Accurate Pulmonary Nodule Detection in Computed Tomography Images Using Deep Convolutional Neural Networks

Early detection of pulmonary cancer is the most promising way to enhance a patient's chance for survival. Accurate pulmonary nodule detection in computed tomography (CT) images is a crucial step in diagnosing pulmonary cancer. In this paper, inspired by the successful use of deep convolutional neural networks (DCNNs) in natural image recognition, we propose a novel pulmonary nodule detection approach based on DCNNs. We first introduce a deconvolutional structure to Faster Region-based Convolutional Neural Network (Faster R-CNN) for candidate detection on axial slices. Then, a three-dimensional DCNN is presented for the subsequent false positive reduction. Experimental results of the LUng Nodule Analysis 2016 (LUNA16) Challenge demonstrate the superior detection performance of the proposed approach on nodule detection(average FROC-score of 0.891, ranking the 1st place over all submitted results).Comment: MICCAI 2017 accepte

Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution

The effect of asymmetry in the transbilayer lipid distribution on the dynamics of phase separation in fluid vesicles is investigated numerically for the first time. This asymmetry is shown to set a spontaneous curvature for the domains that alter the morphology and dynamics considerably. For moderate tension, the domains are capped and the spontaneous curvature leads to anomalously slow dynamics, as compared to the case of symmetric bilayers. In contrast, in the limiting cases of high and low tensions, the dynamics proceeds towards full phase separation.Comment: 4 pages, 5 figure

Are stress-free membranes really 'tensionless'?

In recent years it has been argued that the tension parameter driving the fluctuations of fluid membranes, differs from the imposed lateral stress, the 'frame tension'. In particular, stress-free membranes were predicted to have a residual fluctuation tension. In the present paper, this argument is reconsidered and shown to be inherently inconsistent -- in the sense that a linearized theory, the Monge model, is used to predict a nonlinear effect. Furthermore, numerical simulations of one-dimensional stiff membranes are presented which clearly demonstrate, first, that the internal 'intrinsic' stress in membranes indeed differs from the frame tension as conjectured, but second, that the fluctuations are nevertheless driven by the frame tension. With this assumption, the predictions of the Monge model agree excellently with the simulation data for stiffness and tension values spanning several orders of magnitude

Ergodic and Nonergodic Anomalous Diffusion in Coupled Stochastic Processes

Inspired by problems in biochemical kinetics, we study statistical properties of an overdamped Langevin process whose friction coefficient depends on the state of a similar, unobserved process. Integrating out the latter, we derive the long time behaviour of the mean square displacement. Anomalous diffusion is found. Since the diffusion exponent can not be predicted using a simple scaling argument, anomalous scaling appears as well. We also find that the coupling can lead to ergodic or non-ergodic behaviour of the studied process. We compare our theoretical predictions with numerical simulations and find an excellent agreement. The findings caution against treating biochemical systems coupled with unobserved dynamical degrees of freedom by means of standard, diffusive Langevin descriptions

Model for the unidirectional motion of a dynein molecule

Cytoplasmic dyneins transport cellular organelles by moving on a microtubule filament. It has been found recently that depending on the applied force and the concentration of the adenosine triphosphate (ATP) molecules, dynein's step size varies. Based on these studies, we propose a simple model for dynein's unidirectional motion taking into account the variations in its step size. We study how the average velocity and the relative dispersion in the displacement vary with the applied load. The model is amenable to further extensions by inclusion of details associated with the structure and the processivity of the molecule.Comment: 10 pages, 5 figure

Membrane fluctuations near a plane rigid surface

We use analytical calculations and Monte Carlo simulations to determine the thermal fluctuation spectrum of a membrane patch of a few tens of nanometer in size, whose corners are located at a fixed distance $d$ above a plane rigid surface. Our analysis shows that the surface influence on the bilayer fluctuations can be effectively described in terms of a uniform confining potential that grows quadratically with the height of the membrane $h$ relative to the surface: $V=(1/2)\gamma h^2$. The strength $\gamma$ of the harmonic confining potential vanishes when the corners of the membrane patch are placed directly on the surface ($d=0$), and achieves its maximum value when $d$ is of the order of a few nanometers. However, even at maximum strength the confinement effect is quite small and has noticeable impact only on the amplitude of the largest bending mode.Comment: Accepted for publication in Phys. Rev.

Mean encounter times for cell adhesion in hydrodynamic flow: analytical progress by dimensional reduction

For a cell moving in hydrodynamic flow above a wall, translational and rotational degrees of freedom are coupled by the Stokes equation. In addition, there is a close coupling of convection and diffusion due to the position-dependent mobility. These couplings render calculation of the mean encounter time between cell surface receptors and ligands on the substrate very difficult. Here we show for a two-dimensional model system how analytical progress can be achieved by treating motion in the vertical direction by an effective reaction term in the mean first passage time equation for the rotational degree of freedom. The strength of this reaction term can either be estimated from equilibrium considerations or used as a fit parameter. Our analytical results are confirmed by computer simulations and allow to assess the relative roles of convection and diffusion for different scaling regimes of interest.Comment: Reftex, postscript figures include

Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers

A systematic investigation of the phase separation dynamics in self-assembled multi-component bilayer fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition

Steady-state MreB helices inside bacteria: dynamics without motors

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasi-static evolution of the helical pitch with cell growth, as well as timescales of helix turnover and denovo establishment. We find that while the body of a polarized MreB helix treadmills towards its slow-growing end, the fast-growing tips of laterally associated protofilaments move towards the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.Comment: 7 figures, 1 tabl