bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of sidewall adhesion in surface micromachines due to repetitive impact loading
Authors: Xiang H. , Komvopoulos K.
Published: March 2012

A contact-mode surface micromachine consisting of polycrystalline silicon was used to study the effect of repetitive impact loading on the evolution of adhesion at sidewall contact interfaces under different conditions of contact load, ambient pressure, and relative humidity. All micromachines demonstrated an initial run-in phase of low and stable adhesion force, followed by a surface modification phase characterized by the rapid increase of the interfacial adhesion force. The nonlinear increase of the adhesion force with impact cycles was found to be in direct correlation with the micromachine operation lifetime. A criterion of micromachine failure due to excessive interfacial adhesion (stiction) was formulated based on the observed experimental trend. Micromachine lifetime decreased nonlinearly with the increase of the maximum contact pressure. The adhesion force of micromachines operated in vacuum or high-humidity atmosphere increased faster than those operated in dry atmosphere. Despite the significant increase of the adhesion force with impact cycles, high-magnification scanning electron microscopy did not reveal any discernible changes in the surface topography even after 3 × 107 impact cycles. The evolution of the interfacial adhesion force is attributed to the increase of the real area of contact and the work of adhesion due to nanoscale surface smoothening and the removal of adsorbed contaminant layers, respectively. Physical and chemical surface modification is interpreted in the context of results obtained for different maximum contact pressures, ambient pressures, and relative humidity levels.
A novel method of temperature compensation for piezoresistive microcantilever-based sensors
Authors: Han Jianqiang , Wang Xiaofei , Yan Tianhong , Li Yan , Song Meixuan
Published: March 2012

Microcantilever with integrated piezoresistor has been applied to in situ surface stress measurement in the field of biochemical sensors. It is well known that piezoresistive cantilever-based sensors are sensitive to ambient temperature changing due to highly temperature-dependent piezoresistive effect and mismatch in thermal expansion of composite materials. This paper proposes a novel method of temperature drift compensation for microcantilever-based sensors with a piezoresistive full Wheatstone bridge integrated at the clamped ends by subtracting the amplified output voltage of the reference cantilever from the output voltage of the sensing cantilever through a simple temperature compensating circuit. Experiments show that the temperature drift of microcantilever sensors can be significantly reduced by the method.
Thermally-induced first-order phase transition in the (FC6H4C2H4NH3)2[PbI4] photoluminescent organic-inorganic material
Authors: Koubaa M. , Dammak T. , Garrot D. , Castro M. , Codjovi E. , Mlayah A. , Abid Y. , Boukheddaden K.
Published: March 2012

The thermal properties of the perovskite slab alkylammonium lead iodide (FC6H4C2H4NH3)2[PbI4] are investigated using spectroscopic ellipsometry, differential scanning calorimetry, photoluminescence, and Raman spectroscopy. The spectroscopic ellipsometry, performed in the heating mode, clearly evidenced the presence of a singularity at 375 K. This is corroborated by the temperature dependence of the photoluminescence, which pointed out a first-order order-disorder phase transition at ∼375 K, with a hysteresis loop of 40 K width. Raman spectroscopy data suggest that this transition arises from a dynamic rotational disordering of the ammonium headgroups of the alkylammonium chain. In contrast, differential scanning calorimetry measurements on a pellet sample led to an entropy change value ΔS ≈0.39 J/K/mol at the transition, suggesting the existence of a residual short-range order of the NH3+ on cooling from the high temperature phase.
A global model of the self-pulsing regime of micro-hollow cathode discharges
Authors: Lazzaroni C. , Chabert P.
Published: March 2012

A global (volume-averaged) model of the self-pulsing regime of micro-hollow cathode discharges working in argon gas is proposed. The power balance is done using an equivalent circuit model of the discharge that allows the current and voltage dynamics to be calculated. The fraction of the total power dissipated in the discharge that contributes to electron heating is deduced from a sheath model previously described. The particle balance is first done in a very simplified reaction scheme involving only electrons, argon atomic ions, and argon molecular ions. In a second step, the excited states (the metastable state Ar*(3P2) and the resonant state Ar*(3P1)) are included in the particle balance equations. The models are compared to experiments and several conclusions are drawn. The model without excited states underestimates the electron density and does not capture well the trends in pressure. The model with the excited states is in better agreement which shows that multi-step ionization plays a significant role. The time-evolution of the electron density follows closely that of the discharge current but the excited states density presents two peaks: (i) the first at the early stage of the current peak due to direct excitation with high electron temperature, (ii) the second at the end of the current (and electron density) peak due to large production of excited states by electron-ion recombination at very low electron temperature.
Patterned oxide semiconductor by electrohydrodynamic jet printing for transparent thin film transistors
Authors: Lee Sangkyu , Kim Jeonghyun , Choi Junghyun , Park Hyunjung , Ha Jaehwan , Kim Yongkwan , Rogers John A. , Paik Ungyu
Published: March 2012

This paper explores transport in transparent thin film transistors formed using a liquid precursor to indium zinc oxide, delivered to target substrates by electrohydrodynamic jet (e-jet) printing. Under optimized conditions, we observe field effect mobilities as high as 32 cm2V−1s−1, with on/off current ratios of 103 and threshold voltages of 2 V. These results provide evidence that material manipulated in fine-jet, electric field induced liquid flows can yield semiconductor devices without any adverse effects of residual charge or unintentional doping. E-jet printing methods provide levels of resolution (∼1.5 μm) that provide a path to printed transistors with small critical dimensions.
Local structures in ionic liquids probed and characterized by microscopic thermal diffusion monitored with picosecond time-resolved Raman spectroscopy
Authors: Yoshida Kyousuke , Iwata Koichi , Nishiyama Yoshio , Kimura Yoshifumi , Hamaguchi Hiro-o
Published: March 2012

Vibrational cooling rate of the first excited singlet (S1) state of trans-stilbene and bulk thermal diffusivity are measured for seven room temperature ionic liquids, C2mimTf2N, C4mimTf2N, C4mimPF6, C5mimTf2N, C6mimTf2N, C8mimTf2N, and bmpyTf2N. Vibrational cooling rate measured with picosecond time-resolved Raman spectroscopy reflects solute-solvent and solvent-solvent energy transfer in a microscopic solvent environment. Thermal diffusivity measured with the transient grating method indicates macroscopic heat conduction capability. Vibrational cooling rate of S1 trans-stilbene is known to have a good correlation with bulk thermal diffusivity in ordinary molecular liquids. In the seven ionic liquids studied, however, vibrational cooling rate shows no correlation with thermal diffusivity; the observed rates are similar (0.082 to 0.12 ps−1 in the seven ionic liquids and 0.08 to 0.14 ps−1 in molecular liquids) despite large differences in thermal diffusivity (5.4–7.5 × 10−8 m2 s−1 in ionic liquids and 8.0–10 × 10−8 m2 s−1 in molecular liquids). This finding is consistent with our working hypothesis that there are local structures characteristically formed in ionic liquids. Vibrational cooling rate is determined by energy transfer among solvent ions in a local structure, while macroscopic thermal diffusion is controlled by heat transfer over boundaries of local structures. By using “local” thermal diffusivity, we are able to simulate the vibrational cooling kinetics observed in ionic liquids with a model assuming thermal diffusion in continuous media. The lower limit of the size of local structure is estimated with vibrational cooling process observed with and without the excess energy. A quantitative discussion with a numerical simulation shows that the diameter of local structure is larger than 10 nm. If we combine this lower limit, 10 nm, with the upper limit, 100 nm, which is estimated from the transparency (no light scattering) of ionic liquids, an order of magnitude estimate of local structure is obtained as 10 nm < L < 100 nm, where L is the length or the diameter of the domain of local structure.
Influence of plasma-generated negative oxygen ion impingement on magnetron sputtered amorphous SiO2 thin films during growth at low temperatures
Authors: Macias-Montero M. , Garcia-Garcia F. J. , Álvarez R. , Gil-Rostra J. , González J. C. , Cotrino J. , Gonzalez-Elipe A. R. , Palmero A.
Published: March 2012

Growth of amorphous SiO2 thin films deposited by reactive magnetron sputtering at low temperatures has been studied under different oxygen partial pressure conditions. Film microstructures varied from coalescent vertical column-like to homogeneous compact microstructures, possessing all similar refractive indexes. A discussion on the process responsible for the different microstructures is carried out focusing on the influence of (i) the surface shadowing mechanism, (ii) the positive ion impingement on the film, and (iii) the negative ion impingement. We conclude that only the trend followed by the latter and, in particular, the impingement of O- ions with kinetic energies between 20 and 200 eV, agrees with the resulting microstructural changes. Overall, it is also demonstrated that there are two main microstructuring regimes in the growth of amorphous SiO2 thin films by magnetron sputtering at low temperatures, controlled by the amount of O2 in the deposition reactor, which stem from the competition between surface shadowing and ion-induced adatom surface mobility.
Approach for measuring complex refractive index of molten Sb2Te3 by spectroscopic ellipsometry
Authors: Kuwahara M. , Endo R. , Tsutsumi K. , Morikasa F. , Tsuruoka T. , Fukaya T. , Suzuki M. , Susa M. , Endo T. , Tadokoro T.
Published: March 2012

The complex refractive index of liquid and solid Sb2Te3 around its melting point has been measured by spectroscopic ellipsometry. The real and imaginary parts of the complex refractive index of liquid Sb2Te3 are totally different from those of solid Sb2Te3. The imaginary part of the complex refractive index for the liquid is significantly lower than that of the solid over the observed wavelength range. Our results are consistent with the idea that a molten area created in the center of a focused laser spot can function as a small aperture in the super-resolution readout effect in optical disks.
Existence and removal of Cu2Se second phase in coevaporated Cu2ZnSnSe4 thin films
Authors: Tanaka Tooru , Sueishi Tatsuya , Saito Katsuhiko , Guo Qixin , Nishio Mitsuhiro , Yu Kin M. , Walukiewicz Wladek
Published: March 2012

The composition dependence of the electrical properties of Cu2ZnSnSe4 thin films synthesized by coevaporation and the results of phase analyses are reported. We found that the hole concentration depends on the Cu/(Zn + Sn) ratio and is on the order of 1017 cm−3 for the ratio of 0.7 and increases to over 1020 cm−3 when the ratio exceeds 0.9. Raman spectra indicate the coexistence of semimetallic Cu2Se second phase in the thin films with Cu/(Zn + Sn) ratio above 0.9. In order to remove the Cu2Se phase selectively, we attempted a KCN etching. After the KCN etching for 30 min, the Raman peak attributed to the Cu2Se phase disappeared, and the hole concentration decreased to about 1018 cm−3.
Identification of different origins for s-shaped current voltage characteristics in planar heterojunction organic solar cells
Authors: Wagner Julia , Gruber Mark , Wilke Andreas , Tanaka Yuya , Topczak Katharina , Steindamm Andreas , Hörmann Ulrich , Opitz Andreas , Nakayama Yasuo , Ishii Hisao , Pflaum Jens , Koch Norbert , Brütting Wolfgang
Published: March 2012

We investigate different parameters influencing the occurrence of s-shaped current voltage (j-V) characteristics in planar heterojunction organic solar cells. It is shown how substrate modification, purity of the active organic material as well as variation of the top contact can affect the shape of the j-V curves. The studies are performed on vacuum-evaporated planar heterojunction solar cells with diindenoperylene (DIP) as electron donor and fullerene C60 as acceptor. The focus is on the fill factor and forward current being the most direct indicators for s-shapes in j-V curves. We find that the main effect of substrate heating during film growth can be assigned to changes in energy barriers rather than to the modification of morphology and crystallinity, which is also influenced by elevated substrate temperatures. The decisive role of the barrier height between the anode work function and the HOMO (i.e., highest occupied molecular orbital) level of the donor is approved by comparing hole-injection layers with different work functions. By using donor materials of different purity we find a correlation between charge carrier mobilities and fill factors. Finally, it is demonstrated that an exciton blocking interlayer is essential to get high fill factors when aluminum is used as top contact, but is dispensable for samarium as cathode material. This finding can be ascribed to the protective effect of the interlayer from aluminum diffusion into the active semiconductor rather than to its role as exciton diffusion barrier.
Enhanced carrier density in Nb-doped SrTiO3 thermoelectrics
Authors: Ozdogan K. , Upadhyay Kahaly M. , Sarath Kumar S. R. , Alshareef H. N. , Schwingenschlögl U.
Published: March 2012

We study epitaxial SrTiO3 interfaced with Nb-doped SrTi1-xNbxO3 (x = 0, 0.125, 0.25, 0.375, and 0.5) by full-potential density functional theory. From the electronic band structures obtained by our ab-initio calculations we determine the dependence of the induced metallicity on the Nb concentration. We obtain a monotonous increase of the carrier density with the Nb concentration. The results are confirmed by experiments for SrTi0.88Nb0.12O3 and SrTi0.8Nb0.2O3, demonstrating the predictive power and limitations of our theoretical approach. We also show that the Seebeck coefficient decreases monotonously with increasing temperature.
Temperature dependence of electron-spin relaxation in a single InAs quantum dot at zero applied magnetic field
Authors: Dou X. M. , Sun B. Q. , Jiang D. S. , Ni H. Q. , Niu Z. C.
Published: March 2012

The temperature-dependent electron spin relaxation of positively charged excitons in a single InAs quantum dot was measured by time-resolved photoluminescence spectroscopy at zero applied magnetic fields. The experimental results show that the electron-spin relaxation is clearly divided into two different temperature regimes: (i) at T < 50 K, spin relaxation depends on the dynamical nuclear spin polarization and is approximately temperature-independent, as predicted by Merkulov et al. [Phys. Rev. B 65, 205309 (2002)] (ii) T > about 50 K, spin relaxation speeds up with increasing temperature. A model of a two longitudinal optical phonon scattering process coupled with hyperfine interaction is proposed to account for the accelerated electron spin relaxation at higher temperatures.
Experimental characterization of electrochemical synthesized Fe nanowires for biomedical applications
Authors: Song Shuangqi , Bohuslav Greg , Capitano Adam , Du Jun , Taniguchi Karen , Cai Zhonghou , Sun Li
Published: March 2012

Fe based nanomaterials have shown extensive application promises in medical diagnosis and treatment due to their biocompatibility. Using template assisted electrodeposition, iron based nanowires with controllable size, aspect ratio, and magnetic anisotropy have been fabricated. In situ synchrotron diffraction technique has been used to reveal the nanowire growth mechanism and provide real time compositional and crystallographic information. Biocompatibility of the nanowires with Rat-2 fibroblast cells has been evaluated and compared with magnetite nanoparticles. Using an external magnetic field, cell manipulation through the use of these magnetic nanowires has been demonstrated.
An analysis method for asymmetric resonator transmission applied to superconducting devices
Authors: Khalil M. S. , Stoutimore M. J. A. , Wellstood F. C. , Osborn K. D.
Published: March 2012

We examine the transmission through nonideal microwave resonant circuits. The general analytical resonance line shape is derived for both inductive and capacitive coupling with mismatched input and output transmission impedances, and it is found that, for certain non-ideal conditions, the line shape is asymmetric. We describe an analysis method for extracting an accurate internal quality factor (Qi), the diameter correction method (DCM), and compare it to the conventional method used for millikelvin resonator measurements, the φ rotation method (φRM). We analytically find that the φRM deterministically overestimates Qi when the asymmetry of the resonance line shape is high, and that this error is eliminated with the DCM. A consistent discrepancy between the two methods is observed when they are used to analyze both simulations from a numerical linear solver and data from asymmetric coplanar superconducting thin-film resonators.
Reversible phase transition in laser-shocked 3Y-TZP ceramics observed via nanosecond time-resolved x-ray diffraction
Authors: Hu Jianbo , Ichiyanagi Kouhei , Takahashi Hiroshi , Koguchi Hiroaki , Akasaka Takeaki , Kawai Nobuaki , Nozawa Shunsuke , Sato Tokushi , Sasaki Yuji C. , Adachi Shin-ichi , Nakamura Kazutaka G.
Published: March 2012

The high-pressure phase stability of the metastable tetragonal zirconia is still under debate. The transition dynamics of shocked Y2O3 (3 mol. %) stabilized tetragonal zirconia ceramics under laser-shock compression has been directly studied using nanosecond time-resolved x-ray diffraction. The martensitic phase transformation to the monoclinic phase, which is the stable phase for pure zirconia at ambient pressure and room temperature, has been observed during compression at 5 GPa within 20 ns without any intermediates. This monoclinic phase reverts back to the tetragonal phase during pressure release. The results imply that the stabilization effect due to the addition of Y2O3 is to some extent negated by the shear stress under compression.
Comparison of electrical and electro-optical characteristics of light-emitting capacitors based on silicon-rich Si-oxide fabricated by plasma-enhanced chemical vapor deposition and ion implantation
Authors: González-Fernández A. A. , Juvert J. , Morales-Sánchez Alfredo , Barreto Jorge , Aceves-Mijares M. , Domínguez C.
Published: March 2012

This work presents electrical and electro-optical studies performed on light-emitting capacitors with silicon-rich silicon oxide fabricated by plasma-enhanced chemical vapor deposition and by the implantation of Si ions in thermally grown SiO2. The influence of the fabrication technique and silicon content on electrical, electro-optical, and emission spectra characteristics has been studied. Results on the electrical behavior show a significant dependence on both the fabrication technique and Si content that translates in variations on electroluminescence with fabrication technique and silicon excess.
Evaluation of radiation damage using nonlinear ultrasound
Authors: Matlack K. H. , Wall J. J. , Kim J.-Y. , Qu J. , Jacobs L. J. , Viehrig H.-W.
Published: March 2012

Nonlinear ultrasound was used to monitor radiation damage in two reactor pressure vessel (RPV) steels. The microstructural changes associated with radiation damage include changes in dislocation density and the formation of precipitates, and nonlinear ultrasonic waves are known to be sensitive to such changes. Six samples each of two different RPV steels were previously irradiated in the Rheinsberg power reactor to two fluence levels, up to 1020 n/cm2 (E > 1 MeV). Longitudinal waves were used to measure the acoustic nonlinearity in these samples, and the results show a clear increase in the measured acoustic nonlinearity from the unirradiated state to the medium dose, and then a decrease from medium dose to high dose.
Stimulated supercontinuum generation extends broadening limits in silicon
Authors: DeVore P. T. S. , Solli D. R. , Ropers C. , Koonath P. , Jalali B.
Published: March 2012

We demonstrate that stimulated supercontinuum generation alleviates restrictions on spectral broadening in silicon waveguides. At telecommunications wavelengths, two-photon and free-carrier absorption typically deplete the pump before large broadening factors can be achieved. However, broadening via modulation instability (MI) can be enhanced by seeding, which also substantially improves the energy efficiency of spectral broadening in media with nonlinear loss. Coherent seeding also generates a stable output spectrum, in contrast to conventional approaches where broadening starts from noise. The combination of self-phase modulation and stimulated modulation instability generates broadening factors in excess of 40-fold at moderate intensity levels, with >15-times better energy efficiency.
B14: An all-boron fullerene
Authors: Cheng Longjiu
Published: March 2012

Experiments revealed that small boron cluster anions and cations are (quasi-)planar. For neutral boron cluster, (quasi-)planar motifs are also suggested to be global minimum by many theoretical studies, and a structural transformation from quasi-planar to double-ring tubular structures occurs at B20. However, a missing opportunity is found for neutral B14, which is a flat cage and more stable than the previous quasi-planar one by high level ab initio calculations. The B14 cage has a large HOMO-LUMO gap (2.69 eV), and NICS values reveal that it is even more aromatic than the known most aromatic quasi-planar B12 and double-ring B20, which indicates a close-shell electronic structure. Chemical bonding analysis given by AdNDP reveals that the B14 cage is an all-boron fullerene with 18 delocalized σ-electrons following the 2(n+1)2 rule of spherical aromaticity. The geometry and bonding features of the B14 cage are unique denying conversional thinking.
Investigation of the direct band gaps in Ge1−xSnx alloys with strain control by photoreflectance spectroscopy
Authors: Lin Hai , Chen Robert , Lu Weisheng , Huo Yijie , Kamins Theodore I. , Harris James S.
Published: March 2012

Unstrained and compressive-strained Ge1−xSnx alloys were grown on InGaAs buffer layers by molecular beam epitaxy. Photoreflectance at room temperature determines the direct bandgap energies of Ge1−xSnx alloys from the maxima of the light- and heavy-hole bands to the bottom of Γ valley. The lowest transition energies from photoreflectance are consistent with the energies derived from photoluminescence. The calculated bowing parameter is 2.42 ± 0.04 eV for the direct band gap of Ge1−xSnx alloys. The dilational and shear deformation potentials of the direct band gap are −11.04 ± 1.41 eV and −4.07 ± 0.91 eV, respectively. These basic material parameters are important in designing optoelectronic devices based on Ge1−xSnx alloys.
Measurement of light diffusion in ZnO nanowire forests
Authors: Versteegh Marijn A. M. , van der Wel Ruben E. C. , Dijkhuis Jaap I.
Published: March 2012

Optimum design of efficient nanowire solar cells requires better understanding of light diffusion in a nanowire array. Here we demonstrate that our recently developed ultrafast all-optical shutter can be used to directly measure the dwell time of light in a nanowire array. Our measurements on disordered ZnO nanowire arrays, “nanowire forests,” indicate that the photon mean free path and the dwell time of light can be well predicted from SEM images.
Multifunctional behaviour of mesoporous LiNbO3
Authors: Banerjee Shilpi , Kumar Bhunia Manas , Bhaumik Asim , Chakravorty Dipankar
Published: March 2012

Mesoporous LiNbO3 nanoparticles with BET surface area 185 m2 g−1 were synthesized by using Pluronic P123 as soft template. The samples showed three functionalities, viz., photoluminescence, ferroelectricity, and ferromagnetism. Room temperature photoluminescence was observed at 390 nm wavelength due to oxygen vacancy. The mesoporous LiNbO3 showed ferromagnetic behavior at room temperature. Ferroelectric behavior of the samples was confirmed from the P-E hysteresis loop measurement. The samples showed a magneto-dielectric effect with the dielectric constant increasing by ∼4.5% for an applied magnetic field of 10 kOe due to magnetostriction of the material which changed the lattice parameter to bring about an increase in the dipole moment of the unit cell.
Tapered gold-helix metamaterials as improved circular polarizers
Authors: Gansel Justyna K. , Latzel Michael , Frölich Andreas , Kaschke Johannes , Thiel Michael , Wegener Martin
Published: March 2012

We have previously shown that square arrays of three-dimensional gold helices can serve as compact broadband circular polarizers. Here, we show by heuristic reasoning supported by numerical calculations that the bandwidth of the device can realistically be increased to 1.5 octaves by tapering the gold-helix radius. The tapering also improves the extinction ratio. Depending on the side from which light impinges onto the tapered helices, the polarization conversions are different. Therefore, the structure is either optimal as polarizer or as analyzer. Corresponding structures for the infrared spectral range are fabricated by direct laser writing and gold electroplating.
Study of direct relationship between atomic structures and glass forming abilities of Cu100-x Zrx (0≤x≤10) liquids by molecular dynamics simulations
Authors: Zhang Y. , Mattern N. , Eckert J.
Published: March 2012

We have studied the phase formation of Cu100-xZrx liquids with x = 0, 0.5, 1, 2, 5, 10, and 25 using molecular dynamics simulations, respectively, in order to find a direct relationship between the atomic structures and the glass forming abilities (GFAs). The difference among the critical cooling rates has been identified by at least two orders of magnitude. We introduce a parameter based on the relative change in the factions of Voronoi polyhedra to evaluate the contributions of different clusters to the glass forming ability. Within the studied composition range, it is revealed that the contributions to glass forming ability obey Cu-centered 〈0 0 12 0〉 >Zr-centered 〈0 1 10 5〉 >Cu-centered 〈0 1 9 3〉 and 〈0 1 10 2〉, whereas the Cu-centered 〈0 1 10 3〉, 〈0 1 10 4〉, 〈0 2 8 4〉, 〈0 2 8 5〉 and Zr-centered 〈0 1 10 6〉 and 〈0 1 10 7〉 are not beneficial to GFA, although their absolute fractions also increase upon cooling. Higher degree of chemical short range order corresponds to better GFA in the Cu100-xZrx system for x ≤ 25. By studying the transport properties, it is found that Zr addition increases the atomic friction and viscosity of the Cu100-xZrx liquids. The viscosity of Cu90Zr10 liquid is twice of that of pure Cu at 900 K. The deviation from Einstein-Stokes relation corresponds to GFA very well, indicating that it is also a good indicator to evaluate the glass forming abilities.
Indigenous and modern biomaterials derived from Triodia (‘spinifex’) grasslands in Australia
Authors: Gamage Harshi K. , Mondal Subrata , Wallis Lynley A. , Memmott Paul , Martin Darren , Wright Boyd R. , Schmidt Susanne
Published: March 2012

Plant-derived fibres and resins can provide biomaterials with environmental, health and financial benefits. Australian arid zone grasses have not been explored as sources of modern biomaterials including building materials. Triodia grasslands are a dominant vegetation type in the arid and semiarid regions of Australia covering a third of the continent. Of the 69 identified Triodia species, 26 produce resin from specialised cells in the outer leaf epidermis. In Aboriginal culture, Triodia biomass and resin were valued for their usefulness in cladding shelters and as a hafting agent. Since European settlement, Triodia grasslands have been used for cattle grazing and burning is a common occurrence to improve pasture value and prevent large-scale fires. Although Triodia grasslands are relatively stable to fires, more frequent and large-scale fires impact on other fire sensitive woody and herbaceous species associated with Triodia and invasion of exotic weeds resulting in localised changes in vegetation structure and composition. The extent and change occurring in Triodia grasslands as a result of altered land-use practices, fire regimes, and changing climate warrant careful consideration of their future management. Localised harvesting of Triodia grasslands could have environmental benefits and provide much needed biomaterials for desert living. Research is underway to evaluate the material properties of Triodia biomass and resin in the context of Indigenous and western scientific knowledge. Here, we review uses of Triodia and highlight research needs if sustainable harvesting is to be considered.
Different protein expression patterns associated with polycystic ovary syndrome in human follicular fluid during controlled ovarian hyperstimulation
Authors: Dai Guo , Lu Guangxiu
Published: March 2012

Polycystic ovary syndrome (PCOS) is one of the most common causes of anovulatory infertility, affecting 5–10% of females during their reproductive life. Currently the pathology of PCOS is largely unknown. To identify the differential protein expression in follicular fluids from PCOS and normal subjects during controlled ovarian hyperstimulation, we performed an initial proteomic study including two-dimensional gel electrophoresis (2DE) analysis and mass spectroscopy, and confirmed results by western blot. Thirty-two protein spots were shown to be significantly differentially expressed between PCOS and normal follicular fluids, of which 20 unique proteins were identified to be associated with cellular metabolism and physiological processes; 13 of these proteins were upregulated while seven were downregulated in PCOS follicular fluids. Western blotting analyses confirmed the differential expressions for three randomly selected proteins, i.e. upregulated α1-antitrypsin, apolipoprotein A-I and transferrin in follicular fluid from PCOS patients than normal controls. Furthermore, semiquantitative reverse transcription-polymerase chain reaction (RT–PCR) analyses revealed that mRNA levels of serine palmitoyltransferase 2, serine/threonine-protein kinase male germ cell-associated kinase (MAK) and DNA damage-regulated autophagy modulator protein 2 decreased significantly in granulosa cells of PCOS patients compared with normal samples. These results increase our understanding of PCOS and the identified genes may serve as candidate biomarkers to develop diagnostic and therapeutic tools.
Corrigendum to: A revision of Commersonia including Rulingia (Malvaceae s.l. or Byttneriaceae)
Authors: Wilkins C .F. , Whitlock B. A.
Published: March 2012

A taxonomic revision and DNA sequence analysis of all species previously attributed to Rulingia R.Br. and Commersonia J.R.Forst. & G.Forst. resulted in two major groupings, referred to a redefined Commersonia and a new genus (Androcalva C.F.Wilkins & Whitlock 2011). In total, 25 species are now recognised within Commersonia, including the type species of Rulingia, and 14 species previously included in Rulingia and 10 in Commersonia. Three of these are described as new (C. apella C.F.Wilkins, C. erythrogyna C.F.Wilkins and C. gilva C.F.Wilkins). A new subspecies, C. magniflora subsp. oblongifolia C.F.Wilkins, is recognised and C. bartramia (L.) Merr. var. tahitensis Dorr is raised to species level as C. tahitensis (Dorr) C.F.Wilkins & Whitlock. Two new combinations are made, Rulingia platycalyx Benth. and R. parviflora Endl. as C. parviflora (Endl.) C.F.Wilkins & Whitlock; and R. cistifolia Steetz and R. rugosa Steetz as C. rugosa (Steetz) F.Muell. The redefined Commersonia is monophyletic and characterised by anthers with sublatrorse dehiscence and mainly hairy staminodes, compared with extrorse dehiscence and glabrous staminodes as seen in Androcalva.
An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships
Authors: Syme Anna E. , Murphy Daniel J. , Holmes Gareth D. , Gardner Stuart , Fowler Rachael , Cantrill David J.
Published: March 2012

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.
Modelling firebrand transport in wildfires using HIGRAD/FIRETEC
Authors: Koo Eunmo , Linn Rodman R. , Pagni Patrick J. , Edminster Carleton B.
Published: March 2012

Firebrand transport is studied for disc and cylindrical firebrands by modelling their trajectories with a coupled-physics fire model, HIGRAD/FIRETEC. Through HIGRAD/FIRETEC simulations, the size of possible firebrands and travelled distances are analysed to assess spot ignition hazard. Trajectories modelled with and without the assumption that the firebrands’ relative velocities always equal their terminal velocities are. Various models for the flight and combustion of disc- and cylindrical-shaped firebrands are evaluated. Eight simulations are performed with surface fuel fires and four simulations are performed with combined surface and canopy fuels. Firebrand trajectories without terminal velocity are larger than those from models with terminal velocity. Discs travel further than cylinders, as discs are aerodynamically more favourable. Thin discs burning on their faces and tall cylinders burning around their circumference have shorter lifetimes than thin discs burning from their circumference or longer cylinders burning from their ends. Firebrands from canopy fires, with larger size and potential to ignite recipient fuel, travel further than firebrands from surface fires. In the simulations, which included a line fire ignition in homogeneous fuels on flat terrain, the firebrand launching patterns are very heterogeneous, and the trajectories and landing patterns are dominated by the coupled fire–atmosphere behaviour.
Structure-based model of allostery predicts coupling between distant sites
Authors: Weinkam Patrick , Pons Jaume , Sali Andrej
Published: March 2012

Allostery is a phenomenon that couples effector ligand binding at an allosteric site to a structural and/or dynamic change at a distant regulated site. To study an allosteric transition, we vary the size of the allosteric site and its interactions to construct a series of energy landscapes with pronounced minima corresponding to both the effector bound and unbound crystal structures. We use molecular dynamics to sample these landscapes. The degree of perturbation by the effector, modeled by the size of the allosteric site, provides an order parameter for allostery that allows us to determine how microscopic motions give rise to commonly discussed macroscopic mechanisms: (
i
) induced fit, (
ii
) population shift, and (
iii
) entropy driven. These mechanisms involve decreasing structural differences between the effector bound and unbound populations. A metric (ligand-induced cooperativity) can measure how cooperatively a given regulated site responds to effector binding and therefore what kind of allosteric mechanism is involved. We apply the model to three proteins with experimentally characterized transitions: (
i
) calmodulin-GFP Ca
2+
sensor protein, (
ii
) maltose binding protein, and (
iii
) CSL transcription factor. Remarkably, the model is able to reproduce allosteric motion and predict coupling in a manner consistent with experiment.
RETRACTED: Endothelial expression of hypoxia-inducible factor 1 protects the murine heart and aorta from pressure overload by suppression of TGF-β signaling
Authors: Wei Hong , Bedja Djahida , Koitabashi Norimichi , Xing Dongmei , Chen Jasper , Fox-Talbot Karen , Rouf Rosanne , Chen Shaoping , Steenbergen Charles , Harmon John W. , Dietz Harry C. , Gabrielson Kathleen L. , Kass David A. , Semenza Gregg L.
Published: March 2012

Chronic systemic hypertension causes cardiac pressure overload leading to increased myocardial O
2
consumption. Hypoxia-inducible factor 1 (HIF-1) is a master regulator of O
2
homeostasis. Mouse embryos lacking expression of the O
2
-regulated HIF-1α subunit die at midgestation with severe cardiac malformations and vascular regression. Here we report that

Hif1a
f/f
;Tie2-Cre

conditional knockout mice, which lack HIF-1α expression only in Tie2
+
lineage cells, develop normally, but when subjected to pressure overload induced by transaortic constriction (TAC), they manifest rapid cardiac decompensation, which is accompanied by excess cardiac fibrosis and myocardial hypertrophy, decreased myocardial capillary density, increased myocardial hypoxia and apoptosis, and increased TGF-β signaling through both canonical and noncanonical pathways that activate SMAD2/3 and ERK1/2, respectively, within endothelial cells of cardiac blood vessels. TAC also induces dilatation of the proximal aorta through enhanced TGF-β signaling in

Hif1a
f/f
;Tie2-Cre

mice. Inhibition of TGF-β signaling by treatment with neutralizing antibody or pharmacologic inhibition of MEK–ERK signaling prevented TAC-induced contractile dysfunction and pathological remodeling. Thus, HIF-1 plays a critical protective role in the adaptation of the heart and aorta to pressure overload by negatively regulating TGF-β signaling in endothelial cells. Treatment of wild-type mice with digoxin, which inhibits HIF-1α synthesis, resulted in rapid cardiac failure after TAC. Although digoxin has been used for decades as an inotropic agent to treat heart failure, it does not improve survival, suggesting that the countertherapeutic effects of digoxin observed in the TAC mouse model may have clinical relevance.
Lignin synthesis, transcriptional regulation and potential for useful modification in plants.
Authors: Bedon F. , Legay S.
Published: March 2012

Lignin, the second most abundant plant polymer on earth, has always been of great interest for research with regard to its biological roles and potential for useful modification. Over the last few decades, numerous studies have considerably enriched our knowledge of lignin biosynthesis. In the first part, a revision of lignin composition and synthesis is described, highlighting the key genes shown to be implicated in the lignification process occurring during secondary cell wall (SCW) formation in plants. Availability of genome sequencing data has brought about useful information concerning the different gene families of the lignin biosynthesis pathway. These data can be exploited to isolate the members that are more specific to the SCW formation process through combination of sequence homology or specific transcript-profiling techniques. This review also summarizes our current knowledge on the transcriptional regulation of lignin biosynthesis, particularly the R2R3-MYB and NAC transcription factor (TF) families. Strategies of lignin modification for the production of second-generation biofuels are also discussed.
Assessing safety of biological control introductions.
Authors: Barratt B. I. P.
Published: March 2012

Biological control is an important component of pest management systems. It was generally considered safe and sustainable until the validity of this consensus was challenged by researchers who pointed out that there was a lack of study, and hence evidence, to support it and provided examples of non-target impacts. Biosafety of biological control subsequently received considerable attention from both biocontrol practitioners and regulators. Many countries now have legislation in place, which is focused on risk assessment for biological control and protecting native and valued biota and the environment from potential adverse impacts. This review summarizes the biosafety debate and characterizes the direct and indirect risks of biological control mainly for weeds and insect pests. During a biological control programme, there are several ways in which aspects of biosafety can be considered and addressed: exploration in the native range of the target species; from literature and knowledge of the biological control agent and host; experience from use of the biological control agent elsewhere; and host-range tests. The value of post-release monitoring and retrospective studies for validation of pre-release predictions is discussed. A poorly studied aspect is analysis of the population impacts of non-target attack by biological control agents. The literature from the last 20-30 years can help define some useful principles by which a risk assessment can be conducted to minimize adverse environmental effects. It has become clear over this period that comprehensive assembly of information and robust quarantine testing to provide a well-structured risk assessment can reduce uncertainty in decision-making in this area.
Atomically controlled CVD processing of group IV semiconductors for ultra-large-scale integrations
Authors: Murota Junichi , Sakuraba Masao , Tillack Bernd
Published: March 2012

One of the main requirements for ultra-large-scale integrations (ULSIs) is atomic-order control of process technology. Our concept of atomically controlled processing is based on atomic-order surface reaction control by CVD. By ultraclean low-pressure CVD using SiH
4 and GeH
4 gases, high-quality low-temperature epitaxial growth of Si
1−x

Ge

x
(100) (x=0–1) with atomically flat surfaces and interfaces on Si(100) is achieved. Self-limiting formation of 1–3 atomic layers of group IV or related atoms in the thermal adsorption and reaction of hydride gases on Si
1-x

Ge

x
(100) are generalized based on the Langmuir-type model. By the Si epitaxial growth on top of the material already-formed on Si(100), N, B and C atoms are confined within about a 1 nm thick layer. In Si cap layer growth on the P atomic layer formed on Si
1−x

Ge

x
(100), segregation of P atoms is suppressed by using Si
2
H
6 instead of SiH
4 at a low temperature of 450 °C. Heavy C atomic-layer doping suppresses strain relaxation as well as intermixing between Si and Ge at the Si
1−x

Ge

x
/Si heterointerface. It is confirmed that higher carrier concentration and higher carrier mobility are achieved by atomic-layer doping. These results open the way to atomically controlled technology for ULSIs.
A strategy for building neuroanatomy ontologies
Authors: Osumi-Sutherland David , Reeve Simon , Mungall Christopher J. , Neuhaus Fabian , Ruttenberg Alan , Jefferis Gregory S. X. E. , Armstrong J. Douglas
Published: March 2012

Motivation: Advancing our understanding of how nervous systems work will require the ability to store and annotate 3D anatomical datasets, recording morphology, partonomy and connectivity at multiple levels of granularity from subcellular to gross anatomy. It will also require the ability to integrate this data with other data-types including functional, genetic and electrophysiological data. The web ontology language OWL2 provides the means to solve many of these problems. Using it, one can rigorously define and relate classes of anatomical structure using multiple criteria. The resulting classes can be used to annotate datasets recording, for example, gene expression or electrophysiology. Reasoning software can be used to automate classification and error checking and to construct and answer sophisticated combinatorial queries. But for such queries to give consistent and biologically meaningful results, it is important that both classes and the terms (relations) used to relate them are carefully defined.

Results: We formally define a set of relations for recording the spatial and connectivity relationships of neuron classes and brain regions in a broad range of species, from vertebrates to arthropods. We illustrate the utility of our approach via its application in the ontology that drives the Virtual Fly Brain web resource.

Availability and implementation: The relations we define are available from http://purl.obolibrary.org/obo/ro.owl. They are used in the Drosophila anatomy ontology (http://purl.obolibrary.org/obo/fbbt/2011-09-06/), which drives the web resource http://www.virtualflybrain.org

Contact:  djs93@gen.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure
Authors: Gautier Mathieu , Vitalis Renaud
Published: March 2012

Summary: With the development of next-generation sequencing and genotyping approaches, large single nucleotide polymorphism haplotype datasets are becoming available in a growing number of both model and non-model species. Identifying genomic regions with unexpectedly high local haplotype homozygosity relatively to neutral expectation represents a powerful strategy to ascertain candidate genes responding to natural or artificial selection. To facilitate genome-wide scans of selection based on the analysis of long-range haplotypes, we developed the R package rehh. It provides a versatile tool to detect the footprints of recent or ongoing selection with several graphical functions that help visual interpretation of the results.

Availability and implementation: Stable version is available from CRAN: http://cran.r-project.org/. Development version is available from the R-forge repository: http://r-forge.r-project.org/projects/rehh. Both versions can be installed directly from R. Function documentation and example data files are provided within the package and a tutorial is available as Supplementary Material. rehh is distributed under the GNU General Public Licence (GPL ≥ 2).

Contact:  mathieu.gautier@supagro.inra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.