bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Mom and Dad: Quantitative Genetic Models for Maternal Effects and Genomic Imprinting
Authors: Santure Anna W , Spencer Hamish G
Published: June 2006

The expression of an imprinted gene is dependent on the sex of the parent it was inherited from, and as a result reciprocal heterozygotes may display different phenotypes. In contrast, maternal genetic terms arise when the phenotype of an offspring is influenced by the phenotype of its mother beyond the direct inheritance of alleles. Both maternal effects and imprinting may contribute to resemblance between offspring of the same mother. We demonstrate that two standard quantitative genetic models for deriving breeding values, population variances and covariances between relatives, are not equivalent when maternal genetic effects and imprinting are acting. Maternal and imprinting effects introduce both sex-dependent and generation-dependent effects that result in differences in the way additive and dominance effects are defined for the two approaches. We use a simple example to demonstrate that both imprinting and maternal genetic effects add extra terms to covariances between relatives and that model misspecification may over- or underestimate true covariances or lead to extremely variable parameter estimation. Thus, an understanding of various forms of parental effects is essential in correctly estimating quantitative genetic variance components.
Unequal Sister Chromatid and Homolog Recombination at a Tandem Duplication of the a1 Locus in Maize
Authors: Yandeau-Nelson Marna D , Xia Yiji , Li Jin , Neuffer M Gerald , Schnable Patrick S
Published: June 2006

Tandemly arrayed duplicate genes are prevalent. The maize A1-b haplotype is a tandem duplication that consists of the components, α and β. The rate of meiotic unequal recombination at A1-b is ninefold higher when a homolog is present than when it is absent (i.e., hemizygote). When a sequence heterologous homolog is available, 94% of recombinants (264/281) are generated via recombination with the homolog rather than with the sister chromatid. In addition, 83% (220/264) of homolog recombination events involved α rather than β. These results indicate that: (1) the homolog is the preferred template for unequal recombination and (2) pairing of the duplicated segments with the homolog does not occur randomly but instead favors a particular configuration. The choice of recombination template (i.e., homolog vs. sister chromatid) affects the distribution of recombination breakpoints within a1. Rates of unequal recombination at A1-b are similar to the rate of recombination between nonduplicated a1 alleles. Unequal recombination is therefore common and is likely to be responsible for the generation of genetic variability, even within inbred lines.
A Bayesian Heterogeneous Analysis of Variance Approach to Inferring Recent Selective Sweeps
Authors: Marshall John M , Weiss Robert E
Published: June 2006

The distribution of microsatellite allele sizes in populations aids in understanding the genetic diversity of species and the evolutionary history of recent selective sweeps. We propose a heterogeneous Bayesian analysis of variance model for inferring loci involved in recent selective sweeps by analyzing the distribution of allele sizes at multiple loci in multiple populations. Our model is shown to be consistent with a multilocus test statistic, ln RV, proposed for identifying microsatellite loci involved in recent selective sweeps. Our methodology differs in that it accepts original allele size data rather than summary statistics and allows the incorporation of prior knowledge about allele frequencies using a hierarchical prior distribution consisting of log normal and gamma probability distributions. Interesting features of the model are its ability to simultaneously analyze allele size data for any number of populations and to cope with the presence of any number of selected loci. The utility of the method is illustrated by application to two sets of microsatellite allele size data for a group of West African Anopheles gambiae populations. The results are consistent with the suppressed-recombination model of speciation, and additional candidate loci on chromosomes 2 (079 and 175) and 3 (088) are discovered that escaped former analysis.
Quantitative Trait Linkage Analysis Using Gaussian Copulas
Authors: Li Mingyao , Boehnke Michael , Abecasis Gonçalo R , Song Peter X-K
Published: June 2006

Mapping and identifying variants that influence quantitative traits is an important problem for genetic studies. Traditional QTL mapping relies on a variance-components (VC) approach with the key assumption that the trait values in a family follow a multivariate normal distribution. Violation of this assumption can lead to inflated type I error, reduced power, and biased parameter estimates. To accommodate nonnormally distributed data, we developed and implemented a modified VC method, which we call the “copula VC method,” that directly models the nonnormal distribution using Gaussian copulas. The copula VC method allows the analysis of continuous, discrete, and censored trait data, and the standard VC method is a special case when the data are distributed as multivariate normal. Through the use of link functions, the copula VC method can easily incorporate covariates. We use computer simulations to show that the proposed method yields unbiased parameter estimates, correct type I error rates, and improved power for testing linkage with a variety of nonnormal traits as compared with the standard VC and the regression-based methods.
An Integrated-Likelihood Method for Estimating Genetic Differentiation Between Populations
Authors: Kitakado Toshihide , Kitada Shuichi , Kishino Hirohisa , Skaug Hans Julius
Published: June 2006

The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of θ = 4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.
Scan of Human Genome Reveals No New Loci Under Ancient Balancing Selection
Authors: Bubb K L , Bovee D , Buckley D , Haugen E , Kibukawa M , Paddock M , Palmieri A , Subramanian S , Zhou Y , Kaul R , Green P , Olson M V
Published: June 2006

There has been much speculation as to what role balancing selection has played in evolution. In an attempt to identify regions, such as HLA, at which polymorphism has been maintained in the human population for millions of years, we scanned the human genome for regions of high SNP density. We found 16 regions that, outside of HLA and ABO, are the most highly polymorphic regions yet described; however, evidence for balancing selection at these sites is notably lacking—indeed, whole-genome simulations indicate that our findings are expected under neutrality. We propose that (i) because it is rarely stable, long-term balancing selection is an evolutionary oddity, and (ii) when a balanced polymorphism is ancient in origin, the requirements for detection by means of SNP data alone will rarely be met.
Using Substrate-Binding Variants of the cAMP-Dependent Protein Kinase to Identify Novel Targets and a Kinase Domain Important for Substrate Interactions in Saccharomyces cerevisiae
Authors: Deminoff Stephen J , Howard Susie C , Hester Arelis , Warner Sarah , Herman Paul K
Published: June 2006

Protein kinases mediate much of the signal transduction in eukaryotic cells and defects in kinase function are associated with a variety of human diseases. To understand and correct these defects, we will need to identify the physiologically relevant substrates of these enzymes. The work presented here describes a novel approach to this identification process for the cAMP-dependent protein kinase (PKA) in Saccharomyces cerevisiae. This approach takes advantage of two catalytically inactive PKA variants, Tpk1K336A/H338A and Tpk1R324A, that exhibit a stable binding to their substrates. Most protein kinases, including the wild-type PKA, associate with substrates with a relatively low affinity. The binding observed here was specific to substrates and was dependent upon PKA residues known to be important for interactions with peptide substrates. The general utility of this approach was demonstrated by the ability to identify both previously described and novel PKA substrates in S. cerevisiae. Interestingly, the positions of the residues altered in these variants implicated a particular region within the PKA kinase domain, corresponding to subdomain XI, in the binding and/or release of protein substrates. Moreover, the high conservation of the residues altered and, in particular, the invariant nature of the R324 position suggest that this approach might be generally applicable to other protein kinases.
Deletion Polymorphism ofDisc1Is Common to All 129 Mouse Substrains: Implications for Gene-Targeting Studies of Brain Function
Authors: Clapcote Steven J , Roder John C
Published: June 2006

We report that the Disc1 gene in all extant 129 mouse inbred substrains has a deletion, previously considered specific to the 129S6/SvEv substrain, which is predicted to abolish production of the full-length protein. This finding has implications for the study of knockout mice generated from 129-derived embryonic stem cells.
A study of indentation work in homogeneous materials
Authors: Tan Mengxi
Published: June 2006

The work of indentation is investigated experimentally in this article. A method of using the elastic energy to extract the elastic modulus is proposed and verified. Two types of hardness related to the work of indentation are defined and examined: Hwtis defined as the total work required creating a unit volume of contact deformationand Hwp is defined as the plastic work required creating a unit volume of plastic deformation; experiments show that both hardness definitions are good choices for characterizing hardness. Several features that may provide significant insights in understanding indentation measurements are studied. These features mainly concern some scaling relationships in indentation measurements and the indentation size effects.
Quantitative analysis of thermal stability of CdSe/CdS core-shell nanocrystals under infrared radiation
Authors: Singha A. , Roy Anushree
Published: June 2006

Here, we report investigations on the instability in luminescence of bare (trioctylphosphine oxide [TOPO]-stabilized) and CdS-capped CdSe particles under infrared radiation. During thermal annealing under radiation, the formation of oxide layers on the surfaces of the particles create defect states. Consequently, there is a reduction in particle size. These two effects control the light output from the samples. We make a quantitative comparison of the stability of bare CdSe and core-shell-type CdSe-CdS particles during annealing under infrared radiation. Using diffusion theory, we show that the volume of the oxide layer, adhered to the crystallites, plays a dominant role in controlling the luminosity of the particles.
Modeling of the surface tension of liquid Fe-P alloy by calculation of liquidus line in Fe-P binary system
Authors: Kim Han S. , Kobayashi Y. , Nagai K.
Published: June 2006

The surface tension of the Fe-P binary liquid solution was computed using a Butler's model in wide composition and temperature ranges by adopting the activity coefficient data that were evaluated from the phase diagram calculation. In the surface tension modeling, the Fe-P binary system was assumed as the Fe-Fe3P pseudo-binary system. The results of the computation were critically compared with the experimental data of the literature considering the effects of the size of the adsorbed elements and the interactions among them. The results of the computation at 1823 K showed good agreement with the selected experimental data of the literature in a wide composition range from 0 to 15 mass%P. Furthermore, the results of the computation at 0.5 mass%P showed good correlation with the selected experimental data of the literature in a wide temperature range from 1823 K to 1923 K.
Al2O3scale development on iron aluminides
Authors: Zhang X.F. , Thaidigsmann K. , Ager J. , Hou P.Y.
Published: June 2006

The structure and phase of the Al2O3scale that forms on an Fe3Al-based alloy Fe-28Al-5Cr (at.%) was investigated by transmission electron microscopy and photoluminescence spectroscopy. Oxidation was performed at 900 °C and 1000 °C for up to 190 min. Transmission electron microscopy revealed that single-layer scales were formed after short oxidation times. Electron diffraction was used to show that the scales are composed of nanoscale crystallites of the θ, γ, and α phases of alumina. Band-like structure was observed extending along three 120°-separated directions within the surface plane. Textured θ and γ grains were the main components of the bands, whereas mixed α and transient phases were found between the bands. Extended oxidation produced a double-layered scale structure with a continuous α layer at the scale/alloy interface and a γ/θ layer at the gas surface. The mechanism for the formation of Al2O3scales on iron aluminide alloys is discussed and compared with that for nickel aluminide alloys.
Low-temperature synthesis and sintering of γ-Y2Si2O7
Authors: Sun Ziqi , Zhou Yanchun , Li Meishuan
Published: June 2006

In this article, a novel pressureless solid-liquid reaction method is presented for preparation of yttrium disilicate (γ-Y2Si2O7). Single-phase γ-Y2Si2O7 powder was synthesized by calcination of SiO2 and Y2O3 powders with the addition of LiYO2 at 1400 °C for 4 h. The addition of LiYO2 significantly decreased the synthesis temperature, shortened the calcination time, and enhanced the stability of γ-Y2Si2O7. The sintering of these powders in air and O2 was studied by means of thermal mechanical analyzer. It is shown that the γ-Y2Si2O7 sintered in oxygen had a faster densification rate and a higher density than that sintered in air. Furthermore, single-phase γ-Y2Si2O7 with a density of 4.0 g/cm3 (99% of the theoretical density) was obtained by pressureless sintering at 1400 °C for 2 h in oxygen. Microstructures of the sintered samples are studied by scanning electron microscope.
Mechanical property development in reactively sputtered tantalum carbide/amorphous hydrocarbon thin films
Authors: Evans Ryan D. , Doll Gary L. , Glass Jeffrey T.
Published: June 2006

Hardness, elastic modulus, and stress directly influence the ability of tantalum carbide/amorphous hydrocarbon (TaC/a-C:H) thin films to enhance the wear-resistance of steel tribological component surfaces. Designed factorial experiments enabled an evaluation of the effects of acetylene flow rate (QC2H2), direct current bias voltage level (Vb), and substrate rotation rate (ωRot) during deposition on the mechanical properties of reactively sputtered TaC/a-C:H films. Significant relationships were found between compressive stress level and Vb, whereas hardness and elastic modulus were dependent primarily on Vb and secondarily on QC2H2 within the studied parameter space. It is proposed that effects of ion bombardment on the a-C:H phase during growth are responsible for property dependencies on Vb. Decreases in hardness and elastic modulus with increasing QC2H2 are attributed to increased hydrogen concentration and a concomitant decreased volume fraction of TaC crystallites in the films.
High-temperature tolerance of the silver-copper oxide braze in reducing and oxidizing atmospheres
Authors: Kim J.Y. , Hardy J.S. , Weil K.S.
Published: June 2006

The silver-copper oxide–based reactive air brazing technique was developed as a method of joining complex-shaped ceramic parts. To investigate the viability of this approach for high-temperature application, a series of air-brazed alumina joints were independently exposed to either oxidizing or reducing atmosphere at 800 °C for 100 h. Those samples that were thermally aged in air maintained good joint strength, similar to that of the original as-brazed samples. Microstructural analysis revealed no significant change in joint microstructure after long-term oxidation at elevated temperature, indicating excellent stability of the Ag–CuO-based filler metal in this environment. On the other hand, exposure of the air-brazed alumina joints to hydrogen under the same aging conditions resulted in a measurable decrease in joint strength. Scanning electron microscope analysis conducted on the fracture surfaces of the broken hydrogen-exposed specimens indicated that the source of joint failure was debonding along the interface between the filler metal and alumina substrate. This was due in large part to internal reduction of CuO precipitates within the filler metal to copper and accompanied by the simultaneous formation of porosity at these sites, both within the bulk of the joint as well as along the filler metal/substrate interfaces. Pore formation was noticeably present in filler metals prepared with a high concentration of copper oxide.
Fabrication and properties of HfB2–MoSi2 composites produced by hot pressing and spark plasma sintering
Authors: Sciti Diletta , Silvestroni Laura , Bellosi Alida
Published: June 2006

HfB2–15 vol% MoSi2 composites were produced from powder mixtures and densified through different techniques, namely hot pressing and spark plasma sintering. Dense materials were obtained at 1900 °C by hot pressing and at 1750 °C by spark plasma sintering. Microstructure and mechanical properties were compared. The most relevant result was for high-temperature strength: independent of the processing technique, the flexural strength in air at 1500 °C was higher than 500 MPa.
Morphology studies of a W/Cu alloy synthesized by hydrogen reduction
Authors: Tilliander U. , Bergqvist H. , Seetharaman S.
Published: June 2006

Because of the applications for W/Cu composite materials in high technology, the advantages of synthesizing this alloy by the hydrogen reduction route were investigated, with special attention to the properties of the product that was formed. Kinetic studies of reduction indicated that the mechanism changes significantly at 923 K, and the product had unusual properties. In the present work, morphological studies of the W/Cu alloy with 20 wt% Cu, produced at 923 K, were carried out by x-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) analyses. The structural studies performed by XRD indicated that, at 923 K, Cu dissolved in W, forming a metastable solid solution in the nanocrystalline state. The samples produced at higher as well as lower temperatures, on the other hand, showed the presence of two phases, pure W and pure Cu. The SEM results were in agreement with the XRD analysis and confirmed the formation of W/Cu alloy. TEM analysis results confirmed the above observations and showed that the particle sizes were about 20 nm. The structure of the W/Cu alloy produced in the present work was compared with those for pure Cu, produced from Cu2O produced by hydrogen reduction under similar conditions. This indicated that the presence of W hinders the coalescence of Cu particles, and the alloy retains its nano-grain structure. The present results open up an interesting process route toward the production of intermetallic phases and composite materials under optimized conditions.
Electrical properties of highly oriented Pb(Mg1/3Nb2/3)O3–Pb(Zr,Ti)O3 thin films fabricated by the sol-gel method
Authors: Kang Joon-Koo , Park Chee-Sung , Lee Jae-Wung , Park Gun-Tae , Kim Hyoun-Ee , Choi Jong-Jin
Published: June 2006

Highly (100)- and (111)-oriented lead magnesium niobate–lead zirconate titanate (PMN-PZT) films were deposited on Pt(111)/Ti/SiO2/Si substrates using a sol containing polyvinylpyrrolidone (PVP). The molar ratio of Zr/Ti in the PZT was fixed at 60/40, and the PMN content was changed in the range of 0–30 mol%. The films had a dense and columnar microstructure with a thickness of about 1 μm as a result of being spun four times. The crystallographic orientation of the films was controlled by adjusting the pyrolysis temperature; a (100) orientation was obtained by pyrolyzing at 300 °C and a (111) orientation by pyrolyzing at 350 °C. The electrical properties of the films were strongly dependent on the crystallographic orientation and PMN content. With increasing PMN content, the dielectric constant of all of the films increased. On the other hand, the remnant polarization of the (111)-oriented films decreased steadily with increasing PMN content, while that of the (100)-oriented films remained unchanged up to a PMN content of 20%. The piezoelectric coefficients of the (100)-oriented film were consistently higher than those of the (111)-oriented film with the same composition. The highest piezoelectric coefficient was observed for the (100)-oriented film with a composition of 0.2PMN–0.8PZT, indicating the morphotropic phase boundary between the rhombohedral PZT phase and the pseudocubic PMN phase is in the vicinity of this composition.
Surface evolution of strained SrRuO3 films deposited at various temperatures on SrTiO3 (001) substrates
Authors: Oh Sang Ho , Park Chan Gyung
Published: June 2006

Surface evolution was studied for strained SrRuO3 films with a nominal 75 nm thickness deposited at various substrate temperatures (650–850 °C). Epitaxial growth of the films was achieved on single TiO2-terminated SrTiO3 (001) substrates by using ion-beam sputtering. The surface morphology of the deposited films was investigated by scanning tunneling microscopy in ambient conditions, and their microstructure was characterized by transmission electron microscopy. The self-organized step-terrace structure was observed for the films deposited at lower than 800 °C, suggesting that the epitaxial growth proceeded by step-flow growth. In particular, each film showed characteristic surface evolutions pertinent to the misfit strain relaxation stage, mostly influenced by the moving segment of misfit dislocations threading up to the surface: surface undulations for the film at the initial stage of relaxation (deposited at 650 °C), circular growth spirals during the relaxation stage (700 °C), and well-ordered step-terrace structure after almost full development of misfit dislocations (750 and 800 °C).
Observation of linear defects in Al particles below 7 nm in size
Authors: Louzguine-Luzgin Dmitri V. , Inoue Akihisa
Published: June 2006

An as-solidified structure of an Al-based ribbon sample produced by the melt-spinning technique was studied by x-ray diffractometry and transmission electron microscopy. The addition of Pd to Al-Y-Ni-Co alloys caused formation of the highly dispersed primary α-Al nanoparticles about 3–5 nm in size homogeneously embedded in the glassy matrix upon solidification. The first direct observation of microstrain and dislocations quenched in nanoparticles with a size below 7 nm is provided.
Zr-Cu-Ni-Al-Ta glassy matrix composites with enhanced plasticity
Authors: Dong Wenbo , Zhang Haifeng , Sun Wensheng , Wang Aimin , Li Hong , Hu Zhuangqi
Published: June 2006

(Zr62Cu15.4Ni12.6) (x = 6–12) in situ glassy composites containing uniformly distributed Ta-rich particles were prepared by arc-melting and copper mould casting. The results show that addition of 6–10 at.% Ta to Zr62Cu15.4Ni12.6Al10 results in dissolution of 2.4 to 4.6 at.% Ta in the glassy matrix, which promotes glass-forming ability, and the remaining Ta precipitates out as body-centered cubic (BCC) Ta-rich particles dispersed on the glassy matrix. The critical diameters for the composites with 6, 8, and 10 at.% Ta are 7, 7, and 6 mm, respectively. At 12 at.% Ta addition, the glass-forming ability is dramatically reduced because of the precipitation of secondary dendritic Ta-rich particles and other nanocrystallites from melts during copper mould casting. Also, owing to the solid-liquid reaction during induction heating, some Ta-rich particles formed in the master alloys will redissolve into the glassy matrix, resulting in a smaller volume fraction of Ta-rich particles in the as-cast glassy rods than that of the corresponding ingots. The glassy matrix composites exhibit enhanced plastic strain of about 7.5 to 22.5% at room temperature. The optimum Ta content in the glassy alloys is determined to be 10 at.%, which corresponds to the highest ultimate stress of 2220 MPa and the largest plastic strain of 22.5%. The plastic strain increases with increasing volume fraction of in situ BCC Ta-rich particles. This is apparently ascribed to the impedance of Ta-rich particles to shear bands. Ta-rich particles seed the initiation of multiple shear bands and block the shear band propagation, leading to intensive multiplication and bifurcation of shear bands.
Contact creep compliance of viscoelastic materials via nanoindentation
Authors: Tweedie Catherine A. , Van Vliet Krystyn J.
Published: June 2006

The creep compliance of viscoelastic materials such as synthetic polymers is an established metric of the rate at which strain increases for a constant applied stress and can, in principle, be implemented at the nanoscale to compare quantitatively bulk or thin film polymers of different structures or processing histories. Here, we outline the evolution of contact creep compliance analysis and application for both conical and spherical indenter geometries. Through systematic experiments on four amorphous (glassy) polymers, two semi-crystalline polymers and two epoxies, we show that assumptions of linear viscoelasticity are not maintained for any of these polymers when creep compliance is measured via conical indentation at the nanoscale, regardless of the rate of stress application (step or ramp). Further, we show that these assumptions can be maintained to evaluate the contact creep complianceJc(t) of these bulk polymers, regardless of the rate of stress application, provided that the contact strains are reduced sufficiently through spherical indentation. Finally, we consider the structural and physical properties of these polymers in relation toJc(t), and demonstrate thatJc(t) correlates positively with molecular weight between entanglements or crosslinks of bulk, glassy polymers.
Interfacial reactions and shear strength on Cu and electrolytic Au/Ni metallization with Sn-Zn solder
Authors: Yoon Jeong-Won , Jung Seung-Boo
Published: June 2006

The interfacial reaction between eutectic Sn-9 wt% Zn solder and two different kinds of ball-grid-array substrates (Cu and Au/Ni electroplated Cu) during aging at 150 °C and the shear strength of the resulting joints were investigated. In the Sn-9Zn/Cu joints, only Cu5Zn8 intermetallic compound (IMC) was observed between the solder and Cu layer during the first 100 h of aging. After aging for 1000 h, the layer-type Cu5Zn8 IMC layer was disrupted at the interface, causing it to act as a channel for the diffusion of Sn. As a result, Cu6Sn5 and Cu3Sn IMCs were formed underneath the Cu5Zn8 IMC layer. This interfacial reaction significantly degraded the joint strength. In the case of the Au/Ni/Cu substrate, an AuZn3 IMC layer formed at the interface because of the fast reaction between Au and Zn. In addition, the AuZn3 IMC layer became detached from the interface during reflow. The detachment of the AuZn3 IMC layer is presumably from the mismatch in the coefficients of thermal expansion and weak adhesion between the AuZn3 IMC layer and Ni layer caused by the depletion of the Au layer. When the aging time was extended to 100 h, Ni5Zn21 IMC was observed on the Ni substrate. The shear strength of the aged Sn-9Zn/Au/Ni/Cu joint was significantly related to the detachment of the AuZn3 IMC layer. After aging at 150 °C, fracturing occurred on the detached AuZn3 IMC layer. To ensure the reliability of the Sn-Zn/Au/Ni/Cu joint, the detachment of the AuZn3 IMC needs to be prevented.
Overexpression and Characterization of the Rhodobacter sphaeroides PufX Membrane Protein in Escherichia coli †
Authors: Onodera Shiho , Suzuki Hiroaki , Shimada Yuichiro , Kobayashi Masayuki , Nozawa Tsunenori , Wang Zheng‐Yu
Published: June 2006

Heterologous expression of the PufX membrane protein from purple photosynthetic bacterium Rhodobacter sphaeroides was attempted by using Escherichia (E.) coli cells. The PufX was overexpressed as a recombinant protein with a histidine tag added to the carboxyl terminus, and can be extracted from the cell membrane by various detergents. Circular dichroism measurements showed that the expressed PufX protein had α‐helix contents of 29% in organic solvents and 22–26% in 0.8–2.0% (w/v) n‐octyl β‐d‐glucopyranoside solutions, suggesting that the PufX contains a substantial α‐helical region composed of 18–22 amino acids. The PufX expressed in E. coli was examined by reconstitution experiments with LH1 α‐ and β‐polypeptides and bacteriochlorophyll a. It was shown that the PufX inhibited not only the reconstitution of the LH1 complex, but also the formation of the B820 subunit type complex at high concentrations, indicating that the expressed PufX is biologically active. Large‐scale expression of the functional PufX membrane protein provides sufficient quantity for further biophysical and structural analyses of its biological function, and adds another example for producing highly hydrophobic integral membrane proteins using the E. coli expression system.
Mechanistic Studies on the Photochemical Deprotection of 3′,5′‐Dimethoxybenzoin Esters
Authors: Pirrung Michael C. , Ye Tong , Zhou Zheng , Simon John D.
Published: June 2006

Several mechanistic alternatives proposed for the photochemical deprotection of dimethoxybenzoin esters are presented. Both experimental and theoretical evidence suggest the mechanism is heterolysis of the singlet excited state to form a carbox‐ylate and the α‐ketocation. The α‐ketocation has been observed by transient spectroscopy. We propose the α‐ketocation undergoes electrocyclization to an intermediate with extended conjugation, whose deprotonation gives the observed benzofuran product. A Brønsted study of the rates of benzofuran formation with dimethoxybenzoin esters derived from acids of varying pKa shows the rate is independent of the basicity of the leaving group. In this multistep reaction, benzofuran formation by a final deprotonation is slower than α‐ketocation generation.
Geographic Variation in Somatic Growth of Redside Shiner
Authors: Houston Derek D. , Belk Mark C.
Published: June 2006

The geographic variation in growth rate and resulting body size is poorly known for most fish species. In this paper, we used data derived from otoliths to describe patterns of growth in redside shiners Richardsonius balteatus from seven native populations across the southern portion of its range, and we compare growth with latitude, elevation, and growing season to determine which of these environmental factors best predicts the growth patterns among these populations. To determine whether observed differences in growth resulted from environmental or genetic variation, we conducted a common‐environment experiment on fish from three of the seven populations that showed contrasting patterns between latitude and length of growing season. Redside shiners exhibited about a 60% difference in size at age among populations in their natural environments. Growing season length was the best predictor of body size among these populations (Akaike weight = 0.78). In a common environment, temperature‐specific growth rates differed among populations, indicating that some of the observed differences in size at age among populations are genetically based. Although populations of redside shiners with shorter growing seasons exhibited higher field growth rates than expected, the pattern of variation in individual growth rates among populations in a common environment was not consistent with either a countergradient variation model or a local adaptation model of growth.
Thermal Habitat Use by Lake Trout in Two Contrasting Yukon Territory Lakes
Authors: Mackenzie‐Grieve Jody L. , Post John R.
Published: June 2006

Thermal habitat use by lake trout Salvelinus namaycush in two northern lakes in the southern portion of the Yukon Territory that differ in morphometry and thermal regime was monitored using temperature‐sensitive acoustics and radiotelemetry. We then contrasted in situ temperature selection by lake trout in these lakes with previously published estimates of the species' optimal thermal range of 8–12°C. We found that thermal habitat use by lake trout in the two northern lakes is not consistent with these literature‐derived expectations. In Dezadeash Lake, which is isothermal in summer, temperatures typically exceeded the literature‐derived upper limit of 12°C. Throughout the summer lake trout sought the coldest water in the lake, which was in the form of shallow coldwater plumes derived from alpine ice‐pack meltwater streams. Once lake temperatures declined in the fall, lake trout were distributed throughout the lake. In Kathleen Lake, where water temperatures ranged from approximately 2°C to 12°C in the summer, the majority of lake trout selected habitats throughout the summer and fall that were colder than the 8°C lower limit of their literature‐derived optimal thermal range. Our results highlight the importance of summer thermal refugia for lake trout inhabiting marginal systems and the variation in thermal habitat use among populations inhabiting different thermal environments. Given the established importance of thermal habitat availability to lake trout production, our results suggest the need to better understand optimal thermal habitat characteristics in nature, particularly in light of factors such as climate warming.
Computer Usage and Reading in Elementary Schools: A Cross-Cultural Study
Authors: Lai Shu-Ling , Chang Tai-Shent , Ye Renmin
Published: June 2006

This study uses international data to investigate computer use situations in elementary school reading classes and the impacts of computer usage on students' reading performance across 15 countries. The study compares and reveals computer use levels in reading classes, frequencies of teachers having students use computers, times and places of students' computer usage, computer activities of male and female students, and effects of computer usage on students' reading interests and achievement by country. The results provide worldwide summary views of computer use in elementary school reading classes.
Validation of the Business Computer Self-Efficacy Scale: Assessment of the Computer Literacy of Incoming Business Students
Authors: Stephens Paul
Published: June 2006

The business computer self-efficacy (BCSE) scale is potentially an important tool for researchers studying business students and professionals, but it needs to be validated for use. Content validity was established by Stephens and Shotick (2002). This research analyzes the scale under both criterion-related and construct validation. The scale is compared to a similar scale that has already been validated through research (Murphy, Coover & Owen, 1989). Intercorrelational patterns are examined among these two scales designed to measure the same construct (computer self-efficacy). The results reveal that the two scales are highly correlated. Additionally, the scale is used to demonstrate that it can be used to choose the appropriate type of computer training. Research theorizes that low computer self efficacy will lead individuals to circumvent experiences with computer technology (Stephens & Shotick, 2002). This article provides evidence that subjects with low computer self-efficacy will avoid interacting with computer technology when given a choice.
Addressing the Nets for Students Through Constructivist Technology Use in K–12 Classrooms
Authors: Niederhauser Dale S. , Lindstrom Denise L.
Published: June 2006

The National Educational Technology Standards for Students promote constructivist technology use for K-12 students in U.S. schools. In this study, researchers reported on 716 cases in which teachers described technology-based activities they conducted with their students. Narrative analysis was used to examine case transcripts relative to the NETS*S, and the constructivist principles that support them. Findings suggest teachers' instructional technology use has shifted from the drill-and-practice and word-processing usage that was so pervasive in the 1980s and 1990s, to more constructive hands-on tool-based uses. However, teachers missed opportunities to engage their students in higher-order thinking when they limited problem-solving potential and over-structured student design activities.
Cloud Piercer: Mile High
Authors: Schwinge Jonathan
Published: June 2006

Conceived by Jonathan Schwinge as a hypothetical model for the tallest and largest megastructural project in world ‐ the Thames Estuary ‐ Cloud Piercer would be an oceanic vertical supercity to meet the rate of anticipated economic and population growth throughout the world.
Mass Customisation and the Manufactured Module
Authors: Woudhuysen James
Published: June 2006

James Woudhuysen, Professor of Forecasting and Innovation at De Montfort University, and co‐author of Why is Construction So Backwards? (Wiley‐Academy, 2004), talks to Stephen Kieran and James Timberlake of KieranTimberlake Architects about how they are setting out to refabricate architecture.
Think Big for the Developing World
Authors: Dingle Ceri , Regan Viv
Published: June 2006

2005 was tagged the ‘year of Africa’. In fact, it should go down in history as the year Africa's development was firmly reined in by Western policy‐makers, say Ceri Dingle and Viv Regan, director and assistant director of the education charity, NGO and NVYO WORLD. Africa needs development, but not the small‐minded sustainable variety. Could it be that a lack of confidence and ambition in development among the industrialised nations is holding back the developing world?
Frequency of genomic rearrangements involving the SHFM3 locus at chromosome 10q24 in syndromic and non‐syndromic split‐hand/foot malformation
Authors: Everman David B. , Morgan Chad T. , Lyle Robert , Laughridge Mary E. , Bamshad Michael J. , Clarkson Katie B. , Colby Randall , Gurrieri Fiorella , Innes A. Micheil , Roberson Jacquelyn , Schrander‐Stumpel Connie , van Bokhoven Hans , Antonarakis Stylianos E. , Schwartz Charles E.
Published: June 2006

Split‐hand/foot malformation (SHFM), or ectrodactyly, is characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM occurs as both an isolated finding and a component of many syndromes. SHFM is a heterogeneous condition caused by multiple loci, including SHFM1 (chromosome region 7q21‐q22), SHFM2 (Xq26), SHFM3 (10q24), SHFM4 (3q27), and SHFM5 (2q31). Mutations in TP63 at the SHFM4 locus are known to underlie both syndromic and non‐syndromic forms SHFM, but the causes of most non‐syndromic SHFM cases remain unknown. The recent identification of submicroscopic tandem chromosome duplications affecting the SHFM3 locus in seven families with non‐syndromic SHFM has helped to further unravel the molecular basis of this malformation. In our ongoing studies of the SHFM3 locus in 44 additional cases of syndromic and non‐syndromic SHFM, we have identified similar chromosome rearrangements in eight additional cases (18%), using pulsed‐field gel electrophoresis (PFGE). We have also utilized real‐time quantitative PCR (qPCR) to test for the duplications. Seven of the cases with rearrangements were non‐syndromic. The current findings bring the total of SHFM3‐associated cases with chromosome rearrangements to 15, which constitute 29% (15 of 51) of the cases screened to date. This includes 9 of 9 cases (100%) with known linkage to the SHFM3 locus, all of whom have non‐syndromic SHFM, and 6 of 42 additional cases (14%), four of whom have non‐syndromic SHFM. Thus, SHFM3 abnormalities underlie a substantial proportion of SHFM cases and appear to be a more frequent cause of non‐syndromic SHFM than mutations in TP63. © 2006 Wiley‐Liss, Inc.
Mosaicism for a full mutation, premutation, and deletion of the CGG repeats results in 22% FMRP and elevated FMR1 mRNA levels in a high‐functioning fragile X male
Authors: Han Xiao‐Dong , Powell Berkley R. , Phalin Judith L. , Chehab Farid F.
Published: June 2006

The molecular basis in the majority of fragile X patients results from expansion of the CGG repeats in the FMR1 gene causing its transcriptional silencing and deficiency of its encoded protein FMRP. In this communication, we report on a male patient who lacks the characteristic physical features of fragile X and carries a fully methylated mutation, a premutation, a non‐methylated full mutation, and a microdeletion encompassing the entire CGG repeat region and 42 bp of upstream flanking sequence. Southern blot analysis revealed that the methylated full mutation accounted for only 10% of his genotype while the premutation/non‐methylated full mutation and the microdeletion constituted 37% and 53%, respectively. Immunofluorescent staining of FMRP demonstrated the presence of 22% FMRP in his peripheral blood leukocytes and quantitative RT‐PCR revealed a 3.6‐fold elevation of FMR1 mRNA levels. Developmental assessments indicated that while he has a learning disability, he does not have mental retardation. Because previous reports had noted that 28% FMRP expression is associated with a characteristic fragile X phenotype, we propose that in our patient the association of 22% FMRP levels with normal physical features and a high‐functioning status may have resulted from increased FMRP stability by a mechanism that takes into account the CGG microdeletion and elevated mRNA levels. © 2006 Wiley‐Liss, Inc.
The near universal presence of autism spectrum disorders in children with Smith–Lemli–Opitz syndrome
Authors: Sikora Darryn M. , Pettit‐Kekel Kersti , Penfield Jennifer , Merkens Louise S. , Steiner Robert D.
Published: June 2006

Smith–Lemli–Opitz syndrome (SLOS) is an autosomal recessive condition caused by a defect in cholesterol synthesis. Affected children often have malformations and mental retardation. Autistic behaviors also are evident. The purpose of the present study was to determine the prevalence of autism spectrum disorders (ASDs) in children with SLOS. Fourteen children, 3–16 years old, were evaluated using three different methods to document autistic symptoms: (a) parent interview, (b) direct observation, and (c) a behavior checklist. Blood sterols were also measured at regular intervals. Each subject was determined to have Autistic Disorder, Pervasive Developmental Disorder, not otherwise specified (PDD NOS), or no diagnosis on the autism spectrum, based on DSM‐IV criteria. Correlations among variables were calculated, and blood sterol levels were compared between diagnostic groups. Approximately three‐fourths of the children with SLOS (71–86% depending on the evaluation method) had an ASD, about 50% diagnosed with Autistic Disorder and the rest with PDD NOS. The children's baseline cholesterol, 7‐dehydrocholesterol (7‐DHC), and 8‐dehydrocholesterol (8‐DHC) levels, and cholesterol levels following supplementation did not correlate with the presence or severity of autistic symptoms. These results suggest that most children with SLOS have some variant of autism. SLOS appears to have the most consistent relationship with autism of any single gene disorder. Therefore, a link between cholesterol metabolism and autism is suggested. With further study, these findings, together with knowledge of the genetic and biochemical defects in SLOS, will likely provide valuable insights into the causes of autism in general. © 2006 Wiley‐Liss, Inc.
Stabilization of bzip Peptides through Incorporation of Fluorinated Aliphatic Residues
Authors: Son Soojin , Tanrikulu I. Caglar , Tirrell David A.
Published: June 2006

Two fluorinated amino acids, 5,5,5‐trifluoroisoleucine (5TFI) and (2S,3R)‐4,4,4‐trifluorovaline (4TFV), which have been shown to serve as isoleucine surrogates in protein synthesis in Escherichia coli, have been incorporated in vivo into basic leucine zipper (bzip) peptides derived from GCN4. The extents of residue‐specific incorporation of 5TFI and 4TFV were 90 and 88 %, respectively, of the encoded isoleucine residues, as evidenced by MALDI mass spectrometry and amino acid analysis. Both circular dichroism and equilibrium sedimentation studies of the fluorinated bzip peptides indicated preservation of secondary and higher‐order protein structure. Thermal‐denaturation experiments showed an increase of 27 °C in melting temperature when isoleucine was replaced by 5TFI. However, the Tm of the peptide containing 4TFV was increased by only 4 °C over that of the peptide containing valine. Similar trends were observed in chemical denaturation studies in which ΔΔGunfold in water was determined to be 2.1 or 0.3 kcal mol−1 upon incorporation of 5TFI or 4TFV, respectively. When the fluorinated peptides were tested for DNA binding, both their affinity and specificity were similar to those of the respective hydrogenated peptides. These results suggest that fluorinated amino acids, even when introduced into the same positions, can have markedly different effects on the physical properties of proteins, while having little impact on secondary and higher‐order structure.
Impact of 16‐slice computed tomography in percutaneous coronary intervention of chronic total occlusions
Authors: Yokoyama Naoyuki , Yamamoto Yoshito , Suzuki Shigeru , Suzuki Masatoshi , Konno Kumiko , Kozuma Ken , Kaminaga Tatsuro , Isshiki Takaaki
Published: June 2006

The main reason for failure of percutaneous coronary intervention (PCI) of chronic total occlusion (CTO) is because the calcified plaque prevents the guide wire crossing the occlusion. We aimed to identify the route, and characterize plaque components within CTO, using 16‐slice computed tomography (MSCT). Twenty three angiographic CTO in 22 patients (mean age 69 ±± 5 years, 17 males) were included. All patients had undergone MSCT prior to PCI. Images were analyzed for lesion visibility and plaque characteristics of CTO. The presence and location of calcified plaque within the CTO were systematically assessed. Each lesion was classified as a noncalcified, moderately calcified, or exclusively calcified plaque. Procedural failure was defined as the inability to cross a guide wire through the occlusion. All coronary routes of CTO segment were visualized. MSCT revealed three markedly bent CTO segments (13.0%), which could not be identified by coronary angiography only. Calcified plaques were detected in 30 lesions of 19 CTO segments (82.6%), but were not detected in the other four. The majority of calcified plaque was located in the proximal lesion, or both proximal and distal lesions. Fifteen out of 30 calcified lesions (50.0%) were exclusively calcified plaques. Overall procedural success was obtained in 21 CTOs (91.3%). MSCT can accurately identify the route of the CTO segment and evaluate both distribution and amount of the calcified plaque within it. Even with the complicated and/or calcified lesions, PCI success rate was excellent under MSCT guidance. MSCT should become a useful tool in PCI of CTO. © 2006 Wiley‐Liss, Inc.