Science.gov

Sample records for lung density correction

  1. Variations of lung density and geometry on inhomogeneity correction algorithms: a Monte Carlo dosimetric evaluation.

    PubMed

    Chow, James C L; Leung, Michael K K; Van Dyk, Jake

    2009-08-01

    This work contributed the following new information to the study of inhomogeneity correction algorithm: (1) Evaluation of lung dose calculation methods as a function of lung relative electron density (rhoe,lung) and treatment geometry and (2) comparison of doses calculated using the collapsed cone convolution (CCC) and adaptive convolution (AC) in lung using the Monte Carlo (MC) simulation with the EGSnrc-based code. The variations of rhoe,lung and geometry such as the position and dimension of the lung were studied with different photon beam energies and field sizes. Three groups of inhomogeneous lung phantoms, namely, "slab," "column," and "cube," with different positions, volumes, and shapes of lung in water as well as clinical computed tomography lung images were used. The rhoe,lung in each group of phantoms vary from 0.05 to 0.7. 6 and 18 MV photon beams with small (4 x 4 cm2) and medium (10 x 10 cm2) field sizes produced by a Varian 21 EX linear accelerator were used. This study reveals that doses in the inhomogeneous lung calculated by the CCC match well with those by AC within +/- 1%, indicating that the AC, with an advantage of shorter computing times (three to four times shorter than CCC), is a good substitute for CCC. Comparing the CCC and AC to MC in general, significant dose deviations are found when the rhoe,lung is < or =0.3. The degree of deviation depends on the photon beam energy and field size and is relatively large when high-energy photon beams with small fields are used. For penumbra widths (20%-80%), the CCC and AC agree well with MC for the slab and cube phantoms with the lung volumes at the central beam axis (CAX). However, deviations (>2 mm) occur in the column phantoms, with two lung volumes separated by a unit density column along the CAX in the middle using the 18 MV beam with 4 x 4 cm2 field for rhoe,lung < or =0.1. This study provides new dosimetric data to evaluate the impact of the variations of rhoe,lung and geometry on dose

  2. TBI lung dose comparisons using bilateral and anteroposterior delivery techniques and tissue density corrections.

    PubMed

    Bailey, Daniel W; Wang, Iris Z; Lakeman, Tara; Hales, Lee D; Singh, Anurag K; Podgorsak, Matthew B

    2015-03-08

    This study compares lung dose distributions for two common techniques of total body photon irradiation (TBI) at extended source-to-surface distance calculated with, and without, tissue density correction (TDC). Lung dose correction factors as a function of lateral thorax separation are approximated for bilateral opposed TBI (supine), similar to those published for anteroposterior-posteroanterior (AP-PA) techniques in AAPM Report 17 (i.e., Task Group 29). 3D treatment plans were created retrospectively for 24 patients treated with bilateral TBI, and for whom CT data had been acquired from the head to the lower leg. These plans included bilateral opposed and AP-PA techniques- each with and without - TDC, using source-to-axis distance of 377 cm and largest possible field size. On average, bilateral TBI requires 40% more monitor units than AP-PA TBI due to increased separation (26% more for 23 MV). Calculation of midline thorax dose without TDC leads to dose underestimation of 17% on average (standard deviation, 4%) for bilateral 6 MV TBI, and 11% on average (standard deviation, 3%) for 23 MV. Lung dose correction factors (CF) are calculated as the ratio of midlung dose (with TDC) to midline thorax dose (without TDC). Bilateral CF generally increases with patient separation, though with high variability due to individual uniqueness of anatomy. Bilateral CF are 5% (standard deviation, 4%) higher than the same corrections calculated for AP-PA TBI in the 6 MV case, and 4% higher (standard deviation, 2%) for 23 MV. The maximum lung dose is much higher with bilateral TBI (up to 40% higher than prescribed, depending on patient anatomy) due to the absence of arm tissue blocking the anterior chest. Dose calculations for bilateral TBI without TDC are incorrect by up to 24% in the thorax for 6 MV and up to 16% for 23 MV. Bilateral lung CF may be calculated as 1.05 times the values published in Table 6 of AAPM Report 17, though a larger patient pool is necessary to better

  3. Conservative surgery and radiotherapy for stage I/II breast cancer using lung density correction: 10-year and 15-year results

    SciTech Connect

    Pierce, Lori J. . E-mail: ljpierce@umich.edu; Griffith, Kent A.; Hayman, James A.; Douglas, Kathye R.; Lichter, Allen S.

    2005-04-01

    Purpose: Radiotherapy (RT) planning for breast cancer using lung density correction improves dose homogeneity. Its use obviates the need for a medial wedge, thus reducing scatter to the opposite breast. Although lung density correction is used at many centers in planning for early-stage breast cancer, long-term results of local control and survival have not been reported. Since 1984, we have used lung density correction for dose calculations at the University of Michigan. We now present our 10-year and 15-year results. Methods and Materials: The records of 867 patients with Stage I/II breast cancer treated with breast-conserving surgery and RT with or without systemic therapy were reviewed. Tangential fields delivering 45-50 Gy to the whole breast calculated using lung density correction were used. A boost was added in 96.8% of patients for a total median dose of 61.8 Gy. Results: With a median follow-up of 6.6 years (range, 0.2-18.9 years), 5-, 10-, and 15-year actuarial rates of in-breast tumor recurrence as only first failure were 2.2%, 3.6%, and 5.4%, respectively. With surgical salvage, the 15-year cumulative rate of local control was 99.7%. Factors that significantly predicted for increased rate of local recurrence in multivariate analysis were age {<=} 35 years, hazard ratio 4.8 (95% confidence interval [CI], 1.6-13.9) p = 0.004; negative progesterone receptor status, hazard ratio 6.8 (95% CI, 2.3-20.3) p = < 0.001; negative estrogen receptor status, hazard ratio 4.0 (95% CI, 1.5-11.1) p = 0.007; and lack of adjuvant tamoxifen therapy, hazard ratio 7.7 (95% CI, 1.7-33.3) p = 0.008. Relapse-free survival rates at 5, 10, and 15 years were 84.6%, 70.8%, and 55.9%, respectively; breast cancer-specific survival rates were 94.4%, 90.5%, and 86.9%, respectively; and corresponding estimates for overall survival were 89.7%, 75.7%, and 61.3%. Conclusions: Use of lung density correction was associated with high rates of local control, relapse-free survival, breast

  4. Correction for ‘artificial’ electron disequilibrium due to cone-beam CT density errors: implications for on-line adaptive stereotactic body radiation therapy of lung

    NASA Astrophysics Data System (ADS)

    Disher, Brandon; Hajdok, George; Wang, An; Craig, Jeff; Gaede, Stewart; Battista, Jerry J.

    2013-06-01

    Cone-beam computed tomography (CBCT) has rapidly become a clinically useful imaging modality for image-guided radiation therapy. Unfortunately, CBCT images of the thorax are susceptible to artefacts due to scattered photons, beam hardening, lag in data acquisition, and respiratory motion during a slow scan. These limitations cause dose errors when CBCT image data are used directly in dose computations for on-line, dose adaptive radiation therapy (DART). The purpose of this work is to assess the magnitude of errors in CBCT numbers (HU), and determine the resultant effects on derived tissue density and computed dose accuracy for stereotactic body radiation therapy (SBRT) of lung cancer. Planning CT (PCT) images of three lung patients were acquired using a Philips multi-slice helical CT simulator, while CBCT images were obtained with a Varian On-Board Imaging system. To account for erroneous CBCT data, three practical correction techniques were tested: (1) conversion of CBCT numbers to electron density using phantoms, (2) replacement of individual CBCT pixel values with bulk CT numbers, averaged from PCT images for tissue regions, and (3) limited replacement of CBCT lung pixels values (LCT) likely to produce artificial lateral electron disequilibrium. For each corrected CBCT data set, lung SBRT dose distributions were computed for a 6 MV volume modulated arc therapy (VMAT) technique within the Philips Pinnacle treatment planning system. The reference prescription dose was set such that 95% of the planning target volume (PTV) received at least 54 Gy (i.e. D95). Further, we used the relative depth dose factor as an a priori index to predict the effects of incorrect low tissue density on computed lung dose in regions of severe electron disequilibrium. CT number profiles from co-registered CBCT and PCT patient lung images revealed many reduced lung pixel values in CBCT data, with some pixels corresponding to vacuum (-1000 HU). Similarly, CBCT data in a plastic lung

  5. Correction for 'artificial' electron disequilibrium due to cone-beam CT density errors: implications for on-line adaptive stereotactic body radiation therapy of lung.

    PubMed

    Disher, Brandon; Hajdok, George; Wang, An; Craig, Jeff; Gaede, Stewart; Battista, Jerry J

    2013-06-21

    Cone-beam computed tomography (CBCT) has rapidly become a clinically useful imaging modality for image-guided radiation therapy. Unfortunately, CBCT images of the thorax are susceptible to artefacts due to scattered photons, beam hardening, lag in data acquisition, and respiratory motion during a slow scan. These limitations cause dose errors when CBCT image data are used directly in dose computations for on-line, dose adaptive radiation therapy (DART). The purpose of this work is to assess the magnitude of errors in CBCT numbers (HU), and determine the resultant effects on derived tissue density and computed dose accuracy for stereotactic body radiation therapy (SBRT) of lung cancer. Planning CT (PCT) images of three lung patients were acquired using a Philips multi-slice helical CT simulator, while CBCT images were obtained with a Varian On-Board Imaging system. To account for erroneous CBCT data, three practical correction techniques were tested: (1) conversion of CBCT numbers to electron density using phantoms, (2) replacement of individual CBCT pixel values with bulk CT numbers, averaged from PCT images for tissue regions, and (3) limited replacement of CBCT lung pixels values (LCT) likely to produce artificial lateral electron disequilibrium. For each corrected CBCT data set, lung SBRT dose distributions were computed for a 6 MV volume modulated arc therapy (VMAT) technique within the Philips Pinnacle treatment planning system. The reference prescription dose was set such that 95% of the planning target volume (PTV) received at least 54 Gy (i.e. D95). Further, we used the relative depth dose factor as an a priori index to predict the effects of incorrect low tissue density on computed lung dose in regions of severe electron disequilibrium. CT number profiles from co-registered CBCT and PCT patient lung images revealed many reduced lung pixel values in CBCT data, with some pixels corresponding to vacuum (-1000 HU). Similarly, CBCT data in a plastic lung

  6. A density dependent dispersion correction.

    PubMed

    Steinmann, Stephan N; Corminboeuf, Clémence

    2011-01-01

    Density functional approximations fail to provide an accurate treatment of weak interactions. More recent, but not readily available functionals can lead to significant improvements. A simple alternative to correct for the missing weak interactions is to add, a posteriori, an atom pair-wise dispersion correction. We here present a density dependent dispersion correction, dDXDM, which dramatically improves the performance of popular functionals (e.g., PBE-dDXDM or B3LYP-dDXDM) for a set of 145 systems featuring both inter- and intramolecular interactions. Whereas the highly parameterized M06-2X functional, the long-range corrected LC-BLYP and the fully non-local van der Waals density functional rPW86-W09 also lead to improved results as compared to standard DFT methods, the enhanced performance of dDXDM remains the most impressive.

  7. Evaluation of attenuation corrections using Monte Carlo simulated lung SPECT

    NASA Astrophysics Data System (ADS)

    Gustafsson, Agnetha; Bake, Björn; Jacobsson, Lars; Johansson, Åke; Ljungberg, Michael; Moonen, Michaela

    1998-08-01

    SPECT (single photon emission computed tomography) images are distorted by photon attenuation. The effect is complex in the thoracic region due to different tissue densities. This study compares the effect on the image homogeneity of two different methods of attenuation correction in lung SPECT; one pre-processing and one post-processing method. This study also investigates the impact of attenuation correction parameters such as lung contour, body contour, density of the lung tissue and effective attenuation coefficient. The Monte Carlo technique was used to simulate SPECT studies of a digital thorax phantom containing a homogeneous activity distribution in the lung. Homogeneity in reconstructed images was calculated as the coefficient of variation (CV). The isolated effect of the attenuation correction was assessed by normalizing pixel values from the attenuation corrected lung by pixel values from the lung with no attenuation effects. Results show that the CV decreased from 12.8% with no attenuation correction to 4.4% using the post-processing method and true densities in the thoracic region. The impact of variations in the definition of the body contour was found to be marginal while the corresponding effect of variations in the lung contour was substantial.

  8. A new boundary correction method for lung parenchyma

    NASA Astrophysics Data System (ADS)

    Liang, Junfang; Jiang, Huiqin; Ma, Ling; Liu, Yumin; Toshiya, Nakaguchi

    2017-02-01

    In order to repair the boundary depressions caused by juxtapleural nodules and improve the lung segmentation accuracy, we propose a new boundary correction method for lung parenchyma. Firstly, the top-hat filter is used to enhance the image contrast; Secondly, we employ the Ostu algorithm for image binarization; Thirdly, the connected component labeling algorithm is utilized to remove the main trachea; Fourthly, the initial mask image is obtained by morphological region filling algorithm; Fifthly, the boundary tracing algorithm is applied to extract the initial lung contour; Afterwards, we design a sudden change degree algorithm to modify the initial lung contour; Finally, the complete lung parenchyma image is obtained. The novelty is that sudden change degree algorithm can detect the inflection points more accurately than other methods, which contributes to repairing lung contour efficiently. The experimental results show that the proposed method can incorporate the juxtapleural nodules into the lung parenchyma effectively, and the precision is increased by 6.46% and 2.72% respectively compared with the other two methods, providing favorable conditions for the accurate detection of pulmonary nodules and having important clinical value.

  9. Finite number density corrections to leptogenesis

    NASA Astrophysics Data System (ADS)

    Beneke, Martin; Garbrecht, Björn; Herranen, Matti; Schwaller, Pedro

    2010-10-01

    We derive and solve kinetic equations for leptogenesis within the Closed Time Path (CTP) formalism. It is particularly emphasised how the procedure of real intermediate state subtraction familiar from the Boltzmann approach is realised within the CTP framework; and we show how in time-independent situations no lepton asymmetry emerges, in accordance with the CPT theorem. The CTP approach provides new quantum statistical corrections from evaluating the loop integrals. These lead to an enhancement of the asymmetry originating from the Bose statistics of the Higgs particles. To quantify this effect, we define and evaluate an effective CP-violating parameter. We also solve the kinetic equations and show explicitly that the new quantum statistical corrections can be neglected in the strong-washout regime, while, depending on initial conditions, they can be sizable for weak washout.

  10. Scatter correction associated with dedicated dual-source CT hardware improves accuracy of lung air measures.

    PubMed

    Mobberley, Sean D; Fuld, Matthew K; Sieren, Jered P; Primak, Andrew N; Hoffman, Eric A

    2013-11-01

    Accurate assessment of air density used to quantitatively characterize amount and distribution of emphysema in chronic obstructive pulmonary disease (COPD) subjects has remained challenging. Hounsfield units (HU) within tracheal air can be considerably less negative than -1000 HU. This study has sought to characterize the effects of improved scatter correction used in dual-source pulmonary computed tomography (CT). Dual-source dual-energy (DSDE) and single-source (SS) scans taken at multiple energy levels and scan settings were acquired for quantitative comparison using anesthetized ovine (n = 6), swine (n = 13), and a lung phantom. Data were evaluated for the lung, inferior vena cava, and tracheal segments. To minimize the effect of cross-scatter, the phantom scans in the DSDE mode were obtained by reducing the current of one of the tubes to near zero. A significant shift in mean HU values in the tracheal regions of animals and the phantom is observed, with values consistently closer to -1000 HU in DSDE mode. HU values associated with SS mode demonstrated a positive shift of up to 32 HU. In vivo tracheal air measurements demonstrated considerable variability with SS scanning, whereas these values were more consistent with DSDE imaging. Scatter effects in the lung parenchyma differed from adjacent tracheal measures. Data suggest that the scatter correction introduced into the dual-energy mode of imaging has served to provide more accurate CT lung density measures sought to quantitatively assess the presence and distribution of emphysema in COPD subjects. Data further suggest that CT images, acquired without adequate scatter correction, cannot be corrected by linear algorithms given the variability in tracheal air HU values and the independent scatter effects on lung parenchyma. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

  11. Improved correction for the tissue fraction effect in lung PET/CT imaging

    NASA Astrophysics Data System (ADS)

    Holman, Beverley F.; Cuplov, Vesna; Millner, Lynn; Hutton, Brian F.; Maher, Toby M.; Groves, Ashley M.; Thielemans, Kris

    2015-09-01

    Recently, there has been an increased interest in imaging different pulmonary disorders using PET techniques. Previous work has shown, for static PET/CT, that air content in the lung influences reconstructed image values and that it is vital to correct for this ‘tissue fraction effect’ (TFE). In this paper, we extend this work to include the blood component and also investigate the TFE in dynamic imaging. CT imaging and PET kinetic modelling are used to determine fractional air and blood voxel volumes in six patients with idiopathic pulmonary fibrosis. These values are used to illustrate best and worst case scenarios when interpreting images without correcting for the TFE. In addition, the fractional volumes were used to determine correction factors for the SUV and the kinetic parameters. These were then applied to the patient images. The kinetic parameters K1 and Ki along with the static parameter SUV were all found to be affected by the TFE with both air and blood providing a significant contribution to the errors. Without corrections, errors range from 34-80% in the best case and 29-96% in the worst case. In the patient data, without correcting for the TFE, regions of high density (fibrosis) appeared to have a higher uptake than lower density (normal appearing tissue), however this was reversed after air and blood correction. The proposed correction methods are vital for quantitative and relative accuracy. Without these corrections, images may be misinterpreted.

  12. Method and apparatus for measuring lung density by Compton backscattering

    DOEpatents

    Loo, Billy W.; Goulding, Frederick S.

    1991-01-01

    The density of the lung of a patient suffering from pulmonary edema is monitored by irradiating the lung by a single collimated beam of monochromatic photons and measuring the energies of photons Compton backscattered from the lung by a single high-resolution, high-purity germanium detector. A compact system geometry and a unique data extraction scheme are utilized to monimize systematic errors due to the presence of the chestwall and multiple scattering.

  13. Method and apparatus for measuring lung density by Compton backscattering

    DOEpatents

    Loo, B.W.; Goulding, F.S.

    1988-03-11

    The density of the lung of a patient suffering from pulmonary edema is monitored by irradiating the lung by a single collimated beam of monochromatic photons and measuring the energies of photons compton back-scattered from the lung by a single high-resolution, high-purity germanium detector. A compact system geometry and a unique data extraction scheme are utilized to minimize systematic errors due to the presence of the chestwall and multiple scattering. 11 figs., 1 tab.

  14. Regional differences in alveolar density in the human lung are related to lung height.

    PubMed

    McDonough, John E; Knudsen, Lars; Wright, Alexander C; Elliott, W Mark; Ochs, Matthias; Hogg, James C

    2015-06-01

    The gravity-dependent pleural pressure gradient within the thorax produces regional differences in lung inflation that have a profound effect on the distribution of ventilation within the lung. This study examines the hypothesis that gravitationally induced differences in stress within the thorax also influence alveolar density in terms of the number of alveoli contained per unit volume of lung. To test this hypothesis, we measured the number of alveoli within known volumes of lung located at regular intervals between the apex and base of four normal adult human lungs that were rapidly frozen at a constant transpulmonary pressure, and used microcomputed tomographic imaging to measure alveolar density (number alveoli/mm3) at regular intervals between the lung apex and base. These results show that at total lung capacity, alveolar density in the lung apex is 31.6 ± 3.4 alveoli/mm3, with 15 ± 6% of parenchymal tissue consisting of alveolar duct. The base of the lung had an alveolar density of 21.2 ± 1.6 alveoli/mm3 and alveolar duct volume fraction of 29 ± 6%. The difference in alveolar density can be negated by factoring in the effects of alveolar compression due to the pleural pressure gradient at the base of the lung in vivo and at functional residual capacity.

  15. Association Between RT-Induced Changes in Lung Tissue Density and Global Lung Function

    SciTech Connect

    Ma Jinli; Zhang Junan; Zhou Sumin; Hubbs, Jessica L.; Foltz, Rodney J.; Hollis, Donna R.; Light, Kim L.; Wong, Terence Z.; Kelsey, Christopher R.; Marks, Lawrence B.

    2009-07-01

    Purpose: To assess the association between radiotherapy (RT)-induced changes in computed tomography (CT)-defined lung tissue density and pulmonary function tests (PFTs). Methods and Materials: Patients undergoing incidental partial lung RT were prospectively assessed for global (PFTs) and regional (CT and single photon emission CT [SPECT]) lung function before and, serially, after RT. The percent reductions in the PFT and the average changes in lung density were compared (Pearson correlations) in the overall group and subgroups stratified according to various clinical factors. Comparisons were also made between the CT- and SPECT-based computations using the Mann-Whitney U test. Results: Between 1991 and 2004, 343 patients were enrolled in this study. Of these, 111 patients had a total of 203 concurrent post-RT evaluations of changes in lung density and PFTs available for the analyses, and 81 patients had a total of 141 concurrent post-RT SPECT images. The average increases in lung density were related to the percent reductions in the PFTs, albeit with modest correlation coefficients (range, 0.20-0.43). The analyses also indicated that the association between lung density and PFT changes is essentially equivalent to the corresponding association with SPECT-defined lung perfusion. Conclusion: We found a weak quantitative association between the degree of increase in lung density as defined by CT and the percent reduction in the PFTs.

  16. Adiabatic corrections to density functional theory energies and wave functions.

    PubMed

    Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas

    2008-09-25

    The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT.

  17. A System-Dependent Density-Based Dispersion Correction.

    PubMed

    Steinmann, Stephan N; Corminboeuf, Clemence

    2010-07-13

    Density functional approximations fail to provide a consistent description of weak molecular interactions arising from small electron density overlaps. A simple remedy to correct for the missing interactions is to add a posteriori an attractive energy term summed over all atom pairs in the system. The density-dependent energy correction, presented herein, is applicable to all elements of the periodic table and is easily combined with any electronic structure method, which lacks the accurate treatment of weak interactions. Dispersion coefficients are computed according to Becke and Johnson's exchange-hole dipole moment (XDM) formalism, thereby depending on the chemical environment of an atom (density, oxidation state). The long-range ∼R(-6) potential is supplemented with higher-order correction terms (∼R(-8) and ∼R(-10)) through the universal damping function of Tang and Toennies. A genuine damping factor depending on (iterative) Hirshfeld (overlap) populations, atomic ionization energies, and two adjustable parameters specifically fitted to a given DFT functional is also introduced. The proposed correction, dDXDM, dramatically improves the performance of popular density functionals. The analysis of 30 (dispersion corrected) density functionals on 145 systems reveals that dDXDM largely reduces the errors of the parent functionals for both inter- and intramolecular interactions. With mean absolute deviations (MADs) of 0.74-0.84 kcal mol(-1), PBE-dDXDM, PBE0-dDXDM, and B3LYP-dDXDM outperform the computationally more demanding and most recent functionals such as M06-2X and B2PLYP-D (MAD of 1.93 and 1.06 kcal mol(-1), respectively).

  18. Self-interaction corrections in density functional theory

    SciTech Connect

    Tsuneda, Takao; Hirao, Kimihiko

    2014-05-14

    Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds.

  19. Associations of dairy intake with CT lung density and lung function

    PubMed Central

    Jiang, Rui; Jacobs, David R.; He, Ka; Hoffman, Eric; Hankinson, John; Nettleton, Jennifer A.; Barr, R. Graham

    2013-01-01

    Objective Dairy products contain vitamin D and other nutrients that may be beneficial for lung function, but are also high in fats that may have mixed effects on lung function. However, the overall associations of dairy intake with lung density and lung function have not been studied. Methods We examined the cross-sectional relations between dairy intake and CT lung density and lung function in the Multi-Ethnic Study of Atherosclerosis (MESA). Total, low-fat and high-fat dairy intakes were quantified from food frequency questionnaire responses of men and women, aged 45–84 years, free of clinical cardiovascular disease. The MESA-Lung Study assessed CT lung density from cardiac CT imaging and prebronchodilator spirometry among 3,965 MESA participants. Results Total dairy intake was inversely associated with apical-basilar difference in percent emphysema and positively associated with FVC (the multivariate-adjusted mean difference between the highest and the lowest quintile of total dairy intake was −0.92 (p for trend=0.04) for apical-basilar difference in percent emphysema and 72.0 mL (p=0.01) for FVC). Greater low-fat dairy intake was associated with higher alpha (higher alpha values indicate less emphysema) and lower apical-basilar difference in percent emphysema (corresponding differences in alpha and apical-basilar difference in percent emphysema were 0.04 (p=0.02) and −0.98 (p=0.01) for low-fat dairy intake, respectively). High-fat dairy intake was not associated with lung density measures. Greater low- or high-fat dairy intake was not associated with higher FEV1, FVC and FEV1/FVC. Conclusions Higher low-fat dairy intake but not high-fat dairy intake was associated with moderately improved CT lung density. PMID:21504976

  20. Improved correlation between CT emphysema quantification and pulmonary function test by density correction of volumetric CT data based on air and aortic density.

    PubMed

    Kim, Song Soo; Seo, Joon Beom; Kim, Namkug; Chae, Eun Jin; Lee, Young Kyung; Oh, Yeon Mok; Lee, Sang Do

    2014-01-01

    To determine the improvement of emphysema quantification with density correction and to determine the optimal site to use for air density correction on volumetric computed tomography (CT). Seventy-eight CT scans of COPD patients (GOLD II-IV, smoking history 39.2±25.3 pack-years) were obtained from several single-vendor 16-MDCT scanners. After density measurement of aorta, tracheal- and external air, volumetric CT density correction was conducted (two reference values: air, -1,000 HU/blood, +50 HU). Using in-house software, emphysema index (EI) and mean lung density (MLD) were calculated. Differences in air densities, MLD and EI prior to and after density correction were evaluated (paired t-test). Correlation between those parameters and FEV1 and FEV1/FVC were compared (age- and sex adjusted partial correlation analysis). Measured densities (HU) of tracheal- and external air differed significantly (-990 ± 14, -1016 ± 9, P<0.001). MLD and EI on original CT data, after density correction using tracheal- and external air also differed significantly (MLD: -874.9 ± 27.6 vs. -882.3 ± 24.9 vs. -860.5 ± 26.6; EI: 16.8 ± 13.4 vs. 21.1 ± 14.5 vs. 9.7 ± 10.5, respectively, P<0.001). The correlation coefficients between CT quantification indices and FEV1, and FEV1/FVC increased after density correction. The tracheal air correction showed better results than the external air correction. Density correction of volumetric CT data can improve correlations of emphysema quantification and PFT. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  1. Standardizing CT lung density measure across scanner manufacturers.

    PubMed

    Chen-Mayer, Huaiyu Heather; Fuld, Matthew K; Hoppel, Bernice; Judy, Philip F; Sieren, Jered P; Guo, Junfeng; Lynch, David A; Possolo, Antonio; Fain, Sean B

    2017-03-01

    Computed Tomography (CT) imaging of the lung, reported in Hounsfield Units (HU), can be parameterized as a quantitative image biomarker for the diagnosis and monitoring of lung density changes due to emphysema, a type of chronic obstructive pulmonary disease (COPD). CT lung density metrics are global measurements based on lung CT number histograms, and are typically a quantity specifying either the percentage of voxels with CT numbers below a threshold, or a single CT number below which a fixed relative lung volume, nth percentile, falls. To reduce variability in the density metrics specified by CT attenuation, the Quantitative Imaging Biomarkers Alliance (QIBA) Lung Density Committee has organized efforts to conduct phantom studies in a variety of scanner models to establish a baseline for assessing the variations in patient studies that can be attributed to scanner calibration and measurement uncertainty. Data were obtained from a phantom study on CT scanners from four manufacturers with several protocols at various tube potential voltage (kVp) and exposure settings. Free from biological variation, these phantom studies provide an assessment of the accuracy and precision of the density metrics across platforms solely due to machine calibration and uncertainty of the reference materials. The phantom used in this study has three foam density references in the lung density region, which, after calibration against a suite of Standard Reference Materials (SRM) foams with certified physical density, establishes a HU-electron density relationship for each machine-protocol. We devised a 5-step calibration procedure combined with a simplified physical model that enabled the standardization of the CT numbers reported across a total of 22 scanner-protocol settings to a single energy (chosen at 80 keV). A standard deviation was calculated for overall CT numbers for each density, as well as by scanner and other variables, as a measure of the variability, before and after the

  2. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

    SciTech Connect

    Chai, Jeng-Da; Head-Gordon, Martin

    2008-06-14

    We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

  3. Comprehensive Benchmarking of a Density-Dependent Dispersion Correction.

    PubMed

    Steinmann, Stephan N; Corminboeuf, Clemence

    2011-11-08

    Standard density functional approximations cannot accurately describe interactions between nonoverlapping densities. A simple remedy consists in correcting for the missing interactions a posteriori, adding an attractive energy term summed over all atom pairs. The density-dependent energy correction, dDsC, presented herein, is constructed from dispersion coefficients computed on the basis of a generalized gradient approximation to Becke and Johnson's exchange-hole dipole moment formalism. dDsC also relies on an extended Tang and Toennies damping function accounting for charge-overlap effects. The comprehensive benchmarking on 341 diverse reaction energies divided into 18 illustrative test sets validates the robust performance and general accuracy of dDsC for describing various intra- and intermolecular interactions. With a total MAD of 1.3 kcal mol(-1), B97-dDsC slightly improves the results of M06-2X and B2PLYP-D3 (MAD = 1.4 kcal mol(-1) for both) at a lower computational cost. The density dependence of both the dispersion coefficients and the damping function makes the approach especially valuable for modeling redox reactions and charged species in general.

  4. A corrected effective density fluid model for gassy sediments.

    PubMed

    Zheng, Guangying; Huang, Yiwang; Hua, Jian; Xu, Xiuyu; Wang, Fei

    2017-01-01

    A corrected effective density fluid model is developed for predicting sound speed dispersion and attenuation coefficient in gassy sediments. An acoustic experiment was undertaken to measure the attenuation coefficient in a frequency band of 600 to 3000 Hz in gassy unsaturated sand. The measured frequency spectra of the attenuation coefficient show four peaks due to bubble resonance. Then a method of using several modified Gaussian functions to model bubble size distribution is proposed to fit measured attenuation data, which shows that the magnitudes of the fitted model attenuation coefficients are broadly in agreement with those measured attenuation data.

  5. Dispersion corrections to density functionals for water aromatic interactions.

    PubMed

    Zimmerli, Urs; Parrinello, Michele; Koumoutsakos, Petros

    2004-02-08

    We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C6r(-6) term is introduced that is damped at short range. The coefficient C6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Møller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics.

  6. Simple spin correction of unrestricted density-functional calculation

    NASA Astrophysics Data System (ADS)

    Ovchinnikov, Alexander A.; Labanowski, Jan K.

    1996-06-01

    The unrestricted Hartree-Fock and unrestricted Kohn-Sham calculations generally result in spin-contaminated solutions. Moreover, the energies from these calculations cannot be directly compared with the results of corresponding restricted calculations since the latter yield higher energies due to restrictions imposed on the form of the wave function. We present here a simple method of correcting the mixed spin energies resulting from unrestricted Hartree-Fock or density-functional theory calculations and removing the foreign spin components. The method allows for elimination of higher-multiplet components from the given mixed spin state solution by performing unrestricted calculations at the same fixed geometry for the higher multiplets and the state under consideration. The performance of the method is illustrated with several examples of density-functional calculations of radical species. The current method is also variational in nature and can be further extended in a self-consistent field fashion.

  7. Lung mast cell density defines a subpopulation of patients with idiopathic pulmonary fibrosis.

    PubMed

    Cha, Seung-Ick; Chang, Christine S; Kim, Eun Kyung; Lee, Jae W; Matthay, Michael A; Golden, Jeffrey A; Elicker, Brett M; Jones, Kirk; Collard, Harold R; Wolters, Paul J

    2012-07-01

    The relationship of mast cells to the pathogenesis of lung fibrosis remains undefined despite recognition of their presence in the lungs of patients with pulmonary fibrosis. This study was performed to characterize the relationship of mast cells to fibrotic lung diseases. Lung tissues from patients with idiopathic pulmonary fibrosis (IPF), chronic hypersensitivity pneumonitis (HP), systemic sclerosis (SSc)-related interstitial lung disease (ILD) and normal individuals were subjected to chymase immunostaining and the mast cell density quantified. Eosinophils were quantified by immunostaining for eosinophil peroxidase. Changes in lung function were correlated with mast cell density. Lung tissue obtained from IPF patients had a higher density of chymase-immunoreactive mast cells than that from patients with HP, SSc-related ILD or normal lungs. IPF lung tissue had a higher density of eosinophils than normal lung. There was no correlation between mast cell density and eosinophil density in IPF lung. IPF patients with high mast cell density had a slower rate of decline in forced vital capacity (FVC) than IPF patients with low mast cell density. Mast cell density in IPF lungs is higher than in other fibrotic lung diseases and normal lungs. Increased mast cell density in IPF may predict slower disease progression. © 2012 Blackwell Publishing Ltd.

  8. Lung mast cell density defines a subpopulation of patients with idiopathic pulmonary fibrosis

    PubMed Central

    Cha, Seung-Ick; Chang, Christine S; Kim, Eun Kyung; Lee, Jae W.; Matthay, Michael A; Golden, Jeffrey A; Elicker, Brett M; Jones, Kirk; Collard, Harold R; Wolters, Paul J

    2012-01-01

    Aims The relationship of mast cells to the pathogenesis of lung fibrosis remains undefined despite recognition of their presence in the lungs of patients with pulmonary fibrosis. This study was performed to characterize the relationship of mast cells to fibrotic lung diseases. Methods and results Lung tissues from patients with idiopathic pulmonary fibrosis (IPF), chronic hypersensitivity pneumonitis (HP), systemic sclerosis (SSc)-related interstitial lung disease (ILD) and normal individuals were subjected to chymase immunostaining and the mast cell density quantified. Eosinophils were quantified by immunostaining for eosinophil peroxidase. Changes in lung function were correlated with mast cell density. Lung tissue obtained from IPF patients had a higher density of chymase-immunoreactive mast cells than that from patients with HP, SSc-related ILD or normal lungs. IPF lung tissue had a higher density of eosinophils than normal lung. There was no correlation between mast cell density and eosinophil density in IPF lung. IPF patients with high mast cell density had a slower rate of decline in forced vital capacity (FVC) than IPF patients with low mast cell density. Conclusions Mast cell density in IPF lungs is higher than in other fibrotic lung diseases and normal lungs. Increased mast cell density in IPF may predict slower disease progression. PMID:22394225

  9. Association between lung function and airway wall density

    NASA Astrophysics Data System (ADS)

    Leader, J. Ken; Zheng, Bin; Fuhrman, Carl R.; Tedrow, John; Park, Sang C.; Tan, Jun; Pu, Jiantao; Drescher, John M.; Gur, David; Sciurba, Frank C.

    2009-02-01

    Computed tomography (CT) examination is often used to quantify the relation between lung function and airway remodeling in chronic obstructive pulmonary disease (COPD). In this preliminary study, we examined the association between lung function and airway wall computed attenuation ("density") in 200 COPD screening subjects. Percent predicted FVC (FVC%), percent predicted FEV1 (FEV1%), and the ratio of FEV1 to FVC as a percentage (FEV1/FVC%) were measured post-bronchodilator. The apical bronchus of the right upper lobe was manually selected from CT examinations for evaluation. Total airway area, lumen area, wall area, lumen perimeter and wall area as fraction of the total airway area were computed. Mean HU (meanHU) and maximum HU (maxHU) values were computed across pixels assigned membership in the wall and with a HU value greater than -550. The Pearson correlation coefficients (PCC) between FVC%, FEV1%, and FEV1/FVC% and meanHU were -0.221 (p = 0.002), -0.175 (p = 0.014), and -0.110 (p = 0.123), respectively. The PCCs for maxHU were only significant for FVC%. The correlations between lung function and the airway morphometry parameters were slightly stronger compared to airway wall density. MeanHU was significantly correlated with wall area (PCC = 0.720), airway area (0.498) and wall area percent (0.611). This preliminary work demonstrates that airway wall density is associated with lung function. Although the correlations in our study were weaker than a recent study, airway wall density initially appears to be an important parameter in quantitative CT analysis of COPD.

  10. Emission-based estimation of lung attenuation coefficients for attenuation correction in time-of-flight PET/MR

    NASA Astrophysics Data System (ADS)

    Mehranian, Abolfazl; Zaidi, Habib

    2015-06-01

    In standard segmentation-based MRI-guided attenuation correction (MRAC) of PET data on hybrid PET/MRI systems, the inter/intra-patient variability of linear attenuation coefficients (LACs) is ignored owing to the assignment of a constant LAC to each tissue class. This can lead to PET quantification errors, especially in the lung regions. In this work, we aim to derive continuous and patient-specific lung LACs from time-of-flight (TOF) PET emission data using the maximum likelihood reconstruction of activity and attenuation (MLAA) algorithm. The MLAA algorithm was constrained for estimation of lung LACs only in the standard 4-class MR attenuation map using Gaussian lung tissue preference and Markov random field smoothness priors. MRAC maps were derived from segmentation of CT images of 19 TOF-PET/CT clinical studies into background air, lung, soft tissue and fat tissue classes, followed by assignment of predefined LACs of 0, 0.0224, 0.0864 and 0.0975 cm-1, respectively. The lung LACs of the resulting attenuation maps were then estimated from emission data using the proposed MLAA algorithm. PET quantification accuracy of MRAC and MLAA methods was evaluated against the reference CT-based AC method in the lungs, lesions located in/near the lungs and neighbouring tissues. The results show that the proposed MLAA algorithm is capable of retrieving lung density gradients and compensate fairly for respiratory-phase mismatch between PET and corresponding attenuation maps. It was found that the mean of the estimated lung LACs generally follow the trend of the reference CT-based attenuation correction (CTAC) method. Quantitative analysis revealed that the MRAC method resulted in average relative errors of  -5.2   ±   7.1% and  -6.1   ±   6.7% in the lungs and lesions, respectively. These were reduced by the MLAA algorithm to  -0.8   ±   6.3% and  -3.3   ±   4.7%, respectively. In conclusion, we demonstrated

  11. Singularity Correction for Long-Range-Corrected Density Functional Theory with Plane-Wave Basis Sets.

    PubMed

    Kawashima, Yukio; Hirao, Kimihiko

    2017-03-09

    We introduced two methods to correct the singularity in the calculation of long-range Hartree-Fock (HF) exchange for long-range-corrected density functional theory (LC-DFT) calculations in plane-wave basis sets. The first method introduces an auxiliary function to cancel out the singularity. The second method introduces a truncated long-range Coulomb potential, which has no singularity. We assessed the introduced methods using the LC-BLYP functional by applying it to isolated systems of naphthalene and pyridine. We first compared the total energies and the HOMO energies of the singularity-corrected and uncorrected calculations and confirmed that singularity correction is essential for LC-DFT calculations using plane-wave basis sets. The LC-DFT calculation results converged rapidly with respect to the cell size as the other functionals, and their results were in good agreement with the calculated results obtained using Gaussian basis sets. LC-DFT succeeded in obtaining accurate orbital energies and excitation energies. We next applied LC-DFT with singularity correction methods to the electronic structure calculations of the extended systems, Si and SiC. We confirmed that singularity correction is important for calculations of extended systems as well. The calculation results of the valence and conduction bands by LC-BLYP showed good convergence with respect to the number of k points sampled. The introduced methods succeeded in overcoming the singularity problem in HF exchange calculation. We investigated the effect of the singularity correction on the excitation state calculation and found that careful treatment of the singularities is required compared to ground-state calculations. We finally examined the excitonic effect on the band gap of the extended systems. We calculated the excitation energies to the first excited state of the extended systems using a supercell model at the Γ point and found that the excitonic binding energy, supposed to be small for

  12. Is non-attenuation-corrected PET inferior to body attenuation-corrected PET or PET/CT in lung cancer?

    NASA Astrophysics Data System (ADS)

    Maintas, Dimitris; Houzard, Claire; Ksyar, Rachid; Mognetti, Thomas; Maintas, Catherine; Scheiber, Christian; Itti, Roland

    2006-12-01

    It is considered that one of the great strengths of PET imaging is the ability to correct for body attenuation. This enables better lesion uptake quantification and quality of PET images. The aim of this work is to compare the sensitivity of non-attenuation-corrected (NAC) PET images, the gamma photons (GPAC) and CT attenuation-corrected (CTAC) images in detecting and staging of lung cancer. We have studied 66 patients undergoing PET/CT examinations for detecting and staging NSC lung cancer. The patients were injected with 18-FDG; 5 MBq/kg under fasting conditions and examination was started 60 min later. Transmission data were acquired by a spiral CT X-ray tube and by gamma photons emitting Cs-137l source and were used for the patient body attenuation correction without correction for respiratory motion. In 55 of 66 patients we performed both attenuation correction procedures and in 11 patients only CT attenuation correction. In seven patients with solitary nodules PET was negative and in 59 patients with lung cancer PET/CT was positive for pulmonary or other localization. In the group of 55 patients we found 165 areas of focal increased 18-FDG uptake in NAC, 165 in CTAC and 164 in GPAC PET images.In the patients with only CTAC we found 58 areas of increased 18-FDG uptake on NAC and 58 areas lesions on CTAC. In the patients with positive PET we found 223 areas of focal increased uptake in NAC and 223 areas in CTAC images. The sensitivity of NAC was equal to the sensitivity of CTAC and GPAC images. The visualization of peripheral lesions was better in NAC images and the lesions were better localized in attenuation-corrected images. In three lesions of the thorax the localization was better in GPAC and fused images than in CTAC images.

  13. [Correction of tetralogy of Fallot and its influence to oxygen transport and lung changes. Part II: Lung changes (author's transl)].

    PubMed

    Reichart, B; Brunner, L; Hügel, W; Klinner, W; Weinhold, C; Westerburg, K W; Heinze, G

    1977-02-01

    22 children got lung scans 3 weeks respectively 12 months after the correction of a tetralogy of Fallot. In 18 cases previous operations were done: 12 times a Blalock-Taussig shunt and 6 times a Brock procedure. For the scan 20-70 mu diameter albumin macrospheres were used, which were labeled with Technetium 99m. The following pathologicla lung changes were seen: 1. Loss of perfusion, typical after Blalock-Taussig shunt procedure; these findings were always on the left side, the site of the anastomosis. 2. Anomalous flow distrubution (=more spheres in the upper than in the lower lobe) in the left lung; these changes were also caused by the Blalock-Taussing shunts, but disappeared within the one year follow-up after the correction. 3. Intrapulmonary rigt-left shunts (according to the dilatation of the alveolar capillaries). These decreased within one year from 9.9+/-1.3 to 4.6+/-0.9%.

  14. Short- and long-range corrected hybrid density functionals with the D3 dispersion corrections

    NASA Astrophysics Data System (ADS)

    Wang, Chih-Wei; Hui, Kerwin; Chai, Jeng-Da

    2016-11-01

    We propose a short- and long-range corrected (SLC) hybrid scheme employing 100% Hartree-Fock exchange at both zero and infinite interelectronic distances, wherein three SLC hybrid density functionals with the D3 dispersion corrections (SLC-LDA-D3, SLC-PBE-D3, and SLC-B97-D3) are developed. SLC-PBE-D3 and SLC-B97-D3 are shown to be accurate for a very diverse range of applications, such as core ionization and excitation energies, thermochemistry, kinetics, noncovalent interactions, dissociation of symmetric radical cations, vertical ionization potentials, vertical electron affinities, fundamental gaps, and valence, Rydberg, and long-range charge-transfer excitation energies. Relative to ωB97X-D, SLC-B97-D3 provides significant improvement for core ionization and excitation energies and noticeable improvement for the self-interaction, asymptote, energy-gap, and charge-transfer problems, while performing similarly for thermochemistry, kinetics, and noncovalent interactions.

  15. Metallophilic interactions from dispersion-corrected density-functional theory

    SciTech Connect

    Otero-de-la-Roza, Alberto Mallory, Joel D.; Johnson, Erin R.

    2014-05-14

    In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Møller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH{sub 3}){sub 4}]{sup +} cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.

  16. Improving accuracy through density correction in guided wave tomography

    PubMed Central

    2016-01-01

    The accurate quantification of wall loss caused by corrosion is critical to the reliable life estimation of pipes and pressure vessels. Traditional thickness gauging by scanning a probe is slow and requires access to all points on the surface; this is impractical in many cases as corrosion often occurs where access is restricted, such as beneath supports where water collects. Guided wave tomography presents a solution to this; by transmitting guided waves through the region of interest and exploiting their dispersive nature, it is possible to build up a map of thickness. While the best results have been seen when using the fundamental modes A0 and S0 at low frequency, the complex scattering of the waves causes errors within the reconstruction. It is demonstrated that these lead to an underestimate in wall loss for A0 but an overestimate for S0. Further analysis showed that this error was related to density variation, which was proportional to thickness. It was demonstrated how this could be corrected for in the reconstructions, in many cases resulting in the near-elimination of the error across a range of defects, and greatly improving the accuracy of life estimates from guided wave tomography. PMID:27118904

  17. Quantitative computed tomography of lung parenchyma in patients with emphysema: analysis of higher-density lung regions

    NASA Astrophysics Data System (ADS)

    Lederman, Dror; Leader, Joseph K.; Zheng, Bin; Sciurba, Frank C.; Tan, Jun; Gur, David

    2011-03-01

    Quantitative computed tomography (CT) has been widely used to detect and evaluate the presence (or absence) of emphysema applying the density masks at specific thresholds, e.g., -910 or -950 Hounsfield Unit (HU). However, it has also been observed that subjects with similar density-mask based emphysema scores could have varying lung function, possibly indicating differences of disease severity. To assess this possible discrepancy, we investigated whether density distribution of "viable" lung parenchyma regions with pixel values > -910 HU correlates with lung function. A dataset of 38 subjects, who underwent both pulmonary function testing and CT examinations in a COPD SCCOR study, was assembled. After the lung regions depicted on CT images were automatically segmented by a computerized scheme, we systematically divided the lung parenchyma into different density groups (bins) and computed a number of statistical features (i.e., mean, standard deviation (STD), skewness of the pixel value distributions) in these density bins. We then analyzed the correlations between each feature and lung function. The correlation between diffusion lung capacity (DLCO) and STD of pixel values in the bin of -910HU <= PV < -750HU was -0.43, as compared with a correlation of -0.49 obtained between the post-bronchodilator ratio (FEV1/FVC) measured by the forced expiratory volume in 1 second (FEV1) dividing the forced vital capacity (FVC) and the STD of pixel values in the bin of -1024HU <= PV < -910HU. The results showed an association between the distribution of pixel values in "viable" lung parenchyma and lung function, which indicates that similar to the conventional density mask method, the pixel value distribution features in "viable" lung parenchyma areas may also provide clinically useful information to improve assessments of lung disease severity as measured by lung functional tests.

  18. Decreased lung carcinoma cell density on select polymer nanometer surface features for lung replacement therapies.

    PubMed

    Zhang, Lijuan; Chun, Young Wook; Webster, Thomas J

    2010-05-13

    Poly(lactic-co-glycolic) acid (PLGA) has been widely used as a biomaterial in regenerative medicine because of its biocompatibility and biodegradability properties. Previous studies have shown that cells (such as bladder smooth muscle cells, chondrocytes, and osteoblasts) respond differently to nanostructured PLGA surfaces compared with nanosmooth surfaces. The purpose of the present in vitro research was to prepare PLGA films with various nanometer surface features and determine whether lung cancer epithelial cells respond differently to such topographies. To create nanosurface features on PLGA, different sized (190 nm, 300 nm, 400 nm, and 530 nm diameter) polystyrene beads were used to cast polydimethylsiloxane (PDMS) molds which were used as templates to create nanofeatured PLGA films. Atomic force microscopy (AFM) images and root mean square roughness (RMS) values indicated that the intended spherical surface nanotopographies on PLGA with RMS values of 2.23, 5.03, 5.42, and 36.90 nm were formed by employing 190, 300, 400, and 530 nm beads. A solution evaporation method was also utilized to modify PLGA surface features by using 8 wt% (to obtain an AFM RMS value of 0.62 nm) and 4 wt% (to obtain an AFM RMS value of 2.23 nm) PLGA in chloroform solutions. Most importantly, lung cancer epithelial cells adhered less on the PLGA surfaces with RMS values of 0.62, 2.23, and 5.42 nm after four hours of culture compared with any other PLGA surface created here. After three days, PLGA surfaces with an RMS value of 0.62 nm had much lower cell density than any other sample. In this manner, PLGA with specific nanometer surface features may inhibit lung cancer cell density which may provide an important biomaterial for the treatment of lung cancer (from drug delivery to regenerative medicine).

  19. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated From Patient iPSCs

    PubMed Central

    Firth, Amy L; Menon, Tushar; Parker, Gregory S; Qualls, Susan J; Lewis, Benjamin M; Ke, Eugene; Dargitz, Carl T; Wright, Rebecca; Khanna, Ajai; Gage, Fred H; Verma, Inder M

    2015-01-01

    SUMMARY Lung disease is a major cause of death in the USA, with current therapeutic approaches only serving to manage symptoms. The most common chronic and life-threatening genetic disease of the lung is Cystic fibrosis (CF) caused by mutations in the cystic fibrosis transmembrane regulator (CFTR). We have generated induced pluripotent stem cells (iPSC) from CF patients carrying a homozygous deletion of F508 in the CFTR gene, which results in defective processing of CFTR to the cell membrane. This mutation was precisely corrected using CRISPR to target corrective sequences to the endogenous CFTR genomic locus, in combination with a completely excisable selection system which significantly improved the efficiency of this correction. The corrected iPSC were subsequently differentiated to mature airway epithelial cells where recovery of normal CFTR expression and function was demonstrated. This isogenic iPSC-based model system for CF could be adapted for the development of new therapeutic approaches. PMID:26299960

  20. Corrections and improvements of lung imaging under Optical Coherence Tomography (OCT)

    NASA Astrophysics Data System (ADS)

    Golabchi, Ali

    Visualization and correct assessment of alveolar volume via intact lung imaging is important to study and assess respiratory mechanics. Optical Coherence Tomography (OCT), a real time imaging technique based on near-infrared interferometry, can image several layers of distal alveoli in intact, ex-vivo lung tissue. However optical effects associated with heterogeneity of lung tissue, including the refraction caused by air-tissue interfaces along alveoli and duct walls, and changes in speed of light as it travels through the tissue, result in inaccurate measurement of alveolar volume. Experimentally such errors have been difficult to analyze because of lack of ''ground truth,'' as the lung has a unique microstructure of liquid-coated thin walls surrounding relatively large airspaces, which is difficult to model with synthetic foams. In addition, both lung and foams contain airspaces of highly irregular shape, further complicating quantitative measurement of optical artifacts and correction. To address this we have adapted the Bragg-Nye bubble raft, a crystalline two-dimensional arrangement of elements similar in geometry to alveoli (up to several hundred um in diameter with thin walls) as an inflated lung phantom in order to understand, analyze and correct these errors. By applying exact optical ray tracing on OCT images of the bubble raft, the errors are predicted and corrected. The results are validated by imaging the bubble raft with OCT from one edge and with a charged coupled device (CCD) camera in transillumination from top, providing ground truth for the OCT. We also developed a tomographic technique based on incoherent summation of multiple angle-diverse images by utilizing image registration to increase our depth of imaging and our results were validated by utilizing the inflated lung phantom. In this thesis also, an experimental apparatus for macro-scale mechanical probing of lung with in-situ micro-scale imaging of alveolar deformation was analyzed

  1. Quantitative proton density mapping: correcting the receiver sensitivity bias via pseudo proton densities.

    PubMed

    Volz, Steffen; Nöth, Ulrike; Jurcoane, Alina; Ziemann, Ulf; Hattingen, Elke; Deichmann, Ralf

    2012-10-15

    Most methods for mapping proton densities (PD) in brain tissue are based on measuring all parameters influencing the signal intensity with subsequent elimination of any weighting not related to PD. This requires knowledge of the receiver coil sensitivity profile (RP), the measurement of which can be problematic. Recently, a method for compensating the influence of RP non-uniformities on PD data at a field strength of 3T was proposed, based on bias field correction of spoiled gradient echo image data to remove the low spatial frequency bias imposed by RP variations from uncorrected PD maps. The purpose of the current study was to present and test an independent method, based on the well-known linear relationship between the longitudinal relaxation rate R1 and 1/PD in brain tissue. For healthy subjects, RP maps obtained with this method and the resulting PD maps are very similar to maps based on bias field correction, and quantitative PD values acquired with the new independent method are in very good agreement with literature values. Furthermore, both methods for PD mapping are compared in the presence of several pathologies (multiple sclerosis, stroke, meningioma, recurrent glioblastoma). Copyright © 2012 Elsevier Inc. All rights reserved.

  2. (18)FDG uptake associated with CT density on PET/CT in lungs with and without chronic interstitial lung diseases.

    PubMed

    Inoue, Kentaro; Okada, Ken; Taki, Yasuyuki; Goto, Ryoi; Kinomura, Shigeo; Fukuda, Hiroshi

    2009-05-01

    The dependent-density of computed tomography (CT) images of positron emission tomography (PET)/CT is sometimes difficult to distinguish from chronic interstitial lung disease (ILD) when it accompanies increased (18)F-fluorodeoxy-D: -glucose ((18)FDG) uptake. Though the possible utility of (18)FDG-PET for the diagnosis of active ILD has been reported, the clinical relevance of mild lung (18)FDG uptake in ILD cases without signs and symptoms suggesting acute progression has not been described. This study aimed to test relationships between (18)FDG uptake and lung density on CT using PET/CT in patients with normal lung as well as clinically stable chronic ILD. Thirty-six patients with normal lungs (controls) and 28 patients with chronic ILD (ILD cases) without acute exacerbation were retrospectively selected from (18)FDG-PET/CT scans performed in examination of malignant neoplasms. Elliptical regions of interest (ROIs) were placed on the lung. The relationships between CT density and (18)FDG uptake between the control and ILD cases were tested. The CT density and (18)FDG uptake had a linear correlation in both the controls and the ILD cases without a difference in their regression slopes, and they were overlapped between the controls and the ILD cases with higher mean values in the ILD cases. Lung (18)FDG uptake was considered to reflect a gravity-dependent tissue density in the normal lung. Though the lung (18)FDG uptake as well as the CT density tended to be higher in chronic ILD patients, it may be difficult to distinguish them in normal dependent regions from those related to chronic ILD in some cases.

  3. Analysis of lung density by computed tomography before and during general anaesthesia.

    PubMed

    Hachenberg, T; Lundquist, H; Tokics, L; Brismar, B; Hedenstierna, G

    1993-08-01

    Pulmonary structure was analysed by means of computed tomography (CT) in 20 lung-healthy patients, relating tissue density to the attenuation value (AV) of a picture element. Regional density of pulmonary tissue (rlung) was determined using mean lung density in five regions of interest (ROI1-5) (sector method). Vertical and horizontal distributions of x-ray attenuation were analysed by density profiles, relating AV values to evenly distributed and normalised length scales. In group I (n = 12), CT-densitometry was obtained in awake, supine patients and after induction of general anaesthesia. In group II (n = 8), the effect of mechanical ventilation with positive end-expiratory pressure (PEEP, 1.0 kPa [10 cmH2O]) was studied. In the awake state, a vertical tissue density difference between the top and bottom of the lung was found in all patients, accounting for a mean of 0.235 g.cm-3 (right lung) and 0.199 g.cm-3 (left lung). Only minor changes were seen in the horizontal lung density profiles. After induction of anaesthesia, x-ray attenuation of ROI1-4 showed no significant differences when compared with the awake state. The basal lung areas (ROI5) revealed a significantly increased tissue density (P < or = 0.01), reaching mean values of 0.94 g.cm-3 (right lung) and 0.814 g.cm-3 (left lung). Similarly, vertical density profiles showed a markedly enhanced rlung of the bottom of the lung in all patients, interpreted as atelectasis. The amount of atelectasis accounted for 4.8 +/- 2.6% (right lung) and 4.7 +/- 2.1% (left lung) of the intrapulmonary area.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. A Method for Lung Boundary Correction Using Split Bregman Method and Geometric Active Contour Model

    PubMed Central

    Zhang, Jianxun; Liang, Rui

    2015-01-01

    In order to get the extracted lung region from CT images more accurately, a model that contains lung region extraction and edge boundary correction is proposed. Firstly, a new edge detection function is presented with the help of the classic structure tensor theory. Secondly, the initial lung mask is automatically extracted by an improved active contour model which combines the global intensity information, local intensity information, the new edge information, and an adaptive weight. It is worth noting that the objective function of the improved model is converted to a convex model, which makes the proposed model get the global minimum. Then, the central airway was excluded according to the spatial context messages and the position relationship between every segmented region and the rib. Thirdly, a mesh and the fractal theory are used to detect the boundary that surrounds the juxtapleural nodule. Finally, the geometric active contour model is employed to correct the detected boundary and reinclude juxtapleural nodules. We also evaluated the performance of the proposed segmentation and correction model by comparing with their popular counterparts. Efficient computing capability and robustness property prove that our model can correct the lung boundary reliably and reproducibly. PMID:26089976

  5. A Method for Lung Boundary Correction Using Split Bregman Method and Geometric Active Contour Model.

    PubMed

    Feng, Changli; Zhang, Jianxun; Liang, Rui

    2015-01-01

    In order to get the extracted lung region from CT images more accurately, a model that contains lung region extraction and edge boundary correction is proposed. Firstly, a new edge detection function is presented with the help of the classic structure tensor theory. Secondly, the initial lung mask is automatically extracted by an improved active contour model which combines the global intensity information, local intensity information, the new edge information, and an adaptive weight. It is worth noting that the objective function of the improved model is converted to a convex model, which makes the proposed model get the global minimum. Then, the central airway was excluded according to the spatial context messages and the position relationship between every segmented region and the rib. Thirdly, a mesh and the fractal theory are used to detect the boundary that surrounds the juxtapleural nodule. Finally, the geometric active contour model is employed to correct the detected boundary and reinclude juxtapleural nodules. We also evaluated the performance of the proposed segmentation and correction model by comparing with their popular counterparts. Efficient computing capability and robustness property prove that our model can correct the lung boundary reliably and reproducibly.

  6. Refractive errors and corrections for OCT images in an inflated lung phantom

    PubMed Central

    Golabchi, Ali; Faust, J.; Golabchi, F. N.; Brooks, D. H.; Gouldstone, A.; DiMarzio, C. A.

    2012-01-01

    Visualization and correct assessment of alveolar volume via intact lung imaging is important to study and assess respiratory mechanics. Optical Coherence Tomography (OCT), a real-time imaging technique based on near-infrared interferometry, can image several layers of distal alveoli in intact, ex vivo lung tissue. However optical effects associated with heterogeneity of lung tissue, including the refraction caused by air-tissue interfaces along alveoli and duct walls, and changes in speed of light as it travels through the tissue, result in inaccurate measurement of alveolar volume. Experimentally such errors have been difficult to analyze because of lack of ’ground truth,’ as the lung has a unique microstructure of liquid-coated thin walls surrounding relatively large airspaces, which is difficult to model with cellular foams. In addition, both lung and foams contain airspaces of highly irregular shape, further complicating quantitative measurement of optical artifacts and correction. To address this we have adapted the Bragg-Nye bubble raft, a crystalline two-dimensional arrangement of elements similar in geometry to alveoli (up to several hundred μm in diameter with thin walls) as an inflated lung phantom in order to understand, analyze and correct these errors. By applying exact optical ray tracing on OCT images of the bubble raft, the errors are predicted and corrected. The results are validated by imaging the bubble raft with OCT from one edge and with a charged coupled device (CCD) camera in transillumination from top, providing ground truth for the OCT. PMID:22567599

  7. Indirect measurement of lung density and air volume from electrical impedance tomography (EIT) data.

    PubMed

    Nebuya, Satoru; Mills, Gary H; Milnes, Peter; Brown, Brian H

    2011-12-01

    This paper describes a method for estimating lung density, air volume and changes in fluid content from a non-invasive measurement of the electrical resistivity of the lungs. Resistivity in Ω m was found by fitting measured electrical impedance tomography (EIT) data to a finite difference model of the thorax. Lung density was determined by comparing the resistivity of the lungs, measured at a relatively high frequency, with values predicted from a published model of lung structure. Lung air volume can then be calculated if total lung weight is also known. Temporal changes in lung fluid content will produce proportional changes in lung density. The method was implemented on EIT data, collected using eight electrodes placed in a single plane around the thorax, from 46 adult male subjects and 36 adult female subjects. Mean lung densities (±SD) of 246 ± 67 and 239 ± 64 kg m(-3), respectively, were obtained. In seven adult male subjects estimates of 1.68 ± 0.30, 3.42 ± 0.49 and 4.40 ± 0.53 l in residual volume, functional residual capacity and vital capacity, respectively, were obtained. Sources of error are discussed. It is concluded that absolute differences in lung density of about 30% and changes over time of less than 30% should be detected using the current technology in normal subjects. These changes would result from approximately 300 ml increase in lung fluid. The method proposed could be used for non-invasive monitoring of total lung air and fluid content in normal subjects but needs to be assessed in patients with lung disease.

  8. Convolution kernel design and efficient algorithm for sampling density correction.

    PubMed

    Johnson, Kenneth O; Pipe, James G

    2009-02-01

    Sampling density compensation is an important step in non-cartesian image reconstruction. One of the common techniques to determine weights that compensate for differences in sampling density involves a convolution. A new convolution kernel is designed for sampling density attempting to minimize the error in a fully reconstructed image. The resulting weights obtained using this new kernel are compared with various previous methods, showing a reduction in reconstruction error. A computationally efficient algorithm is also presented that facilitates the calculation of the convolution of finite kernels. Both the kernel and the algorithm are extended to 3D. Copyright 2009 Wiley-Liss, Inc.

  9. High density, optically corrected, micro-channel cooled, v-groove monolithic laser diode array

    DOEpatents

    Freitas, Barry L.

    1998-01-01

    An optically corrected, micro-channel cooled, high density laser diode array achieves stacking pitches to 33 bars/cm by mounting laser diodes into V-shaped grooves. This design will deliver>4kW/cm2 of directional pulsed laser power. This optically corrected, micro-channel cooled, high density laser is usable in all solid state laser systems which require efficient, directional, narrow bandwidth, high optical power density pump sources.

  10. High density, optically corrected, micro-channel cooled, v-groove monolithic laser diode array

    DOEpatents

    Freitas, B.L.

    1998-10-27

    An optically corrected, micro-channel cooled, high density laser diode array achieves stacking pitches to 33 bars/cm by mounting laser diodes into V-shaped grooves. This design will deliver > 4kW/cm{sup 2} of directional pulsed laser power. This optically corrected, micro-channel cooled, high density laser is usable in all solid state laser systems which require efficient, directional, narrow bandwidth, high optical power density pump sources. 13 figs.

  11. Trends in corrected lung cancer mortality rates in Brazil and regions

    PubMed Central

    Malta, Deborah Carvalho; de Abreu, Daisy Maria Xavier; de Moura, Lenildo; Lana, Gustavo C; Azevedo, Gulnar; França, Elisabeth

    2016-01-01

    ABSTRACT OBJECTIVE To describe the trend in cancer mortality rates in Brazil and regions before and after correction for underreporting of deaths and redistribution of ill-defined and nonspecific causes. METHODS The study used data of deaths from lung cancer among the population aged from 30 to 69 years, notified to the Mortality Information System between 1996 and 2011, corrected for underreporting of deaths, non-registered sex and age , and causes with ill-defined or garbage codes according to sex, age, and region. Standardized rates were calculated by age for raw and corrected data. An analysis of time trend in lung cancer mortality was carried out using the regression model with autoregressive errors. RESULTS Lung cancer in Brazil presented higher rates among men compared to women, and the South region showed the highest death risk in 1996 and 2011. Mortality showed a trend of reduction for males and increase for women. CONCLUSIONS Lung cancer in Brazil presented different distribution patterns according to sex, with higher rates among men and a reduction in the mortality trend for men and increase for women. PMID:27355467

  12. Using simulation data to predict lung geometry for inhomogeneity corrections in breast cancer treatments.

    PubMed

    Chen, W; Chu, J C; Griem, K; Hartsell, W F; Saxena, V S

    1995-10-15

    To develop a statistical model based only on simulation measurement data, to predict the lung geometry in the central slice of the tangential radiation treatment fields for breast cancer. A linear regression analysis was performed on 22 patients to determine the shape of lung in the central axis plane of the tangential radiation fields. Data collected include the greatest perpendicular distance (GPD) measured from the chest wall to the field border on computed tomography (CT) images, the central lung distance (CLD) measured from the posterior field border to the chest wall on the simulation portal images, and the lung contours digitized at 1 cm intervals. The lung contours of these patients were fitted to a parabolic curve through a polynomial regression model. A lung template based on the regression model is used to construct a "generic lung" contour on patients' external body contours for treatment planning. The accuracy of this technique was tested on another group of 15 patients for its ability to predict the shape of lung on the central axis plane and the accuracy of dose to the prescription point. The polynomial regression indicates that all the patients' lung contours in the tangential fields follow a parabolic curve: Y = -0.0808 X2 + 0.0096 X + 0.0326. The maximum lung involvement (GPD) can be determined from the value of CLD measured on the simulation film by the linear regression model with a determination coefficient of 0.712. The 15-patient test results indicate that our model predicts the lung separation on the central axis with an average deviation of 1.35 cm, and the average absolute dose deviation to the dose prescription point is 1.46%. The model presented in this article provides an efficient method to estimate the lung geometry for breast cancer treatment planning without the requirement of CT data. The lung contour predicted by our model is useful for calculating dose distributions with inhomogeneity correction and may potentially benefit

  13. Finite-size corrections to the density of states

    NASA Astrophysics Data System (ADS)

    Wörner, C. H.; Muñoz, E.

    2012-09-01

    The counting of states used in the well-known calculus of the density of states is revisited with emphasis on the error involved in the standard calculation. For pedagogical reasons, we restrict our treatment mainly to the two-dimensional case. This question is discussed in connection with the mathematical Gauss circle problem. It is shown that the typical error involved is negligible when the number of states tends to infinity.

  14. Effect of partial liquid ventilation and nebulized perfluorocarbon on CT lung density distribution: randomized controlled study of experimental lung injury.

    PubMed

    Kelly, K P; Stenson, B J; Drummond, G B

    2005-05-01

    Perfluorocarbon (PFC) liquid can improve gas exchange in acute lung injury. How PFC aerosol is distributed in the lung is unknown. We induced lung injury in rabbits with saline lavage, followed by mechanical ventilation in the supine position. The animals were divided into three groups: a control group, a group treated with partial liquid ventilation and a group given nebulized perfluorocarbon (PF 5080). We made CT image slices of the excised lungs. In the apical, middle and caudal slices we defined three regions of interest, from anterior to posterior, and noted the mean attenuation of each area. We also studied two rabbits which had not received lung injury or mechanical ventilation. Group means were different between the normal rabbits and all three study groups. There was a difference between the control and partial liquid ventilation groups, and between the partial liquid ventilation and nebulized groups, but no difference between the nebulized and control groups. Within each treatment group, there was no regional difference in the distribution of density. PF 5080 is not deposited in large amounts by aerosol. Less PFC was found in the lungs after partial liquid ventilation than expected. Within treatment groups, lung densities indicate less gravitational and regional differences than found in other studies.

  15. Lung density on high resolution computer tomography (HRCT) reflects degree of inflammation in smokers

    PubMed Central

    2014-01-01

    Background Smokers have increased cell concentration in the lower respiratory tract indicating a chronic inflammatory state, which in some individuals may lead to development of chronic obstructive pulmonary disease (COPD). Computer tomography (CT) imaging provides means of quantifying pulmonary structure and early signs of disease. We investigated whether lung density on high resolution CT differs between smokers and never-smokers and if this were associated to intensity of inflammation. Methods Forty smoking volunteers with normal pulmonary function, 40 healthy never-smokers and 40 patients with COPD of GOLD stage I-II, were included. Mean lung attenuation and percentage of pixels in the lung with attenuation between −750 and −900 HU (percentage higher density spectrum (%HDS)) were calculated on inspiratory CT-scans. Markers of systemic inflammation in blood and cell counts in bronchoalveolar lavage (BAL) fluid were recorded. Results Lung density expressed as %HDS was increased in smokers (44.0 ± 5.8%) compared to both never-smokers (38.3 ± 5.8%) and patients with COPD (39.1 ± 5.8%), (p < 0.001, for both). Females had denser lungs than males, which was dependent on body height. Cell concentration in BAL were correlated to lung density in smokers (r = 0.50, p < 0.001). Conclusions Lung density on CT is associated with cell concentration in BAL in smokers and may mirror an inflammatory response in the lung. Gender difference in lung density is dependent on height. In COPD with emphysema, loss of lung tissue may counterbalance the expected increase in density due to inflammation. The findings may help to interpret high resolution CT in the context of smoking and gender and highlight the heterogeneity of structural changes in COPD. PMID:24564813

  16. Does early tetralogy of Fallot total correction give better final lung volumes?

    PubMed

    Sadeghi, Hasan Allah; Miri, Seyed Reza; Bakhshandeh, Hooman; Mirmesdagh, Yalda; Paziraee, Nazita

    2013-06-01

    Pulmonary blood flow may affect lung development in adulthood. Early total correction of tetralogy of Fallot may affect development of final lung volumes. We evaluated the effect of age at total correction on lung volumes years after the operation. In a retrospective cohort study on patients with totally corrected tetralogy of Fallot (mean age, 13.40 years at the time of follow-up), forced vital capacity, slow vital capacity, forced expiratory volume in 1 s, and other parameters were measured 154.8 ± 46.25 months after the operation. Comparison were made of 3 groups: ≤2-, 2-8-, and >8-years old at the time of total correction surgery. Among 322 enrolled patients, the mean values of the follow-up spirometry results in ≤2-, 2-8-, >8-year-olds and the percentage of predicted values were respectively: vital capacity: 4.46 ± 0.57 L (107% ± 10.96%), 3.89 ± 0.58 L (91.10% ± 12.25%), 3.25 ± 0.48 L (82.35% ± 10.62%), p < 0.001; forced vital capacity: 4.28 ± 0.63 L (95.90% ± 18.77%), 3.76 ± 0.58 L (90.83% ± 12.52%), 3.14 ± 0.49 L (83.26% ± 11.71%), p < 0.001; forced expiratory volume in 1 s: 4.22 ± 0.63 L (104.84% ± 13.64%), 3.66 ± 0.58 L (90.61% ± 12.59%), 3.02 ± 0.48 L (84.31% ± 12%), p < 0.001. Early correction of defects or reestablishments of perfusion of tetralogy of Fallot before completion of lung development might improve final adulthood lung volumes and capacities. It is better to consider total correction for all tetralogy of Fallot patients below 2-years old, or at least below 8-years old, if it is technically possible.

  17. Empirical corrections to density functional theory highlight the importance of nonbonded intramolecular interactions in alkanes.

    PubMed

    Wodrich, Matthew D; Jana, Daniel F; Schleyer, Paul von Ragué; Corminboeuf, Clémence

    2008-11-13

    Energies of alkanes computed with many popular and even newer density functionals are flawed by systematic errors, which become considerable with larger molecules. The same energies, however, are well described by post-Hartree-Fock methods. Similar DFT shortcomings are well documented for cases involving descriptions of intermolecular van der Waals complexes. One solution to the density functional problem is the addition of an empirical correction term, which more accurately models the known R (-6) dependence of van der Waals energies. Here, we present the first empirical correction to DFT parametrized to reproduce experimental energies associated with intramolecular interactions in alkanes. Our training set used only three reactions involving simple linear and branched alkanes and provides a remarkable improvement over conventional DFT methods and empirical corrections optimized for intermolecular interactions. In contrast to many standard density functionals, the intramolecular empirical correction correctly predicts the lowest energy alkane isomer in addition to performing satisfactorily for describing the interaction energies of intermolecular complexes.

  18. An in-depth Monte Carlo study of lateral electron disequilibrium for small fields in ultra-low density lung: implications for modern radiation therapy

    NASA Astrophysics Data System (ADS)

    Disher, Brandon; Hajdok, George; Gaede, Stewart; Battista, Jerry J.

    2012-03-01

    Modern radiation therapy techniques such as intensity-modulated radiation therapy (IMRT) and stereotactic body radiation therapy (SBRT) use tightly conformed megavoltage x-ray fields to irradiate a tumour within lung tissue. For these conditions, lateral electron disequilibrium (LED) may occur, which systematically perturbs the dose distribution within tumour and nearby lung tissues. The goal of this work is to determine the combination of beam and lung density parameters that cause significant LED within and near the tumour. The Monte Carlo code DOSXYZnrc (National Research Council of Canada, Ottawa, ON) was used to simulate four 20 × 20 × 25 cm3 water-lung-water slab phantoms, which contained lung tissue only, or one of three different centrally located small tumours (sizes: 1 × 1 × 1, 3 × 3 × 3, 5 × 5 × 5 cm3). Dose calculations were performed using combinations of six beam energies (Co-60 up to 18 MV), five field sizes (1 × 1 cm2 up to 15 × 15 cm2), and 12 lung densities (0.001 g cm-3 up to 1 g cm-3) for a total of 1440 simulations. We developed the relative depth-dose factor (RDDF), which can be used to characterize the extent of LED (RDDF <1.0). For RDDF <0.7 severe LED occurred, and both lung and tumour dose were drastically reduced. For example, a 6 MV (3 × 3 cm2) field was used to irradiate a 1 cm3 tumour embedded in lung with ultra-low density of 0.001 g cm-3 (RDDF = 0.2). Dose in up-stream lung and tumour centre were reduced by as much as 80% with respect to the water density calculation. These reductions were worse for smaller tumours irradiated with high energy beams, small field sizes, and low lung density. In conclusion, SBRT trials based on dose calculations in homogeneous tissue are misleading as they do not reflect the actual dosimetric effects due to LED. Future clinical trials should only use dose calculation engines that can account for electron scatter, with special attention given to patients with low lung density (i.e. emphysema

  19. Why Density-Gradient Corrections Improve Atomization Energies and Barrier Heights

    NASA Astrophysics Data System (ADS)

    Perdew, John P.; Ernzerhof, Matthias; Zupan, Ales; Burke, Kieron

    While the Hartree-Fock (HF) approximation typically underestimates the strength of the chemical bond, the local spin density (LSD) approximation overestimates it. Thus LSD overbinds atoms in molecules, and underestimates the heights of energy barriers when the transition state is more highly bonded than the initial state. Generalized gradient approximations (GGA's), which incorporate density-gradient corrections to LSD, improve the agreement between calculated and measured energetics. This has been previously understood as a consequence of the fact that gradient corrections favor density inhomogeneity, which increases when a bond is stretched or broken. We show that gradient corrections also favor high density, which increases when a bond is compressed or formed, but that the inhomogeneity effect usually prevails. To quantify the discussion, we present a thermodynamic-like inequality which is satisfied when gradient corrections favor a process.

  20. Surgical Correction of Gastroesophageal Reflux in Lung Transplant Patients Is Associated With Decreased Effector CD8 Cells in Lung Lavages

    PubMed Central

    Mohammed, Aminu; Ulukpo, Onome; Force, Seth D.; Ramirez, Allan M.; Pelaez, Andres; Lawrence, E. Clinton; Larsen, Christian P.; Kirk, Allan D.

    2010-01-01

    Background: Lung transplantation is associated with a high incidence of gastroesophageal reflux disease (GERD). The presence of GERD is considered a risk factor for the subsequent development of obliterative bronchiolitis (OB), and surgical correction of GERD by gastric fundoplication (GF) may be associated with increased freedom from OB. The mechanisms underlying a protective effect from OB remain elusive. The objective of this study was to analyze the flow cytometric properties of BAL cells in patients who have undergone GF early after transplant. Methods: In a single-center lung transplant center, eight patients with GERD who were in the first transplant year underwent GF. Prior to and immediately following GF, BAL cells were analyzed by polychromatic flow cytometry. Spirometry was performed before and after GF. Results: GF was associated with a significant reduction in the frequency of BAL CD8 lymphocytes expressing the intracellular effector marker granzyme B, compared with the pre-GF levels. Twenty-six percent of CD8 cells were granzyme Bhi pre-GF compared with 12% of CD8 cells post-GF (range 8%-50% pre-GF, 2%-24% post-GF, P = .01). In contrast, GF was associated with a significant interval increase in the frequency of CD8 cells with an exhausted phenotype (granzyme Blo, CD127lo, PD1hi) from 12% of CD8 cells pre-GF to 24% post-GF (range 1.7%-24% pre-GF and 11%-47% post-GF, P = .05). No significant changes in spirometry were observed during the study interval. Conclusions: Surgical correction of GF is associated with a decreased frequency of potentially injurious effector CD8 cells in the BAL of lung transplant recipients. PMID:20522573

  1. Use of Multiple Imputation to Correct for Bias in Lung Cancer Incidence Trends by Histologic Subtype

    PubMed Central

    Yu, Mandi; Feuer, Eric J.; Cronin, Kathleen A.; Caporaso, Neil E.

    2014-01-01

    Background Over the past several decades, advances in lung cancer research and practice have led to refinements of histological diagnosis of lung cancer. The differential use and subsequent alterations of non-specific morphology codes, however, may have caused artifactual fluctuations in the incidence rates for histologic subtypes, thus biasing temporal trends. Methods We developed a multiple imputation (MI) method to correct lung cancer incidence for non-specific histology using data from the Surveillance, Epidemiology, and End Results (SEER) Program during 1975–2010. Results For adenocarcinoma in men and squamous in both genders, the change to a increasing trend around 2005, after more than ten years of decreasing incidence, is apparently an artifact of the changes in histopathology practice and coding system. After imputation, the rates remained decreasing for adenocarcinoma and squamous in men, and became constant for squamous in women. Conclusions As molecular features of distinct histologies are increasingly identified by new technologies, accurate histological distinctions are becoming increasingly relevant to more effective 'targeted' therapies, and therefore, are important to track in patients. However, without incorporating the coding changes, the incidence trends estimated for histologic subtypes could be misleading. Impact The MI approach provides a valuable tool for bridging the different histology definitions, thus permitting meaningful inferences about the long-term trends of lung cancer by histological subtype. PMID:24855099

  2. Use of multiple imputation to correct for bias in lung cancer incidence trends by histologic subtype.

    PubMed

    Yu, Mandi; Feuer, Eric J; Cronin, Kathleen A; Caporaso, Neil E

    2014-08-01

    Over the past several decades, advances in lung cancer research and practice have led to refinements of histologic diagnosis of lung cancer. The differential use and subsequent alterations of nonspecific morphology codes, however, may have caused artifactual fluctuations in the incidence rates for histologic subtypes, thus biasing temporal trends. We developed a multiple imputation (MI) method to correct lung cancer incidence for nonspecific histology using data from the Surveillance, Epidemiology, and End Results Program during 1975 to 2010. For adenocarcinoma in men and squamous in both genders, the change to an increasing trend around 2005, after more than 10 years of decreasing incidence, is apparently an artifact of the changes in histopathology practice and coding system. After imputation, the rates remained decreasing for adenocarcinoma and squamous in men, and became constant for squamous in women. As molecular features of distinct histologies are increasingly identified by new technologies, accurate histologic distinctions are becoming increasingly relevant to more effective "targeted" therapies, and therefore, are important to track in patients. However, without incorporating the coding changes, the incidence trends estimated for histologic subtypes could be misleading. The MI approach provides a valuable tool for bridging the different histology definitions, thus permitting meaningful inferences about the long-term trends of lung cancer by histologic subtype. ©2014 American Association for Cancer Research.

  3. Regional Normal Lung Tissue Density Changes in Patients Treated With Stereotactic Body Radiation Therapy for Lung Tumors

    SciTech Connect

    Diot, Quentin; Kavanagh, Brian; Schefter, Tracey; Gaspar, Laurie; Stuhr, Kelly; Miften, Moyed

    2012-11-15

    Purpose: To describe regional lung tissue density changes in normal lung tissue of patients with primary and metastatic lung tumors who received stereotactic body radiation therapy (SBRT). Methods and Materials: A total of 179 post-SBRT follow-up computed tomography (CT) scans of 62 patients who received SBRT between 2003 and 2009 were studied. Median prescription dose was 54 Gy (range, 30-60 Gy) in 3 to 5 fractions. SBRT-induced lung density changes on post-SBRT follow-up CT were evaluated at approximately 3, 6, 12, 18, 24, and 30 months after treatment. Dose-response curves (DRC) were generated for SBRT-induced lung damage by averaging CT number (HU) changes for regions of the lungs receiving the same dose at 5-Gy intervals. Results: For all follow-up interval periods, CT numbers linearly increased with dose until 35 Gy and were constant thereafter. For 3, 18, 24, and 30 months, the rate of relative electron density increase with dose was approximately 0.24% per Gy. At 6 months, the rate was also similar below 20 Gy but then rose to 0.6% per Gy above this threshold. After 6 months, DRCs were mostly time-independent. When split between patients treated with 3 fractions of 12 to 20 Gy (median, 20 Gy; average tumor volume, 12 {+-} 16 cm{sup 3}) and with >3 fractions of 6 to 12.5 Gy (median, 9 Gy; average tumor volume, 30 {+-} 40 cm{sup 3}), DRCs differed significantly. In both cases, CT changes at 3, 18, 24, and 30 months were identical to those of the population DRC; however, patients who received >3 fractions showed 6-month CT changes that were more than twice those for the group that received 3 fractions. Conclusions: This analysis of SBRT-induced normal lung density changes indicates that lung normal tissue has more pronounced self-limited acute effects than late effects. Differences in acute CT changes following treatments in 3 fractions were considerably less than for treatments in >3 fractions.

  4. Sexual minority population density and incidence of lung, colorectal and female breast cancer in California

    PubMed Central

    Boehmer, Ulrike; Miao, Xiaopeng; Maxwell, Nancy I; Ozonoff, Al

    2014-01-01

    Objective Risk factors for breast, colorectal, and lung cancer are known to be more common among lesbian, gay, and bisexual (LGB) individuals, suggesting they may be more likely to develop these cancers. Our objective was to determine differences in cancer incidence by sexual orientation, using sexual orientation data aggregated at the county level. Methods Data on cancer incidence were obtained from the California Cancer Registry and data on sexual orientation were obtained from the California Health Interview Survey, from which a measure of age-specific LGB population density by county was calculated. Using multivariable Poisson regression models, the association between the age–race-stratified incident rate of breast, lung and colorectal cancer in each county and LGB population density was examined, with race, age group and poverty as covariates. Results Among men, bisexual population density was associated with lower incidence of lung cancer and with higher incidence of colorectal cancer. Among women, lesbian population density was associated with lower incidence of lung and colorectal cancer and with higher incidence of breast cancer; bisexual population density was associated with higher incidence of lung and colorectal cancer and with lower incidence of breast cancer. Conclusions These study findings clearly document links between county-level LGB population density and cancer incidence, illuminating an important public health disparity. PMID:24670430

  5. Sexual minority population density and incidence of lung, colorectal and female breast cancer in California.

    PubMed

    Boehmer, Ulrike; Miao, Xiaopeng; Maxwell, Nancy I; Ozonoff, Al

    2014-03-26

    Risk factors for breast, colorectal, and lung cancer are known to be more common among lesbian, gay, and bisexual (LGB) individuals, suggesting they may be more likely to develop these cancers. Our objective was to determine differences in cancer incidence by sexual orientation, using sexual orientation data aggregated at the county level. Data on cancer incidence were obtained from the California Cancer Registry and data on sexual orientation were obtained from the California Health Interview Survey, from which a measure of age-specific LGB population density by county was calculated. Using multivariable Poisson regression models, the association between the age-race-stratified incident rate of breast, lung and colorectal cancer in each county and LGB population density was examined, with race, age group and poverty as covariates. Among men, bisexual population density was associated with lower incidence of lung cancer and with higher incidence of colorectal cancer. Among women, lesbian population density was associated with lower incidence of lung and colorectal cancer and with higher incidence of breast cancer; bisexual population density was associated with higher incidence of lung and colorectal cancer and with lower incidence of breast cancer. These study findings clearly document links between county-level LGB population density and cancer incidence, illuminating an important public health disparity.

  6. Effect of compression paddle tilt correction on volumetric breast density estimation.

    PubMed

    Kallenberg, Michiel G J; van Gils, Carla H; Lokate, Mariëtte; den Heeten, Gerard J; Karssemeijer, Nico

    2012-08-21

    For the acquisition of a mammogram, a breast is compressed between a compression paddle and a support table. When compression is applied with a flexible compression paddle, the upper plate may be tilted, which results in variation in breast thickness from the chest wall to the breast margin. Paddle tilt has been recognized as a major problem in volumetric breast density estimation methods. In previous work, we developed a fully automatic method to correct the image for the effect of compression paddle tilt. In this study, we investigated in three experiments the effect of paddle tilt and its correction on volumetric breast density estimation. Results showed that paddle tilt considerably affected accuracy of volumetric breast density estimation, but that effect could be reduced by tilt correction. By applying tilt correction, a significant increase in correspondence between mammographic density estimates and measurements on MRI was established. We argue that in volumetric breast density estimation, tilt correction is both feasible and essential when mammographic images are acquired with a flexible compression paddle.

  7. Respiratory effort correction strategies to improve the reproducibility of lung expansion measurements

    SciTech Connect

    Du, Kaifang; Reinhardt, Joseph M.; Christensen, Gary E.; Ding, Kai; Bayouth, John E.

    2013-12-15

    Purpose: Four-dimensional computed tomography (4DCT) can be used to make measurements of pulmonary function longitudinally. The sensitivity of such measurements to identify change depends on measurement uncertainty. Previously, intrasubject reproducibility of Jacobian-based measures of lung tissue expansion was studied in two repeat prior-RT 4DCT human acquisitions. Difference in respiratory effort such as breathing amplitude and frequency may affect longitudinal function assessment. In this study, the authors present normalization schemes that correct ventilation images for variations in respiratory effort and assess the reproducibility improvement after effort correction.Methods: Repeat 4DCT image data acquired within a short time interval from 24 patients prior to radiation therapy (RT) were used for this analysis. Using a tissue volume preserving deformable image registration algorithm, Jacobian ventilation maps in two scanning sessions were computed and compared on the same coordinate for reproducibility analysis. In addition to computing the ventilation maps from end expiration to end inspiration, the authors investigated the effort normalization strategies using other intermediated inspiration phases upon the principles of equivalent tidal volume (ETV) and equivalent lung volume (ELV). Scatter plots and mean square error of the repeat ventilation maps and the Jacobian ratio map were generated for four conditions: no effort correction, global normalization, ETV, and ELV. In addition, gamma pass rate was calculated from a modified gamma index evaluation between two ventilation maps, using acceptance criterions of 2 mm distance-to-agreement and 5% ventilation difference.Results: The pattern of regional pulmonary ventilation changes as lung volume changes. All effort correction strategies improved reproducibility when changes in respiratory effort were greater than 150 cc (p < 0.005 with regard to the gamma pass rate). Improvement of reproducibility was

  8. Assessment of CF lung disease using motion corrected PROPELLER MRI: a comparison with CT.

    PubMed

    Ciet, Pierluigi; Serra, Goffredo; Bertolo, Silvia; Spronk, Sandra; Ros, Mirco; Fraioli, Francesco; Quattrucci, Serena; Assael, M Baroukh; Catalano, Carlo; Pomerri, Fabio; Tiddens, Harm A W M; Morana, Giovanni

    2016-03-01

    To date, PROPELLER MRI, a breathing-motion-insensitive technique, has not been assessed for cystic fibrosis (CF) lung disease. We compared this technique to CT for assessing CF lung disease in children and adults. Thirty-eight stable CF patients (median 21 years, range 6-51 years, 22 female) underwent MRI and CT on the same day. Study protocol included respiratory-triggered PROPELLER MRI and volumetric CT end-inspiratory and -expiratory acquisitions. Two observers scored the images using the CF-MRI and CF-CT systems. Scores were compared with intra-class correlation coefficient (ICC) and Bland-Altman plots. The sensitivity and specificity of MRI versus CT were calculated. MRI sensitivity for detecting severe CF bronchiectasis was 0.33 (CI 0.09-0.57), while specificity was 100% (CI 0.88-1). ICCs for bronchiectasis and trapped air were as follows: MRI-bronchiectasis (0.79); CT-bronchiectasis (0.85); MRI-trapped air (0.51); CT-trapped air (0.87). Bland-Altman plots showed an MRI tendency to overestimate the severity of bronchiectasis in mild CF disease and underestimate bronchiectasis in severe disease. Motion correction in PROPELLER MRI does not improve assessment of CF lung disease compared to CT. However, the good inter- and intra-observer agreement and the high specificity suggest that MRI might play a role in the short-term follow-up of CF lung disease (i.e. pulmonary exacerbations). PROPELLER MRI does not match CT sensitivity to assess CF lung disease. PROPELLER MRI has lower sensitivity than CT to detect severe bronchiectasis. PROPELLER MRI has good to very good intra- and inter-observer variability. PROPELLER MRI can be used for short-term follow-up studies in CF.

  9. Predictive Value of Early Tumor Shrinkage and Density Reduction of Lung Metastases in Patients With Metastatic Colorectal Cancer Treated With Regorafenib.

    PubMed

    Vanwynsberghe, Hannes; Verbeke, Xander; Coolen, Johan; Van Cutsem, Eric

    2017-03-29

    The benefit of regorafenib in colorectal cancer is not very pronounced. At present, there is lack of predictive biological or radiological markers. We studied if density reduction or small changes in size of lung metastases could be a predictive marker. We retrospectively measured density in size of lung metastases of all patients included in the CORRECT and CONSIGN trials at our center. Contrast-enhanced CT scan at baseline and at week 8 were compared. Data of progressive-free survival and overall survival were collected from the CORRECT and CONSIGN trials. A significant difference in progressive-free survival was seen in 3 groups: response or stable disease in size (5.36 vs. 3.96 months), response in density (6.03 vs. 2.72 months), and response in corrected density (6.14 vs. 3.08 months). No difference was seen for response in size versus stable disease or progressive disease in size. For overall survival, a difference was observed in the same 3 groups: response or stable disease in size (9.89 vs. 6.44 months), response in density (9.59 vs. 7.04 months), and response in corrected density (9.09 vs. 7.16 months). No difference was seen for response in size versus stable disease or progressive disease in size. Density reduction in lung metastases might be a good predictive parameter to predict outcome for regorafenib. Early tumor progression might be a negative predictive factor. If further validated, density reduction and early tumor progression might be useful to ameliorate the cost-benefit of regorafenib. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Correction to BrainSCAN central axis dose calculations for 6-MV photon beams to lung with lateral electron disequilibrium

    SciTech Connect

    Geyer, Peter . E-mail: peter.geyer@mailbox.tu-dresden.de; Blank, Hilbert; Zips, Daniel; Alheit, Horst

    2006-11-15

    Purpose: To develop and evaluate a correction method for lateral electron disequilibrium and tissue inhomogeneities in lung tissues applicable to the BrainSCAN treatment planning system. Methods and Materials: Four noncoplanar 6-MV photon beams with different beam diameters were applied to the right lung of a thorax phantom. The measured/calculated dose value ratio was evaluated as a function of a parameter that describes the degree of the lateral electron disequilibrium based on the primary dose. Results: The dose ratio showed a clearcut linear dependency on the disequilibrium parameter. Applying the proposed correction method, only minor differences between the measured and calculated doses were found for lesions >1 cm. However, for lesions <1 cm surrounded by lung tissue the difference was {<=}15%. Conclusion: The data have indicated a relevant magnitude of the correction factor only for lung lesions <1 cm.

  11. Interconnections between atomic-electron density and electron-momentum density: Leading and tail corrections

    NASA Astrophysics Data System (ADS)

    Gadre, Shridhar R.; Chakravorty, Subhas J.

    1986-02-01

    The Burkhardt-Konya-Coulson-March (BKCM) procedure developed by Gadre and Pathak for direct and reverse transformations between atomic-electron density and electron-momentum density has been modified. The modification is based on a work by Allan and March suggesting the use of a square of the Fourier transform of √ρ(r) for obtaining electron-momentum density at small as well as large p values. The new procedure [grafted-BKCM (G-BKCM)] involves an amalgamation of these procedures: the Allan-March procedure being grafted onto the BKCM method for low and high p values. The G-BKCM method has been tested out in direct as well as reverse directions and is seen to lead to extremely good estimates of atomic properties in the conjugate space.

  12. SU-E-T-129: Dosimetric Evaluation of the Impact of Density Correction On Dose Calculation of Breast Cancer Treatment: A Study Based On RTOG 1005 Cases

    SciTech Connect

    Li, J; Yu, Y

    2014-06-01

    Purpose: RTOG 1005 requires density correction in the dose calculation of breast cancer radiation treatment. The aim of the study was to evaluate the impact of density correction on the dose calculation. Methods: Eight cases were studied, which were planned on an XiO treatment planning system with pixel-by-pixel density correction using a superposition algorithm, following RTOG 1005 protocol requirements. Four were protocol Arm 1 (standard whole breast irradiation with sequential boost) cases and four were Arm 2 (hypofractionated whole breast irradiation with concurrent boost) cases. The plans were recalculated with the same monitor units without density correction. Dose calculations with and without density correction were compared. Results: Results of Arm 1 and Arm 2 cases showed similar trends in the comparison. The average differences between the calculations with and without density correction (difference = Without - With) among all the cases were: -0.82 Gy (range: -2.65∼−0.18 Gy) in breast PTV Eval D95, −0.75 Gy (range: −1.23∼0.26 Gy) in breast PTV Eval D90, −1.00 Gy (range: −2.46∼−0.29 Gy) in lumpectomy PTV Eval D95, −0.78 Gy (range: −1.30∼0.11 Gy) in lumpectomy PTV Eval D90, −0.43% (range: −0.95∼−0.14%) in ipsilateral lung V20, −0.81% (range: −1.62∼−0.26%) in V16, −1.95% (range: −4.13∼−0.84%) in V10, −2.64% (−5.55∼−1.04%) in V8, −4.19% (range: −6.92∼−1.81%) in V5, and −4.95% (range: −7.49∼−2.01%) in V4, respectively. The differences in other normal tissues were minimal. Conclusion: The effect of density correction was observed in breast target doses (an average increase of ∼1 Gy in D95 and D90, compared to the calculation without density correction) and exposed ipsilateral lung volumes in low dose region (average increases of ∼4% and ∼5% in V5 and V4, respectively)

  13. Analytic energy-level densities of separable harmonic oscillators including approximate hindered rotor corrections

    NASA Astrophysics Data System (ADS)

    Döntgen, M.

    2016-09-01

    Energy-level densities are key for obtaining various chemical properties. In chemical kinetics, energy-level densities are used to predict thermochemistry and microscopic reaction rates. Here, an analytic energy-level density formulation is derived using inverse Laplace transformation of harmonic oscillator partition functions. Anharmonic contributions to the energy-level density are considered approximately using a literature model for the transition from harmonic to free motions. The present analytic energy-level density formulation for rigid rotor-harmonic oscillator systems is validated against the well-studied CO+O˙ H system. The approximate hindered rotor energy-level density corrections are validated against the well-studied H2O2 system. The presented analytic energy-level density formulation gives a basis for developing novel numerical simulation schemes for chemical processes.

  14. Lung Density Changes After Stereotactic Radiotherapy: A Quantitative Analysis in 50 Patients

    SciTech Connect

    Palma, David A.; Soernsen de Koste, John van; Verbakel, Wilko F.A.R.; Vincent, Andrew; Senan, Suresh

    2011-11-15

    Purpose: Radiologic lung density changes are observed in more than 50% of patients after stereotactic body radiotherapy (SBRT) for lung cancer. We studied the relationship between SBRT dose and posttreatment computed tomography (CT) density changes, a surrogate for lung injury. Methods and Materials: The SBRT fractionation schemes used to treat Stage I lung cancer with RapidArc were three fractions of 18 Gy, five fractions of 11 Gy, or eight fractions of 7.5 Gy, prescribed at the 80% isodose. Follow-up CT scans performed at less than 6 months (n = 50) and between 6 and 9 months (n = 30) after SBRT were reviewed. Posttreatment scans were coregistered with baseline scans using a B-spline deformable registration algorithm. Voxel-Hounsfield unit histograms were created for doses between 0.5 and 50 Gy. Linear mixed effects models were used to assess the effects of SBRT dose on CT density, and the influence of possible confounders was tested. Results: Increased CT density was associated with higher dose, increasing planning target volume size, and increasing time after SBRT (all p < 0.0001). Density increases were apparent in areas receiving >6 Gy, were most prominent in areas receiving >20 Gy, and seemed to plateau above 40 Gy. In regions receiving >36 Gy, the reduction in air-filled fraction of lung after treatment was up to 18%. No increase in CT density was observed in the contralateral lung receiving {>=}3 Gy. Conclusions: A dose-response relationship exists for quantitative CT density changes after SBRT. A threshold of effect is seen at low doses, and a plateau at highest doses.

  15. Spatially coupled low-density parity-check error correction for holographic data storage

    NASA Astrophysics Data System (ADS)

    Ishii, Norihiko; Katano, Yutaro; Muroi, Tetsuhiko; Kinoshita, Nobuhiro

    2017-09-01

    The spatially coupled low-density parity-check (SC-LDPC) was considered for holographic data storage. The superiority of SC-LDPC was studied by simulation. The simulations show that the performance of SC-LDPC depends on the lifting number, and when the lifting number is over 100, SC-LDPC shows better error correctability compared with irregular LDPC. SC-LDPC is applied to the 5:9 modulation code, which is one of the differential codes. The error-free point is near 2.8 dB and over 10-1 can be corrected in simulation. From these simulation results, this error correction code can be applied to actual holographic data storage test equipment. Results showed that 8 × 10-2 can be corrected, furthermore it works effectively and shows good error correctability.

  16. Surface measurement system for the atmospheric electrical vertical conduction current density, with displacement current density correction

    NASA Astrophysics Data System (ADS)

    Bennett, A. J.; Harrison, R. G.

    2008-08-01

    Global thunderstorm and shower cloud activity generate the global electric potential difference between the Earth's surface and the lower ionosphere. The finite conductivity of atmospheric air, which arises from cosmic ray and natural radioactive ionisation, permits a vertical conduction current density (~1 pA m-2) between the lower ionosphere and the surface during fair-weather conditions; this current provides a physical link between the upper and lower atmospheres. A new instrument system is described to measure the conduction current density at the surface (the "air-Earth current"), which operates on a novel principle using two collecting electrodes of different geometry. Simultaneous measurements from two independent co-located systems using the geometrical principle show close agreement (correlation of 0.96 during 2.5 h of 5 min measurements). The sensor design described is durable and successful measurements in fair and disturbed weather have been obtained in air temperatures between -6 and 35 °C, relative humidity between 44% and 100%, fog, rain and snowfall. The uncertainty in conduction current density determinations is 0.20 pA m-2.

  17. Local density corrected three-body distribution functions for probing local structure reorganization in liquids.

    PubMed

    Bhattacharjee, Anirban; Hofer, Thomas S; Rode, Bernd M

    2008-11-28

    Three-body distribution functions are calculated for metal ions in an aqueous medium in order to investigate and characterise solvent structure reorganization. Based on the existing formulation of three body correlation function, a local density correction is introduced to enable a comparison of different sub-regions within a solvate as well as different systems, thus taking into account the varying density arising from the influence of the solute.

  18. Effects of body position on lung density estimated from EIT data

    NASA Astrophysics Data System (ADS)

    Noshiro, Makoto; Ebihara, Kei; Sato, Ena; Nebuya, Satoru; Brown, Brian H.

    2010-04-01

    Normal subjects took the sitting, supine, prone, right lateral and left lateral positions during the measurement procedure. One minute epochs of EIT data were collected at the levels of the 3rd, 4th, 5th and 6th intercostal spaces in each position during normal tidal breathing. Lung density was then determined from the EIT data using the method proposed by Brown5. Lung density at the electrode level of the 6th intercostal space was different from that at almost any other levels in both male and female subjects, and lung density at the electrode levels of the 4th and 5th intercostal spaces in male subjects did not depend upon position.

  19. Relationship between frequency, length, and treatment outcome of exacerbations to baseline lung function and lung density in alpha-1 antitrypsin-deficient COPD

    PubMed Central

    Vijayasaratha, Kesavaperumal; Stockley, Robert A

    2012-01-01

    Background Diary cards are useful for analyzing exacerbations in chronic obstructive pulmonary disease (COPD), although factors influencing the length and frequency of each episode are poorly understood. This study investigated factors that influence the features of exacerbations in patients with alpha-1 antitrypsin (AAT) deficiency (PiZ phenotype) and COPD. Methods Daily diary cards were collected over 2 years. Patients had emphysema visualized and quantified by computed tomography scan, and had at least one documented exacerbation in the previous year. Results The patients (n = 23) had a mean age of 52.5 years, forced expiratory volume in one second (FEV1) of 1.2 L (38.4% predicted), corrected gas transfer (KCO) of 0.90 mmol/min/kPa/L (59.7% predicted), and 15th percentile lung density of 44.55 g/L. Two hundred and sixty-three exacerbations (164 treated) were identified. The frequency of treated exacerbations correlated negatively with KCO% predicted (r = −0.432; P = 0.022). Exacerbation length (determined for 17 of the patients for whom diary card data through the episode were available) correlated negatively with baseline 15th percentile lung density (r = −0.361; P = 0.003), and increased the longer treatment was delayed (r = 0.503; P < 0.001). Treatment delay was shorter with higher day 1 symptom score, lower baseline FEV1, FEV1/forced vital capacity, and lower 15th percentile lung density (r = −0.368, 0.272, 0.461, and 0.786; P = 0.004, 0.036, <0.001, and <0.001, respectively). Time to resolution of exacerbation after treatment initiation was not affected by treatment delay, but correlated negatively with KCO% predicted (r = −0.647; P = 0.007). Conclusion In alpha-1 antitrypsin deficiency, the frequency and length of resolution of exacerbation were related to baseline gas transfer. Treatment delay adversely affected exacerbation length, and lung density was the best independent predictor of delay in starting treatment. PMID:23226015

  20. A perspective on thirty years of the Webb, Pearman and Leuning density corrections

    Treesearch

    Xuhui Lee; William J. Massman

    2011-01-01

    The density correction theory of Webb et al. (1980, Q J Roy Meteorol Soc 106: 85-100, hereafter WPL) is a principle underpinning the experimental investigation of surface fluxes of energy and masses in the atmospheric boundary layer. It has a long-lasting influence in boundary-layer meteorology and micrometeorology, and the year 2010 marks the 30th anniversary of the...

  1. Gradient corrections to the local-density approximation for trapped superfluid Fermi gases

    SciTech Connect

    Csordas, Andras; Almasy, Orsolya; Szepfalusy, Peter

    2010-12-15

    Two species superfluid Fermi gas is investigated on the BCS side up to the Feshbach resonance. Using the Greens's function technique gradient corrections are calculated to the generalized Thomas-Fermi theory including Cooper pairing. Their relative magnitude is found to be measured by the small parameter (d/R{sub TF}){sup 4}, where d is the oscillator length of the trap potential and R{sub TF} is the radial extension of the density n in the Thomas-Fermi approximation. In particular, at the Feshbach resonance the universal corrections to the local density approximation are calculated and a universal prefactor {kappa}{sub W}=7/27 is derived for the von Weizsaecker-type correction {kappa}{sub W}(({h_bar}/2{pi}){sup 2}/2m)({nabla}{sup 2}n{sup 1/2}/n{sup 1/2}).

  2. Spin-wave-induced corrections to the electronic density of states in metallic ferromagnets

    NASA Astrophysics Data System (ADS)

    Ricottone, A.; Danon, J.; Brouwer, P. W.

    2013-12-01

    We calculate the correction to the electronic density of states in a disordered ferromagnetic metal induced by spin-wave mediated interaction between the electrons. Our calculation is valid for the case that the exchange splitting Δ in the ferromagnet is much smaller than the Fermi energy, but we make no assumption on the relative magnitude of Δ and the elastic electronic scattering time τel. In the ‘clean limit’ Δτel/ℏ ≫ 1 we find a correction with a Td/2 temperature dependence, where d is the effective dimensionality of the ferromagnet. In the ‘dirty limit’ Δτel/ℏ ≪ 1, the density-of-states correction is a non-monotonous function of energy and temperature.

  3. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-06-05

    The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

  4. Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

    PubMed

    Guidez, Emilie B; Gordon, Mark S

    2015-03-12

    The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

  5. Size-Consistency, Self-Interaction Correction, and Derivative Discontinuity in Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Perdew, John P.

    Three size-consistency principles of electronic structure theory are set forth. "Separability" and "extensivity" are respected even by local or semilocal density functional approximations, which succeed for that and other reasons. The strong tendency of a separated subsystem to reject fractional electron number is a consequence of the derivative discontinuity of the energy; this "integer preference" is probably not respected by any practical density functional approximation. However, all three size-consistency principles are obeyed by theories which construct the energy from localized orbitals. The self-interaction correction (SIC) to the local spin density approximation favors localized orbitals for most systems. If this fails for metals, then SIC gives rise to a "false surface energy". The self-interaction correction is reviewed, along with its exact-theory "doppelganger", the derivative discontinuity. The latter reveals the physical content of the exact Kohn-Sham orbital energies and resolves the "band-gap problem".

  6. Plasma carbonyls do not correlate with lung function or computed tomography measures of lung density in older smokers

    PubMed Central

    Mesia-Vela, Sonia; Yeh, Chih-Ching; Austin, John H.M.; Dounel, Matthew; Powell, Charles A.; Reeves, Anthony; Santella, Regina M.; Stevenson, Lori; Yankelevitz, David; Barr, R. Graham

    2009-01-01

    Oxidative stress and inflammation are hallmarks of chronic obstructive pulmonary disease (COPD). A critical byproduct of oxidative damage is the introduction of carbonyl groups into amino acid residues. We hypothesize that plasma carbonyl content is inversely correlated with lung function and computed tomography (CT) measures of lung density among smokers and is elevated in COPD. Carbonyl was measured in plasma of participants aged 60 years and older by ELISA. Generalized linear and additive models were used to adjust for potential confounders. Among 541 participants (52% male, mean age 67 years, 41% current smokers), mean plasma carbonyl content was 17.9±2.9 nmol ml−1 and mean forced expiratory volume in one second (FEV1) was 80.7±20.9% of predicted. Plasma carbonyl content was inversely associated with FEV1, but this relationship was largely explained by age. Multivariate analyses ruled out clinically meaningful associations of plasma carbonyl content with FEV1, FEV1/FVC (forced vital capacity) ratio, severity of airflow obstruction, and CT lung density. Plasma carbonyl content is a poor biomarker of oxidative stress in COPD and emphysema. PMID:18484356

  7. Effect of lung and target density on small-field dose coverage and PTV definition

    SciTech Connect

    Higgins, Patrick D. Ehler, Eric D.; Cho, Lawrence C.; Dusenbery, Kathryn E.

    2015-04-01

    We have studied the effect of target and lung density on block margin for small stereotactic body radiotherapy (SBRT) targets. A phantom (50 × 50 × 50 cm{sup 3}) was created in the Pinnacle (V9.2) planning system with a 23-cm diameter lung region of interest insert. Diameter targets of 1.6, 2.0, 3.0, and 4.0 cm were placed in the lung region of interest and centered at a physical depth of 15 cm. Target densities evaluated were 0.1 to 1.0 g/cm{sup 3}, whereas the surrounding lung density was varied between 0.05 and 0.6 g/cm{sup 3}. A dose of 100 cGy was delivered to the isocenter via a single 6-MV field, and the ratio of the average dose to points defining the lateral edges of the target to the isocenter dose was recorded for each combination. Field margins were varied from none to 1.5 cm in 0.25-cm steps. Data obtained in the phantom study were used to predict planning treatment volume (PTV) margins that would match the clinical PTV and isodose prescription for a clinical set of 39 SBRT cases. The average internal target volume (ITV) density was 0.73 ± 0.17, average local lung density was 0.33 ± 0.16, and average ITV diameter was 2.16 ± 0.8 cm. The phantom results initially underpredicted PTV margins by 0.35 cm. With this offset included in the model, the ratio of predicted-to-clinical PTVs was 1.05 ± 0.32. For a given target and lung density, it was found that treatment margin was insensitive to target diameter, except for the smallest (1.6-cm diameter) target, for which the treatment margin was more sensitive to density changes than the larger targets. We have developed a graphical relationship for block margin as a function of target and lung density, which should save time in the planning phase by shortening the design of PTV margins that can satisfy Radiation Therapy Oncology Group mandated treatment volume ratios.

  8. 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

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

    SciTech Connect

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

    2013-12-15

    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'sr, 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'sr increased from 0.86 to 0.92 with the bias field correction

  10. Effect of motion on tracer activity determination in CT attenuation corrected PET images: A lung phantom study

    SciTech Connect

    Pevsner, Alex; Nehmeh, Sadek A.; Humm, John L.; Mageras, Gig S.; Erdi, Yusuf E.

    2005-07-15

    Respiratory motion is known to affect the quantitation of {sup 18}FDG uptake in lung lesions. The aim of the study was to investigate the magnitude of errors in tracer activity determination due to motion, and its dependence upon CT attenuation at different phases of the motion cycle. To estimate these errors we have compared maximum activity concentrations determined from PET/CT images of a lung phantom at rest and under simulated respiratory motion. The NEMA 2001 IEC body phantom, containing six hollow spheres with diameters 37, 28, 22, 17, 13, and 10 mm, was used in this study. To mimic lung tissue density, the phantom (excluding spheres) was filled with low density polystyrene beads and water. The phantom spheres were filled with {sup 18}FDG solution setting the target-to-background activity concentration ratio at 8:1. PET/CT data were acquired with the phantom at rest, and while it was undergoing periodic motion along the longitudinal axis of the scanner with a range of displacement being 2 cm, and a period of 5 s. The phantom at rest and in motion was scanned using manufacturer provided standard helical/clinical protocol, a helical CT scan followed by a PET emission scan. The moving phantom was also scanned using a 4D-CT protocol that provides volume image sets at different phases of the motion cycle. To estimate the effect of motion on quantitation of activities in six spheres, we have examined the activity concentration data for (a) the stationary phantom, (b) the phantom undergoing simulated respiratory motion, and (c) a moving phantom acquired with PET/4D-CT protocol in which attenuation correction was performed with CT images acquired at different phases of motion cycle. The data for the phantom at rest and in motion acquired with the standard helical/clinical protocol showed that the activity concentration in the spheres can be underestimated by as much as 75%, depending on the sphere diameter. We have also demonstrated that fluctuations in sphere

  11. CT analysis of lung density changes in patients undergoing total body irradiation prior to bone marrow transplantation

    SciTech Connect

    Lee, J.Y.; Shank, B.; Bonfiglio, P.; Reid, A.

    1984-10-01

    Sequential changes in lung density measured by CT are potentially sensitive and convenient monitors of lung abnormalities following total body irradiation (TBI). Methods have been developed to compare pre- and post-TBI CT of lung. The average local features of a cross-sectional lung slice are extracted from three peripheral regions of interest in the anterior, posterior, and lateral portions of the CT image. Also, density profiles across a specific region may be obtained. These may be compared first for verification of patient position and breathing status and then for changes between pre- and post-TBI. These may also be compared with radiation dose profiles through the lung. A preliminary study on 21 leukemia patients undergoing total body irradiation indicates the following: (a) Density gradients of patients' lungs in the antero-posterior direction show a marked heterogeneity before and after transplantation compared with normal lungs. The patients with departures from normal density gradients pre-TBI correlate with later pulmonary complications. (b) Measurements of average peripheral lung densities have demonstrated that the average lung density in the younger age group is substantially higher: pre-TBI, the average CT number (1,000 scale) is -638 +/- 39 Hounsfield unit (HU) for 0-10 years old and -739 +/- 53 HU for 21-40 years old. (c) Density profiles showed no post-TBI regional changes in lung density corresponding to the dose profile across the lung, so no differentiation of a radiation-specific effect has yet been possible. Computed tomographic density profiles in the antero-posterior direction are successfully used to verify positioning of the CT slice and the breathing level of the lung.

  12. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

    PubMed

    Soniat, Marielle; Rogers, David M; Rempe, Susan B

    2015-07-14

    A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.

  13. Distributions and averages of electron density parameters: Explaining the effects of gradient corrections

    NASA Astrophysics Data System (ADS)

    Zupan, Ales; Burke, Kieron; Ernzerhof, Matthias; Perdew, John P.

    1997-06-01

    We analyze the electron densities n(r) of atoms, molecules, solids, and surfaces. The distributions of values of the Seitz radius rs=(3/4πn)1/3 and the reduced density gradient s=|∇n|/(2(3π2)1/3n4/3) in an electron density indicate which ranges of these variables are significant for physical processes. We also define energy-weighted averages of these variables, and , from which local spin density (LSD) and generalized gradient approximation (GGA) exchange-correlation energies may be estimated. The changes in these averages upon rearrangement of the nuclei (atomization of molecules or solids, stretching of bond lengths or lattice parameters, change of crystal structure, etc.) are used to explain why GGA corrects LSD in the way it does. A thermodynamic-like inequality (essentially d/>d/2) determines whether the gradient corrections drive a process forward. We use this analysis to explain why gradient corrections usually stretch bonds (but not for example H-H bonds), reduce atomization and surface energies, and raise energy barriers to formation at transition states.

  14. Local respiratory motion correction for PET/CT imaging: Application to lung cancer

    SciTech Connect

    Lamare, F. Fernandez, P.; Fayad, H.; Visvikis, D.

    2015-10-15

    Purpose: Despite multiple methodologies already proposed to correct respiratory motion in the whole PET imaging field of view (FOV), such approaches have not found wide acceptance in clinical routine. An alternative can be the local respiratory motion correction (LRMC) of data corresponding to a given volume of interest (VOI: organ or tumor). Advantages of LRMC include the use of a simple motion model, faster execution times, and organ specific motion correction. The purpose of this study was to evaluate the performance of LMRC using various motion models for oncology (lung lesion) applications. Methods: Both simulated (NURBS based 4D cardiac-torso phantom) and clinical studies (six patients) were used in the evaluation of the proposed LRMC approach. PET data were acquired in list-mode and synchronized with respiration. The implemented approach consists first in defining a VOI on the reconstructed motion average image. Gated PET images of the VOI are subsequently reconstructed using only lines of response passing through the selected VOI and are used in combination with a center of gravity or an affine/elastic registration algorithm to derive the transformation maps corresponding to the respiration effects. Those are finally integrated in the reconstruction process to produce a motion free image over the lesion regions. Results: Although the center of gravity or affine algorithm achieved similar performance for individual lesion motion correction, the elastic model, applied either locally or to the whole FOV, led to an overall superior performance. The spatial tumor location was altered by 89% and 81% for the elastic model applied locally or to the whole FOV, respectively (compared to 44% and 39% for the center of gravity and affine models, respectively). This resulted in similar associated overall tumor volume changes of 84% and 80%, respectively (compared to 75% and 71% for the center of gravity and affine models, respectively). The application of the nonrigid

  15. Ensemble density variational methods with self- and ghost-interaction-corrected functionals

    SciTech Connect

    Pastorczak, Ewa; Pernal, Katarzyna

    2014-05-14

    Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.

  16. Trends in corrected lung cancer mortality rates in Brazil and regions.

    PubMed

    Malta, Deborah Carvalho; Abreu, Daisy Maria Xavier de; Moura, Lenildo de; Lana, Gustavo C; Azevedo, Gulnar; França, Elisabeth

    2016-06-27

    To describe the trend in cancer mortality rates in Brazil and regions before and after correction for underreporting of deaths and redistribution of ill-defined and nonspecific causes. The study used data of deaths from lung cancer among the population aged from 30 to 69 years, notified to the Mortality Information System between 1996 and 2011, corrected for underreporting of deaths, non-registered sex and age , and causes with ill-defined or garbage codes according to sex, age, and region. Standardized rates were calculated by age for raw and corrected data. An analysis of time trend in lung cancer mortality was carried out using the regression model with autoregressive errors. Lung cancer in Brazil presented higher rates among men compared to women, and the South region showed the highest death risk in 1996 and 2011. Mortality showed a trend of reduction for males and increase for women. Lung cancer in Brazil presented different distribution patterns according to sex, with higher rates among men and a reduction in the mortality trend for men and increase for women. Descrever a tendência da mortalidade por câncer de pulmão no Brasil e regiões, antes e após as correções por sub-registro de óbitos, redistribuição de causas mal definidas e causas inespecíficas. Foram utilizados dados de óbitos por câncer de pulmão da população de 30 a 69 anos, notificados ao Sistema de Informação sobre Mortalidade, entre 1996 e 2011, corrigidos para sub-registro de óbitos, declaração de sexo e idade ignorados e causas com códigos mal definidos e inespecíficos segundo sexo, idade e região. Foram calculadas taxas padronizadas por idade para dados brutos e corrigidos. Realizou-se análise da tendência temporal da mortalidade por câncer de pulmão por meio do modelo de regressão com erros autorregressivos. O câncer de pulmão no Brasil apresentou taxas mais elevadas em homens que em mulheres e a região Sul foi a que apresentou maior risco de morte em 1996 e

  17. Measuring Fluxes with Better Certainty without a Need for Density Corrections or Pressure Term

    NASA Astrophysics Data System (ADS)

    Burba, G.; Nakai, T.; Schmidt, A.; Scott, R.; Kathilankal, J.; Fratini, G.; Hanson, C.; Law, B.; McDermitt, D.; Eckles, R.

    2012-04-01

    Eddy Covariance flux measurements using gas analyzers of an enclosed design rely on the covariance between instantaneous vertical wind speed and instantaneous output of gas mixing ratio, such that density data are corrected on-the-fly using instantaneous water vapor, temperature and pressure measurements in the cell, collected and aligned with CO2 or other gas of interest. This approach implicitly accounts for the effects of fluctuations in water vapor, temperature and pressure on the density of the gas of interest. Therefore no sensible heat or latent heat portions of Webb-Pearman-Leuning density corrections (WPL) are required, and the pressure term, which is usually neglected in traditional WPL implementation, is accounted for in these mixing ratio-based measurements. A somewhat similar way of calculating fluxes has been used frequently with traditional closed-path analyzers, with some assumptions: (i) slow temperature measurements were used to convert from density to mixing ratio, assuming fast fluctuations of the air temperature to be fully attenuated in the long intake tube; (ii) slow pressure measurements were used, assuming negligible instantaneous pressure fluctuations. Nine field experiments were conducted in a wide range of environmental conditions from Florida to Alaska using an enclosed CO2/H2O gas analyzer. These experiments presented an opportunity to verify the performance of the mixing ratio approach, and examine the differences from traditional density-based measurements. Results indicate that the mixing ratio-based approach helps to minimize or eliminate a number of uncertainties associated with traditional density-based approach, including: (i) uncertainties associated with correcting the product of fast covariances of gas density using sensible and latent heat flux calculated over half-hour or an hour; (ii) uncertainties in the magnitudes of the sensible and latent heat fluxes used in correcting gas flux; (iii) bias in long-term accumulated CO2

  18. Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms

    SciTech Connect

    Pederson, Mark R.

    2015-02-14

    A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeit slightly too low.

  19. Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms.

    PubMed

    Pederson, Mark R

    2015-02-14

    A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeit slightly too low.

  20. Quantum oscillations in the kinetic energy density: Gradient corrections from the Airy gas

    NASA Astrophysics Data System (ADS)

    Lindmaa, Alexander; Mattsson, Ann E.; Armiento, Rickard

    2014-03-01

    We show how one can systematically derive exact quantum corrections to the kinetic energy density (KED) in the Thomas-Fermi (TF) limit of the Airy gas (AG). The resulting expression is of second order in the density variation and we demonstrate how it applies universally to a certain class of model systems in the slowly varying regime, for which the accuracy of the gradient corrections of the extended Thomas-Fermi (ETF) model is limited. In particular we study two kinds of related electronic edges, the Hermite gas (HG) and the Mathieu gas (MG), which are both relevant for discussing periodic systems. We also consider two systems with finite integer particle number, namely non-interacting electrons subject to harmonic confinement as well as the hydrogenic potential. Finally we discuss possible implications of our findings mainly related to the field of functional development of the local kinetic energy contribution.

  1. Partnering dispersion corrections with modern parameter-free double-hybrid density functionals.

    PubMed

    Sancho-García, J C; Brémond, É; Savarese, M; Pérez-Jiménez, A J; Adamo, C

    2017-03-09

    The PBE-QIDH and SOS1-PBE-QIDH double-hybrid density functionals are merged with a pair of dispersion corrections, namely the pairwise additive D3(BJ) and the non-local correlation functional VV10, leading to the corresponding dispersion-corrected models. The parameters adjusting each of the dispersion corrections to the functionals are obtained by fitting to well-established energy datasets (e.g. S130) used as a benchmark, giving rise to functionals spanning covalent and non-covalent binding forces. The application of the models to challenging systems out of the training set, like those comprising the L7 database of large supramolecular complexes, or the S66x8 dataset of stretched and elongated intermolecular distances, reveals the high accuracy of the coupling.

  2. Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

    NASA Astrophysics Data System (ADS)

    Nocera, A.; Alvarez, G.

    2016-11-01

    Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.

  3. Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

    DOE PAGES

    None, None

    2016-11-21

    Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that themore » Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.« less

  4. Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

    SciTech Connect

    None, None

    2016-11-21

    Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.

  5. Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors.

    PubMed

    Nocera, A; Alvarez, G

    2016-11-01

    Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.

  6. Effect of inhaled gas density on the pendelluft-induced lung injury.

    PubMed

    Alzahrany, Mohammed; Banerjee, Arindam

    2016-12-08

    Helium, sulfur hexafluoride-oxygen, and air were modeled to examine the role of the gas density on the pendelluft-induced lung injury (PILI) under high frequency oscillatory ventilation (HFOV). Large eddy simulation coupled with physiological resistance-compliance boundary conditions was applied to capture pendelluft-induced gas entrapment and mechanical stresses in an image-based human lung model. The flow characteristics were strongly dependent on the inspired gas density. The flow partitioning, globally between the left and right lung and locally between adjacent units branches, was significantly affected by the density of inhaled gas and was more balanced when inspiring lighter gas. The incomplete loops of flow-volume and volume-pressure curves were significantly influenced by the variations of the flow redistribution, resistance, and turbulence associated with the pendelluft mechanism. Inhaling light gas reduced the entrapped gas volume and mechanical stress surrounding carina ridges signifying the important role of inhaled gas properties on PILI. In general, lung ventilation by HFOV with a gas mixture of large amounts of Helium is thought to mitigate ventilator complications.

  7. Unified Inter- and Intramolecular Dispersion Correction Formula for Generalized Gradient Approximation Density Functional Theory.

    PubMed

    Steinmann, Stephan N; Csonka, Gábor; Corminboeuf, Clémence

    2009-11-10

    Density functionals fail to provide a consistent description of weak intra- (i.e., short-range) and inter- (i.e., long-range) molecular interactions arising from nonoverlapping electron densities. An efficient way to correct the long-range errors is to add an empirical atom pair wise interaction-correction, inspired by the Lennard-Jones potential (R(-6) dependence). We show that the universal damping function of Tang and Toennies (TT) that includes higher-order correction terms (R(-8) and R(-10) dependent) reduces the intramolecular errors more efficiently, without altering the long-range correction. For general applicability, the TT damping function is augmented by a Fermi damping to prevent corrections at covalent distances. The performance of the new dD10 correction was tested in combination with three nonempirical GGAs (PBE, PBEsol, RGE2) on 64 illustrative reaction energies featuring both intra- and intermolecular interactions. With only two empirical parameters, PBE-dD10 outperforms the computationally more demanding and most recent functionals such as M06-2X or B2PLYP-D (MAD = 3.78 and 1.95 kcal mol(-1), respectively). At the cc-pVTZ level, PBE-dD10 (MAD = 1.24 kcal mol(-1)) considerably reduces common DFT errors successfully balancing intra- (short-range) and inter- (long-range) molecular interactions. While REG2-dD10 performs closely to PBE-dD10 (MAD = 1.48 kcal mol(-1)), the overall MAD of PBEsol-dD10 is again slightly higher (MAD = 1.76 kcal mol(-1)).

  8. A neural network based error correction method for radio occultation electron density retrieval

    NASA Astrophysics Data System (ADS)

    Pham, Viet-Cuong; Juang, Jyh-Ching

    2015-12-01

    Abel inversion techniques have been widely employed to retrieve electron density profiles (EDPs) from radio occultation (RO) measurements, which are available by observing Global Navigation Satellite System (GNSS) satellites from low-earth-orbit (LEO) satellites. It is well known that the ordinary Abel inversion might introduce errors in the retrieval of EDPs when the spherical symmetry assumption is violated. The error, however, is case-dependent; therefore it is desirable to associate an error index or correction coefficient with respect to each retrieved EDP. Several error indices have been proposed but they only deal with electron density at the F2 peak and suffer from some drawbacks. In this paper we propose an artificial neural network (ANN) based error correction method for EDPs obtained by the ordinary Abel inversion. The ANN is first trained to learn the relationship between vertical total electron content (TEC) measurements and retrieval errors at the F2 peak, 220 km and 110 km altitudes; correction coefficients are then estimated to correct the retrieved EDPs at these three altitudes. Experiments using the NeQuick2 model and real FORMOSAT-3/COSMIC RO geometry show that the proposed method outperforms existing ones. Real incoherent scatter radar (ISR) measurements at the Jicamarca Radio Observatory and the global TEC map provided by the International GNSS Service (IGS) are also used to valid the proposed method.

  9. The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

    NASA Astrophysics Data System (ADS)

    Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

    2016-04-01

    Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

  10. How important is self-consistency for the dDsC density dependent dispersion correction?

    PubMed

    Brémond, Éric; Golubev, Nikolay; Steinmann, Stephan N; Corminboeuf, Clémence

    2014-05-14

    The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.

  11. How important is self-consistency for the dDsC density dependent dispersion correction?

    SciTech Connect

    Brémond, Éric; Corminboeuf, Clémence; Golubev, Nikolay; Steinmann, Stephan N.

    2014-05-14

    The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.

  12. Dosimetric Impact of Online Correction via Cone-Beam CT-Based Image Guidance for Stereotactic Lung Radiotherapy

    SciTech Connect

    Galerani, Ana Paula; Grills, Inga; Hugo, Geoffrey; Kestin, Larry; Mohammed, Nasiruddin; Chao, K. Kenneth; Suen, Andrew; Martinez, Alvaro; Yan, Di

    2010-12-01

    Purpose: To evaluate the dosimetric impact of online cone-beam computed tomography (CBCT) guided correction in lung stereotactic body radiation therapy (SBRT). Methods and Materials: Twenty planning and 162 CBCT images from 20 patients undergoing lung SBRT were analyzed. The precorrection CBCT (CBCT after patient setup, no couch correction) was registered to planning CT using soft tissue; couch shift was applied, with a second CBCT for verification (postcorrection CBCT). Targets and normal structures were delineated on CBCTs: gross tumor volume (GTV), clinical target volume (CTV), cord, esophagus, lung, proximal bronchial tree, and aorta. Dose distributions on all organs manifested on each CBCT were compared with those planned on the CT. Results: Without CBCT guided target position correction, target dose reduced with respect to treatment plan. Mean and standard deviation of treatment dose discrepancy from the plan were -3.2% (4.9%), -2.1% (4.4%), -6.1% (10.7%), and -3.5% (7%) for GTV D{sub 99%}, GTV D{sub 95%}, CTV D{sub 99%}, and CTV D{sub 95%}, respectively. With CBCT correction, the results were -0.4% (2.6%), 0.1% (1.7%), -0.3% (4.2%), and 0.5% (3%). Mean and standard deviation of the difference in normal organ maximum dose were 2.2% (6.5%) before correction and 2.4% (5.9%) after correction for esophagus; 6.1% (14.1%) and 3.8% (8.1%) for cord; 3.1% (17.5%) and 6.2% (9.8%) for proximal bronchial tree; and 17.7% (19.5%) and 14.1% (17%) for aorta. Conclusion: Online CBCT guidance improves the accuracy of target dose delivery for lung SBRT. However, treatment dose to normal tissue can vary regardless of the correction. Normal tissues should be considered during target registration, according to target proximity.

  13. Photodynamic induced uptake of liposomal doxorubicin to rat lung tumors parallels tumor vascular density.

    PubMed

    Wang, Yabo; Gonzalez, Michel; Cheng, Cai; Haouala, Amina; Krueger, Thorsten; Peters, Solange; Decosterd, Laurent-Arthur; van den Bergh, Hubert; Perentes, Jean Y; Ris, Hans-Beat; Letovanec, Igor; Debefve, Elodie

    2012-04-01

    Visudyne®-mediated photodynamic therapy (PDT) at low drug/light conditions has shown to selectively enhance the uptake of liposomal doxorubicin in subpleural localized sarcoma tumors grown on rodent lungs without causing morphological alterations of the lung. The present experiments explore the impact of low-dose PDT on liposomal doxorubicin (Liporubicin™) uptake to different tumor types grown on rodent lungs. Three groups of Fischer rats underwent subpleural generation of sarcoma, mesothelioma, or adenocarcinoma tumors on the left lung. At least five animals of each group (sarcoma, n = 5; mesothelioma, n = 7; adenocarcinoma, n = 5) underwent intraoperative low-dose (10 J/cm(2) at 35 mW/cm(2) ) PDT with 0.0625 mg/kg Visudyne® of the tumor and the lower lobe. This was followed by intravenous (IV) administration of 400 µg Liporubicin™. After a circulation time of 60 min, the tumor-bearing lung was processed for HPLC analyses. At least five animals per group underwent the same procedure but without PDT (sarcoma, n = 5; mesothelioma, n = 5; adenocarcinoma, n = 6). Five untreated animals per group underwent CD31 immunostaining of their tumors with histomorphometrical assessment of the tumor vascularization. Low-dose PDT significantly enhanced Liporubicin™ uptake to all tumor types (sarcoma, P = 0.0007; mesothelioma, P = 0.001; adenocarcinoma, P = 0.02) but not to normal lung tissue compared to IV drug administration alone. PDT led to a significantly increased ratio of tumor to lung tissue drug uptake for all three tumor types (P < 0.05). However, the tumor drug uptake varied between tumor types and paralleled tumor vascular density. The vascular density was significantly higher in sarcoma than in adenocarcinoma (P < 0.001) and mesothelioma (P < 0.001), whereas there was no significant difference between adenocarcinoma and mesothelioma. Low-dose Visudyne®-mediated PDT selectively enhances the uptake of

  14. Intratumoral Immune Cell Densities Are Associated with Lung Adenocarcinoma Gene Alterations.

    PubMed

    Mansuet-Lupo, Audrey; Alifano, Marco; Pécuchet, Nicolas; Biton, Jérôme; Becht, Etienne; Goc, Jeremy; Germain, Claire; Ouakrim, Hanane; Régnard, Jean-François; Cremer, Isabelle; Laurent-Puig, Pierre; Dieu-Nosjean, Marie-Caroline; Blons, Hélène; Damotte, Diane

    2016-12-01

    Tumor-infiltrating immune cells affect lung cancer outcome. However, the factors that influence the composition and function of the tumor immune environment remain poorly defined and need investigation, particularly in the era of immunotherapy. To determine whether the tumoral immune environment is related to lung adenocarcinoma mutations. This retrospective cohort included 316 consecutive patients with lung adenocarcinoma (225 men; 258 smokers) studied from 2001 to 2005 in a single center. We investigated the association of densities of intratumoral mature dendritic cells (mDCs), CD8(+) T cells, neutrophils, and macrophages with clinical and pathological variables and tumor cell mutation profiles obtained by next-generation sequencing. In 282 tumors, we found 460 mutations, mainly in TP53 (59%), KRAS (40%), STK11 (24%), and EGFR (14%). Intratumoral CD8(+) T-cell density was high in smokers (P = 0.02) and TP53-mutated tumors (P = 0.02) and low in BRAF-mutated tumors (P = 0.005). Intratumoral mDC density was high with low pathological tumor stage (P = 0.01) and low with STK11 mutation (P = 0.004). Intratumoral neutrophil density was high and low with BRAF mutation (P = 0.04) and EGFR mutation (P = 0.02), respectively. Intratumoral macrophage density was low with EGFR mutation (P = 0.01). Intratumoral CD8(+) T-cell and mDC densities remained strong independent markers of overall survival (P = 0.001 and P = 0.02, respectively). Intratumoral immune cell densities (mDCs, CD8(+) T cells, neutrophils, macrophages) were significantly associated with molecular alterations in adenocarcinoma underlying the interactions between cancer cells and their microenvironment.

  15. Calculation of correction factors for ionization chamber measurements with small fields in low-density media

    NASA Astrophysics Data System (ADS)

    Pisaturo, O.; Pachoud, M.; Bochud, F. O.; Moeckli, R.

    2012-07-01

    The quantity of interest for high-energy photon beam therapy recommended by most dosimetric protocols is the absorbed dose to water. Thus, ionization chambers are calibrated in absorbed dose to water, which is the same quantity as what is calculated by most treatment planning systems (TPS). However, when measurements are performed in a low-density medium, the presence of the ionization chamber generates a perturbation at the level of the secondary particle range. Therefore, the measured quantity is close to the absorbed dose to a volume of water equivalent to the chamber volume. This quantity is not equivalent to the dose calculated by a TPS, which is the absorbed dose to an infinitesimally small volume of water. This phenomenon can lead to an overestimation of the absorbed dose measured with an ionization chamber of up to 40% in extreme cases. In this paper, we propose a method to calculate correction factors based on the Monte Carlo simulations. These correction factors are obtained by the ratio of the absorbed dose to water in a low-density medium □Dw,Q,V1low averaged over a scoring volume V1 for a geometry where V1 is filled with the low-density medium and the absorbed dose to water □Dw,QV2low averaged over a volume V2 for a geometry where V2 is filled with water. In the Monte Carlo simulations, □Dw,QV2low is obtained by replacing the volume of the ionization chamber by an equivalent volume of water, according to the definition of the absorbed dose to water. The method is validated in two different configurations which allowed us to study the behavior of this correction factor as a function of depth in phantom, photon beam energy, phantom density and field size.

  16. Mechanics, hydrodynamics and energetics of blue whale lunge feeding: efficiency dependence on krill density.

    PubMed

    Goldbogen, J A; Calambokidis, J; Oleson, E; Potvin, J; Pyenson, N D; Schorr, G; Shadwick, R E

    2011-01-01

    Lunge feeding by rorqual whales (Balaenopteridae) is associated with a high energetic cost that decreases diving capacity, thereby limiting access to dense prey patches at depth. Despite this cost, rorquals exhibit high rates of lipid deposition and extremely large maximum body size. To address this paradox, we integrated kinematic data from digital tags with unsteady hydrodynamic models to estimate the energy budget for lunges and foraging dives of blue whales (Balaenoptera musculus), the largest rorqual and living mammal. Our analysis suggests that, despite the large amount of mechanical work required to lunge feed, a large amount of prey and, therefore, energy is obtained during engulfment. Furthermore, we suggest that foraging efficiency for blue whales is significantly higher than for other marine mammals by nearly an order of magnitude, but only if lunges target extremely high densities of krill. The high predicted efficiency is attributed to the enhanced engulfment capacity, rapid filter rate and low mass-specific metabolic rate associated with large body size in blue whales. These results highlight the importance of high prey density, regardless of prey patch depth, for efficient bulk filter feeding in baleen whales and may explain some diel changes in foraging behavior in rorqual whales.

  17. On the validity of density overrides for VMAT lung SBRT planning

    SciTech Connect

    Wiant, David Vanderstraeten, Caroline; Maurer, Jacqueline; Pursley, Jan; Terrell, Jonathon; Sintay, Benjamin J.

    2014-08-15

    Purpose: Modeling dose to a moving target in lung is a very difficult task. Current approaches to planning lung stereotactic body radiotherapy (SBRT) generally calculate dose on either free breathing or average computed tomography (CT) scans, which do not always accurately predict dose to parts of the target volume not occupied by tumor on the planning scan. In this work, the authors look at using density overrides of the target volumes to more accurately predict dose for lung SBRT using the analytic anisotropic algorithm (AAA). Methods: Volumetric modulated arc therapy plans were created on free breathing scans (FBP), time average scans (AVGP), free breathing scans with the internal target volume overridden to tumor density (ITVP), free breathing scans with the planning target volume overridden to tumor density (PTVP), and free breathing scan using a hybrid scheme with the internal target volume set to tumor density and the planning target volume minus the internal target volume set to a density intermediate between lung and tumor (HP) for the case of a 4D motion phantom and five patient cases. Radiochromic film measurements were made for the phantom plans, with gamma analysis used to compare the planned to delivered dose. The patient plans were recalculated on each of the phases of a 4DCT to evaluate tumor coverage and conformity index (CI). A modified modulation complexity score (MCSv) and average open area per control point (AA) metrics were used to evaluate multileaf collimator (MLC) modulation for each of the plans. Results: The HP plans showed significantly higher gamma passing rates (p < 0.05) than the FBP, AVGP, and ITVP for criteria of 2 mm/2% and 1 mm/1%. No significant correlation was observed between gamma values and AA or MCSv. The tumor volume was covered by the prescription dose on all phases of the 4DCT for all patient plans. The PTVP and HP yielded lower mean CI than the other plans for all five patients, with three of the cases showing

  18. Molecular density functional theory for water with liquid-gas coexistence and correct pressure

    SciTech Connect

    Jeanmairet, Guillaume Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  19. Molecular density functional theory for water with liquid-gas coexistence and correct pressure.

    PubMed

    Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  20. Molecular density functional theory for water with liquid-gas coexistence and correct pressure

    NASA Astrophysics Data System (ADS)

    Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-01

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  1. An improved theoretical approach to the empirical corrections of density functional theory

    NASA Astrophysics Data System (ADS)

    Lii, Jenn-Huei; Hu, Ching-Han

    2012-02-01

    An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization-dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond ( 1,2-) and angle ( 1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported Δ H f values of the training set containing alkane, alcohol and ether molecules. The Δ H f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in Δ H f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.

  2. Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-01-01

    We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

  3. Applications of Screened Hybrid Density Functionals with Empirical Dispersion Corrections to Rare Gas Dimers and Solids.

    PubMed

    Yousaf, Kazim E; Brothers, Edward N

    2010-03-09

    An empirical dispersion correction is added to the range-separated hybrid density functionals HSE and HISS via parametrization versus a standard test bed of weakly bound complexes. The performance of the resulting HSE-D and HISS-D functionals is evaluated by calculating the equilibrium bond length, harmonic frequency, and dissociation energy for a number of rare gas dimers, and the lattice constants, band gaps, and sublimation energies of the rare gas solids. Both HSE-D and HISS-D are shown to provide accurate results for both molecules and extended systems, suggesting that the combination of a screened hybrid functional with an empirical dispersion correction provides an accurate, widely applicable method for use in solid-state and gas-phase electronic structure theory.

  4. Fermi orbital self-interaction corrected electronic structure of molecules beyond local density approximation

    SciTech Connect

    Hahn, T. Liebing, S.; Kortus, J.; Pederson, Mark R.

    2015-12-14

    The correction of the self-interaction error that is inherent to all standard density functional theory calculations is an object of increasing interest. In this article, we apply the very recently developed Fermi-orbital based approach for the self-interaction correction [M. R. Pederson et al., J. Chem. Phys. 140, 121103 (2014) and M. R. Pederson, J. Chem. Phys. 142, 064112 (2015)] to a set of different molecular systems. Our study covers systems ranging from simple diatomic to large organic molecules. We focus our analysis on the direct estimation of the ionization potential from orbital eigenvalues. Further, we show that the Fermi orbital positions in structurally similar molecules appear to be transferable.

  5. Discrimination between lung homeostatic and injury-induced epithelial progenitor subsets by cell-density properties.

    PubMed

    Sen, Namita; Weprin, Samuel; Peter, Yakov

    2013-07-15

    Stem/progenitor cells and their lineage derivatives are often identified by patterns and intensity of cell clusters of differentiation presentation. However, the cell biochemical façade can prove to be elusive, transient, and subject to interlaboratory disparities. To enhance current methods of lung stem cell isolation and identification and to investigate biophysical changes, which occur during homeostasis and in response to acute lung injury, we separated cells on a discontinuous density gradient, of 1.025-1.074 g/cm(3), and characterized the eluted lineages. At homeostasis, surfactant protein-C (SFTPC)-expressing cells of the alveolar type (AT)-2 lineage possessed average densities ≥1.039 g/cm(3) and aquaporin-5 producing AT1 cells equilibrated at densities <1.039 g/cm(3). While 0.74%±0.32% of lung cells were determined proliferating or postmitotic by BrdU nucleotide uptake, 73% of CD49f-, 72% of c-KIT-, and 61% of SCA-1-positive cells (putative alveolar progenitor lineage markers) showed densities ≤1.039 g/cm(3). CD49f/EpCAM(hi) progenitors, as well as c-KIT(pos)/CD45(neg) cells, could be enriched at the 1.039 g/cm(3) interface. Following acute bleomycin-induced injury, the frequency of BrdU-incorporating cells rose to 0.92%±0.36% and density could largely explain cell-lineage distribution. Specifically, a decline in the density of mitotic/postmitotic SFTPC-positive cells to ≤1.029 g/cm(3), in conjunction with an increase in CD45-positive, and proliferating CD45 and c-KIT cells in the heaviest fraction (≥1.074 g/cm(3)) were observed. These data attest to the generation of AT2 cells from low-density precursors and emphasize a relationship between cell density and molecular expression following injury, expanding on our current understanding of lung and progenitor cell dynamics.

  6. Discrimination Between Lung Homeostatic and Injury-Induced Epithelial Progenitor Subsets by Cell-Density Properties

    PubMed Central

    Sen, Namita; Weprin, Samuel

    2013-01-01

    Stem/progenitor cells and their lineage derivatives are often identified by patterns and intensity of cell clusters of differentiation presentation. However, the cell biochemical façade can prove to be elusive, transient, and subject to interlaboratory disparities. To enhance current methods of lung stem cell isolation and identification and to investigate biophysical changes, which occur during homeostasis and in response to acute lung injury, we separated cells on a discontinuous density gradient, of 1.025–1.074 g/cm3, and characterized the eluted lineages. At homeostasis, surfactant protein-C (SFTPC)-expressing cells of the alveolar type (AT)-2 lineage possessed average densities ≥1.039 g/cm3 and aquaporin-5 producing AT1 cells equilibrated at densities <1.039 g/cm3. While 0.74%±0.32% of lung cells were determined proliferating or postmitotic by BrdU nucleotide uptake, 73% of CD49f-, 72% of c-KIT-, and 61% of SCA-1-positive cells (putative alveolar progenitor lineage markers) showed densities ≤1.039 g/cm3. CD49f/EpCAMhi progenitors, as well as c-KITpos/CD45neg cells, could be enriched at the 1.039 g/cm3 interface. Following acute bleomycin-induced injury, the frequency of BrdU-incorporating cells rose to 0.92%±0.36% and density could largely explain cell-lineage distribution. Specifically, a decline in the density of mitotic/postmitotic SFTPC-positive cells to ≤1.029 g/cm3, in conjunction with an increase in CD45-positive, and proliferating CD45 and c-KIT cells in the heaviest fraction (≥1.074 g/cm3) were observed. These data attest to the generation of AT2 cells from low-density precursors and emphasize a relationship between cell density and molecular expression following injury, expanding on our current understanding of lung and progenitor cell dynamics. PMID:23461422

  7. Adsorption of imidazole on Au(111) surface: Dispersion corrected density functional study

    NASA Astrophysics Data System (ADS)

    Izzaouihda, Safia; Mahjoubi, Khaled; Abou El Makarim, Hassna; Komiha, Najia; Benoit, David M.

    2016-10-01

    We use density functional theory in the generalized gradient approximation to study the adsorption of imidazole on the Au(111) surface and account for dispersion effect using Grimme's empirical dispersion correction technique. Our results show that the adsorption energy of imidazole depends on the slab size and on the adsorption site. In agreement with other studies, we find the largest adsorption energy for imidazole on a top site of Au(111). However, we also note that the adsorption energy at other sites is substantial.

  8. Long-range corrected density functional theory with linearly-scaled HF exchange

    SciTech Connect

    Song, Jong-Won; Hirao, Kimihiko

    2015-12-31

    Long-range corrected density functional theory (LC-DFT) attracts many chemists’ attentions as a quantum chemical method to be applied to large molecular system and its property calculations. However, the expensive time cost to evaluate the long-range HF exchange is a big obstacle to be overcome to be applied to the large molecular systems and the solid state materials. Upon this problem, we propose a linear-scaling method of the HF exchange integration, in particular, for the LC-DFT hybrid functional.

  9. Long-range corrected density functional theory with linearly-scaled HF exchange

    NASA Astrophysics Data System (ADS)

    Song, Jong-Won; Hirao, Kimihiko

    2015-12-01

    Long-range corrected density functional theory (LC-DFT) attracts many chemists' attentions as a quantum chemical method to be applied to large molecular system and its property calculations. However, the expensive time cost to evaluate the long-range HF exchange is a big obstacle to be overcome to be applied to the large molecular systems and the solid state materials. Upon this problem, we propose a linear-scaling method of the HF exchange integration, in particular, for the LC-DFT hybrid functional.

  10. A density-adaptive SPH method with kernel gradient correction for modeling explosive welding

    NASA Astrophysics Data System (ADS)

    Liu, M. B.; Zhang, Z. L.; Feng, D. L.

    2017-05-01

    Explosive welding involves processes like the detonation of explosive, impact of metal structures and strong fluid-structure interaction, while the whole process of explosive welding has not been well modeled before. In this paper, a novel smoothed particle hydrodynamics (SPH) model is developed to simulate explosive welding. In the SPH model, a kernel gradient correction algorithm is used to achieve better computational accuracy. A density adapting technique which can effectively treat large density ratio is also proposed. The developed SPH model is firstly validated by simulating a benchmark problem of one-dimensional TNT detonation and an impact welding problem. The SPH model is then successfully applied to simulate the whole process of explosive welding. It is demonstrated that the presented SPH method can capture typical physics in explosive welding including explosion wave, welding surface morphology, jet flow and acceleration of the flyer plate. The welding angle obtained from the SPH simulation agrees well with that from a kinematic analysis.

  11. Deconvolution-based correction of alkali beam emission spectroscopy density profile measurements

    SciTech Connect

    Pusztai, I.; Pokol, G.; Refy, D.; Por, G.; Dunai, D.; Anda, G.; Zoletnik, S.; Schweinzer, J.

    2009-08-15

    A deconvolution-based correction method of the beam emission spectroscopy (BES) density profile measurement is demonstrated by its application to simulated measurements of the COMPASS and TEXTOR tokamaks. If the line of sight is far from tangential to the flux surfaces, and the beam width is comparable to the scale length on which the light profile varies, the observation may cause an undesired smoothing of the light profile, resulting in a non-negligible underestimation of the calculated density profile. This effect can be reduced significantly by the emission reconstruction method, which gives an estimate of the emissivity along the beam axis from the measured light profile, taking the finite beam width and the properties of the measurement into account in terms of the transfer function of the observation. Characteristics and magnitude of the mentioned systematic error and its reduction by the introduced method are studied by means of the comprehensive alkali BES simulation code RENATE.

  12. Vibrational and Thermal Properties of β-HMX and TATB from Dispersion Corrected Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Landerville, Aaron; Oleynik, Ivan

    2015-06-01

    Dispersion Corrected Density Functional Theory (DFT+vdW) calculations are performed to predict vibrational and thermal properties of the bulk energetic materials (EMs) β-octahydrocyclotetramethylene-tetranitramine (β-HMX) and triaminotrinitrobenzene (TATB). DFT+vdW calculations of optimized unit cells along the hydrostatic equation of state are followed by frozen-phonon calculations of their respective vibration spectra. These are then used under the quasi-harmonic approximation to obtain zero-point and thermal free energy contributions to the pressure, resulting in PVT equations of state for each material that is in excellent agreement with experiment. Further, heat capacities, thermal expansion coefficients, and Gruneissen parameters as functions of temperature are calculated and compared with experiment. The vibrational properties, including phonon densities of states and pressure dependencies of individual modes, are also analyzed and compared with experiment.

  13. Density-functional correction of random-phase-approximation correlation with results for jellium surface energies

    NASA Astrophysics Data System (ADS)

    Kurth, Stefan; Perdew, John P.

    1999-04-01

    Since long-range electron-electron correlation is treated properly in the random phase approximation (RPA), we define short-range correlation as the correction to the RPA. The effects of short-range correlation are investigated here in the local spin density (LSD) approximation and the generalized gradient approximation (GGA). Results are presented for atoms, molecules, and jellium surfaces. It is found that (1) short-range correlation energies are less sensitive to the inclusion of density gradients than are full correlation energies, and (2) short-range correlation makes a surprisingly small contribution to surface and molecular atomization energies. In order to improve the accuracy of electronic-structure calculations, we therefore combine a GGA treatment of short-range correlation with a full RPA treatment of the exchange-correlation energy. This approach leads to jellium surface energies close to those of the LSD approximation for exchange and correlation together (but not for each separately).

  14. Gas density alters expiratory time constants before and after experimental lung injury.

    PubMed

    Henderson, William R; Molgat-Seon, Yannick; Dominelli, Paolo B; Brasher, Penelope M A; Griesdale, Donald E G; Foster, Glen E; Yacyshyn, Alexandra; Ayas, Najib T; Sheel, A William

    2015-10-01

    What is the central question of this study? Does the induction of a model of lung injury affect the expiratory time constant (τE) in terms of either total duration or morphology? Does ventilation with gases of different densities alter the duration or morphology of τE either before or after injury? What is the main finding and its importance? The use of sulfur hexafluoride in ventilating gas mixtures lengthens total expiratory time constants before and after lung injury compared with both nitrogen and helium mixtures. Sulfur hexafluoride mixtures also decrease the difference and variability of τE between fast- and slow-emptying compartments before and after injury when compared with nitrogen and helium mixtures. Acute lung injury is characterized by regional heterogeneity of lung resistance and elastance that may lead to regional heterogeneity of expiratory time constants (τE). We hypothesized that increasing airflow resistance by using inhaled sulfur hexafluoride (SF6) would lengthen time constants and decrease their heterogeneity in an experimental model of lung injury when compared with nitrogen or helium mixtures. To overcome the limitations of a single-compartment model, we employed a multisegment model of expiratory gas flow. An experimental model of lung injury was created using intratracheal injection of sodium polyacrylate in anaesthetized and mechanically ventilated female Yorkshire-cross pigs (n = 7). The animals were ventilated with 50% O2 and the remaining 50% as nitrogen (N2), helium (He) or sulfur hexafluoride (SF6). Values for τE decreased with injury and were more variable after injury than before (P < 0.001). Values for τE increased throughout expiration both before and after injury, and the rate of increase in τE was lessened by SF6 (P < 0.001 when compared with N2 both before and after injury). Altering the inhaled gas density did not affect indices of oxygenation, dead space or shunt. The use of SF6 in ventilating gas mixtures lengthens

  15. The effects of iterative reconstruction and kernel selection on quantitative computed tomography measures of lung density.

    PubMed

    Rodriguez, Alfonso; Ranallo, Frank N; Judy, Philip F; Fain, Sean B

    2017-06-01

    To determine the effects of iterative reconstruction (IR) and high-frequency kernels on quantitative computed tomography (qCT) density measures at reduced X-ray dose. The COPDGene 2 Phantom (CTP 698, The Phantom Laboratory, Salem, NY) with four embedded lung mimicking foam densities (12lb, 20lb, and 4lb), as well as water, air, and acrylic reference inserts, was imaged using a GE 64 slice CT750 HD scanner in helical mode with four current-time products ranging from 12 to 100 mAs. The raw acquired data were reconstructed using standard (STD - low frequency) and Bone (high frequency) kernels with filtered back projection (FBP), 100% ASiR, and Veo reconstruction algorithms. The reference density inserts were manually segmented using Slicer3D (www.slicer.org), and the mean, standard deviation, and histograms of the segmented regions were generated using Fiji (http://fiji.sc/Fiji) for each reconstruction. Measurements of threshold values placed on the cumulative frequency distribution of voxels determined by these measured histograms at 5%, PD5phant , and 15%, PD15phant , (analogous to the relative area below -950 HU (RA-950) and percent density 15 (PD15) in human lung emphysema quantification, respectively), were also performed. The use of high-resolution kernels in conjunction with ASiR and Veo did not significantly affect the mean Hounsfield units (HU) of each of the density standards (< 4 HU deviation) and current-time products within the phantom when compared with the STD+FBP reconstruction conventionally used in clinical applications. A truncation of the scanner reported HU values at -1024 that shifts the mean toward more positive values was found to cause a systematic error in lower attenuating regions. Use of IR drove convergence toward the mean of measured histograms (~100-137% increase in the number measured voxels at the mean of the histogram), while the combination of Bone+ASiR preserved the standard deviation of HU values about the mean compared to STD

  16. National dosimetric audit network finds discrepancies in AAA lung inhomogeneity corrections.

    PubMed

    Dunn, Leon; Lehmann, Joerg; Lye, Jessica; Kenny, John; Kron, Tomas; Alves, Andrew; Cole, Andrew; Zifodya, Jackson; Williams, Ivan

    2015-07-01

    This work presents the Australian Clinical Dosimetry Service's (ACDS) findings of an investigation of systematic discrepancies between treatment planning system (TPS) calculated and measured audit doses. Specifically, a comparison between the Anisotropic Analytic Algorithm (AAA) and other common dose-calculation algorithms in regions downstream (≥2cm) from low-density material in anthropomorphic and slab phantom geometries is presented. Two measurement setups involving rectilinear slab-phantoms (ACDS Level II audit) and anthropomorphic geometries (ACDS Level III audit) were used in conjunction with ion chamber (planar 2D array and Farmer-type) measurements. Measured doses were compared to calculated doses for a variety of cases, with and without the presence of inhomogeneities and beam-modifiers in 71 audits. Results demonstrate a systematic AAA underdose with an average discrepancy of 2.9 ± 1.2% when the AAA algorithm is implemented in regions distal from lung-tissue interfaces, when lateral beams are used with anthropomorphic phantoms. This systemic discrepancy was found for all Level III audits of facilities using the AAA algorithm. This discrepancy is not seen when identical measurements are compared for other common dose-calculation algorithms (average discrepancy -0.4 ± 1.7%), including the Acuros XB algorithm also available with the Eclipse TPS. For slab phantom geometries (Level II audits), with similar measurement points downstream from inhomogeneities this discrepancy is also not seen.

  17. Impact of PET - CT motion correction in minimizing the gross tumor volume in non-small cell lung cancer

    PubMed Central

    Masoomi, Michael A; McLean, Anne H; Bouchareb, Yassine; Ryder, Will; Robinson, Andy

    2013-01-01

    Objective(s): To investigate the impact of respiratory motion on localization, and quantification of lung lesions for the Gross Tumor Volume utilizing a fully automated Auto3Dreg program and dynamic NURBS-based cardiac-torso digitized phantom (NCAT). Methods: Respiratory motion may result in more than 30% underestimation of the SUV values of lung, liver and kidney tumor lesions. The motion correction technique adopted in this study was an image-based motion correction approach using, a voxel-intensity-based and a multi-resolution multi-optimization (MRMO) algorithm. The NCAT phantom was used to generate CT attenuation maps and activity distribution volumes for the lung regions. All the generated frames were co-registered to a reference frame using a time efficient scheme. Quantitative assessment including Region of Interest (ROI), image fidelity and image correlation techniques, as well as semi-quantitative line profile analysis and qualitatively overlaying non-motion and motion corrected image frames were performed. Results: The largest motion was observed in the Z-direction. The greatest translation was for the frame 3, end inspiration, and the smallest for the frame 5 which was closet frame to the reference frame at 67% expiration. Visual assessment of the lesion sizes, 20-60mm at 3 different locations, apex, mid and base of lung showed noticeable improvement for all the foci and their locations. The maximum improvements for the image fidelity were from 0.395 to 0.930 within the lesion volume of interest. The greatest improvement in activity concentration underestimation was 7.7% below the true activity for the 20 mm lesion in comparison to 34.4% below, prior to correction. The discrepancies in activity underestimation were reduced with increasing the lesion sizes. Overlaying activity distribution on the attenuation map showed improved localization of the PET metabolic information to the anatomical CT images. Conclusion: The respiratory motion correction for the

  18. Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.

    PubMed

    Singh, Raman K; Tsuneda, Takao

    2013-02-15

    The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.

  19. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

    PubMed Central

    van de Streek, Jacco; Neumann, Marcus A.

    2010-01-01

    This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect. PMID:20841921

  20. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

    PubMed

    van de Streek, Jacco; Neumann, Marcus A

    2010-10-01

    This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

  1. Evaluation of tumor localization in respiration motion-corrected cone-beam CT: Prospective study in lung

    SciTech Connect

    Dzyubak, Oleksandr; Kincaid, Russell; Hertanto, Agung; Hu, Yu-Chi; Pham, Hai; Yorke, Ellen; Zhang, Qinghui; Mageras, Gig S.; Rimner, Andreas

    2014-10-15

    Purpose: Target localization accuracy of cone-beam CT (CBCT) images used in radiation treatment of respiratory disease sites is affected by motion artifacts (blurring and streaking). The authors have previously reported on a method of respiratory motion correction in thoracic CBCT at end expiration (EE). The previous retrospective study was limited to examination of reducing motion artifacts in a small number of patient cases. They report here on a prospective study in a larger group of lung cancer patients to evaluate respiratory motion-corrected (RMC)-CBCT ability to improve lung tumor localization accuracy and reduce motion artifacts in Linac-mounted CBCT images. A second study goal examines whether the motion correction derived from a respiration-correlated CT (RCCT) at simulation yields similar tumor localization accuracy at treatment. Methods: In an IRB-approved study, 19 lung cancer patients (22 tumors) received a RCCT at simulation, and on one treatment day received a RCCT, a respiratory-gated CBCT at end expiration, and a 1-min CBCT. A respiration monitor of abdominal displacement was used during all scans. In addition to a CBCT reconstruction without motion correction, the motion correction method was applied to the same 1-min scan. Projection images were sorted into ten bins based on abdominal displacement, and each bin was reconstructed to produce ten intermediate CBCT images. Each intermediate CBCT was deformed to the end expiration state using a motion model derived from RCCT. The deformed intermediate CBCT images were then added to produce a final RMC-CBCT. In order to evaluate the second study goal, the CBCT was corrected in two ways, one using a model derived from the RCCT at simulation [RMC-CBCT(sim)], the other from the RCCT at treatment [RMC-CBCT(tx)]. Image evaluation compared uncorrected CBCT, RMC-CBCT(sim), and RMC-CBCT(tx). The gated CBCT at end expiration served as the criterion standard for comparison. Using automatic rigid image

  2. Evaluation of tumor localization in respiration motion-corrected cone-beam CT: Prospective study in lung

    PubMed Central

    Dzyubak, Oleksandr; Kincaid, Russell; Hertanto, Agung; Hu, Yu-Chi; Pham, Hai; Rimner, Andreas; Yorke, Ellen; Zhang, Qinghui; Mageras, Gig S.

    2014-01-01

    Purpose: Target localization accuracy of cone-beam CT (CBCT) images used in radiation treatment of respiratory disease sites is affected by motion artifacts (blurring and streaking). The authors have previously reported on a method of respiratory motion correction in thoracic CBCT at end expiration (EE). The previous retrospective study was limited to examination of reducing motion artifacts in a small number of patient cases. They report here on a prospective study in a larger group of lung cancer patients to evaluate respiratory motion-corrected (RMC)-CBCT ability to improve lung tumor localization accuracy and reduce motion artifacts in Linac-mounted CBCT images. A second study goal examines whether the motion correction derived from a respiration-correlated CT (RCCT) at simulation yields similar tumor localization accuracy at treatment. Methods: In an IRB-approved study, 19 lung cancer patients (22 tumors) received a RCCT at simulation, and on one treatment day received a RCCT, a respiratory-gated CBCT at end expiration, and a 1-min CBCT. A respiration monitor of abdominal displacement was used during all scans. In addition to a CBCT reconstruction without motion correction, the motion correction method was applied to the same 1-min scan. Projection images were sorted into ten bins based on abdominal displacement, and each bin was reconstructed to produce ten intermediate CBCT images. Each intermediate CBCT was deformed to the end expiration state using a motion model derived from RCCT. The deformed intermediate CBCT images were then added to produce a final RMC-CBCT. In order to evaluate the second study goal, the CBCT was corrected in two ways, one using a model derived from the RCCT at simulation [RMC-CBCT(sim)], the other from the RCCT at treatment [RMC-CBCT(tx)]. Image evaluation compared uncorrected CBCT, RMC-CBCT(sim), and RMC-CBCT(tx). The gated CBCT at end expiration served as the criterion standard for comparison. Using automatic rigid image

  3. Evaluation of tumor localization in respiration motion-corrected cone-beam CT: prospective study in lung.

    PubMed

    Dzyubak, Oleksandr; Kincaid, Russell; Hertanto, Agung; Hu, Yu-Chi; Pham, Hai; Rimner, Andreas; Yorke, Ellen; Zhang, Qinghui; Mageras, Gig S

    2014-10-01

    Target localization accuracy of cone-beam CT (CBCT) images used in radiation treatment of respiratory disease sites is affected by motion artifacts (blurring and streaking). The authors have previously reported on a method of respiratory motion correction in thoracic CBCT at end expiration (EE). The previous retrospective study was limited to examination of reducing motion artifacts in a small number of patient cases. They report here on a prospective study in a larger group of lung cancer patients to evaluate respiratory motion-corrected (RMC)-CBCT ability to improve lung tumor localization accuracy and reduce motion artifacts in Linac-mounted CBCT images. A second study goal examines whether the motion correction derived from a respiration-correlated CT (RCCT) at simulation yields similar tumor localization accuracy at treatment. In an IRB-approved study, 19 lung cancer patients (22 tumors) received a RCCT at simulation, and on one treatment day received a RCCT, a respiratory-gated CBCT at end expiration, and a 1-min CBCT. A respiration monitor of abdominal displacement was used during all scans. In addition to a CBCT reconstruction without motion correction, the motion correction method was applied to the same 1-min scan. Projection images were sorted into ten bins based on abdominal displacement, and each bin was reconstructed to produce ten intermediate CBCT images. Each intermediate CBCT was deformed to the end expiration state using a motion model derived from RCCT. The deformed intermediate CBCT images were then added to produce a final RMC-CBCT. In order to evaluate the second study goal, the CBCT was corrected in two ways, one using a model derived from the RCCT at simulation [RMC-CBCT(sim)], the other from the RCCT at treatment [RMC-CBCT(tx)]. Image evaluation compared uncorrected CBCT, RMC-CBCT(sim), and RMC-CBCT(tx). The gated CBCT at end expiration served as the criterion standard for comparison. Using automatic rigid image registration, each CBCT was

  4. Correction: Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy.

    PubMed

    Amano, Ken-Ichi; Liang, Yunfeng; Miyazawa, Keisuke; Kobayashi, Kazuya; Hashimoto, Kota; Fukami, Kazuhiro; Nishi, Naoya; Sakka, Tetsuo; Onishi, Hiroshi; Fukuma, Takeshi

    2016-08-07

    Correction for 'Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy' by Ken-ichi Amano et al., Phys. Chem. Chem. Phys., 2016, 18, 15534-15544.

  5. Therapeutic strategies to correct proteostasis-imbalance in chronic obstructive lung diseases.

    PubMed

    Bodas, M; Tran, I; Vij, N

    2012-08-01

    Proteostasis is a critical cellular homeostasis mechanism that regulates the concentration of all cellular proteins by controlling protein- synthesis, processing and degradation. This includes protein-conformation, binding interactions and sub-cellular localization. Environmental, genetic or age-related pathogenetic factors can modulate the proteostasis (proteostasis-imbalance) through transcriptional, translational and post-translational changes that trigger the development of several complex diseases. Although these factors are known to be involved in pathogenesis of chronic obstructive pulmonary disease (COPD), the role of proteostasis mechanisms in COPD is scarcely investigated. As a proof of concept, our recent data reveals a novel role of proteostasis-imbalance in COPD pathogenesis. Briefly, cigarette- and biomass- smoke induced proteostasis-imbalance may aggravate chronic inflammatory-oxidative stress and/or protease-anti-protease imbalance resulting in pathogenesis of severe emphysema. In contrast, pathogenesis of other chronic lung diseases like ΔF508-cystic fibrosis (CF), α1-anti-trypsin-deficiency (α-1 ATD) and pulmonary fibrosis (PF) is regulated by other proteostatic mechanisms, involving the degradation of misfolded proteins (ΔF508-CFTR/α1-AT- Z variant) or regulating the concentration of signaling proteins (such as TGF-β1) by the ubiquitin-proteasome system (UPS). The therapeutic strategies to correct proteostasis-imbalance in misfolded protein disorders such as ΔF508-CF have been relatively well studied and involve strategies that rescue functional CFTR protein to treat the underlying cause of the disease. While in the case of COPD-emphysema and/or PF, identification of novel proteostasis-regulators that can control inflammatory-oxidative stress and/or protease-anti-protease balance is warranted.

  6. Correction

    NASA Astrophysics Data System (ADS)

    1995-04-01

    Seismic images of the Brooks Range, Arctic Alaska, reveal crustal-scale duplexing: Correction Geology, v. 23, p. 65 68 (January 1995) The correct Figure 4A, for the loose insert, is given here. See Figure 4A below. Corrected inserts will be available to those requesting copies of the article from the senior author, Gary S. Fuis, U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025. Figure 4A. P-wave velocity model of Brooks Range region (thin gray contours) with migrated wide-angle reflections (heavy red lines) and migreated vertical-incidence reflections (short black lines) superimposed. Velocity contour interval is 0.25 km/s; 4,5, and 6 km/s contours are labeled. Estimated error in velocities is one contour interval. Symbols on faults shown at top are as in Figure 2 caption.

  7. Smooth muscle myosin regulation by serum and cell density in cultured rat lung connective tissue cells.

    PubMed

    Babij, P; Zhao, J; White, S; Woodcock-Mitchell, J; Mitchell, J; Absher, M; Baldor, L; Periasamy, M; Low, R B

    1993-08-01

    RNA and protein analyses were used to detect expression of SM1 and SM2 smooth muscle myosin heavy chain (MHC) in cultured adult rat lung connective tissue cells (RL-90). Smooth muscle MHC mRNA expression in confluent cells grown in 10% serum was approximately 50% of the level in adult stomach. Similar results were obtained in cells cultured at low density (25% confluency) in 1% serum. However, in low-density cultures transferred to 10% serum for 24 h, the level of MHC mRNA decreased to approximately 20% of that in adult stomach. Smooth muscle alpha-actin showed a pattern of expression similar to that for smooth muscle MHC. Expression of nonmuscle MHC-A mRNA was higher in all culture conditions compared to stomach. MHC-A mRNA expression was less in low-density cultures in low serum and increased when low-density cultures were transferred to 10% serum for 24 h. MHC-B mRNA expression was less in low- vs. high-density cultures. In contrast to MHC-A, however, MHC-B mRNA expression in low-density cultures was higher in low serum. Immunofluorescence and immunoblotting with SM1-specific antibody demonstrated the presence of the SM1 protein isoform as well as reactivity to a protein band migrating slightly faster than SM2. These results demonstrate that cultured rat lung connective tissue cells express smooth muscle MHC and that expression is modulated by culture conditions.

  8. Automatic Approach for Lung Segmentation with Juxta-Pleural Nodules from Thoracic CT Based on Contour Tracing and Correction

    PubMed Central

    2016-01-01

    This paper presents a fully automatic framework for lung segmentation, in which juxta-pleural nodule problem is brought into strong focus. The proposed scheme consists of three phases: skin boundary detection, rough segmentation of lung contour, and pulmonary parenchyma refinement. Firstly, chest skin boundary is extracted through image aligning, morphology operation, and connective region analysis. Secondly, diagonal-based border tracing is implemented for lung contour segmentation, with maximum cost path algorithm used for separating the left and right lungs. Finally, by arc-based border smoothing and concave-based border correction, the refined pulmonary parenchyma is obtained. The proposed scheme is evaluated on 45 volumes of chest scans, with volume difference (VD) 11.15 ± 69.63 cm3, volume overlap error (VOE) 3.5057 ± 1.3719%, average surface distance (ASD) 0.7917 ± 0.2741 mm, root mean square distance (RMSD) 1.6957 ± 0.6568 mm, maximum symmetric absolute surface distance (MSD) 21.3430 ± 8.1743 mm, and average time-cost 2 seconds per image. The preliminary results on accuracy and complexity prove that our scheme is a promising tool for lung segmentation with juxta-pleural nodules. PMID:27974907

  9. Automatic Approach for Lung Segmentation with Juxta-Pleural Nodules from Thoracic CT Based on Contour Tracing and Correction.

    PubMed

    Wang, Jinke; Guo, Haoyan

    2016-01-01

    This paper presents a fully automatic framework for lung segmentation, in which juxta-pleural nodule problem is brought into strong focus. The proposed scheme consists of three phases: skin boundary detection, rough segmentation of lung contour, and pulmonary parenchyma refinement. Firstly, chest skin boundary is extracted through image aligning, morphology operation, and connective region analysis. Secondly, diagonal-based border tracing is implemented for lung contour segmentation, with maximum cost path algorithm used for separating the left and right lungs. Finally, by arc-based border smoothing and concave-based border correction, the refined pulmonary parenchyma is obtained. The proposed scheme is evaluated on 45 volumes of chest scans, with volume difference (VD) 11.15 ± 69.63 cm(3), volume overlap error (VOE) 3.5057 ± 1.3719%, average surface distance (ASD) 0.7917 ± 0.2741 mm, root mean square distance (RMSD) 1.6957 ± 0.6568 mm, maximum symmetric absolute surface distance (MSD) 21.3430 ± 8.1743 mm, and average time-cost 2 seconds per image. The preliminary results on accuracy and complexity prove that our scheme is a promising tool for lung segmentation with juxta-pleural nodules.

  10. Optical thickness, spin temperature and correction factor for the density of Galactic H I gas

    NASA Astrophysics Data System (ADS)

    Sofue, Yoshiaki

    2017-07-01

    This paper presents a method to determine the spin temperature of the local (VLSR = 0 km s-1) H I gas using the saturated brightness temperature of the 21-cm line in radial velocity-degenerate regions (VDRs). The spin temperature is determined to be: TS = 146.2 ± 16.1 K by measuring saturated brightness in the VDR towards the Galactic Centre; 146.8 ± 10.7 K by χ2 fitting of the expected brightness distribution to observations around the VDR; and 144.4 ± 6.8 K towards the local arm. Assuming TS = 146 K, a correction factor Γ for the H I density, defined by the ratio of the true H I density for finite optical thickness to that calculated by assuming optically thin H i, was obtained as Γ ˜ 1.2 (optical depth τ ˜ 0.3) in the local H I gas, ˜1.8 (˜1.3) towards the arm and anti-Centre, and as high as ˜3.6 (˜2.7) in the Galactic Centre direction. It is suggested that the H I density and mass in the local arm could be ˜2 times greater than currently estimated values, and that in the inner Galaxy could be ˜3.6 times greater.

  11. The validation of tomotherapy dose calculations in low-density lung media.

    PubMed

    Chaudhari, Summer R; Pechenaya, Olga L; Goddu, S Murty; Mutic, Sasa; Rangaraj, Dharanipathy; Bradley, Jeffrey D; Low, Daniel

    2009-04-21

    The dose-calculation accuracy of the tomotherapy Hi-Art II(R) (Tomotherapy, Inc., Madison, WI) treatment planning system (TPS) in the presence of low-density lung media was investigated. In this evaluation, a custom-designed heterogeneous phantom mimicking the mediastinum geometry was used. Gammex LN300 and balsa wood were selected as two lung-equivalent materials with different densities. Film analysis and ionization chamber measurements were performed. Treatment plans for esophageal cancers were used in the evaluation. The agreement between the dose calculated by the TPS and the dose measured via ionization chambers was, in most cases, within 0.8%. Gamma analysis using 3% and 3 mm criteria for radiochromic film dosimetry showed that 98% and 95% of the measured dose distribution had passing gamma values < or =1 for LN300 and balsa wood, respectively. For a homogeneous water-equivalent phantom, 95% of the points passed the gamma test. It was found that for the interface between the low-density medium and water-equivalent medium, the TPS calculated the dose distribution within acceptable limits. The phantom developed for this work enabled detailed quality-assurance testing under realistic conditions with heterogeneous media.

  12. The validation of tomotherapy dose calculations in low-density lung media

    NASA Astrophysics Data System (ADS)

    Chaudhari, Summer R.; Pechenaya, Olga L.; Goddu, S. Murty; Mutic, Sasa; Rangaraj, Dharanipathy; Bradley, Jeffrey D.; Low, Daniel

    2009-04-01

    The dose-calculation accuracy of the tomotherapy Hi-Art II® (Tomotherapy, Inc., Madison, WI) treatment planning system (TPS) in the presence of low-density lung media was investigated. In this evaluation, a custom-designed heterogeneous phantom mimicking the mediastinum geometry was used. Gammex LN300 and balsa wood were selected as two lung-equivalent materials with different densities. Film analysis and ionization chamber measurements were performed. Treatment plans for esophageal cancers were used in the evaluation. The agreement between the dose calculated by the TPS and the dose measured via ionization chambers was, in most cases, within 0.8%. Gamma analysis using 3% and 3 mm criteria for radiochromic film dosimetry showed that 98% and 95% of the measured dose distribution had passing gamma values <=1 for LN300 and balsa wood, respectively. For a homogeneous water-equivalent phantom, 95% of the points passed the gamma test. It was found that for the interface between the low-density medium and water-equivalent medium, the TPS calculated the dose distribution within acceptable limits. The phantom developed for this work enabled detailed quality-assurance testing under realistic conditions with heterogeneous media.

  13. Density features of screened lung tumors in low-dose computed tomography.

    PubMed

    Shen, Wei-Chih; Liu, Juhn-Cherng; Shieh, Shwn-Huey; Yang, Su-Tso; Tseng, Guan-Chin; Hsu, Wu-Huei; Chen, Chih-Yi; Yu, Yang-Hao

    2014-01-01

    Using low-dose computed tomography (LDCT), small and heterogeneous lung tumors are detected in screening. The criteria for assessing detected tumors are crucial for determining follow-up or resection strategies. The purpose of this study was to investigate the capacity of density features in differentiating lung tumors. From July 2008 to December 2011, 48 surgically confirmed tumors (29 malignancies, comprising 17 cases of adenocarcinoma and 12 cases of adenocarcinoma in situ [AdIs], and 19 benignancies, comprising 11 cases of atypical adenomatous hyperplasia [AAH] and eight cases of benign non-AAH) in 38 patients were retrospectively evaluated, indicating that the positive predictive value (PPV) of physicians is 60.4% (29/48). Three types of density features, tumor disappearance rate (TDR), mean, and entropy, were obtained from the CT values of detected tumors. Entropy is capable of differentiating malignancy from benignancy but is limited in differentiating AdIs from benign non-AAH. The combination of entropy and TDR is effective for predicting malignancy with an accuracy of 87.5% (42/48) and a PPV of 89.7% (26/29), improving the PPV of physicians by 29.3%. The combination of entropy and mean adequately clarifies the four pathology groups with an accuracy of 72.9% (35/48). For tumors with a mean below -400 Hounsfield units, the criterion of an entropy larger than 5.4 might be appropriate for diagnosing malignancy. For others, the pathology is either benign non-AAH or adenocarcinoma; adenocarcinoma has a higher entropy than benign non-AAH, with the exception of tuberculoma. Combining density features enables differentiating heterogeneous lung tumors in LDCT. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  14. Effect of higher implant density on curve correction in dystrophic thoracic scoliosis secondary to neurofibromatosis Type 1.

    PubMed

    Li, Yang; Yuan, Xinxin; Sha, Shifu; Liu, Zhen; Zhu, Weiguo; Qiu, Yong; Wang, Bin; Yu, Yang; Zhu, Zezhang

    2017-10-01

    OBJECTIVE The aim of this study was to investigate how implant density affects radiographic results and clinical outcomes in patients with dystrophic scoliosis secondary to neurofibromatosis Type 1 (NF1). METHODS A total of 41 patients with dystrophic scoliosis secondary to NF1 who underwent 1-stage posterior correction between June 2011 and December 2013 were included. General information about patients was recorded, as were preoperative and postoperative scores from Scoliosis Research Society (SRS)-22 questionnaires. Pearson correlation analysis was used to analyze the associations among implant density, coronal Cobb angle correction rate and correction loss at last follow-up, change of sagittal curve, and apical vertebral translation. Patients were then divided into 2 groups: those with low-density and those with high-density implants. Independent-sample t-tests were used to compare demographic data, radiographic findings, and clinical outcomes before surgery and at last follow-up between the groups. RESULTS Significant correlations were found between the implant density and the coronal correction rate of the main curve (r = 0.505, p < 0.01) and the coronal correction loss at final follow-up (r = -0.379, p = 0.015). There was no significant correlation between implant density and change of sagittal profile (p = 0.662) or apical vertebral translation (p = 0.062). The SRS-22 scores improved in the appearance, activity, and mental health domains within both groups, but there was no difference between the groups in any of the SRS-22 domains at final follow-up (p > 0.05 for all). CONCLUSIONS Although no significant differences between the high- and low-density groups were found in any of the SRS-22 domains at final follow-up, higher implant density was correlated with superior coronal correction and less postoperative correction loss in patients with dystrophic NF1-associated scoliosis.

  15. Corrections.

    PubMed

    2015-07-01

    Lai Y-S, Biedermann P, Ekpo UF, et al. Spatial distribution of schistosomiasis and treatment needs in sub-Saharan Africa: a systematic review and geostatistical analysis. Lancet Infect Dis 2015; published online May 22. http://dx.doi.org/10.1016/S1473-3099(15)00066-3—Figure 1 of this Article should have contained a box stating ‘100 references added’ with an arrow pointing inwards, rather than a box stating ‘199 records excluded’, and an asterisk should have been added after ‘1473 records extracted into GNTD’. Additionally, the positioning of the ‘§ and ‘†’ footnotes has been corrected in table 1. These corrections have been made to the online version as of June 4, 2015.

  16. Correction.

    PubMed

    2016-02-01

    In the article by Guessous et al (Guessous I, Pruijm M, Ponte B, Ackermann D, Ehret G, Ansermot N, Vuistiner P, Staessen J, Gu Y, Paccaud F, Mohaupt M, Vogt B, Pechère-Bertschi A, Martin PY, Burnier M, Eap CB, Bochud M. Associations of ambulatory blood pressure with urinary caffeine and caffeine metabolite excretions. Hypertension. 2015;65:691–696. doi: 10.1161/HYPERTENSIONAHA.114.04512), which published online ahead of print December 8, 2014, and appeared in the March 2015 issue of the journal, a correction was needed.One of the author surnames was misspelled. Antoinette Pechère-Berstchi has been corrected to read Antoinette Pechère-Bertschi.The authors apologize for this error.

  17. Vibrational and thermal properties of β-HMX and TATB from dispersion corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Landerville, Aaron C.; Oleynik, Ivan I.

    2017-01-01

    Dispersion Corrected Density Functional Theory (DFT+vdW) calculations are performed to predict vibrational and thermal properties of the bulk energetic materials (EMs) β-octahydrocyclotetramethylene-tetranitramine (β-HMX) and triaminotrinitrobenzene (TATB). DFT+vdW calculations of pressure-dependent crystal structure and the hydrostatic equation of state are followed by frozen-phonon calculations of their respective vibration spectra at each pressure. These are then used under the quasi-harmonic approximation to obtain zero-point and thermal free energy contributions to the pressure, resulting in pressure-volume-temperature (PVT) EOS for each material that are in excellent agreement with experiment. Heat capacities, and coefficients of thermal expansion as functions of temperature are also calculated and compared with experiment.

  18. Computing approximate random Delta v magnitude probability densities. [for spacecraft trajectory correction

    NASA Technical Reports Server (NTRS)

    Chadwick, C.

    1984-01-01

    This paper describes the development and use of an algorithm to compute approximate statistics of the magnitude of a single random trajectory correction maneuver (TCM) Delta v vector. The TCM Delta v vector is modeled as a three component Cartesian vector each of whose components is a random variable having a normal (Gaussian) distribution with zero mean and possibly unequal standard deviations. The algorithm uses these standard deviations as input to produce approximations to (1) the mean and standard deviation of the magnitude of Delta v, (2) points of the probability density function of the magnitude of Delta v, and (3) points of the cumulative and inverse cumulative distribution functions of Delta v. The approximates are based on Monte Carlo techniques developed in a previous paper by the author and extended here. The algorithm described is expected to be useful in both pre-flight planning and in-flight analysis of maneuver propellant requirements for space missions.

  19. Self-interaction-corrected local-spin-density calculations for rare earth materials

    SciTech Connect

    Svane, A.; Temmerman, W.M.; Szotek, Z.; Laegsgaard, J.; Winter, H.

    2000-04-20

    The ab initio self-interaction-corrected (SIC) local-spin-density (LSD) approximation is discussed with emphasis on the ability to describe localized f-electron states in rare earth solids. Two methods for minimizing the SIC-LSD total energy functional are discussed, one using a unified Hamiltonian for all electron states, thus having the advantages of Bloch's theorem, the other one employing an iterative scheme in real space. Results for cerium and cerium compounds as well as other rare earths are presented. For the cerium compounds the onset of f-electron delocalization can be accurately described, including the intricate isostructural phase transitions in elemental cerium and CeP. In Pr and Sm the equilibrium lattice constant and zero temperature equation of state is greatly improved in comparison with the LSD results.

  20. Water cluster anions studied by the long-range corrected density functional theory.

    PubMed

    Yagi, Kiyoshi; Okano, Yuko; Sato, Takeshi; Kawashima, Yukio; Tsuneda, Takao; Hirao, Kimihiko

    2008-10-09

    Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).

  1. Calibrated and completeness-corrected optical stellar density maps of the northern Galactic plane

    NASA Astrophysics Data System (ADS)

    Farnhill, H. J.; Drew, J. E.; Barentsen, G.; González-Solares, E. A.

    2016-03-01

    Following on from the second release of calibrated photometry from IPHAS, the INT/WFC Photometric Hα Survey of the Northern Galactic Plane, we present incompleteness-corrected stellar density maps in the r and i photometric bands. These have been computed to a range of limiting magnitudes reaching to 20th magnitude in r and 19th in i (Vega system), and with different angular resolutions - the highest resolution available being 1 arcmin2. The maps obtained cover 94 per cent of the 1800 square degree IPHAS footprint, spanning the Galactic latitude range, -5° < b < +5°, north of the celestial equator. The corrections for incompleteness, due to confusion and sensitivity loss at the faint limit, have been deduced by the method of artificial source injection. The presentation of this method is preceded by a discussion of other more approximate methods of determining completeness. Our method takes full account of position-dependent seeing and source ellipticity in the survey data base. The application of the star counts to testing reddened Galactic disc models is previewed by a comparison with predicted counts along three constant-longitude cuts at ℓ ≃ 30°, 90° and 175°: some overprediction of the most heavily reddened ℓ ≃ 30° counts is found, alongside good agreement at ℓ ≃ 90° and 175°.

  2. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations

    SciTech Connect

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-14

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor–acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene–perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.

  3. Evaluation of Density Corrections to Methane Fluxes Measured by Open-Path Eddy Covariance over Contrasting Landscapes

    NASA Astrophysics Data System (ADS)

    Chamberlain, Samuel D.; Verfaillie, Joseph; Eichelmann, Elke; Hemes, Kyle S.; Baldocchi, Dennis D.

    2017-06-01

    Corrections accounting for air density fluctuations due to heat and water vapour fluxes must be applied to the measurement of eddy-covariance fluxes when using open-path sensors. Experimental tests and ecosystem observations have demonstrated the important role density corrections play in accurately quantifying carbon dioxide (CO2) fluxes, but less attention has been paid to evaluating these corrections for methane (CH4) fluxes. We measured CH4 fluxes with open-path sensors over a suite of sites with contrasting CH4 emissions and energy partitioning, including a pavement airfield, two negligible-flux ecosystems (drained alfalfa and pasture), and two high-flux ecosystems (flooded wetland and rice). We found that density corrections successfully re-zeroed fluxes in negligible-flux sites; however, slight overcorrection was observed above pavement. The primary impact of density corrections varied over negligible- and high-flux ecosystems. For negligible-flux sites, corrections led to greater than 100% adjustment in daily budgets, while these adjustments were only 3-10% in high-flux ecosystems. The primary impact to high-flux ecosystems was a change in flux diel patterns, which may affect the evaluation of relationships between biophysical drivers and fluxes if correction bias exists. Additionally, accounting for density effects to high-frequency CH4 fluctuations led to large differences in observed CH4 flux cospectra above negligible-flux sites, demonstrating that similar adjustments should be made before interpreting CH4 cospectra for comparable ecosystems. These results give us confidence in CH4 fluxes measured by open-path sensors, and demonstrate that density corrections play an important role in adjusting flux budgets and diel patterns across a range of ecosystems.

  4. Reproducible isolation of type II pneumocytes from fetal and adult rat lung using nycodenz density gradients.

    PubMed

    Viscardi, R M; Ullsperger, S; Resau, J H

    1992-01-01

    Isolating fresh, relatively pure type II pneumocytes from the lung, particularly of fetal origin, is a difficult process. Separation by buoyant density gradient centrifugation has been used successfully to isolate adult type II cells. There is concern, however, that Percoll, a gradient medium that is commonly used for type II cell isolation, may be toxic to cells. We evaluated a new gradient medium, Nycodenz, that is (1) a true solution, (2) transparent, (3) not metabolized by cells, and (4) nontoxic to cells. Type II pneumocytes were isolated from 19- and 21-day gestation fetal and adult rat lung by elastase digestion and separated on preformed isotonic Nycodenz gradients (2 mL each of 27.6, 20.7, 13.8, and 4.6 (w/v) solutions). Type II pneumocytes were recovered from the density range 1.057-1.061 and identified by binding of FITC-conjugated and gold-complexed Maclura pomifera lectin. Cells derived from 19-day fetal lung contained abundant glycogen and reacted with a monoclonal antibody to the cytokeratins 8 and 18, which are markers of the fetal type II cell. Adult type II cells reacted with antibodies to cytokeratins 8, 18, and 19. Type II cell purity was 79.7 +/- 2.4%, 83.8 +/- 2.8%, and 82.6 +/- 1.8% (means +/- SEM) for 19- and 21-day gestation fetal and adult lung preparations, respectively. Cell viability was greater than 95%. The final cell yield for adult preparations was 17.8 +/- 2.7 x 10(6)/rat (means +/- SEM). To determine if the freshly isolated type II pneumocytes were functionally active, the incorporation of [3H]choline into phosphatidylcholine was measured. The percent saturation of phosphatidylcholine was high for both populations of freshly isolated cells. However, adult type II pneumocytes incorporated [3H]choline into phosphatidylcholine more rapidly than 21-day gestation fetal cells (5.97 x 10(-3) dpm/10(6) cells/h vs. 0.32 x 10(-3) dpm/10(6) cells/h, P less than .005). We have demonstrated that, using the Nycodenz isolation method, it is

  5. Correction of localized shape errors on optical surfaces by altering the localized density of surface or near-surface layers

    SciTech Connect

    Taylor, John S.; Folta, James A.; Montcalm, Claude

    2005-01-18

    Figure errors are corrected on optical or other precision surfaces by changing the local density of material in a zone at or near the surface. Optical surface height is correlated with the localized density of the material within the same region. A change in the height of the optical surface can then be caused by a change in the localized density of the material at or near the surface.

  6. Self-interaction corrected density functional calculations of molecular Rydberg states

    SciTech Connect

    Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes

    2013-11-21

    A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.

  7. Band-structure-corrected local density approximation study of semiconductor quantum dots and wires

    NASA Astrophysics Data System (ADS)

    Li, Jingbo; Wang, Lin-Wang

    2005-09-01

    This paper presents results of ab initio accuracy thousand atom calculations of colloidal quantum dots and wires using the charge patching method. We have used density functional theory under local density approximation (LDA), and we have corrected the LDA bulk band structures by modifying the nonlocal pseudopotentials, so that their effective masses agree with experimental values. We have systematically studied the electronic states of group III-V (GaAs, InAs, InP, GaN, AlN, and InN) and group II-VI (CdSe, CdS, CdTe, ZnSe, ZnS, ZnTe, and ZnO) systems. We have also calculated the electron-hole Coulomb interactions in these systems. We report the exciton energies as functions of the quantum dot sizes and quantum wire diameters for all the above materials. We found generally good agreements between our calculated results and experimental measurements. For CdSe and InP, the currently calculated results agree well with the previously calculated results using semiempirical pseudopotentials. The ratios of band-gap-increases between quantum wires and dots are material-dependent, but a majority of them are close to 0.586, as predicted by the simple effective-mass model. Finally, the size dependence of 1Se-1Pe transition energies of CdSe quantum dots agrees well with the experiment. Our results can be used as benchmarks for future experiments and calculations.

  8. Changes of myocardial capillary density in progression of experimental lung emphysema.

    PubMed

    Sulkowski, S; Musiatowicz, B; Sulkowska, M; Sobaniec-Lotowska, M; Dziechiol, J; Sulik, M; Szynaka, B

    1996-01-01

    A morphometrical analysis of changes in the heart of rats with experimental lung emphysema due to single intratracheal administration of papain solution has been done. Special attention has been paid to quantitative changes of capillaries and to the cardiomyocyte diameter in respective regions of the myocardium after one, three and six months following the administration of papain. A histological and morphometrical analysis of changes in the lungs has also been carried out and partial pressures of oxygen and carbon dioxide in the arterial blood of the examined animals have been marked. It has been found that a single administration of papain caused emphysematous changes in the lungs, growing more intense until the third month of the experiment. The progression of these changes corresponded to a capillary density increase in the right ventricle, interventricular septum and in the subendocardial layer of the left ventricle. The increase in the number of capillaries was interpreted as the first adaptive stage of cor pulmonale development and explained by the occurrence of angiogenesis. The changes co-existed with a decrease in partial pressure of oxygen in the arterial blood. After six months of the experiment, a reduction in capillary density in the heart regions mentioned above and a simultaneous increase in the cardiomycyte transversal diameter were observed, being the exponents of evident myocardial hypertrophy. Development of ultrastructural changes in the hearts of rats has been analysed too. Simultaneous development of changes in the right ventricle muscle and in the subendocardial layer of the heart left ventricle myocardium was observed. The role of hypoxia as a one of essential factors responsible for the observed morphologic changes has been discussed.

  9. Relationship of lung function loss to level of initial function: correcting for measurement error using the reliability coefficient.

    PubMed Central

    Irwig, L; Groeneveld, H; Becklake, M

    1988-01-01

    The regression of lung function change on the initial lung function level is biased when the initial level is measured with random error. Several methods have been proposed to obtain unbiased estimates of regression coefficients in such circumstances. We apply these methods to examine the relationship between lung function loss over 11 years and its initial level in 433 men aged about 20 when first seen. On theoretical and practical grounds the best method is the correction of the regression coefficient using the reliability coefficient. This is defined as the ratio of the error free variance to the variance of the variable measured with error, and is easily estimated as the correlation between repeat measurements of the underlying level. In young men the loss of some lung functions (forced vital capacity [FVC], forced expiratory volume in one second [FEV1], forced expiratory flow in the middle half of expiration, and the ratio FEV1/FVC) do not appear to be related to initial level. PMID:3256581

  10. Correction

    NASA Astrophysics Data System (ADS)

    1998-12-01

    Alleged mosasaur bite marks on Late Cretaceous ammonites are limpet (patellogastropod) home scars Geology, v. 26, p. 947 950 (October 1998) This article had the following printing errors: p. 947, Abstract, line 11, “sepia” should be “septa” p. 947, 1st paragraph under Introduction, line 2, “creep” should be “deep” p. 948, column 1, 2nd paragraph, line 7, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 1, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 5, “19774” should be “1977)” p. 949, column 1, 4th paragraph, line 7, “in particular” should be “In particular” CORRECTION Mammalian community response to the latest Paleocene thermal maximum: An isotaphonomic study in the northern Bighorn Basin, Wyoming Geology, v. 26, p. 1011 1014 (November 1998) An error appeared in the References Cited. The correct reference appears below: Fricke, H. C., Clyde, W. C., O'Neil, J. R., and Gingerich, P. D., 1998, Evidence for rapid climate change in North America during the latest Paleocene thermal maximum: Oxygen isotope compositions of biogenic phosphate from the Bighorn Basin (Wyoming): Earth and Planetary Science Letters, v. 160, p. 193 208.

  11. Association of chronic obstructive pulmonary disease and smoking status with bone density and vertebral fractures in male lung cancer screening participants.

    PubMed

    de Jong, Werner U; de Jong, Pim A; Vliegenthart, Rozemarijn; Isgum, Ivana; Lammers, Jan-Willem J; Oudkerk, Matthijs; van der Aalst, Carlijn; de Koning, Harry J; Mohamed Hoesein, Firdaus A

    2014-10-01

    We studied the vertebral fracture prevalence on low-dose chest computed tomography (CT) in male lung cancer screening participants and the association of fractures and bone density with chronic obstructive pulmonary disease (COPD) and smoking. 1140 male current and former smokers with ≥ 16.5 packyears from the NELSON lung cancer screening trial were included. Age, body mass index, and smoking status were registered. CT scans and pulmonary function tests were obtained on the same day. On CT, vertebral fractures and bone density were measured. The cohort had a mean age of 62.5 years (standard deviation 5.2) old; 531 (46.6%) had quit smoking; and 437 (38.3%) had COPD. Of the group, 100 (8.8%) participants had a vertebral fracture. Fracture prevalence was higher in current compared to former smokers (11.3% versus 5.8%, p = 0.001), but similar in participants with COPD compared to those without (9.6% versus 8.3%, p = 0.430). The multivariable adjusted odds ratio for fracture presence was 1.79 (95% CI: 1.13-2.84) in current smokers and 1.08 (95% CI: 0.69-1.67) in COPD participants. Bone density was lower in current compared to former smokers (103.2 HU versus 108.7 HU, p = 0.006) and in participants with COPD compared to those without [100.7 Hounsfield Units (HU) versus 108.9 HU, p < 0.001]. In multivariate analysis, smoking status and COPD status were independently associated with bone density, corrected for age and body mass index. In conclusion, our study shows that lung cancer screening participants have a substantial vertebral fracture burden. Fractures are more common in current smokers, who also have lower bone density. We could not confirm that COPD is independently associated with vertebral fractures.

  12. Understanding molecular crystals with dispersion-inclusive density functional theory: pairwise corrections and beyond.

    PubMed

    Kronik, Leeor; Tkatchenko, Alexandre

    2014-11-18

    CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids.

  13. Adsorption of benzene on noble metal surfaces studied by density functional theory with Van der Waals correction.

    PubMed

    Toyoda, Kenji; Hamada, Ikutaro; Yanagisawa, Susumu; Morikawa, Yoshitada

    2011-04-01

    We have studied the atomic geometries and the electronic properties of benzene/metal interfaces by using density functional theoretical (DFT) calculations with van der Waals corrections. Adsorption energies of benzene on Cu(111), Ag(111), and Au(111) surfaces calculated by van der Waals density functional proposed by Dion and co-workers agree reasonably well with experimentally reported values, while those calculated by a semi-empirical van der Waals correction proposed by Grimme are overestimated slightly. The work function change induced by benzene adsorption on the three surfaces are quite well reproduced by the semi-empirical correction, suggesting that weak adsorption geometries can be quite well reproduced by DFT with a semi-empirical dispersion correction scheme.

  14. Finite Size Corrections to the Large Deviation Function of the Density in the One Dimensional Symmetric Simple Exclusion Process

    NASA Astrophysics Data System (ADS)

    Derrida, Bernard; Retaux, Martin

    2013-09-01

    The symmetric simple exclusion process is one of the simplest out-of-equilibrium systems for which the steady state is known. Its large deviation functional of the density has been computed in the past both by microscopic and macroscopic approaches. Here we obtain the leading finite size correction to this large deviation functional. The result is compared to the similar corrections for equilibrium systems.

  15. Screened van der Waals correction to density functional theory for solids

    NASA Astrophysics Data System (ADS)

    Tao, Jianmin; Zheng, Fan; Gebhardt, Julian; Perdew, John P.; Rappe, Andrew M.

    2017-07-01

    Lattice constant and cohesive energy are basic properties in the design of materials and devices. However, due to neglect of long-range van der Waals (vdW) interactions, density functional approximations (DFAs) often yield unusually large errors for ionic solids and heavy metals. Here, we propose a model for the dynamically screened vdW correction, including the leading order as well as higher-order contributions. The striking feature of this model is that important screening effects and higher-order contributions are properly considered and that its contribution to the short-range part is removed by a novel damping function for the avoidance of double counting. As a result, the model dramatically reduces the error of the DFA-GGA in lattice constant and cohesive energy. We also find that the three-body interactions are small, due to the screening effects. These observations greatly improve our fundamental understanding of vdW interactions and enhance the applicability of efficient semilocal DFAs.

  16. Universal Correction of Density Functional Theory to Include London Dispersion (up to Lr, Element 103).

    PubMed

    Kim, Hyungjun; Choi, Jeong-Mo; Goddard, William A

    2012-02-02

    Conventional density functional theory (DFT) fails to describe accurately the London dispersion essential for describing molecular interactions in soft matter (biological systems, polymers, nucleic acids) and molecular crystals. This has led to several methods in which atom-dependent potentials are added into the Kohn-Sham DFT energy. Some of these corrections were fitted to accurate quantum mechanical results, but it will be tedious to determine the appropriate parameters to describe all of the atoms of the periodic table. We propose an alternative approach in which a single parameter in the low-gradient (lg) functional form is combined with the rule-based UFF (universal force-field) nonbond parameters developed for the entire periodic table (up to Lr, Z = 103), named as a DFT-ulg method. We show that DFT-ulg method leads to a very accurate description of the properties for molecular complexes and molecular crystals, providing the means for predicting more accurate weak interactions across the periodic table.

  17. Estimation of boiling points using density functional theory with polarized continuum model solvent corrections.

    PubMed

    Chan, Poh Yin; Tong, Chi Ming; Durrant, Marcus C

    2011-09-01

    An empirical method for estimation of the boiling points of organic molecules based on density functional theory (DFT) calculations with polarized continuum model (PCM) solvent corrections has been developed. The boiling points are calculated as the sum of three contributions. The first term is calculated directly from the structural formula of the molecule, and is related to its effective surface area. The second is a measure of the electronic interactions between molecules, based on the DFT-PCM solvation energy, and the third is employed only for planar aromatic molecules. The method is applicable to a very diverse range of organic molecules, with normal boiling points in the range of -50 to 500 °C, and includes ten different elements (C, H, Br, Cl, F, N, O, P, S and Si). Plots of observed versus calculated boiling points gave R²=0.980 for a training set of 317 molecules, and R²=0.979 for a test set of 74 molecules. The role of intramolecular hydrogen bonding in lowering the boiling points of certain molecules is quantitatively discussed.

  18. Effects of Respiration-Induced Density Variations on Dose Distributions in Radiotherapy of Lung Cancer

    SciTech Connect

    Mexner, Vanessa; Wolthaus, Jochem W.H.; Herk, Marcel van; Damen, Eugene M.F.; Sonke, Jan-Jakob

    2009-07-15

    Purpose: To determine the effect of respiration-induced density variations on the estimated dose delivered to moving structures and, consequently, to evaluate the necessity of using full four-dimensional (4D) treatment plan optimization. Methods and Materials: In 10 patients with large tumor motion (median, 1.9 cm; range, 1.1-3.6 cm), the clinical treatment plan, designed using the mid-ventilation ([MidV]; i.e., the 4D-CT frame closest to the time-averaged mean position) CT scan, was recalculated on all 4D-CT frames. The cumulative dose was determined by transforming the doses in all breathing phases to the MidV geometry using deformable registration and then averaging the results. To determine the effect of density variations, this cumulative dose was compared with the accumulated dose after similarly deforming the planned (3D) MidV-dose in each respiratory phase using the same transformation (i.e., 'blurring the dose'). Results: The accumulated tumor doses, including and excluding density variations, were almost identical. Relative differences in the minimum gross tumor volume (GTV) dose were less than 2% for all patients. The relative differences were even smaller in the mean lung dose and the V20 (<0.5% and 1%, respectively). Conclusions: The effect of respiration-induced density variations on the dose accumulated over the respiratory cycle was very small, even in the presence of considerable respiratory motion. A full 4D-dose calculation for treatment planning that takes into account such density variations is therefore not required. Planning using the MidV-CT derived from 4D-CT with an appropriate margin for geometric uncertainties is an accurate and safe method to account for respiration-induced anatomy variations.

  19. Hypoxia induced changes in lung fluid balance in humans is associated with beta-2 adrenergic receptor density on lymphocytes.

    PubMed

    Johnson, Micah W; Taylor, Bryan J; Hulsebus, Minelle L; Johnson, Bruce D; Snyder, Eric M

    2012-08-15

    Previous studies have demonstrated an important role for beta-2 adrenergic receptors (β(2)AR) in lung fluid clearance. The purpose of this investigation was to examine the relationship between β(2)AR density on lymphocytes and indices of lung water in healthy humans exposed to ≈ 17 h of hypoxia (FIO2 = 12.5% in a hypoxia tent). Thirteen adults (mean ± SEM; age=31 ± 3 years, BMI=24 ± 1 kg/m(2), VO2 Peak = 40 ± 2 ml/kg/min ) participated. Pulmonary function, CT derived lung tissue volume (V(tis)-tissue, blood and water), lung diffusing capacity for carbon monoxide (D(CO)) and nitric oxide (D(NO)), alveolar-capillary conductance (D(M)), pulmonary capillary blood volume (V(c)) and lung water (CT V(tis)-V(c)) were assessed before and after ≈ 17 h normobaric hypoxia (FIO2 = 12.5%). β(2)AR density on lymphocytes was measured via radioligand binding. Arterial oxygen saturation (SaO2), cardiac output (Q), right ventricular systolic pressure (RVSP) and blood pressure (BP) were also assessed. After 17 h hypoxia, SaO2 decreased from 97 ± 1 (normoxia) to 82 ± 4% and RVSP increased from 14 ± 3 (normoxia) to 29 ± 2 mmHg (p<0.05) with little change in Q or BP. V(c) and D(M) both increased with hypoxia with a small increase in D(M)/V(c) ratio (p>0.05). CT V(tis) decreased and lung water was estimated to decline 7 ± 13%, respectively. β(2)AR density averaged 1497 ± 187 receptors/lymphocyte and increased 21 ± 34% with hypoxia (range -31 to +86%). The post-hypoxia increase in β(2)AR density was significantly related to the reduction in lung water (r=-0.64, p<0.05), with the subjects with the greatest increase in density demonstrating the largest decline in lung water. Lung water decreases with 17 h normobaric hypoxia are associated with changes in beta adrenergic receptor density on lymphocytes in healthy adults. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Hypoxia Induced Changes in Lung Fluid Balance in Humans is Associated with Beta-2 Adrenergic Receptor Density on Lymphocytes

    PubMed Central

    Johnson, Micah W.; Taylor, Bryan J.; Hulsebus, Minelle L.; Johnson, Bruce D.; Snyder, Eric M.

    2012-01-01

    Background Previous studies have demonstrated an important role for beta-2 adrenergic receptors (β2AR) in lung fluid clearance. The purpose of this investigation was to examine the relationship between β2AR density on lymphocytes and indices of lung water in healthy humans exposed to ~17hr of hypoxia (FIO2 12.5% in a hypoxia tent). Methods Thirteen adults (mean±SEM; age=31±3yr, BMI=24±1 kg/m2, VO2Peak=40±2 ml/kg/min) participated. Pulmonary function, CT derived lung tissue volume (Vtis-tissue, blood & water), lung diffusing capacity for carbon monoxide (DCO) and nitric oxide (DNO), alveolar-capillary conductance (DM), pulmonary capillary blood volume (Vc) and lung water (CT Vtis − Vc) were assessed before and after ~17hr normobaric hypoxia (FIO2 12.5%). β2AR density on lymphocytes was measured via radioligand binding. Arterial oxygen saturation (SaO2), cardiac output (Q), right ventricular systolic pressure (RVSP) and blood pressure (BP) were also assessed. Results After 17hr hypoxia, SaO2 decreased from 97±1 (normoxia) to 82±4% and RVSP increased from 15±9 (normoxia) to 28±4mmHg (p<0.05) with little change in Q or BP. Vc and DM both increased with hypoxia with a small increase in DM/Vc ratio (p>0.05). CT Vtis decreased and lung water was estimated to decline 7±13%, respectively. β2AR density averaged 1497±187 receptors/lymphocyte and increased 21±34% with hypoxia (range −31 to +86%). The post-hypoxia increase in β2AR density was significantly related to the reduction in lung water (r=−0.64, p<0.05), with the subjects with the greatest increase in density demonstrating the largest decline in lung water. Conclusions Lung water decreases with 17hr normobaric hypoxia are associated with changes in beta adrenergic receptor density on lymphocytes in healthy adults. PMID:22772314

  1. Prediction of d^0 magnetism in self-interaction corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Das Pemmaraju, Chaitanya

    2010-03-01

    Over the past couple of years, the phenomenon of ``d^0 magnetism'' has greatly intrigued the magnetism community [1]. Unlike conventional magnetic materials, ``d^0 magnets'' lack any magnetic ions with open d or f shells but surprisingly, exhibit signatures of ferromagnetism often with a Curie temperature exceeding 300 K. Current research in the field is geared towards trying to understand the mechanism underlying this observed ferromagnetism which is difficult to explain within the conventional m-J paradigm [1]. The most widely studied class of d^0 materials are un-doped and light element doped wide gap Oxides such as HfO2, MgO, ZnO, TiO2 all of which have been put forward as possible d0 ferromagnets. General experimental trends suggest that the magnetism is a feature of highly defective samples leading to the expectation that the phenomenon must be defect related. In particular, based on density functional theory (DFT) calculations acceptor defects formed from the O-2p states in these Oxides have been proposed as being responsible for the ferromagnetism [2,3]. However. predicting magnetism originating from 2p orbitals is a delicate problem, which depends on the subtle interplay between covalency and Hund's coupling. DFT calculations based on semi-local functionals such as the local spin-density approximation (LSDA) can lead to qualitative failures on several fronts. On one hand the excessive delocalization of spin-polarized holes leads to half-metallic ground states and the expectation of room-temperature ferromagnetism. On the other hand, in some cases a magnetic ground state may not be predicted at all as the Hund's coupling might be under estimated. Furthermore, polaronic distortions which are often a feature of acceptor defects in Oxides are not predicted [4,5]. In this presentation, we argue that the self interaction error (SIE) inherent to semi-local functionals is responsible for the failures of LSDA and demonstrate through various examples that beyond

  2. Implementation of empirical dispersion corrections to density functional theory for periodic systems.

    PubMed

    Reckien, Werner; Janetzko, Florian; Peintinger, Michael F; Bredow, Thomas

    2012-09-30

    A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT-D3) is implemented in the plane-wave program package VASP. The DFT-D3 implementation is compared with an implementation of the earlier DFT-D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT-D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three-center terms as implemented in the original molecular DFT-D3 version is investigated. The empirical parameters are taken from the original DFT-D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid-state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT-D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106). Copyright © 2012 Wiley Periodicals, Inc.

  3. Effect of spin-orbit nuclear charge density corrections due to the anomalous magnetic moment on halonuclei

    SciTech Connect

    Ong, A.; Berengut, J. C.; Flambaum, V. V.

    2010-07-15

    In this paper we consider the contribution of the anomalous magnetic moments of protons and neutrons to the nuclear charge density. We show that the spin-orbit contribution to the mean-square charge radius, which has been neglected in recent nuclear calculations, can be important in light halonuclei. We estimate the size of the effect in helium, lithium, and beryllium nuclei. It is found that the spin-orbit contribution represents a approx2% correction to the charge density at the center of the {sup 7}Be nucleus. We derive a simple expression for the correction to the mean-square charge radius due to the spin-orbit term and find that in light halonuclei it may be larger than the Darwin-Foldy term and comparable to finite size corrections. A comparison of experimental and theoretical mean-square radii including the spin-orbit contribution is presented.

  4. SU-F-BRD-09: Is It Sufficient to Use Only Low Density Tissue-Margin to Compensate Inter-Fractionation Setup Uncertainties in Lung Treatment?

    SciTech Connect

    Nie, K; Yue, N; Chen, T; Millevoi, R; Qin, S; Guo, J

    2014-06-15

    Purpose: In lung radiation treatment, PTV is formed with a margin around GTV (or CTV/ITV). Although GTV is most likely of water equivalent density, the PTV margin may be formed with the surrounding low-density tissues, which may lead to unreal dosimetric plan. This study is to evaluate whether the concern of dose calculation inside the PTV with only low density margin could be justified in lung treatment. Methods: Three SBRT cases were analyzed. The PTV from the original plan (Plan-O) was created with a 5–10 mm margin outside the ITV to incorporate setup errors and all mobility from 10 respiratory phases. Test plans were generated with the GTV shifted to the PTV edge to simulate the extreme situations with maximum setup uncertainties. Two representative positions as the very posterior-superior (Plan-PS) and anterior-inferior (Plan-AI) edge were considered. The virtual GTV was assigned a density of 1.0 g.cm−3 and surrounding lung, including the PTV margin, was defined as 0.25 g.cm−3. Also, additional plan with a 1mm tissue-margin instead of full lung-margin was created to evaluate whether a composite-margin (Plan-Comp) has a better approximation for dose calculation. All plans were generated on the average CT using Analytical Anisotropic Algorithm with heterogeneity correction on and all planning parameters/monitor unites remained unchanged. DVH analyses were performed for comparisons. Results: Despite the non-static dose distribution, the high-dose region synchronized with tumor positions. This might due to scatter conditions as greater doses were absorbed in the solid-tumor than in the surrounding low-density lungtissue. However, it still showed missing target coverage in general. Certain level of composite-margin might give better approximation for the dosecalculation. Conclusion: Our exploratory results suggest that with the lungmargin only, the planning dose of PTV might overestimate the coverage of the target during treatment. The significance of this

  5. The use of low density high accuracy (LDHA) data for correction of high density low accuracy (HDLA) point cloud

    NASA Astrophysics Data System (ADS)

    Rak, Michal Bartosz; Wozniak, Adam; Mayer, J. R. R.

    2016-06-01

    Coordinate measuring techniques rely on computer processing of coordinate values of points gathered from physical surfaces using contact or non-contact methods. Contact measurements are characterized by low density and high accuracy. On the other hand optical methods gather high density data of the whole object in a short time but with accuracy at least one order of magnitude lower than for contact measurements. Thus the drawback of contact methods is low density of data, while for non-contact methods it is low accuracy. In this paper a method for fusion of data from two measurements of fundamentally different nature: high density low accuracy (HDLA) and low density high accuracy (LDHA) is presented to overcome the limitations of both measuring methods. In the proposed method the concept of virtual markers is used to find a representation of pairs of corresponding characteristic points in both sets of data. In each pair the coordinates of the point from contact measurements is treated as a reference for the corresponding point from non-contact measurement. Transformation enabling displacement of characteristic points from optical measurement to their match from contact measurements is determined and applied to the whole point cloud. The efficiency of the proposed algorithm was evaluated by comparison with data from a coordinate measuring machine (CMM). Three surfaces were used for this evaluation: plane, turbine blade and engine cover. For the planar surface the achieved improvement was of around 200 μm. Similar results were obtained for the turbine blade but for the engine cover the improvement was smaller. For both freeform surfaces the improvement was higher for raw data than for data after creation of mesh of triangles.

  6. Comparison of air sac volume, lung volume, and lung densities determined by use of computed tomography in conscious and anesthetized Humboldt penguins (Spheniscus humboldti) positioned in ventral, dorsal, and right lateral recumbency.

    PubMed

    Nevitt, Benjamin N; Langan, Jennifer N; Adkesson, Michael J; Mitchell, Mark A; Henzler, Margaret; Drees, Randi

    2014-08-01

    To determine the effects of recumbency on air sac volume, lung volume, and lung densities in CT images of healthy, conscious and anesthetized spontaneously breathing Humboldt penguins (Spheniscus humboldti). 25 adult (13 male and 12 female) Humboldt penguins. CT images of conscious penguins in ventral recumbency and anesthetized penguins in dorsal, ventral, and right lateral recumbency were obtained. Air sac volume, lung volume, and lung densities in CT images were calculated. A paired samples t test was used to determine whether right and left lung densities differed among recumbencies. Repeated-measures ANOVA (controlled for sex and order of recumbencies during CT) was used to determine whether air sac or lung volumes differed among recumbencies. Recumbency had a significant effect on air sac volume but not lung volume. Air sac volume was largest in conscious penguins in ventral recumbency (mean ± SD, 347.2 ± 103.1 cm(3)) and lowest in anesthetized penguins in dorsal recumbency (median, 202.0 cm(3); 10th to 90th percentile, 129.2 to 280.3 cm(3)). Lung densities were highest in anesthetized penguins in dorsal recumbency (right lung median, 0.522 g/cm(3); left lung median, 0.511 g/cm(3)) and lowest in anesthetized penguins in ventral recumbency (right lung median, 0.488 g/cm(3); left lung median, 0.482 g/cm(3)). Results indicated that anesthetized Humboldt penguins had the lowest air sac volume and highest lung densities in dorsal recumbency. Therefore, this recumbency may not be recommended. Minimal changes in lung volume were detected among recumbencies or between conscious and anesthetized penguins.

  7. Spatial pattern corrections and sample sizes for forest density estimates of historical tree surveys

    Treesearch

    Brice B. Hanberry; Shawn Fraver; Hong S. He; Jian Yang; Dan C. Dey; Brian J. Palik

    2011-01-01

    The U.S. General Land Office land surveys document trees present during European settlement. However, use of these surveys for calculating historical forest density and other derived metrics is limited by uncertainty about the performance of plotless density estimators under a range of conditions. Therefore, we tested two plotless density estimators, developed by...

  8. The optimized effective potential and the self-interaction correction in density functional theory: Application to molecules

    SciTech Connect

    Garza, Jorge; Nichols, Jeffrey A.; Dixon, David A.

    2000-05-08

    The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation, the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work. (c) 2000 American Institute of Physics.

  9. Long-range corrected density functional theory study on static second hyperpolarizabilities of singlet diradical systems.

    PubMed

    Kishi, Ryohei; Bonness, Sean; Yoneda, Kyohei; Takahashi, Hideaki; Nakano, Masayoshi; Botek, Edith; Champagne, Benoît; Kubo, Takashi; Kamada, Kenji; Ohta, Koji; Tsuneda, Takao

    2010-03-07

    Within the spin-unrestricted density functional theory (DFT) the long-range correction (LC) scheme combined with the Becke-Lee-Yang-Parr exchange-correlation functional, referred to as LC-UBLYP method, has been applied to the calculation of the second hyperpolarizability (gamma) of open-shell singlet diradical systems of increasing complexity and has demonstrated good performance: (i) for the simplest H(2) dissociation model, the gamma values calculated by the LC-UBLYP method significantly overshoot the full configuration interaction result but reproduce qualitatively the evolution of gamma as a function of the diradical character, (ii) for small singlet diradical 1,3-dipole systems, the diradical character dependence of gamma determined by the UCCSD and UCCSD(T) reference methods is reproduced semiquantitatively by the LC-UBLYP method except in the small diradical character region, where the spin-unrestricted solutions coincide with spin-restricted solutions, (iii) the LC-UBLYP method also closely reproduces the UCCSD(T) results on the diradical character dependence of gamma of the p-quinodimethane model system, particularly in the intermediate and large diradical character regions, whereas it shows an abrupt change for a diradical character (y) close to 0.2 originating from the triplet instability, (iv) the reliability of LC-UBLYP to reproduce reference coupled cluster results on open-shell singlet systems with intermediate and large diradical characters has also been substantiated in the case of gamma of 1,4-bis-(imidazol-2-ylidene)-cyclohexa-2,5-diene (BI2Y), then (v), for real systems built from a pair of phenalenyl radicals separated by a conjugated linker, the LC-UBLYP results have been found to closely match the UBHandHLYP values-which, for small systems are in good agreement with those obtained using correlated molecular orbital methods-whereas the UB3LYP results can be much different. These results are not only important from the viewpoint of an efficient

  10. [Ventilation and gas exchange in the lungs during physical exertion in patients following the correction of mitral stenosis].

    PubMed

    Volovoĭ, V L; Guliamov, D S; Gafurov, F Kh

    1985-01-01

    During rehabilitation of 40 patients after correction of mitral stenosis, a study was made of ventilation and gas exchange in the lungs under spirometric bicycle ergometry according to the "standard protocol" until the maximal oxygen consumption (MOC) was attained. The patients were examined 20-30 days, 3 and 6 months after operation. In accordance with the magnitude of the MOC expressed in metabolic equivalents (MET), all the patients were divided into 3 functional classes which corresponded roughly to the NYHA classification. It was revealed that with the same magnitude of the MOC the patients of the worst functional class had a lower production of CO2, a greater volume of the dead space and a higher level of minute ventilation. It is supposed that the described respiratory abnormalities are connected with enhanced ventilation of the poorly perfused alveoli, apparently because of venous congestion in the pulmonary capillaries. The characteristics of gas exchange and ventilation in the lungs investigated under the conditions of the "standard protocol" of spirometric bicycle ergometry objectively mark pump function of the heart and respiratory potentialities of the cardiorespiratory system, which might be the basis for the functional classification of the patients after cardiosurgical interventions.

  11. Configuration Interaction-Corrected Tamm-Dancoff Approximation: A Time-Dependent Density Functional Method with the Correct Dimensionality of Conical Intersections.

    PubMed

    Li, Shaohong L; Marenich, Aleksandr V; Xu, Xuefei; Truhlar, Donald G

    2014-01-16

    Linear response (LR) Kohn-Sham (KS) time-dependent density functional theory (TDDFT), or KS-LR, has been widely used to study electronically excited states of molecules and is the method of choice for large and complex systems. The Tamm-Dancoff approximation to TDDFT (TDDFT-TDA or KS-TDA) gives results similar to KS-LR and alleviates the instability problem of TDDFT near state intersections. However, KS-LR and KS-TDA share a debilitating feature; conical intersections of the reference state and a response state occur in F - 1 instead of the correct F - 2 dimensions, where F is the number of internal degrees of freedom. Here, we propose a new method, named the configuration interaction-corrected Tamm-Dancoff approximation (CIC-TDA), that eliminates this problem. It calculates the coupling between the reference state and an intersecting response state by interpreting the KS reference-state Slater determinant and linear response as if they were wave functions. Both formal analysis and test results show that CIC-TDA gives similar results to KS-TDA far from a conical intersection, but the intersection occurs with the correct dimensionality. We anticipate that this will allow more realistic application of TDDFT to photochemistry.

  12. Relevance of density, size and DNA content of tumour cells to the lung colony assay.

    PubMed Central

    Grdina, D. J.; Hittelman, W. N.; White, R. A.; Meistrich, M. L.

    1977-01-01

    Mouse fibrosarcoma tumours were dissociated and divided into subpopulations of viable cells by centrifugation in linear density gradients of Renografin. Two of these subpopulations, designated Band 2 and Band 4, differed in their clonogenic ability in lung colony assay. The less dense Band 2 cells were significantly more clonogenic than the Band 4 cells (2.9 percent vs 1.4 percent respectively). Each band was further separated on the basis of cell size by centrifugal elutriation. Each size class of cells comprising Band 2 showed higher clonogenic ability than the corresponding size class in Band 4. Thus cell size differences were not responsible for the clonogenic differences between these bands. To determine whether cell-cycle distribution of the tumour cells was responsible for differences in cloning efficiency, flow microfluorometric and premature chromosome condensation methods were utilized. The unseparated and Band 4 populations showed a higher percentage of cells in S and G2 than did the Band 2 populations, but many of the S and G2 tumour cells showed extensive chromosome damage. From this study we conclude that the increased clonogenic ability of the lighter tumour cells is not due to differences in cell size or cell-cycle parameters. Images Fig. 4 Fig. 5 Fig. 6 Fig. 7 PMID:563726

  13. Statistical control process to compare and rank treatment plans in radiation oncology: impact of heterogeneity correction on treatment planning in lung cancer

    PubMed Central

    Balosso, Jacques

    2016-01-01

    Background This study proposes a statistical process to compare different treatment plans issued from different irradiation techniques or different treatment phases. This approach aims to provide arguments for discussion about the impact on clinical results of any condition able to significantly alter dosimetric or ballistic related data. Methods The principles of the statistical investigation are presented in the framework of a clinical example based on 40 fields of radiotherapy for lung cancers. Two treatment plans were generated for each patient making a change of dose distribution due to variation of lung density correction. The data from 2D gamma index (γ) including the pixels having γ≤1 were used to determine the capability index (Cp) and the acceptability index (Cpk) of the process. To measure the strength of the relationship between the γ passing rates and the Cp and Cpk indices, the Spearman’s rank non-parametric test was used to calculate P values. Results The comparison between reference and tested plans showed that 95% of pixels have γ≤1 with criteria (6%, 6 mm). The values of the Cp and Cpk indices were lower than one showing a significant dose difference. The data showed a strong correlation between γ passing rates and the indices with P>0.8. Conclusions The statistical analysis using Cp and Cpk, show the significance of dose differences resulting from two plans in radiotherapy. These indices can be used for adaptive radiotherapy to measure the difference between initial plan and daily delivered plan. The significant changes of dose distribution could raise the question about the continuity to treat the patient with the initial plan or the need for adjustments. PMID:28149763

  14. Efficacy of surface error corrections to density functional theory calculations of vacancy formation energy in transition metals.

    PubMed

    Nandi, Prithwish Kumar; Valsakumar, M C; Chandra, Sharat; Sahu, H K; Sundar, C S

    2010-09-01

    We calculate properties like equilibrium lattice parameter, bulk modulus and monovacancy formation energy for nickel (Ni), iron (Fe) and chromium (Cr) using Kohn-Sham density functional theory (DFT). We compare the relative performance of local density approximation (LDA) and generalized gradient approximation (GGA) for predicting such physical properties for these metals. We also make a relative study between two different flavors of GGA exchange correlation functional, namely PW91 and PBE. These calculations show that there is a discrepancy between DFT calculations and experimental data. In order to understand this discrepancy in the calculation of vacancy formation energy, we introduce a correction for the surface intrinsic error corresponding to an exchange correlation functional using the scheme implemented by Mattsson et al (2006 Phys. Rev. B 73 195123) and compare the effectiveness of the correction scheme for Al and the 3d transition metals.

  15. Level density of a Fermi gas and integer partitions: A Gumbel-like finite-size correction

    SciTech Connect

    Roccia, Jerome; Leboeuf, Patricio

    2010-04-15

    We investigate the many-body level density of a gas of noninteracting fermions. We determine its behavior as a function of the temperature and the number of particles. As the temperature increases, and beyond the usual Sommerfeld expansion that describes the degenerate gas behavior, corrections due to a finite number of particles lead to Gumbel-like contributions. We discuss connections with the partition problem in number theory, extreme value statistics, and differences with respect to the Bose gas.

  16. Density functional theory study of indirect nuclear spin-spin coupling constants with spin-orbit corrections

    NASA Astrophysics Data System (ADS)

    Oprea, Corneliu I.; Rinkevicius, Zilvinas; Vahtras, Olav; Ågren, Hans; Ruud, Kenneth

    2005-07-01

    This work outlines the calculation of indirect nuclear spin-spin coupling constants with spin-orbit corrections using density functional response theory. The nonrelativistic indirect nuclear spin-spin couplings are evaluated using the linear response method, whereas the relativistic spin-orbit corrections are computed using quadratic response theory. The formalism is applied to the homologous systems H2X (X=O,S,Se,Te) and XH4 (X =C,Si,Ge,Sn,Pb) to calculate the indirect nuclear spin-spin coupling constants between the protons. The results confirm that spin-orbit corrections are important for compounds of the H2X series, for which the electronic structure allows for an efficient coupling between the nuclei mediated by the spin-orbit interaction, whereas in the case of the XH4 series the opposite situation is encountered and the spin-orbit corrections are negligible for all compounds of this series. In addition we analyze the performance of the density functional theory in the calculations of nonrelativistic indirect nuclear spin-spin coupling constants.

  17. Tidally distorted exoplanets: Density corrections for short-period hot-Jupiters based solely on observable parameters

    SciTech Connect

    Burton, J. R.; Watson, C. A.; Fitzsimmons, A.; Moulds, V.; Pollacco, D.; Wheatley, P. J.; Littlefair, S. P.

    2014-07-10

    The close proximity of short-period hot-Jupiters to their parent star means they are subject to extreme tidal forces. This has a profound effect on their structure and, as a result, density measurements that assume that the planet is spherical can be incorrect. We have simulated the tidally distorted surface for 34 known short-period hot-Jupiters, assuming surfaces of constant gravitational equipotential for the planet, and the resulting densities have been calculated based only on observed parameters of the exoplanet systems. Comparing these results to the density values, assuming the planets are spherical, shows that there is an appreciable change in the measured density for planets with very short periods (typically less than two days). For one of the shortest-period systems, WASP-19b, we determine a decrease in bulk density of 12% from the spherical case and, for the majority of systems in this study, this value is in the range of 1%-5%. On the other hand, we also find cases where the distortion is negligible (relative to the measurement errors on the planetary parameters) even in the cases of some very short period systems, depending on the mass ratio and planetary radius. For high-density gas planets requiring apparently anomalously large core masses, density corrections due to tidal deformation could become important for the shortest-period systems.

  18. Technical Note: Contrast solution density and cross section errors in inhomogeneity-corrected dose calculation for breast balloon brachytherapy

    SciTech Connect

    Kim, Leonard H.; Zhang Miao; Howell, Roger W.; Yue, Ning J.; Khan, Atif J.

    2013-01-15

    Purpose: Recent recommendations by the American Association of Physicists in Medicine Task Group 186 emphasize the importance of understanding material properties and their effect on inhomogeneity-corrected dose calculation for brachytherapy. Radiographic contrast is normally injected into breast brachytherapy balloons. In this study, the authors independently estimate properties of contrast solution that were expected to be incorrectly specified in a commercial brachytherapy dose calculation algorithm. Methods: The mass density and atomic weight fractions of a clinical formulation of radiographic contrast solution were determined using manufacturers' data. The mass density was verified through measurement and compared with the density obtained by the treatment planning system's CT calibration. The atomic weight fractions were used to determine the photon interaction cross section of the contrast solution for a commercial high-dose-rate (HDR) brachytherapy source and compared with that of muscle. Results: The density of contrast solution was 10% less than that obtained from the CT calibration. The cross section of the contrast solution for the HDR source was 1.2% greater than that of muscle. Both errors could be addressed by overriding the density of the contrast solution in the treatment planning system. Conclusions: The authors estimate the error in mass density and cross section parameters used by a commercial brachytherapy dose calculation algorithm for radiographic contrast used in a clinical breast brachytherapy practice. This approach is adaptable to other clinics seeking to evaluate dose calculation errors and determine appropriate density override values if desired.

  19. Technical note: contrast solution density and cross section errors in inhomogeneity-corrected dose calculation for breast balloon brachytherapy.

    PubMed

    Kim, Leonard H; Zhang, Miao; Howell, Roger W; Yue, Ning J; Khan, Atif J

    2013-01-01

    Recent recommendations by the American Association of Physicists in Medicine Task Group 186 emphasize the importance of understanding material properties and their effect on inhomogeneity-corrected dose calculation for brachytherapy. Radiographic contrast is normally injected into breast brachytherapy balloons. In this study, the authors independently estimate properties of contrast solution that were expected to be incorrectly specified in a commercial brachytherapy dose calculation algorithm. The mass density and atomic weight fractions of a clinical formulation of radiographic contrast solution were determined using manufacturers' data. The mass density was verified through measurement and compared with the density obtained by the treatment planning system's CT calibration. The atomic weight fractions were used to determine the photon interaction cross section of the contrast solution for a commercial high-dose-rate (HDR) brachytherapy source and compared with that of muscle. The density of contrast solution was 10% less than that obtained from the CT calibration. The cross section of the contrast solution for the HDR source was 1.2% greater than that of muscle. Both errors could be addressed by overriding the density of the contrast solution in the treatment planning system. The authors estimate the error in mass density and cross section parameters used by a commercial brachytherapy dose calculation algorithm for radiographic contrast used in a clinical breast brachytherapy practice. This approach is adaptable to other clinics seeking to evaluate dose calculation errors and determine appropriate density override values if desired.

  20. Techniques for correcting velocity and density fluctuations of ion beams in ion inducti on accelerators

    NASA Astrophysics Data System (ADS)

    Woo, K. M.; Yu, S. S.; Barnard, J. J.

    2013-06-01

    It is well known that the imperfection of pulse power sources that drive the linear induction accelerators can lead to time-varying fluctuation in the accelerating voltages, which in turn leads to longitudinal emittance growth. We show that this source of emittance growth is correctable, even in space-charge dominated beams with significant transients induced by space-charge waves. Two correction methods are proposed, and their efficacy in reducing longitudinal emittance is demonstrated with three-dimensional particle-in-cell simulations.

  1. Dynamical Correction to Linear Kohn-Sham Conductances from Static Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Kurth, S.; Stefanucci, G.

    2013-07-01

    For molecules weakly coupled to leads the exact linear Kohn-Sham (KS) conductance can be orders of magnitude larger than the true linear conductance due to the lack of dynamical exchange-correlation (xc) corrections. In this work we show how to incorporate dynamical effects in KS transport calculations. The only quantity needed is the static xc potential in the molecular junction. Our scheme provides a comprehensive description of Coulomb blockade without breaking the spin symmetry. This is explicitly demonstrated in single-wall nanotubes where the corrected conductance is in good agreement with experimental data whereas the KS conductance fails dramatically.

  2. Carrier Density Profiling of Ultra-Shallow Junction Layers Through Corrected C-V Plotting

    SciTech Connect

    Chen, James; Dimitrov, Dimitar; Dimitrova, Tatiana; Timans, Paul; Gelpey, Jeff; McCoy, Steve; Lerch, Wilfried; Paul, Silke; Bolze, Detlef

    2008-11-03

    The aim of this report is to present and justify a new approach for carrier density profiling in ultra-shallow junction (USJ) layer. This new approach is based on a capacitance measurement model, which takes series impedance, shunt resistance and the presence of a boron skin on the USJ layer into account. It allows us to extract the depletion layer capacitances in the USJ layer from C-V plotting more accurately and hence to obtain better carrier density profiles. Based on this new approach the carrier density profiles of different USJ layers with and without halo-style implants are obtained and discussed.

  3. High-density Lipoproteins and Apolipoprotein A-I: Potential New Players in the Prevention and Treatment of Lung Disease.

    PubMed

    Gordon, Elizabeth M; Figueroa, Debbie M; Barochia, Amisha V; Yao, Xianglan; Levine, Stewart J

    2016-01-01

    Apolipoprotein A-I (apoA-I) and high-density lipoproteins (HDL) mediate reverse cholesterol transport out of cells. Furthermore, HDL has additional protective functions, which include anti-oxidative, anti-inflammatory, anti-apoptotic, and vasoprotective effects. In contrast, HDL can become dysfunctional with a reduction in both cholesterol efflux and anti-inflammatory properties in the setting of disease or the acute phase response. These paradigms are increasingly being recognized to be active in the pulmonary system, where apoA-I and HDL have protective effects in normal lung health, as well as in a variety of disease states, including acute lung injury (ALI), asthma, chronic obstructive pulmonary disease, lung cancer, pulmonary arterial hypertension, pulmonary fibrosis, and viral pneumonia. Similar to observations in cardiovascular disease, however, HDL may become dysfunctional and contribute to disease pathogenesis in respiratory disorders. Furthermore, synthetic apoA-I mimetic peptides have been shown to have protective effects in animal models of ALI, asthma, pulmonary hypertension, and influenza pneumonia. These findings provide evidence to support the concept that apoA-I mimetic peptides might be developed into a new treatment that can either prevent or attenuate the manifestations of lung diseases, such as asthma. Thus, the lung is positioned to take a page from the cardiovascular disease playbook and utilize the protective properties of HDL and apoA-I as a novel therapeutic approach.

  4. High-density Lipoproteins and Apolipoprotein A-I: Potential New Players in the Prevention and Treatment of Lung Disease

    PubMed Central

    Gordon, Elizabeth M.; Figueroa, Debbie M.; Barochia, Amisha V.; Yao, Xianglan; Levine, Stewart J.

    2016-01-01

    Apolipoprotein A-I (apoA-I) and high-density lipoproteins (HDL) mediate reverse cholesterol transport out of cells. Furthermore, HDL has additional protective functions, which include anti-oxidative, anti-inflammatory, anti-apoptotic, and vasoprotective effects. In contrast, HDL can become dysfunctional with a reduction in both cholesterol efflux and anti-inflammatory properties in the setting of disease or the acute phase response. These paradigms are increasingly being recognized to be active in the pulmonary system, where apoA-I and HDL have protective effects in normal lung health, as well as in a variety of disease states, including acute lung injury (ALI), asthma, chronic obstructive pulmonary disease, lung cancer, pulmonary arterial hypertension, pulmonary fibrosis, and viral pneumonia. Similar to observations in cardiovascular disease, however, HDL may become dysfunctional and contribute to disease pathogenesis in respiratory disorders. Furthermore, synthetic apoA-I mimetic peptides have been shown to have protective effects in animal models of ALI, asthma, pulmonary hypertension, and influenza pneumonia. These findings provide evidence to support the concept that apoA-I mimetic peptides might be developed into a new treatment that can either prevent or attenuate the manifestations of lung diseases, such as asthma. Thus, the lung is positioned to take a page from the cardiovascular disease playbook and utilize the protective properties of HDL and apoA-I as a novel therapeutic approach. PMID:27708582

  5. Correction factors for the topside IRI electron density during the recent solar minimum derived from CHAMP and GRACE observations

    NASA Astrophysics Data System (ADS)

    Xiong, Chao; Luehr, Hermann; Liu, Yiwen; Bilitza, Dieter

    The International Reference Ionosphere (IRI) is an empirical model based on large collections of satellite and ground-based observations, and it is expected to give a reasonably accurate description of the ionosphere for quiet and moderate geomagnetic conditions. However, our comparisons of IRI predictions with CHAMP and GRACE in-situ electron density measurements during the recent unusually low and extended solar minimum (2008-2009) revealed significant discrepancies at 300-500 km altitudes. Based on nearly 10 years data from CHAMP and GRACE, we have used the data-to-model ratios to established correction factors for the IRI model. These correction factors vary with solar flux levels, local time and modified dip latitude. The results show that at the crest region of the Equatorial Ionization Anomaly (EIA) IRI overestimates the electron density around noon during lower solar activity periods, while it underestimates the electron density after sunset during higher solar activity periods. Around sunrise the IRI always overestimate the electron density in the low- and mid-latitude region irrespective of solar activity. We present functional relations that can be used to improve the representation of the topside ionosphere.

  6. Electron density profiles from ionograms - Underlying ionization corrections and their comparison with rocket results

    NASA Technical Reports Server (NTRS)

    Wright, J. W.; Paul, A. K.; Mechtly, E. A.

    1975-01-01

    Electron density profiles from nine daytime rocket flights at Wallops Island, Va., conducted at high and low levels of solar activity are compared with profiles calculated by inversion of ionograms obtained at the same times and location. Sources of error and uncertainty in the ionogram inversion are discussed, as are means for their amelioration. In most cases, agreement between the two kinds of measurement within a few percent in electron density and within a few percent of a scale height can be achieved.

  7. An algorithm for noise correction of dual-energy computed tomography material density images.

    PubMed

    Maia, Rafael Simon; Jacob, Christian; Hara, Amy K; Silva, Alvin C; Pavlicek, William; Ross, Mitchell J

    2015-01-01

    Dual-energy computed tomography (DECT) images can undergo a two-material decomposition process which results in two images containing material density information. Material density images obtained by that process result in images with increased pixel noise. Noise reduction in those images is desirable in order to improve image quality. A noise reduction algorithm for material density images was developed and tested. A three-level wavelet approach combined with the application of an anisotropic diffusion filter was used. During each level, the resulting noise maps are further processed, until the original resolution is reached and the final noise maps obtained. Our method works in image space and, therefore, can be applied to any type of material density images obtained from any DECT vendor. A quantitative evaluation of the noise-reduced images using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and 2D noise power spectrum was done to quantify the improvements. The noise reduction algorithm was applied to a set of images resulting in images with higher SNR and CNR than the raw density images obtained by the decomposition process. The average improvement in terms of SNR gain was about 49 % while CNR gain was about 52 %. The difference between the raw and filtered regions of interest mean values was far from reaching statistical significance (minimum [Formula: see text], average [Formula: see text]). We have demonstrated through a series of quantitative analyses that our novel noise reduction algorithm improves the image quality of DECT material density images.

  8. Correction of steel casing effect for density log using numerical and experimental methods in the slim borehole

    SciTech Connect

    Hwang, Seho; Shin, Jehyun; Kim, Jongman; Won, Byeongho

    2015-03-10

    Density log is widely applied for a variety of fields such as the petroleum exploration, mineral exploration, and geotechnical survey. The logging condition of density log is normally open holes but there are frequently cased boreholes. The primary calibration curve by slim hole logging manufacturer is normally the calibration curves for the variation of borehole diameter. In this study, we have performed the correction of steel casing effects using numerical and experimental methods. We have performed numerical modeling using the Monte Carlo N-Particle (MCNP) code based on Monte Carlo method, and field experimental method from open and cased hole log. In this study, we used the FDGS (Formation Density Gamma Sonde) for slim borehole with a 100 mCi 137Cs source, three inch borehole and steel casing. The casing effect between numerical and experimental method is well matched.

  9. Lung function reductions associated with motor vehicle density in chronic obstructive pulmonary disease: a cross-sectional study.

    PubMed

    Nitschke, Monika; Appleton, Sarah L; Li, Qiaoyu; Tucker, Graeme R; Shah, Pushan; Bi, Peng; Pisaniello, Dino L; Adams, Robert J

    2016-10-24

    Motor vehicle-related air pollution can potentially impair lung function. The effect of pollution in people with compromised pulmonary function such as in COPD has not been previously investigated. To examine the association of lung function with motor vehicle density in people with spirometrically determined COPD in a cross-sectional study. In 2004-06, The North West Adelaide Health Study (NWAHS), a biomedical cohort of adults assessed pre and post-bronchodilator spirometry (n = 3,103). Traffic density, obtained from the motor vehicle inventory maintained by the South Australian Environment Protection Authority, was expressed as the daily numbers of vehicles travelling within a 200 m diameter zone around participants' geocoded residences. In subjects with COPD (FEV1/FVC <0.7, n = 221, 7.1 %), increasing daily vehicle density was associated with statistically significant decreases in lung function parameters after adjustment for smoking and socio-economic variables. Mean (95 % CI) post-bronchodilator % predicted FEV1 was 81 % (76-87) in the low (≤7179/day) compared with 71 % (67-75) in the high (≥15,270/day) vehicle exposure group (p < 0.05). Linear regression analysis in all subjects with COPD showed significant decrements in post-bronchodilator FEV1/FVC ratio and % predicted FEV1 of 0.03 and 0.05 % respectively per daily increase in 1000 vehicles. In men with COPD (n = 150), the corresponding reductions were 0.03 and 0.06 %. Smaller, non-significant decrements were seen in females. No difference was seen in those without COPD. Vehicle traffic density was associated with significant reductions in lung function in people with COPD. Urban planning should consider the health impacts for those with pre-existing respiratory conditions.

  10. SU-E-J-173: Evaluation of Deformable Registration for Correcting Respiratory Motion in 4DCT Lung Images

    SciTech Connect

    Larrue, A; Kaster, F; Kadir, T; Gooding, M; Elmpt, W van

    2014-06-01

    Purpose: Deformable Image Registration (DIR) is gaining wider clinical acceptance in radiation oncology. The aim of this work is to characterise a DIR algorithm on publically available 4DCT lung images, such that comparison can be performed against other algorithms. We propose an evaluation method of registration accuracy that takes into account the initial misregistration of the datasets. Methods: The “DIR Validation dataset” ( http://www.creatis.insa-lyon.fr/rio/dir{sub v}alidation{sub d}ata ) provides benchmark data for evaluating 3D CT registration algorithms. It consists of six 4DCT lung datasets (1x1x2mm resolution) with 100 landmarks identified on the end-exhalation and end-inhalation phases. Images were registered to end-inhalation using proprietary form of optical flow in commercial software (Mirada RTx, Mirada Medical, UK). Target registration error was measured before and after DIR, referred to as Initial Registration Error (IRE) and Final Registration Error (FRE). Results: The mean FRE over all landmarks was 1.37±1.81mm. FRE increased with IRE. Mean FRE of 0.86, 0.86, 1.53, 3.38, 4.45, 7.58mm was observed for IRE in the ranges 0–5, 5–10, 10–15, 15–20, 20–25, >25 mm. Higher FRE was observed at the inferior lung, where IRE was greater. Out-of-plane motion contributed more to IRE, and therefore to FRE. Maximum FRE of 20.6mm was observed for IRE of 32.1mm, located at the posterior of the middle lobe for dataset 2. Sub-voxel registration accuracy was achieved for up to 10mm IRE, and increased linearly at 0.3mm FRE/mm IRE thereafter. Conclusion: Publicly available clinical datasets enable algorithms to be compared objectively between publications. However, only reporting average TRE after registration can be misleading as the ability of an algorithm to correct for displacements varies with the IRE or position within the patient. Consequently, algorithms should be characterized using the entire range of initial displacements. For the algorithm

  11. High density bit transition requirements versus the effects on BCH error correcting code. [bit synchronization

    NASA Technical Reports Server (NTRS)

    Ingels, F. M.; Schoggen, W. O.

    1982-01-01

    The design to achieve the required bit transition density for the Space Shuttle high rate multiplexes (HRM) data stream of the Space Laboratory Vehicle is reviewed. It contained a recommended circuit approach, specified the pseudo random (PN) sequence to be used and detailed the properties of the sequence. Calculations showing the probability of failing to meet the required transition density were included. A computer simulation of the data stream and PN cover sequence was provided. All worst case situations were simulated and the bit transition density exceeded that required. The Preliminary Design Review and the critical Design Review are documented. The Cover Sequence Generator (CSG) Encoder/Decoder design was constructed and demonstrated. The demonstrations were successful. All HRM and HRDM units incorporate the CSG encoder or CSG decoder as appropriate.

  12. Esmolol Corrects Severe Hypoxemia in Patients with Femoro-Femoral Venoarterial Extracorporeal Life Support for Lung Transplantation

    PubMed Central

    Ghalayini, Mohamed; Brun, Pierre-Yves; Augustin, Pascal; Guivarch, Elise; Dilly, Marie Pierre; Provenchere, Sophie; Mordant, Pierre; Castier, Yves; Montravers, Philippe; Longrois, Dan

    2016-01-01

    Abstract: Competitive flows syndrome result in severe regional hypoxemia when the deoxygenated flow from the native left ventricle (LV) competes with oxygenated flow from extracorporeal life support (ECLS) pump with potentially severe consequences for the cerebral and coronary circulations. Fast correction of hypoxemia could be obtained by decreasing native LV flow by infusion of a short-acting beta-blocker (esmolol). Our purpose was to retrospectively review the efficacy of esmolol in this situation and hypothesize on the potential mechanisms of action and the associated risks. This is a retrospective analysis of five clinical cases, who underwent lung transplantation and a femoro-femoral venoarterial (VA) ECLS. The patients presented severe hypoxemia (SpO2 < 85%) measured through photoplethysmography on a right hand finger. From the patients' medical records and anesthesia flowcharts, hemodynamic, right heart catheterization, echocardiography variables, and arterial blood gas results were noted before and after injection of esmolol. Mechanical ventilation and VA ECLS function variables were optimized and unchanged before and after esmolol injection. All patients had terminal respiratory failure with pulmonary hypertension and conserved LV systolic function. Immediately following esmolol injection (1.3 ± .7 mg/kg; mean ± 1 SD), SpO2 increased from 73% ± 12 to 95% ± 6; blood to arterial partial pressure in CO2 (PaCO2) decreased from 52 ± 18 to 35 ± 7 mmHg systolic pulmonary artery pressure decreased from 61 ± 8 to 50 ± 12 mmHg; the pulmonary artery oxygen saturation (SvO2); increased from 51% ± 24 to 77% ± 12; systemic arterial pressure or catecholamine requirements were unchanged. In conclusion, these results suggest that injection of esmolol allowed rapid correction of regional hypoxemia occurring during lung transplantation despite femoro-femoral VA ECLS. The mechanism is probably a decreased cardiac output of the native LV due to esmolol

  13. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

    NASA Astrophysics Data System (ADS)

    Lutsker, V.; Aradi, B.; Niehaus, T. A.

    2015-11-01

    Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

  14. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

    SciTech Connect

    Lutsker, V.; Niehaus, T. A.; Aradi, B.

    2015-11-14

    Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

  15. Numerical Study of Nonperturbative Corrections to the Chiral Separation Effect in Quenched Finite-Density QCD

    NASA Astrophysics Data System (ADS)

    Puhr, Matthias; Buividovich, P. V.

    2017-05-01

    We demonstrate the nonrenormalization of the chiral separation effect (CSE) in quenched finite-density QCD in both confinement and deconfinement phases using a recently developed numerical method which allows us, for the first time, to address the transport properties of exactly chiral, dense lattice fermions. This finding suggests that CSE can be used to fix renormalization constants for axial current density. Explaining the suppression of the CSE which we observe for topologically nontrivial gauge field configurations on small lattices, we also argue that CSE vanishes for self-dual non-Abelian fields inside instanton cores.

  16. Numerical Study of Nonperturbative Corrections to the Chiral Separation Effect in Quenched Finite-Density QCD.

    PubMed

    Puhr, Matthias; Buividovich, P V

    2017-05-12

    We demonstrate the nonrenormalization of the chiral separation effect (CSE) in quenched finite-density QCD in both confinement and deconfinement phases using a recently developed numerical method which allows us, for the first time, to address the transport properties of exactly chiral, dense lattice fermions. This finding suggests that CSE can be used to fix renormalization constants for axial current density. Explaining the suppression of the CSE which we observe for topologically nontrivial gauge field configurations on small lattices, we also argue that CSE vanishes for self-dual non-Abelian fields inside instanton cores.

  17. Electron intracule densities with correct electron coalescence cusps from Hiller-Sucher-Feinberg-type identities

    NASA Astrophysics Data System (ADS)

    Cioslowski, Jerzy; Stefanov, Boris B.; Tan, Agnes; Umrigar, C. J.

    1995-10-01

    Identities for the electron intracule density I(R) in atoms and molecules are derived within the Hiller-Sucher-Feinberg (HSF) formalism. It is proven that, when applied to arbitrary (exact or approximate) electronic wave functions, these identities produce intracule densities that satisfy a modified condition for the electron coalescence cusp. A corollary of this proof provides a new, simplified derivation of the cusp condition for the exact I(R). An expression for the Hartree-Fock approximation to the HSF electron intracule density that contains only two- and three-electron terms is obtained and its properties are analyzed. A simple scaling of the three-electron contributions in this expression assures integrability of the approximate I(R) and improves its overall accuracy. Numerical tests carried out for the H-, He, Li+, Be2+, Li, and Be systems demonstrate that the application of the scaled HSF-type identity to Hartree-Fock wave functions affords dramatic improvements in the short-range behavior of the electron intracule density.

  18. A study of high density bit transition requirements versus the effects on BCH error correcting coding

    NASA Technical Reports Server (NTRS)

    Ingels, F.; Schoggen, W. O.

    1981-01-01

    The various methods of high bit transition density encoding are presented, their relative performance is compared in so far as error propagation characteristics, transition properties and system constraints are concerned. A computer simulation of the system using the specific PN code recommended, is included.

  19. Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory.

    PubMed

    Baer, Marcel D; Mundy, Christopher J; McGrath, Matthew J; Kuo, I-F Will; Siepmann, J Ilja; Tobias, Douglas J

    2011-09-28

    First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.

  20. Hounsfield Unit inaccuracy in computed tomography lesion size and density, diagnostic quality vs attenuation correction

    NASA Astrophysics Data System (ADS)

    Szczepura, Katy; Thompson, John; Manning, David

    2017-03-01

    In computed tomography the Hounsfield Units (HU) are used as an indicator of the tissue type based on the linear attenuation coefficients of the tissue. HU accuracy is essential when this metric is used in any form to support diagnosis. In hybrid imaging, such as SPECT/CT and PET/CT, the information is used for attenuation correction (AC) of the emission images. This work investigates the HU accuracy of nodules of known size and HU, comparing diagnostic quality (DQ) images with images used for AC.

  1. Human lung density is not altered following normoxic and hypoxic moderate-intensity exercise: implications for transient edema.

    PubMed

    Hodges, Alastair N H; Sheel, A William; Mayo, John R; McKenzie, Donald C

    2007-07-01

    The purpose of this study was to examine the effects of exercise on extravascular lung water as it may relate to pulmonary gas exchange. Ten male humans underwent measures of maximal oxygen uptake (Vo2 max) in two conditions: normoxia (N) and normobaric hypoxia of 15% O2 (H). Lung density was measured by quantified MRI before and 48.0 +/- 7.4 and 100.7 +/- 15.1 min following 60 min of cycling exercise in N (intensity = 61.6 +/- 9.5% Vo2 max) and 55.5 +/- 9.8 and 104.3 +/- 9.1 min following 60 min cycling exercise in H (intensity = 65.4 +/- 7.1% hypoxic Vo2 max), where Vo2 max = 65.0 +/- 7.5 ml x kg(-1) x min(-1) (N) and 54.1 +/- 7.0 ml x kg(-1) x min(-1) (H). Two subjects demonstrated mild exercise-induced arterial hypoxemia (EIAH) [minimum arterial oxygen saturation (SaO2 min) = 94.5% and 93.8%], and seven subjects demonstrated moderate EIAH (SaO2 min = 91.4 +/- 1.1%) as measured noninvasively during the Vo2 max test in N. Mean lung densities, measured once preexercise and twice postexercise, were 0.177 +/- 0.019, 0.181 +/- 0.019, and 0.173 +/- 0.019 g/ml (N) and 0.178 +/- 0.021, 0.174 +/- 0.022, and 0.176 +/- 0.019 g/ml (H), respectively. No significant differences (P > 0.05) were found in lung density following exercise in either condition or between conditions. Transient interstitial pulmonary edema did not occur following sustained steady-state cycling exercise in N or H, indicating that transient edema does not result from pulmonary capillary leakage during sustained submaximal exercise.

  2. Importance of far-field topographic and isostatic corrections for regional density modelling

    NASA Astrophysics Data System (ADS)

    Szwillus, Wolfgang; Ebbing, Jörg; Holzrichter, Nils

    2016-10-01

    The long-wavelength gravity field contains information about processes in the sublithospheric mantle. As satellite-derived gravity models now provide the long to medium-wavelength gravity field at unprecedented accuracy, techniques used to process gravity data need to be updated. We show that when determining these long-wavelengths, the treatment of topographic-isostatic effect (TIE) and isostatic effects (IE) is a likely source of error. We constructed a global isostatic model and calculated global TIE and IE. These calculations were done for ground stations as well as stations at satellite height. We considered both gravity and gravity gradients. Using these results, we determined how much of the gravity signal comes from distant sources. We find that a significant long-wavelength bias is introduced if far-field effects on the topographic effect are neglected. However, due to isostatic compensation far-field effects of the topographic effect are to a large degree compensated by the far-field IE. This means that far-field effects can be reduced effectively by always considering topographic masses together with their compensating isostatic masses. We show that to correctly represent the ultra-long wavelengths, a global background model should be used. This is demonstrated both globally and for a continental-scale case area in North America. In the case of regional modelling, where the ultra-long wavelengths are not of prime importance, gravity gradients can be used to help minimize correction errors caused by far-field effects.

  3. van der Waals forces in density functional theory: Perturbational long-range electron-interaction corrections

    SciTech Connect

    Angyan, Janos G.; Gerber, Iann C.; Savin, Andreas; Toulouse, Julien

    2005-07-15

    Long-range exchange and correlation effects, responsible for the failure of currently used approximate density functionals in describing van der Waals forces, are taken into account explicitly after a separation of the electron-electron interaction in the Hamiltonian into short- and long-range components. We propose a 'range-separated hybrid' functional based on a local density approximation for the short-range exchange-correlation energy, combined with a long-range exact exchange energy. Long-range correlation effects are added by a second-order perturbational treatment. The resulting scheme is general and is particularly well adapted to describe van der Waals complexes, such as rare gas dimers.

  4. The performance of functional methods for correcting non-Gaussian measurement error within Poisson regression: corrected excess risk of lung cancer mortality in relation to radon exposure among French uranium miners.

    PubMed

    Allodji, Rodrigue S; Thiébaut, Anne C M; Leuraud, Klervi; Rage, Estelle; Henry, Stéphane; Laurier, Dominique; Bénichou, Jacques

    2012-12-30

    A broad variety of methods for measurement error (ME) correction have been developed, but these methods have rarely been applied possibly because their ability to correct ME is poorly understood. We carried out a simulation study to assess the performance of three error-correction methods: two variants of regression calibration (the substitution method and the estimation calibration method) and the simulation extrapolation (SIMEX) method. Features of the simulated cohorts were borrowed from the French Uranium Miners' Cohort in which exposure to radon had been documented from 1946 to 1999. In the absence of ME correction, we observed a severe attenuation of the true effect of radon exposure, with a negative relative bias of the order of 60% on the excess relative risk of lung cancer death. In the main scenario considered, that is, when ME characteristics previously determined as most plausible from the French Uranium Miners' Cohort were used both to generate exposure data and to correct for ME at the analysis stage, all three error-correction methods showed a noticeable but partial reduction of the attenuation bias, with a slight advantage for the SIMEX method. However, the performance of the three correction methods highly depended on the accurate determination of the characteristics of ME. In particular, we encountered severe overestimation in some scenarios with the SIMEX method, and we observed lack of correction with the three methods in some other scenarios. For illustration, we also applied and compared the proposed methods on the real data set from the French Uranium Miners' Cohort study.

  5. High pulsed current density β-Ga2O3 MOSFETs verified by an analytical model corrected for interface charge

    NASA Astrophysics Data System (ADS)

    Moser, Neil A.; McCandless, Jonathan P.; Crespo, Antonio; Leedy, Kevin D.; Green, Andrew J.; Heller, Eric R.; Chabak, Kelson D.; Peixoto, Nathalia; Jessen, Gregg H.

    2017-04-01

    We report on Sn-doped β-Ga2O3 MOSFETs grown by molecular beam epitaxy with as-grown carrier concentrations from 0.7 × 1018 to 1.6 × 1018 cm-3 and a fixed channel thickness of 200 nm. A pulsed current density of >450 mA/mm was achieved on the sample with the lowest sheet resistance and a gate length of 2 μm. Our results are explained using a simple analytical model with a measured gate voltage correction factor based on interface charges that accurately predict the electrical performance for all doping variations.

  6. Geometrical correction for the inter- and intramolecular basis set superposition error in periodic density functional theory calculations.

    PubMed

    Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan

    2013-09-26

    We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.

  7. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

    PubMed Central

    van de Streek, Jacco; Neumann, Marcus A.

    2014-01-01

    In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

  8. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

    PubMed

    van de Streek, Jacco; Neumann, Marcus A

    2014-12-01

    In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

  9. Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method.

    PubMed

    Kranz, Julian J; Elstner, Marcus; Aradi, Bálint; Frauenheim, Thomas; Lutsker, Vitalij; Garcia, Adriel Dominguez; Niehaus, Thomas A

    2017-03-21

    We present a consistent linear response formulation of the density functional based tight-binding method for long-range corrected exchange-correlation functionals (LC-DFTB). Besides a detailed account of derivation and implementation of the method, we also test the new scheme on a variety of systems considered to be problematic for conventional local/semilocal time-dependent density functional theory (TD-DFT). To this class belong the optical properties of polyacenes and nucleobases, as well as charge transfer excited states in molecular dimers. We find that the approximate LC-DFTB method exhibits the same general trends and similar accuracy as range-separated DFT methods at significantly reduced computational cost. The scheme should be especially useful in the determination of the electronic excited states of very large molecules, for which conventional TD-DFT is supposed to fail due to a multitude of artificial low energy states.

  10. First Density Correction to the Transport Coefficients for a Square Well Gas: Temperature Dependence and Bound State Effects

    NASA Astrophysics Data System (ADS)

    Garland, Gregory Ellis

    The temperature dependence of transport properties of a moderately dense square well gas is studied in order to understand the effects of attractive forces (particularly bound states). The quantum cluster expansions of the Green -Kubo time correlation functions for the thermal conductivity, shear viscosity, and self-diffusion coefficients are given, and exact expressions to zeroth (Boltzmann level) and first order in the density are obtained. Specializing to Boltzmann statistics and the classical square well potential allows calculations of the kinetic potential parts of the first density correction; the important contributions to the remaining triple collision parts are discussed. Good agreement with molecular dynamics results is found; quantitative difference from real fluids are observed, however. Possible reasons for the discrepancies are discussed. A brief description of the ultility and limitations of the hard sphere model is given for comparison. The dynamics structure factor is calculated for a dense fluid of hard spheres and compared with recent neutron scattering data for Krypton.

  11. Band-gap corrected density functional theory calculations for InAs/GaSb type II superlattices

    SciTech Connect

    Wang, Jianwei; Zhang, Yong

    2014-12-07

    We performed pseudopotential based density functional theory (DFT) calculations for GaSb/InAs type II superlattices (T2SLs), with bandgap errors from the local density approximation mitigated by applying an empirical method to correct the bulk bandgaps. Specifically, this work (1) compared the calculated bandgaps with experimental data and non-self-consistent atomistic methods; (2) calculated the T2SL band structures with varying structural parameters; (3) investigated the interfacial effects associated with the no-common-atom heterostructure; and (4) studied the strain effect due to lattice mismatch between the two components. This work demonstrates the feasibility of applying the DFT method to more exotic heterostructures and defect problems related to this material system.

  12. Analytic derivatives for perturbatively corrected "double hybrid" density functionals: theory, implementation, and applications.

    PubMed

    Neese, Frank; Schwabe, Tobias; Grimme, Stefan

    2007-03-28

    A recently proposed new family of density functionals [S. Grimme, J. Chem. Phys. 124, 34108 (2006)] adds a fraction of nonlocal correlation as a new ingredient to density functional theory (DFT). This fractional correlation energy is calculated at the level of second-order many-body perturbation theory (PT2) and replaces some of the semilocal DFT correlation of standard hybrid DFT methods. The new "double hybrid" functionals (termed, e.g., B2-PLYP) contain only two empirical parameters that have been adjusted in thermochemical calculations on parts of the G2/3 benchmark set. The methods have provided the lowest errors ever obtained by any DFT method for the full G3 set of molecules. In this work, the applicability of the new functionals is extended to the exploration of potential energy surfaces with analytic gradients. The theory of the analytic gradient largely follows the standard theory of PT2 gradients with some additional subtleties due to the presence of the exchange-correlation terms in the self-consistent field operator. An implementation is reported for closed-shell as well as spin-unrestricted reference determinants. Furthermore, the implementation includes external point charge fields and also accommodates continuum solvation models at the level of the conductor like screening model. The density fitting resolution of the identity (RI) approximation can be applied to the evaluation of the PT2 part with large gains in computational efficiency. For systems with approximately 500-600 basis functions the evaluation of the double hybrid gradient is approximately four times more expensive than the calculation of the standard hybrid DFT gradient. Extensive test calculations are provided for main group elements and transition metal containing species. The results reveal that the B2-PLYP functional provides excellent molecular geometries that are superior compared to those from standard DFT and MP2.

  13. A study of high density bit transition requirements versus the effects on BCH error correcting coding

    NASA Technical Reports Server (NTRS)

    Ingels, F.; Schoggen, W. O.

    1981-01-01

    Several methods for increasing bit transition densities in a data stream are summarized, discussed in detail, and compared against constraints imposed by the 2 MHz data link of the space shuttle high rate multiplexer unit. These methods include use of alternate pulse code modulation waveforms, data stream modification by insertion, alternate bit inversion, differential encoding, error encoding, and use of bit scramblers. The psuedo-random cover sequence generator was chosen for application to the 2 MHz data link of the space shuttle high rate multiplexer unit. This method is fully analyzed and a design implementation proposed.

  14. Correction of lung inflammation in a F508del CFTR murine cystic fibrosis model by the sphingosine-1-phosphate lyase inhibitor LX2931.

    PubMed

    Veltman, Mieke; Stolarczyk, Marta; Radzioch, Danuta; Wojewodka, Gabriella; De Sanctis, Juan B; Dik, Willem A; Dzyubachyk, Oleh; Oravecz, Tamas; de Kleer, Ismé; Scholte, Bob J

    2016-11-01

    Progressive lung disease with early onset is the main cause of mortality and morbidity in cystic fibrosis patients. Here we report a reduction of sphingosine-1-phosphate (S1P) in the lung of unchallenged Cftr(tm1EUR) F508del CFTR mutant mice. This correlates with enhanced infiltration by inducible nitric oxide synthase (iNOS)-expressing granulocytes, B cells, and T cells. Furthermore, the ratio of macrophage-derived dendritic cells (MoDC) to conventional dendritic cells (cDC) is higher in mutant mouse lung, consistent with unprovoked inflammation. Oral application of a S1P lyase inhibitor (LX2931) increases S1P levels in mutant mouse tissues. This normalizes the lung MoDC/cDC ratio and reduces B and T cell counts. Lung granulocytes are enhanced, but iNOS expression is reduced in this population. Although lung LyC6+ monocytes are enhanced by LX2931, they apparently do not differentiate to MoDC and macrophages. After challenge with bacterial toxins (LPS-fMLP) we observe enhanced levels of proinflammatory cytokines TNF-α, KC, IFNγ, and IL-12 and the inducible mucin MUC5AC in mutant mouse lung, evidence of deficient resolution of inflammation. LX2931 does not prevent transient inflammation or goblet cell hyperplasia after challenge, but it reduces MUC5AC and proinflammatory cytokine levels toward normal values. We conclude that lung pathology in homozygous mice expressing murine F508del CFTR, which represents the most frequent mutation in CF patients, is characterized by abnormal behavior of infiltrating myeloid cells and delayed resolution of induced inflammation. This phenotype can be partially corrected by a S1P lyase inhibitor, providing a rationale for therapeutic targeting of the S1P signaling pathway in CF patients. Copyright © 2016 the American Physiological Society.

  15. Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters.

    PubMed

    Rapacioli, Mathias; Spiegelman, Fernand; Talbi, Dahbia; Mineva, Tzonka; Goursot, Annick; Heine, Thomas; Seifert, Gotthard

    2009-06-28

    The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

  16. Evaluation of dispersion-corrected density functional theory (B3LYP-DCP) for compounds of biochemical interest.

    PubMed

    Lill, Sten O Nilsson

    2010-09-01

    An evaluation of a dispersion-corrected density functional theory method (B3LYP-DCP) [I.D. Mackie, G.A. DiLabio, Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections, J. Phys. Chem. A 112 (2008) 10968-10976] for three systems of biochemical interest is presented. Firstly, structures and energies of isomers of the tripeptide Phe-Gly-Phe have been compared with CCSD(T)/CBS//RI-MP2/cc-pVTZ literature values. In the system aromatic interactions compete with XH-pi (X=C, N) interactions and hydrogen bonds which makes it a reliable model for proteins. The resulting mean absolute deviation between B3LYP-DCP and CCSD(T)/CBS relative energies is found to be 0.50 kcal mol(-1). Secondly, a phenylalanine derivative featuring a CH-pi interaction has been investigated. A comparison between the optimized geometry and X-ray crystal data shows that B3LYP-DCP accurately predicts the interaction between the two aromatic rings. Thirdly, the dipeptide Ac-Phe-Phe-NH(2) which contains an edge-to-face interaction between two aromatic rings has been studied. The study demonstrates the general applicability of the B3LYP-DCP method on systems which features interactions typically present in biochemical compounds.

  17. Innovative Troxler-free measurement of macular pigment and lens density with correction of the former for the aging lens.

    PubMed

    Bone, Richard A; Mukherjee, Anirbaan

    2013-10-01

    Simplified measurement of macular pigment optical density (MPOD) is important because of the ocular health benefits that are attributed to these retinal carotenoids. Here, we describe a novel instrument designed for this purpose, based on heterochromatic flicker photometry (HFP), which removes a number of difficulties that subjects often experience with traditional HFP. The instrument generates 1.5- and 15-deg diameter, centrally viewed stimuli that alternate between blue and green colors generated by light emitting diodes (LED). The 15 deg stimulus replaces the small, eccentrically viewed stimulus used in traditional HFP. Subjects adjust the blue LED intensity until flicker is eliminated in the case of the 1.5 deg stimulus and eliminated around the periphery in the case of the 15 deg stimulus. A microprocessor computes the subject's MPOD, in addition to the lens OD, and uses the latter to correct the MPOD. Good repeatability was confirmed through test-retest measurements on 52 subjects. The overwhelming majority of them stated that they found the test easy. The importance of the lens correction on MPOD measurements was confirmed in a simulation study. The study showed that, without the correction, MPOD would show an apparent age-related decline in a population for whom there was no real age dependence.

  18. Integrated stereological and biochemical studies on hepatocytic membranes. II. Correction of section thickness effect on volume and surface density estimates.

    PubMed

    Weibel, E R; Paumgartner, D

    1978-05-01

    The basic stereological formulas for estimating volume (Vv) and surface (Sv) densities are strictly valid only for true infinitely thin sections; the use of "ultrathin" sections of finite thickness T introduces systematic errors, mostly in the sense of overestimation of the parameters. These errors depend on the size and shape of the structural elements and on T. Correction factors for this effect of T are derived by considering model structures that simulate the shape and arrangement of subcellular organelles: (a) spherical vesicles, (b) disks as models for rough endoplasmic reticulum (RER) cisternae, (c) cylindrical tublules as models for smooth endoplasmic reticulum (SER) tubules, microvilli, etc. For vesicles, a model of discrete convex spherical particles is assumed; the correction factors consider loss of caps due to grazing sections and size distribution of the vesicles. The disk and tubule models are used in connection with the new integral geometric formulas of R.E. Miles which consider random aggregates of "inter-penetrating" particles so that the resultant structure is non-convex and thus approximates in nature the networks characteristic of endoplasmic reticulum (ER). Some practical examples relative to liver cells show that the errors due to section thickness may be of the order of 20-40% or more. Computation formulas as well as graphs are given for the determination of the correction factors for Vv and Sv.

  19. Incorporating Quantitative Single Photon Emission Computed Tomography into Radiation Therapy Treatment Planning for Lung Cancer: Impact of Attenuation and Scatter Correction on the Single Photon Emission Computed Tomography-Weighted Mean Dose and Functional Lung Segmentation

    SciTech Connect

    Yin Lingshu; Shcherbinin, Sergey; Celler, Anna

    2010-10-01

    Purpose: To assess the impact of attenuation and scatter corrections on the calculation of single photon emission computed tomography (SPECT)-weighted mean dose (SWMD) and functional volume segmentation as applied to radiation therapy treatment planning for lung cancer. Methods and Materials: Nine patients with lung cancer underwent a SPECT lung perfusion scan. For each scan, four image sets were reconstructed using the ordered subsets expectation maximization method with attenuation and scatter corrections ranging from none to a most comprehensive combination of attenuation corrections and direct scatter modeling. Functional volumes were segmented in each reconstructed image using 10%, 20%, ..., 90% of maximum SPECT intensity as a threshold. Systematic effects of SPECT reconstruction methods on treatment planning using functional volume were studied by calculating size and spatial agreements of functional volumes, and V{sub 20} for functional volume from actual treatment plans. The SWMD was calculated for radiation beams with a variety of possible gantry angles and field sizes. Results: Functional volume segmentation is sensitive to the particular method of SPECT reconstruction used. Large variations in functional volumes, as high as >50%, were observed in SPECT images reconstructed with different attenuation/scatter corrections. However, SWMD was less sensitive to the type of scatter corrections. SWMD was consistent within 2% for all reconstructions as long as computed tomography-based attenuation correction was used. Conclusion: When using perfusion SPECT images during treatment planning optimization/evaluation, the SWMD may be the preferred figure of merit, as it is less affected by reconstruction technique, compared with threshold-based functional volume segmentation.

  20. Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase.

    PubMed

    Grimme, Stefan; Steinmetz, Marc

    2013-10-14

    A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.

  1. Traumatic tracheal diverticulum corrected with resection and anastomosis during one-lung ventilation and total intravenous anesthesia in a cat.

    PubMed

    Sayre, Rebecca S; Lepiz, Mauricio; Wall, Corey; Thieman-Mankin, Kelley; Dobbin, Jennifer

    2016-11-01

    This report describes the clinical findings and diagnostic images of a traumatic intrathoracic tracheal avulsion with a tracheal diverticulum in a cat. Furthermore, a complete description of the tracheal resection and anastomosis using one-lung ventilation (OLV) with total and partial intravenous anesthesia is made. A 3-year-old neutered male domestic shorthair cat weighing 6.8 kg was presented to the University Teaching Hospital for evaluation of increased respiratory noise 3 months following unknown trauma. Approximately 12 weeks prior to presentation, the cat had been seen by the primary care veterinarian for respiratory distress. At that time, the cat had undergone a tracheal ballooning procedure for a distal tracheal stricture diagnosed by tracheoscopy. The tracheal ballooning had provided only temporary relief. At presentation to our institution, the cat had increased respiratory effort with harsh upper airway noise auscultated during thoracic examination. The remainder of the physical examination was normal. Diagnostics included a tracheoscopy and a thoracic computed tomographic examination. The cat was diagnosed with tracheal avulsion, pseudotrachea with a tracheal diverticulum, and stenosis of the avulsed tracheal ends. Surgical correction of the tracheal stricture via a thoracotomy was performed using OLV with total and partial intravenous anesthesia. The cat recovered uneventfully and at last follow-up was active and doing well. This case report describes OLV using standard anesthesia equipment that is available at most private practices. Furthermore, this case describes the computed tomographic images of the intrathoracic tracheal avulsion and offers a positive outcome for tracheal resection and anastomosis. © Veterinary Emergency and Critical Care Society 2015.

  2. A correction for the Hartree-Fock density of states for jellium without screening

    SciTech Connect

    Blair, Alexander I.; Kroukis, Aristeidis; Gidopoulos, Nikitas I.

    2015-02-28

    We revisit the Hartree-Fock (HF) calculation for the uniform electron gas, or jellium model, whose predictions—divergent derivative of the energy dispersion relation and vanishing density of states (DOS) at the Fermi level—are in qualitative disagreement with experimental evidence for simple metals. Currently, this qualitative failure is attributed to the lack of screening in the HF equations. Employing Slater’s hyper-Hartree-Fock (HHF) equations, derived variationally, to study the ground state and the excited states of jellium, we find that the divergent derivative of the energy dispersion relation and the zero in the DOS are still present, but shifted from the Fermi wavevector and energy of jellium to the boundary between the set of variationally optimised and unoptimised HHF orbitals. The location of this boundary is not fixed, but it can be chosen to lie at arbitrarily high values of wavevector and energy, well clear from the Fermi level of jellium. We conclude that, rather than the lack of screening in the HF equations, the well-known qualitative failure of the ground-state HF approximation is an artifact of its nonlocal exchange operator. Other similar artifacts of the HF nonlocal exchange operator, not associated with the lack of electronic correlation, are known in the literature.

  3. Monte Carlo dose calculation in presence of low-density media: Application to lung SBRT treated during DIBH.

    PubMed

    Beilla, S; Younes, T; Vieillevigne, L; Bardies, M; Franceries, X; Simon, L

    2017-09-01

    Commercial algorithms used in Radiotherapy include approximations that are generally acceptable. However their limits can be seen when confronted with small fields and low-density media. These conditions exist during the treatment of lung cancers with Stereotactic Body Radiation Therapy (SBRT) achieved with the "Deep Inspiration Breath Hold" (DIBH) technique. A Monte Carlo (MC) model of a linear accelerator was used to assess the performance of two algorithms (Varian Acuros and AAA) in these conditions. This model is validated using phantoms with different densities. Lastly, results for SBRT cases are compared to both Acuros and AAA. A Varian TrueBeam linac was modeled using GATE/Geant4 and validated by comparing dose distributions for simple fields to measurements in water and in heterogeneous phantoms composed of PMMA and two types of cork (corresponding to lung densities during free-breathing and DIBH). Experimental measurements are also compared to AAA and Acuros. Finally, results of Acuros/AAA are compared to MC for a clinical case (SBRT during DIBH). Based on 1D gamma index comparisons with measurements in water, the TrueBeam model was validated (>97% of points passed this test). In heterogeneous phantoms, and in particular for small field sizes, very low density (0.12g.cm(-3)) and at the edge of the field, MC model was still in good agreement with measurements whilst AAA and Acuros showed discrepancies. With the patient CT, similar differences between MC and AAA/Acuros were observed for static fields but disappeared using an SBRT arc field. Our MC model is validated and limits of commercial algorithms are shown in very low densities. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  4. Development of lung function in very low birth weight infants with or without bronchopulmonary dysplasia: Longitudinal assessment during the first 15 months of corrected age

    PubMed Central

    2012-01-01

    Background Very low birth weight (VLBW) infants (< 1,500 g) with bronchopulmonary dysplasia (BPD) develop lung damage caused by mechanical ventilation and maturational arrest. We compared functional lung development after discharge from hospital between VLBW infants with and without BPD. Methods Comprehensive lung function assessment was performed at about 50, 70, and 100 weeks of postmenstrual age in 55 sedated VLBW infants (29 with former BPD [O2 supplementation was given at 36 weeks of gestational age] and 26 VLBW infants without BPD [controls]). Mean gestational age (26 vs. 29 weeks), birth weight (815 g vs. 1,125 g), and the proportion of infants requiring mechanical ventilation for ≥7 d (55% vs. 8%), differed significantly between BPD infants and controls. Results Both body weight and length, determined over time, were persistently lower in former BPD infants compared to controls, but no significant between-group differences were noted in respiratory rate, respiratory or airway resistance, functional residual capacity as determined by body plethysmography (FRCpleth), maximal expiratory flow at the FRC (V'max FRC), or blood gas (pO2, pCO2) levels. Tidal volume, minute ventilation, respiratory compliance, and FRC determined by SF6 multiple breath washout (representing the lung volume in actual communication with the airways) were significantly lower in former BPD infants compared to controls. However, these differences became non-significant after normalization to body weight. Conclusions Although somatic growth and the development of some lung functional parameters lag in former BPD infants, the lung function of such infants appears to develop in line with that of non-BPD infants when a body weight correction is applied. Longitudinal lung function testing of preterm infants after discharge from hospital may help to identify former BPD infants at risk of incomplete recovery of respiratory function; such infants are at risk of later respiratory problems. PMID

  5. van der Waals Corrected Density Functional Theory Calculations on Zeolitic Imidazolate Frameworks

    NASA Astrophysics Data System (ADS)

    Ray, Keith George

    The van der Waals force is ubiquitous in nature, however, first principles calculations of this interaction for large systems, i.e., around 1000 atoms, have been performed only recently. In the following are presented results on the application of the van der Waals density functional (vdW-DF) to gas adsorption and transport in zeolitic imidazolate frameworks (ZIFs). Carbon dioxide and methane binding energies and positions are calculated with the vdW-DF in three distinct binding sites in a series of five rho topology ZIFs. The isostructural set of ZIFs was selected in order to isolate the effect of framework functionalization. Gas molecules are found to bind in locations with high coordination to framework atoms at distances of around 3 A. Contributions to the binding energy from induced polarization and dispersion are quantified in order to elucidate the origins of strong CO2 adsorption and selectivity over CH4. The dispersion energy is found to dominate the interactions, however, CO2 adsorption is also enhanced by electrostatic interactions with asymmetrically functionalized linkers. Steric constraints for methane molecules, that do not impede carbon dioxide binding, further contribute to selectivity. Binding energy landscapes for CO2 and CH4 are calculated using classical force fields for the same set of rho ZIFs and several other ZIFs that differ in functionalization and topology. Quantities extracted from these landscapes are used to explain the effect of framework topology on gas adsorption at low and high pressure as well as how the positions of adsorbed gas molecules evolve as a function of pressure. Materials with large surface areas have greater gas uptake at high pressure, while smaller pores, which are associated with stronger binding, adsorb more gas at low pressure. Finally, the effect of framework flexibility on CO2 transport through the double 8-ring channel of ZIF-97 is investigated with computationally intensive climbing-nudged elastic band

  6. Revisiting the structural pattern and the stability of (H2O)20 clusters using the dispersion corrected density functional method

    NASA Astrophysics Data System (ADS)

    Shilpi, V.; Kaur, Surinder Pal; Ramachandran, C. N.

    2015-04-01

    The structure and relative stability of the most stable isomers of different families of (H2O)20 clusters viz. edge-sharing pentagonal prism, face-sharing pentagonal prism, fused cube, dodecahedron and irregular-dodecahedron are studied using dispersion corrected density functional Becke97-D in conjunction with cc-pVTZ basis set. The relative stability of water clusters followed the order ESPP > FSPP > FC > DD > IDD. It is found that the relative stability depends mainly on degree of fusion, number of AADD water molecules and four-membered rings present. For a given family, the energy of isomers increases with decrease in the number of t1d hydrogen bonds.

  7. Electronic structure of novel charge transfer compounds: application of Fermi orbital self-interaction corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Hahn, Torsten; Rückerl, Florian; Liebing, Simon; Pederson, Mark

    We present our experimental and theoretical results on novel Picene/F4TCNQ and Manganese-Phthalocyanine/F4TCNQ donor / acceptor systems. We apply the recently developed Fermi-orbital based approach for self-interaction corrected density functional theory (FO-SIC DFT) to these materials and compare the results to standard DFT calculations and to experimental data obtained by photoemission spectroscopy. We focus our analysis on the description of the magnitude of the ground state charge transfer and on the details of the formed hybrid orbitals. Further, we show that for weakly bound donor / acceptor systems the FO-SIC approach delivers a more realistic description of the electronic structure compared to standard DFT calculations Support by DFG FOR1154 is greatly acknowledged.

  8. Comparison of radiation-induced normal lung tissue density changes for patients from multiple institutions receiving conventional or hypofractionated treatments.

    PubMed

    Diot, Quentin; Marks, Lawrence B; Bentzen, Soren M; Senan, Suresh; Kavanagh, Brian D; Lawrence, Michael V; Miften, Moyed; Palma, David A

    2014-07-01

    To quantitatively assess changes in computed tomography (CT)-defined normal lung tissue density after conventional and hypofractionated radiation therapy (RT). The pre-RT and post-RT CT scans from 118 and 111 patients receiving conventional and hypofractionated RT, respectively, at 3 institutions were registered to each other and to the 3-dimensional dose distribution to quantify dose-dependent changes in normal lung tissue density. Dose-response curves (DRC) for groups of patients receiving conventional and hypofractionated RT were generated for each institution, and the frequency of density changes >80 Hounsfield Units (HU) was modeled depending on the fractionation type using a Probit model for different follow-up times. For the pooled data from all institutions, there were significant differences in the DRC between the conventional and hypofractionated groups; the respective doses resulting in 50% complication risk (TD50) were 62 Gy (95% confidence interval [CI] 57-67) versus 36 Gy (CI 33-39) at <6 months, 48 Gy (CI 46-51) versus 31 Gy (CI 28-33) at 6-12 months, and 47 Gy (CI 45-49) versus 35 Gy (32-37) at >12 months. The corresponding m values (slope of the DRC) were 0.52 (CI 0.46-0.59) versus 0.31 (CI 0.28-0.34) at <6 months, 0.46 (CI 0.42-0.51) versus 0.30 (CI 0.26-0.34) at 6-12 months, and 0.45 (CI 0.42-0.50) versus 0.31 (CI 0.27-0.35) at >12 months (P<.05 for all comparisons). Compared with conventional fractionation, hypofractionation has a lower TD50 and m value, both suggesting an increased degree of normal tissue density sensitivity with hypofractionation. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Electronic and magnetic properties of T i4O7 predicted by self-interaction-corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Zhong, X.; Rungger, I.; Zapol, P.; Heinonen, O.

    2015-03-01

    Understanding electronic properties of substoichiometric phases of titanium oxide such as Magnéli phase T i4O7 is crucial in designing and modeling resistive switching devices. Here we present our study on Magnéli phase T i4O7 together with rutile Ti O2 and T i2O3 using density functional theory methods with atomic-orbital-based self-interaction correction (ASIC). We predict a new antiferromagnetic (AF) ground state in the low temperature (LT) phase, and we explain energy difference with a competing AF state using a Heisenberg model. The predicted energy ordering of these states in the LT phase is calculated to be robust in a wide range of modeled isotropic strain. We have also investigated the dependence of the electronic structures of the Ti-O phases on stoichiometry. The splitting of titanium t2 g orbitals is enhanced with increasing oxygen deficiency as Ti-O is reduced. The electronic properties of all these phases can be reasonably well described by applying ASIC with a "standard" value for transition metal oxides of the empirical parameter α of 0.5 representing the magnitude of the applied self-interaction correction.

  10. Excited states of DNA base pairs using long-range corrected time-dependent density functional theory.

    PubMed

    Jensen, Lasse; Govind, Niranjan

    2009-09-10

    In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

  11. Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

    SciTech Connect

    Jensen, Lasse; Govind, Niranjan

    2009-09-10

    In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.

  12. Electronic and magnetic properties of Ti4O7 predicted by self-interaction-corrected density functional theory

    DOE PAGES

    Zhong, X.; Rungger, I.; Zapol, P.; ...

    2015-03-15

    Understanding electronic properties of substoichiometric phases of titanium oxide such as Magneli phase Ti4O7 is crucial in designing and modeling resistive switching devices. Here we present our study on Magneli phase Ti4O7 together with rutile TiO2 and Ti2O3 using density functional theory methods with atomic-orbital-based self-interaction correction (ASIC). We predict a new antiferromagnetic (AF) ground state in the low temperature (LT) phase, and we explain energy difference with a competing AF state using a Heisenberg model. The predicted energy ordering of these states in the LT phase is calculated to be robust in a wide range of modeled isotropic strain.more » We have also investigated the dependence of the electronic structures of the Ti-O phases on stoichiometry. The splitting of titanium t2g orbitals is enhanced with increasing oxygen deficiency as Ti-O is reduced. Furthermore, the electronic properties of all these phases can be reasonably well described by applying ASIC with a "standard" value for transition metal oxides of the empirical parameter alpha of 0.5 representing the magnitude of the applied self-interaction correction.« less

  13. Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Jensen, Lasse; Govind, Niranjan

    2009-08-01

    In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

  14. Absorption and fluorescence properties of oligothiophene biomarkers from long-range-corrected time-dependent density functional theory.

    PubMed

    Wong, Bryan M; Piacenza, Manuel; Della Sala, Fabio

    2009-06-14

    The absorption and fluorescence properties in a class of oligothiophene push-pull biomarkers are investigated with a long-range-corrected (LC) density functional method. Using linear-response time-dependent density functional theory (TDDFT), we calculate excitation energies, fluorescence energies, oscillator strengths, and excited-state dipole moments. To benchmark and assess the quality of the LC-TDDFT formalism, an extensive comparison is made between LC-BLYP excitation energies and approximate coupled cluster singles and doubles (CC2) calculations. When using a properly-optimized value of the range parameter, mu, we find that the LC technique provides an accurate description of charge-transfer excitations as a function of biomarker size and chemical functionalization. In contrast, we find that re-optimizing the fraction of Hartree Fock exchange in conventional hybrid functionals still yields an inconsistent description of excitation energies and oscillator strengths for the two lowest excited states in our series of biomarkers. The results of the present study emphasize the importance of a distance-dependent contribution of exchange in TDDFT for investigating excited-state properties.

  15. Technical Note: Is bulk electron density assignment appropriate for MRI-only based treatment planning for lung cancer?

    PubMed

    Prior, Phil; Chen, Xinfeng; Gore, Elizabeth; Johnstone, Candice; Li, X Allen

    2017-07-01

    MRI-based treatment planning in radiation therapy (RT) is prohibitive, in part, due to the lack of electron density (ED) information within the image. The dosimetric differences between MRI- and CT-based planning for intensity modulated RT (IMRT) of lung cancer were investigated to assess the appropriateness of bulk ED assignment. Planning CTs acquired for six representative lung cancer patients were used to generate bulk ED IMRT plans. To avoid the effect of anatomic differences between CT and MRI, "simulated MRI-based plans" were generated by forcing the relative ED (rED) to water on CT-delineated structures using organ specific values from the ICRU Report 46 and using the mean rED value of the internal target volume (ITV) from the planning CT. The "simulated MRI-based plans" were generated using a research planning system (Monaco v5.09.07a, Elekta, AB) and employing Monte Carlo dose calculation. The following dose-volume-parameters (DVPs) were collected from both the "simulated MRI-based plans" and the original planning CT: D95 , the dose delivered to 95% of the ITV & planning target volume (PTV), D5 and V5 , the volume of normal lung irradiated ≥5 Gy. The percent point difference and relative dose difference were used for comparison with the CT based plan for V5 and D95 respectively. A total of five plans per patient were generated; three with the ITV rED (rEDITV ) = 1.06, 1.0 and the mean value from the planning CT while the lung rED (rEDlung ) was fixed at the ICRU value of 0.26 and two with rEDlung = 0.1 and 0.5 while the rEDITV was fixed to the mean value from the planning CT. Noticeable differences in the ITV and PTV DVPs were observed. Variations of the normal lung V5 can be as large as 9.6%. In some instances, varying the rEDITV between rEDmean and 1.06 resulted in D95 increases ranging from 3.9% to 6.3%. Bulk rED assignment on normal lung affected the DVPs of the ITV and PTV by 4.0-9.8% and 0.3-19.6% respectively. Dose volume histograms were presented

  16. Influence of radiation therapy on the lung-tissue in breast cancer patients: CT-assessed density changes and associated symptoms

    SciTech Connect

    Rotstein, S.; Lax, I.; Svane, G. )

    1990-01-01

    The relative electron density of lung tissue was measured from computer tomography (CT) slices in 33 breast cancer patients treated by various techniques of adjuvant radiotherapy. The measurements were made before radiotherapy, 3 months and 9 months after completion of radiation therapy. The changes in lung densities at 3 months and 9 months were compared to radiation induced radiological (CT) findings. In addition, subjective symptoms such as cough and dyspnoea were assessed before and after radiotherapy. It was observed that the mean of the relative electron density of lung tissue varied from 0.25 when the whole lung was considered to 0.17 when only the anterior lateral quarter of the lung was taken into account. In patients with positive radiological (CT) findings the mean lung density of the anterior lateral quarter increased 2.1 times 3 months after radiotherapy and was still increased 1.6 times 6 months later. For those patients without findings, in the CT pictures the corresponding values were 1.2 and 1.1, respectively. The standard deviation of the pixel values within the anterior lateral quarter of the lung increased 3.8 times and 3.2 times at 3 months and 9 months, respectively, in the former group, as opposed to 1.2 and 1.1 in the latter group. Thirteen patients had an increase in either cough or dyspnoea as observed 3 months after completion of radiotherapy. In eleven patients these symptoms persisted 6 months later. No significant correlation was found between radiological findings and subjective symptoms. However, when three different treatment techniques were compared among 29 patients the highest rate of radiological findings was observed in patients in which the largest lung volumes received the target dose. A tendency towards an increased rate of subjective symptoms was also found in this group.

  17. An efficient method to predict and include Bragg curve degradation due to lung-equivalent materials in Monte Carlo codes by applying a density modulation

    NASA Astrophysics Data System (ADS)

    Baumann, Kilian-Simon; Witt, Matthias; Weber, Uli; Engenhart-Cabillic, Rita; Zink, Klemens

    2017-05-01

    Sub-millimetre-sized heterogeneities such as lung parenchyma cause Bragg peak degradation which can lead to an underdose of the tumor and an overdose of healthy tissue when not accounted for in treatment planning. Since commonly used treatment-planning CTs do not resolve the fine structure of lungs, this degradation can hardly be considered. We present a mathematical model capable of predicting and describing Bragg peak degradation due to a lung-equivalent geometry consisting of sub-millimetre voxels filled with either lung tissue or air. The material characteristic ‘modulation power’ is introduced to quantify the Bragg peak degradation. A strategy was developed to transfer the modulating effects of such fine structures to rougher structures such as 2 mm thick CT voxels, which is the resolution of typically used CTs. This is done by using the modulation power to derive a density distribution applicable to these voxels. By replacing the previously used sub-millimetre voxels by 2 mm thick voxels filled with lung tissue and modulating the lung tissue’s density in each voxel individually, we were able to reproduce the Bragg peak degradation. Hence a solution is found to include Bragg curve degradation due to lung-equivalent materials in Monte Carlo-based treatment-planning systems.

  18. Adaptive 4D volume perfusion CT of lung cancer: effects of computerized motion correction and the range of volume coverage on measurement reproducibility.

    PubMed

    Lee, Sang Min; Lee, Hyun-Ju; Kim, Jung Im; Kang, Mi-Jin; Goo, Jin Mo; Park, Chang Min; Im, Jung-Gi

    2013-06-01

    The purpose of this study was to determine whether measurement reproducibility can be improved using computerized motion correction and whole-tumor coverage in adaptive 4D perfusion CT of lung cancer. Perfusion CT covering the entire z-axis of a mass was performed of 40 patients with lung cancer. Each perfusion CT study was performed in 93.5 seconds and included 17 repeated dynamic CT scans obtained using the Adaptive 4D Spiral mode. Tumor blood flow (BF), blood volume (BV), and permeability were measured in four different manners: in the entire tumor (whole-tumor coverage) without the use of motion correction; in the entire tumor with motion correction; in a small volume of interest (VOI) of tumor without motion correction; and in a small VOI with motion correction. Intra- and interobserver reproducibility were assessed through Bland-Altman analyses. The 95% limits of intraobserver reproducibility for BF, BV, and permeability were as follows: -52.1% to 48.0%, -22.4% to 27.8%, and -33.2% to 38.5%, respectively, in the whole tumor without motion correction; -53.3% to 45.6%, -17.7% to 20.6%, and -31.5% to 37.0% in the whole tumor with motion correction; -107.8% to 97.4%, -98.3% to 93.7%, and -132.3% to 100.7% in a small VOI of tumor without motion correction; and -74.9% to 98.6%, -74.5% to 88.1%, and -109.8% to 114.1% in a small VOI with motion correction. The 95% limits of interobserver reproducibility for BF, BV, and permeability were as follows: -57.0% to 62.5%, -36.8% to 52.6%, and -47.7% to 66.0%, respectively, in the whole tumor without motion correction; -55.7% to 55.8%, -25.8% to 42.0%, and -35.3% to 46.7% in the whole tumor with motion correction; -146.6% to 165.1%, -117.1% to 137.7%, and -143.2% to 149.8% in a small VOI of tumor without motion correction; and -106.2% to 133.6%, -99.5% to 122.4%, and -108.6% to 170.0% in a small VOI of tumor with motion correction. Overall, the best reproducibility was obtained when measurements were obtained in the entire

  19. Effect of Complex-Valued Optimal Orbitals on Atomization Energies with the Perdew-Zunger Self-Interaction Correction to Density Functional Theory.

    PubMed

    Lehtola, Susi; Jónsson, Elvar Ö; Jónsson, Hannes

    2016-09-13

    The spurious interaction of an electron with itself-self-interaction error-is one of the biggest problems in modern density-functional theory. Some of its most glaring effects, such as qualitatively incorrect charge separation upon dissociation, can be removed by an approximate self-interaction correction due to Perdew and Zunger (PZ) (Perdew, J.; Zunger, A. Phys. Rev. B 1981, 23, 5048). However, the correction introduces an explicit dependence on the occupied orbital densities, which makes proper minimization of the functional difficult. Previous work (Vydrov et al., J. Chem. Phys. 2006, 124, 094108) has suggested that the application of the PZ correction results in worse atomization energies than those obtained with the uncorrected parent functional. But, it has only recently been found that the correct minimization of the PZ energy functional requires complex-valued orbitals, which have not been used in previous work on atomization energies. Here, we study the effect of the proper use of complex-valued orbitals on the atomization energies of molecules in the W4-11 data set (Karton, A.; Daon, S.; Martin, J. M. Chem. Phys. Lett. 2001, 510, 165). We find that the correction has a tendency to weaken the binding of molecules. The correction using complex-valued orbitals is invariably found to yield better atomization energies than the correction with real-valued orbitals. The correction applied to the PBEsol exchange-correlation functional results in a functional that is more accurate than the (uncorrected) PBE functional.

  20. Variability in CT lung-nodule quantification: Effects of dose reduction and reconstruction methods on density and texture based features

    PubMed Central

    Lo, P.; Young, S.; Kim, H. J.; Brown, M. S.

    2016-01-01

    Purpose: To investigate the effects of dose level and reconstruction method on density and texture based features computed from CT lung nodules. Methods: This study had two major components. In the first component, a uniform water phantom was scanned at three dose levels and images were reconstructed using four conventional filtered backprojection (FBP) and four iterative reconstruction (IR) methods for a total of 24 different combinations of acquisition and reconstruction conditions. In the second component, raw projection (sinogram) data were obtained for 33 lung nodules from patients scanned as a part of their clinical practice, where low dose acquisitions were simulated by adding noise to sinograms acquired at clinical dose levels (a total of four dose levels) and reconstructed using one FBP kernel and two IR kernels for a total of 12 conditions. For the water phantom, spherical regions of interest (ROIs) were created at multiple locations within the water phantom on one reference image obtained at a reference condition. For the lung nodule cases, the ROI of each nodule was contoured semiautomatically (with manual editing) from images obtained at a reference condition. All ROIs were applied to their corresponding images reconstructed at different conditions. For 17 of the nodule cases, repeat contours were performed to assess repeatability. Histogram (eight features) and gray level co-occurrence matrix (GLCM) based texture features (34 features) were computed for all ROIs. For the lung nodule cases, the reference condition was selected to be 100% of clinical dose with FBP reconstruction using the B45f kernel; feature values calculated from other conditions were compared to this reference condition. A measure was introduced, which the authors refer to as Q, to assess the stability of features across different conditions, which is defined as the ratio of reproducibility (across conditions) to repeatability (across repeat contours) of each feature. Results: The

  1. Graphene-supported small transition-metal clusters: A density functional theory investigation within van der Waals corrections

    NASA Astrophysics Data System (ADS)

    Rêgo, Celso R. C.; Tereshchuk, Polina; Oliveira, Luiz N.; Da Silva, Juarez L. F.

    2017-06-01

    Transition-metal nanoparticles adsorbed on graphene are of great interest due to the unique catalytic and magnetic properties resulting from nanoparticles-graphene interactions. Comparison between the physical properties of such systems and those of the same nanoparticles in the gas phase is especially important. Here we report a systematic density functional investigation of the structural, energetic, and magnetic properties of small Nin, Pdn, and Ptn clusters, comprising from n =1 to 6 atoms, in the gas phase and adsorbed on a graphene monolayer. Our results show that the Ni adatom binds to the graphene hollow site, with -1.47 -meV adsorption energy, while Pd and Pt prefer the bridge sites, with -1.14 - and -1.62 -meV adsorption energies, respectively. This difference is determined by a competition between quantum and classical forces. Ni2 and Pt2 dimers bind perpendicularly on hollow and bridge sites, respectively, while Pd2 lies parallel to the graphene sheet, with each adatom on a bridge site. For larger TMn (TM = Ni , Pd , Pt ; n =3 -6 ) clusters, either two or three atoms bind to bridge graphene sites. In almost all cases the adsorbed clusters retain their gas-phase structures. The exceptions are Ni5 and Pt4, which acquire more compact structures with effective coordination number 12 and 19 % larger than in the gas phase, respectively. As the number of atoms grows, the cluster binds more weakly to the graphene, while its binding energy mounts up. Van der Waals corrections to the plain density functional theory (DFT) total energy raise the adsorption energy, but leave the cluster structure unchanged, in the gas phase or upon adsorption. Bader charge analysis shows that adsorption causes minor charge redistribution: the TM atoms bound to C atoms become positively charged, while the remaining metal atoms acquire negative charge. We have derived an approximate analytical expression for the local densities of states for the d orbitals of Ni , Pd , and Pt adatoms

  2. Hydrogen storage on metal oxide model clusters using density-functional methods and reliable van der Waals corrections.

    PubMed

    Gebhardt, Julian; Viñes, Francesc; Bleiziffer, Patrick; Hieringer, Wolfgang; Görling, Andreas

    2014-03-21

    We investigate the capability of low-coordinated sites on small model clusters to act as active centers for hydrogen storage. A set of small magic clusters with the formula (XY)6 (X = Mg, Ba, Be, Zn, Cd, Na, Li, B and Y = O, Se, S, F, I, N) and a "drumlike" hexagonal shape showing a low coordination number of three was screened. Oxide clusters turned out to be the most promising candidates for hydrogen storage. For these ionic compounds we explored the suitability of different van der Waals (vdW) corrections to density-functional calculations by comparing the respective H2 physisorption profile to highly accurate CCSD(T) (Coupled Cluster Singles Doubles with perturbative Triples) calculations. The Grimme D3 vdW correction in combination with the Perdew-Burke-Ernzerhof exchange-correlation functional was found to be the best approach compared to CCSD(T) hydrogen physisorption profiles and is, therefore, suited to study these and other light metal oxide systems. H2 adsorption on sites of oxide model clusters is found to meet the adsorption energy criteria for H2 storage, with bond strengths ranging from 0.15 to 0.21 eV. Energy profiles and estimates of kinetic constants for the H2 splitting reaction reveal that H2 is likely to be adsorbed molecularly on sites of (MgO)6, (BaO)6, and (BeO)6 clusters, suggesting a rapid H2 uptake/release at operating temperatures and moderate pressures. The small mass of beryllium and magnesium makes such systems appealing for meeting the gravimetric criterion for H2 storage.

  3. Prognostic impact of average iodine density assessed by dual-energy spectral imaging for predicting lung tumor recurrence after stereotactic body radiotherapy

    PubMed Central

    Aoki, Masahiko; Hirose, Katsumi; Sato, Mariko; Akimoto, Hiroyoshi; Kawaguchi, Hideo; Hatayama, Yoshiomi; Fujioka, Ichitaro; Tanaka, Mitsuki; Ono, Shuichi; Takai, Yoshihiro

    2016-01-01

    The purpose of this study was to investigate the prognostic significance of average iodine density as assessed by dual-energy computed tomography (DE-CT) for lung tumors treated with stereotactic body radiotherapy (SBRT). From March 2011 to August 2014, 93 medically inoperable patients with 74 primary lung cancers and 19 lung metastases underwent DE-CT prior to SBRT of a total dose of 45–60 Gy in 5–10 fractions. Of these 93 patients, nine patients had two lung tumors. Thus, 102 lung tumors were included in this study. DE-CT was performed for pretreatment evaluation. Regions of interest were set for the entire tumor, and average iodine density was obtained using a dedicated imaging software and evaluated with regard to local control. The median follow-up period was 23.4 months (range, 1.5–54.5 months). The median value of the average iodine density was 1.86 mg/cm3 (range, 0.40–9.27 mg/cm3). Two-year local control rates for the high and low average iodine density groups divided by the median value of the average iodine density were 96.9% and 75.7% (P = 0.006), respectively. Tumors with lower average iodine density showed a worse prognosis, possibly reflecting a hypoxic cell population in the tumor. The average iodine density exhibited a significant impact on local control. Our preliminary results indicate that iodine density evaluated using dual-energy spectral CT may be a useful, noninvasive and quantitative assessment of radio-resistance caused by presumably hypoxic cell populations in tumors. PMID:26826198

  4. Prognostic impact of average iodine density assessed by dual-energy spectral imaging for predicting lung tumor recurrence after stereotactic body radiotherapy.

    PubMed

    Aoki, Masahiko; Hirose, Katsumi; Sato, Mariko; Akimoto, Hiroyoshi; Kawaguchi, Hideo; Hatayama, Yoshiomi; Fujioka, Ichitaro; Tanaka, Mitsuki; Ono, Shuichi; Takai, Yoshihiro

    2016-07-01

    The purpose of this study was to investigate the prognostic significance of average iodine density as assessed by dual-energy computed tomography (DE-CT) for lung tumors treated with stereotactic body radiotherapy (SBRT). From March 2011 to August 2014, 93 medically inoperable patients with 74 primary lung cancers and 19 lung metastases underwent DE-CT prior to SBRT of a total dose of 45-60 Gy in 5-10 fractions. Of these 93 patients, nine patients had two lung tumors. Thus, 102 lung tumors were included in this study. DE-CT was performed for pretreatment evaluation. Regions of interest were set for the entire tumor, and average iodine density was obtained using a dedicated imaging software and evaluated with regard to local control. The median follow-up period was 23.4 months (range, 1.5-54.5 months). The median value of the average iodine density was 1.86 mg/cm(3) (range, 0.40-9.27 mg/cm(3)). Two-year local control rates for the high and low average iodine density groups divided by the median value of the average iodine density were 96.9% and 75.7% (P = 0.006), respectively. Tumors with lower average iodine density showed a worse prognosis, possibly reflecting a hypoxic cell population in the tumor. The average iodine density exhibited a significant impact on local control. Our preliminary results indicate that iodine density evaluated using dual-energy spectral CT may be a useful, noninvasive and quantitative assessment of radio-resistance caused by presumably hypoxic cell populations in tumors.

  5. Initial implementation of the conversion from the energy-subtracted CT number to electron density in tissue inhomogeneity corrections: An anthropomorphic phantom study of radiotherapy treatment planning

    SciTech Connect

    Tsukihara, Masayoshi; Noto, Yoshiyuki; Sasamoto, Ryuta; Hayakawa, Takahide; Saito, Masatoshi

    2015-03-15

    Purpose: To achieve accurate tissue inhomogeneity corrections in radiotherapy treatment planning, the authors had previously proposed a novel conversion of the energy-subtracted computed tomography (CT) number to an electron density (ΔHU–ρ{sub e} conversion), which provides a single linear relationship between ΔHU and ρ{sub e} over a wide range of ρ{sub e}. The purpose of this study is to present an initial implementation of the ΔHU–ρ{sub e} conversion method for a treatment planning system (TPS). In this paper, two example radiotherapy plans are used to evaluate the reliability of dose calculations in the ΔHU–ρ{sub e} conversion method. Methods: CT images were acquired using a clinical dual-source CT (DSCT) scanner operated in the dual-energy mode with two tube potential pairs and an additional tin (Sn) filter for the high-kV tube (80–140 kV/Sn and 100–140 kV/Sn). Single-energy CT using the same DSCT scanner was also performed at 120 kV to compare the ΔHU–ρ{sub e} conversion method with a conventional conversion from a CT number to ρ{sub e} (Hounsfield units, HU–ρ{sub e} conversion). Lookup tables for ρ{sub e} calibration were obtained from the CT image acquisitions for tissue substitutes in an electron density phantom (EDP). To investigate the beam-hardening effect on dosimetric uncertainties, two EDPs with different sizes (a body EDP and a head EDP) were used for the ρ{sub e} calibration. Each acquired lookup table was applied to two radiotherapy plans designed using the XiO TPS with the superposition algorithm for an anthropomorphic phantom. The first radiotherapy plan was for an oral cavity tumor and the second was for a lung tumor. Results: In both treatment plans, the performance of the ΔHU–ρ{sub e} conversion was superior to that of the conventional HU–ρ{sub e} conversion in terms of the reliability of dose calculations. Especially, for the oral tumor plan, which dealt with dentition and bony structures, treatment

  6. Successes and failures of Hubbard-corrected density functional theory. The case of Mg doped LiCoO2

    DOE PAGES

    Santana Palacio, Juan A.; Kim, Jeongnim; Kent, Paul R.; ...

    2014-10-28

    We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO2. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO2. We find that formation of impurity states results in changes on the valency of Co in LiCoO2. Variation of the Co U shifts the energy of the impurity state, resulting inmore » energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO2.« less

  7. Long-range corrected time-dependent density functional study on fluorescence of 4,4'-dimethylaminobenzonitrile.

    PubMed

    Chiba, Mahito; Tsuneda, Takao; Hirao, Kimihiko

    2007-01-21

    Dual fluorescence of 4,4(')-dimethylaminobenzonitrile (DMABN) was theoretically investigated on the basis of long-range corrected time-dependent density functional theory. Excited-state geometry optimization states and single-point energy calculations with and without solvent effect were carried out. It has been explained that DMABN emits dual fluorescence only in polar solvents through locally excited (LE) and charge transfer (CT) states. It was, however, concluded from this study that although the main spectrum of dual fluorescence in acetonitrile solvent is clearly due to twisted intramolecular CT fluorescence, small secondary fluorescence in acetonitrile may also emanate from CT fluorescence during the DMABN twisting process. This conclusion is supported by an experimental interpretation on polarization spectroscopy. It was also found that the optimized DMABN geometries have certain wagging angles for the CT state and no wagging angle for the LE state. This may support an early experimental hypothesis that the dual fluorescence of DMABN is induced by the wagging mode due to vibronic coupling between LE and CT states. Consequently, the authors propose a fluorescence mechanism of DMABN in gas phase and in acetonitrile solvent: the main absorption proceeds to the CT state in both situations. In gas phase, single fluorescence is chiefly emitted from the LE state through the internal conversion from CT to LE states. Dual fluorescence in acetonitrile solvent may only be emitted from the CT state.

  8. A noniterative asymmetric triple excitation correction for the density-fitted coupled-cluster singles and doubles method: Preliminary applications

    NASA Astrophysics Data System (ADS)

    Bozkaya, Uǧur

    2016-04-01

    An efficient implementation of the asymmetric triples correction for the coupled-cluster singles and doubles [ΛCCSD(T)] method [S. A. Kucharski and R. J. Bartlett, J. Chem. Phys. 108, 5243 (1998); T. D. Crawford and J. F. Stanton, Int. J. Quantum Chem. 70, 601 (1998)] with the density-fitting [DF-ΛCCSD(T)] approach is presented. The computational time for the DF-ΛCCSD(T) method is compared with that of ΛCCSD(T). Our results demonstrate that the DF-ΛCCSD(T) method provide substantially lower computational costs than ΛCCSD(T). Further application results show that the ΛCCSD(T) and DF-ΛCCSD(T) methods are very beneficial for the study of single bond breaking problems as well as noncovalent interactions and transition states. We conclude that ΛCCSD(T) and DF-ΛCCSD(T) are very promising for the study of challenging chemical systems, where the coupled-cluster singles and doubles with perturbative triples method fails.

  9. Excited state geometry optimizations by analytical energy gradient of long-range corrected time-dependent density functional theory.

    PubMed

    Chiba, Mahito; Tsuneda, Takao; Hirao, Kimihiko

    2006-04-14

    An analytical excitation energy gradient of long-range corrected time-dependent density functional theory (LC-TDDFT) is presented. This is based on a previous analytical TDDFT gradient formalism, which avoids solving the coupled-perturbed Kohn-Sham equation for each nuclear degree of freedom. In LC-TDDFT, exchange interactions are evaluated by combining the short-range part of a DFT exchange functional with the long-range part of the Hartree-Fock exchange integral. This LC-TDDFT gradient was first examined by calculating the excited state geometries and adiabatic excitation energies of small typical molecules and a small protonated Schiff base. As a result, we found that long-range interactions play a significant role even in valence excited states of small systems. This analytical LC-TDDFT gradient was also applied to the investigations of small twisted intramolecular charge transfer (TICT) systems. By comparing with calculated ab initio multireference perturbation theory and experimental results, we found that LC-TDDFT gave much more accurate absorption and fluorescence energies of these systems than those of conventional TDDFTs using pure and hybrid functionals. For optimized excited state geometries, LC-TDDFT provided fairly different twisting and wagging angles of these small TICT systems in comparison with conventional TDDFT results.

  10. A Correction for the IRI Topside Electron Density Model Based on Alouette/ISIS Topside Sounder Data

    NASA Technical Reports Server (NTRS)

    Bilitza, D.

    2004-01-01

    The topside segment of the International Reference Ionosphere (IRI) electron density model (and also of the Bent model) is based on the limited amount of topside data available at the time (40,OOO Alouette 1 profiles). Being established from such a small database it is therefore not surprising that the models have well-known shortcomings, for example, at high solar activities. Meanwhile a large data base of close to 200,000 topside profiles from Alouette 1,2, and ISIS I, 2 has become available online. A program of automated scaling and inversion of a large volume of digitized ionograms adds continuously to this data pool. We have used the currently available ISIs/Alouette topside profiles to evaluate the IRI topside model and to investigate ways of improving the model. The IRI model performs generally well at middle latitudes and shows discrepancies at low and high latitudes and these discrepancies are largest during high solar activity. In the upper topside IRI consistently overestimates the measurements. Based on averages of the data-model ratios we have established correction factors for the IRI model. These factors vary with altitude, modified dip latitude, and local time.

  11. Unraveling Interactions in Molecular Crystals Using Dispersion Corrected Density Functional Theory: The Case of the Epoxydihydroarsanthrene Molecules.

    PubMed

    Otero-de-la-Roza, A; Luaña, Víctor; Tiekink, Edward R T; Zukerman-Schpector, Julio

    2014-11-11

    Noncovalent interactions are prevalent in crystal packing and supramolecular chemistry. Directional noncovalent interactions such as donor-acceptor bonds (e.g., hydrogen, chalcogen, and pnictogen bonds) as well as nondirectional forces (such as dispersion) come together to stabilize supramolecular assemblies by striking a delicate energetic balance. Typically, a two-pronged approach employing experimental X-ray structures and gas phase quantum chemical modeling has been used to understand and design supramolecular architectures. Drawing from recent advances in molecular crystal modeling with dispersion corrected density functional theory (DFT), we propose in this article a combination of qualitative noncovalent index (NCI) analysis and periodic and gas phase DFT calculations on substitutional crystal analogues to unravel the dominant interactions in a particular crystal packing. We illustrate the possibilities of this approach by studying three crystal packings of epoxydihydroarsanthrene analogues that present a complex combination of donor-acceptor interactions including pnictogen-pnictogen, pnictogen-π, and pnictogen-chalcogen. We show that, in these crystals, the chalcogen-pnictogen interaction dominates over the pnictogen-pnictogen and pnictogen-π. In the latter, the role of donor and acceptor is reversed depending on the interacting moieties. Multiple chalcogen-pnictogen interactions necessitate larger donor atoms, such as sulfur. These observations explain and rationalize the experimentally observed crystal structures.

  12. A Correction for the IRI Topside Electron Density Model Based on Alouette/ISIS Topside Sounder Data

    NASA Technical Reports Server (NTRS)

    Bilitza, D.

    2004-01-01

    The topside segment of the International Reference Ionosphere (IRI) electron density model (and also of the Bent model) is based on the limited amount of topside data available at the time (40,OOO Alouette 1 profiles). Being established from such a small database it is therefore not surprising that the models have well-known shortcomings, for example, at high solar activities. Meanwhile a large data base of close to 200,000 topside profiles from Alouette 1,2, and ISIS I, 2 has become available online. A program of automated scaling and inversion of a large volume of digitized ionograms adds continuously to this data pool. We have used the currently available ISIs/Alouette topside profiles to evaluate the IRI topside model and to investigate ways of improving the model. The IRI model performs generally well at middle latitudes and shows discrepancies at low and high latitudes and these discrepancies are largest during high solar activity. In the upper topside IRI consistently overestimates the measurements. Based on averages of the data-model ratios we have established correction factors for the IRI model. These factors vary with altitude, modified dip latitude, and local time.

  13. Pressure dependent stability and structure of carbon dioxide—A density functional study including long-range corrections

    NASA Astrophysics Data System (ADS)

    Gohr, Sebastian; Grimme, Stefan; Söhnel, Tilo; Paulus, Beate; Schwerdtfeger, Peter

    2013-11-01

    First-principles density functional theory (DFT) is used to study the solid-state modifications of carbon dioxide up to pressures of 60 GPa. All known molecular CO2 structures are investigated in this pressure range, as well as three non-molecular modifications. To account for long-range van der Waals interactions, the dispersion corrected DFT method developed by Grimme and co-workers (DFT-D3) is applied. We find that the DFT-D3 method substantially improves the results compared to the uncorrected DFT methods for the molecular carbon dioxide crystals. Enthalpies at 0 K and cohesive energies support only one possibility of the available experimental solutions for the structure of phase IV: the Roverline{3}c modification, proposed by Datchi and co-workers [Phys. Rev. Lett. 103, 185701 (2009)]. Furthermore, comparing bulk moduli with experimental values, we cannot reproduce the quite large—rather typical for covalent crystal structures—experimental values for the molecular phases II and III.

  14. Comparison of Radiation-Induced Normal Lung Tissue Density Changes for Patients From Multiple Institutions Receiving Conventional or Hypofractionated Treatments

    SciTech Connect

    Diot, Quentin; Marks, Lawrence B.; Bentzen, Soren M.; Senan, Suresh; Kavanagh, Brian D.; Lawrence, Michael V.; Miften, Moyed; Palma, David A.

    2014-07-01

    Purpose: To quantitatively assess changes in computed tomography (CT)–defined normal lung tissue density after conventional and hypofractionated radiation therapy (RT). Methods and Materials: The pre-RT and post-RT CT scans from 118 and 111 patients receiving conventional and hypofractionated RT, respectively, at 3 institutions were registered to each other and to the 3-dimensional dose distribution to quantify dose-dependent changes in normal lung tissue density. Dose-response curves (DRC) for groups of patients receiving conventional and hypofractionated RT were generated for each institution, and the frequency of density changes >80 Hounsfield Units (HU) was modeled depending on the fractionation type using a Probit model for different follow-up times. Results: For the pooled data from all institutions, there were significant differences in the DRC between the conventional and hypofractionated groups; the respective doses resulting in 50% complication risk (TD{sub 50}) were 62 Gy (95% confidence interval [CI] 57-67) versus 36 Gy (CI 33-39) at <6 months, 48 Gy (CI 46-51) versus 31 Gy (CI 28-33) at 6-12 months, and 47 Gy (CI 45-49) versus 35 Gy (32-37) at >12 months. The corresponding m values (slope of the DRC) were 0.52 (CI 0.46-0.59) versus 0.31 (CI 0.28-0.34) at <6 months, 0.46 (CI 0.42-0.51) versus 0.30 (CI 0.26-0.34) at 6-12 months, and 0.45 (CI 0.42-0.50) versus 0.31 (CI 0.27-0.35) at >12 months (P<.05 for all comparisons). Conclusion: Compared with conventional fractionation, hypofractionation has a lower TD{sub 50} and m value, both suggesting an increased degree of normal tissue density sensitivity with hypofractionation.

  15. Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory.

    PubMed

    Hempler, Daniela; Schmidt, Martin U; van de Streek, Jacco

    2017-08-01

    More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å. For 98.5% of 200 molecular crystal structures published with missed symmetry, the correct space group is identified; there are no false positives. Very small, very symmetrical molecules can end up in artificially high space groups upon energy minimization, although this is easily detected through visual inspection. If the space group of a crystal structure determined from powder diffraction data is ambiguous, energy minimization with DFT-D provides a fast and reliable method to select the correct space group.

  16. SU-E-T-24: A Simple Correction-Based Method for Independent Monitor Unit (MU) Verification in Monte Carlo (MC) Lung SBRT Plans

    SciTech Connect

    Pokhrel, D; Badkul, R; Jiang, H; Estes, C; Kumar, P; Wang, F

    2014-06-01

    Purpose: Lung-SBRT uses hypo-fractionated dose in small non-IMRT fields with tissue-heterogeneity corrected plans. An independent MU verification is mandatory for safe and effective delivery of the treatment plan. This report compares planned MU obtained from iPlan-XVM-Calgorithm against spreadsheet-based hand-calculation using most commonly used simple TMR-based method. Methods: Treatment plans of 15 patients who underwent for MC-based lung-SBRT to 50Gy in 5 fractions for PTV V100%=95% were studied. ITV was delineated on MIP images based on 4D-CT scans. PTVs(ITV+5mm margins) ranged from 10.1- 106.5cc(average=48.6cc). MC-SBRT plans were generated using a combination of non-coplanar conformal arcs/beams using iPlan XVM-Calgorithm (BrainLAB iPlan ver.4.1.2) for Novalis-TX consisting of micro-MLCs and 6MV-SRS (1000MU/min) beam. These plans were re-computed using heterogeneity-corrected Pencil-Beam (PB-hete) algorithm without changing any beam parameters, such as MLCs/MUs. Dose-ratio: PB-hete/MC gave beam-by-beam inhomogeneity-correction-factors (ICFs):Individual Correction. For independent-2nd-check, MC-MUs were verified using TMR-based hand-calculation and obtained an average ICF:Average Correction, whereas TMR-based hand-calculation systematically underestimated MC-MUs by ∼5%. Also, first 10 MC-plans were verified with an ion-chamber measurement using homogenous phantom. Results: For both beams/arcs, mean PB-hete dose was systematically overestimated by 5.5±2.6% and mean hand-calculated MU systematic underestimated by 5.5±2.5% compared to XVMC. With individual correction, mean hand-calculated MUs matched with XVMC by - 0.3±1.4%/0.4±1.4 for beams/arcs, respectively. After average 5% correction, hand-calculated MUs matched with XVMC by 0.5±2.5%/0.6±2.0% for beams/arcs, respectively. Smaller dependence on tumor volume(TV)/field size(FS) was also observed. Ion-chamber measurement was within ±3.0%. Conclusion: PB-hete overestimates dose to lung tumor relative to

  17. [The effectiveness of care bundles in maintaining the skin integrity and reducing the incidence density of pressure ulcers in lung cancer inpatients].

    PubMed

    Lin, Wen-Ling; Tseng, Chien-Hua; Chung, Yi-Jen; Chuang, Hsin-Chu; Lin, Yun-Lan; Chang, Pi-Hua

    2014-04-01

    Pressure ulcers are tissue defects that form on the skin as a result of progressive skin damage. Pressure ulcers are a skin-integrity-related care issue and an important clinical indicator of care quality, especially for lung cancer inpatients who face rapidly deteriorating health conditions due to multiple symptoms and the side effects of treatment. Treating severe pressure ulcers may consume considerable manpower, time, and medical resources. Pressure ulcers may be avoided or effectively treated when nurses conduct proper skin assessments and care for wounds properly. This project evaluates the efficacy of skin care bundles in terms of reducing the incidence density of pressure ulcers in lung cancer inpatients. Data gathered between January 2010 and March 2011 showed unstable incidence density for pressure ulcers. The average pressure-ulcer incidence density in lung cancer inpatients was 2.09%, which was 8-times higher than the average for all patients. Using evidence-based care bundles for pressure ulcer prevention, we trained nurse staffs to incorporate these bundles into their clinical daily care of lung cancer patients in our hospital. During the study period between November 2011 and January 2012, the pressure-ulcer incidence density gradually fell to 0.55%. The incidence density continued to fall to 0.33% over the subsequent 8 months. We used the concept of "care bundles" to establish a standard skin-care protocol for advanced lung cancer inpatients. This protocol improved the clinical ability of nursing staffs and effectively maintained skin care quality in lung cancer patients.

  18. Analytical O (αs) corrections to the beam frame double-spin density matrix elements of e+e-→t t ¯

    NASA Astrophysics Data System (ADS)

    Kaldamäe, L.; Groote, S.; Körner, J. G.

    2016-12-01

    We provide analytical results for the O (αs) corrections to the double-spin density matrix elements in the reaction e+e-→t t ¯ . These concern the elements l l , l t , l n , t t , t n , and n n of the double-spin density matrix elements where l , t , n stand for longitudinal, transverse and normal orientations with respect to the beam frame spanned by the electron and the top quark momentum.

  19. Classification of lung nodules in diagnostic CT: an approach based on 3D vascular features, nodule density distribution, and shape features

    NASA Astrophysics Data System (ADS)

    Lo, Shih-Chung B.; Hsu, Li-Yueh; Freedman, Matthew T.; Lure, Yuan Ming F.; Zhao, Hui

    2003-05-01

    We have developed various segmentation and analysis methods for the quantification of lung nodules in thoracic CT. Our methods include the enhancement of lung structures followed by a series of segmentation methods to extract the nodule and to form 3D configuration at an area of interest. The vascular index, aspect ratio, circularity, irregularity, extent, compactness, and convexity were also computed as shape features for quantifying the nodule boundary. The density distribution of the nodule was modeled based on its internal homogeneity and/or heterogeneity. We also used several density related features including entropy, difference entropy as well as other first and second order moments. We have collected 48 cases of lung nodules scanned by thin-slice diagnostic CT. Of these cases, 24 are benign and 24 are malignant. A jackknife experiment was performed using a standard back-propagation neural network as the classifier. The LABROC result showed that the Az of this preliminary study is 0.89.

  20. Using the electron localization function to correct for confinement physics in semi-local density functional theory

    SciTech Connect

    Hao, Feng Mattsson, Ann E.; Armiento, Rickard

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  1. Using soft computing techniques to predict corrected air permeability using Thomeer parameters, air porosity and grain density

    NASA Astrophysics Data System (ADS)

    Nooruddin, Hasan A.; Anifowose, Fatai; Abdulraheem, Abdulazeez

    2014-03-01

    Soft computing techniques are recently becoming very popular in the oil industry. A number of computational intelligence-based predictive methods have been widely applied in the industry with high prediction capabilities. Some of the popular methods include feed-forward neural networks, radial basis function network, generalized regression neural network, functional networks, support vector regression and adaptive network fuzzy inference system. A comparative study among most popular soft computing techniques is presented using a large dataset published in literature describing multimodal pore systems in the Arab D formation. The inputs to the models are air porosity, grain density, and Thomeer parameters obtained using mercury injection capillary pressure profiles. Corrected air permeability is the target variable. Applying developed permeability models in recent reservoir characterization workflow ensures consistency between micro and macro scale information represented mainly by Thomeer parameters and absolute permeability. The dataset was divided into two parts with 80% of data used for training and 20% for testing. The target permeability variable was transformed to the logarithmic scale as a pre-processing step and to show better correlations with the input variables. Statistical and graphical analysis of the results including permeability cross-plots and detailed error measures were created. In general, the comparative study showed very close results among the developed models. The feed-forward neural network permeability model showed the lowest average relative error, average absolute relative error, standard deviations of error and root means squares making it the best model for such problems. Adaptive network fuzzy inference system also showed very good results.

  2. Assessment of density functionals with long-range and/or empirical dispersion corrections for conformational energy calculations of peptides.

    PubMed

    Kang, Young Kee; Byun, Byung Jin

    2010-12-01

    Density functionals with long-range and/or empirical dispersion corrections, including LC-ωPBE, B97-D, ωB97X-D, M06-2X, B2PLYP-D, and mPW2PLYP-D functionals, are assessed for their ability to describe the conformational preferences of Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22-0.40 kcal/mol in conformational energy and 2.0-3.2° in torsion angles φ and ψ using these functionals with the 6-311++G(d,p) basis set against the reference values calculated at the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP-D ≈ mPW2PLYP-D > ωB97X-D ≈ M06-2X > MP2 > LC-ωPBE > B3LYP with the 6-311++G(d,p) basis set. The SMD model at the M06-2X/6-31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP-D/6-311++G(d,p)//SMD M06-2X/6-31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values.

  3. Using the electron localization function to correct for confinement physics in semi-local density functional theory.

    PubMed

    Hao, Feng; Armiento, Rickard; Mattsson, Ann E

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu-O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  4. Modified corrections for London forces in solid-state density functional theory calculations of structure and lattice dynamics of molecular crystals.

    PubMed

    King, Matthew D; Korter, Timothy M

    2012-06-28

    Dispersion forces are critical for defining the crystal structures and vibrational potentials of molecular crystals. It is, therefore, important to include corrections for these forces in periodic density functional theory (DFT) calculations of lattice vibrational frequencies. In this study, DFT was augmented with a correction term for London-type dispersion forces in the simulations of the structures and terahertz (THz) vibrational spectra of the dispersion-bound solids naphthalene and durene. The parameters of the correction term were modified to best reproduce the experimental crystal structures and THz spectra. It was found that the accurate reproduction of the lattice dimensions by adjusting the magnitude of the applied dispersion forces resulted in the highest-quality fit of the calculated vibrational modes with the observed THz absorptions. The method presented for the modification of the dispersion corrections provides a practical approach to accurately simulating the THz spectra of molecular crystals, accounting for inherent systematic errors imposed by computational and experimental factors.

  5. Mitogen-Activated Protein Kinase Phosphatase-1 Is a Key Regulator of Hypoxia-Induced Vascular Endothelial Growth Factor Expression and Vessel Density in Lung

    PubMed Central

    Shields, Kristin M.; Panzhinskiy, Evgeniy; Burns, Nana; Zawada, W. Michael; Das, Mita

    2011-01-01

    Although mitogen-activated protein kinase phosphatase-1 (MKP-1) is a key deactivator of MAP kinases, known effectors of lung vessel formation, whether it plays a role in the expression of proangiogenic vascular endothelial growth factor (VEGF) in hypoxic lung is unknown. We therefore hypothesized that MKP-1 is a crucial modulator of hypoxia-stimulated vessel development by regulating lung VEGF levels. Wild-type MKP-1+/+, heterozygous MKP-1+/−, and deficient MKP-1−/− mice were exposed to sea level (SL), Denver altitude (DA) (1609 m [5280 feet]), and severe high altitude (HYP) (∼5182 m [∼17,000 feet]) for 6 weeks. Hypoxia enhanced phosphorylation of p38 MAP kinase, a substrate of MKP-1, as well as α smooth muscle actin (αSMA) expression in vessels, respiratory epithelium, and interstitium of phosphatase-deficient lung. αSMA-positive vessel (<50 μm outside diameter) densities were markedly reduced, whereas vessel wall thickness was increased in hypoxic MKP-1−/− lung. Mouse embryonic fibroblasts (MEFs) of all three genotypes were isolated to pinpoint the mechanism involved in hypoxia-induced vascular abnormalities of MKP-1−/− lung. Sustained phosphorylation of p38 MAP kinase was observed in MKP-1-null MEFs in response to hypoxia exposure. Although hypoxia up-regulated VEGF levels in MKP-1+/+ MEFs eightfold, only a 70% increase in VEGF expression was observed in MKP-1-deficient cells. Therefore, our data strongly suggest that MKP-1 might be the key regulator of vascular densities through the regulation of VEGF levels in hypoxic lung. PMID:21224048

  6. First-order exchange and self-energy corrections to static density correlation function of a spin-polarized two-dimensional quantum electron fluid

    SciTech Connect

    Arora, Priya; Moudgil, R. K.; Bhukal, Nisha

    2015-05-15

    Static density-density correlation function has been calculated for a spin-polarized two-dimensional quantum electron fluid by including the first-order exchange and self-energy corrections to the random-phase approximation (RPA). This is achieved by determining these corrections to the RPA linear density-density response function, obtained by solving the equation of motion for the single-particle Green’s function. Resulting infinite hierarchy of equations (involving higher-order Green’s functions) is truncated by factorizing the two-particle Green’s function as a product of the single-particle Green’s function and one-particle distribution function. Numerical results of correlation function are compared directly against the quantum Monte Carlo simulation data due to Tanatar and Ceperley for different coupling parameter (r{sub s}) values. We find almost exact agreement for r{sub s}=1, with a noticeable improvement over the RPA. Its quality, however, deteriorates with increasing r{sub s}, but correction to RPA is quite significant.

  7. SU-E-T-513: Investigating Dose of Internal Target Volume After Correcting for Tissue Heterogeneity in SBRT Lung Plans with Homogeneity Calculation

    SciTech Connect

    Qi, P; Zhuang, T; Magnelli, A; Djemil, T; Shang, Q; Balik, S; Andrews, M; Stephans, K; Videtic, G; Xia, P

    2015-06-15

    Purpose It was recommended to use the prescription of 54 Gy/3 with heterogeneity corrections for previously established dose scheme of 60 Gy/3 with homogeneity calculation. This study is to investigate dose coverage for the internal target volume (ITV) with and without heterogeneity correction. Methods Thirty patients who received stereotactic body radiotherapy (SBRT) to a dose of 60 Gy in 3 fractions with homogeneous planning for early stage non-small-cell lung cancer (NSCLC) were selected. ITV was created either from 4DCT scans or a fusion of multi-phase respiratory scans. Planning target volume (PTV) was a 5 mm expansion of the ITV. For this study, we recalculated homogeneous clinical plans using heterogeneity corrections with monitor units set as clinically delivered. All plans were calculated with 3 mm dose grids and collapsed cone convolution algorithm. To account for uncertainties from tumor delineation and image-guided radiotherapy, a structure ITV2mm was created by expanding ITV with 2 mm margins. Dose coverage to the PTV, ITV and ITV2mm were compared with a student paired t-test. Results With heterogeneity corrections, the PTV V60Gy decreased by 10.1% ± 18.4% (p<0.01) while the maximum dose to the PTV increased by 3.7 ± 4.3% (p<0.01). With and without corrections, D99% was 65.8 ± 4.0 Gy and 66.7 ± 4.8 Gy (p=0.15) for the ITV, and 63.9 ± 3.4 Gy and 62.9 ± 4.6 Gy for the ITV2mm (p=0.22), respectively. The mean dose to the ITV and ITV2mm increased 3.6% ± 4.7% (p<0.01) and 2.3% ± 5.2% (p=0.01) with heterogeneity corrections. Conclusion After heterogeneity correction, the peripheral coverage of the PTV decreased to approximately 54 Gy, but D99% of the ITV and ITV2mm was unchanged and the mean dose to the ITV and ITV2mm was increased. Clinical implication of these results requires more investigation.

  8. Scanner conformity in CT densitometry of the lungs.

    PubMed

    Kemerink, G J; Lamers, R J; Thelissen, G R; van Engelshoven, J M

    1995-12-01

    To quantify inter- and intrascanner conformity in computed tomographic (CT) densitometry of the lungs. With six scanners from four manufacturers, a lung densitometry protocol with several variations was applied for performance comparison. Phantoms included water, air, and a humanoid thorax phantom equipped with a dog lung and exchangeable pseudolungs of polyethylene foam. All scanners produced acceptable CT numbers (Hounsfield units) for water, but some not for air. An incorrect calibration of air density affected all CT numbers at lung densities, but the error was easily correctable. Some systems were more sensitive to object size than others were. Sensitivity of CT numbers to section thickness, reconstruction filter, zoom factor, and table height was small, except for two scanners in relation to section thickness. After correction for poor air calibration, scanner conformity was acceptable when the reproducibility of lung densitometry in clinical practice was set as a reference.

  9. Finite-density corrections to the unitary Fermi gas: A lattice perspective from dynamical mean-field theory

    SciTech Connect

    Privitera, Antonio; Capone, Massimo; Castellani, Claudio

    2010-01-01

    We investigate the approach to the universal regime of the dilute unitary Fermi gas as the density is reduced to zero in a lattice model. To this end we study the chemical potential, superfluid order parameter and internal energy of the attractive Hubbard model in three different lattices with densities of states (DOSs) which share the same low-energy behavior of fermions in three-dimensional free space: a cubic lattice, a 'Bethe lattice' with a semicircular DOS, and a 'lattice gas' with parabolic dispersion and a sharp energy cutoff that ensures the normalization of the DOS. The model is solved using dynamical mean-field theory, that treats directly the thermodynamic limit and arbitrarily low densities, eliminating finite-size effects. At densities on the order of one fermion per site the lattice and its specific form dominate the results. The evolution to the low-density limit is smooth and it does not allow to define an unambiguous low-density regime. Such finite-density effects are significantly reduced using the lattice gas, and they are maximal for the three-dimensional cubic lattice. Even though dynamical mean-field theory is bound to reduce to the more standard static mean field in the limit of zero density due to the local nature of the self-energy and of the vertex functions, it compares well with accurate Monte Carlo simulations down to the lowest densities accessible to the latter.

  10. SYNCHROTRON RADIATION, FREE ELECTRON LASER, APPLICATION OF NUCLEAR TECHNOLOGY, ETC.: X-ray beam hardening correction for measuring density in linear accelerator industrial computed tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Ri-Feng; Wang, Jue; Chen, Wei-Min

    2009-07-01

    Due to X-ray attenuation being approximately proportional to material density, it is possible to measure the inner density through Industrial Computed Tomography (ICT) images accurately. In practice, however, a number of factors including the non-linear effects of beam hardening and diffuse scattered radiation complicate the quantitative measurement of density variations in materials. This paper is based on the linearization method of beam hardening correction, and uses polynomial fitting coefficient which is obtained by the curvature of iron polychromatic beam data to fit other materials. Through theoretical deduction, the paper proves that the density measure error is less than 2% if using pre-filters to make the spectrum of linear accelerator range mainly 0.3 MeV to 3 MeV. Experiment had been set up at an ICT system with a 9 MeV electron linear accelerator. The result is satisfactory. This technique makes the beam hardening correction easy and simple, and it is valuable for measuring the ICT density and making use of the CT images to recognize materials.

  11. Asynchrony in respiratory movements between the pulmonary lobes in patients with COPD: continuous measurement of lung density by 4-dimensional dynamic-ventilation CT.

    PubMed

    Yamashiro, Tsuneo; Moriya, Hiroshi; Matsuoka, Shin; Nagatani, Yukihiro; Tsubakimoto, Maho; Tsuchiya, Nanae; Murayama, Sadayuki

    2017-01-01

    Four-dimensional dynamic-ventilation CT imaging demonstrates continuous movement of the lung. The aim of this study was to assess the correlation between interlobar synchrony in lung density and spirometric values in COPD patients and smokers, by measuring the continuous changes in lung density during respiration on the dynamic-ventilation CT. Thirty-two smokers, including ten with COPD, underwent dynamic-ventilation CT during free breathing. CT data were continuously reconstructed every 0.5 sec. Mean lung density (MLD) of the five lobes (right upper [RU], right middle [RM], right lower [RL], left upper [LU], and left lower [LL]) was continuously measured by commercially available software using a fixed volume of volume of interest which was placed and tracked on a single designated point in each lobe. Concordance between the MLD time curves of six pairs of lung lobes (RU-RL, RU-RM, RM-RL, LU-LL, RU-LU, and RL-LL lobes) was expressed by cross-correlation coefficients. The relationship between these cross-correlation coefficients and the forced expiratory volume in one second/forced vital capacity (FEV1.0/FVC) values was assessed by Spearman rank correlation analysis. In all six pairs of the pulmonary lobes, the cross-correlation coefficients of the two MLD curves were significantly positively correlated with FEV1.0/FVC (ρ =0.60-0.73, P<0.001). The mean value of the six coefficients strongly correlated with FEV1.0/FVC (ρ =0.80, P<0.0001). The synchrony of respiratory movements between the pulmonary lobes is limited or lost in patients with more severe airflow limitation.

  12. Identification of early-stage usual interstitial pneumonia from low-dose chest CT scans using fractional high-density lung distribution

    NASA Astrophysics Data System (ADS)

    Xie, Yiting; Salvatore, Mary; Liu, Shuang; Jirapatnakul, Artit; Yankelevitz, David F.; Henschke, Claudia I.; Reeves, Anthony P.

    2017-03-01

    A fully-automated computer algorithm has been developed to identify early-stage Usual Interstitial Pneumonia (UIP) using features computed from low-dose CT scans. In each scan, the pre-segmented lung region is divided into N subsections (N = 1, 8, 27, 64) by separating the lung from anterior/posterior, left/right and superior/inferior in 3D space. Each subsection has approximately the same volume. In each subsection, a classic density measurement (fractional high-density volume h) is evaluated to characterize the disease severity in that subsection, resulting in a feature vector of length N for each lung. Features are then combined in two different ways: concatenation (2*N features) and taking the maximum in each of the two corresponding subsections in the two lungs (N features). The algorithm was evaluated on a dataset consisting of 51 UIP and 56 normal cases, a combined feature vector was computed for each case and an SVM classifier (RBF kernel) was used to classify them into UIP or normal using ten-fold cross validation. A receiver operating characteristic (ROC) area under the curve (AUC) was used for evaluation. The highest AUC of 0.95 was achieved by using concatenated features and an N of 27. Using lung partition (N = 27, 64) with concatenated features had significantly better result over not using partitions (N = 1) (p-value < 0.05). Therefore this equal-volume partition fractional high-density volume method is useful in distinguishing early-stage UIP from normal cases.

  13. Performance of dispersion-corrected double hybrid density functional theory: a computational study of OCS-hydrocarbon van der Waals complexes.

    PubMed

    Pakhira, Srimanta; Sen, Kaushik; Sahu, Chandan; Das, Abhijit K

    2013-04-28

    The performance of double hybrid density functionals (DHDFs) has been assessed by studying the spectroscopic properties and potential energy curves of OCS-C2H4 (carbonyl sulfide-ethylene) and OCS-C4H6 (carbonyl sulfide-dimethylacetylene) van der Waals complexes. Both dispersion corrected and uncorrected DHDF theories have been applied to study the intermolecular interaction energies, stability, spectroscopic parameters, rigidity, and binding energies or depths of the potential well of the weakly bound complexes and also to explore the possibility of formation of three isomers of each complex. The correlation consistent valence triple zeta quality basis set is used to investigate the complexes. The calculated results provide insight into the computational methods applied to the weakly bound complexes. The double hybrid density functional B2PLYP and mPW2PLYP methods with dispersion corrections (B2PLYP-D2, B2PLYP-D3 and mPW2PLYP-D2, mPW2PLYP-D3) performed better over the B2PLYP and mPW2PLYP density functional methods without dispersion correction to deal with the weak dispersion interaction that prevails in these complexes. The results obtained by the dispersion-corrected density functional mPW2PLYP-D2 and mPW2PLYP-D3 methods agree very well with the earlier experimental values wherever available. The contributing components of the interaction energy have been analyzed by the symmetry-adapted perturbation theory (SAPT, here, SAPT0) to get insight into the interaction energy.

  14. Acceleration of Lung Regeneration by Platelet-Rich Plasma Extract through the Low-Density Lipoprotein Receptor-Related Protein 5-Tie2 Pathway.

    PubMed

    Mammoto, Tadanori; Chen, Zhao; Jiang, Amanda; Jiang, Elisabeth; Ingber, Donald E; Mammoto, Akiko

    2016-01-01

    Angiogenesis, the growth of new blood vessels, plays a key role in organ development, homeostasis, and regeneration. The cooperation of multiple angiogenic factors, rather than a single factor, is required for physiological angiogenesis. Recently, we have reported that soluble platelet-rich plasma (PRP) extract, which contains abundant angiopoietin-1 and multiple other angiogenic factors, stimulates angiogenesis and maintains vascular integrity in vitro and in vivo. In this report, we have demonstrated that mouse PRP extract increases phosphorylation levels of the Wnt coreceptor low-density lipoprotein receptor-related protein 5 (LRP5) and thereby activates angiogenic factor receptor Tie2 in endothelial cells (ECs) and accelerates EC sprouting and lung epithelial cell budding in vitro. PRP extract also increases phosphorylation levels of Tie2 in the mouse lungs and accelerates compensatory lung growth and recovery of exercise capacity after unilateral pneumonectomy in mice, whereas soluble Tie2 receptor or Lrp5 knockdown attenuates the effects of PRP extract. Because human PRP extract is generated from autologous peripheral blood and can be stored at -80°C, our findings may lead to the development of novel therapeutic interventions for various angiogenesis-related lung diseases and to the improvement of strategies for lung regeneration.

  15. Asymptotic correction approach to improving approximate exchange-correlation potentials: Time-dependent density-functional theory calculations of molecular excitation spectra

    NASA Astrophysics Data System (ADS)

    Casida, Mark E.; Salahub, Dennis R.

    2000-11-01

    The time-dependent density functional theory (TD-DFT) calculation of excitation spectra places certain demands on the DFT exchange-correlation potential, vxc, that are not met by the functionals normally used in molecular calculations. In particular, for high-lying excitations, it is crucial that the asymptotic behavior of vxc be correct. In a previous paper, we introduced a novel asymptotic-correction approach which we used with the local density approximation (LDA) to yield an asymptotically corrected LDA (AC-LDA) potential [Casida, Casida, and Salahub, Int. J. Quantum Chem. 70, 933 (1998)]. The present paper details the theory underlying this asymptotic correction approach, which involves a constant shift to incorporate the effect of the derivative discontinuity (DD) in the bulk region of finite systems, and a spliced asymptotic correction in the large r region. This is done without introducing any adjustable parameters. We emphasize that correcting the asymptotic behavior of vxc is not by itself sufficient to improve the overall form of the potential unless the effect of the derivative discontinuity is taken into account. The approach could be used to correct vxc from any of the commonly used gradient-corrected functionals. It is here applied to the LDA, using the asymptotically correct potential of van Leeuwen and Baerends (LB94) in the large r region. The performance of our AC-LDA vxc is assessed for the calculation of TD-DFT excitation energies for a large number of excitations, including both valence and Rydberg states, for each of four small molecules: N2, CO, CH2O, and C2H4. The results show a significant improvement over those from either the LB94 or the LDA functionals. This confirms that the DD is indeed an important element in the design of functionals. The quality of TDLDA/LB94 and TDLDA/AC-LDA oscillator strengths were also assessed in what we believe to be the first rigorous assessment of TD-DFT molecular oscillator strengths in comparison with

  16. Non-covalent interactions and thermochemistry using XDM-corrected hybrid and range-separated hybrid density functionals.

    PubMed

    Otero-de-la-Roza, A; Johnson, Erin R

    2013-05-28

    The exchange-hole dipole-moment model (XDM) for dispersion is combined with a collection of semilocal, hybrid, and range-separated hybrid functionals. The resulting XDM-corrected functionals are tested against standard benchmarks for non-covalent interactions at and away from equilibrium, conformer ranking in water clusters, thermochemistry, and kinetics. We show that functionals with the correct -1∕r tail of the exchange potential yield superior accuracy for weak interactions. Thus, balancing long-range exchange with dispersion interactions in XDM is essential in the correct description of dimers with significant non-dispersion contributions to binding. With the exception of the noble gases, the performance of PW86PBE-XDM is improved upon at the semilocal (BLYP), hybrid (B3LYP), and range-separated hybrid (LC-ωPBE) levels. Based on its excellent performance, we propose LC-ωPBE-XDM as an accurate functional for hard and soft matter.

  17. Non-covalent interactions and thermochemistry using XDM-corrected hybrid and range-separated hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Otero-de-la-Roza, A.; Johnson, Erin R.

    2013-05-01

    The exchange-hole dipole-moment model (XDM) for dispersion is combined with a collection of semilocal, hybrid, and range-separated hybrid functionals. The resulting XDM-corrected functionals are tested against standard benchmarks for non-covalent interactions at and away from equilibrium, conformer ranking in water clusters, thermochemistry, and kinetics. We show that functionals with the correct -1/r tail of the exchange potential yield superior accuracy for weak interactions. Thus, balancing long-range exchange with dispersion interactions in XDM is essential in the correct description of dimers with significant non-dispersion contributions to binding. With the exception of the noble gases, the performance of PW86PBE-XDM is improved upon at the semilocal (BLYP), hybrid (B3LYP), and range-separated hybrid (LC-ωPBE) levels. Based on its excellent performance, we propose LC-ωPBE-XDM as an accurate functional for hard and soft matter.

  18. Neighbourhoods matter too: the association between neighbourhood socioeconomic position, population density and breast, prostate and lung cancer incidence in Denmark between 2004 and 2008.

    PubMed

    Meijer, Mathias; Bloomfield, Kim; Engholm, Gerda

    2013-01-01

    Previous studies have shown that cancer incidence is related to a number of individual factors, including socioeconomic status. The aim of this study was to refine the current knowledge about indicators associated with cancer incidence by evaluating the influence of neighbourhood characteristics on breast, prostate and lung cancer incidence in Denmark. All women aged 30-83 years were followed for breast cancer between 2004 and 2008, men between 50 and 83 years were followed for prostate cancer and both sexes between ages 50 and 83 were followed for lung cancer. Registry data obtained from Statistics Denmark included age, sex, availability of breast cancer screening, marital status, education, disposable income and occupational socioeconomic status on the individual level and population density and neighbourhood socioeconomic status (the proportion of unemployed) on the parish level. Frailty modelling with individuals on the first level and parishes on the second level was conducted. A significantly lower HR of breast cancer was found in areas with low population density (HR=0.93; CI 0.88 to 0.99), while neighbourhood unemployment had no effect. Inhabitants of lower unemployment areas had a higher risk of prostate cancer (HR=1.14; CI 1.08 to 1.21) compared with those in higher unemployment areas, whereas population density had no effect. Risk of lung cancer was lower in areas with lowest population density (HR=0.80; CI 0.74 to 0.85) and lowest in areas with lowest unemployment (HR=0.88; CI 0.84 to 0.92). In addition to individual-level factors, characteristics on the neighbourhood level also have an influence on breast, prostate and lung cancer incidence.

  19. BODE-index, modified BODE-index and ADO-score in chronic obstructive pulmonary disease: relationship with COPD phenotypes and CT lung density changes.

    PubMed

    Camiciottoli, Gianna; Bigazzi, Francesca; Bartolucci, Maurizio; Cestelli, Lucia; Paoletti, Matteo; Diciotti, Stefano; Cavigli, Edoardo; Magni, Chiara; Buonasera, Luigi; Mascalchi, Mario; Pistolesi, Massimo

    2012-06-01

    COPD is a heterogeneous disorder whose assessment is going to be increasingly multidimensional. Grading systems such as BODE (Body-Mass Index, Obstruction, Dyspnea, Exercise), mBODE (BODE modified in grading of walked distance), ADO (Age, Dyspnea, Obstruction) are proposed to assess COPD severity and outcome. Computed tomography (CT) is deemed to reflect COPD lung pathologic changes. We studied the relationship of multidimensional grading systems (MGS) with clinically determined COPD phenotypes and CT lung density. Seventy-two patients underwent clinical and chest x-ray evaluation, pulmonary function tests (PFT), 6-minute walking test (6MWT) to derive: predominant COPD clinical phenotype, BODE, mBODE, ADO. Inspiratory and expiratory CT was performed to calculate mean lung attenuation (MLA), relative area with density below-950 HU at inspiration (RAI(-950)), and below -910 HU at expiration (RAE(-910)). MGS, PFT, and CT data were compared between bronchial versus emphysematous COPD phenotype. MGS were correlated with CT data. The prediction of CT density by means of MGS was investigated by direct and stepwise multivariate regression. MGS did not differ in clinically determined COPD phenotypes. BODE was more closely related and better predicted CT findings than mBODE and ADO; the better predictive model was obtained for CT expiratory data; stepwise regression models of CT data did not include 6MWT distance; the dyspnea score MRC was included only to predict RA-950 and RA-910 which quantify emphysema extent. BODE reflect COPD severity better than other MGS, but not its clinical heterogeneity. 6MWT does not significantly increase BODE predictivity of CT lung density changes.

  20. Calibration of megavoltage cone-beam CT for radiotherapy dose calculations: Correction of cupping artifacts and conversion of CT numbers to electron density

    SciTech Connect

    Petit, Steven F.; Elmpt, Wouter J. C. van; Nijsten, Sebastiaan M. J. J. G.; Lambin, Philippe; Dekker, Andre L. A. J.

    2008-03-15

    Megavoltage cone-beam CT (MV CBCT) is used for three-dimensional imaging of the patient anatomy on the treatment table prior to or just after radiotherapy treatment. To use MV CBCT images for radiotherapy dose calculation purposes, reliable electron density (ED) distributions are needed. Patient scatter, beam hardening and softening effects result in cupping artifacts in MV CBCT images and distort the CT number to ED conversion. A method based on transmission images is presented to correct for these effects without using prior knowledge of the object's geometry. The scatter distribution originating from the patient is calculated with pencil beam scatter kernels that are fitted based on transmission measurements. The radiological thickness is extracted from the scatter subtracted transmission images and is then converted to the primary transmission used in the cone-beam reconstruction. These corrections are performed in an iterative manner, without using prior knowledge regarding the geometry and composition of the object. The method was tested using various homogeneous and inhomogeneous phantoms with varying shapes and compositions, including a phantom with different electron density inserts, phantoms with large density variations, and an anthropomorphic head phantom. For all phantoms, the cupping artifact was substantially removed from the images and a linear relation between the CT number and electron density was found. After correction the deviations in reconstructed ED from the true values were reduced from up to 0.30 ED units to 0.03 for the majority of the phantoms; the residual difference is equal to the amount of noise in the images. The ED distributions were evaluated in terms of absolute dose calculation accuracy for homogeneous cylinders of different size; errors decreased from 7% to below 1% in the center of the objects for the uncorrected and corrected images, respectively, and maximum differences were reduced from 17% to 2%, respectively. The

  1. Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals.

    PubMed

    Kocman, Mikuláš; Jurečka, Petr; Dubecký, Matúš; Otyepka, Michal; Cho, Yeonchoo; Kim, Kwang S

    2015-03-07

    Hydrogen storage in carbonaceous materials and their derivatives is currently a widely investigated topic. The rational design of novel adsorptive materials is often attempted with the help of computational chemistry tools, in particular density functional theory (DFT). However, different exchange-correlation functionals provide a very wide range of hydrogen binding energies. The aim of this article is to offer high level QM reference data based on coupled-cluster singles and doubles calculations with perturbative triple excitations, CCSD(T), and a complete basis set limit estimate that can be used to assess the accuracy of various DFT-based predictions. For one complex, the CCSD(T) result is verified against diffusion quantum Monte Carlo calculations. Reference binding curves are calculated for two model compounds representing weak and strong hydrogen adsorption: coronene (-4.7 kJ mol(-1) per H2), and coronene modified with boron and lithium (-14.3 kJ mol(-1)). The reference data are compared to results obtained with widely used density functionals including pure DFT, M06, DFT-D3, PBE-TS, PBE + MBD, optB88-vdW, vdW-DF, vdW-DF2 and VV10. We find that whereas DFT-D3 shows excellent results for weak hydrogen adsorption on coronene, most of the less empirical density based dispersion functionals except VV10 overestimate this interaction. On the other hand, some of the less empirical density based dispersion functionals better describe stronger binding in the more polar coroB2Li22H2 complex which is one of realistic models for high-capacity hydrogen storage materials. Our results may serve as a guide for choosing suitable DFT methods for quickly evaluating hydrogen binding potential and as a reference for assessing the accuracy of the previously published DFT results.

  2. Assessment of density functional theory optimized basis sets for gradient corrected functionals to transition metal systems: the case of small Nin (n

    PubMed

    López Arvizu, Gregorio; Calaminici, Patrizia

    2007-05-21

    Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (ndensity functional theory approach. Newly developed nickel all-electron basis sets optimized for generalized gradient approximation (GGA) as well as an all-electron basis set optimized for the local density approximation were employed. For both neutral and charged systems, several isomers and different multiplicities were studied in order to determine the lowest energy structures. A vibrational analysis was performed in order to characterize these isomers. Structural parameters, harmonic frequencies, binding energies, ionization potentials, and electron affinities are reported. This work shows that the employed GGA basis sets for the nickel atom are important for the correct prediction of the ground state structures of small nickel clusters and that the structural assignment of these systems can be performed, with a good resolution, over the ionization potential.

  3. Application of London-type dispersion corrections to the solid-state density functional theory simulation of the terahertz spectra of crystalline pharmaceuticals.

    PubMed

    King, Matthew D; Buchanan, William D; Korter, Timothy M

    2011-03-14

    The effects of applying an empirical dispersion correction to solid-state density functional theory methods were evaluated in the simulation of the crystal structure and low-frequency (10 to 90 cm(-1)) terahertz spectrum of the non-steroidal anti-inflammatory drug, naproxen. The naproxen molecular crystal is bound largely by weak London force interactions, as well as by more prominent interactions such as hydrogen bonding, and thus serves as a good model for the assessment of the pair-wise dispersion correction term in systems influenced by intermolecular interactions of various strengths. Modifications to the dispersion parameters were tested in both fully optimized unit cell dimensions and those determined by X-ray crystallography, with subsequent simulations of the THz spectrum being performed. Use of the unmodified PBE density functional leads to an unrealistic expansion of the unit cell volume and the poor representation of the THz spectrum. Inclusion of a modified dispersion correction enabled a high-quality simulation of the THz spectrum and crystal structure of naproxen to be achieved without the need for artificially constraining the unit cell dimensions.

  4. Long-range corrected density functional theory with accelerated Hartree-Fock exchange integration using a two-Gaussian operator [LC-ωPBE(2Gau)

    SciTech Connect

    Song, Jong-Won; Hirao, Kimihiko

    2015-10-14

    Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory.

  5. Calculation of gravity and magnetic anomalies along profiles with end corrections and inverse solutions for density and magnetization

    USGS Publications Warehouse

    Cady, John W.

    1977-01-01

    A computer program is presented which performs, for one or more bodies, along a profile perpendicular to strike, both forward calculations for the magnetic and gravity anomaly fields and independent gravity and magnetic inverse calculations for density and susceptibility or remanent magnetization.

  6. Development of a Geomagnetic Storm Correction to the International Reference Ionosphere E-Region Electron Densities Using TIMED/SABER Observations

    NASA Technical Reports Server (NTRS)

    Mertens, C. J.; Xu, X.; Fernandez, J. R.; Bilitza, D.; Russell, J. M., III; Mlynczak, M. G.

    2009-01-01

    Auroral infrared emission observed from the TIMED/SABER broadband 4.3 micron channel is used to develop an empirical geomagnetic storm correction to the International Reference Ionosphere (IRI) E-region electron densities. The observation-based proxy used to develop the storm model is SABER-derived NO+(v) 4.3 micron volume emission rates (VER). A correction factor is defined as the ratio of storm-time NO+(v) 4.3 micron VER to a quiet-time climatological averaged NO+(v) 4.3 micron VER, which is linearly fit to available geomagnetic activity indices. The initial version of the E-region storm model, called STORM-E, is most applicable within the auroral oval region. The STORM-E predictions of E-region electron densities are compared to incoherent scatter radar electron density measurements during the Halloween 2003 storm events. Future STORM-E updates will extend the model outside the auroral oval.

  7. The effect of Fe doping on adsorption of CO2/N2 within carbon nanotubes: a density functional theory study with dispersion corrections.

    PubMed

    Du, A J; Sun, C H; Zhu, Z H; Lu, G Q; Rudolph, V; Smith, Sean C

    2009-09-16

    An ab initio density functional theory (DFT) study with correction for dispersive interactions was performed to study the adsorption of N(2) and CO(2) inside an (8, 8) single-walled carbon nanotube. We find that the approach of combining DFT and van der Waals correction is very effective for describing the long-range interaction between N(2)/CO(2) and the carbon nanotube (CNT). Surprisingly, exohedral doping of an Fe atom onto the CNT surface will only affect the adsorption energy of the quadrupolar CO(2) molecule inside the CNT (20-30%), and not that of molecular N(2). Our results suggest the feasibility of enhancement of CO(2)/N(2) separation in CNT-based membranes by using exohedral doping of metal atoms.

  8. Balanced Description of Ground-State Properties, Valence Excitations, and Charge-Transfer Excitations with Long-Range Corrected Density Functionals

    NASA Astrophysics Data System (ADS)

    Rohrdanz, Mary A.; Herbert, John M.

    2009-06-01

    Time-dependent density functional theory's favorable scaling properties make it an attractive technique for the study of large, condensed-phase systems. However, in such systems conventional generalized gradient approximation functionals are plagued by spurious, low-energy charge transfer (CT) excitations. Long-range corrected (LRC) functionals, which asymptotically turn on full Hartree-Fock exchange at long range, push these CT states to higher energies. Until recently it has seemed impossible to find a long-range corrected functional that performed acceptably well for both ground- and excited-state properties. We have constructed an implemented a LRC hybrid functional that not only performs reasonably well in a battery of tests on ground-state properties and valence excitations, but also achieves reasonable accuracy for a small database of CT excitations.

  9. Respiration-Averaged CT for Attenuation Correction of PET Images – Impact on PET Texture Features in Non-Small Cell Lung Cancer Patients

    PubMed Central

    Cheng, Nai-Ming; Fang, Yu-Hua Dean; Tsan, Din-Li

    2016-01-01

    Purpose We compared attenuation correction of PET images with helical CT (PET/HCT) and respiration-averaged CT (PET/ACT) in patients with non-small-cell lung cancer (NSCLC) with the goal of investigating the impact of respiration-averaged CT on 18F FDG PET texture parameters. Materials and Methods A total of 56 patients were enrolled. Tumors were segmented on pretreatment PET images using the adaptive threshold. Twelve different texture parameters were computed: standard uptake value (SUV) entropy, uniformity, entropy, dissimilarity, homogeneity, coarseness, busyness, contrast, complexity, grey-level nonuniformity, zone-size nonuniformity, and high grey-level large zone emphasis. Comparisons of PET/HCT and PET/ACT were performed using Wilcoxon signed-rank tests, intraclass correlation coefficients, and Bland-Altman analysis. Receiver operating characteristic (ROC) curves as well as univariate and multivariate Cox regression analyses were used to identify the parameters significantly associated with disease-specific survival (DSS). A fixed threshold at 45% of the maximum SUV (T45) was used for validation. Results SUV maximum and total lesion glycolysis (TLG) were significantly higher in PET/ACT. However, texture parameters obtained with PET/ACT and PET/HCT showed a high degree of agreement. The lowest levels of variation between the two modalities were observed for SUV entropy (9.7%) and entropy (9.8%). SUV entropy, entropy, and coarseness from both PET/ACT and PET/HCT were significantly associated with DSS. Validation analyses using T45 confirmed the usefulness of SUV entropy and entropy in both PET/HCT and PET/ACT for the prediction of DSS, but only coarseness from PET/ACT achieved the statistical significance threshold. Conclusions Our results indicate that 1) texture parameters from PET/ACT are clinically useful in the prediction of survival in NSCLC patients and 2) SUV entropy and entropy are robust to attenuation correction methods. PMID:26930211

  10. The adsorption of h-BN monolayer on the Ni(111) surface studied by density functional theory calculations with a semiempirical long-range dispersion correction

    SciTech Connect

    Sun, X.; Pratt, A.; Li, Z. Y.; Ohtomo, M.; Sakai, S.; Yamauchi, Y.

    2014-05-07

    The geometric and spin-resolved electronic structure of a h-BN adsorbed Ni(111) surface has been investigated by density functional theory calculations. Two energy minima (physisorption and chemisorption) are obtained when the dispersive van der Waals correction is included. The geometry of N atom on top site and B atom on fcc site is the most energetically favorable. Strong hybridization with the ferromagnetic Ni substrate induces considerable gap states in the h-BN monolayer. The induced π* states are spin-polarized.

  11. Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

    PubMed

    Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

    2013-06-14

    Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

  12. Self-interaction corrected density functional calculations of Rydberg states of molecular clusters: N,N-dimethylisopropylamine

    SciTech Connect

    Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes

    2014-12-21

    Theoretical calculations of Rydberg excited states of molecular clusters consisting of N,N-dimethylisopropylamine molecules using a Perdew-Zunger self-interaction corrected energy functional are presented and compared with results of resonant multiphoton ionization measurements. The binding energy of the Rydberg electron in the monomer is calculated to be 2.79 eV and 2.27 eV in the 3s and 3p state, respectively, which compares well with measured values of 2.88 eV and 2.21 eV. Three different stable configurations of the dimer in the ground state were found using an energy functional that includes van der Waals interaction. The lowest ground state energy conformation has the two N-atoms widely separated, by 6.2 Å, while the Rydberg state energy is lowest for a configuration where the N-atoms of the two molecules come close together, separated by 3.7 Å. This conformational change is found to lower the Rydberg electron binding energy by 0.2 eV. The self-interaction corrected functional gives a highly localized hole on one of the two molecules, unlike results obtained using the PBE functional or the hybrid B3LYP functional which give a delocalized hole. For the trimer, the self-interaction corrected calculation gives a Rydberg electron binding energy lowered further by 0.13 eV as compared with the dimer. The calculated results compare well with trends observed in experimental measurements. The reduction of the Rydberg electron binding energy with cluster size can be ascribed to an effective delocalization of the positive charge of the hole by the induced and permanent dipole moments of the neighboring molecules. A further decrease observed to occur on a time scale of tens of ps can be ascribed to a structural rearrangement of the clusters in the Rydberg state where molecules rotate to orient their dipoles in response to the formation of the localized hole.

  13. Assessing Hubbard-corrected AM05+U and PBEsol+U density functionals for strongly correlated oxides CeO2 and Ce2O3.

    PubMed

    Weck, Philippe F; Kim, Eunja

    2016-09-29

    The structure-property relationships of bulk CeO2 and Ce2O3 have been investigated using AM05 and PBEsol exchange-correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+U) and density functional perturbation theory (DFPT+U). Compared with conventional PBE+U, RPBE+U, PW91+U and LDA+U functionals, AM05+U and PBEsol+U describe experimental crystalline parameters and properties of CeO2 and Ce2O3 with superior accuracy, especially when +U is chosen close to its value derived by the linear-response approach. The present findings call for a reexamination of some of the problematic oxide materials featuring strong f- and d-electron correlation using AM05+U and PBEsol+U.

  14. Assessing Hubbard-corrected AM05+U and PBEsol+U density functionals for strongly correlated oxides CeO2 and Ce2O3

    DOE PAGES

    Weck, Philippe F.; Kim, Eunja

    2016-09-12

    The structure–property relationships of bulk CeO2 and Ce2O3 have been investigated using AM05 and PBEsol exchange–correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+U) and density functional perturbation theory (DFPT+U). Compared with conventional PBE+U, RPBE+U, PW91+U and LDA+U functionals, AM05+U and PBEsol+U describe experimental crystalline parameters and properties of CeO2 and Ce2O3 with superior accuracy, especially when +U is chosen close to its value derived by the linear-response approach. Lastly, the present findings call for a reexamination of some of the problematic oxide materials featuring strong f- and d-electron correlation using AM05+U and PBEsol+U.

  15. Intravenous augmentation treatment and lung density in severe α1 antitrypsin deficiency (RAPID): a randomised, double-blind, placebo-controlled trial.

    PubMed

    Chapman, Kenneth R; Burdon, Jonathan G W; Piitulainen, Eeva; Sandhaus, Robert A; Seersholm, Niels; Stocks, James M; Stoel, Berend C; Huang, Liping; Yao, Zhenling; Edelman, Jonathan M; McElvaney, Noel G

    2015-07-25

    The efficacy of α1 proteinase inhibitor (A1PI) augmentation treatment for α1 antitrypsin deficiency has not been substantiated by a randomised, placebo-controlled trial. CT-measured lung density is a more sensitive measure of disease progression in α1 antitrypsin deficiency emphysema than spirometry is, so we aimed to assess the efficacy of augmentation treatment with this measure. The RAPID study was a multicentre, double-blind, randomised, parallel-group, placebo-controlled trial of A1PI treatment in patients with α1 antitrypsin deficiency. We recruited eligible non-smokers (aged 18-65 years) in 28 international study centres in 13 countries if they had severe α1 antitrypsin deficiency (serum concentration <11 μM) with a forced expiratory volume in 1 s of 35-70% (predicted). We excluded patients if they had undergone, or were on the waiting list to undergo, lung transplantation, lobectomy, or lung volume-reduction surgery, or had selective IgA deficiency. We randomly assigned patients (1:1; done by Accovion) using a computerised pseudorandom number generator (block size of four) with centre stratification to receive A1PI intravenously 60 mg/kg per week or placebo for 24 months. All patients and study investigators (including those assessing outcomes) were unaware of treatment allocation throughout the study. Primary endpoints were CT lung density at total lung capacity (TLC) and functional residual capacity (FRC) combined, and the two separately, at 0, 3, 12, 21, and 24 months, analysed by modified intention to treat (patients needed at least one evaluable lung density measurement). This study is registered with ClinicalTrials.gov, number NCT00261833. A 2-year open-label extension study was also completed (NCT00670007). Between March 1, 2006, and Nov 3, 2010, we randomly allocated 93 (52%) patients A1PI and 87 (48%) placebo, analysing 92 in the A1PI group and 85 in the placebo group. The annual rate of lung density loss at TLC and FRC combined did not

  16. Including screening in van der Waals corrected density functional theory calculations: The case of atoms and small molecules physisorbed on graphene

    SciTech Connect

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H{sub 2}, H{sub 2}O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

  17. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    PubMed

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-07

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  18. Beam hardening and smoothing correction effects on performance of micro-ct SkyScan 1173 for imaging low contrast density materials

    NASA Astrophysics Data System (ADS)

    Sriwayu, Wa Ode; Haryanto, Freddy; Khotimah, Siti Nurul; Latief, Fourier Dzar Eljabbar

    2015-04-01

    We have designed and fabricated phantom mimicking breast cancer composition known as a region that has low contrast density. The used compositions are a microcalcifications, fatty tissues and tumor mass by using Al2O3, C27H46O, and hard nylon materials. Besides, phantom also has a part to calculate low cost criteria /CNR (Contrast to Noise Ratio). Uniformity will be measured at water distillation medium located in a part of phantom scale contrast. Phantom will be imaged by using micro ct-sky scan 1173 high energy type, and then also can be quantified CT number to examine SkyScan 1173 performance in imaging low contrast density materials. Evaluation of CT number is done at technique configuration parameter using voltage of 30 kV, exposure 0.160 mAs, and camera resolution 560x560 pixel, the effect of image quality to reconstruction process is evaluated by varying image processing parameters in the form of beam hardening corrections with amount of 25%, 66% and100% with each smoothing level S10,S2 and S7. To obtain the better high quality image, the adjustment of beam hardening correction should be 66% and smoothing level reach maximal value at level 10.

  19. Beam hardening and smoothing correction effects on performance of micro-ct SkyScan 1173 for imaging low contrast density materials

    SciTech Connect

    Sriwayu, Wa Ode; Haryanto, Freddy; Khotimah, Siti Nurul; Latief, Fourier Dzar Eljabbar

    2015-04-16

    We have designed and fabricated phantom mimicking breast cancer composition known as a region that has low contrast density. The used compositions are a microcalcifications, fatty tissues and tumor mass by using Al{sub 2}O{sub 3}, C{sub 27}H{sub 46}O, and hard nylon materials. Besides, phantom also has a part to calculate low cost criteria /CNR (Contrast to Noise Ratio). Uniformity will be measured at water distillation medium located in a part of phantom scale contrast. Phantom will be imaged by using micro ct-sky scan 1173 high energy type, and then also can be quantified CT number to examine SkyScan 1173 performance in imaging low contrast density materials. Evaluation of CT number is done at technique configuration parameter using voltage of 30 kV, exposure 0.160 mAs, and camera resolution 560x560 pixel, the effect of image quality to reconstruction process is evaluated by varying image processing parameters in the form of beam hardening corrections with amount of 25%, 66% and100% with each smoothing level S10,S2 and S7. To obtain the better high quality image, the adjustment of beam hardening correction should be 66% and smoothing level reach maximal value at level 10.

  20. London dispersion forces by range-separated hybrid density functional with second order perturbational corrections: the case of rare gas complexes.

    PubMed

    Gerber, I C; Angyán, J G

    2007-01-28

    A satisfactory account of the van der Waals (vdW) (London dispersion) forces is, in general not possible by the Kohn-Sham method using standard local, semilocal generalized gradient approximation (GGA), or meta-GGA density functionals. The recently proposed range-separated hybrid (RSH) approach, supplemented by second order perturbational corrections (MP2) to include long-range dynamic correlation effects, offers a physically consistent, seamless description of dispersion forces. It is based on a rigorous generalization of the Kohn-Sham method, where long-range exchange and correlation effects are treated by wave function methods, while short-range electron exchange and correlation are handled by local or semilocal functionals. The method is tested on a series of rare gas dimers in comparison with standard wave function theory and density functional theory approaches. In contrast to the most successful exchange correlation functionals, which describe at best the vdW minimum, the RSH+MP2 approach is valid also in the asymptotic region and the potential curve displays the correct 1/R(6) behavior at large internuclear separations. In contrast to usual MP2 calculations, the basis set superposition error is considerably reduced, making RSH+MP2 an ideal tool for exploring the potential energy surface of weakly bound molecular complexes.

  1. Ytterbium monopnictides under high pressure and high temperature: Structural and electronic properties studied using local spin density approximation and Hubbard corrections approach

    NASA Astrophysics Data System (ADS)

    Singh, S. K.; Verma, U. P.

    2014-06-01

    The structural and electronic properties of ytterbium monopnictides YbX (X = N, P) compounds have been investigated using full potential linear augmented plane wave plus local orbitals approach within the framework of density functional theory. The local spin-density approximation along with Hubbard- U corrections and spin-orbit coupling have been used for correct prediction of electronic properties. At ambient conditions ytterbium monopnictides stabilize in NaCl ( B1) structure. Also, the equilibrium properties, viz., lattice constants ( a), bulk modulus ( B 0) and its pressure derivative ( B 0 ') and total energy ( E 0) have been calculated in three other phases namely CsCl ( B2), zinc blende ( B3) and body centred tetragonal. Under compression, both YbN and YbP undergo first-order structural transition from B1 to B2 phase at 164.0 and 33.7 GPa of pressure, respectively. Obtained results show that YbX is semi-metallic in B1 phase and metallic in B2 phase. Thermal parameters such as Gruneisen parameter, Debye temperature, specific heat, thermal expansion coefficient and entropy have been determined as a function of pressure and temperature. The calculated lattice and other parameters are in good agreement with experimental and other theoretical values reported earlier.

  2. Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water

    NASA Astrophysics Data System (ADS)

    Bartók, Albert P.; Gillan, Michael J.; Manby, Frederick R.; Csányi, Gábor

    2013-08-01

    We show how machine learning techniques based on Bayesian inference can be used to enhance the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density functional theory (DFT) by themselves give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable one- and two-body corrections to DFT with modest extra resources. The resulting corrected DFT scheme is considerably more accurate than uncorrected DFT for the relative energies of small water clusters and different ice structures and significantly improves the description of the structure and dynamics of liquid water. However, our results for ice structures and the liquid indicate that beyond-two-body DFT errors cannot be ignored, and we suggest how our machine-learning methods can be further developed to correct these errors.

  3. Symmetry-adapted perturbation theory with Kohn-Sham orbitals using non-empirically tuned, long-range-corrected density functionals

    NASA Astrophysics Data System (ADS)

    Lao, Ka Un; Herbert, John M.

    2014-01-01

    The performance of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals is evaluated against benchmark results for intermolecular interactions. Unlike previous studies of this "SAPT(KS)" methodology, the present study uses non-empirically tuned long-range corrected (LRC) functionals for the monomers. The proper {v{}_xc}(r)rArr 0 asymptotic limit is achieved by tuning the range separation parameter in order to satisfy the condition that the highest occupied KS energy level equals minus the molecule's ionization energy, for each monomer unit. Tests for He2, Ne2, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations.

  4. Improved description of the structural and optoelectronic properties of DNA/RNA nucleobase anhydrous crystals: Experiment and dispersion-corrected density functional theory calculations

    NASA Astrophysics Data System (ADS)

    da Silva, M. B.; Francisco, T. S.; Maia, F. F.; Caetano, E. W. S.; Fulco, U. L.; Albuquerque, E. L.; Freire, V. N.

    2017-08-01

    The development of low cost and environmentally friendly organic electronic/optoelectronic devices has attracted a lot of interest. The integration of DNA and RNA nucleobases to improve the performance of organic light-emitting diodes has been proposed recently [Gomez et al., Sci. Rep. 4, 7105 (2014), 10.1038/srep07105], notwithstanding limited experimental and theoretical information on the optoelectronic properties of DNA/RNA thin films. As a contribution to an improved understanding of DNA/RNA-based devices in the solid state, we have performed in this paper dispersion corrected density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to obtain the optimized geometries, Kohn-Sham band structures and orbitals, charge distribution, optical absorption, Frenkel exciton binding energies, and complex dielectric functions of the five DNA/RNA nucleobase anhydrous crystals, namely cytosine, guanine, adenine, thymine, and uracil. Optical absorption measurements on DNA/RNA nucleobase powders were also performed for comparison with the simulations. An improvement on the local density approximation (LDA) description of the lattice parameter estimates was achieved considering the generalized gradient approach (GGA) with a semiempirical dispersion correction scheme in comparison with structural x-ray data found in the literature. Energy gap correction using the Δ-sol methodology provided a good agreement between theory and experimental estimates from our optical absorption data, greatly surpassing the quality of previous simulations. Effective masses for the carriers were also found, indicating that the guanine crystal as well as the cytosine one (although with some drawbacks) has potential applications in optoelectronics as a direct gap semiconductor, with the other nucleobases presenting either a semiconductor or an insulator character depending on the carrier type. The complex dielectric function exhibits a high degree of anisotropy for different states

  5. Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

    PubMed

    Torres, Edmanuel; DiLabio, Gino A

    2013-08-13

    Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

  6. Effects of van der Waals Density Functional Corrections on Trends in Furfural Adsorption and Hydrogenation on Close-Packed Transition Metal Surfaces

    SciTech Connect

    Liu, Bin; Cheng, Lei; Curtiss, Larry A.; Greeley, Jeffrey P.

    2014-04-01

    The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdWDF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the erpendicular distance and the orientation of the aromatic ringwith respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van derWaals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted–Evans–Polanyi relationship developed solely fromPW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

  7. Effects of van der Waals density functional corrections on trends in furfural adsorption and hydrogenation on close-packed transition metal surfaces

    NASA Astrophysics Data System (ADS)

    Liu, Bin; Cheng, Lei; Curtiss, Larry; Greeley, Jeffrey

    2014-04-01

    The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdW-DF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the perpendicular distance and the orientation of the aromatic ring with respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van der Waals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted-Evans-Polanyi relationship developed solely from PW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

  8. Effects of van der Waals density functional corrections on trends in furfural adsorption and hydrogenation on close-packed transition metal surfaces.

    SciTech Connect

    Liu, Bin; Cheng, Lei; Curtiss, Larry; Greeley, Jeffrey

    2014-04-01

    The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdW-DF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of funcfionals, while on Cu(111), modest changes are seen in both the perpendicular distance and the orientation of the aromatic ring with respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van der Waals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brensted-Evans-Polanyi relationship developed solely from PW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfulyl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

  9. Structural and vibrational properties of α-MoO3 from van der Waals corrected density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Ding, Hong; Ray, Keith G.; Ozolins, Vidvuds; Asta, Mark

    2012-01-01

    Structural and vibrational properties of α-MoO3 are studied employing two recently proposed methodologies for incorporating van der Waals (vdW) contributions in density functional theory (DFT) based calculations. The DFT-D2 [S. Grimme, J. Comput. Chem.JCCHDD0192-865110.1002/jcc.20495 27, 1787 (2006)] and optB88 vdW-DFT [J. Klimeš , J. Phys.: Condens. MatterPRBMDO0953-898410.1088/0953-8984/22/2/022201 22, 022201 (2010)] methods are shown to give rise to increased accuracy in predicted lattice parameters, relative to conventional DFT methods. Calculated vibrational frequencies agree with measurements to within 5% and 10% for modes involving bonded and nonbonded interactions in this compound, respectively.

  10. A density functional theory study on the effect of zero-point energy corrections on the methanation profile on Fe(100).

    PubMed

    Govender, Ashriti; Ferré, Daniel Curulla; Niemantsverdriet, J W Hans

    2012-04-23

    The thermodynamics and kinetics of the surface hydrogenation of adsorbed atomic carbon to methane, following the reaction sequence C+4H(-->/<--)CH+3H(-->/<--)CH(2)+2H(-->/<--)CH(3)+H(-->/<--)CH(4), are studied on Fe(100) by means of density functional theory. An assessment is made on whether the adsorption energies and overall energy profile are affected when zero-point energy (ZPE) corrections are included. The C, CH and CH(2) species are most stable at the fourfold hollow site, while CH(3) prefers the twofold bridge site. Atomic hydrogen is adsorbed at both the twofold bridge and fourfold hollow sites. Methane is physisorbed on the surface and shows neither orientation nor site preference. It is easily desorbed to the gas phase once formed. The incorporation of ZPE corrections has a very slight, if any, effect on the adsorption energies and does not alter the trends with regards to the most stable adsorption sites. The successive addition of hydrogen to atomic carbon is endothermic up to the addition of the third hydrogen atom resulting in the methyl species, but exothermic in the final hydrogenation step, which leads to methane. The overall methanation reaction is endothermic when starting from atomic carbon and hydrogen on the surface. Zero-point energy corrections are rarely provided in the literature. Since they are derived from C-H bonds with characteristic vibrations on the order of 2500-3000 cm(-1), the equivalent ZPE of 1/2 hν is on the order of 0.2-0.3 eV and its effect on adsorption energy can in principle be significant. Particularly in reactions between CH(x) and H, the ZPE correction is expected to be significant, as additional C-H bonds are formed. In this instance, the methanation reaction energy of +0.77 eV increased to +1.45 eV with the inclusion of ZPE corrections, that is, less favourable. Therefore, it is crucial to include ZPE corrections when reporting reactions involving hydrogen-containing species.

  11. Systematic approach for simultaneously correcting the band-gap andp-dseparation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

    DOE PAGES

    Wang, Jianwei; Zhang, Yong; Wang, Lin-Wang

    2015-07-31

    We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles methodmore » can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.« less

  12. The role of the exchange-correlation response kernel and scaling corrections in relativistic density functional nuclear magnetic shielding calculations with the zeroth-order regular approximation

    NASA Astrophysics Data System (ADS)

    Autschbach, Jochen

    2013-09-01

    The relativistic NMR module of the Amsterdam Density Functional (ADF) package, which is frequently utilised in studies of heavy atom NMR chemical shifts, is extended to calculate a hitherto neglected term from the response of the exchange-correlation (XC) potential. The term vanishes in the absence of spin-orbit coupling. Further, corrections to the shielding arising from scaling factors in the zeroth-order regular approximation (zora) relativistic framework are investigated. The XC response markedly improves calculated proton chemical shifts for hydrogen halides. Mercury chemical shifts for mercury dihalides are also noticeably altered. Contributions from density-gradient dependent terms in the response kernel contribute about 30-40%. New fully relativistic density functional theory (DFT) benchmark data are compared with zora and literature reference values. In line with previous work, it is found that absolute shielding constants for Hg are not accurately predicted with zora. However, chemical shifts agree well with fully relativistic calculations. The application of 'scaled-zora' scaling factors deteriorates the shielding constants and is therefore not recommended. The scaling hardly affects chemical shifts. zora calculations are not suitable for absolute shielding of heavy atoms but they can be used safely for chemical shifts in most application scenarios.

  13. Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

    PubMed

    Fekete, Attila; Komáromi, István

    2016-12-07

    A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to

  14. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

    NASA Astrophysics Data System (ADS)

    Kruse, Holger; Grimme, Stefan

    2012-04-01

    A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

  15. Empirical Storm-Time Correction to the International Reference Ionosphere Model E-Region Electron and Ion Density Parameterizations Using Observations from TIMED/SABER

    NASA Technical Reports Server (NTRS)

    Mertens, Christoper J.; Winick, Jeremy R.; Russell, James M., III; Mlynczak, Martin G.; Evans, David S.; Bilitza, Dieter; Xu, Xiaojing

    2007-01-01

    The response of the ionospheric E-region to solar-geomagnetic storms can be characterized using observations of infrared 4.3 micrometers emission. In particular, we utilize nighttime TIMED/SABER measurements of broadband 4.3 micrometers limb emission and derive a new data product, the NO+(v) volume emission rate, which is our primary observation-based quantity for developing an empirical storm-time correction the IRI E-region electron density. In this paper we describe our E-region proxy and outline our strategy for developing the empirical storm model. In our initial studies, we analyzed a six day storm period during the Halloween 2003 event. The results of this analysis are promising and suggest that the ap-index is a viable candidate to use as a magnetic driver for our model.

  16. Highly Accelerated, Intravascular T1, T2, and Proton Density Mapping with Linear Algebraic Modeling and Sensitivity Profile Correction at 3T.

    PubMed

    Wang, Guan; Zhang, Yi; Hegde, Shashank Sathyanarayana; Bottomley, Paul A

    2016-05-01

    Vessel wall MRI with intravascular (IV) detectors can produce superior local signal-to-noise ratios (SNR) and generate high-resolution T1, T2, and proton density (PD) maps that could be used to automatically classify atherosclerotic lesion stage. However, long acquisition times potentially limit multi-parametric mapping. Here, for the first time, spectroscopy with linear algebraic modeling (SLAM) is applied to yield accurate compartment-average T1, T2 and PD measures at least 10 times faster compared to a standard full k-space reconstructed MIX-TSE sequence at 3T. Simple phase and magnitude sensitivity corrections are incorporated into the SLAM reconstruction to compensate for IV detector non-uniformity.

  17. Investigation of the pressure dependent thermodynamic and elastic properties of 1,3,5-triamino-2,4,6-trinitrobenzene using dispersion corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Rykounov, A. A.

    2015-06-01

    The influence of pressure on the thermodynamic, structural, and elastic properties of the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecular crystal at T = 0 is systematically studied. Calculations are carried out using density functional theory methods in a plane wave basis set with dispersion corrections for the exchange-correlation part of total energy, and ultrasoft pseudopotentials. The equilibrium unit cell parameters, the cold compression curve in the pressure range of 0-50 GPa and the sound speeds are computed. The effect of finite pressure on the molecular structure of TATB is elucidated from the analysis of relative changes in the intra- and intermolecular geometrical parameters. For the first time, the full set of elastic constants of this crystal at zero and non-zero pressures is determined from ab initio calculations. The resulted structural, elastic, and acoustic properties of TATB are shown to be in a good agreement with available experimental and theoretical data.

  18. Surgical Correction in Patients with Lumbar Degenerative Kyphosis Who Had Low Bone Mineral Density: An Analysis of 40 Patients with a Minimum Follow-Up of Two Years

    PubMed Central

    Kim, Ki Tack; Lee, Sang Hun; Huh, Dae Seok; Son, Eun Seok

    2015-01-01

    Study Design Retrospective study. Purpose To investigate influence of bone mineral density (BMD) on the surgical correction of lumbar degenerative kyphosis (LDK). Overview of Literature No studies so far have reported the influence of BMD on the surgical correction of LDK. Methods Forty LDK patients with more than 2 years follow-up were studied. Pelvic incidence (PI), pelvic tilt, sacral slope, sagittal vertical axis (SVA), lumbar lordosis (LL), and thoracic kyphosis were measured preoperatively, immediate postoperatively and at final follow-up. Adverse outcomes: proximal adjacent fractures, sagittal decompensation, pseudoarthrosis, and cage subsidence were documented. Results There were 37 females and 3 males. Average age was 65.1±4.5 years and mean follow-up was 34.2±16.7 months. 42.5% were Takemitsu type 3 curves, 27.5% type 2, 20.0% type 4 and 10.0% type 1. 37.5% had osteopenia, 40.0% osteoporosis and 22.5% had severe osteoporosis. SVA improved from 237.0±96.7 mm preoperatively to 45.3±41.8 mm postoperatively (p=0.000). LL improved from 10.5°±14.7° to -40.6°±10.9° postoperatively (p=0.000). At final follow-up SVA deteriorated to 89.8±72.2 mm and LL to 34.7°±15.8° (p=0.000). The association between late sagittal decompensation, pseudoarthrosis, or proximal adjacent fractures and osteoporosis was insignificant. The difference between immediate postoperative LL and PI (PIDiff) had a significant association with sagittal decompensation and pseudoarthrosis. Conclusions Osteoporosis did not influence the degree of correction, late sagittal decompensation, proximal adjacent fractures, and pseudoarthrosis in LDK. PIDiff had a significant association with sagittal decompensation and pseudoarthrosis. PMID:25705337

  19. Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

    SciTech Connect

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-14

    The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

  20. Reply to Comment on 'Excited states of DNA base pairs using long-range corrected time-dependent density functional theory

    SciTech Connect

    Jensen, Lasse; Govind, Niranjan

    2009-09-18

    In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.

  1. Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

    NASA Astrophysics Data System (ADS)

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-01

    The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

  2. Estimation of the pKa values of water ligands in transition metal complexes using density functional theory with polarized continuum model solvent corrections.

    PubMed

    Gilson, Ronan; Durrant, Marcus C

    2009-12-14

    The deprotonation energies of the water ligands in a set of 40 d-block metal complexes have been calculated using density functional theory with polarized continuum model solvent corrections. The complexes include 13 aqua ions [M(OH(2))(n)](2+/3+) and a variety of aqua complexes with organic co-ligands, whose experimental pK(a) values have been reported in the literature. For comparison, the deprotonation energies of a set of 60 organic and inorganic molecules with experimental pK(a) values ranging from -25 (HSbF(6)) to +52 (C(2)H(6)) have also been calculated. Three different classes of acids are identified as giving different slopes in plots of pK(a) versus deprotonation energies; namely non-hydroxy acids, hydroxy acids, and the metal complexes. The correlation coefficients for the straight lines obtained for these three classes are 0.96, 0.97 and 0.92 respectively. Better correlations are found for sub-sets of the complexes, such as the 31 first row complexes (correlation coefficient 0.95).For several of the complexes, comparison of the calculated and observed pK(a) values, together with changes in the geometry upon optimization, offer new insights into the possible solution structures. It is concluded that DFT calculations incorporating solvent corrections can be used to give reasonable estimates of pK(a) values for the aqua ligands in a range of complex types.

  3. The effect of image radiometric correction on the accuracy of vegetation canopy density estimate using several Landsat-8 OLI’s vegetation indices: A case study of Wonosari area, Indonesia

    NASA Astrophysics Data System (ADS)

    Dewa, R. P.; Danoedoro, P.

    2017-01-01

    Recent studies on the use of spectral indices have involved radiometric correction as a prerequisite. However, study on the effect of radiometric correction level on the accuracy of biophysical parameters’ estimate is still rare in Indonesia. This study tried to investigate the influence of various radiometric correction levels and the number of vegetation strata on the accuracy of vegetation density estimates using NDVI, MSAVI2 and GEMI of Landsat 8 OLI. In this study, the dataset covering vegetated area in Wonosari, Gunung Kidul Regency, Indonesia was processed radiometrically using eight different methods, i.e. spectral radiance, at sensor reflectance, sun elevation correction, histogram adjustments using original DN, spectal radiance, at sensor reflectance, and sun position correction respectively, as well as dark object subtraction (DOS). Every image with specific correction level was then transformed using the aforementioned indices, in order correlate with the field-measured canopy density. The analysis were carried out by considering the number of canopy layers. This found that different radiometric correction methods resulted canopy density estimates with different accuracies. The number of canopy strata also played an important role. Every vegetation index transformation performed its best accuracy by using different radiometric correction method and different number of canopy layers.

  4. Optimized Long-Range Corrected Density Functionals for Electronic and Optical Properties of Bare and Ligated CdSe Quantum Dots.

    PubMed

    Bokareva, O S; Shibl, M F; Al-Marri, M J; Pullerits, T; Kühn, O

    2017-01-10

    The reliable prediction of optical and fundamental gaps of finite size systems using density functional theory requires to account for the potential self-interaction error, which is notorious for degrading the description of charge transfer transitions. One solution is provided by parametrized long-range corrected functionals such as LC-BLYP, which can be tuned such as to describe certain properties of the particular system at hand. Here, bare and 3-mercaptoprotionic acid covered Cd33Se33 quantum dots are investigated using the optimally tuned LC-BLYP functional. The range separation parameter, which determines the switching on of the exact exchange contribution, is found to be 0.12 bohr(-1) and 0.09 bohr(-1) for the bare and covered quantum dot, respectively. It is shown that density functional optimization indeed yields optical and fundamental gaps and thus exciton binding energies, considerably different compared with standard functionals such as the popular PBE and B3LYP ones. This holds true, despite the well established fact that the leading transitions are localized on the quantum dot and do not show pronounced long-range charge transfer character.

  5. Dispersion-Corrected Density Functional Theory Investigations of Structural and Electronic Properties of Bulk MoS2: Effect of Uniaxial Strain.

    PubMed

    Nguyen, Chuong V; Hieu, Nguyen N; Nguyen, Duong T

    2015-12-01

    Strain-dependent structural and electronic properties of MoS2 materials are investigated using first principles calculations. The structural and electronic band structures of the MoS2 with relaxed unit cells are optimized and calculated by the dispersion-corrected density functional theory (DFT-D2). Calculations within the local density approximation (LDA) and GGA using PAW potentials were also performed for specific cases for the purpose of comparison. The effect of strain on the band gap and the dependence of formation energy on strain of MoS2 are also studied and discussed using the DFT-D2 method. In bulk MoS2, the orbitals shift towards the higher/lower energy area when strain is applied along the z/x direction, respectively. The energy splitting of Mo4d states is in the range from 0 to 2 eV, which is due to the reduction of the electronic band gap of MoS2.

  6. Dispersion-Corrected Density Functional Theory Investigations of Structural and Electronic Properties of Bulk MoS2: Effect of Uniaxial Strain

    NASA Astrophysics Data System (ADS)

    Nguyen, Chuong V.; Hieu, Nguyen N.; Nguyen, Duong T.

    2015-11-01

    Strain-dependent structural and electronic properties of MoS2 materials are investigated using first principles calculations. The structural and electronic band structures of the MoS2 with relaxed unit cells are optimized and calculated by the dispersion-corrected density functional theory (DFT-D2). Calculations within the local density approximation (LDA) and GGA using PAW potentials were also performed for specific cases for the purpose of comparison. The effect of strain on the band gap and the dependence of formation energy on strain of MoS2 are also studied and discussed using the DFT-D2 method. In bulk MoS2, the orbitals shift towards the higher/lower energy area when strain is applied along the z/ x direction, respectively. The energy splitting of Mo4 d states is in the range from 0 to 2 eV, which is due to the reduction of the electronic band gap of MoS2.

  7. Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional.

    PubMed

    McGrath, Matthew J; Kuo, I-Feng William; Siepmann, J Ilja

    2011-11-28

    Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

  8. Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold

    NASA Astrophysics Data System (ADS)

    Casida, Mark E.; Jamorski, Christine; Casida, Kim C.; Salahub, Dennis R.

    1998-03-01

    This paper presents an evaluation of the performance of time-dependent density-functional response theory (TD-DFRT) for the calculation of high-lying bound electronic excitation energies of molecules. TD-DFRT excitation energies are reported for a large number of states for each of four molecules: N2, CO, CH2O, and C2H4. In contrast to the good results obtained for low-lying states within the time-dependent local density approximation (TDLDA), there is a marked deterioration of the results for high-lying bound states. This is manifested as a collapse of the states above the TDLDA ionization threshold, which is at -ɛHOMOLDA (the negative of the highest occupied molecular orbital energy in the LDA). The -ɛHOMOLDA is much lower than the true ionization potential because the LDA exchange-correlation potential has the wrong asymptotic behavior. For this reason, the excitation energies were also calculated using the asymptotically correct potential of van Leeuwen and Baerends (LB94) in the self-consistent field step. This was found to correct the collapse of the high-lying states that was observed with the LDA. Nevertheless, further improvement of the functional is desirable. For low-lying states the asymptotic behavior of the exchange-correlation potential is not critical and the LDA potential does remarkably well. We propose criteria delineating for which states the TDLDA can be expected to be used without serious impact from the incorrect asymptotic behavior of the LDA potential.

  9. Vision-based measurement system for structural vibration monitoring using non-projection quasi-interferogram fringe density enhanced by spectrum correction method

    NASA Astrophysics Data System (ADS)

    Zhong, Jianfeng; Zhong, Shuncong; Zhang, Qiukun; Zhuang, Yizhou; Lu, Huancai; Fu, Xinbin

    2017-01-01

    A non-projection fringe vision measurement system suitable for vibration monitoring was proposed by using the concept of a 2D optical coherence vibration tomography (2D-OCVT) technique. An artificial quasi-interferogram fringe pattern (QIFP), similar to the interferogram of the 2D-OCVT system, was pasted onto the surface of a vibrating structure as a sensor. Image sequences of the QIFP were captured by a high-speed CMOS camera that worked as a detector. It was possible to obtain both the in-plane and out-of-plane vibration simultaneously. The in-plane vibration was obtained by tracking the center of the imaged QIFP using an image cross-correlation method, whilst the out-of-plane vibration was obtained from the changes in period density of the imaged QIFP. The influence of the noise sources from the CMOS image sensor, together with the effect of the imaging distance, the period density of the QIFP and also the key parameters of the fringe density enhanced by the spectrum correction method on the accuracy of the displacement measurement, were investigated by numerical simulations and experiments. Compared with the results from a conventional accelerometer-based measurement system, the proposed method was demonstrated to be an effective and accurate technique for measuring structural vibration without introducing any extra mass from the accelerometer. The significant advantages of this method include its simple installation and real-time dynamic response measurement capability, making the measurement system ideal for the low- and high-frequency vibration monitoring of engineering structures.

  10. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

    PubMed

    Grimme, Stefan; Antony, Jens; Ehrlich, Stephan; Krieg, Helge

    2010-04-21

    The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related

  11. Number of circulating endothelial progenitor cells and intratumoral microvessel density in non-small cell lung cancer patients: differences in angiogenic status between adenocarcinoma histologic subtypes.

    PubMed

    Maeda, Ryo; Ishii, Genichiro; Ito, Masami; Hishida, Tomoyuki; Yoshida, Junji; Nishimura, Mitsuyo; Haga, Hironori; Nagai, Kanji; Ochiai, Atsushi

    2012-03-01

    Angiogenesis plays a significant role in tumor progression. This study examined the association between the number of circulating endothelial progenitor cells (EPCs), intratumoral microvessel density (MVD) (both of which may be markers for neovascularization), and lung cancer histological types, particularly adenocarcinoma histological subtypes. A total of 83 stage I non-small cell lung cancer (NSCLC) patients underwent complete tumor resection between November 2009 and July 2010. The number of EPCs from the pulmonary artery of the resected lungs was measured by assaying CD34/vascular endothelial growth factor receptor 2 positive cells, and the MVD was assessed immunohistochemically in tumor specimens by staining for CD34. A statistically significant correlation between the number of EPCs from pulmonary artery and intratumoral MVD was found (p < 0.001). No statistically significant differences in the number of EPCs and the MVD were observed between the adenocarcinomas and the squamous cell carcinomas. Among the adenocarcinoma histological subtypes, a higher number of EPCs and MVD were found significantly more frequently in solid adenocarcinomas than in nonsolid adenocarcinomas (p < 0.001 and p = 0.011, respectively). In addition, solid adenocarcinomas showed higher levels of vascular endothelial growth factor using quantitative real-time polymerase chain reaction in the tumor tissue samples than in the nonsolid adenocarcinomas (p = 0.005). The higher number of circulating EPCs and the MVD of solid adenocarcinoma may indicate the presence of differences in the tumor angiogenic status between early-stage adenocarcinoma histological subtypes. Among adenocarcinoma patients, patients with solid adenocarcinoma may be the best candidates for antiangiogenic therapies.

  12. Combination of body mass index and oxidized low density lipoprotein receptor 1 in prognosis prediction of patients with squamous non-small cell lung cancer.

    PubMed

    Jiang, Long; Jiang, Shanshan; Lin, Yongbin; Yang, Han; Zhao, Zerui; Xie, Zehua; Lin, Yaobin; Long, Hao

    2015-09-08

    Lung cancer, especially non-small cell lung cancer (NSCLC), represents enormous challenges in continuously achieving treatment improvements. Besides cancer, obesity is becoming ever more prevalent. Obesity is increasingly acknowledged as a major risk factor for several types of common cancers. Significant mechanisms overlap in the pathobiology of obesity and tumorigenesis. One of these mechanisms involves oxidized low density lipoprotein receptor 1 (OLR1), as a link between obesity and cancer. Additionally, body mass index (BMI) has been widely used in exploiting the role of obesity on a series of diseases, including cancer. Significantly, squamous NSCLC revealed to be divergent clinical and molecular phenotypes compared with non-squamous NSCLC. Consequently, OLR1 immunostaining score and BMI were assessed by Fisher's linear discriminant analysis to discriminate if progression-free survival (PFS) would exceed 2 years. In addition, the final model was utilized to calculate the discriminant score in each study participant. Finally, 131 patients with squamous NCSLC were eligible for analysis. And a prediction model was established for PFS based on these 2 markers and validated in a second set of squamous NCSLC patients. The model offers a novel tool for survival prediction and could establish a framework for future individualized therapy for patients with squamous NCSLC.

  13. [Serum and tissue concentration of tegafur and 5-FU after administration of tegafur suppository in patients with lung cancer--correcting the influence of residual blood in the tissue].

    PubMed

    Ohno, K; Nakahara, K; Hashimoto, J; Matsumura, A; Mizuta, T; Akashi, A; Nakagawa, K; Takeda, S; Minami, M; Kawashima, Y

    1989-11-01

    Tissue concentration of tegafur and 5-FU was studied in 25 patients with of primary lung cancer, given 2 x 750 mg of tegafur suppository daily preoperatively (total doses 3.75-9.75 g, mean 5.16 g). Furthermore, the influence of blood remaining in the tissue was corrected in the determination of tegafur and 5-FU concentration. The tegafur level in tumor tissue (9.614 +/- 5.739 micrograms/g) was significantly (p less than 0.01) low compared with those in serum and normal lung tissue (13.185 +/- 8.198 micrograms/ml, 12.954 +/- 10.048 micrograms/g). On the other hand, the 5-FU level in tumor tissue (0.124 +/- 0.208) was significantly (p less than 0.01, p less than 0.05) high compared with those in serum and normal lung tissue (0.019 +/- 0.013 micrograms/ml, 0.035 +/- 0.031 micrograms/g) and showed approximately 2.5 times more minimum effective concentration against tumor cells (0.05 micrograms/g). The results show that preoperative administration of 2 x 750 mg of tegafur suppository daily is effective for the transfer of tegafur and 5-FU to lung cancer tissue.

  14. Iron deposition and increased alveolar septal capillary density in nonfibrotic lung tissue are associated with pulmonary hypertension in idiopathic pulmonary fibrosis.

    PubMed

    Kim, Kyung-Hee; Maldonado, Fabien; Ryu, Jay H; Eiken, Patrick W; Hartman, Thomas E; Bartholmai, Brian J; Decker, Paul A; Yi, Eunhee S

    2010-04-14

    Early diagnosis of pulmonary hypertension (PH) in idiopathic pulmonary fibrosis (IPF) has potential prognostic and therapeutic implications but can be difficult due to the lack of specific clinical manifestations or accurate non-invasive tests. Histopathologic parameters correlating with PH in IPF are also not known. Remodeling of postcapillary pulmonary vessels has been reported in the nonfibrotic areas of explanted lungs from IPF patients. We hypothesized that iron deposition and increased alveolar capillaries, the findings often seen in postcapillary PH, might predict the presence of clinical PH, independent of the severity of fibrosis or ventilatory dysfunction in IPF patients. To test this hypothesis, we examined the association between these histologic parameters and the degree of PH, with consideration of the severity of disease in IPF. Iron deposition and alveolar septal capillary density (ASCD) were evaluated on histologic sections with hematoxylin-eosin, iron, elastin and CD34 stainings. Percentage of predicted forced vital capacity (FVC%) was used for grading pulmonary function status. Fibrosis score assessed on high resolution computed tomography (HRCT) was used for evaluating overall degree of fibrosis in whole lungs. Right ventricular systolic pressure (RVSP) by transthoracic echocardiography was used for the estimation of PH. Univariate and multivariate regression analyses were performed. A cohort of 154 patients was studied who had the clinicopathological diagnosis of IPF with surgical lung biopsies or explants during the period of 1997 to 2006 at Mayo Clinic Rochester. In univariate analysis, RVSP in our IPF cases was associated with both iron deposition and ASCD (p < 0.001). In multivariate analysis with FVC% and HRCT fibrosis score included, iron deposition (p = 0.02), but not ASCD (p = 0.076), maintained statistically significant association with RVSP. FVC% was associated with RVSP on univariate analysis but not on multivariate analysis, while

  15. Force correcting atom centred potentials for generalised gradient approximated density functional theory: Approaching hybrid functional accuracy for geometries and harmonic frequencies in small chlorofluorocarbons

    NASA Astrophysics Data System (ADS)

    Anatole von Lilienfeld, O.

    2013-08-01

    Generalised gradient approximated (GGA) density functional theory (DFT) typically overestimates polarisability and bond-lengths, and underestimates force constants of covalent bonds. To overcome this problem we show that one can use empirical force correcting atom centred potentials (FCACPs), parametrised for every nuclear species. Parameters are obtained through minimisation of a penalty functional that explicitly encodes hybrid DFT forces and static polarisabilities of reference molecules. For hydrogen, fluorine, chlorine and carbon the respective reference molecules consist of H2, F2, Cl2 and CH4. The transferability of this approach is assessed for harmonic frequencies in a small set of chlorofluorocarbon molecules. Numerical evidence, gathered for CF4, CCl4, CCl3F, CCl2F2, CClF3, ClF, HF, HCl, CFH3, CF2H2, CF3H, CHCl3, CH2Cl2 and CH3Cl indicates that the GGA+FCACP level of theory yields harmonic frequencies that are significantly more consistent with hybrid DFT values, as well as slightly reduced molecular polarisability.

  16. Investigation of the pressure dependent thermodynamic and elastic properties of 1,3,5-triamino-2,4,6-trinitrobenzene using dispersion corrected density functional theory

    SciTech Connect

    Rykounov, A. A.

    2015-06-07

    The influence of pressure on the thermodynamic, structural, and elastic properties of the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecular crystal at T = 0 is systematically studied. Calculations are carried out using density functional theory methods in a plane wave basis set with dispersion corrections for the exchange-correlation part of total energy, and ultrasoft pseudopotentials. The equilibrium unit cell parameters, the cold compression curve in the pressure range of 0–50 GPa and the sound speeds are computed. The effect of finite pressure on the molecular structure of TATB is elucidated from the analysis of relative changes in the intra- and intermolecular geometrical parameters. For the first time, the full set of elastic constants of this crystal at zero and non-zero pressures is determined from ab initio calculations. The resulted structural, elastic, and acoustic properties of TATB are shown to be in a good agreement with available experimental and theoretical data.

  17. Successes and failures of Hubbard-corrected density functional theory: The case of Mg doped LiCoO{sub 2}

    SciTech Connect

    Santana, Juan A.; Kim, Jeongnim; Reboredo, Fernando A.; Kent, P. R. C.

    2014-10-28

    We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO{sub 2}. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO{sub 2}. We find that formation of impurity states results in changes on the valency of Co in LiCoO{sub 2}. Variation of the Co U shifts the energy of the impurity state, resulting in energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO{sub 2}.

  18. Benchmarking Density Functional Theory Based Methods To Model NiOOH Material Properties: Hubbard and van der Waals Corrections vs Hybrid Functionals.

    PubMed

    Zaffran, Jeremie; Caspary Toroker, Maytal

    2016-08-09

    NiOOH has recently been used to catalyze water oxidation by way of electrochemical water splitting. Few experimental data are available to rationalize the successful catalytic capability of NiOOH. Thus, theory has a distinctive role for studying its properties. However, the unique layered structure of NiOOH is associated with the presence of essential dispersion forces within the lattice. Hence, the choice of an appropriate exchange-correlation functional within Density Functional Theory (DFT) is not straightforward. In this work, we will show that standard DFT is sufficient to evaluate the geometry, but DFT+U and hybrid functionals are required to calculate the oxidation states. Notably, the benefit of DFT with van der Waals correction is marginal. Furthermore, only hybrid functionals succeed in opening a bandgap, and such methods are necessary to study NiOOH electronic structure. In this work, we expect to give guidelines to theoreticians dealing with this material and to present a rational approach in the choice of the DFT method of calculation.

  19. Charge transfer optical absorption and fluorescence emission of 4-(9-acridyl)julolidine from long-range-corrected time dependent density functional theory in polarizable continuum approach

    NASA Astrophysics Data System (ADS)

    Kityk, A. V.

    2014-07-01

    A long-range-corrected time-dependent density functional theory (LC-TDDFT) in combination with polarizable continuum model (PCM) have been applied to study charge transfer (CT) optical absorption and fluorescence emission energies basing on parameterized LC-BLYP xc-potential. The molecule of 4-(9-acridyl)julolidine selected for this study represents typical CT donor-acceptor dye with strongly solvent dependent optical absorption and fluorescence emission spectra. The result of calculations are compared with experimental spectra reported in the literature to derive an optimal value of the model screening parameter ω. The first absorption band appears to be quite well predictable within DFT/TDDFT/PCM with the screening parameter ω to be solvent independent (ω≈0.245 Bohr-1) whereas the fluorescence emission exhibits a strong dependence on the range separation with ω-value varying on a rising solvent polarity from about 0.225 to 0.151 Bohr-1. Dipolar properties of the initial state participating in the electronic transition have crucial impact on the effective screening.

  20. Successes and failures of Hubbard-corrected density functional theory. The case of Mg doped LiCoO2

    SciTech Connect

    Santana Palacio, Juan A.; Kim, Jeongnim; Kent, Paul R.; Reboredo, Fernando A.

    2014-10-28

    We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO2. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO2. We find that formation of impurity states results in changes on the valency of Co in LiCoO2. Variation of the Co U shifts the energy of the impurity state, resulting in energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO2.

  1. Kohn-Sham calculations with self-interaction-corrected local-spin-density exchange-correlation energy functional for atomic systems

    NASA Astrophysics Data System (ADS)

    Chen, Jiqiang; Krieger, J. B.; Li, Yan; Iafrate, G. J.

    1996-11-01

    We have investigated the accuracy of the local-spin-density approximation with orbital-density-dependent self-interaction correction (LSDSIC) as proposed by Perdew and Zunger within a Kohn-Sham approach in which electrons with a given spin projection all move in a single optimized effective potential (OEP). We have also studied the accuracy of the Krieger-Li-Iafrate (KLI) approximation to the OEP for the same energy functional in order to assess its applicability to systems in which the integral equation for the OEP cannot be reduced to a one-dimensional problem, e.g., molecules. Self-consistent Kohn-Sham LSDSIC calculations have been performed for atoms with atomic number Z=1-20 in the exchange-only case for the total energy, the highest-occupied orbital energy ɛm, and the expectation value of r2. In addition, the structure of the resulting exchange potential is examined and compared with the exact exchange-only density-functional theory (OEP method with Hartree-Fock exchange-energy functional) results. Furthermore, we display ɛm, the ionization potential I, and the electron affinity A when both exchange and correlation energy effects are included. Finally, we also consider the results of evaluating the LSDSIC energy functional by employing the exact (in the central-field approximation) single particle orbitals as proposed by Harrison. We find that the LSDSIC energy functional generally leads to calculated values that are superior to those provided by the LSD approximation and that the KLI approximation yields results in excellent agreement with the corresponding exact OEP results for this energy functional. In particular, quantities strongly related to the behavior of the valence electrons are nearly identical in both the OEP and KLI calculations, i.e., the difference between the and ɛm is less than 0.2% on average, while the difference between the calculated I is less than 0.2 millihartree on average with the corresponding difference of only 0

  2. Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections.

    PubMed

    Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

    2008-04-24

    We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results

  3. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    PubMed

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-07

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  4. Adsorption of water and ethanol on noble and transition-metal substrates: a density functional investigation within van der Waals corrections.

    PubMed

    Freire, Rafael L H; Kiejna, Adam; Da Silva, Juarez L F

    2016-10-26

    We report the results of extensive computational investigation of the adsorption properties of water and ethanol on several Cu-, Pt-, and Au-based substrates, including the close-packed unreconstructed Cu(111), Pt(111), and Au(111) surfaces, defected metal substrates with on-surface low-coordinated sites generated by the intermixing of Pt-Cu and Pt-Au in the topmost surface layers and strained on-surface and sub-surface Pt-layers at Cu(111) and Au(111) substrates. The calculations are based on the density functional theory (DFT) within the van der Waals (vdW) correction. For all the substrates, we found that water and ethanol bind via the anionic O atom to the cationic one-fold coordinated on-top metal sites, which enhances the adsorbate-substrate Coulomb interactions. For water, both DFT and DFT + vdW calculations predict a flat geometry. For ethanol, the DFT and DFT + vdW results are in contrast, namely, DFT yields a perpendicular orientation of the C-C bond with respect to the surface, while we obtained a parallel orientation of the C-C bond using DFT + vdW, which maximizes the adsorption energies. Despite expected deviations due to the nature of the weak adsorbate-substrate interactions, we found that the adsorption energy of water and ethanol shows a linear dependence as a function of the position of the center of gravity of the occupied d-band, and hence, the magnitude of the adsorption energy increases as the d-band center position shifts towards the Fermi energy. Thus, it indicates hybridization between the O p- and metal d-states, which determines the magnitude of the adsorption energy of water and ethanol on clean, low-coordinated, and strained noble and transition-metal substrates.

  5. SU-E-T-541: Measurement of CT Density Model Variations and the Impact On the Accuracy of Monte Carlo (MC) Dose Calculation in Stereotactic Body Radiation Therapy for Lung Cancer

    SciTech Connect

    Xiang, H; Li, B; Behrman, R; Russo, G; Kachnic, L; Lu, H; Fernando, H

    2015-06-15

    Purpose: To measure the CT density model variations between different CT scanners used for treatment planning and impact on the accuracy of MC dose calculation in lung SBRT. Methods: A Gammex electron density phantom (RMI 465) was scanned on two 64-slice CT scanners (GE LightSpeed VCT64) and a 16-slice CT (Philips Brilliance Big Bore CT). All three scanners had been used to acquire CT for CyberKnife lung SBRT treatment planning. To minimize the influences of beam hardening and scatter for improving reproducibility, three scans were acquired with the phantom rotated 120° between scans. The mean CT HU of each density insert, averaged over the three scans, was used to build the CT density models. For 14 patient plans, repeat MC dose calculations were performed by using the scanner-specific CT density models and compared to a baseline CT density model in the base plans. All dose re-calculations were done using the same plan beam configurations and MUs. Comparisons of dosimetric parameters included PTV volume covered by prescription dose, mean PTV dose, V5 and V20 for lungs, and the maximum dose to the closest critical organ. Results: Up to 50.7 HU variations in CT density models were observed over the baseline CT density model. For 14 patient plans examined, maximum differences in MC dose re-calculations were less than 2% in 71.4% of the cases, less than 5% in 85.7% of the cases, and 5–10% for 14.3% of the cases. As all the base plans well exceeded the clinical objectives of target coverage and OAR sparing, none of the observed differences led to clinically significant concerns. Conclusion: Marked variations of CT density models were observed for three different CT scanners. Though the differences can cause up to 5–10% differences in MC dose calculations, it was found that they caused no clinically significant concerns.

  6. Clinicopathological significance of BGP expression in non-small-cell lung carcinoma: relationship with histological type, microvessel density and patients' survival.

    PubMed

    Lee, Min Ki; Kim, Jae Ho; Lee, Chang Hun; Kim, Jong Min; Kang, Chi Duk; Kim, Young Dae; Choi, Kyung Un; Kim, Hwal Woong; Kim, Jee Yeon; Park, Do Youn; Sol, Mee Young

    2006-12-01

    Brain-type glycogen phosphorylase (BGP) is the major isoform of glycogen phosphorylase found in fetal and neoplastic tissues, and is generally thought to induce glucose supply during an ischaemic period. This study was performed to investigate BGP expression in non-small-cell lung carcinoma (NSCLC). A total of 119 cases of NSCLC, including 63 squamous cell carcinomas (SqCCs) and 56 adenocarcinomas (ACs), were imunohistochemically evaluated for BGP expression, and its expression was correlated with clinicopathological parameters. In total, 76.5% were positive, while non-neoplastic bronchial epithelial cells were weakly positive and pneumocytes were negative. High BGP expression was noted in 78.6% of ACs and 36.5% of SqCCs (p=0.001). Microvessel density was higher in the low BGP expression tumours (29.6 +/- 16.9/mm(2)) than in the high expression tumours (22.8+/-13.8/mm(2)) (p=0.017). BGP expression did not correlate with patient age or tumour stage, but was more frequent in females than males. Kaplan-Meier analysis showed that high BGP expression was associated with poorer survival (p=0.032). BGP is expressed in NSCLC, particularly AC, and is an independent poor prognostic factor.

  7. A model for quantitative correction of coronary calcium scores on multidetector, dual source, and electron beam computed tomography for influences of linear motion, calcification density, and temporal resolution: a cardiac phantom study.

    PubMed

    Greuter, M J W; Groen, J M; Nicolai, L J; Dijkstra, H; Oudkerk, M

    2009-11-01

    The objective of this study is to quantify the influence of linear motion, calcification density, and temporal resolution on coronary calcium determination using multidetector computed tomography (MDCT), dual source CT (DSCT), and electron beam tomography (EBT) and to find a quantitative method which corrects for the influences of these parameters using a linear moving cardiac phantom. On a robotic arm with artificial arteries with four calcifications of increasing density, a linear movement was applied between 0 and 120 mm/s (step of 10 mm/s). The phantom was scanned five times on 64-slice MDCT, DSCT, and EBT using a standard acquisition protocol. The average Agatston, volume, and mass scores were determined for each velocity, calcification, and scanner. Susceptibility to motion was quantified using a cardiac motion susceptibility (CMS) index. Resemblance to EBT and physical volume and mass was quantified using a Delta index. Increasing motion artifacts were observed at increasing velocities on all scanners, with increasing severity from EBT to DSCT to 64-slice MDCT. The calcium score showed a linear dependency on motion from which a correction factor could be derived. This correction factor showed a linear dependency on the mean calcification density with a good fit for all three scoring methods and all three scanners (0.73 < or = R2 < or = 0.95). The slope and offset of this correction factor showed a linear dependency on temporal resolution with a good fit for all three scoring methods and all three scanners (0.83 < or = R2 < or = 0.98). CMS was minimal for EBT and increasing values were observed for DSCT and highest values for 64-slice MDCT. CMS was minimal for mass score and increasing values were observed for volume score and highest values for Agatston score. For all densities and scoring methods DSCT showed on average the closest resemblance to EBT calcium scores. When using the correction factor, CMS index decreased on average by 15% and Delta index

  8. A model for quantitative correction of coronary calcium scores on multidetector, dual source, and electron beam computed tomography for influences of linear motion, calcification density, and temporal resolution: A cardiac phantom study

    SciTech Connect

    Greuter, M. J. W.; Groen, J. M.; Nicolai, L. J.; Dijkstra, H.; Oudkerk, M.

    2009-11-15

    Purpose: The objective of this study is to quantify the influence of linear motion, calcification density, and temporal resolution on coronary calcium determination using multidetector computed tomography (MDCT), dual source CT (DSCT), and electron beam tomography (EBT) and to find a quantitative method which corrects for the influences of these parameters using a linear moving cardiac phantom. Methods: On a robotic arm with artificial arteries with four calcifications of increasing density, a linear movement was applied between 0 and 120 mm/s (step of 10 mm/s). The phantom was scanned five times on 64-slice MDCT, DSCT, and EBT using a standard acquisition protocol. The average Agatston, volume, and mass scores were determined for each velocity, calcification, and scanner. Susceptibility to motion was quantified using a cardiac motion susceptibility (CMS) index. Resemblance to EBT and physical volume and mass was quantified using a {Delta} index. Results: Increasing motion artifacts were observed at increasing velocities on all scanners, with increasing severity from EBT to DSCT to 64-slice MDCT. The calcium score showed a linear dependency on motion from which a correction factor could be derived. This correction factor showed a linear dependency on the mean calcification density with a good fit for all three scoring methods and all three scanners (0.73{<=}R{sup 2}{<=}0.95). The slope and offset of this correction factor showed a linear dependency on temporal resolution with a good fit for all three scoring methods and all three scanners (0.83{<=}R{sup 2}{<=}0.98). CMS was minimal for EBT and increasing values were observed for DSCT and highest values for 64-slice MDCT. CMS was minimal for mass score and increasing values were observed for volume score and highest values for Agatston score. For all densities and scoring methods DSCT showed on average the closest resemblance to EBT calcium scores. When using the correction factor, CMS index decreased on average by

  9. Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics-Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections.

    PubMed

    Lin, I-Chun; Seitsonen, Ari P; Tavernelli, Ivano; Rothlisberger, Ursula

    2012-10-09

    We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using ab initio molecular dynamics simulations with density functional theory. The lack of London dispersion forces in generalized gradient approximations (GGAs) is remedied by means of dispersion-corrected atom-centered potentials (DCACPs) or damped atom-pairwise dispersion corrections of the C6R(-6) form. We compare results from simulations using GGA density functionals (BLYP, PBE, and revPBE) with data from their van der Waals (vdW) corrected counterparts. As pointed out previously, all vdW-corrected BLYP simulations give rise to highly mobile water whose softened structure is closer to experimental data than the one predicted by the bare BLYP functional. Including vdW interactions in the PBE functional, on the other hand, has little influence on both structural and dynamical properties of water. Augmenting the revPBE functional with either damped atom-pairwise dispersion corrections or DCACP evokes opposite behaviors. The former further softens the already under-structured revPBE water, whereas the latter makes it more glassy. These results demonstrate the delicacy needed in describing weak interactions in molecular liquids.

  10. Death or neurodevelopmental impairment at 18 to 22 months corrected age in a randomized trial of early dexamethasone to prevent death or chronic lung disease in extremely low birth weight infants.

    PubMed

    Stark, Ann R; Carlo, Waldemar A; Vohr, Betty R; Papile, Lu Ann; Saha, Shampa; Bauer, Charles R; Oh, William; Shankaran, Seetha; Tyson, Jon E; Wright, Linda L; Poole, W Kenneth; Das, Abhik; Stoll, Barbara J; Fanaroff, Avroy A; Korones, Sheldon B; Ehrenkranz, Richard A; Stevenson, David K; Peralta-Carcelen, Myriam; Wilson-Costello, Deanne E; Bada, Henrietta S; Heyne, Roy J; Johnson, Yvette R; Lee, Kimberly Gronsman; Steichen, Jean J

    2014-01-01

    To evaluate the incidence of death or neurodevelopmental impairment (NDI) at 18-22 months corrected age in subjects enrolled in a trial of early dexamethasone treatment to prevent death or chronic lung disease in extremely low birth weight infants. Evaluation of infants at 18-22 months corrected age included anthropomorphic measurements, a standard neurological examination, and the Bayley Scales of Infant Development-II, including the Mental Developmental Index and the Psychomotor Developmental Index. NDI was defined as moderate or severe cerebral palsy, Mental Developmental Index or Psychomotor Developmental Index <70, blindness, or hearing impairment. Death or NDI at 18-22 months corrected age was similar in the dexamethasone and placebo groups (65% vs 66%, P = .99 among those with known outcome). The proportion of survivors with NDI was also similar, as were mean values for weight, length, and head circumference and the proportion of infants with poor growth (50% vs 41%, P = .42 for weight less than 10th percentile); 49% of infants in the placebo group received treatment with corticosteroid compared with 32% in the dexamethasone group (P = .02). The risk of death or NDI and rate of poor growth were high but similar in the dexamethasone and placebo groups. The lack of a discernible effect of early dexamethasone on neurodevelopmental outcome may be due to frequent clinical corticosteroid use in the placebo group. Copyright © 2014 Mosby, Inc. All rights reserved.

  11. Density-functional approaches to non-bonding interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

    SciTech Connect

    Burns, Lori A; Sherrill, David; Vazquez-Mayagoitia, Alvaro; Sumpter, Bobby G

    2011-01-01

    A systematic study of techniques for treating non-covalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength com- piled for molecular complexes of diverse size and nature. In particular, the effi- cacy of functionals deliberately crafted to encompass long-range forces, a posteri- ori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, B97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double- or robust triple- basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunc- tion with aug-cc-pVDZ, for a mean absolute deviation of 0.41 0.49 kcal/mol, and B3LYP-D3, B97-D3, B97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, af- fording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 0.38 kcal/mol.

  12. Political Correctness--Correct?

    ERIC Educational Resources Information Center

    Boase, Paul H.

    1993-01-01

    Examines the phenomenon of political correctness, its roots and objectives, and its successes and failures in coping with the conflicts and clashes of multicultural campuses. Argues that speech codes indicate failure in academia's primary mission to civilize and educate through talk, discussion, thought,166 and persuasion. (SR)

  13. Automated lung segmentation in digital chest tomosynthesis

    PubMed Central

    Wang, Jiahui; Dobbins, James T.; Li, Qiang

    2012-01-01

    Purpose: The purpose of this study was to develop an automated lung segmentation method for computerized detection of lung nodules in digital chest tomosynthesis. Methods: The authors collected 45 digital tomosynthesis scans and manually segmented reference lung regions in each scan to assess the performance of the method. The authors automated the technique by calculating the edge gradient in an original image for enhancing lung outline and transforming the edge gradient image to polar coordinate space. The authors then employed a dynamic programming technique to delineate outlines of the unobscured lungs in the transformed edge gradient image. The lung outlines were converted back to the original image to provide the final segmentation result. The above lung segmentation algorithm was first applied to the central reconstructed tomosynthesis slice because of the absence of ribs overlapping lung structures. The segmented lung in the central slice was then used to guide lung segmentation in noncentral slices. The authors evaluated the segmentation method by using (1) an overlap rate of lung regions, (2) a mean absolute distance (MAD) of lung borders, (3) a Hausdorff distance of lung borders between the automatically segmented lungs and manually segmented reference lungs, and (4) the fraction of nodules included in the automatically segmented lungs. Results: The segmentation method achieved mean overlap rates of 85.7%, 88.3%, and 87.0% for left lungs, right lungs, and entire lungs, respectively; mean MAD of 4.8, 3.9, and 4.4 mm for left lungs, right lungs, and entire lungs, respectively; and mean Hausdorrf distance of 25.0 mm, 25.5 mm, and 30.1 mm for left lungs, right lungs, and entire lungs, respectively. All of the nodules inside the reference lungs were correctly included in the segmented lungs obtained with the lung segmentation method. Conclusions: The method achieved relatively high accuracy for lung segmentation and will be useful for computer-aided detection

  14. Two novel susceptibility loci for non-small cell lung cancer map to low-density lipoprotein receptor-related protein 5

    PubMed Central

    Wang, Ying; Zhang, Yongjun; Fang, Meiyu; Bao, Wenglong; Deng, Dehou

    2016-01-01

    This study investigated the effect of single-nucleotide polymorphisms (SNPs) of low-density lipoprotein receptor-related protein 5 (LRP5) on the risk of developing non-small cell lung cancer (NSCLC). A total of 500 NSCLC patients and 500 healthy controls were recruited for genotyping of 11 SNPs of LRP5. The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses. Eleven Tag SNPs were detected. The frequency of the LRP5 rs3736228 T allele (18.9% in male NSCLC cases and 23.9% in male controls) was statistically different between male NSCLCs and male controls (P=0.03), and the T allele was associated with a lower risk of NSCLC (OR=0.74; 95% CI, 0.56–0.67), whereas the C/C homozygous genotype and the LRP5 rs64843 T/T genotype were associated with an increased risk of NSCLC and squamous cell carcinoma (SCC), respectively (OR=1.43 and 1.77, respectively). Using Haploview software, the frequency of the haplotypes of rs312009/rs3120015/rs3120014 CCC was was significantly higher in female SCC cases compared with female controls (0.064 vs. 0.009, P=0.04). LRP5 rs3736228 and rs64843 SNPs were significantly associated with an increased risk of NSCLC and SCC, respectively. Further studies are required to investigate the functional changes in LRP5 expression and activity in NSCLC in vitro. PMID:27698794

  15. A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4(+) T cell receptor repertoire clonality.

    PubMed

    Zhu, Wei; Germain, Claire; Liu, Zheng; Sebastian, Yinong; Devi, Priyanka; Knockaert, Samantha; Brohawn, Philip; Lehmann, Kim; Damotte, Diane; Validire, Pierre; Yao, Yihong; Valge-Archer, Viia; Hammond, Scott A; Dieu-Nosjean, Marie-Caroline; Higgs, Brandon W

    2015-12-01

    T and B cell receptor (TCR and BCR, respectively) Vβ or immunoglobulin heavy chain complementarity-determining region 3 sequencing allows monitoring of repertoire changes through recognition, clonal expansion, affinity maturation, and T or B cell activation in response to antigen. TCR and BCR repertoire analysis can advance understanding of antitumor immune responses in the tumor microenvironment. TCR and BCR repertoires of sorted CD4(+), CD8(+) or CD19(+) cells in tumor, non-tumoral distant tissue (NT), and peripheral compartments (blood/draining lymph node [P]) from 47 non-small cell lung cancer (NSCLC) patients (agemedian = 68 y) were sequenced. The clonotype spectra were assessed among different tissues and correlated with clinical and immunological parameters. In all tissues, CD4(+) and CD8(+) TCR repertoires had greater clonality relative to CD19(+) BCR. CD4(+) T cells exhibited greater clonality in NT compared to tumor (p = 0.002) and P (p < 0.001), concentrated among older patients (age > 68). Younger patients exhibited greater CD4(+) T cell diversity in P compared to older patients (p = 0.05), and greater CD4(+) T cell clonality in tumor relative to P (p < 0.001), with fewer shared clonotypes between tumor and P than older patients (p = 0.04). More interestingly, greater CD4(+) and CD8(+) T cell clonality in tumor and P, respectively (both p = 0.05), correlated with high density of tumor-associated tertiary lymphoid structure (TLS) B cells, a biomarker of higher overall survival in NSCLC. Results indicate distinct adaptive immune responses in NSCLC, where peripheral T cell diversity is modulated by age, and tumor T cell clonal expansion is favored by the presence of TLSs in the tumor microenvironment.

  16. A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+ T cell receptor repertoire clonality

    PubMed Central

    Zhu, Wei; Germain, Claire; Liu, Zheng; Sebastian, Yinong; Devi, Priyanka; Knockaert, Samantha; Brohawn, Philip; Lehmann, Kim; Damotte, Diane; Validire, Pierre; Yao, Yihong; Valge-Archer, Viia; Hammond, Scott A; Dieu-Nosjean, Marie-Caroline; Higgs, Brandon W

    2015-01-01

    T and B cell receptor (TCR and BCR, respectively) Vβ or immunoglobulin heavy chain complementarity-determining region 3 sequencing allows monitoring of repertoire changes through recognition, clonal expansion, affinity maturation, and T or B cell activation in response to antigen. TCR and BCR repertoire analysis can advance understanding of antitumor immune responses in the tumor microenvironment. TCR and BCR repertoires of sorted CD4+, CD8+ or CD19+ cells in tumor, non-tumoral distant tissue (NT), and peripheral compartments (blood/draining lymph node [P]) from 47 non-small cell lung cancer (NSCLC) patients (agemedian = 68 y) were sequenced. The clonotype spectra were assessed among different tissues and correlated with clinical and immunological parameters. In all tissues, CD4+ and CD8+ TCR repertoires had greater clonality relative to CD19+ BCR. CD4+ T cells exhibited greater clonality in NT compared to tumor (p = 0.002) and P (p < 0.001), concentrated among older patients (age > 68). Younger patients exhibited greater CD4+ T cell diversity in P compared to older patients (p = 0.05), and greater CD4+ T cell clonality in tumor relative to P (p < 0.001), with fewer shared clonotypes between tumor and P than older patients (p = 0.04). More interestingly, greater CD4+ and CD8+ T cell clonality in tumor and P, respectively (both p = 0.05), correlated with high density of tumor-associated tertiary lymphoid structure (TLS) B cells, a biomarker of higher overall survival in NSCLC. Results indicate distinct adaptive immune responses in NSCLC, where peripheral T cell diversity is modulated by age, and tumor T cell clonal expansion is favored by the presence of TLSs in the tumor microenvironment. PMID:26587322

  17. FLASH proton density imaging for improved surface coil intensity correction in quantitative and semi-quantitative SSFP perfusion cardiovascular magnetic resonance.

    PubMed

    Nielles-Vallespin, Sonia; Kellman, Peter; Hsu, Li-Yueh; Arai, Andrew E

    2015-02-17

    A low excitation flip angle (α < 10°) steady-state free precession (SSFP) proton-density (PD) reference scan is often used to estimate the B1-field inhomogeneity for surface coil intensity correction (SCIC) of the saturation-recovery (SR) prepared high flip angle (α = 40-50°) SSFP myocardial perfusion images. The different SSFP off-resonance response for these two flip angles might lead to suboptimal SCIC when there is a spatial variation in the background B0-field. The low flip angle SSFP-PD frames are more prone to parallel imaging banding artifacts in the presence of off-resonance. The use of FLASH-PD frames would eliminate both the banding artifacts and the uneven frequency response in the presence of off-resonance in the surface coil inhomogeneity estimate and improve homogeneity of semi-quantitative and quantitative perfusion measurements. B0-field maps, SSFP and FLASH-PD frames were acquired in 10 healthy volunteers to analyze the SSFP off-resonance response. Furthermore, perfusion scans preceded by both FLASH and SSFP-PD frames from 10 patients with no myocardial infarction were analyzed semi-quantitatively and quantitatively (rest n = 10 and stress n = 1). Intra-subject myocardial blood flow (MBF) coefficient of variation (CoV) over the whole left ventricle (LV), as well as intra-subject peak contrast (CE) and upslope (SLP) standard deviation (SD) over 6 LV sectors were investigated. In the 6 out of 10 cases where artifacts were apparent in the LV ROI of the SSFP-PD images, all three variability metrics were statistically significantly lower when using the FLASH-PD frames as input for the SCIC (CoVMBF-FLASH = 0.3 ± 0.1, CoVMBF-SSFP = 0.4 ± 0.1, p = 0.03; SDCE-FLASH = 10 ± 2, SDCE-SSFP = 32 ± 7, p = 0.01; SDSLP-FLASH = 0.02 ± 0.01, SDSLP-SSFP = 0.06 ± 0.02, p = 0.03). Example rest and stress data sets from the patient pool demonstrate that the low flip angle SSFP protocol

  18. Lung Transplant

    MedlinePlus

    Lung transplant Overview By Mayo Clinic Staff A lung transplant is a surgical procedure to replace a diseased or ... lung, usually from a deceased donor. A lung transplant is reserved for people who have tried other ...

  19. Lung surgery

    MedlinePlus

    ... lung tissue that is diseased or damaged from emphysema or bronchiectasis Remove blood or blood clots ( hemothorax ) ... Editorial team. Related MedlinePlus Health Topics Collapsed Lung Emphysema Lung Cancer Lung Diseases Pleural Disorders Browse the ...

  20. Lung Emergencies

    MedlinePlus

    ... Emergencies Cardiac Emergencies Eye Emergencies Lung Emergencies Surgeries Lung Emergencies People with Marfan syndrome can be at ... should be considered an emergency. Symptoms of sudden lung collapse (pneumothorax) Symptoms of a sudden lung collapse ...

  1. Lung Cancer

    MedlinePlus

    ... version of this page please turn Javascript on. Lung Cancer What is Lung Cancer? How Tumors Form The body is made ... button on your keyboard.) Two Major Types of Lung Cancer There are two major types of lung ...

  2. Lung cancer

    SciTech Connect

    Aisner, J.

    1985-01-01

    This book contains 13 chapters. Some of the chapter titles are: The Pathology of Lung Cancer; Radiotherapy for Non-Small-Cell Cancer of the Lung; Chemotherapy for Non-Small-Cell Lung Cancer; Immunotherapy in the Management of Lung Cancer; Preoperative Staging and Surgery for Non-Small-Cell Lung Cancer; and Prognostic Factors in Lung Cancer.

  3. Inter-scanner differences in in vivo QCT measurements of the density and strength of the proximal femur remain after correction with anthropomorphic standardization phantoms.

    PubMed

    Carpenter, R Dana; Saeed, Isra; Bonaretti, Serena; Schreck, Carole; Keyak, Joyce H; Streeper, Timothy; Harris, Tamara B; Lang, Thomas F

    2014-10-01

    In multicenter studies and longitudinal studies that use two or more different quantitative computed tomography (QCT) imaging systems, anthropomorphic standardization phantoms (ASPs) are used to correct inter-scanner differences and allow pooling of data. In this study, in vivo imaging of 20 women on two imaging systems was used to evaluate inter-scanner differences in hip integral BMD (iBMD), trabecular BMD (tBMD), cortical BMD (cBMD), femoral neck yield moment (My) and yield force (Fy), and finite-element derived strength of the femur under stance (FEstance) and fall (FEfall) loading. Six different ASPs were used to derive inter-scanner correction equations. Significant (p<0.05) inter-scanner differences were detected in all measurements except My and FEfall, and no ASP-based correction was able to reduce inter-scanner variability to corresponding levels of intra-scanner precision. Inter-scanner variability was considerably higher than intra-scanner precision, even in cases where the mean inter-scanner difference was statistically insignificant. A significant (p<0.01) effect of body size on inter-scanner differences in BMD was detected, demonstrating a need to address the effects of body size on QCT measurements. The results of this study show that significant inter-scanner differences in QCT-based measurements of BMD and bone strength can remain even when using an ASP. Copyright © 2014 IPEM. All rights reserved.

  4. {sup 63}Cu and {sup 197}Au nuclear quadrupole moments from four-component relativistic density-functional calculations using correct long-range exchange

    SciTech Connect

    Thierfelder, Christian; Schwerdtfeger, Peter; Saue, Trond

    2007-09-15

    The electric field gradient in late transition metal compounds is incorrectly determined by most density functionals. We show that the coupling of short-range density functional based with long-range wave function based methods using a reparametrization of the Coulomb-attenuated Becke three-parameter Lee-Yang-Parr approximation gives reliable results for the electric field gradients of copper and gold for a series of compounds. This results in nuclear quadrupole moments of -0.208 b for {sup 63}Cu and +0.526 b for {sup 197}Au in good agreement with experimental values of -0.220(15) and +0.547(16)b, respectively.

  5. Correction of Apolipoprotein A-I-mediated Lipid Efflux and High Density Lipoprotein Particle Formation in Human Niemann-Pick Type C Disease Fibroblasts

    USDA-ARS?s Scientific Manuscript database

    Impaired cell cholesterol trafficking in Niemann-Pick type C (NPC) disease results in the first known instance of impaired regulation of the ATP-binding cassette transporter A1 (ABCA1), a lipid transporter mediating the rate-limiting step in high density lipoprotein (HDL) formation, as a cause of lo...

  6. Second-order M{umlt o}ller-Plesset and Epstein-Nesbet corrections to the molecular charge density: distributed computing on a cluster of heterogeneous workstations with the PVM system

    SciTech Connect

    Bendrider, M.; Leclercq, J.

    1995-04-01

    We perform distributed calculations of the MP2 and EN2 corrections to the charge density of a lot of molecules. A heterogeneous cluster of IBM RS/600 and Silicon Graphics workstations is used. These network-based distributed concurrent calculations are developed with the {bold P}arallel {bold V}irtual {bold M}achine system of the Oak Ridge National Laboratory, with the ETHERNET IP mode and, for the RS/6000s, the SOCC IP mode. (AIP) {copyright}{ital 1995 American Institute of Physics}

  7. Lung Transplantation

    MedlinePlus

    ... who have severe COPD Cystic fibrosis Idiopathic pulmonary fibrosis Alpha-1 antitrypsin deficiency Pulmonary hypertension Complications of lung transplantation include rejection of the transplanted lung and infection. NIH: National Heart, Lung, and Blood Institute

  8. Lung disease

    MedlinePlus

    ... the lungs to take in oxygen and release carbon dioxide. People with this type of lung disorder often ... the lungs to take up oxygen and release carbon dioxide. These diseases may also affect heart function. An ...

  9. Collapsed Lung

    MedlinePlus

    A collapsed lung happens when air enters the pleural space, the area between the lung and the chest wall. If it is a ... is called pneumothorax. If only part of the lung is affected, it is called atelectasis. Causes of ...

  10. Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

    PubMed

    Casida, Mark E; Huix-Rotllant, Miquel

    2016-01-01

    In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

  11. Evaluation of a semiautomated lung mass calculation technique for internal dosimetry applications

    SciTech Connect

    Busse, Nathan; Erwin, William; Pan, Tinsu

    2013-12-15

    calculated using the formula (lung HU − air HU)/(tissue HU − air HU), and mass = specific gravity × total volume × 1.04 g/cm{sup 3}.Results: The range of calculated lung masses was 0.51–1.29 kg. The average male and female lung masses during FB CT were 0.80 and 0.71 kg, respectively. The calculated lung mass varied across the respiratory cycle but changed to a lesser degree than did lung volume measurements (7.3% versus 15.4%). Lung masses calculated using deep inspiration breath-hold and average CT were significantly larger (p < 0.05) than were some masses calculated using respiratory-phase and FB CT. Increased voxel size and smooth reconstruction kernels led to high lung mass estimates owing to partial volume effects.Conclusions: Organ mass correction is an important component of patient-specific internal radionuclide dosimetry. Lung mass calculation necessitates scan-based density correction to account for volume changes owing to respiration. The range of lung masses in the authors’ patient population represents lung doses for the same absorbed energy differing from 25% below to 64% above the dose found using reference phantom organ masses. With proper management of acquisition parameters and selection of FB or midexpiration breath hold scans, lung mass estimates with about 10% population precision may be achieved.

  12. Lowest excited states and optical absorption spectra of donor-acceptor copolymers for organic photovoltaics: a new picture emerging from tuned long-range corrected density functionals.

    PubMed

    Pandey, Laxman; Doiron, Curtis; Sears, John S; Brédas, Jean-Luc

    2012-11-07

    Polymers with low optical gaps are of importance to the organic photovoltaics community due to their potential for harnessing a large portion of the solar energy spectrum. The combination along their backbones of electron-rich and electron-deficient fragments contributes to the presence of low-lying excited states that are expected to display significant charge-transfer character. While conventional hybrid functionals are known to provide unsatisfactory results for charge-transfer excitations at the time-dependent DFT level, long-range corrected (LRC) functionals have been reported to give improved descriptions in a number of systems. Here, we use such LRC functionals, considering both tuned and default range-separation parameters, to characterize the absorption spectra of low-optical-gap systems of interest. Our results indicate that tuned LRC functionals lead to simulated optical-absorption properties in good agreement with experimental data. Importantly, the lowest-lying excited states (excitons) are shown to present a much more localized nature than initially anticipated.

  13. Impact of red blood cells count on the relationship between high density lipoproteins and the prevalence and extent of coronary artery disease: a single centre study [corrected].

    PubMed

    Schaffer, Alon; Verdoia, Monica; Cassetti, Ettore; Barbieri, Lucia; Perrone-Filardi, Pasquale; Marino, Paolo; De Luca, Giuseppe

    2015-07-01

    We have hypothesized that high red blood cells (RBC) count can potentially play an atheroprotective role in patients with coronary atherosclerosis. We, therefore, have investigated the relationship between high density lipoproteins cholesterol (HDL-C) and RBC levels in patients undergoing coronary angiography. Coronary artery disease (CAD) is a major cause of mortality. Impaired lipid profile represents a major risk factor for atherosclerosis. High density lipoprotein (HDL) is a key factor in atherosclerosis disease development. RBC can mimic HDL's reverse cholesterol transportation with a potential atheroprotective role. Coronary angiography has been evaluated in 3,534 patients. Fasting samples were collected for haematology and lipids levels assessment. Coronary disease was defined for at least 1 vessel stenosis >50 %. Patients were divided according to HDL-C and RBC tertiles. Lower HDL-C was significantly associated to the prevalence of CAD (84.8 vs 78.5 vs 67.3 %, p ≤ 0.001; adjusted OR [95 % CI] = 1.55 [1.3-1.8], p < 0.001) and severe CAD (30 % vs 30 % vs 24.4 %, p = 0.002; adjusted OR [95 % CI] = 1.08 [1.01-1.16], p = 0.02), this relationship was maintained even dividing our population according to RBC tertiles (p < 0.001).In conclusion, HDL-C levels are directly related to RBC count and inversely to the prevalence and extent of coronary disease. Higher RBC levels can reduce the risk of CAD in patients with lower HDL-C levels, suggesting an important atheroprotective role.

  14. Interaction between n-Alkane Chains:  Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

    PubMed

    Goursot, Annick; Mineva, Tzonka; Kevorkyants, Ruslan; Talbi, Dahbia

    2007-05-01

    The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.

  15. Adsorption of CO on the rutile TiO2(110) surface: a dispersion-corrected density functional theory study.

    PubMed

    Prates Ramalho, João P; Illas, Francesc; Gomes, José R B

    2017-01-18

    The geometry, energy and stretching frequency of carbon monoxide on the rutile TiO2(110) surface for coverages between 0.125 and 1.5 ML are investigated by means of density functional theory calculations. Four different approaches were considered, namely, the PBE exchange-correlation functional and the PBE-D2, vdW-DF and vdW-DF2 methods incorporating van der Waals dispersion interactions of different theoretical complexity and empiricism. It is found that upon the increase of the surface coverage, the adsorption becomes less favorable due to lateral destabilizing interactions between adsorbed molecules. The preferred geometry for CO changes from an upright configuration at 0.125 ML to tilted configurations at 1.5 ML and the tilting of the C-O axis from the surface normal increases with the increase of the surface coverage. At 1 ML, all computational approaches predict alternate tilted configurations which contradict the interpretation of recent experimental infrared reflection-absorption spectroscopic findings suggesting upright CO geometries. Encouragingly, a very good agreement between calculated and experimental shifts of the C-O stretching frequency of adsorbed CO at different coverages with respect to gaseous CO species was reached.

  16. Histopathologic approach to the surgical lung biopsy in interstitial lung disease.

    PubMed

    Jones, Kirk D; Urisman, Anatoly

    2012-03-01

    Interpretation of lung biopsy specimens is an integral part in the diagnosis of interstitial lung disease (ILD). The process of evaluating a surgical lung biopsy for disease involves answering several questions. Unlike much of surgical pathology of neoplastic lung disease, arriving at the correct diagnosis in nonneoplastic lung disease often requires correlation with clinical and radiologic findings. The topic of ILD or diffuse infiltrative lung disease covers several hundred entities. This article is meant to be a launching point in the clinician's approach to the histologic evaluation of lung disease. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Geological Corrections in Gravimetry

    NASA Astrophysics Data System (ADS)

    Mikuška, J.; Marušiak, I.

    2015-12-01

    Applying corrections for the known geology to gravity data can be traced back into the first quarter of the 20th century. Later on, mostly in areas with sedimentary cover, at local and regional scales, the correction known as gravity stripping has been in use since the mid 1960s, provided that there was enough geological information. Stripping at regional to global scales became possible after releasing the CRUST 2.0 and later CRUST 1.0 models in the years 2000 and 2013, respectively. Especially the later model provides quite a new view on the relevant geometries and on the topographic and crustal densities as well as on the crust/mantle density contrast. Thus, the isostatic corrections, which have been often used in the past, can now be replaced by procedures working with an independent information interpreted primarily from seismic studies. We have developed software for performing geological corrections in space domain, based on a-priori geometry and density grids which can be of either rectangular or spherical/ellipsoidal types with cells of the shapes of rectangles, tesseroids or triangles. It enables us to calculate the required gravitational effects not only in the form of surface maps or profiles but, for instance, also along vertical lines, which can shed some additional light on the nature of the geological correction. The software can work at a variety of scales and considers the input information to an optional distance from the calculation point up to the antipodes. Our main objective is to treat geological correction as an alternative to accounting for the topography with varying densities since the bottoms of the topographic masses, namely the geoid or ellipsoid, generally do not represent geological boundaries. As well we would like to call attention to the possible distortions of the corrected gravity anomalies. This work was supported by the Slovak Research and Development Agency under the contract APVV-0827-12.

  18. Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci

    PubMed Central

    Kachuri, Linda; Amos, Christopher I.; McKay, James D.; Johansson, Mattias; Vineis, Paolo; Bueno-de-Mesquita, H.Bas; Boutron-Ruault, Marie-Christine; Johansson, Mikael; Quirós, J.Ramón; Sieri, Sabina; Travis, Ruth C.; Weiderpass, Elisabete; Le Marchand, Loic; Henderson, Brian E.; Wilkens, Lynne; Goodman, Gary E.; Chen, Chu; Doherty, Jennifer A.; Christiani, David C.; Wei, Yongyue; Su, Li; Tworoger, Shelley; Zhang, Xuehong; Kraft, Peter; Zaridze, David; Field, John K.; Marcus, Michael W.; Davies, Michael P.A.; Hyde, Russell; Caporaso, Neil E.; Landi, Maria Teresa; Severi, Gianluca; Giles, Graham G.; Liu, Geoffrey; McLaughlin, John R.; Li, Yafang; Xiao, Xiangjun; Fehringer, Gord; Zong, Xuchen; Denroche, Robert E.; Zuzarte, Philip C.; McPherson, John D.; Brennan, Paul; Hung, Rayjean J.

    2016-01-01

    Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases and 5716 controls of European ancestry. After adjusting for known risk loci, rs2736100 and rs401681, we identified a new, independent lung cancer susceptibility variant in LPCAT1: rs139852726 (OR = 0.46, P = 4.73×10–9), and three new adenocarcinoma risk variants in TERT: rs61748181 (OR = 0.53, P = 2.64×10–6), rs112290073 (OR = 1.85, P = 1.27×10–5), rs138895564 (OR = 2.16, P = 2.06×10–5; among young cases, OR = 3.77, P = 8.41×10–4). In addition, we found that rs139852726 (P = 1.44×10–3) was associated with telomere length in a sample of 922 healthy individuals. The gene-based SKAT-O analysis implicated TERT as the most relevant gene in the 5p15.33 region for adenocarcinoma (P = 7.84×10–7) and lung cancer (P = 2.37×10–5) risk. In this largest fine-mapping study to investigate a large number of rare and novel variants within 5p15.33, we identified novel lung and adenocarcinoma susceptibility loci with large effects and provided support for the role of telomere length as the potential underlying mechanism. PMID:26590902

  19. Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci.

    PubMed

    Kachuri, Linda; Amos, Christopher I; McKay, James D; Johansson, Mattias; Vineis, Paolo; Bueno-de-Mesquita, H Bas; Boutron-Ruault, Marie-Christine; Johansson, Mikael; Quirós, J Ramón; Sieri, Sabina; Travis, Ruth C; Weiderpass, Elisabete; Le Marchand, Loic; Henderson, Brian E; Wilkens, Lynne; Goodman, Gary E; Chen, Chu; Doherty, Jennifer A; Christiani, David C; Wei, Yongyue; Su, Li; Tworoger, Shelley; Zhang, Xuehong; Kraft, Peter; Zaridze, David; Field, John K; Marcus, Michael W; Davies, Michael P A; Hyde, Russell; Caporaso, Neil E; Landi, Maria Teresa; Severi, Gianluca; Giles, Graham G; Liu, Geoffrey; McLaughlin, John R; Li, Yafang; Xiao, Xiangjun; Fehringer, Gord; Zong, Xuchen; Denroche, Robert E; Zuzarte, Philip C; McPherson, John D; Brennan, Paul; Hung, Rayjean J

    2016-01-01

    Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases and 5716 controls of European ancestry. After adjusting for known risk loci, rs2736100 and rs401681, we identified a new, independent lung cancer susceptibility variant in LPCAT1: rs139852726 (OR = 0.46, P = 4.73×10(-9)), and three new adenocarcinoma risk variants in TERT: rs61748181 (OR = 0.53, P = 2.64×10(-6)), rs112290073 (OR = 1.85, P = 1.27×10(-5)), rs138895564 (OR = 2.16, P = 2.06×10(-5); among young cases, OR = 3.77, P = 8.41×10(-4)). In addition, we found that rs139852726 (P = 1.44×10(-3)) was associated with telomere length in a sample of 922 healthy individuals. The gene-based SKAT-O analysis implicated TERT as the most relevant gene in the 5p15.33 region for adenocarcinoma (P = 7.84×10(-7)) and lung cancer (P = 2.37×10(-5)) risk. In this largest fine-mapping study to investigate a large number of rare and novel variants within 5p15.33, we identified novel lung and adenocarcinoma susceptibility loci with large effects and provided support for the role of telomere length as the potential underlying mechanism.

  20. Morphometric examination of native lungs in human lung allograft recipients.

    PubMed

    Wiebe, B M; Burton, C M; Milman, N; Iversen, M; Andersen, C B

    2006-11-01

    The aim of the study was to estimate the degree of lung damage in patients with alpha(1)-antitrypsin (alpha1AT) deficiency, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF) at the time of lung transplantation. Using unbiased stereological methods, lung-, bronchial- and vessel-volume, capillary length, and alveolar surface area and densities were estimated in recipient lungs from 21 consecutive patients with pre-transplant diagnoses including COPD (n=7), alpha1AT deficiency (n=6) and CF (n=8). Six unused adult donor lungs served as controls. Information relating to patient demography and pre-transplant lung function was obtained by retrospective chart review. Disease groups differed significantly with respect to demographics and pre-transplant lung function. Total lung volume was similar in all groups. Bronchial volume was significantly larger in CF patients compared to the control group (p<0.0001) and to the other two diagnostic groups: alpha1AT deficiency (p=0.0001) and COPD (p<0.0001). Alveolar surface density and capillary length density were significantly lower in patients with alpha1AT deficiency and COPD compared to controls (p<0.0001, respectively) and to patients with CF (p<0.0002, respectively). There were no correlations between clinical lung function and morphometric measurements. We conclude that unbiased microscopic stereological morphometry is an evolving science with the potential to elucidate pulmonary disease pathogenesis.

  1. Bone mass density, fracture history, self-reported osteoporosis as proxy variables for estrogen and the risk of non-small-cell lung cancer--a population based cohort study, the HUNT study: are proxy variables friends or faults?

    PubMed

    Hatlen, Peter; Langhammer, Arnulf; Forsmo, Siri; Carlsen, Sven M; Amundsen, Tore

    2013-07-01

    Lung cancer has the highest mortality of all cancers. Patients with early stage disease have the best cure rates and that emphasizes the importance of early detection. About half of all non-small cell lung cancers (NSCLC) are estrogen receptor positive. The impact of estrogen and its receptors for NSCLC carcinogenesis has been studied but is still unclear. Low estrogen levels are associated with osteoporosis. We hypothesize that low bone mineral density (BMD), a positive history of fracture or self-reported osteoporosis, used as a proxy variable for life time estrogen exposure, are associated with a low incidence of NSCLC. We analyzed data from a cohort study, the Nord-Trøndelag Health Study 2 (1995-1997) linked to the Norwegian Cancer Registry. Using the logistic regression model we calculated the odds ratio (OR) with a 95% confidence interval (CI) for the risk of NSCLC for the three proxy variables, stratified by sex. Participants older than 50 years of age, having measured bone density (N = 18,156), having answered the questions on self-reported fracture (N = 37,883) and osteoporosis (N = 25,701) and known body mass index (BMI) (N = 29,291), were evaluated for inclusion. In 6996 participants all these information was available in addition to tobacco use, and in women also hormonal replacement therapy (HRT). Lung function (FEV1 percent of predicted) was included in a sensitivity analysis. We identified 132 (1.9%) cases of NSCLC, 59 (1.2%) and 73 (3.3%) cases in women and men, respectively. Low BMD was associated with a higher risk of NSCLC, OR: 2.38, 95% CI: 1.09-5.18 and OR: 2.67, 95% CI: 1.39-5.16 in women and men, respectively. No association was found between the two other proxy variables and the risk of NSCLC. Inclusion of lung function in the model did not change the results. Contrary to our hypothesis, women and men with low BMD had a higher risk for NSCLC. In addition the study demonstrates that the risk depends on which proxy variable was chosen, and we

  2. Electronic and thermoelectric properties of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} computed with density functional theory with on-site Coulomb interaction correction

    SciTech Connect

    Vo, Trinh; Allmen, Paul von; Huang, Chen-Kuo; Ma, James; Bux, Sabah; Fleurial, Jean-Pierre

    2014-10-07

    The electronic properties and Seebeck coefficients of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} are computed using Density Functional Theory with on-site Coulomb interaction correction. We found that the Seebeck coefficients of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} are almost equal at temperatures larger than the Curie temperature of Ce{sub 3}Te{sub 4}, and in good agreement with the measurements reported by May et al. [Phys. Rev. B 86, 035135 (2012)]. At temperatures below the Curie temperature, the Seebeck coefficient of Ce{sub 3}Te{sub 4} increases due to the ferromagnetic ordering, which leads the f-electron of Ce to contribute to the Seebeck coefficient in the relevant range of electron concentration.

  3. Spin-flip, tensor equation-of-motion configuration interaction with a density-functional correction: A spin-complete method for exploring excited-state potential energy surfaces

    SciTech Connect

    Zhang, Xing; Herbert, John M.

    2015-12-21

    We revisit the formalism of the spin-adapted, spin-flip (SA-SF) configuration-interaction singles (CIS) method based on a tensor equation-of-motion formalism that affords proper spin eigenstates without sacrificing single-reference simplicity. Matrix elements for SA-SF-CIS are then modified in a manner similar to collinear spin-flip time-dependent density functional theory (SF-TDDFT), to include a DFT exchange-correlation correction. The performance of this method, which we call SA-SF-DFT, is evaluated numerically and we find that it systematically improves the energies of electronic states that exhibit significant spin contamination within the conventional SF-TDDFT approach. The new method cures the state assignment problem that plagues geometry optimizations and ab initio molecular dynamics simulations using traditional SF-TDDFT, without sacrificing computational efficiency, and furthermore provides correct topology at conical intersections, including those that involve the ground state, unlike conventional TDDFT. As such, SA-SF-DFT appears to be a promising method for generating excited-state potential energy surfaces at DFT cost.

  4. Regional tidal lung strain in mechanically ventilated normal lungs.

    PubMed

    Paula, Luis Felipe; Wellman, Tyler J; Winkler, Tilo; Spieth, Peter M; Güldner, Andreas; Venegas, Jose G; Gama de Abreu, Marcelo; Carvalho, Alysson R; Vidal Melo, Marcos F

    2016-12-01

    Parenchymal strain is a key determinant of lung injury produced by mechanical ventilation. However, imaging estimates of volumetric tidal strain (ε = regional tidal volume/reference volume) present substantial conceptual differences in reference volume computation and consideration of tidally recruited lung. We compared current and new methods to estimate tidal volumetric strains with computed tomography, and quantified the effect of tidal volume (VT) and positive end-expiratory pressure (PEEP) on strain estimates. Eight supine pigs were ventilated with VT = 6 and 12 ml/kg and PEEP = 0, 6, and 12 cmH2O. End-expiratory and end-inspiratory scans were analyzed in eight regions of interest along the ventral-dorsal axis. Regional reference volumes were computed at end-expiration (with/without correction of regional VT for intratidal recruitment) and at resting lung volume (PEEP = 0) corrected for intratidal and PEEP-derived recruitment. All strain estimates demonstrated vertical heterogeneity with the largest tidal strains in middependent regions (P < 0.01). Maximal strains for distinct estimates occurred at different lung regions and were differently affected by VT-PEEP conditions. Values consistent with lung injury and inflammation were reached regionally, even when global measurements were below critical levels. Strains increased with VT and were larger in middependent than in nondependent lung regions. PEEP reduced tidal-strain estimates referenced to end-expiratory lung volumes, although it did not affect strains referenced to resting lung volume. These estimates of tidal strains in normal lungs point to middependent lung regions as those at risk for ventilator-induced lung injury. The different conditions and topography at which maximal strain estimates occur allow for testing the importance of each estimate for lung injury.

  5. Role of electronic correlation in high-low temperature phase transition of hexagonal nickel sulfide: a comparative density functional theory study with and without correction for on-site Coulomb interaction.

    PubMed

    Zhang, Wei-Bing; Li, Jie; Tang, Bi-Yu

    2013-06-28

    The structural, electronic, magnetic, and elastic properties of hexagonal nickel sulfide (NiS) have been investigated comparatively by Density Functional theory (DFT) and DFT plus correction for on-site Coulomb interaction (DFT+U), in which two different exchange correlation functionals local density approximations (LDA) and general gradient approximations (GGA) in the form of Perdew-Burke-Ernzerhof (PBE) are used. Our results indicate LDA and PBE methods predict hexagonal NiS to be a paramagnetic metal whereas LDA(PBE)+U calculations with reasonable on-site Coulomb interaction energy give the antiferromagnetic insulating state of low temperature hexagonal NiS successfully. Meanwhile, compared with LDA(PBE) results, LDA(PBE)+U methods give larger lattice parameters, crystal volume, and shear constant c44, consistent with the experimental picture during high-low temperature phase transition of hexagonal NiS, in which an increase of the shear constant c44 and lattice parameters were found in the low-temperature antiferromagnetic phase. The present DFT and DFT+U calculations provide a reasonable description for the properties of high temperature and low temperature hexagonal NiS respectively, which indicates that electronic correlation is responsible for this high-low temperature phase transition.

  6. Assessing Hubbard-corrected AM05+U and PBEsol+U density functionals for strongly correlated oxides CeO2 and Ce2O3

    SciTech Connect

    Weck, Philippe F.; Kim, Eunja

    2016-09-12

    The structure–property relationships of bulk CeO2 and Ce2O3 have been investigated using AM05 and PBEsol exchange–correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+U) and density functional perturbation theory (DFPT+U). Compared with conventional PBE+U, RPBE+U, PW91+U and LDA+U functionals, AM05+U and PBEsol+U describe experimental crystalline parameters and properties of CeO2 and Ce2O3 with superior accuracy, especially when +U is chosen close to its value derived by the linear-response approach. Lastly, the present findings call for a reexamination of some of the problematic oxide materials featuring strong f- and d-electron correlation using AM05+U and PBEsol+U.

  7. Assessing Hubbard-corrected AM05+U and PBEsol+U density functionals for strongly correlated oxides CeO2 and Ce2O3

    SciTech Connect

    Weck, Philippe F.; Kim, Eunja

    2016-09-12

    The structure–property relationships of bulk CeO2 and Ce2O3 have been investigated using AM05 and PBEsol exchange–correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+U) and density functional perturbation theory (DFPT+U). Compared with conventional PBE+U, RPBE+U, PW91+U and LDA+U functionals, AM05+U and PBEsol+U describe experimental crystalline parameters and properties of CeO2 and Ce2O3 with superior accuracy, especially when +U is chosen close to its value derived by the linear-response approach. Lastly, the present findings call for a reexamination of some of the problematic oxide materials featuring strong f- and d-electron correlation using AM05+U and PBEsol+U.

  8. Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

    SciTech Connect

    Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan

    2014-04-14

    A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0–100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMX and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.

  9. Corrective work.

    ERIC Educational Resources Information Center

    Hill, Leslie A.

    1978-01-01

    Discusses some general principles for planning corrective instruction and exercises in English as a second language, and follows with examples from the areas of phonemics, phonology, lexicon, idioms, morphology, and syntax. (IFS/WGA)

  10. Lung pair phantom

    DOEpatents

    Olsen, Peter C.; Gordon, N. Ross; Simmons, Kevin L.

    1993-01-01

    The present invention is a material and method of making the material that exhibits improved radiation attenuation simulation of real lungs, i.e., an "authentic lung tissue" or ALT phantom. Specifically, the ALT phantom is a two-part polyurethane medium density foam mixed with calcium carbonate, potassium carbonate if needed for K-40 background, lanthanum nitrate, acetone, and a nitrate or chloride form of a radionuclide. This formulation is found to closely match chemical composition and linear attenuation of real lungs. The ALT phantom material is made according to established procedures but without adding foaming agents or preparing thixotropic concentrate and with a modification for ensuring uniformity of density of the ALT phantom that is necessary for accurate simulation. The modification is that the polyurethane chemicals are mixed at a low temperature prior to pouring the polyurethane mixture into the mold.

  11. Lung pair phantom

    DOEpatents

    Olsen, P.C.; Gordon, N.R.; Simmons, K.L.

    1993-11-30

    The present invention is a material and method of making the material that exhibits improved radiation attenuation simulation of real lungs, i.e., an ``authentic lung tissue`` or ALT phantom. Specifically, the ALT phantom is a two-part polyurethane medium density foam mixed with calcium carbonate, potassium carbonate if needed for K-40 background, lanthanum nitrate, acetone, and a nitrate or chloride form of a radionuclide. This formulation is found to closely match chemical composition and linear attenuation of real lungs. The ALT phantom material is made according to established procedures but without adding foaming agents or preparing thixotropic concentrate and with a modification for ensuring uniformity of density of the ALT phantom that is necessary for accurate simulation. The modification is that the polyurethane chemicals are mixed at a low temperature prior to pouring the polyurethane mixture into the mold.

  12. Lung transplant

    MedlinePlus

    ... diseases that may require a lung transplant are: Cystic fibrosis Damage to the arteries of the lung because ... BC; Clinical Practice Guidelines for Pulmonary Therapies Committee; ... Therapies Committee. Cystic fibrosis pulmonary guidelines: ...

  13. Systematic approach for simultaneously correcting the band-gap andp-dseparation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

    SciTech Connect

    Wang, Jianwei; Zhang, Yong; Wang, Lin-Wang

    2015-07-31

    We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles method can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.

  14. MAGNETIC RESONANCE ELASTOGRAPHY OF HUMAN LUNG PARENCHYMA: TECHNICAL DEVELOPMENT, THEORETICAL MODELING AND IN VIVO VALIDATION

    PubMed Central

    Mariappan, Yogesh K; Glaser, Kevin J; Hubmayr, Rolf D; Manduca, Armando; Ehman, Richard L; McGee, Kiaran P

    2011-01-01

    Purpose To develop a novel MR-based method for visualizing the elastic properties of human lung parenchyma in vivo and to evaluate the ability of this method to resolve differences in parenchymal stiffness at different respiration states in healthy volunteers. Materials and Methods A spin-echo MR Elastography (MRE) pulse sequence was developed to provide both high shear wave motion sensitivity and short TE for improved visualization of lung parenchyma. The improved motion sensitivity of this approach was modeled and tested with phantom experiments. In vivo testing was then performed on ten healthy volunteers at the respiratory states of residual volume (RV) and total lung capacity (TLC). Results Shear wave propagation was visualized within the lungs of all volunteers and was processed to provide parenchymal shear stiffness maps of all ten subjects. Density corrected stiffness values at TLC (1.83 ± 0.22 kPa) were higher than those at the RV (1.14 ± 0.14 kPa) with the difference being statistically significant (p<0.0001). Conclusion 1H-based MR Elastography can noninvasively measure the shear stiffness of human lung parenchyma in vivo and can quantitate the change in shear stiffness due to respiration. The values obtained were consistent with previously reported in vitro assessments of cadaver lungs. Further work is required to increase the flexibility of the current acquisition and to investigate the clinical potential of lung MRE. PMID:21591003

  15. Lung Organogenesis

    PubMed Central

    Warburton, David; El-Hashash, Ahmed; Carraro, Gianni; Tiozzo, Caterina; Sala, Frederic; Rogers, Orquidea; De Langhe, Stijn; Kemp, Paul J.; Riccardi, Daniela; Torday, John; Bellusci, Saverio; Shi, Wei; Lubkin, Sharon R; Jesudason, Edwin

    2011-01-01

    Developmental lung biology is a field that has the potential for significant human impact: lung disease at the extremes of age continues to cause major morbidity and mortality worldwide. Understanding how the lung develops holds the promise that investigators can use this knowledge to aid lung repair and regeneration. In the decade since the “molecular embryology” of the lung was first comprehensively reviewed, new challenges have emerged—and it is on these that we focus the current review. Firstly, there is a critical need to understand the progenitor cell biology of the lung in order to exploit the potential of stem cells for the treatment of lung disease. Secondly, the current familiar descriptions of lung morphogenesis governed by growth and transcription factors need to be elaborated upon with the reinclusion and reconsideration of other factors, such as mechanics, in lung growth. Thirdly, efforts to parse the finer detail of lung bud signaling may need to be combined with broader consideration of overarching mechanisms that may be therapeutically easier to target: in this arena, we advance the proposal that looking at the lung in general (and branching in particular) in terms of clocks may yield unexpected benefits. PMID:20691848

  16. Assessment of hybrid, meta-hybrid-GGA, and long-range corrected density functionals for the estimation of enthalpies of formation, barrier heights, and ionisation potentials of selected C1-C5 oxygenates

    NASA Astrophysics Data System (ADS)

    El-Nahas, Ahmed M.; Simmie, John M.; Mangood, Ahmed H.; Hirao, Kimihiko; Song, Jong-Won; Watson, Mark A.; Taketsugu, Tetsuya; Koga, Nobuaki

    2015-07-01

    The enthalpies of formation for some selected oxygenates have been calculated by the atomisation energy approach using B3LYP, BHandHLYP, MPW3LYP, MPW1K, MPWB1K, BB1K, MPW1B95, BMK, and long-range corrected (LC-ωPBE, LC-BOP, LCgau-BOP, LC-BOP12, LCgau-B97) density functionals, as well as the composite CBS-QB3 method. Compared with experiment, BMK, LC-ωPBE, LCgau-BOP, LC-BOP12, LCgau-B97, MPW195, MPW3LYP functionals and CBS-QB3 give root mean square errors (RMSE) in enthalpies of formation no greater than 4 kcal/mol, whilst MPW1K and BHandHLYP show much worse performance (RMSE of 20-40 kcal/mol). The B3LYP, MPWB1K, and BB1K results fall between the two extremes. Energy barriers for the dominant paths in the unimolecular decomposition of simple esters (HCO2CH3, C2H5CO2C2H5), C1-C3 acids, and 1-butanol are reproduced well by CBS-QB3, BMK, BB1K, LCgau-B97, and PW1B95 (RMSE = 1-2 kcal/mol), while other LC methods (LC-ωPBE, LC-BOP, LCgau-BOP, and LC-BOP12) show a deviation of up to 4 kcal/mol. For the ionisation potentials, calculated from Koopman's theorem, all of the investigated LC-methods give good results compared with other density functional theory functionals with a maximum deviation of 0.4 eV, except for LCgau-B97, which has an RMSE of 0.7 eV.

  17. Jitter Correction

    NASA Technical Reports Server (NTRS)

    Waegell, Mordecai J.; Palacios, David M.

    2011-01-01

    Jitter_Correct.m is a MATLAB function that automatically measures and corrects inter-frame jitter in an image sequence to a user-specified precision. In addition, the algorithm dynamically adjusts the image sample size to increase the accuracy of the measurement. The Jitter_Correct.m function takes an image sequence with unknown frame-to-frame jitter and computes the translations of each frame (column and row, in pixels) relative to a chosen reference frame with sub-pixel accuracy. The translations are measured using a Cross Correlation Fourier transformation method in which the relative phase of the two transformed images is fit to a plane. The measured translations are then used to correct the inter-frame jitter of the image sequence. The function also dynamically expands the image sample size over which the cross-correlation is measured to increase the accuracy of the measurement. This increases the robustness of the measurement to variable magnitudes of inter-frame jitter

  18. [The lung].

    PubMed

    Martinod, Emmanuel; Uzunhan, Yurdagül; Radu, Dana M; Seguin, Agathe; Boddaert, Guillaume; Valeyre, Dominique; Planès, Carole; Carpentier, Alain

    2011-10-01

    Lung transplantation is still the only curative treatment for end-stage pulmonary diseases. The results remain poor, however, because of the limited availability of lung donors, chronic rejection, and complications related to immunosuppressive therapy. The use of a bioartificial lung generated from autologous cells could offer a solution. We have demonstrated that in vivo epithelial and cartilage regeneration of the airways is feasible with the use of an aortic tissue matrix. Other studies show that in vitro and in vivo airway regeneration, respectively, can be obtained by using bio-engineering and heterotopic allograft implantation. A more complex challenge is the creation of an artificial lung Indeed, this would require the use of an elastic matrix that can promote regeneration of the different lung components (airways, alveoli, vessels) over a large surface area, thus allowing ventilation, blood perfusion and gas exchanges. Recent studies have demonstrated the possibility of in vitro and in vivo regeneration of lung tissue from autologous cells, and especially stem cells. This emerging research field is currently dominated by the use of decellularized lung matrices and autologous epithelial and endothelial cells. Implantation of such a recellularized matrix in animals has proved the feasibility of a functional bio-artificial lung. The first human transplantation of a bio-artificial lung should be possible within 10-20 years.

  19. Lung transplantation

    PubMed Central

    Afonso, José Eduardo; Werebe, Eduardo de Campos; Carraro, Rafael Medeiros; Teixeira, Ricardo Henrique de Oliveira Braga; Fernandes, Lucas Matos; Abdalla, Luis Gustavo; Samano, Marcos Naoyuki; Pêgo-Fernandes, Paulo Manuel

    2015-01-01

    ABSTRACT Lung transplantation is a globally accepted treatment for some advanced lung diseases, giving the recipients longer survival and better quality of life. Since the first transplant successfully performed in 1983, more than 40 thousand transplants have been performed worldwide. Of these, about seven hundred were in Brazil. However, survival of the transplant is less than desired, with a high mortality rate related to primary graft dysfunction, infection, and chronic graft dysfunction, particularly in the form of bronchiolitis obliterans syndrome. New technologies have been developed to improve the various stages of lung transplant. To increase the supply of lungs, ex vivo lung reconditioning has been used in some countries, including Brazil. For advanced life support in the perioperative period, extracorporeal membrane oxygenation and hemodynamic support equipment have been used as a bridge to transplant in critically ill patients on the waiting list, and to keep patients alive until resolution of the primary dysfunction after graft transplant. There are patients requiring lung transplant in Brazil who do not even come to the point of being referred to a transplant center because there are only seven such centers active in the country. It is urgent to create new centers capable of performing lung transplantation to provide patients with some advanced forms of lung disease a chance to live longer and with better quality of life. PMID:26154550

  20. Lung Diseases

    MedlinePlus

    When you breathe, your lungs take in oxygen from the air and deliver it to the bloodstream. The cells in your body need oxygen to ... you breathe nearly 25,000 times. People with lung disease have difficulty breathing. Millions of people in ...

  1. Lung Cancer

    MedlinePlus

    Lung cancer is one of the most common cancers in the world. It is a leading cause of cancer death in men and women in the United States. Cigarette smoking causes most lung cancers. The more cigarettes you smoke per day and ...

  2. Interactive lung segmentation in abnormal human and animal chest CT scans

    SciTech Connect

    Kockelkorn, Thessa T. J. P. Viergever, Max A.; Schaefer-Prokop, Cornelia M.; Bozovic, Gracijela; Muñoz-Barrutia, Arrate; Rikxoort, Eva M. van; Brown, Matthew S.; Jong, Pim A. de; Ginneken, Bram van

    2014-08-15

    Purpose: Many medical image analysis systems require segmentation of the structures of interest as a first step. For scans with gross pathology, automatic segmentation methods may fail. The authors’ aim is to develop a versatile, fast, and reliable interactive system to segment anatomical structures. In this study, this system was used for segmenting lungs in challenging thoracic computed tomography (CT) scans. Methods: In volumetric thoracic CT scans, the chest is segmented and divided into 3D volumes of interest (VOIs), containing voxels with similar densities. These VOIs are automatically labeled as either lung tissue or nonlung tissue. The automatic labeling results can be corrected using an interactive or a supervised interactive approach. When using the supervised interactive system, the user is shown the classification results per slice, whereupon he/she can adjust incorrect labels. The system is retrained continuously, taking the corrections and approvals of the user into account. In this way, the system learns to make a better distinction between lung tissue and nonlung tissue. When using the interactive framework without supervised learning, the user corrects all incorrectly labeled VOIs manually. Both interactive segmentation tools were tested on 32 volumetric CT scans of pigs, mice and humans, containing pulmonary abnormalities. Results: On average, supervised interactive lung segmentation took under 9 min of user interaction. Algorithm computing time was 2 min on average, but can easily be reduced. On average, 2.0% of all VOIs in a scan had to be relabeled. Lung segmentation using the interactive segmentation method took on average 13 min and involved relabeling 3.0% of all VOIs on average. The resulting segmentations correspond well to manual delineations of eight axial slices per scan, with an average Dice similarity coefficient of 0.933. Conclusions: The authors have developed two fast and reliable methods for interactive lung segmentation in

  3. Fibroblast Growth Factor Receptor 1 (FGFR1), Partly Related to Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) and Microvessel Density, is an Independent Prognostic Factor for Non-Small Cell Lung Cancer

    PubMed Central

    Pu, Dan; Liu, Jiewei; Li, Zhixi; Zhu, Jiang; Hou, Mei

    2017-01-01

    Background This study aimed to explore the correlation between FGFR1 and clinical features, including survival analysis and the promotion of angiogenesis by fibroblast growth factor receptor 1 (FGFR1) and vascular endothelial growth factor receptor 2 (VEGFR2). FGFR1 gene amplification has been found in non-small cell lung cancer (NSCLC). However, the prognostic value of FGFR1 and the correlation between FGFR1 and clinical features are still controversial. Material/Methods A total of 92 patients with NSCLC who underwent R0 resection between July 2006 and July 2008 were enrolled in the study. The expression of FGFR1, VEGFR2, and CD34 was detected by immunohistochemistry. The correlations between the aforementioned markers and the patients’ clinical features were analyzed by the chi-square test. The impact factors of prognosis were evaluated by Cox regression analyses. Results The expression ratios of FGFR1 and VEGFR2 were 26.1% and 43.4%, respectively. The intensity of FGFR1 expression was related to VEGFR2 and histopathology. To some extent, the average microvessel density (MVD) had correlation to the expression of FGFR1 and VGEFR2. The pathological stages III–IV and high expression of FGFR1 were found to be independent prognostic factors. Conclusions The expression intensity of FGFR1 and VEGFR2 was associated with MVD, and the expression of FGFR1 is one of the independent prognostic indicators for NSCLC. PMID:28088809

  4. What Is Lung Cancer?

    MedlinePlus

    ... Graphics Infographic Stay Informed Cancer Home What Is Lung Cancer? Language: English Español (Spanish) Recommend on Facebook Tweet ... cancer starts in the lungs, it is called lung cancer. Lung cancer begins in the lungs and may ...

  5. Lung Cancer Screening

    MedlinePlus

    ... Treatment Lung Cancer Prevention Lung Cancer Screening Research Lung Cancer Screening (PDQ®)–Patient Version What is screening? ... These are called diagnostic tests . General Information About Lung Cancer Key Points Lung cancer is a disease ...

  6. Lung Cancer Prevention

    MedlinePlus

    ... Treatment Lung Cancer Prevention Lung Cancer Screening Research Lung Cancer Prevention (PDQ®)–Patient Version What is prevention? ... to keep cancer from starting. General Information About Lung Cancer Key Points Lung cancer is a disease ...

  7. Particles causing lung disease.

    PubMed Central

    Kilburn, K H

    1984-01-01

    The lung has a limited number of patterns of reaction to inhaled particles. The disease observed depends upon the location: conducting airways, terminal bronchioles and alveoli, and upon the nature of inflammation induced: acute, subacute or chronic. Many different agents cause narrowing of conducting airways (asthma) and some of these cause permanent distortion or obliteration of airways as well. Terminal bronchioles appear to be particularly susceptible to particles which cause goblet cell metaplasia, mucous plugging and ultimately peribronchiolar fibrosis. Cancer is the last outcome at the bronchial level and appears to depend upon continuous exposure to or retention of an agent in the airway and failure of the affected cells to be exfoliated which may be due to squamous metaplasia. Alveoli are populated by endothelial cells, Type I or pavement epithelial cells and metabolically active cuboidal Type II cells that produce the lungs specific surfactant, dipalmytol lecithin. Disturbances of surfactant lead to edema in distal lung while laryngeal edema due to anaphylaxis or fumes may produce asphyxia. Physical retention of indigestible particles or retention by immune memory responses may provoke hyaline membranes, stimulate alveolar lipoproteinosis and finally fibrosis. This later exuberant deposition of connective tissue has been best studied in the occupational pneumoconioses especially silicosis and asbestosis. In contrast emphysema a catabolic response, appears frequently to result from leakage or release of lysosomal proteases into the lung during processing of cigarette smoke particles. The insidious and probably most important human lung disease due to particles is bronchiolar obstruction and obliteration, producing progressive impairment of air flow. The responsible particle is the complex combination of poorly digestive lipids and complex carbohydrates with active chemicals which we call cigarette smoke. More research is needed to perfect, correct and

  8. Metallic artifact mitigation and organ-constrained tissue assignment for Monte Carlo calculations of permanent implant lung brachytherapy.

    PubMed

    Sutherland, J G H; Miksys, N; Furutani, K M; Thomson, R M

    2014-01-01

    To investigate methods of generating accurate patient-specific computational phantoms for the Monte Carlo calculation of lung brachytherapy patient dose distributions. Four metallic artifact mitigation methods are applied to six lung brachytherapy patient computed tomography (CT) images: simple threshold replacement (STR) identifies high CT values in the vicinity of the seeds and replaces them with estimated true values; fan beam virtual sinogram replaces artifact-affected values in a virtual sinogram and performs a filtered back-projection to generate a corrected image; 3D median filter replaces voxel values that differ from the median value in a region of interest surrounding the voxel and then applies a second filter to reduce noise; and a combination of fan beam virtual sinogram and STR. Computational phantoms are generated from artifact-corrected and uncorrected images using several tissue assignment schemes: both lung-contour constrained and unconstrained global schemes are considered. Voxel mass densities are assigned based on voxel CT number or using the nominal tissue mass densities. Dose distributions are calculated using the EGSnrc user-code BrachyDose for (125)I, (103)Pd, and (131)Cs seeds and are compared directly as well as through dose volume histograms and dose metrics for target volumes surrounding surgical sutures. Metallic artifact mitigation techniques vary in ability to reduce artifacts while preserving tissue detail. Notably, images corrected with the fan beam virtual sinogram have reduced artifacts but residual artifacts near sources remain requiring additional use of STR; the 3D median filter removes artifacts but simultaneously removes detail in lung and bone. Doses vary considerably between computational phantoms with the largest differences arising from artifact-affected voxels assigned to bone in the vicinity of the seeds. Consequently, when metallic artifact reduction and constrained tissue assignment within lung contours are employed

  9. Metallic artifact mitigation and organ-constrained tissue assignment for Monte Carlo calculations of permanent implant lung brachytherapy

    SciTech Connect

    Sutherland, J. G. H.; Miksys, N.; Thomson, R. M.; Furutani, K. M.

    2014-01-15

    Purpose: To investigate methods of generating accurate patient-specific computational phantoms for the Monte Carlo calculation of lung brachytherapy patient dose distributions. Methods: Four metallic artifact mitigation methods are applied to six lung brachytherapy patient computed tomography (CT) images: simple threshold replacement (STR) identifies high CT values in the vicinity of the seeds and replaces them with estimated true values; fan beam virtual sinogram replaces artifact-affected values in a virtual sinogram and performs a filtered back-projection to generate a corrected image; 3D median filter replaces voxel values that differ from the median value in a region of interest surrounding the voxel and then applies a second filter to reduce noise; and a combination of fan beam virtual sinogram and STR. Computational phantoms are generated from artifact-corrected and uncorrected images using several tissue assignment schemes: both lung-contour constrained and unconstrained global schemes are considered. Voxel mass densities are assigned based on voxel CT number or using the nominal tissue mass densities. Dose distributions are calculated using the EGSnrc user-code BrachyDose for{sup 125}I, {sup 103}Pd, and {sup 131}Cs seeds and are compared directly as well as through dose volume histograms and dose metrics for target volumes surrounding surgical sutures. Results: Metallic artifact mitigation techniques vary in ability to reduce artifacts while preserving tissue detail. Notably, images corrected with the fan beam virtual sinogram have reduced artifacts but residual artifacts near sources remain requiring additional use of STR; the 3D median filter removes artifacts but simultaneously removes detail in lung and bone. Doses vary considerably between computational phantoms with the largest differences arising from artifact-affected voxels assigned to bone in the vicinity of the seeds. Consequently, when metallic artifact reduction and constrained tissue

  10. Metallic artifact mitigation and organ-constrained tissue assignment for Monte Carlo calculations of permanent implant lung brachytherapy

    SciTech Connect

    Sutherland, J. G. H.; Miksys, N.; Thomson, R. M.; Furutani, K. M.

    2014-01-15

    Purpose: To investigate methods of generating accurate patient-specific computational phantoms for the Monte Carlo calculation of lung brachytherapy patient dose distributions. Methods: Four metallic artifact mitigation methods are applied to six lung brachytherapy patient computed tomography (CT) images: simple threshold replacement (STR) identifies high CT values in the vicinity of the seeds and replaces them with estimated true values; fan beam virtual sinogram replaces artifact-affected values in a virtual sinogram and performs a filtered back-projection to generate a corrected image; 3D median filter replaces voxel values that differ from the median value in a region of interest surrounding the voxel and then applies a second filter to reduce noise; and a combination of fan beam virtual sinogram and STR. Computational phantoms are generated from artifact-corrected and uncorrected images using several tissue assignment schemes: both lung-contour constrained and unconstrained global schemes are considered. Voxel mass densities are assigned based on voxel CT number or using the nominal tissue mass densities. Dose distributions are calculated using the EGSnrc user-code BrachyDose for{sup 125}I, {sup 103}Pd, and {sup 131}Cs seeds and are compared directly as well as through dose volume histograms and dose metrics for target volumes surrounding surgical sutures. Results: Metallic artifact mitigation techniques vary in ability to reduce artifacts while preserving tissue detail. Notably, images corrected with the fan beam virtual sinogram have reduced artifacts but residual artifacts near sources remain requiring additional use of STR; the 3D median filter removes artifacts but simultaneously removes detail in lung and bone. Doses vary considerably between computational phantoms with the largest differences arising from artifact-affected voxels assigned to bone in the vicinity of the seeds. Consequently, when metallic artifact reduction and constrained tissue

  11. A CORRECTION.

    PubMed

    Johnson, D

    1940-03-22

    IN a recently published volume on "The Origin of Submarine Canyons" the writer inadvertently credited to A. C. Veatch an excerpt from a submarine chart actually contoured by P. A. Smith, of the U. S. Coast and Geodetic Survey. The chart in question is Chart IVB of Special Paper No. 7 of the Geological Society of America entitled "Atlantic Submarine Valleys of the United States and the Congo Submarine Valley, by A. C. Veatch and P. A. Smith," and the excerpt appears as Plate III of the volume fist cited above. In view of the heavy labor involved in contouring the charts accompanying the paper by Veatch and Smith and the beauty of the finished product, it would be unfair to Mr. Smith to permit the error to go uncorrected. Excerpts from two other charts are correctly ascribed to Dr. Veatch.

  12. 77 FR 72199 - Technical Corrections; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-05

    ... COMMISSION 10 CFR Part 171 RIN 3150-AJ16 Technical Corrections; Correction AGENCY: Nuclear Regulatory... corrections, including updating the street address for the Region I office, correcting authority citations and... rule. DATES: The correction is effective on December 5, 2012. FOR FURTHER INFORMATION CONTACT:...

  13. Lung cancer

    MedlinePlus

    ... Sputum test to look for cancer cells Thoracentesis (sampling of fluid buildup around the lung) In most ... quitting, talk with your provider. There are many methods to help you quit, from support groups to ...

  14. Lung Transplant

    MedlinePlus

    ... will recover in the hospital’s intensive care unit (ICU) before moving to a hospital room for one to three weeks. Your doctor may recommend pulmonary rehabilitation after your lung transplant surgery to help you ...

  15. Quantification of lung surface area using computed tomography.

    PubMed

    Yuan, Ren; Nagao, Taishi; Paré, Peter D; Hogg, James C; Sin, Don D; Elliott, Mark W; Loy, Leanna; Xing, Li; Kalloger, Steven E; English, John C; Mayo, John R; Coxson, Harvey O

    2010-10-31

    To refine the CT prediction of emphysema by comparing histology and CT for specific regions of lung. To incorporate both regional lung density measured by CT and cluster analysis of low attenuation areas for comparison with histological measurement of surface area per unit lung volume. The histological surface area per unit lung volume was estimated for 140 samples taken from resected lung specimens of fourteen subjects. The region of the lung sampled for histology was located on the pre-operative CT scan; the regional CT median lung density and emphysematous lesion size were calculated using the X-ray attenuation values and a low attenuation cluster analysis. Linear mixed models were used to examine the relationships between histological surface area per unit lung volume and CT measures. The median CT lung density, low attenuation cluster analysis, and the combination of both were important predictors of surface area per unit lung volume measured by histology (p < 0.0001). Akaike's information criterion showed the model incorporating both parameters provided the most accurate prediction of emphysema. Combining CT measures of lung density and emphysematous lesion size provides a more accurate estimate of lung surface area per unit lung volume than either measure alone.

  16. Unexpandable lung.

    PubMed

    Pereyra, Marco F; Ferreiro, Lucía; Valdés, Luis

    2013-02-01

    Unexpandable lung is a mechanical complication by which the lung does not expand to the chest wall, impeding a normal apposition between the two pleural layers. The main mechanism involved is the restriction of the visceral pleura due to the formation of a fibrous layer along this pleural membrane. This happens because of the presence of an active pleural disease (lung entrapment), which can be resolved if proper therapeutic measures are taken, or a remote disease (trapped lung), in which an irreversible fibrous pleural layer has been formed. The clinical suspicion arises with the presence of post-thoracocentesis hydropneumothorax or a pleural effusion that cannot be drained due to the appearance of thoracic pain. The diagnosis is based on the analysis of the pleural liquid, the determination of pleural pressures as we drain the effusion and on air-contrast chest CT. As both represent the continuity of one same process, the results will depend on the time at which these procedures are done. If, when given a lung that is becoming entrapped, the necessary therapeutic measures are not taken, the final result will be a trapped lung. In this instance, most patients are asymptomatic or have mild exertional dyspnea and therefore they do not require treatment. Nevertheless, in cases of incapacitating dyspnea, it may be necessary to use pleural decortication in order to resolve the symptoms. Copyright © 2012 SEPAR. Published by Elsevier Espana. All rights reserved.

  17. No evidence of linkage between the very-low-density lipoprotein receptor gene and fasting serum insulin or homeostasis model assessment insulin resistance index: the National Heart, Lung, and Blood Institute Family Heart Study.

    PubMed

    Hong, Y; Leppert, M F; Lin, J; Hunt, S C; Rich, S S; Arnett, D K; Myers, R H; Eckfeldt, J; Williams, R R; Province, M A

    2000-03-01

    A major gene effect on the fasting insulin level and insulin resistance has been suggested in previous studies. Several candidate genes for insulin resistance in rare syndromes have been proposed. However, there has been limited success in finding genes for common forms of insulin resistance. There is accumulating evidence of a relationship between insulin resistance and a disturbance of free fatty acid (FFA) metabolism. The very-low-density lipoprotein (VLDL) receptor, which is associated with FFA metabolism, could serve as a possible candidate gene for insulin resistance. We performed linkage analyses between the VLDL receptor gene and fasting insulin and the homeostasis model assessment (HOMA) insulin resistance index (fasting insulin x fasting glucose/22.5) in 1,050 sibpairs participating in the phase II physical examination of the National Heart, Lung, and Blood Institute Family Heart Study (FHS). Data analyses were completed using the SIBPAL component of the SAGE software package (SAGE, Statistical Analysis for Genetic Epidemiology, Version 3.1; Computer program package available from the Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 1997). We did not find evidence for linkage of the fasting insulin or the HOMA insulin resistance index with a polymorphic marker at the VLDL locus (P = .316 and .402, respectively). Adjustment of fasting insulin and the HOMA insulin resistance index for the body mass index (BMI) did not change the results (P = .319 and .472, respectively). In conclusion, no evidence was found for a linkage between a locus controlling the fasting insulin level or HOMA insulin resistance index and a VLDL polymorphism in the present study. Additional adjustment of fasting insulin or the HOMA insulin resistance index for the BMI did not change the linkage results significantly.

  18. Bias atlases for segmentation-based PET attenuation correction using PET-CT and MR

    PubMed Central

    Ouyang, Jinsong; Chun, Se Young; Petibon, Yoann; Bonab, Ali A.; Alpert, Nathaniel; Fakhri, Georges El

    2014-01-01

    This study was to obtain voxel-wise PET accuracy and precision using tissue-segmentation for attenuation correction. We applied multiple thresholds to the CTs of 23 patients to classify tissues. For six of the 23 patients, MR images were also acquired. The MR fat/in-phase ratio images were used for fat segmentation. Segmented tissue classes were used to create attenuation maps, which were used for attenuation correction in PET reconstruction. PET bias images were then computed using the PET reconstructed with the original CT as the reference. We registered the CTs for all the patients and transformed the corresponding bias images accordingly. We then obtained the mean and standard deviation bias atlas using all the registered bias images. Our CT-based study shows that four-class segmentation (air, lungs, fat, other tissues), which is available on most PET-MR scanners, yields 15.1%, 4.1%, 6.6%, and 12.9% RMSE bias in lungs, fat, non-fat soft-tissues, and bones, respectively. An accurate fat identification is achievable using fat/in-phase MR images. Furthermore, we have found that three-class segmentation (air, lungs, other tissues) yields less than 5% standard deviation of bias within the heart, liver, and kidneys. This implies that three-class segmentation can be sufficient to achieve small variation of bias for imaging these three organs. Finally, we have found that inter- and intra-patient lung density variations contribute almost equally to the overall standard deviation of bias within the lungs. PMID:24966415

  19. Measurement of lung function using Electrical Impedance Tomography (EIT) during mechanical ventilation

    NASA Astrophysics Data System (ADS)

    Nebuya, Satoru; Koike, Tomotaka; Imai, Hiroshi; Noshiro, Makoto; Brown, Brian H.; Soma, Kazui

    2010-04-01

    The consistency of regional lung density measurements as estimated by Electrical Impedance Tomography (EIT), in eleven patients supported by a mechanical ventilator, was validated to verify the feasibility of its use in intensive care medicine. There were significant differences in regional lung densities between the normal lung and diseased lungs associated with pneumonia, atelectasis and pleural effusion (Steel-Dwass test, p < 0.05). Temporal changes in regional lung density of patients with atelectasis were observed to be in good agreement with the results of clinical diagnosis. These results indicate that it is feasible to obtain a quantitative value for regional lung density using EIT.

  20. 78 FR 75449 - Miscellaneous Corrections; Corrections

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ..., 50, 52, and 70 RIN 3150-AJ23 Miscellaneous Corrections; Corrections AGENCY: Nuclear Regulatory... final rule in the Federal Register on June 7, 2013, to make miscellaneous corrections to its regulations... miscellaneous corrections to its regulations in chapter I of Title 10 of the Code of Federal Regulations (10...

  1. CT densitometry of the lungs: Scanner performance

    SciTech Connect

    Kemerink, G.J.; Lamers, R.J.S.; Thelissen, G.R.P.; Engelshoven, J.M.A. van

    1996-01-01

    Our goal was to establish the reproducibility and accuracy of the CT scanner in densitometry of the lungs. Scanner stability was assessed by analysis of daily quality checks. Studies using a humanoid phantom and polyethylene foams for lung were performed to measure reproducibility and accuracy. The dependence of the CT-estimated density on reconstruction filter, zoom factor, slice thickness, table height, data truncation, and objects outside the scan field was determined. Stability of the system at air density was within {approx}1 HU and at water density within {approx}2 HU. Reproducibility and accuracy for densities found for lung were within 2-3%. Dependence on the acquisition and reconstruction parameters was neglible, with the exceptions of the ultra high resolution reconstruction algorithm in the case of emphysema, and objects outside the scan field. The performance of the CT scanner tested is quite adequate for densitometry of the lungs. 26 refs., 5 figs., 4 tabs.

  2. Model-based dose calculations for {sup 125}I lung brachytherapy

    SciTech Connect

    Sutherland, J. G. H.; Furutani, K. M.; Garces, Y. I.; Thomson, R. M.

    2012-07-15

    Purpose: Model-baseddose calculations (MBDCs) are performed using patient computed tomography (CT) data for patients treated with intraoperative {sup 125}I lung brachytherapy at the Mayo Clinic Rochester. Various metallic artifact correction and tissue assignment schemes are considered and their effects on dose distributions are studied. Dose distributions are compared to those calculated under TG-43 assumptions. Methods: Dose distributions for six patients are calculated using phantoms derived from patient CT data and the EGSnrc user-code BrachyDose. {sup 125}I (GE Healthcare/Oncura model 6711) seeds are fully modeled. Four metallic artifact correction schemes are applied to the CT data phantoms: (1) no correction, (2) a filtered back-projection on a modified virtual sinogram, (3) the reassignment of CT numbers above a threshold in the vicinity of the seeds, and (4) a combination of (2) and (3). Tissue assignment is based on voxel CT number and mass density is assigned using a CT number to mass density calibration. Three tissue assignment schemes with varying levels of detail (20, 11, and 5 tissues) are applied to metallic artifact corrected phantoms. Simulations are also performed under TG-43 assumptions, i.e., seeds in homogeneous water with no interseed attenuation. Results: Significant dose differences (up to 40% for D{sub 90}) are observed between uncorrected and metallic artifact corrected phantoms. For phantoms created with metallic artifact correction schemes (3) and (4), dose volume metrics are generally in good agreement (less than 2% differences for all patients) although there are significant local dose differences. The application of the three tissue assignment schemes results in differences of up to 8% for D{sub 90}; these differences vary between patients. Significant dose differences are seen between fully modeled and TG-43 calculations with TG-43 underestimating the dose (up to 36% in D{sub 90}) for larger volumes containing higher proportions of

  3. Rheumatoid lung disease

    MedlinePlus

    Lung disease - rheumatoid arthritis; Rheumatoid nodules; Rheumatoid lung ... Lung problems are common in rheumatoid arthritis. They often cause no symptoms. The cause of lung disease associated with rheumatoid arthritis is unknown. Sometimes, the medicines used to ...

  4. Nutrition for Lung Cancer

    MedlinePlus

    ... by zip code or Select your state State Lung Cancer www.lung.org > Lung Health and Diseases > ... I Stay Healthy Share this page: Nutrition for Lung Cancer Key Points There is no prescribed diet ...

  5. Lung Nodules: Overview

    MedlinePlus

    ... Research & Science Education & Training Home Conditions Lung Nodules Lung Nodules Make an Appointment Find a Doctor Ask ... Kern, MD (June 01, 2016) What is a lung nodule? A lung nodule is also called a ...

  6. Eosinophilic Lung Disorders

    MedlinePlus

    ... Education & Training Home Conditions Eosinophilic Lung Disorders Eosinophilic Lung Disorders Make an Appointment Find a Doctor Ask ... Rafeul Alam, MD, PhD (July 01, 2012) Eosinophilic lung disorders are a category of lung problems characterized ...

  7. Lung Nodules: Overview

    MedlinePlus

    ... Research & Science Education & Training Home Conditions Lung Nodules Lung Nodules Make an Appointment Find a Doctor Ask ... Kern, MD (June 01, 2016) What is a lung nodule? A lung nodule is also called a ...

  8. Lung Cancer Screening

    MedlinePlus

    Lung cancer screening Overview By Mayo Clinic Staff Lung cancer screening is a process that's used to detect the presence ... with a high risk of lung cancer. Lung cancer screening is recommended for older adults who are longtime ...

  9. Lung cancer - small cell

    MedlinePlus

    Cancer - lung - small cell; Small cell lung cancer; SCLC ... About 15% of all lung cancer cases are SCLC. Small cell lung cancer is slightly more common in men than women. Almost all cases of SCLC are ...

  10. Furrier's lung

    PubMed Central

    Pimentel, J. Cortez

    1970-01-01

    As is known, the inhalation of animal hairs can provoke immunological reactions in the respiratory tract affecting the naso-tracheo-bronchial sector and giving rise to asthma-like syndromes. Another form of disease, found in furriers with long exposure to `hair dust', is described. It is characterized by a granulomatous interstitial pneumonia, of the tuberculoid type, very similar to that described in other diseases related to the inhalation of organic dusts, both vegetable and animal, such as `farmer's lung' and `bird fancier's lung'. This new disease—which we experimentally reproduced—can be diagnosed from the occupational history together with the finding on lung biopsy of hair shafts within granulomatous lesions (birefringence and histo-chemical reactions). As in other diseases of this type, a host factor of probable immunological nature is suggested. Attention is drawn to the need to protect workers in the furrier's trade. Images PMID:5484998

  11. Tsunami lung.

    PubMed

    Inoue, Yoshihiro; Fujino, Yasuhisa; Onodera, Makoto; Kikuchi, Satoshi; Shozushima, Tatsuyori; Ogino, Nobuyoshi; Mori, Kiyoshi; Oikawa, Hirotaka; Koeda, Yorihiko; Ueda, Hironobu; Takahashi, Tomohiro; Terui, Katsutoshi; Nakadate, Toshihide; Aoki, Hidehiko; Endo, Shigeatsu

    2012-04-01

    We encountered three cases of lung disorders caused by drowning in the recent large tsunami that struck following the Great East Japan Earthquake. All three were females, and two of them were old elderly. All segments of both lungs were involved in all the three patients, necessitating ICU admission and endotracheal intubation and mechanical ventilation. All three died within 3 weeks. In at least two cases, misswallowing of oil was suspected from the features noted at the time of the detection. Sputum culture for bacteria yielded isolation of Stenotrophomonas maltophilia, Legionella pneumophila, Burkholderia cepacia, and Pseudomonas aeruginosa. The cause of tsunami lung may be a combination of chemical induced pneumonia and bacterial pneumonia.

  12. The impact of breathing motion versus heterogeneity effects in lung cancer treatment planning.

    PubMed

    Rosu, Mihaela; Chetty, Indrin J; Tatro, Daniel S; Ten Haken, Randall K

    2007-04-01

    The purpose of this study is to investigate the effects of tissue heterogeneity and breathing-induced motion/deformation on conformal treatment planning for pulmonary tumors and to compare the magnitude and the clinical importance of changes induced by these effects. Treatment planning scans were acquired at normal exhale/inhale breathing states for fifteen patients. The internal target volume (ITV) was defined as the union of exhale and inhale gross tumor volumes uniformly expanded by 5 mm. Anterior/posterior opposed beams (AP/PA) and three-dimensional (3D)-conformal plans were designed using the unit-density exhale ("static") dataset. These plans were further used to calculate (a) density-corrected ("heterogeneous") static dose and (b) heterogeneous cumulative dose, including breathing deformations. The DPM Monte Carlo code was used for dose computations. For larger than coin-sized tumors, relative to unit-density plans, tumor and lung doses increased in the heterogeneity-corrected plans. In comparing cumulative and static plans, larger normal tissue complication probability changes were observed for tumors with larger motion amplitudes and uncompensated breathing-induced hot/cold spots in lung. Accounting for tissue heterogeneity resulted in average increases of 9% and 7% in mean lung dose (MLD) for the 6 MV and 15 MV photon beams, respectively. Breathing-induced effects resulted in approximately 1% and 2% average decreases in MLD from the static value, for the 6 and 15 MV photon beams, respectively. The magnitude of these effects was not found to correlate with the treatment plan technique, i.e., AP/PA versus 3D-CRT. Given a properly designed ITV, tissue heterogeneity effects are likely to have a larger clinical significance on tumor and normal lung treatment evaluation metrics than four-dimensional respiratory-induced changes.

  13. The impact of breathing motion versus heterogeneity effects in lung cancer treatment planning

    SciTech Connect

    Rosu, Mihaela; Chetty, Indrin J.; Tatro, Daniel S.; Haken, Randall K. ten

    2007-04-15

    The purpose of this study is to investigate the effects of tissue heterogeneity and breathing-induced motion/deformation on conformal treatment planning for pulmonary tumors and to compare the magnitude and the clinical importance of changes induced by these effects. Treatment planning scans were acquired at normal exhale/inhale breathing states for fifteen patients. The internal target volume (ITV) was defined as the union of exhale and inhale gross tumor volumes uniformly expanded by 5 mm. Anterior/posterior opposed beams (AP/PA) and three-dimensional (3D)-conformal plans were designed using the unit-density exhale (''static'') dataset. These plans were further used to calculate (a) density-corrected (''heterogeneous'') static dose and (b) heterogeneous cumulative dose, including breathing deformations. The DPM Monte Carlo code was used for dose computations. For larger than coin-sized tumors, relative to unit-density plans, tumor and lung doses increased in the heterogeneity-corrected plans. In comparing cumulative and static plans, larger normal tissue complication probability changes were observed for tumors with larger motion amplitudes and uncompensated breathing-induced hot/cold spots in lung. Accounting for tissue heterogeneity resulted in average increases of 9% and 7% in mean lung dose (MLD) for the 6 MV and 15 MV photon beams, respectively. Breathing-induced effects resulted in approximately 1% and 2% average decreases in MLD from the static value, for the 6 and 15 MV photon beams, respectively. The magnitude of these effects was not found to correlate with the treatment plan technique, i.e., AP/PA versus 3D-CRT. Given a properly designed ITV, tissue heterogeneity effects are likely to have a larger clinical significance on tumor and normal lung treatment evaluation metrics than four-dimensional respiratory-induced changes.

  14. Lung imaging.

    PubMed

    Ley, Sebastian

    2015-06-01

    Imaging of the lung is a mainstay of respiratory medicine. It provides local information about morphology and function of the lung parenchyma that is unchallenged by other noninvasive techniques. During the 2014 European Respiratory Society International Congress in Munich, Germany, a Clinical Year in Review session was held focusing on the latest developments in pulmonary imaging. This review summarises some of the main findings of peer-reviewed articles that were published in the 12-month period prior to the 2014 International Congress. Copyright ©ERS 2015.

  15. Quantitative assessment of scatter correction techniques incorporated in next generation dual-source computed tomography

    NASA Astrophysics Data System (ADS)

    Mobberley, Sean David

    Accurate, cross-scanner assessment of in-vivo air density used to quantitatively assess amount and distribution of emphysema in COPD subjects has remained elusive. Hounsfield units (HU) within tracheal air can be considerably more positive than -1000 HU. With the advent of new dual-source scanners which employ dedicated scatter correction techniques, it is of interest to evaluate how the quantitative measures of lung density compare between dual-source and single-source scan modes. This study has sought to characterize in-vivo and phantom-based air metrics using dual-energy computed tomography technology where the nature of the technology has required adjustments to scatter correction. Anesthetized ovine (N=6), swine (N=13: more human-like rib cage shape), lung phantom and a thoracic phantom were studied using a dual-source MDCT scanner (Siemens Definition Flash. Multiple dual-source dual-energy (DSDE) and single-source (SS) scans taken at different energy levels and scan settings were acquired for direct quantitative comparison. Density histograms were evaluated for the lung, tracheal, water and blood segments. Image data were obtained at 80, 100, 120, and 140 kVp in the SS mode (B35f kernel) and at 80, 100, 140, and 140-Sn (tin filtered) kVp in the DSDE mode (B35f and D30f kernels), in addition to variations in dose, rotation time, and pitch. To minimize the effect of cross-scatter, the phantom scans in the DSDE mode was obtained by reducing the tube current of one of the tubes to its minimum (near zero) value. When using image data obtained in the DSDE mode, the median HU values in the tracheal regions of all animals and the phantom were consistently closer to -1000 HU regardless of reconstruction kernel (chapters 3 and 4). Similarly, HU values of water and blood were consistently closer to their nominal values of 0 HU and 55 HU respectively. When using image data obtained in the SS mode the air CT numbers demonstrated a consistent positive shift of up to 35 HU

  16. Lung vasculature imaging using speckle variance optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Cua, Michelle; Lee, Anthony M. D.; Lane, Pierre M.; McWilliams, Annette; Shaipanich, Tawimas; MacAulay, Calum E.; Yang, Victor X. D.; Lam, Stephen

    2012-02-01

    Architectural changes in and remodeling of the bronchial and pulmonary vasculature are important pathways in diseases such as asthma, chronic obstructive pulmonary disease (COPD), and lung cancer. However, there is a lack of methods that can find and examine small bronchial vasculature in vivo. Structural lung airway imaging using optical coherence tomography (OCT) has previously been shown to be of great utility in examining bronchial lesions during lung cancer screening under the guidance of autofluorescence bronchoscopy. Using a fiber optic endoscopic OCT probe, we acquire OCT images from in vivo human subjects. The side-looking, circumferentially-scanning probe is inserted down the instrument channel of a standard bronchoscope and manually guided to the imaging location. Multiple images are collected with the probe spinning proximally at 100Hz. Due to friction, the distal end of the probe does not spin perfectly synchronous with the proximal end, resulting in non-uniform rotational distortion (NURD) of the images. First, we apply a correction algorithm to remove NURD. We then use a speckle variance algorithm to identify vasculature. The initial data show a vascaulture density in small human airways similar to what would be expected.

  17. [Humidifier lung].

    PubMed

    Gerber, P; de Haller, R; Pyrozynski, W J; Sturzenegger, E R; Brändli, O

    1981-02-07

    Breathing air from a humidifier or an air conditioning unit contaminated by various microorganisms can cause an acute lung disease involving fever, cough and dyspnea, termed "humidifier fever". This type of hypersensitivity pneumonitis was first described in 1959 by PESTALOZZI in the Swiss literature and subsequently by BANASZAK et al. in the Anglo-American. Here a chronic form of this disease which led to pulmonary fibrosis is described: A 37-year-old woman who works in a cheese shop presented with dyspnea which had been progressive over two years, weight loss, a diffuse reticular pattern radiographically and a severe restrictive defect in lung function tests. Open lung biopsy revealed chronic interstitial and alveolar inflammation with non-caseating granulomas and fibrotic changes. Circulating immune complexes and precipitins against the contaminated humidifier water and cheese mites were found, but no antibodies suggesting legionnaires' disease. Two out of five otherwise healthy employees of this cheese shop, where a new humidifying system had been installed 7 years earlier, also had precipitins against the contaminated water from the humidifier and the cheese mites. Despite ending of exposure and longterm steroid and immunosuppressive therapy, the signs and symptoms of pulmonary fibrosis persisted. Contrary to the acute disease, this chronic form is termed "humidifier lung". The importance is stressed of investigating the possibility of exposure to contaminated humidifiers or air conditioning units in all cases of newly detected pulmonary fibrosis.

  18. Partition Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Wasserman, Adam

    2012-02-01

    Partition Density Functional Theory (PDFT) is a formally exact method for obtaining molecular properties from self-consistent calculations on isolated fragments [1,2]. For a given choice of fragmentation, PDFT outputs the (in principle exact) molecular energy and density, as well as fragment densities that sum to the correct molecular density. I describe our progress understanding the behavior of the fragment energies as a function of fragment occupations, derivative discontinuities, practical implementation, and applications of PDFT to small molecules. I also discuss implications for ground-state Density Functional Theory, such as the promise of PDFT to circumvent the delocalization error of approximate density functionals. [4pt] [1] M.H. Cohen and A. Wasserman, J. Phys. Chem. A, 111, 2229(2007).[0pt] [2] P. Elliott, K. Burke, M.H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010).

  19. What Are Lung Carcinoid Tumors?

    MedlinePlus

    ... Carcinoid Tumor About Lung Carcinoid Tumors What Are Lung Carcinoid Tumors? Lung carcinoid tumors (also known as ... lungs, as well as the neuroendocrine system. The lungs The lungs are 2 sponge-like organs in ...

  20. Gluon density in nuclei

    SciTech Connect

    Ayala, A.L.; Ducati, M.B.G.; Levin, E.M.

    1996-10-01

    In this talk we present our detailed study (theory and numbers) on the shadowing corrections to the gluon structure functions for nuclei. Starting from rather controversial information on the nucleon structure function which is originated by the recent HERA data, we develop the Glauber approach for the gluon density in a nucleus based on Mueller formula and estimate the value of the shadowing corrections in this case. Then we calculate the first corrections to the Glauber approach and show that these corrections are big. Based on this practical observation we suggest the new evolution equation which takes into account the shadowing corrections and solve it. We hope to convince you that the new evolution equation gives a good theoretical tool to treat the shadowing corrections for the gluons density in a nucleus and, therefore, it is able to provide the theoretically reliable initial conditions for the time evolution of the nucleus-nucleus cascade. The initial conditions should be fixed both theoretically and phenomenologically before to attack such complicated problems as the mixture of hard and soft processes in nucleus-nucleus interactions at high energy or the theoretically reliable approach to hadron or/and parton cascades for high energy nucleus-nucleus interaction. 35 refs., 24 figs., 1 tab.

  1. Lung tissue classification using wavelet frames.

    PubMed

    Depeursinge, Adrien; Sage, Daniel; Hidki, Asmâa; Platon, Alexandra; Poletti, Pierre-Alexandre; Unser, Michael; Müller, Henning

    2007-01-01

    We describe a texture classification system that identifies lung tissue patterns from high-resolution computed tomography (HRCT) images of patients affected with interstitial lung diseases (ILD). This pattern recognition task is part of an image-based diagnostic aid system for ILDs. Five lung tissue patterns (healthy, emphysema, ground glass, fibrosis and microdules) selected from a multimedia database are classified using the overcomplete discrete wavelet frame decompostion combined with grey-level histogram features. The overall multiclass accuracy reaches 92.5% of correct matches while combining the two types of features, which are found to be complementary.

  2. 77 FR 2435 - Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-18

    ...- Free Treatment Under the Generalized System of Preferences and for Other Purposes Correction In... following correction: On page 407, the date following the proclamation number should read ``December...

  3. 78 FR 2193 - Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-10

    ... United States-Panama Trade Promotion Agreement and for Other Purposes Correction In Presidential document... correction: On page 66507, the proclamation identification heading on line one should read...

  4. Mild loss of lung aeration augments stretch in healthy lung regions.

    PubMed

    Cereda, Maurizio; Xin, Yi; Hamedani, Hooman; Clapp, Justin; Kadlecek, Stephen; Meeder, Natalie; Zeng, Johnathan; Profka, Harrilla; Kavanagh, Brian P; Rizi, Rahim R

    2016-02-15

    Inspiratory stretch by mechanical ventilation worsens lung injury. However, it is not clear whether and how the ventilator damages lungs in the absence of preexisting injury. We hypothesized that subtle loss of lung aeration during general anesthesia regionally augments ventilation and distension of ventilated air spaces. In eight supine anesthetized and intubated rats, hyperpolarized gas MRI was performed after a recruitment maneuver following 1 h of volume-controlled ventilation with zero positive end-expiratory pressure (ZEEP), FiO2 0.5, and tidal volume 10 ml/kg, and after a second recruitment maneuver. Regional fractional ventilation (FV), apparent diffusion coefficient (ADC) of (3)He (a measurement of ventilated peripheral air space dimensions), and gas volume were measured in lung quadrants of ventral and dorsal regions of the lungs. In six additional rats, computed tomography (CT) images were obtained at each time point. Ventilation with ZEEP decreased total lung gas volume and increased both FV and ADC in all studied regions. Increases in FV were more evident in the dorsal slices. In each lung quadrant, higher ADC was predicted by lower gas volume and by increased mean values (and heterogeneity) of FV distribution. CT scans documented 10% loss of whole-lung aeration and increased density in the dorsal lung, but no macroscopic atelectasis. Loss of pulmonary gas at ZEEP increased fractional ventilation and inspiratory dimensions of ventilated peripheral air spaces. Such regional changes could help explain a propensity for mechanical ventilation to contribute to lung injury in previously uninjured lungs.

  5. Gene expression profiling allows distinction between primary and metastatic squamous cell carcinomas in the lung.

    PubMed

    Talbot, Simon G; Estilo, Cherry; Maghami, Ellie; Sarkaria, Inderpal S; Pham, Duy Khanh; O-charoenrat, Pornchai; Socci, Nicholas D; Ngai, Ivan; Carlson, Diane; Ghossein, Ronald; Viale, Agnes; Park, Bernard J; Rusch, Valerie W; Singh, Bhuvanesh

    2005-04-15

    Lung neoplasms commonly develop in patients previously treated for head and neck carcinomas. The derivation of these tumors, either as new primary lung cancers or as metastatic head and neck cancers, is difficult to establish based on clinical or histopathologic criteria since both are squamous cell carcinomas and have identical features under light microscopy. However, this distinction has significant treatment and prognostic implications. Gene expression profiling was performed on a panel of 52 sequentially collected patients with either primary lung (n = 21) or primary head and neck (n = 31) carcinomas using the Affymetrix HG_U95Av2 high-density oligonucleotide microarray. Unsupervised hierarchical clustering with Ward linkage and the Pearson correlation metric was performed. To assess robustness, bootstrap resampling was performed with 1,000 iterations. A t test of the normalized values for each gene was used to determine the genes responsible for segregating head and neck from lung primary carcinomas, and those with the most differential expression were used for later analyses. In the absence of a large "test" set of tumors, we used a supervised leave-one-out cross-validation to test how well we could predict the tumor origin. Once a gene expression profile was established, 12 lung lesions taken from patients with previously treated head and neck cancers were similarly analyzed by gene expression profiling to determine their sites of origin. Unsupervised clustering analysis separated the study cohort into two distinct groups which reliably remained segregated with bootstrap resampling. Group 1 consisted of 30 tongue carcinomas. Group 2 consisted of 21 lung cancers and 1 tongue carcinoma. The clustering was not changed even when normal lung or tongue profiles were subtracted from the corresponding carcinomatous lesions, and a leave-one-out cross-validation showed a 98% correct prediction (see Supplementary Data 1). A minimum set of 500 genes required to

  6. Early lung function abnormalities in acromegaly.

    PubMed

    Benfante, A; Ciresi, A; Bellia, M; Cannizzaro, F; Bellia, V; Giordano, C; Scichilone, N

    2015-06-01

    Acromegaly is an insidious disorder caused by a pituitary growth hormone (GH)-secreting adenoma resulting in high circulating levels of GH and insulin-like growth factor I (IGF-I). Respiratory disorders are common complications in acromegaly, and can severely impact on quality of life, eventually affecting mortality. The present study aimed to explore structural and functional lung alterations of acromegalic subjects. We enrolled 10 consecutive patients (M/F: 5/5) affected by acromegaly. In all patients, magnetic resonance imaging (MRI) revealed the presence of pituitary tumor. All patients underwent clinical, lung functional, biological, and radiological assessments. Ten healthy