bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical consequences of sedlin mutations that cause spondyloepiphyseal dysplasia tarda
Authors: Choi Mei Y. , Chan Caleb C. Y. , Chan Danny , Luk Keith D. K. , Cheah Kathryn S. E. , Tanner Julian A.
Published: August 2009

SEDT (spondyloepiphyseal dysplasia tarda) is a late-onset X-linked recessive skeletal dysplasia caused by mutations in the gene SEDL coding for sedlin. In the present paper, we investigated four missense mutations observed in SEDT and compare biochemical and cellular characteristics relative to the wild-type protein to address the mechanism of disease and to gain insight into the function of the sedlin protein. In situ hybridization and immunohistochemical experiments in mouse growth plates revealed sedlin to be predominantly expressed in proliferating and hypertrophic chondrocytes. Cell culture studies showed that the wild-type protein localized predominantly in the vicinity of the nucleus and the Golgi, with further localization around the cytoplasm, whereas mutation resulted in mislocalization. The D47Y mutant was expressed similarly to the wild-type, but the S73L, F83S and V130D mutants showed particularly low levels of expression that were rescued in the presence of the proteasome inhibitor MG132 (benzyloxycarbonyl-leucylleucylleucinal). Furthermore, whereas the D47Y mutant folded similarly and had similar stability to the wild-type sedlin as shown by CD and fluorescence, the S73L, F83S and V130D mutants all misfolded during expression. Two independent assays showed that the D47Y mutation resulted in an increased affinity for the transport protein particle component Bet3 compared with the wild-type sedlin. Our results suggest that the sedlin mutations S73L, F83S and V130D cause SEDT by sedlin misfolding, whereas the D47Y mutation may influence normal TRAPP (transport protein particle) dynamics.
Combined polarized Raman and atomic force microscopy: In situ study of point defects and mechanical properties in individual ZnO nanobelts
Authors: Lucas Marcel , Wang Zhong Lin , Riedo Elisa
Published: August 2009

We present a method, polarized Raman (PR) spectroscopy combined with atomic force microscopy (AFM), to characterize in situ and nondestructively the structure and the physical properties of individual nanostructures. PR-AFM applied to individual ZnO nanobelts reveals the interplay between growth direction, point defects, morphology, and mechanical properties of these nanostructures. In particular, we find that the presence of point defects can decrease the elastic modulus of the nanobelts by one order of magnitude. More generally, PR-AFM can be extended to different types of nanostructures, which can be in as-fabricated devices.
Extending the Navier–Stokes solutions to transition regime in two-dimensional micro- and nanochannel flows using information preservation scheme
Authors: Roohi Ehsan , Darbandi Masoud
Published: August 2009

The kinetic-theory-based numerical schemes, such as direct simulation Monte Carlo (DSMC) and information preservation (IP), can be readily used to solve transition flow regimes. However, their high computational cost still promotes the researchers to extend the Navier–Stokes (NS) equations beyond the slip flow and to the transition regime applications. Evidently, a suitable extension would accurately predict both the local velocity profiles and the mass flow rate magnitude as well as the streamwise pressure distribution. The second-order slip velocity model derived from kinetic theory can provide relatively accurate velocity profiles up to a Knudsen (Kn) number of around 0.5; however, its mass flow rate accuracy decreases as Knudsen number approaches the upper bound. One remedy is to consider the rarefaction effects in calculating the NS viscosity coefficient. In this work, we use the shear stress distribution derived from our IP simulations, extend an analytical expression for the viscosity coefficient, impose it in the NS equations, and evaluate it via solving the transition regime. Using the new viscosity coefficient, we also derive an analytical expression for the mass flow rate, which provides accurate solutions for Kn<0.5 and even beyond in micro- and nanochannel flows. We also show that the obtained streamwise pressure distribution agrees well with that of the DSMC-IP in this range. The current study is concerned with low speed diatomic gas flow through two-dimensional micro- and nanochannels.
Multiple scattering x-ray photoelectron diffraction study of the SrTiO3(100) surface
Authors: Pancotti A. , Barrett N. , Zagonel L. F. , Vanacore G. M.
Published: August 2009

The atomic surface structure of SrTiO3(100) after annealing at 630 °C in vacuum is investigated by x-ray photoelectron diffraction (XPD) using the Sr 3d5/2 core level. The photoelectron diffraction peaks are successfully assigned by considering the forward scattering of photoelectrons by the atomic potential near the emitter atom in the lattice. The strongest diffraction peaks are aligned along the single crystal internuclear axes. We compare the results of photoelectron multiple scattering calculations (MSC) of SrO and TiO2 terminated SrTiO3(100) surfaces, including surface relaxation and rumpling, with the experimental data. For TiO2 and SrO terminated SrTiO3(100) surfaces, all top-layer cations relax inward, whereas second-layer atoms relax outward. The surface rumpling for SrO- and TiO2-terminated surfaces agrees well with low-energy electron diffraction results. Using a genetic algorithm the best agreement of MSC to the experimental XPD data is obtained for a SrO terminated surface with a 30% coverage of 3 ML SrO(100) islands.
Arrangement of band structure for organic-inorganic photovoltaics embedded with silicon nanowire arrays grown on indium tin oxide glass
Authors: Kuo Cheng Yung , Gau Chie
Published: August 2009

Silicon nanowires (SiNWs) arrays grown vertically on an indium tin oxide glass substrate by the vapor liquid solid process are covered with poly (3-hexylthiophene) (P3HT) mixed with [6,6]-phenyl-C60-butyric acid methyl ester (PCBM) to make into a hybrid solar cell. With proper control of the nanowire size and arrangement of the band structure suitable for charge carrier transport, the P3HT/SiNWs solar cell can have a much better energy conversion efficiency than the P3HT+PCBM solar cell. Poor band structure arrangement can lead to band barrier and enhanced electron-hole pair recombination and much lower efficiency even with more light absorption.
Generating function of spin correlation functions for kinetic Glauber–Ising model with time-dependent transition rates
Authors: Aliev M. A.
Published: August 2009

The exact analytical solution in quadratures have been found for the generating function of spin correlation functions for the Reiss variant of the kinetic Ising model that is the extension of the Glauber–Ising model to account for the dependence of heat bath temperature on time.
Micrometric spatial control of rare earth ion emission in LiNbO3: A two-dimensional multicolor array
Authors: Molina P. , Ramírez M. O. , García-Santizo J. V. , Álvarez-García S. , Pazik R. , Strek W. , Dereń P. J. , Bausá L. E.
Published: August 2009

We report on the preparation and optical characterization of a two-dimensional multicolor emission arrangement obtained by embedding high refractive-index Er3+ doped CaTiO3 nanoparticles into a Nd3+ doped LiNbO3 crystal substrate prepatterned with an array of microvoids. By controlling the spatial location of the rare earth ions at the micrometer scale, we show the possibility of simultaneous spatial and spectral control of the spontaneous emission in a two-dimensional rare earth optically activated array. The results can be useful for the development of microcomposite rare earth based photonic devices, such as multicolor emission displays or pixelated color structures.
Surface relief grating formation on nano-objects
Authors: Barillé R. , Tajalli P. , Zielinska S. , Ortyl E. , Kucharski S. , Nunzi J. M.
Published: August 2009

We exploit the photoinduced migration effect in azopolymer thin films to induce surface relief patterning of nano-objects. Manipulation and precise control of the molecular order is achieved at the nanoscale. Interaction between a laser beam from an argon laser and the azopolymer nano-objects induces structures on the surface. The self-patterning process is observed to depend on the laser beam polarization.
Morphology, orientation relationship, and stability analysis of Cu2O nanoclusters on SrTiO3 (100)
Authors: Kuchibhatla Satyanarayana V. N. T. , Hu S. Y. , Yu Z. Q. , Shutthanandan V. , Li Y. L. , Nachimuthu P. , Jiang W. , Thevuthasan S. , Henager C. H. , Sundaram S. K.
Published: August 2009

Reflection high energy electron diffraction, atomic force microscopy, and theoretical studies based on classical nucleation theory have been used to interpret the morphology, orientation relationship, and stability of Cu2O nanoclusters on SrTiO3 (100) (STO). We propose that the competing interfacial and elastic energies facilitate an in-plane rotation of the Cu2O clusters by 45° with respect to the STO substrate and stabilize Cu2O clusters on STO(100) with an orientation relationship of (001)Cu2O//(001)SrTiO3 and ⟨100⟩Cu2O//⟨110⟩SrTiO3. Our preliminary theoretical analysis also suggests that this particular orientation results in smaller critical nucleus sizes and lower nucleation barriers and also indicates a chemical potential (growth rate) dependence of the orientation relationship.
Nanostructured semiconductor heterojunctions from quantum dot layers
Authors: Könenkamp R. , Nadarajah A. , Word Robert C.
Published: August 2009

We report the deposition of conformal thin layers of 10–50 nm thickness from II-VI quantum dot suspensions on ZnO nanowire substrates. Smooth polycrystalline films of high electronic quality can be obtained from CdSe quantum dots after annealing at moderate temperatures. The electronic properties are adequate for detector and solar cell applications. The growth and annealing temperatures permit deposition on light-weight and flexible substrates. Some elemental diffusion of Se across the CdSe/ZnO interface occurs in the film formation. A comparison with CdS/ZnO junctions indicates that the low Se diffusion rates are essential for efficient charge transfer.
Blue-emitting LaSi3N5:Ce3+ fine powder phosphor for UV-converting white light-emitting diodes
Authors: Suehiro Takayuki , Hirosaki Naoto , Xie Rong-Jun , Sato Tsugio
Published: August 2009

We have synthesized the pure ternary nitride phosphor, LaSi3N5:Ce3+ from the multicomponent oxide system La2O3–CeO2–SiO2, by using the gas-reduction-nitridation method. Highly pure, single-phase LaSi3N5:Ce3+ powders possessing particle sizes of ∼0.4–0.6 μm were obtained with the processing temperature ≤1500 °C. The synthesized LaSi3N5:Ce3+ exhibits tunable blue broadband emission with the dominant wavelength of 464–475 nm and the external quantum efficiency of ∼34%–67% under excitation of 355–380 nm. A high thermal stability of LaSi3N5:Ce3+ compared to the existing La–Si–O–N hosts was demonstrated, indicating the promising applicability as a blue-emitting phosphor for UV-converting white light-emitting diodes.
Transition from static to kinetic friction of metallic nanoparticles
Authors: Dietzel Dirk , Feldmann Michael , Fuchs Harald , Schwarz Udo D. , Schirmeisen André
Published: August 2009

Nanometer scale metallic islands were manipulated on a graphite surface by placing the tip of an atomic force microscope on top of the particles. Above a certain lateral force threshold particle sliding is observed, which allows us to quantify the transition from static to kinetic friction. This transition shows hysteretic character in the force domain and is characterized by a constant ratio of kinetic versus static friction of one half.
Time-dependent barrier passage of two-dimensional non-Ohmic damping system
Authors: Wang Chun-Yang
Published: August 2009

The time-dependent barrier passage of two-dimensional non-Ohmic damping system is studied in the framework of statistical Langevin reactive dynamics. The stationary transmission coefficient is found to be a nonmonotonic function of the exponent δ which reveals an intrinsic effect of the friction’s non-Markovian character on the two-dimensional reactive process; the coupling between nonreactive and reactive modes results in an optimal path for the reactant in all cases of non-Ohmic friction. A big net flux resulted from the less barrier recrossing behavior in the two-dimensional non-Ohmic friction case.
Burn-in mechanism of 450nm InGaN ridge laser test structures
Authors: Müller Jens , Brüderl Georg , Schillgalies Marc , Tautz Sönke , Dini Dimitri , Breidenassel Andreas , Galler Bastian , Lutgen Stephan
Published: August 2009

We investigated the short term stability of the optical output power of 450nm InGaN test lasers. The short term degradation strongly depended on ridge width. It was mainly caused by an increase in threshold current. From measurements of subthreshold wave-length blueshift, carrier lifetime, and output power, we found a decrease in carrier density after 15h of aging. We show a direct correlation of the short term aging with current spreading effects.
The role of stress in the time-dependent optical response of silicon photonic band gap crystals
Authors: Wei H. , Underwood D. F. , Han S. E. , Blank D. A. , Norris D. J.
Published: August 2009

Amorphous silicon inverse opals with a complete photonic band gap have been studied with optical pump-probe spectroscopy. The pump-generated free carriers cause the reflection near the band gap to be lowered for the first few picoseconds due to induced absorption. After ∼5 ps, this effect disappears and an unexpected blue spectral shift is seen in the photonic band gap. The shift appears consistent with photoinduced stress caused by the thermal expansion mismatch between the silicon and its native oxide. However, simple mechanical models fail to quantify this behavior.
Polarized micro-Raman study of the field-induced phase transition in the relaxor 0.67PbMg1/3Nb2/3O3–0.33PbTiO3 single crystal
Authors: Yang Y. , Liu Y. L. , Ma S. Y. , Zhu K. , Zhang L. Y. , Cheng J. , Siu G. G. , Xu Z. K. , Luo H. S.
Published: August 2009

Polarized Raman spectroscopy has been performed to investigate the effects of the electric field on 0.67PbMg1/3Nb2/3O3–0.33PbTiO3 (PMN–33%PT) single crystal. The electric-field-evolution of Raman spectra differed from one microarea to another. In the crossed polarization geometry, the abrupt changes in the intensities of the Raman bands at around 570 and 780 cm−1 indicated the occurrence of the field induced phase transition from the MC-type to the MA-type monoclinic structure. On the other hand, the Raman spectra for the microarea that was initially in the MA phase exhibited no obvious changes. All these results revealed the microheterogeneity in PMN–33%PT single crystal, which is useful for understanding the field-induced superior electromechanical properties.
Complete characterization of the constrained geometry bimolecular reaction O(D1)+N2O→NO+NO by three-dimensional velocity map imaging
Authors: Gödecke Niels , Maul Christof , Chichinin Alexey I. , Kauczok Sebastian , Gericke Karl-Heinz
Published: August 2009

The bimolecular reaction O(D1)+N2O→NO+NO was photoinitiated in the (N2O)2 dimer at a wavelength of 193 nm and was investigated by three-dimensional (3D) velocity map imaging. State selective 3D momentum vector distributions were monitored and analyzed. For the first time, kinetic energy resolution and stereodynamic information about the reaction under constrained geometry conditions is available. Directly observable NO products exhibit moderate vibrational excitation and are rotationally and translationally cold. Speed and spatial distributions suggest a pronounced backward scattering of the observed products with respect to the direction of motion of the O(D1) atom. Forward scattered partner products, which are not directly detectable are also translationally cold, but carry very large internal energy as vibration or rotation. The results confirm and extend previous studies on the complex initiated reaction system. The restricted geometry of the van der Waals complex seems to favor an abstraction reaction of the terminal nitrogen atom by the O(D1) atom, which is in striking contrast to the behavior observed for the unrestricted gas phase reaction under bulk conditions.
A charge-passivated codoping approach for enhancing ferromagnetism and electron transport on rutile TiO2(110) surface
Authors: Liu Qinghua , He Jingfu , Mai Cong , Yao Tao , Pan Zhiyun , Sun Zhihu , Yan Wensheng , Wu Ziyu , Wei Shiqiang
Published: August 2009

We performed a first-principles study on the magnetism and electronic character of rutile Fe:TiO2(110) mediated by oxygen vacancies (OVs) and codopant. The results show the magnetic interaction between Fe ions is a ferromagnetic (FM) superexchange nature, while the presence of OV makes it turn to an antiferromagnetic behavior. It is found when the system is codoped with oppositely charged P, the interactions are rehabilitated to FM coupling. The electronic structure analysis reveals that this is principally attributed to the sp-d hybridizations between P and Fe, which finally activate a long-ranged FM interaction between the Fe ions, and substantially facilitate the electron transport.
Tailoring of inclined crystal orientation in layered cobaltite thin films for the development of off-diagonal thermoelectric effect
Authors: Takahashi Kouhei , Sakai Akihiro , Kanno Tsutomu , Adachi Hideaki
Published: August 2009

A highly inclined CoO2 plane orientation was realized in CaxCoO2 thin films grown on sapphire single crystal substrates. The inclination angle of the CoO2 plane orientation was controlled by changing the inclination angle of the sapphire(0001) plane with respect to the substrate surface and additionally by introducing an epitaxial buffer layer of hematite. We demonstrate that the highly inclined crystal orientation results in a unique off-diagonal thermoelectric effect with a potential to produce a voltage signal of up to 600 mV along the film in-plane direction by a unit temperature difference along the film out-of-plane direction.
Increasing permittivity in HfZrO thin films by surface manipulation
Authors: Böscke T. S. , Hung P. Y. , Kirsch P. D. , Quevedo-Lopez M. A. , Ramírez-Bon R.
Published: August 2009

We report on the electrical and physical characterization of nanoscale crystalline HfxZr1−xO2 films by x-ray diffraction (XRD) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. Increasing the ZrO2 content generally led to an increase in tetragonal phase fraction and dielectric constant. This was reflected in both XRD and ATR-FTIR measurements. We demonstrate that not only the composition, but also the distribution of ZrO2 throughout the film determines phase formation. Concentrating ZrO2 at the top surface of the film allowed the dielectric constant to be optimized for a given composition. These observations are explained by a surface energy thermodynamic model.
Freestanding high quality GaN substrate by associated GaN nanorods self-separated hydride vapor-phase epitaxy
Authors: Chao C. L. , Chiu C. H. , Lee Y. J. , Kuo H. C. , Liu Po-Chun , Tsay Jeng Dar , Cheng S. J.
Published: August 2009

This work proposes a method for fabricating 2 in. freestanding GaN substrates of high crystallographic quality and low residual strain. Arrays of GaN nanorods with sidewalls coated with silicon dioxide (SiO2) were randomly arranged on the sapphire substrate as a growth template for subsequent hydride vapor-phase epitaxy (HVPE). The passivation of the sidewalls coated with SiO2 prevents the coalescence of GaN grains in spaces between the rods, causing them to grow preferentially on the top of individual rods. The proposed method significantly improves GaN crystal quality and results in self-separation from the underlying host sapphire substrate due to the relaxation of thermal strains in the HVPE cooling-down process.
Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations
Authors: Chen Shilu , Fang Wei-Hai
Published: August 2009

In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH3CHO). Stationary structures for H2 and CO eliminations in the ground state (S0) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C–C and C–H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH3CHO (265 nm<λ<318 nm), the T1 C–C bond fission following intersystem crossing from the S1 state is the predominant channel and the minor channel, the ground-state elimination to CH4+CO after internal conversion (IC) from S1 to S0, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S1/S0 intersection point resulting from the S1 C–C bond fission, becomes accessible and increases the yield of CH4+CO.
Quantitative study of interior nanostructure in hollow zinc oxide particles on the basis of nondestructive x-ray nanotomography
Authors: Li Wenjie , Wang Ning , Chen Jie , Liu Gang , Pan Zhiyun , Guan Yong , Yang Yunhao , Wu Wenquan , Tian Jinping , Wei Shiqiang , Wu Ziyu , Tian Yangchao , Guo Lin
Published: August 2009

The complicated three-dimensional interior structures of the polycrystalline hollow zinc oxide microspheres were clearly obtained by the nondestructive nanocomputed tomography (nano-CT) technique. The parameters such as diameter, volume, porosity, and surface area were calculated by the quantitative analysis of reconstructed data. Especially, three single selected particles with different typical structures were separated and compared. With these results, the distinction of the particles can be clearly understood in nanoscale. This study reveals that nano-CT is an effective and competent tool for investigating the three-dimensional interior structures of nanomaterials in the natural environment.
Influence of lattice symmetry on ultrasound transmission through plates with subwavelength aperture arrays
Authors: Estrada Héctor , Candelas Pilar , Uris Antonio , Belmar Francisco , García de Abajo F. Javier , Meseguer Francisco
Published: August 2009

We study the transmission of sound waves through aluminum plates perforated with square and triangular hole arrays. We demonstrate both theoretically and experimentally that lattice symmetry affects the position of the Wood anomalies and the width of the transmission peaks. The angle and frequency dependence of sound transmission through perforated plates are thoroughly discussed. Finally, we observe unexpected anisotropic behavior in the long-wavelength Lamb-mode bands of perforated plates.
Semitransparent inverted polymer solar cells with MoO3/Ag/MoO3 as transparent electrode
Authors: Tao Chen , Xie Guohua , Liu Caixia , Zhang Xindong , Dong Wei , Meng Fanxu , Kong Xiangzi , Shen Liang , Ruan Shengping , Chen Weiyou
Published: August 2009

Semitransparent inverted polymer solar cells were developed using thermally evaporable MoO3/Ag/MoO3 as transparent anode. The ultrathin inner MoO3 layer was introduced as a buffer layer to improve hole collection, while the outer MoO3 layer served as a light coupling layer to enhance optical transmittance of the device. The dependence of the device performances on the thickness of the outer MoO3 layer was investigated. The results showed that the addition of the outer MoO3 layer improves the transmittance of the anode compared to MoO3/Ag anode and the performances of the semitransparent devices with the outer MoO3 layer are improved due to the reduced series resistance.
Dynamic dipolar interaction effect on spin-transfer switching with perpendicular anisotropy
Authors: Qiu Yongcheng , Zhang Zongzhi , Jin Q. Y. , Liu Yaowen
Published: August 2009

Micromagnetic simulation is employed to study the influence of neighboring cells on spin torque switching in a matrix of nanopillars with perpendicular magnetic anisotropy. We find that with the decreased separation the critical switching current densities can be strongly modified for different matrix configurations as compared to an isolated disk element. Such variations are attributed to the stray fields rather than the resonant effect, although both of them arise from the dipolar interaction between the target and neighboring cells. The Bloch wall mediated switching process is evidenced by the magnetization snapshots, which agrees with the recent experimental results.
The origin of stretched exponential function in dynamic response of photodarkening in amorphous chalcogenides
Authors: Shimakawa K. , Nakagawa N. , Itoh T.
Published: August 2009

An increase in the optical absorption coefficient during illumination [photodarkening (PD)] is known to be described by a stretched exponential function (SEF) 1−exp[−(t/τ)β], where τ and β, respectively, are the effective response time and the dispersion parameter. τ and β deduced experimentally depend on the thickness of films. A model calculation, assuming a series sequence of PD along the thickness direction from the illuminated surface to the back surface, produces the SEF and replicates well the experimental results.
Focusing properties of microspheres containing multiconcentric metallic rings
Authors: Chang Chin-Kai , Yeh Chau-Shioung , Lee Chih-Kung , Lai Ming-Wei , Yeh Ji-Tian , Liu Jung-Ming
Published: August 2009

We fabricated multiconcentric metallic rings on a polystyrene microbead by using a focused ion beam. We found this type of structure possesses good focusing properties unlike planar multiconcentric metallic rings, which require varying the width of each ring. In addition, we found that we can change the shape of the bead by heating it, after which we then fabricated multiconcentric metallic rings around it. Our results showed that the focal distance of the structure as well as the size of the focal spot increased as the heating time increased. These kinds of structures have good potential for application to optical imaging and photolithography.
Drag on random assemblies of spheres in shear-thinning and thixotropic liquids
Authors: Derksen J. J.
Published: August 2009

The flow and resulting drag force in suspensions consisting of monodisperse, solid spheres, and non-Newtonian liquids have been studied via direct numerical simulations. The liquids are purely viscous (i.e., nonelastic) with shear thinning and/or thixotropic (time-dependent) behavior. The configuration of spheres is static. The interstitial liquid flow is solved by means of the lattice-Boltzmann method. Only creeping flow conditions have been considered. Thixotropy enters via a network integrity parameter that relates to the local, apparent viscosity and for which a transport equation has been solved. The results show that the shear-thinning character of the liquid manifests itself more pronounced at higher solids volume fractions. Thixotropy tends to increase the drag force due to the decoupling of locations of high deformation rates and low viscosity.
Australian grains free-air carbon dioxide enrichment (AGFACE) facility: design and performance
Authors: Mollah Mahabubur , Norton Rob , Huzzey Jeff
Published: August 2009

The AGFACE project commenced in June 2007 at Horsham (36°45′07″S, 142°06′52″E; 127 m elevation), Victoria, Australia. Its aim is to quantify the interactive effects of elevated atmospheric carbon dioxide concentration (e[CO2]), nitrogen, temperature (accomplished by early and late sowing times), and soil moisture on the growth, yield, and water use of wheat (Triticum aestivum L.) under Australian conditions. The main engineering goal of the project was to maintain an even temporal and spatial distribution of carbon dioxide (CO2) at 550 μmol/mol within AGFACE rings containing the experimental treatments. Monitoring showed that e[CO2] at the ring-centres was maintained at or above 90% of the target (495 μmol/mol) between 93 and 98% of the operating time across the 8 rings and within ±10% of the target (495–605 μmol/mol) between 86 and 94% of the time. The carbon dioxide concentration ([CO2]) measured inside the rings declined non-linearly with increasing distance downwind of the CO2 source and differed by 3–13% in concentration between the two canopy heights in each ring, but was not affected by wind speed or small variations in [CO2] at the ring-centres. The median values for model-predicted concentrations within the inner 11-m-diameter portion of the rings (>80% of the ring area) varied between 524 and 871 μmol/mol but remained close to target near the centres. The design criteria adopted from existing pure CO2 fumigating FACE systems and new ideas incorporated in the AGFACE system provided a performance similar to its equivalent systems. This provides confidence in the results that will be generated from experiments using the AGFACE system.
Establishment and persistence of perennial grass and herb cultivars and lines in a recharge area, North-West Slopes, New South Wales
Authors: Boschma S. P. , Lodge G. M. , Harden S.
Published: August 2009

Two adjacent sites, one previously cropped and the other a native pasture, were sown with perennial temperate and tropical grasses and herbs (Expt 1), Phalaris aquatica (phalaris) and Festuca arundinacea (tall fescue) cultivars or lines (Expt 2), and perennial tropical grasses (Expt 3) near Manilla, NSW. Establishment, herbage mass and plant frequency were assessed in 2003–06 to (i) identify cultivars/lines with superior persistence, (ii) detect possible mechanisms required for successful production and persistence in a summer-dominant rainfall environment, and (iii) examine the comparative performance of the species groups when sown into previously cropped and native pasture areas. Plots were fertilised annually and grazed or mown at least seasonally. Most cultivars/lines persisted at the previously cropped site, while those on the native pasture site had to be resown and generally failed to persist beyond the first year. At the previously cropped site, summer-dormant tall fescue cv. Resolute MaxP® was the most persistent of the grasses evaluated in Expt 1. Grasses such as Lolium perenne cv. Avalon and Bromus stamineus cv. Gala did not perenneate, but regenerated annually from seed. Native grasses generally had poor establishment; however, Austrodanthonia richardsonii and A. fulva tended to increase in plant frequency over time. Chloris gayana (Rhodes grass) cv. Katambora and Panicum maximum (panic) cv. Gatton were the only tropical grasses that established in Expt 1, and both had plant frequencies similar (P > 0.05) to the temperate grasses at the final assessment. In Expt 2, Resolute MaxP again was the most persistent cultivar/line. Several experimental lines of phalaris (e.g. T39 and M225) had high herbage mass and good persistence compared with commercial cultivars. In Expt 3, Katambora Rhodes grass and Digitaria eriantha ssp. eriantha (digit grass) cv. Premier were the most persistent cultivars and had the highest herbage mass. These data highlighted summer dormancy in temperate grasses and frost tolerance in tropical grasses as two possible mechanisms important for persistence of grasses on the North-West Slopes of NSW and the risks associated with sowing perennial grasses into established native pastures.
Variation for and relationships among biomass and grain yield component traits conferring improved yield and grain weight in an elite wheat population grown in variable yield environments
Authors: Rattey Allan , Shorter Ray , Chapman Scott , Dreccer Fernanda , van Herwaarden Anthony
Published: August 2009

Grain yield and kernel size (grain weight) are important industry traits for wheat in the water-limited environments of the north-eastern wheatbelt of Australia. These, and underpinning morphological and physiological traits, were evaluated in a population of recombinant inbred lines from the elite CIMMYT cross Seri/Babax, segregating for the presence of the rye translocation (T1BL.1RS). The population was examined to determine the variation among lines, relationships among traits, the extent of line × environment interactions, potential efficiency of direct and indirect selection, and to identify trait combinations that are associated with higher grain yield and grain weight. Transgressive segregation was observed for all traits, and line × environment interaction effects were frequently larger than line main effects. Across six environments ranging in yield from 202 to 660 g/m2, the T1BL.1RS wheat-rye translocation had a positive effect on grain weight (+3.4%) but resulted in decreased grain number per m2 (–6.5%) and grain yield (–3.1%). Realised selection responses indicated that broad adaptation was best achieved by selection for mean performance across the range of target environments. However, specific adaptation for performance in high- or low-yielding environments was best detected by direct selection in those types of environments. A group of broadly adapted Seri/Babax lines exceeded the mean of five cultivars grown commercially in the north-eastern wheatbelt by 8% for grain yield and 17% for grain weight. These Seri/Babax lines with both high grain yield and grain weight were associated with a combination of several traits: earlier flowering, reduced tillering, a greater proportion of tillers that produce grain-bearing spikes at maturity, high water-soluble carbohydrate stem reserves at anthesis, a higher proportion of competent florets at anthesis to maximise grains per spikelet leading to a high harvest index, and possibly a greater capacity to extract soil water. These results suggest a suitable ideotype for breeding high-yielding wheat cultivars with high grain weight adapted to environments with hotter, drier conditions during the post-anthesis period.
GATA6
mutations cause human cardiac outflow tract defects by disrupting semaphorin-plexin signaling
Authors: Kodo Kazuki , Nishizawa Tsutomu , Furutani Michiko , Arai Shoichi , Yamamura Eiji , Joo Kunitaka , Takahashi Takao , Matsuoka Rumiko , Yamagishi Hiroyuki
Published: August 2009

Congenital heart diseases (CHD) occur in nearly 1% of all live births and are the major cause of infant mortality and morbidity. Although an improved understanding of the genetic causes of CHD would provide insight into the underlying pathobiology, the genetic etiology of most CHD remains unknown. Here we show that mutations in the gene encoding the transcription factor GATA6 cause CHD characteristic of a severe form of cardiac outflow tract (OFT) defect, namely persistent truncus arteriosus (PTA). Two different
GATA6
mutations were identified by systematic genetic analysis using DNA from patients with PTA. Genes encoding the neurovascular guiding molecule semaphorin 3C (SEMA3C) and its receptor plexin A2 (PLXNA2) appear to be regulated directly by GATA6, and both GATA6 mutant proteins failed to transactivate these genes. Transgenic analysis further suggests that, in the developing heart, the expression of SEMA3C in the OFT/subpulmonary myocardium and PLXNA2 in the cardiac neural crest contributing to the OFT is dependent on GATA transcription factors. Together, our data implicate mutations in
GATA6
as genetic causes of CHD involving OFT development, as a result of the disruption of the direct regulation of semaphorin-plexin signaling.
A Rab GAP cascade defines the boundary between two Rab GTPases on the secretory pathway
Authors: Rivera-Molina Félix E. , Novick Peter J.
Published: August 2009

Membrane traffic along the endocytic and exocytic pathways relies on the appropriate localization and activation of a series of different Rab GTPases. Rabs are activated by specific guanine nucleotide exchange factors (GEFs) and inactivated by GTPase-activating proteins (GAPs). GEF cascades, in which one Rab in its GTP-bound form recruits the GEF that activates the next Rab along the pathway, can account for the sequential activation of a series of Rabs, but it does not explain how the first Rab is inactivated after the next Rab has been activated. We present evidence for a counter-current GAP cascade that serves to restrict the spatial and temporal overlap of 2 Rabs, Ypt1p and Ypt32p, on the exocytic pathway in
Saccharomyces cerevisiae
. We show that Gyp1p, a GAP for Ypt1p, specifically interacts with Ypt32p, and that this interaction is important for the localization and stability of Gyp1p. Moreover, we demonstrate that, in WT cells, Ypt1p compartments are converted over time into Ypt32p compartments, whereas in
gyp1
Δ cells there is a significant increase in compartments containing both proteins that reflects a slower transition from Ypt1p to Ypt32p. GEF cascades working in concert with counter-current GAP cascades could generate a programmed series of Rab conversions responsible for regulating the choreography of membrane traffic.
Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells
Authors: Chan Keith Syson , Espinosa Inigo , Chao Mark , Wong David , Ailles Laurie , Diehn Max , Gill Harcharan , Presti Joseph , Chang Howard Y. , van de Rijn Matt , Shortliffe Linda , Weissman Irving L.
Published: August 2009

Major clinical issues in bladder cancer include the identification of prediction markers and novel therapeutic targets for invasive bladder cancer. In the current study, we describe the isolation and characterization of a tumor-initiating cell (T-IC) subpopulation in primary human bladder cancer, based on the expression of markers similar to that of normal bladder basal cells (Lineage-CD44
+
CK5
+
CK20
−
). The bladder T-IC subpopulation was defined functionally by its enriched ability to induce xenograft tumors in vivo that recapitulated the heterogeneity of the original tumor. Further, molecular analysis of more than 300 bladder cancer specimens revealed heterogeneity among activated oncogenic pathways in T-IC (e.g., 80% Gli1, 45% Stat3, 10% Bmi-1, and 5% β-catenin). Despite this molecular heterogeneity, we identified a unique bladder T-IC gene signature by gene chip analysis. This T-IC gene signature, which effectively distinguishes muscle-invasive bladder cancer with worse clinical prognosis from non-muscle-invasive (superficial) cancer, has significant clinical value. It also can predict the progression of a subset of recurring non-muscle-invasive cancers. Finally, we found that CD47, a protein that provides an inhibitory signal for macrophage phagocytosis, is highly expressed in bladder T-ICs compared with the rest of the tumor. Blockade of CD47 by a mAb resulted in macrophage engulfment of bladder cancer cells in vitro. In summary, we have identified a T-IC subpopulation with potential prognostic and therapeutic value for invasive bladder cancer.
Retrotransposon overdose and genome integrity
Authors: Scheifele Lisa Z. , Cost Gregory J. , Zupancic Margaret L. , Caputo Emerita M. , Boeke Jef D.
Published: August 2009

Yeast and mammalian genomes are replete with nearly identical copies of long dispersed repeats in the form of retrotransposons. Mechanisms clearly exist to maintain genome structure in the face of potential rearrangement between the dispersed repeats, but the nature of this machinery is poorly understood. Here we describe a series of distinct “retrotransposon overdose” (RO) lineages in which the number of Ty1 elements in the
Saccharomyces cerevisiae
genome has been increased by as much as 10 fold. Although these RO strains are remarkably normal in growth rate, they demonstrate an intrinsic supersensitivity to DNA-damaging agents. We describe the identification of mutants in the DNA replication pathway that enhance this RO-specific DNA damage supersensitivity by promoting ectopic recombination between Ty1 elements. Abrogation of normal DNA replication leads to rampant genome instability primarily in the form of chromosomal aberrations and confirms the central role of DNA replication accuracy in the stabilization of repetitive DNA.
CD4+CD25−LAG3+regulatory T cells controlled by the transcription factor Egr-2
Authors: Okamura Tomohisa , Fujio Keishi , Shibuya Mihoko , Sumitomo Shuji , Shoda Hirofumi , Sakaguchi Shimon , Yamamoto Kazuhiko
Published: August 2009

Regulatory T cells (Tregs) are engaged in the maintenance of immunological self-tolerance and immune homeostasis. IL-10 has an important role in maintaining the normal immune state. Here, we show that IL-10-secreting Tregs can be delineated in normal mice as CD4+CD25−Foxp3−T cells that express lymphocyte activation gene 3 (LAG-3), an MHC-class-II-binding CD4 homolog. Although ≈2% of the CD4+CD25−T cell population consisted of CD4+CD25−LAG3+T cells in the spleen, CD4+CD25−LAG3+T cells are enriched to ≈8% in the Peyer's patch. They are hypoproliferative upon in vitro antigenic stimulation and suppress in vivo development of colitis. Gene expression analysis reveals that CD4+CD25−LAG3+Tregs characteristically express early growth response gene 2 (Egr-2), a key molecule for anergy induction. Retroviral gene transfer of Egr-2 converts naïve CD4+T cells into the IL-10-secreting and LAG-3-expressing phenotype, and Egr-2-transduced CD4+T cells exhibit antigen-specific immunosuppressive capacity in vivo. Unlike Foxp3+natural Tregs, high-affinity interactions with selecting peptide/MHC ligands expressed in the thymus do not induce the development of CD4+CD25−LAG3+Tregs. In contrast, the number of CD4+CD25−LAG3+Tregs is influenced by the presence of environmental microbiota. Thus, IL-10-secreting Egr-2+LAG3+CD4+Tregs can be exploited for the control of peripheral immunity.
How is inflectional morphology learned?
Authors: Slabakova Roumyana
Published: August 2009

This article considers recent explanations of variability in the second language (L2) comprehension of inflectional morphology. The predictions of five accounts are spelled out: the emergentist account, the Feature Assembly Hypothesis, the Contextual Complexity Hypothesis, the Morphological Underspecification Hypothesis and the Combinatorial Variability Hypothesis. These predictions are checked against the results of an experimental study on the L2 acquisition of inflectional morphology (based on an extension of Slabakova and Gajdos 2008). English-native learners of German at beginning and intermediate proficiency levels took a multiple-choice test where they had to supply appropriate missing subjects. The predictions of the Morphological Underspecification Hypothesis and the Combinatorial Variability Hypothesis were largely supported by the experimental findings. It is argued that only accounts looking at mental representation of lexical features adequately explain L2 morphological variability.
On L1 attrition and the linguistic system
Authors: Schmid Monika S.
Published: August 2009

One of the most puzzling observations for linguists is the difference between learning a language from birth and later in life: while all normally developing children can attain full native language proficiency, there is considerable variability in ultimate attainment among older speakers who attempt to acquire a second language (L2). There is an ongoing controversy in linguistic research on whether this discrepancy is due to a maturationally constrained window of linguistic development making language learning difficult or impossible after puberty, or to general cognitive factors linked to the fact that the later an L2 is established, the stronger the competition it has to overcome from the more deeply entrenched first language (L1). Studies attempting to resolve this controversy have so far focussed exclusively on the development of L2 skills. New insights may be provided by investigating the first language skills of migrants who have become dominant in the L2 (referred to as L1 attriters). Such speakers learned their L1 as monolinguals during childhood, and were therefore not impeded by maturational constraints in the acquisitional process. Having lived in an L2 environment for a long period of time, however, their seldom-used L1 shows signs of the influence of their highly active L2. A systematic comparison of L1 attriters and L2 learners may therefore be able to shed some light on the question of whether there is a qualitative or merely a quantitative difference between L1 acquisition in childhood and L2 acquisition later in life: If being a native speaker is maturationally constrained, even attrited L1 systems should remain native-like. But if the persistent problems of L2 learners are due to issues such as lack of practice and exposure, and competition between their two language systems, bilinguals who use their second language dominantly should become more similar to L2 speakers.
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
Authors: Clément-Ziza Mathieu , Malabat Christophe , Weber Christian , Moszer Ivan , Aittokallio Tero , Letondal Catherine , Rousseau Sandrine
Published: August 2009

Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.

Availability: Genoscape is an open-source software freely available from the Genoscape webpage (http://www.pasteur.fr/recherche/unites/Gim/genoscape/). Installation instructions and tutorial can also be found at this URL.

Contact:  Mathieu.clement-ziza@biotec.tu-dresden.de; sandrine.rousseau@pasteur.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance
Authors: Buendia Patricia , Cadwallader Brice , DeGruttola Victor
Published: August 2009

Motivation: Modern HIV-1, hepatitis B virus and hepatitis C virus antiviral therapies have been successful at keeping viruses suppressed for prolonged periods of time, but therapy failures attributable to the emergence of drug resistant mutations continue to be a distressing reminder that no therapy can fully eradicate these viruses from their host organisms. To better understand the emergence of drug resistance, we combined phylogenetic and statistical models of viral evolution in a 2-phase computational approach that reconstructs mutational pathways of drug resistance.

Results: The first phase of the algorithm involved the modeling of the evolution of the virus within the human host environment. The inclusion of longitudinal clonal sequence data was a key aspect of the model due to the progressive fashion in which multiple mutations become linked in the same genome creating drug resistant genotypes. The second phase involved the development of a Markov model to calculate the transition probabilities between the different genotypes. The proposed method was applied to data from an HIV-1 Efavirenz clinical trial study. The obtained model revealed the direction of evolution over time with greater detail than previous models. Our results show that the mutational pathways facilitate the identification of fast versus slow evolutionary pathways to drug resistance.

Availability: Source code for the algorithm is publicly available at http://biorg.cis.fiu.edu/vPhyloMM/

Contact:  pbuendia@miami.edu