Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Force-free equilibria of magnetized jets

Force-free equilibrium configurations of magnetic-pressure-dominated magnetized supersonic jets confined by slowly varying external pressure are investigated analytically. For the case where internal dissipation mechanisms are active, the lowest-energy field configuration is found to be the superposition of an axisymmetric mode and a helical mode with a wavelength equal to 5 times the jet radius, and the pressure below which the nonaxisymmetric mode becomes energetically favorable is given as 2700 times the product of the 4th power of the magnetic helicity per unit length and the -6th power of the magnetic flux. A model of the total and polarized emission of such a configuration is developed and applied to the extended well-collimated astronomically resolved jet NGC 6251. The model is shown to reproduce significant features such as transverse oscillations of the ridge line, width oscillations and emission knots, the projected magnetic-field configuration, oscillations of the degree of polarization, and the distribution of the Faraday rotation measure.

Magnetic energy dissipation in force-free jets

It is shown that a magnetic-pressure-dominated, supersonic jet which expands (or contracts) in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to take place, the effective reconnection time must be a fraction ɛ ⪉ 1 of the expansion time. The amount of energy dissipation is calculated, and it is concluded that magnetic energy dissipation could, in principle, power the observed synchrotron emission in extragalactic radio jets such as NGC 6251. However, this mechanism is only viable if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

Mechanism of failure in a free-standing Pt-aluminide bond coat during tensile testing at room temperature

The room temperature (RT) tensile behaviour of a free-standing high activity Pt-aluminide bond coat has been evaluated by microtensile testing technique. The coating had a typical three-layer microstructure. The stress-strain plot for the free-standing coating was linear, indicating the coating to be brittle at RT. Different fracture features were observed across the coating layers, namely quasi-cleavage in the outer layer and inner interdiffusion zone, and cleavage in the intermediate layer. By employing interrupted tensile test and observing the cross-sectional microstructure of the tested specimens, it was determined that failure of the microtensile samples occurred by the initiation of a single crack in the intermediate layer of the coating and its subsequent inside-out propagation. Such a mechanism of failure has been explained in terms of the fracture features observed across the sample thickness. This mechanism of failure is consistent with fracture toughness values of the individual coating layers. (C) 2009 Elsevier B.V. All rights reserved.

A germanium/single-walled carbon nanotube composite paper as a free-standing anode for lithium-ion batteries

Paper-like free-standing germanium (Ge) and single-walled carbon nanotube (SWCNT) composite anodes were synthesized by the vacuum filtration of Ge/SWCNT composites, which were prepared by a facile aqueous-based method. The samples were characterized by X-ray diffraction, field emission scanning electron microscopy, and transmission electron microscopy. Electrochemical measurements demonstrate that the Ge/SWCNT composite paper anode with the weight percentage of 32% Ge delivered a specific discharge capacity of 417 mA h g-1 after 40 cycles at a current density of 25 mA g-1, 117% higher than the pure SWCNT paper anode. The SWCNTs not only function as a flexible mechanical support for strain release, but also provide excellent electrically conducting channels, while the nanosized Ge particles contribute to improving the discharge capacity of the paper anode.

3D hierarchical rutile TiO2 and metal-free organic sensitizer producing dye-sensitized solar cells 8.6% conversion efficiency

Three-dimensional (3D) hierarchical nanoscale architectures comprised of building blocks, with specifically engineered morphologies, are expected to play important roles in the fabrication of 'next generation' microelectronic and optoelectronic devices due to their high surface-to-volume ratio as well as opto-electronic properties. Herein, a series of well-defined 3D hierarchical rutile TiO2 architectures (HRT) were successfully prepared using a facile hydrothermal method without any surfactant or template, simply by changing the concentration of hydrochloric acid used in the synthesis. The production of these materials provides, to the best of our knowledge, the first identified example of a ledgewise growth mechanism in a rutile TiO2 structure. Also for the first time, a Dye-sensitized Solar Cell (DSC) combining a HRT is reported in conjunction with a high-extinction-coefficient metal-free organic sensitizer (D149), achieving a conversion efficiency of 5.5%, which is superior to ones employing P25 (4.5%), comparable to state-of-the-art commercial transparent titania anatase paste (5.8%). Further to this, an overall conversion efficiency 8.6% was achieved when HRT was used as the light scattering layer, a considerable improvement over the commercial transparent/reflector titania anatase paste (7.6%), a significantly smaller gap in performance than has been seen previously.

Genistein and 17β-estradiol fatty acid esters in blood and adipose tissue and the structure-related antioxidant activity of estrogens on lipoproteins

Soy-derived phytoestrogen genistein and 17β-estradiol (E2), the principal endogenous estrogen in women, are also potent antioxidants protecting LDL and HDL lipoproteins against oxidation. This protection is enhanced by esterification with fatty acids, resulting in lipophilic molecules that accumulate in lipoproteins or fatty tissues. The aims were to investigate, whether genistein becomes esterified with fatty acids in human plasma accumulating in lipoproteins, and to develop a method for their quantitation; to study the antioxidant activity of different natural and synthetic estrogens in LDL and HDL; and to determine the E2 esters in visceral and subcutaneous fat in late pregnancy and in pre- and postmenopause. Human plasma was incubated with [3H]genistein and its esters were analyzed from lipoprotein fractions. Time-resolved fluoroimmunoassay (TR-FIA) was used to quantitate genistein esters in monkey plasma after subcutaneous and oral administration. The E2 esters in women s serum and adipose tissue were also quantitated using TR-FIA. The antioxidant activity of estrogen derivatives (n=43) on LDL and HDL was assessed by monitoring the copper induced formation of conjugated dienes. Human plasma was shown to produce lipoprotein-bound genistein fatty acid esters, providing a possible explanation for the previously reported increased oxidation resistance of LDL particles during intake of soybean phytoestrogens. Genistein esters were introduced into blood by subcutaneous administration. The antioxidant effect of estrogens on lipoproteins is highly structure-dependent. LDL and HDL were protected against oxidation by many unesterified, yet lipophilic derivatives. The strongest antioxidants had an unsubstituted A-ring phenolic hydroxyl group with one or two adjacent methoxy groups. E2 ester levels were high during late pregnancy. The median concentration of E2 esters in pregnancy serum was 0.42 nmol/l (n=13) and in pre- (n=8) and postmenopause (n=6) 0.07 and 0.06 nmol/l, respectively. In pregnancy visceral fat the concentration of E2 esters was 4.24 nmol/l and in pre- and postmenopause 0.82 and 0.74 nmol/l. The results from subcutaneous fat were similar. In serum and fat during pregnancy, E2 esters constituted about 0.5 and 10% of the free E2. In non-pregnant women most of the E2 in fat was esterified (the ester/free ratio 150 - 490%). In postmenopause, E2 levels in fat highly exceeded those in serum, the majority being esterified. The pathways for fatty acid esterification of steroid hormones are found in organisms ranging from invertebrates to vertebrates. The evolutionary preservation and relative abundance of E2 esters, especially in fat tissue, suggest a biological function, most likely in providing a readily available source of E2. The body s own estrogen reservoir could be used as a source of E2 by pharmacologically regulating the E2 esterification or hydrolysis.

Organic–inorganic bismuth (III)-based material: A lead-free, air-stable and solution-processable light-absorber beyond organolead perovskites

Methylammonium bismuth (III) iodide single crystals and films have been developed and investigated. We have further presented the first demonstration of using this organic–inorganic bismuth-based material to replace lead/tin-based perovskite materials in solution-processable solar cells. The organic–inorganic bismuth-based material has advantages of non-toxicity, ambient stability, and low-temperature solution-processability, which provides a promising solution to address the toxicity and stability challenges in organolead- and organotin-based perovskite solar cells. We also demonstrated that trivalent metal cation-based organic–inorganic hybrid materials can exhibit photovoltaic effect, which may inspire more research work on developing and applying organic-inorganic hybrid materials beyond divalent metal cations (Pb (II) and Sn (II)) for solar energy applications.

Free-volume dependent pressure sensitivity of Zr-based bulk metallic glass

Instrumented indentation experiments on a Zr-based bulk metallic glass (BMG) in as-cast, shot-peened and structurally relaxed conditions were conducted to examine the dependence of plastic deformation on its structural state. Results show significant differences in hardness, H, with structural relaxation increasing it and shot peening markedly reducing it, and slightly changed morphology of shear bands around the indents. This is in contrast to uniaxial compressive yield strength, sigma(y), which remains invariant with the change in the structural state of the alloys investigated. The plastic constraint factor, C = H/sigma(y), of the relaxed BMG increases compared with that of the as-cast glass, indicating enhanced pressure sensitivity upon annealing. In contrast, C of the shot-peened layer was found to be similar to that observed in crystalline metals, indicating that severe plastic deformation could eliminate pressure sensitivity. Microscopic origins for this result, in terms of shear transformation zones and free volume, are discussed.

Assessment of code bias variations of BDS triple-frequency signals and their impacts on ambiguity resolution for long baselines

Carrier phase ambiguity resolution over long baselines is challenging in BDS data processing. This is partially due to the variations of the hardware biases in BDS code signals and its dependence on elevation angles. We present an assessment of satellite-induced code bias variations in BDS triple-frequency signals and the ambiguity resolutions procedures involving both geometry-free and geometry-based models. First, since the elevation of a GEO satellite remains unchanged, we propose to model the single-differenced fractional cycle bias with widespread ground stations. Second, the effects of code bias variations induced by GEO, IGSO and MEO satellites on ambiguity resolution of extra-wide-lane, wide-lane and narrow-lane combinations are analyzed. Third, together with the IGSO and MEO code bias variations models, the effects of code bias variations on ambiguity resolution are examined using 30-day data collected over the baselines ranging from 500 to 2600 km in 2014. The results suggest that although the effect of code bias variations on the extra-wide-lane integer solution is almost ignorable due to its long wavelength, the wide-lane integer solutions are rather sensitive to the code bias variations. Wide-lane ambiguity resolution success rates are evidently improved when code bias variations are corrected. However, the improvement of narrow-lane ambiguity resolution is not obvious since it is based on geometry-based model and there is only an indirect impact on the narrow-lane ambiguity solutions.

Geometry-free stochastic analysis of BDS triple frequency signals

The paper presents a geometry-free approach to assess the variation of covariance matrices of undifferenced triple frequency GNSS measurements and its impact on positioning solutions. Four independent geometryfree/ ionosphere-free (GFIF) models formed from original triple-frequency code and phase signals allow for effective computation of variance-covariance matrices using real data. Variance Component Estimation (VCE) algorithms are implemented to obtain the covariance matrices for three pseudorange and three carrier-phase signals epoch-by-epoch. Covariance results from the triple frequency Beidou System (BDS) and GPS data sets demonstrate that the estimated standard deviation varies in consistence with the amplitude of actual GFIF error time series. The single point positioning (SPP) results from BDS ionosphere-free measurements at four MGEX stations demonstrate an improvement of up to about 50% in Up direction relative to the results based on a mean square statistics. Additionally, a more extensive SPP analysis at 95 global MGEX stations based on GPS ionosphere-free measurements shows an average improvement of about 10% relative to the traditional results. This finding provides a preliminary confirmation that adequate consideration of the variation of covariance leads to the improvement of GNSS state solutions.

Injection laryngoplasty with autologous fascia for treatment of unilateral vocal fold paralysis

The purpose of this dissertation was to study the applicability of minced autologous fascia graft for injection laryngoplasty of unilateral vocal fold paralysis (UVFP). Permanence of augmentation and host versus graft tissue reactions were of special interest. The topic deals with phonosurgery, which is a subdivision of the Ear, Nose and Throat-speciality of medicine. UVFP results from an injury to the recurrent or the vagal nerve. The main symptom is a hoarse and weak voice. Surgery is warranted for patients in whom spontaneous reinnervation and a course of voice therapy fails to improve the voice. Injection laryngoplasty is a widespread surgical technique which aims to restore glottic closure by augmenting the atrophied vocal muscle, and also by turning the paralyzed vocal fold towards midline. Currently, there exists a great diversity of synthetic, xenologous, homologous, and autologous substances available for injection. An autologous graft is perfect in terms of biocompatibility. Free fascia grafts have been successfully used in the head and neck surgery for decades, but fascia had not been previously applied into the vocal fold. The fascia is harvested from the lateral thigh under local anesthesia and minced into paste by scissors. Injection of the vocal fold is performed in laryngomicroscopy under general anesthesia. Three series of clinical trials of injection laryngoplasty with autologous fascia (ILAF) for patients with UVFP were conducted at the Department of Otorhinolaryngology of the Helsinki University Central Hospital. The follow-up ranged from a few months to ten years. The aim was to document the vocal results and possible morbidity related to graft harvesting and vocal fold injection. To address the tissue reactions and the degree of reabsoprtion of the graft, an animal study with a follow-up ranging from 3 days to 12 months was performed at the National Laboratory Animal Center, University of Kuopio. Harvesting of the graft and injection was met with minor morbidity. Histological analysis of the vocal fold tissue showed that fascia was well tolerated. Although some resorption or compaction of the graft during the first months is evident, graft volume is maintained well. When injected deep and laterally into the vocalis muscle, the fascia graft allows normal vibration of the vocal fold mucosa to occur during phonation. Improvement of voice quality was seen in all series by multiple objective parameters of voice evaluation. However, the vocal results were poor in cases where the nerve trauma was severe, such as UVFP after chest surgery. ILAF is most suitable for correction of mild to moderate glottic gaps related to less severe nerve damage. Our results indicate that autologous fascia is a feasible and safe new injection material with good and stable vocal results. It offers a practical solution for surgeons who treat this complex issue.

On the Cubicity of AT-Free Graphs and Circular-Arc Graphs

A unit cube in k dimensions (k-cube) is defined as the Cartesian product R-1 x R-2 x ... x R-k where R-i (for 1 <= i <= k) is a closed interval of the form [a(i), a(i) + 1] on the real line. A graph G on n nodes is said to be representable as the intersection of k-cubes (cube representation in k dimensions) if each vertex of C can be mapped to a k-cube such that two vertices are adjacent in G if and only if their corresponding k-cubes have a non-empty intersection. The cubicity of G denoted as cub(G) is the minimum k for which G can be represented as the intersection of k-cubes. An interesting aspect about cubicity is that many problems known to be NP-complete for general graphs have polynomial time deterministic algorithms or have good approximation ratios in graphs of low cubicity. In most of these algorithms, computing a low dimensional cube representation of the given graph is usually the first step. We give an O(bw . n) algorithm to compute the cube representation of a general graph G in bw + 1 dimensions given a bandwidth ordering of the vertices of G, where bw is the bandwidth of G. As a consequence, we get O(Delta) upper bounds on the cubicity of many well-known graph classes such as AT-free graphs, circular-arc graphs and cocomparability graphs which have O(Delta) bandwidth. Thus we have: 1. cub(G) <= 3 Delta - 1, if G is an AT-free graph. 2. cub(G) <= 2 Delta + 1, if G is a circular-arc graph. 3. cub(G) <= 2 Delta, if G is a cocomparability graph. Also for these graph classes, there axe constant factor approximation algorithms for bandwidth computation that generate orderings of vertices with O(Delta) width. We can thus generate the cube representation of such graphs in O(Delta) dimensions in polynomial time.