Dynamical Imaging with Interferometry

By linking widely separated radio dishes, the technique of very long baseline interferometry (VLBI) can greatly enhance angular resolution in radio astronomy. However, at any given moment, a VLBI array only sparsely samples the information necessary to form an image. Conventional imaging techniques partially overcome this limitation by making the assumption that the observed cosmic source structure does not evolve over the duration of an observation, which enables VLBI networks to accumulate information as the Earth rotates and changes the projected array geometry. Although this assumption is appropriate for nearly all VLBI, it is almost certainly violated for submillimeter observations of the Galactic Center supermassive black hole, Sagittarius A* (Sgr A*), which has a gravitational timescale of only ~20 seconds and exhibits intra-hour variability. To address this challenge, we develop several techniques to reconstruct dynamical images ("movies") from interferometric data. Our techniques are applicable to both single-epoch and multi-epoch variability studies, and they are suitable for exploring many different physical processes including flaring regions, stable images with small time-dependent perturbations, steady accretion dynamics, or kinematics of relativistic jets. Moreover, dynamical imaging can be used to estimate time-averaged images from time-variable data, eliminating many spurious image artifacts that arise when using standard imaging methods. We demonstrate the effectiveness of our techniques using synthetic observations of simulated black hole systems and 7mm Very Long Baseline Array observations of M87, and we show that dynamical imaging is feasible for Event Horizon Telescope observations of Sgr A*.Comment: 16 Pages, 12 Figures, Accepted for publication in Ap

Non-parametric PSF estimation from celestial transit solar images using blind deconvolution

Context: Characterization of instrumental effects in astronomical imaging is important in order to extract accurate physical information from the observations. The measured image in a real optical instrument is usually represented by the convolution of an ideal image with a Point Spread Function (PSF). Additionally, the image acquisition process is also contaminated by other sources of noise (read-out, photon-counting). The problem of estimating both the PSF and a denoised image is called blind deconvolution and is ill-posed. Aims: We propose a blind deconvolution scheme that relies on image regularization. Contrarily to most methods presented in the literature, our method does not assume a parametric model of the PSF and can thus be applied to any telescope. Methods: Our scheme uses a wavelet analysis prior model on the image and weak assumptions on the PSF. We use observations from a celestial transit, where the occulting body can be assumed to be a black disk. These constraints allow us to retain meaningful solutions for the filter and the image, eliminating trivial, translated and interchanged solutions. Under an additive Gaussian noise assumption, they also enforce noise canceling and avoid reconstruction artifacts by promoting the whiteness of the residual between the blurred observations and the cleaned data. Results: Our method is applied to synthetic and experimental data. The PSF is estimated for the SECCHI/EUVI instrument using the 2007 Lunar transit, and for SDO/AIA using the 2012 Venus transit. Results show that the proposed non-parametric blind deconvolution method is able to estimate the core of the PSF with a similar quality to parametric methods proposed in the literature. We also show that, if these parametric estimations are incorporated in the acquisition model, the resulting PSF outperforms both the parametric and non-parametric methods.Comment: 31 pages, 47 figure

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

EgoFace: Egocentric Face Performance Capture and Videorealistic Reenactment

Face performance capture and reenactment techniques use multiple cameras and sensors, positioned at a distance from the face or mounted on heavy wearable devices. This limits their applications in mobile and outdoor environments. We present EgoFace, a radically new lightweight setup for face performance capture and front-view videorealistic reenactment using a single egocentric RGB camera. Our lightweight setup allows operations in uncontrolled environments, and lends itself to telepresence applications such as video-conferencing from dynamic environments. The input image is projected into a low dimensional latent space of the facial expression parameters. Through careful adversarial training of the parameter-space synthetic rendering, a videorealistic animation is produced. Our problem is challenging as the human visual system is sensitive to the smallest face irregularities that could occur in the final results. This sensitivity is even stronger for video results. Our solution is trained in a pre-processing stage, through a supervised manner without manual annotations. EgoFace captures a wide variety of facial expressions, including mouth movements and asymmetrical expressions. It works under varying illuminations, background, movements, handles people from different ethnicities and can operate in real time

Patterns of the electric organ discharge during courtship and spawning in the mormyrid fish, Pollimyrus isidori

Pollimyrus isidori's electric organ discharge (EOD) is of the pulse type. Patterns of EOD intervals were investigated prior to, during and following spawning behaviors as related with overt behaviors, and with the sound production by the nestbuilding male. Prior to the time of reproduction, isolated and socially interacting fish (n=15) showed characteristic discharge interval patterns for resting, swimming, probing, hovering and hiding activities. Males (n=8) and females (n=6) did not differ in their mean EOD repetition rates during resting (11.6±2.5 Hz), nor Short Bursts/min (less than 20 intervals of 8–13 ms). In interacting fish Long Bursts (greater than 20 intervals of 8–13 ms, lasting for more than 300 ms) were observed only during the attack and bite sequence. A pursuing fish displayed a rapid alternation of Long Bursts with Discharge Breaks (300–1000 ms silence) during the chase behavior. Avoidance behavior which followed from several attacks was correlated with a Medium Uniform Rate (8–12 Hz) normally lasting for 20 to 60 s, or a Discharge Arrest (silence greater than 1 s) in the submissive fish. The nocturnal courtship behavior began soon after dark (1900 h). Spawning typically started 2 to 5 h after dark, continuing for 2 to 6 h until about 0200 h. During courtship and spawning the female's brief visits (15–25 s) to the male's territory recurred every 30–60 s. At all other times the female was aggressively excluded from the nest region. Courtship and spawning behaviors are described along with the electrical displays identified from 19 spawnings in three fish pairs (from a total of 37 spawnings in 4 males and 4 females). Just prior to the onset of courtship behavior, with male territorial aggression beginning to decline, females switched from a Medium Sporadic Rate pattern (resting and hiding patterns; 13 Hz) to a Medium Uniform Rate pattern (6–8 Hz) while still in their hiding area. Females continued to display this uniform rate throughout the courship and spawning period, including the courtship and spawning bouts when Discharge Breaks or Arrests also occurred. This persistance distinguishes the courtship pattern from the similar avoidance pattern (see above). The male courtship and spawning EOD pattern was similar to the female's and unique for a territorial male. He switched from a High Sporadic Rate (swimming EOD pattern; about 18 Hz) to a regularized Medium Uniform Rate (about 9 to 11 Hz) only during courtship and spawning bouts, including 1–3 EOD Breaks during Vent-to-Vent coupling (average interval: 272±71 ms, n=37). No sooner had the female left the spawning site than he resumed displaying a High Sporadic Rate. This temporal correlation of reproductive behaviors with electrical displays suggests their instrumental role in mutual acceptance of mates. Males showed their sex-specific type of EOD phase-locking, the Preferred Latency Response, only during the first few hours of entry of a fish in their tank. Two females with EOD waveform features more typical of males also spawned repeatedly; waveform does not appear to be critical. Males stopped their nocturnal sound production for the later part of courtship and the whole spawning period. Except for infrequent attacks on the female between spawning bouts, the male did not resume singing until the end of spawning when all eggs were shed (around 0200 h); from this time on the male sang until dawn. The sequencing of the three acoustic elements (moans, grunts, growls) are described. A catalogue of discharge patterns correlated with overt behaviors (Tables 1, 2), and an integrated summary time table of P. isidori's complex reproductive behavior are presented

Single-particle cryo-electron microscopy studies of ribosomes with fragmented 28S rRNA

In the past five years, single-particle cryo-electron microscopy (cryo-EM) has revolutionized structural biology. Recent advances in detector technology and powerful computational methods now allow images of unprecedented detail to be recorded and structures to be determined at near-atomic resolution. For my PhD studies, I took advantage of this technique to study the structure of uniquely fragmented ribosomes. Ribosomes, are large macromolecular complexes that translate genetic information carried by messenger RNAs (mRNAs) into polypeptide chains. They are the protein production factories of all living cells and are thus involved in virtually all aspects of cellular development and maintenance. By virtue of their core role in the cell, ribosomes share a highly evolutionarily conserved core that carries out the fundamental processes of protein synthesis [1]. However, outside of this core, ribosome composition varies considerably. The main differences among eukaryotic ribosomes are due to rRNA expansion segments (ESs) and variations of ribosomal proteins (r-proteins) [1, 2]. Further, rRNA fragmentation occurring in regions of high variability has been reported in several organisms from bacteria to protozoa, insects, helminths, fish, and surprisingly mammals [3-15]. Recently, the naked mole-rat (Heterocephalus glaber) was discovered to have unusual cleavage sites in its 28S rRNA resulting in the deletion of the major part of the D6 variable region (ES15L) and leaving the two rRNA fragments disconnected [14]. The cleaved 28S rRNA has been associated with the naked mole rat’s increased translational fidelity [14]. The only other known mammals having fragmented rRNA are the tuco-tuco rodent (of the genus Ctenomys) and the degu (in the related genus Octodontomys) [13]. Here we present the high-resolution structures of the naked mole-rat, tuco-tuco, and guinea pig (Cavia porcellus) ribosomes. Guinea pig, which has canonical (non-fragmented) 28S rRNA is used as a rodent model for comparisons to the naked mole-rat and tuco-tuco ribosomes. During my PhD studies, I also looked at another uniquely fragmented ribosome, that of the protozoan parasite, Trypanosoma cruzi (T. cruzi), the causative agent of Chagas disease. The T. cruzi large subunit (LSU) rRNA is assembled from 8 pieces-5S, 5.8S, and six pieces forming jointly the 28S rRNA. Together with my colleagues from Joachim Frank’s and Liang Tong’s research groups, we solved the structure of the T. Cruzi LSU and identified distinctive trypanosome interactions, which allowed us to propose a tentative model for assembly of the large ribosomal subunit (60S) [16, 17]

Probing dynamics of elliptical vortex rings via direct vorticity measurements with digital inline holography

Investigating vorticity dynamics provides an effective way for understanding the fundamental mechanisms of fluid flows across diverse scales. However, experimental vorticity measurements often suffer from limited spatial and temporal resolution, hindering our capability to probe into small-scale dynamics in various flows, particularly turbulence. In Li et al. (EXIF, 2022, vol. 63, 161), we introduced a novel holographic vorticimetry technique for direct vorticity measurements by tracking the three-dimensional rotations of tracers with internal markers. This study further extends it to investigate the intricate vorticity dynamics during the evolution of elliptical vortex rings with different aspect ratios. Based on the shadowgraph imaging quantifying the axis-switching cycles and vortex ring deformation, holographic vorticimetry is applied to measure the vorticity distribution within the millimeter-size core of elliptical vortex rings during their evolution. Specifically, our method resolves an even vorticity spread near the core center that rapidly decays within a few hundred microns. Additionally, our results reveal the intricate vorticity fluctuations associated with the folding-unfolding behaviors during the vortex ring evolution. These subtle vorticity changes informed by simulations have not been captured by previous experiments due to limited resolution. Furthermore, we find that higher aspect ratios yield larger initial vorticity and vorticity fluctuations but also prompt earlier inception of instabilities, causing vortex core distortion. These opposing effects result in a non-monotonic vorticity evolution trend. Overall, our measurements demonstrate the efficacy of holographic vorticimetry by measuring the intricate vorticity variations in unsteady vortex flows, paving the way for capturing the vorticity dynamics of small-scale turbulence structures