Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe.

Which variables determine the constraints on gene sequence evolution is one of the most central questions in molecular evolution. In the fission yeast Schizosaccharomyces pombe, an important model organism, the variables influencing the rate of sequence evolution have yet to be determined. Previous studies in other single celled organisms have generally found gene expression levels to be most significant, with numerous other variables such as gene length and functional importance identified as having a smaller impact. Using publicly available data, we used partial least squares regression, principal components regression, and partial correlations to determine the variables most strongly associated with sequence evolution constraints. We identify centrality in the protein-protein interactions network, amino acid composition, and cellular location as the most important determinants of sequence conservation. However, each factor only explains a small amount of variance, and there are numerous variables having a significant or heterogeneous influence. Our models explain more than half of the variance in dN, raising the possibility that future refined models could quantify the role of stochastics in evolutionary rate variation.

Optical phantoms with adjustable subdiffusive scattering parameters.

A new epoxy-resin-based optical phantom system with adjustable subdiffusive scattering parameters is presented along with measurements of the intrinsic absorption, scattering, fluorescence, and refractive index of the matrix material. Both an aluminium oxide powder and a titanium dioxide dispersion were used as scattering agents and we present measurements of their scattering and reduced scattering coefficients. A method is theoretically described for a mixture of both scattering agents to obtain continuously adjustable anisotropy values g between 0.65 and 0.9 and values of the phase function parameter γ in the range of 1.4 to 2.2. Furthermore, we show absorption spectra for a set of pigments that can be added to achieve particular absorption characteristics. By additional analysis of the aging, a fully characterized phantom system is obtained with the novelty of g and γ parameter adjustment.

In-vivo multilaboratory investigation of the optical properties of the human head.

The in-vivo optical properties of the human head are investigated in the 600-1100 nm range on different subjects using continuous wave and time domain diffuse optical spectroscopy. The work was performed in collaboration with different research groups and the different techniques were applied to the same subject. Data analysis was carried out using homogeneous and layered models and final results were also confirmed by Monte Carlo simulations. The depth sensitivity of each technique was investigated and related to the probed region of the cerebral tissue. This work, based on different validated instruments, is a contribution to fill the existing gap between the present knowledge and the actual in-vivo values of the head optical properties.

Surface layering properties of Intralipid phantoms.

Intralipid has become an extensively studied and widely used reference and calibration phantom for diffuse optical imaging technologies. In this study we call attention to the layering properties of Intralipid emulsions, which are commonly assumed to have homogeneous optical properties. By measurement of spatial frequency domain reflectance in combination with an analytical solution of the radiative transfer equation for two-layered media, we make quantitative investigations on the formation of a surface layer on different dilutions of Intralipid. Our findings are verified by an independent spatially resolved reflectance setup giving evidence of a time dependent, thin and highly scattering surface layer on top of Intralipid-water emulsions. This layer should be considered when using Intralipid as an optical calibration or reference phantom.

Time-resolved measurements of the optical properties of fibrous media using the anisotropic diffusion equation.

Transmittance and reflectance from spruce wood and bovine ligamentum nuchae as two different fibrous media are examined by time-of-flight spectroscopy for varying source detector separations and several orientations of the fibers in the sample. The anisotropic diffusion theory is used to obtain the absorption coefficient and the diffusion coefficients parallel and perpendicular to the fibers. The results are compared to those obtained with the isotropic diffusion theory. It is shown that for increasing source detector separations, the retrieved optical properties change as expected from Monte Carlo simulations performed in a previous study. This confirms that the anisotropic diffusion theory yields useful results for certain experimental conditions.

Hybrid Green's function of the time-dependent radiative transfer equation for anisotropically scattering semi-infinite media.

A semi-infinite space Green's function of the time-dependent radiative transfer equation is derived based upon an exact solution for anisotropic scattering in infinite space and the approximated extrapolated boundary condition. The obtained solution is compared to Monte Carlo simulations and used for retrieving the optical parameters of simulated data in a nonlinear fit. It is shown that the solution performs well for boundaries with mismatched refractive indices. The relative errors in the fitted optical parameters are considerably smaller than by using the diffusion theory.