Fourier-Domain Wavefield Rendering for Rapid Simulation of Synthetic Aperture Sonar Data

This paper introduces a new method for simulating synthetic aperture sonar (SAS) raw coherent echo data that is orders of magnitude faster than the commonly used point and facet diffraction models. The new approach uses Fourier wavefield generation and propagation in combination with a highly optimised optical rendering engine. It has been shown to produce a quantifiably similar quality of data and data products (i.e., images and spectra) to a point-diffraction model, capturing the important coherent wave physics (including diffraction, speckle, aspect-dependence, and layover) as well as effects of the SAS processing chain (including image focusing errors and artefacts). This new simulation capability may be an enabler for augmenting data sets with physically accurate and diverse synthetic data for robust machine learning

Occlusion Modeling for Coherent Echo Data Simulation:A Comparison Between Ray-Tracing and Convex-Hull Methods

The ability to simulate realistic coherent datasets for synthetic aperture imaging systems is crucial for the design, development and evaluation of the sensors and their signal processing pipelines, machine learning algorithms and autonomy systems. In the case of synthetic aperture sonar (SAS), collecting experimental data is expensive and it is rarely possible to obtain ground truth of the sensor’s path, the speed of sound in the medium, and the geometry of the imaged scene. Simulating sonar echo data allows signal processing algorithms to be tested with known ground truth, enabling rapid and inexpensive development and evaluation of signal processing algorithms. The de-facto standard for simulating conventional high-frequency (i.e., > 100 kHz) SAS echo data from an arbitrary sensor, path and scene is to use a point-based or facet-based diffraction model. A crucial part of this process is acoustic occlusion modeling. This article describes a SAS simulation pipeline and compares implementations of two occlusion methods; ray-tracing, and a newer approximate method based on finding the convex hull of a transformed point cloud. The full capability of the simulation pipeline is demonstrated using an example scene based on a high-resolution 3D model of the SS Thistlegorm shipwreck which was obtained using photogrammetry. The 3D model spans a volume of 220 × 130 × 25 m and is comprised of over 30 million facets that are decomposed into a cloud of almost 1 billion points. The convex-hull occlusion model was found to result in simulated SAS imagery that is qualitatively indistinguishable from the ray-tracing approach and quantitatively very similar, demonstrating that use of this alternative method has potential to improve speed while retaining high fidelity of simulation.The convex-hull approach was found to be up to 4 times faster in a fair speed comparison with serial and parallel CPU implementations for both methods, with the largest performance increase for wide-beam systems. The fastest occlusion modeling algorithm was found to be GPU-accelerated ray-tracing over the majority of scene scales tested, which was found to be up to 2 times faster than the parallel CPU convex-hull implementation. Although GPU implementations of convex hull algorithms are not currently readily available, future development of GPU-accelerated convex-hull finding could make the new approach much more viable. However, in the meantime, ray-tracing is still preferable, since it has higher accuracy and can leverage existing implementations for high performance computing architectures for better performance

Simulations of the angular dependence of the dipole-dipole interaction among Rydberg atoms

The dipole-dipole interaction between two Rydberg atoms depends on the relative orientation of the atoms and on the change in the magnetic quantum number. We simulate the effect of this anisotropy on the energy transport in an amorphous many atom system subject to a homogeneous applied electric field. We consider two experimentally feasible geometries and find that the effects should be measurable in current generation imaging experiments. In both geometries atoms of $p$ character are localized to a small region of space which is immersed in a larger region that is filled with atoms of $s$ character. Energy transfer due to the dipole-dipole interaction can lead to a spread of $p$ character into the region initially occupied by $s$ atoms. Over long timescales the energy transport is confined to the volume near the border of the $p$ region which is suggestive of Anderson localization. We calculate a correlation length of 6.3~$\mu$m for one particular geometry.Comment: 6 pages, 5 figures, revised draf

Circularization of flavivirus genomic RNA inhibits de novo translation initiation.

Members of the Flaviviridae family, including dengue virus (DENV) and yellow fever virus, cause serious disease in humans, whilst maternal infection with Zika virus (ZIKV) can induce microcephaly in newborns. Following infection, flaviviral RNA genomes are translated to produce the viral replication machinery but must then serve as a template for the transcription of new genomes. However, the ribosome and viral polymerase proceed in opposite directions along the RNA, risking collisions and abortive replication. Whilst generally linear, flavivirus genomes can adopt a circular conformation facilitated by long-range RNA-RNA interactions, shown to be essential for replication. Using an in vitro reconstitution approach, we demonstrate that circularization inhibits de novo translation initiation on ZIKV and DENV RNA, whilst the linear conformation is translation-competent. Our results provide a mechanism to clear the viral RNA of ribosomes in order to promote efficient replication and, therefore, define opposing roles for linear and circular conformations of the flavivirus genome

Current scaling of axially radiated power in dynamic hohlraums and dynamic hohlraum load design for ZR.

We present designs for dynamic hohlraum z-pinch loads on the 28 MA, 140 ns driver ZR. The scaling of axially radiated power with current in dynamic hohlraums is reviewed. With adequate stability on ZR this scaling indicates that 30 TW of axially radiated power should be possible. The performance of the dynamic hohlraum load on the 20 MA, 100 ns driver Z is extensively reviewed. The baseline z-pinch load on Z is a nested tungsten wire array imploding onto on-axis foam. Data from a variety of x-ray diagnostics fielded on Z are presented. These diagnostics include x-ray diodes, bolometers, fast x-ray imaging cameras, and crystal spectrometers. Analysis of these data indicates that the peak dynamic radiation temperature on Z is between 250 and 300 eV from a diameter less than 1 mm. Radiation from the dynamic hohlraum itself or from a radiatively driven pellet within the dynamic hohlraum has been used to probe a variety of matter associated with the dynamic hohlraum: the tungsten z-pinch itself, tungsten sliding across the end-on apertures, a titanium foil over the end aperture, and a silicon aerogel end cap. Data showing the existence of asymmetry in radiation emanating from the two ends of the dynamic hohlraum is presented, along with data showing load configurations that mitigate this asymmetry. 1D simulations of the dynamic hohlraum implosion are presented and compared to experimental data. The simulations provide insight into the dynamic hohlraum behavior but are not necessarily a reliable design tool because of the inherently 3D behavior of the imploding nested tungsten wire arrays

Rapid, widespread transduction of the murine myocardium using self-complementary Adeno-associated virus

Adeno-associated virus (AAV) has shown great promise as a gene transfer vector. However, the incubation time needed to attain significant levels of gene expression is often too long for some clinical applications. Self-complementary AAV (scAAV) enters the cell as double stranded DNA, eliminating the step of second-strand synthesis, proven to be the rate-limiting step for gene expression of single-stranded AAV (ssAAV). The aim of this study was to compare the efficiency of these two types of AAV vectors in the murine myocardium. Four day old CD-1 mice were injected with either of the two AAV constructs, both expressing GFP and packaged into the AAV1 capsid. The animals were held for 4, 6, 11 or 21 days, after which they were euthanized and their hearts were excised. Serial sections of the myocardial tissue were used for real-time PCR quantification of AAV genome copies and for confocal microscopy. Although we observed similar numbers of AAV genomes at each of the different time points present in both the scAAV and the ssAAV infected hearts, microscopic analysis showed expression of GFP as early as 4 days in animals injected with the scAAV, while little or no expression was observed with the ssAAV constructs until day 11. AAV transduction of murine myocardium is therefore significantly enhanced using scAAV constructs

Downstream evolution of the Kuroshio's time-varying transport and velocity structure

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 3519–3542, doi:10.1002/2016JC012519.Observations from two companion field programs—Origins of the Kuroshio and Mindanao Current (OKMC) and Observations of Kuroshio Transport Variability (OKTV)—are used here to examine the Kuroshio's temporal and spatial evolution. Kuroshio strength and velocity structure were measured between June 2012 and November 2014 with pressure-sensor equipped inverted echo sounders (PIESs) and upward-looking acoustic Doppler current profilers (ADCPs) deployed across the current northeast of Luzon, Philippines, and east of Taiwan with an 8 month overlap in the two arrays' deployment periods. The time-mean net (i.e., integrated from the surface to the bottom) absolute transport increases downstream from 7.3 Sv (±4.4 Sv standard error) northeast of Luzon to 13.7 Sv (±3.6 Sv) east of Taiwan. The observed downstream increase is consistent with the return flow predicted by the simple Sverdrup relation and the mean wind stress curl field over the North Pacific (despite the complicated bathymetry and gaps along the North Pacific western boundary). Northeast of Luzon, the Kuroshio—bounded by the 0 m s−1 isotach—is shallower than 750 dbar, while east of Taiwan areas of positive flow reach to the seafloor (3000 m). Both arrays indicate a deep counterflow beneath the poleward-flowing Kuroshio (–10.3 ± 2.3 Sv by Luzon and −12.5 ± 1.2 Sv east of Taiwan). Time-varying transports and velocities indicate the strong influence at both sections of westward propagating eddies from the ocean interior. Topography associated with the ridges east of Taiwan also influences the mean and time-varying velocity structure there.Office of Naval Research (ONR) Grant Numbers: N00014-15-12593 , N00014-16-13069; Taiwan's Ministry of Science and Technology Grant Numbers: NSC 101-2611-M-002-018-MY3 , MOST 103-2611-M-002-011 , MOST 105-2119-M-002-042; ONR Grant Numbers: N00014-10-1-0308 , N00015-10-1-04692017-11-0

IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA.

Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5' end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and ribosome recruitment. The presence of IFIT1 imposes a requirement on viruses that replicate in the cytoplasm to maintain mechanisms to avoid its restrictive effects. Interaction of different IFIT family members is well described, but little is known of the molecular basis of IFIT association or its impact on function. Here, we reconstituted different complexes of IFIT1, IFIT2 and IFIT3 in vitro, which enabled us to reveal critical aspects of IFIT complex assembly. IFIT1 and IFIT3 interact via a YxxxL motif present in the C-terminus of each protein. IFIT2 and IFIT3 homodimers dissociate to form a more stable heterodimer that also associates with IFIT1. We show for the first time that IFIT3 stabilizes IFIT1 protein expression, promotes IFIT1 binding to a cap0 Zika virus reporter mRNA and enhances IFIT1 translation inhibition. This work reveals molecular aspects of IFIT interaction and provides an important missing link between IFIT assembly and function.This work was supported by a joint Royal Society/Wellcome Trust Sir Henry Dale Fellowship (202471/Z/16/Z) and a Royal Society Research Grant (RG140708) to TRS. HVM is supported by a University of Cambridge, Department of Pathology PhD studentship. XYL is supported by a King’s Scholarship from the Malaysian government. TJS is supported by a Wellcome Trust PhD studentship (105389/Z/14/Z). RCF and DSM are supported by CAPES Computational Biology (23038.010048/2013-27). DSM is also supported by the Academy of Medical Sciences/UK (NAF004/1005). SCG is a Sir Henry Dale Fellow (098406/Z/12/Z) co-funded by the Wellcome Trust and Royal Society