A two-armed pattern in flickering maps of the nova-like variable UU aquarii

We report the analysis of a uniform sample of 31 light curves of the nova-like variable UU Aqr with eclipse-mapping techniques. The data were combined to derive eclipse maps of the average steady-light component, the long-term brightness changes, and the low- and high-frequency flickering components. The long-term variability responsible for the ""low-brightness`` and ""high-brightness`` states is explained in terms of the response of a viscous disk to changes of 20%-50% in the mass transfer rate from the donor star. Low- and high-frequency flickering maps are dominated by emission from two asymmetric arcs reminiscent of those seen in the outbursting dwarf nova IP Peg, and they are similarly interpreted as manifestations of a tidally induced spiral shock wave in the outer regions of a large accretion disk. The asymmetric arcs are also seen in the map of the steady light aside from the broad brightness distribution of a roughly steady-state disk. The arcs account for 25% of the steady-light flux and are a long-lasting feature in the accretion disk of UU Aqr. We infer an opening angle of 10 degrees +/- 3 degrees for the spiral arcs. The results suggest that the flickering in UU Aqr is caused by turbulence generated after the collision of disk gas with the density-enhanced spiral wave in the accretion disk.

Curiously composite structures of a retrotransposon and a complex repeat associated with chromosome ends of Rhynchosciara americana (Diptera: Sciaridae)

In Drosophila, telomere retrotransposons counterbalance the loss of telomeric DNA. The exceptional mechanism of telomere recovery characterized in Drosophila has not been found in lower dipterans (Nematocera). However, a retroelement resembling a telomere transposon and termed ""RaTART"" has been described in the nematoceran Rhynchosciara americana. In this work, DNA and protein sequence analyses, DNA cloning, and chromosomal localization of probes obtained either by PCR or by screening a genomic library were carried out in order to examine additional features of this retroelement. The analyses performed raise the possibility that RaTART represents a genomic clone composed of distinct repetitive elements, one of which is likely to be responsible for its apparent enrichment at chromosome ends. RaTART sequence in addition allowed to assess a novel subtelomeric region of R. americana chromosomes that was analyzed in this work after subcloning a DNA fragment from a phage insert. It contains a complex repeat that is located in the vicinity of simple and complex tandem repeats characterized previously. Quantification data suggest that the copy number of the repeat is significantly lower than that observed for the ribosomal DNA in the salivary gland of R. americana. A short insertion of the RaTART was identified in the cloned segment, which hybridized preferentially to subtelomeres. Like RaTART, it displays truncated sequences related to distinct retrotransposons, one of which has a conceptual translation product with significant identity with an endonuclease from a lepidopteran retrotransposon. The composite structure of this DNA stretch probably reflects mobile element activity in the subtelomeric region analyzed in this work.

Fractal structures in nonlinear plasma physics

Fractal structures appear in many situations related to the dynamics of conservative as well as dissipative dynamical systems, being a manifestation of chaotic behaviour. In open area-preserving discrete dynamical systems we can find fractal structures in the form of fractal boundaries, associated to escape basins, and even possessing the more general property of Wada. Such systems appear in certain applications in plasma physics, like the magnetic field line behaviour in tokamaks with ergodic limiters. The main purpose of this paper is to show how such fractal structures have observable consequences in terms of the transport properties in the plasma edge of tokamaks, some of which have been experimentally verified. We emphasize the role of the fractal structures in the understanding of mesoscale phenomena in plasmas, such as electromagnetic turbulence.

Group IV Graphene- and Graphane-Like Nanosheets

We performed a first-principles investigation on the structural and electronic properties of group IV (C, SiC, Si, Ge, and Sn) graphene-like sheets in flat and buckled configurations and the respective hydrogenated or fluorinated graphane-like ones. The analysis on the energetics, associated with the formation of those structures, showed that fluorinated graphane-like sheets are very stable and should be easily synthesized in the laboratory. We also studied the changes of the properties of the graphene-like sheets as a result of hydrogenation or fluorination. The interatomic distances in those graphane-like sheets are consistent with the respective crystalline ones, a property that may facilitate integration of those sheets within three-dimensional nanodevices.

From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

Vanadium complexes with 2-pyridineformamide thiosemicarbazones: In vitro studies of insulin-like activity

Reaction of VOCl(2) with 2-pyridineformamide thiosemicarbazone (H2Am4DH) and its N(4)-methyl (H2Am4Me), N(4)-ethyl (H2Am4Et) and N(4)-phenyl (H2Am4Ph) derivatives in ethanol gave as products [VO(H2Am4DH) Cl(2)] (1), [VO(H2Am4Me) Cl(2)] center dot 1/2HCl (2), [VO(H2Am4Et) Cl(2)] center dot HCl (3) and [VO(2Am4Ph) Cl] (4). Upon the dissolution of 1-4 in water, oxidation immediately occurs with the formation of [VO(2)(2Am4DH)] (5), [VO(2)(2Am4Me)] (6), [VO(2)(2Am4Et)] (7) and [VO(2)(2Am4Ph)] (8). The crystal and molecular structures of 5 and 6 were determined. Complexes 5-8 inhibited glycerol release in a similar way to that observed with insulin but showed a low enhancing effect on glucose uptake by rat adipocytes. (C) 2008 Elsevier B.V. All rights reserved.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Human endogenous RNAs: Implications for the immunomodulation of Toll-like receptor 3

Toll-like receptors (TLRs), a family of mammalian receptors, are able to recognize nucleic acids. TLR3 recognizes double-stranded (ds)RNA, a product of the replication of certain viruses. Polyinosinic-polycytidylic acid, referred to as poly(I:C), an analog of viral dsRNA, interacts with TLR3 thereby eliciting immunoinflammatory responses characteristic of viral infection or down-regulating the expression of chemokine receptor CXCR4. It is known that dsRNA also directly activates interferon (IFN)-induced enzymes, such as the RNA-dependent protein kinase (PKR). In the present study, the mRNA expression of TLR3, CXCR4, IFN gamma and PKR was investigated in a culture of peripheral blood mononuclear cells (PBMCs) stimulated with poly(I:C) and endogenous RNA from human PBMCs. No cytotoxic effect on the cells or on the proliferation of CD3(+), CD4(+) and CD8(+) cells was observed. TLR3 expression in the PBMCs in the presence of poly(I:C) was up-regulated 9.5-fold, and TLR3 expression in the PBMCs treated with endogenous RNA was down-regulated 1.8-fold (p=0.002). The same trend was observed for IFN gamma where in the presence of poly(I:C) an 8.7-fold increase was noted and in the presence of endogenous RNA a 3.1-fold decrease was observed. In the culture activated with poly(1:C), mRNA expression of CXCR4 increased 8.0-fold and expression of PKR increased 33.0-fold. Expression of these genes decreased in the culture treated with endogenous RNA when compared to the culture without stimulus. Thus, high expression of mRNA for TLR3, IFN gamma, CXCR4 and PKR was observed in the presence of poly(I:C) and low expression was observed in the cells cultured with endogenous RNA. In conclusion, TLR3 may play major physiological roles that are not in the context of viral infection. It is possible that RNA released from cells could contain enough double-stranded structures to regulate cell activation. The involvement of endogenous RNA in endogenous gene expression and its implications in the regulation thereof, are still being studied, and will have significant implications in the future.

Oxovanadium(IV) and (V) complexes of acetylpyridine-derived semicarbazones exhibit insulin-like activity

Reaction of 2-acetylpyridine semicarbazone (H2APS), 3-acetylpyridine semicarbazone (H3APS) and 4-acetylpyridine semicarbazone (H4APS) with [VO(acac)(2)] (acac = acetylacetonate) gave [VO(H2APS)(acac)(2)] (1), (VO(H3APS)(acac)(2)] (2) and [VO(4APS)(acac) (H2O)] center dot 1/2H(2)O (3). Oxidation of complex 1 in acetonitrile gave [VO2(2APS)] (4). The crystal structures of complexes 1 and 4 have been determined. Complexes 1-3 were able to enhance glucose uptake and to inhibit glycerol release from adipocytes, which indicate their potential to act as insulin-mimics. (C) 2008 Elsevier Ltd. All rights reserved.

Adiabatic propagation in potential structures

In this work the adiabatic approximation is applied to the propagation of matter waves in confined geometries like those experimentally realized in recent atom optical experiments. Adiabatic propagation along a channel is assumed not to mix the various transverse modes. Nonadiabatic corrections arise from the potential squeezing and bending. Here we investigate the effect of the former. Detailed calculations of two-dimensional propagation are carried out both exactly and in an adiabatic approximation. This offers the possibility to analyze the validity of adiabaticity criteria. A semiclassical (sc) approach, based on the sc Massey parameter is shown to be inadequate, and the diffraction due to wave effects must be included separately. This brings in the Fresnel parameter well known from optical systems. Using these two parameters, we have an adequate understanding of adiabaticity on the system analyzed. Thus quantum adiabaticity must also take cognizance of the intrinsic diffraction of matter waves.

Permian soft-sediment deformation structures related to earthquake in the Southern Sydney Basin, Eastern Australia

Sydney Basin is located in the eastern part of Australia, Lachlan Fold Belt, and between the New England Fold Belt. From the Sydney basin at the end of the Late Carboniferous to Middle Triassic experienced back-arc spreading to the foreland basin at different stages: back-arc spreading stage (Carboniferous ), A passive thermal subsidence stage (early in the Permian Berry) and load deflection extruding stage (in Broughton Permian - Triassic). This time at the Sydney basin on the eastern side of the New England Fold Belt for the island Background of the arc. As a result, back-arc in the Permian Basin of the South Sydney basin by the back-arc spreading the eastern side of the arc and trench subduction before the impact of strong seismic activity, the development of a series of earthquake-related seismites to form various types and Seismic activity related to the deformation of soft sediment structure. Permian Basin, South Sydney's soft sediment deformation including cracks in shock-fold, liquefied vein, volcanic sand, load structure, flame Construction, pillow-like structure, spherical structure, pillow Layer structure slump, and so breccia. To which the cracks in shock-fold fibrillation is a direct result of earthquake faults and folds; pillow is a layer of sand caused by the earthquake fibrillation dehydration, the formation of the sinking; liquefied vein, Volcanic sand for the liquefaction of sand penetration of the formation of earthquake fissures formed; load structure, flame Construction, pillow-like structure, spherical structure is affected by the earthquake fibrillation in the sand, mudstone interface because of the sinking sand, mud layer formed through ; Slump structures and breccia of the earthquake was caused by the gravitational collapse or the formation of the debris flow. Fissures, earthquake-fold, liquefied vein, volcanic sand, load structure, flame Construction, pillow-like structure, spherical structure, pillow-like layer Equivalent to the original earthquake rocks the plot, and the slump structures and breccia of the plot belong to different earthquake rocks.

The prediction of damage condition in regards to damage factor influence of light structures on expansive soils in Victoria, Australia

This paper proposes a neural network model using genetic algorithm for a model for the prediction of the damage condition of existing light structures founded in expansive soils in Victoria, Australia. It also accounts for both individual effects and interactive effects of the damage factors influencing the deterioration of light structures. A Neural Network Model was chosen because it can deal with 'noisy' data while a Genetic Algorithm was chosen because it does not get `trapped' in local optimum like other gradient descent methods. The results obtained were promising and indicate that a Neural Network Model trained using a Genetic Algorithm has the ability to develop an interactive relationship and a Predicted Damage Conditions Model.

Inorganic-organic hybrids of the p,p'-diphenylmethylenediphosphinate, pcp2-. synthesis, characterization and XRPD structures of [Sn(pcp)] and [Cu(pcp)]

Two new inorganic-organic polymeric hybrids [Sn(pcp)] and [Cu(pcp)], pcp = CH₂(PhPO₂)₂^2-, have been synthesized and structurally chracterized. The tin derivative has been obtained by reaction of the p,p'-diphenylmethylenediphosphinic acid (H₂pcp) in water with SnCl₂·2H₂O, while the copper derivative has been synthesized through a hydrothermal reaction from the same H₂pcp acid and Cu(O₂CMe)₂·H₂O. The structures of these compounds have been solved "ab initio" by X-ray powder diffraction (XRPD) data. [Sn(pcp)] has a ladder-like polymeric structure, with tin(II) centers bridged by diphenylmethylenediphosphinate ligands, and alternating six- and eight-membered rings. The hemilectic coordination around the metal shows the tin(II) lone pair to be operative, resulting in significant interaction mainly with a C-C bond of one phenyl ring. The [Cu(pcp)] complex displays a polymeric columnar structure formed by two intersecting sinusoidal ribbons of copper(II) ions bridged by the bifunctional phosphinate ligands. The intersections of the ribbons are made of dimeric units of pentacoordinated copper ions. Crystal data for [Sn(pcp)]: monoclinic, space group P2₁Ic, a = 11.2851(1), b = 15.4495(6), c = 8.6830(1) Å, ^β= 107.546(1)°, V = 1443.44(9) Å, Z = 4. Crystal data for [Cu(pcp)]: triclinic, space group P, a = 10.7126(4), b = 13.0719(4), c = 4.9272(3) Å, α= 92.067(5), β= 95.902(7), γ= 87.847(4)°, V = 685.47(7), Z = 2. The tin compound has been characterized by ¹¹⁹Sn MAS NMR (magic-angle spinning NMR), revealing asymmetry in the valence electron cloud about tin. Low-temperature magnetic measurements of the copper compound have indicated the presence of weak antiferromagnetic interactions below 50 K.

Exploiting monge structures in optimum subwindow search

Optimum subwindow search for object detection aims to find a subwindow so that the contained subimage is most similar to the query object. This problem can be formulated as a four dimensional (4D) maximum entry search problem wherein each entry corresponds to the quality score of the subimage contained in a subwindow. For n x n images, a naive exhaustive search requires O(n⁴) sequential computations of the quality scores for all subwindows. To reduce the time complexity, we prove that, for some typical similarity functions like Euclidian metric, χ² metric on image histograms, the associated 4D array carries some Monge structures and we utilise these properties to speed up the optimum subwindow search and the time complexity is reduced to O(n³). Furthermore, we propose a locally optimal alternating column and row search method with typical quadratic time complexity O(n²). Experiments on PASCAL VOC 2006 demonstrate that the alternating method is significantly faster than the well known efficient subwindow search (ESS) method whilst the performance loss due to local maxima problem is negligible.

A systems approach to shape and topology optimisation of mechanical structures

Optimisation techniques have become more and more important as the possibility of simulating complex mechanical structures has become a reality. A common tool in the layout design of structural parts is the topology optimisation method, which finds an optimum material distribution within a given geometrical design space to best meet loading conditions and constraints. Another important method is shape optimisation, which optimises weight given parametric geometric constraints. In the case of complex shaped parts or elaborate assemblies, for example automobile body structures, shape optimisation is still hard to do; mainly due to the difficulty in translating shape design parameters into meaningful analysis models. Tools like the parametric geometry package SFE CONCEPT are designed to mitigate these issues. Nevertheless, shape methods usually cannot suggest new load path configurations, while topology methods are often confined to single parts. To overcome these limitations the authors have developed a method that combines both approaches into an Integral Shape/Topology Method (IST) that is capable of finding new optimal solutions. This is achieved by an automated optimisation loop and can be applied for both thin walled structures as well as solid 3D geometries. When optimising structures by applying IST, global optimum solutions can be determined that may not be obtained with isolated shape- or topology-optimisation methods.