bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of symmetry mismatch on heteroepitaxial growth of perovskite thin films
Authors: Proffit D. L. , Jang H. W. , Lee S. , Nelson C. T. , Pan X. Q. , Rzchowski M. S. , Eom C. B.
Published: September 2008

Epitaxial thin films of (110) orthorhombic CaRuO3 grown on orthorhombic (110) NdGaO3 and cubic (001) (LaAlO3)0.3–(Sr2AlTaO6)0.7 (LSAT) substrates serve as a model system isolating the influence of oxygen octahedron distortion on epitaxial growth of thin films. CaRuO3 grows as a coherent single crystal on NdGaO3 with an atomically smooth surface, whereas CaRuO3 on LSAT is multidomain with a rough surface despite the equivalent film stoichoimetry and average lattice mismatch between CaRuO3 and the substrates. Anisotropic metallic resistivity of the single crystal CaRuO3 was observed at 10 K with different electrical behaviors as a function of temperature for [1¯10] and [001] in-plane directions.
Proper orthogonal decomposition methods for noise reduction in particle-based transport calculations
Authors: del-Castillo-Negrete D. , Spong D. A. , Hirshman S. P.
Published: September 2008

Proper orthogonal decomposition techniques to reduce noise in the reconstruction of the distribution function in particle-based transport calculations are explored. For two-dimensional steady-state problems, the method is based on low rank truncations of the singular value decomposition of a coarse-grained representation of the particle distribution function. For time-dependent two-dimensional problems or three-dimensional time-independent problems, the use of a generalized low-rank approximation of matrices technique is proposed. The methods are illustrated and tested with Monte Carlo particle simulation data of plasma collisional relaxation and guiding-center transport with collisions in a magnetically confined plasma in toroidal geometry. It is observed that the proposed noise reduction methods achieve high levels of smoothness in the particle distribution function by using significantly fewer particles in the computations.
A kinetic equation for unstable plasmas in a finite space-time domain
Authors: Baalrud S. D. , Callen J. D. , Hegna C. C.
Published: September 2008

A generalization of the Lenard–Balescu equation is derived that includes wave-particle scattering by collective instabilities in finite space-time domain plasmas. It is shown that wave-particle interactions can dominate conventional particle-particle Coulomb scattering when finite times are considered or convective instabilities are present in a medium of finite spatial extent before the instabilities grow to nonlinear or turbulent amplitudes. The modified Lenard–Balescu operator retains important physical properties including particle, momentum, and energy conservation laws and the Boltzmann H-theorem. To demonstrate its utility, the theory is applied to the simple example of convectively growing ion-acoustic instabilities in a finite spatial domain.
Microphase separation in multigraft copolymer melts studied by random-phase approximation and self-consistent field theory
Authors: Wang Liquan , Zhang Liangshun , Lin Jiaping
Published: September 2008

Microphase separation of AB multigraft copolymers with various numbers of graft arms per junction along the backbone was examined by the random-phase approximation and real-space implemented self-consistent field theory. The calculations carried out show that the number of graft arms per junction exerts a marked effect on the phase behavior of the multigraft copolymers. The spinodal shows an upward shift with increasing number of graft arms per junction. The order-order transitions shift toward the higher volume fraction of backbone and the ordered region becomes narrower when the number of graft arms per junction increases. The influence of the number of graft arms per junction on the domain size and the interfacial width has also been examined. It was found that the characteristic domain size decreases and the interfacial width broadens with increasing number of graft arms per junction. The theoretical results at a strong segregation were compared with the existing experimental observations and a good agreement is shown.
Equivalent circuit model for organic single-layer diodes
Authors: Haldi A. , Sharma A. , Potscavage W. J. , Kippelen B.
Published: September 2008

A simple equivalent circuit is proposed to model single-layer organic diodes. The circuit is based on thermionic emission to describe carrier injection from the electrode into the organic semiconductor and on space-charge limited currents across the semiconductor. By fitting the electrical characteristics measured as a function of temperature with the model, intrinsic material and interface parameters such as the mobility and the injection barrier energy are extracted. The resulting parameters agree well with independently measured values in the literature.
Reversed Cherenkov radiation in a waveguide filled with anisotropic double-negative metamaterials
Authors: Duan Zhaoyun , Wu Bae-Ian , Lu Jie , Au Kong Jin , Chen Min
Published: September 2008

The physical properties of Cherenkov radiation (CR) are theoretically investigated for a charged particle traveling along the axis of a cylindrical waveguide filled with anisotropic double-negative metamaterials (DNMs). The reversed CR and CR conditions are obtained using analytical method. The influence of the particle velocity, the waveguide radius, and the constitutive parameters of the anisotropic DNMs are discussed. A numerical example illustrates that the total radiated energy increases with increasing particle velocity, the radiated energy spectral density has different poles at the different frequencies for different anisotropic DNMs when the loss of the anisotropic DNM is smaller, and when the radius has the same order as the operating wavelength, the influence of the waveguide radius on the total radiated energy is smaller on the whole. Since most of the metamaterials realized so far are anisotropic, our theoretical work based on anisotropic DNMs will be helpful for future experimental realizations.
Electrons and holes in Si quantum well: A room-temperature transport and drag resistance study
Authors: Prunnila M. , Laakso S. J. , Kivioja J. M. , Ahopelto J.
Published: September 2008

We investigate carrier transport in a single 22-nm-thick double-gate Si quantum well device, which has independent contacts to electrons and holes. Conductance, Hall density and Hall mobility are mapped in a broad double-gate voltage window. When the gate voltage asymmetry is not too large only either electrons or holes occupy the Si well and the Hall mobility shows the fingerprints of volume inversion/accumulation. At strongly asymmetric double-gate voltage an electric field induced electron-hole (EH) bilayer is formed inside the well. The EH drag resistance Rhe is explored at balanced carrier densities: Rhe decreases monotonically from 860to37Ω when the electron and hole densities are varied between ∼0.4×1016 and 1.7×1016m−2.
Highly sensitive NO2 sensor array based on undecorated single-walled carbon nanotube monolayer junctions
Authors: Maeng Sunglyul , Moon Seungeon , Kim Sanghyeob , Lee Hong-Yeol , Park So-Jeong , Kwak Jun-Hyuk , Park Kang-Ho , Park Jonghyurk , Choi Youngjin , Udrea Florin , Milne William I. , Lee Byung Yang , Lee Minbaek , Hong Seunghun
Published: September 2008

Using the surface-programmed assembly technique, we have fabricated a uniform array of NO2 sensors based on undecorated single-walled carbon nanotube (SWNT) monolayer junctions. The sensitivity of the SWNT monolayer network-based sensors to NO2 gas was investigated at room temperature. We have found that the response of the gas sensors is inversely proportional to the initial conductance of the SWNT network. This behavior is different from conventional gas sensors based on uniform films, and it may be critical for the calibration of sensors in practical applications. An analytical model based on standard percolation theory is proposed to explain this behavior.
Nonlinear structure in a current-carrying collisional dusty plasma
Authors: Haas F. , Shukla P. K.
Published: September 2008

A perpendicular ion drift is proposed as a possible mechanism for the generation of magnetic field structures in a highly collisional dusty plasma. The basic dissipation mechanism is assumed to be the dust-neutral momentum exchange, so that plasmas with a small ionization fraction are natural candidates for experiments. The model reduces to a nonlinear partial differential equation for the vector potential. The conditions for linear instability are presented. Possible stationary states are periodic arrangements for the magnetic field, described by a Lienard equation. The fully depleted (ion-dust) case is also considered in detail. Applications of the present work to magnetic field structures in planetary rings, comets, and low-temperature dusty plasma experiments are discussed. A necessary condition for the validity of the model is a sufficiently slow time scale of the generated magnetic fields in dusty plasmas.
Electrostatic drift vortices in quantum magnetoplasmas
Authors: Haque Q.
Published: September 2008

A nonlinear equation similar to the Hasegawa–Mima equation for drift waves in dense quantum plasmas has been obtained. Therefore, electrostatic drift vortices can appear in nonuniform dense magnetoplasmas. These nonlinear structures can be of dipolar form as well as street-type vortices. It is noticed that these structures are formed on very short spatial scales. Further, it is discussed that quantum drift waves can couple with quantum ion acoustic waves, like classical plasmas, if the ion parallel dynamics is also considered.
Projecting deep-subwavelength patterns from diffraction-limited masks using metal-dielectric multilayers
Authors: Xiong Yi , Liu Zhaowei , Zhang Xiang
Published: September 2008

We utilize a metal-dielectric multilayer structure to generate deep-subwavelength one-dimensional and two-dimensional periodic patterns with diffraction-limited masks. The working wavelength and the pattern are set by the flexible design of the multilayer structure. This scheme is suitable to be applied to deep-subwavelength photolithography. As an example, we numerically demonstrate pattern periods down to 50nm under 405nm light illumination.
Static and dynamic properties of vortices in anisotropic magnetic disks
Authors: Machado Tiago S. , Rappoport Tatiana G. , Sampaio Luiz C.
Published: September 2008

We investigate the effect of the magnetic anisotropy (Kz) on the static and dynamic properties of magnetic vortices in small disks. Our micromagnetic calculations reveal that for a range of Kz there is an enlargement of the vortex core. We analyze the influence of Kz on the dynamics of the vortex core magnetization reversal under the excitation of a pulsed field. The presence of Kz, which lead to better resolved vortex structures, allows us to discuss in more details the role played by the in-plane and perpendicular components of the gyrotropic field during the vortex-antivortex nucleation and annihilation.
Memory characteristics of self-assembled tungsten nanodots dispersed in silicon nitride
Authors: Pei Yanli , Nishijima Masahiko , Fukushima Takafumi , Tanaka Tetsu , Koyanagi Mitsumasa
Published: September 2008

In this letter, tungsten nanodots (W-NDs) in silicon nitride formed by a self-assembled nanodot deposition method have been investigated as a floating gate of nonvolatile memory (NVM). Observations from transmission electron microscopy and x-ray diffraction pattern clearly confirm the formation of crystallized W-NDs with a diameter of ∼5 nm. The metal-oxide-semiconductor device with W-NDs in silicon nitride exhibits a larger memory window (∼4.1 V at ±12 V sweep), indicating charge trapping and distrapping between the W-ND and a silicon substrate. The program/erase behaviors and data retention characteristics were evaluated. After 10 years retention, a large memory window of ∼3.4 V with a low charge loss of ∼15% was extrapolated. These results demonstrate advantages of W-NDs in silicon nitride for the NVM application.
ZnO based oxide system with continuous bandgap modulation from 3.7 to 4.9 eV
Authors: Yang C. , Li X. M. , Gu Y. F. , Yu W. D. , Gao X. D. , Zhang Y. W.
Published: September 2008

ZnO based oxide system Zn1−x−yBexMgyO has been prepared by pulsed laser deposition. By incorporating different amounts of beryllium and magnesium into ZnO, the bandgap of ZnBeMgO has been modulated from 3.7 to 4.9 eV continuously. The crystal quality of ZnBeMgO film has been improved significantly comparing with that of either ZnMgO or BeZnO. These ZnBeMgO films are promising for fabricating high-efficiency optoelectronic devices such as solar-blind UV detectors.
High photocurrent gain in SnO2 nanowires
Authors: Lin Cheng-Hua , Chen Reui-San , Chen Tzung-Te , Chen Hsin-Yi , Chen Yang-Fang , Chen Kuei-Hsien , Chen Li-Chyong
Published: September 2008

Huge photocurrent gains with a value of 10 000 detected in air and 100 000 detected in vacuum have been obtained from SnO2 nanowires. Unlike previous reports that emphasized on carrier trapping by charge oxygen molecules in metal oxide nanostructures, we point out that spatial separation of photoexcited electrons and holes due to built-in electric field induced by surface charge defects does plays a significant role especially for nanostructured materials with a large surface-to-volume ratio. The study shown here provides a useful guideline to achieve photodetectors based on nanostructured materials with high sensitivity.
Comparison of n-type and p-type GaAs oxide growth and its effects on frequency dispersion characteristics
Authors: Hinkle C. L. , Sonnet A. M. , Milojevic M. , Aguirre-Tostado F. S. , Kim H. C. , Kim J. , Wallace R. M. , Vogel E. M.
Published: September 2008

The electrical characteristics of n- and p-type gallium arsenide (GaAs) capacitors show a striking difference in the “accumulation” capacitance frequency dispersion. This difference has been attributed by some to a variation in the oxide growth, possibly due to photoelectrochemical properties of the two substrates. We show that the oxide growth on n- and p-type GaAs substrates is identical when exposed to identical environmental and chemical conditions while still maintaining the diverse electrical characteristics. The difference in electron and hole trap time constants is suggested as the source of the disparity of the frequency dispersion for n-type versus p-type GaAs devices.
Facile fabrication of suspended as-grown carbon nanotube devices
Authors: Sangwan V. K. , Ballarotto V. W. , Fuhrer M. S. , Williams E. D.
Published: September 2008

A simple scalable scheme is reported for fabricating suspended carbon nanotube field effect transistors (CNT-FETs) without exposing pristine as-grown carbon nanotubes to subsequent chemical processing. Versatility and ease of the technique is demonstrated by controlling the density of suspended nanotubes and reproducing devices multiple times on the same electrode set. Suspending the carbon nanotubes results in ambipolar transport behavior with negligible hysteresis. The Hooge’s constant of the suspended CNT-FETs (2.6×10−3) is about 20 times lower than for control CNT-FETs on SiO2 (5.6×10−2).
Si nanophotonics based cantilever sensor
Authors: Lee Chengkuo , Thillaigovindan Jayaraj , Chen Chii-Chang , Chen Xian Tong , Chao Ya-Ting , Tao Shaohua , Xiang Wenfeng , Yu Aibin , Feng Hanhua , Lo G. Q.
Published: September 2008

We present design and simulation results of a novel nanomechanical sensor using silicon cantilever embedded with a two-dimensional photonic crystal microcavity resonator. Both of resonant wavelength and resonant wavelength shift could be measured as a function of various physical parameters such as applied force, strain, and displacement. Rather linear relationship is derived for strain and resonant wavelength shift. This new nanomechanical sensor shows promising features for biomolecules detection.
Reduction in coherent phonon lifetime in Bi2Te3/Sb2Te3 superlattices
Authors: Wang Yaguo , Xu Xianfan , Venkatasubramanian Rama
Published: September 2008

Femtosecond pulses are used to excite A1g optical phonons in Bi2Te3, Sb2Te3, and Bi2Te3/Sb2Te3 superlattice. Time-resolved reflectivity measurements show both the low-frequency and high-frequency components of A1g phonon modes. By comparing the phonon lifetime, it is found that the scattering rate (inverse of lifetime) in superlattice is significantly higher than those in Bi2Te3 and Sb2Te3. This represents the direct measurement of coherent phonon lifetime reduction in superlattice structures, consistent with the observed reduction in thermal conductivity in superlattices.
The atomic hydrogen flux to silicon growth flux ratio during microcrystalline silicon solar cell deposition
Authors: Dingemans G. , van den Donker M. N. , Hrunski D. , Gordijn A. , Kessels W. M. M. , van de Sanden M. C. M.
Published: September 2008

The H flux to Si growth flux ratio is experimentally determined under state-of-the-art silicon thin-film deposition conditions by employing the recently introduced etch product detection technique. Under the technologically relevant high-pressure depletion conditions and for different process parameter settings such as pressure, SiH4 concentration, rf power, and excitation frequency, it was demonstrated that the microcrystalline to amorphous silicon phase transition is uniquely and reactor independently determined by the flux ratio of H and Si growth species.
Alloying strongly influences the structure, dynamics, and glass forming ability of metallic supercooled liquids
Authors: Cheng Y. Q. , Ma E. , Sheng H. W.
Published: September 2008

The addition of a relatively small amount of alloying element(s) can induce major changes in the viscosity, fragility, and glass forming ability of supercooled liquids. A microscopic understanding of this behavior from the structural perspective has been elusive. Through comparisons between Cu–Zr–Al and Cu–Zr supercooled liquids, here we demonstrate the strong effects of Al alloying on the atomic-scale structure, in particular, the evolution of icosahedral local motifs, as well as the resulting dramatic slowing down of relaxation dynamics. The composition-structure-dynamics relationship uncovered for realistic bulk metallic glass forming liquids is important for understanding the glass transition and glass forming ability.
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria
Authors: Johansson Malin E. V. , Phillipson Mia , Petersson Joel , Velcich Anna , Holm Lena , Hansson Gunnar C.
Published: September 2008

We normally live in symbiosis with ∼10
13
bacteria present in the colon. Among the several mechanisms maintaining the bacteria/host balance, there is limited understanding of the structure, function, and properties of intestinal mucus. We now demonstrate that the mouse colonic mucus consists of two layers extending 150 μm above the epithelial cells. Proteomics revealed that both of these layers have similar protein composition, with the large gel-forming mucin Muc2 as the major structural component. The inner layer is densely packed, firmly attached to the epithelium, and devoid of bacteria. In contrast, the outer layer is movable, has an expanded volume due to proteolytic cleavages of the Muc2 mucin, and is colonized by bacteria. Muc2
−/−
mice have bacteria in direct contact with the epithelial cells and far down in the crypts, explaining the inflammation and cancer development observed in these animals. These findings show that the Muc2 mucin can build a mucus barrier that separates bacteria from the colon epithelia and suggest that defects in this mucus can cause colon inflammation.
Effective rescue of dystrophin improves cardiac function in dystrophin-deficient mice by a modified morpholino oligomer
Authors: Wu Bo , Moulton Hong M. , Iversen Patrick L. , Jiang Jiangang , Li Juan , Li Jianbin , Spurney Christopher F. , Sali Arpana , Guerron Alfredo D. , Nagaraju Kanneboyina , Doran Timothy , Lu Peijuan , Xiao Xiao , Lu Qi Long
Published: September 2008

Antisense oligonucleotide-mediated exon skipping is able to correct out-of-frame mutations in Duchenne muscular dystrophy and restore truncated yet functional dystrophins. However, its application is limited by low potency and inefficiency in systemic delivery, especially failure to restore dystrophin in heart. Here, we conjugate a phosphorodiamidate morpholino oligomer with a designed cell-penetrating peptide (PPMO) targeting a mutated dystrophin exon. Systemic delivery of the novel PPMO restores dystrophin to almost normal levels in the cardiac and skeletal muscles in dystrophic
mdx
mouse. This leads to increase in muscle strength and prevents cardiac pump failure induced by dobutamine stress
in vivo
. Muscle pathology and function continue to improve during the 12-week course of biweekly treatment, with significant reduction in levels of serum creatine kinase. The high degree of potency of the oligomer in targeting all muscles and the lack of detectable toxicity and immune response support the feasibility of testing the novel oligomer in treating Duchenne muscular dystrophy patients.
Sustained induction of epithelial to mesenchymal transition activates DNA methylation of genes silenced in basal-like breast cancers
Authors: Dumont Nancy , Wilson Matthew B. , Crawford Yongping G. , Reynolds Paul A. , Sigaroudinia Mahvash , Tlsty Thea D.
Published: September 2008

The active acquisition of epigenetic changes is a poorly understood but important process in development, differentiation, and disease. Our work has shown that repression of the p16/pRb pathway in human epithelial cells, a condition common to stem cells and many tumor cells, induces dynamic epigenetic remodeling resulting in the targeted methylation of a selected group of CpG islands. We hypothesized that cells in this epigenetically plastic state could be programmed by the microenvironment to acquire epigenetic changes associated with tumorigenesis. Here, we describe an
in vitro
model system where epigenetically plastic cells were placed in an environment that induced epithelial to mesenchymal transition (EMT) and led to a program of acquired
de novo
DNA methylation at targeted sites. In this model, we found that repression of E-cadherin transcription preceded the subsequent acquisition of methylated CpG sites. Furthermore, the induction of EMT was accompanied by
de novo
methylation of several other gene promoters, including those of the estrogen receptor and Twist. These data demonstrate that signals from the microenvironment can induce phenotypic and gene expression changes associated with targeted
de novo
epigenetic alterations important in tumor progression, and that these alterations occur through a deterministic, rather than stochastic, mechanism. Given the dynamic epigenetic reprogramming that occurs in these cells, DNA methylation profiles observed in human tumors may reflect the history of environmental exposures during the genesis of a tumor.
The convergence of carbohydrate active gene repertoires in human gut microbes
Authors: Lozupone Catherine A. , Hamady Micah , Cantarel Brandi L. , Coutinho Pedro M. , Henrissat Bernard , Gordon Jeffrey I. , Knight Rob
Published: September 2008

The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.
Backtracking on the folding landscape of the β-trefoil protein interleukin-1β?
Authors: Capraro Dominique T. , Roy Melinda , Onuchic José N. , Jennings Patricia A.
Published: September 2008

Interleukin-1β (IL-1β) is a cytokine within the β-trefoil family. Our data indicate that the folding/unfolding routes are geometrically frustrated. Follow-up theoretical studies predicted backtracking events that could contribute to the broad transition barrier and the experimentally observed long-lived intermediate. The backtracking route is attributed to the topological frustration introduced by the packing of the functional loop (the β-bulge, residues 47–53) to the nascent barrel. We used real-time refolding NMR experiments to test for the presence of backtracking events predicted from our theoretical studies. Structural variants of IL-1β, a β-bulge deletion, and a circular permutation that opens the protein in the middle of the experimentally observed kinetic intermediate, were also refolded and studied to determine the affects on the observed folding reactions. The functional loop deletion variant demonstrated less backtracking than in WT protein whereas the permutation still maintains backtracking in agreement with theoretical predictions. Taken together, these findings indicate that the backtracking results from geometric frustration introduced into the fold for functional purposes.
Pancreatic exocrine insufficiency in LXRβ
−/−
mice is associated with a reduction in aquaporin-1 expression
Authors: Gabbi Chiara , Kim Hyun-Jin , Hultenby Kjell , Bouton Didier , Toresson Gudrun , Warner Margaret , Gustafsson Jan-Åke
Published: September 2008

Liver X receptors (LXRs) α and β are nuclear oxysterol receptors with a key role in cholesterol, triglyceride, and glucose metabolism. In LXRβ
−/−
mice on a normal diet, there is a reduction in size of perigonadal fat pad and, on high-fat diet there is resistance to obesity. In the present study, we investigated the reason for the resistance of LXRβ
−/−
mice to weight gain. In LXRβ
−/−
mice we found pancreatic exocrine insufficiency with reduced serum levels of amylase and lipase, reduced proteolytic activity in feces, chronic inflammatory infiltration, and, in the ductal epithelium, an increased apoptosis without compensatory proliferation. Electron microscopy revealed ductal dilatation with intraductal laminar structures characteristic of cystic fibrosis. To investigate the relationship between LXRβ and pancreatic secretion, we studied the expression of LXRβ and the water channel, aquaporin-1 (AQP1), in the ductal epithelium of the pancreas. In WT mice, ductal epithelial cells expressed LXRβ in the nuclei and AQP1 on the plasma membrane. In LXRβ
−/−
mice neither LXRβ nor AQP1 was detectable. Moreover, in WT mice the LXR agonist (T2320) increased AQP1 gene expression. These data demonstrate that in LXRβ
−/−
mice dietary resistance to weight gain is caused by pancreatic insufficiency and that LXRβ regulates pancreatic exocrine secretion through the control of AQP1 expression. Pancreatic exocrine insufficiency is the main cause of malabsorption syndrome responsible for weight loss in adults and growth failure in children. Several genes are known to be involved in the pathogenesis and susceptibility to pancreatic insufficiency. LXRβ should be included in that list.
Microstructure and magnetic properties of bulk nanocomposite magnets prepared by crystallizing amorphous Nd3.6Pr5.4Fe80Co3B7Nb1under high pressure
Authors: Liang Baoyi , Xie Yanwu , Li Wei , Wu Wei , Zhang Xiangyi
Published: September 2008

The microstructures and magnetic properties of bulk α-Fe/R2Fe14B (R= Nd, Pr) nanocomposite magnets prepared by crystallizing amorphous Nd3.6Pr5.4Fe80Co3B7Nb1at 923 K under different pressures were studied. The average size ofR2Fe14B nanocrystals decreases monotonically from 42.9 to 12.1 nm with an increase in pressure from normal pressure to 6 GPa, while that for α-Fe nanocrystals first increases from 16.9 to 24.8 nm when a pressure of 1 GPa is applied and then decreases monotonically with a further increase in pressure, and a small size of about 10 nm was obtained at a pressure ofp= 6 GPa. Compared with the nanocomposite α-Fe/R2Fe14B ribbons produced by annealing the amorphous alloy under normal pressure, the bulk nanocomposite magnets prepared under high pressures have much more homogeneous microstructures and thus show enhanced magnetic properties. The effect of the pressure on the microstructures of the bulk nanocomposite magnets is discussed.
Optimal stepwise experimental design for pairwise functional interaction studies
Authors: Casey Fergal P. , Cagney Gerard , Krogan Nevan J. , Shields Denis C.
Published: September 2008

Motivation: Pairwise experimental perturbation is increasingly used to probe gene and protein function because these studies offer powerful insight into the activity and regulation of biological systems. Symmetric two-dimensional datasets, such as pairwise genetic interactions are amenable to an optimally designed measurement procedure because of the equivalence of cases and conditions where fewer experimental measurements may be required to extract the underlying structure.

Results: We show that optimal experimental design can provide improvements in efficiency when collecting data in an iterative manner. We develop a method built on a statistical clustering model for symmetric data and the Fisher information uncertainty estimates, and we also provide simple heuristic approaches that have comparable performance. Using yeast epistatic miniarrays as an example, we show that correct assignment of the major subnetworks could be achieved with <50% of the measurements in the complete dataset. Optimization is likely to become critical as pairwise functional studies extend to more complex mammalian systems where all by all experiments are currently intractable.

Contact:  fergal.p.casey@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Empirically modelling the potential effects of changes in temperature and prey availability on the growth of cod larvae in UK shelf seas
Authors: Pitois Sophie G. , Fox Clive J.
Published: September 2008

Pitois, S. G., and Fox, C. J. 2008. Empirically modelling the potential effects of changes in temperature and prey availability on the growth of cod larvae in UK shelf seas. – ICES Journal of Marine Science, 65: 1559–1572. It has been hypothesized that changes in zooplankton community structure over the past four decades led to reduced growth and survival of prerecruit Atlantic cod (Gadus morhua) and that this was a key factor underlying poor year classes, contributing to stock collapse, and inhibiting the recovery of stocks around the UK. To evaluate whether observed changes in plankton abundance, species composition and temperature could have led to periods of poorer growth of cod larvae, we explored the effect of prey availability and temperature on early larval growth using an empirical trophodynamic model. Prey availability was parameterized using species abundance data from the Continuous Plankton Recorder. Our model suggests that the observed changes in plankton community structure in the North Sea may have had less impact on cod larval growth, at least for the first 40 days following hatching, than previously suggested. At least in the short term, environmental and prey conditions should be able to sustain growth of cod larvae and environmental changes acting on this early life stage should not limit stock recovery.
Genomic predictors of interindividual differences in response to DNA damaging agents
Authors: Fry Rebecca C. , Svensson J. Peter , Valiathan Chandni , Wang Emma , Hogan Brad J. , Bhattacharya Sanchita , Bugni James M. , Whittaker Charles A. , Samson Leona D.
Published: September 2008

Human lymphoblastoid cells derived from different healthy individuals display considerable variation in their transcription profiles. Here we show that such variation in gene expression underlies interindividual susceptibility to DNA damaging agents. The results demonstrate the massive differences in sensitivity across a diverse cell line panel exposed to an alkylating agent. Computational models identified 48 genes with basal expression that predicts susceptibility with 94% accuracy. Modulating transcript levels for two member genes, MYH and C21ORF56, confirmed that their expression does indeed influence alkylation sensitivity. Many proteins encoded by these genes are interconnected in cellular networks related to human cancer and tumorigenesis.
TAp73 knockout shows genomic instability with infertility and tumor suppressor functions
Authors: Tomasini Richard , Tsuchihara Katsuya , Wilhelm Margareta , Fujitani Masashi , Rufini Alessandro , Cheung Carol C. , Khan Fatima , Itie-Youten Annick , Wakeham Andrew , Tsao Ming-sound , Iovanna Juan L. , Squire Jeremy , Jurisica Igor , Kaplan David , Melino Gerry , Jurisicova Andrea , Mak Tak W.
Published: September 2008

TheTrp53gene family memberTrp73encodes two major groups of protein isoforms, TAp73 and ΔNp73, with opposing pro- and anti-apoptotic functions; consequently, their relative ratio regulates cell fate. However, the precise roles of p73 isoforms in cellular events such as tumor initiation, embryonic development, and cell death remain unclear. To determine which aspects of p73 function are attributable to the TAp73 isoforms, we generated and characterized mice in which exons encoding the TAp73 isoforms were specifically deleted to create a TAp73-deficient (TAp73−/−) mouse. Here we show that mice specifically lacking in TAp73 isoforms develop a phenotype intermediate between the phenotypes ofTrp73−/−andTrp53−/−mice with respect to incidence of spontaneous and carcinogen-induced tumors, infertility, and aging, as well as hippocampal dysgenesis. In addition, cells from TAp73−/−mice exhibit genomic instability associated with enhanced aneuploidy, which may account for the increased incidence of spontaneous tumors observed in these mutants. Hence, TAp73 isoforms exert tumor-suppressive functions and indicate an emerging role forTrp73in the maintenance of genomic stability.
Impact of PsbTc on Forward and Back Electron Flow, Assembly, and Phosphorylation Patterns of Photosystem II in Tobacco
Authors: Umate Pavan , Fellerer Christine , Schwenkert Serena , Zoryan Mikael , Eichacker Lutz A. , Sadanandam Abbagani , Ohad Itzhak , Herrmann Reinhold G. , Meurer Jörg
Published: September 2008

Photosystem II (PSII) of oxygen-evolving cyanobacteria, algae, and land plants mediates electron transfer from the Mn4Ca cluster to the plastoquinone pool. It is a dimeric supramolecular complex comprising more than 30 subunits per monomer, of which 16 are bitopic or peripheral, low-molecular-weight components. Directed inactivation of the plastid gene encoding the low-molecular-weight peptide PsbTc in tobacco (Nicotiana tabacum) does not prevent photoautotrophic growth. Mutant plants appear normal green, and levels of PSII proteins are not affected. Yet, PSII-dependent electron transport, stability of PSII dimers, and assembly of PSII light-harvesting complexes (LHCII) are significantly impaired. PSII light sensitivity is moderately increased and recovery from photoinhibition is delayed, leading to faster D1 degradation in ΔpsbTc under high light. Thermoluminescence emission measurements revealed alterations of midpoint potentials of primary/secondary electron-accepting plastoquinone of PSII interaction. Only traces of CP43 and no D1/D2 proteins are phosphorylated, presumably due to structural changes of PSII in ΔpsbTc. In striking contrast to the wild type, LHCII in the mutant is phosphorylated in darkness, consistent with its association with PSI, indicating an increased pool of reduced plastoquinone in the dark. Finally, our data suggest that the secondary electron-accepting plastoquinone of PSII site, the properties of which are altered in ΔpsbTc, is required for oxidation of reduced plastoquinone in darkness in an oxygen-dependent manner. These data present novel aspects of plastoquinone redox regulation, chlororespiration, and redox control of LHCII phosphorylation.
Transcriptional Profiling of Mature Arabidopsis Trichomes Reveals That NOECK Encodes the MIXTA-Like Transcriptional Regulator MYB106
Authors: Jakoby Marc J. , Falkenhan Doris , Mader Michael T. , Brininstool Ginger , Wischnitzki Elisabeth , Platz Nicole , Hudson Andrew , Hülskamp Martin , Larkin John , Schnittger Arp
Published: September 2008

Leaf hairs (trichomes) of Arabidopsis (Arabidopsis thaliana) have been extensively used as a model to address general questions in cell and developmental biology. Here, we lay the foundation for a systems-level understanding of the biology of this model cell type by performing genome-wide gene expression analyses. We have identified 3,231 genes that are up-regulated in mature trichomes relative to leaves without trichomes, and we compared wild-type trichomes with two mutants, glabra3 and triptychon, that affect trichome morphology and physiology in contrasting ways. We found that cell wall-related transcripts were particularly overrepresented in trichomes, consistent with their highly elaborated structure. In addition, trichome expression maps revealed high activities of anthocyanin, flavonoid, and glucosinolate pathways, indicative of the roles of trichomes in the biosynthesis of secondary compounds and defense. Interspecies comparisons revealed that Arabidopsis trichomes share many expressed genes with cotton (Gossypium hirsutum) fibers, making them an attractive model to study industrially important fibers. In addition to identifying physiological processes involved in the development of a specific cell type, we also demonstrated the utility of transcript profiling for identifying and analyzing regulatory gene function. One of the genes that are differentially expressed in fibers is the MYB transcription factor GhMYB25. A combination of transcript profiling and map-based cloning revealed that the NOECK gene of Arabidopsis encodes AtMYB106, a MIXTA-like transcription factor and homolog of cotton GhMYB25. However, in contrast to Antirrhinum, in which MIXTA promotes epidermal cell outgrowth, AtMYB106 appears to function as a repressor of cell outgrowth in Arabidopsis.
Alterations in Cytosolic Glucose-Phosphate Metabolism Affect Structural Features and Biochemical Properties of Starch-Related Heteroglycans
Authors: Fettke Joerg , Nunes-Nesi Adriano , Alpers Jessica , Szkop Michal , Fernie Alisdair R. , Steup Martin
Published: September 2008

The cytosolic pools of glucose-1-phosphate (Glc-1-P) and glucose-6-phosphate are essential intermediates in several biosynthetic paths, including the formation of sucrose and cell wall constituents, and they are also linked to the cytosolic starch-related heteroglycans. In this work, structural features and biochemical properties of starch-related heteroglycans were analyzed as affected by the cytosolic glucose monophosphate metabolism using both source and sink organs from wild-type and various transgenic potato (Solanum tuberosum) plants. In leaves, increased levels of the cytosolic phosphoglucomutase (cPGM) did affect the cytosolic heteroglycans, as both the glucosyl content and the size distribution were diminished. By contrast, underexpression of cPGM resulted in an unchanged size distribution and an unaltered or even increased glucosyl content of the heteroglycans. Heteroglycans prepared from potato tubers were found to be similar to those from leaves but were not significantly affected by the level of cPGM activity. However, external glucose or Glc-1-P exerted entirely different effects on the cytosolic heteroglycans when added to tuber discs. Glucose was directed mainly toward starch and cell wall material, but incorporation into the constituents of the cytosolic heteroglycans was very low and roughly reflected the relative monomeric abundance. By contrast, Glc-1-P was selectively taken up by the tuber discs and resulted in a fast increase in the glucosyl content of the heteroglycans that quantitatively reflected the level of the cytosolic phosphorylase activity. Based on 14C labeling experiments, we propose that in the cytosol, glucose and Glc-1-P are metabolized by largely separated paths.
High Glycolate Oxidase Activity Is Required for Survival of Maize in Normal Air
Authors: Zelitch Israel , Schultes Neil P. , Peterson Richard B. , Brown Patrick , Brutnell Thomas P.
Published: September 2008

A mutant in the maize (Zea mays) Glycolate Oxidase1 (GO1) gene was characterized to investigate the role of photorespiration in C4 photosynthesis. An Activator-induced allele of GO1 conditioned a seedling lethal phenotype when homozygous and had 5% to 10% of wild-type GO activity. Growth of seedlings in high CO2 (1%–5%) was sufficient to rescue the mutant phenotype. Upon transfer to normal air, the go1 mutant became necrotic within 7 d and plants died within 15 d. Providing [1-14C]glycolate to leaf tissue of go1 mutants in darkness confirmed that the substrate is inefficiently converted to 14CO2, but both wild-type and GO-deficient mutant seedlings metabolized [1-14C]glycine similarly to produce [14C]serine and 14CO2 in a 1:1 ratio, suggesting that the photorespiratory pathway is otherwise normal in the mutant. The net CO2 assimilation rate in wild-type leaves was only slightly inhibited in 50% O2 in high light but decreased rapidly and linearly with time in leaves with low GO. When go1 mutants were shifted from high CO2 to air in light, they accumulated glycolate linearly for 6 h to levels 7-fold higher than wild type and 11-fold higher after 25 h. These studies show that C4 photosynthesis in maize is dependent on photorespiration throughout seedling development and support the view that the carbon oxidation pathway evolved to prevent accumulation of toxic glycolate.
A Protracted and Dynamic Maturation Schedule UnderliesArabidopsisLeaf Development
Authors: Efroni Idan , Blum Eyal , Goldshmidt Alexander , Eshed Yuval
Published: September 2008

Leaf development has been monitored chiefly by following anatomical markers. Analysis of transcriptome dynamics during leaf maturation revealed multiple expression patterns that rise or fall with age or that display age-specific peaks. These were used to formulate a digital differentiation index (DDI) based on a set of selected markers with informative expression during leaf ontogeny. The leaf-based DDI reliably predicted the developmental state of leaf samples from diverse sources and was independent of mitotic cell division transcripts or propensity of specific cell types. When calibrated by informative root markers, the same algorithm accurately diagnosed dissected root samples. We used the DDI to characterize plants with reduced activities of multiple CINCINNATA (CIN)-TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCF) growth regulators. These plants had giant curled leaves made up of small cells with abnormal shape, low DDI scores, and low expression of mitosis markers, depicting the primary role of CIN-TCPs as promoters of differentiation. Delayed activity of several CIN-TCPs resulted in abnormally large but flat leaves with regular cells. The application of DDI has therefore portrayed the CIN-TCPs as heterochronic regulators that permit the development of a flexible and robust leaf form through an ordered and protracted maturation schedule.
Genetic Analysis Reveals That C19-GA 2-Oxidation Is a Major Gibberellin Inactivation Pathway inArabidopsis
Authors: Rieu Ivo , Eriksson Sven , Powers Stephen J. , Gong Fan , Griffiths Jayne , Woolley Lindsey , Benlloch Reyes , Nilsson Ove , Thomas Stephen G. , Hedden Peter , Phillips Andrew L.
Published: September 2008

Bioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.
Civilisation and its disconnects
Authors: Hunt Robin
Published: September 2008

Purpose

This paper aims to explore some initial and necessarily broad ideas about the effects of the world wide web on our methods of understanding and trusting, online and off.

Design/methodology/approach

The paper considers the idea of trust via some of the revolutionary meanings inherent in the world wide web at its public conception in 1994, and some of its different meanings now. It does so in the context of the collaborative reader‐writer Web2.0 (of today), and also through a brief exploration of our relationship to the grand narratives (and some histories) of the post‐war West. It uses a variety of formal approaches taken from information science, literary criticism, philosophy, history, and journalism studies – together with some practical analysis based on 15 years as a web practitioner and content creator. It is a starting point.

Findings

This paper suggests that a pronounced effect of the world wide web is the further atomising of many once‐shared Western post‐war narratives, and the global democratising of doubt as a powerful though not necessarily helpful epistemological tool. The world wide web is the place that most actively demonstrates contemporary doubt.

Research limitations/implications

This is the starting place for a piece of larger cross‐faculty (and cross‐platform) research into the arena of trust and doubt. In particular, the relationship of concepts such as news, event, history and myth with the myriad content platforms of new media, the idea of the digital consumer, and the impact of geography on knowledge that is enshrined in the virtual. This paper attempts to frame a few of the initial issues inherent in the idea of “trust” in the digital age and argues that without some kind of shared aesthetics of narrative judgment brought about through a far broader public understanding of (rather than an interpretation of) oral, visual, literary and multi‐media narratives, stories and plots, we cannot be said to trust many types of knowledge – not just in philosophical terms but also in our daily actions and behaviours.

Originality/value

This paper initiates debate about whether the creation of a new academic “space” in which cross‐faculty collaborations into the nature of modern narrative (in terms of production and consumption; producers and consumers) might be able to help us to understand more of the social implications of the collaborative content produced for consumption on the world wide web.