Jožef Stefan Institute

About: Jožef Stefan Institute is a facility organization based out in Ljubljana, Slovenia. It is known for research contribution in the topics: Liquid crystal & Dielectric. The organization has 3828 authors who have published 12614 publications receiving 291025 citations.

Evolutionary Genomics of Chromoviruses in Eukaryotes

Abstract: The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.

Regulation of the activity of lysosomal cysteine proteinases by pH-induced inactivation and/or endogenous protein inhibitors, cystatins.

Abstract: The kinetics of pH-induced inactivation of human cathepsins B and L was studied by conventional and stopped-flow methods. The inactivation of both enzymes was found to be an irreversible, first-order process. The inactivation rate constants increased exponentially with pH for both enzymes. From log kinac vs pH plots, 3.0 and 1.7 protons were calculated to be desorbed for pH-induced inactivation of cathepsins L and B. Cathepsin B was thus substantially more stable than cathepsin L (approximately 15-fold at pH 7.0 and 37 degrees C). Cathepsin B was efficiently inhibited by cystatin C at pH 7.4, whereas the inhibition by stefin B and high molecular weight kininogen was only moderate. In contrast, cathepsin L was efficiently inhibited by both chicken cystatin and stefin B at this pH kass approximately 3.3 x 10(7) m-1 s-1).

Off-center Ti model of barium titanate

Abstract: It has recently been shown by NMR techniques that in the high-temperature cubic phase of ${\mathrm{BaTiO}}_{3}$ the $\mathrm{Ti}$ ions are not confined to the high-symmetry cubic sites, but rather occupy one of the eight off-center positions along the $[111]$ directions. The off-center $\mathrm{Ti}$ picture is in apparent contrast with most soft-mode-type theoretical descriptions of this classical perovskite ferroelectric. Here we apply the Girshberg-Yacoby off-center cation model of perovskite ferroelectrics assuming that the symmetrized occupation operators or ``pseudospins'' for the $\mathrm{Ti}$ off-center sites are linearly coupled to the normal coordinates for $\mathrm{TO}$ lattice vibrations. In the adiabatic limit, the coupling is eliminated by transforming to displaced phonon coordinates, and after excluding the self-interaction terms an effective $\mathrm{Ti}\text{\ensuremath{-}}\mathrm{Ti}$ interaction is obtained. Using the Langevin equations of motion and the soft-spin formalism for the $\mathrm{Ti}$ pseudospin degrees of freedom with ${T}_{1u}$ symmetry, the dynamic response of the coupled system is derived. The results are shown to be in qualitative agreement with the experimental data of Vogt et al. [Phys. Rev. B, 26, 5904 (1982)] obtained by hyper-Raman scattering. The nature of the phase transition, which is of a mixed displacive and order-disorder type, is discussed.

Comparisons between MCNP, EGS4 and experiment for clinical electron beams

Abstract: Understanding the limitations of Monte Carlo codes is essential in order to avoid systematic errors in simulations, and to suggest further improvement of the codes. MCNP and EGS4, Monte Carlo codes commonly used in medical physics, were compared and evaluated against electron depth dose data and experimental backscatter results obtained using clinical radiotherapy beams. Different physical models and algorithms used in the codes give significantly different depth dose curves and electron backscattering factors. The default version of MCNP calculates electron depth dose curves which are too penetrating. The MCNP results agree better with experiment if the ITS-style energy-indexing algorithm is used. EGS4 underpredicts electron backscattering for high-Z materials. The results slightly improve if optimal PRESTA-I parameters are used. MCNP simulates backscattering well even for high-Z materials. To conclude the comparison, a timing study was performed. EGS4 is generally faster than MCNP and use of a large number of scoring voxels dramatically slows down the MCNP calculation. However, use of a large number of geometry voxels in MCNP only slightly affects the speed of the calculation.