bluuebunny/crossref_metadata_2025 huggingface dataset:
Ligand field photofragmentation spectroscopy of [Ag(L)N]2+ complexes in the gas phase: Experiment and theory
Authors: Guan Jingang , Puškar Ljiljana , Esplugas Ricardo O. , Cox Hazel , Stace Anthony J.
Published: August 2007

Experiments have been undertaken to record photofragmentation spectra from a series of [Ag(L)N]2+ complexes in the gas phase. Spectra have been obtained for silver(II) complexed with the ligands (L): acetone, 2-pentanone, methyl-vinyl ketone, pyridine, and 4-methyl pyridine (4-picoline) with N in the range of 4–7. A second series of experiments using 1,1,1,3-fluoroacetone, acetonitrile, and CO2 as ligands failed to show any evidence of photofragmentation. Interpretation of the experimental data has come from time-dependent density functional theory (TDDFT), which very successfully accounts for trends in the spectra in terms of subtle differences in the properties of the ligands. Taking a sample of three ligands, acetone, pyridine, and acetonitrile, the calculations show all the spectral transitions to involve ligand-to-metal charge transfer, and that wavelength differences (or lack of spectra) arise from small changes in the energies of the molecular orbitals concerned. The calculations account for an absence in the spectra of any effects due to Jahn-Teller distortion, and they also reveal structural differences between complexes where the coordinating atom is either oxygen or nitrogen that have implications for the stability of silver(II) compounds. Where possible, comparisons have also been made with the physical properties of condensed phase silver(II) complexes.
Molecular quantum-dot cellular automata: From molecular structure to circuit dynamics
Authors: Lu Yuhui , Liu Mo , Lent Craig
Published: August 2007

We establish a method for exploring the dynamics of molecular quantum-dot cellular automata (QCA) devices by hierarchically combining the techniques of quantum chemistry with the nonequilibrium time-dependent coherence vector formalism. Single QCA molecules are characterized using ab initio quantum chemistry methods. We show how to construct a simple model Hamiltonian for each QCA cell based on parameters extracted from the ab initio calculation. The model Hamiltonian captures well the relevant switching behavior and can then be used to calculate the time-dependent coherence vector, including thermal and nonequilibrium behavior. This enables us to explore dynamic behavior and power dissipation for various QCA devices and circuits.
Demonstration of high-performance compact magnetic shields for chip-scale atomic devices
Authors: Donley E. A. , Hodby E. , Hollberg L. , Kitching J.
Published: August 2007

We have designed and tested a set of five miniature nested magnetic shields constructed of high-permeability material, with external volumes for the individual shielding layers ranging from 0.01to2.5cm3. We present measurements of the longitudinal and transverse shielding factors (the ratio of external to internal magnetic field) of both individual shields and combinations of up to three layers. The largest shielding factor measured was 6×106 for a nested set of three shields, and from our results we predict a shielding factor of up to 1×1013 when all five shields are used. Two different techniques were used to measure the internal field: a chip-scale atomic magnetometer and a commercially available magnetoresistive sensor. Measurements with the two methods were in good agreement.
Wakefield generation in metamaterial-loaded waveguides
Authors: Antipov S. , Spentzouris L. , Liu W. , Gai W. , Power J. G.
Published: August 2007

Metamaterials (MTMs) are artificial structures made of periodic elements and are designed to obtain specific electromagnetic properties. As long as the periodicity and the size of the elements are much smaller than the wavelength of interest, an artificial structure can be assigned a permittivity and permeability, just like natural materials. Metamaterials can be customized to have the permittivity and permeability desired for a particular application. When the permittivity and permeability are made simultaneously negative in some frequency range, the metamaterial is called double-negative or left-handed and has some unusual properties. For example, Cherenkov radiation (CR) in a left-handed metamaterial is backward; radiated energy propagates in the opposite direction to particle velocity. This property can be used to improve the design of particle detectors. Waveguides loaded with metamaterials are of interest because the metamaterials can change the dispersion relation of the waveguide significantly. Slow backward waves, for example, can be produced in a MTM-loaded waveguide without corrugations. In this paper we present theoretical studies of waveguides loaded with an anisotropic and dispersive medium (metamaterial). The dispersion relation of a MTM-loaded waveguide has several interesting frequency bands which are described. We present a universal method to simulate wakefield (CR) generation in a waveguide loaded with a dispersive and anisotropic medium. This method allows simulation of different waveguide cross sections, any transverse beam distribution, and any physical dispersion, of the medium. The method is benchmarked against simple cases, which can be theoretically calculated. Results show excellent agreement.
Aluminum-nitride codoped zinc oxide films prepared using a radio-frequency magnetron cosputtering system
Authors: Liu Day-Shan , Sheu Chia-Sheng , Lee Ching-Ting
Published: August 2007

Al–N codoped zinc oxide films were prepared using a radio-frequency magnetron cosputtering system at room temperature. AlN and ZnO materials were employed as the cosputtered targets. The as-deposited cosputtered films at various theoretical atomic ratios [Al∕(Al+Zn)at.%] showed n-type conductive behavior in spite of the N atoms exceeding that of the Al dopants, indicating that the N-related acceptors were still inactive. The crystalline structure was obviously correlated with the cosputtered AlN contents and eventually evolved into an amorphous structure for the Al–N codoped ZnO film at a theoretical Al doping level reaching 60%. With an adequate postannealing treatment, the N-related acceptors were effectively activated and the p-type ZnO conductive behavior achieved. The appearance of the Zn3N2 phase in the x-ray diffraction pattern of the annealed Al–N codoped ZnO film provided evidence of the nitrification of zinc ions. The redshift of the shallow level transition and the apparent suppression of the oxygen-related deep level emission investigated from the photoluminescence spectrum measured at room temperature were concluded to be influenced by the activated N-related acceptors. In addition, the activation of the N acceptors denoted as N–Zn bond and the chemical bond related to the Zn3N2 crystalline structure were also observed from the associated x-ray photoelectron spectroscopy spectra.
Synthesis and electronic-property control of Cs-encapsulated single- and double-walled carbon nanotubes by plasma ion irradiation
Authors: Hatakeyama R. , Li Y. F.
Published: August 2007

The synthesis of Cs-encapsulated single-walled carbon nanotubes (Cs@SWNTs) and double-walled carbon nanotubes (Cs@DWNTs) is realized by a plasma ion-irradiation method. Transmission electron microscopy observations confirm that chainlike and amorphous Cs fill SWNTs and DWNTs, respectively. The electronic transport properties of Cs@SWNTs and Cs@DWNTs are experimentally investigated at both room and low temperatures by fabricating them as the channels of field-effect transistor devices. Our results reveal that both Cs@SWNTs and Cs@DWNTs exhibit n-type semiconducting behavior at room temperature. The electronic properties of the Cs-encapsulated nanotubes can be controlled by adjusting the Cs filling levels during the plasma ion irritation process. At low temperatures, Coulomb blockade transport characteristics are observed for both encapsulated nanotubes, and the size of quantum dots formed in Cs@DWNTs is much smaller than that formed in Cs@SWNTs. More importantly, the n-type characteristics of Cs@SWNTs and Cs@DWNTs are found to remain stable, even in air, owing to Cs encapsulation.
High resolution microresonator-based digital temperature sensor
Authors: Jha C. M. , Bahl G. , Melamud R. , Chandorkar S. A. , Hopcroft M. A. , Kim B. , Agarwal M. , Salvia J. , Mehta H. , Kenny T. W.
Published: August 2007

A digital temperature sensing technique using a complementary metal oxide semiconductor (CMOS) compatible encapsulated microresonator is presented. This technique leverages our ability to select the temperature dependence of the resonant frequency for micromechanical silicon resonators by adjusting the relative thickness of a SiO2 compensating layer. A dual-resonator design is described that includes a pair of resonators with differential temperature compensations so that the difference between the two resonant frequencies is a sensitive function of temperature. The authors demonstrate a temperature resolution of approximately 0.008°C for 1s averaging time, which is better than that of the best CMOS temperature sensors available today.
p
-type conduction in unintentional carbon-doped ZnO thin films
Authors: Tan S. T. , Sun X. W. , Yu Z. G. , Wu P. , Lo G. Q. , Kwong D. L.
Published: August 2007

p -type conduction has been observed in unintentional carbon-doped ZnO thin films grown by metal organic chemical vapor deposition through postgrowth annealing treatment. The existence of carbon, which has been verified by secondary ion mass spectrometry and x-ray photoelectron spectroscopy, was predicted to immobilize the oxygen in the interstitial site in ZnO thin films after annealing. Using first principles calculations, the formation of carbon-oxygen cluster defect in ZnO was found to be favorable and acts as a shallow acceptor. The cryogenic photoluminescence of the p-type carbon-doped ZnO thin films shows an additional peak located at 3.3564eV, which was attributed to the acceptor (carbon-oxygen cluster defect) bound exciton emission.
Selective epitaxial germanium on silicon-on-insulator high speed photodetectors using low-temperature ultrathin Si0.8Ge0.2 buffer
Authors: Loh T. H. , Nguyen H. S. , Murthy R. , Yu M. B. , Loh W. Y. , Lo G. Q. , Balasubramanian N. , Kwong D. L. , Wang J. , Lee S. J.
Published: August 2007

The authors report the performance of selective epitaxial Ge (400nm) on Si-on-insulator p-i-n mesa-type normal incidence photodiodes using ∼14nm low-temperature Si0.8Ge0.2 buffer without cyclic annealing. At −1V, very low bulk dark current densities of 1.5–2mA∕cm2 were obtained indicating good material quality, and the peripheral surface leakage current densities were 14–19.5μA∕cm. For 28μm diameter round photodiode, the highest achieved external quantum efficiencies at −5V were 27%, 9%, and 2.9% for 850nm, 1.3μm, and 1.56μm optical wavelengths, respectively. 15×15μm2 square photodiode has 3dB bandwidth ⩾15GHz at −1V. Good performance was achieved without high-temperature annealing, suggesting easy integration of Ge∕Si photodiode unto existing complementary metal-oxide-semiconductor process.
Branched growth of degenerately Sb-doped SnO2 nanowires
Authors: Huang Jin , Lu Aixia , Zhao Bin , Wan Qing
Published: August 2007

The authors report the growth of degenerately Sb-doped SnO2 single crystalline nanowires with three-dimensionally branched morphology by a two-step Au-catalyzed vapor-liquid-solid growth approach. Raman scattering and transmission electron microscopy results indicate that the crystal phase of Sb-doped SnO2 nanowires is rutile. Electrical transport measurements indicate that Sb-doped SnO2 nanowire has a resistivity of 1.92×10−3Ωcm and an electron concentration of 2.8×1020cm3. Branched conducting nanowires are promising candidates for catalyst supports, biologic molecule detection, and three-dimensional nanodevices integration.
Effect of edge roughness in graphene nanoribbon transistors
Authors: Yoon Youngki , Guo Jing
Published: August 2007

The effects of edge irregularity and mixed-edge shapes on the characteristics of graphene nanoribbon transistors are examined by self-consistent atomistic simulations based on the nonequilibrium Green’s function formalism. The minimal leakage current increases due to the localized states induced in the band gap, and the on current decreases due to smaller quantum transmission and the self-consistent electrostatic effect in general. Although the ratio between the on current and minimal leakage current decreases, the transistor still switches even in the presence of edge roughness. The variation between devices, however, can be large, especially for a short channel length.
In-plane bistable nematic liquid crystal devices based on nanoimprinted surface relief
Authors: Gwag Jin Seog , Fukuda Jun-ichi , Yoneya Makoto , Yokoyama Hiroshi
Published: August 2007

The authors present a bistable nematic device, using a fourfold symmetrical bidirection nanometer-scale surface grating fabricated by the nanoimprinting lithography. The bistability is achieved by a composite action between two orthogonal surface undulations, which tend to stabilize the nematic director along either of the two diagonal axes. The switching between the bistable states is easily driven by orthogonal in-plane electric fields. A recent model of groove-induced surface anchoring due to Fukuda et al. [Phys. Rev. Lett. 98, 187803 (2007)] accounts for the azimuthal bistability in the present system.
1.54
μ
m
photoluminescence from β-FeSi2 as-deposited film
Authors: Akiyama Kensuke , Kaneko Satoru , Funakubo Hiroshi , Itakura Masaru
Published: August 2007

The authors succeeded in preparing high-crystal-quality β-FeSi2 as-deposited film emitting a photoluminescence spectrum strong in intensity. The density of the nonradiative center at the interface and in the β-FeSi2 film remained low by depositing a Cu-treated Si layer such as amorphous Si. The recrystallization of the Cu-treated Si layer during β-FeSi2 deposition contributed to improving the β-FeSi2∕Si interface and the crystallinity of the β-FeSi2 film.
Optical manipulable polymer optical fiber Bragg gratings with azopolymer as core material
Authors: Luo Yanhua , Zhou Jingli , Yan Qing , Su Wei , Li Zengchang , Zhang Qijin , Huang Jintang , Wang Keyi
Published: August 2007

Polymer optical fiber (POF) with a core of azopolymer has been fabricated. Based on the photoinduced birefringence of azopolymer materials, a mechanism for writing POF gratings is presented. After writing in azopolymer optical fiber (APOF) by two beams of mutually orthogonal polarizations, a birefringence grating was formed, and then the gratings could be erased almost totally for a short time by the circularly polarized beam at the same wavelength. By manipulating the APOF gratings, the transmittance through APOF at 632.8nm can be adjustable as revealed by the transmittance change during write-erase-write procedure.
Microwave absorption saturation and decay heating of surface electrons on liquid helium
Authors: Monarkha Y. , Konstantinov D. , Kono K.
Published: August 2007

The microwave (MW) resonance absorption and decay heating of surface electrons (SEs) on liquid He4 are studied theoretically for the vapor atom scattering regime. The decay heating is shown to be an essential occurrence in a MW resonance experiment, appearing even at low excitation rates. It strongly affects the occupancies of surface levels and the broadening of resonance lines long before the absorption saturation condition is reached. Contrary to the model of cold SEs usually used for description of the MW resonance, the new theory leads to MW absorption saturation when only a very small fraction of electrons (less than 10%) is left at the ground and the first excited levels.
Liquid crystal surface alignments by using ion beam sputtered magnetic thin films
Authors: Wu Hsin-Ying , Pan Ru-Pin
Published: August 2007

A method for liquid crystal surface alignment by using a one-step, ion beam bombardment of the glass substrates is demonstrated. Precoating by polyimide is not necessary. The authors show that the homeotropic alignment is achieved due to orientation of the diamagnetic nematogenic molecules by the magnetic field from the γ-Fe2O3 ferrimagnetic thin films created on the substrates by ion beam bombardment. The film exhibits a high Curie temperature well above 300K and a compensation temperature which is the typical feature of ferrimagnetism. This is a simple, noncontact, and reliable alignment method for liquid crystal devices.
Diffusion of nitrogen molecules in amorphous SiO2
Authors: Kajihara Koichi , Hirano Masahiro , Takimoto Yasuyuki , Skuja Linards , Hosono Hideo
Published: August 2007

Nitrogen molecules (N2) are incorporated in interstitial voids in amorphous silica (a-SiO2) thermally annealed in N2 atmosphere. The Raman band associated with the infrared N–N stretching mode of interstitial N2 (Q band) is located at ∼2325cm−1 and is shifted to low energy compared to that of N2 molecules in air (∼2330cm−1). From depth profiling of the Raman band intensity in the samples thermally annealed at 800, 900, or 1000°C, the authors determined the diffusion coefficient and solubility of N2 in a-SiO2 as 1.3×10−4±0.5exp(−1.28±0.1eV∕kT)cm2s−1 and 7.0×1015±0.5exp(0.07±0.1eV∕kT)cm−3atm−1, respectively.
Optical signal storage and switching between two wavelengths
Authors: Song Xiao-Li , Wang Lei , Kang Zhi-Hui , Lin Rui-Zhu , Li Xin , Jiang Yun , Gao Jin-Yue
Published: August 2007

The authors report an experiment in which optical pulses are effectively stored via maximal atomic coherence in a three-level Λ-type Rb87 atomic system, and then selectively released at one of the two different wavelengths by turning on the retrieve control pulse at 794.9842 or 794.9698nm. The storage time up to 360ns was demonstrated.
Planar ZnO ultraviolet modulator
Authors: Zhang X. Y. , Dhawan A. , Wellenius P. , Suresh A. , Muth J. F.
Published: August 2007

A planar electroabsorption modulator suitable for spatial light modulation has been constructed. The device operates near the band edge of zinc oxide at 3.3eV and is based on broadening and shifting of the unconfined exciton with an externally applied electric field. The ZnO active layer was deposited on an aluminum/titanium oxide dielectric on an indium tin oxide conducting layer on glass. A transparent conductive InGaZnO layer on a spin on glass insulator served as the top contact, allowing high electric fields to be applied transverse to the ZnO layer. The modulator operates at room temperature in transmission mode with +45% modulation at 373nm and −18% modulation at 380nm at 140V applied bias, corresponding to ∼450kV∕cm electric field across the ZnO active layer.
Strain-induced single-domain growth of epitaxial SrRuO3 layers on SrTiO3: A high-temperature x-ray diffraction study
Authors: Vailionis Arturas , Siemons Wolter , Koster Gertjan
Published: August 2007

Temperature dependent structural phase transitions of SrRuO3 thin films epitaxially grown on SrTiO3(001) single crystal substrates have been studied using high-resolution x-ray diffraction. In contrast to bulk SrRuO3, coherently strained epitaxial layers do not display cubic symmetry up to ∼730°C and remain tetragonal. The cause of this behavior is believed to be the compressive strain in the SrRuO3 layer due to the lattice mismatch with SrTiO3 substrate due to lattice mismatch. The tetragonal symmetry during growth explains the single domain growth on miscut SrTiO3 substrates with step edges running along the [100] or [010] direction.
Anomalous photoconductivity of CeO2 nanowires in air
Authors: Fu X. Q. , Wang C. , Feng P. , Wang T. H.
Published: August 2007

The conductance of the CeO2 nanowire film is found to decrease by about two orders of magnitude in air under ultraviolet illumination. Such a drastic decrease in conductance is attributed to light-induced desorption of H2O from the nanowire’s surface. When exposed in air, the surface conductivity of the nanowire increases significantly due to the adsorption of H2O. Considering the large surface-to-volume ratio of the nanowire, the conductance of the nanowire film is mainly controlled by surface conduction. Upon ultraviolet illumination, desorption of H2O results in the decrease of the conductance of the nanowire film, thus leading to the anomalous photoconductivity.
Optically actuated thermocapillary movement of gas bubbles on an absorbing substrate
Authors: Ohta Aaron T. , Jamshidi Arash , Valley Justin K. , Hsu Hsan-Yin , Wu Ming C.
Published: August 2007

The authors demonstrate an optical manipulation mechanism of gas bubbles for microfluidic applications. Air bubbles in a silicone oil medium are manipulated via thermocapillary forces generated by the absorption of a laser in an amorphous silicon thin film. In contrast to previous demonstrations of optically controlled thermally driven bubble movement, transparent liquids can be used, as the thermal gradient is formed from laser absorption in the amorphous silicon substrate, and not in the liquid. A variety of bubbles with volumes ranging from 19plto23nl was transported at measured velocities of up to 1.5mm∕s.
Electric field effect on BiFeO3 single crystal investigated by Raman spectroscopy
Authors: Cazayous M. , Malka D. , Lebeugle D. , Colson D.
Published: August 2007

Micro-Raman spectroscopy has been used to study lattice dynamics associated with the ferroelectric domains of a BiFeO3 single crystal at low temperature. The phonon assignment shows a large frequency splitting between the transverse and longitudinal components of the A1 phonon mode related to the Bi–O bonds in contrast with thin films where the splitting is negligible. Applying an external electric field induces frequency shifts of the low energy modes related to the Bi–O bonds. These softenings are due to a tensile stress via the piezoelectric effect. The authors give estimates of the phonon deformation potentials.
Low-loss optical Er3+-activated glass-ceramics planar waveguides fabricated by bottom-up approach
Authors: Jestin Y. , Armellini C. , Chiasera A. , Chiappini A. , Ferrari M. , Moser E. , Retoux R. , Righini G. C.
Published: August 2007

A low-loss optical erbium activated silica-hafnia glass-ceramic planar waveguide was fabricated using a bottom-up approach. Hafnia nanoparticles were first prepared by colloidal route and then mixed in a silica-hafnia:Er3+ sol. The resulting sol was deposited on SiO2 substrate. Analysis of the photoluminescence has demonstrated that erbium ions are embedded in a crystalline phase. A lifetime enhancement of the I13∕24 metastable level was observed. Losses measurements at 1542nm highlight a very low attenuation coefficient (0.3dB∕cm) making this nanostructured material suitable for single band waveguide amplifier in the C band of telecommunications.
Labile soil organic matter pools under a mixed grass/lucerne pasture and adjacent native bush in Western Australia
Authors: Macdonald A. J. , Murphy D. V. , Mahieu N. , Fillery I. R. P.
Published: August 2007

Total C and N were measured in whole soils (0–0.15, 0.15–0.35, and 0.35–0.65 m), light organic matter fractions (<1 g/cm3 (LF 1.0) and 1.0–1.7 g/cm3 (LF 1.7)) in surface soils, and in leaf litter collected from a mixed grass/lucerne pasture and adjacent native bush at Moora, Western Australia. The C content of the plant material and light fractions was characterised by 13C cross-polarisation/magic angle spinning nuclear magnetic resonance (13C CP/MAS NMR) spectroscopy. Water-extractable organic C (WEOC) and N (WEON) were measured in soil, and dissolved organic C (DOC) and N (DON) were measured in soil solutions. In addition, both NO3-N and NH4-N (SMN) were measured in soil solutions and water extracts.
Total soil C (0–0.65 m) did not differ significantly between land uses, but there was clear evidence of N enrichment under the pasture system, which contained significantly (P < 0.05) more total N in the surface soil (0–0.15 m) compared with that under native bush. The significantly (P < 0.05) smaller C/N ratios of the surface soil, plant litter, and light fractions (LF 1.0 and 1.7) under the pasture provided further evidence of N enrichment. The 13C CP/MAS NMR spectra for plant material and light fractions did not differ greatly between landuses, but in both cases the O-alkyl : alkyl carbon ratio declined with increasing density. The decomposition and subsequent mineralisation of the relatively N-rich organic matter fractions in the pasture system may have contributed to the significantly (P < 0.05) greater DOC, DON, and SMN concentration measured in soil solutions under pasture compared with those under native bush.
Effects of 15 years of conservation tillage on soil structure and productivity of wheat cultivation in northern China
Authors: Li Hongwen , Gao Huanwen , Wu Hongdan , Li Wenying , Wang Xiaoyan , He Jin
Published: August 2007

An understanding of long-term tillage and straw management impact on soil structure and productivity is necessary for the further development of conservation tillage practice in dryland farming areas. Data from a 15-year field experiment conducted in Shanxi, on the loess plateau of northern China, were used to compare the long-term effects of no-till and residue cover (NTSC) with conventional tillage (CT) in a winter wheat (Triticum aestivum L.) monoculture.
Long-term CT and straw removal resulted in poor soil structure and low productivity. Mean soil bulk density in NTSC was 1.5% less than in CT and capillary porosity (<60 μm) 3.2% greater. Water stability of macro-aggregates >2 mm was much greater for NTSC in the 0–0.20 m profile. Soil organic matter and total N and P were 27.9%, 25.6%, and 4.4% greater in NTSC, respectively, and earthworms (19/m2) were found only in the no tillage treatment.
Crop yield and water use efficiency tended to be higher under NTSC than under CT, especially in the years of low rainfall, suggesting that the change in soil structure has provided a better environment for crop development. Our 15-year experimental data indicate that NTSC is a more sustainable farming system, which can improve soil structure, and increase productivity with positive environmental impacts in the rainfed dryland farming areas of northern China.
Chemical fractionation of fluorine in soils with a long-term phosphate fertiliser history
Authors: Loganathan P. , Liu Q. , Hedley M. J. , Gray C. W.
Published: August 2007

Elevated concentrations of fluorine (F) in pasture topsoils resulting from phosphorus (P) fertiliser (1–4% F) use are potentially toxic to grazing livestock if F absorption from ingested soil is high. Fluorine absorption by animals and the potential F toxicity is expected to vary depending on the chemical nature of the F in the ingested soil. In this paper we assess the solubility of F in 6 acidic topsoils (0–75 mm depth) under grazed pastures in New Zealand with widely different chemical characteristics, using a sequential soil P fractionation technique involving a cation/anion exchange resin, 0.1 m NaOH, 0.5 m H2SO4, and a residual fraction (17 m NaOH fusion). The results showed that F accumulates mainly in the NaOH-Fi fraction (inorganic F (Fi) adsorbed to Fe and Al oxides) and residual fractions (occluded F and recalcitrant organic F). In contrast, P accumulates mainly in the NaOH-Po (labile organic P fraction) and H2SO4-P (calcium phosphate compounds) fractions, with minor amounts in the NaOH-Pi fraction. The NaOH-Fo (labile organic F) fraction was not determined but the total F concentration calculated by summing all the extracted F fractions, except NaOH-Fo, was approximately equal to the total F concentration determined by NaOH fusion, indicating negligible F was in the NaOH-Fo fraction. Therefore, we suggest that the mechanisms of release of P and F in soils are different. Some of the F found in the residual fraction may have been derived from the previously extracted H2SO4-F fraction which was precipitated by the Al dissolved during H2SO4 extraction. It may therefore have been an artefact of the fractionation method.
Varying environments can speed up evolution
Authors: Kashtan Nadav , Noor Elad , Alon Uri
Published: August 2007

Simulations of biological evolution, in which computers are used to evolve systems toward a goal, often require many generations to achieve even simple goals. It is therefore of interest to look for generic ways, compatible with natural conditions, in which evolution in simulations can be speeded. Here, we study the impact of temporally varying goals on the speed of evolution, defined as the number of generations needed for an initially random population to achieve a given goal. Using computer simulations, we find that evolution toward goals that change over time can, in certain cases, dramatically speed up evolution compared with evolution toward a fixed goal. The highest speedup is found under modularly varying goals, in which goals change over time such that each new goal shares some of the subproblems with the previous goal. The speedup increases with the complexity of the goal: the harder the problem, the larger the speedup. Modularly varying goals seem to push populations away from local fitness maxima, and guide them toward evolvable and modular solutions. This study suggests that varying environments might significantly contribute to the speed of natural evolution. In addition, it suggests a way to accelerate optimization algorithms and improve evolutionary approaches in engineering.
Empirical evidence for a recent slowdown in irrigation-induced cooling
Authors: Bonfils Céline , Lobell David
Published: August 2007

Understanding the influence of past land use changes on climate is needed to improve regional projections of future climate change and inform debates about the tradeoffs associated with land use decisions. The effects of rapid expansion of irrigated area in the 20th century has remained unclear relative to other land use changes, such as urbanization, that affected a similar total land area. Using spatial and temporal variations in temperature and irrigation extent observed in California, we show that irrigation expansion has had a large cooling effect on summertime average daily daytime temperatures (−0.14°C to −0.25°C per decade), which corresponds to an estimated cooling of −1.8°C to −3.2°C since the introduction of irrigation practices. Irrigation has negligible effects on nighttime temperatures, leading to a net cooling effect of irrigation on climate (−0.06°C to −0.19°C per decade). Stabilization of irrigated area has occurred in California since 1980 and is expected in the near future for many irrigated regions. The suppression of past human-induced greenhouse warming by increased irrigation is therefore likely to slow in the future, and a potential decrease in irrigation may even contribute to a more rapid warming. Changes in irrigation alone are not expected to influence broad-scale temperatures, but they may introduce large uncertainties in climate projections for irrigated agricultural regions, which provide ≈40% of global food production.
Genetics of microenvironmental canalization in
Arabidopsis thaliana
Authors: Hall Megan C. , Dworkin Ian , Ungerer Mark C. , Purugganan Michael
Published: August 2007

Canalization is a fundamental feature of many developmental systems, yet the genetic basis for this property remains elusive. We examine the genetic basis of microenvironmental canalization in the model plant
Arabidopsis thaliana
, focusing on differential developmental stability between genotypes in one fitness and four quantitative morphological traits. We measured developmental stability in genetically identical replicates of two populations of recombinant inbred (RI) lines and one population of geographically widespread accessions of
A. thaliana
grown in two different photoperiod-controlled environments. We were able to map quantitative trait loci associated with developmental stability. We also identified a candidate gene,
ERECTA
, that may contribute to microenvironmental canalization in rosette leaf number under long-day photoperiods, and analysis of mutant lines indicates that the
er
-105 allele results in increased canalization for this trait.
ERECTA
, which encodes a signaling protein, appears to act as an ecological amplifier by transducing developmental noise (e.g., microenvironmental variation) into phenotypic differentiation. We also measured genotypic selection on four plant architecture traits and find evidence for selection for both increased and decreased canalization at various traits.
The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP
Authors: Bange Gert , Petzold Georg , Wild Klemens , Parlitz Richard O. , Sinning Irmgard
Published: August 2007

Flagella are well characterized as the organelles of locomotion and allow bacteria to react to environmental changes. The assembly of flagella is a multistep process and relies on a complex type III export machinery located in the cytoplasmic membrane. The FlhF protein is essential for the placement and assembly of polar flagella and has been classified as a signal-recognition particle (SRP)-type GTPase. SRP GTPases appeared early in evolution and form a unique subfamily within the guanine nucleotide binding proteins with only three members: the signal sequence-binding protein SRP54, the SRP receptor FtsY, and FlhF. We report the crystal structures of FlhF from
Bacillus subtilis
in complex with GTP and GMPPNP. FlhF shares SRP GTPase-specific features such as the presence of an N-terminal α-helical domain and the I-box insertion. It forms a symmetric homodimer sequestering a composite active site that contains two head-to-tail arranged nucleotides similar to the heterodimeric SRP-targeting complex. However, significant differences to the GTPases of SRP and the SRP receptor include the formation of a stable homodimer with GTP as well as severe modifications and even the absence of motifs involved in regulation of the other two SRP GTPases. Our results provide insights into SRP GTPases and their roles in two fundamentally different protein-targeting routes that both rely on efficient protein delivery to a secretion channel.
Anomalous compression behavior in lanthanum/cerium-based metallic glass under high pressure
Authors: Zeng Q. S. , Li Y. C. , Feng C. M. , Liermann P. , Somayazulu M. , Shen G. Y. , Mao H.-k. , Yang R. , Liu J. , Hu T. D. , Jiang J. Z.
Published: August 2007

In situ
high-pressure x-ray diffraction, low-temperature resistivity, and magnetization experiments were performed on a La
32
Ce
32
Al
16
Ni
5
Cu
15
bulk metallic glass (BMG). A sudden change in compressibility at ≈14 GPa and a rapid increase of resistivity at ≈12 K were detected, whereas magnetic phase transformation and magnetic field dependence of the low-temperature resistivity do not occur at temperatures down to 4.2 K. An interaction between conduction electrons and the two-level systems is suggested to explain the temperature and field dependences of resistivity of the BMG alloy. Although the cause of the unusual change in compressibility at ≈14 GPa is not clear, we believe that it could be linked with the unique electron structure of cerium in the amorphous matrix. An electronic phase transition in BMG alloys, most likely a second-order amorphous-to-amorphous phase transition, is suggested.
Stabilized immune modulatory RNA compounds as agonists of Toll-like receptors 7 and 8
Authors: Lan Tao , Kandimalla Ekambar R. , Yu Dong , Bhagat Lakshmi , Li Yukui , Wang Daqing , Zhu FuGang , Tang Jimmy X. , Putta Mallikarjuna R. , Cong YanPing , Trombino Anthony F. , Sullivan Tim , Agrawal Sudhir
Published: August 2007

Viral and synthetic single-stranded RNAs are the ligands for Toll-like receptor (TLR)7 and TLR8. However, single-stranded RNA is rapidly degraded by ubiquitous RNases, and the studies reported to date have used RNA with lipid carriers. To overcome nuclease susceptibility of RNA, we have synthesized several RNAs incorporating a range of chemical modifications. The present study describes one pool of RNA compounds, referred to as stabilized immune modulatory RNA (SIMRA) compounds, in which two RNA segments are attached through their 3′ ends. SIMRA compounds showed greater stability in human serum compared with linear RNA and activated human TLR8, but not TLR7, in HEK293 cells without using lipid carriers. Interestingly, another set of SIMRA compounds containing 7-deazaguanosine substituted for natural guanosine activated human TLR7 and TLR8. Additionally, TLR7- and TLR8-activating compounds, but not the compounds that activated only TLR8, stimulated mouse immune cellsin vitroandin vivoand produced dose-dependent T helper 1-type cytokines. Both types of compounds activated human peripheral blood mononuclear cells, but only TLR7- and TLR8-activating compounds activated plasmacytoid dendritic cells and produced high levels of IFN-α. In monkeys, s.c. administration of both types of SIMRA compounds induced transient changes in peripheral blood monocytes and neutrophils, and activated T lymphocytes, monocytes, and NK cells. Both types of compounds induced IFN-γ-inducible protein 10, but only the 7-deazaguanosine-containing compound that activated both TLR7 and TLR8 induced IFN-α in monkeys. This is a comprehensive study of RNA-based compounds containing structures and synthetic stimulatory motifs in mouse, monkey, and human systems without using lipid carriers.
One at a time, live tracking of NGF axonal transport using quantum dots
Authors: Cui Bianxiao , Wu Chengbiao , Chen Liang , Ramirez Alfredo , Bearer Elaine L. , Li Wei-Ping , Mobley William C. , Chu Steven
Published: August 2007

Retrograde axonal transport of nerve growth factor (NGF) signals is critical for the survival, differentiation, and maintenance of peripheral sympathetic and sensory neurons and basal forebrain cholinergic neurons. However, the mechanisms by which the NGF signal is propagated from the axon terminal to the cell body are yet to be fully elucidated. To gain insight into the mechanisms, we used quantum dot-labeled NGF (QD-NGF) to track the movement of NGF in real time in compartmentalized culture of rat dorsal root ganglion (DRG) neurons. Our studies showed that active transport of NGF within the axons was characterized by rapid, unidirectional movements interrupted by frequent pauses. Almost all movements were retrograde, but short-distance anterograde movements were occasionally observed. Surprisingly, quantitative analysis at the single molecule level demonstrated that the majority of NGF-containing endosomes contained only a single NGF dimer. Electron microscopic analysis of axonal vesicles carrying QD-NGF confirmed this finding. The majority of QD-NGF was found to localize in vesicles 50–150 nm in diameter with a single lumen and no visible intralumenal membranous components. Our findings point to the possibility that a single NGF dimer is sufficient to sustain signaling during retrograde axonal transport to the cell body.
Constructing subdivision rules from rational maps
Authors: Cannon J. , Floyd W. , Parry W.
Published: August 2007

This paper deepens the connections between critically finite rational maps and finite subdivision rules. The main theorem is that if

f
f

is a critically finite rational map with no periodic critical points, then for any sufficiently large integer

n
n

the iterate

f

∘
n

f^{\circ n}

is the subdivision map of a finite subdivision rule. This enables one to give essentially combinatorial models for the dynamics of such iterates.
Mining complex genotypic features for predicting HIV-1 drug resistance
Authors: Saigo Hiroto , Uno Takeaki , Tsuda Koji
Published: August 2007

Motivation: Human immunodeficiency virus type 1 (HIV-1) evolves in human body, and its exposure to a drug often causes mutations that enhance the resistance against the drug. To design an effective pharmacotherapy for an individual patient, it is important to accurately predict the drug resistance based on genotype data. Notably, the resistance is not just the simple sum of the effects of all mutations. Structural biological studies suggest that the association of mutations is crucial: even if mutations A or B alone do not affect the resistance, a significant change might happen when the two mutations occur together. Linear regression methods cannot take the associations into account, while decision tree methods can reveal only limited associations. Kernel methods and neural networks implicitly use all possible associations for prediction, but cannot select salient associations explicitly.

Results: Our method, itemset boosting, performs linear regression in the complete space of power sets of mutations. It implements a forward feature selection procedure where, in each iteration, one mutation combination is found by an efficient branch-and-bound search. This method uses all possible combinations, and salient associations are explicitly shown. In experiments, our method worked particularly well for predicting the resistance of nucleotide reverse transcriptase inhibitors (NRTIs). Furthermore, it successfully recovered many mutation associations known in biological literature.

Availability:  http://www.kyb.mpg.de/bs/people/hiroto/iboost/

Contact:  koji.tsuda@tuebingen.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian and Likelihood Inference for 2 × 2 Ecological Tables: An Incomplete-Data Approach
Authors: Imai Kosuke , Lu Ying , Strauss Aaron
Published: August 2007

Ecological inference is a statistical problem where aggregate-level data are used to make inferences about individual-level behavior. In this article, we conduct a theoretical and empirical study of Bayesian and likelihood inference for 2 × 2 ecological tables by applying the general statistical framework of incomplete data. We first show that the ecological inference problem can be decomposed into three factors:distributional effects, which address the possible misspecification of parametric modeling assumptions about the unknown distribution of missing data;contextual effects, which represent the possible correlation between missing data and observed variables; andaggregation effects, which are directly related to the loss of information caused by data aggregation. We then examine how these three factors affect inference and offer new statistical methods to address each of them. To deal with distributional effects, we propose a nonparametric Bayesian model based on a Dirichlet process prior, which relaxes common parametric assumptions. We also identify the statistical adjustments necessary to account for contextual effects. Finally, although little can be done to cope with aggregation effects, we offer a method to quantify the magnitude of such effects in order to formally assess its severity. We use simulated and real data sets to empirically investigate the consequences of these three factors and to evaluate the performance of our proposed methods. C code, along with an easy-to-use R interface, is publicly available for implementing our proposed methods (Imai, Lu, and Strauss, forthcoming).
Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling
Authors: Jang In-Cheol , Yang Seong Wook , Yang Jun-Yi , Chua Nam-Hai
Published: August 2007

Several positive regulators of phytochrome A signaling—e.g., LAF1, HFR1, and HY5—operate downstream from the photoreceptor, but their relative sites of action in the transduction pathway are unknown. Here, we show that HFR1RNAi/laf1 or hfr1-201/LAF1RNAi generated by RNA interference (RNAi) has an additive phenotype under FR light compared with the single mutants, hfr1-201 or laf1. This result indicates that LAF1 and HFR1 function in largely independent pathways. LAF1, an R2R3-MYB factor, interacts with HFR1, a basic helix–loop–helix (bHLH) factor, and this interaction is abolished by the R97A mutation in the LAF1 R2R3 domain. Polyubiquitinations of LAF1 and HFR1 by the COP1 E3 ligase in vitro are inhibited by LAF1/HFR1 association. Consistent with this result, endogenous HFR1 is less stable in laf1 compared with wild type, and similarly, LAF1-3HA expressed from a transgene is also less stable in hfr1-201 than wild type. In transgenic plants, HFR1 levels are significantly elevated upon induced expression of LAF1 but not LAF1(R97A). Moreover, induced expression of LAF1 but not LAF1(R97A) delays post-translational HFR1 degradation in FR light. Constitutive coexpression of HFR1 and LAF1 but not HFR1 and LAF1 (R97A) confers FR hypersensitivity in double transgenic plants. Our results show that in addition to their independent functions in phyA signaling, LAF1 and HFR1 also cooperate post-translationally to stabilize each other through inhibition of ubiquitination by COP1, thereby enhancing phyA photoresponses.
Supported Nafion Membrane for Direct Methanol Fuel Cell
Authors: Jung Guo-Bin , Su Ay , Tu Cheng-Hsin , Weng Fang-Bor , Chan Shih-Hung , Lee Ruey-Yi , Wu Szu-Han
Published: August 2007

The performances of direct methanol fuel cells are largely dependent on the methanol crossover, while the amount of methanol crossover is reported to strongly rely on membrane materials and thickness. In this research, two new membranes (Nafion 211 and Nx-424), along with well-known Nafion 117 and 112 were studied as electrolytes in the direct methanol fuel cells (DMFC). The Nafion 211 is the thinnest and latest membrane of Nafion series products and Nx-424 is a Nafion membrane with polytetrafluoroethylene (PTFE) fibers as mechanical reinforcement. Nx-424 is used primarily for chloro-alkali production and the electrolytic processes. Although open circuit voltage provides a quick way to evaluate the effect of methanol crossover, the amount of methanol crossover through the membranes was studied in detail via the electrochemical oxidation technique. Both methods show the same trend of methanol crossover of different membranes in this study. Nafion 211 was found to present the highest degree of methanol crossover, however, its’ best performance implied the fact that the influence of the cell resistance (membrane thickness) is dominated in the traditional Nafion system. Although Nafion membrane with thicker thickness and PTFE fiber within Nx-424 provided higher resistance for methanol to cross through, the negative effects of its’ hydrophobic properties also prevent the transport of H2O accompanied by the proton. Therefore, the cell performance of Nx-424 is lower both due to poor proton conductivity and thickest membrane. In other words, the cell performances of traditional Nafion series membranes (Nafion 211, 112, 117) were fully controlled by the thickness while Nx-424 was controlled both by its’ blend properties (hydrophilic-Nafion and hydrophobic-PTFE ) and thickness.
Thermal Dynamic Modeling and Nonlinear Control of a Proton Exchange Membrane Fuel Cell Stack
Authors: Kolodziej Jason R.
Published: August 2007

The purpose of this paper is to present a nonlinear control method for accurately maintaining coolant temperature within a proton exchange membrane (PEM) fuel cell stack by controlling coolant flow rate. Due to the current sensitive nature of the membrane and a strict relative humidity requirement it is critical to precisely control the internal temperature of the fuel cell. First, an optimization-based parameter identification is applied to determine unknown coefficients to the nonlinear thermal model of the fuel cell stack. The stack is modeled according to a lumped parameter continuous-flow stirred tank reactor (CSTR) form. The paper then presents a nonlinear disturbance rejection control technique to accomplish the necessary temperature control. Experimental data from a 17-cell fuel cell stack is used for both the modeling and the control portions of this work.