Collisionless microinstabilities in stellarators I - analytical theory of trapped-particle modes

This is the first of two papers about collisionless, electrostatic micro-instabilities in stellarators, with an emphasis on trapped-particle modes. It is found that, in so-called maximum-$J$ configurations, trapped-particle instabilities are absent in large regions of parameter space. Quasi-isodynamic stellarators have this property (approximately), and the theory predicts that trapped electrons are stabilizing to all eigenmodes with frequencies below the electron bounce frequency. The physical reason is that the bounce-averaged curvature is favorable for all orbits, and that trapped electrons precess in the direction opposite to that in which drift waves propagate, thus precluding wave-particle resonance. These considerations only depend on the electrostatic energy balance, and are independent of all geometric properties of the magnetic field other than the maximum-$J$ condition. However, if the aspect ratio is large and the instability phase velocity differs greatly from the electron and ion thermal speeds, it is possible to derive a variational form for the frequency showing that stability prevails in a yet larger part of parameter space than what follows from the energy argument. Collisionless trapped-electron modes should therefore be more stable in quasi-isodynamic stellarators than in tokamaks.Comment: 9 pages, 1 figur

Salt and Pepper for Point-of-Care Diagnostics

AbstractCurrently available Point-Of-Care-Testing (POCT) devices usually suffer from complex test formats and transduction technologies unfavorable for automation. Among optical sensor technologies, the Reflectometric Interference Spectroscopy (RIfS) is particularly well suited for generating miniaturized, robust and disposable sensors. RIfS systems are not only suitable for diagnostic applications, but are also a good choice for other areas of life-science analytics including biotechnology, food monitoring and safety engineering. Users take advantage of the direct test format by avoiding laborious sample pre-treatment as well as addition of costly reagents, both being common disadvantages of competing test systems

Available energy of trapped electrons in Miller tokamak equilibria

Available energy (\AE{}), which quantifies the maximum amount of thermal energy that may be liberated and converted into instabilities and turbulence, has shown to be a useful metric for predicting saturated energy fluxes in trapped-electron-mode-driven turbulence. Here, we calculate and investigate the \AE{} in the analytical tokamak equilibria introduced by \citet{Miller1998NoncircularModel}. The \AE{} of trapped electrons reproduces various trends also observed in experiments; negative shear, increasing Shafranov shift, vertical elongation, and negative triangularity can all be stabilising, as indicated by a reduction in \AE{}, although it is strongly dependent on the chosen equilibrium. Comparing \AE{} with saturated energy flux estimates from the \textsc{tglf} model, we find fairly good correspondence, showcasing that \AE{} can be useful to predict trends. We go on to investigate \AE{} and find that negative triangularity is especially beneficial in vertically elongated configurations with positive shear or low gradients. We furthermore extract a gradient threshold-like quantity from \AE{} and find that it behaves similarly to gyrokinetic gradient thresholds: it tends to increase linearly with magnetic shear, and negative triangularity leads to an especially high threshold. We next optimise the device geometry for minimal \AE{} and find that the optimum is strongly dependent on equilibrium parameters, e.g. magnetic shear or pressure gradient. Investigating the competing effects of increasing the density gradient, the pressure gradient, and decreasing the shear, we find regimes that have steep gradients yet low \AE{}, and that such a regime is inaccessible in negative-triangularity tokamaks.Comment: 31 pages, 16 figure

Distinct cellular responses differentiating alcohol- and hepatitis C virus-induced liver cirrhosis

BACKGROUND: Little is known at the molecular level concerning the differences and/or similarities between alcohol and hepatitis C virus induced liver disease. Global transcriptional profiling using oligonucleotide microarrays was therefore performed on liver biopsies from patients with cirrhosis caused by either chronic alcohol consumption or chronic hepatitis C virus (HCV). RESULTS: Global gene expression patterns varied significantly depending upon etiology of liver disease, with a greater number of differentially regulated genes seen in HCV-infected patients. Many of the gene expression changes specifically observed in HCV-infected cirrhotic livers were expectedly associated with activation of the innate antiviral immune response. We also compared severity (CTP class) of cirrhosis for each etiology and identified gene expression patterns that differentiated ethanol-induced cirrhosis by class. CTP class A ethanol-cirrhotic livers showed unique expression patterns for genes implicated in the inflammatory response, including those related to macrophage activation and migration, as well as lipid metabolism and oxidative stress genes. CONCLUSION: Stages of liver cirrhosis could be differentiated based on gene expression patterns in ethanol-induced, but not HCV-induced, disease. In addition to genes specifically regulating the innate antiviral immune response, mechanisms responsible for differentiating chronic liver damage due to HCV or ethanol may be closely related to regulation of lipid metabolism and to effects of macrophage activation on deposition of extracellular matrix components

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers

<p>Abstract</p> <p>Background</p> <p>Hepatitis C virus (HCV) is a major cause of chronic liver disease by infecting over 170 million people worldwide. Recent studies have shown that microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are involved in the regulation of HCV infection, but their functions have not been systematically studied. We propose an integrative strategy for identifying the miRNA-mRNA regulatory modules that are associated with HCV infection. This strategy combines paired expression profiles of miRNAs and mRNAs and computational target predictions. A miRNA-mRNA regulatory module consists of a set of miRNAs and their targets, in which the miRNAs are predicted to coordinately regulate the level of the target mRNA.</p> <p>Results</p> <p>We simultaneously profiled the expression of cellular miRNAs and mRNAs across 30 HCV positive or negative human liver biopsy samples using microarray technology. We constructed a miRNA-mRNA regulatory network, and using a graph theoretical approach, identified 38 miRNA-mRNA regulatory modules in the network that were associated with HCV infection. We evaluated the direct miRNA regulation of the mRNA levels of targets in regulatory modules using previously published miRNA transfection data. We analyzed the functional roles of individual modules at the systems level by integrating a large-scale protein interaction network. We found that various biological processes, including some HCV infection related canonical pathways, were regulated at the miRNA level during HCV infection.</p> <p>Conclusion</p> <p>Our regulatory modules provide a framework for future experimental analyses. This report demonstrates the utility of our approach to obtain new insights into post-transcriptional gene regulation at the miRNA level in complex human diseases.</p