Understanding Simulations of Thin Accretion Disks by Energy Equation

We study the fluctuations of standard thin accretion disks by linear analysis of the time-dependent energy equation together with the vertical hydrostatic equilibrium and the equation of state. We show that some of the simulation results in Hirose et al. (2009b), such as the time delay, the relationship of power spectra, and the correlation between magnetic energy and radiation energy, can be well understood by our analytic results.Comment: 13 pages, 3 figure, accepted for publication in Ap

The relationship between cation exchange capacity, total bases, and exchange acidity in certain Oregon soils

Two soils representative of the coast and three representing the Willamette Valley have been studied for their general chemical characteristics. Exchange capacity and exchangeable cations were determined by the ammonium acetate and the BaCl₂-triethanolamine buffer methods. Exchange capacity was also obtained from conductimetric titrations which were run on each soil before and after destroying the organic matter.Potentiometric titrations were run before and after leaching each soil with HCl. Lime requirement was determined by Woodruff's method and also obtained from the pH-lime curves. The two coastal soils, Astoria and Clatsop, have lower pH and base saturation and higher organic matter content and exchange capacity than the Melbourne, Olympic, and Willamette soils from the valley. The Melbourne soil had the highest base saturation percentage and Astoria had the lowest. The amount of exchangeable aluminum was also higher in the coastal soils. The amount of exchange capacity contributed to the organic fraction was 65 per cent in the Olympic and Willamette soils and 50 per cent in the other three. The value for exchange capacity by the different methods was in good agreement in the three valley soils before and after the organic matter was destroyed. In the coastal soils there was no agreement between methods in any case. This would indicate that in the latter two soils, type of clay mineral present may be more of an influence than in the former soils. The potentiometric titration curves showed that the two coastal soils were well buffered and the valley soils were only slightly buffered. After the soils were leached with HCl the Melbourne soil was the only one which indicated a strong acid property. The exchange properties of the soils as affected by additions of lime were studied by incubating the soils for four weeks with added increments of lime. With each added increment of lime the pH increased and exchangeable acidity decreased in each soil. The amount of lime to bring the soils to any given degree of base saturation appeared to be proportional to the magnitude of the exchange capacity and inversely proportional to the degree of base saturation. At any given pH value there was a considerable difference in the degree of base saturation for these soils. This might well be a reflection of the type of minerals present in the different soils. More lime was required to bring the two coastal soils up to pH 6.5 as indicated by the pH-lime relationship curve than that estimated by the Woodruff method. Consistent results were observed in the three valley soils. This suggests that the buffer solution at pH 7 as recommended by Woodruff was not strong enough to neutralize the acidity in the coastal soils. There was good agreement between the two methods in the determination of the exchangeable bases. The BaCl₂-buffer method gave much higher values of exchangeable acidity than did the ammonium acetate method. These values, when converted to tons of calcium carbonate, agree fairly closely with the amount of lime required to bring the soils to pH 7 when added directly to the soil. When lime was added above the saturation point the amount of exchangeable calcium as determined by the ammonium acetate method increased but remained relatively constant for the BaCl₂-buffer method. The various analysis seem to indicate that the Astoria and Clatsop soils contain predominantly 2:1 type clay minerals while the Olympic and Willamette soils contain predominantly the 1:1 type. The Melbourne soil exhibits properties more closely associated with the coastal soils

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons

GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbers of gene annotations verified by experiments, it is feasible to identify genes in the newly sequenced genomes by comparing to annotated genes of phylogenetically close organisms. GeneAlign applies CORAL, a heuristic linear time alignment tool, to determine if regions flanked by the candidate signals (initiation codon-GT, AG-GT and AG-STOP codon) are similar to annotated coding exons. Employing the conservation of gene structures and sequence homologies between protein coding regions increases the prediction accuracy. GeneAlign was tested on Projector dataset of 491 human–mouse homologous sequence pairs. At the gene level, both the average sensitivity and the average specificity of GeneAlign are 81%, and they are larger than 96% at the exon level. The rates of missing exons and wrong exons are smaller than 1%. GeneAlign is a free tool available at

Functional role of NF-IL6β and its sumoylation and acetylation modifications in promoter activation of cyclooxygenase 2 gene

NF-IL6β regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6β expression in A431 cells. NF-IL6β coordinated with c-Jun on cox-2 transcriptional activation by reporter and small interfering RNA assays. NF-IL6β could directly bind to CCAAT/enhancer-binding protein (C/EBP) and cyclic AMP-response element (CRE) sites of the cox-2 promoter by in vitro-DNA binding assay. The C/EBP site was important for basal and, to a lesser extent, for EGF-regulated cox-2 transcription, while the CRE site was a more specific response to EGF inducibility of cox-2 gene. SUMO1 expression attenuated EGF- and NF-IL6β-induced cox-2 promoter activities. NF-IL6β was found to be sumoylated by in vivo- and in vitro-sumoylation assays, and the SUMO1-NF-IL6β (suNF-IL6β) lost its ability to interact with p300 in in vitro-binding assay. NF-IL6β was also acetylated by p300, and acetylation of NF-IL6β enhanced the cox-2 promoter activity stimulated by NF-IL6β itself. In vivo-DNA binding assay demonstrated that EGF stimulated the recruitment of p300 and NF-IL6β to the cox-2 promoter, yet promoted the dissociation of SUMO1-modificated proteins from the promoter. These results indicated that NF-IL6β plays a pivotal role in the regulation of basal and EGF-induced cox-2 transcription