Overview and first measurements of the MAST Upgrade bolometer diagnostic

A suite of multi-channel resistive bolometers has been implemented to measure the total radiation from Mega Amp Spherical Tokamak Upgrade plasmas, with cameras covering the core plasma and lower divertor chamber. Data are digitized and processed using novel field-programmable gate array-based electronics, offering improved compactness and new operational capabilities. A synthetic diagnostic has been developed to explore the quality of 2D reconstructions available from the system and to quantify the uncertainty on quantities such as the total radiated power. Measurements in the first campaign have demonstrated correct functioning of the diagnostic while also highlighting issues with electrical noise and some failure mechanisms of the detectors, as well as significant neutral beam fast-particle losses.

Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci

RNA polymerase II (RNAPII) pausing in early elongation is critical for gene regulation. Paused RNAPII can be released into productive elongation by the kinase P-TEFb or targeted for premature termination by the Integrator complex. Integrator comprises endonuclease and phosphatase activities, driving termination by cleavage of nascent RNA and removal of stimulatory phosphorylation. We generated a degron system for rapid Integrator endonuclease (INTS11) depletion to probe the direct consequences of Integrator-mediated RNA cleavage. Degradation of INTS11 elicits nearly universal increases in active early elongation complexes. However, these RNAPII complexes fail to achieve optimal elongation rates and exhibit persistent Integrator phosphatase activity. Thus, only short transcripts are significantly upregulated following INTS11 loss, including transcription factors, signaling regulators, and non-coding RNAs. We propose a uniform molecular function for INTS11 across all RNAPII-transcribed loci, with differential effects on particular genes, pathways, or RNA biotypes reflective of transcript lengths rather than specificity of Integrator activity.

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes

The cerebral cortex has expanded in size and complexity in primates, yet the molecular innovations that enabled primate-specific brain attributes remain obscure. We generated cerebral cortex organoids from human, chimpanzee, orangutan, and rhesus pluripotent stem cells and sequenced their transcriptomes at weekly time points for comparative analysis. We used transcript structure and expression conservation to discover gene regulatory long non-coding RNAs (lncRNAs). Of 2,975 human, multi-exonic lncRNAs, 2,472 were structurally conserved in at least one other species and 920 were conserved in all. Three hundred eighty-six human lncRNAs were transiently expressed (TrEx) and many were also TrEx in great apes (46%) and rhesus (31%). Many TrEx lncRNAs are expressed in specific cell types by single-cell RNA sequencing. Four TrEx lncRNAs selected based on cell-type specificity, gene structure, and expression pattern conservation were ectopically expressed in HEK293 cells by CRISPRa. All induced trans gene expression changes were consistent with neural gene regulatory activity.

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and is a determinant of neuronal number in the mammalian cortex. We find that three paralogs of human-specific NOTCH2NL are highly expressed in radial glia. Functional analysis reveals that different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation into cortical neurons. Furthermore, NOTCH2NL genes provide the breakpoints in 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism and deletions with microcephaly and schizophrenia. Thus, the emergence of human-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger human neocortex, accompanied by loss of genomic stability at the 1q21.1 locus and resulting recurrent neurodevelopmental disorders.

Experimental signatures of critically balanced turbulence in MAST

Beam emission spectroscopy (BES) measurements of ion-scale density fluctuations in the MAST tokamak are used to show that the turbulence correlation time, the drift time associated with ion temperature or density gradients, the particle (ion) streaming time along the magnetic field, and the magnetic drift time are consistently comparable, suggesting a "critically balanced" turbulence determined by the local equilibrium. The resulting scalings of the poloidal and radial correlation lengths are derived and tested. The nonlinear time inferred from the density fluctuations is longer than the other times; its ratio to the correlation time scales as ν(*i)(-0.8 ± 0.1), where ν(*i) = ion  collision rate/streaming rate. This is consistent with turbulent decorrelation being controlled by a zonal component, invisible to the BES, with an amplitude exceeding those of the drift waves by ∼ ν(*i)(-0.8).

Beam emission spectroscopy turbulence imaging system for the MAST spherical tokamak

A new beam emission spectroscopy turbulence imaging system has recently been installed onto the MAST spherical tokamak. The system utilises a high-throughput, direct coupled imaging optics, and a single large interference filter for collection of the Doppler shifted D(α) emission from the ~2 MW heating beam of ~70 keV injection energy. The collected light is imaged onto a 2D array detector with 8 × 4 avalanche photodiode sensors which is incorporated into a custom camera unit to perform simultaneous 14-bit digitization at 2 MHz of all 32 channels. The array is imaged at the beam to achieve a spatial resolution of ~2 cm in the radial (horizontal) and poloidal (vertical) directions, which is sufficient for detection of the ion-scale plasma turbulence. At the typical photon fluxes of ~10(11) s(-1) the achieved signal-to-noise ratio of ~300 at the 0.5 MHz analogue bandwidth is sufficient for detection of relative density fluctuations at the level of a few 0.1%. The system is to be utilised for the study of the characteristics of the broadband, ion-scale turbulence, in particular its interaction with flow shear, as well as coherent fluctuations due to various types of MHD activity.

Avalanche photodiode based detector for beam emission spectroscopy

An avalanche photodiode based (APD) detector for the visible wavelength range was developed for low light level, high frequency beam emission spectroscopy (BES) experiments in fusion plasmas. This solid state detector has higher quantum efficiency than photomultiplier tubes, and unlike normal photodiodes, it has internal gain. This paper describes the developed detector as well as the noise model of the electronic circuit. By understanding the noise sources and the amplification process, the optimal amplifier and APD reverse voltage setting can be determined, where the signal-to-noise ratio is the highest for a given photon flux. The calculations are compared to the absolute calibration results of the implemented circuit. It was found that for a certain photon flux range, relevant for BES measurements (≈10(8)-10(10) photons/s), the new detector is superior to both photomultipliers and photodiodes, although it does not require cryogenic cooling of any component. The position of this photon flux window sensitively depends on the parameters of the actual experimental implementation (desired bandwidth, detector size, etc.) Several detector units based on these developments have been built and installed in various tokamaks. Some illustrative results are presented from the 8-channel trial BES system installed at Mega-Ampere Spherical Tokamak (MAST) and the 16-channel BES system installed at the Torus Experiment for Technology Oriented Research (TEXTOR).

Calculation of spatial response of 2D beam emission spectroscopy diagnostic on MAST

The beam emission spectroscopy (BES) turbulence diagnostic on MAST is to be upgraded in June 2010 from a one-dimensional trial system to a two-dimensional imaging system (8 radial×4 poloidal channels) based on a newly developed avalanche photodiode array camera. The spatial resolution of the new system is calculated in terms of the point spread function to account for the effects of field-line curvature, observation geometry, the finite lifetime of the excited state of the beam atoms, and beam attenuation and divergence. It is found that the radial spatial resolution is ∼2-3 cm and the poloidal spatial resolution ∼1-5 cm depending on the radial viewing location. The absolute number of detected photons is also calculated, hence the photon noise level can be determined.

Beam emission spectroscopy for density turbulence measurements on the MAST spherical tokamak

Beam emission spectroscopy (BES) of the energetic deuterium (D(0)) heating beams can provide a means of characterizing the density turbulence in tokamak plasmas. First such measurements have been performed on the MAST spherical tokamak using a trial BES system, which shares the collection optics of the charge-exchange recombination spectroscopy system. This system, with eight spatial channels covering the outer part of the plasma cross section, uses avalanche photodiode detectors with custom preamplifiers to provide measurements at 1 MHz bandwidth with a spatial resolution of 4 cm. Simulations of the measurement, including the beam absorption and excitation, line-of-sight integration of the emission spectrum, and the characteristics of the detection system have been benchmarked against the measured absolute intensity of the Doppler shifted Dalpha fluorescence from the 50 keV beam. This gives confidence in predictions of the performance of a two-dimensional imaging BES system planned for MAST. Correlation techniques have also provided information on the characteristics of the density turbulence at the periphery of L-mode plasmas as well as density perturbations due to coherent magnetohydrodynamic activity at the edge of H-mode plasmas. Precursor oscillations of the density in the pedestal region to edge-localized modes occurring during H-mode plasmas with a single-null diverted magnetic configuration are also observable in the raw signals from the trial BES system.

L-H transition in the mega-amp spherical tokamak

H-mode plasmas have been achieved on the MAST spherical tokamak at input power considerably higher than predicted by conventional threshold scalings. Following L- H transition, a clear improvement in energy confinement is obtained, exceeding recent international scalings even at densities approaching the Greenwald density limit. Transition is accompanied by an order-of-magnitude increase in edge-density gradient, a marked decrease in turbulence, the efficient conversion of internal electron Bernstein waves into free space waves, and the onset and saturation of edge poloidal rotation.