bluuebunny/crossref_metadata_2025 huggingface dataset:
Spin-dependent synchrotron x-ray excitations studied by scanning tunneling microscopy
Authors: Rose V. , Chien T. Y. , Freeland J. W. , Rosenmann D. , Hiller J. , Metlushko V.
Published: February 2012

The ability to position a sharp probe in close proximity to a sample while the surface is illuminated by synchrotron x-rays opens a path to localized spectroscopy and imaging with chemical and magnetic contrast. We have employed a scanning tunneling microscope for the local study of synchrotron x-ray magnetic circular dichroism of micron-sized NiFe rings. Spectra have been obtained by an insulator-coated tip positioned about 200 nm over the sample surface. A negative sample bias is required in order to enhance the dichroism signal at the tip.
A magnetoelectric multiglass state in multiferroic YbFe2O4
Authors: Sun Y. , Liu Y. , Ye F. , Chi S. , Ren Y. , Zou T. , Wang F. , Yan L.
Published: February 2012

A multiglass state in which two distinct glassy phases coexist has been identified in multiferroic YbFe2O4. A collective magnetic freezing, as evidenced by AC susceptibility, magnetization, and coercivity measurements, develops at a freezing temperature TF ∼ 80 K. Meanwhile, the low-temperature dielectric and pyroelectric measurements suggest that an electric polar-glass state develops at the same freezing temperature. The simultaneous freezing of spin and polar clusters implies a strong magnetoelectric coupling and leads to a magnetoelectric multiglass state.
Effect of indium doping on physical properties of nanocrystallized SnS zinc blend thin films grown by chemical bath deposition
Authors: Reghima Meriem , Akkari Anis , Guasch Cathy , Kamoun-Turki Najoua
Published: February 2012

SnS:In thin films have been successfully prepared on Pyrex substrates using low cost chemical bath deposition technique with different indium concentrations (y=[In][Sn]=4%,6%,8%,and10%). The structure, the surface morphology, and the optical properties of the SnS:In films were studied by x-ray diffraction, scanning electron microscope, atomic force microscopy, and spectrophotometer measurements. In order to obtain a thickness of the order of 308 ± 10 nm for potential applications in solar cell devices, a multilayer deposition has been prepared. It is found that the physical properties of tin sulphide are affected by indium concentration. In fact, x-ray diffraction study showed that better crystallinity in zinc blend structure with preferential orientations (111)ZB and (200)ZB was obtained for y equal to 6%. According to the AFM analysis, we remark that low average surface roughness value of SnS(ZB) thin film is obtained with In concentrations equal to y = 6%. Energy dispersive spectroscopy showed the existence of In, Sn, and S in the films. Optical analyses by means of transmission T(λ) and reflection R(λ) measurements show 1.57 eV as an optical band gap value of SnS:In(6%), which is lower than the previously obtained value (1.76 eV) for undoped tin sulphide. In doped tin sulphide exhibits a high absorption coefficient 2.5 × 106 cm−1, indicating that SnS:In can be used as absorber thin layer in photovoltaic structure such as SnS:In/ZnS/SnO2:F and SnS:In/In2S3/SnO2:F, where ZnS and In2S3 are chemically deposited as described in a previous work. In this study, the hetero-junctions SnS/In2S3:Al and SnS/ZnS:In are also investigated.
Fully kinetic description of the linear excitation and nonlinear saturation of fast-ion-driven geodesic acoustic mode instability
Authors: Zarzoso D. , Garbet X. , Sarazin Y. , Dumont R. , Grandgirard V.
Published: February 2012

We show in this paper that geodesic acoustic modes (GAMs) can be efficiently excited by a population of fast ions even when Landau damping on thermal ions is accounted for. We report in particular fully kinetic calculations of the GAM dispersion relation and its complete solution. Written under a variational form, the quasi-neutrality condition, together with the kinetic Vlasov equation, leads to the density of exchanged energy between particles and the mode. In particular, a linear threshold for the GAMs excitation is derived. Two examples of fast ion distribution have been discussed analytically. It turns out that particles with high perpendicular energy compared to the parallel resonance energy are most responsible for the excitation of the mode. Subsequent numerical simulations of circular plasmas using gysela code have been carried out. In particular, the linear kinetic threshold has been reproduced during the excitation phase, and a nonlinear saturation has been observed. Analysis in the phase space of the evolution of the equilibrium distribution function is presented and the saturation level quantified.
Properties of single crystalline AZn2Sb2 (A = Ca,Eu,Yb)
Authors: May Andrew F. , McGuire Michael A. , Ma Jie , Delaire Olivier , Huq Ashfia , Custelcean Radu
Published: February 2012

Single crystals of CaZn2Sb2, EuZn2Sb2, and YbZn2Sb2 were grown from melts of nominal composition AZn5Sb5 (A = Ca,Eu,Yb) with the excess melt being removed at 1073 K. The electrical transport properties are consistent with those previously reported for polycrystalline samples. This confirms that the p-type carrier concentrations ranging from 2 × 1019 cm−3 to ∼1 × 1020 cm−3 are intrinsic to these materials. Also consistent with transport in polycrystalline materials, the carrier mobility is found to be lowest in CaZn2Sb2, suggesting the trends in mobility and thermoelectric efficiency within these compounds are inherent to the material systems and not due to inhomogeneity or impurities in polycrystalline samples. These results suggest CaZn2Sb2 has the strongest coupling between the doping/defects and the electronic framework. Magnetization measurements reveal an antiferromagnetic transition near 13 K in EuZn2Sb2, and the observed magnetic anisotropy indicates the spins align parallel and anti-parallel to c in the trigonal lattice. Powder neutron diffraction on polycrystalline samples of CaZn2Sb2 and YbZn2Sb2 reveals smooth lattice expansion to 1000 K, with c expanding faster than a. The Debye temperatures calculated from specific heat capacity data and the isotropic displacement parameters are found to correlate with the carrier mobility, with the CaZn2Sb2 displaying the largest Debye temperature and smallest mobility.
Imaging of magnetic flux distribution in vicinity of insulating particles in high-Tc superconductor by electron holography
Authors: Akase Zentaro , Kasai Hiroto , Mamishin Shuichi , Shindo Daisuke , Morita Mitsuru , Tonomura Akira
Published: February 2012

REBaCuO (RE: rare earth) bulk superconductors, whose microstructures can be controlled by quench and melt growth (QMG) processing, have a high critical current density Jc, which makes them well suited for use in practical applications. Through a combination of electron holography and a focused ion-beam technique, we succeeded in visualizing a fluxon pinned by an insulating particle in a QMG bulk Y-Ba-Cu-O superconductor. We also clarified the magnetic flux distribution in the vicinity of the insulating particles at different temperatures in a uniform external magnetic field.
Selective probe of the morphology and local vibrations at carbon nanoasperities
Authors: Fujimori Toshihiko , Urita Koki , Tománek David , Ohba Tomonori , Moriguchi Isamu , Endo Morinobu , Kaneko Katsumi
Published: February 2012

We introduce a way to selectively probe local vibration modes at nanostructured asperities such as tips of carbon nanohorns. Our observations benefit from signal amplification in surface-enhanced Raman scattering (SERS) at sites near a silver surface. We observe nanohorn tip vibration modes in the range 200–500 cm−1, which are obscured in regular Raman spectra. Ab initio density functional calculations assign modes in this frequency range to local vibrations at the nanohorn cap resembling the radial breathing mode of fullerenes. Careful interpretation of our SERS spectra indicates presence of caps with 5 or 6 pentagons, which are chemically the most active sites. Changes in the peak intensities and frequencies with time indicate that exposure to laser irradiation may cause structural rearrangements at the cap.
Mesoscopic analysis of Gibbs’ criterion for sessile nanodroplets on trapezoidal substrates
Authors: Dutka F. , Napiórkowski M. , Dietrich S.
Published: February 2012

By taking into account precursor films accompanying nanodroplets on trapezoidal substrates we show that on a mesoscopic level of description one does not observe the phenomenon of liquid-gas-substrate contact line pinning at substrate edges. This phenomenon is present in a macroscopic description and leads to non-unique contact angles which can take values within a range determined by the so-called Gibbs’ criterion. Upon increasing the volume of the nanodroplet the apparent contact angle evaluated within the mesoscopic approach changes continuously between two limiting values fulfilling Gibbs’ criterion, while the contact line moves smoothly across the edge of the trapezoidal substrate. The spatial extent of the range of positions of the contact line, corresponding to the variations of the contact angle between the values given by Gibbs’ criterion, is of the order of ten fluid particle diameters.
High-throughput study of alpha-synuclein expression in yeast using microfluidics for control of local cellular microenvironment
Authors: Rosa Patrícia , Tenreiro Sandra , Chu Virginia , Outeiro Tiago F. , Conde João Pedro
Published: February 2012

Microfluidics is an emerging technology which allows the miniaturization, integration, and automation of fluid handling processes. Microfluidic systems offer low sample consumption, significantly reduced processing time, and the prospect of massive parallelization. A microfluidic platform was developed for the control of the soluble cellular microenvironment of Saccharomyces cerevisiae cells, which enabled high-throughput monitoring of the controlled expression of alpha-synuclein (aSyn), a protein involved in Parkinson’s disease. Y-shaped structures were fabricated using particle desorption mass spectrometry-based soft-lithography techniques to generate biomolecular gradients along a microchannel. Cell traps integrated along the microchannel allowed the positioning and monitoring of cells in precise locations, where different, well-controlled chemical environments were established. S. cerevisiae cells genetically engineered to encode the fusion protein aSyn-GFP (green fluorescent protein) under the control of GAL1, a galactose inducible promoter, were loaded in the microfluidic structure. A galactose concentration gradient was established in the channel and a time-dependent aSyn-GFP expression was obtained as a function of the positioning of cells along the galactose gradient. Our results demonstrate the applicability of this microfluidic platform to the spatiotemporal control of cellular microenvironment and open a range of possibilities for the study of cellular processes based on single-cell analysis.
The long range voice coil atomic force microscope
Authors: Barnard H. , Randall C. , Bridges D. , Hansma P. K.
Published: February 2012

Most current atomic force microscopes (AFMs) use piezoelectric ceramics for scan actuation. Piezoelectric ceramics provide precision motion with fast response to applied voltage potential. A drawback to piezoelectric ceramics is their inherently limited ranges. For many samples this is a nonissue, as imaging the nanoscale details is the goal. However, a key advantage of AFM over other microscopy techniques is its ability to image biological samples in aqueous buffer. Many biological specimens have topography for which the range of piezoactuated stages is limiting, a notable example of which is bone. In this article, we present the use of voice coils in scan actuation for an actuation range in the Z-axis an order of magnitude larger than any AFM commercially available today. The increased scan size will allow for imaging an important new variety of samples, including bone fractures.
High-strength titanium alloy nanopillars with stacking faults and enhanced plastic flow
Authors: Yu Qian , Li Suzhi , Minor Andrew M. , Sun Jun , Ma Evan
Published: February 2012

Through ex situ and in situ compression and tension tests of micrometer- and submicrometer-sized single crystal hexagonal close packed (HCP) Ti alloy pillars oriented for prismatic slip, we have observed that “smaller is stronger” and the larger samples exhibit obvious strain bursts. However, for extremely small samples, the plastic flow becomes much more stable both in compression and tension, mainly due to the emergence of a high density of basal stacking faults (SFs) driven by extremely high stress, which rarely appear in larger samples and bulk counterpart. This work demonstrates a recipe towards ultra-high strength (GPa level) nanoscale samples with continous plastic flow.
Energy band engineering and controlled p-type conductivity of CuAlO2 thin films by nonisovalent Cu-O alloying
Authors: Yao Z. Q. , He B. , Zhang L. , Zhuang C. Q. , Ng T. W. , Liu S. L. , Vogel M. , Kumar A. , Zhang W. J. , Lee C. S. , Lee S. T. , Jiang X.
Published: February 2012

The electronic band structure and p-type conductivity of CuAlO2 films were modified via synergistic effects of energy band offset and partial substitution of less-dispersive Cu+ 3d10 with Cu2+ 3d9 orbitals in the valence band maximum by alloying nonisovalent Cu-O with CuAlO2 host. The Cu-O/CuAlO2 alloying films show excellent electronic properties with tunable wide direct bandgaps (∼3.46–3.87 eV); Hall measurements verify the highest hole mobilities (∼11.3–39.5 cm2/Vs) achieved thus far for CuAlO2 thin films and crystals. Top-gate thin film transistors constructed on p-CuAlO2 films were presented, and the devices showed pronounced performance with Ion/Ioff of ∼8.0 × 102 and field effect mobility of 0.97 cm2/Vs.
High mobility thin film transistors with indium oxide/gallium oxide bi-layer structures
Authors: Wang S.-L. , Yu J.-W. , Yeh P.-C. , Kuo H.-W. , Peng L.-H. , Fedyanin A. A. , Mishina E. D. , Sigov A. S.
Published: February 2012

We investigate the transport properties of thin-film transistors using indium oxide (In2O3)/gallium oxide (Ga2O3) bi-layer stacks as the channel material. At low gate bias, we observe the transistor field-effect mobility increases with the film resistivity to μFE = 51.3 cm2/Vs and ON/OFF current ratio to 108 due to combinatorial layer thickness modulation. With the Ga2O3 layer thickness ratio increase to R = 14.35%, these observations are accompanied with one-order-of-magnitude reduction in the transistor subthreshold swing to 0.38 V/decade and suggest a trap-limited conduction mechanism upon which the reduced scattering centers due to annihilation of subgap states improve the device electric characteristics without post-growth annealing.
Understanding on the current-induced crystallization process and faster set write operation thereof in non-volatile phase change memory
Authors: Kang Dae-Hwan , Young Kim Nan , Jeong Hongsik , Cheong Byung-ki
Published: February 2012

We experimentally demonstrate that the crystallization process of Ge-Sb-Te crystallites during the set operation in non-volatile phase change memory commences after threshold switching event. It is also shown that the nucleation and growth rates have opposite behaviors with the increase of set operation power: the incubation time in nucleation stage can be minimized at higher power, whereas the percolation time in growth stage is smaller at lower power. Based on these results, we introduce a two-step set pulse of high-power nucleation and low-power growth making the set write operation much faster than conventional simple rectangular or slow-quenched form.
Atomic layer deposited (TiO2)x(Al2O3)1−x/In0.53Ga0.47As gate stacks for III-V based metal-oxide-semiconductor field-effect transistor applications
Authors: Mahata C. , Mallik S. , Das T. , Maiti C. K. , Dalapati G. K. , Tan C. C. , Chia C. K. , Gao H. , Kumar M. K. , Chiam S. Y. , Tan H. R. , Seng H. L. , Chi D. Z. , Miranda E.
Published: February 2012

Atomic layer deposited (ALD) (TiO2)x(Al2O3)1-x(TiAlO) alloy gate dielectrics on In0.47Ga0.53As/InP substrates are shown to produce high quality interfaces between TiAlO and InGaAs. The surface morphology and interfacial reaction of nanolaminate ALD TiAlO on In0.53Ga0.47As are studied using atomic force microscopy and x-ray photoelectron spectroscopy. Measured valence and conduction band offsets are found to be 2.85 ± 0.05 and 1.25 ± 0.05 eV, respectively. Capacitance-voltage characteristics show low frequency dispersion (∼11%), interface state density (∼4.2 × 1011 cm−2eV−1), and hysteresis voltage (∼90 mV). Ga-O and As-O bonding are found to get suppressed in the gate stacks after post deposition annealing. Our experimental results suggest that higher oxidation states of In and Ga at the In0.53Ga0.47As surface and As diffusion in the dielectric are effectively controlled by Ti incorporation in Al2O3.
Surface plasmon resonance-enabled antibacterial digital versatile discs
Authors: Dou Xuan , Chung Pei-Yu , Jiang Peng , Dai Jianli
Published: February 2012

We report the achievement of effective sterilization of exemplary bacteria including Escherichia coli and Geobacillus stearothermophilus spores on a digital versatile disc (DVD). The spiral arrangement of aluminum-covered pits generates strong surface plasmon resonance (SPR) absorption of near-infrared light, leading to high surface temperature that could even damage the DVD plastics. Localized protein denaturation and high sterilization efficiency have been demonstrated by using a fluorescence microscope and cell cultures. Numerical simulations have also been conducted to model the SPR properties and the surface temperature distribution of DVDs under laser illumination. The theoretical predictions agree reasonably well with the experimental results.
Electron gas dimensionality engineering in AlGaN/GaN high electron mobility transistors using polarization
Authors: Sung Park Pil , Nath Digbijoy N. , Krishnamoorthy Sriram , Rajan Siddharth
Published: February 2012

We propose and demonstrate a two dimensional/three dimensional hybrid channel AlGaN/GaN high electron mobility transistor (HEMT) structure with a flat transconductance profile using polarization-induced channel engineering. A quasi three dimensional electron gas profile with 5–6 nm of vertical channel depth was formed by grading the channel region linearly from GaN to Al0.15Ga0.85 N over 50 Å. We demonstrate a flat gm profile in an AlGaN/GaN HEMT with high current density of 1 A/mm and peak gm of 168 mS/mm over 85% of the input bias range under dc conditions. This approach simultaneously enables vertical device scaling and transconductance engineering in a HEMT structure.
Coexistence of bi-stable memory and mono-stable threshold resistance switching phenomena in amorphous NbOx films
Authors: Bae Jieun , Hwang Inrok , Jeong Yuhyun , Kang Sung-Oong , Hong Sahwan , Son Jongwan , Choi Jinsik , Kim Jinsoo , Park June , Seong Maeng-Je , Jia Quanxi , Ho Park Bae
Published: February 2012

Both bi-stable memory and mono-stable threshold switching are observed in amorphous NbOx films. In addition, the transition between memory and threshold switching can be induced by changing external electrical stress. Raman spectroscopy and transmission electron microscope data show that the NbOx film is self-assembled into a layered structure consisting of a top metal-rich region and a bottom oxygen-rich region. The volume ratio of the two regions depends on the film thickness. Our experimental results suggest that different characteristics of conducting filaments in the two regions result in thickness dependence of switching types and the transition between memory and threshold switching.
Communication: Angle-resolved thermal dissociative sticking of CH4 on Pt(111): Further indication that rotation is a spectator to the gas-surface reaction dynamics
Authors: Navin J. K. , Donald S. B. , Tinney D. G. , Cushing G. W. , Harrison I.
Published: February 2012

Effusive molecular beam measurements of angle-resolved thermal dissociative sticking coefficients for CH4 impinging on a Pt(111) surface, at a temperature of 700 K, are reported and compared to theoretical predictions. The reactivity falls off steeply as the molecular angle of incidence increases away from the surface normal. Successful modeling of the thermal dissociative sticking behavior, consistent with existent CH4 supersonic molecular beam experiments involving rotationally cold molecules, required that rotation be treated as a spectator degree of freedom.
Microstructure, AC impedance and DC electrical conductivity characteristics of NiFe2-xGdxO4 (x = 0, 0.05 and 0.075)
Authors: Kamala Bharathi K. , Markandeyulu G. , Ramana C. V.
Published: February 2012

The structure and electrical characteristics of Gd doped Ni ferrite materials, namely NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4, are reported to demonstrate their improved electrical properties compared to that of pure NiFe2O4. NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds crystallize in the cubic inverse spinel phase with a very small amount of GdFeO3 additional phase while pure NiFe2O4 crystallize in inverse spinel phase without any impurity phase. The back scattered electron imaging analysis indicate the primary and secondary formation in NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds. Atomic force microscopy measurements indicate that the bulk grains are ∼2-5 micron size while the grain boundaries are thin compared to bulk grains. Impedance spectroscopic analysis at different temperature indicates the different relaxation mechanisms and their variation with temperature, bulk grain and grain-boundary contributions to the electrical conductivity (Rg) and capacitance (Cg) of these materials. The conductivity in pure NiFeO4 is found to be predominantly due to intrinsic bulk contribution (Rg=213 kΩ and Cg=4.5 x 10-8 F). In the case of NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds, grain and grain-boundary contributions to the conductivity are clearly observed. The DC conductivity values (at 300 K) of NiFe2O4, NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds are found to be 1.06 x 10-7 Ω-1 cm-1, 5.73 x 10-8 Ω-1 cm-1 and 1.28 x 10-8 Ω-1 cm-1 respectively.
Triboelectric charging of insulating polymers–some new perspectives
Authors: Williams Meurig W.
Published: February 2012

Tribolectric charging results from contact between surfaces, but precisely what is meant by each is not defined or understood, as they relate to charging. The recent microscopic evidence that contact charging can result from material transfer provides incentive to examine how contact charging is affected by these two factors. It is suggested that vigorous rubbing or pressing of two polymers results in transfer of deeper layers than would result from light contacts. Different layers can have substantially different compositions because polymers are typically not homogeneous as a function of depth, so contact and surface are related in this way. This could account for charge transfer between identical polymers, especially in asymmetric contacts in which the frictional force on one polymer differs from that on the other, so that material from different depths is transferred. This review outlines the roles of physics, chemistry and surface analysis in sufficient detail to focus on these subjects. It also makes suggestions how these concepts could be applied to some of the current leading edge research in this area.
Relationship between oil tocopherol concentration and oil weight per grain in several crop species
Authors: Izquierdo N. G. , Nolasco S. , Mateo C. , Santos D. , Aguirrezábal L. A. N.
Published: February 2012

The objectives of this work were (i) to analyse the effect of intercepted solar radiation (ISR) per plant during grain filling on oil tocopherol concentration in soybean, maize and rape and (ii) to investigate in these species if variations in oil tocopherol concentration are well accounted for by variations in oil weight per grain. Field experiments were conducted with genotypes of soybean, maize and rape. A genotype of sunflower was included as ‘control species’ as its behaviour was known from previous works. ISR was modified during grain filling by shading or thinning plants. Plants were harvested at physiological maturity and oil tocopherol concentration was determined by high performance liquid chromatography. Samples from other field or growth chamber experiments were also processed. In the four species, increasing radiation increased the oil and tocopherol weight per grain. Increasing ISR reduced oil tocopherol concentration in sunflower, soybean and rape but not in maize. The oil tocopherol concentration would be reduced by ISR in those species, with high oil contents in their grains, where the oil synthesis is more increased than tocopherol synthesis. The variations in oil tocopherol concentration were accounted for by variations in oil weight per grain only in those species with high and variable oil concentration.
Physiological and morphological factors influencing wear resistance and recovery in C3 and C4 turfgrass species
Authors: Lulli Filippo , Volterrani Marco , Grossi Nicola , Armeni Roberto , Stefanini Sara , Guglielminetti Lorenzo
Published: February 2012

High turfgrass wear resistance and recovery are the most sought after characteristics in turfgrass species when used for sports turf, but they are also very important in home gardens and public parks. Several wear resistance investigations have been conducted in field conditions in recent years, but these investigations involved the use of machinery and techniques that are not able to segregate the plant wounding and death effects from soil compaction effects that are generally associated with turfgrass wear. The same can be said of wear recovery investigations, with an extensive use of agronomical machinery for field trials. This study focussed on the wear resistance and recovery of mature swards of Cynodon dactylon (L.) Pers. var. dactylon × C. transvaalensis Burt-Davy cv. Tifway 419, Zoysia matrella (L.) Merr. cv. Zeon and Paspalum vaginatum Swartz. cv. Salam and a typical sports-type mix of Lolium perenne L. (cvv. Speedster 35% and Greenway 35%) + Poa pratensis L. (cvv. SR2100 15% and Greenknight 15%). The goal of this trial was to evaluate turfgrass wear resistance and recovery devoid of climatic and soil effects and thus, sward growing, wear simulation and recovery were conducted in controlled environment. Furthermore, wear simulation was conducted with FIFA-approved, numerical control machinery (Lisport). Wear resistance and recovery data was plotted against results from laboratory investigations on key tissue constituents. Zoysia matrella proved to be the most wear resistant, but the slowest in recovery, whereas the bermudagrass hybrid showed the exact opposite behaviour. Lignin and carbohydrate concentrations proved to be the two factors most closely correlated with wear resistance and recovery respectively. These two classes of compounds were present in an equilibrium that was species specific, with a frequent mutual exclusion between lignin and starch concentrations that deserves further investigation at the intra-specific level.
A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks
Authors: Gallos Lazaros K. , Makse Hernán A. , Sigman Mariano
Published: February 2012

The human brain is organized in functional modules. Such an organization presents a basic conundrum: Modules ought to be sufficiently independent to guarantee functional specialization and sufficiently connected to bind multiple processors for efficient information transfer. It is commonly accepted that small-world architecture of short paths and large local clustering may solve this problem. However, there is intrinsic tension between shortcuts generating small worlds and the persistence of modularity, a global property unrelated to local clustering. Here, we present a possible solution to this puzzle. We first show that a modified percolation theory can define a set of hierarchically organized modules made of strong links in functional brain networks. These modules are “large-world” self-similar structures and, therefore, are far from being small-world. However, incorporating weaker ties to the network converts it into a small world preserving an underlying backbone of well-defined modules. Remarkably, weak ties are precisely organized as predicted by theory maximizing information transfer with minimal wiring cost. This trade-off architecture is reminiscent of the “strength of weak ties” crucial concept of social networks. Such a design suggests a natural solution to the paradox of efficient information flow in the highly modular structure of the brain.
Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria
Authors: Kamileri Irene , Karakasilioti Ismene , Sideri Aria , Kosteas Theodoros , Tatarakis Antonis , Talianidis Iannis , Garinis George A.
Published: February 2012

Nucleotide excision repair (NER) defects are associated with cancer, developmental disorders and neurodegeneration. However, with the exception of cancer, the links between defects in NER and developmental abnormalities are not well understood. Here, we show that the ERCC1-XPF NER endonuclease assembles on active promoters in vivo and facilitates chromatin modifications for transcription during mammalian development. We find that

Ercc1
−/−

mice demonstrate striking physiological, metabolic and gene expression parallels with

Taf10
−/−

animals carrying a liver-specific transcription factor II D (TFIID) defect in transcription initiation. Promoter occupancy studies combined with expression profiling in the liver and in vitro differentiation cell assays reveal that ERCC1-XPF interacts with TFIID and assembles with POL II and the basal transcription machinery on promoters in vivo. Whereas ERCC1-XPF is required for the initial activation of genes associated with growth, it is dispensable for ongoing transcription. Recruitment of ERCC1-XPF on promoters is accompanied by promoter-proximal DNA demethylation and histone marks associated with active hepatic transcription. Collectively, the data unveil a role of ERCC1/XPF endonuclease in transcription initiation establishing its causal contribution to NER developmental disorders.
Skeletal muscle transcriptional coactivator PGC-1α mediates mitochondrial, but not metabolic, changes during calorie restriction
Authors: Finley Lydia W. S. , Lee Jaewon , Souza Amanda , Desquiret-Dumas Valérie , Bullock Kevin , Rowe Glenn C. , Procaccio Vincent , Clish Clary B. , Arany Zoltan , Haigis Marcia C.
Published: February 2012

Calorie restriction (CR) is a dietary intervention that extends lifespan and healthspan in a variety of organisms. CR improves mitochondrial energy production, fuel oxidation, and reactive oxygen species (ROS) scavenging in skeletal muscle and other tissues, and these processes are thought to be critical to the benefits of CR. PGC-1α is a transcriptional coactivator that regulates mitochondrial function and is induced by CR. Consequently, many of the mitochondrial and metabolic benefits of CR are attributed to increased PGC-1α activity. To test this model, we examined the metabolic and mitochondrial response to CR in mice lacking skeletal muscle PGC-1α (MKO). Surprisingly, MKO mice demonstrated a normal improvement in glucose homeostasis in response to CR, indicating that skeletal muscle PGC-1α is dispensable for the whole-body benefits of CR. In contrast, gene expression profiling and electron microscopy (EM) demonstrated that PGC-1α is required for the full CR-induced increases in mitochondrial gene expression and mitochondrial density in skeletal muscle. These results demonstrate that PGC-1α is a major regulator of the mitochondrial response to CR in skeletal muscle, but surprisingly show that neither PGC-1α nor mitochondrial biogenesis in skeletal muscle are required for the whole-body metabolic benefits of CR.
Neutralizing antibodies against the preactive form of respiratory syncytial virus fusion protein offer unique possibilities for clinical intervention
Authors: Magro Margarita , Mas Vicente , Chappell Keith , Vázquez Mónica , Cano Olga , Luque Daniel , Terrón María C. , Melero José A. , Palomo Concepción
Published: February 2012

Human respiratory syncytial virus (hRSV) is the most important viral agent of pediatric respiratory infections worldwide. The only specific treatment available today is a humanized monoclonal antibody (Palivizumab) directed against the F glycoprotein, administered prophylactically to children at very high risk of severe hRSV infections. Palivizumab, as most anti-F antibodies so far described, recognizes an epitope that is shared by the two conformations in which hRSV_F can fold, the metastable prefusion form and the highly stable postfusion conformation. We now describe a unique class of antibodies specific for the prefusion form of this protein that account for most of the neutralizing activity of either a rabbit serum raised against a vaccinia virus recombinant expressing hRSV_F or a human Ig preparation (Respigam), which was used for prophylaxis before Palivizumab. These antibodies therefore offer unique possibilities for immune intervention against hRSV, and their production should be assessed in trials of hRSV vaccines.
“Evolution Canyon,” a potential microscale monitor of global warming across life
Authors: Nevo Eviatar
Published: February 2012

Climatic change and stress is a major driving force of evolution. The effects of climate change on living organisms have been shown primarily on regional and global scales. Here I propose the “Evolution Canyon” (EC) microscale model as a potential life monitor of global warming in Israel and the rest of the world. The EC model reveals evolution in action at a microscale involving biodiversity divergence, adaptation, and incipient sympatric speciation across life from viruses and bacteria through fungi, plants, and animals. The EC consists of two abutting slopes separated, on average, by 200 m. The tropical, xeric, savannoid, “African” south-facing slope (AS = SFS) abuts the forested “European” north-facing slope (ES = NFS). The AS receives 200–800% higher solar radiation than the ES. The ES represents the south European forested maquis. The AS and ES exhibit drought and shade stress, respectively. Major adaptations on the AS are because of solar radiation, heat, and drought, whereas those on the ES relate to light stress and photosynthesis. Preliminary evidence suggests the extinction of some European species on the ES and AS. In
Drosophila,
a 10-fold higher migration was recorded in 2003 from the AS to ES. I advance some predictions that could be followed in diverse species in EC. The EC microclimatic model is optimal to track global warming at a microscale across life from viruses and bacteria to mammals in Israel, and in additional ECs across the planet.
The structural, optical and electrical properties of Y-doped SnO thin films and their p-type TFT application
Authors: Liang Ling Yan , Liu Zhi Min , Cao Hong Tao , Xu Wang Ying , Sun Xi Lian , Luo Hao , Cang Kai
Published: February 2012

Unintentionally doped and Y-doped SnO thin films were prepared and characterized by x-ray diffraction, spectroscopic ellipsometry, and Hall-effect measurements. SnO-based thin-film transistors were also fabricated and investigated. Preferred (0 0 l) grain orientation present in the undoped films is alleviated by Y doping, inducing the deterioration of crystallinity as well as the decrease in Hall-effect and saturation field-effect mobilities. However, both the films and the transistor devices always possess p-type characteristics in this study. As the Y content increases, the optical band gap, the real part of the dielectric constant of the films and the on/off current ratio of the devices increase. Moreover, the threshold voltage was observed to shift towards the positive direction as more yttrium content is introduced. These results give evidence that the yttrium element is incorporated into the SnO lattice successfully and higher hole concentration can be generated.
Judging Farmers' Willingness to Trade Distance and Taxes for Extension Services
Authors: Diekmann Florian , Loibl Cäzilia , Batte Marvin T. , Yen Meng‐Fen
Published: February 2012

Is it necessary for the U.S. Cooperative Extension Service system to maintain an extension office in every county? Using stated choice data from a conjoint analysis experimental design, we examine the tradeoffs that farmers are willing to make when choosing between local offices based on differences in educational programs offered, expertise level of staffing educators, distance to the local office, and the level of local taxation required to support an extension office. Our results show farmers' willingness to travel further and/or pay higher taxes in support of their “local” extension office depends on access to specialized expertise, crop, economics/finance, and 4‐H programs, and shared facilities with USDA agencies. However, farmers may not be willing to pay enough for local offices to actually cover their costs.
Discriminating response groups in metabolic and regulatory pathway networks
Authors: Van Hemert John L. , Dickerson Julie A.
Published: February 2012

Motivation: Analysis of omics experiments generates lists of entities (genes, metabolites, etc.) selected based on specific behavior, such as changes in response to stress or other signals. Functional interpretation of these lists often uses category enrichment tests using functional annotations like Gene Ontology terms and pathway membership. This approach does not consider the connected structure of biochemical pathways or the causal directionality of events.

Results: The Omics Response Group (ORG) method, described in this work, interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Statistical results for all response groups are visualized in a novel Pathway Flow plot. The statistical tests are based on the Erlang distribution model under the assumption of independent and identically Exponential-distributed random walk flows through pathways. As a proof of concept, we applied our method to an Escherichia coli transcriptomics dataset where we confirmed common knowledge of the E.coli transcriptional response to Lipid A deprivation. The main response is related to osmotic stress, and we were also able to detect novel responses that are supported by the literature. We also applied our method to an Arabidopsis thaliana expression dataset from an abscisic acid study. In both cases, conventional pathway enrichment tests detected nothing, while our approach discovered biological processes beyond the original studies.

Availability: We created a prototype for an interactive ORG web tool at http://ecoserver.vrac.iastate.edu/pathwayflow (source code is available from https://subversion.vrac.iastate.edu/Subversion/jlv/public/jlv/pathwayflow). The prototype is described along with additional figures and tables in Supplementary Material.

Contact:  julied@iastate.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
IDEOM: an Excel interface for analysis of LC–MS-based metabolomics data
Authors: Creek Darren J. , Jankevics Andris , Burgess Karl E. V. , Breitling Rainer , Barrett Michael P.
Published: February 2012

Summary: The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates filtering and identification of metabolite peaks, paying particular attention to common sources of noise and false identifications generated by liquid chromatography–mass spectrometry (LC–MS) platforms. Building on advanced processing tools such as mzMatch and XCMS, it allows users to run a comprehensive pipeline for data analysis and visualization from a graphical user interface within Microsoft Excel, a familiar program for most biological scientists.

Availability and implementation: IDEOM is provided free of charge at http://mzmatch.sourceforge.net/ideom.html, as a macro-enabled spreadsheet (.xlsb). Implementation requires Microsoft Excel (2007 or later). R is also required for full functionality.

Contact:  michael.barrett@glasgow.ac.uk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Improving your target-template alignment with MODalign
Authors: Barbato Alessandro , Benkert Pascal , Schwede Torsten , Tramontano Anna , Kosinski Jan
Published: February 2012

Summary: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information.

Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported.

Contact:  jan.kosinski@uniroma1.it
Biophysical assessment of aquaporin‐9 as principal facilitative pathway in mouse liver import of glucogenetic glycerol
Authors: Calamita Giuseppe , Gena Patrizia , Ferri Domenico , Rosito Anna , Rojek Aleksandra , Nielsen Søren , Marinelli Raúl A. , Frühbeck Gema , Svelto Maria
Published: February 2012

Background information

Lipolytic glycerol, released from adipocytes, flows through the bloodstream to the liver, where its utilisation in supplying hepatocyte gluconeogenesis is rate‐limited by the permeation step. An aquaglyceroporin expressed in hepatocytes, aquaporin‐9 (AQP9), has been often linked to liver uptake of glycerol. However, the truthfulness of this postulation and the potential existence of additional pathways of glycerol import by hepatocytes have never been assessed directly. Here, we define the identity and extent of liver glycerol transport and evaluate the correlation between hepatic AQP9 expression and glycerol permeability (Pgly) in AQP9+/+ wild‐type mice in different nutritional states and circulating insulin levels. The liver Pgly of AQP9 null mice is also assessed.

Results

By stopped‐flow light scattering, facilitated diffusion of glycerol into hepatocytes was indicated by the low Arrhenius activation energy (3.5 kcal/mol) and strong inhibition by phloretin, an AQP9 blocker, that characterised the transport. Although fasting markedly increased hepatic AQP9, a straight parallelism was seen both in quantitative and time–space terms between Pgly and AQP9 protein in AQP9+/+ mice kept in fed or fasted/refed states. In line with these findings, the highest Pgly (Pgly ≈ 14.0 × 10−6 cm/s at 20°C) at 18‐h fasting coincided with the highest percent of phloretin inhibition (63%). Besides being markedly lower than that in AQP9+/+ mice, the liver Pgly of the AQP9 null mice did not increase during fasting. Reverse‐transcription PCR analysis showed lack of compensation by AQP3 and AQP7, the other known murine glycerol facilitators, in AQP9 null mice.

Conclusions

Overall, these results experimentally prove major functional significance for AQP9 in maximising liver glycerol import during states requiring increased glucose production. If any, alternative facilitated pathways would be of minor importance in transporting glucogenetic glycerol into hepatocytes during starvation. Refining the understanding of liver AQP9 in metabolic and energy homeostasis may reveal helpful for therapeutic purposes.
Cancer‐associated orthotopic myofibroblasts stimulates the motility of gastric carcinoma cells
Authors: Fuyuhiro Yuhiko , Yashiro Masakazu , Noda Satoru , Matsuoka Junko , Hasegawa Tsuyoshi , Kato Yukihiro , Sawada Tetsuji , Hirakawa Kosei
Published: February 2012

Tumor progression has been recognized as the product of evolving crosstalk between cancer cells and the surrounding stromal cells. Cancer‐associated orthotopic myofibroblasts may be linked to the progression of gastric carcinomas. To understand the significance of orthotopic myofibroblasts, we examined the effects of cancer‐associated orthotopic myofibroblasts on the malignant phenotype of gastric cancer cells. Three human gastric cancer cell lines (OCUM‐2MD3, OCUM‐12, MKN‐45) and four human gastric fibroblast cell lines (cancer‐associated orthotopic fibroblast [CaF]‐29, CaF‐33, normal orthotopic fibroblast [NF]‐29, NF‐33) were used. The cancer‐associated orthotopic fibroblast cell lines CaF‐29 and CaF‐33 were established from a tumoral gastric wall, and normal orthotopic fibroblast NF‐29 and NF‐33 were established from a non‐tumoral gastric wall. Fibroblasts that were α‐smooth muscle actin‐positive were defined as myofibroblasts. We examined the effects of cancer‐associated orthotopic myofibroblasts on the aggressiveness of gastric cancer cells by wound‐healing assay, invasion assay, and RT‐PCR. The ratios of myofibroblasts in CaF‐29 (33%) and CaF‐33 (46%) were significantly (P < 0.001) greater than those in NF‐29 (11%) or NF‐33 (13%). Although all four orthotopic fibroblast lines increased the motility of gastric cancer cells, including migration and invasion ability, the motility‐stimulating activity of cancer‐associated fibroblasts (CaF‐29 and CaF‐33) was significantly higher than that of normal fibroblasts (NF‐29 and NF‐33). These motility‐stimulating activities of cancer‐associated orthotopic fibroblasts were downregulated by Smad2 siRNA treatment and anti‐transforming growth factor‐β neutralizing antibody. These findings suggest that cancer‐associated orthotopic myofibroblasts may play an important role in the progression of gastric cancers and that transforming growth factor‐β produced by myofibroblasts may be one of the factors associated with the aggressiveness of gastric carcinoma cells. (Cancer Sci 2012; 103: 797–805)
Cytokine and chemokine modification by Toll‐like receptor polymorphisms is associated with nasopharyngeal carcinoma
Authors: Yang Zhi‐Hui , Dai Qiong , Gu Ying‐Jiang , Guo Qing‐Xi , Gong Li
Published: February 2012

Toll‐like receptors (TLR) play a pivotal role in sensing a wide range of pathogens, including bacteria, fungi and viruses. A dysregulation of TLR signaling may increase the risk of developing chronic inflammatory diseases and cancers. The aim of this study was to investigate the association of TLR2 R753Q, TLR4 D299G, and T399I polymorphisms with nasopharyngeal carcinoma (NPC) and to explore the effects of these polymorphisms on cytokine and chemokine expression in NPC biopsies. The genotypes of the three loci among 236 patients with NPC and 287 healthy controls were determined by PCR‐RFLP. Cytokines and chemokines mRNA and protein in NPC biopsies were measured by real‐time quantitative PCR and ELISA, respectively. Results showed that the combined CT/TT genotype of T399I was associated with increased NPC risk, with an odds ratio of 1.853 (95% confidence interval: 1.184–2.961). Also, individuals with the T allele of T399I showed a 1.842‐fold increase in NPC risk compared to those with the T399I C allele (95% confidence interval: 1.213–3.015). Messenger RNA levels of interleukin (IL)‐1α, tumor necrosis factor‐α and IL‐10 were significantly elevated in patients with T399I combined CT/TT genotype; IL‐1α and IL‐10 protein concentration significantly increased in NPC patients with T399I combined CT/TT genotype compared to those with the T399I CC genotype. Our data suggest that TLR4 T399I modify cytokines and chemokines patterns and play a role in the development of NPC. (Cancer Sci 2012; 103: 653–658)