM assessed by Segment MaR. The bias and correlation was, -1.9 ± 6.4% of LVM, R = 0.81 (p < 0.001) for Segment MaR, -2.3 ± 4.9%, R = 0.91 (p < 0.001) for inter observer variability of manual delineation, -7.7 ± 11.4%, R = 0.38 (p = 0.008) for 2SD, -21.0 ± 9.9%, R = 0.41 (p = 0.004) for FWHM, and 5.3 ± 9.6%, R = 0.47 (p < 0.001) for Otsu. There is a good agreement between automatic Segment MaR and manually assessed MaR in T2-weighted CMR. Thus, the proposed algorithm seems to be a promising, objective method for standardized MaR quantification in T2-weighted CMR.

Development of device for quantifying magnetic nanoparticle tracers accumulating in sentinel lymph nodes

NASA Astrophysics Data System (ADS)

Kuwahata, Akihiro; Kaneko, Miki; Chikaki, Shinichi; Kusakabe, Moriaki; Sekino, Masaki

2018-05-01

The developed device with electromagnetic coils and small permanent magnets quantifies the iron contents of superparamagnetic iron oxide nanoparticles for sentinel lymph node (SLN) biopsy. To remove diamagnetic and paramagnetic components and detect only superparamagnetic components, a 2nd harmonics signal is detected by a gradiometer under a moderate AC magnetic field (1-2 mT) with the fundamental frequency (2.944 kHz) of the coils and DC magnetic field (1-2 mT) of the magnets. The detection limit with a signal-to-noise ratio of 5 is approximately 0.28 μg of iron, and the device has a wide dynamic range of 104, 0.28 μg-2.8 mg. Additional coils and permanent magnets play an important role producing the optimum distribution of AC/DC magnetic fields for an iron distribution-independent and SLN size-independent quantification. We demonstrated the quantification of the iron in phantoms, which have a size of 3-20 mm with varied iron distributions and contain magnetic nanoparticles numerically. These results indicate that the developed device is useful for quantifying the magnetic nanoparticles accumulating in SLNs.

Surface smoothness: cartilage biomarkers for knee OA beyond the radiologist

NASA Astrophysics Data System (ADS)

Tummala, Sudhakar; Dam, Erik B.

2010-03-01

Fully automatic imaging biomarkers may allow quantification of patho-physiological processes that a radiologist would not be able to assess reliably. This can introduce new insight but is problematic to validate due to lack of meaningful ground truth expert measurements. Rather than quantification accuracy, such novel markers must therefore be validated against clinically meaningful end-goals such as the ability to allow correct diagnosis. We present a method for automatic cartilage surface smoothness quantification in the knee joint. The quantification is based on a curvature flow method used on tibial and femoral cartilage compartments resulting from an automatic segmentation scheme. These smoothness estimates are validated for their ability to diagnose osteoarthritis and compared to smoothness estimates based on manual expert segmentations and to conventional cartilage volume quantification. We demonstrate that the fully automatic markers eliminate the time required for radiologist annotations, and in addition provide a diagnostic marker superior to the evaluated semi-manual markers.

T1ρ MRI Quantification of Arthroscopically-Confirmed Cartilage Degeneration

PubMed Central

Witschey, Walter RT; Borthakur, Arijitt; Fenty, Matt; Kneeland, J Bruce; Lonner, Jess H; McArdle, Erin L.; Sochor, Matt; Reddy, Ravinder

2010-01-01

9 asymptomatic subjects and 6 patients underwent T1ρ MRI to determine whether Outerbridge grade 1 or 2 cartilage degeneration observed during arthroscopy could be detected noninvasively. MRI was performed 2–3 months post-arthroscopy using sagittal T1-weighted and axial and coronal T1ρ MRI from which spatial T1ρ relaxation maps were calculated from segmented T1-weighted images. Median T1ρ relaxation times of patients with arthroscopically documented cartilage degeneration and asymptomatic subjects were significantly different (p < 0.001) and median T1ρ exceeded asymptomatic articular cartilage median T1ρ by 2.5 to 9.2 ms. In 8 observations of mild cartilage degeneration at arthroscopy (Outerbridge grades 1 and 2), mean compartment T1ρ was elevated in 5, but in all observations, large foci of increased T1ρ were observed. It was determined that T1ρ could detect some, but not all, Outerbridge grade 1 and 2 cartilage degeneration but that a larger patient population is needed to determine the sensitivity to these changes. PMID:20432308

Evaluation of a transvaginal mesh delivery system for the correction of pelvic organ prolapse: subjective and objective findings at least 1 year after surgery.

PubMed

Culligan, Patrick J; Littman, Paul M; Salamon, Charbel G; Priestley, Jennifer L; Shariati, Amir

2010-11-01

We sought to track objective and subjective outcomes ≥1 year after transvaginal mesh system to correct prolapse. This was a retrospective cohort study of 120 women who received a transvaginal mesh procedure (Avaulta Solo, CR Bard Inc, Covington, GA). Outcomes were pelvic organ prolapse quantification values; Pelvic Floor Distress Inventory, Short Form 20/Pelvic Floor Impact Questionnaire, Short Form 7 scores; and a surgical satisfaction survey. "Surgical failure" was defined as pelvic organ prolapse quantification point >0, and/or any reports of vaginal bulge. Of 120 patients, 116 (97%) were followed up for a mean of 14.4 months (range, 12-30). In all, 74 patients had only anterior mesh, 21 only posterior mesh, and 21 both meshes. Surgical cure rate was 81%. Surgical failure was more common if preoperative point C ≥+2 (35% vs 16%; P = .04). Mesh erosion and de novo pain occurred in 11.7% and 3.3%, respectively. Pelvic Floor Distress Inventory, Short Form 20/Pelvic Floor Impact Questionnaire, Short Form 7 scores improved (P < .01). Objective and subjective improvements occurred at ≥1 year, yet failure rates were high when preoperative point C was ≥+2. Copyright © 2010 Mosby, Inc. All rights reserved.

Influence of amplitude-related perfusion parameters in the parotid glands by non-fat-saturated dynamic contrast-enhanced magnetic resonance imaging.

PubMed

Chiu, Su-Chin; Cheng, Cheng-Chieh; Chang, Hing-Chiu; Chung, Hsiao-Wen; Chiu, Hui-Chu; Liu, Yi-Jui; Hsu, Hsian-He; Juan, Chun-Jung

2016-04-01

To verify whether quantification of parotid perfusion is affected by fat signals on non-fat-saturated (NFS) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and whether the influence of fat is reduced with fat saturation (FS). This study consisted of three parts. First, a retrospective study analyzed DCE-MRI data previously acquired on different patients using NFS (n = 18) or FS (n = 18) scans. Second, a phantom study simulated the signal enhancements in the presence of gadolinium contrast agent at six concentrations and three fat contents. Finally, a prospective study recruited nine healthy volunteers to investigate the influence of fat suppression on perfusion quantification on the same subjects. Parotid perfusion parameters were derived from NFS and FS DCE-MRI data using both pharmacokinetic model analysis and semiquantitative parametric analysis. T tests and linear regression analysis were used for statistical analysis with correction for multiple comparisons. NFS scans showed lower amplitude-related parameters, including parameter A, peak enhancement (PE), and slope than FS scans in the patients (all with P < 0.0167). The relative signal enhancement in the phantoms was proportional to the dose of contrast agent and was lower in NFS scans than in FS scans. The volunteer study showed lower parameter A (6.75 ± 2.38 a.u.), PE (42.12% ± 14.87%), and slope (1.43% ± 0.54% s(-1)) in NFS scans as compared to 17.63 ± 8.56 a.u., 104.22% ± 25.15%, and 9.68% ± 1.67% s(-1), respectively, in FS scans (all with P < 0.005). These amplitude-related parameters were negatively associated with the fat content in NFS scans only (all with P < 0.05). On NFS DCE-MRI, quantification of parotid perfusion is adversely affected by the presence of fat signals for all amplitude-related parameters. The influence could be reduced on FS scans.

Correction for FDG PET dose extravasations: Monte Carlo validation and quantitative evaluation of patient studies.

PubMed

Silva-Rodríguez, Jesús; Aguiar, Pablo; Sánchez, Manuel; Mosquera, Javier; Luna-Vega, Víctor; Cortés, Julia; Garrido, Miguel; Pombar, Miguel; Ruibal, Alvaro

2014-05-01

Current procedure guidelines for whole body [18F]fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography (PET) state that studies with visible dose extravasations should be rejected for quantification protocols. Our work is focused on the development and validation of methods for estimating extravasated doses in order to correct standard uptake value (SUV) values for this effect in clinical routine. One thousand three hundred sixty-seven consecutive whole body FDG-PET studies were visually inspected looking for extravasation cases. Two methods for estimating the extravasated dose were proposed and validated in different scenarios using Monte Carlo simulations. All visible extravasations were retrospectively evaluated using a manual ROI based method. In addition, the 50 patients with higher extravasated doses were also evaluated using a threshold-based method. Simulation studies showed that the proposed methods for estimating extravasated doses allow us to compensate the impact of extravasations on SUV values with an error below 5%. The quantitative evaluation of patient studies revealed that paravenous injection is a relatively frequent effect (18%) with a small fraction of patients presenting considerable extravasations ranging from 1% to a maximum of 22% of the injected dose. A criterion based on the extravasated volume and maximum concentration was established in order to identify this fraction of patients that might be corrected for paravenous injection effect. The authors propose the use of a manual ROI based method for estimating the effectively administered FDG dose and then correct SUV quantification in those patients fulfilling the proposed criterion.

Correction for FDG PET dose extravasations: Monte Carlo validation and quantitative evaluation of patient studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silva-Rodríguez, Jesús, E-mail: jesus.silva.rodriguez@sergas.es; Aguiar, Pablo, E-mail: pablo.aguiar.fernandez@sergas.es; Servicio de Medicina Nuclear, Complexo Hospitalario Universidade de Santiago de Compostela

Purpose: Current procedure guidelines for whole body [18F]fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography (PET) state that studies with visible dose extravasations should be rejected for quantification protocols. Our work is focused on the development and validation of methods for estimating extravasated doses in order to correct standard uptake value (SUV) values for this effect in clinical routine. Methods: One thousand three hundred sixty-seven consecutive whole body FDG-PET studies were visually inspected looking for extravasation cases. Two methods for estimating the extravasated dose were proposed and validated in different scenarios using Monte Carlo simulations. All visible extravasations were retrospectively evaluated using a manualmore » ROI based method. In addition, the 50 patients with higher extravasated doses were also evaluated using a threshold-based method. Results: Simulation studies showed that the proposed methods for estimating extravasated doses allow us to compensate the impact of extravasations on SUV values with an error below 5%. The quantitative evaluation of patient studies revealed that paravenous injection is a relatively frequent effect (18%) with a small fraction of patients presenting considerable extravasations ranging from 1% to a maximum of 22% of the injected dose. A criterion based on the extravasated volume and maximum concentration was established in order to identify this fraction of patients that might be corrected for paravenous injection effect. Conclusions: The authors propose the use of a manual ROI based method for estimating the effectively administered FDG dose and then correct SUV quantification in those patients fulfilling the proposed criterion.« less

Quantification of free fatty acids in human stratum corneum using tandem mass spectrometry and surrogate analyte approach.

PubMed

Dapic, Irena; Kobetic, Renata; Brkljacic, Lidija; Kezic, Sanja; Jakasa, Ivone

2018-02-01

The free fatty acids (FFAs) are one of the major components of the lipids in the stratum corneum (SC), the uppermost layer of the skin. Relative composition of FFAs has been proposed as a biomarker of the skin barrier status in patients with atopic dermatitis (AD). Here, we developed an LC-ESI-MS/MS method for simultaneous quantification of a range of FFAs with long and very long chain length in the SC collected by adhesive tape (D-Squame). The method, based on derivatization with 2-bromo-1-methylpyridinium iodide and 3-carbinol-1-methylpyridinium iodide, allowed highly sensitive detection and quantification of FFAs using multiple reaction monitoring. For the quantification, we applied a surrogate analyte approach and internal standardization using isotope labeled derivatives of FFAs. Adhesive tapes showed the presence of several FFAs, which are also present in the SC, a problem encountered in previous studies. Therefore, the levels of FFAs in the SC were corrected using C12:0, which was present on the adhesive tape, but not detected in the SC. The method was applied to SC samples from patients with atopic dermatitis and healthy subjects. Quantification using multiple reaction monitoring allowed sufficient sensitivity to analyze FFAs of chain lengths C16-C28 in the SC collected on only one tape strip. Copyright © 2017 John Wiley & Sons, Ltd.

Separation, identification, quantification, and method validation of anthocyanins in botanical supplement raw materials by HPLC and HPLC-MS.

PubMed

Chandra, A; Rana, J; Li, Y

2001-08-01

A method has been established and validated for identification and quantification of individual, as well as total, anthocyanins by HPLC and LC/ES-MS in botanical raw materials used in the herbal supplement industry. The anthocyanins were separated and identified on the basis of their respective M(+) (cation) using LC/ES-MS. Separated anthocyanins were individually calculated against one commercially available anthocyanin external standard (cyanidin-3-glucoside chloride) and expressed as its equivalents. Amounts of each anthocyanin calculated as external standard equivalent were then multiplied by a molecular-weight correction factor to afford their specific quantities. Experimental procedures and use of a molecular-weight correction factors are substantiated and validated using Balaton tart cherry and elderberry as templates. Cyanidin-3-glucoside chloride has been widely used in the botanical industry to calculate total anthocyanins. In our studies on tart cherry and elderberry, its use as external standard followed by use of molecular-weight correction factors should provide relatively accurate results for total anthocyanins, because of the presence of cyanidin as their major anthocyanidin backbone. The method proposed here is simple and has a direct sample preparation procedure without any solid-phase extraction. It enables selection and use of commercially available anthocyanins as external standards for quantification of specific anthocyanins in the sample matrix irrespective of their commercial availability as analytical standards. It can be used as a template and applied for similar quantification in several anthocyanin-containing raw materials for routine quality control procedures, thus providing consistency in analytical testing of botanical raw materials used for manufacturing efficacious and true-to-the-label nutritional supplements.

Quantification of nimesulide in human plasma by high-performance liquid chromatography with ultraviolet detector (HPLC-UV): application to pharmacokinetic studies in 28 healthy Korean subjects.

PubMed

Kim, Mi-Sun; Park, Yoo-Sin; Kim, Shin-Hee; Kim, Sang-Yeon; Lee, Min-Ho; Kim, Youn-Hee; Kim, Do-Wan; Yang, Seok-Chul; Kang, Ju-Seop

2012-05-01

Nimesulide is a selective COX-2 inhibitor that is as effective as the classical non-acidic nonsteroidal anti-inflammatory drugs in the relief of various pain and inflammatory conditions, but is better tolerated with lower incidences of adverse effects than other drugs. After oral dose of 100 mg nimesulide to western subjects, a mean maximal concentration (C(max)) of 2.86 ∼ 6.5 µg/mL was reached at 1.22 ∼ 2.75 h and mean t(1/2β) of 1.8 ∼ 4.74 h. This study developed a robust method for quantification of nimesulide for the pharmacokinetics and suitability of its dosage in Korea and compared its suitability with other racial populations. Nimesulide and internal standard were extracted from acidified samples with methyl tert-butyl ether and analyzed by high-performance liquid chromatography with ultraviolet detection (HPLC-UV). The 28 healthy volunteers took 2 tablets of 100 mg nimesulide and blood concentrations were analyzed during the 24 h post dose. Several pharmacokinetic parameters were represented: AUC(0-infinity) = 113.0 mg-h/mL, C(max) = 12.06 mg/mL, time for maximal concentrations (T(max)) = 3.19 h and t(1/2β) = 4.51 h. These were different from those of western populations as follows: AUC was 14.5% and C(max) was 28% that of of Korean subjects and T(max) and t(1/2β) were also different. The validated HPLC-UV method was successfully applied for the pharmacokinetic studies of nimesulide in Korean subjects. Because the pharmacokinetics of nimesulide were different from western populations, its dosage regimen needs to be adjusted for Koreans. © The Author [2012]. Published by Oxford University Press. All rights reserved.

The Impact of a Common MDM2 SNP on the Sensitivity of Breast Cancer to Treatment

DTIC Science & Technology

2011-06-01

Kirchhoff T, Alexe G, Bond EE, Robins H, Bartel F, Taubert H, Wuerl P, Hait W, Toppmeyer D, Offit K, and Levine A. MDM2 SNP309 accelerates tumor...the Western blot analysis corresponding to the quantification in the upper graphs . 29 Figure 5. Effect of

Effect of background correction on peak detection and quantification in online comprehensive two-dimensional liquid chromatography using diode array detection.

PubMed

Allen, Robert C; John, Mallory G; Rutan, Sarah C; Filgueira, Marcelo R; Carr, Peter W

2012-09-07

A singular value decomposition-based background correction (SVD-BC) technique is proposed for the reduction of background contributions in online comprehensive two-dimensional liquid chromatography (LC×LC) data. The SVD-BC technique was compared to simply subtracting a blank chromatogram from a sample chromatogram and to a previously reported background correction technique for one dimensional chromatography, which uses an asymmetric weighted least squares (AWLS) approach. AWLS was the only background correction technique to completely remove the background artifacts from the samples as evaluated by visual inspection. However, the SVD-BC technique greatly reduced or eliminated the background artifacts as well and preserved the peak intensity better than AWLS. The loss in peak intensity by AWLS resulted in lower peak counts at the detection thresholds established using standards samples. However, the SVD-BC technique was found to introduce noise which led to detection of false peaks at the lower detection thresholds. As a result, the AWLS technique gave more precise peak counts than the SVD-BC technique, particularly at the lower detection thresholds. While the AWLS technique resulted in more consistent percent residual standard deviation values, a statistical improvement in peak quantification after background correction was not found regardless of the background correction technique used. Copyright © 2012 Elsevier B.V. All rights reserved.

Colorectal cancer and 18FDG-PET/CT: What about adding the T to the N parameter in loco-regional staging?

PubMed Central

Mainenti, Pier Paolo; Iodice, Delfina; Segreto, Sabrina; Storto, Giovanni; Magliulo, Mario; Palma, Giovanni Domenico De; Salvatore, Marco; Pace, Leonardo

2011-01-01

AIM: To evaluate whether FDG-positron emission tomography (PET)/computed tomography (CT) may be an accurate technique in the assessment of the T stage in patients with colorectal cancer. METHODS: Thirty four consecutive patients (20 men and 14 women; mean age: 63 years) with a histologically proven diagnosis of colorectal adenocarcinoma and scheduled for surgery in our hospital were enrolled in this study. All patients underwent FDG-PET/CT preoperatively. The primary tumor site and extent were evaluated on PET/CT images. Colorectal wall invasion was analysed according to a modified T classification that considers only three stages (≤ T2, T3, T4). Assessment of accuracy was carried out using 95% confidence intervals for T. RESULTS: Thirty five/37 (94.6%) adenocarcinomas were identified and correctly located on PET/CT images. PET/CT correctly staged the T of 33/35 lesions identified showing an accuracy of 94.3% (95% CI: 87%-100%). All T1, T3 and T4 lesions were correctly staged, while two T2 neoplasms were overstated as T3. CONCLUSION: Our data suggest that FDG-PET/CT may be an accurate modality for identifying primary tumor and defining its local extent in patients with colorectal cancer. PMID:21472100

Correlation between Serum Levels of 3,3',5'-Triiodothyronine and Thyroid Hormones Measured by Liquid Chromatography-Tandem Mass Spectrometry and Immunoassay.

PubMed

Sakai, Hiroyuki; Nagao, Hidenori; Sakurai, Mamoru; Okumura, Takako; Nagai, Yoshiyuki; Shikuma, Junpei; Ito, Rokuro; Imazu, Tetsuya; Miwa, Takashi; Odawara, Masato

2015-01-01

For measuring serum 3,3',5'-triiodothyronine (rT3) levels, radioimmunoassay (RIA) has traditionally been used owing to the lack of other reliable methods; however, it has recently become difficult to perform. Meanwhile, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has recently been attracting attention as a novel alternative method in clinical chemistry. To the best of our knowledge, there are no studies to date comparing results of the quantification of human serum rT3 between LC-MS/MS and RIA. We therefore examined the feasibility of LC-MS/MS as a novel alternative method for measuring serum rT3, thyroxine (T4), and 3,5,3'-triiodothyronine (T3) levels. Assay validation was performed by LC-MS/MS using quality control samples of rT3, T4, and T3 at 4 various concentrations which were prepared from reference compounds. Serum samples of 50 outpatients in our department were quantified both by LC-MS/MS and conventional immunoassay for rT3, T4, and T3. Correlation coefficients between the 2 measurement methods were statistically analyzed respectively. Matrix effects were not observed with our method. Intra-day and inter-day precisions were less than 10.8% and 9.6% for each analyte at each quality control level, respectively. Intra-day and inter-day accuracies were between 96.2% and 110%, and between 98.3% and 108.6%, respectively. The lower limit of quantification was 0.05 ng/mL. Strong correlations were observed between the 2 measurement methods (correlation coefficient, T4: 0.976, p < 0.001; T3: 0.912, p < 0.001; rT3: 0.928, p < 0.001). Our LC-MS/MS system requires no manual cleanup operation, and the process after application of a sample is fully automated; furthermore, it was found to be highly sensitive, and superior in both precision and accuracy. The correlation between the 2 methods over a wide range of concentrations was strong. LC-MS/MS is therefore expected to become a useful tool for clinical diagnosis and research.

Characterization and MCNP simulation of neutron energy spectrum shift after transmission through strong absorbing materials and its impact on tomography reconstructed image.

PubMed

Hachouf, N; Kharfi, F; Boucenna, A

2012-10-01

An ideal neutron radiograph, for quantification and 3D tomographic image reconstruction, should be a transmission image which exactly obeys to the exponential attenuation law of a monochromatic neutron beam. There are many reasons for which this assumption does not hold for high neutron absorbing materials. The main deviations from the ideal are due essentially to neutron beam hardening effect. The main challenges of this work are the characterization of neutron transmission through boron enriched steel materials and the observation of beam hardening. Then, in our work, the influence of beam hardening effect on neutron tomographic image, for samples based on these materials, is studied. MCNP and FBP simulation are performed to adjust linear attenuation coefficients data and to perform 2D tomographic image reconstruction with and without beam hardening corrections. A beam hardening correction procedure is developed and applied based on qualitative and quantitative analyses of the projections data. Results from original and corrected 2D reconstructed images obtained shows the efficiency of the proposed correction procedure. Copyright © 2012 Elsevier Ltd. All rights reserved.

CO2 flux from Javanese mud volcanism.

PubMed

Queißer, M; Burton, M R; Arzilli, F; Chiarugi, A; Marliyani, G I; Anggara, F; Harijoko, A

2017-06-01

Studying the quantity and origin of CO 2 emitted by back-arc mud volcanoes is critical to correctly model fluid-dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO 2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO 2 with a volume fraction of at least 16 vol %. A lower limit CO 2 flux of 1.4 kg s -1 (117 t d -1 ) was determined, in line with the CO 2 flux from the Javanese mud volcano LUSI. Extrapolating these results to mud volcanism from the whole of Java suggests an order of magnitude total CO 2 flux of 3 kt d -1 , comparable with the expected back-arc efflux of magmatic CO 2 . After discussing geochemical, geological, and geophysical evidence we conclude that the source of CO 2 observed at Bledug Kuwu is likely a mixture of thermogenic, biogenic, and magmatic CO 2 , with faulting controlling potential pathways for magmatic fluids. This study further demonstrates the merit of man-portable active remote sensing instruments for probing natural gas releases, enabling bottom-up quantification of CO 2 fluxes.

CO2 flux from Javanese mud volcanism

PubMed Central

Burton, M. R.; Arzilli, F.; Chiarugi, A.; Marliyani, G. I.; Anggara, F.; Harijoko, A.

2017-01-01

Abstract Studying the quantity and origin of CO2 emitted by back‐arc mud volcanoes is critical to correctly model fluid‐dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO2 with a volume fraction of at least 16 vol %. A lower limit CO2 flux of 1.4 kg s−1 (117 t d−1) was determined, in line with the CO2 flux from the Javanese mud volcano LUSI. Extrapolating these results to mud volcanism from the whole of Java suggests an order of magnitude total CO2 flux of 3 kt d−1, comparable with the expected back‐arc efflux of magmatic CO2. After discussing geochemical, geological, and geophysical evidence we conclude that the source of CO2 observed at Bledug Kuwu is likely a mixture of thermogenic, biogenic, and magmatic CO2, with faulting controlling potential pathways for magmatic fluids. This study further demonstrates the merit of man‐portable active remote sensing instruments for probing natural gas releases, enabling bottom‐up quantification of CO2 fluxes. PMID:28944134

Reproducibility measurement of glutathione, GABA, and glutamate: Towards in vivo neurochemical profiling of multiple sclerosis with MR spectroscopy at 7T.

PubMed

Prinsen, Hetty; de Graaf, Robin A; Mason, Graeme F; Pelletier, Daniel; Juchem, Christoph

2017-01-01

To determine the reproducibility of a comprehensive single-session measurement of glutathione (GSH), γ-aminobutyric acid (GABA), glutamate, and other biochemicals implicated in the pathophysiology of multiple sclerosis (MS) in the human brain with 1 H magnetic resonance spectroscopy (MRS). Five healthy subjects were studied twice in separate 1-hour sessions at 7T. One MS patient was also scanned once. GSH and GABA were measured with J-difference editing using a semilocalized by adiabatic selective refocusing sequence (semi-LASER, TE = 72 msec). A stimulated echo acquisition mode sequence (STEAM, TE = 10 msec) was used to detect glutamate along with the overall biochemical profile. Spectra were quantified with LCModel. Quantification accuracy was assessed through Cramer-Rao lower bounds (CRLB). Reproducibility of the metabolite quantification was tested using coefficients of variation (CoV). CRLB were ≤7% for GSH, GABA, and glutamate and average CoV of 7.8 ± 3.2%, 9.5 ± 7.0%, and 3.2 ± 1.7% were achieved, respectively. The average test/retest concentration differences at this measurement reproducibility and quantification accuracy were smaller for GABA and glutamate than intersubject variations in metabolite content with CoV ratios of 0.6 and 0.8, respectively. As proof of principle, GSH, GABA, and glutamate were also detected in an MS patient. GSH, GABA, glutamate, and other metabolites relevant in MS can be quantified at 7T with high accuracy and reproducibility in a single 1-hour session. This methodology might serve as a clinical research tool to investigate biochemical markers associated with MS. 2 J. Magn. Reson. Imaging 2017;45:187-198. © 2016 International Society for Magnetic Resonance in Medicine.

T1 mapping with the variable flip angle technique: A simple correction for insufficient spoiling of transverse magnetization.

PubMed

Baudrexel, Simon; Nöth, Ulrike; Schüre, Jan-Rüdiger; Deichmann, Ralf

2018-06-01

The variable flip angle method derives T 1 maps from radiofrequency-spoiled gradient-echo data sets, acquired with different flip angles α. Because the method assumes validity of the Ernst equation, insufficient spoiling of transverse magnetization yields errors in T 1 estimation, depending on the chosen radiofrequency-spoiling phase increment (Δϕ). This paper presents a versatile correction method that uses modified flip angles α' to restore the validity of the Ernst equation. Spoiled gradient-echo signals were simulated for three commonly used phase increments Δϕ (50°/117°/150°), different values of α, repetition time (TR), T 1 , and a T 2 of 85 ms. For each parameter combination, α' (for which the Ernst equation yielded the same signal) and a correction factor C Δϕ (α, TR, T 1 ) = α'/α were determined. C Δϕ was found to be independent of T 1 and fitted as polynomial C Δϕ (α, TR), allowing to calculate α' for any protocol using this Δϕ. The accuracy of the correction method for T 2 values deviating from 85 ms was also determined. The method was tested in vitro and in vivo for variable flip angle scans with different acquisition parameters. The technique considerably improved the accuracy of variable flip angle-based T 1 maps in vitro and in vivo. The proposed method allows for a simple correction of insufficient spoiling in gradient-echo data. The required polynomial parameters are supplied for three common Δϕ. Magn Reson Med 79:3082-3092, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Quantification of traumatic meningeal injury using dynamic contrast enhanced (DCE) fluid-attenuated inversion recovery (FLAIR) imaging

NASA Astrophysics Data System (ADS)

Castro, Marcelo A.; Williford, Joshua P.; Cota, Martin R.; MacLaren, Judy M.; Dardzinski, Bernard J.; Latour, Lawrence L.; Pham, Dzung L.; Butman, John A.

2016-03-01

Traumatic meningeal injury is a novel imaging marker of traumatic brain injury, which appears as enhancement of the dura on post-contrast T2-weighted FLAIR images, and is likely associated with inflammation of the meninges. Dynamic Contrast Enhanced MRI provides a better discrimination of abnormally perfused regions. A method to properly identify those regions is presented. Images of seventeen patients scanned within 96 hours of head injury with positive traumatic meningeal injury were normalized and aligned. The difference between the pre- and last post-contrast acquisitions was segmented and voxels in the higher class were spatially clustered. Spatial and morphological descriptors were used to identify the regions of enhancement: a) centroid; b) distance to the brain mask from external voxels; c) distance from internal voxels; d) size; e) shape. The method properly identified thirteen regions among all patients. The method failed in one case due to the presence of a large brain lesion that altered the mask boundaries. Most false detections were correctly rejected resulting in a sensitivity and specificity of 92.9% and 93.6%, respectively.

Detection and Quantification of Viable and Nonviable Trypanosoma cruzi Parasites by a Propidium Monoazide Real-Time Polymerase Chain Reaction Assay

PubMed Central

Cancino-Faure, Beatriz; Fisa, Roser; Alcover, M. Magdalena; Jimenez-Marco, Teresa; Riera, Cristina

2016-01-01

Molecular techniques based on real-time polymerase chain reaction (qPCR) allow the detection and quantification of DNA but are unable to distinguish between signals from dead or live cells. Because of the lack of simple techniques to differentiate between viable and nonviable cells, the aim of this study was to optimize and evaluate a straightforward test based on propidium monoazide (PMA) dye action combined with a qPCR assay (PMA-qPCR) for the selective quantification of viable/nonviable epimastigotes of Trypanosoma cruzi. PMA has the ability to penetrate the plasma membrane of dead cells and covalently cross-link to the DNA during exposure to bright visible light, thereby inhibiting PCR amplification. Different concentrations of PMA (50–200 μM) and epimastigotes of the Maracay strain of T. cruzi (1 × 105–10 parasites/mL) were assayed; viable and nonviable parasites were tested and quantified by qPCR with a TaqMan probe specific for T. cruzi. In the PMA-qPCR assay optimized at 100 μM PMA, a significant qPCR signal reduction was observed in the nonviable versus viable epimastigotes treated with PMA, with a mean signal reduction of 2.5 logarithm units and a percentage of signal reduction > 98%, in all concentrations of parasites assayed. This signal reduction was also observed when PMA-qPCR was applied to a mixture of live/dead parasites, which allowed the detection of live cells, except when the concentration of live parasites was low (10 parasites/mL). The PMA-qPCR developed allows differentiation between viable and nonviable epimastigotes of T. cruzi and could thus be a potential method of parasite viability assessment and quantification. PMID:27139452

Quantitative analysis of MRI-guided attenuation correction techniques in time-of-flight brain PET/MRI.

PubMed

Mehranian, Abolfazl; Arabi, Hossein; Zaidi, Habib

2016-04-15

In quantitative PET/MR imaging, attenuation correction (AC) of PET data is markedly challenged by the need of deriving accurate attenuation maps from MR images. A number of strategies have been developed for MRI-guided attenuation correction with different degrees of success. In this work, we compare the quantitative performance of three generic AC methods, including standard 3-class MR segmentation-based, advanced atlas-registration-based and emission-based approaches in the context of brain time-of-flight (TOF) PET/MRI. Fourteen patients referred for diagnostic MRI and (18)F-FDG PET/CT brain scans were included in this comparative study. For each study, PET images were reconstructed using four different attenuation maps derived from CT-based AC (CTAC) serving as reference, standard 3-class MR-segmentation, atlas-registration and emission-based AC methods. To generate 3-class attenuation maps, T1-weighted MRI images were segmented into background air, fat and soft-tissue classes followed by assignment of constant linear attenuation coefficients of 0, 0.0864 and 0.0975 cm(-1) to each class, respectively. A robust atlas-registration based AC method was developed for pseudo-CT generation using local weighted fusion of atlases based on their morphological similarity to target MR images. Our recently proposed MRI-guided maximum likelihood reconstruction of activity and attenuation (MLAA) algorithm was employed to estimate the attenuation map from TOF emission data. The performance of the different AC algorithms in terms of prediction of bones and quantification of PET tracer uptake was objectively evaluated with respect to reference CTAC maps and CTAC-PET images. Qualitative evaluation showed that the MLAA-AC method could sparsely estimate bones and accurately differentiate them from air cavities. It was found that the atlas-AC method can accurately predict bones with variable errors in defining air cavities. Quantitative assessment of bone extraction accuracy based on Dice similarity coefficient (DSC) showed that MLAA-AC and atlas-AC resulted in DSC mean values of 0.79 and 0.92, respectively, in all patients. The MLAA-AC and atlas-AC methods predicted mean linear attenuation coefficients of 0.107 and 0.134 cm(-1), respectively, for the skull compared to reference CTAC mean value of 0.138cm(-1). The evaluation of the relative change in tracer uptake within 32 distinct regions of the brain with respect to CTAC PET images showed that the 3-class MRAC, MLAA-AC and atlas-AC methods resulted in quantification errors of -16.2 ± 3.6%, -13.3 ± 3.3% and 1.0 ± 3.4%, respectively. Linear regression and Bland-Altman concordance plots showed that both 3-class MRAC and MLAA-AC methods result in a significant systematic bias in PET tracer uptake, while the atlas-AC method results in a negligible bias. The standard 3-class MRAC method significantly underestimated cerebral PET tracer uptake. While current state-of-the-art MLAA-AC methods look promising, they were unable to noticeably reduce quantification errors in the context of brain imaging. Conversely, the proposed atlas-AC method provided the most accurate attenuation maps, and thus the lowest quantification bias. Copyright © 2016 Elsevier Inc. All rights reserved.

Toward real-time quantification of fluorescence molecular probes using target/background ratio for guiding biopsy and endoscopic therapy of esophageal neoplasia.

PubMed

Jiang, Yang; Gong, Yuanzheng; Rubenstein, Joel H; Wang, Thomas D; Seibel, Eric J

2017-04-01

Multimodal endoscopy using fluorescence molecular probes is a promising method of surveying the entire esophagus to detect cancer progression. Using the fluorescence ratio of a target compared to a surrounding background, a quantitative value is diagnostic for progression from Barrett's esophagus to high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC). However, current quantification of fluorescent images is done only after the endoscopic procedure. We developed a Chan-Vese-based algorithm to segment fluorescence targets, and subsequent morphological operations to generate background, thus calculating target/background (T/B) ratios, potentially to provide real-time guidance for biopsy and endoscopic therapy. With an initial processing speed of 2 fps and by calculating the T/B ratio for each frame, our method provides quasireal-time quantification of the molecular probe labeling to the endoscopist. Furthermore, an automatic computer-aided diagnosis algorithm can be applied to the recorded endoscopic video, and the overall T/B ratio is calculated for each patient. The receiver operating characteristic curve was employed to determine the threshold for classification of HGD/EAC using leave-one-out cross-validation. With 92% sensitivity and 75% specificity to classify HGD/EAC, our automatic algorithm shows promising results for a surveillance procedure to help manage esophageal cancer and other cancers inspected by endoscopy.

Application of the CC(P;Q) Hierarchy of Coupled-Cluster Methods to the Beryllium Dimer.

PubMed

Magoulas, Ilias; Bauman, Nicholas P; Shen, Jun; Piecuch, Piotr

2018-02-08

The performance of coupled-cluster approaches with higher-than-doubly excited clusters, including the CCSD(T), CCSD(2) T , CR-CC(2,3), CCSD(TQ), and CR-CC(2,4) corrections to CCSD, the active-space CCSDt, CCSDtq, and CCSDTq methods, and the CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) corrections to CCSDt, CCSDtq, and CCSDTq resulting from the CC(P;Q) formalism, in reproducing the CCSDT and CCSDTQ potential energy curves and vibrational term values characterizing Be 2 in its electronic ground state is assessed. The correlation-consistent aug-cc-pVnZ and aug-cc-pCVnZ (n = T and Q) basis sets are employed. Among the CCSD-based corrections, the completely renormalized CR-CC(2,3) and CR-CC(2,4) approaches perform the best. The CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) methods, especially CC(t;3) and CC(q;4), outperform other employed approaches in reproducing the CCSDT and CCSDTQ data. Composite schemes combining the all-electron CCSDT calculations extrapolated to the complete basis set limit with the frozen-core CC(q;4) and CCSDTQ computations using the aug-cc-pVTZ basis to account for connected quadruple excitations reproduce the latest experimental vibrational spectrum of Be 2 to within 4-5 cm -1 , when the vibrational spacings are examined, with typical errors being below 1-2 cm -1 . The resulting binding energies and equilibrium bond lengths agree with their experimentally derived counterparts to within ∼10 cm -1 and 0.01 Å.

Direct sampling graphite furnace atomic absorption spectrometry - feasibility of Na and K determination in desalted crude oil

NASA Astrophysics Data System (ADS)

Seeger, Tassia S.; Machado, Eduarda Q.; Flores, Erico M. M.; Mello, Paola A.; Duarte, Fabio A.

2018-03-01

In this study, Na and K were determined in desalted crude oil by direct sampling graphite furnace atomic absorption spectrometry (DS-GF AAS), with the use of a Zeeman-effect background correction system with variable magnetic field. The analysis was performed in low and high sensitivity conditions. Sodium determination was performed in two low-sensitivity conditions: 1) main absorption line (589.0 nm), gas stop flow during the atomization step and 3-field dynamic mode (0.6-0.8 T); and 2) secondary absorption line (330.3 nm), gas stop flow during the atomization and 2-field mode (0.8 T). In K determination, some parameters, such as high-sensitivity mode, main absorption line (766.5 nm), gas stop flow during the atomization and 2-field mode (0.8 T), were used. Suitability of chemical modifiers, such as Pd and W-Ir was also evaluated. The heating program for Na and K was based on the pyrolysis and atomization curves. Calibration was performed by aqueous standards. Accuracy was evaluated by the analysis of Green Petroleum Coke (SRM NIST 2718) and Trace Elements in Fuel Oil (SRM NIST 1634c). Recovery tests were also performed and results were compared with those obtained by GF AAS after crude oil digestion by microwave-assisted digestion. The characteristic mass of Na was 17.1 pg and 0.46 ng in conditions 1 and 2, respectively, while the one of K was 1.4 pg. Limits of detection and quantification by DS-GF AAS were 30 and 40 ng g-1 for Na and 3.2 and 4.2 ng g-1 for K, respectively. Sodium and K were determined in three crude oil samples with API density ranging from 20.9 to 28.0. Sodium and K concentration ranged from 1.5 to 73 μg g-1 and from 23 to 522 ng g-1, respectively.

Joint correction of respiratory motion artifact and partial volume effect in lung/thoracic PET/CT imaging.

PubMed

Chang, Guoping; Chang, Tingting; Pan, Tinsu; Clark, John W; Mawlawi, Osama R

2010-12-01

Respiratory motion artifacts and partial volume effects (PVEs) are two degrading factors that affect the accuracy of image quantification in PET/CT imaging. In this article, the authors propose a joint motion and PVE correction approach (JMPC) to improve PET quantification by simultaneously correcting for respiratory motion artifacts and PVE in patients with lung/thoracic cancer. The objective of this article is to describe this approach and evaluate its performance using phantom and patient studies. The proposed joint correction approach incorporates a model of motion blurring, PVE, and object size/shape. A motion blurring kernel (MBK) is then estimated from the deconvolution of the joint model, while the activity concentration (AC) of the tumor is estimated from the normalization of the derived MBK. To evaluate the performance of this approach, two phantom studies and eight patient studies were performed. In the phantom studies, two motion waveforms-a linear sinusoidal and a circular motion-were used to control the motion of a sphere, while in the patient studies, all participants were instructed to breathe regularly. For the phantom studies, the resultant MBK was compared to the true MBK by measuring a correlation coefficient between the two kernels. The measured sphere AC derived from the proposed method was compared to the true AC as well as the ACs in images exhibiting PVE only and images exhibiting both PVE and motion blurring. For the patient studies, the resultant MBK was compared to the motion extent derived from a 4D-CT study, while the measured tumor AC was compared to the AC in images exhibiting both PVE and motion blurring. For the phantom studies, the estimated MBK approximated the true MBK with an average correlation coefficient of 0.91. The tumor ACs following the joint correction technique were similar to the true AC with an average difference of 2%. Furthermore, the tumor ACs on the PVE only images and images with both motion blur and PVE effects were, on average, 75% and 47.5% (10%) of the true AC, respectively, for the linear (circular) motion phantom study. For the patient studies, the maximum and mean AC/SUV on the PET images following the joint correction are, on average, increased by 125.9% and 371.6%, respectively, when compared to the PET images with both PVE and motion. The motion extents measured from the derived MBK and 4D-CT exhibited an average difference of 1.9 mm. The proposed joint correction approach can improve the accuracy of PET quantification by simultaneously compensating for the respiratory motion artifacts and PVE in lung/thoracic PET/CT imaging.

Increased numbers of CD38 molecules on bright CD8+ T lymphocytes in infectious mononucleosis caused by Epstein–Barr virus infection

PubMed Central

ŽIDOVEC LEPEJ, S; VINCE, A; ÐAKOVIĆ RODE, O; REMENAR, A; JEREN, T

2003-01-01

The aim of this study was to quantify the expression of CD38 on CD8+ T lymphocytes of patients with infectious mononucleosis (IM) caused by Epstein–Barr virus (EBV) and cytomegalovirus (CMV). CD38 quantification technique chosen for this study was based on the enumeration of CD38 antibody binding sites in comparison to the quantification standards rather than determining relative fluorescence, which is difficult to standardize. The study enrolled 19 patients with typical clinical and laboratory parameters compatible with EBV-induced IM as well as 10 patients with atypical clinical presentation of this disease. Furthermore, CD38 expression was analysed in a group of 13 patients with IM caused by CMV infection. CD38 quantification was performed within 6 days of the presentation of symptoms. All three groups of IM patients showed a statistically significant increase in the number of anti-CD38 antibody binding sites (which correspond to the number of CD38 molecules) on bright CD8+ T lymphocytes compared to healthy controls. The numbers of CD38 molecules expressed on CD8+ T lymphocytes did not differ significantly between IM patients with typical and atypical clinical presentation of the disease. Patients with CMV-induced IM had significantly lower numbers of CD38 molecules expressed on CD8+ T lymphocytes. Therefore, we conclude that CD38 quantification could be helpful in differential diagnostics of IM cases with atypical clinical presentation. PMID:12930365

Installation Restoration Program. Phase II. Confirmation/Quantification. Stage 1. Volume 2. Appendices A-M. Cannon AFB, New Mexico.

DTIC Science & Technology

1986-09-01

0’ - N tT qT -0 t" C-r C-, M z a <CLW 4 0 a. o.CL- C= un z LJJIIr-= r -I CiA c= cot ’ rcli LAJI LUU CLCL LLI- IOUa a. IF LLJLm I-l - ( Cft - 4 CL...Depth Graphic Core Sample Sample Cft ) Log Interval/ID Taken* Lithologic Description 0- .. ~.G TOPSOIL; with some wood and other debris. 5-.~J SB-lA-1 ST...Date Recev 7 T ime~ L Transported By La- aml No. 0,; 0 Comments_____________________ ________ ___ Inclusive Dates of Possession

SU-D-303-03: Impact of Uncertainty in T1 Measurements On Quantification of Dynamic Contrast Enhanced MRI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aryal, M; Cao, Y

2015-06-15

Purpose: Quantification of dynamic contrast enhanced (DCE) MRI requires native longitudinal relaxation time (T1) measurement. This study aimed to assess uncertainty in T1 measurements using two different methods. Methods and Materials: Brain MRI scans were performed on a 3T scanner in 9 patients who had low grade/benign tumors and partial brain radiotherapy without chemotherapy at pre-RT, week-3 during RT (wk-3), end-RT, and 1, 6 and 18 months after RT. T1-weighted images were acquired using gradient echo sequences with 1) 2 different flip angles (50 and 150), and 2) 5 variable TRs (100–2000ms). After creating quantitative T1 maps, average T1 wasmore » calculated in regions of interest (ROI), which were distant from tumors and received a total of accumulated radiation doses < 5 Gy at wk-3. ROIs included left and right normal Putamen and Thalamus (gray matter: GM), and frontal and parietal white matter (WM). Since there were no significant or even a trend of T1 changes from pre-RT to wk-3 in these ROIs, a relative repeatability coefficient (RC) of T1 as a measure of uncertainty was estimated in each ROI using the data pre-RT and at wk-3. The individual T1 changes at later time points were evaluated compared to the estimated RCs. Results: The 2-flip angle method produced small RCs in GM (9.7–11.7%) but large RCs in WM (12.2–13.6%) compared to the saturation-recovery (SR) method (11.0–17.7% for GM and 7.5–11.2% for WM). More than 81% of individual T1 changes were within T1 uncertainty ranges defined by RCs. Conclusion: Our study suggests that the impact of T1 uncertainty on physiological parameters derived from DCE MRI is not negligible. A short scan with 2 flip angles is able to achieve repeatability of T1 estimates similar to a long scan with 5 different TRs, and is desirable to be integrated in the DCE protocol. Present study was supported by National Institute of Health (NIH) under grant numbers; UO1 CA183848 and RO1 NS064973.« less

SU-G-IeP1-07: Inaccuracy of Lesion Blood Flow Quantification Related to the Proton Density Reference Image in Arterial Spin Labeling MRI of Brain Tumors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jen, M; Johnson, J; Hou, P

Purpose: Cerebral blood flow quantification in arterial spin labeling (ASL) MRI requires an estimate of the equilibrium magnetization of blood, which is often obtained by a set of proton density (PD) reference image. Normally, a constant blood-brain partition coefficient is assumed across the brain. However, this assumption may not be valid for brain lesions. This study aimed to evaluate the impact of lesion-related PD variations on ASL quantification in patients with brain tumors. Methods: MR images for posttreatment evaluation of 42 patients with brain tumors were retrospectively analyzed. These images were acquired on a 3T MRI scanner, including T2-weighted FLAIR,more » 3D pseudo-continuous ASL and post-contrast T1-weighted images. Anatomical images were coregistered with ASL images using the SPM software. Regions of interest (ROIs) of the enhancing and FLAIR lesions were manually drawn on the coregistered images. ROIs of the contralateral normal appearing tissues were also determined, with the consideration of approximating coil sensitivity patterns in lesion ROIs. Relative lesion blood flow (lesion/contralateral tissue) was calculated from both the CBF map (dependent on the PD) and the ΔM map for comparison. Results: The signal intensities in both enhancing and FLAIR lesions were significantly different than contralateral tissues on the PD reference image (p<0.001). The percent signal difference ranged from −15.9 to 19.2%, with a mean of 5.4% for the enhancing lesion, and from −2.8 to 22.9% with a mean of 10.1% for the FLAIR lesion. The high/low lesion-related PD signal resulted in inversely proportional under-/over-estimation of blood flow in both enhancing and FLAIR lesions. Conclusion: Significant signal differences were found between lesions and contralateral tissues in the PD reference image, which introduced errors in blood flow quantification in ASL. The error can be up to 20% in individual patients with an average of 5- 10% for the group of patients with brain tumors.« less

Impact of a Serious Videogame Designed for Flexible Insulin Therapy on the Knowledge and Behaviors of Children with Type 1 Diabetes: The LUDIDIAB Pilot Study.

PubMed

Joubert, Michael; Armand, Coline; Morera, Julia; Tokayeva, Leyla; Guillaume, Aurore; Reznik, Yves

2016-02-01

Flexible (or functional) insulin therapy method is a self-management education approach for intensive insulin therapy in patients with type 1 diabetes. The serious game (or applied game) "L'Affaire Birman" ("Mr. Birman's File") (available at www.gluciweb.com ) was specifically designed as an educational tool for the flexible insulin therapy method. Its educational impact was evaluated in children with type 1 diabetes. This prospective multicenter pilot study evaluated the effect of this videogame on the therapeutic knowledge and behavior of children with type 1 diabetes. PedCarbQuiz (PCQ) and Diabetes Self-Management Profile (DSMP) questionnaires were used before (T0), immediately after (T1), and 6 months after (T2) the unstructured use of the videogame. The 38 children enrolled in the study were 42% boys and 58% girls; they had a mean age of 13.7 ± 2.1 years old, a diabetes duration of 6.0 ± 3.8 years, and hemoglobin A1c (HbA1c) levels of 8.5 ± 1.4% (69.4 ± 9.4 mmol/mol). The children connected to the game 3.3 ± 2.8 times during this 6-month study. Their PCQ score increased from 31.6 ± 4.9 at T0 to 36.0 ± 4.0 at T2 (P < 0.05). Two PCQ subscores also increased significantly: the insulin titration score at T1 and T2 and the carbohydrate quantification score at T2. Conversely, the DSMP score was not different at T0, T1, and T2 (59.1 ± 9.9, 60.2 ± 9.8, and 60.0 ± 10.0, respectively), and HbA1c levels also remained stable throughout the study (8.4 ± 1.3%, 8.4 ± 1.2%, and 8.5 ± 1.5% at T0, T1, and T2, respectively). Subgroup analysis found a greater impact of the game in children with poor glycemic control and low knowledge at baseline. Adherence to the game was rather low (half of the children played less than 2.5 bouts), but no criterion was found to be predictive of this low attractiveness. Nonsupervised usage of the serious game "L'Affaire Birman" was able to improve insulin titration and carbohydrate quantification in children with type 1 diabetes.

Robustness of Fat Quantification using Chemical Shift Imaging

PubMed Central

Hansen, Katie H; Schroeder, Michael E; Hamilton, Gavin; Sirlin, Claude B; Bydder, Mark

2011-01-01

This purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: 2D/3D sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to known effects of T1 bias and the two forms of noise bias. PMID:22055856

Estimating changes in mean body temperature for humans during exercise using core and skin temperatures is inaccurate even with a correction factor.

PubMed

Jay, Ollie; Reardon, Francis D; Webb, Paul; Ducharme, Michel B; Ramsay, Tim; Nettlefold, Lindsay; Kenny, Glen P

2007-08-01

Changes in mean body temperature (DeltaT(b)) estimated by the traditional two-compartment model of "core" and "shell" temperatures and an adjusted two-compartment model incorporating a correction factor were compared with values derived by whole body calorimetry. Sixty participants (31 men, 29 women) cycled at 40% of peak O(2) consumption for 60 or 90 min in the Snellen calorimeter at 24 or 30 degrees C. The core compartment was represented by esophageal, rectal (T(re)), and aural canal temperature, and the shell compartment was represented by a 12-point mean skin temperature (T(sk)). Using T(re) and conventional core-to-shell weightings (X) of 0.66, 0.79, and 0.90, mean DeltaT(b) estimation error (with 95% confidence interval limits in parentheses) for the traditional model was -95.2% (-83.0, -107.3) to -76.6% (-72.8, -80.5) after 10 min and -47.2% (-40.9, -53.5) to -22.6% (-14.5, -30.7) after 90 min. Using T(re), X = 0.80, and a correction factor (X(0)) of 0.40, mean DeltaT(b) estimation error for the adjusted model was +9.5% (+16.9, +2.1) to -0.3% (+11.9, -12.5) after 10 min and +15.0% (+27.2, +2.8) to -13.7% (-4.2, -23.3) after 90 min. Quadratic analyses of calorimetry DeltaT(b) data was subsequently used to derive best-fitting values of X for both models and X(0) for the adjusted model for each measure of core temperature. The most accurate model at any time point or condition only accounted for 20% of the variation observed in DeltaT(b) for the traditional model and 56% for the adjusted model. In conclusion, throughout exercise the estimation of DeltaT(b) using any measure of core temperature together with mean skin temperature irrespective of weighting is inaccurate even with a correction factor customized for the specific conditions.

Correcting Too Much or Too Little? The Performance of Three Chi-Square Corrections.

PubMed

Foldnes, Njål; Olsson, Ulf Henning

2015-01-01

This simulation study investigates the performance of three test statistics, T1, T2, and T3, used to evaluate structural equation model fit under non normal data conditions. T1 is the well-known mean-adjusted statistic of Satorra and Bentler. T2 is the mean-and-variance adjusted statistic of Sattertwaithe type where the degrees of freedom is manipulated. T3 is a recently proposed version of T2 that does not manipulate degrees of freedom. Discrepancies between these statistics and their nominal chi-square distribution in terms of errors of Type I and Type II are investigated. All statistics are shown to be sensitive to increasing kurtosis in the data, with Type I error rates often far off the nominal level. Under excess kurtosis true models are generally over-rejected by T1 and under-rejected by T2 and T3, which have similar performance in all conditions. Under misspecification there is a loss of power with increasing kurtosis, especially for T2 and T3. The coefficient of variation of the nonzero eigenvalues of a certain matrix is shown to be a reliable indicator for the adequacy of these statistics.

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis

NASA Astrophysics Data System (ADS)

Mailhiot, Sarah E.; Zong, Fangrong; Maneval, James E.; June, Ronald K.; Galvosas, Petrik; Seymour, Joseph D.

2018-02-01

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

Installation Restoration Program. Phase II. Confirmation/Quantification. Stage 1 for Cannon AFB, New Mexico. Volume 1. Text.

DTIC Science & Technology

1986-03-24

interbedded sands and silts in5 the lower portion of the profile. The sand units within the caliche are gen- erally pink . quartzose. fine grained and...C1426 I- 0 .J C U-I 0 c 0 o .1. 00 44I -14 u -4 >u~ 0i c FloI ~ -r4 ra t-o 14 co 00 z -4 -t cc ’w4t ibe 4-39 C1426 ~-~-~2 o IL _ Cl) 0*l *IJ. *0 0 00 U.U 0

Determination of hydroxylated polychlorinated biphenyls (HO-PCBs) in blood plasma by high-performance liquid chromatography-electrospray ionization-tandem quadrupole mass spectrometry.

PubMed

Letcher, R J; Li, H X; Chu, S G

2005-01-01

Hydroxylated metabolites of polychlorinated biphenyls (HO-PCBs) and pentachlorophenol (PCP) are halogenated phenolic compounds, and they are increasingly common as environmental contaminants mainly in the blood of wildlife and humans. A methodology based on high-performance liquid chromatography (reversed-phase)-electrospray (negative) ionization-tandem quadrupole mass spectrometry (LC-ESI(-)-MS-MS) in the select ion monitoring or multiple reaction monitoring modes was developed for HO-PCB and PCP determination in blood plasma and serum. Among 11 environmentally relevant HO-PCB congeners and PCP spiked to fetal calf serum, quantitative assessments, including matrix effects on ESI(-) suppression/ enhancement, showed process (recovery) efficiencies of 73% to 89% without internal standard (IS) correction, and 88% to 103% with IS correction, and method limits of quantification ranging from 1 to 50 pg/g (wet weight). Using the developed LC-ESI(-)-MS methodology in comparison with GC-MS and GC-ECD based approaches, similar results were found for HO-PCB identification and quantification in the plasma of polar bear (Ursus maritimus) from the Canadian arctic. LC-ESI(-)-MS identified four HO-PCB congeners [4'-HO-2,2',4,6,6'-pentachlorobiphenyl (4'-HO-CB104), 4-HO-2,3,3',4',5-pentachlorobiphenyl (4-HO-CB107), 4-HO-2,3,3',5,5',6-hexachlorobiphenyl (4-HO-CB165) and 3'-HO-2,2',3,4,4',5,5'-heptachlorobiphenyl (3'-HO-CB180)], and 14 additional tetra- to hepta-chlorinated HO-PCBs isomers in the polar bear plasma.

[Method of correcting sensitivity nonuniformity using gaussian distribution on 3.0 Tesla abdominal MRI].

PubMed

Hayashi, Norio; Miyati, Tosiaki; Takanaga, Masako; Ohno, Naoki; Hamaguchi, Takashi; Kozaka, Kazuto; Sanada, Shigeru; Yamamoto, Tomoyuki; Matsui, Osamu

2011-01-01

In the direction where the phased array coil used in parallel magnetic resonance imaging (MRI) is perpendicular to the arrangement, sensitivity falls significantly. Moreover, in a 3.0 tesla (3T) abdominal MRI, the quality of the image is reduced by changes in the relaxation time, reinforcement of the magnetic susceptibility effect, etc. In a 3T MRI, which has a high resonant frequency, the signal of the depths (central part) is reduced in the trunk part. SCIC, which is sensitivity correction processing, has inadequate correction processing, such as that edges are emphasized and the central part is corrected. Therefore, we used 3T with a Gaussian distribution. The uneven compensation processing for sensitivity of an abdomen MR image was considered. The correction processing consisted of the following methods. 1) The center of gravity of the domain of the human body in an abdomen MR image was calculated. 2) The correction coefficient map was created from the center of gravity using the Gaussian distribution. 3) The sensitivity correction image was created from the correction coefficient map and the original picture image. Using the Gaussian correction to process the image, the uniformity calculated using the NEMA method was improved significantly compared to the original image of a phantom. In a visual evaluation by radiologists, the uniformity was improved significantly using the Gaussian correction processing. Because of the homogeneous improvement of the abdomen image taken using 3T MRI, the Gaussian correction processing is considered to be a very useful technique.

Initial evaluation of 18F-GE-179, a putative PET Tracer for activated N-methyl D-aspartate receptors.

PubMed

McGinnity, Colm J; Hammers, Alexander; Riaño Barros, Daniela A; Luthra, Sajinder K; Jones, Paul A; Trigg, William; Micallef, Caroline; Symms, Mark R; Brooks, David J; Koepp, Matthias J; Duncan, John S

2014-03-01

N-methyl D-aspartate (NMDA) ion channels play a key role in a wide range of physiologic (e.g., memory and learning tasks) and pathologic processes (e.g., excitotoxicity). To date, suitable PET markers of NMDA ion channel activity have not been available. (18)F-GE-179 is a novel radioligand that selectively binds to the open/active state of the NMDA receptor ion channel, displacing the binding of (3)H-tenocyclidine from the intrachannel binding site with an affinity of 2.4 nM. No significant binding was observed with 10 nM GE-179 at 60 other neuroreceptors, channels, or transporters. We describe the kinetic behavior of the radioligand in vivo in humans. Nine healthy participants (6 men, 3 women; median age, 37 y) each underwent a 90-min PET scan after an intravenous injection of (18)F-GE-179. Continuous arterial blood sampling over the first 15 min was followed by discrete blood sampling over the duration of the scan. Brain radioactivity (KBq/mL) was measured in summation images created from the attenuation- and motion-corrected dynamic images. Metabolite-corrected parent plasma input functions were generated. We assessed the abilities of 1-, 2-, and 3-compartment models to kinetically describe cerebral time-activity curves using 6 bilateral regions of interest. Parametric volume-of-distribution (V(T)) images were generated by voxelwise rank-shaping regularization of exponential spectral analysis (RS-ESA). A 2-brain-compartment, 4-rate-constant model best described the radioligand's kinetics in normal gray matter of subjects at rest. At 30 min after injection, 37% of plasma radioactivity represented unmetabolized (18)F-GE-179. The highest mean levels of gray matter radioactivity were seen in the putamina and peaked at 7.5 min. A significant positive correlation was observed between K1 and V(T) (Spearman ρ = 0.398; P = 0.003). Between-subject coefficients of variation of V(T) ranged between 12% and 16%. Voxelwise RS-ESA yielded similar V(T)s and coefficients of variation. (18)F-GE-179 exhibits high and rapid brain extraction, with a relatively homogeneous distribution in gray matter and acceptable between-subject variability. Despite its rapid peripheral metabolism, quantification of (18)F-GE-179 VT is feasible both within regions of interest and at the voxel level. The specificity of (18)F-GE-179 binding, however, requires further characterization with in vivo studies using activation and disease models.

Intensity inhomogeneity correction for magnetic resonance imaging of human brain at 7T.

PubMed

Uwano, Ikuko; Kudo, Kohsuke; Yamashita, Fumio; Goodwin, Jonathan; Higuchi, Satomi; Ito, Kenji; Harada, Taisuke; Ogawa, Akira; Sasaki, Makoto

2014-02-01

To evaluate the performance and efficacy for intensity inhomogeneity correction of various sequences of the human brain in 7T MRI using the extended version of the unified segmentation algorithm. Ten healthy volunteers were scanned with four different sequences (2D spin echo [SE], 3D fast SE, 2D fast spoiled gradient echo, and 3D time-of-flight) by using a 7T MRI system. Intensity inhomogeneity correction was performed using the "New Segment" module in SPM8 with four different values (120, 90, 60, and 30 mm) of full width at half maximum (FWHM) in Gaussian smoothness. The uniformity in signals in the entire white matter was evaluated using the coefficient of variation (CV); mean signal intensities between the subcortical and deep white matter were compared, and contrast between subcortical white matter and gray matter was measured. The length of the lenticulostriate (LSA) was measured on maximum intensity projection (MIP) images in the original and corrected images. In all sequences, the CV decreased as the FWHM value decreased. The differences of mean signal intensities between subcortical and deep white matter also decreased with smaller FWHM values. The contrast between white and gray matter was maintained at all FWHM values. LSA length was significantly greater in corrected MIP than in the original MIP images. Intensity inhomogeneity in 7T MRI can be successfully corrected using SPM8 for various scan sequences.

Multiband Spectral-Spatial RF Excitation for Hyperpolarized [2-13C]Dihydroxyacetone 13C-MR Metabolism Studies

PubMed Central

Marco-Rius, Irene; Cao, Peng; von Morze, Cornelius; Merrit, Matthew; Moreno, Karlos X; Chang, Gene-Yuan; Ohliger, Michael A.; Pearce, David; Kurhanewicz, John; Larson, Peder E. Z.; Vigneron, Daniel B.

2016-01-01

Purpose To develop a specialized multislice, single-acquisition approach to detect the metabolites of hyperpolarized [2-13C]dihydroxyacetone (DHAc) to probe gluconeogenesis in vivo, which have a broad 144 ppm spectral range (~4.6 KHz at 3T). A novel multiband RF excitation pulse was designed for independent flip angle control over 5-6 spectral-spatial (SPSP) excitation bands, each corrected for chemical shift misregistration effects. Methods Specialized multi-band SPSP RF pulses were designed, tested and applied to investigate hyperpolarized [2-13C]DHAc metabolism in kidney and liver of fasted rats with dynamic 13C-MRS and an optimal flip angle scheme. For comparison, experiments were also performed with narrow-band slice-selective RF pulses and a sequential change of the frequency offset to cover the five frequency bands of interest. Results The SPSP pulses provided a controllable spectral profile free of baseline distortion with improved signal to noise of the metabolite peaks, allowing for quantification of the metabolic products. We observed organ-specific differences in DHAc metabolism. There was 2-5 times more [2-13C]phosphoenolpyruvate and about 19 times more [2-13C]glycerol 3-phosphate in the liver than in the kidney. Conclusion A multiband SPSP RF pulse covering a spectral range over 144 ppm enabled in vivo characterization of HP [2-13C]dihydroxyacetone metabolism in rat liver and kidney. PMID:27017966

A semi-automatic method for quantification and classification of erythrocytes infected with malaria parasites in microscopic images.

PubMed

Díaz, Gloria; González, Fabio A; Romero, Eduardo

2009-04-01

Visual quantification of parasitemia in thin blood films is a very tedious, subjective and time-consuming task. This study presents an original method for quantification and classification of erythrocytes in stained thin blood films infected with Plasmodium falciparum. The proposed approach is composed of three main phases: a preprocessing step, which corrects luminance differences. A segmentation step that uses the normalized RGB color space for classifying pixels either as erythrocyte or background followed by an Inclusion-Tree representation that structures the pixel information into objects, from which erythrocytes are found. Finally, a two step classification process identifies infected erythrocytes and differentiates the infection stage, using a trained bank of classifiers. Additionally, user intervention is allowed when the approach cannot make a proper decision. Four hundred fifty malaria images were used for training and evaluating the method. Automatic identification of infected erythrocytes showed a specificity of 99.7% and a sensitivity of 94%. The infection stage was determined with an average sensitivity of 78.8% and average specificity of 91.2%.

Reproducibility of CMRO2 determination using dynamic 17 O MRI.

PubMed

Niesporek, Sebastian C; Umathum, Reiner; Lommen, Jonathan M; Behl, Nicolas G R; Paech, Daniel; Bachert, Peter; Ladd, Mark E; Nagel, Armin M

2018-06-01

To assess the reproducibility of 17 O MRI-based determination of the cerebral metabolic rate of oxygen consumption (CMRO 2 ) in healthy volunteers. To assess the influence of image acquisition and reconstruction parameters on dynamic quantification of functional parameters such as CMRO 2 . Dynamic 17 O MRI data were simulated and used to investigate influences of temporal resolution (Δt) and partial volume correction (PVC) on the determination of CMRO 2 . Three healthy volunteers were examined in two separate examinations. In vivo 17 O MRI measurements were conducted with a nominal spatial resolution of (7.5 mm) 3 using a density-adapted radial sequence with golden angle acquisition scheme. In each measurement, 4.0 ± 0.1 L of 70%-enriched 17 O gas were administered using a rebreathing system. Data were corrected with a PVC algorithm, and CMRO 2 was determined in gray matter (GM) and white matter (WM) compartments using a three-phase metabolic model (baseline, 17 O inhalation, decay phase). Comparison with the ground truth of simulations revealed improved CMRO 2 determination after application of PVC and with Δt ≤ 2:00 min. Evaluation of in vivo data yields to CMRO 2,GM  = 2.31 ± 0.1 μmol/g/min and to CMRO 2,WM  = 0.69 ± 0.04 μmol/g/min with coefficients of variation (CoV) of 0.3-5.5% and 4.3-5.0% for intra-volunteer and inter-volunteer data, respectively. This in vivo 17 O inhalation study demonstrated that the proposed experimental setup enables reproducible determination of CMRO 2 in healthy volunteers. Magn Reson Med 79:2923-2934, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Planning of vessel grafts for reconstructive surgery in congenital heart diseases

NASA Astrophysics Data System (ADS)

Rietdorf, U.; Riesenkampff, E.; Schwarz, T.; Kuehne, T.; Meinzer, H.-P.; Wolf, I.

2010-02-01

The Fontan operation is a surgical treatment for patients with severe congenital heart diseases, where a biventricular correction of the heart can't be achieved. In these cases, a uni-ventricular system is established. During the last step of surgery a tunnel segment is placed to connect the inferior caval vein directly with the pulmonary artery, bypassing the right atrium and ventricle. Thus, the existing ventricle works for the body circulation, while the venous blood is passively directed to the pulmonary arteries. Fontan tunnels can be placed intra- and extracardially. The location, length and shape of the tunnel must be planned accurately. Furthermore, if the tunnel is placed extracardially, it must be positioned between other anatomical structures without constraining them. We developed a software system to support planning of the tunnel location, shape, and size, making pre-operative preparation of the tunnel material possible. The system allows for interactive placement and adjustment of the tunnel, affords a three-dimensional visualization of the virtual Fontan tunnel inside the thorax, and provides a quantification of the length, circumferences and diameters of the tunnel segments. The visualization and quantification can be used to plan and prepare the tunnel material for surgery in order to reduce the intra-operative time and to improve the fit of the tunnel patch.

Statistical models to predict type 2 diabetes remission after bariatric surgery.

PubMed

Ramos-Levi, Ana M; Matia, Pilar; Cabrerizo, Lucio; Barabash, Ana; Sanchez-Pernaute, Andres; Calle-Pascual, Alfonso L; Torres, Antonio J; Rubio, Miguel A

2014-09-01

Type 2 diabetes (T2D) remission may be achieved after bariatric surgery (BS), but rates vary according to patients' baseline characteristics. The present study evaluates the relevance of several preoperative factors and develops statistical models to predict T2D remission 1 year after BS. We retrospectively studied 141 patients (57.4% women), with a preoperative diagnosis of T2D, who underwent BS in a single center (2006-2011). Anthropometric and glucose metabolism parameters before surgery and at 1-year follow-up were recorded. Remission of T2D was defined according to consensus criteria: HbA1c <6%, fasting glucose (FG) <100 mg/dL, absence of pharmacologic treatment. The influence of several preoperative factors was explored and different statistical models to predict T2D remission were elaborated using logistic regression analysis. Three preoperative characteristics considered individually were identified as the most powerful predictors of T2D remission: C-peptide (R2  = 0.249; odds ratio [OR] 1.652, 95% confidence interval [CI] 1.181-2.309; P = 0.003), T2D duration (R2  = 0.197; OR 0.869, 95% CI 0.808-0.935; P < 0.001), and previous insulin therapy (R2  = 0.165; OR 4.670, 95% CI 2.257-9.665; P < 0.001). High C-peptide levels, a shorter duration of T2D, and the absence of insulin therapy favored remission. Different multivariate logistic regression models were designed. When considering sex, T2D duration, and insulin treatment, remission was correctly predicted in 72.4% of cases. The model that included age, FG and C-peptide levels resulted in 83.7% correct classifications. When sex, FG, C-peptide, insulin treatment, and percentage weight loss were considered, correct classification of T2D remission was achieved in 95.9% of cases. Preoperative characteristics determine T2D remission rates after BS to different extents. The use of statistical models may help clinicians reliably predict T2D remission rates after BS. © 2014 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

Hypergravity-induced immunomodulation in a rodent model: lymphocytes and lymphoid organs

NASA Technical Reports Server (NTRS)

Gridley, Daila S.; Pecaut, Michael J.; Green, Lora M.; Miller, Glen M.; Nelson, Gregory A.

2002-01-01

The major goal of this study was to quantify changes in lymphoid organs and cells over time due to centrifugation-induced hypergravity. C57BL/6 mice were exposed to 1, 2 and 3 G and the following assays were performed on days 1, 4, 7, 10, and 21: spleen, thymus, lung, and liver masses; total leukocyte, lymphocyte, monocyte/macrophage, and granulocyte counts; level of splenocyte apoptosis; enumeration of CD3+ T, CD3+/CD4+ T helper, CD3+/CD8+ T cytotoxic, B220+ B, and NK1.1+ natural killer cells; and quantification of cells expressing CD25, CD69, and CD71 activation markers. The data show that increased gravity resulted in decreased body, spleen, thymus, and liver, but not lung, mass. Significant reductions were noted in all three major leukocyte populations (lymphocytes, granulocytes, monocyte/macrophages) [correction of macrphages] with increased gravity; persistent depletion was noted in blood but not spleen. Among the various lymphocyte populations, the CD3+/CD8+ T cells and B220+ B cells were the most affected and NK1.1+ NK cells the least affected. Overall, the changes were most evident during the first week, with a greater influence noted for cells in the spleen. A linear relationship was found between some of the measurements and the level of gravity, especially on day 4. These findings indicate that hypergravity profoundly alters leukocyte number and distribution in a mammalian model and that some aberrations persisted throughout the three weeks of the study. In certain cases, the detected changes were similar to those observed after whole-body irradiation. In future investigations we hope to combine hypergravity with low-dose rate irradiation and immune challenge.

Magnetic resonance cell-tracking studies: spectrophotometry-based method for the quantification of cellular iron content after loading with superparamagnetic iron oxide nanoparticles.

PubMed

Böhm, Ingrid

2011-08-01

The purpose of this article is to present a user-friendly tool for quantifying the iron content of superparamagnetic labeled cells before cell tracking by magnetic resonance imaging (MRI). Iron quantification was evaluated by using Prussian blue staining and spectrophotometry. White blood cells were labeled with superparamagnetic iron oxide (SPIO) nanoparticles. Labeling was confirmed by light microscopy. Subsequently, the cells were embedded in a phantom and scanned on a 3 T magnetic resonance tomography (MRT) whole-body system. Mean peak wavelengths λ(peak) was determined at A(720 nm) (range 719-722 nm). Linearity was proven for the measuring range 0.5 to 10 μg Fe/mL (r  =  .9958; p  =  2.2 × 10(-12)). The limit of detection was 0.01 μg Fe/mL (0.1785 mM), and the limit of quantification was 0.04 μg Fe/mL (0.714 mM). Accuracy was demonstrated by comparison with atomic absorption spectrometry. Precision and robustness were also proven. On T(2)-weighted images, signal intensity varied according to the iron concentration of SPIO-labeled cells. Absorption spectrophotometry is both a highly sensitive and user-friendly technique that is feasible for quantifying the iron content of magnetically labeled cells. The presented data suggest that spectrophotometry is a promising tool for promoting the implementation of magnetic resonance-based cell tracking in routine clinical applications (from bench to bedside).

A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

NASA Astrophysics Data System (ADS)

Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

2007-09-01

This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it improves not only the interpretation, but also the quantification.

Assessment of using digital manipulation tools for diagnosing mandibular radiolucent lesions

PubMed Central

Raitz, R; Assunção Junior, JNR; Fenyo-Pereira, M; Correa, L; de Lima, LP

2012-01-01

Objective The purpose of this study was to analyse the use of digital tools for image enhancement of mandibular radiolucent lesions and the effects of this manipulation on the percentage of correct radiographic diagnoses. Methods 24 panoramic radiographs exhibiting radiolucent lesions were selected, digitized and evaluated by non-experts (undergraduate and newly graduated practitioners) and by professional experts in oral diagnosis. The percentages of correct and incorrect diagnoses, according to the use of brightness/contrast, sharpness, inversion, highlight and zoom tools, were compared. All dental professionals made their evaluations without (T1) and with (T2) a list of radiographic diagnostic parameters. Results Digital tools were used with low frequency mainly in T2. The most preferred tool was sharpness (45.2%). In the expert group, the percentage of correct diagnoses did not change when any of the digital tools were used. For the non-expert group, there was an increase in the frequency of correct diagnoses when brightness/contrast was used in T2 (p=0.008) and when brightness/contrast and sharpness were not used in T1 (p=0.027). The use or non-use of brightness/contrast, zoom and sharpness showed moderate agreement in the group of experts [kappa agreement coefficient (κ)=0.514, 0.425 and 0.335, respectively]. For the non-expert group there was slight agreement for all the tools used (κ≤0.237). Conclusions Consulting the list of radiographic parameters before image manipulation reduced the frequency of tool use in both groups of examiners. Consulting the radiographic parameters with the use of some digital tools was important for improving correct diagnosis only in the group of non-expert examiners. PMID:22116126

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

PubMed

Blumers, Ansel L; Tang, Yu-Hang; Li, Zhen; Li, Xuejin; Karniadakis, George E

2017-08-01

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

Multiparameter fluorescence imaging for quantification of TH-1 and TH-2 cytokines at the single-cell level

NASA Astrophysics Data System (ADS)

Fekkar, Hakim; Benbernou, N.; Esnault, S.; Shin, H. C.; Guenounou, Moncef

1998-04-01

Immune responses are strongly influenced by the cytokines following antigenic stimulation. Distinct cytokine-producing T cell subsets are well known to play a major role in immune responses and to be differentially regulated during immunological disorders, although the characterization and quantification of the TH-1/TH-2 cytokine pattern in T cells remained not clearly defined. Expression of cytokines by T lymphocytes is a highly balanced process, involving stimulatory and inhibitory intracellular signaling pathways. The aim of this study was (1) to quantify the cytokine expression in T cells at the single cell level using optical imaging, (2) and to analyze the influence of cyclic AMP- dependent signal transduction pathway in the balance between the TH-1 and TH-2 cytokine profile. We attempted to study several cytokines (IL-2, IFN-(gamma) , IL-4, IL-10 and IL-13) in peripheral blood mononuclear cells. Cells were prestimulated in vitro using phytohemagglutinin and phorbol ester for 36h, and then further cultured for 8h in the presence of monensin. Cells were permeabilized and then simple-, double- or triple-labeled with the corresponding specific fluorescent monoclonal antibodies. The cell phenotype was also determined by analyzing the expression of each of CD4, CD8, CD45RO and CD45RA with the cytokine expression. Conventional images of cells were recorded with a Peltier- cooled CCD camera (B/W C5985, Hamamatsu photonics) through an inverted microscope equipped with epi-fluorescence (Diaphot 300, Nikon). Images were digitalized using an acquisition video interface (Oculus TCX Coreco) in 762 by 570 pixels coded in 8 bits (256 gray levels), and analyzed thereafter in an IBM PC computer based on an intel pentium processor with an adequate software (Visilog 4, Noesis). The first image processing step is the extraction of cell areas using an edge detection and a binary thresholding method. In order to reduce the background noise of fluorescence, we performed an opening procedure of the original image using a structuring element. The opened image was therefore subtracted from the original one, and the gray intensities were subsequently measured. Fluorescence intensities are mapped in MD representation using Matlab software. Consequently, quantitative comparative expression of intracellular cytokines and cell membrane markers was achieved. Using this technique, we showed that CD4+ and CD8+T lymphocytes expressed a large panel of cytokines, and that protein kinase A (PKA) activation pathway induced a polarization of activated human T cells to the TH-2 type profile. Data also showed different sensitivities of CD45 RO/CD45RA lymphocytes to the activation of PKA, thus suggesting the implication of memory CD4+- and CD8+-T cells in the T cell specific immune and inflammatory processes and their control by PKA activation pathway. Finally, this method represents a powerful tool for the detection and quantification of intracellular cytokine expression and the analysis of the functional properties of T lymphocytes during immune responses.

Abdominal adipose tissue quantification on water-suppressed and non-water-suppressed MRI at 3T using semi-automated FCM clustering algorithm

NASA Astrophysics Data System (ADS)

Valaparla, Sunil K.; Peng, Qi; Gao, Feng; Clarke, Geoffrey D.

2014-03-01

Accurate measurements of human body fat distribution are desirable because excessive body fat is associated with impaired insulin sensitivity, type 2 diabetes mellitus (T2DM) and cardiovascular disease. In this study, we hypothesized that the performance of water suppressed (WS) MRI is superior to non-water suppressed (NWS) MRI for volumetric assessment of abdominal subcutaneous (SAT), intramuscular (IMAT), visceral (VAT), and total (TAT) adipose tissues. We acquired T1-weighted images on a 3T MRI system (TIM Trio, Siemens), which was analyzed using semi-automated segmentation software that employs a fuzzy c-means (FCM) clustering algorithm. Sixteen contiguous axial slices, centered at the L4-L5 level of the abdomen, were acquired in eight T2DM subjects with water suppression (WS) and without (NWS). Histograms from WS images show improved separation of non-fatty tissue pixels from fatty tissue pixels, compared to NWS images. Paired t-tests of WS versus NWS showed a statistically significant lower volume of lipid in the WS images for VAT (145.3 cc less, p=0.006) and IMAT (305 cc less, p<0.001), but not SAT (14.1 cc more, NS). WS measurements of TAT also resulted in lower fat volumes (436.1 cc less, p=0.002). There is strong correlation between WS and NWS quantification methods for SAT measurements (r=0.999), but poorer correlation for VAT studies (r=0.845). These results suggest that NWS pulse sequences may overestimate adipose tissue volumes and that WS pulse sequences are more desirable due to the higher contrast generated between fatty and non-fatty tissues.

The impact of physiologic noise correction applied to functional MRI of pain at 1.5 and 3.0 T.

PubMed

Vogt, Keith M; Ibinson, James W; Schmalbrock, Petra; Small, Robert H

2011-07-01

This study quantified the impact of the well-known physiologic noise correction algorithm RETROICOR applied to a pain functional magnetic resonance imaging (FMRI) experiment at two field strengths: 1.5 and 3.0 T. In the 1.5-T acquisition, there was an 8.2% decrease in time course variance (σ) and a 227% improvement in average model fit (increase in mean R(2)(a)). In the 3.0-T acquisition, significantly greater improvements were seen: a 10.4% decrease in σ and a 240% increase in mean R(2)(a). End-tidal carbon dioxide data were also collected during scanning and used to account for low-frequency changes in cerebral blood flow; however, the impact of this correction was trivial compared to applying RETROICOR. Comparison between two implementations of RETROICOR demonstrated that oversampled physiologic data can be applied by either downsampling or modification of the timing in the RETROICOR algorithm, with equivalent results. Furthermore, there was no significant effect from manually aligning the physiologic data with corresponding image slices from an interleaved acquisition, indicating that RETROICOR accounts for timing differences between physiologic changes and MR signal changes. These findings suggest that RETROICOR correction, as it is commonly implemented, should be included as part of the data analysis for pain FMRI studies performed at 1.5 and 3.0 T. Copyright © 2011 Elsevier Inc. All rights reserved.

Quantitative Evaluation of Atlas-based Attenuation Correction for Brain PET in an Integrated Time-of-Flight PET/MR Imaging System.

PubMed

Yang, Jaewon; Jian, Yiqiang; Jenkins, Nathaniel; Behr, Spencer C; Hope, Thomas A; Larson, Peder E Z; Vigneron, Daniel; Seo, Youngho

2017-07-01

Purpose To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain positron emission tomography (PET) in an integrated time-of-flight (TOF) PET/magnetic resonance (MR) imaging system. Materials and Methods Thirty recruited patients provided informed consent in this institutional review board-approved study. All patients underwent whole-body fluorodeoxyglucose PET/computed tomography (CT) followed by TOF PET/MR imaging. With use of TOF PET data, PET images were reconstructed with four different attenuation correction (AC) methods: PET with patient CT-based AC (CTAC), PET with ATAC (air and bone from an atlas), PET with ATAC patientBone (air and tissue from the atlas with patient bone), and PET with ATAC boneless (air and tissue from the atlas without bone). For quantitative evaluation, PET mean activity concentration values were measured in 14 1-mL volumes of interest (VOIs) distributed throughout the brain and statistical significance was tested with a paired t test. Results The mean overall difference (±standard deviation) of PET with ATAC compared with PET with CTAC was -0.69 kBq/mL ± 0.60 (-4.0% ± 3.2) (P < .001). The results were patient dependent (range, -9.3% to 0.57%) and VOI dependent (range, -5.9 to -2.2). In addition, when bone was not included for AC, the overall difference of PET with ATAC boneless (-9.4% ± 3.7) was significantly worse than that of PET with ATAC (-4.0% ± 3.2) (P < .001). Finally, when patient bone was used for AC instead of atlas bone, the overall difference of PET with ATAC patientBone (-1.5% ± 1.5) improved over that of PET with ATAC (-4.0% ± 3.2) (P < .001). Conclusion ATAC in PET/MR imaging achieves similar quantification accuracy to that from CTAC by means of atlas-based bone compensation. However, patient-specific anatomic differences from the atlas causes bone attenuation differences and misclassified sinuses, which result in patient-dependent performance variation of ATAC. © RSNA, 2017 Online supplemental material is available for this article.

[Research on Residual Aberrations Correction with Adaptive Optics Technique in Patients Undergoing Orthokeratology].

PubMed

Gong, Rui; Yang, Bi; Liu, Longqian; Dai, Yun; Zhang, Yudong; Zhao, Haoxin

2016-06-01

We conducted this study to explore the influence of the ocular residual aberrations changes on contrast sensitivity(CS)function in eyes undergoing orthokeratology using adaptive optics technique.Nineteen subjects’ nineteen eyes were included in this study.The subjects were between 12 and 20years(14.27±2.23years)of age.An adaptive optics(AO)system was adopted to measure and compensate the residual aberrations through a 4-mm artificial pupil,and at the same time the contrast sensitivities were measured at five spatial frequencies(2,4,8,16,and 32 cycles per degree).The CS measurements with and without AO correction were completed.The sequence of the measurements with and without AO correction was randomly arranged without informing the observers.A two-interval forced-choice procedure was used for the CS measurements.The paired t-test was used to compare the contrast sensitivity with and without AO correction at each spatial frequency.The results revealed that the AO system decreased the mean total root mean square(RMS)from 0.356μm to 0.160μm(t=10.517,P<0.001),and the mean total higher-order RMS from 0.246μm to 0.095μm(t=10.113,P<0.001).The difference in log contrast sensitivity with and without AO correction was significant only at 8cpd(t=-2.51,P=0.02).Thereby we concluded that correcting the ocular residual aberrations using adaptive optics technique could improve the contrast sensitivity function at intermediate spatial frequency in patients undergoing orthokeratology.

Improved δ(13)C analysis of amino sugars in soil by ion chromatography-oxidation-isotope ratio mass spectrometry.

PubMed

Dippold, Michaela A; Boesel, Stefanie; Gunina, Anna; Kuzyakov, Yakov; Glaser, Bruno

2014-03-30

Amino sugars build up microbial cell walls and are important components of soil organic matter. To evaluate their sources and turnover, δ(13)C analysis of soil-derived amino sugars by liquid chromatography was recently suggested. However, amino sugar δ(13)C determination remains challenging due to (1) a strong matrix effect, (2) CO2 -binding by alkaline eluents, and (3) strongly different chromatographic behavior and concentrations of basic and acidic amino sugars. To overcome these difficulties we established an ion chromatography-oxidation-isotope ratio mass spectrometry method to improve and facilitate soil amino sugar analysis. After acid hydrolysis of soil samples, the extract was purified from salts and other components impeding chromatographic resolution. The amino sugar concentrations and δ(13)C values were determined by coupling an ion chromatograph to an isotope ratio mass spectrometer. The accuracy and precision of quantification and δ(13)C determination were assessed. Internal standards enabled correction for losses during analysis, with a relative standard deviation <6%. The higher magnitude peaks of basic than of acidic amino sugars required an amount-dependent correction of δ(13)C values. This correction improved the accuracy of the determination of δ(13)C values to <1.5‰ and the precision to <0.5‰ for basic and acidic amino sugars in a single run. This method enables parallel quantification and δ(13)C determination of basic and acidic amino sugars in a single chromatogram due to the advantages of coupling an ion chromatograph to the isotope ratio mass spectrometer. Small adjustments of sample amount and injection volume are necessary to optimize precision and accuracy for individual soils. Copyright © 2014 John Wiley & Sons, Ltd.

Magnetic resonance imaging of pulmonary infection in immunocompromised children: comparison with multidetector computed tomography.

PubMed

Ozcan, H Nursun; Gormez, Ayşegul; Ozsurekci, Yasemin; Karakaya, Jale; Oguz, Berna; Unal, Sule; Cetin, Mualla; Ceyhan, Mehmet; Haliloglu, Mithat

2017-02-01

Computed tomography (CT) is commonly used to detect pulmonary infection in immunocompromised children. To compare MRI and multidetector CT findings of pulmonary abnormalities in immunocompromised children. Seventeen neutropaenic children (6 girls; ages 2-18 years) were included. Non-contrast-enhanced CT was performed with a 64-detector CT scanner. Axial and coronal non-enhanced thoracic MRI was performed using a 1.5-T scanner within 24 h of the CT examination (true fast imaging with steady-state free precession, fat-saturated T2-weighted turbo spin echo with motion correction, T2-weighted half-Fourier single-shot turbo spin echo [HASTE], fat-saturated T1-weighted spoiled gradient echo). Pulmonary abnormalities (nodules, consolidations, ground glass opacities, atelectasis, pleural effusion and lymph nodes) were evaluated and compared among MRI sequences and between MRI and CT. The relationship between MRI sequences and nodule sizes was examined by chi- square test. Of 256 CT lesions, 207 (81%, 95% confidence interval [CI] 76-85%) were detected at MRI. Of 202 CT-detected nodules, 157 (78%, 95% CI 71-83%) were seen at motion-corrected MRI. Of the 1-5-mm nodules, 69% were detected by motion-corrected T2-weighted MRI and 38% by HASTE MRI. Sensitivity of MRI (both axial fat-saturated T2-weighted turbo spin echo with variable phase encoding directions (BLADE) images and HASTE sequences) to detect pulmonary abnormalities is promising.

Cutaneous T-cell lymphoma (CTCL): Current practices in blood assessment and the utility of T-cell receptor (TCR)-Vβ chain restriction.

PubMed

Gibson, Juliet F; Huang, Jing; Liu, Kristina J; Carlson, Kacie R; Foss, Francine; Choi, Jaehyuk; Edelson, Richard; Hussong, Jerry W; Mohl, Ramsey; Hill, Sally; Girardi, Michael

2016-05-01

Accurate quantification of malignant cells in the peripheral blood of patients with cutaneous T-cell lymphoma is important for early detection, prognosis, and monitoring disease burden. We sought to determine the spectrum of current clinical practices; critically evaluate elements of current International Society for Cutaneous Lymphomas (ISCL) B1 and B2 staging criteria; and assess the potential role of T-cell receptor-Vβ analysis by flow cytometry. We assessed current clinical practices by survey, and performed a retrospective analysis of 161 patients evaluated at Yale (2011-2014) to compare the sensitivity, specificity, positive predictive value, and negative predictive value of parameters for ISCL B2 staging. There was heterogeneity in clinical practices among institutions. ISCL B1 criteria did not capture 5 Yale cohort cases with immunophenotypic abnormalities that later progressed. T-cell receptor-Vβ testing was more specific than polymerase chain reaction and aided diagnosis in detecting clonality, but was of limited benefit in quantification of tumor burden. Because of limited follow-up involving a single center, further investigation will be necessary to conclude whether our proposed diagnostic algorithm is of general clinical benefit. We propose further study of modified B1 criteria: CD4/CD8 ratio 5 or greater, %CD4(+) CD26(-) 20% or greater, or %CD4(+) CD7(-) 20% or greater, with evidence of clonality. T-cell receptor-Vβ testing should be considered in future diagnostic and staging algorithms. Copyright © 2015 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

SU-E-T-146: Reference Dosimetry for Protons and Light-Ion Beams Based on Graphite Calorimetry.

PubMed

Rossomme, S; Palmans, H; Thomas, R; Lee, N; Bailey, M; Shipley, D; Al-Sulaiti, L; Cirrone, P; Romano, F; Kacperek, A; Bertrand, D; Vynckier, S

2012-06-01

The IAEA TRS-398 code of practice can be applied for the measurement of absorbed dose to water under reference conditions with an ionization chamber. For protons, the combined relative standard uncertainty on those measurements is less than 2% while for light-ion beams, it is considerably larger, i.e. 3.2%, mainly due to the higher uncertainty contributions for the water to air stopping power ration and the W air-value on the beam quality correction factors kQ,Q 0 . To decrease this uncertainty, a quantification of kQ,Q 0 is proposed using a primary standard level graphite calorimeter. This work includes numerical and experimental determinations of dose conversion factors to derive dose to water from graphite calorimetry. It also reports on the first experimental data obtained with the graphite calorimeter in proton, alpha and carbon ion beams. Firstly, the dose conversion has been calculated with by Geant4 Monte-Carlo simulations through the determination of the water to graphite stopping power ratio and the fluence correction factor. The latter factor was also derived by comparison of measured ionization curves in graphite and water. Secondly, kQ,Q 0 was obtained by comparison of the dose response of ionization chambers with that of the calorimeter. Stopping power ratios are found to vary by no more than 0.35% up to the Bragg peak, while fluence correction factors are shown to increase slightly above unity close to the Bragg peak. The comparison of the calorimeter with ionization chambers is currently under analysis. For the modulated proton beam, preliminary results on W air confirm the value recommended in TRS-398. Data in both the non-modulated proton and light-ion beams indicate higher values but further investigation of heat loss corrections is needed. The application of graphite calorimetry to proton, alpha and carbon ion beams has been demonstrated successfully. Other experimental campaigns will be held in 2012. This work is supported by the BioWin program of the Wallon Government. © 2012 American Association of Physicists in Medicine.

MO-G-18C-07: Improving T2 Determination and Quantification of Lipid Methylene Protons in Proton Magnetic Resonance Spectroscopy at 3 T

DOE Office of Scientific and Technical Information (OSTI.GOV)

Breitkreutz, D.; Fallone, B. G.; Yahya, A.

2014-06-15

Purpose: To improve proton magnetic resonance spectroscopy (MRS) transverse relaxation (T{sub 2}) determination and quantification of lipid methylene chain (1.3 ppm) protons by rewinding their J-coupling evolution. Methods: MRS experiments were performed on four lipid phantoms, namely, almond, corn, sunflower and oleic acid, using a 3 T Philips MRI scanner with a transmit/receive birdcage head coil. Two PRESS (Point RESolved Spectroscopy) pulse sequences were used. The first PRESS sequence employed standard bandwidth (BW) (∼550 Hz) RF (radiofrequency) refocussing pulses, while the second used refocussing pulses of narrow BW (∼50 Hz) designed to rewind J-coupling evolution of the methylene protons inmore » the voxel of interest. Signal was acquired with each sequence from a 5×5×5 mm{sup 3} voxel, with a repetition time (TR) of 3000 ms, and with echo times (TE) of 100 to 200 ms in steps of 20 ms. 2048 sample points were measured with a 2000 Hz sampling bandwidth. Additionally, 30 mm outer volume suppression slabs were used to suppress signal outside the voxel of interest. The frequency of the RF pulses was set to that of the methylene resonance. Methylene peak areas were calculated and fitted in MATLAB to a monexponentially decaying function of the form M{sub 0}exp(-TE/T{sub 2}), where M{sub 0} is the extrapolated area when TE = 0 ms and yields a measure of concentration. Results: The determined values of M{sub 0} and T{sub 2} increased for all fatty acids when using the PRESS sequence with narrow BW refocussing pulses. M{sub 0} and T{sub 2} values increased by an average amount (over all the phantoms) of 31% and 14%, respectively. Conclusion: This investigation has demonstrated that J-coupling interactions of lipid methylene protons causes non-negligible signal losses which, if not accounted for, Result in underestimations of their levels and T{sub 2} values when performing MRS measurements. Funded by the Natural Sciences and Engineering Research Council of Canada and the Canadian Breast Cancer Foundation - Prairies.NWT.« less

First-in-human PET quantification study of cerebral α4β2* nicotinic acetylcholine receptors using the novel specific radioligand (-)-[(18)F]Flubatine.

PubMed

Sabri, Osama; Becker, Georg-Alexander; Meyer, Philipp M; Hesse, Swen; Wilke, Stephan; Graef, Susanne; Patt, Marianne; Luthardt, Julia; Wagenknecht, Gudrun; Hoepping, Alexander; Smits, René; Franke, Annegret; Sattler, Bernhard; Habermann, Bernd; Neuhaus, Petra; Fischer, Steffen; Tiepolt, Solveig; Deuther-Conrad, Winnie; Barthel, Henryk; Schönknecht, Peter; Brust, Peter

2015-09-01

α4β2* nicotinic receptors (α4β2* nAChRs) could provide a biomarker in neuropsychiatric disorders (e.g., Alzheimer's and Parkinson's diseases, depressive disorders, and nicotine addiction). However, there is a lack of α4β2* nAChR specific PET radioligands with kinetics fast enough to enable quantification of nAChR within a reasonable time frame. Following on from promising preclinical results, the aim of the present study was to evaluate for the first time in humans the novel PET radioligand (-)-[(18)F]Flubatine, formerly known as (-)-[(18)F]NCFHEB, as a tool for α4β2* nAChR imaging and in vivo quantification. Dynamic PET emission recordings lasting 270min were acquired on an ECAT EXACT HR+ scanner in 12 healthy male non-smoking subjects (71.0±5.0years) following the intravenous injection of 353.7±9.4MBq of (-)-[(18)F]Flubatine. Individual magnetic resonance imaging (MRI) was performed for co-registration. PET frames were motion-corrected, before the kinetics in 29 brain regions were characterized using 1- and 2-tissue compartment models (1TCM, 2TCM). Given the low amounts of metabolite present in plasma, we tested arterial input functions with and without metabolite corrections. In addition, pixel-based graphical analysis (Logan plot) was used. The model's goodness of fit, with and without metabolite correction was assessed by Akaike's information criterion. Model parameters of interest were the total distribution volume VT (mL/cm(3)), and the binding potential BPND relative to the corpus callosum, which served as a reference region. The tracer proved to have high stability in vivo, with 90% of the plasma radioactivity remaining as untransformed parent compound at 90min, fast brain kinetics with rapid uptake and equilibration between free and receptor-bound tracer. Adequate fits of brain TACs were obtained with the 1TCM. VT could be reliably estimated within 90min for all regions investigated, and within 30min for low-binding regions such as the cerebral cortex. The rank order of VT by region corresponded well with the known distribution of α4β2* receptors (VT [thalamus] 27.4±3.8, VT [putamen] 12.7±0.9, VT [frontal cortex] 10.0±0.8, and VT [corpus callosum] 6.3±0.8). The BPND, which is a parameter of α4β2* nAChR availability, was 3.41±0.79 for the thalamus, 1.04±0.25 for the putamen and 0.61±0.23 for the frontal cortex, indicating high specific tracer binding. Use of the arterial input function without metabolite correction resulted in a 10% underestimation in VT, and was without important biasing effects on BPND. Altogether, kinetics and imaging properties of (-)-[(18)F]Flubatine appear favorable and suggest that (-)-[(18)F]Flubatine is a very suitable and clinically applicable PET tracer for in vivo imaging of α4β2* nAChRs in neuropsychiatric disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

Alkaline saponification results in decomposition of tocopherols in milk and ovine blood plasma.

PubMed

Czauderna, M; Kowalczyk, J

2007-10-15

Alkaline saponification of entire sample matrixes for quantification of alpha-, gamma-, delta-tocopherols (alpha-T, gamma-T, delta-T) and alpha-tocopherol acetate (alpha-TAc) was examined. High-performance liquid chromatography was used to measure alpha-T, gamma-T, delta-T and alpha-TAc in tocopherol standard solutions, milk and ovine blood plasma. Saponification in the presence of vitamin C decreases the concentration of tocopherols, especially alpha-T and gamma-T. The poor recovery of tocopherols is due to the decomposition of tocopherols in saponified standard solutions, milk or plasma. Saponification of samples in the presence of 2,[6]-ditertbutyl-p-cresol or flushed only with a stream of Ar resulted in a major decrease in the concentrations of alpha-T, gamma-T, delta-T and alpha-TAc in comparison with saponification in the presence of vitamin C.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soliman, A; Elzibak, A; Fatemi, A

Purpose: To quantitatively evaluate the MR image quality of a novel direction modulated brachytherapy (DMBT) tandem applicator for cervical cancer, using the clinical MRI scanning protocol for image guided brachytherapy. Methods: The tungsten alloy-based applicator was placed in a water phantom and clinical imaging protocol was performed. Axial images were acquired using 2D turbo-spin echo (TSE) T2-weighted sequence on a 1.5T GE 450w MR scanner and an 8-channel body coil. As multi-channel receiver coil was used, inhomogeneities in the B1 receive field must be considered before performing the quantification process. Therefore the applicator was removed from the phantom and themore » whole imaging session was performed again for the water phantom with the same parameters. Images from the two scans were then subtracted, resulting in a difference image that only shows the applicator with its surrounding magnetic susceptibility dipole artifact. Line profiles were drawn and plotted on the difference image at various angles and locations along the tandem. Full width at half maximum (FWHM) was measured at all the line profiles to quantify the extent of the artifact. Additionally, the extent of the artifact along the diameter of the tandem was measured at various angles and locations. Results: After removing the background inhomogeneities of the receiver coil, FWHM of the tandem measured 5.75 ± 0.35 mm (the physical tandem diameter is 5.4 mm). The average extent of the artifacts along the diameter of the tandem measured is 2.14 ± 0.56 mm. In contrast to CT imaging of the same applicator (not shown here), the tandem can be easily identified without additional correction algorithms. Conclusion: This work demonstrated that the novel DMBT tandem applicator has minimal susceptibility artifact in T2-weighted images employed in clinical practice for MRI-guided brachytherapy of cervical cancer.« less

Machine vs. human translation of SNOMED CT terms.

PubMed

Schulz, Stefan; Bernhardt-Melischnig, Johannes; Kreuzthaler, Markus; Daumke, Philipp; Boeker, Martin

2013-01-01

In the context of past and current SNOMED CT translation projects we compare three kinds of SNOMED CT translations from English to German by: (t1) professional medical translators; (t2) a free Web-based machine translation service; (t3) medical students. 500 SNOMED CT fully specified names from the (English) International release were randomly selected. Based on this, German translations t1, t2, and t3 were generated. A German and an Austrian physician rated the translations for linguistic correctness and content fidelity. Kappa for inter-rater reliability was 0.4 for linguistic correctness and 0.23 for content fidelity. Average ratings of linguistic correctness did not differ significantly between human translation scenarios. Content fidelity was rated slightly better for student translators compared to professional translators. Comparing machine to human translation, the linguistic correctness differed about 0.5 scale units in favour of the human translation and about 0.25 regarding content fidelity, equally in favour of the human translation. The results demonstrate that low-cost translation solutions of medical terms may produce surprisingly good results. Although we would not recommend low-cost translation for producing standardized preferred terms, this approach can be useful for creating additional language-specific entry terms. This may serve several important use cases. We also recommend testing this method to bootstrap a crowdsourcing process, by which term translations are gathered, improved, maintained, and rated by the user community.

In vivo visualization and ex vivo quantification of murine breast cancer cells in the mouse brain using MRI cell tracking and electron paramagnetic resonance.

PubMed

Danhier, Pierre; Magat, Julie; Levêque, Philippe; De Preter, Géraldine; Porporato, Paolo E; Bouzin, Caroline; Jordan, Bénédicte F; Demeur, Gladys; Haufroid, Vincent; Feron, Olivier; Sonveaux, Pierre; Gallez, Bernard

2015-03-01

Cell tracking could be useful to elucidate fundamental processes of cancer biology such as metastasis. The aim of this study was to visualize, using MRI, and to quantify, using electron paramagnetic resonance (EPR), the entrapment of murine breast cancer cells labeled with superparamagnetic iron oxide particles (SPIOs) in the mouse brain after intracardiac injection. For this purpose, luciferase-expressing murine 4 T1-luc breast cancer cells were labeled with fluorescent Molday ION Rhodamine B SPIOs. Following intracardiac injection, SPIO-labeled 4 T1-luc cells were imaged using multiple gradient-echo sequences. Ex vivo iron oxide quantification in the mouse brain was performed using EPR (9 GHz). The long-term fate of 4 T1-luc cells after injection was characterized using bioluminescence imaging (BLI), brain MRI and immunofluorescence. We observed hypointense spots due to SPIO-labeled cells in the mouse brain 4 h after injection on T2 *-weighted images. Histology studies showed that SPIO-labeled cancer cells were localized within blood vessels shortly after delivery. Ex vivo quantification of SPIOs showed that less than 1% of the injected cells were taken up by the mouse brain after injection. MRI experiments did not reveal the development of macrometastases in the mouse brain several days after injection, but immunofluorescence studies demonstrated that these cells found in the brain established micrometastases. Concerning the metastatic patterns of 4 T1-luc cells, an EPR biodistribution study demonstrated that SPIO-labeled 4 T1-luc cells were also entrapped in the lungs of mice after intracardiac injection. BLI performed 6 days after injection of 4 T1-luc cells showed that this cell line formed macrometastases in the lungs and in the bones. Conclusively, EPR and MRI were found to be complementary for cell tracking applications. MRI cell tracking at 11.7 T allowed sensitive detection of isolated SPIO-labeled cells in the mouse brain, whereas EPR allowed the assessment of the number of SPIO-labeled cells in organs shortly after injection. Copyright © 2015 John Wiley & Sons, Ltd.

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reeve, Samuel Temple; Strachan, Alejandro, E-mail: strachan@purdue.edu

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated undermore » three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.« less

Corrections of the finite relativistic contributions to the synodic month period Earth-Moon range oscillations: Agreement between the geocentric and the solar-system barycentric inertial-frame calculations

NASA Astrophysics Data System (ADS)

Nordtvedt, Ken

1993-04-01

We have corrected our calculation of the finite general relativistic contribution to the synodic month period Earth-Moon range oscillation by including previously overlooked terms in the Moon's post-Newtonian equation of motion: the corrected result x(t)~=(3gSr2/c2) cos(ω-Ω)t agrees with the Shahid-Saless calculation which was performed in the geocentric frame. It is also pointed out that at the level of a few millimeters synodic month period amplitude, the Moon's orbit is polarized by the solar radiation pressure force on the Moon.

Precision of MRI-based body composition measurements of postmenopausal women

PubMed Central

Romu, Thobias; Thorell, Sofia; Lindblom, Hanna; Berin, Emilia; Holm, Anna-Clara Spetz; Åstrand, Lotta Lindh; Karlsson, Anette; Borga, Magnus; Hammar, Mats; Leinhard, Olof Dahlqvist

2018-01-01

Objectives To determine precision of magnetic resonance imaging (MRI) based fat and muscle quantification in a group of postmenopausal women. Furthermore, to extend the method to individual muscles relevant to upper-body exercise. Materials and methods This was a sub-study to a randomized control trial investigating effects of resistance training to decrease hot flushes in postmenopausal women. Thirty-six women were included, mean age 56 ± 6 years. Each subject was scanned twice with a 3.0T MR-scanner using a whole-body Dixon protocol. Water and fat images were calculated using a 6-peak lipid model including R2*-correction. Body composition analyses were performed to measure visceral and subcutaneous fat volumes, lean volumes and muscle fat infiltration (MFI) of the muscle groups’ thigh muscles, lower leg muscles, and abdominal muscles, as well as the three individual muscles pectoralis, latissimus, and rhomboideus. Analysis was performed using a multi-atlas, calibrated water-fat separated quantification method. Liver-fat was measured as average proton density fat-fraction (PDFF) of three regions-of-interest. Precision was determined with Bland-Altman analysis, repeatability, and coefficient of variation. Results All of the 36 included women were successfully scanned and analysed. The coefficient of variation was 1.1% to 1.5% for abdominal fat compartments (visceral and subcutaneous), 0.8% to 1.9% for volumes of muscle groups (thigh, lower leg, and abdomen), and 2.3% to 7.0% for individual muscle volumes (pectoralis, latissimus, and rhomboideus). Limits of agreement for MFI was within ± 2.06% for muscle groups and within ± 5.13% for individual muscles. The limits of agreement for liver PDFF was within ± 1.9%. Conclusion Whole-body Dixon MRI could characterize a range of different fat and muscle compartments with high precision, including individual muscles, in the study-group of postmenopausal women. The inclusion of individual muscles, calculated from the same scan, enables analysis for specific intervention programs and studies. PMID:29415060

Optimization of training periods for the estimation model of three-dimensional target positions using an external respiratory surrogate.

PubMed

Iramina, Hiraku; Nakamura, Mitsuhiro; Iizuka, Yusuke; Mitsuyoshi, Takamasa; Matsuo, Yukinori; Mizowaki, Takashi; Kanno, Ikuo

2018-04-19

During therapeutic beam irradiation, an unvisualized three-dimensional (3D) target position should be estimated using an external surrogate with an estimation model. Training periods for the developed model with no additional imaging during beam irradiation were optimized using clinical data. Dual-source 4D-CBCT projection data for 20 lung cancer patients were used for validation. Each patient underwent one to three scans. The actual target positions of each scan were equally divided into two equal parts: one for the modeling and the other for the validating session. A quadratic target position estimation equation was constructed during the modeling session. Various training periods for the session-i.e., modeling periods (T M )-were employed: T M  ∈ {5,10,15,25,35} [s]. First, the equation was used to estimate target positions in the validating session of the same scan (intra-scan estimations). Second, the equation was then used to estimate target positions in the validating session of another temporally different scan (inter-scan estimations). The baseline drift of the surrogate and target between scans was corrected. Various training periods for the baseline drift correction-i.e., correction periods (T C s)-were employed: T C  ∈ {5,10,15; T C  ≤ T M } [s]. Evaluations were conducted with and without the correction. The difference between the actual and estimated target positions was evaluated by the root-mean-square error (RMSE). The range of mean respiratory period and 3D motion amplitude of the target was 2.4-13.0 s and 2.8-34.2 mm, respectively. On intra-scan estimation, the median 3D RMSE was within 1.5-2.1 mm, supported by previous studies. On inter-scan estimation, median elapsed time between scans was 10.1 min. All T M s exhibited 75th percentile 3D RMSEs of 5.0-6.4 mm due to baseline drift of the surrogate and the target. After the correction, those for each T M s fell by 1.4-2.3 mm. The median 3D RMSE for both the 10-s T M and the T C period was 2.4 mm, which plateaued when the two training periods exceeded 10 s. A widely-applicable estimation model for the 3D target positions during beam irradiation was developed. The optimal T M and T C for the model were both 10 s, to allow for more than one respiratory cycle. UMIN000014825 . Registered: 11 August 2014.

Dental and skeletal changes in patients with mandibular retrognathism following treatment with Herbst and pre-adjusted fixed appliance

PubMed Central

Vigorito, Fabio de Abreu; Dominguez, Gladys Cristina; Aidar, Luís Antônio de Arruda

2014-01-01

Objective To assess the dentoskeletal changes observed in treatment of Class II, division 1 malocclusion patients with mandibular retrognathism. Treatment was performed with the Herbst orthopedic appliance during 13 months (phase I) and pre-adjusted orthodontic fixed appliance (phase II). Methods Lateral cephalograms of 17 adolescents were taken in phase I onset (T1) and completion (T2); in the first thirteen months of phase II (T3) and in phase II completion (T4). Differences among the cephalometric variables were statistically analyzed (Bonferroni variance and multiple comparisons). Results From T1 to T4, 42% of overall maxillary growth was observed between T1 and T2 (P < 0.01), 40.3% between T2 and T3 (P < 0.05) and 17.7% between T3 and T4 (n.s.). As for overall mandibular movement, 48.2% was observed between T1 and T2 (P < 0.001) and 51.8% between T2 and T4 (P < 0.01) of which 15.1% was observed between T2 and T3 (n.s.) and 36.7% between T3 and T4 (P < 0.01). Class II molar relationship and overjet were properly corrected. The occlusal plane which rotated clockwise between T1 and T2, returned to its initial position between T2 and T3 remaining stable until T4. The mandibular plane inclination did not change at any time during treatment. Conclusion Mandibular growth was significantly greater in comparison to maxillary, allowing sagittal maxillomandibular adjustment. The dentoalveolar changes (upper molar) that overcorrected the malocclusion in phase I, partially recurred in phase II, but did not hinder correction of the malocclusion. Facial type was preserved. PMID:24713559

Development of an LC-MS/MS Determination Method for T-2 Toxin and Its Glucoside and Acetyl Derivatives for Estimating the Contamination of Total T-2 Toxins in Staple Flours.

PubMed

Nakagawa, Hiroyuki; Matsuo, Yosuke; McCormick, Susan; Lim, Chee Wei

2018-05-01

A determination method previously validated for trichothecenes and zearalenone by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS) was adapted for the quantification of T-2 toxin (T-2) as well as its glucoside and acetyl derivatives, T-2-3-glucoside (T-2-3G) and 3-acetyl-T-2 (3A-T-2). HT-2 toxin (HT-2) and its acetyl derivative 3-acetyl-HT-2 (3A-HT-2) were also included as the target chemicals. Staple flours (56 samples collected from the Singapore market) were examined for contamination from T-2 and/or HT-2 and their derivatives. Among them, 16 flours were found to be contaminated with T-2 and/or HT-2, whereas none was contaminated with T-2-3G and 3A-HT-2, except for trace 3A-T-2 detected in 2 rye samples. Rye flour samples were frequently contaminated with both T-2 and HT-2. Some of the reference materials (RMs) were further analyzed, and T-2-3G and 3A-T-2 were quantitatively detected in corn and wheat RMs. The ratio of T-2-3G to T-2 in the RMs seemed to be much lower than the ratio of deoxynivalenol-3-glucoside to deoxynivalenol usually reported in former studies. To the best of our knowledge, the natural contamination of 3A-T-2 in staple flour is reported here for the first time.

Implementation of the O(αt2) MSSM Higgs-mass corrections in FeynHiggs

NASA Astrophysics Data System (ADS)

Hahn, Thomas; Paßehr, Sebastian

2017-05-01

We describe the implementation of the two-loop Higgs-mass corrections of O(αt2) in the complex MSSM in FeynHiggs. The program for the calculation is comprised of several scripts which flexibly use FeynArts and FormCalc together with other packages. It is included in FeynHiggs and documented here in some detail so that it can be re-used as a template for similar calculations.

Chemical shift-based MRI to measure fat fractions in dystrophic skeletal muscle

PubMed Central

Triplett, William T.; Baligand, Celine; Forbes, Sean C.; Willcocks, Rebecca J.; Lott, Donovan J.; DeVos, Soren; Pollaro, Jim; Rooney, William D.; Sweeney, H. Lee; Bönnemann, Carsten; Wang, Dah-Jyuu; Vandenborne, Krista; Walter, Glenn A.

2014-01-01

Purpose The relationship between FF determined based on multiple TE, unipolar GE images and 1H-MRS was evaluated using different models for fat-water decomposition, signal-to-noise ratios (SNR), and excitation flip angles. Methods A combination of single voxel proton spectroscopy (1H-MRS) and gradient echo (GE) imaging was used to determine muscle fat fractions (FF) in both normal and dystrophic muscles. In order to cover a large range of FF, the soleus and vastus lateralis muscles of 22 unaffected control (CON), 16 subjects with Collagen VI (COL6), and 71 subjects with Duchenne muscular dystrophy (DMD) were studied. 1H-MRS based FF were corrected for the increased muscle 1H2O T1 and T2 values observed in dystrophic muscles. Results Excellent agreement was found between co-registered FF derived from GE images fit to a multipeak model with noise bias correction and the relaxation corrected 1H-MRS FF (y= 0.93×+0.003; R2=0.96) across the full range of FF. Relaxation corrected 1H-MRS FF and imaging based FF were significantly elevated (p<0.01) in both COL6 and DMD muscles. Conclusion FF, T2, and T1 were all sensitive to muscle involvement in dystrophic muscle. MRI offered an additional advantage over single voxel spectroscopy in that the tissue heterogeneity in FF could be readily determined. PMID:24006208

Validation of the AMSU-B Bias Corrections Based on Satellite Measurements from SSM/T-2

NASA Technical Reports Server (NTRS)

Kolodner, Marc A.

1999-01-01

The NOAA-15 Advanced Microwave Sounding Unit-B (AMSU-B) was designed in the same spirit as the Special Sensor Microwave Water Vapor Profiler (SSM/T-2) on board the DMSP F11-14 satellites, to perform remote sensing of spatial and temporal variations in mid and upper troposphere humidity. While the SSM/T-2 instruments have a 48 km spatial resolution at nadir and 28 beam positions per scan, AMSU-B provides an improvement with a 16 km spatial resolution at nadir and 90 beam positions per scan. The AMSU-B instrument, though, has been experiencing radio frequency interference (RFI) contamination from the NOAA-15 transmitters whose effect is dependent upon channel, geographic location, and current spacecraft antenna configuration. This has lead to large cross-track biases reaching as high as 100 Kelvin for channel 17 (150 GHz) and 50 Kelvin for channel 19 (183 +/-3 GHz). NOAA-NESDIS has recently provided a series of bias corrections for AMSU-B data starting from March, 1999. These corrections are available for each of the five channels, for every third field of view, and for three cycles within an eight second period. There is also a quality indicator in each data record to indicate whether or not the bias corrections should be applied. As a precursor to performing retrievals of mid and upper troposphere humidity, a validation study is performed by statistically analyzing the differences between the F14 SSM/T-2 and the bias corrected AMSU-B brightness temperatures for three months in the spring of 1999.

Critical assessment of digital PCR for the detection and quantification of genetically modified organisms.

PubMed

Demeke, Tigst; Dobnik, David

2018-07-01

The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.

Quantification of red myotomal muscle volume and geometry in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis) using T1-weighted magnetic resonance imaging.

PubMed

Perry, Cameron N; Cartamil, Daniel P; Bernal, Diego; Sepulveda, Chugey A; Theilmann, Rebecca J; Graham, Jeffrey B; Frank, Lawrence R

2007-04-01

T1-weighted magnetic resonance imaging (MRI) in conjunction with image and segmentation analysis (i.e., the process of digitally partitioning tissues based on specified MR image characteristics) was evaluated as a noninvasive alternative for differentiating muscle fiber types and quantifying the amounts of slow, red aerobic muscle in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis). MRI-determinations of red muscle quantity and position made for the mid-body sections of three mako sharks (73.5-110 cm fork length, FL) are in close agreement (within the 95% confidence intervals) with data obtained for the same sections by the conventional dissection method involving serial cross-sectioning and volumetric analyses, and with previously reported findings for this species. The overall distribution of salmon shark red muscle as a function of body fork length was also found to be consistent with previously acquired serial dissection data for this species; however, MR imaging revealed an anterior shift in peak red muscle cross-sectional area corresponding to an increase in body mass. Moreover, MRI facilitated visualization of the intact and anatomically correct relationship of tendon linking the red muscle and the caudal peduncle. This study thus demonstrates that MRI is effective in acquiring high-resolution three-dimensional digital data with high contrast between different fish tissue types. Relative to serial dissection, MRI allows more precise quantification of the position, volume, and other details about the types of muscle within the fish myotome, while conserving specimen structural integrity. Copyright (c) 2007 Wiley-Liss, Inc.

Non-cancellation of electroweak logarithms in high-energy scattering

DOE PAGES

Manohar, Aneesh V.; Shotwell, Brian; Bauer, Christian W.; ...

2015-01-01

We study electroweak Sudakov corrections in high energy scattering, and the cancellation between real and virtual Sudakov corrections. Numerical results are given for the case of heavy quark production by gluon collisions involving the rates gg→t¯t, b¯b, t¯bW, t¯tZ, b¯bZ, t¯tH, b¯bH. Gauge boson virtual corrections are related to real transverse gauge boson emission, and Higgs virtual corrections to Higgs and longitudinal gauge boson emission. At the LHC, electroweak corrections become important in the TeV regime. At the proposed 100TeV collider, electroweak interactions enter a new regime, where the corrections are very large and need to be resummed.

Quantification of Tumor Vessels in Glioblastoma Patients Using Time-of-Flight Angiography at 7 Tesla: A Feasibility Study

PubMed Central

Radbruch, Alexander; Eidel, Oliver; Wiestler, Benedikt; Paech, Daniel; Burth, Sina; Kickingereder, Philipp; Nowosielski, Martha; Bäumer, Philipp; Wick, Wolfgang; Schlemmer, Heinz-Peter; Bendszus, Martin; Ladd, Mark; Nagel, Armin Michael; Heiland, Sabine

2014-01-01

Purpose To analyze if tumor vessels can be visualized, segmented and quantified in glioblastoma patients with time of flight (ToF) angiography at 7 Tesla and multiscale vessel enhancement filtering. Materials and Methods Twelve patients with newly diagnosed glioblastoma were examined with ToF angiography (TR = 15 ms, TE = 4.8 ms, flip angle = 15°, FOV = 160×210 mm2, voxel size: 0.31×0.31×0.40 mm3) on a whole-body 7 T MR system. A volume of interest (VOI) was placed within the border of the contrast enhancing part on T1-weighted images of the glioblastoma and a reference VOI was placed in the non-affected contralateral white matter. Automated segmentation and quantification of vessels within the two VOIs was achieved using multiscale vessel enhancement filtering in ImageJ. Results Tumor vessels were clearly visible in all patients. When comparing tumor and the reference VOI, total vessel surface (45.3±13.9 mm2 vs. 29.0±21.0 mm2 (p<0.035)) and number of branches (3.5±1.8 vs. 1.0±0.6 (p<0.001) per cubic centimeter were significantly higher, while mean vessel branch length was significantly lower (3.8±1.5 mm vs 7.2±2.8 mm (p<0.001)) in the tumor. Discussion ToF angiography at 7-Tesla MRI enables characterization and quantification of the internal vascular morphology of glioblastoma and may be used for the evaluation of therapy response within future studies. PMID:25415327

Evaluation and Analysis of SEASAT-A Scanning Multichannel Microwave Radiometer (SSMR) Antenna Pattern Correction (APC) Algorithm. Sub-task 4: Interim Mode T Sub B Versus Cross and Nominal Mode T Sub B

NASA Technical Reports Server (NTRS)

Kitzis, J. L.; Kitzis, S. N.

1979-01-01

The brightness temperature data produced by the SMMR Antenna Pattern Correction algorithm are evaluated. The evaluation consists of: (1) a direct comparison of the outputs of the interim, cross, and nominal APC modes; (2) a refinement of the previously determined cos beta estimates; and (3) a comparison of the world brightness temperature (T sub B) map with actual SMMR measurements.

NMR quantification of diffusional exchange in cell suspensions with relaxation rate differences between intra and extracellular compartments.

PubMed

Eriksson, Stefanie; Elbing, Karin; Söderman, Olle; Lindkvist-Petersson, Karin; Topgaard, Daniel; Lasič, Samo

2017-01-01

Water transport across cell membranes can be measured non-invasively with diffusion NMR. We present a method to quantify the intracellular lifetime of water in cell suspensions with short transverse relaxation times, T2, and also circumvent the confounding effect of different T2 values in the intra- and extracellular compartments. Filter exchange spectroscopy (FEXSY) is specifically sensitive to exchange between compartments with different apparent diffusivities. Our investigation shows that FEXSY could yield significantly biased results if differences in T2 are not accounted for. To mitigate this problem, we propose combining FEXSY with diffusion-relaxation correlation experiment, which can quantify differences in T2 values in compartments with different diffusivities. Our analysis uses a joint constrained fitting of the two datasets and considers the effects of diffusion, relaxation and exchange in both experiments. The method is demonstrated on yeast cells with and without human aquaporins.

NMR quantification of diffusional exchange in cell suspensions with relaxation rate differences between intra and extracellular compartments

PubMed Central

Eriksson, Stefanie; Elbing, Karin; Söderman, Olle; Lindkvist-Petersson, Karin; Topgaard, Daniel

2017-01-01

Water transport across cell membranes can be measured non-invasively with diffusion NMR. We present a method to quantify the intracellular lifetime of water in cell suspensions with short transverse relaxation times, T2, and also circumvent the confounding effect of different T2 values in the intra- and extracellular compartments. Filter exchange spectroscopy (FEXSY) is specifically sensitive to exchange between compartments with different apparent diffusivities. Our investigation shows that FEXSY could yield significantly biased results if differences in T2 are not accounted for. To mitigate this problem, we propose combining FEXSY with diffusion-relaxation correlation experiment, which can quantify differences in T2 values in compartments with different diffusivities. Our analysis uses a joint constrained fitting of the two datasets and considers the effects of diffusion, relaxation and exchange in both experiments. The method is demonstrated on yeast cells with and without human aquaporins. PMID:28493928

Remote Quantification of Smokestack Total Effluent Mass Flow Rates Using Imaging Fourier-Transform Spectroscopy

DTIC Science & Technology

2011-03-01

between plume and air: ∆ρρ = Tair ∆T , where Tair was taken to be 300 ◦ K and ∆T to be 100◦ K . This resulted in final values of M = 735m4/s2, B = 2999m4/s3...37 Appendix A. Extended velocity discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 vi Page Appendix B . Additional... B . Lastly, Appendix C contains MATLAB code developed specifically for the brightness feature tracking method and plume flow anal- ysis. Each primary

Characterisation of Special Sensor Microwave Water Vapor Profiler (SSM/T-2) radiances using radiative transfer simulations from global atmospheric reanalyses

NASA Astrophysics Data System (ADS)

Kobayashi, Shinya; Poli, Paul; John, Viju O.

2017-02-01

The near-global and all-sky coverage of satellite observations from microwave humidity sounders operating in the 183 GHz band complement radiosonde and aircraft observations and satellite infrared clear-sky observations. The Special Sensor Microwave Water Vapor Profiler (SSM/T-2) of the Defense Meteorological Satellite Program began operations late 1991. It has been followed by several other microwave humidity sounders, continuing today. However, expertise and accrued knowledge regarding the SSM/T-2 data record is limited because it has remained underused for climate applications and reanalyses. In this study, SSM/T-2 radiances are characterised using several global atmospheric reanalyses. The European Centre for Medium-Range Weather Forecasts (ECMWF) Interim Reanalysis (ERA-Interim), the first ECMWF reanalysis of the 20th-century (ERA-20C), and the Japanese 55-year Reanalysis (JRA-55) are projected into SSM/T-2 radiance space using a fast radiative transfer model. The present study confirms earlier indications that the polarisation state of SSM/T-2 antenna is horizontal (not vertical) in the limit of nadir viewing. The study also formulates several recommendations to improve use of the SSM/T-2 measurement data in future fundamental climate data records or reanalyses. Recommendations are (1) to correct geolocation errors, especially for DMSP 14; (2) to blacklist poor quality data identified in the paper; (3) to correct for inter-satellite biases, estimated here on the order of 1 K, by applying an inter-satellite recalibration or, for reanalysis, an automated (e.g., variational) bias correction; and (4) to improve precipitating cloud filtering or, for reanalysis, consider an all-sky assimilation scheme where radiative transfer simulations account for the scattering effect of hydrometeors.

Proposed Tier 2 Screening Criteria and Tier 3 Field Procedures for Evaluation of Vapor Intrusion (ESTCP Cost and Performance Report)

DTIC Science & Technology

2012-08-01

Interstate Technology & Regulatory Council, Washington, DC, Copyright 2007. McHugh T.E., D.E. Hammond, T. Nickels , and B. Hartman. 2008. Use of...based corrective action have realized significant cost savings for their corrective action programs (Connor and McHugh , 2002). As described above...Groundwater (Tier 2) VOCs USEPA 8260B 40 mL VOA vial HCl 14 days Vapor (Tier 2 and Tier 3) Radon McHugh et al., 2008 500 mL Tedlar bag None 14

Effects of transaldolase exchange on estimates of gluconeogenesis in type 2 diabetes

PubMed Central

Rajpal, Aman; Dube, Simmi; Carvalho, Filipa; Simoes, Ana Rita; Figueiredo, Angelo; Basu, Ananda; Jones, John

2013-01-01

Transaldolase (TA) exchange overestimates gluconeogenesis measured with deuterated water (2H2O). However, it is unknown whether TA differs in people with type 2 diabetes (T2DM). 2H2O was ingested, and [1-13C]acetate and [3-3H]glucose were infused in T2DM (n = 10) and healthy nondiabetic (ND; n = 8) subjects. TA was assessed from the ratio of 13C3 to 13C4 glucose enrichment (13C3/13C4) measured by 13C NMR. Glucose turnover was measured before (∼16-h fast) and during hyperglycemic (∼10 mM) moderate-dose insulin (∼0.35 mU·kg−1·min−1) clamp. 13C3/13C4 in T2DM vs. ND was <1.0 and not different at baseline and clamp, indicating equivalent TA. To determine whether incomplete triose phosphate isomerase (TPI) exchange contributed to asymmetric 13C3/13C4, [U-13C]glycerol was infused in lieu of [1-13C]acetate during a separate visit in a subset of ND (n = 7) subjects. Ratio of 13C3/13C4 obtained following either tracer was <1.0 at baseline and during clamp, indicating that TPI exchange was essentially complete and did not contribute to asymmetric glucose enrichment. Uncorrected and corrected rates of gluconeogenesis were no different (P = not significant) in T2DM vs. ND both at baseline and during clamp. TA correction resulted in equivalent estimates of corrected gluconeogenesis in T2DM and ND that were ∼25–35% lower than uncorrected gluconeogenesis both at baseline and during the clamp. The asymmetric enrichment of glucose from 13C-gluconeogenic tracers is attributable to TA exchange and can be utilized to correct for TA exchange. In conclusion, TA exchange does not differ between T2DM and ND under fasting or hyperglycemic clamp conditions, and the 2H2O method continues to provide an accurate estimation of gluconeogenesis. PMID:23736541

Quantification of [11C]GB67 binding to cardiac alpha1-adrenoceptors with positron emission tomography: validation in pigs.

PubMed

Park-Holohan, So-Jin; Asselin, Marie-Claude; Turton, David R; Williams, Sharron L; Hume, Susan P; Camici, Paolo G; Rimoldi, Ornella E

2008-09-01

An increase in human cardiac alpha(1)-adrenoceptor (alpha(1)-AR) density is associated with various diseases such as myocardial ischemia, congestive heart failure, hypertrophic cardiomyopathy and hypertension. Positron emission tomography (PET) with an appropriate radioligand offers the possibility of imaging receptor function in the normal and diseased heart. [(11)C]GB67, an analogue of prazosin, has been shown in rats to have potential as a PET ligand with high selectivity to alpha(1)-AR. However, alpha(1)-AR density is up to ten times higher in rat heart compared to that in man. The aim of the present preclinical study was to extend the previous evaluation to a large mammal heart, where the alpha(1)-AR density is comparable to man, and to validate a method for quantification before PET studies in man. Seven [(11)C]GB67 PET studies, with weight-adjusted target dose of either 5.29 MBq kg(-1) (pilot, test-retest and baseline-predose studies) or 8.22 MBq kg(-1) (baseline-displacement studies), were performed in four anaesthetised pigs (39.5 +/- 3.9 kg). Total myocardial volume of distribution (V (T)) was estimated under different pharmacological conditions using compartmental analysis with a radiolabelled metabolite-corrected arterial plasma input function. A maximum possible blocking dose of 0.12 mumol kg(-1) of unlabeled GB67 was given 20 min before [(11)C]GB67 administration in the predose study and 45 min after administration of [(11)C]GB67 in the displacement study. In addition, [(15)O]CO (3,000 MBq) and [(15)O]H(2)O, with weight adjusted target dose of 10.57 MBq kg(-1), were also administered for estimation of blood volume recovery (RC) of the left ventricular cavity and myocardial perfusion (MBF), respectively. [(11)C]GB67 V (T) values (in ml cm(-3)) were estimated to be 24.2 +/- 5.5 (range, 17.3-31.3), 10.1 (predose) and 11.6 (displacement). MBF did not differ within each pig, including between baseline and predose conditions. Predose and displacement studies showed that specific binding of [(11)C]GB67 to myocardial alpha(1)-ARs accounts for approximately 50% of V (T). The present study offers a methodology for using [(11)C]GB67 as a radioligand to quantify human myocardial alpha(1)-ARs in clinical PET studies.

Circumferential thoracolumbar corrective fusion with an anterior interbody fresh-frozen femoral head allograft for osteoporotic lower acute kyphosis: a case report

PubMed Central

2009-01-01

Introduction Lower acute kyphosis (LAK) is a postural deformity caused by severe osteoporotic vertebral collapse at the thoracolumbar junction. Corrective surgery is indicated for severe cases, but no case report using a fresh-frozen femoral head allograft was found in the English literature. Case presentation A 69-year-old Japanese woman with severe LAK with osteoporotic vertebral fractures from T11 to L2 complained of severe back pain and difficulty in walking. The rigid kyphosis measured 74° from T10 to L3. The patient underwent an anterior release and interbody fusion using a fresh-frozen femoral head allograft (T11-L3) and a posterior instrumented fusion (T10-L3). Postoperatively, kyphosis was corrected to 28°, and the patient's symptoms were alleviated. The allograft bone was fully incorporated 1 year postoperatively. A new vertebral fracture at T10 occurred after 2 years, resulting in a slight loss of correction. A kyphosis angle of 35° at 2 years was maintained at 12 years (age, 81 years). She remained free of back pain and able to walk without a cane over the 12-year follow-up. Conclusion For treatment of severe osteoporotic LAK, anterior reconstruction is essential to obtain good spinal alignment and prevent recurrence. A fresh-frozen femoral head allograft, in combination with rigid posterior instrumented fixation, fulfills this function. PMID:19946544

Uncertainty quantification in Eulerian-Lagrangian models for particle-laden flows

NASA Astrophysics Data System (ADS)

Fountoulakis, Vasileios; Jacobs, Gustaaf; Udaykumar, Hs

2017-11-01

A common approach to ameliorate the computational burden in simulations of particle-laden flows is to use a point-particle based Eulerian-Lagrangian model, which traces individual particles in their Lagrangian frame and models particles as mathematical points. The particle motion is determined by Stokes drag law, which is empirically corrected for Reynolds number, Mach number and other parameters. The empirical corrections are subject to uncertainty. Treating them as random variables renders the coupled system of PDEs and ODEs stochastic. An approach to quantify the propagation of this parametric uncertainty to the particle solution variables is proposed. The approach is based on averaging of the governing equations and allows for estimation of the first moments of the quantities of interest. We demonstrate the feasibility of our proposed methodology of uncertainty quantification of particle-laden flows on one-dimensional linear and nonlinear Eulerian-Lagrangian systems. This research is supported by AFOSR under Grant FA9550-16-1-0008.

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 1 for Pease Air Force Base, New Hampshire. Volume 2. Appendices.

DTIC Science & Technology

1987-08-01

total recoverable trivalent - ambient water, the estimated level is 2 more sensitive than those tested. No chromium the avallabe data indicate - mg/L...freshwater aquatic chronic toxicity of trivalent chromium to life occurs at concentrations as low as sensitive saltwater aquatic life...epoxide Lindane Nethoxyohlor Diazinon Malathion Parathion Toxaphene 2.4- 2,A.5-T 2,JI,5-TP (silvex) barsenic barium cadmiumn chromium (total). copper Iron

76 FR 36995 - Requirements for Taxpayers Filing Form 5472; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-24

... * * * 0 Par. 2. Section 1.6038A-1T is amended by adding paragraph (o) to read as follows: Sec. 1.6038A-1T... section expires on June 10, 2014. * * * * * 0 Par. 3. Section 1.6038A-2T is amended by adding paragraph (i...

Simple and rapid quantification of serotonin transporter binding using [11C]DASB bolus plus constant infusion.

PubMed

Gryglewski, G; Rischka, L; Philippe, C; Hahn, A; James, G M; Klebermass, E; Hienert, M; Silberbauer, L; Vanicek, T; Kautzky, A; Berroterán-Infante, N; Nics, L; Traub-Weidinger, T; Mitterhauser, M; Wadsak, W; Hacker, M; Kasper, S; Lanzenberger, R

2017-04-01

In-vivo quantification of serotonin transporters (SERT) in human brain has been a mainstay of molecular imaging in the field of neuropsychiatric disorders and helped to explore the underpinnings of several medical conditions, therapeutic and environmental influences. The emergence of PET/MR hybrid systems and the heterogeneity of SERT binding call for the development of efficient methods making the investigation of larger or vulnerable populations with limited scanner time and simultaneous changes in molecular and functional measures possible. We propose [ 11 C]DASB bolus plus constant infusion for these applications and validate it against standard analyses of dynamic PET data. [ 11 C]DASB bolus/infusion optimization was performed on data acquired after [ 11 C]DASB bolus in 8 healthy subjects. Subsequently, 16 subjects underwent one scan using [ 11 C]DASB bolus plus constant infusion with K bol 160-179min and one scan after [ 11 C]DASB bolus for inter-method reliability analysis. Arterial blood sampling and metabolite analysis were performed for all scans. Distribution volumes (V T ) were obtained using Logan plots for bolus scans and ratios between tissue and plasma parent activity for bolus plus infusion scans for different time spans of the scan (V T-70 for 60-70min after start of tracer infusion, V T-90 for 75-90min, V T-120 for 100-120min) in 9 subjects. Omitting blood data, binding potentials (BP ND ) obtained using multilinear reference tissue modeling (MRTM2) and cerebellar gray matter as reference region were compared in 11 subjects. A K bol of 160min was observed to be optimal for rapid equilibration in thalamus and striatum. V T-70 showed good intraclass correlation coefficients (ICCs) of 0.61-0.70 for thalamus, striatal regions and olfactory cortex with bias ≤5.1% compared to bolus scans. ICCs increased to 0.72-0.78 for V T-90 and 0.77-0.93 for V T-120 in these regions. BP ND-90 had negligible bias ≤2.5%, low variability ≤7.9% and ICCs of 0.74-0.87; BP ND-120 had ICCs of 0.73-0.90. Low-binding cortical regions and cerebellar gray matter showed a positive bias of ~8% and ICCs 0.57-0.68 at V T-90 . Cortical BP ND suffered from high variability and bias, best results were obtained for olfactory cortex and anterior cingulate cortex with ICC=0.74-0.75 for BP ND-90 . High-density regions amygdala and midbrain had a negative bias of -5.5% and -22.5% at V T-90 with ICC 0.70 and 0.63, respectively. We have optimized the equilibrium method with [ 11 C]DASB bolus plus constant infusion and demonstrated good inter-method reliability with accepted standard methods and for SERT quantification using both V T and BP ND in a range of different brain regions. With as little as 10-15min of scanning valid estimates of SERT V T and BP ND in thalamus, amygdala, striatal and high-binding cortical regions could be obtained. Blood sampling seems vital for valid quantification of SERT in low-binding cortical regions. These methods allow the investigation of up to three subjects with a single radiosynthesis. Copyright © 2017 Elsevier Inc. All rights reserved.

Validation and Clinical Evaluation of a Novel Method To Measure Miltefosine in Leishmaniasis Patients Using Dried Blood Spot Sample Collection

PubMed Central

Rosing, H.; Hillebrand, M. J. X.; Blesson, S.; Mengesha, B.; Diro, E.; Hailu, A.; Schellens, J. H. M.; Beijnen, J. H.

2016-01-01

To facilitate future pharmacokinetic studies of combination treatments against leishmaniasis in remote regions in which the disease is endemic, a simple cheap sampling method is required for miltefosine quantification. The aims of this study were to validate a liquid chromatography-tandem mass spectrometry method to quantify miltefosine in dried blood spot (DBS) samples and to validate its use with Ethiopian patients with visceral leishmaniasis (VL). Since hematocrit (Ht) levels are typically severely decreased in VL patients, returning to normal during treatment, the method was evaluated over a range of clinically relevant Ht values. Miltefosine was extracted from DBS samples using a simple method of pretreatment with methanol, resulting in >97% recovery. The method was validated over a calibration range of 10 to 2,000 ng/ml, and accuracy and precision were within ±11.2% and ≤7.0% (≤19.1% at the lower limit of quantification), respectively. The method was accurate and precise for blood spot volumes between 10 and 30 μl and for Ht levels of 20 to 35%, although a linear effect of Ht levels on miltefosine quantification was observed in the bioanalytical validation. DBS samples were stable for at least 162 days at 37°C. Clinical validation of the method using paired DBS and plasma samples from 16 VL patients showed a median observed DBS/plasma miltefosine concentration ratio of 0.99, with good correlation (Pearson's r = 0.946). Correcting for patient-specific Ht levels did not further improve the concordance between the sampling methods. This successfully validated method to quantify miltefosine in DBS samples was demonstrated to be a valid and practical alternative to venous blood sampling that can be applied in future miltefosine pharmacokinetic studies with leishmaniasis patients, without Ht correction. PMID:26787691

Validation of ethnomedicinal potential of Tinospora cordifolia for anticancer and immunomodulatory activities and quantification of bioactive molecules by HPTLC.

PubMed

Bala, Manju; Pratap, Kunal; Verma, Praveen Kumar; Singh, Bikram; Padwad, Yogendra

2015-12-04

Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thomas. (Menispermaceae) is one of the most widely used plants in various traditional medicinal systems including "Ayurveda". The plant is used for the treatment of jaundice, rheumatism, urinary disorder, skin diseases, diabetes and anemia. The phytoconstituents present in the plant belongs to different class of compounds such as alkaloids, diterpenoids lactones, glycosides, steroids, phenol, aliphatic compounds and polysaccharides. The aim of present study was the isolation, structure elucidation, quantification and pharmacological evaluation of secondary metabolites from T. cordifolia for anticancer and immunomodulatory activities. Different extracts and fractions were prepared from the stem of T. cordifolia. Pure molecules were isolated using normal phase chromatography and characterized on the basis of NMR and mass spectroscopic techniques. The anti-cancer and immunomodulatory activities of different extracts, fractions and isolated compounds were evaluated against four different human cancer cell lines, KB (human oral squamous carcinoma), CHOK-1 (hamster ovary), HT-29 (human colon cancer) and SiHa (human cervical cancer) and murine primary cells respectively. A simple, normal phase HPTLC method was also developed for the quantification of three bioactive compounds i.e N-formylannonain (1), 11-hydroxymustakone (5) and yangambin (8) in the stem of T. cordifolia hosted on fifteen different plants. Chromatographic purification of different fractions led to the isolation of eight pure molecules i.e N-formylannonain (1), magnoflorine (2), jatrorrhizine (3) palmatine (4), 11-hydroxymustakone (5), cordifolioside A (6), tinocordiside (7) and yangambin (8). All extracts and fractions were active against KB and CHOK-1 cells whereas among the pure molecules palmatine (4) was found to be active against KB and HT-29; tinocordiside (7) against KB and CHOK-1; yangambin (8) against KB cells however N-formylannonain (1) and 11-hydroxymustakone (5), was found active for immunomodulatory activity. HPTLC quantification of three active molecules i.e N-formylannonain (1), 11-hydroxymustakone (5), and yangambin (8) were found in highest quantity in the stem of T. cordifolia hosted on Mangifera indica, however, other two active molecules were not quantified due to their insufficient quantity. Eight compounds have been isolated and characterized belonging to different classes. The pharmacological evaluation of extract, fractions and pure molecules revealed the ethnomedicinal value of T. cordifolia for anticancer and immunomodulatory activities. Copyright © 2015. Published by Elsevier Ireland Ltd.

Evaluation of prospective motion correction of high-resolution 3D-T2-FLAIR acquisitions in epilepsy patients.

PubMed

Vos, Sjoerd B; Micallef, Caroline; Barkhof, Frederik; Hill, Andrea; Winston, Gavin P; Ourselin, Sebastien; Duncan, John S

2018-03-02

T2-FLAIR is the single most sensitive MRI contrast to detect lesions underlying focal epilepsies but 3D sequences used to obtain isotropic high-resolution images are susceptible to motion artefacts. Prospective motion correction (PMC) - demonstrated to improve 3D-T1 image quality in a pediatric population - was applied to high-resolution 3D-T2-FLAIR scans in adult epilepsy patients to evaluate its clinical benefit. Coronal 3D-T2-FLAIR scans were acquired with a 1mm isotropic resolution on a 3T MRI scanner. Two expert neuroradiologists reviewed 40 scans without PMC and 40 with navigator-based PMC. Visual assessment addressed six criteria of image quality (resolution, SNR, WM-GM contrast, intensity homogeneity, lesion conspicuity, diagnostic confidence) on a seven-point Likert scale (from non-diagnostic to outstanding). SNR was also objectively quantified within the white matter. PMC scans had near-identical scores on the criteria of image quality to non-PMC scans, with the notable exception that intensity homogeneity was generally worse. Using PMC, the percentage of scans with bad image quality was substantially lower than without PMC (3.25% vs. 12.5%) on the other five criteria. Quantitative SNR estimates revealed that PMC and non-PMC had no significant difference in SNR (P=0.07). Application of prospective motion correction to 3D-T2-FLAIR sequences decreased the percentage of low-quality scans, reducing the number of scans that need to be repeated to obtain clinically useful data. Copyright © 2018 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Simultaneous detection of valine and lactate using MEGA-PRESS editing in pyogenic brain abscess.

PubMed

Lange, Thomas; Ko, Cheng-Wen; Lai, Ping-Hong; Dacko, Michael; Tsai, Shang-Yueh; Buechert, Martin

2016-12-01

Valine and lactate have been recognized as important metabolic markers to diagnose brain abscess by means of MRS. However, in vivo unambiguous detection and quantification is hampered by macromolecular contamination. In this work, MEGA-PRESS difference editing of valine and lactate is proposed. The method is validated in vitro and applied for quantitative in vivo experiments in one healthy subject and two brain abscess patients. It is demonstrated that with this technique the overlapping lipid signal can be reduced by more than an order of magnitude and thus the robustness of valine and lactate detection in vivo can be enhanced. Quantification of the two abscess MEGA-PRESS spectra yielded valine/lactate concentration ratios of 0.10 and 0.27. These ratios agreed with the concentration ratios determined from concomitantly acquired short-T E PRESS data and were in line with literature values. The quantification accuracy of lactate (as measured with Cramér-Rao lower bounds in LCModel processing) was better for MEGA-PRESS than for short-T E PRESS in all acquired in vivo datasets. The Cramér-Rao lower bounds of valine were only better for MEGA-PRESS in one of the two abscess cases, while in the other case coediting of isoleucine confounded the quantification in the MEGA-PRESS analysis. MEGA-PRESS and short-T E PRESS should be combined for unambiguous quantification of amino acids in abscess measurements. Simultaneous valine/lactate MEGA-PRESS editing might benefit the distinction of brain abscesses from tumors, and further categorization of bacteria with reasonable sensitivity and specificity. Copyright © 2016 John Wiley & Sons, Ltd.

Cardiac Iron Determines Cardiac T2*, T2, and T1 in the Gerbil Model of Iron Cardiomyopathy

PubMed Central

Wood, John C.; Otto-Duessel, Maya; Aguilar, Michelle; Nick, Hanspeter; Nelson, Marvin D.; Coates, Thomas D.; Pollack, Harvey; Moats, Rex

2010-01-01

Background Transfusional therapy for thalassemia major and sickle cell disease can lead to iron deposition and damage to the heart, liver, and endocrine organs. Iron causes the MRI parameters T1, T2, and T2* to shorten in these organs, which creates a potential mechanism for iron quantification. However, because of the danger and variability of cardiac biopsy, tissue validation of cardiac iron estimates by MRI has not been performed. In this study, we demonstrate that iron produces similar T1, T2, and T2* changes in the heart and liver using a gerbil iron-overload model. Methods and Results Twelve gerbils underwent iron dextran loading (200 mg · kg−1 · wk−1) from 2 to 14 weeks; 5 age-matched controls were studied as well. Animals had in vivo assessment of cardiac T2* and hepatic T2 and T2* and postmortem assessment of cardiac and hepatic T1 and T2. Relaxation measurements were performed in a clinical 1.5-T magnet and a 60-MHz nuclear magnetic resonance relaxometer. Cardiac and liver iron concentrations rose linearly with administered dose. Cardiac 1/T2*, 1/T2, and 1/T1 rose linearly with cardiac iron concentration. Liver 1/T2*, 1/T2, and 1/T1 also rose linearly, proportional to hepatic iron concentration. Liver and heart calibrations were similar on a dry-weight basis. Conclusions MRI measurements of cardiac T2 and T2* can be used to quantify cardiac iron. The similarity of liver and cardiac iron calibration curves in the gerbil suggests that extrapolation of human liver calibration curves to heart may be a rational approximation in humans. PMID:16027257

Myocardial perfusion quantification using simultaneously acquired 13 NH3 -ammonia PET and dynamic contrast-enhanced MRI in patients at rest and stress.

PubMed

Kunze, Karl P; Nekolla, Stephan G; Rischpler, Christoph; Zhang, Shelley HuaLei; Hayes, Carmel; Langwieser, Nicolas; Ibrahim, Tareq; Laugwitz, Karl-Ludwig; Schwaiger, Markus

2018-04-19

Systematic differences with respect to myocardial perfusion quantification exist between DCE-MRI and PET. Using the potential of integrated PET/MRI, this study was conceived to compare perfusion quantification on the basis of simultaneously acquired 13 NH 3 -ammonia PET and DCE-MRI data in patients at rest and stress. Twenty-nine patients were examined on a 3T PET/MRI scanner. DCE-MRI was implemented in dual-sequence design and additional T 1 mapping for signal normalization. Four different deconvolution methods including a modified version of the Fermi technique were compared against 13 NH 3 -ammonia results. Cohort-average flow comparison yielded higher resting flows for DCE-MRI than for PET and, therefore, significantly lower DCE-MRI perfusion ratios under the common assumption of equal arterial and tissue hematocrit. Absolute flow values were strongly correlated in both slice-average (R 2  = 0.82) and regional (R 2  = 0.7) evaluations. Different DCE-MRI deconvolution methods yielded similar flow result with exception of an unconstrained Fermi method exhibiting outliers at high flows when compared with PET. Thresholds for Ischemia classification may not be directly tradable between PET and MRI flow values. Differences in perfusion ratios between PET and DCE-MRI may be lifted by using stress/rest-specific hematocrit conversion. Proper physiological constraints are advised in model-constrained deconvolution. © 2018 International Society for Magnetic Resonance in Medicine.

Quantification des besoins en intrants antipaludiques: contribution à l'actualisation des hypothèses pour la quantification des intrants de prise en charge des cas de paludisme grave en République Démocratique du Congo

PubMed Central

Likwela, Joris Losimba; Otokoye, John Otshudiema

2015-01-01

Les formes graves de paludisme à Plasmodium falciparum sont une cause majeure de décès des enfants de moins de 5 ans en Afrique Sub-saharienne. Un traitement rapide dépend de la disponibilité de médicaments appropriés au niveau des points de prestation de service. La fréquence des ruptures de stock des commodités antipaludiques, en particuliers celles utilisées pour le paludisme grave, avait nécessité une mise à jour des hypothèses de quantification. Les données issues de la collecte de routine du PNLP de 2007 à 2012 ont été comparées à celles rapportés par d'autres pays africains et utilisées pour orienter les discussions au cours d'un atelier organisé par le PNLP et ses partenaires techniques et financiers afin de dégager un consensus national. La proportion des cas de paludisme rapportés comme grave en RDC est resté autour d'une médiane de 7% avec un domaine de variation de 6 à 9%. Hormis la proportion rapportée au Kenya (2%), les pays africains ont rapporté une proportion de cas grave variant entre 5 et 7%. Il apparaît que la proportion de 1% précédemment utilisée pour la quantification en RDC a été sous-estimée dans le contexte de la gestion des cas graves sur terrain. Un consensus s'est dégagé autour de la proportion de 5% étant entendu que des efforts de renforcement des capacités seraient déployés afin d'améliorer le diagnostic au niveau des points de prestation des services. PMID:26213595

A brain phantom for motion-corrected PROPELLER showing image contrast and construction similar to those of in vivo MRI.

PubMed

Saotome, Kousaku; Matsushita, Akira; Matsumoto, Koji; Kato, Yoshiaki; Nakai, Kei; Murata, Koichi; Yamamoto, Tetsuya; Sankai, Yoshiyuki; Matsumura, Akira

2017-02-01

A fast spin-echo sequence based on the Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction (PROPELLER) technique is a magnetic resonance (MR) imaging data acquisition and reconstruction method for correcting motion during scans. Previous studies attempted to verify the in vivo capabilities of motion-corrected PROPELLER in real clinical situations. However, such experiments are limited by repeated, stray head motion by research participants during the prescribed and precise head motion protocol of a PROPELLER acquisition. Therefore, our purpose was to develop a brain phantom set for motion-corrected PROPELLER. The profile curves of the signal intensities on the in vivo T 2 -weighted image (T 2 WI) and 3-D rapid prototyping technology were used to produce the phantom. In addition, we used a homemade driver system to achieve in-plane motion at the intended timing. We calculated the Pearson's correlation coefficient (R 2 ) between the signal intensities of the in vivo T 2 WI and the phantom T 2 WI and clarified the rotation precision of the driver system. In addition, we used the phantom set to perform initial experiments to show the rotational angle and frequency dependences of PROPELLER. The in vivo and phantom T 2 WIs were visually congruent, with a significant correlation (R 2 ) of 0.955 (p<.001). The rotational precision of the driver system was within 1 degree of tolerance. The experiment on the rotational angle dependency showed image discrepancies between the rotational angles. The experiment on the rotational frequency dependency showed that the reconstructed images became increasingly blurred by the corruption of the blades as the number of motions increased. In this study, we developed a phantom that showed image contrasts and construction similar to the in vivo T 2 WI. In addition, our homemade driver system achieved precise in-plane motion at the intended timing. Our proposed phantom set could perform systematic experiments with a real clinical MR image, which to date has not been possible in in vivo studies. Further investigation should focus on the improvement of the motion-correction algorithm in PROPELLER using our phantom set for what would traditionally be considered problematic patients (children, emergency patients, elderly, those with dementia, and so on). Copyright © 2016 Elsevier Inc. All rights reserved.

Validation of a Multimodality Flow Phantom and Its Application for Assessment of Dynamic SPECT and PET Technologies.

PubMed

Gabrani-Juma, Hanif; Clarkin, Owen J; Pourmoghaddas, Amir; Driscoll, Brandon; Wells, R Glenn; deKemp, Robert A; Klein, Ran

2017-01-01

Simple and robust techniques are lacking to assess performance of flow quantification using dynamic imaging. We therefore developed a method to qualify flow quantification technologies using a physical compartment exchange phantom and image analysis tool. We validate and demonstrate utility of this method using dynamic PET and SPECT. Dynamic image sequences were acquired on two PET/CT and a cardiac dedicated SPECT (with and without attenuation and scatter corrections) systems. A two-compartment exchange model was fit to image derived time-activity curves to quantify flow rates. Flowmeter measured flow rates (20-300 mL/min) were set prior to imaging and were used as reference truth to which image derived flow rates were compared. Both PET cameras had excellent agreement with truth ( [Formula: see text]). High-end PET had no significant bias (p > 0.05) while lower-end PET had minimal slope bias (wash-in and wash-out slopes were 1.02 and 1.01) but no significant reduction in precision relative to high-end PET (<15% vs. <14% limits of agreement, p > 0.3). SPECT (without scatter and attenuation corrections) slope biases were noted (0.85 and 1.32) and attributed to camera saturation in early time frames. Analysis of wash-out rates from non-saturated, late time frames resulted in excellent agreement with truth ( [Formula: see text], slope = 0.97). Attenuation and scatter corrections did not significantly impact SPECT performance. The proposed phantom, software and quality assurance paradigm can be used to qualify imaging instrumentation and protocols for quantification of kinetic rate parameters using dynamic imaging.

Antagonistic role of vertebral translation against vertebral rotation in the spontaneous postoperative modulation of the anterior chest wall contour in thoracic idiopathic scoliosis.

PubMed

Qian, Bang-ping; Mao, Sai-hu; Zhu, Ze-zhang; Zhu, Feng; Liu, Zhen; Xu, Lei-lei; Wang, Bing; Yu, Yang; Qiu, Yong

2013-09-01

A computed tomography study. To identify the best scoliotic deformity components that show impact upon the spontaneous postoperative modulation of the deformed anterior chest wall contour in right convex thoracic adolescent idiopathic scoliosis. Spontaneous postoperative aggravation of the anterior concave costal projection was a common occurrence in adolescent idiopathic scoliosis, yet the risk factors that effectively bridged the gap between what the surgeons did in the interior and how the rib cages reacted on the exterior were still open to debate. Pre- and postoperative computed tomographic scans of 77 patients with right convex thoracic adolescent idiopathic scoliosis were retrieved and analyzed. According to the postoperative variation of anterior chest wall angle (CWA), the patients were divided into 2 groups with either aggravated or improved CWA. Multiple scoliotic deformity parameters and their surgical correction rates were evaluated, correlated, and then compared between the 2 groups. Moreover, patients with apex located at T9 were isolated and evaluated independently. A logistic regression analysis was used to determine the independent predictors of the spontaneous postoperative modulation of the anterior chest wall contour. The surgical correction rate of Cobb angle (supine), the rotational angle with respect to the sagittal plane (RAsag angle), the rotational angle with respect to the anterior midline of the body (RAml angle), the angle of lateral deviation of the apical vertebrae from the midline (MLdev angle), the posterior hemithorax ratio, the vertebral translation (VT), and the thoracic rotation averaged 64.6%, 19.5%, 30.8%, 39.2%, 15.0%, 41.2%, and 28.7%, respectively. Ratio of aggravated anterior chest wall contour was the highest at the T7 apex group (84.6%) as compared with T8 apex group (47.1%), T9 apex group (19.5%), and T10 apex group (0.0%). The preoperative CWA was significantly lower in the aggravated CWA group when compared with the improved group (2.1 ± 1.8°vs. 6.6 ± 2.4°, P < 0.001). Besides, in the aggravated CWA group, significantly greater surgical correction of VT and lesser correction of RAsag angle were demonstrated when compared with the improved CWA group (VT: 53.0% vs. 34.8%, P = 0.001; RAsag: 2.5% vs. 28.7%, P = 0.000). In the T9 subgroup, remarkably different correction rate of VT and RAsag were similarly observed (VT: 54.9% vs. 35.3%, P = 0.046; RAsag: 4.9% vs. 23.5%, P = 0.034). In terms of other deformity parameters, no significantly different correction rate was consistently detected. In the logistic regression analysis, apex location, CWA, and correction rate of RAsag were demonstrated to be independent factors predictive of the alteration of chest wall contour. In addition to the smaller preoperative CWA and higher apex location, lesser correction of vertebral rotation, if accompanied by great surgical correction of apical VT, could also largely result in a poor postoperative anterior chest wall contour.

Tumor Cell-Free DNA Copy Number Instability Predicts Therapeutic Response to Immunotherapy.

PubMed

Weiss, Glen J; Beck, Julia; Braun, Donald P; Bornemann-Kolatzki, Kristen; Barilla, Heather; Cubello, Rhiannon; Quan, Walter; Sangal, Ashish; Khemka, Vivek; Waypa, Jordan; Mitchell, William M; Urnovitz, Howard; Schütz, Ekkehard

2017-09-01

Purpose: Chromosomal instability is a fundamental property of cancer, which can be quantified by next-generation sequencing (NGS) from plasma/serum-derived cell-free DNA (cfDNA). We hypothesized that cfDNA could be used as a real-time surrogate for imaging analysis of disease status as a function of response to immunotherapy and as a more reliable tool than tumor biomarkers. Experimental Design: Plasma cfDNA sequences from 56 patients with diverse advanced cancers were prospectively collected and analyzed in a single-blind study for copy number variations, expressed as a quantitative chromosomal number instability (CNI) score versus 126 noncancer controls in a training set of 23 and a blinded validation set of 33. Tumor biomarker concentrations and a surrogate marker for T regulatory cells (Tregs) were comparatively analyzed. Results: Elevated CNI scores were observed in 51 of 56 patients prior to therapy. The blinded validation cohort provided an overall prediction accuracy of 83% (25/30) and a positive predictive value of CNI score for progression of 92% (11/12). The combination of CNI score before cycle (Cy) 2 and 3 yielded a correct prediction for progression in all 13 patients. The CNI score also correctly identified cases of pseudo-tumor progression from hyperprogression. Before Cy2 and Cy3, there was no significant correlation for protein tumor markers, total cfDNA, or surrogate Tregs. Conclusions: Chromosomal instability quantification in plasma cfDNA can serve as an early indicator of response to immunotherapy. The method has the potential to reduce health care costs and disease burden for cancer patients following further validation. Clin Cancer Res; 23(17); 5074-81. ©2017 AACR . ©2017 American Association for Cancer Research.

Precise Correction of Disease Mutations in Induced Pluripotent Stem Cells Derived From Patients With Limb Girdle Muscular Dystrophy.

PubMed

Turan, Soeren; Farruggio, Alfonso P; Srifa, Waracharee; Day, John W; Calos, Michele P

2016-04-01

Limb girdle muscular dystrophies types 2B (LGMD2B) and 2D (LGMD2D) are degenerative muscle diseases caused by mutations in the dysferlin and alpha-sarcoglycan genes, respectively. Using patient-derived induced pluripotent stem cells (iPSC), we corrected the dysferlin nonsense mutation c.5713C>T; p.R1905X and the most common alpha-sarcoglycan mutation, missense c.229C>T; p.R77C, by single-stranded oligonucleotide-mediated gene editing, using the CRISPR/Cas9 gene-editing system to enhance the frequency of homology-directed repair. We demonstrated seamless, allele-specific correction at efficiencies of 0.7-1.5%. As an alternative, we also carried out precise gene addition strategies for correction of the LGMD2B iPSC by integration of wild-type dysferlin cDNA into the H11 safe harbor locus on chromosome 22, using dual integrase cassette exchange (DICE) or TALEN-assisted homologous recombination for insertion precise (THRIP). These methods employed TALENs and homologous recombination, and DICE also utilized site-specific recombinases. With DICE and THRIP, we obtained targeting efficiencies after selection of ~20%. We purified iPSC corrected by all methods and verified rescue of appropriate levels of dysferlin and alpha-sarcoglycan protein expression and correct localization, as shown by immunoblot and immunocytochemistry. In summary, we demonstrate for the first time precise correction of LGMD iPSC and validation of expression, opening the possibility of cell therapy utilizing these corrected iPSC.

T-duality constraints on higher derivatives revisited

NASA Astrophysics Data System (ADS)

Hohm, Olaf; Zwiebach, Barton

2016-04-01

We ask to what extent are the higher-derivative corrections of string theory constrained by T-duality. The seminal early work by Meissner tests T-duality by reduction to one dimension using a distinguished choice of field variables in which the bosonic string action takes a Gauss-Bonnet-type form. By analyzing all field redefinitions that may or may not be duality covariant and may or may not be gauge covariant we extend the procedure to test T-duality starting from an action expressed in arbitrary field variables. We illustrate the method by showing that it determines uniquely the first-order α' corrections of the bosonic string, up to terms that vanish in one dimension. We also use the method to glean information about the O({α}^' 2}) corrections in the double field theory with Green-Schwarz deformation.

Oxygen Consumption of Tilapia and Preliminary Mass Flows through a Prototype Closed Aquaculture System

NASA Technical Reports Server (NTRS)

Muller, Matthew S.; Bauer, Clarence F.

1994-01-01

Performance of NASA's prototype CELSS Breadboard Project Closed Aquaculture System was evaluated by estimating gas exchange quantification and preliminary carbon and nitrogen balances. The total system oxygen consumption rate was 535 mg/hr kg/fish (cv = 30%) when stocked with Tilapia aurea populations (fresh weights of 97 +/- 19 to 147 +/- 36 g/fish for various trials). Oxygen consumption by T. aurea (260 mg/hr kg/fish) contributed to approximately one-half of total system demand. Continuous carbon dioxide quantification methods were analyzed using the,relation of carbon dioxide to oxygen consumption. Overall food conversion rates averaged 18.2 +/- 3.2%. Major pathways for nitrogen and carbon in the system were described with preliminary mass closure of 60-80% and 60% for nitrogen and carbon.

Quantification of OH and HO2 radicals during the low-temperature oxidation of hydrocarbons by Fluorescence Assay by Gas Expansion technique

PubMed Central

Blocquet, Marion; Schoemaecker, Coralie; Amedro, Damien; Herbinet, Olivier; Battin-Leclerc, Frédérique; Fittschen, Christa

2013-01-01

•OH and •HO2 radicals are known to be the key species in the development of ignition. A direct measurement of these radicals under low-temperature oxidation conditions (T = 550–1,000 K) has been achieved by coupling a technique named fluorescence assay by gas expansion, an experimental technique designed for the quantification of these radicals in the free atmosphere, to a jet-stirred reactor, an experimental device designed for the study of low-temperature combustion chemistry. Calibration allows conversion of relative fluorescence signals to absolute mole fractions. Such radical mole fraction profiles will serve as a benchmark for testing chemical models developed to improve the understanding of combustion processes. PMID:24277836

Influence of amplitude-related perfusion parameters in the parotid glands by non-fat-saturated dynamic contrast-enhanced magnetic resonance imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiu, Su-Chin; Cheng, Cheng-Chieh; Chang, Hing-Chiu

Purpose: To verify whether quantification of parotid perfusion is affected by fat signals on non-fat-saturated (NFS) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and whether the influence of fat is reduced with fat saturation (FS). Methods: This study consisted of three parts. First, a retrospective study analyzed DCE-MRI data previously acquired on different patients using NFS (n = 18) or FS (n = 18) scans. Second, a phantom study simulated the signal enhancements in the presence of gadolinium contrast agent at six concentrations and three fat contents. Finally, a prospective study recruited nine healthy volunteers to investigate the influence of fatmore » suppression on perfusion quantification on the same subjects. Parotid perfusion parameters were derived from NFS and FS DCE-MRI data using both pharmacokinetic model analysis and semiquantitative parametric analysis. T tests and linear regression analysis were used for statistical analysis with correction for multiple comparisons. Results: NFS scans showed lower amplitude-related parameters, including parameter A, peak enhancement (PE), and slope than FS scans in the patients (all with P < 0.0167). The relative signal enhancement in the phantoms was proportional to the dose of contrast agent and was lower in NFS scans than in FS scans. The volunteer study showed lower parameter A (6.75 ± 2.38 a.u.), PE (42.12% ± 14.87%), and slope (1.43% ± 0.54% s{sup −1}) in NFS scans as compared to 17.63 ± 8.56 a.u., 104.22% ± 25.15%, and 9.68% ± 1.67% s{sup −1}, respectively, in FS scans (all with P < 0.005). These amplitude-related parameters were negatively associated with the fat content in NFS scans only (all with P < 0.05). Conclusions: On NFS DCE-MRI, quantification of parotid perfusion is adversely affected by the presence of fat signals for all amplitude-related parameters. The influence could be reduced on FS scans.« less

Stable isotope dilution HILIC-MS/MS method for accurate quantification of glutamic acid, glutamine, pyroglutamic acid, GABA and theanine in mouse brain tissues.

PubMed

Inoue, Koichi; Miyazaki, Yasuto; Unno, Keiko; Min, Jun Zhe; Todoroki, Kenichiro; Toyo'oka, Toshimasa

2016-01-01

In this study, we developed the stable isotope dilution hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-MS/MS) technique for the accurate, reasonable and simultaneous quantification of glutamic acid (Glu), glutamine (Gln), pyroglutamic acid (pGlu), γ-aminobutyric acid (GABA) and theanine in mouse brain tissues. The quantification of these analytes was accomplished using stable isotope internal standards and the HILIC separating mode to fully correct the intramolecular cyclization during the electrospray ionization. It was shown that linear calibrations were available with high coefficients of correlation (r(2)  > 0.999, range from 10 pmol/mL to 50 mol/mL). For application of the theanine intake, the determination of Glu, Gln, pGlu, GABA and theanine in the hippocampus and central cortex tissues was performed based on our developed method. In the region of the hippocampus, the concentration levels of Glu and pGlu were significantly reduced during reality-based theanine intake. Conversely, the concentration level of GABA increased. This result showed that transited theanine has an effect on the metabolic balance of Glu analogs in the hippocampus. Copyright © 2015 John Wiley & Sons, Ltd.

Correction of the lack of commutability between plasmid DNA and genomic DNA for quantification of genetically modified organisms using pBSTopas as a model.

PubMed

Zhang, Li; Wu, Yuhua; Wu, Gang; Cao, Yinglong; Lu, Changming

2014-10-01

Plasmid calibrators are increasingly applied for polymerase chain reaction (PCR) analysis of genetically modified organisms (GMOs). To evaluate the commutability between plasmid DNA (pDNA) and genomic DNA (gDNA) as calibrators, a plasmid molecule, pBSTopas, was constructed, harboring a Topas 19/2 event-specific sequence and a partial sequence of the rapeseed reference gene CruA. Assays of the pDNA showed similar limits of detection (five copies for Topas 19/2 and CruA) and quantification (40 copies for Topas 19/2 and 20 for CruA) as those for the gDNA. Comparisons of plasmid and genomic standard curves indicated that the slopes, intercepts, and PCR efficiency for pBSTopas were significantly different from CRM Topas 19/2 gDNA for quantitative analysis of GMOs. Three correction methods were used to calibrate the quantitative analysis of control samples using pDNA as calibrators: model a, or coefficient value a (Cva); model b, or coefficient value b (Cvb); and the novel model c or coefficient formula (Cf). Cva and Cvb gave similar estimated values for the control samples, and the quantitative bias of the low concentration sample exceeded the acceptable range within ±25% in two of the four repeats. Using Cfs to normalize the Ct values of test samples, the estimated values were very close to the reference values (bias -13.27 to 13.05%). In the validation of control samples, model c was more appropriate than Cva or Cvb. The application of Cf allowed pBSTopas to substitute for Topas 19/2 gDNA as a calibrator to accurately quantify the GMO.

An enhanced in vivo stable isotope labeling by amino acids in cell culture (SILAC) model for quantification of drug metabolism enzymes.

PubMed

MacLeod, A Kenneth; Fallon, Padraic G; Sharp, Sheila; Henderson, Colin J; Wolf, C Roland; Huang, Jeffrey T-J

2015-03-01

Many of the enzymes involved in xenobiotic metabolism are maintained at a low basal level and are only synthesized in response to activation of upstream sensor/effector proteins. This induction can have implications in a variety of contexts, particularly during the study of the pharmacokinetics, pharmacodynamics, and drug-drug interaction profile of a candidate therapeutic compound. Previously, we combined in vivo SILAC material with a targeted high resolution single ion monitoring (tHR/SIM) LC-MS/MS approach for quantification of 197 peptide pairs, representing 51 drug metabolism enzymes (DME), in mouse liver. However, as important enzymes (for example, cytochromes P450 (Cyp) of the 1a and 2b subfamilies) are maintained at low or undetectable levels in the liver of unstimulated metabolically labeled mice, quantification of these proteins was unreliable. In the present study, we induced DME expression in labeled mice through synchronous ligand-mediated activation of multiple upstream nuclear receptors, thereby enhancing signals for proteins including Cyps 1a, 2a, 2b, 2c, and 3a. With this enhancement, 115 unique, lysine-containing, Cyp-derived peptides were detected in the liver of a single animal, as opposed to 56 in a pooled sample from three uninduced animals. A total of 386 peptide pairs were quantified by tHR/SIM, representing 68 Phase I, 30 Phase II, and eight control proteins. This method was employed to quantify changes in DME expression in the hepatic cytochrome P450 reductase null (HRN) mouse. We observed compensatory induction of several enzymes, including Cyps 2b10, 2c29, 2c37, 2c54, 2c55, 2e1, 3a11, and 3a13, carboxylesterase (Ces) 2a, and glutathione S-transferases (Gst) m2 and m3, along with down-regulation of hydroxysteroid dehydrogenases (Hsd) 11b1 and 17b6. Using DME-enhanced in vivo SILAC material with tHR/SIM, therefore, permits the robust analysis of multiple DME of importance to xenobiotic metabolism, with improved utility for the study of drug pharmacokinetics, pharmacodynamics, and of chemically treated and genetically modified mouse models. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Non-invasive detection and quantification of brain microvascular deficits by near-infrared spectroscopy in a rat model of Vascular Cognitive Impairment

NASA Astrophysics Data System (ADS)

Hallacoglu, Bertan; Sassaroli, Angelo M.; Rosenberg, Irwin H.; Troen, Aron; Fantini, Sergio

2011-02-01

Structural abnormalities in brain microvasculature are commonly associated with Alzheimer's Disease and other dementias. However, the extent to which structural microvascular abnormalities cause functional impairments in brain circulation and thereby to cognitive impairment is unclear. Non-invasive, near-infrared spectroscopy (NIRS) methods can be used to determine the absolute hemoglobin concentration and saturation in brain tissue, from which additional parameters such as cerebral blood volume (a theoretical correlate of brain microvascular density) can be derived. Validating such NIRS parameters in animal models, and understanding their relationship to cognitive function is an important step in the ultimate application of these methods to humans. To this end we applied a non-invasive multidistance NIRS method to determine the absolute concentration and saturation of cerebral hemoglobin in rat, by separately measuring absorption and reduced scattering coefficients without relying on pre- or post-correction factors. We applied this method to study brain circulation in folate deficient rats, which express brain microvascular pathology1 and which we have shown to develop cognitive impairment.2 We found absolute brain hemoglobin concentration ([HbT]) and oxygen saturation (StO2) to be significantly lower in folate deficient rats (n=6) with respect to control rats (n=5) (for [HbT]: 73+/-10 μM vs. 95+/-14 μM for StO2: 55%+/-7% vs. 66% +/-4%), implicating microvascular pathology and diminished oxygen delivery as a mechanism of cognitive impairment. More generally, our study highlights how noninvasive, absolute NIRS measurements can provide unique insight into the pathophysiology of Vascular Cognitive Impairment. Applying this method to this and other rat models of cognitive impairment will help to validate physiologically meaningful NIRS parameters for the ultimate goal of studying cerebral microvascular disease and cognitive decline in humans.

Vertebral derotation in adolescent idiopathic scoliosis causes hypokyphosis of the thoracic spine

PubMed Central

2012-01-01

Background The purpose of this study was to test the hypothesis that direct vertebral derotation by pedicle screws (PS) causes hypokyphosis of the thoracic spine in adolescent idiopathic scoliosis (AIS) patients, using computer simulation. Methods Twenty AIS patients with Lenke type 1 or 2 who underwent posterior correction surgeries using PS were included in this study. Simulated corrections of each patient’s scoliosis, as determined by the preoperative CT scan data, were performed on segmented 3D models of the whole spine. Two types of simulated extreme correction were performed: 1) complete coronal correction only (C method) and 2) complete coronal correction with complete derotation of vertebral bodies (C + D method). The kyphosis angle (T5-T12) and vertebral rotation angle at the apex were measured before and after the simulated corrections. Results The mean kyphosis angle after the C + D method was significantly smaller than that after the C method (2.7 ± 10.0° vs. 15.0 ± 7.1°, p < 0.01). The mean preoperative apical rotation angle of 15.2 ± 5.5° was completely corrected after the C + D method (0°) and was unchanged after the C method (17.6 ± 4.2°). Conclusions In the 3D simulation study, kyphosis was reduced after complete correction of the coronal and rotational deformity, but it was maintained after the coronal-only correction. These results proved the hypothesis that the vertebral derotation obtained by PS causes hypokyphosis of the thoracic spine. PMID:22691717

Lung perfusion measured using magnetic resonance imaging: New tools for physiological insights into the pulmonary circulation.

PubMed

Hopkins, Susan R; Prisk, G Kim

2010-12-01

Since the lung receives the entire cardiac output, sophisticated imaging techniques are not required in order to measure total organ perfusion. However, for many years studying lung function has required physiologists to consider the lung as a single entity: in imaging terms as a single voxel. Since imaging, and in particular functional imaging, allows the acquisition of spatial information important for studying lung function, these techniques provide considerable promise and are of great interest for pulmonary physiologists. In particular, despite the challenges of low proton density and short T2* in the lung, noncontrast MRI techniques to measure pulmonary perfusion have several advantages including high reliability and the ability to make repeated measurements under a number of physiologic conditions. This brief review focuses on the application of a particular arterial spin labeling (ASL) technique, ASL-FAIRER (flow sensitive inversion recovery with an extra radiofrequency pulse), to answer physiologic questions related to pulmonary function in health and disease. The associated measurement of regional proton density to correct for gravitational-based lung deformation (the "Slinky" effect (Slinky is a registered trademark of Pauf-Slinky incorporated)) and issues related to absolute quantification are also discussed. Copyright © 2010 Wiley-Liss, Inc.

Hepatic fat quantification: a prospective comparison of magnetic resonance spectroscopy and analysis methods for chemical-shift gradient echo magnetic resonance imaging with histologic assessment as the reference standard.

PubMed

Kang, Bo-Kyeong; Yu, Eun Sil; Lee, Seung Soo; Lee, Youngjoo; Kim, Namkug; Sirlin, Claude B; Cho, Eun Yoon; Yeom, Suk Keu; Byun, Jae Ho; Park, Seong Ho; Lee, Moon-Gyu

2012-06-01

The aims of this study were to assess the confounding effects of hepatic iron deposition, inflammation, and fibrosis on hepatic steatosis (HS) evaluation by magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) and to assess the accuracies of MRI and MRS for HS evaluation, using histology as the reference standard. In this institutional review board-approved prospective study, 56 patients gave informed consents and underwent chemical-shift MRI and MRS of the liver on a 1.5-T magnetic resonance scanner. To estimate MRI fat fraction (FF), 4 analysis methods were used (dual-echo, triple-echo, multiecho, and multi-interference), and MRS FF was calculated with T2 correction. Degrees of HS, iron deposition, inflammation, and fibrosis were analyzed in liver resection (n = 37) and biopsy (n = 19) specimens. The confounding effects of histology on fat quantification were assessed by multiple linear regression analysis. Using the histologic degree of HS as the reference standard, the accuracies of each method in estimating HS and diagnosing an HS of 5% or greater were determined by linear regression and receiver operating characteristic analyses. Iron deposition significantly confounded estimations of FF by the dual-echo (P < 0.001) and triple-echo (P = 0.033) methods, whereas no histologic feature confounded the multiecho and multi-interference methods or MRS. The MRS (r = 0.95) showed the strongest correlation with histologic degree of HS, followed by the multiecho (r = 0.92), multi-interference (r = 0.91), triple-echo (r = 0.90), and dual-echo (r = 0.85) methods. For diagnosing HS, the areas under the curve tended to be higher for MRS (0.96) and the multiecho (0.95), multi-interference (0.95), and triple-echo (0.95) methods than for the dual-echo method (0.88) (P ≥ 0.13). The multiecho and multi-interference MRI methods and MRS can accurately quantify hepatic fat, with coexisting histologic abnormalities having no confounding effects.

Comparison of astigmatism correction using either peripheral corneal relaxing incisions or toric intraocular lenses.

PubMed

Muftuoglu, Ilkay Kilic; Aydin Akova, Yonca; Aksoy, Sibel; Unsal, Erkan

2016-01-01

To compare the efficacy and short-term stability of toric intraocular lenses (tIOL) and peripheral cornea relaxing incisions (PCRI) during phacoemulsification. Patients with preexisting corneal astigmatism had cataract surgery either with tIOL (AcrySof Toric) (39 eyes of 35 patients) or standard intraocular lens (AcrySof) + PCRIs (38 eyes of 33 patients). Patients were retrospectively evaluated for manifest refraction, corneal topography, and uncorrected and corrected visual acuities preoperatively and at postoperative 1 and 6 months. The Alpins vectorial method was used to analyze the target induced astigmatism (TIA) and surgically induced astigmatism (SIA), magnitude of error (the difference between the magnitude of SIA and TIA) (ME), and correction index. Mean preoperative corneal astigmatism was 2.21 ± 1.32 D in the tIOL group and 2.24 ± 0.96 D in the PCRI group; the difference was not significant. The decrease in astigmatism was significant in both groups at last follow-up (64% tIOL group, 32% PCRI group, p<0.01, Wilcoxon signed rank test). The mean remaining refractive astigmatism was significantly higher in the PCRI group than in the tIOL group at 1-month (1.42 ± 1.22, 0.89 ± 0.68, respectively) and 6-month follow-ups (1.75 ± 1.37 D, 0.92 ± 0.72, respectively) (p<0.01). The mean ME was significantly lower (-0.35 versus -0.88) with a higher correction index (0.96 versus 0.56) in the tIOL group at 6 months postoperatively. Both tIOL implantation and using PCRI were effective methods to reduce preoperative astigmatism at the time of the cataract surgery. However, tIOLs provided better remaining astigmatism with a more stable refraction than PCRI.

Efficacy and workload analysis of a fixed vertical couch position technique and a fixed‐action–level protocol in whole‐breast radiotherapy

PubMed Central

Verhoeven, Karolien; Weltens, Caroline; Van den Heuvel, Frank

2015-01-01

Quantification of the setup errors is vital to define appropriate setup margins preventing geographical misses. The no‐action–level (NAL) correction protocol reduces the systematic setup errors and, hence, the setup margins. The manual entry of the setup corrections in the record‐and‐verify software, however, increases the susceptibility of the NAL protocol to human errors. Moreover, the impact of the skin mobility on the anteroposterior patient setup reproducibility in whole‐breast radiotherapy (WBRT) is unknown. In this study, we therefore investigated the potential of fixed vertical couch position‐based patient setup in WBRT. The possibility to introduce a threshold for correction of the systematic setup errors was also explored. We measured the anteroposterior, mediolateral, and superior–inferior setup errors during fractions 1–12 and weekly thereafter with tangential angled single modality paired imaging. These setup data were used to simulate the residual setup errors of the NAL protocol, the fixed vertical couch position protocol, and the fixed‐action–level protocol with different correction thresholds. Population statistics of the setup errors of 20 breast cancer patients and 20 breast cancer patients with additional regional lymph node (LN) irradiation were calculated to determine the setup margins of each off‐line correction protocol. Our data showed the potential of the fixed vertical couch position protocol to restrict the systematic and random anteroposterior residual setup errors to 1.8 mm and 2.2 mm, respectively. Compared to the NAL protocol, a correction threshold of 2.5 mm reduced the frequency of mediolateral and superior–inferior setup corrections with 40% and 63%, respectively. The implementation of the correction threshold did not deteriorate the accuracy of the off‐line setup correction compared to the NAL protocol. The combination of the fixed vertical couch position protocol, for correction of the anteroposterior setup error, and the fixed‐action–level protocol with 2.5 mm correction threshold, for correction of the mediolateral and the superior–inferior setup errors, was proved to provide adequate and comparable patient setup accuracy in WBRT and WBRT with additional LN irradiation. PACS numbers: 87.53.Kn, 87.57.‐s

Multi-frequency interpolation in spiral magnetic resonance fingerprinting for correction of off-resonance blurring.

PubMed

Ostenson, Jason; Robison, Ryan K; Zwart, Nicholas R; Welch, E Brian

2017-09-01

Magnetic resonance fingerprinting (MRF) pulse sequences often employ spiral trajectories for data readout. Spiral k-space acquisitions are vulnerable to blurring in the spatial domain in the presence of static field off-resonance. This work describes a blurring correction algorithm for use in spiral MRF and demonstrates its effectiveness in phantom and in vivo experiments. Results show that image quality of T1 and T2 parametric maps is improved by application of this correction. This MRF correction has negligible effect on the concordance correlation coefficient and improves coefficient of variation in regions of off-resonance relative to uncorrected measurements. Copyright © 2017 Elsevier Inc. All rights reserved.

[Performance evaluation of a fluorescamine-HPLC method for determination of histamine in fish and fish products].

PubMed

Kikuchi, Hiroyuki; Tsutsumi, Tomoaki; Matsuda, Rieko

2012-01-01

A method for the quantification of histamine in fish and fish products using tandem solid-phase extraction and fluorescence derivatization with fluorescamine was previously developed. In this study, we improved this analytical method to develop an official test method for quantification of histamine in fish and fish products, and performed a single laboratory study to validate it. Recovery tests of histamine from fillet (Thunnus obesus), and two fish products (fish sauce and salted and dried whole big-eye sardine) that were spiked at the level of 25 and 50 µg/g for T. obesus, and 50 and 100 µg/g for the two fish products, were carried out. The recoveries of histamine from the three samples tested were 88.8-99.6% with good repeatability (1.3-2.1%) and reproducibility (2.1-4.7%). Therefore, this method is acceptable for the quantification of histamine in fish and fish products. Moreover, surveillance of histamine content in food on the market was conducted using this method, and high levels of histamine were detected in some fish products.

Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients.

PubMed

Bezrukov, Ilja; Schmidt, Holger; Gatidis, Sergios; Mantlik, Frédéric; Schäfer, Jürgen F; Schwenzer, Nina; Pichler, Bernd J

2015-07-01

Pediatric imaging is regarded as a key application for combined PET/MR imaging systems. Because existing MR-based attenuation-correction methods were not designed specifically for pediatric patients, we assessed the impact of 2 potentially influential factors: inter- and intrapatient variability of attenuation coefficients and anatomic variability. Furthermore, we evaluated the quantification accuracy of 3 methods for MR-based attenuation correction without (SEGbase) and with bone prediction using an adult and a pediatric atlas (SEGwBONEad and SEGwBONEpe, respectively) on PET data of pediatric patients. The variability of attenuation coefficients between and within pediatric (5-17 y, n = 17) and adult (27-66 y, n = 16) patient collectives was assessed on volumes of interest (VOIs) in CT datasets for different tissue types. Anatomic variability was assessed on SEGwBONEad/pe attenuation maps by computing mean differences to CT-based attenuation maps for regions of bone tissue, lungs, and soft tissue. PET quantification was evaluated on VOIs with physiologic uptake and on 80% isocontour VOIs with elevated uptake in the thorax and abdomen/pelvis. Inter- and intrapatient variability of the bias was assessed for each VOI group and method. Statistically significant differences in mean VOI Hounsfield unit values and linear attenuation coefficients between adult and pediatric collectives were found in the lungs and femur. The prediction of attenuation maps using the pediatric atlas showed a reduced error in bone tissue and better delineation of bone structure. Evaluation of PET quantification accuracy showed statistically significant mean errors in mean standardized uptake values of -14% ± 5% and -23% ± 6% in bone marrow and femur-adjacent VOIs with physiologic uptake for SEGbase, which could be reduced to 0% ± 4% and -1% ± 5% using SEGwBONEpe attenuation maps. Bias in soft-tissue VOIs was less than 5% for all methods. Lung VOIs showed high SDs in the range of 15% for all methods. For VOIs with elevated uptake, mean and SD were less than 5% except in the thorax. The use of a dedicated atlas for the pediatric patient collective resulted in improved attenuation map prediction in osseous regions and reduced interpatient bias variation in femur-adjacent VOIs. For the lungs, in which intrapatient variation was higher for the pediatric collective, a patient- or group-specific attenuation coefficient might improve attenuation map accuracy. Mean errors of -14% and -23% in bone marrow and femur-adjacent VOIs can affect PET quantification in these regions when bone tissue is ignored. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

31 P magnetic resonance fingerprinting for rapid quantification of creatine kinase reaction rate in vivo.

PubMed

Wang, Charlie Y; Liu, Yuchi; Huang, Shuying; Griswold, Mark A; Seiberlich, Nicole; Yu, Xin

2017-12-01

The purpose of this work was to develop a 31 P spectroscopic magnetic resonance fingerprinting (MRF) method for fast quantification of the chemical exchange rate between phosphocreatine (PCr) and adenosine triphosphate (ATP) via creatine kinase (CK). A 31 P MRF sequence (CK-MRF) was developed to quantify the forward rate constant of ATP synthesis via CK ( kfCK), the T 1 relaxation time of PCr ( T1PCr), and the PCr-to-ATP concentration ratio ( MRPCr). The CK-MRF sequence used a balanced steady-state free precession (bSSFP)-type excitation with ramped flip angles and a unique saturation scheme sensitive to the exchange between PCr and γATP. Parameter estimation was accomplished by matching the acquired signals to a dictionary generated using the Bloch-McConnell equation. Simulation studies were performed to examine the susceptibility of the CK-MRF method to several potential error sources. The accuracy of nonlocalized CK-MRF measurements before and after an ischemia-reperfusion (IR) protocol was compared with the magnetization transfer (MT-MRS) method in rat hindlimb at 9.4 T (n = 14). The reproducibility of CK-MRF was also assessed by comparing CK-MRF measurements with both MT-MRS (n = 17) and four angle saturation transfer (FAST) (n = 7). Simulation results showed that CK-MRF quantification of kfCK was robust, with less than 5% error in the presence of model inaccuracies including dictionary resolution, metabolite T 2 values, inorganic phosphate metabolism, and B 1 miscalibration. Estimation of kfCK by CK-MRF (0.38 ± 0.02 s -1 at baseline and 0.42 ± 0.03 s -1 post-IR) showed strong agreement with MT-MRS (0.39 ± 0.03 s -1 at baseline and 0.44 ± 0.04 s -1 post-IR). kfCK estimation was also similar between CK-MRF and FAST (0.38 ± 0.02 s -1 for CK-MRF and 0.38 ± 0.11 s -1 for FAST). The coefficient of variation from 20 s CK-MRF quantification of kfCK was 42% of that by 150 s MT-MRS acquisition and was 12% of that by 20 s FAST acquisition. This study demonstrates the potential of a 31 P spectroscopic MRF framework for rapid, accurate and reproducible quantification of chemical exchange rate of CK in vivo. Copyright © 2017 John Wiley & Sons, Ltd.

ERRATUM: Quantification of scattering corrections to the Beer-Lambert law for transmittance measurements in turbid media

NASA Astrophysics Data System (ADS)

Wind, L.; Szymanski, W. W.

2002-06-01

Figure 3 of this paper has not printed correctly. Specifically, the character ψ is missing five times. The correct figure is reproduced below. The electronic version is unaffected. Figure 3. Schematic diagram of the lp detector system. The angle subtained by the cone of light that will be detected is constant and is determined by the focal length of the lens and the radius of the pinhole. To the left of the position indicated by z* the lp geometry behaves in the same way as the open detector geometry.

Singleshot T1 Mapping using Simultaneous Acquisitions of Spin- and STimulated-Echo Planar Imaging (2D ss-SESTEPI)

PubMed Central

Shi, Xianfeng; Kim, Seong-Eun; Jeong, Eun-Kee

2011-01-01

The conventional stimulated-echo NMR sequence only measures the longitudinal component, while discarding the transverse component, after tipping up the prepared magnetization. This transverse magnetization can be used to measure a spin-echo, in addition to the stimulated-echo. 2D ss-SESTEPI is an EPI-based singleshot imaging technique that simultaneously acquires a spin-echo-planar image (SEPI) and a stimulated-echo-planar image (STEPI) after a single RF excitation. The magnitudes of SEPI and STEPI differ by T1 decay and diffusion weighting for perfect 90° RF, and thus can be used to rapidly measure T1. However, the spatial variation of B1 amplitude induces un-even splitting of the transverse magnetization for SEPI and STEPI within the imaging FOV. Correction for B1 inhomogeneity is therefore critical for 2D ss-SESTEPI to be used for T1 measurement. We developed a method for B1 inhomogeneity correction by acquiring an additional STEPI with minimal mixing time, calculating the difference between the spin-echo and the stimulated-echo and multiplying the STEPI by the inverse functional map. Diffusion-induced decay is corrected by measuring the average diffusivity during the prescanning. Rapid singleshot T1 mapping may be useful for various applications, such as dynamic T1 mapping for real-time estimation of the concentration of contrast agent in DCE-MRI. PMID:20564579

78 FR 5195 - Filing of Plats of Survey: California

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-24

... sections accepted October 18, 2012. T. 18 N., R. 10 W., dependent resurvey and subdivision accepted... Meridian, California T. 11 N., R. 3 E., corrective dependent resurvey, resurvey and subdivision accepted November 27, 2012. T. 2 N., R. 2 and 3 W., dependent resurvey and metes-and-bounds survey accepted November...

Quantitation of Human Cytochrome P450 2D6 Protein with Immunoblot and Mass Spectrometry Analysis

PubMed Central

Yu, Ai-Ming; Qu, Jun; Felmlee, Melanie A.; Cao, Jin; Jiang, Xi-Ling

2009-01-01

Accurate quantification of cytochrome P450 (P450) protein contents is essential for reliable assessment of drug safety, including the prediction of in vivo clearance from in vitro metabolism data, which may be hampered by the use of uncharacterized standards and existence of unknown allelic isozymes. Therefore, this study aimed to delineate the variability in absolute quantification of polymorphic CYP2D6 drug-metabolizing enzyme and compare immunoblot and nano liquid chromatography coupled to mass spectrometry (nano-LC/MS) methods in identification and relative quantification of CYP2D6.1 and CYP2D6.2 allelic isozymes. Holoprotein content of in-house purified CYP2D6 isozymes was determined according to carbon monoxide difference spectrum, and total protein was quantified with bicinchoninic acid protein assay. Holoprotein/total CYP2D6 protein ratio was markedly higher for purified CYP2D6.1 (71.0%) than that calculated for CYP2D6.1 Supersomes (35.5%), resulting in distinct linear calibration range (0.05–0.50 versus 0.025–0.25 pmol) that was determined by densitometric analysis of immunoblot bands. Likewise, purified CYP2D6.2 and CYP2D6.10 and the CYP2D6.10 Supersomes all showed different holoprotein/total CYP2D6 protein ratios and distinct immunoblot linear calibration ranges. In contrast to immunoblot, nano-LC/MS readily distinguished CYP2D6.2 (R296C and S486T) from CYP2D6.1 by isoform-specific proteolytic peptides that contain the altered amino acid residues. In addition, relative quantitation of the two allelic isozymes was successfully achieved with label-free protein quantification, consistent with the nominated ratio. Because immunoblot and nano-LC/MS analyses measure total P450 protein (holoprotein and apoprotein) in a sample, complete understanding of holoprotein and apoprotein contents in P450 standards is desired toward reliable quantification. Our data also suggest that nano-LC/MS not only facilitates P450 quantitation but also provides genotypic information. PMID:18832475

N -jettiness subtractions for g g →H at subleading power

NASA Astrophysics Data System (ADS)

Moult, Ian; Rothen, Lorena; Stewart, Iain W.; Tackmann, Frank J.; Zhu, Hua Xing

2018-01-01

N -jettiness subtractions provide a general approach for performing fully-differential next-to-next-to-leading order (NNLO) calculations. Since they are based on the physical resolution variable N -jettiness, TN , subleading power corrections in τ =TN/Q , with Q a hard interaction scale, can also be systematically computed. We study the structure of power corrections for 0-jettiness, T0, for the g g →H process. Using the soft-collinear effective theory we analytically compute the leading power corrections αsτ ln τ and αs2τ ln3τ (finding partial agreement with a previous result in the literature), and perform a detailed numerical study of the power corrections in the g g , g q , and q q ¯ channels. This includes a numerical extraction of the αsτ and αs2τ ln2τ corrections, and a study of the dependence on the T0 definition. Including such power suppressed logarithms significantly reduces the size of missing power corrections, and hence improves the numerical efficiency of the subtraction method. Having a more detailed understanding of the power corrections for both q q ¯ and g g initiated processes also provides insight into their universality, and hence their behavior in more complicated processes where they have not yet been analytically calculated.

Myocardial T2* Mapping at Ultrahigh Field: Physics and Frontier Applications

NASA Astrophysics Data System (ADS)

Huelnhagen, Till; Paul, Katharina; Ku, Min-Chi; Serradas Duarte, Teresa; Niendorf, Thoralf

2017-06-01

Cardiovascular magnetic resonance imaging (CMR) has become an indispensable clinical tool for the assessment of morphology, function and structure of the heart muscle. By exploiting quantification of the effective transverse relaxation time (T2*) CMR also affords myocardial tissue characterization and probing of cardiac physiology, both being in the focus of ongoing research. These developments are fueled by the move to ultrahigh magnetic field strengths, which permits enhanced sensitivity and spatial resolution that help to overcome limitations of current clinical MR systems with the goal to contribute to a better understanding of myocardial (patho)physiology in vivo. In this context, the aim of this report is to introduce myocardial T2* mapping at ultrahigh magnetic fields as a promising technique to non-invasively assess myocardial (patho)physiology. For this purpose the basic principles of T2* assessment, the biophysical mechanisms determining T2* and (pre)clinical applications of myocardial T2* mapping are presented. Technological challenges and solutions for T2* sensitized CMR at ultrahigh magnetic field strengths are discussed followed by a review of acquisition techniques and post processing approaches. Preliminary results derived from myocardial T2* mapping in healthy subjects and cardiac patients at 7.0 Tesla are presented. A concluding section discusses remaining questions and challenges and provides an outlook on future developments and potential clinical applications.

Development and validation of a colorimetric assay for simultaneous quantification of neutral and uronic sugars.

PubMed

Rondel, Caroline; Marcato-Romain, Claire-Emmanuelle; Girbal-Neuhauser, Elisabeth

2013-05-15

A colorimetric assay based on the conventional anthrone reaction was investigated for specific quantification of uronic acids (UA) in the presence of neutral sugars and/or proteins. Scanning of glucose (Glu) and glucuronic acid (GlA) was performed after the reaction with anthrone and a double absorbance reading was made, at 560 nm and at 620 nm, in order to quantify the UA and neutral sugars separately. The assay was implemented on binary or ternary solutions containing Glu, GlA and bovine serum albumin (BSA) in order to validate its specificity towards sugars and check possible interference with other biochemical components such as proteins. Statistical analysis indicated that this assay provided correct quantification of uronic sugars from 50 to 400 mg/l and of neutral sugars from 20 to 80 mg/l, in the presence of proteins with concentrations reaching 600 mg/l. The proposed protocol can be of great interest for simultaneous determination of uronic and neutral sugars in complex biological samples. In particular, it can be used to correctly quantify the Extracellular Polymeric Substances (EPS) isolated from the biological matrix of many bacterial aggregates, even in the presence of EPS extractant such as EDTA. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparative Chemometric Analysis for Classification of Acids and Bases via a Colorimetric Sensor Array.

PubMed

Kangas, Michael J; Burks, Raychelle M; Atwater, Jordyn; Lukowicz, Rachel M; Garver, Billy; Holmes, Andrea E

2018-02-01

With the increasing availability of digital imaging devices, colorimetric sensor arrays are rapidly becoming a simple, yet effective tool for the identification and quantification of various analytes. Colorimetric arrays utilize colorimetric data from many colorimetric sensors, with the multidimensional nature of the resulting data necessitating the use of chemometric analysis. Herein, an 8 sensor colorimetric array was used to analyze select acid and basic samples (0.5 - 10 M) to determine which chemometric methods are best suited for classification quantification of analytes within clusters. PCA, HCA, and LDA were used to visualize the data set. All three methods showed well-separated clusters for each of the acid or base analytes and moderate separation between analyte concentrations, indicating that the sensor array can be used to identify and quantify samples. Furthermore, PCA could be used to determine which sensors showed the most effective analyte identification. LDA, KNN, and HQI were used for identification of analyte and concentration. HQI and KNN could be used to correctly identify the analytes in all cases, while LDA correctly identified 95 of 96 analytes correctly. Additional studies demonstrated that controlling for solvent and image effects was unnecessary for all chemometric methods utilized in this study.

Simple and Fast Sample Preparation Followed by Gas Chromatography-Tandem Mass Spectrometry (GC-MS/MS) for the Analysis of 2- and 4-Methylimidazole in Cola and Dark Beer.

PubMed

Choi, Sol Ji; Jung, Mun Yhung

2017-04-01

We have developed a simple and fast sample preparation technique in combination with a gas chromatography-tandem mass spectrometry (GC-MS/MS) for the quantification of 2-methylimidazole (2-MeI) and 4-methylimidazole (4-MeI) in colas and dark beers. Conventional sample preparation technique for GC-MS requires laborious and time-consuming steps consisting of sample concentration, pH adjustment, ion pair extraction, centrifugation, back-extraction, centrifugation, derivatization, and extraction. Our sample preparation technique consists of only 2 steps (in situ derivation and extraction) which requires less than 3 min. This method provided high linearity, low limit of detection and limit of quantification, high recovery, and high intra- and interday repeatability. It was found that internal standard method with diluted stable isotope (4-MeI-d 6 ) and 2-ethylimidazole (2-EI) could not correctly compensate the matrix effects. Thus, standard addition technique was used for the quantification of 2- and 4-MeI. The established method was successfully applied to colas and dark beers for the determination of 2-MeI and 4-MeI. The 4-MeI contents in colas and dark beers ranged from 8 to 319 μg/L and from trace to 417 μg/L, respectively. Small quantity (0 to 8 μg/L) of 2-MeI was found only in dark beers. The contents of 4-MeI (22 μg/L) in colas obtained from fast food restaurants were significantly lower than those (177 μg/L) in canned or bottled colas. © 2017 Institute of Food Technologists®.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

Röst, Hannes L.; Liu, Yansheng; D’Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C.; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329

Sequence optimization to reduce velocity offsets in cardiovascular magnetic resonance volume flow quantification - A multi-vendor study

PubMed Central

2011-01-01

Purpose Eddy current induced velocity offsets are of concern for accuracy in cardiovascular magnetic resonance (CMR) volume flow quantification. However, currently known theoretical aspects of eddy current behavior have not led to effective guidelines for the optimization of flow quantification sequences. This study is aimed at identifying correlations between protocol parameters and the resulting velocity error in clinical CMR flow measurements in a multi-vendor study. Methods Nine 1.5T scanners of three different types/vendors were studied. Measurements were performed on a large stationary phantom. Starting from a clinical breath-hold flow protocol, several protocol parameters were varied. Acquisitions were made in three clinically relevant orientations. Additionally, a time delay between the bipolar gradient and read-out, asymmetric versus symmetric velocity encoding, and gradient amplitude and slew rate were studied in adapted sequences as exploratory measurements beyond the protocol. Image analysis determined the worst-case offset for a typical great-vessel flow measurement. Results The results showed a great variation in offset behavior among scanners (standard deviation among samples of 0.3, 0.4, and 0.9 cm/s for the three different scanner types), even for small changes in the protocol. Considering the absolute values, none of the tested protocol settings consistently reduced the velocity offsets below the critical level of 0.6 cm/s neither for all three orientations nor for all three scanner types. Using multilevel linear model analysis, oblique aortic and pulmonary slices showed systematic higher offsets than the transverse aortic slices (oblique aortic 0.6 cm/s, and pulmonary 1.8 cm/s higher than transverse aortic). The exploratory measurements beyond the protocol yielded some new leads for further sequence development towards reduction of velocity offsets; however those protocols were not always compatible with the time-constraints of breath-hold imaging and flow-related artefacts. Conclusions This study showed that with current systems there was no generic protocol which resulted into acceptable flow offset values. Protocol optimization would have to be performed on a per scanner and per protocol basis. Proper optimization might make accurate (transverse) aortic flow quantification possible for most scanners. Pulmonary flow quantification would still need further (offline) correction. PMID:21388521

α '-corrected black holes in String Theory

NASA Astrophysics Data System (ADS)

Cano, Pablo A.; Meessen, Patrick; Ortín, Tomás; Ramírez, Pedro F.

2018-05-01

We consider the well-known solution of the Heterotic Superstring effective action to zeroth order in α ' that describes the intersection of a fundamental string with momentum and a solitonic 5-brane and which gives a 3-charge, static, extremal, supersymmetric black hole in 5 dimensions upon dimensional reduction on T5. We compute explicitly the first-order in α ' corrections to this solution, including SU(2) Yang-Mills fields which can be used to cancel some of these corrections and we study the main properties of this α '-corrected solution: supersymmetry, values of the near-horizon and asymptotic charges, behavior under α '-corrected T-duality, value of the entropy (using Wald formula directly in 10 dimensions), existence of small black holes etc. The value obtained for the entropy agrees, within the limits of approximation, with that obtained by microscopic methods. The α ' corrections coming from Wald's formula prove crucial for this result.

Utilization of a deuterated derivatization agent to synthesize internal standards for gas chromatography-tandem mass spectrometry quantification of silylated metabolites.

PubMed

Lien, Stina K; Kvitvang, Hans Fredrik Nyvold; Bruheim, Per

2012-07-20

GC-MS analysis of silylated metabolites is a sensitive method that covers important metabolite groups such as sugars, amino acids and non-amino organic acids, and it has become one of the most important analytical methods for exploring the metabolome. Absolute quantitative GC-MS analysis of silylated metabolites poses a challenge as different metabolites have different derivatization kinetics and as their silyl-derivates have varying stability. This report describes the development of a targeted GC-MS/MS method for quantification of metabolites. Internal standards for each individual metabolite were obtained by derivatization of a mixture of standards with deuterated N-methyl-N-trimethylsilyltrifluoroacetamide (d9-MSTFA), and spiking this solution into MSTFA derivatized samples prior to GC-MS/MS analysis. The derivatization and spiking protocol needed optimization to ensure that the behaviour of labelled compound responses in the spiked sample correctly reflected the behaviour of unlabelled compound responses. Using labelled and unlabelled MSTFA in this way enabled normalization of metabolite responses by the response of their deuterated counterpart (i.e. individual correction). Such individual correction of metabolite responses reproducibly resulted in significantly higher precision than traditional data correction strategies when tested on samples both with and without serum and urine matrices. The developed method is thus a valuable contribution to the field of absolute quantitative metabolomics. Copyright © 2012 Elsevier B.V. All rights reserved.

Motor fatigue measurement by distance-induced slow down of walking speed in multiple sclerosis.

PubMed

Phan-Ba, Rémy; Calay, Philippe; Grodent, Patrick; Delrue, Gael; Lommers, Emilie; Delvaux, Valérie; Moonen, Gustave; Belachew, Shibeshih

2012-01-01

Motor fatigue and ambulation impairment are prominent clinical features of people with multiple sclerosis (pMS). We hypothesized that a multimodal and comparative assessment of walking speed on short and long distance would allow a better delineation and quantification of gait fatigability in pMS. Our objectives were to compare 4 walking paradigms: the timed 25-foot walk (T25FW), a corrected version of the T25FW with dynamic start (T25FW(+)), the timed 100-meter walk (T100MW) and the timed 500-meter walk (T500MW). Thirty controls and 81 pMS performed the 4 walking tests in a single study visit. The 4 walking tests were performed with a slower WS in pMS compared to controls even in subgroups with minimal disability. The finishing speed of the last 100-meter of the T500MW was the slowest measurable WS whereas the T25FW(+) provided the fastest measurable WS. The ratio between such slowest and fastest WS (Deceleration Index, DI) was significantly lower only in pMS with EDSS 4.0-6.0, a pyramidal or cerebellar functional system score reaching 3 or a maximum reported walking distance ≤ 4000 m. The motor fatigue which triggers gait deceleration over a sustained effort in pMS can be measured by the WS ratio between performances on a very short distance and the finishing pace on a longer more demanding task. The absolute walking speed is abnormal early in MS whatever the distance of effort when patients are unaware of ambulation impairment. In contrast, the DI-measured ambulation fatigability appears to take place later in the disease course.

Association of tumor-infiltrating T-cell density with molecular subtype, racial ancestry and clinical outcomes in prostate cancer.

PubMed

Kaur, Harsimar B; Guedes, Liana B; Lu, Jiayun; Maldonado, Laneisha; Reitz, Logan; Barber, John R; De Marzo, Angelo M; Tosoian, Jeffrey J; Tomlins, Scott A; Schaeffer, Edward M; Joshu, Corinne E; Sfanos, Karen S; Lotan, Tamara L

2018-05-30

The inflammatory microenvironment plays an important role in the pathogenesis and progression of tumors and may be associated with somatic genomic alterations. We examined the association of tumor-infiltrating T-cell density with clinical-pathologic variables, tumor molecular subtype, and oncologic outcomes in surgically treated primary prostate cancer occurring in patients of European-American or African-American ancestry. We evaluated 312 primary prostate tumors, enriched for patients with African-American ancestry and high grade disease. Tissue microarrays were immunostained for CD3, CD8, and FOXP3 and were previously immunostained for ERG and PTEN using genetically validated protocols. Image analysis for quantification of T-cell density in tissue microarray tumor spots was performed. Automated quantification of T-cell densities in tumor-containing regions of tissue microarray spots and standard histologic sections were correlated (r = 0.73, p < 0.00001) and there was good agreement between visual and automated T-cell density counts on tissue microarray spots (r = 0.93, p < 0.00001). There was a significant correlation between CD3+, CD8+, and FOXP3+ T-cell densities (p < 0.00001), but these were not associated with most clinical or pathologic variables. Increased T-cell density was significantly associated with ERG positivity (median 309 vs. 188 CD3+ T cells/mm 2 ; p = 0.0004) and also with PTEN loss (median 317 vs. 192 CD3+ T cells/mm 2 ; p = 0.001) in the combined cohort of matched European-American and African-American ancestry patients. The same association or a similar trend was present in patients of both ancestries when analyzed separately. When the African-American patients from the matched race set were combined with a separate high grade set of African-American cases, there was a weak association of increased FOXP3+ T-cell densities with increased risk of metastasis in multivariable analysis. Though high T-cell density is associated with specific molecular subclasses of prostate cancer, we did not find an association of T-cell density with racial ancestry.

Effects of EPI distortion correction pipelines on the connectome in Parkinson's Disease

NASA Astrophysics Data System (ADS)

Galvis, Justin; Mezher, Adam F.; Ragothaman, Anjanibhargavi; Villalon-Reina, Julio E.; Fletcher, P. Thomas; Thompson, Paul M.; Prasad, Gautam

2016-03-01

Echo-planar imaging (EPI) is commonly used for diffusion-weighted imaging (DWI) but is susceptible to nonlinear geometric distortions arising from inhomogeneities in the static magnetic field. These inhomogeneities can be measured and corrected using a fieldmap image acquired during the scanning process. In studies where the fieldmap image is not collected, these distortions can be corrected, to some extent, by nonlinearly registering the diffusion image to a corresponding anatomical image, either a T1- or T2-weighted image. Here we compared two EPI distortion correction pipelines, both based on nonlinear registration, which were optimized for the particular weighting of the structural image registration target. The first pipeline used a 3D nonlinear registration to a T1-weighted target, while the second pipeline used a 1D nonlinear registration to a T2-weighted target. We assessed each pipeline in its ability to characterize high-level measures of brain connectivity in Parkinson's disease (PD) in 189 individuals (58 healthy controls, 131 people with PD) from the Parkinson's Progression Markers Initiative (PPMI) dataset. We computed a structural connectome (connectivity map) for each participant using regions of interest from a cortical parcellation combined with DWI-based whole-brain tractography. We evaluated test-retest reliability of the connectome for each EPI distortion correction pipeline using a second diffusion scan acquired directly after the participants' first. Finally, we used support vector machine (SVM) classification to assess how accurately each pipeline classified PD versus healthy controls using each participants' structural connectome.

Posterior Surgery for Adolescent Idiopathic Scoliosis With Pedicle Screws and Ultrahigh-Molecular Weight Polyethylene Tape: Achieving the Ideal Thoracic Kyphosis.

PubMed

Imagama, Shiro; Ito, Zenya; Wakao, Norimitsu; Ando, Kei; Hirano, Kenichi; Tauchi, Ryoji; Muramoto, Akio; Matsui, Hiroki; Matsumoto, Tomohiro; Sakai, Yoshihito; Katayama, Yoshito; Matsuyama, Yukihiro; Ishiguro, Naoki

2016-10-01

Prospective clinical case series. To describe our surgical procedure and results for posterior correction and fusion with a hybrid approach using pedicle screws, hooks, and ultrahigh-molecular weight polyethylene tape with direct vertebral rotation (DVR) (the PSTH-DVR procedure) for treatment of adolescent idiopathic scoliosis (AIS) with satisfactory correction in the coronal and sagittal planes. Introduction of segmental pedicle screws in posterior surgery for AIS has facilitated good correction and fusion. However, procedures using only pedicle screws have risks during screw insertion, higher costs, and decreased postoperative thoracic kyphosis. We have obtained good outcomes compared with segmental pedicle screw fixation in surgery for AIS using a relatively simple operative procedure (PSTH-DVR) that uses fewer pedicle screws. The subjects were 30 consecutive patients with AIS who underwent the PSTH-DVR procedure and were followed for a minimum of 2 years. Preoperative flexibility, preoperative and postoperative Cobb angles, correction rates, loss of correction, thoracic kyphotic angles (T5-T12), coronal balance, sagittal balance, and shoulder balance were measured on plain radiographs. Rib hump, operation time, estimated blood loss, spinal cord monitoring findings, complications, and scoliosis research society (SRS)-22 scores were also examined. The mean preoperative curve of 58.0 degrees (range, 40-96 degrees) was corrected to a mean of 9.9 degrees postoperatively, and the correction rate was 83.6%. Fusion was obtained in all patients without loss of correction. In 10 cases with preoperative kyphosis angles (T5-T12) <10 degrees, the preoperative mean of 5.8 degrees improved to 20.2 degrees at the final follow-up. Rib hump and coronal, sagittal and shoulder balances were also improved, and good SRS-22 scores were achieved at final follow-up. The correction of deformity with PSTH-DVR is equivalent to that of all-pedicle screw constructs. The procedure gives favorable correction, is advantageous for kyphosis compared with segmental screw fixation, and uses the minimum number of pedicle screws. Therefore, the PSTH-DVR procedure may be useful for treatment of idiopathic scoliosis.

MR fingerprinting using fast imaging with steady state precession (FISP) with spiral readout.

PubMed

Jiang, Yun; Ma, Dan; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A

2015-12-01

This study explores the possibility of using gradient echo-based sequences other than balanced steady-state free precession (bSSFP) in the magnetic resonance fingerprinting (MRF) framework to quantify the relaxation parameters . An MRF method based on a fast imaging with steady-state precession (FISP) sequence structure is presented. A dictionary containing possible signal evolutions with physiological range of T1 and T2 was created using the extended phase graph formalism according to the acquisition parameters. The proposed method was evaluated in a phantom and a human brain. T1 , T2 , and proton density were quantified directly from the undersampled data by the pattern recognition algorithm. T1 and T2 values from the phantom demonstrate that the results of MRF FISP are in good agreement with the traditional gold-standard methods. T1 and T2 values in brain are within the range of previously reported values. MRF-FISP enables a fast and accurate quantification of the relaxation parameters. It is immune to the banding artifact of bSSFP due to B0 inhomogeneities, which could improve the ability to use MRF for applications beyond brain imaging. © 2014 Wiley Periodicals, Inc.

MR Fingerprinting Using Fast Imaging with Steady State Precession (FISP) with Spiral Readout

PubMed Central

Jiang, Yun; Ma, Dan; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A.

2015-01-01

Purpose This study explores the possibility of using gradient echo based sequences other than bSSFP in the magnetic resonance fingerprinting (MRF) framework to quantify the relaxation parameters. Methods An MRF method based on a fast imaging with steady state precession (FISP) sequence structure is presented. A dictionary containing possible signal evolutions with physiological range of T1 and T2 was created using the extended phase graph (EPG) formalism according to the acquisition parameters. The proposed method was evaluated in a phantom and a human brain. T1, T2 and proton density were quantified directly from the undersampled data by the pattern recognition algorithm. Results T1 and T2 values from the phantom demonstrate that the results of MRF FISP are in good agreement with the traditional gold-standard methods. T1 and T2 values in brain are within the range of previously reported values. Conclusion MRF FISP enables a fast and accurate quantification of the relaxation parameters, while is immune to the banding artifact of bSSFP due to B0 inhomogeneities, which could improve the ability to use MRF for applications beyond brain imaging. PMID:25491018

Effects of transaldolase exchange on estimates of gluconeogenesis in type 2 diabetes.

PubMed

Rajpal, Aman; Dube, Simmi; Carvalho, Filipa; Simoes, Ana Rita; Figueiredo, Angelo; Basu, Ananda; Jones, John; Basu, Rita

2013-08-15

Transaldolase (TA) exchange overestimates gluconeogenesis measured with deuterated water (²H₂O). However, it is unknown whether TA differs in people with type 2 diabetes (T2DM). ²H₂O was ingested, and [1-¹³C]acetate and [3-³H]glucose were infused in T2DM (n = 10) and healthy nondiabetic (ND; n = 8) subjects. TA was assessed from the ratio of ¹³C3 to ¹³C4 glucose enrichment (¹³C3/¹³C4) measured by ¹³C NMR. Glucose turnover was measured before (~16-h fast) and during hyperglycemic (~10 mM) moderate-dose insulin (~0.35 mU·kg⁻¹·min⁻¹) clamp. ¹³C3/¹³C4 in T2DM vs. ND was <1.0 and not different at baseline and clamp, indicating equivalent TA. To determine whether incomplete triose phosphate isomerase (TPI) exchange contributed to asymmetric ¹³C3/¹³C4, [U-¹³C]glycerol was infused in lieu of [1-¹³C]acetate during a separate visit in a subset of ND (n = 7) subjects. Ratio of ¹³C3/¹³C4 obtained following either tracer was <1.0 at baseline and during clamp, indicating that TPI exchange was essentially complete and did not contribute to asymmetric glucose enrichment. Uncorrected and corrected rates of gluconeogenesis were no different (P = not significant) in T2DM vs. ND both at baseline and during clamp. TA correction resulted in equivalent estimates of corrected gluconeogenesis in T2DM and ND that were ~25-35% lower than uncorrected gluconeogenesis both at baseline and during the clamp. The asymmetric enrichment of glucose from ¹³C-gluconeogenic tracers is attributable to TA exchange and can be utilized to correct for TA exchange. In conclusion, TA exchange does not differ between T2DM and ND under fasting or hyperglycemic clamp conditions, and the ²H₂O method continues to provide an accurate estimation of gluconeogenesis.

Hemoglobin analyses in the Netherlands reveal more than 80 different variants including six novel ones.

PubMed

van Zwieten, Rob; Veldthuis, Martijn; Delzenne, Barend; Berghuis, Jeffrey; Groen, Joke; Ait Ichou, Fatima; Clifford, Els; Harteveld, Cornelis L; Stroobants, An K

2014-01-01

More than 20,000 blood samples of individuals living in The Netherlands and suspected of hemolytic anemia or diabetes were analyzed by high resolution cation exchange high performance liquid chromatography (HPLC). Besides common disease-related hemoglobins (Hbs), rare variants were also detected. The variant Hbs were retrospectively analyzed by capillary zone electrophoresis (CZE) and by isoelectric focusing (IEF). For unambiguous identification, the globin genes were sequenced. Most of the 80 Hb variants detected by initial screening on HPLC were also separated by capillary electrophoresis (CE), but a few variants were only detectable with one of these methods. Some variants were unstable, had thalassemic properties or increased oxygen affinity, and some interfered with Hb A2 measurement, detection of sickle cell Hb or Hb A1c quantification. Two of the six novel variants, Hb Enschede (HBA2: c.308G  > A, p.Ser103Asn) and Hb Weesp (HBA1: c.301C > T, p.Leu101Phe), had no clinical consequences. In contrast, two others appeared clinically significant: Hb Ede (HBB: c.53A > T, p.Lys18Met) caused thalassemia and Hb Waterland (HBB: c.428C > T, pAla143Val) was related to mild polycytemia. Hb A2-Venlo (HBD: c.193G > A, p.Gly65Ser) and Hb A2-Rotterdam (HBD: c.38A > C, p.Asn13Thr) interfered with Hb A2 quantification. This survey shows that HPLC analysis followed by globin gene sequencing of rare variants is an effective method to reveal Hb variants.

Self-consistent expansion for the molecular beam epitaxy equation

NASA Astrophysics Data System (ADS)

Katzav, Eytan

2002-03-01

Motivated by a controversy over the correct results derived from the dynamic renormalization group (DRG) analysis of the nonlinear molecular beam epitaxy (MBE) equation, a self-consistent expansion for the nonlinear MBE theory is considered. The scaling exponents are obtained for spatially correlated noise of the general form D(r-->-r',t-t')=2D0\\|r-->- r'\\|2ρ-dδ(t-t'). I find a lower critical dimension dc(ρ)=4+2ρ, above which the linear MBE solution appears. Below the lower critical dimension a ρ-dependent strong-coupling solution is found. These results help to resolve the controversy over the correct exponents that describe nonlinear MBE, using a reliable method that proved itself in the past by giving reasonable results for the strong-coupling regime of the Kardar-Parisi-Zhang system (for d>1), where DRG failed to do so.

Self-consistent expansion for the molecular beam epitaxy equation.

PubMed

Katzav, Eytan

2002-03-01

Motivated by a controversy over the correct results derived from the dynamic renormalization group (DRG) analysis of the nonlinear molecular beam epitaxy (MBE) equation, a self-consistent expansion for the nonlinear MBE theory is considered. The scaling exponents are obtained for spatially correlated noise of the general form D(r-r('),t-t('))=2D(0)[r-->-r(')](2rho-d)delta(t-t(')). I find a lower critical dimension d(c)(rho)=4+2rho, above which the linear MBE solution appears. Below the lower critical dimension a rho-dependent strong-coupling solution is found. These results help to resolve the controversy over the correct exponents that describe nonlinear MBE, using a reliable method that proved itself in the past by giving reasonable results for the strong-coupling regime of the Kardar-Parisi-Zhang system (for d>1), where DRG failed to do so.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ericsson, F.; Odar-Cederloef, I.E.; Eriksson, C.G.

The authors determined total body water (TBW) with tritium in 11 patients on chronic hemodialysis and compared this space to that estimated by 60% of body weight, and removal spaces of urea, creatinine, uric acid, and phosphate (PO4). The latter spaces were determined by dividing the total amount of substance (measured in total dialysate) by pre- minus post-dialysis concentrations. Body water X 0.6 was more than 10% less than the tritium space, and showed a maximal variation of 10 liters, or 24%. The removal space of urea was 80% of the tritium space, but correlated closely with it. The differencemore » between total body water and urea removal space was variable and dependent on fluid excess (edema) in the patients. Creatinine, uric acid, and phosphate removal spaces were highly variable and not correlated to total body water. The authors suggest that actual measured TBW should be used, rather than estimations using BW X 0.6, for V in K X T/V, where K = clearance, T = duration of dialysis, and V = the removal space of urea. Furthermore, one may need to introduce a correction factor for urea removal space over TBW in the equation to allow better quantification of dialysis in edematous patients and during very fast dialyses.« less

A correlated ab initio study of the A2 pi <-- X2 sigma+ transition in MgCCH

NASA Technical Reports Server (NTRS)

Woon, D. E.

1997-01-01

The A2 pi <-- X2 sigma+ transition in MgCCH was studied with correlation consistent basis sets and single- and multireference correlation methods. The A2 pi excited state was characterized in detail; the x2 sigma+ ground state has been described elsewhere recently. The estimated complete basis set (CBS) limits for valence correlation, including zero-point energy corrections, are 22668, 23191, and 22795 for the RCCSD(T), MRCI, and MRCI + Q methods, respectively. A core-valence correction of +162 cm-1 shifts the RCCSD(T) value to 22830 cm-1, in good agreement with the experimental result of 22807 cm-1.

[Clinical significance of Q-angle under different conditions in recurrent patellar dislocation].

PubMed

Wang, Zhijie; Chen, You; Li, Anping; Long, Yi

2014-01-01

To investigate the clinical significance of Q-angle measuring under different conditions in female recurrent patellar dislocation female patients. Between August 2012 and March 2013, 10 female patients (11 knees) with recurrent patellar dislocation were collected as trial group; 20 female patients (20 knees) with simple meniscus injury were collected as control group at the same time. Q-angle was measured in extension, 30 degrees flexion, 30 degrees flexion with manual correction, and surgical correction in the trial group, and only in extension and 30 degrees flexion in the control group. Then the difference value of Q-angle between extension and 30 degrees flexion (Q-angle in extension subtracts Q-angle in 30 flexion) were calculated. Independent sample t-test was used to analyze Q-angle degrees in extension, 30 degrees flexion, and the changed degrees of 2 groups. The Q-angle between manual correction and surgical correction of the trial group was analyzed by paired t-test. The Q-angle in extension, Q-angle in 30 degrees flexion, and difference value of Q-angle between extension and 30 degrees flexion were (17.2 +/- 3.6), (14.3 +/- 3.0), and (2.9 +/- 1.9) degrees in the trial group and were (15.2 +/- 3.4), (14.4 +/- 3.5), and (0.8 +/- 1.7) degrees in the control group. No significant difference was found in Q-angle of extension or Q-angle of 30 degrees flexion between 2 groups (P > 0.05), but the difference value of Q-angle between extension and 30 degrees flexion in the trial group was significantly larger than that in the control group (t = 3.253, P = 0.003). The Q-angle in 30 degrees flexion with manual correction and surgical correction in the trial group was (19.8 +/- 3.4) degrees and (18.9 +/- 3.8) degrees respectively, showing no significant difference (t = 2.193, P = 0.053). When a female patient's Q-angle in 30 degrees flexion knee changes obviously compared with Q-angle in extension position, recurrent patellar dislocation should be considered. For female patients with recurrent patellar dislocation, the preoperative Q-angle in 30 degrees flexion with manual correction should be measured, which can help increasing the accuracy of evaluation whether rearrangement should be performed.

Attenuation correction of emission PET images with average CT: Interpolation from breath-hold CT

NASA Astrophysics Data System (ADS)

Huang, Tzung-Chi; Zhang, Geoffrey; Chen, Chih-Hao; Yang, Bang-Hung; Wu, Nien-Yun; Wang, Shyh-Jen; Wu, Tung-Hsin

2011-05-01

Misregistration resulting from the difference of temporal resolution in PET and CT scans occur frequently in PET/CT imaging, which causes distortion in tumor quantification in PET. Respiration cine average CT (CACT) for PET attenuation correction has been reported to improve the misalignment effectively by several papers. However, the radiation dose to the patient from a four-dimensional CT scan is relatively high. In this study, we propose a method to interpolate respiratory CT images over a respiratory cycle from inhalation and exhalation breath-hold CT images, and use the average CT from the generated CT set for PET attenuation correction. The radiation dose to the patient is reduced using this method. Six cancer patients of various lesion sites underwent routine free-breath helical CT (HCT), respiration CACT, interpolated average CT (IACT), and 18F-FDG PET. Deformable image registration was used to interpolate the middle phases of a respiratory cycle based on the end-inspiration and end-expiration breath-hold CT scans. The average CT image was calculated from the eight interpolated CT image sets of middle respiratory phases and the two original inspiration and expiration CT images. Then the PET images were reconstructed by these three methods for attenuation correction using HCT, CACT, and IACT. Misalignment of PET image using either CACT or IACT for attenuation correction in PET/CT was improved. The difference in standard uptake value (SUV) from tumor in PET images was most significant between the use of HCT and CACT, while the least significant between the use of CACT and IACT. Besides the similar improvement in tumor quantification compared to the use of CACT, using IACT for PET attenuation correction reduces the radiation dose to the patient.

Long term measurement of lake evaporation using a pontoon mounted Eddy Covariance system

NASA Astrophysics Data System (ADS)

McGowan, H. A.; McGloin, R.; McJannet, D.; Burn, S.

2011-12-01

Accurate quantification of evaporation from water storages is essential for design of water management and allocation policy that aims to balance demands for water without compromising the sustainability of future water resources, particularly during periods of prolonged and severe drought. Precise measurement of evaporation from lakes and dams however, presents significant research challenges. These include design and installation of measurement platforms that can withstand a range of wind and wave conditions; accurate determination of the evaporation measurement footprint and the influence of changing water levels. In this paper we present results from a two year long deployment of a pontoon mounted Eddy Covariance (EC) system on a 17.2ha irrigation reservoir in southeast Queensland, Australia. The EC unit included a CSAT-3 sonic anemometer (Campbell Scientific, Utah, United States) and a Li-Cor CS7500 open-path H2O/CO2 infrared gas analyzer (LiCor, Nebraska, United States) at a height of 2.2m, a net radiometer (CNR1, Kipp & Zonen, Netherlands) at a height of 1.2m and a humidity and temperature probe (HMP45C,Vaisala, Finland) at 2.3m. The EC unit was controlled by a Campbell Scientific CR3000 data logger with flux measurements made at 10 Hz and block averaged values logged every 15 minutes. Power to the EC system was from mounted solar panels that charged deep cycle lead-acid batteries while communication was via a cellphone data link. The pontoon was fitted with a weighted central beam and gimbal ring system that allowed self-levelling of the instrumentation and minimized dynamic influences on measurements (McGowan et al 2010; Wiebe et al 2011). EC measurements were corrected for tilt errors using the double rotation method for coordinate rotation described by Wilczak et al. (2001). High and low frequency attenuation of the measured co-spectrum was corrected using Massman's (2000) method for estimating frequency response corrections, while measurements were corrected for density fluctuations using the method of Webb-Pearman-Leuning (Webb et al. 1980). The evaporation measurement footprint over the reservoir was determined using the SCADIS one and a half order turbulence closure footprint model (Sogachev and Lloyd, 2004). Comparison of EC measured evaporation rates show excellent agreement with independent measurement of evaporation by scintillometer under a wide range of conditions (McJannet et al 2011). They confirm that pontoon mounted EC systems offer a robust, highly portable and reliable cost effective approach for accurate quantification of evaporation from reservoirs.

Correction to: Gamma-delta (γδ) T cells: friend or foe in cancer development?

PubMed

Zhao, Yijing; Niu, Chao; Cui, Jiuwei

2018-05-08

Following publication of the original article [1], the authors reported that they omitted to state that parts of Fig. 2 were adapted from Van Acker et al. [2] published by Taylor & Francis Ltd ( www.tandfonline.com ). The authors apologise for this omission. Figure 2 and its corrected caption are given below.

Reading in the Social Studies: What Not to Do

ERIC Educational Resources Information Center

Parsons, James; Tomas, Douglas

1978-01-01

Five points are: (1) don't assume students know how to use their textbooks; (2) don't ignore the problem or take only short term measures for improvement; (3) don't give undirected assignments; (4) don't force students to pronounce every word correctly; (5) don't send students to the dictionary for words they don't know. (Author/JK)

Sensitive and rapid liquid chromatography/tandem mass spectrometric assay for the quantification of piperaquine in human plasma.

PubMed

Singhal, Puran; Gaur, Ashwani; Gautam, Anirudh; Varshney, Brijesh; Paliwal, Jyoti; Batra, Vijay

2007-11-01

A simple, sensitive and rapid liquid chromatography/tandem mass spectrometric (LC-MS/MS) method was developed and validated for quantification of piperaquine, an antimalarial drug, in human plasma using its structural analogue, piperazine bis chloroquinoline as internal standard (IS). The method involved a simple protein precipitation with methanol followed by rapid isocratic elution of analytes with 10mM ammonium acetate buffer/methanol/formic acid/ammonia solution (25/75/0.2/0.15, v/v) on Chromolith SpeedROD RP-18e reversed phase chromatographic column and quantification by mass spectrometry in the multiple reaction monitoring mode (MRM). The precursor to product ion transitions of m/z 535.3-->288.2 and m/z 409.1-->205.2 were used to measure the analyte and the IS, respectively. The assay exhibited a linear dynamic range of 1.0-250.2 ng/mL for piperaquine in plasma. The limit of detection (LOD) and lower limit of quantification (LLOQ) in plasma were 0.2 and 1.0 ng/mL, respectively. Acceptable precision and accuracy (+/-20% deviation for LLOQ standard and +/-15% deviation for other standards from the respective nominal concentration) were obtained for concentrations over the standard curve ranges. A run time of 2.5 min for a sample made it possible to achieve a throughput of more than 400 plasma samples analyzed per day. The validated method was successfully applied to analyze human plasma samples from phase-1 clinical studies. The mean pharmacokinetic parameters of piperaquine following 1000 mg oral dose: observed maximum plasma concentration (Cmax), time to maximum plasma concentration (Tmax) and elimination half-life (T1/2) were 46.1 ng/mL, 3.8h and 13 days, respectively.

CCSD(T) potential energy and induced dipole surfaces for N2–H2(D2): retrieval of the collision-induced absorption integrated intensities in the regions of the fundamental and first overtone vibrational transitions.

PubMed

Buryak, Ilya; Lokshtanov, Sergei; Vigasin, Andrey

2012-09-21

The present work aims at ab initio characterization of the integrated intensity temperature variation of collision-induced absorption (CIA) in N(2)-H(2)(D(2)). Global fits of potential energy surface (PES) and induced dipole moment surface (IDS) were made on the basis of CCSD(T) (coupled cluster with single and double and perturbative triple excitations) calculations with aug-cc-pV(T,Q)Z basis sets. Basis set superposition error correction and extrapolation to complete basis set (CBS) limit techniques were applied to both energy and dipole moment. Classical second cross virial coefficient calculations accounting for the first quantum correction were employed to prove the quality of the obtained PES. The CIA temperature dependence was found in satisfactory agreement with available experimental data.

Cutaneous T cell lymphoma: Current practices in blood assessment and the utility of T-cell receptor Vβ chain restriction

PubMed Central

Gibson, Juliet F; Huang, Jing; Liu, Kristina J; Carlson, Kacie R; Foss, Francine; Choi, Jaehyuk; Edelson, Richard; Hussong, Jerry W.; Mohl, Ramsey; Hill, Sally; Girardi, Sally

2016-01-01

Background Accurate quantification of malignant cells in the peripheral blood of patients with cutaneous T cell lymphoma (CTCL) is important for early detection, prognosis, and monitoring disease burden. Objective Determine the spectrum of current clinical practices; critically evaluate elements of current ISCL B1 and B2 staging criteria; and assess the potential role of TCR-Vβ analysis by flow cytometry. Methods We assessed current clinical practices by survey, and performed a retrospective analysis of 161 patients evaluated at Yale (2011-2014) to compare the sensitivity, specificity, PPV, and NPV of parameters for ISCL B2 staging. Results There was heterogeneity in clinical practices among institutions. ISCL B1 criteria did not capture five Yale cohort patients with immunophenotypic abnormalities who later progressed. TCR-Vβ testing was more specific than PCR and aided diagnosis in detecting clonality, but was of limited benefit in quantification of tumor burden. Limitations Because of limited follow-up involving a single center, further investigation will be necessary to conclude whether our proposed diagnostic algorithm is of general clinical benefit. Conclusion We propose further study of “modified B1 criteria”: CD4/CD8 ratio ≥5, %CD4+/CD26- ≥ 20%, %CD4+/CD7- ≥ 20%, with evidence of clonality. TCR-Vβ testing should be considered in future diagnostic and staging algorithms. PMID:26874819

Quantification of fructo-oligosaccharides based on the evaluation of oligomer ratios using an artificial neural network.

PubMed

Onofrejová, Lucia; Farková, Marta; Preisler, Jan

2009-04-13

The application of an internal standard in quantitative analysis is desirable in order to correct for variations in sample preparation and instrumental response. In mass spectrometry of organic compounds, the internal standard is preferably labelled with a stable isotope, such as (18)O, (15)N or (13)C. In this study, a method for the quantification of fructo-oligosaccharides using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS) was proposed and tested on raftilose, a partially hydrolysed inulin with a degree of polymeration 2-7. A tetraoligosaccharide nystose, which is chemically identical to the raftilose tetramer, was used as an internal standard rather than an isotope-labelled analyte. Two mathematical approaches used for data processing, conventional calculations and artificial neural networks (ANN), were compared. The conventional data processing relies on the assumption that a constant oligomer dispersion profile will change after the addition of the internal standard and some simple numerical calculations. On the other hand, ANN was found to compensate for a non-linear MALDI response and variations in the oligomer dispersion profile with raftilose concentration. As a result, the application of ANN led to lower quantification errors and excellent day-to-day repeatability compared to the conventional data analysis. The developed method is feasible for MS quantification of raftilose in the range of 10-750 pg with errors below 7%. The content of raftilose was determined in dietary cream; application can be extended to other similar polymers. It should be stressed that no special optimisation of the MALDI process was carried out. A common MALDI matrix and sample preparation were used and only the basic parameters, such as sampling and laser energy, were optimised prior to quantification.

Adaptive support ventilation may deliver unwanted respiratory rate-tidal volume combinations in patients with acute lung injury ventilated according to an open lung concept.

PubMed

Dongelmans, Dave A; Paulus, Frederique; Veelo, Denise P; Binnekade, Jan M; Vroom, Margreeth B; Schultz, Marcus J

2011-05-01

With adaptive support ventilation, respiratory rate and tidal volume (V(T)) are a function of the Otis least work of breathing formula. We hypothesized that adaptive support ventilation in an open lung ventilator strategy would deliver higher V(T)s to patients with acute lung injury. Patients with acute lung injury were ventilated according to a local guideline advising the use of lower V(T) (6-8 ml/kg predicted body weight), high concentrations of positive end-expiratory pressure, and recruitment maneuvers. Ventilation parameters were recorded when the ventilator was switched to adaptive support ventilation, and after recruitment maneuvers. If V(T) increased more than 8 ml/kg predicted body weight, airway pressure was limited to correct for the rise of V(T). Ten patients with a mean (±SD) Pao(2)/Fio(2) of 171 ± 86 mmHg were included. After a switch from pressure-controlled ventilation to adaptive support ventilation, respiratory rate declined (from 31 ± 5 to 21 ± 6 breaths/min; difference = 10 breaths/min, 95% CI 3-17 breaths/min, P = 0.008) and V(T) increased (from 6.5 ± 0.8 to 9.0 ± 1.6 ml/kg predicted body weight; difference = 2.5 ml, 95% CI 0.4-4.6 ml/kg predicted body weight, P = 0.02). Pressure limitation corrected for the rise of V(T), but minute ventilation declined, forcing the user to switch back to pressure-controlled ventilation. Adaptive support ventilation, compared with pressure-controlled ventilation in an open lung strategy setting, delivers a lower respiratory rate-higher V(T) combination. Pressure limitation does correct for the rise of V(T), but leads to a decline in minute ventilation.

Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography–Mass Spectrometry Data

PubMed Central

Kuich, P. Henning J. L.; Hoffmann, Nils; Kempa, Stefan

2015-01-01

A current bottleneck in GC–MS metabolomics is the processing of raw machine data into a final datamatrix that contains the quantities of identified metabolites in each sample. While there are many bioinformatics tools available to aid the initial steps of the process, their use requires both significant technical expertise and a subsequent manual validation of identifications and alignments if high data quality is desired. The manual validation is tedious and time consuming, becoming prohibitively so as sample numbers increase. We have, therefore, developed Maui-VIA, a solution based on a visual interface that allows experts and non-experts to simultaneously and quickly process, inspect, and correct large numbers of GC–MS samples. It allows for the visual inspection of identifications and alignments, facilitating a unique and, due to its visualization and keyboard shortcuts, very fast interaction with the data. Therefore, Maui-Via fills an important niche by (1) providing functionality that optimizes the component of data processing that is currently most labor intensive to save time and (2) lowering the threshold of expertise required to process GC–MS data. Maui-VIA projects are initiated with baseline-corrected raw data, peaklists, and a database of metabolite spectra and retention indices used for identification. It provides functionality for retention index calculation, a targeted library search, the visual annotation, alignment, correction interface, and metabolite quantification, as well as the export of the final datamatrix. The high quality of data produced by Maui-VIA is illustrated by its comparison to data attained manually by an expert using vendor software on a previously published dataset concerning the response of Chlamydomonas reinhardtii to salt stress. In conclusion, Maui-VIA provides the opportunity for fast, confident, and high-quality data processing validation of large numbers of GC–MS samples by non-experts. PMID:25654076

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

PubMed

Liu, Ruolin; Dickerson, Julie

2017-11-01

We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.

Accounting for the Confound of Meninges in Segmenting Entorhinal and Perirhinal Cortices in T1-Weighted MRI.

PubMed

Xie, Long; Wisse, Laura E M; Das, Sandhitsu R; Wang, Hongzhi; Wolk, David A; Manjón, Jose V; Yushkevich, Paul A

2016-10-01

Quantification of medial temporal lobe (MTL) cortices, including entorhinal cortex (ERC) and perirhinal cortex (PRC), from in vivo MRI is desirable for studying the human memory system as well as in early diagnosis and monitoring of Alzheimer's disease. However, ERC and PRC are commonly over-segmented in T1-weighted (T1w) MRI because of the adjacent meninges that have similar intensity to gray matter in T1 contrast. This introduces errors in the quantification and could potentially confound imaging studies of ERC/PRC. In this paper, we propose to segment MTL cortices along with the adjacent meninges in T1w MRI using an established multi-atlas segmentation framework together with super-resolution technique. Experimental results comparing the proposed pipeline with existing pipelines support the notion that a large portion of meninges is segmented as gray matter by existing algorithms but not by our algorithm. Cross-validation experiments demonstrate promising segmentation accuracy. Further, agreement between the volume and thickness measures from the proposed pipeline and those from the manual segmentations increase dramatically as a result of accounting for the confound of meninges. Evaluated in the context of group discrimination between patients with amnestic mild cognitive impairment and normal controls, the proposed pipeline generates more biologically plausible results and improves the statistical power in discriminating groups in absolute terms comparing to other techniques using T1w MRI. Although the performance of the proposed pipeline is inferior to that using T2-weighted MRI, which is optimized to image MTL sub-structures, the proposed pipeline could still provide important utilities in analyzing many existing large datasets that only have T1w MRI available.

Accelerated acquisition of tagged MRI for cardiac motion correction in simultaneous PET-MR: Phantom and patient studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Chuan, E-mail: chuan.huang@stonybrookmedicine.edu; Department of Radiology, Harvard Medical School, Boston, Massachusetts 02115; Departments of Radiology, Psychiatry, Stony Brook Medicine, Stony Brook, New York 11794

2015-02-15

Purpose: Degradation of image quality caused by cardiac and respiratory motions hampers the diagnostic quality of cardiac PET. It has been shown that improved diagnostic accuracy of myocardial defect can be achieved by tagged MR (tMR) based PET motion correction using simultaneous PET-MR. However, one major hurdle for the adoption of tMR-based PET motion correction in the PET-MR routine is the long acquisition time needed for the collection of fully sampled tMR data. In this work, the authors propose an accelerated tMR acquisition strategy using parallel imaging and/or compressed sensing and assess the impact on the tMR-based motion corrected PETmore » using phantom and patient data. Methods: Fully sampled tMR data were acquired simultaneously with PET list-mode data on two simultaneous PET-MR scanners for a cardiac phantom and a patient. Parallel imaging and compressed sensing were retrospectively performed by GRAPPA and kt-FOCUSS algorithms with various acceleration factors. Motion fields were estimated using nonrigid B-spline image registration from both the accelerated and fully sampled tMR images. The motion fields were incorporated into a motion corrected ordered subset expectation maximization reconstruction algorithm with motion-dependent attenuation correction. Results: Although tMR acceleration introduced image artifacts into the tMR images for both phantom and patient data, motion corrected PET images yielded similar image quality as those obtained using the fully sampled tMR images for low to moderate acceleration factors (<4). Quantitative analysis of myocardial defect contrast over ten independent noise realizations showed similar results. It was further observed that although the image quality of the motion corrected PET images deteriorates for high acceleration factors, the images were still superior to the images reconstructed without motion correction. Conclusions: Accelerated tMR images obtained with more than 4 times acceleration can still provide relatively accurate motion fields and yield tMR-based motion corrected PET images with similar image quality as those reconstructed using fully sampled tMR data. The reduction of tMR acquisition time makes it more compatible with routine clinical cardiac PET-MR studies.« less

Installation Restoration Program. Phase 2. Confirmation/Quantification Stage 2, Moody Air Force Base, Georgia. Appendices. Volume 1

DTIC Science & Technology

1988-11-01

Light gray NB, clayey (kaolin). Poetv al - quartz mad to fine sand, mod. (0 Locking Cap plastic , saturated. 3 COMPILED BY B. Painter (EWM) t DATE 11-21...Painter (EUM) -SAMPLE PNTAINSOIL DESCRIIPTION COMMENTS ZTEST NAME. GRADATION OR PLASTICITY ,. DEPTH Of CASING, W ~ 1NPARTICLE SIZE DISTRIBUTION. COLOR...L. Grayish orange 10 YR 7/4. quart. RNDEVAI: very tine Sandy clay, dense, DIAMETER: 2-inrh Srhe So PVC moderately plastics dry. DEPTH: 2 - fenot[ 1

Erosion / Corrosion Resistant Coatings for Compressor Airfoils

DTIC Science & Technology

2012-08-29

Platforms in Evaluation / Qualification T56 for C-130 AE1107 for V-22 T700 for H-60 T55 for MH-47 GE38 for H-53K Gem for Lynx T58 for H-46... T56 Performance Summary Uncoated vs Coated Engine Uncoated Engine (April – May 2011) With “sand turbine” at San Antonio: Coated Engine (July...power retention 2-3% Corrected Fuel Flow 1-2% Specific Fuel Consumption decrease @ 95% shp Coated Engine T56 Sand Ingestion Test 10 Pressure

Application of phase correction to improve the interpretation of crude oil spectra obtained using 7 T Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Cho, Yunju; Qi, Yulin; O'Connor, Peter B; Barrow, Mark P; Kim, Sunghwan

2014-01-01

In this study, a phase-correction technique was applied to the study of crude oil spectra obtained using a 7 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). 7 T FT-ICR MS had not been widely used for oil analysis due to the lower resolving power compared with high field FT-ICR MS. For low field instruments, usage of data that has not been phase-corrected results in an inability to resolve critical mass splits of C3 and SH4 (3.4 mDa), and (13)C and CH (4.5 mDa). This results in incorrect assignments of molecular formulae, and discontinuous double bond equivalents (DBE) and carbon number distributions of S1, S2, and hydrocarbon classes are obtained. Application of phase correction to the same data, however, improves the reliability of assignments and produces continuous DBE and carbon number distributions. Therefore, this study clearly demonstrates that phase correction improves data analysis and the reliability of assignments of molecular formulae in crude oil anlayses.

Quantification of fibre polymerization through Fourier space image analysis

PubMed Central

Nekouzadeh, Ali; Genin, Guy M.

2011-01-01

Quantification of changes in the total length of randomly oriented and possibly curved lines appearing in an image is a necessity in a wide variety of biological applications. Here, we present an automated approach based upon Fourier space analysis. Scaled, band-pass filtered power spectral densities of greyscale images are integrated to provide a quantitative measurement of the total length of lines of a particular range of thicknesses appearing in an image. A procedure is presented to correct for changes in image intensity. The method is most accurate for two-dimensional processes with fibres that do not occlude one another. PMID:24959096

Quantification of Rifapentine, a Potent Antituberculosis Drug, from Dried Blood Spot Samples Using Liquid Chromatographic-Tandem Mass Spectrometric Analysis

PubMed Central

Parsons, Teresa L.; Marzinke, Mark A.; Hoang, Thuy; Bliven-Sizemore, Erin; Weiner, Marc; Mac Kenzie, William R.; Dorman, Susan E.

2014-01-01

The quantification of antituberculosis drug concentrations in multinational trials currently requires the collection of modest blood volumes, centrifugation, aliquoting of plasma, freezing, and keeping samples frozen during shipping. We prospectively enrolled healthy individuals into the Tuberculosis Trials Consortium Study 29B, a phase I dose escalation study of rifapentine, a rifamycin under evaluation in tuberculosis treatment trials. We developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying rifapentine in whole blood on dried blood spots (DBS) to facilitate pharmacokinetic/pharmacodynamic analyses in clinical trials. Paired plasma and whole-blood samples were collected by venipuncture, and whole blood was spotted on Whatman protein saver 903 cards. The methods were optimized for plasma and then validated for DBS. The analytical measuring range for quantification of rifapentine and its metabolite was 50 to 80,000 ng/ml in whole-blood DBS. The analyte was stable on the cards for 11 weeks with a desiccant at room temperature and protected from light. The method concordance for paired plasma and whole-blood DBS samples was determined after correcting for participant hematocrit or population-based estimates of bias from Bland-Altman plots. The application of either correction factor resulted in acceptable correlation between plasma and whole-blood DBS (Passing-Bablok regression corrected for hematocrit; y = 0.98x + 356). Concentrations of rifapentine may be determined from whole-blood DBS collected via venipuncture after normalization in order to account for the dilutional effects of red blood cells. Additional studies are focused on the application of this methodology to capillary blood collected by finger stick. The simplicity of processing, storage, shipping, and low blood volume makes whole-blood DBS attractive for rifapentine pharmacokinetic evaluations, especially in international and pediatric trials. PMID:25182637

Hybrid two-dimensional navigator correction: a new technique to suppress respiratory-induced physiological noise in multi-shot echo-planar functional MRI

PubMed Central

Barry, Robert L.; Klassen, L. Martyn; Williams, Joy M.; Menon, Ravi S.

2008-01-01

A troublesome source of physiological noise in functional magnetic resonance imaging (fMRI) is due to the spatio-temporal modulation of the magnetic field in the brain caused by normal subject respiration. fMRI data acquired using echo-planar imaging is very sensitive to these respiratory-induced frequency offsets, which cause significant geometric distortions in images. Because these effects increase with main magnetic field, they can nullify the gains in statistical power expected by the use of higher magnetic fields. As a study of existing navigator correction techniques for echo-planar fMRI has shown that further improvements can be made in the suppression of respiratory-induced physiological noise, a new hybrid two-dimensional (2D) navigator is proposed. Using a priori knowledge of the slow spatial variations of these induced frequency offsets, 2D field maps are constructed for each shot using spatial frequencies between ±0.5 cm−1 in k-space. For multi-shot fMRI experiments, we estimate that the improvement of hybrid 2D navigator correction over the best performance of one-dimensional navigator echo correction translates into a 15% increase in the volume of activation, 6% and 10% increases in the maximum and average t-statistics, respectively, for regions with high t-statistics, and 71% and 56% increases in the maximum and average t-statistics, respectively, in regions with low t-statistics due to contamination by residual physiological noise. PMID:18024159

Improvements to sample processing and measurement to enable more widespread environmental application of tritium.

PubMed

Moran, James; Alexander, Thomas; Aalseth, Craig; Back, Henning; Mace, Emily; Overman, Cory; Seifert, Allen; Freeburg, Wilcox

2017-08-01

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. We present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. We identify a current quantification limit of 92.2 TU which, combined with our small sample sizes, correlates to as little as 0.00133Bq of total T activity. This enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps in our understanding of both natural and artificial T behavior in the environment. Copyright © 2017. Published by Elsevier Ltd.

Improvements to sample processing and measurement to enable more widespread environmental application of tritium

DOE PAGES

Moran, James; Alexander, Thomas; Aalseth, Craig; ...

2017-01-26

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. Here, we present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120 mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. We also identify a current quantification limit of 92.2 TU which, combined with our small sample sizes, correlates to as little as 0.00133 Bq of total T activity. Furthermore, this enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps inmore » our understanding of both natural and artificial T behavior in the environment.« less

Standardizing Type Ia supernovae optical brightness using near-infrared rebrightening time

NASA Astrophysics Data System (ADS)

Shariff, H.; Dhawan, S.; Jiao, X.; Leibundgut, B.; Trotta, R.; van Dyk, D. A.

2016-12-01

Accurate standardization of Type Ia supernovae (SNIa) is instrumental to the usage of SNIa as distance indicators. We analyse a homogeneous sample of 22 low-z SNIa, observed by the Carnegie Supernova Project in the optical and near-infrared (NIR). We study the time of the second peak in the J band, t2, as an alternative standardization parameter of SNIa peak optical brightness, as measured by the standard SALT2 parameter mB. We use BAHAMAS, a Bayesian hierarchical model for SNIa cosmology, to estimate the residual scatter in the Hubble diagram. We find that in the absence of a colour correction, t2 is a better standardization parameter compared to stretch: t2 has a 1σ posterior interval for the Hubble residual scatter of σΔμ = {0.250, 0.257} mag, compared to σΔμ = {0.280, 0.287} mag when stretch (x1) alone is used. We demonstrate that when employed together with a colour correction, t2 and stretch lead to similar residual scatter. Using colour, stretch and t2 jointly as standardization parameters does not result in any further reduction in scatter, suggesting that t2 carries redundant information with respect to stretch and colour. With a much larger SNIa NIR sample at higher redshift in the future, t2 could be a useful quantity to perform robustness checks of the standardization procedure.

Methods for discovering and validating relationships among genotyped animals

USDA-ARS?s Scientific Manuscript database

Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, t...

Consistency of signal intensity and T2* in frozen ex vivo heart muscle, kidney, and liver tissue.

PubMed

Kaye, Elena A; Josan, Sonal; Lu, Aiming; Rosenberg, Jarrett; Daniel, Bruce L; Pauly, Kim Butts

2010-03-01

To investigate tissue dependence of the MRI-based thermometry in frozen tissue by quantification and comparison of signal intensity and T2* of ex vivo frozen tissue of three different types: heart muscle, kidney, and liver. Tissue samples were frozen and imaged on a 0.5 Tesla MRI scanner with ultrashort echo time (UTE) sequence. Signal intensity and T2* were determined as the temperature of the tissue samples was decreased from room temperature to approximately -40 degrees C. Statistical analysis was performed for (-20 degrees C, -5 degrees C) temperature interval. The findings of this study demonstrate that signal intensity and T2* are consistent across three types of tissue for (-20 degrees C, -5 degrees C) temperature interval. Both parameters can be used to calculate a single temperature calibration curve for all three types of tissue and potentially in the future serve as a foundation for tissue-independent MRI-based thermometry.

Accurate ab initio binding energies of the benzene dimer.

PubMed

Park, Young Choon; Lee, Jae Shin

2006-04-20

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.

Mathematical simulations for bioanalytical assay development: the (un-)necessity and (im-)possibility of free drug quantification.

PubMed

Staack, Roland F; Jordan, Gregor; Heinrich, Julia

2012-02-01

For every drug development program it needs to be discussed whether discrimination between free and total drug concentrations is required to accurately describe its pharmacokinetic behavior. This perspective describes the application of mathematical simulation approaches to guide this initial decision based on available knowledge about target biology, binding kinetics and expected drug concentrations. We provide generic calculations that can be used to estimate the necessity of free drug quantification for different drug molecules. In addition, mathematical approaches are used to simulate various assay conditions in bioanalytical ligand-binding assays: it is demonstrated that due to the noncovalent interaction between the binding partners and typical assay-related interferences in the equilibrium, a correct quantification of the free drug concentration is highly challenging and requires careful design of different assay procedure steps.

Sensitivity and specificity of human brain glutathione concentrations measured using short-TE (1)H MRS at 7 T.

PubMed

Deelchand, Dinesh K; Marjańska, Małgorzata; Hodges, James S; Terpstra, Melissa

2016-05-01

Although the MR editing techniques that have traditionally been used for the measurement of glutathione (GSH) concentrations in vivo address the problem of spectral overlap, they suffer detriments associated with inherently long TEs. The purpose of this study was to characterize the sensitivity and specificity for the quantification of GSH concentrations without editing at short TE. The approach was to measure synthetically generated changes in GSH concentrations from in vivo stimulated echo acquisition mode (STEAM) spectra after in vitro GSH spectra had been added to or subtracted from them. Spectra from five test subjects were synthetically altered to mimic changes in the GSH signal. To account for different background noise between measurements, retest spectra (from the same individuals as used to generate the altered data) and spectra from five other individuals were compared with the synthetically altered spectra to investigate the reliability of the quantification of GSH concentration. Using STEAM spectroscopy at 7 T, GSH concentration differences on the order of 20% were detected between test and retest studies, as well as between differing populations in a small sample (n = 5) with high accuracy (R(2) > 0.99) and certainty (p ≤ 0.01). Both increases and decreases in GSH concentration were reliably quantified with small impact on the quantification of ascorbate and γ-aminobutyric acid. These results show the feasibility of using short-TE (1)H MRS to measure biologically relevant changes and differences in human brain GSH concentration. Although these outcomes are specific to the experimental approach used and the spectral quality achieved, this study serves as a template for the analogous scrutiny of quantification reliability for other compounds, methodologies and spectral qualities. Copyright © 2016 John Wiley & Sons, Ltd.

Magnetic resonance imaging metallic artifact of commonly encountered surgical implants and foreign material.

PubMed

Sutherland-Smith, James; Tilley, Brenda

2012-01-01

Magnetic resonance imaging (MRI) artifacts secondary to metallic implants and foreign bodies are well described. Herein, we provide quantitative data from veterinary implants including total hip arthroplasty implants, cranial cruciate repair implants, surgical screws, a skin staple, ligation clips, an identification microchip, ameroid constrictor, and potential foreign bodies including air gun and BB projectiles and a sewing needle. The objects were scanned in a gelatin phantom with plastic grid using standardized T2-weighted turbo-spin echo (TSE), T1-weighted spin echo, and T2*-weighted gradient recalled echo (GRE) image acquisitions at 1.5 T. Maximum linear dimensions and areas of signal voiding and grid distortion were calculated using a DICOM workstation for each sequence and object. Artifact severity was similar between the T2-weighted TSE and T1-weighted images, while the T2*-weighted images were most susceptible to artifact. Metal type influenced artifact size with the largest artifacts arising from steel objects followed by surgical stainless steel, titanium, and lead. For animals with metallic surgical implants or foreign bodies, the quantification of the artifact size will help guide clinicians on the viability of MRI. © 2012 Veterinary Radiology & Ultrasound.

Exploring conformational preferences of alanine tetrapeptide by CCSD(T), MP2, and dispersion-corrected DFT methods

NASA Astrophysics Data System (ADS)

Kang, Young Kee; Park, Hae Sook

2018-06-01

The 129 local minima of the alanine tetrapeptide with relative energy < 10 kcal/mol were identified at the ωB97X-D/6-311++G(d,p) level of theory from initial structures generated by combining nine local minima of each residue. The CCSD(T), MP2, and dispersion-corrected DFT levels of theory with various basis sets were assessed for relative energies of the 24 representative conformations. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol against the CCSD(T)/CBS-limit energies. The ωB97X-D/def2-QZVP and CAM-B3LYP-D3BJ/def2-QZVP levels of theory can be an alternative level of theory with marginal deviations for conformational study of peptides.

Inter- and intra-rater reliability of patellofemoral kinematic and contact area quantification by fast spin echo MRI and correlation with cartilage health by quantitative T1ρ MRI☆

PubMed Central

Lau, Brian C.; Thuillier, Daniel U.; Pedoia, Valentina; Chen, Ellison Y.; Zhang, Zhihong; Feeley, Brian T.; Souza, Richard B.

2016-01-01

Background Patellar maltracking is a leading cause of patellofemoral pain syndrome (PFPS). The aim of this study was to determine the inter- and intra-rater reliability of a semi-automated program for magnetic resonance imaging (MRI) based patellofemoral kinematics. Methods Sixteen subjects (10 with PFPS [mean age 32.3; SD 5.2; eight females] and six controls without PFPS 19 [mean age 28.6; SD 2.8; three females]) participated in the study. One set of T2-weighted, fat-saturated fast spin-echo (FSE) MRIs were acquired from each subject in full extension and 30° of knee flexion. MRI including axial T1ρ relaxation time mapping sequences was also performed on each knee. Following image acquisitions, regions of interest for kinematic MRI, and patellar and trochlear cartilage were segmented and quantified with in-house designed spline- based MATLAB semi-automated software. Results Intraclass Correlations Coefficients (ICC) of calculated kinematic parameters were good to excellent, ICC > 0.8 in patellar flexion, rotation, tilt, and translation (anterior -posterior, medial -lateral, and superior -inferior), and contact area translation. Only patellar tilt in the flexed position and motion from extended to flexed state was significantly different between PFPS and control patients (p = 0.002 and p = 0.006, respectively). No significant correlations were identified between patellofemoral kinematics and contact area with T1ρ relaxation times. Conclusions A semi-automated, spline-based kinematic MRI technique for patellofemoral kinematic and contact area quantification is highly reproducible with the potential to help better understand the role of patellofemoral maltracking in PFPS and other knee disorders. PMID:26746045

Inter- and intra-rater reliability of patellofemoral kinematic and contact area quantification by fast spin echo MRI and correlation with cartilage health by quantitative T1ρ MRI.

PubMed

Lau, Brian C; Thuillier, Daniel U; Pedoia, Valentina; Chen, Ellison Y; Zhang, Zhihong; Feeley, Brian T; Souza, Richard B

2016-01-01

Patellar maltracking is a leading cause of patellofemoral pain syndrome (PFPS). The aim of this study was to determine the inter- and intra-rater reliability of a semi-automated program for magnetic resonance imaging (MRI) based patellofemoral kinematics. Sixteen subjects (10 with PFPS [mean age 32.3; SD 5.2; eight females] and six controls without PFPS 19 [mean age 28.6; SD 2.8; three females]) participated in the study. One set of T2-weighted, fat-saturated fast spin-echo (FSE) MRIs were acquired from each subject in full extension and 30° of knee flexion. MRI including axial T1ρ relaxation time mapping sequences was also performed on each knee. Following image acquisitions, regions of interest for kinematic MRI, and patellar and trochlear cartilage were segmented and quantified with in-house designed spline- based MATLAB semi-automated software. Intraclass Correlations Coefficients (ICC) of calculated kinematic parameters were good to excellent, ICC > 0.8 in patellar flexion, rotation, tilt, and translation (anterior -posterior, medial -lateral, and superior -inferior), and contact area translation. Only patellar tilt in the flexed position and motion from extended to flexed state was significantly different between PFPS and control patients (p=0.002 and p=0.006, respectively). No significant correlations were identified between patellofemoral kinematics and contact area with T1ρ relaxation times. A semi-automated, spline-based kinematic MRI technique for patellofemoral kinematic and contact area quantification is highly reproducible with the potential to help better understand the role of patellofemoral maltracking in PFPS and other knee disorders. Level IV. Published by Elsevier B.V.

Native T1 mapping of the heart - a pictorial review.

PubMed

Germain, Philippe; El Ghannudi, Soraya; Jeung, Mi-Young; Ohlmann, Patrick; Epailly, Eric; Roy, Catherine; Gangi, Afshin

2014-01-01

T1 mapping is now a clinically feasible method, providing pixel-wise quantification of the cardiac structure's T1 values. Beyond focal lesions, well depicted by late gadolinium enhancement sequences, it has become possible to discriminate diffuse myocardial alterations, previously not assessable by noninvasive means. The strength of this method includes the high reproducibility and immediate clinical applicability, even without the use of contrast media injection (native or pre-contrast T1). The two most important determinants of native T1 augmentation are (1) edema related to tissue water increase (recent infarction or inflammation) and (2) interstitial space increase related to fibrosis (infarction scar, cardiomyopathy) or to amyloidosis. Conversely, lipid (Anderson-Fabry) or iron overload diseases are responsible for T1 reduction. In this pictorial review, the main features provided by native T1 mapping are discussed and illustrated, with a special focus on the awaited clinical purpose of this unique, promising new method.

Ginzburg-Landau theory, strong coupling corrections and exchange enhancements: Can spin fluctuations give high T c's?

NASA Astrophysics Data System (ADS)

Quader, Khandker F.; Salamon, M. B.

1988-06-01

Ginzburg-Landau theory is used to explore the thermodynamic and electrodynamic properties of YBa 2Cu 3O 7-δ, and to determine γ, m ∗/m and the exchange enhancement. This material is found to be in a moderately strong coupling regime, intermediate between dirty and clean limits; strong coupling corrections are estimated. It is shown that, irrespective of the choice of the carrier density, spin fluctuations are unable to give a sufficiently large T c. An upper bound is given for the T c due spin-fluctuation-mediated pairing.

Validation of an integrated software for the detection of rapid eye movement sleep behavior disorder.

PubMed

Frauscher, Birgit; Gabelia, David; Biermayr, Marlene; Stefani, Ambra; Hackner, Heinz; Mitterling, Thomas; Poewe, Werner; Högl, Birgit

2014-10-01

Rapid eye movement sleep without atonia (RWA) is the polysomnographic hallmark of REM sleep behavior disorder (RBD). To partially overcome the disadvantages of manual RWA scoring, which is time consuming but essential for the accurate diagnosis of RBD, we aimed to validate software specifically developed and integrated with polysomnography for RWA detection against the gold standard of manual RWA quantification. Academic referral center sleep laboratory. Polysomnographic recordings of 20 patients with RBD and 60 healthy volunteers were analyzed. N/A. Motor activity during REM sleep was quantified manually and computer assisted (with and without artifact detection) according to Sleep Innsbruck Barcelona (SINBAR) criteria for the mentalis ("any," phasic, tonic electromyographic [EMG] activity) and the flexor digitorum superficialis (FDS) muscle (phasic EMG activity). Computer-derived indices (with and without artifact correction) for "any," phasic, tonic mentalis EMG activity, phasic FDS EMG activity, and the SINBAR index ("any" mentalis + phasic FDS) correlated well with the manually derived indices (all Spearman rhos 0.66-0.98). In contrast with computerized scoring alone, computerized scoring plus manual artifact correction (median duration 5.4 min) led to a significant reduction of false positives for "any" mentalis (40%), phasic mentalis (40.6%), and the SINBAR index (41.2%). Quantification of tonic mentalis and phasic FDS EMG activity was not influenced by artifact correction. The computer algorithm used here appears to be a promising tool for REM sleep behavior disorder detection in both research and clinical routine. A short check for plausibility of automatic detection should be a basic prerequisite for this and all other available computer algorithms. © 2014 Associated Professional Sleep Societies, LLC.

A Novel Triplex Quantitative PCR Strategy for Quantification of Toxigenic and Nontoxigenic Vibrio cholerae in Aquatic Environments

PubMed Central

Bliem, Rupert; Schauer, Sonja; Plicka, Helga; Obwaller, Adelheid; Sommer, Regina; Steinrigl, Adolf; Alam, Munirul; Reischer, Georg H.; Farnleitner, Andreas H.

2015-01-01

Vibrio cholerae is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of V. cholerae in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic V. cholerae in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected V. cholerae abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6 × 102 to 2.3 × 104 cell equivalents liter−1, whereas GR-corrected abundances ranged from 4.7 × 103 to 1.6 × 106 cell equivalents liter−1. GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic V. cholerae in various aquatic environments for ecological studies as well as for risk assessment programs. PMID:25724966

Highly automatic quantification of myocardial oedema in patients with acute myocardial infarction using bright blood T2-weighted CMR

PubMed Central

2013-01-01

Background T2-weighted cardiovascular magnetic resonance (CMR) is clinically-useful for imaging the ischemic area-at-risk and amount of salvageable myocardium in patients with acute myocardial infarction (MI). However, to date, quantification of oedema is user-defined and potentially subjective. Methods We describe a highly automatic framework for quantifying myocardial oedema from bright blood T2-weighted CMR in patients with acute MI. Our approach retains user input (i.e. clinical judgment) to confirm the presence of oedema on an image which is then subjected to an automatic analysis. The new method was tested on 25 consecutive acute MI patients who had a CMR within 48 hours of hospital admission. Left ventricular wall boundaries were delineated automatically by variational level set methods followed by automatic detection of myocardial oedema by fitting a Rayleigh-Gaussian mixture statistical model. These data were compared with results from manual segmentation of the left ventricular wall and oedema, the current standard approach. Results The mean perpendicular distances between automatically detected left ventricular boundaries and corresponding manual delineated boundaries were in the range of 1-2 mm. Dice similarity coefficients for agreement (0=no agreement, 1=perfect agreement) between manual delineation and automatic segmentation of the left ventricular wall boundaries and oedema regions were 0.86 and 0.74, respectively. Conclusion Compared to standard manual approaches, the new highly automatic method for estimating myocardial oedema is accurate and straightforward. It has potential as a generic software tool for physicians to use in clinical practice. PMID:23548176

MRI-based quantification of Duchenne muscular dystrophy in a canine model

NASA Astrophysics Data System (ADS)

Wang, Jiahui; Fan, Zheng; Kornegay, Joe N.; Styner, Martin A.

2011-03-01

Duchenne muscular dystrophy (DMD) is a progressive and fatal X-linked disease caused by mutations in the DMD gene. Magnetic resonance imaging (MRI) has shown potential to provide non-invasive and objective biomarkers for monitoring disease progression and therapeutic effect in DMD. In this paper, we propose a semi-automated scheme to quantify MRI features of golden retriever muscular dystrophy (GRMD), a canine model of DMD. Our method was applied to a natural history data set and a hydrodynamic limb perfusion data set. The scheme is composed of three modules: pre-processing, muscle segmentation, and feature analysis. The pre-processing module includes: calculation of T2 maps, spatial registration of T2 weighted (T2WI) images, T2 weighted fat suppressed (T2FS) images, and T2 maps, and intensity calibration of T2WI and T2FS images. We then manually segment six pelvic limb muscles. For each of the segmented muscles, we finally automatically measure volume and intensity statistics of the T2FS images and T2 maps. For the natural history study, our results showed that four of six muscles in affected dogs had smaller volumes and all had higher mean intensities in T2 maps as compared to normal dogs. For the perfusion study, the muscle volumes and mean intensities in T2FS were increased in the post-perfusion MRI scans as compared to pre-perfusion MRI scans, as predicted. We conclude that our scheme successfully performs quantitative analysis of muscle MRI features of GRMD.

CORRECTING ENERGY EXPENDITURES FOR FATIGUE AND EXCESS POST-EXERCISE OXYGEN CONSUMPTION

EPA Science Inventory

The EPA's human exposure and dose models often require a quantification of oxygen consumption for a simulated individual. Oxygen consumption is dependent on the individual's current level of physical activity (PA), which is determined from activity diaries selected from the Conso...

Characterization of 3-Dimensional PET Systems for Accurate Quantification of Myocardial Blood Flow.

PubMed

Renaud, Jennifer M; Yip, Kathy; Guimond, Jean; Trottier, Mikaël; Pibarot, Philippe; Turcotte, Eric; Maguire, Conor; Lalonde, Lucille; Gulenchyn, Karen; Farncombe, Troy; Wisenberg, Gerald; Moody, Jonathan; Lee, Benjamin; Port, Steven C; Turkington, Timothy G; Beanlands, Rob S; deKemp, Robert A

2017-01-01

Three-dimensional (3D) mode imaging is the current standard for PET/CT systems. Dynamic imaging for quantification of myocardial blood flow with short-lived tracers, such as 82 Rb-chloride, requires accuracy to be maintained over a wide range of isotope activities and scanner counting rates. We proposed new performance standard measurements to characterize the dynamic range of PET systems for accurate quantitative imaging. 82 Rb or 13 N-ammonia (1,100-3,000 MBq) was injected into the heart wall insert of an anthropomorphic torso phantom. A decaying isotope scan was obtained over 5 half-lives on 9 different 3D PET/CT systems and 1 3D/2-dimensional PET-only system. Dynamic images (28 × 15 s) were reconstructed using iterative algorithms with all corrections enabled. Dynamic range was defined as the maximum activity in the myocardial wall with less than 10% bias, from which corresponding dead-time, counting rates, and/or injected activity limits were established for each scanner. Scatter correction residual bias was estimated as the maximum cavity blood-to-myocardium activity ratio. Image quality was assessed via the coefficient of variation measuring nonuniformity of the left ventricular myocardium activity distribution. Maximum recommended injected activity/body weight, peak dead-time correction factor, counting rates, and residual scatter bias for accurate cardiac myocardial blood flow imaging were 3-14 MBq/kg, 1.5-4.0, 22-64 Mcps singles and 4-14 Mcps prompt coincidence counting rates, and 2%-10% on the investigated scanners. Nonuniformity of the myocardial activity distribution varied from 3% to 16%. Accurate dynamic imaging is possible on the 10 3D PET systems if the maximum injected MBq/kg values are respected to limit peak dead-time losses during the bolus first-pass transit. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Intercalibration between HIRS/2 and HIRS/3 channel 12 based on physical considerations

NASA Astrophysics Data System (ADS)

Gierens, Klaus; Eleftheratos, Kostas; Sausen, Robert

2018-02-01

High-resolution Infrared Radiation Sounder (HIRS) brightness temperatures at channel 12 (T12) can be used to assess the water vapour content of the upper troposphere. The transition from HIRS/2 to HIRS/3 in 1999 involved a shift in the central wavelength of channel 12 from 6.7 to 6.5 µm, causing a discontinuity in the time series of T12. To understand the impact of this change in the measured brightness temperatures, we have performed radiative transfer calculations for channel 12 of HIRS/2 and HIRS/3 instruments, using a large set of radiosonde profiles of temperature and relative humidity from three different sites. Other possible changes within the instrument, apart from the changed spectral response function, have been assumed to be of minor importance, and in fact, it was necessary to assume as a working hypothesis that the spectral and radiometric calibration of the two instruments did not change during the relatively short period of their common operation. For each radiosonde profile we performed two radiative transfer calculations, one using the HIRS/2 channel response function of NOAA 14 and one using the HIRS/3 channel response function of NOAA 15, resulting in negative differences of T12 (denoted as ΔT12 := T12/15 - T12/14) ranging between -12 and -2 K. Inspection of individual profiles for large, medium and small values of ΔT12 pointed to the role of the mid-tropospheric humidity. This guided us to investigate the relation between ΔT12 and the channel 11 brightness temperatures which are typically used to detect signals from the mid-troposphere. This allowed us to construct a correction for the HIRS/3 T12, which leads to a pseudo-channel 12 brightness temperature as if a HIRS/2 instrument had measured it. By applying this correction we find an excellent agreement between the original HIRS/2 T12 and the HIRS/3 data inferred from the correction method with R = 0.986. Upper-tropospheric humidity (UTH) derived from the pseudo HIRS/2 T12 data compared well with that calculated from intersatellite-calibrated data, providing independent justification for using the two intercalibrated time series (HIRS/2 and HIRS/3) as a continuous HIRS time series for long-term UTH analyses.

In vivo quantification of T2* anisotropy in white matter fibers in marmoset monkeys

PubMed Central

Sati, P.; Silva, A. C.; van Gelderen, P.; Gaitan, M. I.; Wohler, J. E.; Jacobson, S.; Duyn, J. H.; Reich, D. S.

2011-01-01

T2*-weighted MRI at high field is a promising approach for studying noninvasively the tissue structure and composition of the brain. However, the biophysical origin of T2* contrast, especially in white matter, remains poorly understood. Recent work has shown that R2* (=1/T2*) may depend on the tissue’s orientation relative to the static magnetic field (B0) and suggested that this dependence could be attributed to local anisotropy in the magnetic properties of brain tissue. In the present work, we analyzed high-resolution, multi-gradient-echo images of in vivo marmoset brains at 7T, and compared them with ex vivo diffusion tensor images, to show that R2* relaxation in white matter is highly sensitive to the fiber orientation relative to the main field. We directly demonstrate this orientation dependence by performing in vivo multi-gradient-echo acquisitions in two orthogonal brain positions, uncovering a nearly 50% change in the R2*relaxation rate constant of the optic radiations. We attribute this substantial R2* anisotropy to local subvoxel susceptibility effects arising from the highly ordered and anisotropic structure of the myelin sheath. PMID:21906687

Correction of murine Rag2 severe combined immunodeficiency by lentiviral gene therapy using a codon-optimized RAG2 therapeutic transgene.

PubMed

van Til, Niek P; de Boer, Helen; Mashamba, Nomusa; Wabik, Agnieszka; Huston, Marshall; Visser, Trudi P; Fontana, Elena; Poliani, Pietro Luigi; Cassani, Barbara; Zhang, Fang; Thrasher, Adrian J; Villa, Anna; Wagemaker, Gerard

2012-10-01

Recombination activating gene 2 (RAG2) deficiency results in severe combined immunodeficiency (SCID) with complete lack of T and B lymphocytes. Initial gammaretroviral gene therapy trials for other types of SCID proved effective, but also revealed the necessity of safe vector design. We report the development of lentiviral vectors with the spleen focus forming virus (SF) promoter driving codon-optimized human RAG2 (RAG2co), which improved phenotype amelioration compared to native RAG2 in Rag2(-/-) mice. With the RAG2co therapeutic transgene, T-cell receptor (TCR) and immunoglobulin repertoire, T-cell mitogen responses, plasma immunoglobulin levels and T-cell dependent and independent specific antibody responses were restored. However, the thymus double positive T-cell population remained subnormal, possibly due to the SF virus derived element being sensitive to methylation/silencing in the thymus, which was prevented by replacing the SF promoter by the previously reported silencing resistant element (ubiquitous chromatin opening element (UCOE)), and also improved B-cell reconstitution to eventually near normal levels. Weak cellular promoters were effective in T-cell reconstitution, but deficient in B-cell reconstitution. We conclude that immune functions are corrected in Rag2(-/-) mice by genetic modification of stem cells using the UCOE driven codon-optimized RAG2, providing a valid optional vector for clinical implementation.

Comparison of T1-weighted 2D TSE, 3D SPGR, and two-point 3D Dixon MRI for automated segmentation of visceral adipose tissue at 3 Tesla.

PubMed

Fallah, Faezeh; Machann, Jürgen; Martirosian, Petros; Bamberg, Fabian; Schick, Fritz; Yang, Bin

2017-04-01

To evaluate and compare conventional T1-weighted 2D turbo spin echo (TSE), T1-weighted 3D volumetric interpolated breath-hold examination (VIBE), and two-point 3D Dixon-VIBE sequences for automatic segmentation of visceral adipose tissue (VAT) volume at 3 Tesla by measuring and compensating for errors arising from intensity nonuniformity (INU) and partial volume effects (PVE). The body trunks of 28 volunteers with body mass index values ranging from 18 to 41.2 kg/m 2 (30.02 ± 6.63 kg/m 2 ) were scanned at 3 Tesla using three imaging techniques. Automatic methods were applied to reduce INU and PVE and to segment VAT. The automatically segmented VAT volumes obtained from all acquisitions were then statistically and objectively evaluated against the manually segmented (reference) VAT volumes. Comparing the reference volumes with the VAT volumes automatically segmented over the uncorrected images showed that INU led to an average relative volume difference of -59.22 ± 11.59, 2.21 ± 47.04, and -43.05 ± 5.01 % for the TSE, VIBE, and Dixon images, respectively, while PVE led to average differences of -34.85 ± 19.85, -15.13 ± 11.04, and -33.79 ± 20.38 %. After signal correction, differences of -2.72 ± 6.60, 34.02 ± 36.99, and -2.23 ± 7.58 % were obtained between the reference and the automatically segmented volumes. A paired-sample two-tailed t test revealed no significant difference between the reference and automatically segmented VAT volumes of the corrected TSE (p = 0.614) and Dixon (p = 0.969) images, but showed a significant VAT overestimation using the corrected VIBE images. Under similar imaging conditions and spatial resolution, automatically segmented VAT volumes obtained from the corrected TSE and Dixon images agreed with each other and with the reference volumes. These results demonstrate the efficacy of the signal correction methods and the similar accuracy of TSE and Dixon imaging for automatic volumetry of VAT at 3 Tesla.

Flutriciclamide (18F-GE180) PET: First-in-Human PET Study of Novel Third-Generation In Vivo Marker of Human Translocator Protein.

PubMed

Fan, Zhen; Calsolaro, Valeria; Atkinson, Rebecca A; Femminella, Grazia D; Waldman, Adam; Buckley, Christopher; Trigg, William; Brooks, David J; Hinz, Rainer; Edison, Paul

2016-11-01

Neuroinflammation is associated with neurodegenerative disease. PET radioligands targeting the 18-kDa translocator protein (TSPO) have been used as in vivo markers of neuroinflammation, but there is an urgent need for novel probes with improved signal-to-noise ratio. Flutriciclamide ( 18 F-GE180) is a recently developed third-generation TSPO ligand. In this first study, we evaluated the optimum scan duration and kinetic modeling strategies for 18 F-GE180 PET in (older) healthy controls. Ten healthy controls, 6 TSPO high-affinity binders, and 4 mixed-affinity binders were recruited. All subjects underwent detailed neuropsychologic tests, MRI, and a 210-min 18 F-GE180 dynamic PET/CT scan using metabolite-corrected arterial plasma input function. We evaluated 5 different kinetic models: irreversible and reversible 2-tissue-compartment models, a reversible 1-tissue model, and 2 models with an extra irreversible vascular compartment. The minimal scan duration was established using 210-min scan data. The feasibility of generating parametric maps was also investigated using graphical analysis. 18 F-GE180 concentration was higher in plasma than in whole blood during the entire scan duration. The volume of distribution (V T ) was 0.17 in high-affinity binders and 0.12 in mixed-affinity binders using the kinetic model. The model that best represented brain 18 F-GE180 kinetics across regions was the reversible 2-tissue-compartment model (2TCM4k), and 90 min resulted as the optimum scan length required to obtain stable estimates. Logan graphical analysis with arterial input function gave a V T highly consistent with V T in the kinetic model, which could be used for voxelwise analysis. We report for the first time, to our knowledge, the kinetic properties of the novel third-generation TSPO PET ligand 18 F-GE180 in humans: 2TCM4k is the optimal method to quantify the brain uptake, 90 min is the optimal scan length, and the Logan approach could be used to generate parametric maps. Although these control subjects have shown relatively low V T , the methodology presented here forms the basis for quantification for future PET studies using 18 F-GE180 in different pathologies. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Reproducibility of Lobar Perfusion and Ventilation Quantification Using SPECT/CT Segmentation Software in Lung Cancer Patients.

PubMed

Provost, Karine; Leblond, Antoine; Gauthier-Lemire, Annie; Filion, Édith; Bahig, Houda; Lord, Martin

2017-09-01

Planar perfusion scintigraphy with 99m Tc-labeled macroaggregated albumin is often used for pretherapy quantification of regional lung perfusion in lung cancer patients, particularly those with poor respiratory function. However, subdividing lung parenchyma into rectangular regions of interest, as done on planar images, is a poor reflection of true lobar anatomy. New tridimensional methods using SPECT and SPECT/CT have been introduced, including semiautomatic lung segmentation software. The present study evaluated inter- and intraobserver agreement on quantification using SPECT/CT software and compared the results for regional lung contribution obtained with SPECT/CT and planar scintigraphy. Methods: Thirty lung cancer patients underwent ventilation-perfusion scintigraphy with 99m Tc-macroaggregated albumin and 99m Tc-Technegas. The regional lung contribution to perfusion and ventilation was measured on both planar scintigraphy and SPECT/CT using semiautomatic lung segmentation software by 2 observers. Interobserver and intraobserver agreement for the SPECT/CT software was assessed using the intraclass correlation coefficient, Bland-Altman plots, and absolute differences in measurements. Measurements from planar and tridimensional methods were compared using the paired-sample t test and mean absolute differences. Results: Intraclass correlation coefficients were in the excellent range (above 0.9) for both interobserver and intraobserver agreement using the SPECT/CT software. Bland-Altman analyses showed very narrow limits of agreement. Absolute differences were below 2.0% in 96% of both interobserver and intraobserver measurements. There was a statistically significant difference between planar and SPECT/CT methods ( P < 0.001) for quantification of perfusion and ventilation for all right lung lobes, with a maximal mean absolute difference of 20.7% for the right middle lobe. There was no statistically significant difference in quantification of perfusion and ventilation for the left lung lobes using either method; however, absolute differences reached 12.0%. The total right and left lung contributions were similar for the two methods, with a mean difference of 1.2% for perfusion and 2.0% for ventilation. Conclusion: Quantification of regional lung perfusion and ventilation using SPECT/CT-based lung segmentation software is highly reproducible. This tridimensional method yields statistically significant differences in measurements for right lung lobes when compared with planar scintigraphy. We recommend that SPECT/CT-based quantification be used for all lung cancer patients undergoing pretherapy evaluation of regional lung function. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Nonlinear microscopy as diagnostic tool for the discrimination of activated T cells

NASA Astrophysics Data System (ADS)

Gavgiotaki, E.; Filippidis, G.; Zerva, I.; Agelaki, S.; Georgoulias, V.; Athanassakis, I.

2017-07-01

Third Harmonic Generation (THG) imaging was applied to mouse resting and activated T-cells. Quantification of THG signal, which corresponded to lipid droplets, could distinguish activated Tcells, allowing follow-up of immune response development.

Suitability of [18F]altanserin and PET to determine 5-HT2A receptor availability in the rat brain: in vivo and in vitro validation of invasive and non-invasive kinetic models.

PubMed

Kroll, Tina; Elmenhorst, David; Matusch, Andreas; Wedekind, Franziska; Weisshaupt, Angela; Beer, Simone; Bauer, Andreas

2013-08-01

While the selective 5-hydroxytryptamine type 2a receptor (5-HT2AR) radiotracer [18F]altanserin is well established in humans, the present study evaluated its suitability for quantifying cerebral 5-HT2ARs with positron emission tomography (PET) in albino rats. Ten Sprague Dawley rats underwent 180 min PET scans with arterial blood sampling. Reference tissue methods were evaluated on the basis of invasive kinetic models with metabolite-corrected arterial input functions. In vivo 5-HT2AR quantification with PET was validated by in vitro autoradiographic saturation experiments in the same animals. Overall brain uptake of [18F]altanserin was reliably quantified by invasive and non-invasive models with the cerebellum as reference region shown by linear correlation of outcome parameters. Unlike in humans, no lipophilic metabolites occurred so that brain activity derived solely from parent compound. PET data correlated very well with in vitro autoradiographic data of the same animals. [18F]Altanserin PET is a reliable tool for in vivo quantification of 5-HT2AR availability in albino rats. Models based on both blood input and reference tissue describe radiotracer kinetics adequately. Low cerebral tracer uptake might, however, cause restrictions in experimental usage.

Analytical Performance of a Multiplex Real-Time PCR Assay Using TaqMan Probes for Quantification of Trypanosoma cruzi Satellite DNA in Blood Samples

PubMed Central

Abate, Teresa; Cayo, Nelly M.; Parrado, Rudy; Bello, Zoraida Diaz; Velazquez, Elsa; Muñoz-Calderon, Arturo; Juiz, Natalia A.; Basile, Joaquín; Garcia, Lineth; Riarte, Adelina; Nasser, Julio R.; Ocampo, Susana B.; Yadon, Zaida E.; Torrico, Faustino; de Noya, Belkisyole Alarcón; Ribeiro, Isabela; Schijman, Alejandro G.

2013-01-01

Background The analytical validation of sensitive, accurate and standardized Real-Time PCR methods for Trypanosoma cruzi quantification is crucial to provide a reliable laboratory tool for diagnosis of recent infections as well as for monitoring treatment efficacy. Methods/Principal Findings We have standardized and validated a multiplex Real-Time quantitative PCR assay (qPCR) based on TaqMan technology, aiming to quantify T. cruzi satellite DNA as well as an internal amplification control (IAC) in a single-tube reaction. IAC amplification allows rule out false negative PCR results due to inhibitory substances or loss of DNA during sample processing. The assay has a limit of detection (LOD) of 0.70 parasite equivalents/mL and a limit of quantification (LOQ) of 1.53 parasite equivalents/mL starting from non-boiled Guanidine EDTA blood spiked with T. cruzi CL-Brener stock. The method was evaluated with blood samples collected from Chagas disease patients experiencing different clinical stages and epidemiological scenarios: 1- Sixteen Venezuelan patients from an outbreak of oral transmission, 2- Sixty three Bolivian patients suffering chronic Chagas disease, 3- Thirty four Argentinean cases with chronic Chagas disease, 4- Twenty seven newborns to seropositive mothers, 5- A seronegative receptor who got infected after transplantation with a cadaveric kidney explanted from an infected subject. Conclusions/Significance The performing parameters of this assay encourage its application to early assessment of T. cruzi infection in cases in which serological methods are not informative, such as recent infections by oral contamination or congenital transmission or after transplantation with organs from seropositive donors, as well as for monitoring Chagas disease patients under etiological treatment. PMID:23350002

Diffusion tensor spectroscopic imaging of the human brain in children and adults.

PubMed

Fotso, Kevin; Dager, Stephen R; Landow, Alec; Ackley, Elena; Myers, Orrin; Dixon, Mindy; Shaw, Dennis; Corrigan, Neva M; Posse, Stefan

2017-10-01

We developed diffusion tensor spectroscopic imaging (DTSI), based on proton-echo-planar-spectroscopic imaging (PEPSI), and evaluated the feasibility of mapping brain metabolite diffusion in adults and children. PRESS prelocalized DTSI at 3 Tesla (T) was performed using navigator-based correction of movement-related phase errors and cardiac gating with compensation for repetition time (TR) related variability in T 1 saturation. Mean diffusivity (MD) and fractional anisotropy (FA) of total N-acetyl-aspartate (tNAA), total creatine (tCr), and total choline (tCho) were measured in eight adults (17-60 years) and 10 children (3-24 months) using b max  = 1734 s/mm 2 , 1 cc and 4.5 cc voxel sizes, with nominal scan times of 17 min and 8:24 min. Residual movement-related phase encoding ghosting (PEG) was used as a regressor across scans to correct overestimation of MD. After correction for PEG, metabolite slice-averaged MD estimated at 20% PEG were lower (P < 0.042) for adults (0.17/0.20/0.18 × 10 -3 mm 2 /s) than for children (0.26/0.27/0.24 × 10 -3 mm 2 /s). Extrapolated to 0% PEG, the MD estimates decreased further (0.09/0.11/0.11 × 10 -3 mm 2 /s versus 0.15/0.16/0.15 × 10 -3 mm 2 /s). Slice-averaged FA of tNAA (P = 0.049), tCr (P = 0.067), and tCho (P = 0.003) were higher in children. This high-speed DTSI approach with PEG regression allows for estimation of metabolite MD and FA with improved tolerance to movement. Our preliminary data suggesting age-related changes support DTSI as a sensitive technique for investigating intracellular markers of biological processes. Magn Reson Med 78:1246-1256, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Automated lobar quantification of emphysema in patients with severe COPD.

PubMed

Revel, Marie-Pierre; Faivre, Jean-Baptiste; Remy-Jardin, Martine; Deken, Valérie; Duhamel, Alain; Marquette, Charles-Hugo; Tacelli, Nunzia; Bakai, Anne-Marie; Remy, Jacques

2008-12-01

Automated lobar quantification of emphysema has not yet been evaluated. Unenhanced 64-slice MDCT was performed in 47 patients evaluated before bronchoscopic lung-volume reduction. CT images reconstructed with a standard (B20) and high-frequency (B50) kernel were analyzed using a dedicated prototype software (MevisPULMO) allowing lobar quantification of emphysema extent. Lobar quantification was obtained following (a) a fully automatic delineation of the lobar limits by the software and (b) a semiautomatic delineation with manual correction of the lobar limits when necessary and was compared with the visual scoring of emphysema severity per lobe. No statistically significant difference existed between automated and semiautomated lobar quantification (p > 0.05 in the five lobes), with differences ranging from 0.4 to 3.9%. The agreement between the two methods (intraclass correlation coefficient, ICC) was excellent for left upper lobe (ICC = 0.94), left lower lobe (ICC = 0.98), and right lower lobe (ICC = 0.80). The agreement was good for right upper lobe (ICC = 0.68) and moderate for middle lobe (IC = 0.53). The Bland and Altman plots confirmed these results. A good agreement was observed between the software and visually assessed lobar predominance of emphysema (kappa 0.78; 95% CI 0.64-0.92). Automated and semiautomated lobar quantifications of emphysema are concordant and show good agreement with visual scoring.

Fast mapping of the T2 relaxation time of cerebral metabolites using proton echo-planar spectroscopic imaging (PEPSI).

PubMed

Tsai, Shang-Yueh; Posse, Stefan; Lin, Yi-Ru; Ko, Cheng-Wen; Otazo, Ricardo; Chung, Hsiao-Wen; Lin, Fa-Hsuan

2007-05-01

Metabolite T2 is necessary for accurate quantification of the absolute concentration of metabolites using long-echo-time (TE) acquisition schemes. However, lengthy data acquisition times pose a major challenge to mapping metabolite T2. In this study we used proton echo-planar spectroscopic imaging (PEPSI) at 3T to obtain fast T2 maps of three major cerebral metabolites: N-acetyl-aspartate (NAA), creatine (Cre), and choline (Cho). We showed that PEPSI spectra matched T2 values obtained using single-voxel spectroscopy (SVS). Data acquisition for 2D metabolite maps with a voxel volume of 0.95 ml (32 x 32 image matrix) can be completed in 25 min using five TEs and eight averages. A sufficient spectral signal-to-noise ratio (SNR) for T2 estimation was validated by high Pearson's correlation coefficients between logarithmic MR signals and TEs (R2 = 0.98, 0.97, and 0.95 for NAA, Cre, and Cho, respectively). In agreement with previous studies, we found that the T2 values of NAA, but not Cre and Cho, were significantly different between gray matter (GM) and white matter (WM; P < 0.001). The difference between the T2 estimates of the PEPSI and SVS scans was less than 9%. Consistent spatial distributions of T2 were found in six healthy subjects, and disagreement among subjects was less than 10%. In summary, the PEPSI technique is a robust method to obtain fast mapping of metabolite T2. (c) 2007 Wiley-Liss, Inc.

Correction of the equilibrium temperature caused by slight evaporation of water in protein crystal growth cells during long-term space experiments at International Space Station.

PubMed

Fujiwara, Takahisa; Suzuki, Yoshihisa; Yoshizaki, Izumi; Tsukamoto, Katsuo; Murayama, Kenta; Fukuyama, Seijiro; Hosokawa, Kouhei; Oshi, Kentaro; Ito, Daisuke; Yamazaki, Tomoya; Tachibana, Masaru; Miura, Hitoshi

2015-08-01

The normal growth rates of the {110} faces of tetragonal hen egg-white lysozyme crystals, R, were measured as a function of the supersaturation σ parameter using a reflection type interferometer under μG at the International Space Station (NanoStep Project). Since water slightly evaporated from in situ observation cells during a long-term space station experiment for several months, equilibrium temperature T(e) changed, and the actual σ, however, significantly increased mainly due to the increase in salt concentration C(s). To correct σ, the actual C(s) and protein concentration C(p), which correctly represent the measured T(e) value in space, were first calculated. Second, a new solubility curve with the corrected C(s) was plotted. Finally, the revised σ was obtained from the new solubility curve. This correction method successfully revealed that the 2.8% water was evaporated from the solution, leading to 2.8% increase in the C(s) and C(p) of the solution.

High resolution T2(*)-weighted Magnetic Resonance Imaging at 3 Tesla using PROPELLER-EPI.

PubMed

Krämer, Martin; Reichenbach, Jürgen R

2014-05-01

We report the application of PROPELLER-EPI for high resolution T2(*)-weighted imaging with sub-millimeter in-plane resolution on a clinical 3 Tesla scanner. Periodically rotated blades of a long-axis PROPELLER-EPI sequence were acquired with fast gradient echo readout and acquisition matrix of 320 × 50 per blade. Images were reconstructed by using 2D-gridding, phase and geometric distortion correction and compensation of resonance frequency drifts that occurred during extended measurements. To characterize these resonance frequency offsets, short FID calibration measurements were added to the PROPELLER-EPI sequence. Functional PROPELLER-EPI was performed with volunteers using a simple block design of right handed finger tapping. Results indicate that PROPELLER-EPI can be employed for fast, high resolution T2(*)-weighted imaging provided geometric distortions and possible resonance frequency drifts are properly corrected. Even small resonance frequency drifts below 10 Hz as well as non-corrected geometric distortions degraded image quality substantially. In the initial fMRI experiment image quality and signal-to-noise ratio was sufficient for obtaining high resolution functional activation maps. Copyright © 2014. Published by Elsevier GmbH.

Metabolite-cycled STEAM and semi-LASER localization for MR spectroscopy of the human brain at 9.4T.

PubMed

Giapitzakis, Ioannis-Angelos; Shao, Tingting; Avdievich, Nikolai; Mekle, Ralf; Kreis, Roland; Henning, Anke

2018-04-01

Metabolite cycling (MC) is an MRS technique for the simultaneous acquisition of water and metabolite spectra that avoids chemical exchange saturation transfer effects and for which water may serve as a reference signal or contain additional information in functional or diffusion studies. Here, MC was developed for human investigations at ultrahigh field. MC-STEAM and MC-semi-LASER are introduced at 9.4T with an optimized inversion pulse and elaborate coil setup. Experimental and simulation results are given for the implementation of adiabatic inversion pulses for MC. The two techniques are compared, and the effect of frequency and phase correction based on the MC water spectra is evaluated. Finally, absolute quantification of metabolites is performed. The proposed coil configuration results in a maximum B1 + of 48 μΤ in a voxel within the occipital lobe. Frequency and phase correction of single acquisitions improve signal-to-noise ratio (SNR) and linewidth, leading to high-resolution spectra. The improvement of SNR of N-acetylaspartate (SNR NAA ) for frequency aligned data, acquired with MC-STEAM and MC-semi-LASER, are 37% and 30%, respectively (P < 0.05). Moreover, a doubling of the SNR NAA for MC-semi-LASER in comparison with MC-STEAM is observed (P < 0.05). Concentration levels for 18 metabolites from the human occipital lobe are reported, as acquired with both MC-STEAM and MC-semi-LASER. This work introduces a novel methodology for single-voxel MRS on a 9.4T whole-body scanner and highlights the advantages of semi-LASER compared to STEAM in terms of excitation profile. In comparison with MC-STEAM, MC-semi-LASER yields spectra with higher SNR. Magn Reson Med 79:1841-1850, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Evaluation of the new capture vapourizer for aerosol mass spectrometers (AMS) through laboratory studies of inorganic species

DOE PAGES

Hu, Weiwei; Campuzano-Jost, Pedro; Day, Douglas A.; ...

2017-08-15

Aerosol mass spectrometers (AMSs) and Aerosol Chemical Speciation Monitors (ACSMs) commercialized by Aerodyne are widely used to measure the non-refractory species in submicron particles. With the standard vapourizer (SV) that is installed in all commercial instruments to date, the quantification of ambient aerosol mass concentration requires the use of the collection efficiency (CE) to correct for the loss of particles due to bounce. A new capture vapourizer (CV) has been designed to reduce the need for a bounce-related CE correction. Two high-resolution AMS instruments, one with a SV and one with a CV, were operated side by side in themore » laboratory. Four standard species, NH 4NO 3, NaNO 3, (NH 4) 2SO 4 and NH 4Cl, which typically constitute the majority of the mass of ambient submicron inorganic species, are studied. The effect of vapourizer temperature ( T v ∼ 200–800 °C) on the detected fragments, CE and size distributions are investigated. A T v of 500–550 °C for the CV is recommended. In the CV, CE was identical (around unity) for more volatile species (e.g. NH 4NO 3) and comparable to or higher than the SV for less-volatile species (e.g. (NH 4) 2SO 4), demonstrating an improvement in CE for laboratory inorganic species in the CV. The detected relative intensities of fragments of NO 3 and SO 4 species observed with the CV are different from those observed with the SV, and are consistent with additional thermal decomposition arising from the increased residence time and multiple collisions. Increased residence times with the CV also lead to broader particle size distribution measurements than with the SV. A method for estimating whether pure species will be detected in AMS sizing mode is proposed. Production of CO 2(g) from sampled nitrate on the vapourizer surface, which has been reported for the SV, is negligible for the CV for NH 4NO 3 and comparable to the SV for NaNO 3. . We observe an extremely consistent fragmentation for ammonium compared to very large changes for the associated anions. Together with other evidence, this indicates that it is unlikely that a major fraction of inorganic species vapourizes as intact salts in the AMS.« less

Evaluation of the new capture vapourizer for aerosol mass spectrometers (AMS) through laboratory studies of inorganic species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Weiwei; Campuzano-Jost, Pedro; Day, Douglas A.

Aerosol mass spectrometers (AMSs) and Aerosol Chemical Speciation Monitors (ACSMs) commercialized by Aerodyne are widely used to measure the non-refractory species in submicron particles. With the standard vapourizer (SV) that is installed in all commercial instruments to date, the quantification of ambient aerosol mass concentration requires the use of the collection efficiency (CE) to correct for the loss of particles due to bounce. A new capture vapourizer (CV) has been designed to reduce the need for a bounce-related CE correction. Two high-resolution AMS instruments, one with a SV and one with a CV, were operated side by side in themore » laboratory. Four standard species, NH 4NO 3, NaNO 3, (NH 4) 2SO 4 and NH 4Cl, which typically constitute the majority of the mass of ambient submicron inorganic species, are studied. The effect of vapourizer temperature ( T v ∼ 200–800 °C) on the detected fragments, CE and size distributions are investigated. A T v of 500–550 °C for the CV is recommended. In the CV, CE was identical (around unity) for more volatile species (e.g. NH 4NO 3) and comparable to or higher than the SV for less-volatile species (e.g. (NH 4) 2SO 4), demonstrating an improvement in CE for laboratory inorganic species in the CV. The detected relative intensities of fragments of NO 3 and SO 4 species observed with the CV are different from those observed with the SV, and are consistent with additional thermal decomposition arising from the increased residence time and multiple collisions. Increased residence times with the CV also lead to broader particle size distribution measurements than with the SV. A method for estimating whether pure species will be detected in AMS sizing mode is proposed. Production of CO 2(g) from sampled nitrate on the vapourizer surface, which has been reported for the SV, is negligible for the CV for NH 4NO 3 and comparable to the SV for NaNO 3. . We observe an extremely consistent fragmentation for ammonium compared to very large changes for the associated anions. Together with other evidence, this indicates that it is unlikely that a major fraction of inorganic species vapourizes as intact salts in the AMS.« less

qRT-PCR quantification of the biological control agent Trichoderma harzianum in peat and compost-based growing media.

PubMed

Beaulieu, Robert; López-Mondéjar, Rubén; Tittarelli, Fabio; Ros, Margarita; Pascual, José Antonio

2011-02-01

To ensure proper use of Trichoderma harzianum in agriculture, accurate data must be obtained in population monitoring. The effectiveness of qRT-PCR to quantify T. harzianum in different growing media was compared to the commonly used techniques of colony counting and qPCR. Results showed that plate counting and qPCR offered similar T. harzianum quantification patterns of an initial rapid increase in fungal population that decreased over time. However, data from qRT-PCR showed a population curve of active T. harzianum with a delayed onset of initial growth which then increased throughout the experiment. Results demonstrated that T. harzianum can successfully grow in these media and that qRT-PCR can offer a more distinct representation of active T. harzianum populations. Additionally, compost amended with T. harzianum exhibited a lower Fusarium oxysporum infection rate (67%) and lower percentage of fresh weight loss (11%) in comparison to amended peat (90% infection rate, 23% fresh weight loss). Copyright © 2010 Elsevier Ltd. All rights reserved.

Classification and quantification of solar wind driver gases leading to intense geomagnetic storms

NASA Astrophysics Data System (ADS)

Adekoya, B. J.; Chukwuma, V. U.

2018-01-01

Classification and quantification of the interplanetary structures causing intense geomagnetic storms (Dst ≤ -100 nT) that occurred during 1997-2016 are studied. The subject of this consists of solar wind parameters of seventy-three intense storms that are associated with the southward interplanetary magnetic field. About 30.14% of the storms were driven by a combination of the sheath and ejecta (S + E), magnetic clouds (MC) and sheath field (S) are 26% each, 10.96% by combined sheath and MCs (S + C), while 5.48% of the storms were driven by ejecta (E) alone. Therefore, we want to aver that for storms driven by: (1) S + E. The Bz is high (≥10 nT), high density (ρ) (>10 N/cm3), high plasma beta (β) (>0.8), and unspecified (i.e. high or low) structure of the plasma temperature (T) and the flow speed (V); (2) MC. The Bz is ≥10 nT, low temperature (T ≤ 400,000 K), low ρ (≤10 N/cm3), high V (≥450 km), and low β (≤0.8); (3) The structures of S + C are similar to that of MC except that the V is low (V ≤ 450 km); (4) S. The Bz is high, low T, high ρ, unspecified V, and low β; and (5) E. Is when the structures are directly opposite of the one driven by MCs except for high V. Although, westward ring current indicates intense storms, but the large intensity of geomagnetic storms is determined by the intense nature of the electric field strength and the Bz. Therefore, great storms (i.e. Dst ≤ -200 nT) are manifestation of high electric field strength (≥13 mV/m).

Hepatic fat quantification magnetic resonance for monitoring treatment response in pediatric nonalcoholic steatohepatitis.

PubMed

Koh, Hong; Kim, Seung; Kim, Myung-Joon; Kim, Hyun Gi; Shin, Hyun Joo; Lee, Mi-Jung

2015-09-07

To evaluate the possibility of treatment effect monitoring using hepatic fat quantification magnetic resonance (MR) in pediatric nonalcoholic steatohepatitis (NASH). We retrospectively reviewed the medical records of patients who received educational recommendations and vitamin E for NASH and underwent hepatic fat quantification MR from 2011 to 2013. Hepatic fat fraction (%) was measured using dual- and triple-echo gradient-recalled-echo sequences at 3T. The compliant and non-compliant groups were compared clinically, biochemically, and radiologically. Twenty seven patients (M:F = 24:3; mean age: 12 ± 2.3 years) were included (compliant group = 22, non-compliant = 5). None of the baseline findings differed between the 2 groups, except for triglyceride level (compliant vs non-compliant, 167.7 mg/dL vs 74.2 mg/dL, P = 0.001). In the compliant group, high-density lipoprotein increased and all other parameters decreased after 1-year follow-up. However, there were various changes in the non-compliant group. Dual-echo fat fraction (-19.2% vs 4.6, P < 0.001), triple-echo fat fraction (-13.4% vs 3.5, P < 0.001), alanine aminotransferase (-110.7 IU/L vs -10.6 IU/L, P = 0.047), total cholesterol (-18.1 mg/dL vs 3.8 mg/dL, P = 0.016), and triglyceride levels (-61.3 mg/dL vs 11.2 mg/dL, P = 0.013) were significantly decreased only in the compliant group. The change in body mass index and dual-echo fat fraction showed a positive correlation (ρ = 0.418, P = 0.030). Hepatic fat quantification MR can be a non-invasive, quantitative and useful tool for monitoring treatment effects in pediatric NASH.

Fat fraction bias correction using T1 estimates and flip angle mapping.

PubMed

Yang, Issac Y; Cui, Yifan; Wiens, Curtis N; Wade, Trevor P; Friesen-Waldner, Lanette J; McKenzie, Charles A

2014-01-01

To develop a new method of reducing T1 bias in proton density fat fraction (PDFF) measured with iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL). PDFF maps reconstructed from high flip angle IDEAL measurements were simulated and acquired from phantoms and volunteer L4 vertebrae. T1 bias was corrected using a priori T1 values for water and fat, both with and without flip angle correction. Signal-to-noise ratio (SNR) maps were used to measure precision of the reconstructed PDFF maps. PDFF measurements acquired using small flip angles were then compared to both sets of corrected large flip angle measurements for accuracy and precision. Simulations show similar results in PDFF error between small flip angle measurements and corrected large flip angle measurements as long as T1 estimates were within one standard deviation from the true value. Compared to low flip angle measurements, phantom and in vivo measurements demonstrate better precision and accuracy in PDFF measurements if images were acquired at a high flip angle, with T1 bias corrected using T1 estimates and flip angle mapping. T1 bias correction of large flip angle acquisitions using estimated T1 values with flip angle mapping yields fat fraction measurements of similar accuracy and superior precision compared to low flip angle acquisitions. Copyright © 2013 Wiley Periodicals, Inc.

Long-term treatment effects of the FR-2 appliance: a prospective evalution 7 years post-treatment

PubMed Central

Franchi, Lorenzo; Cevidanes, Lucia H. S.; Scanavini, Marco A.; McNamara, James A.

2014-01-01

AIM To examine the long-term effects induced by treatment with the function regulator (FR-2) appliance 7 years post-treatment compared with untreated class II subjects. SUBJECTS AND METHODS The FR-2 sample was collected prospectively and comprised 17 subjects (10 boys and 7 girls, mean age 10.8 years) who were treated with the FR-2 appliance for 1.7 years and re-evaluated 7.1 years after treatment. The step-by-step mandibular advancement was performed gradually (increments up to 3–4 mm), until a ‘super class I’ molar relationship was obtained. The control group consisted of 17 class II subjects (9 boys and 8 girls, mean age 11.3 years) with class II malocclusion, excessive overjet, and class II molar relationship, matched to the treated group as to ages at all times, gender distribution, and stages of skeletal maturity (evaluated by the cervical vertebral maturation method). The lateral cephalograms were analysed at T1 (initial), T2 (final), and T3 (7.1 years post-treatment). The compatibility between the groups and the comparisons of their changes at T1–T2, T2–T3, and T1–T3 intervals were examined by independent sample t-tests (P < 0.05). RESULTS FR-2 treatment provided a significant improvement in the maxillomandibular relationship due to an increase in mandibular length compared with controls, which remained stable over time. Also overjet, overbite, and molar relationship corrections demonstrated stability. Among dentoalveolar changes, only the increased mesial movement of the mandibular molars in the FR-2 group demonstrated stability. CONCLUSIONS Correction of class II malocclusion remained stable 7 years after FR-2 treatment mainly due to the stability of the skeletal changes. PMID:23736378

Integrated PET/MR breast cancer imaging: Attenuation correction and implementation of a 16-channel RF coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oehmigen, Mark, E-mail: mark.oehmigen@uni-due.de

Purpose: This study aims to develop, implement, and evaluate a 16-channel radiofrequency (RF) coil for integrated positron emission tomography/magnetic resonance (PET/MR) imaging of breast cancer. The RF coil is designed for optimized MR imaging performance and PET transparency and attenuation correction (AC) is applied for accurate PET quantification. Methods: A 16-channel breast array RF coil was designed for integrated PET/MR hybrid imaging of breast cancer lesions. The RF coil features a lightweight rigid design and is positioned with a spacer at a defined position on the patient table of an integrated PET/MR system. Attenuation correction is performed by generating andmore » applying a dedicated 3D CT-based template attenuation map. Reposition accuracy of the RF coil on the system patient table while using the positioning frame was tested in repeated measurements using MR-visible markers. The MR, PET, and PET/MR imaging performances were systematically evaluated using modular breast phantoms. Attenuation correction of the RF coil was evaluated with difference measurements of the active breast phantoms filled with radiotracer in the PET detector with and without the RF coil in place, serving as a standard of reference measurement. The overall PET/MR imaging performance and PET quantification accuracy of the new 16-channel RF coil and its AC were then evaluated in first clinical examinations on ten patients with local breast cancer. Results: The RF breast array coil provides excellent signal-to-noise ratio and signal homogeneity across the volume of the breast phantoms in MR imaging and visualizes small structures in the phantoms down to 0.4 mm in plane. Difference measurements with PET revealed a global loss and thus attenuation of counts by 13% (mean value across the whole phantom volume) when the RF coil is placed in the PET detector. Local attenuation ranging from 0% in the middle of the phantoms up to 24% was detected in the peripheral regions of the phantoms at positions closer to attenuating hardware structures of the RF coil. The position accuracy of the RF coil on the patient table when using the positioning frame was determined well below 1 mm for all three spatial dimensions. This ensures perfect position match between the RF coil and its three-dimensional attenuation template during the PET data reconstruction process. When applying the CT-based AC of the RF coil, the global attenuation bias was mostly compensated to ±0.5% across the entire breast imaging volume. The patient study revealed high quality MR, PET, and combined PET/MR imaging of breast cancer. Quantitative activity measurements in all 11 breast cancer lesions of the ten patients resulted in increased mean difference values of SUV{sub max} 11.8% (minimum 3.2%; maximum 23.2%) between nonAC images and images when AC of the RF breast coil was applied. This supports the quantitative results of the phantom study as well as successful attenuation correction of the RF coil. Conclusions: A 16-channel breast RF coil was designed for optimized MR imaging performance and PET transparency and was successfully integrated with its dedicated attenuation correction template into a whole-body PET/MR system. Systematic PET/MR imaging evaluation with phantoms and an initial study on patients with breast cancer provided excellent MR and PET image quality and accurate PET quantification.« less

Enhanced processing of threat stimuli under limited attentional resources.

PubMed

De Martino, Benedetto; Kalisch, Raffael; Rees, Geraint; Dolan, Raymond J

2009-01-01

The ability to process stimuli that convey potential threat, under conditions of limited attentional resources, confers adaptive advantages. This study examined the neurobiology underpinnings of this capacity. Employing an attentional blink paradigm, in conjunction with functional magnetic resonance imaging, we manipulated the salience of the second of 2 face target stimuli (T2), by varying emotionality. Behaviorally, fearful T2 faces were identified significantly more than neutral faces. Activity in fusiform face area increased with correct identification of T2 faces. Enhanced activity in rostral anterior cingulate cortex (rACC) accounted for the benefit in detection of fearful stimuli reflected in a significant interaction between target valence and correct identification. Thus, under conditions of limited attention resources activation in rACC correlated with enhanced processing of emotional stimuli. We suggest that these data support a model in which a prefrontal "gate" mechanism controls conscious access of emotional information under conditions of limited attentional resources.

QCD corrections to decay-lepton polar and azimuthal angular distributions in e+e- --> tt(bar) in the soft-gluon approximation

NASA Astrophysics Data System (ADS)

Rindani, Saurabh D.

2002-04-01

QCD corrections to order as in the soft-gluon approximation to angular distributions of decay charged leptons in the process e+e- --> t t(bar), followed by semileptonic decay of t or t(bar), are obtained in the e+e- centre-of-mass frame. As compared to distributions in the top rest frame, these have the advantage that they would allow direct comparison with experiment without the need to reconstruct the top rest frame. The results also do not depend on the choice of a spin quantization axis for t or t (bar). Analytic expression for the triple distribution in the polar angle of t and polar and azimuthal angles of the lepton is obtained. Analytic expression is also derived for the distribution in the charged-lepton polar angle. Numerical values are discussed for (s) 1/2 = 400, 800 and 1500 GeV.

Flow harmonics from self-consistent particlization of a viscous fluid

NASA Astrophysics Data System (ADS)

Wolff, Zack; Molnar, Denes

2017-10-01

The quantitative extraction of quark-gluon plasma (QGP) properties from heavy-ion data, such as its specific shear viscosity η /s , typically requires comparison to viscous hydrodynamic or "hybrid" hydrodynamics + transport simulations. In either case, one has to convert the fluid to hadrons, yet without additional theory input the conversion is ambiguous for dissipative fluids. Here, shear viscous phase-space corrections calculated using linearized transport theory are applied in Cooper-Frye freeze-out to quantify the effects on anisotropic flow coefficients vn(pT) at the energies available at both the BNL Relativistic Heavy Ion Collider and the CERN Large Hadron Collider. Expanding upon our previous flow harmonics studies [D. Molnar and Z. Wolff, Phys. Rev. C 95, 024903 (2017), 10.1103/PhysRevC.95.024903; Z. Wolff and D. Molnar, J. Phys.: Conf. Ser. 535, 012020 (2014), 10.1088/1742-6596/535/1/012020], we calculate pion and proton v2(pT) , v4(pT) , and v6(pT) , but here we incorporate a hadron gas that is chemically frozen below a temperature of 175 MeV and use hypersurfaces from realistic viscous hydrodynamic simulations. For additive quark model cross sections and relative phase-space corrections with p3 /2 momentum dependence rather than the quadratic Grad form, we find at moderately high transverse momentum noticeably higher v4(pT) and v6(pT) for protons than for pions. In addition, the value of η /s deduced from elliptic flow data differs by nearly 50% from the value extracted using the naive "democratic Grad" form of freeze-out distributions. To facilitate the use of the self-consistent viscous corrections calculated here in hydrodynamic and hybrid calculations, we also present convenient parametrizations of the corrections for the various hadron species.

SU-E-J-233: Effect of Brachytherapy Seed Artifacts in T2 and Proton Density Maps in MR Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mashouf, S; University of Toronto, Dept of Radiation Oncology, Toronto, Ontario; Fatemi-Ardekani, A

Purpose: This study aims at investigating the influence of brachytherapy seeds on T2 and proton density (PD) maps generated from MR images. Proton density maps can be used to extract water content. Since dose absorbed in tissue surrounding low energy brachytherapy seeds are highly influenced by tissue composition, knowing the water content is a first step towards implementing a heterogeneity correction algorithm using MR images. Methods: An LDR brachytherapy (IsoAid Advantage Pd-103) seed was placed in the middle of an agar-based gel phantom and imaged using a 3T Philips MR scanner with a 168-channel head coil. A multiple echo sequencemore » with TE=20, 40, 60, 80, 100 (ms) with large repetition time (TR=6259ms) was used to extract T2 and PD maps. Results: Seed artifacts were considerably reduced on T2 maps compared to PD maps. The variation of PD around the mean was obtained as −97% to 125% (±1%) while for T2 it was recorded as −71% to 24% (±1%). Conclusion: PD maps which are required for heterogeneity corrections are susceptible to artifacts from seeds. Seed artifacts on T2 maps, however, are significantly reduced due to not being sensitive to B0 field variation.« less

The image evaluation of iterative motion correction reconstruction algorithm PROPELLER T2-weighted imaging compared with MultiVane T2-weighted imaging

NASA Astrophysics Data System (ADS)

Lee, Suk-Jun; Yu, Seung-Man

2017-08-01

The purpose of this study was to evaluate the usefulness and clinical applications of MultiVaneXD which was applying iterative motion correction reconstruction algorithm T2-weighted images compared with MultiVane images taken with a 3T MRI. A total of 20 patients with suspected pathologies of the liver and pancreatic-biliary system based on clinical and laboratory findings underwent upper abdominal MRI, acquired using the MultiVane and MultiVaneXD techniques. Two reviewers analyzed the MultiVane and MultiVaneXD T2-weighted images qualitatively and quantitatively. Each reviewer evaluated vessel conspicuity by observing motion artifacts and the sharpness of the portal vein, hepatic vein, and upper organs. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated by one reviewer for quantitative analysis. The interclass correlation coefficient was evaluated to measure inter-observer reliability. There were significant differences between MultiVane and MultiVaneXD in motion artifact evaluation. Furthermore, MultiVane was given a better score than MultiVaneXD in abdominal organ sharpness and vessel conspicuity, but the difference was insignificant. The reliability coefficient values were over 0.8 in every evaluation. MultiVaneXD (2.12) showed a higher value than did MultiVane (1.98), but the difference was insignificant ( p = 0.135). MultiVaneXD is a motion correction method that is more advanced than MultiVane, and it produced an increased SNR, resulting in a greater ability to detect focal abdominal lesions.

75 FR 44901 - Extended Carryback of Losses to or From a Consolidated Group; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-30

.... 7805 * * * 0 Par. 2. Section 1.1502-21T(b)(3)(v) is amended by revising paragraphs (B), (C)(1), (C)(2...: Grid Glyer, (202) 622-7930 (not a toll-free number). SUPPLEMENTARY INFORMATION: Background The final... in 26 CFR Part 1 Income taxes, Reporting and recordkeeping requirements. Correction of Publication 0...

Analyzing diffuse scattering with supercomputers. Corrigendum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michels-Clark, Tara M.; Lynch, Vickie E.; Hoffmann, Christina M.

2016-03-01

The study by Michels-Clark et al. (2013 [Michels-Clark, T. M., Lynch, V. E., Hoffmann, C. M., Hauser, J., Weber, T., Harrison, R. & Bürgi, H. B. (2013). J. Appl. Cryst. 46, 1616-1625.]) contains misleading errors which are corrected here. The numerical results reported in that paper and the conclusions given there are not affected and remain unchanged. The transition probabilities in Table 1 (rows 4, 5, 7, 8) and Fig. 2 (rows 1 and 2) of the original paper were different from those used in the numerical calculations. Corrected transition probabilities as used in the computations are given in Tablemore » 1 and Fig. 1 of this article. The Δ parameter in the stacking model expresses the preference for the fifth layer in a five-layer stack to be eclipsed with respect to the first layer. This statement corrects the original text on p. 1622, lines 4–7. In the original Fig. 2 the helicity of the layer stacks b L and b R in rows 3 and 4 had been given as opposite to those in rows 1, 2 and 5. Fig. 1 of this article shows rows 3 and 4 corrected to correspond to rows 1, 2 and 5.« less

Qualitative and quantitative analysis of milk for the detection of adulteration by Laser Induced Breakdown Spectroscopy (LIBS).

PubMed

Moncayo, S; Manzoor, S; Rosales, J D; Anzano, J; Caceres, J O

2017-10-01

The present work focuses on the development of a fast and cost effective method based on Laser Induced Breakdown Spectroscopy (LIBS) to the quality control, traceability and detection of adulteration in milk. Two adulteration cases have been studied; a qualitative analysis for the discrimination between different milk blends and quantification of melamine in adulterated toddler milk powder. Principal Component Analysis (PCA) and neural networks (NN) have been used to analyze LIBS spectra obtaining a correct classification rate of 98% with a 100% of robustness. For the quantification of melamine, two methodologies have been developed; univariate analysis using CN emission band and multivariate calibration NN model obtaining correlation coefficient (R 2 ) values of 0.982 and 0.999 respectively. The results of the use of LIBS technique coupled with chemometric analysis are discussed in terms of its potential use in the food industry to perform the quality control of this dairy product. Copyright © 2017 Elsevier Ltd. All rights reserved.

SU-E-J-215: Towards MR-Only Image Guided Identification of Calcifications and Brachytherapy Seeds: Application to Prostate and Breast LDR Implant Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elzibak, A; Fatemi-Ardekani, A; Soliman, A

Purpose: To identify and analyze the appearance of calcifications and brachytherapy seeds on magnitude and phase MRI images and to investigate whether they can be distinguished from each other on corrected phase images for application to prostate and breast low dose rate (LDR) implant dosimetry. Methods: An agar-based gel phantom containing two LDR brachytherapy seeds (Advantage Pd-103, IsoAid, 0.8mm diameter, 4.5mm length) and two spherical calcifications (large: 7mm diameter and small: 4mm diameter) was constructed and imaged on a 3T Philips MR scanner using a 16-channel head coil and a susceptibility weighted imaging (SWI) sequence (2mm slices, 320mm FOV, TR/more » TE= 26.5/5.3ms, 15 degree flip angle). The phase images were unwrapped and corrected using a 32×32, 2D Hanning high pass filter to remove background phase noise. Appearance of the seeds and calcifications was assessed visually and quantitatively using Osirix (http://www.osirix-viewer.com/). Results: As expected, calcifications and brachytherapy seeds appeared dark (hypointense) relative to the surrounding gel on the magnitude MRI images. The diameter of each seed without the surrounding artifact was measured to be 0.1 cm on the magnitude image, while diameters of 0.79 and 0.37 cm were measured for the larger and smaller calcifications, respectively. On the corrected phase images, the brachytherapy seeds and the calcifications appeared bright (hyperintense). The diameter of the seeds was larger on the phase images (0.17 cm) likely due to the dipole effect. Conclusion: MRI has the best soft tissue contrast for accurate organ delineation leading to most accurate implant dosimetry. This work demonstrated that phase images can potentially be useful in identifying brachytherapy seeds and calcifications in the prostate and breast due to their bright appearance, which helps in their visualization and quantification for accurate dosimetry using MR-only. Future work includes optimizing phase filters to best identify and delineate seeds and calcifications.« less

Accurate computer-aided quantification of left ventricular parameters: experience in 1555 cardiac magnetic resonance studies from the Framingham Heart Study.

PubMed

Hautvast, Gilion L T F; Salton, Carol J; Chuang, Michael L; Breeuwer, Marcel; O'Donnell, Christopher J; Manning, Warren J

2012-05-01

Quantitative analysis of short-axis functional cardiac magnetic resonance images can be performed using automatic contour detection methods. The resulting myocardial contours must be reviewed and possibly corrected, which can be time-consuming, particularly when performed across all cardiac phases. We quantified the impact of manual contour corrections on both analysis time and quantitative measurements obtained from left ventricular short-axis cine images acquired from 1555 participants of the Framingham Heart Study Offspring cohort using computer-aided contour detection methods. The total analysis time for a single case was 7.6 ± 1.7 min for an average of 221 ± 36 myocardial contours per participant. This included 4.8 ± 1.6 min for manual contour correction of 2% of all automatically detected endocardial contours and 8% of all automatically detected epicardial contours. However, the impact of these corrections on global left ventricular parameters was limited, introducing differences of 0.4 ± 4.1 mL for end-diastolic volume, -0.3 ± 2.9 mL for end-systolic volume, 0.7 ± 3.1 mL for stroke volume, and 0.3 ± 1.8% for ejection fraction. We conclude that left ventricular functional parameters can be obtained under 5 min from short-axis functional cardiac magnetic resonance images using automatic contour detection methods. Manual correction more than doubles analysis time, with minimal impact on left ventricular volumes and ejection fraction. Copyright © 2011 Wiley Periodicals, Inc.

Particle Tracking Facilitates Real Time Capable Motion Correction in 2D or 3D Two-Photon Imaging of Neuronal Activity.

PubMed

Aghayee, Samira; Winkowski, Daniel E; Bowen, Zachary; Marshall, Erin E; Harrington, Matt J; Kanold, Patrick O; Losert, Wolfgang

2017-01-01

The application of 2-photon laser scanning microscopy (TPLSM) techniques to measure the dynamics of cellular calcium signals in populations of neurons is an extremely powerful technique for characterizing neural activity within the central nervous system. The use of TPLSM on awake and behaving subjects promises new insights into how neural circuit elements cooperatively interact to form sensory perceptions and generate behavior. A major challenge in imaging such preparations is unavoidable animal and tissue movement, which leads to shifts in the imaging location (jitter). The presence of image motion can lead to artifacts, especially since quantification of TPLSM images involves analysis of fluctuations in fluorescence intensities for each neuron, determined from small regions of interest (ROIs). Here, we validate a new motion correction approach to compensate for motion of TPLSM images in the superficial layers of auditory cortex of awake mice. We use a nominally uniform fluorescent signal as a secondary signal to complement the dynamic signals from genetically encoded calcium indicators. We tested motion correction for single plane time lapse imaging as well as multiplane (i.e., volume) time lapse imaging of cortical tissue. Our procedure of motion correction relies on locating the brightest neurons and tracking their positions over time using established techniques of particle finding and tracking. We show that our tracking based approach provides subpixel resolution without compromising speed. Unlike most established methods, our algorithm also captures deformations of the field of view and thus can compensate e.g., for rotations. Object tracking based motion correction thus offers an alternative approach for motion correction, one that is well suited for real time spike inference analysis and feedback control, and for correcting for tissue distortions.

Particle Tracking Facilitates Real Time Capable Motion Correction in 2D or 3D Two-Photon Imaging of Neuronal Activity

PubMed Central

Aghayee, Samira; Winkowski, Daniel E.; Bowen, Zachary; Marshall, Erin E.; Harrington, Matt J.; Kanold, Patrick O.; Losert, Wolfgang

2017-01-01

The application of 2-photon laser scanning microscopy (TPLSM) techniques to measure the dynamics of cellular calcium signals in populations of neurons is an extremely powerful technique for characterizing neural activity within the central nervous system. The use of TPLSM on awake and behaving subjects promises new insights into how neural circuit elements cooperatively interact to form sensory perceptions and generate behavior. A major challenge in imaging such preparations is unavoidable animal and tissue movement, which leads to shifts in the imaging location (jitter). The presence of image motion can lead to artifacts, especially since quantification of TPLSM images involves analysis of fluctuations in fluorescence intensities for each neuron, determined from small regions of interest (ROIs). Here, we validate a new motion correction approach to compensate for motion of TPLSM images in the superficial layers of auditory cortex of awake mice. We use a nominally uniform fluorescent signal as a secondary signal to complement the dynamic signals from genetically encoded calcium indicators. We tested motion correction for single plane time lapse imaging as well as multiplane (i.e., volume) time lapse imaging of cortical tissue. Our procedure of motion correction relies on locating the brightest neurons and tracking their positions over time using established techniques of particle finding and tracking. We show that our tracking based approach provides subpixel resolution without compromising speed. Unlike most established methods, our algorithm also captures deformations of the field of view and thus can compensate e.g., for rotations. Object tracking based motion correction thus offers an alternative approach for motion correction, one that is well suited for real time spike inference analysis and feedback control, and for correcting for tissue distortions. PMID:28860973

Temperature Dependence of the Upper Critical Field in Disordered Hubbard Model with Attraction

NASA Astrophysics Data System (ADS)

Kuchinskii, E. Z.; Kuleeva, N. A.; Sadovskii, M. V.

2017-12-01

We study disorder effects upon the temperature behavior of the upper critical magnetic field in an attractive Hubbard model within the generalized DMFT+Σ approach. We consider the wide range of attraction potentials U—from the weak coupling limit, where superconductivity is described by BCS model, up to the strong coupling limit, where superconducting transition is related to Bose-Einstein condensation (BEC) of compact Cooper pairs, formed at temperatures significantly higher than superconducting transition temperature, as well as the wide range of disorder—from weak to strong, when the system is in the vicinity of Anderson transition. The growth of coupling strength leads to the rapid growth of H c2( T), especially at low temperatures. In BEC limit and in the region of BCS-BEC crossover H c2( T), dependence becomes practically linear. Disordering also leads to the general growth of H c2( T). In BCS limit of weak coupling increasing disorder lead both to the growth of the slope of the upper critical field in the vicinity of the transition point and to the increase of H c2( T) in the low temperature region. In the limit of strong disorder in the vicinity of the Anderson transition localization corrections lead to the additional growth of H c2( T) at low temperatures, so that the H c2( T) dependence becomes concave. In BCS-BEC crossover region and in BEC limit disorder only slightly influences the slope of the upper critical field close to T c . However, in the low temperature region H c2 ( T may significantly grow with disorder in the vicinity of the Anderson transition, where localization corrections notably increase H c2 ( T = 0) also making H c2( T) dependence concave.

Fusarium mycotoxin content of UK organic and conventional oats.

PubMed

Edwards, S G

2009-07-01

Every year between 2002 and 2005 approximately 100 samples of oats from fields of known agronomy were analysed by GC/MS for 10 trichothecenes: deoxynivalenol (DON), nivalenol, 3-acetylDON, 15-acetylDON, fusarenone X, T-2 toxin (T2), HT-2 toxin (HT2), diacetoxyscirpenol, neosolaniol and T-2 triol. Samples were also analysed for moniliformin and zearalenone by HPLC. Of the 10 trichothecenes analysed from 458 harvest samples of oat only three, 15-acetylDON, fusarenone X and diacetoxyscirpenol, were not detected. Moniliformin and zearalenone were absent or rarely detected, respectively. HT2 and T2 were the most frequently detected fusarium mycotoxins, present above the limit of quantification (10 microg kg(-1)) in 92 and 84% of samples, respectively, and were usually present at the highest concentrations. The combined mean and median for HT2 and T2 (HT2 + T2) was 570 and 213 microg kg(-1), respectively. There were good correlations between concentrations of HT2 and all other type A trichothecenes detected (T2, T2 triol and neosolaniol). Year and region had a significant effect on HT2 + T2 concentration. There was also a highly significant difference between HT2 + T2 content in organic and conventional samples, with the predicted mean for organic samples five times lower than that of conventional samples. This is the largest difference reported for any mycotoxin level in organic and conventional cereals. No samples exceeded the legal limits for DON or zearalenone in oats intended for human consumption. Legislative limits for HT2 and T2 are currently under consideration by the European Commission. Depending on the limits set for unprocessed oats intended for human consumption, the levels detected here could have serious consequences for the UK oat-processing industry.

Quantification of extra virgin olive oil in dressing and edible oil blends using the representative TMS-4,4'-desmethylsterols gas-chromatographic-normalized fingerprint.

PubMed

Pérez-Castaño, Estefanía; Sánchez-Viñas, Mercedes; Gázquez-Evangelista, Domingo; Bagur-González, M Gracia

2018-01-15

This paper describes and discusses the application of trimethylsilyl (TMS)-4,4'-desmethylsterols derivatives chromatographic fingerprints (obtained from an off-line HPLC-GC-FID system) for the quantification of extra virgin olive oil in commercial vinaigrettes, dressing salad and in-house reference materials (i-HRM) using two different Partial Least Square-Regression (PLS-R) multivariate quantification methods. Different data pre-processing strategies were carried out being the whole one: (i) internal normalization; (ii) sampling based on The Nyquist Theorem; (iii) internal correlation optimized shifting, icoshift; (iv) baseline correction (v) mean centering and (vi) selecting zones. The first model corresponds to a matrix of dimensions 'n×911' variables and the second one to a matrix of dimensions 'n×431' variables. It has to be highlighted that the proposed two PLS-R models allow the quantification of extra virgin olive oil in binary blends, foodstuffs, etc., when the provided percentage is greater than 25%. Copyright © 2017 Elsevier Ltd. All rights reserved.

A systematic comparison of error correction enzymes by next-generation sequencing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lubock, Nathan B.; Zhang, Di; Sidore, Angus M.

Gene synthesis, the process of assembling genelength fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared sixmore » different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.« less

A systematic comparison of error correction enzymes by next-generation sequencing

DOE PAGES

Lubock, Nathan B.; Zhang, Di; Sidore, Angus M.; ...

2017-08-01

Gene synthesis, the process of assembling genelength fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared sixmore » different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.« less

Crack Turning and Arrest Mechanisms for Integral Structure

NASA Technical Reports Server (NTRS)

Pettit, Richard; Ingraffea, Anthony

1999-01-01

In the course of several years of research efforts to predict crack turning and flapping in aircraft fuselage structures and other problems related to crack turning, the 2nd order maximum tangential stress theory has been identified as the theory most capable of predicting the observed test results. This theory requires knowledge of a material specific characteristic length, and also a computation of the stress intensity factors and the T-stress, or second order term in the asymptotic stress field in the vicinity of the crack tip. A characteristic length, r(sub c), is proposed for ductile materials pertaining to the onset of plastic instability, as opposed to the void spacing theories espoused by previous investigators. For the plane stress case, an approximate estimate of r(sub c), is obtained from the asymptotic field for strain hardening materials given by Hutchinson, Rice and Rosengren (HRR). A previous study using of high order finite element methods to calculate T-stresses by contour integrals resulted in extremely high accuracy values obtained for selected test specimen geometries, and a theoretical error estimation parameter was defined. In the present study, it is shown that a large portion of the error in finite element computations of both K and T are systematic, and can be corrected after the initial solution if the finite element implementation utilizes a similar crack tip discretization scheme for all problems. This scheme is applied for two-dimensional problems to a both a p-version finite element code, showing that sufficiently accurate values of both K(sub I) and T can be obtained with fairly low order elements if correction is used. T-stress correction coefficients are also developed for the singular crack tip rosette utilized in the adaptive mesh finite element code FRANC2D, and shown to reduce the error in the computed T-stress significantly. Stress intensity factor correction was not attempted for FRANC2D because it employs a highly accurate quarter-point scheme to obtain stress intensity factors.

Bleed-through correction for rendering and correlation analysis in multi-colour localization microscopy

PubMed Central

Kim, Dahan; Curthoys, Nikki M.; Parent, Matthew T.; Hess, Samuel T.

2015-01-01

Multi-colour localization microscopy has enabled sub-diffraction studies of colocalization between multiple biological species and quantification of their correlation at length scales previously inaccessible with conventional fluorescence microscopy. However, bleed-through, or misidentification of probe species, creates false colocalization and artificially increases certain types of correlation between two imaged species, affecting the reliability of information provided by colocalization and quantified correlation. Despite the potential risk of these artefacts of bleed-through, neither the effect of bleed-through on correlation nor methods of its correction in correlation analyses has been systematically studied at typical rates of bleed-through reported to affect multi-colour imaging. Here, we present a reliable method of bleed-through correction applicable to image rendering and correlation analysis of multi-colour localization microscopy. Application of our bleed-through correction shows our method accurately corrects the artificial increase in both types of correlations studied (Pearson coefficient and pair correlation), at all rates of bleed-through tested, in all types of correlations examined. In particular, anti-correlation could not be quantified without our bleed-through correction, even at rates of bleed-through as low as 2%. Demonstrated with dichroic-based multi-colour FPALM here, our presented method of bleed-through correction can be applied to all types of localization microscopy (PALM, STORM, dSTORM, GSDIM, etc.), including both simultaneous and sequential multi-colour modalities, provided the rate of bleed-through can be reliably determined. PMID:26185614

Bleed-through correction for rendering and correlation analysis in multi-colour localization microscopy.

PubMed

Kim, Dahan; Curthoys, Nikki M; Parent, Matthew T; Hess, Samuel T

2013-09-01

Multi-colour localization microscopy has enabled sub-diffraction studies of colocalization between multiple biological species and quantification of their correlation at length scales previously inaccessible with conventional fluorescence microscopy. However, bleed-through, or misidentification of probe species, creates false colocalization and artificially increases certain types of correlation between two imaged species, affecting the reliability of information provided by colocalization and quantified correlation. Despite the potential risk of these artefacts of bleed-through, neither the effect of bleed-through on correlation nor methods of its correction in correlation analyses has been systematically studied at typical rates of bleed-through reported to affect multi-colour imaging. Here, we present a reliable method of bleed-through correction applicable to image rendering and correlation analysis of multi-colour localization microscopy. Application of our bleed-through correction shows our method accurately corrects the artificial increase in both types of correlations studied (Pearson coefficient and pair correlation), at all rates of bleed-through tested, in all types of correlations examined. In particular, anti-correlation could not be quantified without our bleed-through correction, even at rates of bleed-through as low as 2%. Demonstrated with dichroic-based multi-colour FPALM here, our presented method of bleed-through correction can be applied to all types of localization microscopy (PALM, STORM, dSTORM, GSDIM, etc.), including both simultaneous and sequential multi-colour modalities, provided the rate of bleed-through can be reliably determined.

Characterization of [11C]Lu AE92686 as a PET radioligand for phosphodiesterase 10A in the nonhuman primate brain.

PubMed

Yang, Kai-Chun; Stepanov, Vladimir; Amini, Nahid; Martinsson, Stefan; Takano, Akihiro; Nielsen, Jacob; Bundgaard, Christoffer; Bang-Andersen, Benny; Grimwood, Sarah; Halldin, Christer; Farde, Lars; Finnema, Sjoerd J

2017-02-01

[ 11 C]Lu AE92686 is a positron emission tomography (PET) radioligand that has recently been validated for examining phosphodiesterase 10A (PDE10A) in the human striatum. [ 11 C]Lu AE92686 has high affinity for PDE10A (IC 50  = 0.39 nM) and may also be suitable for examination of the substantia nigra, a region with low density of PDE10A. Here, we report characterization of regional [ 11 C]Lu AE92686 binding to PDE10A in the nonhuman primate (NHP) brain. A total of 11 PET measurements, seven baseline and four following pretreatment with unlabeled Lu AE92686 or the structurally unrelated PDE10A inhibitor MP-10, were performed in five NHPs using a high resolution research tomograph (HRRT). [ 11 C]Lu AE92686 binding was quantified using a radiometabolite-corrected arterial input function and compartmental and graphical modeling approaches. Regional time-activity curves were best described with the two-tissue compartment model (2TCM). However, the distribution volume (V T ) values for all regions were obtained by the Logan plot analysis, as reliable cerebellar V T values could not be derived by the 2TCM. For cerebellum, a proposed reference region, V T values increased by ∼30 % with increasing PET measurement duration from 63 to 123 min, while V T values in target regions remained stable. Both pretreatment drugs significantly decreased [ 11 C]Lu AE92686 binding in target regions, while no significant effect on cerebellum was observed. Binding potential (BP ND ) values, derived with the simplified reference tissue model (SRTM), were 13-17 in putamen and 3-5 in substantia nigra and correlated well to values from the Logan plot analysis. The method proposed for quantification of [ 11 C]Lu AE92686 binding in applied studies in NHP is based on 63 min PET data and SRTM with cerebellum as a reference region. The study supports that [ 11 C]Lu AE92686 can be used for PET examinations of PDE10A binding also in substantia nigra.

Effect of Genital Sampling Site on the Detection and Quantification of Ureaplasma Species with Quantitative Polymerase Chain Reaction during Pregnancy.

PubMed

Faron, Gilles; Vancutsem, Ellen; Naessens, Anne; Buyl, Ronald; Gucciardo, Leonardo; Foulon, Walter

2017-01-01

Objective . This study aimed to compare the qualitative and quantitative reproducibility of quantitative PCR (qPCR) for Ureaplasma species (Ureaplasma spp.) throughout pregnancy and according to the genital sampling site. Study Design . Between 5 and 14 weeks of gestation (T1), vaginal, fornix, and two cervical samples were taken. Sampling was repeated during the 2nd (T2) and 3rd (T3) trimester in randomly selected T1 positive and negative women. Qualitative and quantitative reproducibility were evaluated using, respectively, Cohen's kappa ( κ ) and interclass correlation coefficients (ICC) and repeated measures ANOVA on the log-transformed mean number of DNA copies for each sampling site. Results . During T1, 51/127 women were positive for U. parvum and 8 for U. urealyticum (4 patients for both). Sampling was repeated for 44/55 women at T2 and/or T3; 43 (97.7%) remained positive at the three timepoints. κ ranged between 0.83 and 0.95 and the ICC for cervical samples was 0.86. Conclusions . Colonization by Ureaplasma spp. seems to be very constant during pregnancy and vaginal samples have the highest detection rate.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pangaro, L.; Burman, K.D.; Wartofsky, L.

The present report describes a RIA for 3,5-diiodothyronine (3,5T/sub 2/) which uses inner ring-labeled 3,5-(/sup 125/I)T/sub 2/ as the ligand and has a lower limit of detectability of 0.5 ng/dl. Cross-reaction was 0.14% with T/sub 3/, less than 0.001% with T/sub 4/, 1.2% with 3,3',5-triiodothyroacetic acid, and 6.1% with 3,5-diiodothyroacetic acid. No cross-reaction was detectable for iodothyronines within their physiological ranges. Intraassay variation ranged from 2.2 to 7.8%, and interassay variation ranged from 12.7 to 14%. The mean (+-SE) serum 3.5T/sub 2/ concentration in 70 normal subjects was 4.3 +- 0.2 ng/dl. The mean (+-SE) 3.5T/sub 2/ in 14 hyperthyroidmore » patients was increased to 18.4 +- 2.3 ng/dl (P < 0.001), and all but 1 patient had an elevated level. In 10 hypothyroid patients the mean (+-SE) 3,5T/sub 2/ level was decreased to 1.4 +- 0.3 ng/dl (P < 0.001). In 4 patients, levels overlapped with the normal range. In 4 hypothyroid subjects treated with L-T/sub 1/, 3,5T/sub 2/ levels were normal, suggesting that the majority of 3,5T/sub 2/ originates from extrathyroidal conversion from T/sub 3/. Studies in fasting obese subjects demonstrated that serum 3,5T/sub 2/ (mean +- SE) levels fell from 3.4 +- 0.3 to 2.5 +- 0.7 ng/dl during fasting. This fall was significant (P < 0.001) and in parallel with the fall in T/sub 3/ levels of 182 +- 20 to 126 +- 12 ng/dl. In fasting subjects given 100 ..mu..g oral L-T/sub 3//day T/sub 3/ levels rose from 138 +- 11 to 362 +- 26 ng/dl. 3,5T/sub 2/ levels (corrected for cross-reaction and for contamination of oral T/sub 3/ with 3,5T/sub 2/) rose from 2.2 +- 0.7 to 6.4 +- 1.0 ng/dl. In fasting subjects given 25 ..mu..g oral L-T/sub 3//day, T/sub 3/ levels fell from 165 +- 5.1 to 139 +- 6.9 ng/dl. Corrected 3,5T/sub 2/ levels changed from 3.7 +- 0.4 to 2.5 +- 0.3 ng/dl. Neither change were significant.« less

Fast magnetic resonance fingerprinting for dynamic contrast-enhanced studies in mice.

PubMed

Gu, Yuning; Wang, Charlie Y; Anderson, Christian E; Liu, Yuchi; Hu, He; Johansen, Mette L; Ma, Dan; Jiang, Yun; Ramos-Estebanez, Ciro; Brady-Kalnay, Susann; Griswold, Mark A; Flask, Chris A; Yu, Xin

2018-05-09

The goal of this study was to develop a fast MR fingerprinting (MRF) method for simultaneous T 1 and T 2 mapping in DCE-MRI studies in mice. The MRF sequences based on balanced SSFP and fast imaging with steady-state precession were implemented and evaluated on a 7T preclinical scanner. The readout used a zeroth-moment-compensated variable-density spiral trajectory that fully sampled the entire k-space and the inner 10 × 10 k-space with 48 and 4 interleaves, respectively. In vitro and in vivo studies of mouse brain were performed to evaluate the accuracy of MRF measurements with both fully sampled and undersampled data. The application of MRF to dynamic T 1 and T 2 mapping in DCE-MRI studies were demonstrated in a mouse model of heterotopic glioblastoma using gadolinium-based and dysprosium-based contrast agents. The T 1 and T 2 measurements in phantom showed strong agreement between the MRF and the conventional methods. The MRF with spiral encoding allowed up to 8-fold undersampling without loss of measurement accuracy. This enabled simultaneous T 1 and T 2 mapping with 2-minute temporal resolution in DCE-MRI studies. Magnetic resonance fingerprinting provides the opportunity for dynamic quantification of contrast agent distribution in preclinical tumor models on high-field MRI scanners. © 2018 International Society for Magnetic Resonance in Medicine.

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 2. Volume 3. Luke Air Force Base, Arizona.

DTIC Science & Technology

1988-06-01

4 1r0 S tI I ;C;C 00000000 88 8888 mH I lu-It u~W I C In 1 0 Al0 * I " 1 a lei 0 !’. *’ 0 t I I UpV N MM w k4Ř I in N inM n in in in in in r4 4...John Forrest Luke AFB Richard Johnson WESTON Greg Hill WESTON Synopsis: The first portion of the meeting was a general discussion of well specifications...ore 1963-1964 Lancaster County General Hospital processing operations, 6 6Research laboratory for analytical Mr. Marks air contaminant testing

Quantitation of tumor uptake with molecular breast imaging.

PubMed

Bache, Steven T; Kappadath, S Cheenu

2017-09-01

We developed scatter and attenuation-correction techniques for quantifying images obtained with Molecular Breast Imaging (MBI) systems. To investigate scatter correction, energy spectra of a 99m Tc point source were acquired with 0-7-cm-thick acrylic to simulate scatter between the detector heads. System-specific scatter correction factor, k, was calculated as a function of thickness using a dual energy window technique. To investigate attenuation correction, a 7-cm-thick rectangular phantom containing 99m Tc-water simulating breast tissue and fillable spheres simulating tumors was imaged. Six spheres 10-27 mm in diameter were imaged with sphere-to-background ratios (SBRs) of 3.5, 2.6, and 1.7 and located at depths of 0.5, 1.5, and 2.5 cm from the center of the water bath for 54 unique tumor scenarios (3 SBRs × 6 sphere sizes × 3 depths). Phantom images were also acquired in-air under scatter- and attenuation-free conditions, which provided ground truth counts. To estimate true counts, T, from each tumor, the geometric mean (GM) of the counts within a prescribed region of interest (ROI) from the two projection images was calculated as T=C1C2eμtF, where C are counts within the square ROI circumscribing each sphere on detectors 1 and 2, μ is the linear attenuation coefficient of water, t is detector separation, and the factor F accounts for background activity. Four unique F definitions-standard GM, background-subtraction GM, MIRD Primer 16 GM, and a novel "volumetric GM"-were investigated. Error in T was calculated as the percentage difference with respect to in-air. Quantitative accuracy using the different GM definitions was calculated as a function of SBR, depth, and sphere size. Sensitivity of quantitative accuracy to ROI size was investigated. We developed an MBI simulation to investigate the robustness of our corrections for various ellipsoidal tumor shapes and detector separations. Scatter correction factor k varied slightly (0.80-0.95) over a compressed breast thickness range of 6-9 cm. Corrected energy spectra recovered general characteristics of scatter-free spectra. Quantitatively, photopeak counts were recovered to <10% compared to in-air conditions after scatter correction. After GM attenuation correction, mean errors (95% confidence interval, CI) for all 54 imaging scenarios were 149% (-154% to +455%), -14.0% (-38.4% to +10.4%), 16.8% (-14.7% to +48.2%), and 2.0% (-14.3 to +18.3%) for the standard GM, background-subtraction GM, MIRD 16 GM, and volumetric GM, respectively. Volumetric GM was less sensitive to SBR and sphere size, while all GM methods were insensitive to sphere depth. Simulation results showed that Volumetric GM method produced a mean error within 5% over all compressed breast thicknesses (3-14 cm), and that the use of an estimated radius for nonspherical tumors increases the 95% CI to at most ±23%, compared with ±16% for spherical tumors. Using DEW scatter- and our Volumetric GM attenuation-correction methodology yielded accurate estimates of tumor counts in MBI over various tumor sizes, shapes, depths, background uptake, and compressed breast thicknesses. Accurate tumor uptake can be converted to radiotracer uptake concentration, allowing three patient-specific metrics to be calculated for quantifying absolute uptake and relative uptake change for assessment of treatment response. © 2017 American Association of Physicists in Medicine.

Whole-Body Computed Tomography-Based Body Mass and Body Fat Quantification: A Comparison to Hydrostatic Weighing and Air Displacement Plethysmography.

PubMed

Gibby, Jacob T; Njeru, Dennis K; Cvetko, Steve T; Heiny, Eric L; Creer, Andrew R; Gibby, Wendell A

We correlate and evaluate the accuracy of accepted anthropometric methods of percent body fat (%BF) quantification, namely, hydrostatic weighing (HW) and air displacement plethysmography (ADP), to 2 automatic adipose tissue quantification methods using computed tomography (CT). Twenty volunteer subjects (14 men, 6 women) received head-to-toe CT scans. Hydrostatic weighing and ADP were obtained from 17 and 12 subjects, respectively. The CT data underwent conversion using 2 separate algorithms, namely, the Schneider method and the Beam method, to convert Hounsfield units to their respective tissue densities. The overall mass and %BF of both methods were compared with HW and ADP. When comparing ADP to CT data using the Schneider method and Beam method, correlations were r = 0.9806 and 0.9804, respectively. Paired t tests indicated there were no statistically significant biases. Additionally, observed average differences in %BF between ADP and the Schneider method and the Beam method were 0.38% and 0.77%, respectively. The %BF measured from ADP, the Schneider method, and the Beam method all had significantly higher mean differences when compared with HW (3.05%, 2.32%, and 1.94%, respectively). We have shown that total body mass correlates remarkably well with both the Schneider method and Beam method of mass quantification. Furthermore, %BF calculated with the Schneider method and Beam method CT algorithms correlates remarkably well with ADP. The application of these CT algorithms have utility in further research to accurately stratify risk factors with periorgan, visceral, and subcutaneous types of adipose tissue, and has the potential for significant clinical application.

Disease quantification on PET/CT images without object delineation

NASA Astrophysics Data System (ADS)

Tong, Yubing; Udupa, Jayaram K.; Odhner, Dewey; Wu, Caiyun; Fitzpatrick, Danielle; Winchell, Nicole; Schuster, Stephen J.; Torigian, Drew A.

2017-03-01

The derivation of quantitative information from images to make quantitative radiology (QR) clinically practical continues to face a major image analysis hurdle because of image segmentation challenges. This paper presents a novel approach to disease quantification (DQ) via positron emission tomography/computed tomography (PET/CT) images that explores how to decouple DQ methods from explicit dependence on object segmentation through the use of only object recognition results to quantify disease burden. The concept of an object-dependent disease map is introduced to express disease severity without performing explicit delineation and partial volume correction of either objects or lesions. The parameters of the disease map are estimated from a set of training image data sets. The idea is illustrated on 20 lung lesions and 20 liver lesions derived from 18F-2-fluoro-2-deoxy-D-glucose (FDG)-PET/CT scans of patients with various types of cancers and also on 20 NEMA PET/CT phantom data sets. Our preliminary results show that, on phantom data sets, "disease burden" can be estimated to within 2% of known absolute true activity. Notwithstanding the difficulty in establishing true quantification on patient PET images, our results achieve 8% deviation from "true" estimates, with slightly larger deviations for small and diffuse lesions where establishing ground truth becomes really questionable, and smaller deviations for larger lesions where ground truth set up becomes more reliable. We are currently exploring extensions of the approach to include fully automated body-wide DQ, extensions to just CT or magnetic resonance imaging (MRI) alone, to PET/CT performed with radiotracers other than FDG, and other functional forms of disease maps.

Recombinant interleukin 2 therapy in severe combined immunodeficiency disease.

PubMed Central

Pahwa, R; Chatila, T; Pahwa, S; Paradise, C; Day, N K; Geha, R; Schwartz, S A; Slade, H; Oyaizu, N; Good, R A

1989-01-01

Severe combined immunodeficiency disease (SCID) is a congenital disorder of severe B- and T-lymphocyte dysfunction in which several pathogenic mechanisms have been identified. The present study describes a female child with SCID who had a primary defect in the ability of T cells to secrete interleukin 2 (IL-2). B- and T-cell numbers were normal, but their functions were severely deficient. Mitogen and antigen-driven lymphoproliferative responses were diminished but were correctable in vitro with recombinant IL-2 (rIL-2). The patient's phytohemagglutinin-stimulated lymphocytes expressed IL-2 receptors normally. Despite the presence of the gene for IL-2, the patient's cells were grossly deficient in messenger RNA for IL-2 and endogenous IL-2 production. Pokeweed mitogen-driven B-cell differentiation was decreased and was not corrected by the addition of normal T cells to the B cells. Two attempts at immune reconstitution by haploidentical bone marrow transplantation failed. Therapy with rIL-2 (30,000 units/kg, given daily i.v.) resulted in marked clinical improvement as well in improved T-cell functions. The child, now 3 yr old, has been on rIL-2 therapy for 2 yr and receives rIL-2 (30,000 units/kg) three times weekly at home. This case study points to a new direction in the treatment of such disorders with rIL-2. Images PMID:2787027

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.

PubMed

Lemke, Kono H

2017-06-21

This study presents results for the binding energy and geometry of the H 2 S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of D e , E ZPE , D o , and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of D e are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance r SS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H 2 S dimer geometry and binding energy. As regards the structure of (H 2 S) 2 , MPn, CCSD, and CCSD(T) level values of r SS , obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy D e are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies D e with E ZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields D o = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

High-performance thin-layer chromatography (HPTLC) for the simultaneous quantification of the cyclic lipopeptides Surfactin, Iturin A and Fengycin in culture samples of Bacillus species.

PubMed

Geissler, Mareen; Oellig, Claudia; Moss, Karin; Schwack, Wolfgang; Henkel, Marius; Hausmann, Rudolf

2017-02-15

A high-performance thin-layer chromatography method has been established for the identification and simultaneous quantification of the cyclic lipopeptides Surfactin, Iturin A and Fengycin in Bacillus culture samples. B. subtilis DSM 10 T , B. amyloliquefaciens DSM 7 T and B. methylotrophicus DSM 23117 were used as model strains. Culture samples indicated that a sample pretreatment is necessary in order to run HPTLC analyses. A threefold extraction of the cell-free broth with the solvent chloroform/methanol (2:1, v/v) gave best results, when all three lipopeptides were included in the analysis. For the mobile phase, a two-step development was considered most suitable. The first development is conducted with chloroform/methanol/water (65:25:4, v/v/v) over a migration distance of 60mm and the second development using butanol/ethanol/0.1% acetic acid (1:4:1, v/v/v) over a migration distance of 60mm, as well. The method was validated according to Validation of Analytical Procedures: Methodology (FDA Guidance) with respect to the parameters linearity, limit of detection (LOD), limit of quantification (LOQ), precision, accuracy and recovery rate. A linear range with R 2 >0.99 was obtained for all samples from 30ng/zone up to 600ng/zone. The results indicated that quantification of Surfactin has to be performed after the first development (hR F =44), while Fengycin is quantified after the second development (hR F =36, hR F range=20-40). For Iturin A, the results demonstrated that quantification is in favor after the first (hR F =19) development, but also possible after the second (hR F =59) development. LOD and LOQ for Surfactin and Iturin A after the first development, and Fengycin after the second development were determined to be 16ng/zone and 47ng/zone, 13ng/zone and 39ng/zone, and 27ng/zone and 82ng/zone, respectively. Results further revealed the highly accurate and precise character of the developed method with a good inter- and intraday reproducibility. For the precision and accuracy, expressed as % recovery and relative standard deviation, respectively, the determined values did not exceed ±15% as specified by the FDA Guidance. The recovery assay conducted for samples obtained from two strains with the solvent chloroform/methanol (2:1, v/v), which was determined to be most suitable if all three lipopeptides are of interest, gave recoveries of 96.5% and 99.6%, 68.6% and 71.6%, and 102.5% and 95.2% for Surfactin, Iturin A and Fengycin, respectively. Overall, a suitable and reliable method for the simultaneous quantification of the lipopeptides Surfactin, Iturin A and Fengycin in biological samples using HPTLC was successfully developed and validated. Copyright © 2016 Elsevier B.V. All rights reserved.

Multi-Scale Validation of a Nanodiamond Drug Delivery System and Multi-Scale Engineering Education

ERIC Educational Resources Information Center

Schwalbe, Michelle Kristin

2010-01-01

This dissertation has two primary concerns: (i) evaluating the uncertainty and prediction capabilities of a nanodiamond drug delivery model using Bayesian calibration and bias correction, and (ii) determining conceptual difficulties of multi-scale analysis from an engineering education perspective. A Bayesian uncertainty quantification scheme…

Is the Image Quality of I-124-PET Impaired by an Automatic Correction of Prompt Gammas?

PubMed Central

Preylowski, Veronika; Schlögl, Susanne; Schoenahl, Frédéric; Jörg, Gerhard; Samnick, Samuel; Buck, Andreas K.; Lassmann, Michael

2013-01-01

Objectives The aim of this study is to evaluate the quality of I-124 PET images with and without prompt gamma compensation (PGC) by comparing the recovery coefficients (RC), the signal to noise ratios (SNR) and the contrast to F-18 and Ga-68. Furthermore, the influence of the PGC on the quantification and image quality is evaluated. Methods For measuring the image quality the NEMA NU2-2001 PET/SPECT-Phantom was used containing 6 spheres with a diameter between 10 mm and 37 mm placed in water with different levels of background activity. Each sphere was filled with the same activity concentration measured by an independently cross-calibrated dose calibrator. The “hot” sources were acquired with a full 3D PET/CT (Biograph mCT®, Siemens Medical USA). Acquisition times were 2 min for F-18 and Ga-68, and 10 min for I-124. For reconstruction an OSEM algorithm was applied. For I-124 the images were reconstructed with and without PGC. For the calculation of the RCs the activity concentrations in each sphere were determined; in addition, the influence of the background correction was studied. Results The RCs of Ga-68 are the smallest (79%). I-124 reaches similar RCs (87% with PGC, 84% without PGC) as F-18 (84%). showing that the quantification of I-124 images is similar to F-18 and slightly better than Ga-68. With background activity the contrast of the I-124 PGC images is similar to Ga-68 and F-18 scans. There was lower background activity in the I-124 images without PGC, which probably originates from an overcorrection of the scatter contribution. Consequently, the contrast without PGC was much higher than with PGC. As a consequence PGC should be used for I-124. Conclusions For I-124 there is only a slight influence on the quantification depending on the use of the PGC. However, there are considerable differences with respect to I-124 image quality. PMID:24014105

Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet.

PubMed

Candela, Marco; Biagi, Elena; Soverini, Matteo; Consolandi, Clarissa; Quercia, Sara; Severgnini, Marco; Peano, Clelia; Turroni, Silvia; Rampelli, Simone; Pozzilli, Paolo; Pianesi, Mario; Fallucca, Francesco; Brigidi, Patrizia

2016-07-01

The gut microbiota exerts a role in type 2 diabetes (T2D), and deviations from a mutualistic ecosystem layout are considered a key environmental factor contributing to the disease. Thus, the possibility of improving metabolic control in T2D by correcting gut microbiome dysbioses through diet has been evaluated. Here, we explore the potential of two different energy-restricted dietary approaches - the fibre-rich macrobiotic Ma-Pi 2 diet or a control diet recommended by Italian professional societies for T2D treatment - to correct gut microbiota dysbioses in T2D patients. In a previous 21-d open-label MADIAB trial, fifty-six overweight T2D patients were randomised to the Ma-Pi 2 or the control diet. For the present study, stools were collected before and after intervention from a subset of forty MADIAB participants, allowing us to characterise the gut microbiota by 16S rRNA sequencing and imputed metagenomics. To highlight microbiota dysbioses in T2D, the gut microbiota of thirteen normal-weight healthy controls were characterised. According to our findings, both diets were effective in modulating gut microbiome dysbioses in T2D, resulting in an increase of the ecosystem diversity and supporting the recovery of a balanced community of health-promoting SCFA producers, such as Faecalibacterium, Roseburia, Lachnospira, Bacteroides and Akkermansia. The Ma-Pi 2 diet, but not the control diet, was also effective in counteracting the increase of possible pro-inflammatory groups, such as Collinsella and Streptococcus, in the gut ecosystem, showing the potential to reverse pro-inflammatory dysbioses in T2D, and possibly explaining the greater efficacy in improving the metabolic control.

Effect of bypass fat supplementation on productive performance and blood biochemical profile in lactating Murrah (Bubalus bubalis) buffaloes.

PubMed

Ranjan, Amit; Sahoo, Biswanath; Singh, Vijay Kumar; Srivastava, Susant; Singh, Suresh Pratap; Pattanaik, Ashok Kumar

2012-10-01

The study investigated the effect of dietary supplementation of bypass fat on productive performance and blood biochemical profile of lactating Murrah buffaloes (Bubalus bubalis). Fifteen multiparous buffaloes (2-4 lactation) of early to mid lactation were divided in three homogenous groups T(1) (control), T(2), and T(3) of five each. The animals in T(1) were fed with a basal diet consisting of a concentrate mixture, green sorghum, and wheat straw as per requirements, while the animals in group T(2) and T(3) were fed with same ration supplemented with 0.7 % (100 g/day) and 1.4 % (200 g/day) bypass fat (on dry matter intake (DMI) basis), respectively. The feed intake, milk yield, and milk composition were not influenced by supplemental bypass fat. However, fat-corrected milk (6.5 %) yield was higher (P < 0.05) in T(3) (14.21) than that of T(1) (9.83) and similar with T(2) (11.05). Feed efficiency (milk yield/kg DMI) was higher (P < 0.05) in group T(3) (0.51) than that of T(1) (0.38) and T(2) (0.41) indicating that buffaloes fed with bypass fat which is 1.4 % (200 g/day) of the diet were economically more efficient. The serum cholesterol level was higher (P < 0.01) in bypass fat-supplemented group (T(2) and T(3)) of animals. Serum high density lipoprotein (HDL) cholesterol (good cholesterol) level was more (P < 0.05) than LDL cholesterol (bad cholesterol) level with higher dose of bypass fat in T(3) than T(2). It was concluded that bypass fat supplementation with 1.4 % of the diet (200 g/day) increased the fat-corrected milk production and feed efficiency along with serum HDL cholesterol level in lactating Murrah buffaloes.

Investigation of P213S SELL gene polymorphism in type 2 diabetes mellitus and related end stage renal disease. A case-control study.

PubMed

Stavarachi, Monica; Panduru, N M; Serafinceanu, C; Moţa, E; Moţa, Maria; Cimponeriu, D; Ion, Daniela Adriana

2011-01-01

SELL (L-selectin) is a candidate gene for several complex diseases including diabetes mellitus and renal failure. Our aim was to investigate the involvement of P213S SELL gene polymorphism (rs2229569) in type 2 diabetes mellitus (T2DM) and related end stage renal disease (ESRD). Type 2 diabetes mellitus patients without ESRD (n=250) or with ESRD (n=90), ESRD patients without diabetes (n=119) and sex and age matched healthy subjects (n=459) were analyzed in this study. DNA samples from all these subjects were genotyped for the P213S polymorphism by PCR-RFLP technique. Statistical analysis indicated that SELL P213S genotypes and alleles were similar distributed in the patients and control groups (ORSS=0.37, CI 95%: 0.131>0.372>1.06, p=0.05, Yate's correction p=0.09, for T2DM patients without ESRD, ORSS=2.04, CI 95%: 0.365>2.047>1.465, p=0.4, Yate's correction p=0.67, for T2DM patients with ESRD and ORSS=1, CI95%: 0.198>1>5.057, p=1, Yate's correction p=0.67, for non-diabetic with ESRD patients). Also, no significant differences were noticed when we compared the ESRD subjects with diabetes vs. non-diabetic ones (OR=1.798, CI 95%: 0.392>1.798>8.245, p=0.44, Yate's correction p=0.7). No statistically significant results were found in order to sustain the hypothesis of association between SELL gene P213S polymorphism, type 2 diabetes mellitus and end stage renal disease.

The effect of applied transducer force on acoustic radiation force impulse quantification within the left lobe of the liver.

PubMed

Porra, Luke; Swan, Hans; Ho, Chien

2015-08-01

Introduction: Acoustic Radiation Force Impulse (ARFI) Quantification measures shear wave velocities (SWVs) within the liver. It is a reliable method for predicting the severity of liver fibrosis and has the potential to assess fibrosis in any part of the liver, but previous research has found ARFI quantification in the right lobe more accurate than in the left lobe. A lack of standardised applied transducer force when performing ARFI quantification in the left lobe of the liver may account for some of this inaccuracy. The research hypothesis of this present study predicted that an increase in applied transducer force would result in an increase in SWVs measured. Methods: ARFI quantification within the left lobe of the liver was performed within a group of healthy volunteers (n = 28). During each examination, each participant was subjected to ARFI quantification at six different levels of transducer force applied to the epigastric abdominal wall. Results: A repeated measures ANOVA test showed that ARFI quantification was significantly affected by applied transducer force (p = 0.002). Significant pairwise comparisons using Bonferroni correction for multiple comparisons showed that with an increase in applied transducer force, there was a decrease in SWVs. Conclusion: Applied transducer force has a significant effect on SWVs within the left lobe of the liver and it may explain some of the less accurate and less reliable results in previous studies where transducer force was not taken into consideration. Future studies in the left lobe of the liver should take this into account and control for applied transducer force.

tRNAs as Biomarkers and Regulators for Breast Cancer

DTIC Science & Technology

2009-08-01

codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific...CONTRACTING ORGANIZATION : The University of Chicago Chicago, IL 60637 REPORT...Geslain, Q. Dai. 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT

Understanding the atmospheric measurement and behavior of perfluorooctanoic acid.

PubMed

Webster, Eva M; Ellis, David A

2012-09-01

The recently reported quantification of the atmospheric sampling artifact for perfluorooctanoic acid (PFOA) was applied to existing gas and particle concentration measurements. Specifically, gas phase concentrations were increased by a factor of 3.5 and particle-bound concentrations by a factor of 0.1. The correlation constants in two particle-gas partition coefficient (K(QA)) estimation equations were determined for multiple studies with and without correcting for the sampling artifact. Correction for the sampling artifact gave correlation constants with improved agreement to those reported for other neutral organic contaminants, thus supporting the application of the suggested correction factors for perfluorinated carboxylic acids. Applying the corrected correlation constant to a recent multimedia modeling study improved model agreement with corrected, reported, atmospheric concentrations. This work confirms that there is sufficient partitioning to the gas phase to support the long-range atmospheric transport of PFOA. Copyright © 2012 SETAC.

Sensitivity estimation in time-of-flight list-mode positron emission tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herraiz, J. L.; Sitek, A., E-mail: sarkadiu@gmail.com

Purpose: An accurate quantification of the images in positron emission tomography (PET) requires knowing the actual sensitivity at each voxel, which represents the probability that a positron emitted in that voxel is finally detected as a coincidence of two gamma rays in a pair of detectors in the PET scanner. This sensitivity depends on the characteristics of the acquisition, as it is affected by the attenuation of the annihilation gamma rays in the body, and possible variations of the sensitivity of the scanner detectors. In this work, the authors propose a new approach to handle time-of-flight (TOF) list-mode PET data,more » which allows performing either or both, a self-attenuation correction, and self-normalization correction based on emission data only. Methods: The authors derive the theory using a fully Bayesian statistical model of complete data. The authors perform an initial evaluation of algorithms derived from that theory and proposed in this work using numerical 2D list-mode simulations with different TOF resolutions and total number of detected coincidences. Effects of randoms and scatter are not simulated. Results: The authors found that proposed algorithms successfully correct for unknown attenuation and scanner normalization for simulated 2D list-mode TOF-PET data. Conclusions: A new method is presented that can be used for corrections for attenuation and normalization (sensitivity) using TOF list-mode data.« less

Sensitivity estimation in time-of-flight list-mode positron emission tomography.

PubMed

Herraiz, J L; Sitek, A

2015-11-01

An accurate quantification of the images in positron emission tomography (PET) requires knowing the actual sensitivity at each voxel, which represents the probability that a positron emitted in that voxel is finally detected as a coincidence of two gamma rays in a pair of detectors in the PET scanner. This sensitivity depends on the characteristics of the acquisition, as it is affected by the attenuation of the annihilation gamma rays in the body, and possible variations of the sensitivity of the scanner detectors. In this work, the authors propose a new approach to handle time-of-flight (TOF) list-mode PET data, which allows performing either or both, a self-attenuation correction, and self-normalization correction based on emission data only. The authors derive the theory using a fully Bayesian statistical model of complete data. The authors perform an initial evaluation of algorithms derived from that theory and proposed in this work using numerical 2D list-mode simulations with different TOF resolutions and total number of detected coincidences. Effects of randoms and scatter are not simulated. The authors found that proposed algorithms successfully correct for unknown attenuation and scanner normalization for simulated 2D list-mode TOF-PET data. A new method is presented that can be used for corrections for attenuation and normalization (sensitivity) using TOF list-mode data.

Development and validation of a liquid chromatography isotope dilution mass spectrometry method for the reliable quantification of alkylphenols in environmental water samples by isotope pattern deconvolution.

PubMed

Fabregat-Cabello, Neus; Sancho, Juan V; Vidal, Andreu; González, Florenci V; Roig-Navarro, Antoni Francesc

2014-02-07

We present here a new measurement method for the rapid extraction and accurate quantification of technical nonylphenol (NP) and 4-t-octylphenol (OP) in complex matrix water samples by UHPLC-ESI-MS/MS. The extraction of both compounds is achieved in 30min by means of hollow fiber liquid phase microextraction (HF-LPME) using 1-octanol as acceptor phase, which provides an enrichment (preconcentration) factor of 800. On the other hand we have developed a quantification method based on isotope dilution mass spectrometry (IDMS) and singly (13)C1-labeled compounds. To this end the minimal labeled (13)C1-4-(3,6-dimethyl-3-heptyl)-phenol and (13)C1-t-octylphenol isomers were synthesized, which coelute with the natural compounds and allows the compensation of the matrix effect. The quantification was carried out by using isotope pattern deconvolution (IPD), which permits to obtain the concentration of both compounds without the need to build any calibration graph, reducing the total analysis time. The combination of both extraction and determination techniques have allowed to validate for the first time a HF-LPME methodology at the required levels by legislation achieving limits of quantification of 0.1ngmL(-1) and recoveries within 97-109%. Due to the low cost of HF-LPME and total time consumption, this methodology is ready for implementation in routine analytical laboratories. Copyright © 2013 Elsevier B.V. All rights reserved.

Single-Step Transepithelial PRK vs Alcohol-Assisted PRK in Myopia and Compound Myopic Astigmatism Correction.

PubMed

Kaluzny, Bartlomiej J; Cieslinska, Iwona; Mosquera, Samuel A; Verma, Shwetabh

2016-02-01

Transepithelial photorefractive keratectomy (tPRK), where both the epithelium and stroma are removed in a single-step, is a relatively new procedure of laser refractive error correction. This study compares the 3-month results of myopia and compound myopic astigmatism correction by tPRK or conventional alcohol-assisted PRK (aaPRK).This prospective, nonrandomized, case-control study recruited 148 consecutive patients; 93 underwent tPRK (173 eyes) and 55 aaPRK (103 eyes). Refractive results, predictability, safety, and efficacy were evaluated during the 3-month follow-up. The main outcome measures were uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), and mean refractive spherical equivalent (MRSE).Mean preoperative MRSE was -4.30 ± 1.72 D and -4.33 ± 1.96 D, respectively (P = 0.87). The 3-month follow-up rate was 82.1% in the tPRK group (n = 145) and 86.4% in aaPRK group (n = 90), P = 0.81. Postoperative UDVA was 20/20 or better in 97% and 94% of eyes, respectively (P = 0.45). In the tPRK and aaPRK groups, respectively, 13% and 21% of eyes lost 1 line of CDVA, and 30% and 31% gained 1 or 2 lines (P = 0.48). Mean postoperative MRSE was -0.14 ± 0.26 D in the tPRK group and -0.12 ± 0.20 D in the aaPRK group (P = 0.9). The correlation between attempted versus achieved MRSE was equally high in both groups.Single-step transepithelial PRK and conventional PRK provide very similar results 3 months postoperatively. These procedures are predictable, effective, and safe for correction of myopia and compound myopic astigmatism.

Pulsed glow discharge enables direct mass spectrometric measurement of fluorine in crystal materials - Fluorine quantification and depth profiling in fluorine doped potassium titanyl phosphate

NASA Astrophysics Data System (ADS)

Bodnar, Victoria; Ganeev, Alexander; Gubal, Anna; Solovyev, Nikolay; Glumov, Oleg; Yakobson, Viktor; Murin, Igor

2018-07-01

A pulsed direct current glow discharge time-of-flight mass spectrometry (GD TOF MS) method for the quantification of fluorine in insoluble crystal materials with fluorine doped potassium titanyl phosphate (KTP) KTiOPO4:KF as an example has been proposed. The following parameters were optimized: repelling pulse delay, discharge duration, discharge voltage, and pressure in the discharge cell. Effective ionization of fluorine in the space between sampler and skimmer under short repelling pulse delay, related to the high-energy electron impact at the discharge front, has been demonstrated. A combination of instrumental and mathematical correction approaches was used to cope for the interferences of 38Ar2+ and 1H316O + on 19F+. To maintain surface conductivity in the dielectric KTP crystals and insure its effective sputtering in combined hollow cathode cell, silver suspension applied by the dip-coating method was employed. Fluorine quantification was performed using relative sensitivity factors. The analysis of a reference material and scanning electron microscope-energy dispersive X-ray spectroscopy was used for validation. Fluorine limit of detection by pulsed direct current GD TOF MS was 0.01 mass%. Real sample analysis showed that fluorine seems to be inhomogeneously distributed in the crystals. That is why depth profiling of F, K, O, and P was performed to evaluate the crystals' non-stoichiometry. The approaches designed allow for fluorine quantification in insoluble dielectric materials with minimal sample preparation and destructivity as well as performing depth profiling to assess crystal non-stoichiometry.

Identification and accurate quantification of structurally related peptide impurities in synthetic human C-peptide by liquid chromatography-high resolution mass spectrometry.

PubMed

Li, Ming; Josephs, Ralf D; Daireaux, Adeline; Choteau, Tiphaine; Westwood, Steven; Wielgosz, Robert I; Li, Hongmei

2018-06-04

Peptides are an increasingly important group of biomarkers and pharmaceuticals. The accurate purity characterization of peptide calibrators is critical for the development of reference measurement systems for laboratory medicine and quality control of pharmaceuticals. The peptides used for these purposes are increasingly produced through peptide synthesis. Various approaches (for example mass balance, amino acid analysis, qNMR, and nitrogen determination) can be applied to accurately value assign the purity of peptide calibrators. However, all purity assessment approaches require a correction for structurally related peptide impurities in order to avoid biases. Liquid chromatography coupled to high resolution mass spectrometry (LC-hrMS) has become the key technique for the identification and accurate quantification of structurally related peptide impurities in intact peptide calibrator materials. In this study, LC-hrMS-based methods were developed and validated in-house for the identification and quantification of structurally related peptide impurities in a synthetic human C-peptide (hCP) material, which served as a study material for an international comparison looking at the competencies of laboratories to perform peptide purity mass fraction assignments. More than 65 impurities were identified, confirmed, and accurately quantified by using LC-hrMS. The total mass fraction of all structurally related peptide impurities in the hCP study material was estimated to be 83.3 mg/g with an associated expanded uncertainty of 3.0 mg/g (k = 2). The calibration hierarchy concept used for the quantification of individual impurities is described in detail. Graphical abstract ᅟ.

T2 Relaxometry MRI Predicts Cerebral Palsy in Preterm Infants.

PubMed

Chen, L-W; Wang, S-T; Huang, C-C; Tu, Y-F; Tsai, Y-S

2018-01-18

T2-relaxometry brain MR imaging enables objective measurement of brain maturation based on the water-macromolecule ratio in white matter, but the outcome correlation is not established in preterm infants. Our study aimed to predict neurodevelopment with T2-relaxation values of brain MR imaging among preterm infants. From January 1, 2012, to May 31, 2015, preterm infants who underwent both T2-relaxometry brain MR imaging and neurodevelopmental follow-up were retrospectively reviewed. T2-relaxation values were measured over the periventricular white matter, including sections through the frontal horns, midbody of the lateral ventricles, and centrum semiovale. Periventricular T2 relaxometry in relation to corrected age was analyzed with restricted cubic spline regression. Prediction of cerebral palsy was examined with the receiver operating characteristic curve. Thirty-eight preterm infants were enrolled for analysis. Twenty patients (52.6%) had neurodevelopmental abnormalities, including 8 (21%) with developmental delay without cerebral palsy and 12 (31.6%) with cerebral palsy. The periventricular T2-relaxation values in relation to age were curvilinear in preterm infants with normal development, linear in those with developmental delay without cerebral palsy, and flat in those with cerebral palsy. When MR imaging was performed at >1 month corrected age, cerebral palsy could be predicted with T2 relaxometry of the periventricular white matter on sections through the midbody of the lateral ventricles (area under the receiver operating characteristic curve = 0.738; cutoff value of >217.4 with 63.6% sensitivity and 100.0% specificity). T2-relaxometry brain MR imaging could provide prognostic prediction of neurodevelopmental outcomes in premature infants. Age-dependent and area-selective interpretation in preterm brains should be emphasized. © 2018 by American Journal of Neuroradiology.

Impulsive correction to the elastic moduli obtained using the stress-fluctuation formalism in systems with truncated pair potential

NASA Astrophysics Data System (ADS)

Xu, H.; Wittmer, J. P.; Polińska, P.; Baschnagel, J.

2012-10-01

The truncation of a pair potential at a distance rc is well known to imply, in general, an impulsive correction to the pressure and other moments of the first derivatives of the potential. That, depending on rc, the truncation may also be of relevance to higher derivatives is shown theoretically for the Born contributions to the elastic moduli obtained using the stress-fluctuation formalism in d dimensions. Focusing on isotropic liquids for which the shear modulus G must vanish by construction, the predicted corrections are tested numerically for binary mixtures and polydisperse Lennard-Jones beads in, respectively, d=3 and 2 dimensions. Both models being glass formers, we comment briefly on the temperature (T) dependence of the (corrected) shear modulus G(T) around the glass transition temperature Tg.

Intelligent and automatic in vivo detection and quantification of transplanted cells in MRI.

PubMed

Afridi, Muhammad Jamal; Ross, Arun; Liu, Xiaoming; Bennewitz, Margaret F; Shuboni, Dorela D; Shapiro, Erik M

2017-11-01

Magnetic resonance imaging (MRI)-based cell tracking has emerged as a useful tool for identifying the location of transplanted cells, and even their migration. Magnetically labeled cells appear as dark contrast in T2*-weighted MRI, with sensitivities of individual cells. One key hurdle to the widespread use of MRI-based cell tracking is the inability to determine the number of transplanted cells based on this contrast feature. In the case of single cell detection, manual enumeration of spots in three-dimensional (3D) MRI in principle is possible; however, it is a tedious and time-consuming task that is prone to subjectivity and inaccuracy on a large scale. This research presents the first comprehensive study on how a computer-based intelligent, automatic, and accurate cell quantification approach can be designed for spot detection in MRI scans. Magnetically labeled mesenchymal stem cells (MSCs) were transplanted into rats using an intracardiac injection, accomplishing single cell seeding in the brain. T2*-weighted MRI of these rat brains were performed where labeled MSCs appeared as spots. Using machine learning and computer vision paradigms, approaches were designed to systematically explore the possibility of automatic detection of these spots in MRI. Experiments were validated against known in vitro scenarios. Using the proposed deep convolutional neural network (CNN) architecture, an in vivo accuracy up to 97.3% and in vitro accuracy of up to 99.8% was achieved for automated spot detection in MRI data. The proposed approach for automatic quantification of MRI-based cell tracking will facilitate the use of MRI in large-scale cell therapy studies. Magn Reson Med 78:1991-2002, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies.

PubMed

Mackie, Iain D; DiLabio, Gino A

2011-10-07

The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X = D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)∕aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)∕aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcal/mol, a maximum absolute deviation of 0.05 kcal/mol, and a mean percent absolute deviation of only 1.7%, relative to the (estimated) complete basis set CCSD(T) results. Use of this composite approach to an additional set of eight dimers gave binding energies to within 1% of previously published high-level data. It is also shown that binding within parallel and parallel-crossed conformations of naphthalene dimer is predicted by the composite approach to be 9% greater than that previously reported in the literature. The ability of some recently developed dispersion-corrected density-functional theory methods to predict the binding energies of the set of ten small dimers was also examined. © 2011 American Institute of Physics

Corrigendum to "CSigma graphs: A new approach for plasma characterization in laser-induced breakdown spectroscopy" [J. Quant. Spectrosc. Radiat. Transf. 149 (2014) 90-102

NASA Astrophysics Data System (ADS)

Aragón, C.; Aguilera, J. A.

2015-07-01

The authors regret that Tables 2 and 5 provided in the concerned paper contain erroneous values for the line cross section σl. The correct data are listed in the following tables. Also, the σl values in Tables 4 and 6 are calculated for T=14,000 K and Ne=2.5×1017 cm-3, instead of the T, Ne values indicated in the table footnotes. These corrections do not change the results presented in the manuscript J. Quant. Spectrosc. Radiat. Transf. 149 (2014) 90-102.

Theoretical study on the dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides

NASA Astrophysics Data System (ADS)

Cheng, Li; Shen, Zuochun; Lu, Jianye; Gao, Huide; Lü, Zhiwei

2005-11-01

Dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides, CF 3I, C 2F 5I, and i-C 3F 7I are calculated accurately with B3LYP, MP n ( n = 2-4), QCISD, QCISD(T), CCSD, and CCSD(T) methods. Calculations are performed by using large-core correlation-consistent pseudopotential basis set (SDB-aug-cc-pVTZ) for iodine atom. In all energy calculations, the zero point vibration energy is corrected. And the basis set superposition error is corrected by counterpoise method in the calculation of dissociation energy. Theoretical results are compared with the experimental values.

Two-loop top and bottom Yukawa corrections to the Higgs-boson masses in the complex MSSM

NASA Astrophysics Data System (ADS)

Paßehr, Sebastian; Weiglein, Georg

2018-03-01

Results for the two-loop corrections to the Higgs-boson masses of the MSSM with complex parameters of O{( α _t^2+α _tα _b+α _b^2) } from the Yukawa sector in the gauge-less limit are presented. The corresponding self-energies and their renormalization have been obtained in the Feynman-diagrammatic approach. The impact of the new contributions on the Higgs spectrum is investigated. Furthermore, a comparison with an existing result in the limit of the MSSM with real parameters is carried out. The new results will be included in the public code FeynHiggs.

Volterra Transfer Functions from Pulse Tests for Mildly Nonlinear Channels.

DTIC Science & Technology

1983-07-01

printing(1215) = 0 minimal printing = 1 maximum printing IFIX noise correction option = 0 no correction S1 do noise correction IPLI and IPL2 plot options...TITLE READ(5,1)N1,tI,ISKIP,IREM,IBIAS,IO)LY,DELTA, +OSAV,VAR,DFAC READ(5,1021)TITLE READ(5,I001)IPR, IFIX,IPL1, IPL2 IF(II.EQ.10000)GO To 4320...1)VIRITE (6,1004) IF(IPLT.EQ.1.OR. IPLT.EQ.3) +CALL PLOTIT(DATA2,2,11I~l,,rP,ISEIP,NIAXPL,1,1.0) IFCIPLT. EQ.1.OR. IPL2 .EQ. 0)GO TO 6544 C LABEL(18

Enantiomeric separation and quantification of R/S-amphetamine in urine by ultra-high performance supercritical fluid chromatography tandem mass spectrometry.

PubMed

Hegstad, S; Havnen, H; Helland, A; Spigset, O; Frost, J

2018-03-01

To distinguish between legal and illegal consumption of amphetamine reliable analytical methods for chiral separation of the R- and S-enantiomers of amphetamine in biological specimens are required. In this regard, supercritical fluid chromatography (SFC) has several potential advantages over liquid chromatography, including rapid separation of enantiomers due to low viscosity and high diffusivity of supercritical carbon dioxide, the main component in the SFC mobile phase. A method for enantiomeric separation and quantification of R- and S-amphetamine in urine was developed and validated using ultra-high performance supercritical fluid chromatography-tandem mass spectrometry (UHPSFC-MS/MS). Sample preparation prior to UHPSFC-MS/MS analysis was a semi-automatic solid phase extraction method. The UHPSFC-MS/MS method used a Chiralpak AD-3 column with a mobile phase consisting of CO 2 and 0.2% cyclohexylamine in 2-propanol. The injection volume was 2 μL and run-time was 6 min. MS/MS detection was performed with positive electrospray ionization and two multiple reaction monitoring transitions (m/z 136.1 > 119.0 and m/z 136.1 > 91.0). The calibration range was 50-10,000 ng/mL for each enantiomer. The between-assay relative standard deviations were in the range of 3.7-7.6%. Recovery was 92-93% and matrix effects ranged from 100 to 104% corrected with internal standard. After development and validation, the method has been successfully implemented in routine use at our laboratory for both separation and quantification of R/S-amphetamine, and has proved to be a reliable and useful tool for distinguishing intake of R- and S-amphetamine in authentic patient samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Simultaneous acquisition of perfusion and permeability from corrected relaxation rates with dynamic susceptibility contrast dual gradient echo.

PubMed

Kim, Eun-Ju; Kim, Dae-Hong; Lee, Sang Hoon; Huh, Yong-Min; Song, Ho-Taek; Suh, Jin-Suck

2004-04-01

This study compared two methods, corrected (separation of T(1) and T(2)* effects) and uncorrected, in order to determine the suitability of the perfusion and permeability measures through Delta R(2)* and Delta R(1) analyses. A dynamic susceptibility contrast dual gradient echo (DSC-DGE) was used to image the fixed phantoms and flow phantoms (Sephadex perfusion phantoms and dialyzer phantom for the permeability measurements). The results confirmed that the corrected relaxation rate was linearly proportional to gadolinium-diethyltriamine pentaacetic acid (Gd-DTPA) concentration, whereas the uncorrected relaxation rate did not in the fixed phantom and simulation experiments. For the perfusion measurements, it was found that the correction process was necessary not only for the Delta R(1) time curve but also for the Delta R(2)* time curve analyses. Perfusion could not be measured without correcting the Delta R(2)* time curve. The water volume, which was expressed as the perfusion amount, was found to be closer to the theoretical value when using the corrected Delta R(1) curve in the calculations. However, this may occur in the low concentration of Gd-DTPA in tissue used in this study. For the permeability measurements based on the two-compartment model, the permeability factor (k(ev); e = extravascular, v = vascular) from the outside to the inside of the hollow fibers was greater in the corrected Delta R(1) method than in the uncorrected Delta R(1) method. The differences between the corrected and the uncorrected Delta R(1) values were confirmed by the simulation experiments. In conclusion, this study proposes that the correction for the relaxation rates, Delta R(2)* and Delta R(1), is indispensable in making accurate perfusion and permeability measurements, and that DSC-DGE is a useful method for obtaining information on perfusion and permeability, simultaneously.

Reduced thalamic N-acetylaspartate in idiopathic normal pressure hydrocephalus: a controlled 1H-magnetic resonance spectroscopy study of frontal deep white matter and the thalamus using absolute quantification.

PubMed

Lundin, F; Tisell, A; Dahlqvist Leinhard, O; Tullberg, M; Wikkelsö, C; Lundberg, P; Leijon, G

2011-07-01

Patients with idiopathic normal pressure hydrocephalus (INPH) frequently have a reduction in cerebral blood flow in the subcortical frontal lobe/basal ganglia/thalamic areas. With magnetic resonance spectroscopy, the metabolism in the brain can be examined. The aim of this study was to investigate if there was a compromised metabolism in the thalamus and in the subcortical frontal areas in INPH patients. This was done by measuring total creatine, myo-inositol, total choline, N-acetylaspartate (NAA), total N-acetylaspartate (tNA), glutamate and lactate levels. A comparison was made with healthy individuals (HI). 16 patients (nine males, seven females, mean age 74 years, range 49-83) diagnosed as INPH and 15 HI (nine males, six females, mean age 74 years, range 62-89) were examined. (1)H magnetic resonance spectroscopy (1.5 T, point-resolved spectroscopy, echo time/relaxation time 30/3000 ms, volume of interest 2.5-3 ml) was performed in frontal deep white matter and in the thalamus. Absolute quantification with internal water as a reference was used. INPH patients had lower NAA (p=0.02) and lower tNA (p=0.05) concentrations in the thalamus compared with HI. NAA and tNA in the frontal deep white matter did not differ between patients and HI. The absolute metabolic concentrations of total creatine, myo-inositol total choline, tNA, lactate and Cr ratios in frontal deep white matter and in the thalamus were similar in INPH patients and HI. Reduced thalamic NAA and tNA in INPH patients suggest a compromised metabolic neuronal function in these regions. Thus, the thalamus might have an important role in the pathogenesis of INPH.

Therapeutic evaluation of GM2 gangliosidoses by ELISA using anti-GM2 ganglioside antibodies.

PubMed

Tsuji, Daisuke; Higashine, Yukari; Matsuoka, Kazuhiko; Sakuraba, Hitoshi; Itoh, Kohji

2007-03-01

GM2 gangliosidoses, including Tay-Sachs disease, Sandhoff disease and the AB variant, comprise deficiencies of beta-hexosaminidase isozymes and GM2 ganglioside activator protein associated with accumulation of GM2 ganglioside (GM2) in lysosomes and neurosomatic clinical manifestations. A simple assay system for intracellular quantification of GM2 is required to evaluate the therapeutic effects on GM2-gangliosidoses. We newly established a cell-ELISA system involving anti-GM2 monoclonal antibodies for measuring GM2 storage in fibroblasts from Tay-Sachs and Sandhoff disease patients. We succeeded in detecting the corrective effect of enzyme replacement on elimination of GM2 in the cells with this ELISA system. This simple and sensitive system should be useful as additional diagnosis tool as well as therapeutic evaluation of GM2 gangliosidoses.

Brain Volume Estimation Enhancement by Morphological Image Processing Tools.

PubMed

Zeinali, R; Keshtkar, A; Zamani, A; Gharehaghaji, N

2017-12-01

Volume estimation of brain is important for many neurological applications. It is necessary in measuring brain growth and changes in brain in normal/abnormal patients. Thus, accurate brain volume measurement is very important. Magnetic resonance imaging (MRI) is the method of choice for volume quantification due to excellent levels of image resolution and between-tissue contrast. Stereology method is a good method for estimating volume but it requires to segment enough MRI slices and have a good resolution. In this study, it is desired to enhance stereology method for volume estimation of brain using less MRI slices with less resolution. In this study, a program for calculating volume using stereology method has been introduced. After morphologic method, dilation was applied and the stereology method enhanced. For the evaluation of this method, we used T1-wighted MR images from digital phantom in BrainWeb which had ground truth. The volume of 20 normal brain extracted from BrainWeb, was calculated. The volumes of white matter, gray matter and cerebrospinal fluid with given dimension were estimated correctly. Volume calculation from Stereology method in different cases was made. In three cases, Root Mean Square Error (RMSE) was measured. Case I with T=5, d=5, Case II with T=10, D=10 and Case III with T=20, d=20 (T=slice thickness, d=resolution as stereology parameters). By comparing these results of two methods, it is obvious that RMSE values for our proposed method are smaller than Stereology method. Using morphological operation, dilation allows to enhance the estimation volume method, Stereology. In the case with less MRI slices and less test points, this method works much better compared to Stereology method.

Drug Transporter Protein Quantification of Immortalized Human Lung Cell Lines Derived from Tracheobronchial Epithelial Cells (Calu-3 and BEAS2-B), Bronchiolar-Alveolar Cells (NCI-H292 and NCI-H441), and Alveolar Type II-like Cells (A549) by Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

Sakamoto, Atsushi; Matsumaru, Takehisa; Yamamura, Norio; Suzuki, Shinobu; Uchida, Yasuo; Tachikawa, Masanori; Terasaki, Tetsuya

2015-09-01

Understanding the mechanisms of drug transport in the human lung is an important issue in pulmonary drug discovery and development. For this purpose, there is an increasing interest in immortalized lung cell lines as alternatives to primary cultured lung cells. We recently reported the protein expression in human lung tissues and pulmonary epithelial cells in primary culture, (Sakamoto A, Matsumaru T, Yamamura N, Uchida Y, Tachikawa M, Ohtsuki S, Terasaki T. 2013. J Pharm Sci 102(9):3395-3406) whereas comprehensive quantification of protein expressions in immortalized lung cell lines is sparse. Therefore, the aim of the present study was to clarify the drug transporter protein expression of five commercially available immortalized lung cell lines derived from tracheobronchial cells (Calu-3 and BEAS2-B), bronchiolar-alveolar cells (NCI-H292 and NCI-H441), and alveolar type II cells (A549), by liquid chromatography-tandem mass spectrometry-based approaches. Among transporters detected, breast cancer-resistance protein in Calu-3, NCI-H292, NCI-H441, and A549 and OCTN2 in BEAS2-B showed the highest protein expression. Compared with data from our previous study,(Sakamoto A, Matsumaru T, Yamamura N, Uchida Y, Tachikawa M, Ohtsuki S, Terasaki T. 2013. J Pharm Sci 102(9):3395-3406) NCI-H441 was the most similar with primary lung cells from all regions in terms of protein expression of organic cation/carnitine transporter 1 (OCTN1). In conclusion, the protein expression profiles of transporters in five immortalized lung cell lines were determined, and these findings may contribute to a better understanding of drug transport in immortalized lung cell lines. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

[Contribution of echogradient magnetic resonance imaging in the study of subacromial diseases. Surgical and arthrographic correlations].

PubMed

Touzard, R C; Pigeau, I; Doursounian, L; Maigne, J Y; Vadrot, D

1991-01-01

Fifteen asymptomatic volunteers and 300 patients with suspected lesions of the rotator cuff were examined with T2*- and proton density-weighted gradient echo (T2*-Rho-GEI) MRI sequences (500-700 ms/30 ms/30 degrees) with a 0.5 T (GE-CGR) system and an adapted surface coil. For the patients, the findings were compared with those of arthrography in 130 cases and of surgery in 42 cases. For the operated patients, T2*-Rho-GEI and arthrography allowed correctly diagnosing 31 complete ruptures (CR). However, surgical exploration of the ruptures showed that T2*-Rho-GEI showed the actual extent of the rupture and the degree of tendon retraction better than arthrography. T2*-Rho-GEI also provides information about the thickness and trophicity of the remaining cuff and on local muscle trophicity. T2*-Rho-GEI allows directly evaluating the tendon of the long head of the biceps both in its extra-articular and its intra-articular parts. In 3 cases of complete cuff rupture, MRI allowed detecting 3 associated lesions of the anterior labrum, which had not been suspected on the clinical examination and had not been demonstrated by conventional arthrography. Lastly, out of 12 cases of deep incomplete rupture (n = 12) correctly diagnosed with MRI, 5 had been undetected on arthrography. Similarly, 8 cases of inflammatory alterations suspected with T2*-Rho-GEI and confirmed by surgery had not been recognized with arthrography. For the non-operated patients, T2*-Rho-GEI and arthrography had corresponding results for the diagnosis of CR (8 cases), of DIR (6 cases) and of intact cuff (6 cases).(ABSTRACT TRUNCATED AT 250 WORDS)

The Ethics of Quantification and Why It Doesn't Work; or Life among the Numerologists, Inumerates, and Qualitatives.

ERIC Educational Resources Information Center

Sax, Gilbert

The paper states that quantification is neither ethical nor unethical, but is ethically neutral. It is the behavior or intent of the human being that is clearly a matter of ethical concern. Like numerology and the sects of inumerates and qualitatives, there is not so much an unethical practice that is supported as there is a lack of vision and…

Non-invasive evaluation of blood oxygen saturation and hematocrit from T1 and T2 relaxation times: In-vitro validation in fetal blood.

PubMed

Portnoy, Sharon; Seed, Mike; Sled, John G; Macgowan, Christopher K

2017-12-01

We propose an analytical method for calculating blood hematocrit (Hct) and oxygen saturation (sO 2 ) from measurements of its T 1 and T 2 relaxation times. Through algebraic substitution, established two-compartment relationships describing R1=T1-1 and R2=T2-1 as a function of hematocrit and oxygen saturation were rearranged to solve for Hct and sO 2 in terms of R 1 and R 2 . Resulting solutions for Hct and sO 2 are the roots of cubic polynomials. Feasibility of the method was established by comparison of Hct and sO 2 estimates obtained from relaxometry measurements (at 1.5 Tesla) in cord blood specimens to ground-truth values obtained by blood gas analysis. Monte Carlo simulations were also conducted to assess the effect of T 1 , T 2 measurement uncertainty on precision of Hct and sO 2 estimates. Good agreement was observed between estimated and ground-truth blood properties (bias = 0.01; 95% limits of agreement = ±0.13 for Hct and sO 2 ). Considering the combined effects of biological variability and random measurement noise, we estimate a typical uncertainty of ±0.1 for Hct, sO 2 estimates. Results demonstrate accurate quantification of Hct and sO 2 from T 1 and T 2 . This method is applicable to noninvasive fetal vessel oximetry-an application where existing oximetry devices are unusable or require risky blood-sampling procedures. Magn Reson Med 78:2352-2359, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

[Follow-up of resting-state brain function with magnetic resonance imaging in patients with type 2 diabetes mellitus].

PubMed

Qi, N; Cui, Y; Liu, J C; Yu, M; Teng, G J

2017-10-24

Objective: To investigate the changes of resting brain function with time in patients with type 2 diabetes mellitus (T2DM) by using regional homogeneity (ReHo) with resting-state functional magnetic resonance imaging (rs-fMRI). Methods: Multidimensional cognitive function tests and rs-fMRI scans were performed in 21 T2DM patients and 12 healthy controls in 2012 and 2015 respectively.The differences in clinical variables and the ReHo values before and after were measured by paired sample t test, and the correlation between the change of ReHo value and the change of clinical variables was measured by Pearson correlation analysis based on voxel. Results: The delayed score (14±6) of the T2DM patients in 2015 was significantly lower than that in 2012 (18±6) ( t =-2.88, P =0.009); while the value of ReHo in the bilateral occipital lobe and right middle frontal gyrus was significantly lower than that in 2012 ( P <0.01, Alphasim correction). And the decreased ReHo value in the left occipital lobe was significantly correlated with the change of complex figure test (CFT) delay score and the trail making test-B (TMT-B)( r =0.52, -0.46, both P <0.05). No significant change in cognitive function tests in the healthy control group was found between the two years, ReHo value in right cuneus decreased significantly ( P <0.01, Alphasim correction), but it increased significantly in superior frontal gyrus ( P <0.01, Alphasim correction) in 2015.No significant correlation between the changes of the ReHo values in the right cuneus and right superior frontal gyrus and the changes of cognitive function scores was found in the healthy controls. Conclusions: The visual memory is significantly declined in T2DM patients within 3 years.The reduced neural activity areas in T2DM patients are in the bilateral occipitai lobes and the right middle frontal lobe. Decreased neural activity in the left occipital area is related to visual impairment, information processing speed and attention drops.

Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

PubMed

Karthikeyan, S; Singh, Jiten N; Park, Mina; Kumar, Rajesh; Kim, Kwang S

2008-06-28

Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

Structures, energetics, vibrational spectra of NH4+(H2O)n=4,6 clusters: Ab initio calculations and first principles molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Karthikeyan, S.; Singh, Jiten N.; Park, Mina; Kumar, Rajesh; Kim, Kwang S.

2008-06-01

Important structural isomers of NH4+(H2O)n=4,6 have been studied by using density functional theory, Møller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n=4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.

Quantification of concentrated Chinese medicine granules by quantitative polymerase chain reaction.

PubMed

Lo, Yat-Tung; Shaw, Pang-Chui

2017-10-25

Determination of the amount of constituent in a multi-herb product is important for quality control. In concentrated Chinese medicine granules (CCMG), no dregs are left after dissolution of the CCMG. This study is the first to examine the feasibility of using quantitative polymerase chain reaction (qPCR) to find the amount of CCMG in solution form. DNA was extracted from Hirudo and Zaocys CCMG mixed at different ratios and amplified in qPCR using species-specific primers. The threshold cycle (C T ) obtained was compared with the respective standard curves. Results showed that reproducible quantification results could be obtained (1) for 5-50mg CCMG using a modified DNA extraction protocol, (2) amongst DNA extracted from the same batch of CCMG and (3) amongst different batches of CCMG from the same company. This study demonstrated the constitute amount of CCMG in a mixture could be determined using qPCR. This work has extended the application of DNA techniques for the quantification of herbal products and this approach may be developed for quality assurance in the CCMG industry. Copyright © 2017 Elsevier B.V. All rights reserved.

Paternal behavior in the Mongolian gerbil (Meriones unguiculatus): Estrogenic and androgenic regulation.

PubMed

Martínez, Ana; Ramos, Guillermo; Martínez-Torres, Martín; Nicolás, Leticia; Carmona, Agustín; Cárdenas, Mario; Luis, Juana

2015-05-01

Here, we analyzed the effects of testosterone (T) and its metabolites, estradiol (E2) and dihydrotestosterone (DHT), on the onset of paternal behavior in virgin male Mongolian gerbils (Meriones unguiculatus). We hypothesized that T and E2, but not DHT, would facilitate the onset of paternal behavior. Seventy males displaying aggression toward pups were selected through a paternal behavior screening test. Forty males were bilaterally castrated. Of them, 10 were implanted with T, 10 with E2, and 10 with DHT, and 10 received no treatment. Another 30 males underwent a sham procedure. In these gerbils, T, E2 and DHT were measured to obtain the basal levels of these hormones. After treatment, the paternal behavior test was conducted again. Blood samples were obtained immediately after the administration of the test for the quantification of T, E2 and DHT by radioimmunoassay. Surprisingly, 100% of the males that received T, E2 and DHT implants stopped being aggressive and became paternal. Castrated and sham-operated males displayed no changes in their aggressive behaviors. This is the first report that T and its metabolites are involved in neuroendocrine mechanisms that inhibit aggression toward pups and facilitate paternal behavior in virgin male Mongolian gerbils. In addition, this is the first report of regulation of paternal behavior in a rodent by estrogenic and androgenic pathways. Copyright © 2015 Elsevier Inc. All rights reserved.

Parallel imaging of knee cartilage at 3 Tesla.

PubMed

Zuo, Jin; Li, Xiaojuan; Banerjee, Suchandrima; Han, Eric; Majumdar, Sharmila

2007-10-01

To evaluate the feasibility and reproducibility of quantitative cartilage imaging with parallel imaging at 3T and to determine the impact of the acceleration factor (AF) on morphological and relaxation measurements. An eight-channel phased-array knee coil was employed for conventional and parallel imaging on a 3T scanner. The imaging protocol consisted of a T2-weighted fast spin echo (FSE), a 3D-spoiled gradient echo (SPGR), a custom 3D-SPGR T1rho, and a 3D-SPGR T2 sequence. Parallel imaging was performed with an array spatial sensitivity technique (ASSET). The left knees of six healthy volunteers were scanned with both conventional and parallel imaging (AF = 2). Morphological parameters and relaxation maps from parallel imaging methods (AF = 2) showed comparable results with conventional method. The intraclass correlation coefficient (ICC) of the two methods for cartilage volume, mean cartilage thickness, T1rho, and T2 were 0.999, 0.977, 0.964, and 0.969, respectively, while demonstrating excellent reproducibility. No significant measurement differences were found when AF reached 3 despite the low signal-to-noise ratio (SNR). The study demonstrated that parallel imaging can be applied to current knee cartilage quantification at AF = 2 without degrading measurement accuracy with good reproducibility while effectively reducing scan time. Shorter imaging times can be achieved with higher AF at the cost of SNR. (c) 2007 Wiley-Liss, Inc.

Pattern recognition of estradiol, testosterone and dihydrotestosterone in children's saliva samples using stochastic microsensors

NASA Astrophysics Data System (ADS)

Staden, Raluca-Ioana Stefan-Van; Gugoaşă, Livia Alexandra; Calenic, Bogdan; Legler, Juliette

2014-07-01

Stochastic microsensors based on diamond paste and three types of electroactive materials (maltodextrin (MD), α-cyclodextrin (α-CD) and 5,10,15,20-tetraphenyl-21H,23H porphyrin (P)) were developed for the assay of estradiol (E2), testosterone (T2) and dihydrotestosterone (DHT) in children's saliva. The main advantage of utilization of such tools is the possibility to identify and quantify all three hormones within minutes in small volumes of childen's saliva. The limits of quantification obtained for DHT, T2, and E2 (1 fmol/L for DHT, 1 pmol/L for T2, and 66 fmol/L for E2) determined using the proposed tools allows the utilization of these new methods with high reliability for the screening of saliva samples from children. This new method proposed for the assay of the three hormones overcomes the limitations (regarding limits of determination) of ELISA method which is the standard method used in clinical laboratories for the assay of DHT, T2, and E2 in saliva samples. The main feature of its utilization for children's saliva is to identify earlier problems related to early puberty and obesity.

KiT: a MATLAB package for kinetochore tracking.

PubMed

Armond, Jonathan W; Vladimirou, Elina; McAinsh, Andrew D; Burroughs, Nigel J

2016-06-15

During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present 'KiT' (Kinetochore Tracking)-an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development. Supplementary data are available at Bioinformatics online. jonathan.armond@warwick.ac.uk. © The Author 2016. Published by Oxford University Press.

MR Fingerprinting Using The Quick Echo Splitting NMR Imaging Technique

PubMed Central

Jiang, Yun; Ma, Dan; Jerecic, Renate; Duerk, Jeffrey; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A.

2016-01-01

Purpose The purpose of the study is to develop a quantitative method for the relaxation properties with a reduced radio frequency (RF) power deposition by combining Magnetic Resonance Fingerprinting (MRF) technique with Quick Echo Splitting NMR Imaging Technique (QUEST). Methods A QUEST-based MRF sequence was implemented to acquire high order echoes by increasing the gaps between RF pulses. Bloch simulations were used to calculate a dictionary containing the range of physically plausible signal evolutions using a range of T1 and T2 values based on the pulse sequence. MRF-QUEST was evaluated by comparing to the results of spin-echo methods. The SAR of QUEST-MRF was compared to the clinically available methods. Results MRF-QUEST quantifies the relaxation properties with good accuracy at the estimated head Specific Absorption Rate (SAR) of 0.03 W/kg. T1 and T2 values estimated by MRF-QUEST are in good agreement with the traditional methods. Conclusion The combination of the MRF and the QUEST provides an accurate quantification of T1 and T2 simultaneously with reduced RF power deposition. The resulting lower SAR may provide a new acquisition strategy for MRF when RF energy deposition is problematic. PMID:26924639

Quantification of 18F-fluorocholine kinetics in patients with prostate cancer.

PubMed

Verwer, Eline E; Oprea-Lager, Daniela E; van den Eertwegh, Alfons J M; van Moorselaar, Reindert J A; Windhorst, Albert D; Schwarte, Lothar A; Hendrikse, N Harry; Schuit, Robert C; Hoekstra, Otto S; Lammertsma, Adriaan A; Boellaard, Ronald

2015-03-01

Choline kinase is upregulated in prostate cancer, resulting in increased (18)F-fluoromethylcholine uptake. This study used pharmacokinetic modeling to validate the use of simplified methods for quantification of (18)F-fluoromethylcholine uptake in a routine clinical setting. Forty-minute dynamic PET/CT scans were acquired after injection of 204 ± 9 MBq of (18)F-fluoromethylcholine, from 8 patients with histologically proven metastasized prostate cancer. Plasma input functions were obtained using continuous arterial blood-sampling as well as using image-derived methods. Manual arterial blood samples were used for calibration and correction for plasma-to-blood ratio and metabolites. Time-activity curves were derived from volumes of interest in all visually detectable lymph node metastases. (18)F-fluoromethylcholine kinetics were studied by nonlinear regression fitting of several single- and 2-tissue plasma input models to the time-activity curves. Model selection was based on the Akaike information criterion and measures of robustness. In addition, the performance of several simplified methods, such as standardized uptake value (SUV), was assessed. Best fits were obtained using an irreversible compartment model with blood volume parameter. Parent fractions were 0.12 ± 0.4 after 20 min, necessitating individual metabolite corrections. Correspondence between venous and arterial parent fractions was low as determined by the intraclass correlation coefficient (0.61). Results for image-derived input functions that were obtained from volumes of interest in blood-pool structures distant from tissues of high (18)F-fluoromethylcholine uptake yielded good correlation to those for the blood-sampling input functions (R(2) = 0.83). SUV showed poor correlation to parameters derived from full quantitative kinetic analysis (R(2) < 0.34). In contrast, lesion activity concentration normalized to the integral of the blood activity concentration over time (SUVAUC) showed good correlation (R(2) = 0.92 for metabolite-corrected plasma; 0.65 for whole-blood activity concentrations). SUV cannot be used to quantify (18)F-fluoromethylcholine uptake. A clinical compromise could be SUVAUC derived from 2 consecutive static PET scans, one centered on a large blood-pool structure during 0-30 min after injection to obtain the blood activity concentrations and the other a whole-body scan at 30 min after injection to obtain lymph node activity concentrations. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Phase aberration simulation study of MRgFUS breast treatments

PubMed Central

Farrer, Alexis I.; Almquist, Scott; Dillon, Christopher R.; Neumayer, Leigh A.; Parker, Dennis L.; Christensen, Douglas A.; Payne, Allison

2016-01-01

Purpose: This simulation study evaluates the effects of phase aberration in breast MR-guided focused ultrasound (MRgFUS) ablation treatments performed with a phased-array transducer positioned laterally to the breast. A quantification of these effects in terms of thermal dose delivery and the potential benefits of phase correction is demonstrated in four heterogeneous breast numerical models. Methods: To evaluate the effects of varying breast tissue properties on the quality of the focus, four female volunteers with confirmed benign fibroadenomas were imaged using 3T MRI. These images were segmented into numerical models with six tissue types, with each tissue type assigned standard acoustic properties from the literature. Simulations for a single-plane 16-point raster-scan treatment trajectory centered in a fibroadenoma in each modeled breast were performed for a breast-specific MRgFUS system. At each of the 16 points, pressure patterns both with and without applying a phase correction technique were determined with the hybrid-angular spectrum method. Corrected phase patterns were obtained using a simulation-based phase aberration correction technique to adjust each element’s transmit phase to obtain maximized constructive interference at the desired focus. Thermal simulations were performed for both the corrected and uncorrected pressure patterns using a finite-difference implementation of the Pennes bioheat equation. The effect of phase correction was evaluated through comparison of thermal dose accumulation both within and outside a defined treatment volume. Treatment results using corrected and uncorrected phase aberration simulations were compared by evaluating the power required to achieve a 20 °C temperature rise at the first treatment location. The extent of the volumes that received a minimum thermal dose of 240 CEM at 43 °C inside the intended treatment volume as well as the volume in the remaining breast tissues was also evaluated in the form of a dose volume ratio (DVR), a DVR percent change between corrected and uncorrected phases, and an additional metric that measured phase spread. Results: With phase aberration correction applied, there was an improvement in the focus for all breast anatomies as quantified by a reduction in power required (13%–102%) to reach 20 °C when compared to uncorrected simulations. Also, the DVR percent change increased by 5%–77% in seven out of eight cases, indicating an improvement to the treatment as measured by a reduction in thermal dose deposited to the nontreatment tissues. Breast compositions with a higher degree of heterogeneity along the ultrasound beam path showed greater reductions in thermal dose delivered outside of the treatment volume with correction applied than beam trajectories that propagated through more homogeneous breast compositions. An increasing linear trend was observed between the DVR percent change and the phase-spread metric (R2 = 0.68). Conclusions: These results indicate that performing phase aberration correction for breast MRgFUS treatments is beneficial for the small-aperture transducer (14.4 × 9.8 cm) evaluated in this work. While all breast anatomies could benefit from phase aberration correction, greater benefits are observed in more heterogeneous anatomies. PMID:26936722