bluuebunny/crossref_metadata_2025 huggingface dataset:
Breastfeeding by Aboriginal mothers in Perth
Authors: BINNS Colin W. , GILCHRIST Dawn , WOODS Beth , GRACEY Michael , SCOTT Jane , SMITH Hannah , ZHANG Min , ROBERMAN Brian
Published: March 2006

Objective:  To document the breastfeeding practices of Aboriginal mothers delivering in Perth.

Design and methods:  A cohort of mothers was followed from the time of delivery for six months to obtain details of infant feeding practices.

Subjects:  A total of 455 mothers delivered during the study period and were asked to participate. A total of 425 mothers completed the initial questionnaire.

Setting:  The study was undertaken in six public hospitals in Perth, Western Australia.

Data analyses:  The data were analysed using spss. Breastfeeding duration was calculated using Kaplan–Meier survival analysis.

Main outcome measures:  Breastfeeding initiation and duration.

Results:  The mean age of the Aboriginal mothers was 21.8 years (range 14–39 years, SD 5.32) and the average gestational age was 38.3 weeks. Almost 50% of the mothers in the study delivered by Caesarean section. At discharge from hospital 89.4% (CI 86.6–92.1) of mothers were breastfeeding, declining to 58.8% (CI 53.5–64.1) at six months. When compared with non‐Aboriginal mothers, the Aboriginal breastfeeding rates were higher than the non‐Aboriginal average breastfeeding rates, but lower than the highest socioeconomic group.

Conclusions:  The breastfeeding rates of Aboriginal mothers are higher than for other Australians. This is despite the low maternal age and level of education and the high rates of low‐birth‐weight infants and Caesarean section among this population. The World Health Organization recommendation for infant feeding is exclusive breastfeeding until six months, but less than one‐third of Aboriginal mothers achieved this recommendation.
Household factors associated with older Australian's purchasing a varied diet: Results from household expenditure data
Authors: TEMPLE Jeromey B.
Published: March 2006

Objective:  To examine the household factors associated with older Australian's (aged 55 years and over) purchasing a varied diet.

Design and methods:  National cross‐sectional survey.

Setting:  All states and territories of Australia.

Subjects:  A total of 1898 households headed by adults aged 55 years and over.

Main outcome measures:  Food diversity was measured using the Dietary Variety Score (DVS). The DVS is the total number of food items purchased within a two‐week period, from a possible 110 individual food expenditure items.

Data analysis:  Negative binomial regression was used to examine the association between the respondent's individual and household characteristics with the DVS, after controlling for all factors in the model.

Results:  Among the demographic factors, living arrangements, age and education are found to be associated with dietary diversity. Lone males, lone females, and households headed by people with no secondary school education, or aged over 75 years were most likely to experience lower levels of dietary diversity.

Conclusions:  The finding that both poor education and low income in old age are associated with dietary diversity suggests the need for early life‐course interventions to improve nutritional outcomes. Nutrition education programs that also focus on those with poor education and low income, as well as lone person households and those aged over 75 years, may improve nutritional wellbeing, and thereby reduce public health costs.
Development of food groupings to guide dietary advice for people with diabetes
Authors: GILLEN Lynda J. , TAPSELL Linda C.
Published: March 2006

Objective:  To describe the development and characteristics of a food categorisation system and its application to guide advice for diabetes treatment.

Design and methods:  Foods commonly consumed by 16 adults with diabetes were grouped by macronutrient content and type of fat to form a set of reference food groups for dietary advice. Means for energy and macronutrients from individual food groups were then used to construct an overall intake pattern targeting 8000 kJ and relative amounts of carbohydrate, protein and fat (saturated fatty acids (SFA) < 10%E and (polyunsaturated fatty acids) PUFA ∼ 10%E). Variation in energy and macronutrients contributed by all foods partitioned into each food group was assessed by the coefficient of variation of data on the whole diet.

Results:  To differentiate between sources of fat, 13 food groups emerged and 10 were deemed acceptable to nutritional guidelines for diabetes treatment. The food group pattern was judged adequate for the achievement of dietary recommendations with low‐potential variation in total energy (5%) and macronutrient proportions (protein 6%, fat 6%, carbohydrate 3%), but higher for fat types (SFA 22%, (monounsaturated fatty acids) MUFA 11%, PUFA 12%). Targeted proportions for fat types were achieved only when daily servings of PUFA‐rich, oils, nuts and oily fish or soy were included in an ideal intake pattern.

Conclusions:  In theory, a dietary pattern constructed from food group sources of macronutrients and individual fat types results in low‐potential variation from recommended nutrient targets and, therefore, is appropriate to guide advice for the treatment of diabetes.
Disturbance alters habitat isolation's effect on biodiversity in aquatic microcosms
Authors: Östman Örjan , Kneitel Jamie M , Chase Jonathan M
Published: March 2006

Isolated habitats generally have fewer species at local spatial scales than more connected habitats. However, over larger spatial scales, the response of species richness to variation in the degree of isolation is variable. Here, we hypothesized that the effects of habitat isolation on patterns of regional level species richness may depend at least in part on the level of disturbances those habitats receive. We tested this hypothesis in a microcosm experiment using an aquatic community consisting of container dwelling protists and rotifers by manipulating disturbance and dispersal to experimental regions factorially. In disturbed regions, regional species richness was lower in regions with isolated patches compared to regions where patches were experimentally connected by dispersal. A likely mechanism for this result is that dispersal from adjacent undisturbed local patches allowed disturbance‐intolerant species a temporary refugia, thereby allowing regional coexistence of disturbance‐tolerant and intolerant species. In contrast, without disturbances (and thus no temporal heterogeneity) it is likely that dispersal homogenized communities, leading to overall lower richness with higher dispersal. Our results emphasize the importance of simultaneously considering multiple limiting factors, disturbance and dispersal in this case, as well as the spatial scale of the response, in order to fully understand factors that control biodiversity.
Stress anisotropy and stress gradient in magnetron sputtered films with different deposition geometries
Authors: Zhao Z. B. , Yalisove S. M. , Bilello J. C.
Published: March 2006

Mo films were deposited via magnetron sputtering with two different deposition geometries: dynamic deposition (moving substrate) and static deposition (fixed substrate). The residual stress and structural morphologies of these films were investigated, with particular focus on in-plane anisotropy of the biaxial stress and stress gradient across the film thickness. The results revealed that the Mo films developed distinct states of residual stress, which depended on both deposition geometry and film thickness. With the dynamic geometry, the Mo films generally exhibited anisotropic stress. Both the degree of anisotropy and the magnitude of stress varied as functions of film thickness. The variation of stress was linked to the evolution of anisotropic microstructures in the films. The Mo films from the static geometry developed isotropic residual stress, which was more compressive and noticeably larger in magnitude than that of the Mo films from the dynamic geometry. Aside from these disparities, the two types of Mo films (i.e., anisotropic and isotropic) exhibited notably similar trends of stress variation with film thickness. Depth profiling indicated the presence of large stress gradients for the Mo films, irrespective of the deposition geometries. This observation seems to be consistent with the premise that Mo films develop a zone T structure, which is inherently inhomogeneous along the film thickness. Moreover, the largest stress gradient for both types of deposition geometries arises at roughly the same film depth (∼240nm from substrate), where the stresses sharply transits from highly compressive to less compressive or even tensile. This appears to correspond to the boundary region that separates two distinct stages of microstructural evolution, a feature unique to zone T-type structure.
Optical emission from the aggregated state in poly [2-methoxy-5-(2′-ethyl-hexyloxy)-p-phenylene vinylene]
Authors: Kong F. , Wu X. L. , Yuan R. K. , Yang C. Z. , Siu G. G. , Chu Paul K.
Published: March 2006

We report the photoluminescence characteristics of solid solutions of poly[2-methox-5-(2′-ethyl-hexyloxy)-p-phenylene vinylene] (MEH-PPV) with different concentrations in polystyrene. Reduction in the distances between the MEH-PPV chains with increased MEH-PPV concentrations makes the conjugation segments aggregated in the solid solution. Absorption by the conjugation segments in the aggregated state leads to a redshift absorption edge. By comparing the photoluminescence and absorption spectra of the solid solutions with those of the 100% MEH-PPV film, it is shown that the emission from the 100% MEH-PPV film originates from the radiative recombination of excitons in the aggregated state.
Structural and optical characteristics of tantalum oxide grown by pulsed Nd:YAG laser oxidation
Authors: Atanassova E. , Aygun G. , Turan R. , Babeva Tz.
Published: March 2006

Tantalum pentoxide (Ta2O5) thin films (20–50nm) have been grown by 1064nm Nd:YAG laser oxidation of Ta film deposited on Si. The chemical bonding, structure, and optical properties of the films have been studied by Fourier transform infrared spectroscopy, x-ray diffraction, and reflectance measurements at normal light incidence in the spectral range of 350–800nm. The effect of the substrate temperature (250–400°C) during oxidation and its optimization with respect to the used laser beam energy density (3.2–3.4J∕cm2 per pulse) is discussed. It is established that the substrate temperature is a critical factor for the effectiveness of the oxidation process and can be used to control the composition and amorphous status of the films. The film density explored by refractive index is improved with increasing film thickness. The refractive index of the layers grown under the higher laser beam energy density and at substrate temperature of 350–400°C was found to be close to the value of bulk Ta2O5. The films are amorphous at substrate temperature below 350°C and possessed an orthorhombic (β-Ta2O5) crystal structure at higher temperatures. The thinner layers crystallize at a little higher temperature.
Experimental and numerical evaluations of adhesion strength and stress in TiN films deposited on ti-implanted aluminum
Authors: Xu Ming , Liu Youming , Li Liuhe , Cai Xun , Chen Qiulong , Chu Paul K.
Published: March 2006

Titanium ions were implanted into aluminum substrates at 40kV prior to magnetron sputtering deposition of the Ti interlayer and TiN film using our custom-designed multifunctional ion implanter without breaking vacuum. An 82-nm-thick modified layer was formed between the TiN film and the substrate. The characteristics of the implanted samples were compared to those of TiN∕Al and TiN∕Ti∕Al samples that were not preimplanted. Based on our scratch tests, the critical loading Lc of the TiN∕Ti∕Ti-implanted Al sample was significantly improved compared to the unimplanted TiN∕Al and TiN∕Ti∕Al samples. Finite element analysis was conducted to simulate the scratch process to help reveal the stress distributions in the vicinity of the interlayer. The results show that the stress around the interface is largely reduced in the TiN∕Ti∕Ti-implanted Al sample. Consequently, the mechanical properties such as resistance to loadings are enhanced.
Texture of Ru columns grown by oblique angle sputter deposition
Authors: Morrow P. , Tang F. , Karabacak T. , Wang P.-I. , Ye D.-X , Wang G.-C. , Lu T.-M.
Published: March 2006

Ru films were sputter deposited on native oxide p-Si(100) substrates under normal incidence and oblique angle incidence with and without substrate rotation. We characterized the crystalline texture and morphology of the Ru films by x-ray diffraction, transmission electron microscopy, and scanning electron microscopy. For the case of normal incidence, a smooth, uniform surface layer was observed, and pole figure analysis showed coexisting {101¯0}, {0002}, and {101¯1} normally oriented textures. For oblique angle incidence, we found that the films grown by uniform substrate rotation consist of isolated, vertical columnar structures with a clear pyramidal-shaped apex and display a normal {101¯0} fiber texture. Individual vertical columns were found to possess a single-crystal structure. In comparison, Ru films grown without substrate rotation possess a slanted columnar structure. They mainly show a tilted {101¯1}{101¯0} two-orientation (II-O) texture, with non-negligible {101¯0}{112¯0} and {0002} {112¯0} II-O textures as well. The formation of textures under oblique angle deposition was ascribed to the competition between crystalline planes having different vertical growth rates, where the planes associated with a higher rate survive from the shadowing effects. We argue that the vertical growth rate is determined by the atom mobility. Under substrate rotation this mobility is correlated with the overall atomic roughness of the crystalline planes. For a fixed substrate the adatom mobility exhibits anisotropic behavior, which is reflected in the biased diffusion.
Laser deposition and dielectric properties of cubic pyrochlore bismuth zinc niobate thin films
Authors: Jiang S. W. , Jiang B. , Liu X. Z. , Li Y. R.
Published: March 2006

The Bi1.5ZnNb1.5O7 (BZN) thin films with cubic pyrochlore structure were prepared on Pt∕SiO2∕Si substrates by pulsed laser deposition from a stoichiometric target. The crystallinity, surface morphology, and dielectric properties of BZN thin films at different substrate temperatures were investigated. It was found that the BZN films had a pure cubic pyrochlore structure when deposited at 550–650°C and the strong (222) texture at 650°C. The cubic BZN thin films deposited at 600°C had a dielectric loss lower than 0.004 and maximum voltage tunability of 6% with an applied bias field of 0.5MV∕cm under 100kHz.
Attenuated total reflection infrared spectroscopy for studying adsorbates on planar model catalysts: CO adsorption on silica supported Rh nanoparticles
Authors: Leewis C. M. , Kessels W. M. M. , van de Sanden M. C. M. , Niemantsverdriet J. W.
Published: March 2006

A sensitive method is presented for studying adsorption of gaseous species on metal surfaces in vacuum by attenuated total internal reflection Fourier transform infrared spectroscopy (ATR). The method is illustrated by CO adsorption experiments on silica supported Rh nanoparticles. An experimental setup and a procedure are described in detail to obtain a sensitivity of reflectance change of ∼5×10−5 absorbance units. Here, a silicon ATR crystal with a 50nm layer of hydroxylated silica acts as the support for the Rh nanoparticles. These particles are easily prepared by spincoat impregnation from a RhCl3 solution followed by H2 reduction. X-ray photoelectron spectroscopy before and after reduction shows that rhodium is reduced to Rh0 and that all chlorine is removed. Atomic force microscope images the distribution of the particles, which are 3–4nm in height. When the crystal is exposed to pressures up to 1mbar of CO, a gas which is inert to the silica support, the stretch vibration of linearly adsorbed CO on the Rh nanoparticles is detected at 2023cm−1, while no bridged CO or geminal dicarbonyl species can be distinguished. The minimum detectable coverage is estimated ∼0.005COpernm2 substrate area or ∼5×10−4ML.
Magnetic anisotropy of (Ga,Mn)As films grown on Si (001) substrates
Authors: Sato Shin’ya , Jinbo Yoshio , Uchitomi Naotaka
Published: March 2006

We investigated the anisotropic magnetotransport and magnetic properties of (Ga,Mn)As films on GaAs buffer layers grown on Si (001) substrates. The in-plane magnetoresistance (MR) showed similar dependence on the applied magnetic field at 10K for crystallographically equivalent [110] and [1¯10] directions. On the other hand, the in-plane MRs for [110] and [100] directions in an as-grown sample were observed to have slightly different magnetic field dependence, which disappeared after low-temperature annealing. The behavior observed in this experiment was different from that observed from (Ga,Mn)As∕GaAs systems. This difference was probably related to the competition between uniaxial magnetic anisotropy and cubic magnetic anisotropy induced by the antiphase domains observed for our samples grown on Si (001) substrates.
Radio frequency dual magnetron sputtering deposition and characterization of nanocomposite Al2O3–ZrO2 thin films
Authors: Trinh D. H. , Högberg H. , Andersson J. M. , Collin M. , Reineck I. , Helmersson U. , Hultman L.
Published: March 2006

Radio frequency magnetron sputtering from oxide targets has been used to synthesize crystalline alumina–zirconia nanocomposites at a relatively low temperature of 450°C. Films of different compositions have been deposited ranging from pure zirconia to pure alumina, the compositions being measured with Rutherford backscattering and elastic recoil detection analysis. X-ray diffraction studies show the presence of the monoclinic zirconia phase in pure zirconia films. Addition of alumina into the film results in the growth of the cubic zirconia phase and amorphous alumina. No crystalline alumina was detected in either the composite or the pure alumina film. The microstructure of the films as studied by high resolution electron microscopy and scanning transmission electron microscopy shows a columnar growth mode in both the pure zirconia and nanocomposite films, but reveals differences in the intracolumnar structure. For the nanocomposite small equiaxed grains, ∼5nm in size, are found at the base of the columns at the interface with the substrate. An amorphous tissue of alumina was present between the small crystallites in the case of the nanocomposite.
Crystallization and (Al,Ti)-oxide growth in annealed TiO2–Al2O3 multilayers
Authors: Omari M. A. , Sorbello R. S. , Aita C. R.
Published: March 2006

A family of TiO2–Al2O3 multilayers (Λ=2–72nmTiO2∕7nmAl2O3) is sputter deposited on fused silica substrates, sequentially annealed at 973 and 1273K, and analyzed by x-ray diffraction. The goal is to examine crystallization behavior upon annealing at temperatures at which thermodynamically stable mixed-cation phases should not form. The results show: (1) After the 973K anneal, films with Λ=18–72nmTiO2∕7nmAl2O3 weakly crystallize with a preferred (110) rutile orientation. In addition, enhancement of (200) rutile diffraction increases with increasing TiO2 layer thickness. (2) Significant crystallization occurs in films after the 1273K anneal. In films with Λ=36–72nmTiO2∕7nmAl2O3, a metastable pseudobrookite phase, Al0.95Ti2.05O5, crystallizes along with (110)r. However, only rutile TiO2 and α-Al2O3 crystallize in films with thinner TiO2 layers. An architecture-sensitive crystallization model is presented in which the first step common to all architectures is diffusive amorphization of TiO2 by Al2O3 at 973K to produce an amorphous mixed-cation solid solution, a-ATO. As the reaction interface sweeps through a TiO2 layer in architectures with thicker TiO2 layers, (200)r preferentially crystallizes from a-ATO because (200)r planes can accommodate Al species with the least rutile lattice strain. We suggest that (200)r provides crystallization sites for Al0.95Ti2.05O5 at 1273K.
Influence of process parameters on the properties of the tantalum oxynitride thin films deposited by pulsing reactive gas sputtering
Authors: Banakh O. , Heulin T. , Schmid P. E. , Le Dréo H. , Tkalcec I. , Lévy F. , Steinmann P.-A.
Published: March 2006

Thin films of tantalum oxynitride were prepared by reactive magnetron sputtering using a tantalum target and argon mixed with nitrogen and oxygen as reactive gases. The nitrogen flow was kept constant, while the oxygen flow was turned on and off periodically. This process prevents the complete target oxidation and controls the chemical composition of the films by varying the oxygen pulse duration. The choice of the process parameters was made by studying the evolution of the target potential during the sputtering process. The film composition evolves progressively from TaO0.46N1.34 to TaO2.04N0.5 while increasing the oxygen pulse duty cycle without any abrupt change in the elemental content. The optical transmission spectra collected on films deposited on glass show a blueshift of the absorption edge with increasing oxygen content. X-ray diffraction (XRD) patterns of all films exhibit broad peaks typical for nanocrystalline materials, which makes the phase identification difficult. Cross-section film morphology and surface topography observations support the results obtained by XRD. The optical and mechanical properties of the films are very sensitive to the chemical composition of the films and show a systematic evolution with the duty cycle.
Effects of nitrogen content on microstructure and oxidation behaviors of Ti–B–N nanocomposite thin films
Authors: Lu Y. H. , Shen Y. G. , Zhou Z. F. , Li K. Y.
Published: March 2006

Several different types of thin films, TiB0.65,TiB0.62N0.18,TiB0.61N1.04, and pure TiN, were deposited on Si(100) substrates at 500 °C by reactive unbalanced close-field dc-magnetron sputtering using two Ti and two TiB2 targets. The oxidation experiments of these films were carried out in air at fixed temperatures in a temperature regime of 600–1000 °C. As-deposited and oxidized films were characterized and analyzed using x-ray diffraction, plan-view and cross-sectional scanning electron microscopies, atomic force microscopy, and x-ray photoelectron spectroscopy (XPS). It was found that the microstructure and bonding configuration of Ti–B–N thin films were strongly dependent on nitrogen flow rate during deposition. Depending upon the amount of N addition, the films showed two- or three-phase nanocomposite structure. Nitrogen-free films were amorphous compound comprising of Ti and TiB2 (Ti–TiB2 compound). At 10 at. % N addition (TiB0.62N0.18), the films consisted of mainly TiN and TiB2 bondings with microstructures comprising of nanocrystalline (nc)-Ti(N) embedded in an amorphous (a)-TiB2 matrix. As the N concentration increased up to 38 at. % (TiB0.61N1.04), the films consisted of nc-TiN in a-(TiB2, BN) matrix. The oxidation experiment illustrated that the nanocomposite TiB0.61N1.04 thin films exhibited a much higher high-temperature oxidation resistance than TiN, TiB0.65, and TiB0.62N0.18 thin films. A two-stage oxidation process took place in these nanocomposite films in the whole temperature regime. A low oxidation rate accompanied with formation of small-grained Ti oxide occurred below 800 °C, while above 800 °C a rapid oxidation process accompanied with formation of large-grained Ti oxide with rough surface took place. It is believed that the two-stage oxidation process was related to oxidation resistance of nanocrystallites and thermal stability of amorphous matrix phase. By XPS, the oxides were determined to consist mainly of various types of Ti oxides in the oxidation temperatures of 600–1000 °C, such as TiO, TiNxOy, Ti2O3, and TiO2. It was also found that no elemental B was detected in oxide formed above 600 °C, which may be due to a low melting temperature of B2O3.
Transparent conductive Cd3TeO6 thin films with perovskite structure
Authors: Tetsuka Hiroyuki , Shan Yue Jin , Tezuka Keitaro , Imoto Hideo , Wasa Kiyotaka
Published: March 2006

Transparent conductive Cd3TeO6 thin films were deposited by radio-frequency magnetron sputtering using a target composed of CdO and TeO2 powders, and these films’ electrical and optical properties were examined. The electrical resistivity of 1.9×10−2Ωcm and an average transmittance above 85% in the visible region (400–800 nm) were obtained after annealing the film at 500 °C. The film’s carrier density and Hall mobility were 8.7×1019cm−3 and 6.8cm2V−1s−1, respectively. The absorption edge of the films was shifted to a lower wavelength by increasing the carrier density. The maximum band gap of these films was found to be 3.69 eV.
Electrical and physical properties of room temperature deposited, mixed TiO2∕SiO2 oxides
Authors: Busani T. , Devine R. A. B. , Yu Xiangkun , Seo Hye-Won
Published: March 2006

Mixed oxide TiO2∕SiO2 dielectrics have been deposited at room temperature by microwave excited plasma enhanced chemical vapor deposition from SiH4 and TiCl4 precursor gases. The low frequency dielectric constant and the refractive index at 632.8 nm are observed to increase linearly with increasing Ti concentration. No anomalous enhancement of the dielectric constant at low Ti concentrations is observed, consistent with the conclusion that the Ti ion replaces the Si ion directly in fourfold coordination. A compound dielectric constant of 25 can be achieved for a concentration ∼50% Ti where it is anticipated the optical band gap would be ∼6.25eV.
Systematic studies of SiGe∕Si islands nucleated via separate in situ or ex situ Ga+ focused ion beam-guided growth techniques
Authors: Vandervelde Thomas E. , Atha Surajit , Hull Robert , Pernell Timothy L. , Bean John C.
Published: March 2006

In this study, we use 25 keV in situ and 30 keV ex situ Ga+ focused ion beams (FIBs) to locally modify the substrate before deposition and determine their effects on nucleation of molecular beam epitaxy grown Ge∕Si islands. FIB processing may alter island formation in at least five ways: the surfactant effect of Ga+, doping effects of subsurface Ga+, local strains, crystalline damage, and surface roughening. To explore these possibilities, we milled square regions of increasing Ga+ doses and used atomic force microscopy to monitor islanding in and around these regions. For in situ experiments, doses ranged from ∼1013 to 5×1017ions∕cm2 (0.04–400 ML). We began to observe changes in island topology at doses as low as ∼1014ions∕cm2. For doses of ∼1015 to ∼8×1016ions∕cm2 (2–160 ML), implanted areas were surrounded by denuded zones that grew from ∼0.5 to 6μm with increasing dose. Immediately inside the implanted area, island size and concentration appeared to peak. At doses above ∼6×1016ions∕cm2 (120 ML), Ga+ produced noticeable surface depressions, which were often surrounded by enhanced island densities, rather than a denuded zone. For ex situ FIB patterning, samples underwent both pregrowth cleaning and growth of a thin capping layer (0–100 nm). Doses ranging from 7.5×1013 to ∼1017ions∕cm2 (0.15–200 ML) were used in concert with varied capping layer thicknesses to study their combined affect on island nucleation. The results correspond well with in situ experiments for thin capping layers. Increased capping layer thickness resulted in muted modifications to island formation for low Ga+ doses, while for higher doses trends similar to those obtained in situ are seen.
Cross Talk between a Fungal Blue-Light Perception System and the Cyclic AMP Signaling Pathway
Authors: Casas-Flores Sergio , Rios-Momberg Mauricio , Rosales-Saavedra Teresa , Martínez-Hernández Pedro , Olmedo-Monfil Vianey , Herrera-Estrella Alfredo
Published: March 2006

Blue light regulates many physiological and developmental processes in fungi. In
Trichoderma atroviride
the complex formed by the BLR-1 and BLR-2 proteins appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Here we demonstrate that the BLR proteins are necessary for carbon deprivation induced conidiation, even in the absence of light, pointing to the existence of an unprecedented cross talk between light and carbon sensing. Further, in contrast to what has been found in all other fungal systems, clear BLR-independent blue-light responses, including the activation of protein kinase A (PKA) and the regulation of gene expression, were found. Expression of an antisense version of the
pkr-1
gene, encoding the regulatory subunit of PKA, resulted in a nonsporulating phenotype, whereas overexpression of the gene produced colonies that conidiate even in the dark. In addition, overexpression of
pkr-1
blocked the induction of early light response genes. Thus, our data demonstrate that PKA plays an important role in the regulation of light responses in
Trichoderma
. Together, these observations suggest that the BLR complex plays a general role in sensing environmental cues that trigger conidiation and that such a role can be separated from its function as a transcription factor.
The RIM101 Pathway Contributes to Yeast Cell Wall Assembly and Its Function Becomes Essential in the Absence of Mitogen-Activated Protein Kinase Slt2p
Authors: Castrejon F. , Gomez A. , Sanz M. , Duran A. , Roncero C.
Published: March 2006

The
Saccharomyces cerevisiae ynl294cΔ
(
rim21Δ
) mutant was identified in our lab owing to its moderate resistance to calcofluor, although it also displayed all of the phenotypic traits associated with its function as the putative sensor (Rim21p) of the RIM101 pathway.
rim21Δ
also showed moderate hypersensitivity to sodium dodecyl sulfate, caffeine, and zymolyase, and the cell wall compensatory response in this mutant was very poor, as indicated by the almost complete absence of Slt2 phosphorylation and the modest increase in chitin synthesis after calcofluor treatment. However, the cell integrity pathway appeared functional after caffeine treatment or thermal stress.
rim21Δ
and
rim101Δ
mutant strains shared all of the cell-wall-associated phenotypes, which were reverted by the expression of Rim101-531p, the constitutively active form of this transcription factor. Therefore, the absence of a functional RIM101 pathway leads to cell wall defects.
rim21Δ
, as well as
rim101Δ
, was synthetic lethal with
slt2Δ
, a synthetic defect alleviated by osmotic stabilization of the media. The double mutants grown in osmotically stabilized media were extremely hypersensitive to zymolyase and showed thicker cell walls, with poorly defined mannoprotein layers. In contrast,
rim21Δ rlm1Δ
and
rim101Δ rlm1Δ
double mutants were fully viable. Taken together, these results show that the RIM101 pathway participates directly in cell wall assembly and that it acts in parallel with the protein kinase C pathway (PKC) in this process independently of the transcriptional effect of the compensatory response mediated by this route. In addition, these results provide new experimental evidence of the direct involvement of the PKC signal transduction pathway through the Sltp2 kinase in the construction of yeast cell walls.
Mapping of an Internal Protease Cleavage Site in the Ssy5p Component of the Amino Acid Sensor of
Saccharomyces cerevisiae
and Functional Characterization of the Resulting Pro- and Protease Domains by Gain-of-Function Genetics
Authors: Poulsen Peter , Lo Leggio Leila , Kielland-Brandt Morten C.
Published: March 2006

Ssy5p is a 77-kDa protein believed to be a component of the SPS amino acid sensor complex in the plasma membrane of
Saccharomyces cerevisiae
. Ssy5p has been suggested to be a chymotrypsin-like serine protease that activates the transcription factor Stp1p upon exposure of the yeast to extracellular amino acid. Here we overexpressed and partially purified Ssy5p to improve our understanding of its structure and function. Antibodies against Ssy5p expressed in
Escherichia coli
were isolated and used to detect Ssy5p processing in
S. cerevisiae
cells. Partial purification and N-terminal sequencing of processed Ssy5p revealed in vivo cleavage of Ssy5p between amino acids 381 and 382. We also isolated constitutively signaling
SSY5
mutants and quantified target promoter activation and Stp1p processing. One mutant contained an amino acid substitution in the prodomain, whereas three others harbored amino acid substitutions in the protease domain. Dose-response analysis indicated that all four mutants exhibited increased basal levels of Stp1p processing. Interestingly, whereas the three constitutive mutants mapping to the protease domain of Ssy5p exhibited the decreased 50% effective concentration (EC
50
) characteristic of constitutive mutations previously found in Ssy1p, Ptr3p, and Ssy5p, the EC
50
of the mutation that maps to the prodomain of Ssy5p remained essentially unchanged. In a model of Ssy5p derived from its similarities with α-lytic protease from
Lysobacter enzymogenes
, the sites corresponding to the mutations in the protease domain are clustered in a region facing the prodomain, suggesting that this region interacts with the prodomain and participates in the conformational dynamics of sensing.
Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases
Authors: Trinh Vincent , Langelier Marie-France , Archambault Jacques , Coulombe Benoit
Published: March 2006

High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.
Chemoenzymatic and Template-Directed Synthesis of Bioactive Macrocyclic Peptides
Authors: Grünewald Jan , Marahiel Mohamed A.
Published: March 2006

Non-ribosomally synthesized peptides have compelling biological activities ranging from antimicrobial to immunosuppressive and from cytostatic to antitumor. The broad spectrum of applications in modern medicine is reflected in the great structural diversity of these natural products. They contain unique building blocks, such as
d
-amino acids, fatty acids, sugar moieties, and heterocyclic elements, as well as halogenated, methylated, and formylated residues. In the past decades, significant progress has been made toward the understanding of the biosynthesis of these secondary metabolites by nonribosomal peptide synthetases (NRPSs) and their associated tailoring enzymes. Guided by this knowledge, researchers genetically redesigned the NRPS template to synthesize new peptide products. Moreover, chemoenzymatic strategies were developed to rationally engineer nonribosomal peptides products in order to increase or alter their bioactivities. Specifically, chemical synthesis combined with peptide cyclization mediated by nonribosomal thioesterase domains enabled the synthesis of glycosylated cyclopeptides, inhibitors of integrin receptors, peptide/polyketide hybrids, lipopeptide antibiotics, and streptogramin B antibiotics. In addition to the synthetic potential of these cyclization catalysts, which is the main focus of this review, different enzymes for tailoring of peptide scaffolds as well as the manipulation of carrier proteins with reporter-labeled coenzyme A analogs are discussed.
Characterization of a Novel Virus Causing a Lethal Disease in Carp and Koi
Authors: Ilouze Maya , Dishon Arnon , Kotler Moshe
Published: March 2006

Since 1998 a lethal disease of carp and ornamental koi (Cyprinus carpio) has afflicted fisheries in North America, Europe, and Asia, causing severe economic losses to the fish farming industry. This review summarizes the isolation and identification of the disease-causing agent and describes the currently known molecular characteristics of this newly isolated virus, distinguishing it from other known large DNA viruses. In addition, we summarize the clinical and histopathological manifestations of the disease. Providing information on the immune response to this virus and evaluating the available means of diagnosis and protection should help to reduce the damage induced by this disease. This review does not discuss the economic aspects of the disease or the debate on whether the disease should be registered; both of these issues were recently reviewed in detail (O. L. M. Haenen, K. Way, S. M. Bergmann, and E. Ariel, Bull. Eur. Assoc. Fish Pathol.
24:
293-307, 2004; D. Pokorova, T. Vesely, V. Piackova, S. Reschova, and J. Hulova, Vet. Med. Czech.
50:
139-147, 2005).
Glucose Signaling in
Saccharomyces cerevisiae
Authors: Santangelo George M.
Published: March 2006

Eukaryotic cells possess an exquisitely interwoven and fine-tuned series of signal transduction mechanisms with which to sense and respond to the ubiquitous fermentable carbon source glucose. The budding yeast Saccharomyces cerevisiae has proven to be a fertile model system with which to identify glucose signaling factors, determine the relevant functional and physical interrelationships, and characterize the corresponding metabolic, transcriptomic, and proteomic readouts. The early events in glucose signaling appear to require both extracellular sensing by transmembrane proteins and intracellular sensing by G proteins. Intermediate steps involve cAMP-dependent stimulation of protein kinase A (PKA) as well as one or more redundant PKA-independent pathways. The final steps are mediated by a relatively small collection of transcriptional regulators that collaborate closely to maximize the cellular rates of energy generation and growth. Understanding the nuclear events in this process may necessitate the further elaboration of a new model for eukaryotic gene regulation, called “reverse recruitment.” An essential feature of this idea is that fine-structure mapping of nuclear architecture will be required to understand the reception of regulatory signals that emanate from the plasma membrane and cytoplasm. Completion of this task should result in a much improved understanding of eukaryotic growth, differentiation, and carcinogenesis.
CXCR3 chemokine receptor immunoreactivity in primary cutaneous malignant melanoma: correlation with clinicopathological prognostic factors
Authors: Monteagudo C , Martin J M , Jorda E , Llombart-Bosch A
Published: March 2006

Background:A role for CXCR3, the receptor for chemokines Mig, IP-10 and interferon-inducible T cell α-chemoattractant, in tumour cell migration during melanoma progression has been proposed.

Aims:To analyse CXCR3 expression in primary cutaneous malignant melanomas and its comparison with clinicopathological and prognostic factors.

Methods:A retrospective immunohistochemical study was carried out on formalin-fixed paraffin-wax-embedded sections from 82 patients with primary invasive cutaneous melanomas, with a monoclonal antibody to CXCR3 (clone 49801.111; R&D Systems). Immunoreactivity was semiquantitatively evaluated: labelling intensity (0, absent; 1, weak; 2, moderate; 3, strong) multiplied by the percentage of cells in each of the four intensity categories. A positive staining was considered when the score was >100. Melanomas were categorised by age, sex, primary site, tumour thickness, growth phase, ulceration, lymphocytic infiltration, recurrence, lymph node and distant metastasis, and survival. Univariate and multivariate statistical analyses were carried out.

Results:Of the 82 patients, a positive CXCR3 staining was found in 26 (31.7%) patients, whereas 56 (68.3%) were negative. In univariate analysis, a significant association of CXCR3-positive tumour cell immunostaining with tumour thickness >1 mm (p = 0.003), absence of lymphocytic infiltration (p = 0.04) and the presence of distant metastasis (p = 0.048) was found. Multivariate analysis found tumour thickness as the only independent factor with considerable association with distant metastases.

Conclusions:Our findings of a positive correlation of CXCR3 tumour cell immunoreactivity in human primary cutaneous melanoma with tumour thickness >1 mm and absence of intratumoral lymphocytic infiltration support the biological implication of CXCR3 in the tumour progression of cutaneous malignant melanoma.
INTERPRETING GRAPH COLORABILITY IN FINITE SEMIGROUPS
Authors: JACKSON MARCEL , McKENZIE RALPH
Published: March 2006

We show that a number of natural membership problems for classes associated with finite semigroups are computationally difficult. In particular, we construct a 55-element semigroup S such that the finite membership problem for the variety of semigroups generated by S interprets the graph 3-colorability problem.
THE ALGEBRA OF STRAND SPLITTING II: A PRESENTATION FOR THE BRAID GROUP ON ONE STRAND
Authors: BRIN MATTHEW G.
Published: March 2006

The author previously introduced groups BV and [Formula: see text] as braided versions of groups introduced by Richard J. Thompson, and as having connections to braided tensor categories. Here we show that BV and [Formula: see text] are finitely presented by exhibiting finite presentations for them. We show that these groups are "Artinifications" of the older Thompson groups V and [Formula: see text] by showing that presentations for V and [Formula: see text] can be obtained from presentations for BV and [Formula: see text] by adding relations that trivialize the squares of the generators of the latter groups.
ELEMENTARY SUBGROUPS OF RELATIVELY HYPERBOLIC GROUPS AND BOUNDED GENERATION
Authors: OSIN DENIS V.
Published: March 2006

Let G be a group hyperbolic relative to a collection of subgroups {Hλ, λ ∈ Λ}. We say that a subgroup Q ≤ G is hyperbolically embedded into G, if G is hyperbolic relative to {Hλ, λ ∈ Λ} ∪ {Q}. In this paper we obtain a characterization of hyperbolically embedded subgroups. In particular, we show that if an element g ∈ G has infinite order and is not conjugate to an element of some Hλ, λ ∈ Λ, then the (unique) maximal elementary subgroup containing g is hyperbolically embedded into G. This allows us to prove that if G is boundedly generated, then G is elementary or Hλ = G for some λ ∈ Λ.
CHARGED PARTICLES WITH SPIN IN A GRAVITATIONAL WAVE AND A UNIFORM MAGNETIC FIELD
Authors: MOHSENI MORTEZA
Published: March 2006

We study the motion of a pseudo-classical charged particle with spin in the space–time of a gravitational pp wave in the presence of a uniform magnetic field.
TESTING A NEW MESH REFINEMENT CODE IN THE EVOLUTION OF A SPHERICALLY SYMMETRIC KLEIN–GORDON FIELD
Authors: CSIZMADIA PÉTER
Published: March 2006

Numerical evolution of the spherically symmetric, massive Klein–Gordon field is presented using a new adaptive mesh refinement (AMR) code with fourth order discretization in space and time, along with compactification in space. The system is non-interacting, thus the initial disturbance is entirely radiated away. The main aim is to simulate its propagation until it vanishes near [Formula: see text]. By numerical investigations of the violation of the energy balance relations, the space–time boundaries of "well-behaving" regions are determined for different values of the AMR parameters. An important result is that mesh refinement maintains precision in the central region for a longer time even if the mesh is only refined outside of this region. The speed of the algorithm was also tested; in the case of ten refinement levels the algorithm was two orders of magnitude faster than the extrapolated time of the corresponding unigrid run.
EMPIRICAL EXERCISE BEHAVIOR OF WARRANT HOLDERS AND ITS CONSEQUENCES FOR WARRANT VALUES
Authors: KOZIOL CHRISTIAN
Published: March 2006

In this paper, we analyze the exercise behavior of warrant holders and its impact on warrant values. For this purpose, we propose a parametric model to describing the exercise volume of warrants and calibrate it to exercise data of 40 warrants from the German market. We find that few too-early exercises but also a significant number of too-late exercises occur. This observed exercise behavior results in warrant values that are more than 3% below those under the optimal exercise strategy for at-the-money warrants and the differences are even much higher for in- and out-of-the-money warrants.
OPTIMAL TIMING OF THE ANNUITY PURCHASE: COMBINED STOCHASTIC CONTROL AND OPTIMAL STOPPING PROBLEM
Authors: STABILE GABRIELE
Published: March 2006

The paper examines the optimal annuitization time and the optimal consumption/investment strategies for a retired individual subject to a constant force of mortality in an all-or-nothing framework. We allow for a different utility of consumption before and after annuitization. For a general family of preferences we characterize the value function and the optimal controls of the resulting combined stochastic control and optimal stopping problem. Assuming power utility functions we obtain explicit solutions. We show that if the individual evaluates the consumption flow and the annuity payments stream in the same way, then, depending on the parameters of the economy, the annuity is purchased at retirement or never. In the case when the individual is more risk averse in the annuity assessment, it is optimal to defer the annuitization until her wealth reaches a threshold, and such threshold depends on the parameters of the economy.
WOULD THERE EVER BE CONSENSUS VALUE AND SOURCE OF THE EQUITY RISK PREMIUM? A REVIEW OF THE EXTANT LITERATURE
Authors: OYEFESO OLUWATOBI
Published: March 2006

This paper reviews the extant studies on the equity premium. While paper attempts to make the review comprehensive, describing all of the work in this area is difficult considering the numerous researches that have been done in this area. Essentially, the paper assesses the relationship between the excess return and the equity risk premium and draws attention to their interchangeable use in the finance literature. Existing literature is reviewed around possible theories explaining the equity premium puzzle and followed by the empirical evidence on the theories. Finally, this paper focuses on the problems of attaining consensus value and source of the market risk premium, which makes equity premium puzzle an unresolved issue among the academics and finance practitioners.