Characterization of density fluctuations during the search for an I-mode regime on the DIII-D tokamak

The I-mode regime, routinely observed on the Alcator C-Mod tokamak, is characterized by an edge energy transport barrier without an accompanying particle barrier and with broadband instabilities, known as weakly coherent modes (WCM), believed to regulate particle transport at the edge. Recent experiments on the DIII-D tokamak exhibit I-mode characteristics in various physical quantities. These DIII-D plasmas evolve over long periods, lasting several energy confinement times, during which the edge electron temperature slowly evolves towards an H-mode-like profile, while maintaining a typical L-mode edge density profile. During these periods, referred to as I-mode phases, the radial electric field at the edge also gradually reaches values typically observed in H-mode. Density fluctuations measured with the phase contrast imaging diagnostic during I-mode phases exhibit three features typically observed in H-mode on DIII-D, although they develop progressively with time and without a sharp transition: the intensity of the fluctuations is reduced; the frequency spectrum is broadened and becomes non-monotonic; two dimensional space-time spectra appear to approach those in H-mode, showing phase velocities of density fluctuations at the edge increasing to about 10 km s−1. However, in DIII-D there is no clear evidence of the WCM. Preliminary linear gyro-kinetic simulations are performed in the pedestal region with the GS2 code and its recently upgraded model collision operator that conserves particles, energy and momentum. The increased bootstrap current and flow shear generated by the temperature pedestal are shown to decrease growth rates, thus possibly generating a feedback mechanism that progressively stabilizes fluctuations.United States. Department of Energy. Office of Fusion Energy Sciences (Award DE-FG02- 94ER54235)United States. Department of Energy. Office of Fusion Energy Sciences (Award DE-FG02-94ER54084)United States. Department of Energy. Office of Fusion Energy Sciences (Award DE-FG02-08ER54984)United States. Department of Energy. Office of Fusion Energy Sciences (Award DE-FC02-04ER54698

The effects of main-ion dilution on turbulence in low q95 C-Mod ohmic plasmas, and comparisons with nonlinear GYRO

Recent experiments on C-mod seeding nitrogen into ohmic plasmas with [subscript q]95 = 3.4 found that the seeding greatly reduced long-wavelength (ITG-scale) turbulence. The long-wavelength turbulence that was reduced by the nitrogen seeding was localized to the region of r/a≈0.85, where the turbulence is well above marginal stability (as evidenced by Q[subscript i]/Q[subscript GB]≫1). The nonlinear gyrokinetic code GYRO was used to simulate the expected turbulence in these plasmas, and the simulated turbulent density fluctuations and turbulent energy fluxes quantitatively agreed with the experimental measurements both before and after the nitrogen seeding. Unexpectedly, the intrinsic rotation of the plasma was also found to be affected by the nitrogen seeding, in a manner apparently unrelated to a change in the electron-ion collisionality that was proposed by other experiments.United States. Dept. of Energy. Office of Fusion Energy Sciences (Award E-FG02-94-ER54235

Application of ECH to the Study of Transport in ITER Baseline Scenario-like Discharges in DIII-D

Recent DIII-D experiments in the ITER Baseline Scenario (IBS) have shown strong increases in fluctuations and correlated reduction of confinement associated with entering the electron-heating-dominated regime with strong electron cyclotron heating (ECH). The addition of 3.2 MW of 110 GHz EC power deposited at ρ~0.42 to IBS discharges with ~3 MW of neutral beam injection causes large increases in low-k and medium-k turbulent density fluctuations observed with Doppler backscatter (DBS), beam emission spectroscopy (BES) and phase-contrast imaging (PCI) diagnostics, correlated with decreases in the energy, particle, and momentum confinement times. Power balance calculations show the electron heat diffusivity χ[subscript e] increases significantly in the mid-radius region 0.4<ρ<0.8, which is roughly the same region where the DBS and BES diagnostics show the increases in turbulent density fluctuations. Confinement of angular momentum is also reduced during ECH. Studies with the TGYRO transport solver show that the model of turbulent transport embodied in the TGLF code quantitatively reproduces the measured transport in both the neutral beam (NB)-only and in the NB plus EC cases. A simple model of the decrease in toroidal rotation with EC power is set forth, which exhibits a bifurcation in the rotational state of the discharge.United States. Dept. of Energy (DE-FC02-04ER54698)United States. Dept. of Energy (DE-FC02-08ER54966)United States. Dept. of Energy (DE-AC03-09CH11466)United States. Dept. of Energy (DE-FG02-04ER54235)United States. Dept. of Energy (DE-FG0289ER53296)United States. Dept. of Energy (DE-FG02-08ER54999)United States. Dept. of Energy (DE-FG02-08ER54984)United States. Dept. of Energy (DE-FG02-04ER54461

Short wavelength turbulence generated by shear in the quiescent H-mode edge on DIII–D

A region of turbulence with large radial wavenumber (k[subscript r]ρ[subscript s] > 1) is found in the high-shear portion of the plasma edge in Quiescent H-mode (QH-mode) on DIII–D using the Phase Contrast Imaging (PCI) diagnostic. At its peak outside the minimum of the Er well, the turbulence exhibits large amplitude [~ over n]/n ~ 40%, with large radial wavenumber ∣[¯over k][subscript r]/[¯ over k][subscript θ]∣ ~ 11 and short radial correlation length L[subscript r]/ρ[subscript i] ~ 0.2. The turbulence inside the E[subscript r] well minimum is characterized by the opposite sign in radial wavenumber from that of turbulence outside the minimum, consistent with the expected effects of velocity shear. The PCI diagnostic provides a line-integrated measurement of density fluctuations, so data are taken during a scan of plasma position at constant parameters to allow the PCI to sample a range in k[subscript r]/k[subscript θ]. Analysis of the Doppler shift and plasma geometry allows the turbulence to be localized to a narrow region 3 mm inside the last closed flux surface, outside the minimum of the E[subscript r] well. The turbulence amplitude and radial wavenumber and correlation length are determined by fitting the PCI results with a simple non-isotropic turbulence model with two regions of turbulence. These PCI observations, made in QH-mode, are qualitatively similar to those made in standard edge localized modes (ELM)-free H-mode and between ELMs, suggesting a similar role for large k[subscript r] turbulence there.United States. Dept. of Energy (DE-FG02-94ER54235)United States. Dept. of Energy (DE-FC02-04ER54698

Development and Evaluation of MR-Based Radiogenomic Models to Differentiate Atypical Lipomatous Tumors from Lipomas

Background: The aim of this study was to develop and validate radiogenomic models to predict the MDM2 gene amplification status and differentiate between ALTs and lipomas on preoperative MR images. Methods: MR images were obtained in 257 patients diagnosed with ALTs (n = 65) or lipomas (n = 192) using histology and the MDM2 gene analysis as a reference standard. The protocols included T2-, T1-, and fat-suppressed contrast-enhanced T1-weighted sequences. Additionally, 50 patients were obtained from a different hospital for external testing. Radiomic features were selected using mRMR. Using repeated nested cross-validation, the machine-learning models were trained on radiomic features and demographic information. For comparison, the external test set was evaluated by three radiology residents and one attending radiologist. Results: A LASSO classifier trained on radiomic features from all sequences performed best, with an AUC of 0.88, 70% sensitivity, 81% specificity, and 76% accuracy. In comparison, the radiology residents achieved 60–70% accuracy, 55–80% sensitivity, and 63–77% specificity, while the attending radiologist achieved 90% accuracy, 96% sensitivity, and 87% specificity. Conclusion: A radiogenomic model combining features from multiple MR sequences showed the best performance in predicting the MDM2 gene amplification status. The model showed a higher accuracy compared to the radiology residents, though lower compared to the attending radiologist

The prokaryotic enzyme DsbB may share key structural features with eukaryotic disulfide bond forming oxidoreductases

Three different classes of thiol-oxidoreductases that facilitate the formation of protein disulfide bonds have been identified. They are the Ero1 and SOX/ALR family members in eukaryotic cells, and the DsbB family members in prokaryotic cells. These enzymes transfer oxidizing potential to the proteins PDI or DsbA, which are responsible for directly introducing disulfide bonds into substrate proteins during oxidative protein folding in eukaryotes and prokaryotes, respectively. A comparison of the recent X-ray crystal structure of Ero1 with the previously solved structure of the SOX/ALR family member Erv2 reveals that, despite a lack of primary sequence homology between Ero1 and Erv2, the core catalytic domains of these two proteins share a remarkable structural similarity. Our search of the DsbB protein sequence for features found in the Ero1 and Erv2 structures leads us to propose that, in a fascinating example of structural convergence, the catalytic core of this integral membrane protein may resemble the soluble catalytic domain of Ero1 and Erv2. Our analysis of DsbB also identified two new groups of DsbB proteins that, based on sequence homology, may also possess a catalytic core similar in structure to the catalytic domains of Ero1 and Erv2

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains

We identified key residues from the structural alignment of families of protein domains from SCOP which we represented in the form of sparse protein signatures. A signature-generating algorithm (SigGen) was developed and used to automatically identify key residues based on several structural and sequence-based criteria. The capacity of the signatures to detect related sequences from the SWISSPROT database was assessed by receiver operator characteristic (ROC) analysis and jack-knife testing. Test signatures for families from each of the main SCOP classes are described in relation to the quality of the structural alignments, the SigGen parameters used, and their diagnostic performance. We show that automatically generated signatures are potently diagnostic for their family (ROC50 scores typically >0.8), consistently outperform random signatures, and can identify sequence relationships in the “twilight zone” of protein sequence similarity (<40%). Signatures based on 15%–30% of alignment positions occurred most frequently among the best-performing signatures. When alignment quality is poor, sparser signatures perform better, whereas signatures generated from higher-quality alignments of fewer structures require more positions to be diagnostic. Our validation of signatures from the Globin family shows that when sequences from the structural alignment are removed and new signatures generated, the omitted sequences are still detected. The positions highlighted by the signature often correspond (alignment specificity >0.7) to the key positions in the original (non-jack-knifed) alignment. We discuss potential applications of sparse signatures in sequence annotation and homology modeling