Ion acceleration during internal magnetic reconnection events in TST-2

Characteristics of ion acceleration in the internal magnetic reconnection events (IRE) have been studied by means of a neutral particle energy analyzer (NPA) in Tokyo Spherical Tokamak (TST-2). The major and minor radii are 0.38 m and 0.25m, respectively. The magnetic field strength is 0.3T and the maximum plasma current is up to 140 kA. The electron and ion temperatures are 0.4-0.5 keV and 0.1 keV, respectively and the electron density is ~1x1019 m-3. The NPA can be scanned toroidally from q = 74&deg; (cw) to q = 114&deg; (ccw), where q = 90&deg; corresponds to the perpendicular sightline. The direction of the plasma current is cw. The NPA signals are digitized at every 50 ms. The NPA is calibrated in the energy range of 0.1 keV < E < 8.4 keV. When the IRE occurs, it is observed that the plasma current increases by ~ 20% and the loop voltage drops from 0.6 V to-5 V for ~ 0.1 ms. The enhanced charge exchange flux is observed by more than one order of magnitude at ~ 1 keV for this reconnection phase. The ion temperature increases by 80 eV at IREs. The angle q dependence of increment of Ti shows that DTi (q = 74&deg;) is higher than that for q = 114&deg;. This observation suggests that an ion is accelerated initially in the direction of magnetic field lines. The time evolution of the ion distribution function is simulated with a Fokker-Planck code taking into account the electric field effects.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Transport barrier formation by LHCD on TRIAM-1M

Internal transport barrier (ITB) has been obtained in full lower hybrid current driven (LHCD) plasmas on a superconducting tokamak, TRIMA-1M (R=0.84m, a x b=0.12mx0.18m, BT<8T). The formation of ITB depends on the current density profile, j(r), varied by the power deposition of the lower hybrid (LH). The plasma with ITB can be maintained by the LH power deposited around the foot point of ITB up to 25 sec, which corresponds to more than 100 times of current diffusion time, $\tau$L/R. ITB is terminated by the reduction of current drive efficiency caused by metal impurities accumulation. In some condition, self-organized slow sawtooth oscillations (SSSO) of plasma current, density, temperature, and so on with the period comparable to the current diffusion time have been also observed during ITB discharge. The oscillation has the capability of particle exhaust, as the result, it may play an role in the avoidance of the impurity accumulation and the dilution in the future steady state fusion plasma with ITB, as the edge-localized mode in H-mode.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity

The synthesis of oligonucleotides containing 2′-deoxy-2′-fluoro-4′-thioarabinonucleotides is described. 2′-Deoxy-2′-fluoro-5-methyl-4′-thioarabinouridine (4′S-FMAU) was incorporated into 18-mer antisense oligonucleotides (AONs). 4′S-FMAU adopts a predominantly northern sugar conformation. Oligonucleotides containing 4′S-FMAU, unlike those containing FMAU, were unable to elicit E. coli or human RNase H activity, thus corroborating the hypothesis that RNase H prefers duplexes containing oligonucleotides that can adopt eastern conformations in the antisense strand. The duplex structure and stability of these oligonucleotides was also investigated via circular dichroism (CD)- and UV- binding studies. Replacement of the 4′-oxygen by a sulfur atom resulted in a marked decrease in melting temperature of AON:RNA as well as AON:DNA duplexes. 2′-Deoxy-2′-fluoro-4′-thioarabinouridine (4′S-FAU) was incorporated into 21-mer small interfering RNA (siRNA) and the resulting siRNA molecules were able to trigger RNA interference with good efficiency. Positional effects were explored, and synergy with 2′F-ANA, which has been previously established as a functional siRNA modification, was demonstrated

Increased Nitric Oxide Production and GFAP Expression in the Brains of Influenza A/NWS Virus Infected Mice

The cause of influenza to the brain was investigated using the A/NWS/33 influenza virus infected BALB/c mouse model. NOS-2 mRNA levels in the infected mouse brain was greater than in control mice in all brain regions examined, particularly in the olfactory bulb and hippocampus by 1 day p.i. On the contrary, no differences in NOS-1 or NOS-3 mRNA levels were found between infected and control mice. There was also a marked increase in the levels of metabolites of nitric oxide in the olfactory bulb and hippocampus. Immunohistochemistry showed positive staining for anti-NOS-2 primarily in the hippocampus of infected mice. Further, anti-NOS-2 and GFAP staining was mostly found around capillary blood vessels of the hippocampus starting early in the course of the disease. These results indicate that the NWS enhances the activation of astrocytes and NOS-2 expression which in turn enhances NO production and the expansion of capillary blood vessels

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

<p>Abstract</p> <p>Background</p> <p>RNA interference (RNAi) is a naturally occurring phenomenon that results in the suppression of a target RNA sequence utilizing a variety of possible methods and pathways. To dissect the factors that result in effective siRNA sequences a regression kernel Support Vector Machine (SVM) approach was used to quantitatively model RNA interference activities.</p> <p>Results</p> <p>Eight overall feature mapping methods were compared in their abilities to build SVM regression models that predict published siRNA activities. The primary factors in predictive SVM models are position specific nucleotide compositions. The secondary factors are position independent sequence motifs (<it>N</it>-grams) and guide strand to passenger strand sequence thermodynamics. Finally, the factors that are least contributory but are still predictive of efficacy are measures of intramolecular guide strand secondary structure and target strand secondary structure. Of these, the site of the 5' most base of the guide strand is the most informative.</p> <p>Conclusion</p> <p>The capacity of specific feature mapping methods and their ability to build predictive models of RNAi activity suggests a relative biological importance of these features. Some feature mapping methods are more informative in building predictive models and overall <it>t</it>-test filtering provides a method to remove some noisy features or make comparisons among datasets. Together, these features can yield predictive SVM regression models with increased predictive accuracy between predicted and observed activities both within datasets by cross validation, and between independently collected RNAi activity datasets. Feature filtering to remove features should be approached carefully in that it is possible to reduce feature set size without substantially reducing predictive models, but the features retained in the candidate models become increasingly distinct. Software to perform feature prediction and SVM training and testing on nucleic acid sequences can be found at the following site: <url>ftp://scitoolsftp.idtdna.com/SEQ2SVM/</url>.</p