ALBERT

Description: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states.

Description: In the quest for high- k dielectrics with decent magnetodielectric (MD) response, ball-milled processed (Li, Ti) doped NiO ceramics have been evaluated by various experimental techniques. Magnetic properties in these ceramics manifest with a pronounced anomaly appearing at ∼260 K, suggesting ferrimagnetic phase (related to cluster magnetism) and co-existence with a glassy-like antiferromagnetic phase at ∼7 K. Room temperature neutron diffraction pattern shows the existence of short-range magnetic correlations. In the magnetically ordered state below 250 K, the magnetic structure is found to be phase coexistence of G -type antiferromagnet and ferrimagnet. Impedance spectroscopy measurements over a wide temperature range can be perfectly described with appropriate microstructural model (internal barrier layer capacitor), based on domain and domain boundary relaxations, justifying the enhancement of the dielectric response. The low-temperature (T 

Description: We study the influence of electrical poling, carried out at room temperature, on the structure and magnetism of Pb(Fe 0.5 Nb 0.5 )O 3 by analyzing the differences observed in structural and magnetic properties before and after the electrical poling. The changes observed in magnetization of Pb(Fe 0.5 Nb 0.5 )O 3 before and after electrical poling exhibit considerably strong converse magnetoelectric effect at room temperature. In addition, the strengthening of Fe/Nb-O bond due to electrical poling is discussed on the basis of Raman spectral studies and analysis of neutron diffraction patterns. The potential tunability of magnetization with electrical poling can be an ideal tool for realization of application potential of this multiferroic material.

Description: The molecular mechanism of antimony-resistant Leishmania donovani (SbRLD)–driven up-regulation of IL-10 and multidrug-resistant protein 1 (MDR1) in infected macrophages (Mϕs) has been investigated. This study showed that both promastigote and amastigote forms of SbRLD, but not the antimony-sensitive form of LD, express a unique glycan with N-acetylgalactosamine as a terminal...

Description: Author(s): J. Nehrkorn, S. Mukherjee, S. Stuiber, H. Mutka, Th. Strässle, G. Christou, and O. Waldmann Structurally, the two mixed-valence manganese disks Mn 7 -11 and Mn 7 -16 differ only in the peripheral ligand but, as a result of a subtle interplay of intramolecular exchange interactions, differ strongly in their magnetic properties, e.g., Mn 7 -11 possesses a ground-state spin of S =11 and Mn 7 -16 of S =... [Phys. Rev. B 86, 134417] Published Fri Oct 19, 2012

Description: Evidence of intense naticid drilling predation occurs on turritelline prey from a turritelline-dominated assemblage (TDA) which lies below the K-T boundary sections in Rajahmundry, India. Previously, it was believed that drilling frequency (DF) on turritelline taxa was low during the Cretaceous. Data from the study area indicates that the Cenozoic level of predation on turritelline taxa already occurred by the Late Cretaceous in the study area. The paleobiogeography of naticid predation is extended from the western world to India, which was located in the southern hemisphere during the Cretaceous. In addition to the high drilling frequency, the Indian fossil record shows that many aspects of naticid behavior; for example, size and site stereotypy, which are characteristic features of Cenozoic predators, were also established by the Late Cretaceous. These data support previous views that the Mesozoic Marine Revolution had minimal influence on morphological change in Late Cretaceous turritelline gastropods and that turritelline gastropods may have developed behavioral and/or physiological antipredatory adaptations. TDAs in general may indicate tremendous fecundity that may act as a buffer against high juvenile mortality due to predation.

Description: 〈span〉〈div〉Abstract〈/div〉A calc-silicate rock from part of the Chotanagpur Granite Gneiss Complex, East India, develops veins and patches of vesuvianite (F: 2.3–3.9 apfu, Fe〈sup〉3+〈/sup〉: 1.7–2.1 apfu) and garnet (Gr〈sub〉71–80〈/sub〉Alm〈sub〉12–17〈/sub〉Adr〈sub〉1–9〈/sub〉) proximal to amphibole-bearing quartzo-feldspathic pegmatitic veins. The host calc-silicate rock exhibits a prominent gneissic banding that is defined by alternate clinopyroxene- and plagioclase-rich layers. The vesuvianite-garnet veins are both parallel and cross-cutting the gneissic banding of the host calc-silicate rock. Two contrasting mineralogical domains that are rich in garnet and vesuvianite, respectively, develop within the vesuvianite-garnet veins. Textural studies support the view that the garnet- and vesuvianite-rich domains preferentially develop in the clinopyroxene- and plagioclase-rich layers of the host calc-silicate rocks, respectively. Some of the vesuvianite-rich domains of the veins develop the assemblage vesuvianite + quartz + calcite + anorthite (as a result of the reaction diopside + quartz + calcite + anorthite = vesuvianite) that was deemed metastable in the commonly used qualitative isobaric 〈span〉T-X〈/span〉〈sub〉CO〈sub〉2〈/sub〉〈/sub〉 topology in the system CaO-MgO-Al〈sub〉2〈/sub〉O〈sub〉3〈/sub〉-SiO〈sub〉2〈/sub〉-H〈sub〉2〈/sub〉O-CO〈sub〉2〈/sub〉 (CMASV).Using an internally consistent thermodynamic database, quantitative petrogenetic grids in the 〈span〉P-T〈/span〉 and isobaric 〈span〉T-X〈/span〉〈sub〉CO〈sub〉2〈/sub〉〈/sub〉 spaces have been computed in the CMASV system. The influence of the non-CMASV components (e.g., Na, Fe〈sup〉3+〈/sup〉, F) on the CMASV topologies have been discussed using the published 〈span〉a-X〈/span〉 relations of the minerals. Our study shows topological inversion in the isobaric 〈span〉T-X〈/span〉〈sub〉CO〈sub〉2〈/sub〉〈/sub〉 space that primarily depends upon the composition of the vesuvianite. The quantitative CMASV topologies presented in this study successfully explain the stabilities of the natural vesuvianite-bearing assemblages including the paradoxical assemblage vesuvianite + quartz + calcite + anorthite.Application of the activity-corrected CMASV topology suggests that infiltration of F-bearing oxidizing aqueous fluids into the calc-silicate rocks develop the vesuvianite-garnet veins in the studied area. A genetic link between quartzo-feldspathic pegmatites and the vesuvianite-garnet veins seems plausible.This study demonstrates controls of topological inversion in the complex natural system, owing to which certain mineral assemblages develop in nature that are otherwise deemed metastable in one set of reaction geometry.〈/span〉