Longitudinal detection of radiological abnormalities with time-modulated LSTM

Convolutional neural networks (CNNs) have been successfully employed in recent years for the detection of radiological abnormalities in medical images such as plain x-rays. To date, most studies use CNNs on individual examinations in isolation and discard previously available clinical information. In this study we set out to explore whether Long-Short-Term-Memory networks (LSTMs) can be used to improve classification performance when modelling the entire sequence of radiographs that may be available for a given patient, including their reports. A limitation of traditional LSTMs, though, is that they implicitly assume equally-spaced observations, whereas the radiological exams are event-based, and therefore irregularly sampled. Using both a simulated dataset and a large-scale chest x-ray dataset, we demonstrate that a simple modification of the LSTM architecture, which explicitly takes into account the time lag between consecutive observations, can boost classification performance. Our empirical results demonstrate improved detection of commonly reported abnormalities on chest x-rays such as cardiomegaly, consolidation, pleural effusion and hiatus hernia.Comment: Submitted to 4th MICCAI Workshop on Deep Learning in Medical Imaging Analysi

Spatiotemporal variation of methane and other trace hydrocarbon concentrations in the valley of Mexico

Mexico City is the world's largest and most polluted urban center. We examine the distribution of methane and other hydrocarbons within the Valley of Mexico, using it as a model for the role developing megacities will play in the next century of geochemical cycling. Seventy-five whole air samples were analyzed with multivariate statistical techniques, including factor analysis using principal components. Methane concentrations are highly variable in space and time, due to air circulations and source distribution. Landfills and open sewage canals are major inputs. Emissions into and out from the valley are modeled to be ∼515 t per day. Per capita emission is 0.01 t per annum per person, consistent with the global average for human related anaerobic generation. Natural gas leaks are small, and likely to be higher in other developing megacities; Mexican natural gas use has been discouraged out of earthquake safety concerns. In contrast, liquefied petroleum gas loss constitutes the major emission of propane and butane estimated at a leak rate of 5-10%. Kyoto and other environmental conventions have ignored methane as a greenhouse gas. Our analysis underscores the need to consider methane and other hydrocarbons, and the urbanization process, in future emission protocols. © 2002 Elsevier Science Ltd. All rights reserved

Spherical Functions Associated With the Three Dimensional Sphere

In this paper, we determine all irreducible spherical functions \Phi of any K -type associated to the pair (G,K)=(\SO(4),\SO(3)). This is accomplished by associating to \Phi a vector valued function H=H(u) of a real variable u, which is analytic at u=0 and whose components are solutions of two coupled systems of ordinary differential equations. By an appropriate conjugation involving Hahn polynomials we uncouple one of the systems. Then this is taken to an uncoupled system of hypergeometric equations, leading to a vector valued solution P=P(u) whose entries are Gegenbauer's polynomials. Afterward, we identify those simultaneous solutions and use the representation theory of \SO(4) to characterize all irreducible spherical functions. The functions P=P(u) corresponding to the irreducible spherical functions of a fixed K-type \pi_\ell are appropriately packaged into a sequence of matrix valued polynomials (P_w)_{w\ge0} of size (\ell+1)\times(\ell+1). Finally we proved that \widetilde P_w={P_0}^{-1}P_w is a sequence of matrix orthogonal polynomials with respect to a weight matrix W. Moreover we showed that W admits a second order symmetric hypergeometric operator \widetilde D and a first order symmetric differential operator \widetilde E.Comment: 49 pages, 2 figure

Superspace Formulation in a Three-Algebra Approach to D=3, N=4,5 Superconformal Chern-Simons Matter Theories

We present a superspace formulation of the D=3, N=4,5 superconformal Chern-Simons Matter theories, with matter supermultiplets valued in a symplectic 3-algebra. We first construct an N=1 superconformal action, and then generalize a method used by Gaitto and Witten to enhance the supersymmetry from N=1 to N=5. By decomposing the N=5 supermultiplets and the symplectic 3-algebra properly and proposing a new super-potential term, we construct the N=4 superconformal Chern-Simons matter theories in terms of two sets of generators of a (quaternion) symplectic 3-algebra. The N=4 theories can also be derived by requiring that the supersymmetry transformations are closed on-shell. The relationship between the 3-algebras, Lie superalgebras, Lie algebras and embedding tensors (proposed in [E. A. Bergshoeff, O. Hohm, D. Roest, H. Samtleben, and E. Sezgin, J. High Energy Phys. 09 (2008) 101.]) is also clarified. The general N=4,5 superconformal Chern-Simons matter theories in terms of ordinary Lie algebras can be rederived in our 3-algebra approach. All known N=4,5 superconformal Chern-Simons matter theories can be recovered in the present superspace formulation for super-Lie-algebra realization of symplectic 3-algebras.Comment: 37 pages, minor changes, published in PR

Finite time decoherence could be suppressed efficiently in photonic crystal

The decoherence of two initially entangled qubits in anisotropic band gap photonic crystal has been studied analytically without Born or Markovian approximation. It is shown that the decoherence dynamics of two qubits in photonic crystal is greatly different from that of two qubits in vacuum or subjected to usual non-Markovian reservoir. The results also show that the finite time decoherence invoked by spontaneous emission could be suppressed efficiently and the entanglement of the Bell state possesses odd parity is more easily preserved in photonic crystal than that of the Bell state possesses even parity under the same condition. A store scheme for entangled particle pair is proposed.Comment: 4 pages, 7 figure

Quantum interference in deformed carbon nanotube waveguides

Quantum interference (QI) in two types of deformed carbon nanotubes (CNTs), i.e., axially stretched and AFM tip-deformed CNTs, has been investigated by the pi-electron only and four-orbital tight-binding (TB) method. It is found that the rapid conductance oscillation (RCO) period is very sensitive to the applied strains, and decreases in an inverse proportion to the deformation degree, which could be used as a powerful experimental tool to detect precisely the deformation degree of the deformed CNTs. Also, the sigma-pi coupling effect is found to be negligible under axially stretched strain, while it works on the transport properties of the tip-deformed CNTs.Comment: 14 pages and 5 figure

Thermalized Displaced Squeezed Thermal States

In the coordinate representation of thermofield dynamics, we investigate the thermalized displaced squeezed thermal state which involves two temperatures successively. We give the wavefunction and the matrix element of the density operator at any time, and accordingly calculate some quantities related to the position, momentum and particle number operator, special cases of which are consistent with the results in the literature. The two temperatures have diffenent correlations with the squeeze and coherence components. Moreover, different from the properties of the position and momentum, the average value and variance of the particle number operator as well as the second-order correlation function are time-independent.Comment: 7 pages, no figures, Revtex fil

RNomics: a computational search for box C/D snoRNA genes in the D. melanogaster genome.

Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Availability: Additional information is available at http://www. bioinformatica.unito.it/bioinformatics/snoRNA

A distinct sortase SrtB anchors and processes a streptococcal adhesin AbpA with a novel structural property.

Surface display of proteins by sortases in Gram-positive bacteria is crucial for bacterial fitness and virulence. We found a unique gene locus encoding an amylase-binding adhesin AbpA and a sortase B in oral streptococci. AbpA possesses a new distinct C-terminal cell wall sorting signal. We demonstrated that this C-terminal motif is required for anchoring AbpA to cell wall. In vitro and in vivo studies revealed that SrtB has dual functions, anchoring AbpA to the cell wall and processing AbpA into a ladder profile. Solution structure of AbpA determined by NMR reveals a novel structure comprising a small globular α/β domain and an extended coiled-coil heliacal domain. Structural and biochemical studies identified key residues that are crucial for amylase binding. Taken together, our studies document a unique sortase/adhesion substrate system in streptococci adapted to the oral environment rich in salivary amylase