Counter-propagating radiative shock experiments on the Orion laser and the formation of radiative precursors

We present results from new experiments to study the dynamics of radiative shocks, reverse shocks and radiative precursors. Laser ablation of a solid piston by the Orion high-power laser at AWE Aldermaston UK was used to drive radiative shocks into a gas cell initially pressurised between $0.1$ and $1.0 \ bar with different noble gases. Shocks propagated at {80 \pm 10 \ km/s} and experienced strong radiative cooling resulting in post-shock compressions of { \times 25 \pm 2}. A combination of X-ray backlighting, optical self-emission streak imaging and interferometry (multi-frame and streak imaging) were used to simultaneously study both the shock front and the radiative precursor. These experiments present a new configuration to produce counter-propagating radiative shocks, allowing for the study of reverse shocks and providing a unique platform for numerical validation. In addition, the radiative shocks were able to expand freely into a large gas volume without being confined by the walls of the gas cell. This allows for 3-D effects of the shocks to be studied which, in principle, could lead to a more direct comparison to astrophysical phenomena. By maintaining a constant mass density between different gas fills the shocks evolved with similar hydrodynamics but the radiative precursor was found to extend significantly further in higher atomic number gases (\sim$$4$ times further in xenon than neon). Finally, 1-D and 2-D radiative-hydrodynamic simulations are presented showing good agreement with the experimental data.Comment: HEDLA 2016 conference proceeding

Strange Stars with a Density-Dependent Bag Parameter

We have studied strange quark stars in the framework of the MIT bag model, allowing the bag parameter B to depend on the density of the medium. We have also studied the effect of Cooper pairing among quarks, on the stellar structure. Comparison of these two effects shows that the former is generally more significant. We studied the resulting equation of state of the quark matter, stellar mass-radius relation, mass-central-density relation, radius-central-density relation, and the variation of the density as a function of the distance from the centre of the star. We found that the density-dependent B allows stars with larger masses and radii, due to stiffening of the equation of state. Interestingly, certain stellar configurations are found to be possible only if B depends on the density. We have also studied the effect of variation of the superconducting gap parameter on our results.Comment: 23 pages, 8 figs; v2: 25 pages, 9 figs, version to be published in Phys. Rev. (D

Delayed developmental changes in neonatal vocalizations correlates with variations in ventral medial hypothalamus and central amygdala development in the rodent infant: Effects of prenatal cocaine

While variations in neonatal distress vocalizations have long been shown to reflect the integrity of nervous system development following a wide range of prenatal and perinatal insults, a paucity of research has explored the neurobiological basis of these variations. To address this, virgin Sprague-Dawley rats were bred and divided into three groups: (1) untreated, (2) chronic-cocaine treated (30mg/kg/day, gestation days (GDs) 1–20); or (3) chronic-saline treated (2mg/kg/day, GDs 1–20). Pregnant dams were injected with Bromodeoxyuridine (10mg/kg) on GDs 13–15 to label proliferating cells in limbic regions of interest. Ultrasonic vocalizations (USVs) were recorded on PNDs 1, 14, and 21, from one male and female pup per litter. Variations in acoustic properties of USVs following cocaine-exposure were age and sex-dependent including measures of total number, total duration and amplitude of USVs, and percent of USVs with at least one harmonic. Following USV testing brains were stained with standard fluorescent immunohistochemistry protocols and examined for variations in neuronal development and if variations were associated with acoustic characteristics. Limbic region developmental differences following cocaine-exposure were sex- and age-dependent with variations in the ventral medial hypothalamus and central amygdala correlating with variations in vocalizations on PND 14 and 21. Results suggest maturation of the ventral medial hypothalamus and central amygdala may provide the basis for variations in the sound and production of USVs. As vocalizations may serve as a neurobehavioral marker for nervous system integrity, understanding the neurobiological basis of neonatal vocalizations may provide the basis for early intervention strategies in high-risk infant populations

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Stochastic Acceleration by Turbulence

The subject of this paper is stochastic acceleration by plasma turbulence, a process akin to the original model proposed by Fermi. We review the relative merits of different acceleration models, in particular the so called first order Fermi acceleration by shocks and second order Fermi by stochastic processes, and point out that plasma waves or turbulence play an important role in all mechanisms of acceleration. Thus, stochastic acceleration by turbulence is active in most situations. We also show that it is the most efficient mechanism of acceleration of relatively cool non relativistic thermal background plasma particles. In addition, it can preferentially accelerate electrons relative to protons as is needed in many astrophysical radiating sources, where usually there are no indications of presence of shocks. We also point out that a hybrid acceleration mechanism consisting of initial acceleration by turbulence of background particles followed by a second stage acceleration by a shock has many attractive features. It is demonstrated that the above scenarios can account for many signatures of the accelerated electrons, protons and other ions, in particular $^3$He and $^4$He, seen directly as Solar Energetic Particles and through the radiation they produce in solar flares.Comment: 29 pages 7 figures for proceedings of ISSI-Bern workshop on Particle Acceleration 201

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM