SNAI transcription factors mediate epithelial--mesenchymal transition in lung fibrosis

Background: Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterised by accumulation of activated (myo)fibroblasts and excessive extracellular matrix deposition. The enhanced accumulation of (myo)fibroblasts may be attributed, in part, to the process of transforming growth factor \textgreekb1 (TGF\textgreekb1)-induced epithelial--mesenchymal transition (EMT), the phenotypic switching of epithelial to fibroblast-like cells. Although alveolar epithelial type II (ATII) cells have been shown to undergo EMT, the precise mediators and mechanisms remain to be resolved. The objective of this study is to investigate the role of SNAI transcription factors in the process of EMT and in IPF.Methods: Using quantitative reverse transcription-PCR (RT-PCR), immunofluorescence, immunohistochemistry, western blotting, as well as gain- and loss-of-function studies and functional assays, the role of SNAI1 and SNAI2 in TGF\textgreekb1-induced EMT in ATII cells in vitro was assessed; and the expression of SNAI transcription factors was analysed in experimental and human IPF in vivo.Results: TGF\textgreekb1 treatment increased the expression and nuclear accumulation of SNAI1 and SNAI2, in concert with induction of EMT in ATII cells. SNAI overexpression was sufficient to induce EMT, and small interfering RNA (siRNA)-mediated SNAI depletion attenuated TGF\textgreekb1-induced ATII cell migration and EMT. SNAI expression was elevated in experimental and human IPF and localised to hyperplastic ATII cells in vivo.Conclusions: The results demonstrate that TGF\textgreekb1-induced EMT in ATII cells is essentially controlled by the expression and nuclear translocation of SNAI transcription factors. Increased SNAI1 and SNAI2 expression in experimental and human IPF in vivo suggests that SNAI-mediated EMT may contribute to the fibroblast pool in idiopathic pulmonary fibrosis

Effect of nonequilibrium phonons on hot-electron spin relaxation in n-type GaAs quantum wells

We have studied the effect of nonequilibrium longitudinal optical phonons on hot-electron spin relaxation in $n$-type GaAs quantum wells. The longitudinal optical phonons, due to the finite relaxation rate, are driven to nonequilibrium states by electrons under an in-plane electric field. The nonequilibrium phonons then in turn influence the electron spin relaxation properties via modifying the electron heating and drifting. The spin relaxation time is elongated due to the enhanced electron heating and thus the electron-phonon scattering in the presence of nonequilibrium phonons. The frequency of spin precession, which is roughly proportional to the electron drift velocity, can be either increased (at low electric field and/or high lattice temperature) or decreased (at high electric field and/or low lattice temperature). The nonequilibrium phonon effect is more pronounced when the electron density is high and the impurity density is low.Comment: 6 pages, 3 figure

LINVIEW: Incremental View Maintenance for Complex Analytical Queries

Many analytics tasks and machine learning problems can be naturally expressed by iterative linear algebra programs. In this paper, we study the incremental view maintenance problem for such complex analytical queries. We develop a framework, called LINVIEW, for capturing deltas of linear algebra programs and understanding their computational cost. Linear algebra operations tend to cause an avalanche effect where even very local changes to the input matrices spread out and infect all of the intermediate results and the final view, causing incremental view maintenance to lose its performance benefit over re-evaluation. We develop techniques based on matrix factorizations to contain such epidemics of change. As a consequence, our techniques make incremental view maintenance of linear algebra practical and usually substantially cheaper than re-evaluation. We show, both analytically and experimentally, the usefulness of these techniques when applied to standard analytics tasks. Our evaluation demonstrates the efficiency of LINVIEW in generating parallel incremental programs that outperform re-evaluation techniques by more than an order of magnitude.Comment: 14 pages, SIGMO

Theory of Electron Spin Relaxation in ZnO

Doped ZnO is a promising material for spintronics applications. For such applications, it is important to understand the spin dynamics and particularly the spin coherence of this II-VI semiconductor. The spin lifetime $\tau_{s}$ has been measured by optical orientation experiments, and it shows a surprising non-monotonic behavior with temperature. We explain this behavior by invoking spin exchange between localized and extended states. Interestingly, the effects of spin-orbit coupling are by no means negligible, in spite of the relatively small valence band splitting. This is due to the wurtzite crystal structure of ZnO. Detailed analysis allows us to characterize the impurity binding energies and densities, showing that optical orientation experiments can be used as a characterization tool for semiconductor samples.Comment: 7 pages, 1 figure: minor changes Accepted by Phys. Rev.

Mixed quark-nucleon phase in neutron stars and nuclear symmetry energy

The influence of the nuclear symmetry energy on the formation of a mixed quark-nucleon phase in neutron star cores is studied. We use simple parametrizations of the nuclear matter equation of state, and the bag model for the quark phase. The behavior of nucleon matter isobars, which is responsible for the existence of the mixed phase, is investigated. The role of the nuclear symmetry energy changes with the value of the bag constant B. For lower values of B the properties of the mixed phase do not depend strongly on the symmetry energy. For larger B we find that a critical pressure for the first quark droplets to form is strongly dependent on the nuclear symmetry energy, but the pressure at which last nucleons disappear is independent of it.Comment: 12 pages, 16 figures, Phys. Rev. C in pres

Fast non-negative deconvolution for spike train inference from population calcium imaging

Calcium imaging for observing spiking activity from large populations of neurons are quickly gaining popularity. While the raw data are fluorescence movies, the underlying spike trains are of interest. This work presents a fast non-negative deconvolution filter to infer the approximately most likely spike train for each neuron, given the fluorescence observations. This algorithm outperforms optimal linear deconvolution (Wiener filtering) on both simulated and biological data. The performance gains come from restricting the inferred spike trains to be positive (using an interior-point method), unlike the Wiener filter. The algorithm is fast enough that even when imaging over 100 neurons, inference can be performed on the set of all observed traces faster than real-time. Performing optimal spatial filtering on the images further refines the estimates. Importantly, all the parameters required to perform the inference can be estimated using only the fluorescence data, obviating the need to perform joint electrophysiological and imaging calibration experiments.Comment: 22 pages, 10 figure

R-Process in Collapsing O/Ne/Mg Cores

Several circumstantial arguments point to the formation of the third r-process peak at A about 190, near platinum, in stars of mass of about 8-10 solar masses: 1) The delayed production of europium with respect to iron imposes a time scale that restricts the progenitor stars to less than about 10 solar masses; 2) the r-process demands a dominant robust mechanism at least for barium and above, since the relative abundance pattern of those r-process elements in low-metallicity stars is consistent with the solar pattern; 3) stars of about 8-10 solar masses produce nearly identical degenerate O/Ne/Mg cores that collapse due to electron capture; and 4) the resulting low-mass cores may produce both an r-process in a prompt explosion and a subsequent r-process in a neutrino driven wind. The prompt explosion of an O/Ne/Mg core yields low entropy and low electron fraction, and hence may produce a reasonable r-process peak at A about 190 as well as all of the r-process elements with Z greater than 56. The possible differences in the neutrino-driven wind and associated r-process due to the low-mass neutron stars expected in this mass range are also discussed.Comment: 16 pages, LaTeX aasms4; to be published in ApJ Letter