Radiative transfer in disc galaxies −- V. The accuracy of the KB approximation

We investigate the accuracy of an approximate radiative transfer technique that was first proposed by Kylafis & Bahcall (hereafter the KB approximation) and has been popular in modelling dusty late-type galaxies. We compare realistic galaxy models calculated with the KB approximation with those of a three-dimensional Monte Carlo radiative transfer code SKIRT. The SKIRT code fully takes into account of the contribution of multiple scattering whereas the KB approximation calculates only single scattered intensity and multiple scattering components are approximated. We find that the KB approximation gives fairly accurate results if optically thin, face-on galaxies are considered. However, for highly inclined ($i \gtrsim 85^{\circ}$) and/or optically thick (central face-on optical depth $\gtrsim1$) galaxy models, the approximation can give rise to substantial errors, sometimes, up to $\gtrsim 40\%$. Moreover, it is also found that the KB approximation is not always physical, sometimes producing infinite intensities at lines of sight with high optical depth in edge-on galaxy models. There is no "simple recipe" to correct the errors of the KB approximation that is universally applicable to any galaxy models. Therefore, it is recommended that the full radiative transfer calculation be used, even though it's slower than the KB approximation.Comment: 10 pages, 6 figures, accepted for publication in MNRA

Renal protective effects of vicenin-2 and scolymoside in a mouse model of sepsis

This study was initiated to determine whether 2 structurally related flavonoids found in Cyclopia subternata—vicenin-2 (VCN) and scolymoside (SCL)—could modulate renal functional damage in a mouse model of sepsis, and to elucidate the relevant underlying mechanisms. The potential of VCN and SCL treatment to reduce renal damage induced by cecal ligation and puncture (CLP) surgery in mice was measured via assessment of serum creatinine, blood urea nitrogen (BUN), lipid peroxidation, total glutathione, glutathione peroxidase activity, catalase activity, and superoxide dismutase activity. Treatment with either VCN or SCL resulted in elevated plasma levels of BUN and creatinine, and of protein in the urine of mice with CLP-induced renal damage. Moreover, both VCN and SCL inhibited nuclear factor κB activation and reduced the induction of nitric oxide synthase and excessive production of nitric acid. VCN and SCL treatment also reduced the plasma levels of interleukin-6, and tumor necrosis factor-α, reduced lethality due to CLP-induced sepsis, increased lipid peroxidation, and markedly enhanced the antioxidant defense system by restoring the levels of superoxide dismutase, glutathione peroxidase, and catalase in kidney tissues. The present results suggest that VCN and SCL protect mice from sepsis-triggered renal injury

Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications

With the advent of automated and high-throughput techniques, the number of patent applications containing biological sequences has been increasing rapidly. However, they have attracted relatively little attention compared to other sequence resources. We have built a database server called Patome, which contains biological sequence data disclosed in patents and published applications, as well as their analysis information. The analysis is divided into two steps. The first is an annotation step in which the disclosed sequences were annotated with RefSeq database. The second is an association step where the sequences were linked to Entrez Gene, OMIM and GO databases, and their results were saved as a gene–patent table. From the analysis, we found that 55% of human genes were associated with patenting. The gene–patent table can be used to identify whether a particular gene or disease is related to patenting. Patome is available at ; the information is updated bimonthly

Estimates of Discharge Coefficient in Levee Breach Under Two Different Approach Flow Types

The amount of released water (discharge) in a levee breach is a primary input variable to establish an emergency action plan for the area next to the levee. However, although several studies have been conducted, there is still no widely applicable discharge coefficient formula; this needs to be known to estimate discharge amount through an opening caused by a levee breach. Sometimes, the discharge coefficient developed for a sharp crested side weir is used to rate the discharge, but, in case of a levee breach, the resulting geometry and flow types are similar to that over a broad crested weir. Thus, in this study, two different openings—rectangular and trapezoidal shape—are constructed in the center of a levee at a height of 0.6m to replicate levee breach scenarios, and the effect of two different approach flow types—the river type approach and reservoir type approach—are explored to suggest a discharge coefficient formula applicable for discharge rating for a levee breach. The results show that the ratio of head above the bottom of an opening and the opening width is a key variable for calculating the discharge coefficient of a reservoir type, but the approach Froude number should also be considered for a river type approach. The measured data are used to improve rating equations and will be useful in the future to validate computational fluid dynamics simulations of wave propagation during levee failure into the inundation area

Radiative Transfer in Ly{\alpha} Nebulae: I. Modeling a Continuous or Clumpy Spherical Halo with a Central Source

To understand the mechanism behind high-$z$ Ly${\alpha}$ nebulae, we simulate the scattering of Ly${\alpha}$ in a $\rm H\,I$ halo about a central Ly${\alpha}$ source. For the first time, we consider both smooth and clumpy distributions of halo gas, as well as a range of outflow speeds, total $\rm H\,I$ column densities, $\rm H\,I$ spatial concentrations, and central source galaxies (e.g., with Ly${\alpha}$ line widths corresponding to those typical of AGN or star-forming galaxies). We compute the spatial-frequency diffusion and the polarization of the Ly${\alpha}$ photons scattered by atomic hydrogen. Our scattering-only model reproduces the typical size of Ly${\alpha}$ nebulae ($\sim 100\,$kpc) at total column densities $N_{\rm HI} \geq 10^{20} \rm cm^{-2}$ and predicts a range of positive, flat, and negative polarization radial gradients. We also find two general classes of Ly${\alpha}$ nebula morphologies: with and without bright cores. Cores are seen when $N_{\rm HI}$ is low, i.e., when the central source is directly visible, and are associated with a polarization jump, a steep increase in the polarization radial profile just outside the halo center. Of all the parameters tested in our smooth or clumpy medium model, $N_{\rm HI}$ dominates the trends. The radial behaviors of the Ly${\alpha}$ surface brightness, spectral line shape, and polarization in the clumpy model with covering factor $f_c \gtrsim 5$ approach those of the smooth model at the same $N_{\rm HI}$. A clumpy medium with high $N_{\rm HI}$ and low $f_c \lesssim 2$ generates Ly${\alpha}$ features via scattering that the smooth model cannot: a bright core, symmetric line profile, and polarization jump.Comment: 42 pages, 27 figures, accepted for publication in ApJ, Comments welcome