A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

Detection of the white dwarf and the secondary star in the new SU UMa dwarf nova HS 2219+1824

We report the discovery of a new, non-eclipsing SU UMa-type dwarf nova, HS 2219+1824. Photometry obtained in quiescence (V ≈ 17.5) reveals a double-humped light curve from which we derive an orbital period of 86.2 min. Additional photometry obtained during a superoutburst reaching V 12.0 clearly shows superhumps with a period of 89.05 min. The optical spectrum contains double-peaked Balmer and He I emission lines from the accretion disc as well as broad absorption troughs of Hβ, Hγ, and Hδ from the white dwarf primary star. Modelling of the optical spectrum implies a white dwarf temperature of 13 000 K < ∼ T eff < ∼ 17 000 K, a distance of 180 pc < ∼ d < ∼ 230 pc, and suggests that the spectral type of the donor star is later than M 5. Phase-resolved spectroscopy obtained during quiescence reveals a narrow Hα emission line component which has a radial velocity amplitude and phase consistent with an origin on the secondary star, possibly on the irradiated hemisphere facing the white dwarf. This constitutes the first detection of line emission from the secondary star in a quiescent SU UMa star

Geometric analysis of macromolecule organization within cryo-electron tomograms

Cryo-electron tomography (CET) provides unprecedented views into the native cellular environment at molecular resolution. While subtomogram analysis yields high-resolution native structures of molecular complexes, it also determines the precise positions and orientations of these macromolecules within the cell. Analyzing the geometric relationships between adjacent macromolecules can offer structural insights into molecular interactions and identify supramolecular ensembles. However, computation..

Roche tomography of cataclysmic variables - V. A high-latitude star-spot on RU Pegasi

We present Roche tomograms of the secondary star in the dwarf nova system RU Pegasi derived from blue and red arm ISIS data taken on the 4.2-m William Herschel Telescope. We have applied the entropy landscape technique to determine the system parameters and obtained component masses of M1 = 1.06 Msun, M2 = 0.96 Msun, an orbital inclination angle of i = 43 degrees, and an optimal systemic velocity of gamma = 7 km/s. These are in good agreement with previously published values. Our Roche tomograms of the secondary star show prominent irradiation of the inner Lagrangian point due to illumination by the disc and/or bright spot, which may have been enhanced as RU Peg was in outburst at the time of our observations.We find that this irradiation pattern is axi-symmetric and confined to regions of the star which have a direct view of the accretion regions. This is in contrast to previous attempts to map RU Peg which suggested that the irradiation pattern was non-symmetric and extended beyond the terminator. We also detect additional inhomogeneities in the surface distribution of stellar atomic absorption that we ascribe to the presence of a large star-spot. This spot is centred at a latitude of about 82 degrees and covers approximately 4 per cent of the total surface area of the secondary. In keeping with the high latitude spots mapped on the cataclysmic variables AE Aqr and BV Cen, the spot on RU Peg also appears slightly shifted towards the trailing hemisphere of the star. Finally, we speculate that early mapping attempts which indicated non-symmetric irradiation patterns which extended beyond the terminator of CV donors could possibly be explained by a superposition of symmetric heating and a large spot.Comment: 14 pages, 10 figures, 3 tables Accepted for publication in Monthly Notices of the Royal Astronomical Societ

Towards higher precision and operational use of optical homodyne tomograms

We present the results of an operational use of experimentally measured optical tomograms to determine state characteristics (purity) avoiding any reconstruction of quasiprobabilities. We also develop a natural way how to estimate the errors (including both statistical and systematic ones) by an analysis of the experimental data themselves. Precision of the experiment can be increased by postselecting the data with minimal (systematic) errors. We demonstrate those techniques by considering coherent and photon-added coherent states measured via the time-domain improved homodyne detection. The operational use and precision of the data allowed us to check for the first time purity-dependent uncertainty relations and uncertainty relations for Shannon and R\'{e}nyi entropies.Comment: 11 pages, 6 figures, 1 table, some results are extende

Tomography of X-ray Nova Muscae 1991: Evidence for ongoing mass transfer and stream-disc overflow

We present a spectroscopic analysis of the black hole binary Nova Muscae 1991 in quiescence using data obtained in 2009 with MagE on the Magellan Clay telescope and in 2010 with IMACS on the Magellan Baade telescope at the Las Campanas Observatory. Emission from the disc is observed in H alpha, H beta and Ca II (8662 A). A prominent hotspot is observed in the Doppler maps of all three emission lines. The existence of this spot establishes ongoing mass transfer from the donor star in 2009-2010 and, given its absence in the 1993-1995 observations, demonstrates the presence of a variable hotspot in the system. We find the radial distance to the hotspot from the black hole to be consistent with the circularization radius. Our tomograms are suggestive of stream-disc overflow in the system. We also detect possible Ca II (8662 A) absorption from the donor star.Comment: 10 pages, 11 figures, 1 table. Accepted for publication in MNRA

FUSE Observations of a Full Orbit of Hercules X-1: Signatures of Disk, Star, and Wind

We observed an entire 1.7 day orbit of the X-ray binary Hercules X-1 with the Far Ultraviolet Spectroscopic Explorer (FUSE). Changes in the O VI 1032,1037 line profiles through eclipse ingress and egress indicate a Keplerian accretion disk spinning prograde with the orbit. These observations may show the first double-peaked accretion disk line profile to be seen in the Hercules X-1 system. Doppler tomograms of the emission lines show a bright spot offset from the Roche lobe of the companion star HZ Her, but no obvious signs of the accretion disk. Simulations show that the bright spot is too far offset from the Roche lobe to result from uneven X-ray heating of its surface. The absence of disk signatures in the tomogram can be reproduced in simulations which include absorption from a stellar wind. We attempt to diagnose the state of the emitting gas from the C III 977, C III 1175, and N III 991 emission lines. The latter may be enhanced through Bowen fluorescence.Comment: Accepted for publication in The Astrophysical Journa