Deep learning-based segmentation of malignant pleural mesothelioma tumor on computed tomography scans: application to scans demonstrating pleural effusion

Tumor volume is a topic of interest for the prognostic assessment, treatment response evaluation, and staging of malignant pleural mesothelioma. Many mesothelioma patients present with, or develop, pleural fluid, which may complicate the segmentation of this disease. Deep convolutional neural networks (CNNs) of the two-dimensional U-Net architecture were trained for segmentation of tumor in the left and right hemithoraces, with the networks initialized through layers pretrained on ImageNet. Networks were trained on a dataset of 5230 axial sections from 154 CT scans of 126 mesothelioma patients. A test set of 94 CT sections from 34 patients, who all presented with both tumor and pleural effusion, in addition to a more general test set of 130 CT sections from 43 patients, were used to evaluate segmentation performance of the deep CNNs. The Dice similarity coefficient (DSC), average Hausdorff distance, and bias in predicted tumor area were calculated through comparisons with radiologist-provided tumor segmentations on the test sets. The present method achieved a median DSC of 0.690 on the tumor and effusion test set and achieved significantly higher performance on both test sets when compared with a previous deep learning-based segmentation method for mesothelioma

Influence of shape of quantum dots on their far-infrared absorption

We investigate the effects of the shape of quantum dots on their far-infrared absorption in an external magnetic field by a model calculation. We focus our attention on dots with a parabolic confinement potential deviating from the common circular symmetry, and dots having circular doughnut shape. For a confinement where the generalized Kohn theorem does not hold we are able to interprete the results in terms of a mixture of a center-of-mass mode and collective modes reflecting an excitation of relative motion of the electrons. The calculations are performed within the time-dependent Hartree approximation and the results are compared to available experimental results.Comment: RevTeX, 16 pages with 10 postscript figures included. Submitted to Phys. Rev.

Geometrical effects and signal delay in time-dependent transport at the nanoscale

The nonstationary and steady-state transport through a mesoscopic sample connected to particle reservoirs via time-dependent barriers is investigated within the reduced density operator method. The generalized Master equation is solved via the Crank-Nicolson algorithm by taking into account the memory kernel which embodies the non-Markovian effects that are commonly disregarded. We propose a physically reasonable model for the lead-sample coupling which takes into account the match between the energy of the incident electrons and the levels of the isolated sample, as well as their overlap at the contacts. Using a tight-binding description of the system we investigate the effects induced in the transient current by the spectral structure of the sample and by the localization properties of its eigenfunctions. In strong magnetic fields the transient currents propagate along edge states. The behavior of populations and coherences is discussed, as well as their connection to the tunneling processes that are relevant for transport.Comment: 26 pages, 13 figures. To appear in New Journal of Physic

Radio-frequency discharges in Oxygen. Part 1: Modeling

In this series of three papers we present results from a combined experimental and theoretical effort to quantitatively describe capacitively coupled radio-frequency discharges in oxygen. The particle-in-cell Monte-Carlo model on which the theoretical description is based will be described in the present paper. It treats space charge fields and transport processes on an equal footing with the most important plasma-chemical reactions. For given external voltage and pressure, the model determines the electric potential within the discharge and the distribution functions for electrons, negatively charged atomic oxygen, and positively charged molecular oxygen. Previously used scattering and reaction cross section data are critically assessed and in some cases modified. To validate our model, we compare the densities in the bulk of the discharge with experimental data and find good agreement, indicating that essential aspects of an oxygen discharge are captured.Comment: 11 pages, 10 figure

Ion structure factors and electron transport in dense Coulomb plasmas

The dynamical structure factor of a Coulomb crystal of ions is calculated at arbitrary temperature below the melting point taking into account multi-phonon processes in the harmonic approximation. In a strongly coupled Coulomb ion liquid, the static structure factor is split into two parts, a Bragg-diffraction-like one, describing incipient long-range order structures, and an inelastic part corresponding to thermal ion density fluctuations. It is assumed that the diffractionlike scattering does not lead to the electron relaxation in the liquid phase. This assumption, together with the inclusion of multi-phonon processes in the crystalline phase, eliminates large discontinuities of the transport coefficients (jumps of the thermal and electric conductivities, as well as shear viscosity, reported previously) at a melting point.Comment: 4 pages, 2 figures, REVTeX using epsf.sty. Phys. Rev. Lett., in pres

Magnetoplasmon excitations in arrays of circular and noncircular quantum dots

We have investigated the magnetoplasmon excitations in arrays of circular and noncircular quantum dots within the Thomas-Fermi-Dirac-von Weizs\"acker approximation. Deviations from the ideal collective excitations of isolated parabolically confined electrons arise from local perturbations of the confining potential as well as interdot Coulomb interactions. The latter are unimportant unless the interdot separations are of the order of the size of the dots. Local perturbations such as radial anharmonicity and noncircular symmetry lead to clear signatures of the violation of the generalized Kohn theorem. In particular, the reduction of the local symmetry from SO(2) to $C_4$ results in a resonant coupling of different modes and an observable anticrossing behaviour in the power absorption spectrum. Our results are in good agreement with recent far-infrared (FIR) transmission experiments.Comment: 25 pages, 6 figures, typeset in RevTe

Orthogonal localized wave functions of an electron in a magnetic field

We prove the existence of a set of two-scale magnetic Wannier orbitals w_{m,n}(r) on the infinite plane. The quantum numbers of these states are the positions {m,n} of their centers which form a von Neumann lattice. Function w_{00}localized at the origin has a nearly Gaussian shape of exp(-r^2/4l^2)/sqrt(2Pi) for r < sqrt(2Pi)l,where l is the magnetic length. This region makes a dominating contribution to the normalization integral. Outside this region function, w_{00}(r) is small, oscillates, and falls off with the Thouless critical exponent for magnetic orbitals, r^(-2). These functions form a convenient basis for many electron problems.Comment: RevTex, 18 pages, 5 ps fi

How caldera collapse shapes the shallow emplacement and transfer of magma in active volcanoes

Calderas are topographic depressions formed by the collapse of a partly drained magma reservoir. At volcanic edifices with calderas, eruptive fissures can circumscribe the outer caldera rim, be oriented radially and/or align with the regional tectonic stress field. Constraining the mechanisms that govern this spatial arrangement is fundamental to understand the dynamics of shallow magma storage and transport and evaluate volcanic hazard. Here we show with numerical models that the previously unappreciated unloading effect of caldera formation may contribute significantly to the stress budget of a volcano. We first test this hypothesis against the ideal case of Fernandina, Galápagos, where previous models only partly explained the peculiar pattern of circumferential and radial eruptive fissures and the geometry of the intrusions determined by inverting the deformation data. We show that by taking into account the decompression due to the caldera formation, the modeled edifice stress field is consistent with all the observations. We then develop a general model for the stress state at volcanic edifices with calderas based on the competition of caldera decompression, magma buoyancy forces and tectonic stresses. These factors control: 1) the shallow accumulation of magma in stacked sills, consistently with observations; 2) the conditions for the development of circumferential and/or radial eruptive fissures, as observed on active volcanoes. This top-down control exerted by changes in the distribution of mass at the surface allows better understanding of how shallow magma is transferred at active calderas, contributing to forecasting the location and type of opening fissures

Far-infrared edge modes in quantum dots

We have investigated edge modes of different multipolarity sustained by quantum dots submitted to external magnetic fields. We present a microscopic description based on a variational solution of the equation of motion for any axially symmetric confining potential and multipole mode. Numerical results for dots with different number of electrons whose ground-state is described within a local Current Density Functional Theory are discussed. Two sum rules, which are exact within this theory, are derived. In the limit of a large neutral dot at B=0, we have shown that the classical hydrodynamic dispersion law for edge waves \omega(q) \sim \sqrt{q \ln (q_0/q)} holds when quantum and finite size effects are taken into account.Comment: We have changed some figures as well as a part of the tex

A PTAS for planar group Steiner tree via spanner bootstrapping and prize collecting

We present the first polynomial-time approximation scheme (PTAS), i.e., (1 + ϵ)-approximation algorithm for any constant ϵ > 0, for the planar group Steiner tree problem (in which each group lies on a boundary of a face). This result improves on the best previous approximation factor of O(logn(loglogn)O(1)). We achieve this result via a novel and powerful technique called spanner bootstrapping, which allows one to bootstrap from a superconstant approximation factor (even superpolynomial in the input size) all the way down to a PTAS. This is in contrast with the popular existing approach for planar PTASs of constructing lightweight spanners in one iteration, which notably requires a constant-factor approximate solution to start from. Spanner bootstrapping removes one of the main barriers for designing PTASs for problems which have no known constant-factor approximation (even on planar graphs), and thus can be used to obtain PTASs for several difficult-to-approximate problems. Our second major contribution required for the planar group Steiner tree PTAS is a spanner construction, which reduces the graph to have total weight within a factor of the optimal solution while approximately preserving the optimal solution. This is particularly challenging because group Steiner tree requires deciding which terminal in each group to connect by the tree, making it much harder than recent previous approaches to construct spanners for planar TSP by Klein [SIAM J. Computing 2008], subset TSP by Klein [STOC 2006], Steiner tree by Borradaile, Klein, and Mathieu [ACM Trans. Algorithms 2009], and Steiner forest by Bateni, Hajiaghayi, and Marx [J. ACM 2011] (and its improvement to an efficient PTAS by Eisenstat, Klein, and Mathieu [SODA 2012]. The main conceptual contribution here is realizing that selecting which terminals may be relevant is essentially a complicated prize-collecting process: we have to carefully weigh the cost and benefits of reaching or avoiding certain terminals in the spanner. Via a sequence of involved prize-collecting procedures, we can construct a spanner that reaches a set of terminals that is sufficient for an almost-optimal solution. Our PTAS for planar group Steiner tree implies the first PTAS for geometric Euclidean group Steiner tree with obstacles, as well as a (2 + ϵ)-approximation algorithm for group TSP with obstacles, improving over the best previous constant-factor approximation algorithms. By contrast, we show that planar group Steiner forest, a slight generalization of planar group Steiner tree, is APX-hard on planar graphs of treewidth 3, even if the groups are pairwise disjoint and every group is a vertex or an edge