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These files contain code used to segment D. virilis acoustic duets, quantification of courtship behaviors during acoustic duets, and measurements of duet song features.
Hepatitis B virus (HBV) infection remains a major public health problem and, in associated co-infection with hepatitis delta virus (HDV), causes the most severe viral hepatitis and accelerated liver disease progression. As a defective satellite RNA virus, HDV can only propagate in the presence of HBV infection, which makes HBV DNA and HDV RNA the standard biomarkers for monitoring the virological response upon antiviral therapy, in co-infected patients. Although assays have been described to quantify these viral nucleic acids in circulation independently, a method for monitoring both viruses simultaneously is not available, thus hampering characterization of their complex dynamic interactions. Here, we describe the development of a dual fluorescence channel detection system for pan-genotypic, simultaneous quantification of HBV DNA and HDV RNA through a one-step quantitative PCR. The sensitivity for both HBV and HDV is about 10 copies per microliter without significant interference between these two detection targets. This assay provides reliable detection for HBV and HDV basic research in vitro and in human liver chimeric mice. Preclinical validation of this system on serum samples from patient on or off antiviral therapy also illustrates a promising application that is rapid and cost-effective in monitoring HBV and HDV viral loads simultaneously.
Nies, Richard; Paul, Elizabeth J.; Panici, Dario; Hudson, Stuart R.; Bhattacharjee, Amitava
Abstract:
Optimising stellarators for quasisymmetry leads to strongly reduced collisional transport
and energetic particle losses compared to unoptimised configurations. Though stellarators
with precise quasisymmetry have been obtained in the past, it remains unclear how broad
the parameter space is where good quasisymmetry may be achieved. We here study the
range of aspect ratio and rotational transform values for which stellarators with excellent
quasisymmetry on the boundary can be obtained. A large number of Fourier harmonics
is included in the boundary representation, which is made computationally tractable
by the use of adjoint methods to enable fast gradient-based optimisation, and by the
direct optimisation of vacuum magnetic fields, which converge more robustly compared to
solutions from magnetohydrostatics. Several novel configurations are presented, including
stellarators with record levels of quasisymmetry on a surface, three field period quasi-
axisymmetric stellarators with substantial magnetic shear, and compact quasisymmetric
stellarators at low aspect ratios similar to tokamaks.
Scrape-off layer (SOL) and edge plasma turbulence contribute significantly to the radial particle and heat transport lowering plasma confinement and increasing heat load on the plasma facing components. SOL turbulence is predominantly intermittent which manifest in the occurrence of isolated density filaments or blobs. Filaments propagate radially outwards towards plasma facing components limiting their lifetime by erosion and sputtering. To characterize this phenomenon in detail few diagnostic techniques are available. Beam emission spectroscopy is a diagnostic capable of measuring plasma turbulence in both SOL and edge plasmas. Due to the finite lifetime of the excitation states during the beam - plasma interaction, and the misalignment between the optics and the magnetic field, spatial smearing is introduced in the measurement. In this paper a novel method is introduced to overcome this hindering effect by inverting the fluctuation response matrix on an optimally smoothed signal. We show that this method is fast and provides significantly more accurate absolute density fluctuation reconstruction than the direct inversion technique. The presented method is usable for all types of beam emission diagnostics where the spatial resolution is higher than the combined smearing of the atomic physics and the observation.
Fusion power output from spherical tokamaks would benefit from increased confined plasma density, but there exists a limit on the density before confinement is lost and the plasma current is disrupted. This density limit has long been characterized by a simple, global Greenwald limit proportional to the plasma current and inversely proportional to the cross sectional area of the plasma. It is shown that in the database of discharges from the NSTX and MAST spherical tokamaks, the likelihood of disruption does increase above the Greenwald limit, and especially in the plasma current rampdown phase. The physics of the density limit has been recently theoretically explored through local criteria. Several of these are tested using the disruption event characterization and forecasting (DECAFTM) code for their potential effectiveness as disruption warning signals. For a limited set of NSTX discharges, a local island power balance criteria was found to be less reliable, presently, than the Greenwald limit. An empirical critical edge line density and a boundary turbulent transport limit were both tested for MAST-U, which has an electron density profile measurement with high spatial resolution in the outer part of the plasma. Both were found to have similar dependencies on key plasma parameters. In a limited set of MAST-U discharges that appear to disrupt due to rising density at values under the Greenwald limit, crossing of the boundary turbulent transport limit occurred close to the time of disruption. Finally, these limits were evaluated for their potential use in real-time, and it was found that with the necessary real-time inputs and with refinement through further testing, these limits could be implemented in a real-time disruption forecasting system.
Chronic hepatitis B (CHB), caused by hepatitis B virus (HBV), remains a major medical problem. HBV has a high propensity for progressing to chronicity and can result in severe liver disease, including fibrosis, cirrhosis and hepatocellular carcinoma. CHB patients frequently present with viral coinfection, including HIV and hepatitis delta virus. About 10% of chronic HIV carriers are also persistently infected with HBV which can result in more exacerbated liver disease. Mechanistic studies of HBV-induced immune responses and pathogenesis, which could be significantly influenced by HIV infection, have been hampered by the scarcity of immunocompetent animal models. Here, we demonstrate that humanized mice dually engrafted with components of a human immune system and a human liver supported HBV infection, which was partially controlled by human immune cells, as evidenced by lower levels of serum viremia and HBV replication intermediates in the liver. HBV infection resulted in priming and expansion of human HLA-restricted CD8+ T cells, which acquired an activated phenotype. Notably, our dually humanized mice support persistent coinfections with HBV and HIV which opens opportunities for analyzing immune dysregulation during HBV and HIV coinfection and preclinical testing of novel immunotherapeutics.
