Convolutional LSTM Networks for Subcellular Localization of Proteins

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks

Crystallographic structure of ultrathin Fe films on Cu(100)

We report bcc-like crystal structures in 2-4 ML Fe films grown on fcc Cu(100) using scanning tunneling microscopy. The local bcc structure provides a straightforward explanation for their frequently reported outstanding magnetic properties, i.e., ferromagnetic ordering in all layers with a Curie temperature above 300 K. The non-pseudomorphic structure, which becomes pseudomorphic above 4 ML film thickness is unexpected in terms of conventional rules of thin film growth and stresses the importance of finite thickness effects in ferromagnetic ultrathin films.Comment: 4 pages, 3 figures, RevTeX/LaTeX2.0

Dark Current Random Telegraph Signals in Solid-State Image Sensors

This paper focuses on the Dark Current-Random Telegraph Signal (DC-RTS) in solid-state image sensors. The DCRTS is investigated in several bulk materials, for different surface interfaces and for different trench isolation interfaces. The main parameter used to characterize the DC-RTS is the transition maximum amplitude which seems to be the most appropriate for studying the phenomenon and identifying its origin. Proton, neutron and Co-60 Gamma-ray irradiations are used to study DC-RTS induced by both Total Ionizing Dose (TID) and Displacement damage (Dd) dose. Conclusions are drawn by analyzing the correlation between the exponential slope of the transition maximum amplitude histogram and the location of the DC-RTS-induced defects. The presented results can be extrapolated to predict DC-RTS distributions in various kinds of solid state image sensors

Transport and Magnetic Properties of R1-xAxCoO3 (R=La, Pr and Nd; A=Ba, Sr and Ca)

Transport and magnetic measurements have been carried out on perovskite Co-oxides R1-xAxCoO3 (R=La, Pr, and Nd; A=Ba, Sr and Ca; 0<x<0.5: All sets of the R and A species except Nd1-xBaxCoO3 have been studied.). With increasing the Sr- or Ba-concentration x, the system becomes metallic ferromagnet with rather large magnetic moments. For R=Pr and Nd and A=Ca, the system approaches the metal- insulator phase boundary but does not become metallic. The magnetic moments of the Ca-doped systems measured with the magnetic field H=0.1 T are much smaller than those of the Ba- and Sr-doped systems. The thermoelectric powers of the Ba- and Sr-doped systems decrease from large positive values of lightly doped samples to negative ones with increasing doping level, while those of Ca-doped systems remain positive. These results can be understood by considering the relationship between the average ionic radius of R1-xAx and the energy difference between the low spin and intermediate spin states. We have found the resistivity-anomaly in the measurements of Pr1-xCaxCoO3 under pressure in the wide region of x, which indicates the existence of a phase transition different from the one reported in the very restricted region of x~0.5 at ambient pressure [Tsubouchi et al. Phys. Rev. B 66 (2002) 052418.]. No indication of this kind of transition has been observed in other species of R.Comment: 9 pages, 8 figures. J. Phys. Soc. Jpn. 72 (2003) No.

Flight of the dragonflies and damselflies

This work is a synthesis of our current understanding of the mechanics, aerodynamics and visually mediated control of dragonfly and damselfly flight, with the addition of new experimental and computational data in several key areas. These are: the diversity of dragonfly wing morphologies, the aerodynamics of gliding flight, force generation in flapping flight, aerodynamic efficiency, comparative flight performance and pursuit strategies during predatory and territorial flights. New data are set in context by brief reviews covering anatomy at several scales, insect aerodynamics, neuromechanics and behaviour. We achieve a new perspective by means of a diverse range of techniques, including laser-line mapping of wing topographies, computational fluid dynamics simulations of finely detailed wing geometries, quantitative imaging using particle image velocimetry of on-wing and wake flow patterns, classical aerodynamic theory, photography in the field, infrared motion capture and multi-camera optical tracking of free flight trajectories in laboratory environments. Our comprehensive approach enables a novel synthesis of datasets and subfields that integrates many aspects of flight from the neurobiology of the compound eye, through the aeromechanical interface with the surrounding fluid, to flight performance under cruising and higher-energy behavioural modes

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s)=1.96 TeV using Lepton + Jets Events with Lifetime b-tagging

We present a measurement of the top quark pair ($t\bar{t}$) production cross section ($\sigma_{t\bar{t}}$) in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV using 230 pb$^{-1}$ of data collected by the D0 experiment at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), missing transverse energy, and jets in the final state. We employ lifetime-based b-jet identification techniques to further enhance the $t\bar{t}$ purity of the selected sample. For a top quark mass of 175 GeV, we measure $\sigma_{t\bar{t}}=8.6^{+1.6}_{-1.5}(stat.+syst.)\pm 0.6(lumi.)$ pb, in agreement with the standard model expectation.Comment: 7 pages, 2 figures, 3 tables Submitted to Phys.Rev.Let

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE