Transport and drift-driven plasma flow components in the Alcator C-Mod boundary plasma

Boundary layer flows in the Alcator C-Mod tokamak are systematically examined as magnetic topology (upper versus lower-null) and plasma density are changed. Utilizing a unique set of scanning Langmuir–Mach probes, including one on the high-field side (HFS) midplane, the poloidal variation of plasma flow components in the parallel, diamagnetic and radial directions are resolved in detail. It is found that the plasma flow pattern can be decomposed into two principal parts: (1) a drift-driven component, which lies within a magnetic flux surface and is divergence-free and (2) a transport-driven component, which gives rise to near-sonic parallel flows on the HFS scrape-off layer (SOL). Toroidal rotation, Pfirsch–Schlüter and transport-driven contributions are unambiguously identified. Transport-driven parallel flows are found to dominate the HFS particle fluxes; the total poloidal-directed flow accounts for ~1/3 to all of the ion flux arriving on the inner divertor. As a result, heat convection is found to be an important player in this region, consistent with the observation of divertor asymmetries that depend on the direction of B × ∇B relative to the active x-point. In contrast, the poloidal projection of parallel flow in the low-field SOL largely cancels with E[subscript r] × B flow; toroidal rotation is the dominant plasma motion there. The magnitude of the transport-driven poloidal flow is found to be quantitatively consistent with fluctuation-induced radial particle fluxes on the low-field side (LFS), identifying this as the primary drive mechanism. Fluctuation-induced fluxes on the HFS are found to be essentially zero, excluding turbulent inward transport as the mechanism that closes the circulation loop in this region.United States. Dept. of Energy (Cooperative Agreement DE-FC02-99ER54512

X chromosome inactivation does not necessarily determine the severity of the phenotype in Rett syndrome patients

Rett syndrome (RTT) is a severe neurological disorder usually caused by mutations in the MECP2 gene. Since the MECP2 gene is located on the X chromosome, X chromosome inactivation (XCI) could play a role in the wide range of phenotypic variation of RTT patients; however, classical methylation-based protocols to evaluate XCI could not determine whether the preferentially inactivated X chromosome carried the mutant or the wild-type allele. Therefore, we developed an allele-specific methylation-based assay to evaluate methylation at the loci of several recurrent MECP2 mutations. We analyzed the XCI patterns in the blood of 174 RTT patients, but we did not find a clear correlation between XCI and the clinical presentation. We also compared XCI in blood and brain cortex samples of two patients and found differences between XCI patterns in these tissues. However, RTT mainly being a neurological disease complicates the establishment of a correlation between the XCI in blood and the clinical presentation of the patients. Furthermore, we analyzed MECP2 transcript levels and found differences from the expected levels according to XCI. Many factors other than XCI could affect the RTT phenotype, which in combination could influence the clinical presentation of RTT patients to a greater extent than slight variations in the XCI pattern