Position preference and diffusion path of an oxygen ion in apatite-type lanthanum silicate La9.33Si6O26: A density functional study

Using density functional theory, we investigated the position preference and diffusion mechanisms of interstitial oxygen ions in lanthanum silicate La9.33Si6O26, which is an apatite-structured oxide and a promising candidate electrolyte material for solid oxide fuel cells. The reported lanthanum vacancies were explicitly taken into account by theoretically determining their arrangement with a supercell model. The most stable structures and the formation energies of oxygen interstitials were determined for each charged state. It was found that the double-negatively charged state is stable over a wide range of the Fermi level, and that the excess oxygen ions form split interstitials with the original oxygen ions, while the neutral and the single-negatively charged states preferably form molecular oxygen. These species were found near the lanthanum vacancy site. The theoretically determined migration pathway along the c-axis essentially follows an interstitialcy mechanism. The obtained migration barrier is sensitive to the charge state, and is also affected by the lanthanum vacancy. The barrier height of the double-negatively charged state was calculated to be 0.58 eV for the model structure, which is consistent with the measured activation energy.

Alignment of the ALICE Inner Tracking System with cosmic-ray tracks

ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 micron in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10^5 charged tracks from cosmic rays that have been collected during summer 2008, with the ALICE solenoidal magnet switched off.

Group fission in Nilgiri langurs (Presbytis johnii)

During a field study on habituated groups of wild Nilgiri langurs (Presbytis johnii), four cases of group fission were observed which differed markedly from group changes reported in other species of the same genus. All fissions occurred in groups with more than one mature male and roughly coincided with the onset of loud call vocalization by the second mature male group member. As a result of the fission the founder group factions acquired the structure of a onemale group. The filial factions consisted of both mature males and females and occupied, at least temporarily, a part of, or an area adjacent to, the founder group. During fission, the amount of aggressive interactions between the two mature males increased. However, the majority of agonistic interactions involved ritualized threat and intimidation behavior without physical aggression. In at least three cases the two mature males involved in the fission had not joined recently but had lived in these groups for three years or more. Although the presence of all male bands and single males in the two study populations indicate that male replacement by invasive takeovers may occur, it is suggested that in Nilgiri langurs, noninvasive fissions are probably another common mechanism for the foundation and maintenance of bisexual one-male groups.

Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7(+) (spslu7(+)) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3' splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3' splice site distance, intron length, and the impact of its A/U content at the 5' end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1(+), a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.

Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7(+) (spslu7(+)) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3' splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3' splice site distance, intron length, and the impact of its A/U content at the 5' end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1(+), a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species-Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast.

Vortex dynamics in the studies of looping in tropical cyclone tracks

This paper proposes criteria for predicting the tendency of looping in tropical cyclone tracks using the approach of vortex dynamics. We model the asymmetric structure of a cyclone by a system of vortex patches. The evolution of such system of vortices is simulated by the method of contour dynamics. A new set of exact analytic formulas for contour dynamics calculations is derived, which is shown to be more computationally effective. Based on point-vortex models, we derive analytic formulas for the criteria of looping in a cyclone track. From numerical experiments, the simulated trajectories obtained from the point-vortex system and vortex patch system agree quite well. Hence, the looping criteria obtained from the point-vortex system can be applied by forecasters to stay alert for tendency of looping in a cyclone track. To demonstrate the applicability of the proposed criteria, the trajectory of Typhoon Yancy (9012), whose field data are available from ''TCM-90'', is simulated. The case study shows that the asymmetric structure similar to the pattern of a beta gyre is responsible for its recurvature when Yancy landed Fujian Province, China on 20 August 1990.

Fission of solitary wave in stratified fluid

In this paper, we study the fission of a solitary wave in the stratified fluid with a free surface. It has been discovered that there is no difference between the fissions of the internal solitary waves in odd or even modes, and the effect of the stratification on the fission of a surface solitary wave can almost be neglected

Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

Gene fission and fusion, the processes by which a single gene is split into two separate genes and two adjacent genes are fused into a single gene, respectively, are among the primary processes that generate new genes(1-4). Despite their seeming reversibi

In-plane critical current density measurements of straight and curved tracks in RABiTS-MOD coated conductors

Depending on the temperature and the magnitude and orientation of an external magnetic field, the critical current density, J c , of a coated conductor can be limited either by the properties of the grain boundaries or by those of the grains. In order to ascertain what governs J c under different conditions, we have measured straight and curved tracks, patterned into RABiTS-MOD samples, while a magnetic field was swept in the plane of the films. Significantly different results were obtained at different field and temperature ranges, which we were able to attribute to J c being limited by either grain boundaries or grains.