Fiber Orientation Estimation Guided by a Deep Network

Diffusion magnetic resonance imaging (dMRI) is currently the only tool for noninvasively imaging the brain's white matter tracts. The fiber orientation (FO) is a key feature computed from dMRI for fiber tract reconstruction. Because the number of FOs in a voxel is usually small, dictionary-based sparse reconstruction has been used to estimate FOs with a relatively small number of diffusion gradients. However, accurate FO estimation in regions with complex FO configurations in the presence of noise can still be challenging. In this work we explore the use of a deep network for FO estimation in a dictionary-based framework and propose an algorithm named Fiber Orientation Reconstruction guided by a Deep Network (FORDN). FORDN consists of two steps. First, we use a smaller dictionary encoding coarse basis FOs to represent the diffusion signals. To estimate the mixture fractions of the dictionary atoms (and thus coarse FOs), a deep network is designed specifically for solving the sparse reconstruction problem. Here, the smaller dictionary is used to reduce the computational cost of training. Second, the coarse FOs inform the final FO estimation, where a larger dictionary encoding dense basis FOs is used and a weighted l1-norm regularized least squares problem is solved to encourage FOs that are consistent with the network output. FORDN was evaluated and compared with state-of-the-art algorithms that estimate FOs using sparse reconstruction on simulated and real dMRI data, and the results demonstrate the benefit of using a deep network for FO estimation.Comment: A shorter version is accepted by MICCAI 201

Edge states in graphene quantum dots: Fractional quantum Hall effect analogies and differences at zero magnetic field

We investigate the way that the degenerate manifold of midgap edge states in quasicircular graphene quantum dots with zig-zag boundaries supports, under free-magnetic-field conditions, strongly correlated many-body behavior analogous to the fractional quantum Hall effect (FQHE), familiar from the case of semiconductor heterostructures in high magnetic fields. Systematic exact-diagonalization (EXD) numerical studies are presented for the first time for 5 <= N <= 8 fully spin-polarized electrons and for total angular momenta in the range of N(N-1)/2 <= L <= 150. We present a derivation of a rotating-electron-molecule (REM) type wave function based on the methodology introduced earlier [C. Yannouleas and U. Landman, Phys. Rev. B 66, 115315 (2002)] in the context of the FQHE in two-dimensional semiconductor quantum dots. The EXD wave functions are compared with FQHE trial functions of the Laughlin and the derived REM types. It is found that a variational extension of the REM offers a better description for all fractional fillings compared with that of the Laughlin functions (including total energies and overlaps), a fact that reflects the strong azimuthal localization of the edge electrons. In contrast with the multiring arrangements of electrons in circular semiconductor quantum dots, the graphene REMs exhibit in all instances a single (0,N) polygonal-ring molecular (crystalline) structure, with all the electrons localized on the edge. Disruptions in the zig-zag boundary condition along the circular edge act effectively as impurities that pin the electron molecule, yielding single-particle densities with broken rotational symmetry that portray directly the azimuthal localization of the edge electrons.Comment: Revtex. 14 pages with 13 figures and 2 tables. Physical Review B, in press. For related papers, see http://www.prism.gatech.edu/~ph274cy

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche.

Epithelial surfaces form critical barriers to the outside world and are continuously renewed by adult stem cells1. Whereas dynamics of epithelial stem cells during homeostasis are increasingly well understood, how stem cells are redirected from a tissue-maintenance program to initiate repair after injury remains unclear. Here we examined infection by Heligmosomoides polygyrus, a co-evolved pathosymbiont of mice, to assess the epithelial response to disruption of the mucosal barrier. H. polygyrus disrupts tissue integrity by penetrating the duodenal mucosa, where it develops while surrounded by a multicellular granulomatous infiltrate2. Crypts overlying larvae-associated granulomas did not express intestinal stem cell markers, including Lgr53, in spite of continued epithelial proliferation. Granuloma-associated Lgr5- crypt epithelium activated an interferon-gamma (IFN-γ)-dependent transcriptional program, highlighted by Sca-1 expression, and IFN-γ-producing immune cells were found in granulomas. A similar epithelial response accompanied systemic activation of immune cells, intestinal irradiation, or ablation of Lgr5+ intestinal stem cells. When cultured in vitro, granuloma-associated crypt cells formed spheroids similar to those formed by fetal epithelium, and a sub-population of H. polygyrus-induced cells activated a fetal-like transcriptional program, demonstrating that adult intestinal tissues can repurpose aspects of fetal development. Therefore, re-initiation of the developmental program represents a fundamental mechanism by which the intestinal crypt can remodel itself to sustain function after injury

CHIANTI - an Atomic Database for Emission Lines. Paper VI: Proton Rates and Other Improvements

The CHIANTI atomic database contains atomic energy levels, wavelengths, radiative transition probabilities and electron excitation data for a large number of ions of astrophysical interest. Version 4 has been released, and proton excitation data is now included, principally for ground configuration levels that are close in energy. The fitting procedure for excitation data, both electrons and protons, has been extended to allow 9 point spline fits in addition to the previous 5 point spline fits. This allows higher quality fits to data from close-coupling calculations where resonances can lead to significant structure in the Maxwellian-averaged collision strengths. The effects of photoexcitation and stimulated emission by a blackbody radiation field in a spherical geometry on the level balance equations of the CHIANTI ions can now be studied following modifications to the CHIANTI software. With the addition of H I, He I and N I, the first neutral species have been added to CHIANTI. Many updates to existing ion data-sets are described, while several new ions have been added to the database, including Ar IV, Fe VI and Ni XXI. The two-photon continuum is now included in the spectral synthesis routines, and a new code for calculating the relativistic free-free continuum has been added. The treatment of the free-bound continuum has also been updated.Comment: CHIANTI is available at http://wwwsolar.nrl.navy.mil/chianti.htm

Four electrons in a two-leg Hubbard ladder: exact ground states

In the case of a two-leg Hubbard ladder we present a procedure which allows the exact deduction of the ground state for the four particle problem in arbitrary large lattice system, in a tractable manner, which involves only a reduced Hilbert space region containing the ground state. In the presented case, the method leads to nine analytic, linear, and coupled equations providing the ground state. The procedure which is applicable to few particle problems and other systems as well is based on an r-space representation of the wave functions and construction of symmetry adapted orthogonal basis wave vectors describing the Hilbert space region containing the ground state. Once the ground state is deduced, a complete quantum mechanical characterization of the studied state can be given. Since the analytic structure of the ground state becomes visible during the use of the method, its importance is not reduced only to the understanding of theoretical aspects connected to exact descriptions or potential numerical approximation scheme developments, but is relevant as well for a large number of potential technological application possibilities placed between nano-devices and quantum calculations, where the few particle behavior and deep understanding are important key aspects to know.Comment: 19 pages, 5 figure

The role of structural evolution on the quantum conductance behavior of gold nanowires during stretching

Gold nanowires generated by mechanical stretching have been shown to adopt only three kinds of configurations where their atomic arrangements adjust such that either the [100], [111] or [110] zone axes lie parallel to the elongation direction. We have analyzed the relationship between structural rearrangements and electronic transport behavior during the elongation of Au nanowires for each of the three possibilities. We have used two independent experiments to tackle this problem, high resolution transmission high resolution electron microscopy to observe the atomic structure and a mechanically controlled break junction to measure the transport properties. We have estimated the conductance of nanowires using a theoretical method based on the extended H\"uckel theory that takes into account the atom species and their positions. Aided by these calculations, we have consistently connected both sets of experimental results and modeled the evolution process of gold nanowires whose conductance lies within the first and third conductance quanta. We have also presented evidence that carbon acts as a contaminant, lowering the conductance of one-atom-thick wires.Comment: 10 page