Kinematic Effects on Probability Density Functions of Energy Dissipation Rate and Enstrophy in Turbulence.

Direct numerical simulation and theoretical analyses showed that the probability density functions (PDFs) of the energy dissipation rate and enstrophy in turbulence are asymptotically stretched gamma distributions with the same stretching exponent, and both the left and right tails of the enstrophy PDF are longer than those of the energy dissipation rate regardless of the Reynolds number. The differences in PDF tails arise due to the kinematics, with differences in the number of terms contributing to the dissipation rate and enstrophy. Meanwhile, the stretching exponent is determined by the dynamics and likeliness of singularities.

Phantom-Less Nonlinear Magnetic Resonance Imaging Calibration With Multiple Input Blood Flow Model.

PURPOSE: Previous work used phantoms to calibrate the nonlinear relationship between the gadolinium contrast concentration and the intensity of the magnetic resonance imaging signal. This work proposes a new nonlinear calibration procedure without phantoms and considers the variation of contrast agent mass minimum combined with the multiple input blood flow system. This also proposes a new single-input method with meaningful variables that is not influenced by reperfusion or noise generated by aliasing. The reperfusion in the lung is usually neglected and is not considered by the indicator dilution method. However, in cases of lung cancer, reperfusion cannot be neglected. A new multiple input method is formulated, and the contribution of the pulmonary artery and bronchial artery to lung perfusion can be considered and evaluated separately. METHODS: The calibration procedure applies the minimum variation of contrast agent mass in 3 different regions: (1) pulmonary artery, (2) left atrium, and (3) aorta. It was compared with four dimensional computerized tomography with iodine, which has a very high proportional relationship between contrast agent concentration and signal intensity. RESULTS: Nonlinear calibration was performed without phantoms, and it is in the range of phantom calibration. It successfully separated the contributions of the pulmonary and bronchial arteries. The proposed multiple input method was verified in 6 subjects with lung cancer, and perfusion from the bronchial artery, rich in oxygen, was identified as very high in the cancer region. CONCLUSIONS: Nonlinear calibration of the contrast agent without phantoms is possible. Separate contributions of the pulmonary artery and aorta can be determined.

Transition of fluctuations from Gaussian state to turbulent state.

Variation of the statistical properties of an incompressible velocity, passive vector and passive scalar in isotropic turbulence was studied using direct numerical simulation. The structure functions of the gradients, and the moments of the dissipation rates, began to increase at about [Formula: see text] from the Gaussian state and grew rapidly at [Formula: see text] in the turbulent state. A contour map of the probability density functions (PDFs) indicated that PDF expansion of the gradients of the passive vector and passive scalar begins at around [Formula: see text], whereas that of the longitudinal velocity gradient PDF is more gradual. The left tails of the dissipation rate PDF were found to follow a power law with an exponent of 3/2 for the incompressible velocity and passive vector dissipation rates, and 1/2 for the scalar dissipation rate and the enstrophy; they remained constant for all Reynolds numbers, indicating the universality of the left tail. The analytical PDFs of the dissipation rates and enstrophy of the Gaussian state were obtained and found to be the Gamma distribution. It was shown that the number of terms contributing to the dissipation rates and the enstrophy determines the decay rates of the two PDFs for low to moderate amplitudes. This article is part of the theme issue 'Scaling the turbulence edifice (part 1)'.

Hall magnetohydrodynamic turbulence with a magnetic Prandtl number larger than unity.

Turbulence structures with the magnetic Prandtl number larger than unity are studied by means of direct numerical simulations of homogeneous, isotropic, and incompressible Hall magnetohydrodynamic (MHD) turbulence driven by a random force. Spectral and spatial structures on the scales smaller than the ion skin depth are focused upon in this numerical paper. The numerical simulations reveal the emergence of a new power law in the velocity field whereas it is not observed in MHD turbulence simulation without the Hall term. An order estimate of the energy budget in the spectral space shows that this new power law appears in association with the Hall effect and that a balance between the Lorentz force and the viscous dissipation is crucial for formation of the power law. A resemblance to an elastic turbulence is found in the power-law-formation mechanism. Frequent eruptions of strong current ribbons accompanying strong palinstrophy density are observed, showing generation of the palinstrophy density by the Lorentz force at the scales below the ion skin depth. These properties in spectral and spatial structures characterize a high magnetic Prandtl number Hall MHD turbulence at the scales smaller than the ion skin depth.

Early Archean planktonic mode of life: Implications from fluid dynamics of lenticular microfossils.

Lenticular, and commonly flanged, microfossils in 3.0-3.4 Ga sedimentary deposits in Western Australia and South Africa are unusually large (20-80 µm across), robust, and widespread in space and time. To gain insight into the ecology of these organisms, we performed simulations of fluid dynamics of virtual cells mimicking lenticular forms of variable sizes, oblateness, flange presence, and flange thickness. Results demonstrate that (a) the flange reduces sedimentation velocity, (b) this flange function works more effectively in larger cells, and (c) modest oblateness lowers sedimentation rate. These observations support interpretations that the lenticular microbes were planktonic-a lifestyle that could have been advantageous in an early Earth harsh environment including violent volcanic activities, repeated asteroid impacts, and relatively high UV-radiation. Although the robustness of these organisms could have provided additional protection on the early Earth, this architecture may have impeded a planktonic lifestyle by increasing cell density. However, our data suggest that this disadvantage could have been compensated by enlargement of cell volume, which could have enhanced the ability of the flange to slow sedimentation rate, especially if coupled with vacuolation. The results of this simulation study may help to explain the unique morphology and unusually large size of these Archean microfossils.

Size distribution spectrum of noninertial particles in turbulence.

Collision-coalescence growth of noninertial particles in three-dimensional homogeneous isotropic turbulence is studied. Smoluchowski's coagulation equation describes the evolution of the size distribution of particles in this system. By applying a methodology based on turbulence theory, the equation is shown to have a steady-state solution, which corresponds to the Kolmogorov-type power-law spectrum. Direct numerical simulations of turbulence and Lagrangian particles are conducted. The result shows that the size distribution in a statistically steady state agrees accurately with the theoretical prediction.

Extraction of the subpleural lung region from computed tomography images to detect interstitial lung disease.

PURPOSE: To quantify lesions in the subpleural lung region (SubPL) on computed tomography (CT) images and to evaluate whether they are useful for detecting interstitial lung disease (ILD). MATERIALS AND METHODS: The subjects were 40 patients with idiopathic pulmonary fibrosis (IPF) diagnosed by multidisciplinary methods and 35 age-matched patients without ILDs. The lungs and SubPL were extracted from CT images using a Gaussian histogram normalized correlation system and evaluated for the mean CT attenuation value (CTmean) and the percentage of high attenuation area (%HAA), exceeding -700 Hounsfield units. The H pattern was defined as a honeycomb appearance and/or fibrosis with traction bronchiectasis, and the H-pattern volume ratios for the whole lung and the 2-mm-wide SubPL were measured. The utility of the SubPL for detecting ILD was evaluated by receiver operating characteristic (ROC) analysis. RESULTS: The areas under the ROC curves (AUCs) of CTmean and %HAA for the SubPL were greater than those for the whole lung. The AUCs for the whole lung and the SubPL were 0.990 and 0.994, respectively, for H-pattern volume; 0.875 and 0.994, respectively, for CTmean; and 0.965 and 0.991, respectively, for %HAA. CONCLUSION: The SubPL extraction method may be helpful for distinguishing patients with ILD from those without ILD.

The importance of subpleural fibrosis in the prognosis of patients with idiopathic interstitial pneumonias.

PURPOSE: To compare computer-aided diagnostic results with histological findings obtained by surgical biopsy and evaluate whether subpleural lesion volumes can aid identification of idiopathic pulmonary fibrosis (IPF). MATERIALS AND METHODS: We retrospectively analyzed computed tomography (CT) images of 79 patients (43 with fibrosing nonspecific interstitial pneumonia (fNSIP) and 36 with IPF) using the Gaussian Histogram Normalized Correlation (GHNC) system. We determined the H-pattern based on honeycomb and/or fibrosis with traction bronchiectasis on CT, and measured the H-pattern volume ratio at the biopsy sites and in the subpleural area. The biopsy site CT data were compared with biopsy specimens using Spearman's correlation. H-pattern volumes in the subpleural area within 2mm under the pleura (H2) were analyzed to predict IPF diagnosis and patients prognosis. RESULTS: The H-pattern volume ratio at the biopsy sites showed significant correlation with histological honeycomb (r=0.355, p<0.001), subpleural collapse (r=0.410, p<0.001), and heterogeneity (r=0.484, p<0.001). Multivariate regression analysis, adjusting for age, sex, and CT results, revealed that the H2 was a significant independent predictor of IPF diagnosis (odds ratio: 1.073; p=0.048). H2 correlated with patients' survival after adjusting for age (p=0.003). CONCLUSION: The computer-aided H-pattern volume ratio of the subpleural area indicates subpleural abnormalities quantitatively and may help diagnose IPF.

Multicenter study of quantitative computed tomography analysis using a computer-aided three-dimensional system in patients with idiopathic pulmonary fibrosis.

PURPOSE: To evaluate the feasibility of automated quantitative analysis with a three-dimensional (3D) computer-aided system (i.e., Gaussian histogram normalized correlation, GHNC) of computed tomography (CT) images from different scanners. MATERIALS AND METHODS: Each institution's review board approved the research protocol. Informed patient consent was not required. The participants in this multicenter prospective study were 80 patients (65 men, 15 women) with idiopathic pulmonary fibrosis. Their mean age was 70.6 years. Computed tomography (CT) images were obtained by four different scanners set at different exposures. We measured the extent of fibrosis using GHNC, and used Pearson's correlation analysis, Bland-Altman plots, and kappa analysis to directly compare the GHNC results with manual scoring by radiologists. Multiple linear regression analysis was performed to determine the association between the CT data and forced vital capacity (FVC). RESULTS: For each scanner, the extent of fibrosis as determined by GHNC was significantly correlated with the radiologists' score. In multivariate analysis, the extent of fibrosis as determined by GHNC was significantly correlated with FVC (p < 0.001). There was no significant difference between the results obtained using different CT scanners. CONCLUSION: Gaussian histogram normalized correlation was feasible, irrespective of the type of CT scanner used.

Power and nonpower laws of passive scalar moments convected by isotropic turbulence.

The scaling behavior of the moments of two passive scalars that are excited by two different methods and simultaneously convected by the same isotropic steady turbulence at R_{λ}=805 and Sc=0.72 is studied by using direct numerical simulation with N=4096^{3} grid points. The passive scalar θ is excited by a random source that is Gaussian and white in time, and the passive scalar q is excited by the mean uniform scalar gradient. In the inertial convective range, the nth-order moments of the scalar increment δθ(r) do not obey a simple power law, but have the local scaling exponents ξ_{n}^{θ}+ß_{n}log(r/r_{*}) with ß_{n}>0. In contrast, the local scaling exponents of q have well-developed plateaus and saturate with increasing order. The power law of passive scalar moments is not trivial. The universality of passive scalars is found not in the moments, but in the normalized moments.

Quantitative analysis of intraneuronal transport in human iPS neurons.

Induced pluripotent stem (iPS) cells are promising tools to investigate disease mechanism and develop new drugs. Intraneuronal transport, which is fundamental for neuronal survival and function, is vulnerable to various pharmacological and chemical agents and is disrupted in some neurodegenerative disorders. We applied a quantification method for axonal transport by counting CM-DiI-labeled particles traveling along the neurite, which allowed us to monitor and quantitate, for the first time, intraneuronal transport in human neurons differentiated from iPS cells (iCell neurons). We evaluated the acute effects of several anti-neoplastic agents that have been previously shown to affect intraneuronal transport. Vincristine, paclitaxel and oxaliplatin decreased the number of moving particle along neurites. Cisplatin, however, produced no effect on intraneuronal transport, which is in contrast to our previous report indicating that it inhibits transport in chick dorsal root ganglion neurons. Our system may be a useful method for assessing intraneuronal transport and neurotoxicity in human iPS neurons.

CT analysis of the effect of pirfenidone in patients with idiopathic pulmonary fibrosis.

PURPOSE: Pirfenidone is a new, anti-fibrotic drug used for the treatment of idiopathic pulmonary fibrosis (IPF). The aim of this study was to evaluate the utility of computed tomography (CT) in the imaging assessment of the response to pirfenidone therapy. MATERIALS AND METHODS: Subjects were 78 patients with IPF who underwent CT on two occasions with one-year interval (38 consecutive patients treated with pirfenidone and 40 age-matched control). Changes in the fibrous lesion on sequential CTs were assessed as visual score by two radiologists. We measured the volume and change per year of fibrous pattern (F-pattern) quantitatively using a computer-aided system on sequential CTs. RESULTS: The baseline vital capacity (%pred VC) was 74.0 ± 14.0% in the pirfenidone group and 74.6 ± 16.6% in controls (p=NS). Deterioration of respiratory status was defined as 10% or greater decline in %pred VC value after 12-month treatment. A significantly larger proportion of pirfenidone-treated patients showed stable respiratory status (21 of 38, 65.6%) than the control (15 of 40, 37.5%). The change in fibrous lesion was significantly smaller in the pirfenidone group than the control in both of visual score (p=0.006) and computer analysis (p<0.001). The decline in VC correlated significantly with the increase in fibrotic lesion (p<0.001). CONCLUSION: CT can be used to assess pirfenidone-induced slowing of progression of pulmonary fibrosis.

Fusion of lung MR/CT images through lung vessel registration.

Lung perfusion analysis with sequential contrasted MRI is an important clinical tool. This work is part of larger research in which the objective of fusing lung perfusion analysis and lung anatomical structures. In this work, it is proposed a multimodality MR/CT lung fusion algorithm based on lung vessel determination that analyzes lung perfusion. 3D contrasted MR and 3D CT images are first normalized (slice thickness, resolution and pixel intensity), then lung features are determined and elastically registered. The registration algorithm was checked by mapping in both directions, from MR to CT and vice-versa. A MR perfusion analysis result is fused with a 3D CT segmented lung vessel tree.

Mesh-loosening quantification of inhibition of angiogenic tube formation through image analysis.

Angiogenesis is a key step in tumor development, and anti-angiogenesis processes are important for drug discovery and development. The dose-response relationship for an inhibitor is studied using images of endothelial cells captured in vitro by Matrigel assay. In order to improve the quantification of anti-angiogenic processes for faithful synchronization with continuous variation of an inhibitor dose, we have developed an automated image analysis method-mesh-loosening analysis-to evaluate the disruption of tube formation from endothelial cells. The method is based on numerical and morphological changes of mesh regions surrounded by tubes and perceived by considering the spaces between the tubes rather than the tubes themselves. The anti-angiogenic effect of suramin is analyzed comprehensively using four attributes obtained from the mesh regions. The relation between the dose of suramin and response shows an exponential curve that can be approximated as a sigmoid function, even though human assessments yield strong inhibition at moderate doses. The calculated half-minimal inhibitory concentration was in agreement with prior published reports. The results show that mesh-loosening analysis is useful and appropriate for screening applications that need precise and comprehensive quantification of the anti-angiogenic process to compensate for the inadequacy of human assessment. Feasibility study with shikonin shows the robustness of the mesh-loosening analysis.

Computational analysis of axonal transport: a novel assessment of neurotoxicity, neuronal development and functions.

Axonal transport plays a crucial role in neuronal morphogenesis, survival and function. Despite its importance, however, the molecular mechanisms of axonal transport remain mostly unknown because a simple and quantitative assay system for monitoring this cellular process has been lacking. In order to better characterize the mechanisms involved in axonal transport, we formulate a novel computer-assisted monitoring system of axonal transport. Potential uses of this system and implications for future studies will be discussed.

Automatic tracking of the respiratory motion of lung parenchyma on dynamic magnetic resonance imaging: comparison with pulmonary function tests in patients with chronic obstructive pulmonary disease.

PURPOSE: This study evaluated the respiratory motion of the lung parenchyma using dynamic magnetic resonance imaging and clarified differences between healthy individuals and patients with chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS: The study comprised 6 healthy volunteers and 42 patients diagnosed with smoking-related COPD. We captured 80 sequential frames from the mid-sagittal portion of the right lung while repeating forced deep breathing using a balanced fast-field echo sequence (repetition time, 2.2 ms; echo time, 1.1 ms; slice thickness, 10 mm; field of view, 450 mm; matrix size, 128 × 256; and acquisition time, 0.28 s/frame). We traced 15 points on pulmonary vessels using a computer-aided system and measured the maximal motion distance of each tracked point. Movement of these points was then compared with spirometric data using the Pearson correlation coefficient. RESULTS: Patients with COPD showed reduced respiratory motion compared with healthy volunteers. Respiratory motion and spirometric data such as forced expiratory volume in 1 s (FEV1) and FEV1/forced vital capacity showed highly significant positive correlations (correlation between normalized motion distance for the whole lung and FEV1, r = 0.75; P < 0.01). CONCLUSIONS: The respiratory motion of the pulmonary vessels reflects expansion and deflation of the lung parenchyma, and such motion is restricted in patients with COPD due to airflow limitation.

Influence of the distribution of emphysema on diaphragmatic motion in patients with chronic obstructive pulmonary disease.

PURPOSE: We investigated whether the distribution of emphysema on computed tomography (CT) images can affect chest wall motion in patients with chronic obstructive lung disease (COPD). MATERIALS AND METHODS: The subjects were 35 male patients with COPD (age, 69.7 ± 6.2 years). The RA-950 (the ratio of lung volume under -950 HU to total lung volume on CT) was measured separately for the upper and lower halves of the lung. We analyzed the flatness of the diaphragm (Kdome) and its motion (ΔLappo) using dynamic magnetic resonance imaging. Paradoxical motion (Mpr) represented the ratio of the paradoxical diaphragmatic movement (downward or upward) when the lung area decreased or increased, respectively, to he total diaphragm movement (expressed as a percent). These parameters were analyzed in correlation with pulmonary function tests and St. George Respiratory Questionnaire (SGRQ) scores. RESULTS: The RA-950 of the lower lung zone correlated significantly with the Kdome (P = 0.033), ΔLappo (P = 0.006), Mpr (%) (P = 0.001), forced expiratory volume at 1 s (% predicted; P < 0.001), and activity score of the SGRQ (p = 0.017). The RA-950 of the upper lung zone did not correlate with these parameters. CONCLUSION: In COPD patients, the distribution of emphysema on CT correlates with airflow obstruction and abnormal diaphragmatic motion.

Effects of finite mass ratio and inelastic reflection on the interaction between graphene and laminar flow.

A modified boundary condition for the distribution function in the Lattice Boltzmann method at the interface between solid and fluid that takes into account a finite mass ratio between two phases and an inelastic reflection is proposed. The new boundary condition is built into the immersed boundary method to compute the interaction between graphene and laminar flow. Numerical simulations are carried out at a Reynolds number of 40, and drag and lift acting on the graphene and its deformation are examined by changing the mass ratio and the coefficient of restitution. It is found that the amplitude of the oscillating motion of the graphene is enhanced when compared with the case of infinite mass ratio with perfect collision.

Temporal segmentation of lung region from MRI sequences using multiple active contours.

Segmentation of the lung is particularly difficult because of the large variation in image quality. A modified Hough transform in combination with a mask creation algorithm can robustly determine synchronous respiratory patterns. The synchronicity restriction is relaxed by applying a greedy active contour algorithm. The respiratory patterns define a point cloud near the lung region boundary representing a subjective contour. The gravitation vector field (GVF) active contour algorithm is used to create an initial segmentation exclusively based on the point cloud. A final active contours algorithm is executed to adjust the boundary to the images. The algorithm was tested with healthy subjects and COPD patients, and the result was checked through temporal registration of coronal and sagittal images.

Pneumothorax and idiopathic pulmonary fibrosis.

PURPOSE: We evaluated the relation between the severity of idiopathic pulmonary fibrosis (IPF) and the incidence of pneumothorax on computed tomography (CT) images. MATERIALS AND METHODS: In this retrospective study, we evaluated the presence of pneumothorax in 56 consecutive patients who died of IPF from the initial CT to death. We quantitatively analyzed a total of 207 CT images and measured the volume of the normal pattern (N-pattern) and each lesion pattern on the initial CT and their serial changes. The effects of pneumothorax and clinical and CT features on survival were evaluated using Cox regression analysis. RESULTS: Pneumothorax occurred in 17 of 56 patients. Comparison of the pneumothorax (+) and (-) groups showed the initial vital capacity (VC) was lower (P = 0.005) and the follow-up period was shorter (P = 0.03) in the former group. The decrease in the N-pattern volume in the pneumothorax(+) group was significantly faster than in the pneumothorax(-) group (P = 0.013). Cox regression analyses identified a rapid decrease in N-pattern volume (P = 0.008) and a rapid decrease in VC (P = 0.002), but not pneumothorax, as significant predictors of poor survival. CONCLUSION: Pneumothorax in IPF patients is associated with lower VC and rapid deterioration of CT findings. The findings suggest that pneumothorax is a complication of advanced IPF.