Projected iterative algorithms for complex symmetric systems arising in magnetized multicomponent transport

We investigate iterative algorithms for solving complex symmetric constrained singular systems arising in magnetized multicomponent transport. The matrices of the corresponding linear systems are symmetric with a positive semi-definite real part and an imaginary part with a compatible nullspace. We discuss well posedness, the symmetry of generalized inverses and Cholesky methods. We investigate projected stationary iterative methods as well as projected orthogonal residuals algorithms generalizing previous results on real systems. As an application, we consider the linear systems arising from the kinetic theory of gases and providing transport coefficients of partially ionized gas mixtures subjected to a magnetic field.     

Dynamics of Decision Making in Animal Group Motion

We analyze a continuous-time model of a multi-agent system motivated by simulation studies on dynamics of decision making in animal groups in motion. Each individual moves at constant speed in the plane and adjusts its heading in response to relative headings of others in the population. The population includes two subgroups that are “informed” such that individuals in each subgroup have a preferred direction of motion. The model exhibits fast and slow time scales allowing for a reduction in the dimension of the problem. The stable solutions for the reduced model correspond to compromise by individuals with conflicting preferences. We study the global phase space for the proposed reduced model by computing equilibria and exploring stability and bifurcations. B. Nabet’s and N.E. Leonard’s work is supported in part by AFOSR grant FA9550-07-1-0-0528 and ONR grants N00014-02-1-0826 and N00014-04-1-0534. I.D. Couzin’s work was supported by the Royal Society, Balliol College and EPSRC grants GR/S04765/01 and GR/T11234/01, a Searle Scholar Award and DARPA grant HR001-05-1-0057. S.A. Levin’s work was supported in part by DARPA grant HR0011-05-1-0057 and NSF grant EF-0434319.     

Superstructure in RE2-xFe4Si14-y (RE = Y, Gd-Lu) characterized by diffraction, electron microscopy, and Mössbauer spectroscopy

Ternary rare-earth iron silicides RE(2-x)Fe4Si(14-y) (RE = Y, Gd-Lu; x approximately equal to 0.8; y approximately equal to 4.1) crystallize in the hexagonal system with a approximately equal to 3.9 A, c approximately equal to 15.3 A, Pearson symbol hP20-4.9. Their structures involve rare-earth silicide planes with approximate compositions of "RE1.2Si1.9" alternating with beta-FeSi2-derived slabs and are part of a growing class of rare-earth/transition-metal/main-group compounds based on rare-earth/main-group element planes interspersed with (distorted) fluorite-type transition-metal/main-group element layers. The rare-earth silicide planes in the crystallographic unit cells show partial occupancies of both the RE and Si sites because of interatomic distance constraints. Transmission electron microscopy reveals a 4a x 4b x c superstructure for these compounds, whereas further X-ray diffraction experiments suggest ordering within the ab planes but disordered stacking along the c direction. A 4a x 4b structural model for the rare-earth silicide plane is proposed, which provides good agreement with the electron microscopy results and creates two distinct Fe environments in a 15:1 ratio. Fe-57 M?ssbauer spectra confirm these two different iron environments in the powder samples. Magnetic susceptibilities suggest weak (essentially no) magnetic coupling between rare-earth elements, and resistivity measurements indicate poor metallic behavior with a large residual resistivity at low temperatures, which is consistent with disorder. First-principles electronic-structure calculations on model structures identify a pseudogap in the densities of states for specific valence-electron counts that provides a basis for a useful electron-counting scheme for this class of rare-earth/transition-metal/main-group compounds.     

Protein profile of osteoarthritic human articular cartilage using tandem mass spectrometry

Articular cartilage contains both chondrocyte cells and extracellular matrix (ECM) components. Currently, comprehensive information concerning the protein composition of human articular cartilage tissue is somewhat lacking. In this report we detail the use of tandem mass spectrometry (MS/MS) for a preliminary global identification of proteins from human articular knee cartilage tissue from patients diagnosed with osteoarthritis. Knee cartilage supernatant was fractionated using one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE), in-gel digested and peptide sequences were then determined by performing on-line nano-liquid chromatography (LC)/MS/MS experiments using an ion trap mass spectrometer. Altogether, over 100 different proteins from nearly 700 unique peptide sequences were detected by MS/MS. The majority of the proteins identified are involved in ECM organization (35%), signal transduction and cell communication (14%), immune response (11%) and metabolism and energy pathways (11%). Proteins observed included several well-known cartilage components as well as lower abundant lesser known ECM proteins. Possible degradation products in the cartilage sample, such as from cartilage link protein, could also be detected by our mass spectrometry methods. We show here that mass spectrometry can be utilized as a tool for a fast, accurate and sensitive analysis of a complex mixture of cartilage proteins. It is believed that this type of proteomic analysis will aid future work centered on investigating the pathology of this and other related joint diseases.     

Building up key segments of N-glycans in the gas phase: intrinsic structural preferences of the alpha(1,3) and alpha(1,6) dimannosides

The intrinsic conformer specific vibrational spectra of two important subunits of the core pentasaccharide of N-linked glycans, the alpha(1,3) and alpha(1,6) dimannosides, have been recorded in the gas phase. Coupling these measurements with a computational exploration of their conformational landscapes has enabled their conformational assignment and has identified characteristic vibrational signatures associated with particular conformational families-including those that do or do not display inter-ring hydrogen bonding across the glycosidic linkage. In addition, the IR spectra of the monosaccharide moieties provide benchmarks, through which the conformational assignments can be refined. This introduces a general concept of modularity and secondary structure in oligosaccharides--essential for the success of similar studies on larger oligosaccharides in the future.     

De novo structure-based design of bisurea hosts for tetrahedral oxoanion guests

This paper presents a computational approach to the deliberate design of improved host architectures. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential structures. The efficacy of this computer-aided design methodology is illustrated with a search for bisurea podands that are structurally organized for complexation with tetrahedral oxoanions.     

Production and reactions of organic-soluble lanthanide complexes of the monolacunary Dawson [alpha1-P2W17O61]10- polyoxotungstate

The incorporation of lanthanides into polyoxometalates provides entry to new classes of potentially useful materials that combine the intrinsic properties of both constituents. To utilize the [alpha1-Ln(H2O)4P2W17O61]7- species in applications of catalysis and development of luminescent materials, the chemistry of this family of lanthanide polyoxometalates in organic solvents has been developed. Organic-soluble polyoxometalate-lanthanide complexes TBA5H2[alpha1-Ln(H2O)4P2W17O61] (Ln = La(III), Sm(III), Eu(III), Yb(III)) were prepared and characterized by elemental analysis, acid-base titration, IR, 31P NMR, and mass spectrometry. The synthetic procedure involves a cation metathesis reaction in aqueous solution under strict pH control. A solid-liquid-phase transfer protocol yielded a unique species (TBA)8K3[Yb(alpha1-YbP2W17O61)2] with three ytterbium ions and two [alpha1-P2W17O61]10- polyoxotungstates. A centrosymmetric dimeric complex [{alpha1-La(H2O)4P2W17O61}2]14- was crystallized from aqueous solution and characterized by X-ray diffraction. ESI mass spectral analysis of the complexes TBA5H2[alpha1-Ln(H2O)4P2W17O61] shows that similar dimers exist in organic solution, in particular for the early lanthanides. Fragmentation in the mass spectrometer of the complexes from dry acetonitrile solution involves double protonation of an oxo ligand and loss of one water molecule. Low mass tungstate fragments combine into [(WO3)n]2- (n = 1-5) ions and their condensation products with phosphate. Reaction of TBA5H2[alpha1-Eu(H2O)4P2W17O61] with 1,10-phenanthroline or 2,2'-bipyridine showed an increase of the europium luminescence. This result is explained by the formation of a ternary complex of [alpha1-Eu(H2O)4P2W17O61]7- and two sensitizing ligands.     

Ultraviolet B light stimulates interleukin-20 expression by human epithelial keratinocytes

The proinflammatory cytokine interleukin-20 (IL-20) may exert the majority of its activity in the skin. We examined the effect of various treatments including several forms of phototherapy on IL-20 expression using cultured normal human epithelial keratinocytes (NHEK). Broadband UVB light, recombinant (r) IL-1 and rIL-8 increased, while hydrocortisone reduced, NHEK supernatant IL-20 levels. Elevation of NHEK IL-20 mRNA and maximal supernatant IL-20 levels occurred with a UVB light dose (40 mJ cm(-2)) that reduced cell viability by approximately 50%. While this UVB light dose also elevated supernatant IL-1 alpha and IL-8 levels, antibody neutralization studies indicated that neither of these cytokines was directly responsible for this increase in IL-20 expression. However, the elevation in IL-20 levels was fully inhibited by the p38 mitogen-activated protein kinase (MAPK) inhibitor SB-203580, suggesting involvement of this stress signaling pathway in this UVB light response. Photodynamic therapy (PDT) with the photosensitizer lemuteporfin, UVA light, cisplatin, lipopolysaccharide (LPS), tumor necrosis factor-alpha (TNF-alpha) or recombinant interferon-gamma (rIFN-gamma) either had little effect or decreased NHEK supernatant IL-20 levels. Reduced IL-20 levels paralleled the cytotoxic actions of PDT, UVA light or cisplatin and the antiproliferative effect of rIFN-gamma. Neither rIL-20 supplementation nor anti-IL-20 antibody treatments affected cell viability indicating that soluble IL-20 did not affect the short-term survival of UVB light-irradiated NHEK. Stimulation of IL-20 expression in keratinocytes by UVB light suggests that this cytokine might participate in skin responses to this ever-present environmental factor and potentially has a role in UV light-associated dermatoses.     

Reactions with dye free radicals reveal weak redox properties of drugs

The calcium release channel (CRC) of the skeletal sarcoplasmic reticulum is rich in thiol groups and is strongly regulated by covalent modification of these thiols. Oxidizing reagents activate the release channel, whereas reducing reagents inhibit the channel. However, most CRC regulators are not thiol reagents. Here, we propose that reversible redox interactions are involved in regulation of the CRC by nonthiol reagents. This hypothesis was tested with several CRC regulators. The local anesthetics tetracaine, procaine and QX-314, which block the CRC, behaved as electron donors in reactions with dye free radicals. In contrast, ryanodine, caffeine, doxorubicin and daunorubicin, compounds known to activate the release channel, all accepted electrons from dye anion radicals. Moreover, release of Ca2+ from SR initiated by doxorubicin (acceptor) was antagonized by local anesthetics (donors). Based on the redox characterization of CRC modulators, we propose a functional model in which channel inhibitors and activators act as weak electron donors and acceptors, respectively, and shift the thiol-disulfide balance within the release protein. The consequence of this model is that, in spite of the chemical diversity of CRC modulators, a common mechanism of channel regulation involves the transient exchange of electrons between the activator/inhibitor and the CRC.